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Date: 2007/09/20 02:13:39, Link
Author: Daniel Smith
Hello to all,

Thanks Alan for the invitation and the thread.  I don't really know what to say here.  The reference to the evolution of the horse was one of many that Schindewolf uses in his book for his position against gradualism.

Berg essentially argues against selection using many examples from modern biological history.

I've also read recently, the excellent books "Evolution: A Theory in Crisis" and "Nature's Destiny" by Michael Denton.

I also respect immensely Dr. John Davison's Prescribed Evolutionary Hypothesis, although I must admit, much of it is over my head.

I myself am no scientist.  As far as formal training, I'm more than ignorant.  What little I know has been self taught. I spent a lot of time on the talk.origins newsgroup sharpening my views, but my positions are not set in stone.  I have not yet decided what I think really happened in the "history of life" on this planet, but I am convinced of one thing: whatever happened was by design.

Also, I must say that I have very little free time to devote to this discussion - probably 1 or 2 hours a week - so there might be some long delays between posts for me.

Date: 2007/09/22 04:07:01, Link
Author: Daniel Smith
Quote (C.J.O'Brien @ Sep. 20 2007,12:29)
The key difference between science and apologetics is that scientific inquiry begins with the data and moves toward the best explanation...

Science, therefore, seeks consilience. Whatever explanation is proposed for a set of observations must not only be the best fit for those data, it must also fit within the framework of all the other observations and conclusions drawn in the field.

I agree that this is what science should be.  

What then, is your position on the lack of evidence in the fossil record for gradualism?

Date: 2007/09/22 04:11:25, Link
Author: Daniel Smith
Quote (JAM @ Sep. 20 2007,17:43)
 
Quote (Daniel Smith @ Sep. 20 2007,02:13)
I've also read recently, the excellent books "Evolution: A Theory in Crisis" and "Nature's Destiny" by Michael Denton.

Didja happen to notice that the latter book walks back from the position taken in the former book?

Not really.  In the first book, he doesn't really give us an alternative hypothesis; all he does is point out the many deficiencies of the currently held evolutionary theory.

In the second book, he starts to give us his own alternative: a designed universe and directed evolution.

I see no conflict.

Date: 2007/09/22 04:14:13, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Sep. 20 2007,02:48)
As almost every living thing that has ever existed is extinct, why would that be by design? Seems wasteful to me

What's your take on the "designed to go extinct" issue?

I don't know "why" many designers do what they do.  I don't think that in any way negates the fact that their products are designed.  Do you?

Date: 2007/09/22 04:48:52, Link
Author: Daniel Smith
Quote (Peter Henderson @ Sep. 20 2007,14:52)
In fact, in order to be successful in these disciplines they must be approached from an evolutionary viewpoint. Astronomy/cosmology for example, just doesn't make sense when viewed from a YEC perspective despite what people like Dr Jason Lisle say (even he had to learn evolutionary concepts in order to obtain his Phd). What we observe is this field certainly does not confirm a young Earth/Universe.

There are many things I have yet to make up my mind about.  For instance; I have not made my mind up in regard to the age of the earth/cosmos as I have not seen all the evidence and probably do not have the expertise to rightly interpret it.

My main problem is that I want to see unbiased and unadulterated evidence; not evidence that is made-to-fit the observers viewpoint.  I'm finding that hard to do - since both sides of this issue tend to color the evidence with their own interpretive brush.

The first book I read on the subject (other than my high school science books) was "Scientific Creationism" by Dr. Henry Morris, and, although he makes some good points, I found some of his views to be a bit of a stretch and recognized his attempts to fit science to the bible.

I then spent quite some time on talk.origins and did much research on the internet looking at the case for the currently held theory of evolution.  I found that much of the evidence for the theory was being interpreted under the assumption of the theory.

I decided what I needed was just to see the evidence for myself.

This is the reason I have sought out authors such as Berg, Schindewolf, Denton, Davison and others.  First, they are true scientists - there are no religious views expressed in their books.  Second, they hold to no preconceived paradigm and they have (or had) nothing to gain by publishing their views.  Most were either ridiculed or shunned, or just put on a shelf and forgotten, but their works stand the test of time (at least so far).  These are the type of people I want to get my information from.

Date: 2007/09/22 04:53:23, Link
Author: Daniel Smith
Quote (Wesley R. Elsberry @ Sep. 22 2007,04:38)
What meaning of "gradualism" are you interested in?

I mean the smooth, gradual, incremental, evolution of forms throughout biological history.

Date: 2007/09/22 04:55:46, Link
Author: Daniel Smith
Quote (Wesley R. Elsberry @ Sep. 22 2007,04:38)
Might it be the "phyletic gradualism" described by Eldredge and Gould in 1972?

   
Quote

    In this Darwinian perspective, paleontology formulated its picture for the origin of new taxa. This picture, though rarely articulated, is familiar to all of us. We refer to it here as “phyletic gradualism” and identify the following as its tenets:

   (1) New species arise by the transformation of an ancestral population into its modified descendants.

   (2) The transformation is even and slow.

   (3) The transformation involves large numbers, usually the entire ancestral population.

   (4) The transformation occurs over all or a large part of the ancestral species’ geographic range.

Of these I'd pick 1 and 2, but not necessarily 3 or 4.

Date: 2007/09/22 14:26:17, Link
Author: Daniel Smith
Quote (Wesley R. Elsberry @ Sep. 22 2007,04:58)
Uh, no, it's a package deal. Either you are endorsing all four of the definitional components, or you should be using another term.

OK, let me be more specific:
Gradualism is what one would expect to see if the mechanism for evolutionary change were random mutations and natural selection.  If you think that it must entail entire populations and their entire geographical range, then fine - show that by the evidence in the fossil record.

Date: 2007/09/22 15:01:34, Link
Author: Daniel Smith
Quote (jeannot @ Sep. 22 2007,05:02)
         
Quote (Daniel Smith @ Sep. 22 2007,04:07)
What then, is your position on the lack of evidence in the fossil record for gradualism?

Mine is rather straightforward:
Given the billions of animal and plant species that have existed, we've only collected a very small fraction of them as fossils.

We don't expect to find most transitional forms.

But we have found millions of fossil remains for many types of organisms.  Why then do we still find no evidence of smooth, gradual transitions between types?  

         
Quote
"As we all know, Darwin's theory of evolutionary descent asserts that organisms evolve slowly and very gradually through the smallest of individual steps, through the accumulation of an infinite number of small transformations.  Consequently, the fossil organic world would have to consist of an uninterrupted, undivided continuum of forms; as Darwin himself said, geological strata must be filled with the remains of every conceivable transitional form between taxonomic groups, between types of organizations and structural designs of differing magnitudes.

Fossil material did not then and, based on the present state of our knowledge, does not today meet this challenge, not by a long shot. It is true that we know of countless lineages with continuous transformation, in as uninterrupted a sequence as could be desired.  However, each time we go back to the beginning of these consistent, abundantly documented series, we stand before an unbridgeable gulf.  The series break off and do not lead beyond the boundaries of their own particular structural type.  The link connecting them is not discernible; the individual structural designs stand apart, beside one another or in sequence, without true transitional forms"

Otto H. Schindewolf, "Basic Questions in Paleontology", pp 102-103


And later, when speaking of the sudden appearance of new structural types, Schindewolf comments:
     
Quote
" And these are by no means just isolated occurrences; these strange new forms are usually also represented by large numbers of individuals.  Nonetheless, there is no connecting link with the stock from which they derived.  The continuity of the other species gives us no reason to suspect interruptions in the deposition of the layers, or subsequent destruction of layers already deposited, which, furthermore, would be revealed by other geological criteria.  Nothing is missing here, and even drastic changes in living conditions are excluded, for the facies remain the same.

Further, when we see this situation repeated in all stratigraphic sequences of the same time period all over the world... we cannot resort to attributing this phenomenon to immigration of the new type from areas not yet investigated, where perhaps a gradual, slowly progressing evolution had taken place. What we have here must be primary discontinuities, natural evolutionary leaps, and not circumstantial accidents of discovery and gaps in the fossil record"

ibid. pp 104-105 (emphasis his)

Date: 2007/09/22 21:57:32, Link
Author: Daniel Smith
Quote (Peter Henderson @ Sep. 22 2007,11:43)
If you saw 10 clocks Daniel, and 9 of them were reading the same time and the tenth was different which one would you choose ? I know what I would think. I would assume the one that was different was in error.

We are talking about people here - not clocks.
If you were in a meeting, and nine out of ten people agreed with everything the boss said, but one disagreed, would you automatically go along with the 9 or listen closely to the 1?

Date: 2007/09/22 22:04:21, Link
Author: Daniel Smith
Quote (Wesley R. Elsberry @ Sep. 22 2007,17:13)
Actually, it is Daniel's claim that the fossil record is in a particular state. I'd be interested to know what experience Daniel has that would underwrite his confidence in his claim. But even more basic than that is getting some concrete idea of what the claim is... that is, I'd like to see some anchors tying the goalposts in place before going any much further with the game. As it stands, Daniel says that one doesn't see something in the fossil record, but he doesn't seem to have any clear notion of just what it is or what actual paleontologists would call it.

My main source for my argument about paleontology is Otto Schindewolf's "Basic Questions in Paleontology".  

I'm pretty sure Schindewolf qualifies as an "actual paleontologist".  

Did you read the quotes I supplied from that book in any of my posts so far?

Date: 2007/09/23 04:07:57, Link
Author: Daniel Smith
Quote (creeky belly @ Sep. 23 2007,00:24)
     
Quote
"As we all know, Darwin's theory of evolutionary descent asserts that organisms evolve slowly and very gradually through the smallest of individual steps, through the accumulation of an infinite number of small transformations.  Consequently, the fossil organic world would have to consist of an uninterrupted, undivided continuum of forms; as Darwin himself said, geological strata must be filled with the remains of every conceivable transitional form between taxonomic groups, between types of organizations and structural designs of differing magnitudes.

This assumes that fossilization is a uniform process throughout the lineage of a species. Unfortunately, fossilization is a relatively rare event, and to see such a process is very unlikely. This doesn't mean we see nothing.

Schindewolf was a paleontologist.  He knew how fossilization occurred.  To accuse him of assuming something when (I'm pretty sure) you haven't read the book is presumptuous.  He bases his arguments on a multitude of fossil lineages that are thoroughly understood. He spends 55 pages discussing evolutionary patterns among the Cephalopods and the Stony Corals.  He uses real world examples in support of his arguments.
   
Quote
and to see such a process is very unlikely.
But we do see it (transitional forms) over and over and over again - only they are not transitional between types, but only within types.  Now I ask you: Why is it that only these transitional forms are preserved?
           
Quote
   
Quote

Fossil material did not then and, based on the present state of our knowledge, does not today meet this challenge, not by a long shot. It is true that we know of countless lineages with continuous transformation, in as uninterrupted a sequence as could be desired.  However, each time we go back to the beginning of these consistent, abundantly documented series, we stand before an unbridgeable gulf.  The series break off and do not lead beyond the boundaries of their own particular structural type.  The link connecting them is not discernible; the individual structural designs stand apart, beside one another or in sequence, without true transitional forms"

This is demonstrably false. It's like staring at a puzzle after a few pieces have been laid out and saying "We'll never see the picture of Garfield." It's absurd. Look at whale evolution: this use to be trotted out by creationists as an impossible transition only to find that it existed in the fossil record.. You can quote this book all you want, but you're in a poor position to rebut considering that the book is about 60 years old. There have been numerous discoveries of transitional forms in fish, birds, and mammals since then, all of which dispute this point. This doesn't even get into disciplines like genetics, where you'll have an even worse time. Please continue, though. I'm interested what this man from the past thinks we'll never find.

Schindewolf had no arguments against whale evolution to my knowledge.  He did point out that - despite their similar habitats, ichthyosaurs and whales remained reptiles and mammals respectively and did not revert to "the organizations found in fish".  

You have to remember that Schindewolf is no creationist.  He advocated saltational evolution of types, followed by gradual evolution within types.  He did something remarkable: he tailored his views to fit the evidence rather than trying to make the evidence fit his views.

Date: 2007/09/23 04:14:21, Link
Author: Daniel Smith
Quote (JAM @ Sep. 22 2007,21:05)
Has Denton ever published any data?


Have a look.

Have you?

Date: 2007/09/23 04:22:10, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Sep. 23 2007,04:12)
Daniel,
Just to get a feel for your position, if we say that 100% is every living creature that ever existed then what % would you say are represented in the fossil record?

I.E what % of all living creatures fossilize?

No idea.  

I have a question for you:
What % of transitional versus non-transitional forms are fossilized?

Is there some difference that makes the transitional forms more resistant to fossilization than their non-transitional counterparts?

Date: 2007/09/23 17:17:19, Link
Author: Daniel Smith
Quote (JAM @ Sep. 23 2007,10:37)

But that's a book, not the primary literature.

But the opinions of an actual paleontologist aren't actual evidence.  

But quotes aren't evidence, either.

How about opinions quoted from a book by Richard Dawkins?

Date: 2007/09/23 22:01:22, Link
Author: Daniel Smith
Quote (creeky belly @ Sep. 23 2007,05:40)
I'm sure he understood the process of fossilization and I've seen his data (although I'm surprised with the amount of life that's inhabited the planet compared to the number of fossils, he would be so shocked to see gaps in the fossil record. I guess he wanted a poster child for the transition). He could have spent 250 pages and it still wouldn't make a difference, this is not 1950. He used the evidence that he had at the time to construct an argument and made a case.  Now we have something like this:

And here

The saltational events that Schindewolf proposed would go where the dotted lines are on your chart - the part subtitled "suggested lines of descent".             
Quote

Do you mean "archetypes" like he writes on page 411? As he says: "In contrast, we stay with the objective natural data and strive to arrange the morphological steps in the system in their natural sequence." So let's look at fossils that have been discovered since 1950: how about the Therapsid-Mammal transition, are they far enough apart? Try Colbert and Morales (1991) or Strahler(1987). Reptile-Amphibian? Try here. Fish-Amphibian? Try here!

I don't have the book in front of me right now, so I'll have to get back to you on that.

Date: 2007/09/24 04:52:58, Link
Author: Daniel Smith
Quote (Alan Fox @ Sep. 23 2007,06:40)
       
Quote
We are very lucky to have fossils at all. After an animal dies many conditions have to be met if it is to become a fossil, and one or other of those conditions usually is not met. Personally, I would consider it an honor to be fossilized but I don't have much hope of it. If all the creatures which had ever lived had in fact been fossilized we would be wading knee deep in fossils. The world would be filled with fossils. Perhaps it is just as well that it hasn't happened that way.

Because it is particularly difficult for an animal without a hard skeleton to be fossilized, most of the fossils we find are of animals with hard skeletons - vertebrates with bones, mollusks with their shells, arthropods with their external skeleton. If the ancestors of these were all soft and then same offspring evolved a hard skeleton, the only fossilized animals would be those more recent varieties. Therefore, we expect fossils to appear suddenly in the geologic record and that's one reason groups of animals suddenly appear in the Cambrian Explosion.

There are rare instances in which the soft parts of animals are preserved as fossils. One case is the famous Burgess Shale which is one of the best beds from the Cambrian Era (between 500 million and 600 million years ago) mentioned in this quotation. What must have happened is that the ancestors of these creatures were evolving by the ordinary slow processes of evolution, but they were evolving before the Cambrian when fossilizing conditions were not very good and many of them did not have skeletons anyway. It is probably genuinely true that in the Cambrian there was a very rapid flowering of multicellular life and this may have been when a large number of the great animal phyla did evolve. If they did, their essential divergence during a period of about 10 million years is very fast. However, bearing in mind the Stebbins calculation and the Nilsson calculation, it is actually not all that fast. There is some recent evidence from molecular comparisons among modern animals which suggests that there may not have been a Cambrian explosion at all, anyway. Modern phyla may well have their most recent common ancestors way back in the Precambrian.

As I said, we're actually lucky to have fossils at all. In any case, it is misleading to think that fossils are the most important evidence for evolution. Even if there were not a single fossil anywhere in the earth, the evidence for evolution would still be utterly overwhelming.* We would be in the position of a detective who comes upon a crime after the fact. You can't see the crime being committed because it has already happened. But there is evidence lying all around. To pursue any case, most detectives and most courts of law are happy with 2-3 clues that point in the right direction.
(*my emphasis)

Richard Dawkins

Of course I am not surprised at all that Dawkins would minimize the importance of the fossil record.  Surely if it teemed with evidence for his theory, he would feel differently about it.

I am a bit surprised that he thinks the theory of evolution via RM+NS is essentially beyond reproach.  I read through his lecture (which I mistakenly referred to as a book earlier) and I looked for this "utterly overwhelming" evidence he speaks of, but did not find it.

From the same lecture:
       
Quote
These are all domestic dogs (Slide 1) except the top one which is a wolf. The point of it is, as observed by Darwin, how remarkable that we could go by human artificial selection from a wolf ancestor to all these breeds - a Great Dane, a Bulldog, a Whippet, etc. They were all produced by a process analogous to natural selection - artificial selection. Humans did the choosing whereas in natural selection, as you know, it is nature that does the choosing. Nature selects the ones that survive and are good at reproducing, to leave their genes behind. With artificial selection, humans do the choosing of which dogs should breed and with whom they should mate.

These plants (Slide 2) are all members of the same species. They are all descended quite recently from the wild cabbage Brassica olearacea and they are very different cauliflower, brussels sprouts, kale, broccoli, etc. This great variety of vegetables, which look completely different, has been shaped - they have been sculpted - by the process of artificial selection from the same common ancestor.

The problem with Dawkins' logic here is that it doesn't match reality:

(As you and I have discussed before), artificial selection is not "analogous to natural selection", as Dawkins argues. Artificial selection only works by shielding organisms from natural selection.

Throw all domesticated dogs back into the wild and watch as all these breeds go away - to be replaced by mutt dogs which will gradually lose many of their unique, bred-for characteristics and more and more closely resemble the wolf from which they came.

The same goes for these cultivated plants.  Throw them back into the wild and eventually they revert back to the original wild cabbage species - all the domesticated varieties would disappear.

These things can be verified in your own back yard.

Date: 2007/09/24 14:54:45, Link
Author: Daniel Smith
Quote (JAM @ Sep. 24 2007,10:58)
 
Quote (Daniel Smith @ Sep. 24 2007,04:52)
         
Quote
Even if there were not a single fossil anywhere in the earth, the evidence for evolution would still be utterly overwhelming.*
Richard Dawkins

Of course I am not surprised at all that Dawkins would minimize the importance of the fossil record.

You're quote mining, Daniel, and avoiding the real evidence.

It wasn't my quote so how could I be "mining" it?
 
Quote

He's not minimizing its importance. He's pointing out that evidence from other sources is much more extensive and complete:
     
Quote
The evidence comes from comparative studies of modern animals. If you look at the millions of modern species and compare them with each other - looking at the comparative evidence of biochemistry, especially molecular evidence - you get a pattern, an exceedingly significant pattern, whereby some pairs of animals like rats and mice are very similar to each other. Other pairs of animals like rats and squirrels are a bit more different. Pairs like rats and porcupines are a bit more different still in all their characteristics. Others like rats and humans are a bit more different still, and so forth. The pattern that you see is a pattern of cousinship; that is the only way to interpret it. Some are close cousins like rats and mice; others are slightly more distant cousins (rats and porcupines) which means they have a common ancestor that lived a bit longer ago. More distinctly different cousins like rats and humans had a common ancestor who lived a bit longer ago still. Every single fact that you can find about animals is compatible with that pattern.

Big deal.  Things that are alike are built alike - even at the molecular level.  No one disputes this. What the molecular evidence shows, however is not always consistent with RM+NS.  For instance, Denton points out the "Molecular Equidistance of all Eucaryotic Organisms from Bacteria" (in "Evolution: A Theory In Crisis", Figure 12.2, page 280), which is more consistent with the Schindewolf/Berg/Davison et al hypotheses of prescribed/directed/planned/designed evolution.

   
Quote
Surely if it teemed with evidence for his theory, he would feel differently about it.

He's saying that other sources are more complete and more than sufficient. That's why creationists generally avoid discussing the sequence evidence, and when they do, they grossly misrepresent it.

How many trees have you constructed from sequences (evidence) using tools like CLUSTAL and BLAST, Daniel?

None.  And in answer to your previous question about the primary literature:  I read what I can online.  I've often searched for articles on google scholar, but most require memberships to read - so I am not nearly as well informed as you I'm sure.
   
Quote
   
Quote
I am a bit surprised that he thinks the theory of evolution via RM+NS is essentially beyond reproach.


That's because you're afraid of grappling with evidence for yourself. If you any real confidence in your position, you'd be discussing evidence instead of quote mining.

I didn't quote mine.  And I'm happy to discuss any evidence you want to discuss.  It may take me awhile to understand what you're getting at sometimes and you may have to bring it down to my level, but don't accuse me of not being willing to discuss evidence when you haven't even given me the chance.
Quote

     
Quote
I read through his lecture (which I mistakenly referred to as a book earlier) and I looked for this "utterly overwhelming" evidence he speaks of, but did not find it.

What part of this don't you understand?
     
Quote
If you look at the millions of modern species and compare them with each other - looking at the comparative evidence of biochemistry, especially molecular evidence - you get a pattern, an exceedingly significant pattern, whereby some pairs of animals like rats and mice are very similar to each other.

I understand all of it.  None of it is inconsistent with Nomogenesis, Orthogenesis, or the PEH.  
Quote

     
Quote
The same goes for these cultivated plants.  Throw them back into the wild and eventually they revert back to the original wild cabbage species - all the domesticated varieties would disappear.

These things can be verified in your own back yard.

And have you done so?

No, but Berg cites many examples of similar types of experiments.  His arguments against evolution via natural selection are very well constructed and empirically based.

Date: 2007/09/24 15:02:56, Link
Author: Daniel Smith
Quote (creeky belly @ Sep. 23 2007,05:40)
Do you mean "archetypes" like he writes on page 411? As he says: "In contrast, we stay with the objective natural data and strive to arrange the morphological steps in the system in their natural sequence." So let's look at fossils that have been discovered since 1950: how about the Therapsid-Mammal transition, are they far enough apart? Try Colbert and Morales (1991) or Strahler(1987). Reptile-Amphibian? Try here. Fish-Amphibian? Try here!

I'm not sure what you're arguing against here.  The passage you quoted was from the chapter on taxonomy and he was discussing phylogenetic classification (which he deemed subjective) as opposed to morphological classification (which he called objective).  

You seem to be arguing as if he denied common descent or evolution in general.  He denied neither.  His contention was with the mechanism of evolution.

Schindewolf proposed that evolution proceeded according to patterns.  He gave the example of the marsupial and placental wolves.  These obviously unrelated animals developed eerily similar features quite independently of each other.  

He also proposed that evolution proceeded as if constrained by a goal.  He gives the example of the evolution of the one-toed foot on the horse - which began long before the horse moved onto the plains and the one-toed foot became advantageous.

He also proposed that evolution occurred during ontogeny and gave several examples of ammonoid suture and coral septal apparatus evolution to support his views.

Again, I'm not sure what you are arguing against.

Date: 2007/09/25 01:58:26, Link
Author: Daniel Smith
Quote (Albatrossity2 @ Sep. 24 2007,06:12)
The fact that dogs under artificial selection have one set of characters, and another set of characters when they are feral and subject to a different kind of selective pressure, is not a problem for evolutionary theory. It is, in fact, a prediction of that theory.

I didn't know the theory had any predictions.
Quote

Do you have any testable predictions from your theory (whatever it is at the moment) that would lead to a different outcome than that predicted by evolutionary theory?

Since my view holds that selection is a conservative function, my statements about dogs and cabbage would probably qualify as predictions.

Date: 2007/09/25 02:11:22, Link
Author: Daniel Smith
Quote (Erasmus @ FCD,Sep. 24 2007,08:44)
Daniel, it is also not true.  the genetic milieu is changed by selection (artificial is just another form, and it's not really artificial is it?  unless you are arguing it is sooooopernatcheral).
It's artificial in the sense that it's not natural - man selects the breeding partners - not nature.  
Quote

offspring of different lineages (or hybrids if you will) can have phenotypes that are completely outside the range of variation in the parents.  if there is any positive selective pressure on those traits then they will persist.  if there is then a mate preference, they will diverge.  it is that simple, and 'throwing dogs into the wild and they all turn back into wolves' is just wrong for a litany of reasons.  think about why that might be.  no way can a chihuaha turn 'back into' a wolf.  for one, it never was one.

I never predicted that a chihuahua would "turn into" a wolf.  Chihuahuas and great danes would probably be the first breeds to go extinct - due to a lack of reproductive partners.  Medium sized dogs would have more partners to breed with and dog size would most likely gravitate towards that median.  All the super-specialized breeds would probably also eventually go away - as their gene pool became more and more watered down through breeding as well.
Quote


fancy types of lettuce don't go back to being one single muddy lettuce, there is a quantitative legacy of mutation and selection.  same as the dogs.  new traits can be formed from recombination during contact between different lineages (See the Helianthus sunflower examples, it blows your contentions out of the water in the first paragraph)

No idea what sunflower example you're talking about.  Perhaps a link?

Date: 2007/09/25 02:16:36, Link
Author: Daniel Smith
Quote (improvius @ Sep. 24 2007,09:12)

So you actually think that by simply removing natural selection, dogs just magically developed into all of these breeds with very specific purposes?  That's absurd.

Come on now.  You're really can't be that dense, can you?
I said artificial selection (that's the part where people actively protect their dogs from breeding with any other breed of dogs) works by shielding (i.e.: protecting) the dogs from natural selection (that is, what would happen if the dogs got out and just ran the streets, breeding with any dog they felt like).

Date: 2007/09/25 03:08:38, Link
Author: Daniel Smith
Quote (JAM @ Sep. 24 2007,16:02)
             
Quote

Big deal.  Things that are alike are built alike - even at the molecular level.

That's not remotely close to what he's saying. He's talking about mathematical analyses of the similarities AND DIFFERENCES. They fit nested hierarchies. The hierarchies of the organisms can be superimposed upon the hierarchies of their components, which are even more complex, because we can see how different proteins are related to each other.

Nested hierarchies are evidence of "top-down" evolution - where the higher categories are emplaced first - as opposed to evolution by speciation which would not create a nested hierarchy at all but would look more like a road map with lineages wandering aimlessly around.
           
Quote

Oh, and Daniel, no set of designed objects has these characteristics, so please save your lying for ignorant lay people.

Lots of designed objects fit into nested hierarchies.  One could make a nested hierarchy for automobiles - starting with horse drawn carriages and branching out.
               
Quote
             
Quote
What the molecular evidence shows, however is not always consistent with RM+NS.

Obviously, much of it is consistent with drift, which is not RM+NS, and a small subset is consistent with horizontal transfer.

If you had the slightest clue, you'd know that modern evolutionary theory is not limited to RM+NS.
Why do you have to be so mean and accusatory?
               
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For instance, Denton points out the "Molecular Equidistance of all Eucaryotic Organisms from Bacteria" (in "Evolution: A Theory In Crisis", Figure 12.2, page 280), which is more consistent with the Schindewolf/Berg/Davison et al hypotheses of prescribed/directed/planned/designed evolution.

No. Denton fundamentally misunderstood evolutionary theory, and has since backtracked on that ignorant claim. MET (particularly drift) predicts that. Denton assumed a ladder, not a bush.
What claim did he backtrack on?
Denton's last book supports directed evolution.
               
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Why not construct some trees, then, unless you weren't being truthful about your interest in evidence?

So, in order to show that I'm interested in evidence, I must construct trees?
             
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And in answer to your previous question about the primary literature:  I read what I can online.

That doesn't answer my question. Have you ever read a paper from the primary literature?
I guess I don't know what you mean by "primary literature".  Is that only peer-reviewed journals?
         
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I've often searched for articles on google scholar, but most require memberships to read - so I am not nearly as well informed as you I'm sure.

So why do you consider your uninformed conclusions to be more correct than mine?
Well, so far you've mostly called me names, and you haven't (yet) shown me anything that convinces me I'm wrong.
           
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Let's discuss this paper, then:
http://www.biolbull.org/cgi/content/full/202/2/104
...let's start with Figure 2. Note that vertical line length is irrelevant, only the horizontal lines represent sequence divergence.

Alright, I read it.  As I understand it, they found a gene in a fish that would allow it to get high on pot, :D then they sequenced that gene along with the same gene in humans and mice and fed all that info into a couple computer programs that spit out a comparative sequence and a chart that shows a theoretical phylogenetic divergence based on the similarities and differences and... mutation rates I'm guessing?
I'm not sure what I'm supposed to learn from this, but I'm open to whatever it is you think this shows.  You'll just have to spell it out in layman's terms for me.
               
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It may take me awhile to understand what you're getting at sometimes and you may have to bring it down to my level, but don't accuse me of not being willing to discuss evidence when you haven't even given me the chance.

Sorry, but you're supposed to familiarize yourself with the evidence before reaching a firm conclusion.
But I've reached no firm conclusion as of yet.  Unless you are talking about my statement that whatever happened was by design.  In that case, I've yet to see any evidence that doesn't strengthen that conviction.
               
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I understand all of it.  None of it is inconsistent with Nomogenesis, Orthogenesis, or the PEH.      

I don't think you understand it at all, since you blew it off as mere similarity.
Similarities and differences can be mapped out into a neat hierarchal pattern.  What part of that is inconsistent with evolution by law?
               
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No, but Berg cites many examples of similar types of experiments.  His arguments against evolution via natural selection are very well constructed and empirically based.

To know that, you'd have to be familiar with the evidence, not just that someone offered citations. Are you familiar with these data, or are you faking it? Do you realize that science is not about appraising arguments, but about predicting and grappling with the actual evidence, not what anyone says about it?

Berg spent years in the field documenting case after case that confounded those he called "Selectionists".  I respect his findings because they are not arguments but are documented observances.  Many here and at talk.origins who fervently hold to the evolution by RM+NS (and drift and horizontal transfer) seem to be more interested in theoretical arguments than documented field work.

Date: 2007/09/25 03:33:37, Link
Author: Daniel Smith
Quote (jeannot @ Sep. 24 2007,16:38)
         
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Big deal.  Things that are alike are built alike - even at the molecular level.

If you're going to argue for "common design" as we see you coming, you'll have to explain why closely related species share homologies at synonymous or neutral sites, which have nothing to do with "design".

How about this?
         
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"The new view transforms our view of the genomic fabric," explained Dr Tim Hubbard, from the Wellcome Trust Sanger Institute, "The majority of the genome is copied, or transcribed, into RNA, which is the active molecule in our cells, relaying information from the archival DNA copy to the cellular machinery. This is a remarkable finding, since most prior research suggested only a fraction of the genome was transcribed."

"But it is our new understanding of regulation of genes that stands out. The integrated approach has helped us to identify new regions of gene regulation and altered our view of how gene regulation occurs."...

The team showed that transcription of DNA is pervasive across the genome, and that RNA transcripts overlap known genes and are found in what were previously thought to be gene 'deserts'.(all emphasis mine)



I am especially interested in these overlapping coding areas.  What that means, as near as I can tell, is that the coding in DNA is more elaborate and more sophisticated than previously thought - with regions that code for regulatory RNA overlapping (sharing parts of the same code with) regions that code for proteins.

If this is true (and it looks like it is), it would seem to be a nightmare for any theory based on random mutations - since one mutation would have to not only improve the protein produced, but the RNA as well.

Of course those of us who hold to a designed life theory have been predicting that there is no such thing as "junk DNA" all along.

I'm sure, however, that many of you will say that the ToE predicts this as well.

Date: 2007/09/26 04:39:38, Link
Author: Daniel Smith
Quote (jeannot @ Sep. 25 2007,10:18)
       
Quote (Daniel Smith @ Sep. 25 2007,03:33)

How about this?

This has hardly anything to do with my objection. JAM was right about your misconception regarding pseudognes and junk DNA.
Regions of unknown functions (what you like to call “junk”) may actually have some phenotypic effects. And, guess what? This is tested by building phylogenies on those regions, and detecting evidence of selection acting on them.

In a typical gene, synonymous mutations are far more frequent that non-synonymous ones. (To give you an example, the 30 point mutations that separate two species of aphids that I study at a 700 bp locus are all synonymous).
These kinds of observations have been the primary argument of Kimura, who first formulated the neutral theory of evolution.
We know that synonymous mutations lead to the same proteins, and are very unlikely to have a significant effect on the organism. Hence they are not eliminated by natural selection.
Same goes for pseudogenes, once they are knocked-out (typically by a frame shift or a stop mutation), we notice an acceleration of their mutation rates. This is expected if they are no longer active.
So again, why do related species share mutations that have no effect?

First, I don't use the term "junk" to describe any sequence of DNA.  I am against the use of that term - as are most ID proponents.  I've always said that there's no such thing as junk DNA, so saying that I "like to call" it junk is untrue.

Second, I'm arguing that these so-called "junk" regions are important - that they likely do have an effect (something it appears you are noticing too).  The ENCODE study shows that that's true - since it shows that "most" (their word - no idea what the percentage is) of the genome is transcribed.

So to answer your question: Related species share mutations (if that's what they are) that most likely do have an effect.      
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And you should think about my second objection: human, lungfish and trout. What does common design predict about their genes?
Common Design would predict that lungfish and trout would be closer to each other than to humans.  Perhaps, once they get the entire genomes sorted out, they'll find this to be true.  For now, with the concentration seemingly focused on coding regions - it appears not to be true.  I guess we'll have to wait and see.

Date: 2007/09/26 06:01:50, Link
Author: Daniel Smith
Quote (JAM @ Sep. 25 2007,10:58)

D:Nested hierarchies are evidence of "top-down" evolution - where the higher categories are emplaced first - as opposed to evolution by speciation which would not create a nested hierarchy at all but would look more like a road map with lineages wandering aimlessly around.

Please explain how Darwin was wrong when he predicted nested hierarchies, then.

Can you supply that quote from Darwin?
 
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They fit into multiple NHs, but one of "these characteristics" that you socleverly omitted was the superimposability of the NH of the assembled objects over any NH independently constructed from their components. Why did you omit that, Daniel? And if you disagree, show me the NHs you can construct from the relationships between lug nuts for GM cars and trucks.
...
But it couldn't be superimposed on NHs derived from their components. In fact, virtually none of the components of cars can be organized into nested hierarchies.

That's not true.  Most components can also be organized into nested hierarchies. Speaking from experience (since my job involves troubleshooting and repairing very large, complex, industrial CNC machinery) I can verify that the parts of a machine evolve right along with the machine and can be placed in separate but superimposable NHs.
Right now, the company I work for is talking about rebuilding 8 machines (which are pretty much exact duplicates of one another) - one a year - over an 8 year period.  Even though we'll have the same company come in and do the work, we'll end up with 8 very different machines - since the technology will change every year as the machines go in.
   
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The ladder part. It's stupid. The equidistance is predicted.

Where did Denton assume a ladder?  I don't remember that part.
     
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Denton's last book supports directed evolution.

Evidence supports positions, not books. You don't give a damn about evidence, do you?

Like I said, I'm willing to look at any and all evidence.  I'm less interested in opinions though.
     
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Since the relationships between these sequences represent the overwhelming evidence favoring MET that make fossils unnecessary, it would be the inevitable prediction for someone who claimed an interest in evidence.

Fossils are unnecessary? Wow. You do realize that fossils are empirical, observable evidence don't you?                
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Within most journals, there are both primary (those with new data) and secondary (reviews). Usually, only the former are peer-reviewed. So I'll ask again: have you ever read a paper from the primary literature--meaning one that reports data that have never been reported before?

I don't subscribe to the journals and their online articles all seem to require a subscription.  I've been consigned to reading mostly abstracts and summations of these articles.        
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Well, so far you've mostly called me names, and you haven't (yet) shown me anything that convinces me I'm wrong.

Mostly? Show me a single instance in which I called you a name, Daniel.

OK,
       
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you have the appealing quality of massive arrogance, made even more appealing by massive ignorance... so please save your lying for ignorant lay people.

Does that qualify?
       
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Let's discuss this paper, then:
http://www.biolbull.org/cgi/content/full/202/2/104
...let's start with Figure 2. Note that vertical line length is irrelevant, only the horizontal lines represent sequence divergence.

Alright, I read it.  As I understand it, they found a gene in a fish that would allow it to get high on pot, :D then they sequenced that gene along with the same gene in humans and mice

No, those were already sequenced.

OK my bad.
       
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and fed all that info into a couple computer programs that spit out a comparative sequence and a chart that shows a theoretical phylogenetic divergence based on the similarities and differences and... mutation rates I'm guessing?

Sorry, but you're fudging already. The tree is not theoretical in any way. It is simply a graphic representation of the actual evidence--the identities and differences between the sequences.

OK
       
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What do you conclude from these relationships? If CB2 was designed, when was it designed?

When was it designed or when was it implemented?  I have no idea when it was designed, but when it was first implemented can be found out I guess - if you find the earliest fossil evidence for that fish.                
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I'm not sure what I'm supposed to learn from this, but I'm open to whatever it is you think this shows.  You'll just have to spell it out in layman's terms for me.

It's a starting point for examining the evidence and making predictions, something I predict that you're afraid to do. Where will a reptilian CB2 branch off on this tree? Why do both CB1 and CB2 fit into a single nested hierarchy?

I don't know the answers to those questions but I'm not afraid of them - I just need to figure out what you're asking and how you're arriving at your conclusions.  I need to see the evidence for myself - I won't just take your word for it.      
       
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Unless you are talking about my statement that whatever happened was by design.  In that case, I've yet to see any evidence that doesn't strengthen that conviction.

That's because you haven't looked at evidence. Look at how you misrepresented the tree as "theoretical" above.

The tree is theoretical in that it is just a graphic representation of a proposed relationship.  How do you know these genes are not convergent?

Date: 2007/09/27 01:54:00, Link
Author: Daniel Smith
Quote (Wesley R. Elsberry @ Sep. 26 2007,06:42)
<cop drama>
</cop drama>

I have my own cop drama for you.

Lt. DS: The lab boys found the murder weapon with the fingerprints of a known ex-con on it, plus a broken window with size 12 boot prints leading in and out of the house through it.  We'll have to arrest this man for the murder of this woman.

Lt. JAM: Why would we do that? The lab boys also found the husband's DNA all over the house and even on the wife's body.  He had obviously had recent contact with her.  Besides everyone knows that the husband always murders the wife in these cases. The fingerprints, weapon and bootprints are unnecessary.

Lt. DS: Fingerprints are unnecessary? Wow. You do realize that fingerprints are empirical, observable evidence don't you?

Lt. JAM: It doesn't matter - we've got the DNA!

[Rest of people in room look at Lt. JAM, jaws dropping  in amazement at his excellent police work.]

OK, now that we've dispensed with that foolishness, can we get back to talking about the evidence?

Date: 2007/09/27 03:05:12, Link
Author: Daniel Smith
Quote (Richard Simons @ Sep. 26 2007,07:54)
Daniel:                          
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Right now, the company I work for is talking about rebuilding 8 machines (which are pretty much exact duplicates of one another) - one a year - over an 8 year period.  Even though we'll have the same company come in and do the work, we'll end up with 8 very different machines - since the technology will change every year as the machines go in.

But will any of this new technology be used in any machines made by any other company? Or in any machines made by your company to do other things?

You are right that different designers can have different hierarchies - and so the superimposability will not match exactly.  Many manufacturers tend to stick with the same suppliers for quite some time however, and when they do, you can track the evolution of the various parts - right alongside the evolution of the machine's design.                      
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Because in biology that is not the case. A new technology, say mammary glands, that is successful in one group of organisms is never picked up by another group, fish for example. You will never find a fern with flowers or a treefrog with dragonfly wings. The one exception is in some micro-organisms, in which the transfer of genetic material is well-established.
You will also never find a CD player with a microwave oven in it, or a dresser with a 357 chevy motor... but that's another argument.

A possible reason that the nested hierarchy in nature is more perfect than that of other designed objects is for the simple reason that nature might just be the result of a single designer.  

If every part of a machine was designed by a single designer who could not borrow from any other designs or consult with any other designers, but could only refine and build upon his own ideas, we'd see a set of completely superimposable hierarchies for all the various components of a machine and for the machine itself.

This is what we see in nature - correct?

You are right about biological lineages; they do not borrow from one another (although many arrive at similar places) - they do seem to proceed as though constrained along a certain path though.  Once they get lungs, they don't lose them.  They don't ever revert back to an earlier lung-less state.  Schindewolf made many arguments from the evidence in the fossil record for the irreversibility of evolution and for it's procession down a seemingly defined pathway.  Berg also showed that organisms seem to develop features as if by law - and not through the arbitrary process of minute variations and selection.

If the nested hierarchy proves anything, it proves that higher order taxonomic groups came first, then proceeded to differentiate into lower and lower orders until finally arriving at the species level.  If differentiation started at the species level (as Darwin predicted), the higher orders would come last because - at their root - they would be almost exactly alike.  So you'd have species gradually becoming genuses that would gradually become families, then orders,... etc., until the most recent organisms would define the domain.

This is why the fossil record does not match Darwin's illustration.  The fossil record (from what I've seen, if you remove all the dotted lines - which are theoretical organisms anyway), looks like a grove of bushes - not one single bush.  If you take Darwins illustration and cover up the bottom half, it will look much closer to the graph that creeky belly supplied earlier in this thread.

Let me ask you - and all the other members here:
Does the process of cell differentiation during ontogeny produce superimposable nested hierarchies?

Because I think that ontogeny is a perfect model of how directed evolution would unfurl.

Schindewolf and Davison also championed this view and it makes perfect sense - since it reconciles the rapid differentiation found at the beginning of the fossil record with the overall genetic continuity that flows throughout.

       
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BTW, although fossils loom large in the general public's mind (and I include creationists and IDers here) as far as biologists are concerned they form a minor part of the evidence for the theory of evolution. This has been the case right from Origin of Species.

I'd guess that the fossil record would be a major part of the case for the theory of natural selection if it wasn't so ambiguous in its support of it.

Date: 2007/09/27 03:21:22, Link
Author: Daniel Smith
Quote (Wesley R. Elsberry @ Sep. 26 2007,09:44)


We don't have to wait to know that Denton's assertion is incorrect.

You seem to be saying that the rate of mutational change is the same for all species over time.  Is that correct?

But we know that bacteria, fruit flies and mice - due to their rapid reproduction rates - will have more mutational changes over time than animals with slower reproduction rates.  That's why we use them for such studies isn't it?

So how do you reconcile these two seemingly polar opposite realities?

Date: 2007/09/27 03:24:03, Link
Author: Daniel Smith
Quote (Reciprocating Bill @ Sep. 26 2007,06:24)
I'd like to hear about your commitments and community identifications, a description of the non-scientific allegiances from which your biases arise.

OK.

You first.

Date: 2007/09/27 05:30:39, Link
Author: Daniel Smith
Quote (Reciprocating Bill @ Sep. 25 2007,06:51)
But Daniel himself, per his own frank and repeated self-description, is operating from a decisive bias (one you appear to endorse), specifically that he prefers to learn from those who have been ignored, laughed at and shunned.

That's right.  I like scientists who are laughed at and shunned by the majority.  The majority are usually just empty headed sheep anyway. The majority just loves pablum.  Always has, always will.  They're the reason radio stations play the same songs over and over and over - they never want to hear new things.   They suck at the teet of mediocrity.

Me, I've always been this way.  When everyone was listening to ABBA, The Steve Miller Band, and all the other "happy, party, one-beat-fits-all" bands, I was listening to Black Sabbath - a band that cut against the grain and made people uncomfortable.  I liked that.  I was a social outcast and I liked it that way.  People who can't think for themselves gravitate towards the lowest common denominator.  They have to look around and see what everyone else is doing before they'll take a "stand" on anything.  They're afraid of being made fun of and they poke fun at anyone who doesn't "go along".  They're into whatever is "in" at the moment. I hate that.

I don't give a crap what any of you think of me either.  Laugh, shun - who cares.  I don't see any of you coming out with original ideas.  Most of you are probably committed atheists who need science to validate your belief system (or lack thereof).  You not only can't tolerate the thought of "a God", (oh my!), but you must make sure that science never reaches anything but atheistic conclusions.  So you laugh at and shun anyone who dares to bring a different interpretation to the evidence - any interpretation that makes you feel uncomfortable (weez), any interpretation that opens the door - even just a crack - to something remotely theistic.  No, anything like that  has to immediately be ridiculed.  Then you can all pat each other on the back and say "My don't we all think alike!".  It's sad because your minds are closed to anything new or different.  Majority rules!  Better stay safe - stick with whatever the MAJORITY says!

So, yeah, when the majority say one thing, I'm looking for a guy who's saying another.  Guys like Schindewolf, Berg, Davison, Bateson, Goldshmidt, Denton, Spetner - all of them.  These are guys who have the cahonas to take a real stand (without having to look around first).  

I don't think that's a bad way to be.

Date: 2007/09/27 06:35:49, Link
Author: Daniel Smith
Quote (JAM @ Sep. 26 2007,09:45)
   
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you have the appealing quality of massive arrogance, made even more appealing by massive ignorance... so please save your lying for ignorant lay people.

Does that qualify?

No, because there's not a single name in there.

I guess - since you didn't actually call me an arrogant, ignorant liar, but only implied that I'm an arrogant, ignorant liar - technically I cannot say you called me names.

Please accept my sincerest apologies for accusing you of being a name-caller.  You're obviously only a name-implier.

Date: 2007/09/27 06:38:17, Link
Author: Daniel Smith
Quote (Alan Fox @ Sep. 27 2007,05:41)
So, shall I cancel my order to Amazon, Daniel?

Leo Berg was a biologist who traveled the world collecting samples and analyzing flora and fauna.  He then proposed his own theory of evolution based on his years of observations in the field.

What has Dawkins done?

Date: 2007/09/28 02:38:39, Link
Author: Daniel Smith
Quote (JAM @ Sep. 25 2007,09:09)
   
Quote (Daniel Smith @ Sep. 25 2007,02:11)
All the super-specialized breeds would probably also eventually go away - as their gene pool became more and more watered down through breeding as well.

The gene pool would be enriched. Domesticated dogs have high homozygosity from inbreeding, not low.

Yes, but most dogs breeds are too domesticated to survive in the wild.  Surely many have lost the ability to hunt, others will have lost the ability to defend themselves against predators.  Reintroducing them to the wild would probably result in an immediate knockout of many of these breeds - thereby removing much of that enrichment from the gene pool.
Natural selection is a cold mistress.  It works by killing.
As Schindewolf said, "Selection is only a negative principle, an eliminator, and as such is trivial." (pg. 360)

Date: 2007/09/28 03:31:33, Link
Author: Daniel Smith
Quote (Alan Fox @ Sep. 27 2007,11:25)
If you recall, this thread was originally intended for you to show how the evolution of the horse is a problem for the current theory of evolution. I have not seen a great deal of evidence from you, yet.

You're right.  

In order to keep this thread on topic, I will try to keep my posts focused on the work of Schindewolf and Berg and (at least in the case of Schindewolf) also on the evolution of the horse.

Berg doesn't say a lot about horses other than this from section IV, "Convergence":
               
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"At the very time when in North America the Equidae were being evolved, forms of the order Litopterna were being elaborated in South America in the plains of the Argentine.  The latter are extinct ungulates, in many respects recalling horses: they had also lost the lateral digits of their limbs, and for progression made use of the median digit; their extremities and neck were likewise lengthened, and in the former, the ball-and-socket joints, by which movements in all directions could be accomplished, were being gradually supplanted by pulley joints, which restricted their limbs to being moved only backwards and forwards; their teeth lengthened and grew more complex (although no cement was present).  This group was extinct in South America before the arrival of horses. The Litopterna, or pseudo-horses, thus copied the horses in many ways.
The same course (as to limbs and teeth) as in horses was followed in the evolution of camels in the New World, and of deer, antelopes, sheep and oxen in the Old"
Nomogenesis, pg. 212.

As for Schindewolf's position, why don't I just start by using the same quote I provided for you over at Brainstorms:        
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To this extent,the one toed horse must be regarded as the ideal running animal of the plains. It's early Tertiary ancestors had four digits on the front feet and three on the hind feet, and low crowned cheek teeth. Since in the later Tertiary, an expansion of plains at the expense of forests has been observed, this change in environmental conditions and the consequent change in the mode of life has been represented as the cause of linear, progressive selection leading up to the modern horse.
However, in the formulation of this view, not enough consideration has been given to the fact that the evolutionary trend of reduction in the number of toes had already been introduced long before the plains were occupied in the early Tertiary by the precursors of the horse; these inhabited dense scrub, meaning that they lived in an environment where the reduction of the primitive five-toed protoungulate foot was not an advantage at all. In the descendants, then, the rest of the lateral toes degenerated and the teeth grew longer step by step... regardless of the mode of life, which... fluctuated repeatedly, with habitats switching around among forests, savannas, shrubby plains, tundra, and so on.
If selection alone were decisive in this specialization trend, we would have to ascribe to it a completely incomprehensible purposefulness...
Basic Questions in Paleontology pp. 358-359, (emphasis his)

Both of these men intently studied real examples from nature and the fossil record and came to the same conclusions:
1. That evolution of types happened suddenly - not gradually.
2. That subsequent evolution proceeded as if constrained by laws.
3. That natural selection had nothing to do with the formation of any organ.

Date: 2007/09/28 04:05:22, Link
Author: Daniel Smith
Quote (Richard Simons @ Sep. 27 2007,21:51)


Coming back to the nested hierarchies that you seem to persist in misunderstanding; you write
             
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You will also never find a CD player with a microwave oven in it, or a dresser with a 357 chevy motor

But you could find exactly the same electronic chip in a truck, a ship, a railway locomotive, an elevator, a sewing machine and a cash register. On the other hand, not one of the 'ancestors' of these machines would have the same kind of electronic chip, or even anything electrical.

That's demonstrably not true.  In electric circuits, the precursors to IC chips were soldered transistor circuit boards, the precursors to those were hand-wired transistor circuit boards, the precursors to those were relay logic and tube circuits, the precursors to those were manually switched electric circuits.   So the ancestors to a modern elevator controlled with IC chips would be an elevator controlled with soldered transistor circuit boards, then one with hand-wired circuit boards, then relays and tubes, then manually operated electric switches.
         
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This situation never arises in biology. Whenever organisms share a particular feature you will find that this group of organisms also has other features that are absent in others, or the feature serves the same purpose in each organism but is structurally different (e.g. wings, eyes).

Every organism has features that are absent in others - even within the same species.  That proves little to nothing.  But it's the similarities in different lineages that are the most troublesome for your theory since many are structurally similar.

Berg's book is filled with examples, but I'll give you one of his brief summations:    
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The comparative anatomy of animals supplies a number of striking examples of a definite direction in evolution.  Among vertebrates we may mention the evolution of teeth in reptiles and mammals, the gradual ossification of the vertebral column, a reduction in the number of the bones in the skull, the transformation of a two-chambered heart into a three- and four-chambered organ in connection with a corresponding complexity in the circulatory system, the evolution of the brain... the whole subject of comparative anatomy literally bristles with facts exemplifying development in a definite direction
Nomogenesis, pg.121
         
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In another post you suggest the same effect could have arisen if there were multiple designers. True. I have often thought it looks as though one god started it off then farmed it out to other gods, who in turn subcontracted to lesser gods - a sort of pyramid scheme of gods ('Here, I've got mammals started off. Now you take a few off to Australia and we'll see how you do. Don't muck around with the basics and no sneaking a look at what gods are doing anywhere else'). How many gods are you suggesting?
You misread me.  I said the nested hierarchy is evidence of a single designer - since the parts and the organisms both make for superimposable nested hierarchies - without the anomalies sometimes seen when parts are produced by multiple designers.

Date: 2007/09/28 04:09:45, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Sep. 28 2007,02:47)
 
Have you been to the western world lately? There's not many predators that could take on a sausage dog anymore. And there are also cities full of feral cats (descended no doubt from domesticated stock).

And my Siamese cat, bred to the point of insanity, would have no trouble surviving in the wild

I've lived in the city and the country.  Your Siamese cat might survive in the wild, but judging by the number of wild barn cats that almost starved to death on our ranch (until we started feeding them), I'd say that's no guarantee.

Date: 2007/09/28 04:12:07, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Sep. 28 2007,02:47)
 
And there are also cities full of feral cats (descended no doubt from domesticated stock).

OH, And the city doesn't really count as "the wild" now does it?

Date: 2007/09/28 05:45:56, Link
Author: Daniel Smith
Quote (Wesley R. Elsberry @ Sep. 26 2007,09:44)
We don't have to wait to know that Denton's assertion is incorrect.

So what I hear you saying is that the equidistant sequence space between Cytochrome-C among the various groups is more a function of time than anything else.  Is that correct?

If that is correct, then that is completely in keeping with (and in fact would be a prediction of) common descent by design.

Common descent by design would predict that there would be mathematical patterns within the evolution of sequences and that those patterns would be based on time and other internal factors rather than any outside factors - since divergence would occur according to plan - not according to chance, environment, or any other external influences.

Date: 2007/09/30 15:32:57, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Sep. 28 2007,06:05)
 
Is there anything that design predicts that evolution does not?

Seems as everything evolution can do, the designer(s) can also do. So your position is essentially meaningless unless you can somehow differentiate the two.

Is there a differentiation somewhere between the two things?

I could say the same thing about the currently held theory.  Is there anything that will ever be found that you won't somehow make to fit and eventually make to be a prediction of the currently held theory?
Are  protein synthesis, cell division, sexual reproduction, intelligence, speech, flight, sight, hearing, circulatory systems, etc. predicted by the current theory?
Since the current theory predicts "happy accidents", anything useful is then said to be predicted.
ID predicts useful features as well, so we're back to square one aren't we?
   
Quote

Are there any predictions of design that are not retrospective? I.E make a prediction for a something that's currently unknown that can be tested and the result will unambigiously say "designed" or "evolved".

If not, it seems to be all "design predictions" are worthless if they predict exactly the same things that evolution does.

Pointless.

Can you point me to a list of as yet untested "predictions" that common descent by design makes, or are they only available retrospectively? If the latter, then give up now, you'll never be able to convince anybody.

Some predictions (these are my own and in no way represent predictions of the ID movement in general):

Because evolution is proactive, not reactive:

Organisms will show evidence of preparation for anticipated environments; rudiments of organs not yet needed will be found.
When confronted with environmental changes, organisms will adapt using pre-existing features (already coded for in the genome) or will become extinct - no new features will develop slowly over time.
Patterns and laws will be found that govern how evolution works.

From the fossil record:
Lineages will be found to have begun before environments in which they later flourished began.
Mass extinctions will have been preceded by the introduction of new types that would dominate the next phase in earth’s cycle.
Organisms will be found to have begun the adaptive process before adaptation was necessary.
Patterns will be found in the origin, differentiation and eventual extinction of lineages that are not dependent upon environmental factors but exist across all manner of differing environments, geographical locations, types of organisms and ages.

Genetically:
Mathematical patterns not explainable by the current theory will be found when comparing sequences of different organisms.
The genetic code will be found to be more sophisticated and more robust than previously thought.
Embedded and overlapping coding will be found to be more prevalent than previously thought.
Careful examination of genomes will find preparatory and adaptive codes “waiting in the wings” ready to be utilized in case of environmental changes- many just a frame shift away.
Frame shifting will be found to be a more common mechanism for sudden evolutionary change than previously thought.
Every part of the entire genome of any organism will be found to either be used at some time in the organisms life, or be of future use.  There are no unusable “Leftovers”.
No adequate explanation other than design will ever be found for the origin of life’s most basic components - i.e. protein synthesis, cell division, sexual reproduction, etc.

Universally:
Because the earth, and the solar system were specifically designed for life, no life or signs of previous life will be found on any other planets within our field of exploration.

Date: 2007/09/30 15:35:39, Link
Author: Daniel Smith
Quote (JAM @ Sep. 29 2007,14:17)
If they suggest design, their designer was an idiot.

Many are.
What's your point?

Date: 2007/09/30 15:53:10, Link
Author: Daniel Smith
Quote (jeannot @ Sep. 28 2007,14:21)
Common descent by design?
Can you develop, Daniel?

Basically common descent by design (or designed descent) is the view the evolution of organisms was planned out in advance.  
I have to clarify here that this was not Schindewolf's view.  He held "mysticism" (as he called it) in contempt and thought that evolution proceeded by internal factors alone - which constrained it along certain paths.  For this reason he also held Darwinism in contempt.

Date: 2007/09/30 16:03:42, Link
Author: Daniel Smith
Quote (Reciprocating Bill @ Sep. 28 2007,05:24)

This may be contrasted with Darwin's predictions: to fail to find nested hierarchy in nature would be to falsify his model of evolution.

But the nested hierarchy was developed to classify organisms before Darwin's time!
Ever heard of Linnaeus?
So how then can it be a prediction of Darwinism?

   
Quote
(Daniel: Still waiting for you to retract your patently false claim vis interest in data with no biases or preconceptions.)

Thanks for continually telling me what I'm thinking and how best I should express my thoughts.  (I bet you're a big hit at parties!)

BTW, do you know what I'm thinking right now?

Date: 2007/09/30 16:15:22, Link
Author: Daniel Smith
Quote (carlsonjok @ Sep. 28 2007,06:11)
 
Quote (Daniel Smith @ Sep. 28 2007,04:12)
 
OH, And the city doesn't really count as "the wild" now does it?

For whom?  Certainly, it isn't the wild for humans inasmuch as it consolidates all sorts of things, like grocery stores and homes, for our convenience.  But for feral cats, alas without currency to buy themselves a bag of Friskies or take out a mortgage, it is the wild.

Well, cats and dogs rely on humans for their sustenance, therefore the cities (which have dumpsters, trash cans and gutters full of food scraps) don't really qualify as an environment of the type where natural selection was proposed to have done all of it's major work now does it?
So, let me rephrase this:
Remove humans from the world and what happens to dogs, cats and cultivated plants?
It is my contention that natural selection will reduce varieties.
 
Quote
Never mind.  After over six pages and you haven't even mentioned a horse and that is the reason you are here, no?

If you go back to Brainstorms, you'll see that the horse was just one example I used in a discussion with Alan Fox while discussing the theory of evolution in general.  I don't know why he decided to start this thread making that the sole subject.  That was not my doing.  Schindewolf's main argument from horse evolution was that the horse developed a single toed foot before it was advantageous to do so.  So far no one has disputed his position with any evidence that shows it to be a false claim.

Date: 2007/09/30 16:56:01, Link
Author: Daniel Smith
Quote (George @ Sep. 28 2007,07:44)
 
Quote (Daniel Smith @ Sep. 28 2007,03:31)
   
Quote
However, in the formulation of this view, not enough consideration has been given to the fact that the evolutionary trend of reduction in the number of toes had already been introduced long before the plains were occupied in the early Tertiary by the precursors of the horse; these inhabited dense scrub, meaning that they lived in an environment where the reduction of the primitive five-toed protoungulate foot was not an advantage at all. In the descendants, then, the rest of the lateral toes degenerated and the teeth grew longer step by step... regardless of the mode of life, which... fluctuated repeatedly, with habitats switching around among forests, savannas, shrubby plains, tundra, and so on.
If selection alone were decisive in this specialization trend, we would have to ascribe to it a completely incomprehensible purposefulness...
Basic Questions in Paleontology pp. 358-359, (emphasis his)

So basically Schindewolf is saying that horses developed single-toed hooves regardless of the selection pressures applied?  How does he know what those pressures were?  How does he know the scrub was dense?  Paleoecologists today can identify what species were present in the landscape at a point in time, but have much more difficulty in determining vegetation structure.  This has led to disagreements over what the European landscape of most of the Holocene was.  Yes there were lots of oak trees present, but was it closed forest?  Was it patches of scrub interspersed with grassy plains?  Was it widely spaced parkland-like trees?

In other words, what was the quality of his data and how far is he spreading it with rhetoric?

He doesn't go into any details (in this book at least - he may have in others or in one of his papers) about how he knew the environmental conditions were such as he described, so I can't tell you how he determined that.

I'm assuming that the man described in 1965 by Stephen Jay Gould's advisor, Dr. Norman Newell as "the greatest living paleontologist", used the scientific method and the accepted evidence of his day to determine these factors.

You might be in a position to show that he made a false claim, but you must base that on evidence from that time period.

Date: 2007/09/30 18:32:17, Link
Author: Daniel Smith
Quote (Alan Fox @ Sep. 29 2007,04:17)

So, is there another example that better illustrates Berg's alternative to RM + NS?    

Berg's book is full of examples.  He makes his case on cumulative evidence, making mention of so many species, orders, organs, locations, periods, races, genera, etc. and etc... that I can't remember half of them, (his examples probably average at least one per page, and there are over 400 pages!).  So once again, I'll be unable to provide a "best" example, but I'll give you one example:
           
Quote
Osborn (1902, 1907), basing his inferences on the study of the teeth of various groups of mammals, comes to the conclusion that teeth have "predispositions" to vary in a definite direction: in the process of the evolution of teeth full development is reached only by what had previously existed in a potential condition.  Therefore, similar characters in teeth appear quite independently in various groups, such as horses, rhinoceroses, Titanotheria.  Nor is this all.  It is possible to detect a similar evolution of the tubercles of the molars in such widely separate groups as Perissodactyla, and Primates (including the Lemuroidea).  Tubercles appear in a strictly definite position, so that there can be no question of chance.  We have to deal here, says Osborn (1902, p.267; 1907, p. 228), with a definite and determined evolution, governed by certain rules.  This may be seen from the following (Osborn, 1902, pp. 267-268; 1907, pp. 235-236):--

1.  Teeth are distinguished by a very singular property, i.e. that they are laid down and formed under the gums.  Consequently use or disuse cannot exert any effect upon their form.  On the contrary, the more they are used, the sooner they wear out.

2.  At the same time, teeth are one of the most progressive organs.

3.  The different families and orders of the Mammalia diverged from one another at the time when their upper molars possessed three tubercles each, the lower from three to five.  Therefore, only those tubercles are homologous which may be compared to the above mentioned primary ones.

4.  New supplementary tubercles are consequently not homologous, but convergent.  At the same time the occurrence of such tubercles is independent of individual variation.

Natural selection could thus play no part in the evolution of teeth in mammals, because they appear in perfectly definite positions.

Had the supplementary tubercles appeared without any definite order, at random, we should then have observed an unusual diversity in the teeth of mammals in all parts of the world.  But such is not the case: as we have seen, the occurrence of new tubercles follows definite rules in various families; in the upper molars from one to eight supplementary tubercles develop at strictly definite points.  We thus unavoidably come to the conclusion that even in the primary tritubercular condition of the molars a tendency has been inherent which to a certain extent predetermines their future variation and evolution (1907, p. 237).
Not only do the teeth, says Osborn, develop independently of chance variations being selected (for tubercles are predetermined); but the skull, the vertebral column and the extremities are subject to the same principle  of development in a definite direction (1907, p. 237)
Nomogenesis, pp. 123-124, (emphasis his)
BTW, the "Osborn" quoted above is Henry Fairfield Osborn
           
Quote

OK. The RM + NS theory claims that organisms are shaped by their environments. Where a population exists and is subject to change in that environment, selection will result in adaptive change or extinction. Adaptation is not predictive.

From your quote, Schindewolf is claiming that horses began adapting to life on the plains before arriving in that environment. If true, this would indeed be a grave problem for evolution.

How does Schindewolf establish the prevailing climate and vegetation associated with a particular fossil?

I don't know the answer to that.  But normally, when he is about to give a disputed position, he gives the alternate view as well.  He gives no alternate view here, so I'm assuming it was the accepted view at that time.

Date: 2007/09/30 18:55:28, Link
Author: Daniel Smith
Quote (jeannot @ Sep. 30 2007,15:55)
   
Quote (Daniel Smith @ Sep. 30 2007,15:53)
   
Quote (jeannot @ Sep. 28 2007,14:21)
Common descent by design?
Can you develop, Daniel?

Basically common descent by design (or designed descent) is the view the evolution of organisms was planned out in advance.  
I have to clarify here that this was not Schindewolf's view.  He held "mysticism" (as he called it) in contempt and thought that evolution proceeded by internal factors alone - which constrained it along certain paths.  For this reason he also held Darwinism in contempt.

What's your position? Do you support common descent?

I'm not sure.  Berg didn't appear to, Schindewolf did.  My opinion is still developing.

I'm interested in the truth - that's all.  My goal is to find out what really happened.

Date: 2007/09/30 18:58:33, Link
Author: Daniel Smith
Quote (carlsonjok @ Sep. 30 2007,16:22)
How interesting that you managed to quote my entire post except one sentence.  That sentence read:

   
Quote
Perhaps you would like to define the characteristics of an eco-system and then explain to us how an urban environment is not one?


I am sure that was an unintentional oversight that you will correct now.

Well, since it was "the wild" and not "an ecosystem" that I originally specified, perhaps you will now explain to me how the city fits my definition of "the wild"?

Date: 2007/10/01 19:37:42, Link
Author: Daniel Smith
Quote (George @ Oct. 01 2007,07:22)
You misunderstand me.  I'm not saying he was lying.  I'm questioning how he knew what Tertiary environmental conditions were like and how good were the data he based his conclusions on.  As I said before, it is difficult enough for today's paleoecologists to reconstruct past vegetation.  It would have been much more difficult and imprecise for the ecologists of a century ago.  Palynology, one of the more powerful tools, was only in its infancy.

To summarise:  he may have based his theories on the understanding of the day, but if that understanding is wrong, his ideas crumble.

Schindewolf's book was published (originally - in German) in 1950.  While technically that was in the last century, (so was 1999), it wasn't "a century ago".  

This is what he said:
 
Quote
Since in the later Tertiary, an expansion of plains at the expense of forests has been observed, this change in environmental conditions and the consequent change in the mode of life has been represented as the cause of linear, progressive selection leading up to the modern horse.
(emphasis mine)

I assume "has been observed" means that it was well accepted.  Perhaps newer data has proved him wrong, I don't know.

Date: 2007/10/01 19:45:29, Link
Author: Daniel Smith
Quote (carlsonjok @ Oct. 01 2007,05:14)
   
Quote (Daniel Smith @ Sep. 30 2007,18:58)
  Well, since it was "the wild" and not "an ecosystem" that I originally specified, perhaps you will now explain to me how the city fits my definition of "the wild"?

Well, you haven't defined "the wild" with sufficient rigor other than to imply that an urban environment isn't it because it is an environment where natural selection ceases to operate.  Indeed, "the wild" isn't even a scientific term.  That is why I am asking you to define what an eco-system is and then explain why an urban environment, as experienced by feral animals, is not such a thing.



I didn't think I had to define "the wild" when I made my statement.  I think most people here understood what I meant.  

Lets just say "the wild" is what exists outside cities, towns, or anywhere else man dwells.  That was what the ecosystem was like before man arrived on the scene and throughout the majority of natural selection's functional influence.

 
Quote
EDIT: corrected a very badly written sentence.

BTW, How do you edit posts here?

Date: 2007/10/01 21:26:41, Link
Author: Daniel Smith
Quote (Alan Fox @ Oct. 01 2007,07:31)
Re the search for evidence of life on Mars, there are three possible outcomes that I can foresee.

1:Evidence is found for a life-form totally different from anything seen on Earth, say, not even based on carbon, but, for instance, built on silicon.

2: Evidence is found for a life-form bearing distinct similarities to terrestrial lifeforms.

3; No evidence found.

If 1, abiogenesis is almost inevitable on any suitable planet, given enough time.

If 2, lifeforms such as bacterial spores may travel across space as passengers in meteorites. (Panspermia)

If 3, we still don't know.

One other option for #2:

If we find life on another planet that is distinctly similar to our own, it could mean that abiogenesis acts according to laws as well.

Denton's position, as expressed in "Nature's Destiny", was that any life, anywhere else in the universe, would have to be remarkably similar to our own.

Date: 2007/10/01 21:33:11, Link
Author: Daniel Smith
Quote (Reciprocating Bill @ Oct. 01 2007,19:57)
Planned in advance essentially = frontloading, which presents problems that render the hypothesis unworkable on the face of it.

The processes of adaptation and speciation described in the standard RM+NS model have enabled living organisms to track the countless contingent changes in environments and ecosystems in which those organisms have been embedded over the last 38 million centuries (or so). Even with such tracking a vast majority of species ended in extinction, presumably when these variations become too extreme to track. Indeed, the successes, failures and interactions of some species mold the ecological context for the successes and failures of others, all embedded in a contingently changing physical and environment.  

"Planned in advance" would require storage in advance of the countless adaptations, speciation events, ecoloogical interactions, and even extinction events that have been entailed in the story of the survival of life on earth within this endless succession of changing environments and ecosystems, as well as a program determining in advance the order in which these changes unfold. Yet the environmental transitions with with life has been confronted, and that demand these changes, result from physical processes (planetary, geological, meteorological, astronomical, etc.) that are themselves inherently contingent and unguided and which cannot themselves possibly have been "arranged," "planned," or "predicted." Moreover, we are talking the varied environments and apposite adaptations of every extinct and every extant lineage of descent that have taken their places among the astronomical number of ramifications of the tree of life.

With that in mind, "preplanned" becomes utterly implausible and even absurd, in my view.

Yes.  It would be a remarkable feat wouldn't it?

But the more we learn about DNA, the more remarkable it becomes.  For instance, the embedding and overlapping of coding areas radically changes the amount of information that can be stored in a genome.

Things that seem impossible, might just not be after all.

Date: 2007/10/02 02:10:46, Link
Author: Daniel Smith
Quote (jeannot @ Sep. 30 2007,16:13)
Linné's classification was flawed. His nested hierarchy is largely inconsistent across characters, it is full of contradictions.
And I fail to see how this undermines Darwin's prediction. Linné formulated no hypothesis behind his classification, expect perhaps something similar to common design, which can predict anything (hence nothing).

Linnaeus first published his Systema Naturae in 1738.  How could it not be flawed by today's standards?  Hierarchies and evolutionary trees are still hotly disputed amongst those who classify organisms.
You are right that he formed no new hypothesis based on his hierarchy, but he was an adherent to natural theology - so that would be his "hypothesis" I suppose.
The point is that a nested hierarchy was postulated before Darwin's time so how could it be a prediction?

Date: 2007/10/02 02:25:15, Link
Author: Daniel Smith
Quote (Reciprocating Bill @ Oct. 01 2007,21:40)
 
Daniel, your response doesn't appear to reflect any comprehension of my objection whatsoever. Read it again.

OK, I see that I missed some of your points (I was at work and answering your post while on a break - so I didn't give it a thorough review).

 
Quote (Reciprocating Bill @ Oct. 01 2007,19:57)
Planned in advance essentially = frontloading, which presents problems that render the hypothesis unworkable on the face of it.

The processes of adaptation and speciation described in the standard RM+NS model have enabled living organisms to track the countless contingent changes in environments and ecosystems in which those organisms have been embedded over the last 38 million centuries (or so). Even with such tracking a vast majority of species ended in extinction, presumably when these variations become too extreme to track. Indeed, the successes, failures and interactions of some species mold the ecological context for the successes and failures of others, all embedded in a contingently changing physical and environment.  

"Planned in advance" would require storage in advance of the countless adaptations, speciation events, ecoloogical interactions, and even extinction events that have been entailed in the story of the survival of life on earth within this endless succession of changing environments and ecosystems, as well as a program determining in advance the order in which these changes unfold.

It would not require storage of all of these events.  It would only require knowledge of them by the designer, who would then implement programs that would be set up to anticipate such things.  How do animals anticipate natural disasters?  We don't know, but they do.  Perhaps there is some long-range anticipatory mechanism.
 
Quote
Yet the environmental transitions with with life has been confronted, and that demand these changes, result from physical processes (planetary, geological, meteorological, astronomical, etc.) that are themselves inherently contingent and unguided and which cannot themselves possibly have been "arranged," "planned," or "predicted."

Unless there really is an all knowing God.  
Quote
 Moreover, we are talking the varied environments and apposite adaptations of every extinct and every extant lineage of descent that have taken their places among the astronomical number of ramifications of the tree of life.

With that in mind, "preplanned" becomes utterly implausible and even absurd, in my view.

In your view (which I assume is an atheistic one), pre-planning would seem ridiculous.  In my view, it's perfectly conceptual.

Date: 2007/10/02 03:03:19, Link
Author: Daniel Smith
Quote (Richard Simons @ Oct. 01 2007,23:27)
   
Quote
I have to clarify here that this was not Schindewolf's view.  He held "mysticism" (as he called it) in contempt and thought that evolution proceeded by internal factors alone - which constrained it along certain paths.

How does this differ from the views of Lamark?

Schindewolf did not subscribe at all to Lamarckism:
   
Quote
an unbiased examination of the fossil material itself also reveals that absolutely no direct response to environmental influences or appropriate adaptations in the Lamarckian sense must necessarily be inferred...
Formerly, in emphasizing the supremacy of the environment, the properties and qualities of organisms were unduly disregarded.  Yet it should be obvious that in such chains of reactions and complexes of conditions the objects themselves must be credited with critical significance.  When I heat two chemical substances together, it is not the rise in temperature but the composition of the original material that is decisive.  The rise in temperature only triggers the reaction; under certain circumstances, it can be replaced by a different physical or chemical action (pressure, catalysts), and the result, determined by the original material, will still be the same.  At most, the environment plays only a similar role with regard to organisms; it can only provoke and set in motion some potential that is already present.
Basic Questions in Paleontology, pp. 312-313 (emphasis his)
   
Quote (Richard Simons @ Oct. 01 2007,23:27)
How do these 'internal factors', whatever they might be, get translated into mutations and changes in gene frequences? Schindewolf, obviously, could not have expressed much of an opinion on the subject as at the time it was not even known what material carried genetic information.
Schindewolf was familiar with the relatively new science of genetics:
   
Quote
For our phylogenetic approach, then, we shall take from genetics the basic pair of factors, random mutability and directive selection.
These two factors and their mechanisms provide a satisfactory understanding of microevolution, of the experimentally ascertainable modification of forms of lesser rank.  The changes observed here are usually confined to species and have nothing to do with innovation, with the creation of new organs, but always only with relatively trivial, gradual changes regarding size, shape, number, color, and so on in organs that are already present.
ibid., pg. 329 (emphasis his)
 
Quote (Richard Simons @ Oct. 01 2007,23:27)
However, what is your explanation. Presumably you have thought about it as you are carrying the torch for Schindewolf.

I have thought about it, but I'm not sure what my explanation is yet.  I fully expect more discoveries to reveal that DNA is deeper than originally thought, and that things like this will be found more and more often.
Quote (Richard Simons @ Oct. 01 2007,23:27)


       
Quote
He also proposed that evolution proceeded as if constrained by a goal.  He gives the example of the evolution of the one-toed foot on the horse - which began long before the horse moved onto the plains and the one-toed foot became advantageous.

You say he held mysticism in contempt yet at the same time believed that somehow horses not only knew that at some time in the future they would benefit from having fewer toes but were actually able to evolve towards that state? To me, that is a prime example of mysticism. Again, what mechanism do you propose?

He never said horses "knew" any such thing, and I'm not sure how you got that from my posts.  I'm afraid though, that I mischaracterized Schindewolf's views here.  He never used the term "goal" when describing his views - that was my word.

Date: 2007/10/02 03:09:08, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Oct. 02 2007,02:41)
As almost everything that has ever lived is extinct what does that say about the ability of this "designer" to plan?

Why bother to front-load if the organism is going extinct anyway?

Every living thing dies.  Everything.

It would sure seem that natural selection would have overcome that little hiccup by now doesn't it?

Date: 2007/10/03 02:06:56, Link
Author: Daniel Smith
Quote (Louis @ Oct. 02 2007,06:01)
"Natural selection" isn't "trying" to maximise individual survivability, "natural selection" is "trying" to maximise individual survivability to the point of successful reproduction.

Don't those individuals within a species that live longer, reproduce more?  Isn't this exactly what NS is supposed to select for?
       
Quote (Albatrossity2 @ Oct. 02 2007,06:46)
Besides missing the point that the discussion was about extinction of species, and not the death of organisms, this statement implies an inability to think about the consequences/predictions of one's hypotheses, as well as ignorance of well-known thermodynamic laws governing ecosystem functions.

Think about this for a nanosecond. If natural selection, or any process not involving miracles, was able to produce organisms that overcame death, how long would it take for them to consume all the resources on this planet? And then what? Without death, there is no life as we know it; death provides resources for not just the consumers, but the producers as well.

OK, so let me get this straight.  Even though all the "tools" necessary to achieve longer life and even immortality are already in every genome - being in use during the developmental and adolescent cycles of every organism...  And even though these tools are able to "cheat" the 2nd law of thermodynamics throughout those periods...  
If an organism gets a mutation that somehow disables the aging process and keeps these processes working - thereby increasing it's progeny considerably - natural selection will look ahead, decide that one species living too long is not good for the planet, and then cause that organism to die early anyway?

You're going to have to explain to me how this unthinking, uncaring, unintelligent force can suddenly show this kind of forethought!  
       
Quote
Death is not just a "little hiccup". If you think that immortality is something that can be achieved by natural selection, or even if you think it is a good thing, then you are not thinking at all. You are taking your theological constructs (the immortal soul) and trying to shoehorn reality into that construct. Sorry, but reality is gonna win this one.

I'm doing no such thing.  It's my contention that everything dies because death is a law which no living (organic) being can violate.

Date: 2007/10/03 02:22:03, Link
Author: Daniel Smith
Quote (George @ Oct. 02 2007,07:57)
     
Quote (Daniel Smith @ Oct. 01 2007,19:37)
Schindewolf's book was published (originally - in German) in 1950.  While technically that was in the last century, (so was 1999), it wasn't "a century ago".
 

My mistake.  I thought you said he worked and wrote in the 1920s.

Perhaps you were thinking of Leo Berg?  He wrote Nomogenesis in 1922.    
Quote

I wasn't questioning this statement:

       
Quote
Since in the later Tertiary, an expansion of plains at the expense of forests has been observed, this change in environmental conditions and the consequent change in the mode of life has been represented as the cause of linear, progressive selection leading up to the modern horse.


I was questioning this one:

       
Quote
However, in the formulation of this view, not enough consideration has been given to the fact that the evolutionary trend of reduction in the number of toes had already been introduced long before the plains were occupied in the early Tertiary by the precursors of the horse; these inhabited dense scrub, meaning that they lived in an environment where the reduction of the primitive five-toed protoungulate foot was not an advantage at all.
(emphasis mine)

My question is how did he know the environment at the time was entirely comprised of dense scrub?  If I were to guess, this statement is based on finds of macrofossils or pollen of scrub species coupled with other proxy data that gave clues about climate.  This may have been the prevailing view at the time.  Don't know.  Doesn't matter.  But I suspect hand-waving.

So, after admitting that you "don't know" what evidence Schindewolf based his argument on, you say that it "doesn't matter", because you "suspect hand-waving".  Is this how science is done?
   
Quote
My point is that knowledge of what species were present at the time doesn't give an accurate picture of what the vegetation structure was at the time, especially over large areas.  I presume the ancestors of horses were widely distributed and not confined to a small isolated valley or two.

As you can see as you walk around in "the wild", vegetation structure varies considerably depending on climate, soil and other things, including the activities of grazing animals.  It is extremely unlikely that the landscape where the ancestors of horses evolved was completely dominated by "dense scrub".  It is extremely likely that there were some more open areas where having fewer toes increased fitness.

Schindewolf was overstating the case that the environment required to select for single-toedness was not present in the early Tertiary.  Because of this, he has no grounds for claiming that development of the trait preceeded selection pressure.

So based on your experience 'walking around in the wild', you've now decided that Schindewolf, one of the premier paleontologists in all of Europe, overstated his case? (a case which, I'm sure, was based on slightly more research than that!)

It's amazing to me how you can delude yourself into thinking you have actually refuted his arguments while presenting no evidence to the contrary from the Tertiary period at all!

Date: 2007/10/03 02:52:54, Link
Author: Daniel Smith
Quote (Richard Simons @ Oct. 02 2007,08:48)
It is interesting that, when asked questions, those who accept the theory of evolution answer in their own words, with links to sources, while those who don't accept it cut and paste more or less lengthy excerpts of other people's writings.

I can't win!  First I'm told to bring it back to the subject - which was Schindewolf's take on horse evolution - then I'm chided for quoting Schindewolf!  
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Schindewolf did not subscribe at all to Lamarckism:

"an unbiased examination of the fossil material itself also reveals that absolutely no direct response to environmental influences or appropriate adaptations in the Lamarckian sense must necessarily be inferred...
Formerly, in emphasizing the supremacy of the environment, the properties and qualities of organisms were unduly disregarded.  Yet it should be obvious that in such chains of reactions and complexes of conditions the objects themselves must be credited with critical significance.  When I heat two chemical substances together, it is not the rise in temperature but the composition of the original material that is decisive.  The rise in temperature only triggers the reaction; under certain circumstances, it can be replaced by a different physical or chemical action (pressure, catalysts), and the result, determined by the original material, will still be the same.  At most, the environment plays only a similar role with regard to organisms; it can only provoke and set in motion some potential that is already present. "

Basic Questions in Paleontology, pp. 312-313 (emphasis his)

And this differs from Lamarkism how (your own words, please)? As I see it, he is saying "Lamark claims they adapt to present conditions, I say they adapt to future conditions". This is less mystic and more reasonable because . . . (own words, please)?

You want me to explain Schindewolf's position without quoting Schindewolf?
OK, basically, Schindewolf believed that a lineage's evolutionary path was set from the first saltational event that created that type.  He documented what he interpreted as evolutionary patterns throughout the fossil record - which he then used to construct the framework of his "typostrophic theory".  This theory consisted of three stages; "typogenesis", which was the saltational evolution of types; "typostasis", which was a period of gradual development in a way that was constrained by the original typogenetic phase; and finally, "typolysis" which was a period of over-specialization that would usually end in the extinction of the species.
He did not believe that anyone was guiding these processes, he believed them to be totally self-contained.
 
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Schindewolf was familiar with the relatively new science of genetics:

That does not address the question. The question was "How do these 'internal factors', whatever they might be, get translated into mutations and changes in gene frequences?" In other words, how do the required changes in the DNA (that he could not have known about) take place? What makes a specific alanine change to leucine? Please answer in your own words.
He believed that these saltational changes took place during ontogeny.  He cited the many ontogenetic phases documented in the fossils of ammonites, corals, and other lineages in the fossil record as evidence of this.  
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Being able to answer in your own words is significant because it shows that you have thought about the issues to at least some degree.

     
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Linnaeus first published his Systema Naturae in 1738.  How could it not be flawed by today's standards?  Hierarchies and evolutionary trees are still hotly disputed amongst those who classify organisms.
You are right that he formed no new hypothesis based on his hierarchy, but he was an adherent to natural theology - so that would be his "hypothesis" I suppose.
The point is that a nested hierarchy was postulated before Darwin's time so how could it be a prediction?

Hierarchies are hotly disputed? Perhaps at some level, but they are being refined all the time. There is general agreement about the broad outlines and many of the finer details. Could you give an example of a hot dispute in taxonomy?

A nested hierarchy was postulated before Darwin's time? Could we please have a reference.

I think you still have not grasped the significance of a nested hierarchy and are confusing it with Linnaeus' use of a nested hierarchy in his classification scheme. The crucial thing as regards evolution is that it predicts the nested hierarchies will all be the same and that is what is observed.

You just said Linnaeus used a nested hierarchy to classify organisms.  Linnaeus did this more than 100 years before Darwin.  Yet you want me to show that a nested hierarchy was postulated before Darwin's time?
As for your second point.  Maybe you're right.  I'm assuming that nested hierarchies based on morphological characters, or homologous characters, or analogous characters, or genetic sequences will all be different.  I haven't seen how they all line up.

Date: 2007/10/03 02:59:06, Link
Author: Daniel Smith
Quote (Erasmus @ FCD,Oct. 02 2007,09:53)
Schindewolf and the german school are at best mechanist idealists.  They see forms as internally generated by biochemical and physical restraints.  Many of these guys had a completely material theory, but some of them did not.  

Gould says that they have received a bad rap, and that there is an underlying reality to the idea that evolution has constraints.  Of course this is true, but I don't think it is true in the sense that Daniel means it.

Daniel, if you believe that species are not fixed entities (maybe you don't, I dunno, you tell me) then what is the barrier to speciation as an explanation for everything?

I don't believe that the process of RM+NS has been shown capable of producing anything innovative.

Date: 2007/10/05 03:24:19, Link
Author: Daniel Smith
Well I don't have time to answer everybody right now, so let me just make some comments that will (hopefully) get me caught up with most of your objections.

First, Schindewolf's stand on horse evolution is not well spelled out - and he only devotes a couple pages to it, so it doesn't really do his theory justice to use that example.  What I should have done was brought out his position on the evolution of cephalopods or stony corals - since these are his main areas of expertise and the subject to which he devotes probably a good third of his book.  So maybe we can shift gears as regards Schindewolf?

Now, as to the nested hierarchies (the analogous one was out of place BTW):  I don't know why I started arguing against superimposable nested hierarchies - since that is entirely consistent with designed descent.  I guess it's just the old creationist in me that got me caught up in that.  I do admit that I don't have a real good grasp of the subject, and need to learn more.  Really my main objection to the current theory of evolution is in regards to mechanism.

Which brings me to your questions of what genetic mechanism I would propose for designed descent.  First let me say that we have witnessed a saltational evolutionary event consistent with designed descent in our lifetime - the nylon bug.  That this was saltational is pretty straightforward since an entirely new enzyme was created in one step.  That the code for this enzyme was pre-existing also makes it consistent with designed descent.  I know most of you will probably disagree with my assessment of this, but I believe it could very well be a window into how saltational evolution could occur - especially as genomes are found to contain more embedded, overlapping codes.

I should also mention here Schindewolf's observation that the evolution of cephalopod shells and sutures; and corals' septal developments can be traced to earlier and earlier stages of ontogeny - suggesting an ontogenetic mechanism.  Dr. John Davison's semi-meiotic hypothesis follows this principle.

Next, in an effort to better understand the molecular side of things, I picked up a book called "Patterns in Evolution" by Roger Lewin (who is a Darwinist BTW).  Now, first let me say that I just started reading it and also that it came out in 1997 (I got it at a used bookstore) so it's 10 years old already and may not represent the latest thinking on the subject.  Some of the things he says so far have really struck me though:

First, he contrasts morphological evolution with molecular evolution - saying that morphological evolution proceeds in starts and jumps (my words - not his) due to varying reproduction/replication rates, selective pressures, environments, geological periods, etc., but that molecular evolution remains rather constant across the board due to it's main activity being in neutral, non-coding areas of the genome - thereby largely immune from selective pressure.

He goes on to say that convergent evolution is an issue for both molecular and morphological theory to explain.  He gives the morphological example of the placental and marsupial wolves and gives analogous gene sequences as the molecular example.

So here are my thoughts on the subject so far:
First, if convergent evolution can produce similar genes, then how do we know what's convergent and what isn't?  How also can we tell the distance between analogous sequences - since they are so alike?

Second, molecular evolution is thought to take place at a fairly regular rate because it occurs at mostly neutral, non-coding sites; but what if there aren't any neutral sites (as new research may now show)?  The ENCODE study showed that most of the genome is being transcribed into RNA.  If this RNA is being used (which it most likely is), then isn't it also subject to selective pressure?  And if subject to selection, then wouldn't that pretty much throw the molecular clock right out the window?

Perhaps equidistant sequences represent saltational divergences which produced types whose core structures have changed very little genetically since, (possibly drifting back and forth within certain windows), while their peripheral structures evolved more freely within their own wider constraints.

Date: 2007/10/05 21:19:36, Link
Author: Daniel Smith
Quote (Reciprocating Bill @ Oct. 05 2007,06:38)
 
Quote (Daniel Smith @ Oct. 05 2007,04:24)
Which brings me to your questions of what genetic mechanism I would propose for designed descent.  First let me say that we have witnessed a saltational evolutionary event consistent with designed descent in our lifetime - the nylon bug.  That this was saltational is pretty straightforward since an entirely new enzyme was created in one step.  That the code for this enzyme was pre-existing also makes it consistent with designed descent.  I know most of you will probably disagree with my assessment of this, but I believe it could very well be a window into how saltational evolution could occur - especially as genomes are found to contain more embedded, overlapping codes.

Now you would have us include, among the pre-envisioned contingent environmental events for which the genome contains pre-planned, pre-sequenced adaptations, the entire history of cumulative human technological advances, particularly mastery of chemical and manufacturing processes that lead to the introduction of nylon in 1938, and its subsequent widespread use.

Which returns us to:    

"An omniscient supernatural being (an all knowing God) with foreknowledge of every environmental shift in every inhabited environment on earth over 3.8 billion years (shifts that resulted from everything from chaotic fluctuations in the sun's output to the Yucatan asteroid) front-loaded into the first prokaryotic life appropriate preplanned sequences of evolutionary transitions (adaptations, speciations, extinction events) for every one of the countless lineages of organisms that would descend from those first organism over those ensuing billions of years."

Does this fairly summarize your view? The "designer" pre-envisioned Dupont, and planned for it along with the Yucatan asteroid?

If you're going to make a list of everything an all-knowing God would know, you've got a long way to go.
(don't forget your birthday! ... and the number of hairs on your head, and ...)

Date: 2007/10/06 03:15:51, Link
Author: Daniel Smith
Quote (Reciprocating Bill @ Oct. 05 2007,21:25)
OK - but the question was: Does this fairly summarize your view?

Pretty close - yeah.  Of course, I'm not sure if the info was pre-loaded into one or many organisms.

You make it sound so far fetched, but remember, there was a time when it would have seemed far fetched to think that all the info that determines what you will be, and all the info that reveals where you came from, could be contained in one single cell - yet we now know that to be true.

Date: 2007/10/06 04:26:41, Link
Author: Daniel Smith
Quote (Alan Fox @ Oct. 05 2007,04:09)
           
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First, Schindewolf's stand on horse evolution is not well spelled out - and he only devotes a couple pages to it, so it doesn't really do his theory justice to use that example.  What I should have done was brought out his position on the evolution of cephalopods or stony corals - since these are his main areas of expertise and the subject to which he devotes probably a good third of his book.  So maybe we can shift gears as regards Schindewolf?


It does seem to boil down to how clear the evidence is that selective pressure to single toe was occurring before or after horse ancestors were in a savannah or plains environment. If you now concede this evidence is problematic and wish to look at molecular issues, why not start a new thread on the subject when you have marshaled your argument.

I'm not saying the evidence is problematic - just that Schindewolf doesn't say much about it.
I did find this:
           
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The global tropical forest type of ecosystem of the early Tertiary was disrupted by Late Eocene climatic changes, with the extinction of most archaic mammalian lineages and the appearance of most modern families. Later Tertiary trends reflect increasing aridity, with the appearance of open-habitat mammals such as grazing ungulates, although true grasslands probably did not appear until the Late Miocene in the New World and the Pliocene in the Old World....

The relative dryness of the Oligocene (68, 111), as well as evidence from mammalian dental and locomotor adaptations (136, 139, 140) and from paleosols (98), has led to the suggestion that savanna habitats existed in northern latitudes. However, although the faunas were more derived and probably occupied more open habitats than in the Late Eocene, the mammals appear to reflect a woodland rather than a savanna type of community(5 5, 128). The paleosol evidence can be reinterpreted as a dense "woody savanna," without underlying herbs and grasses, a type of vegetation that has no counterpart in modern floras (68).
TERTIARY MAMMAL EVOLUTION IN THE CONTEXT OF CHANGING CLIMATES, VEGETATION, AND TECTONIC EVENTS, Christine M. Janis, 1993 Annual Reviews, (Emphasis mine)(link)
   
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That this was saltational is pretty straightforward since an entirely new enzyme was created in one step.


Whilst mutation events are random, in that they are not predictable, some non-lethal mutations occur relatively frequently. Take the mutation that causes achondroplasia (dwarfism). This is a single-point mutation that produces dramatic and extensive changes in the phenotype of the individual with the mutation. This is the result of a single nucleic acid substitution in the genome, the smallest possible change that can happen. The mutation that occured in bacteria enabling them to digest nylon is thought to be a frame shift, caused by the addition or deletion of one* nucleotide. Again the change is as small as can happen, but the consequences are huge, and often catastrophic.

If you define this as saltation then all mutations are saltations.

(* or a larger no. not divisible by three)

(Added in edit)

"Saltational" (to my mind) refers to the results - not necessarily the cause.  Dwarfism is morphologically saltational even though it has the smallest of causes.  The same with the frame shift that caused the nylon bug.
If (as I'm alleging) genomes are replete with embedded codes just waiting for a signal, such as a frame shift, to set them in action, then a saltational change can happen with just one substitution.  These substitutions would be non-random of course.
   
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PS: If I were to play Devil's advocate, I might suggest you have a look at transfer-RNA, and how each specific t-RNA could have evolved to carry its own particular amino acid. :)

I just downloaded most of the ENCODE articles and will be spending quite some time trying to digest them.  I don't know if I'll have time for another rabbit trail!

Date: 2007/10/06 04:40:41, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Oct. 06 2007,04:01)

As we've now sequenced some organisms, is it your belief that evidence for "front loading" is present in these sequences waiting to be found?
Yes.    
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If so, how do you propose going to look for it?
I don't know.  It would be difficult to foresee usefulness.  (Although the ENCODE study does mention a "large pool of neutral elements" that "may serve as a 'warehouse' for natural selection".)
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In the case of flavobacterium Sp. K17 (nylon eating bacteria) would it be logical to expect that if we sequenced "older" versions of the bacteria that the sequences required for making nylonase would be found, even though they were not enabled in that particular strain?

That would be logical.    
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If not, what exactly do you mean by "front loaded" if not "contains instructions for dealing with future events"?
That's pretty much exactly what I mean.    
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EDIT: Oh, here is "Answers in Genesis" take on it
     
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It seems clear that plasmids are designed features of bacteria that enable adaptation to new food sources or the degradation of toxins. The details of just how they do this remains to be elucidated. The results so far clearly suggest that these adaptations did not come about by chance mutations, but by some designed mechanism. This mechanism might be analogous to the way that vertebrates rapidly generate novel effective antibodies with hypermutation in B-cell maturation, which does not lend credibility to the grand scheme of neo-Darwinian evolution.11 Further research will, I expect, show that there is a sophisticated, irreducibly complex, molecular system involved in plasmid-based adaptation—the evidence strongly suggests that such a system exists. This system will once again, as the black box becomes illuminated, speak of intelligent creation, not chance. Understanding this adaptation system could well lead to a breakthrough in disease control, because specific inhibitors of the adaptation machinery could protect antibiotics from the development of plasmid-based resistance in the target pathogenic microbes.


Try to avoid sounding like them huh?

Link

Never read that, but I can't say that I disagree with it.

Date: 2007/10/06 19:15:53, Link
Author: Daniel Smith
Quote (JAM @ Oct. 05 2007,10:05)
Why not grow some balls and make a prediction instead of hiding from the evidence and making assertions?

How about this?

I predict that sometime in the near future, the idea that evolutionary constraint is evidence of the functionality of a given sequence - will have to be abandoned.

You can add that prediction to the list I've already posted.

Date: 2007/10/06 19:55:36, Link
Author: Daniel Smith
Quote (Reciprocating Bill @ Oct. 06 2007,07:42)
 
Well, I've stated your thesis, and you've ruled it "pretty close" to summarizing your own views - yet also say that it "sounds far fetched."

I submit to you that I haven't made it "sound" far fetched. It simply IS far fetched.  

And, Daniel, speaking to your preference for outliers and scientific rebels, "being far fetched" is NOT a positive argument - particularly when you YOURSELF find that your position defies credulity when it is compactly stated.

You have a way of misinterpreting the meaning of my words.  I didn't say "it sounds far fetched" I said "You make it sound so far fetched".

There's a difference.  

Nowhere did I say it defies credulity, nor do I think that it does.  I think the evidence for design in both the universe and in life's systems is overwhelming.  We are discussing intricate, networked, molecular coding systems that define sophisticated, self-replicating machinery (though the term 'machinery' does not do it justice).  We are talking about cellular systems more complex, more orderly, more efficient, more multi-functional, than anything man can ever hope to invent.  Even the simplest self-replicator had to be more complex than anything man has ever built.  

I work on complex machinery for a living and I see the results of many years of engineering diligence up close and personal every day, yet nothing I've seen at work compares with the type of engineering I've seen in even the simplest bacterial systems or in something as taken-for-granted as the human auditory system.  The more I learn about such systems, the more amazed I am at the mind of God.

Yet you seem fine with dismissing such obvious ingenuity with a simple wave of the hand.  Opting instead for this fairy tale of how happy accidents and the seemingly all-powerful, semi-intelligent, forward-thinking force called "natural selection" designed such complicated efficient structures.

It may sound far fetched to you, that such systems are designed, but it doesn't seem that way at all to those of us who believe in God, nor does it contradict anything we know about designs and designers.

I submit to you that the basis of your objections are not scientific, but atheistic.  Science is your main defense against those pesky thoughts of God that keep popping into your head, and you must do everything in your power to make sure that science cannot reach anything other than atheistic conclusions.

Date: 2007/10/06 20:10:00, Link
Author: Daniel Smith
Quote (JAM @ Oct. 06 2007,19:27)
   
Quote (Daniel Smith @ Oct. 06 2007,19:15)
     
Quote (JAM @ Oct. 05 2007,10:05)
Why not grow some balls and make a prediction instead of hiding from the evidence and making assertions?

How about this?

I predict that sometime in the near future, the idea that evolutionary constraint is evidence of the functionality of a given sequence - will have to be abandoned.

You can add that prediction to the list I've already posted.

Daniel,

None of those represent what scientists mean by predictions. Scientific hypotheses don't make predictions about what ideas people will have; they make predictions about the results of discrete experiments or observations that have yet to be made.

Here is an example of testing a series of predictions in evolutionary biology (not my field). The last paragraph is probably the clearest example.

IOW, you don't have the balls to do it yet. Front-loading makes plenty of predictions, but you're afraid to.

The concept of evolutionary constraint (as I understand it) is based on the theory that mutations are generally rejected in functional sequences because they are usually deleterious, but mutations in neutral sites are not rejected.  Therefore the sequences that have remained alike (are constrained) across related lineages can be inferred to be functional while those that have changed a lot are inferred non-functional (neutral).
My prediction is that there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.
So when I say evolutionary constraint as an indicator of functionality will have to be abandoned, I am expecting my prediction to be experimentally verified.

Date: 2007/10/07 05:17:26, Link
Author: Daniel Smith
Quote (Reciprocating Bill @ Oct. 06 2007,20:48)
At any rate, your position is that God is the author of the world, including the biological world, in all of its detail, complexity, and apparent design. I appreciate that frankness; so often advocates of ID are coy to the point of dishonesty about the commitments that motivate their position.

However, that isn't a notion amenable to scientific investigation, because God can do anything, in any order, at any time, outside the constraints of natural law, and hence no empirical test can be devised to put this notion to empirical test. This simple fact leaves us no choice but to pursue biological and evolutionary science within the constraints of methodological naturalism, regardless of the personal spiritual beliefs of the investigator. Fortunately this powerful epistemology has yielded countless active and productive lines of research that daily increase our understanding of the history and nature of the biological world - including the facts we all find quite astounding.

I sympathize with your frustration over my "goddidit" explanation.  I feel the same way about natural selection:  Often NS is presented as if it can do anything and everything.  If something works, it's because of natural selection; and since pretty much everything works, natural selection becomes this all-powerful entity that can build anything - a lot like God.  In fact the two are essentially interchangeable - they both explain everything and therefore explain nothing.
What's needed are direct observations.  But since we cannot directly observe God or macroevolution, we must look at what we can observe and see if it matches the evidence.  Fortunately for us, natural selection can be observed.  Natural selection needs to be put to the test to assay it's capabilities in the real world.  This is why I have so much respect for scientists like Leo Berg: he spent years, up to his waist, in rivers and streams, observing natural selection in action.  He felt that it was not up to the task.  How many scientists today experimentally verify the ability of NS to produce or conserve innovations?  Probably not many since most take it's capabilities for granted.

Also, when people say that science cannot investigate God or the supernatural, that's not entirely correct.  Science can (and does) investigate claims of supernatural activity - so long as the supernatural activity is supposed to have affected the physical world.  If for example, someone claims that "a ghost" is moving a chair, science can investigate and see if the evidence fits the claim.  More than likely, science will find that some other force is actually moving the chair (if it moves at all), but sometimes they might find no natural explanation.  They can then conclude that the evidence does not rule out the ghost explanation - though they can never actually verify that it is really a ghost.
The same goes for design theories.  If these theories make claims that God affected the natural world, the evidence (the natural world) can be examined to see whether or not it is consistent with such claims.  
One thing that design theories pretty much all do is use the most observed designer - man -  and his designs as a template for what they expect to find when looking for design in nature.  That's what I do.  Of course, if the design theory postulates a God of infinite intelligence, it would expect to find designs that are infinitely more sophisticated than man's.  This is what I expect as well.
So when I examine the evidence, is that what I find?  Yes, that is exactly what I find.  I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on.  Does that mean that science has proven there is a God?  No, it only proves that the physical world is consistent with the design theory and that it cannot be ruled out.
Are such systems within the capabilities of RM+NS?  You tell me.

Date: 2007/10/07 05:46:59, Link
Author: Daniel Smith
Quote (JAM @ Oct. 06 2007,20:52)
         
Quote (Daniel Smith @ Oct. 06 2007,20:10)
The concept of evolutionary constraint (as I understand it) is based on the theory that mutations are generally rejected in functional sequences because they are usually deleterious, but mutations in neutral sites are not rejected.  Therefore the sequences that have remained alike (are constrained) across related lineages can be inferred to be functional while those that have changed a lot are inferred non-functional (neutral).
My prediction is that there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.

Daniel,

Much better! I retract and apologize for my insult; it was mainly a strategy to get you to respond in a coherent way. It's also an example of how hypotheses yield new data even when they are incorrect.

The main criterion you're missing is that you need to apply your hypothesis to something more specific. I'm here to help.

One clarification--when you wrote "functional sequences," you meant groups of sequences with the same or similar biological function(s), correct?
             
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So when I say evolutionary constraint as an indicator of functionality will have to be abandoned, I am expecting my prediction to be experimentally verified.

Luckily for you, the "experiment" has already been done. The scientific method works even when the data already exist--the power of the method is in the prediction. Shall we sample a protein family or ten? Any functions that you find particularly interesting?

I think that I need to clarify my position before we can decide how best to test it.

When I say "functional sequences" I mean functional as in "used within the cell".  By this definition, I'd say that anything that is transcribed would qualify as functional - since the cellular machinery is going through the trouble of transcribing it.  So this would include protein coding sequences as well as ncRNA sequences, and anything else that's transcribed.

I also must clarify that I do actually believe that all functional sequences (as I've defined them) are evolutionarily constrained.  It's just that I don't think you can find functionality or constraint by comparing sequences to other lineages (since I posit that there are no truly neutral sites).  If comparing to other lineages, the function must first be known and then the entire sequence that provides that function compared.  However, the only true test of constraint is comparison to ancestral DNA within the same lineage.  

So, with that in mind, how do we go about testing this?

Date: 2007/10/07 05:59:45, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Oct. 07 2007,05:43)
 
Quote (Daniel Smith @ Oct. 07 2007,05:17)
If these theories make claims that God affected the natural world, the evidence (the natural world) can be examined to see whether or not it is consistent with such claims.

Excluding biology for a moment, what other evidence do you claim also shows this proof? Everything?
You say
 
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So when I examine the evidence, is that what I find?  Yes, that is exactly what I find.  I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on.

Is this level of detail also to be found, for instance, in rocks? The sun? The solar system?

Daniel, when you say
 
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design theories pretty much all do is use the most observed designer - man -  and his designs as a template for what they expect to find when looking for design in nature

Can you apply that template to non-biological entities also?

If so, do you have an example?

If not, well, do you claim there was one designer for biology
one for the mountains
one for the seas
one for the coastline of denmark?

etc etc?

I think similar levels of detail can be found in the earth's various systems in regards to their near perfect fitness for life.  Also, the cosmos, the sun, the moon, all these things are so arranged and physical properties so ordered as to be perfect for life on this planet as well.  Certainly atomic principles and the composition of matter and energy are also remarkable.  The properties of water, carbon, oxygen, hydrogen, light, gravity, etc. are all things which appear to behave as if planned out in advance for the purpose of life on this planet.  I can't think of anything that just appears to be random.  Can you?

So I guess my example would be to compare a human laboratory - where man provides a controlled environment for certain lifeforms to reside - to the earth and its environment.

Date: 2007/10/08 02:18:57, Link
Author: Daniel Smith
Quote (JAM @ Oct. 07 2007,13:27)
           
Quote (Daniel Smith @ Oct. 07 2007,05:46)
I think that I need to clarify my position before we can decide how best to test it.

I feel a breeze.
             
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When I say "functional sequences" I mean functional as in "used within the cell".

That works for me.
             
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By this definition, I'd say that anything that is transcribed would qualify as functional - since the cellular machinery is going through the trouble of transcribing it.

That is a prediction of an intelligent design hypothesis, but MET (non-Darwinian) predicts that there will be loads of RNA that has no function.

Then this is what we need to test.
             
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So this would include protein coding sequences as well as ncRNA sequences, and anything else that's transcribed.

But if we find anything that's transcribed but not functional, your hypothesis is dead, correct?

As for my hypothesis being "dead" if we find anything that conflicts with what I've predicted:  I don't really think that's fair since scientists are constantly finding things they don't expect and simply adjust their hypotheses to fit the evidence when they do.  I will not therefore totally abandon my hypothesis if the results are different, I will simply adjust it (unless the results completely shoot it out of the water).
             
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I also must clarify that I do actually believe that all functional sequences (as I've defined them) are evolutionarily constrained.  It's just that I don't think you can find functionality or constraint by comparing sequences to other lineages (since I posit that there are no truly neutral sites).

What if some sites have far greater rates of change over time, Daniel?

This is precisely the issue.  How do we know the rate if it turns out that there are no neutral sites?  We must first determine that these sites are truly neutral and are actually accumulating mutations.
             
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What sequences are used for forensic DNA analysis?

That's a tough question, and I'm not sure I know the best answer for that.
             
Quote

             
Quote
If comparing to other lineages, the function must first be known and then the entire sequence that provides that function compared.

Not a problem.
             
Quote
However, the only true test of constraint is comparison to ancestral DNA within the same lineage.

Oh-oh...it looks like I'm going to have to retract my retraction. Your prediction:              
Quote
there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.

makes clear predictions about the relationships between modern sequences. No ancestral sequences are required.

I'm not backing off my original prediction, but I think certain terms mean different things to both of us, so I'm just trying to clarify.

I believe that most (if not all) sequences in a genome are functional and therefore resistive to mutation (constrained).  This means there are no neutral sites that are accumulating mutations.

I also believe that macroevolution (when it happens) is not the result of accumulating mutations but is rather; saltational - that is - it creates new types that may have sequences that are radically different from the sequences from which they diverged (hence my earlier prediction).

Therefore, this is what I expect:

1.  Sequence comparisons between related lineages will result in a mixture of like and unlike functional sequences.  

2.  Sequence comparisons within the same lineage will show evolutionary constraint across the board - even in what are presently considered neutral sites.

3.  What are presently considered neutral sites will be found to be "instructional" - that is, they will carry the instructions that tell the various proteins, RNA and enzymes where to go, when to go and what to do when they get there.

Now, the third prediction is more of a guess, but I think it makes sense.  We know about sequences that code for proteins, and we know about sequences that regulate them, but we don't know how a certain protein "knows" where to go, what to do and when to do it.  My guess is that these instructions are carried in what are presently considered neutral sites and - for that reason - these sites resist mutations just like all other evolutionarily constrained sites.

I hope that's clearer.

Date: 2007/10/08 02:34:19, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Oct. 07 2007,06:25)
 
Quote (Daniel Smith @ Oct. 07 2007,05:59)
I think similar levels of detail can be found in the earth's various systems in regards to their near perfect fitness for life.  Also, the cosmos, the sun, the moon, all these things are so arranged and physical properties so ordered as to be perfect for life on this planet as well.  Certainly atomic principles and the composition of matter and energy are also remarkable.  The properties of water, carbon, oxygen, hydrogen, light, gravity, etc. are all things which appear to behave as if planned out in advance for the purpose of life on this planet.  I can't think of anything that just appears to be random.  Can you?

So I guess my example would be to compare a human laboratory - where man provides a controlled environment for certain lifeforms to reside - to the earth and its environment.

Well, what about the rest of the known universe. In the entire volume of the known universe this planet hosts the only known lifeforms.

Therefore the composition of "matter and energy" may seem remarkable to you for hosting life as we know it, but to me it seems more remarkable that this same matter and energy configuration appears to only host that life at one particular locus. Why would that be, if that configuration is explicitly designed to foster life as we know it?
More remarkable is the lack of ET then the finding of it here, if indeed our particular solar system is designed and the rules are designed, why not the planet next door? Why is Mars not thriving? It's very earth like, at least as good as we're gonna get anytime soon in person. Hollywood are already there!

If it was all planned out in advance, why for only 1 planet in the known universe?

We've started to identify details about extrasolar planets now. Photos even.

What does your theory say about life elsewhere in the universe? Predicts it? Y/N?

I suppose what I'm really asking Daniel, is do you consider the entire known universe intelligently designed for the purpose of hosting life on this planet?

I mean, if the solar system is designed, why stop there?

If it is designed, then why did it appear to end there?

I know it sounds like a cop-out but all designers make choices that many of us don't understand.  If we cannot directly ask a designer why they made certain choices, the best we can hope for is to examine their designs and try to make an educated guess based on what we observe.  

I can't do any more than guess as to "why" God did what he did, but my best guess is that he made life rare in the universe so that; as we delve more deeply into it's intricacies, we might become more keenly aware of the delicate and highly improbable balances required for it's mere existence and might be more deeply in awe of the mind that created - not only life - but the very conditions in which it thrives.

As for there being other lifeforms on other planets; we've already covered that in this thread and I made a couple predictions:

1.  That we won't find other planets with life on them.

and (to cover my butt),

2.  If we do find life elsewhere it will be remarkably similar to life on earth.

Date: 2007/10/08 03:22:07, Link
Author: Daniel Smith
Quote (Reciprocating Bill @ Oct. 07 2007,08:14)
         
Quote (Daniel Smith @ Oct. 07 2007,06:17)
Also, when people say that science cannot investigate God or the supernatural, that's not entirely correct.  Science can (and does) investigate claims of supernatural activity - so long as the supernatural activity is supposed to have affected the physical world...

This passage is correct, and also encapsulates the challenge you have set for yourself. I'll sharpen my earlier statement to reflect your comment: "The existence of God is not amenable to scientific investigation, because God can do anything, in any order, at any time, outside the constraints of natural law, and hence no empirical test can be devised to verify God's existence. However, specific claims regarding God's actions in the physical world can be put to empirical test."

One source of assertions regarding God's actions has been the Bible, which makes very specific, testable claims about the world as God created it (e.g. the age of the earth) and his actions within the world (creation of animals and human beings ex nihilo a few thousand years ago; a subsequent world wide flood). One reason why friction has arisen between those who are inclined to Biblical literalism and the advances of the natural sciences is that many Biblical claims about the actions of God CAN be tested, have been tested, and have been found to be obviously false.  
I am not as quick to abandon biblical claims as you might think, since many biblical claims have not been proven false.  For instance the biblical claims about death and disease, war and poverty, human childbirth, even weeds, all still hold true today.  But that's another subject.          
Quote


However, you are not drawing from Biblical claims about God's actions (although I gather you once did). Your claims are much more sophisticated, and concern the origination of the astounding complexity we observe in the biological world. You don't find current theory about the origination of such complexity believable (for reasons you are happy to enumerate). You claim, instead, that the emergence of biological complexity was accomplished by an all knowing God.

Here you've already gone much beyond the claims of the intelligent design movement generally, as represented by Behe, Dembski, Meyer etc.  They have carefully avoided publicly speculating about the identity and nature of the designer, and have repeatedly declined to make any claims whatsoever regarding the designer's characteristics, modes of action, etc. Because they have been unwilling to propose a model of the design or of the designer, and claim they are solely interested in design detection, that brand of ID has been utterly incapable of generating unique testable predictions about future empirical findings, and fails to rise to the level of a an empirical science.
I can't speak for them but I suspect their reluctance is due to the fact that they are trying to make their theory fit into the realm of naturalistic science - and thus they feel they can't identify the designer as God.
I feel differently.  I feel that we can speculate about how the "mind of God" has affected the physical universe and make testable predictions based on those speculations.          
Quote


You've identified the designer. God is the designer. You've also offered some speculations about the manner in which he originated design: he did it by means of "front-loading" information into the genome or genomes of one or more early organisms, front-loading that reflected foreknowledge of the history of the world in all of its detail, as I described above. You see the outcome of that designer's actions in nature - "I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on."

OK, now a careful distinction: "Complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management" are the phenomena that (you say) still demand explanation.
Yes that's true.      
Quote
Your explanation is that these complex systems were designed by an all knowing God.
Yes that's true also, but I went beyond that - since I first pointed out their analogous qualities with known designs - thereby establishing the precedent of the designer/design as a workable, observable explanation for such systems.      
Quote
I think you can see that it would be circular to then point to those self-same "complex intricate systems" as proof that your explanation for their existence is correct - those complex systems that so amaze us all are the very phenomena that call for explanation in the first place. Poring over and expressing amazement at biological complexity, even if that complexity has been elucidated by science, is not itself a scientific activity.  
That's true, but I've done more than that:  I've suggested a source - an all knowing God that (as you say) "can do anything, in any order, at any time, outside the constraints of natural law", and I hope to show that the evidence actually requires such a being.
I believe that any unbiased look at all the requirements for life on this planet will lead any honest person to rule out chance as a cause.  We are then left with only non-random causes.  My argument is that - once we get to that point - if we examine the delicate balances that exist in nature, and all the intricate complexities of the literally trillions of systems involved in life, a mind of infinite intelligence is the only logical, non-random cause for all of this.      
Quote


Rather, to rise to the level of a scientific assertion, your model must make testable empirical predictions that uniquely "put your theory at risk." That is, you must formulate predictions regarding future empirical findings that, if disconfirmed, indicate that the model from which those predictions arose must be modified or discarded. Because you have already asserted that the designer is an omnipotent, all knowing God, you have put yourself in the position of having to make specific predictions regarding God's actions in the world, predictions with power to put your model at risk of disconfirmation.

I think you will agree that this is a problem. It is inherent in the definition of any "God" of sufficient capability to set the entire universe into motion that there are no limitations upon his activities. As I stated earlier, God can do anything, anywhere, anytime, without constraint of the laws of physics. He even specified the laws of physics themselves. Given that, any empirical finding regarding his proposed actions in the world would appear to be compatible with the God hypothesis. Hence it falls to YOU, as you formulate your model of the origins of biological complexity in a scientific manner, to make statements about God's characteristics of sufficient specificity to predict future empirical findings regarding his actions in the world. These assertions must limit God's scope in some way, either based upon constraints (God can do this, but he can't do that) or upon other more intentional characteristics (God would do this, but wouldn't do that). It falls to you to do this before making the relevant observations, in such a way that subsequent disconfirmation would prompt you to conclude, "God does not have the characteristics I proposed."

That's a tall order. In a some respects you've already made some such assertions, although you haven't described how they arise from a specific model of God, or how to test them. Nevertheless, since front-loading is an action in the world, it is potentially testable. I could easily generate some unique testable predictions regarding future empirical findings that arise from front-loading. However, because I find front-loading implausible for reasons I have already described and believe such tests are likely to be a waste of time, it falls to YOU to devise unique empirical predictions that put your theory at risk and then conduct the relevant tests. Ideally, your predictions would put your assertions about God's actions in the world, and hence his characteristics, at risk, as well.

You've got your work cut out for you.

You are right - and I'm feeling the pressure!

Date: 2007/10/08 03:23:34, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Oct. 08 2007,02:57)
Quote (Daniel Smith @ Oct. 08 2007,02:34)
I know it sounds like a cop-out but all designers make choices that many of us don't understand.  If we cannot directly ask a designer why they made certain choices, the best we can hope for is to examine their designs and try to make an educated guess based on what we observe.

Then please make an educated guess as to the reason for the huge variety of beetle species.

God likes beetles?

Date: 2007/10/08 03:32:39, Link
Author: Daniel Smith
Quote (jeannot @ Oct. 07 2007,13:47)
 
Quote
there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.

That's unclear. How will you know that differences are not the result of mutations? Drift, positive selection and negative selection can lead to different level of divergence between regions.
And what to you mean by "being of designed origin"? Do new genes appear (from God knows where) instantaneously in a lineage? Or were they front loaded in the first cell?

Good questions.
The only fool-proof way to know if differences in sequences are the result of mutations is to study sequences for long periods of time within the same lineage and see if certain areas drift or are changed due to selection.  We can ascertain differences between lineages, but we can't be sure of the mechanism that produced the differences.
As for new genes.  I'd say that at least the template for them was front loaded into the root of every lineage - whether that means one common ancestor or many.

I suspect that that is one of the reasons the entire genome is transcribed - to error check and keep intact these templates.  Another guess.

Date: 2007/10/08 04:27:27, Link
Author: Daniel Smith
Quote (mitschlag @ Oct. 07 2007,06:09)
You are the scientist, DS.  You are responsible for devising the test.

Well, I'm not a scientist, but I think I've got an idea for a test:

Take two members of the same species that have been geographically and reproductively isolated for a long period of time (the longer the better), sequence their genomes and compare them.

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.

Date: 2007/10/09 21:27:29, Link
Author: Daniel Smith
Quote (Steverino @ Oct. 08 2007,06:59)
While it may not be a cop out, it's BULLSHIT.  It's based on the premise that when we see gaps of information, you feel that God should be included in the discussion until proven otherwise.

No, I'm actually giving God credit for everything - not just the gaps.  You might want to go back and catch up on the previous 10 pages before you jump in and post.

Date: 2007/10/10 02:25:00, Link
Author: Daniel Smith
Quote (Henry J @ Oct. 09 2007,15:59)
Is there a limit on nesting of quotes? I don't see any apparent syntax errors in that last note, but some of the quotes didn't take for some reason.

Henry

There seems to be.  I had the same trouble with an earlier reply and could only rectify it by eliminating some quotes.

Date: 2007/10/10 02:30:35, Link
Author: Daniel Smith
Quote (mitschlag @ Oct. 08 2007,07:02)
   
Quote (Daniel Smith @ Oct. 08 2007,04:27)
Take two members of the same species that have been geographically and reproductively isolated for a long period of time (the longer the better), sequence their genomes and compare them.

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.

Please define "evolutionary constraint."

Predict the expected results that would falsify your hypothesis.

I am using the term "evolutionary constraint" to mean a sequence that resists or rejects mutations.
As I understand it, this is the common usage of the term.

The results that would falsify my hypothesis would be if the coding sequences showed evolutionary constraint while the non-coding sequences didn't.

Date: 2007/10/10 03:17:09, Link
Author: Daniel Smith
Quote (JAM @ Oct. 09 2007,18:19)
             
Quote (C.J.O'Brien @ Oct. 09 2007,17:12)
               
Quote
So when I examine the evidence, is that what I find?  Yes, that is exactly what I find.  I find complex intricate systems analogous (but far superior) to power plants, factories with automated assembly lines, communication networks, super highway systems, waste management (with recycling!), and on and on.

Bob O'H already made this point, but at some length.
For concision: None of that is evidence in the scientific sense. It's a restatement of the question in explicitly teleological terms. To consider this evidence (the result of empirical investigation beyond a cursory glance) is to beg the question.

Not only that, but most of it is false.

If our superhighway systems were anything like the cell's, trucks crashing into each other (combining their cargos), useless detours, and multiple tractors on the same cargo trailer pulling in different directions would play an integral role in every journey.

If human-designed waste management systems were designed analogously to the cell's, we'd have 20% raw sewage in our drinking water and call it delicious.

The amazing thing is that when you work in these fields, you see massive teleological biases among the scientists, so that extra data are required to overcome these analogies.

I've not seen any descriptions of any biological functions that come across as haphazard and random as you describe them.  In fact I find the opposite to be true.  Whenever I learn the details of how a biological system functions, I'm struck by the sheer brilliance of the system's design (and I'm not going to creationist sources for this info).
Take the process of protein synthesis for example.  Please explain how that process is just a hodgepodge of cobbled together mish-mash that somehow, almost by accident, gets the job done.
Or explain how the brain is just a random lucky accident, or the various visual systems, or the mammalian kidney, or the avian lung, or the central nervous system, or all the various systems of flight, or any other system.  In fact, I challenge you to provide details of how any biological system is just a cobbled together hodge-podge.

Also, explain to me how the qualities observed in an object are not evidence that can be used to determine the object's origin?

What evidence leads us to believe that Stonehenge is designed - if not the qualities of Stonehenge itself?  Do we say it is designed because there were people in the area at that time?  No.  If we did, we'd have to say that every rock, every stone, in fact everything is designed if there are people in the area at the time.  No, it's the organization of the stones and the fact that that organization is analogous to the organization of other designed objects (such as tables, chairs and benches) that leads us to believe that Stonehenge was designed.  This organization is a quality of the object in question - the object that needs explaining.  Yet we can certainly use these qualities to deduce design here.  Why not elsewhere?

Are the qualities of "the thing that needs explaining" and analogies excluded also from random or naturalistic explanations?  Do you not observe the makeup of the organism in question when trying to discern its origin?  Do you not compare the qualities of one object with another?  Do you not say that this sequence is like that one?  Is this not analogy?  If not, then what is it?

And if statements such as mine are not evidence, then why is this statement not challenged equally as vigorously?        
Quote (C.J.O'Brien @ Oct. 09 2007,17:12)
When you actually get in depth and look at some of that cellular machinery, Daniel, you'll see that it does not resemble at all the products of a rational design process. It rather resembles a Rube Goldberg-type cobbled-together mess eerily similar to the sorts of engineering solutions arrived at by evolutionary algorithms.


In short, analogies are a form of evidence.  I'm guessing that you just don't like the fact that I'm comparing biological systems to designed systems.

Date: 2007/10/13 13:22:40, Link
Author: Daniel Smith
Quote (Wesley R. Elsberry @ Oct. 12 2007,07:35)
ISI's Web of Knowledge says, on search for "linkage disequilibrium" in papers of the last 5 years,

 
Quote

9,966 results found


Hmmm. The crickets seem to have come out.

I've been trying to wrap my head around the concept of linkage disequilibrium but am not having much luck.  It's a bit over my head - which is why I haven't responded to your post yet.  Perhaps if you could explain the concept in layman's terms I could give you an answer.  Either that, or you'll have to wait awhile.

Date: 2007/10/13 13:50:05, Link
Author: Daniel Smith
Quote (Erasmus @ FCD,Oct. 10 2007,07:36)
Daniel we know people make things like stonehenge.

What designer do we know of that makes cells and platypi and the grand canyon?  People?  Or something else?  I'll wait for your answer.
That's Right!!!!  We don't know of any such designer!!!  You Lose!!!

I'm proposing that the designer is not human but has qualities similar to human qualities (intelligence, free agency, etc.).

I am proposing this entity has infinite intelligence and that it would require intelligence of that kind to design the universe and life.

IOW, if all this is designed (including us), whatever designed it is as far above us intellectually as the cosmos are above us physically.

Date: 2007/10/13 13:53:22, Link
Author: Daniel Smith
Quote (mitschlag @ Oct. 10 2007,12:47)
 
Quote (Daniel Smith @ Oct. 10 2007,02:30)
The results that would falsify my hypothesis would be if the coding sequences showed evolutionary constraint while the non-coding sequences didn't.
There's a fair amount of evidence showing that (contrary to expectation) non-coding sequences have fewer base changes than coding sequences, see, for example:
http://www.biomedcentral.com/1471-2148/7/66
   
Quote
The primary result is that the mean rate of intergenic nucleotide substitution is two-thirds that of the synonymous coding data, with an absolute rate estimated to be 1.05 × 10-8 substitutions per site per year. This result holds with alternative nucleotide models (see Methods), and thus does not appear to be solely an issue of estimation procedures.

Slower rates in non-coding regions relative to synonymous sites are becoming a surprisingly frequent observation. For example, a recent study of Drosophila demonstrated that non-coding DNA evolves considerably slower than synonymous sites in terms of both divergence between species and polymorphism within species [16]. By comparing studies, one can also make the case that pseudogenes [32,33] and introns [34,35] evolve more slowly than synonymous sites in apes and other mammals [13,36-38]. Studies of mammalian intergenic regions have also found slower rates than synonymous sites [35,39,40]. Although most of these studies encompass only a handful of genes, an overall picture of relatively slow non-coding rates is emerging.

What do you make of that?

If this is true, then it would be a confirmation of my hypothesis with better than expected results.

Date: 2007/10/13 14:00:39, Link
Author: Daniel Smith
Quote (JAM @ Oct. 10 2007,10:40)

Here's an opposing hypothesis:

Known functional sequences will be evolutionarily conserved. Most sequences will not be conserved. We will continue to find functions for some conserved sequences for which no function has been identified.

What do you think? Shall we look at the evidence to see which hypothesis is better supported?

Yes, let's look.  But be warned, I'll be approaching the evidence from a different perspective than you and won't accept any preconceived ideas as part of the interpretation.  What I mean is that the perceived "rate of mutation" is often calculated by a comparison of species that are assumed to have evolved from a common ancestor via an accumulation of random mutations.  Since I am opposing that theory, I won't accept that assumption.  You must show me that the evidence supports this assumed buildup of random mutations first, then we can move on from there.

Fair enough?

Date: 2007/10/13 14:17:56, Link
Author: Daniel Smith
Quote (JAM @ Oct. 11 2007,11:00)
 
Quote (Daniel Smith @ Oct. 08 2007,02:18)
3.  What are presently considered neutral sites will be found to be "instructional" - that is, they will carry the instructions that tell the various proteins, RNA and enzymes where to go, when to go and what to do when they get there.

This is testable. It makes clear predictions about what will happen when we remove the nucleus, for example by cutting off a part of the cell with a laser, creating a cytoplast, or if we sever the axon tethering a neuronal growth cone to its cell body.

It predicts that these proteins will no longer "know what to do." Do you agree, Daniel?

Well, I'm not sure what affect removing the nucleus would have on existing, functioning proteins - since they should already know what to do.  If however, you were able to remove non-coding regions (by this I mean supposed neutral sequences) while leaving the coding sequences intact, then (according to my prediction) the proteins produced would not know what to do.

Date: 2007/10/13 14:41:49, Link
Author: Daniel Smith
Quote (C.J.O'Brien @ Oct. 10 2007,12:35)
That there is a certain kind of elegance to biochemical processes is not in question. They work well enough to have sustained evolving life on Earth for billions of years, and are perfectly capable of supporting the functions of big, complex animals like ourselves. So I am not saying that they barely "get the job done." I am saying, though, that all of the highly-touted complexity of the cell, when it is actually investigated, not simply remarked upon, seems to owe its existence to a maddeningly short-sighted designer --one that seems incabable of building a structure or pathway using anything other than pre-existing components, often themselves integral parts of other, fully functioning systems. But you challenged me for examples.

Here is Ken Miller on the vertebrate blood-clotting cascade

Here is a TalkOrigins summary of several articles on the evolution of the Krebs Cycle

Here is an abstract of a Science paper on the evolution of a steroid-hormone receptor

The articles and abstracts you cite are just explanations of how such systems theoretically could have evolved - not evidence that these systems are cobbled together "Rube Goldberg" type systems.

I found this item from the article on blood clotting interesting:  
Quote
If the modern fibrinogen gene really was recruited from a duplicated ancestral gene, one that had nothing to do with blood clotting, then we ought to be able to find a fibrinogen-like gene in an animal that does not possess the vertebrate clotting pathway. In other words, we ought to be able to find a non-clotting fibrinogen protein in an invertebrate. That's a mighty bold prediction, because if it could not be found, it would cast Doolittle's whole evolutionary scheme into doubt.

Not to worry. In 1990, Xun Yu and Doolittle won their own bet, finding a fibrinogen-like sequence in the sea cucumber, an echinoderm. The vertebrate fibrinogen gene, just like genes for the other proteins of the clotting sequence, was formed by the duplication and modification of pre-existing genes.

This prediction does not seem that "bold" to me - since we already know that convergent evolution produces analogous sequences in unrelated animals.  In fact, I'll be even bolder and predict that you can take any gene and find something "like it" somewhere in some unrelated organism's genome.

Date: 2007/10/13 14:58:37, Link
Author: Daniel Smith
Quote (JAM @ Oct. 13 2007,13:49)
Maybe while you're trying to wrap your head around linkage disequilibrium, you can point us to a designed mechanism involving large numbers of similar, but not identical, parts, that have only partially overlapping functions.

That mechanism would be analogous to living ones.

So we're accepting analogies as evidence now?  
Quote


Also, you can directly test your hypothesis that noncoding regions are conserved by peeking at the VISTA genome browser:

http://pipeline.lbl.gov/cgi-bin/gateway2?bg=hg16

You're not gonna like what you see, so you probably should blow it off and not try to grapple with any real evidence. Here's an idea--pretend that our calling you out on your false claims is mean, which automatically makes your false claims correct (at least in your mind).

I went to the vista site, but I'm not sure how to use it.  I'll have to read the help file I guess.

BTW, you are generally mean - but I'm still here.
Your meanness has nothing to do with your rightness.

Date: 2007/10/13 15:02:51, Link
Author: Daniel Smith
Quote (Wesley R. Elsberry @ Oct. 13 2007,05:23)
The "edit" and "quote" buttons are right next to each other.

I see no "Edit" button with my browser (Mozilla Firefox).  All I see is a question mark (?) next to the "Quote" button - even on my own posts.

Date: 2007/10/13 15:07:47, Link
Author: Daniel Smith
Quote (jeannot @ Oct. 13 2007,14:57)
Daniel, you still need explain what your hypothesis is.
You merely provided one prediction, which is a totally different thing. Without your hypothesis clearly detailed, a prediction is useless.

I still don't see why you'd expect similar "evolutionary constraint" in coding and non coding sites.

Because my hypothesis - which I have already explained here - is that most (if not all) of the genome is used (non-neutral), and so because of this, there are not a bunch of random mutations accumulating in non-coding (neutral) sites.
I've restated it several times, I'm not sure how I can make it any clearer.

Date: 2007/10/13 23:01:21, Link
Author: Daniel Smith
Quote (jeannot @ Oct. 13 2007,15:16)
So what about the fact that mutation rates are far higher at synonymous sites?

As I understand it (and I just learned this) synonymous sites are sites that will accept a substitution with no functional change.  Therefore, there's no reason that these sites wouldn't show higher mutation rates.  The question is: why do sites that are supposedly non-functional show more constraint than synonymous sites?

Date: 2007/10/13 23:32:02, Link
Author: Daniel Smith
Quote (JAM @ Oct. 13 2007,17:14)
   
Quote (Daniel Smith @ Oct. 13 2007,14:00)
     
Quote (JAM @ Oct. 10 2007,10:40)

Here's an opposing hypothesis:

Known functional sequences will be evolutionarily conserved. Most sequences will not be conserved. We will continue to find functions for some conserved sequences for which no function has been identified.

What do you think? Shall we look at the evidence to see which hypothesis is better supported?

Yes, let's look.  But be warned, I'll be approaching the evidence from a different perspective than you and won't accept any preconceived ideas as part of the interpretation.

Daniel, this is why real, honest scientists make predictions BEFORE they get the data.

My hypothesis predicts that when we graph position on the x axis and % identity on the Y axis, we will see this, with the high points representing conserved sequences, which include, but are definitely not limited to, protein-coding sequences:
/\_/\___

Your hypothesis predicts that we will see a flat line wherever we look:

--------------

My hypothesis does not predict a flat line - except within a lineage.  By "lineage" I mean either the same species or very closely related species.  As an example I would think something along the lines of the African vs. Asian elephant.  This is why I said that the test needs to be done within the lineage to test my hypothesis.  
Quote

   
Quote
What I mean is that the perceived "rate of mutation" is often calculated by a comparison of species that are assumed to have evolved from a common ancestor via an accumulation of random mutations.

Not even remotely close, Daniel. Mutation rates are much more directly measured by quantitating new mutations; for example, we can measure the rate of new cases of autosomal dominant diseases that aren't inherited from parents. No assumptions are necessary to distinguish between our hypotheses. We are simply looking at differences between lineages for orthologous regions of the genome.
But orthologous regions are regions that are thought to be homologous due to speciation - which is assumed to have occurred by an accumulation of mutations - isn't that correct?  
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Since I am opposing that theory, I won't accept that assumption.

I'm not making any such assumption, so your desperate evasion won't work. You might want to reread the hypothesis we're testing.

Isn't it my hypothesis we're testing?  
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You must show me that the evidence supports this assumed buildup of random mutations first, then we can move on from there.

Nope. That's not how science works. We use hypotheses to make predictions, and then we look at the evidence to see whether it is consistent or inconsistent.

Only pseudoscientists who have zero confidence in their hypotheses make petulant demands like yours.

What demands?  My hypothesis predicts that there is no buildup of random mutations within the genome - even in non-coding sites.  Isn't that what we're testing?

Date: 2007/10/13 23:32:23, Link
Author: Daniel Smith
Speaking of predictions, I have another one for you:
It's my prediction that random mutations are only neutral or deleterious - never advantageous.  All advantageous mutations are non-random and are therefore experimentally repeatable.
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.

Date: 2007/10/14 10:16:45, Link
Author: Daniel Smith
Quote (Wesley R. Elsberry @ Oct. 13 2007,16:36)
Quote

I see no "Edit" button with my browser (Mozilla Firefox).


You should see an edit button on your own posts, but not other people's posts.

With moderator privileges, the edit button is on every comment.

I have no Edit button on my posts.  Not with Mozilla, not with IE.

Date: 2007/10/14 10:20:03, Link
Author: Daniel Smith
[EDIT]
Speaking of predictions, I have another one for you:
It's my hypothesis that random mutations are only neutral or deleterious - never advantageous.  All advantageous mutations are non-random and are therefore experimentally repeatable and will occurr too rapidly to be random.
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.

Better?

Date: 2007/10/14 10:37:00, Link
Author: Daniel Smith
Quote (JAM @ Oct. 14 2007,00:01)
I already gave you a URL for such a pair--rat vs. mouse. You, predictably, completely ignored the data.

I went there, but I'm not sure what I'm looking at.  What I want to see is the rat and mouse genome side by side, sequence by sequence.  That program appears to pick pieces out of the genome and line them up independently of their position in the chromosome.  Basically, I want to start at chromosome 1, bp 1, and see the rat and mouse side by side.  Is that possible?
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Quote
But orthologous regions are regions that are thought to be homologous due to speciation - which is assumed to have occurred by an accumulation of mutations - isn't that correct?    

Not even close. All orthologs are homologs, but not all homologs are orthologs. Orthologs are not merely homologous, but have the same function. Operationally, we're only really sure about these when we have complete genome sequences or when we rescue a mouse mutant with its human ortholog as a transgene. There are orthologous stretches along huge segments of chromosomes, in which gene order is preserved. This is called synteny. How do you explain that?
Designed descent.

Date: 2007/10/14 14:26:40, Link
Author: Daniel Smith
Quote (Wesley R. Elsberry @ Oct. 08 2007,07:49)
 
Quote

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.


So, why does the term "linkage disequilibrium" seem to get used by geneticists? Wouldn't your prediction mean that we should see the same degree of linkage disequilibrium everywhere we look? If not, what consequences do you think your "prediction" actually has?

First, here's a definition of linkage disequilibrium that I can understand:
 
Quote
The occurrence of some genes together, more often than would be expected. Thus, in the HLA system of histocompatibility antigens, HLA A1 is commonly associated with B8 and DR3 and A2 with B7 and DR2, presumably because the combination confers some selective advantage.
link
Do you agree with this definition?

Second, if so, I'm not sure how this applies to my hypothesis.  Why would you think that evolutioary constraint of non-coding sites would lead to "the same degree of linkage disequilibrium everywhere we look"?

I guess I'm not understanding the connection.

Date: 2007/10/14 14:34:54, Link
Author: Daniel Smith
First, I'm trimming the accusations that I somehow called you a liar because I don't fully understand how VISTA works.    
Quote (JAM @ Oct. 14 2007,11:25)
 
Quote
 
Quote
All orthologs are homologs, but not all homologs are orthologs. Orthologs are not merely homologous, but have the same function. Operationally, we're only really sure about these when we have complete genome sequences or when we rescue a mouse mutant with its human ortholog as a transgene. There are orthologous stretches along huge segments of chromosomes, in which gene order is preserved. This is called synteny. How do you explain that?
Designed descent.

How do you explain the breakpoints between syntenic regions in your design hypothesis, then? How do you explain the extensive synteny that crosses what you idiosyncratically define as "lineages"?

The designed descent hypothesis accepts that some genetic regions are passed on intact - while others are changed during the saltational phase of evolution.  I'm not sure how your objection applies.

Date: 2007/10/16 14:00:34, Link
Author: Daniel Smith
[quote=David Holland,Oct. 15 2007,15:51]  
Quote (Daniel Smith @ Oct. 14 2007,10:20)
[EDIT]
Speaking of predictions, I have another one for you:
It's my hypothesis that random mutations are only neutral or deleterious - never advantageous.  All advantageous mutations are non-random and are therefore experimentally repeatable and will occurr too rapidly to be random.
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.

Better?

Quote


I want to go back to this one for a minute. Suppose I set up a vat with a bazillion Acromobacter guttatus and nylon as the primary source of carbon. If one of the bacteria developes the ability to digest nylon has your hypothesis been supported? Without numbers I can't tell.

Only if it develops the same exact frame shift and only if it happens consistenty faster than random mutation rates can account for.
BTW, I don't have any idea what those rates are, but I'm sure whoever was doing the test would get that info first.

Date: 2007/10/16 18:44:53, Link
Author: Daniel Smith
[quote=JAM,Oct. 16 2007,15:07]  
Quote (Daniel Smith @ Oct. 16 2007,14:00)
   
Quote (David Holland @ Oct. 15 2007,15:51)
       
Quote (Daniel Smith @ Oct. 14 2007,10:20)
[EDIT]
Speaking of predictions, I have another one for you:
It's my hypothesis that random mutations are only neutral or deleterious - never advantageous.  All advantageous mutations are non-random and are therefore experimentally repeatable and will occurr too rapidly to be random.
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.

Better?

     
Quote


I want to go back to this one for a minute. Suppose I set up a vat with a bazillion Acromobacter guttatus and nylon as the primary source of carbon. If one of the bacteria developes the ability to digest nylon has your hypothesis been supported? Without numbers I can't tell.

Only if it develops the same exact frame shift and only if it happens consistenty faster than random mutation rates can account for.
BTW, I don't have any idea what those rates are, but I'm sure whoever was doing the test would get that info first.

What does your hypothesis predict if a different bacterial species is selected on nylon?

I've already made my prediction, why are asking me to make another one?    
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1) Will multiple selections give the same result, and/or
2) Will the enzymes that evolved be the orthologs of the ones that evolved in Achromobacter?

My prediction was that exactly the same frame shift will occur - so I'm guessing it will be #1.      
Quote

P.S. Did you check out the mouse vs. rat sequences yet?

I've been there several times.  Let me give you a blow by blow of my most recent visit:
I want to see the mouse and rat genomes side by side so I go to VISTA and select the Mouse Feb. 2006 genome as a base genome, then I figure the best place to start is at the beginning, so I select ch1:1-1000000 and click GO, I get an error saying "No such contig. or chromosome".  This is a bit confusing.  How can the mouse genome not have a chromosome 1?  So then I select ch2:1-1000000 and get the same error. Ch3 and 4 give the same results. So then I decided to try the Rat June 2003 and go with the default chr10:10000001-10100000, which then gives me some results.  I click on Browse alignment so I can see the coding (the Cs, As, Ts, and Gs).  I zoom in on a spot and when I put my mouse over the Rat code, it gives the number 10034062, when I cursor over the Mouse genome in the same spot, it gives the number 5312532.  I'm assuming these are the numbers for the position of that site within the chromosome.  So, (if that's the case) it's not showing me the Rat and Mouse genomes, side by side - starting at position 10000001 and ending at position 10100000.  If it was, they'd both give the number 10034062 - wouldn't they?
So, like I said, I'm not sure what I'm looking at and I'm not sure the correct way to use the site, but it doesn't appear to be giving me what I was looking for.  So, if you have something you want me to see, you'll have to specifically tell me what it is I'm looking at and how it reflects on my hypothesis.

Date: 2007/10/16 18:53:16, Link
Author: Daniel Smith
Quote (mitschlag @ Oct. 13 2007,18:22)
 
Quote (Daniel Smith @ Oct. 13 2007,13:53)
     
Quote (mitschlag @ Oct. 10 2007,12:47)
       
Quote (Daniel Smith @ Oct. 10 2007,02:30)
The results that would falsify my hypothesis would be if the coding sequences showed evolutionary constraint while the non-coding sequences didn't.
There's a fair amount of evidence showing that (contrary to expectation) non-coding sequences have fewer base changes than coding sequences, see, for example:
http://www.biomedcentral.com/1471-2148/7/66
         
Quote
The primary result is that the mean rate of intergenic nucleotide substitution is two-thirds that of the synonymous coding data, with an absolute rate estimated to be 1.05 × 10-8 substitutions per site per year. This result holds with alternative nucleotide models (see Methods), and thus does not appear to be solely an issue of estimation procedures.

Slower rates in non-coding regions relative to synonymous sites are becoming a surprisingly frequent observation. For example, a recent study of Drosophila demonstrated that non-coding DNA evolves considerably slower than synonymous sites in terms of both divergence between species and polymorphism within species [16]. By comparing studies, one can also make the case that pseudogenes [32,33] and introns [34,35] evolve more slowly than synonymous sites in apes and other mammals [13,36-38]. Studies of mammalian intergenic regions have also found slower rates than synonymous sites [35,39,40]. Although most of these studies encompass only a handful of genes, an overall picture of relatively slow non-coding rates is emerging.

What do you make of that?

If this is true, then it would be a confirmation of my hypothesis with better than expected results.

It's true, all right, but it doesn't confirm your hypothesis.

To learn why, read the cited paper.  Hint: TE=transposable element.

(Sorry that I won't be able to participate in this discussion for the next two weeks due to travel in arcane regions.  In the meantime, I want to commend DS for  his courteous and patient responses to the many challenges that have been addressed to him.)

I read the cited paper.  It was very interesting - a bit over my head - but interesting nonetheless.
Your suggestion to read up on transposable elements was very fruitful as well as now these have piqued my interest.  I, of course, don't believe these to be randomly generated or to be degenerate copies of working genes.  I think they are more likely functional switches for some as yet undefined purpose.  I'm going to read more about them.
Oh and thanks for the commendation.  I appreciate a good civil discussion.  Unfortunately, when things get hostile, I have a tendency to get my guard up and push back a little harder than I have the right to.  Thanks for putting up with that as well.

Date: 2007/10/16 18:55:07, Link
Author: Daniel Smith
Quote (swbarnes2 @ Oct. 16 2007,14:34)
Quote
Only if it develops the same exact frame shift


Okay, so let's get this straight.

Do you agree that the ability to resist antibiotics is "beneficial"?

If so, you then predict that if 50 labs all over the country screen put every post-doc and lab tech they had to work screening plates for 3 months to find resistant mutants, they will ALL find the exact same mutation?

What if I'm screening for a mutation that cripples a certain pathway, and when I find a colony with the mutation I want, I will keep it and cultivate it for the next 20 years, and all the other ones just get incinerated.

Doesn't that make that mutation beneficial?  You certainly can't claim that its bearers fare worse in their environment than the wild-type kind.

I made a specific prediction.  Why do you want me to modify it to fit your scenario?

Date: 2007/10/17 18:31:14, Link
Author: Daniel Smith
Quote (JAM @ Oct. 16 2007,21:44)
   
Quote (Daniel Smith @ Oct. 16 2007,18:44)
My prediction was that exactly the same frame shift will occur - so I'm guessing it will be #1.

Wrong! Completely different, nonhomologous gene. Would you like to see the data?
Yes, I would be interested in seeing that.      
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P.S. Did you check out the mouse vs. rat sequences yet?

I've been there several times.  Let me give you a blow by blow of my most recent visit:
I want to see the mouse and rat genomes side by side so I go to VISTA and select the Mouse Feb. 2006 genome as a base genome, then I figure the best place to start is at the beginning,...

Probably not. There are repeats, called telomeres, at the ends.
I'd like to see those - just for my own curiosity.      
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so I select ch1:1-1000000 and click GO, I get an error saying "No such contig. or chromosome".  This is a bit confusing.  How can the mouse genome not have a chromosome 1?

There's probably no contig for that region. The repeats make it complicated.
What is "contig"?      
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So then I select ch2:1-1000000 and get the same error. Ch3 and 4 give the same results. So then I decided to try the Rat June 2003 and go with the default chr10:10000001-10100000, which then gives me some results.

Yes, because you're in the middle, away from the junk at the ends that you thought would be conserved.
         
Quote
I click on Browse alignment so I can see the coding (the Cs, As, Ts, and Gs).  I zoom in on a spot and when I put my mouse over the Rat code, it gives the number 10034062, when I cursor over the Mouse genome in the same spot, it gives the number 5312532.  I'm assuming these are the numbers for the position of that site within the chromosome.

Correct, but it's not the same chromosome number. Why do you think that I tried to explain synteny to you?
         
Quote
So, (if that's the case) it's not showing me the Rat and Mouse genomes, side by side - starting at position 10000001 and ending at position 10100000.  If it was, they'd both give the number 10034062 - wouldn't they?

No, because contra your hypothesis, they aren't colinear. The autosomes are numbered according to their length, not their content. In fact, the place in which you were looking on rat chr10 has been inverted, and lines up with a bit of mouse chromosome 16, as VISTA tells you. These relationships are illustrated here:
http://www.softberry.com/synt_pl....chr_2=*
and in a different way, as well as conversely, here:
http://www.informatics.jax.org/reports/homologymap/mouse_rat.shtml
         
Quote
So, like I said, I'm not sure what I'm looking at and I'm not sure the correct way to use the site, but it doesn't appear to be giving me what I was looking for.

Since your hypothesis is incorrect, what you're looking for doesn't exist. Rat chromosome 10 doesn't align with mouse chromosome 1, it aligns with chunks of mouse chromosomes 16, 17, and 11. Those represent translocations and inversions from the past. Therefore, none of those breakpoints have been conserved, and your hypothesis is incorrect. But all you had to do was look at the graph to see that between rat and mouse, there are big regions of no conservation between the pink lumps that are 80-100% conserved.
         
Quote
So, if you have something you want me to see, you'll have to specifically tell me what it is I'm looking at and how it reflects on my hypothesis.

Why are there gaps between the pink lumps that are the conserved sequences when we align orthologous sequences from two species within the same lineage?

Thank you for the explanations and the data.  The second page you cited really helped me understand what I was looking at (and not understanding) in the VISTA program.
Let me ask you this:
The rat genome appears to be a re-arrangement of the mouse genome, so how do we know that the "junk" (as you call it) wasn't rearranged in similar manner?  
Does the VISTA program check for this?  
Or does it only compare genes?

Date: 2007/10/17 18:37:56, Link
Author: Daniel Smith
Quote (swbarnes2 @ Oct. 16 2007,19:29)
 
Quote
I made a specific prediction.  Why do you want me to modify it to fit your scenario?


If your hypothesis is to be of any value, it has to be applicable to more than just one organism and one survival challange, surely you see that.

So, 50 labs, 5 post-docs and techs a piece, selecting for resistance to a particular antibiotic, for 3 months.

Do you predict that all the resistant strains found will carry the exact same resistance-granting mutation?

No I don't.  Mainly because I think bacteria are designed to mutate and evolve quickly - so I'd predict a number of different mutations in that scenario.

Now, if these 50 labs had all started with the same pre-nylon-eating bacteria and subjected all of them to a nylon environment, I'd be surprised if a significant percentage of them didn't develop the same frame shift.

I'm interested to see JAMs data about the nylon though.

Date: 2007/10/19 18:14:11, Link
Author: Daniel Smith
Quote (JAM @ Oct. 17 2007,20:35)
       
Quote (Daniel Smith @ Oct. 17 2007,18:31)
Yes, I would be interested in seeing that.      
         
http://jb.asm.org/cgi/reprint/174/24/7948?view=long&pmid=1459943

I apologize because I garbled it; unfortunately, it's more bad news for your hypothesis.

It turns out that it was the same bug, Flavobacterium. One of the nylonase genes was deleted, and selection produced a completely new one.
While these results are interesting, they don't really meet the criteria of my prediction since they started with the already frame-shifted bacteria.  If you remember, my prediction involved the pre-frame-shifted bacteria Acromobacter guttatus.  My prediction was that if that bacteria was subjected to nylon, the same frame shift would occur.
This study appears to involve a mutation of the Flavobacterium sp. strain KI72 - which already has the plasmid pOAD2 that was the result of the original frame shift.
DISCLAIMER - I'm not calling you a liar or anything - I'm just hoping you can appreciate the difference from my perspective. - END DISCLAIMER
       
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Thank you for the explanations and the data.  The second page you cited really helped me understand what I was looking at (and not understanding) in the VISTA program.

You're most welcome. How's your hypothesis?

It's not in as bad of shape as you think it is.        
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The rat genome appears to be a re-arrangement of the mouse genome, so how do we know that the "junk" (as you call it) wasn't rearranged in similar manner?

It clearly was--it just wasn't conserved, as is clearly shown by the spaces between the pink humps of conserved sequences. Why are you not acknowledging my point about all the breakpoint sequences?

In order to acknowledge that you are correct, I must first determine what exactly you're talking about, (no small task for me!), then I have to know what the parameters of VISTA are (does it ignore the non-coding sites? etc.), and finally I have to interpret these results in the light of designed descent.  If, after careful examination, it appears your evidence falsifies my hypothesis, I'll surely admit it.  I am not going to just throw up my hands and give up because you say so though!      
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Does the VISTA program check for this?  

Specifically? No, but it answers your question clearly. The spaces between conserved sequences are mostly still there, but they aren't conserved. Do you understand that the spaces in between the conserved pink humps mean that your hypothesis is DOA?
No, I don't understand that - because there's no data showing me what those spaces represent.  The only thing I have to go on is your insistence that they falsify my hypothesis.  

What I really need is a program that will...
a.) allow me to select any region (coding or non-coding) of the mouse genome and
b.) search the rat genome for a closely matching sequence.
That's what I'd like to do.  Is there such a program?
       
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Or does it only compare genes?

It compares genomes. Genes are only a part of it.

Obviously I have much more research to do, but I find it extremely hard to believe that you can take a working genome, cut it into pieces, shuffle it around, and come up with another working genome.  It defies credulity.  It's like taking a book, cutting up all the pages, shuffling them around and coming up with an equally coherent story.
I know you'll probably say that millions of years+selection can accomplish this, but where's the data to support that assumption?

Date: 2007/10/19 18:30:22, Link
Author: Daniel Smith
Quote (JAM @ Oct. 17 2007,21:03)
 
Quote (Daniel Smith @ Oct. 17 2007,18:31)
I'd like to see those - just for my own curiosity.  
 
http://en.wikipedia.org/wiki/Telomere
http://learn.genetics.utah.edu/features/telomeres/
http://users.rcn.com/jkimbal....es.html
Thank you.  Once again I'm amazed at the forethought of God!  Telomeres accomplish two things: they help to conserve genetic information while still guaranteeing that the aging process will eventually take its toll on all of us.  These might seem like contradictory functions to you, but they make perfect sense from my perspective.
   
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What is "contig"?      

An assembly of overlapping sequences. Sometimes it's impossible to get overlap.

No doubt.  The fact that there are such things as overlapping sequences makes me wonder at the mind of God.  
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The rat genome appears to be a re-arrangement of the mouse genome,...

The human genome just has many more (relative) rearrangements, as one would predict from evolutionary theory:

http://www.informatics.jax.org/reports/homologymap/mouse_human.shtml

Are you seeing anything in what I've shown you that is consistent with your hypothesis?

Yes I am.  I know that's hard for you to believe, but the more mixed up these genomes are relative to each other, the more confident I am of a designed mechanism for that rearrangement.

Date: 2007/10/19 18:34:04, Link
Author: Daniel Smith
Quote (swbarnes2 @ Oct. 18 2007,13:36)


     
Quote
Now, if these 50 labs had all started with the same pre-nylon-eating bacteria and subjected all of them to a nylon environment, I'd be surprised if a significant percentage of them didn't develop the same frame shift.


Oh no.  This is just transparently dishonest.  You previously claimed that you predicted:

     
Quote
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.


Believe me, we all understand.  Creationists are constantly moving the goalposts.  It's inevitable for them if they want to pretend to be reasonable.  It's totally dishonest, but that's inevitable too.

But to change the goalposts within, what, two days and one page of posts?  That's dishonest and sloppy.  

What's the difference between those two predictions?

Date: 2007/10/19 18:54:16, Link
Author: Daniel Smith
Quote (swbarnes2 @ Oct. 18 2007,13:36)
   
Quote
so how do we know that the "junk" (as you call it) wasn't rearranged in similar manner?  


Well, why can't you do the BLASTs that would prove this?

"BLAST stands for Basic Local Alignment Search Tool. It is used to compare a novel sequence with those contained in nucleotide and protein databases by aligning the novel sequence with previously characterised genes." (emphasis added) (link)

I'm not interested in comparing genes.

Date: 2007/10/20 11:43:19, Link
Author: Daniel Smith
Quote (JAM @ Oct. 20 2007,01:00)
 
Quote (Daniel Smith @ Oct. 19 2007,18:14)
   
Quote (JAM @ Oct. 17 2007,20:35)
             
Quote (Daniel Smith @ Oct. 17 2007,18:31)
Yes, I would be interested in seeing that.      
         
http://jb.asm.org/cgi/reprint/174/24/7948?view=long&pmid=1459943

I apologize because I garbled it; unfortunately, it's more bad news for your hypothesis.

It turns out that it was the same bug, Flavobacterium. One of the nylonase genes was deleted, and selection produced a completely new one.
While these results are interesting, they don't really meet the criteria of my prediction since they started with the already frame-shifted bacteria.  If you remember, my prediction involved the pre-frame-shifted bacteria Acromobacter guttatus.

First, if you'll do me the courtesy of rereading what I wrote, I noted that it is still bad news for your HYPOTHESIS, which is an accurate assessment. Your hypothesis makes many testable predictions, and your hypothesis is global, not just about one species.
What exactly are these predictions?
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Second, frameshifts happen to individual genes. The term "frame-shifted bacteria" is gibberish.

   
Quote
My prediction was that if that bacteria was subjected to nylon, the same frame shift would occur.

But your hypothesis makes a very clear prediction in this case, too.
Which is?
Quote
Moreover, your prediction was based on a false assumption, because more than one enzyme is involved.
Where specifically did I make this "false assumption"?
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In this case, we started without one of the two, and got a completely different new one from a different origin to replace its function. This falsifies your hypothesis.
How does this falsify my hypothesis?
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In case you've forgotten, here's your hypothesis, improperly stated as a prediction:
 
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It's my prediction that random mutations are only neutral or deleterious - never advantageous.

How do you know the mutation was random?

Date: 2007/10/20 18:35:19, Link
Author: Daniel Smith
From Wikipedia:
Quote
Recent evidence suggests that "junk DNA" may in fact be employed by proteins created from coding DNA. An experiment concerning the relationship between introns and coded proteins provided evidence for a theory that "junk DNA" is just as important as coding DNA. This experiment consisted of damaging a portion of noncoding DNA in a plant which resulted in a significant change in the leaf structure because structural proteins depended on information contained in introns.

Date: 2007/10/20 19:09:06, Link
Author: Daniel Smith
Quote (JAM @ Oct. 20 2007,14:14)

Yes, VISTA. You're so afraid of what you'll find that you won't explore it. If you need spoonfeeding, here's a larger region:
http://pipeline.lbl.gov/servlet....llbar=0

1) Switch "# rows:" to 1.
2) Read the legend at lower left. See the symbol for genes? This region has four genes: Mtap7, Bclaf1, 260016C23Rik (a putative gene), and Pde7b.
3) Note the color of Exons in the legend: dark blue. See how the exons (protein-coding regions) are within the genes? The exons also are represented on the gene arrows at the top. Exons include all protein-coding regions, but they contain other sequences, such as UTRs, which have function.
4) Look at the scale for the Y axis on the right. It represents % identity.
5) Bonus question: why doesn't the scale go below 50%?
6) Do you see that the exons are highly conserved?
7) Do you see that there is less conservation outside the exons?
7) Look at the mouse vs. rat graph. These species are within the same "lineage" as you defined the term. What do the spaces between the pink bumps represent in that graph?

If you'd like to browse, it's easiest to change chromosome number in the address bar. Here's a gene-rich region:

http://pipeline.lbl.gov/servlet....llbar=0

First, thanks for making it a bit clearer.
Second, if the protein coding regions are dark blue and UTRs are light blue, what are the pink (CNS) regions?
Are these non-coding?  
If so, why are they also so highly conserved between rat and mouse?
Like this?        
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Obviously I have much more research to do, but I find it extremely hard to believe that you can take a working genome, cut it into pieces, shuffle it around, and come up with another working genome.  It defies credulity. It's like taking a book, cutting up all the pages, shuffling them around and coming up with an equally coherent story.

That's the power of selection. There's no coherent design hypothesis that can explain it.
Sure there is.  Every kid who ever rearranged someone else's book report to try to "put it in his own words" knows about it.

BTW, giving credit to "selection" without showing the steps that were selected for is only an assumption and is not grounded in the evidence.  
Quote

               
Quote
I know you'll probably say that millions of years+selection can accomplish this, but where's the data to support that assumption?

These *are* the data. There also are data from shorter time periods that, when extrapolated, are consistent with this.
Isn't that the classic case of using the thing that must be explained as an explanation?  I was told that was taboo around here.

Date: 2007/10/20 19:15:25, Link
Author: Daniel Smith
Another example.
In this one, the pink regions outside the coding areas, are more highly conserved between rat and mouse than the coding areas.

Date: 2007/10/20 19:18:58, Link
Author: Daniel Smith
Oops!  When I click on the links I just provided, they take you to the page JAM originally pointed me to - not the pages I created in VISTA.
I'll have to figure out how to get the correct URL.

Date: 2007/10/20 19:22:32, Link
Author: Daniel Smith
Try this.

Date: 2007/10/20 21:04:21, Link
Author: Daniel Smith
Found it!
CNS = conserved noncoding sequences.
So the pink areas in VISTA are confirmations of my hypothesis.
My, there are quite a lot of them when comparing the rat and mouse genomes!

Date: 2007/10/21 12:53:06, Link
Author: Daniel Smith
Quote (JAM @ Oct. 20 2007,23:59)
   
Quote (Daniel Smith @ Oct. 20 2007,21:04)
Found it!
CNS = conserved noncoding sequences.
So the pink areas in VISTA are confirmations of my hypothesis.

No, they are conserved noncoding sequences. Your hypothesis would only be confirmed if there weren't white areas between the pink areas, remember?
   
Quote
My, there are quite a lot of them when comparing the rat and mouse genomes!

Of course there are! But "quite a lot" of them doesn't fulfill your prediction that there wouldn't be any spaces (nonconserved noncoding sequences) between them at all!
Here's your prediction:
     
Quote
My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.

A lot isn't all, Daniel. Your hypothesis is dead meat. A hefty chunk of noncoding sequences aren't conserved. Did you find any coding sequences that weren't conserved?

Yes!  There are also white spaces amongst the coding sequences.  If you look at the gene markers at the top, you'll see they often extend over white spaces. Like this.

As I see it, there is significant constraint amongst coding and noncoding sequences - as well as significant changes.
Nothing here contradicts my hypothesis.

Date: 2007/10/21 12:55:46, Link
Author: Daniel Smith
Quote (JAM @ Oct. 21 2007,00:19)
Quote (Daniel Smith @ Oct. 20 2007,19:15)
Another example.
In this one, the pink regions outside the coding areas, are more highly conserved between rat and mouse than the coding areas.

You're cherry-picking, and your hypothesis predicts that all noncoding areas will be pink, not just some of them or most of them.

No it doesn't.  My hypothesis predicts that there will be equal amounts of constraint amongst coding and noncoding areas - not that all of it will be conserved. I never said that!

Date: 2007/10/21 13:29:04, Link
Author: Daniel Smith

This wide view of a random portion of the mouse/rat genome illustrates my point.  The fact that there are so many pink regions shows that the noncoding sites are generally conserved just as the coding sites are within lineages.  The question remains as to how closely mice are related to rats, but I don't see anything here that is unexpected from my point of view.  Remember, my hypothesis is that the splitting of lineages is a saltational event.  I would expect big chunks of the genome to be conserved in such an event, but I would also expect some significant changes as well.
Couple this with the significant evidence in the fossil record for adaptive radiation followed by long periods of gradual evolutionary specialization, along with the mounting evidence for non-random mutation and you have the designed descent hypothesis in a nutshell:
Saltational, non-random divergence of types, followed by non-random specialization within types, followed by over-specialization amongst most members of a lineage, resulting in the extinction of the overspecialized members - leaving just those members that have not (for whatever reason) become overly specialized.
From my perspective therefore, concepts such as "evolutionary constraint"  - as they are generally accepted - are meaningless - since all evolutionary events are non-random.

Date: 2007/10/21 13:40:14, Link
Author: Daniel Smith
Quote
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72.

           
Quote
Now, if these 50 labs had all started with the same pre-nylon-eating bacteria and subjected all of them to a nylon environment, I'd be surprised if a significant percentage of them didn't develop the same frame shift.


I see here that the wording of my first prediction has caused some confusion.  
When I said:
"anytime Acromobacter guttatus Sp. K172 is subjected to... the same frame shift will occur...",
I didn't mean that the frame shift would occur in every bacteria.  

What I should have said was:
"anytime a colony of Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur within some members of that colony, resulting in Flavobacterium Sp. KI72".

That would have made my intent clearer.

Date: 2007/10/21 14:09:01, Link
Author: Daniel Smith
Let me also say this:

My view is that proteins are essentially the components of biological machinery - therefore I'd expect that coding for proteins would largely be similar amongst related organisms.  The (so-called)* noncoding regions, however, I believe to be instructional regions that determine how these proteins are used.  Hence, I'd expect these regions to show significant differences amongst morphologically different organisms and similarities between morphologically similar organisms.
I also believe there are regions that are designed for adaptation - a kind of "working lab" cooking up non-random adaptive elements (within limits).  I'd expect these regions to change as environments change.

So, to compare this to VISTA:  The dark blue / light blue regions should be similar amongst related organisms; the pink regions should be similar amongst morphologically similar, related organisms and increasingly dissimilar amongst morphologically dissimilar, related organisms; and the white regions should be dissimilar amongst all organisms.

* (I say "so-called noncoding" because I believe these regions actually "code for" something - just not proteins.)

Date: 2007/10/22 19:26:13, Link
Author: Daniel Smith
Quote (JAM @ Oct. 21 2007,16:57)
           
Quote
- not that all of it will be conserved. I never said that!

               
Quote (Daniel Smith @ Oct. 08 2007,04:27)
My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.


What exactly does basically all sequences mean, then?

Don't trip over your feet while you're backpedaling, OK?

And don't forget...
           
Quote (Daniel Smith @ Oct. 19 2007,18:14)
If, after careful examination, it appears your evidence falsifies my hypothesis, I'll surely admit it.

First, why did you take my prediction out of context?

Here's the full prediction:
           
Quote (Daniel Smith @ Oct. 08 2007,04:27)
Take two members of the same species that have been geographically and reproductively isolated for a long period of time (the longer the better), sequence their genomes and compare them.

My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint.

I also said this:            
Quote (Daniel Smith @ Oct. 06 2007,20:10)
My prediction is that there are many functional sequences that are different (even radically so) amongst related lineages - this due to their being of designed, not mutational, origin.

And this:
           
Quote (Daniel Smith @ Oct. 08 2007,02:18)
1.  Sequence comparisons between related lineages will result in a mixture of like and unlike functional sequences.  

2.  Sequence comparisons within the same lineage will show evolutionary constraint across the board - even in what are presently considered neutral sites.

Now, I'm not sure how closely related rats and mice are, but I think the data suggests that they're at least closely related species, within the same lineage.  The true test however, (as I've said all along) is to take samples from geographically isolated specimens of the same species and see how close they are.

I've recently learned of two examples where this was done and the results are consistent with my hypothesis.

The first was a study of the Ascension Island green sea turtles.  These turtles, which are notoriously faithful in returning to their breeding grounds every year, have been geographically isolated from other sea turtle populations for 60-80 million years (since the separation of South America and Africa).  A study by Brian Bowen and John Avise (abstract) found that the turtles are too genetically similar to other turtles to have been isolated for that length of time.  Their estimate - based on a sequence divergence rate of 2% per million years - was less than 1 million years.  They then go on to postulate that these sea turtles probably interbred with other populations; this despite the fact that sea turtles have never been observed to do so.  In fact, of the 28,000 females tagged over the past 30 years (at another rookery in Costa Rica), none has ever been observed at another nesting site.

Another example is a study done by Scott Baker (from the abstracts on Google Scholar, I was unsure which one corresponds to this study) between Atlantic and Pacific humpback whales - which have been geographically isolated for 3 million years (since the isthmus of Panama separated the two oceans).  Again - based on a sequence divergence rate of 2% per million years - the estimated difference between these two isolated species was 6%.  The actual difference however, was found to be 0.27%.  Again, this forced the scientists to speculate about gene flows occurring between the oceans from time to time, or much slower sequence divergence rates.

In any event, the results in both of these studies are consistent with, and predicted by, my hypothesis, but are not consistent with, or predicted by, the current theory of evolution.  My hypothesis accommodates the known 60-80 million year isolation of the turtles and the known 3 million year isolation of the humpbacks with no extra speculations added to make the data fit!

And, I'll go out on a limb and make another prediction here:
Whenever studies of this type - between geographically isolated members of the same species - are done, the results will be consistent with my hypothesis.

Date: 2007/10/24 20:59:23, Link
Author: Daniel Smith
Quote (swbarnes2 @ Oct. 22 2007,20:55)
 
Quote
anytime a colony of Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur within some members of that colony, resulting in Flavobacterium Sp. KI72".


So I take a sample of Acromobacter, I spread it on a plate.  I grow colonies from that.

I replica plate those colonies onto nylon plates, and you claim that there will be a survivor in every colony?

Of every plate, prepped by every lab worker in 50 labs?

Now, claiming that all of the survivors (because, you suppose, there is only a single possible evolutionary solution to the problem, which is ridiculous) would have the exact same mutation, that's at least imaginable.  But what you suggest now is certifiably crazy.  

So yes, you made it clear.  Clear that your understanding of biology is insane.

Well, I guess you weren't interested in hearing the evidence that nylon-eating can be acquired through mutations in other genes after all.  Which makes it a lie when you said you were.  A pretty pathically transparent one at that.

I never said there was only one possible solution to the nylon problem.  I merely said that I would expect the same frame shift to occur more often and more rapidly than random mutations could account for.

Date: 2007/10/24 21:41:53, Link
Author: Daniel Smith
Quote (W. Kevin Vicklund @ Oct. 23 2007,15:01)
Your claims as to what Bowen and Avise wrote are rather... odd.  Let me guess: you read the abstract, but did not actually read the paper, which is freely avaible from the link you provided.  This is extremely dishonest for anyone who claims to be interested in the evidence.

First, the hypothesized isolation was 40 million years or longer, rather than 60-80 million years.  While this is certainly nitpicking on my part (since 60-80 million years is longer than 40), it suggests that you didn't read the paper - very poor scholarship indeed.  But this is merely a semantic error.  Your other errors are much worse.  For example, the study included a Pacific colony as an outgroup.  The Pacific isolation only occured 3 million years ago (as you yourself noted), yet the Pacific colony showed more changes than the putative 40 million year separation!  Another major error is that you claim they postulated these populations interbred.  This is not quite true - they considered and mostly rejected it, and gave reasons for that rejection.  Rather, they postulated that it was the result of a recent colonization event, and that these events occur periodically.  Bonus question: what is their explanation for why and how periodic colonization events occur?  Finally, you claim that sea turtles have never been observed to change nesting sites.  Yet the paper clearly identifies several instances of this occuring - in the same paragraph they largely rejected the interbreeding argument.

I highly recommend that in the future you read your sources before citing them, if at all possible.  It will help prevent you from making such egregious errors.  Unfortunately, some people never do learn this lesson, and I enjoy rubbing their face in it after the first few times they make that error.  Of course, not all articles are free, and you might find yourself taking a calculated risk to make a point.  Just be prepared for the fall-out if your interpretation of the abstract is incorrect.

For now, I will assume poor scholarship on your part, rather than deliberate dishonesty.  Keep it up, though, and you will soon find yourself being called a pubjacker.

You are right.  I did not read the paper.  My source was a book I've been reading called "Patterns in Evolution" by Roger Lewin.  I decided that it would be better to try to find a link when I posted it; so I found the abstract and just linked to it.
Now that I've read the paper, I see that it's not exactly what I characterized it to be.  I was however, struck by their hypothesis that sea turtles do not accumulate mutations in their mitochondrial DNA as fast as they had expected - and even the 3 million year Atlantic/Pacific separation produced far less variation than the 2% per million years that has generally been accepted.

I must say also here that I've been a bit presumptuous in declaring my "hypothesis" - since (as I said when I first arrived here) my ideas are still in development.  My main goal is to find out what really happened.  I will go wherever the data leads.  So I don't really have a hypothesis that's set in stone.  I have more in the way of expectations due to my variant interpretation of the data.

One thing I've learned recently (from the same book) is that; even among interbreeding populations, sequence divergence can vary widely (one study found a species of skink with an 8% divergence and a subwren species with 0.1% sequence divergence in the same Australian environment).

This has led me to re-evaluate my views.

I'm thinking that perhaps these divergence percentages correlate to Schindewolf's proposed three-stage evolutionary theory; with the "typolosis" (or degenerative, over-specialized) phase corresponding to the species with the lowest sequence diversity.

I'll have to do more study.

Date: 2007/10/25 13:50:08, Link
Author: Daniel Smith
Quote (Richard Simons @ Oct. 25 2007,00:00)
Back to Schindewolf! I am not sure why a hypothesis that has been essentially dead for 50 years holds so much fascination for you. However, given that it does perhaps you could explain how the information to constrain an organism's evolutionary pathway is held. What conceivable mechanism could stop evolution from taking place, or enable parts to evolve before they became useful?

I am also curious about the saltational events. Do you see these as creating a new genus, order, phylum or what? What actually occurs during a saltational event? How does the DNA get changed and how does it know what to become, as I gather it is preparing for the next few million years of evolution and changing conditions? When did the last saltational event take place? I don't even know if the proposal is that one day a dinosaur chick hatched that had feathers and wings or if the process was spread over many generations, which might make it little different from the rapid evolution phase of punctuated equilibrium.

I'm looking forward to your answers.

I don't know.

Date: 2007/10/25 20:56:17, Link
Author: Daniel Smith
Quote (swbarnes2 @ Oct. 25 2007,14:36)
       
Quote
I never said there was only one possible solution to the nylon problem.


And I never said you claimed that.  Why are you lying about what I said?

I was referring to this:
       
Quote (swbarnes2 @ Oct. 22 2007,20:55)
Now, claiming that all of the survivors (because, you suppose, there is only a single possible evolutionary solution to the problem, which is ridiculous) would have the exact same mutation, that's at least imaginable.

Now that I re-read it, I can see that you weren't really saying that I supposed there to be "only a single possible evolutionary solution to the problem" (although it came across that way when I first read it).  So I misinterpreted.
Sorry I'm such a "liar".
       
Quote

Your posts are perfectly easy to look up.  

You said:

           
Quote
anytime a colony of Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur within some members of that colony, resulting in Flavobacterium Sp. KI72.


It means what it says.  You predict that a replica experiment will result in every colony re-establishing itself on the nylon plate because every colony will have a member with that frameshift.

I'm sorry if your prediction is stupid, but that's your responsibility.  You write it.

You got me there.  I guess I'll have to stick with the prediction until it's proven wrong.
       
Quote

           
Quote
I merely said that I would expect the same frame shift to occur more often and more rapidly than random mutations could account for.


No, you said what I quoted above.  
Here's the full context of that quote:
       
Quote (Daniel Smith @ Oct. 14 2007,10:20)
Speaking of predictions, I have another one for you:
It's my hypothesis that random mutations are only neutral or deleterious - never advantageous.  All advantageous mutations are non-random and are therefore experimentally repeatable and will occurr too rapidly to be random.
Therefore, I predict that anytime Acromobacter guttatus Sp. K172 is subjected to an environment where it must consume nylon to survive, the same frame shift will occur, resulting in Flavobacterium Sp. KI72. (emphasis added)
So, as you can see, I actually said both things.        
Quote


Every colony exposed gets the frameshift.

We understand, believe me, we do.

You have already concluded that evolution is wrong because you don't like it, so you are "predicting" that the evidence will show that it doesn't happen.

I have concluded that the currently held theory of evolution is wrong because I have yet to see any convincing evidence of it's mechanism.        
Quote


But you don't honetly care about the content of your predictions.  They aren't relevant.  That's why you can't keep them straight over the course of two days.

This is really one of those cases where you are better off with the truth, because lies are too hard to keep straight.

People who care about the evidence look it up first, and then draw their conclusions.
Is that what you did?
Quote
 Do you honestly think that anyone reading this board would call you a "look at the data first" kind of person?
Maybe not.  I don't really care what the readers of this board think of me.  The truth is, I was invited here.  I was supposed to come here and discuss Berg and Schindewolf, but I was immediately told that the fossil record doesn't matter because molecular evidence outweighs it.  I was then challenged to produce a hypothesis and predictions - so I did.  I probably shouldn't have jumped in so quickly, but oh well.  Now that we're here, let's see how it turns out.  Of all the predictions I've made, how many have been shown false?        
Quote


So embrace the truth about yourself.  You like your Creationism for reasons that have nothing to do with the evidence (since you don't know what any of it is).

I'll admit that my belief in God greatly weighs against any belief in random causes.  In fact what I'm actually advocating is Natural Theology - the belief that the study of nature reveals the mind and qualities of God.  I don't try to hide that.  I started this journey as a young earth creationist, but I've changed much about what I believe because of the evidence.  I refuse, however, to be an unthinking, uncritical lemming.  I will not blindly accept a theory for which there is very little in the way of true evidence.  Much of what I've seen of the case for the theory of evolution is circular.  It presupposes it's conclusion.  In fact the conclusion is a foregone one.  It's very hard sometimes to sift through the evidence without being caught up in the tautology in which it is interpreted.    
Quote


Then you can stop making posts that make you look like a braindead moron, or a pathetic liar.

Thanks.

Date: 2007/10/25 21:06:41, Link
Author: Daniel Smith
And, another thing:

If I were really only interested in reaffirming my own ideas with no concerns for opposing data or evidence, why on earth would I come here?!?!

Date: 2007/10/26 13:48:27, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Oct. 26 2007,02:50)
 
Quote (Daniel Smith @ Oct. 25 2007,20:56)
In fact what I'm actually advocating is Natural Theology - the belief that the study of nature reveals the mind and qualities of God.

And what have you found out so far?

You've presumably been studying nature for a while now.

What has Natural Theology revealed so far about the mind and qualities of God?

Anything?

I've learned that God is an infinitely brilliant chemist, physisict and engineer.
I still might not know much about how or why he did what he did (who does?), but I can surely see the elegance of it.

Date: 2007/10/26 13:51:30, Link
Author: Daniel Smith
Quote (IanBrown_101 @ Oct. 25 2007,22:57)
   
Quote (Daniel Smith @ Oct. 26 2007,03:06)
And, another thing:

If I were really only interested in reaffirming my own ideas with no concerns for opposing data or evidence, why on earth would I come here?!?!

1. I don't recall anyone saying you were here to reaffirm your beliefs, they said you were rock steady in them.

2. In order to convince us you are right, because you subconsciously think this will work, since you clearly think that they trump absolutely anything we can throw at them. Whenever someone gets an idea they believe is totally impervious to attack they immediately want to test it on the opposition because they expect them to fall on their knees and shield their eyes from it's brilliance. It's that simple, if you seriously think that your idea is absolutely, no matter what right, then you think deep down we will, eventually succumb to it.

There might be some truth to #2.

Date: 2007/10/26 13:56:24, Link
Author: Daniel Smith
Quote (Louis @ Oct. 26 2007,13:50)
Quote (Daniel Smith @ Oct. 26 2007,19:48)
I've learned that God is an infinitely brilliant chemist...

I call bullshit! Since the synthesis of azadirachtin I think we can conclude that Steve Ley is an infinitely brilliant chemist!

Louis

Where did he get the idea for azadirachtin?

Date: 2007/10/28 13:08:35, Link
Author: Daniel Smith
I'm going to ignore most of your post because it is laced with personal insults which have little or nothing to do with the subject.  You have attempted to make this thread about me, when it should be about the evidence.  Something you have devoted almost no time to discussing.  For instance, you say that my prediction about Acromobacter guttatus Sp. K172 has been falsified, but where is the cited study?  What specific parameters were used?  How many plates were used?  Were all the bacteria on each plate Acromobacter guttatus Sp. K172?  In short, where is your evidence?

 
Quote (swbarnes2 @ Oct. 26 2007,15:52)
So you believe that the persistant adaptiveness of parasites that kill a hundred thousand children a year reveals...what, exactly about God?

Please, be specific.

Or, you can say nothing, and we'll all understand why.

I will address this one thing you brought up, because it keeps getting asked (in one form or another - "Why HIV/AIDS ?", etc.).

The standard theological answer as to why there is disease and death, is due to the "Curse".  I don't know if you're familiar with Christian doctrine or not, but disease and death are expected from this theological perspective.

Date: 2007/10/28 13:10:04, Link
Author: Daniel Smith
What is your explanation as to why disease and death continue?

Date: 2007/10/28 13:20:03, Link
Author: Daniel Smith
Quote (Louis @ Oct. 26 2007,14:11)
   
Quote (Albatrossity2 @ Oct. 26 2007,19:59)
   
Quote (Daniel Smith @ Oct. 26 2007,13:56)
Where did he get the idea for azadirachtin?

From pixies.

Prove that he didn't!

WAS NOT!

It was leprechauns.

PROVE ME WRONG!!!!! (All science so far)

Louis

I'd argue that he got the idea from azadirachtin.

Arguing that Steve Ley is an "infinitely brilliant chemist", because he figured out how to synthesize something that already exists in a natural form, is like arguing that a cover band is brilliant because they can play someone else's music.  They might be great musicians, but they have not shown any creativity or originality by merely copying someone else's work.  They (and he) surely have not shown "infinite brilliance"!

Date: 2007/10/28 15:22:02, Link
Author: Daniel Smith
Back to another prediction I made:
   
Quote (Daniel Smith @ Sep. 30 2007,15:32)

The genetic code will be found to be more sophisticated and more robust than previously thought.
Embedded and overlapping coding will be found to be more prevalent than previously thought.


In researching the phenomena of overlapping genes, I found that their initial discovery in bacteriophages was followed by speculation that perhaps they evolved due to a lack of informational space in small genomes.  Their subsequent discovery in viruses  seemed to confirm this hypothesis.  
They were then discovered in mammalian mitochondrial DNA (example) - which led to speculation that they might be more common than previously thought.
They are.  I found this article. which shows that not only are overlapping genes fairly common in mammalian genomes, but there are even triple and quadruple overlaps! (Table of triple overlaps for human and mouse genomes)
And:
   
Quote
In the human genome we also found a segment with four exon overlapping genes: LOC338549, IDI2, HT009, and IDI1.


So it would seem, from a cursory browsing of the scientific literature, that my prediction is holding true so far.  Of course, one could argue that this data was already available when I made the prediction - so my prediction was dishonest.  Of course such an accusation would fly in the face of your collective observation regarding my complete lack of knowledge on the subjects of which I speak!  So either I'm much more cunning and aware than I let on, or my prediction is (for the time being at least) a good one.

Date: 2007/10/30 13:52:23, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Oct. 28 2007,16:16)
 
Quote (Daniel Smith @ Oct. 28 2007,15:22)
Back to another prediction I made:
         
Quote (Daniel Smith @ Sep. 30 2007,15:32)

The genetic code will be found to be more sophisticated and more robust than previously thought.
Embedded and overlapping coding will be found to be more prevalent than previously thought.



Not really. It's like saying "there is more to find out" and when more is found out, it confirms your prediction.

Make a specific prediction, and then maybe crow about it when it comes true. I don't see the word "overlapping" in there.

You must've missed it.

Date: 2007/10/30 13:59:49, Link
Author: Daniel Smith
Quote (JAM @ Oct. 29 2007,00:10)
Random mutation doesn't do it by itself. You've bought into the lie that evolution is random, just because a part of it (mutation) is random only in a very limited way (wrt fitness). Why would you buy into such an obvious lie?
You're right.  Evolution is not random.
Quote
How do you explain the fact that starting with a random sequence, we can use mutation and selection to evolve a function in real time?

My guess is that it has to do with the selection criteria.  With a specific goal in mind, random solutions can be consecutively selected until they actually build something useful.

The main reason these types of selection algorithms work is because they select for potential.

Natural selection is not so kind.

Date: 2007/10/31 18:20:42, Link
Author: Daniel Smith
Quote (IanBrown_101 @ Oct. 30 2007,14:18)
Is it just me, or are you Daniel trying to force God into some real science?

I mean when you say things like it's your "guess" that structures are being designed by evolution, aren't you just saying that since the general direction of evolution after stages a and b seems to be towards z, therefore something designed it to be z?

Seems like a whole lot of straw clutching there.

I'm talking about computer simulations - not real evolution.

Date: 2007/10/31 18:25:38, Link
Author: Daniel Smith
Quote (C.J.O'Brien @ Oct. 30 2007,14:19)
Quote
My guess is that it has to do with the selection criteria.  With a specific goal in mind, random solutions can be consecutively selected until they actually build something useful.

The main reason these types of selection algorithms work is because they select for potential.

Natural selection is not so kind.


You're wrong, Daniel.
See
here and here for an object lesson in Evolutionary Computation.

He doesn't give us his selection algorithm, so how can we know if it selects for potential?

Date: 2007/10/31 18:27:17, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Oct. 30 2007,14:22)
Quote (Daniel Smith @ Oct. 30 2007,13:52)
Quote (oldmanintheskydidntdoit @ Oct. 28 2007,16:16)
   
Quote (Daniel Smith @ Oct. 28 2007,15:22)
Back to another prediction I made:
           
Quote (Daniel Smith @ Sep. 30 2007,15:32)

The genetic code will be found to be more sophisticated and more robust than previously thought.
Embedded and overlapping coding will be found to be more prevalent than previously thought.



Not really. It's like saying "there is more to find out" and when more is found out, it confirms your prediction.

Make a specific prediction, and then maybe crow about it when it comes true. I don't see the word "overlapping" in there.

You must've missed it.

Permalink? Not that I don't trust you or anything, but I am willing to be proven wrong.

Permalink

Date: 2007/10/31 18:35:41, Link
Author: Daniel Smith
Quote (JAM @ Oct. 30 2007,15:05)
 
Quote (Daniel Smith @ Oct. 30 2007,13:59)
     
Quote
How do you explain the fact that starting with a random sequence, we can use mutation and selection to evolve a function in real time?

My guess is that it has to do with the selection criteria.

There was a single criterion in the case to which I'm referring: reproduction. Does that help?
     
Quote
With a specific goal in mind, random solutions can be consecutively selected until they actually build something useful.

But there was no specific goal in this case, just reproduction.
   
Quote
The main reason these types of selection algorithms work is because they select for potential.

There was no selection for potential in this case. I'm amazed at the way you view your speculations as more relevant than reality.
     
Quote
Natural selection is not so kind.

This was no different, with the exception of the elimination of competition from outside the initial pool. How do you explain it? More importantly, why would you attempt to explain it when you don't have a clue to begin with?

The more you say, the less I understand you.

If you want specific, detailed answers, why don't you try starting with a specific example - rather than a vague question?
This:
Quote
How do you explain the fact that starting with a random sequence, we can use mutation and selection to evolve a function in real time?

Gives us no information.  I was forced to speculate that you were referring to computer simulations of evolution.  Is that what you were talking about?  Or were you referring to something else?  If a simulation, please show me the info - including the selection algorithm - so I can get a better idea how it works.  
If you're not willing to give any more info, then be satisfied with general answers.

Date: 2007/10/31 19:08:53, Link
Author: Daniel Smith
More confirmation:

From the paper, "Unbiased Mapping of Transcription Factor Binding Sites along Human Chromosomes 21 and 22 Points to Widespread Regulation of Noncoding RNAs"
link
         
Quote
To further explore properties of the transcriptome and to identify functional attributes of the noncoding transcripts, binding sites for a collection of transcription factors have been mapped along chromosomes 21 and 22 in an unbiased approach, as a means of identifying possible regulatory regions for a wide variety of cellular RNAs. Interestingly, only 22% of the transcription factor binding sites (TFBS) are located at the canonical 5? termini of well-characterized protein-coding genes, while 36% lie within of immediately 3? to well-characterized genes and are significantly correlated with noncoding RNAs. A number of these noncoding RNAs are regulated in response to retinoic acid stimulation, and coregulation of overlapping pairs of protein-coding and noncoding RNAs occurs at a frequency significantly greater than chance. These data point to evidence that protein coding and noncoding genes have similar functional attributes regarding (1) the existence of common transcription factors in their promoter regions and (2) their ability to respond to environmental and developmental conditions, which together suggest that that they may be controlled by the same transcriptional regulatory machinery. These functional attributes argue against the idea that these noncoding RNAs merely represent transcriptional noise, but instead suggest that they may have biological functions. (my emphasis)
And...        
Quote
Additionally, overlapping novel transcripts from the genes encoding nuclear protein UBASH3A (Supplemental Figures S2A and S2B), phosphatidylinositol transfer-like protein SEC14L2 (Supplemental Figures S2C and S2D), TBC/rabGAP domain protein EPI64 (Supplemental Figures S2E and S2F), guanine-nucleotide exchange factor TIAM1 (Supplemental Figures S2G and S2H), KIAA0376 protein (Supplemental Figures S2I and S2J), and GTSE1 (Supplemental Figures S2K and S2L) were verified by RT-PCR and/or Northern blot analyses (Supplemental Figure S3). In many of these cases, the TFBS that are located on the 3? end of the well-characterized gene appear to be located 5? of the overlapping novel transcript, which suggests that these transcripts may be regulated by these factors and in precisely the same way as protein coding genes. (my emphasis)


So not only is the myth of "junk DNA" being systematically shattered, but they are also finding evidence that coding and non-coding sequences not only overlap each other, but also share regulatory factors.

Date: 2007/10/31 19:42:18, Link
Author: Daniel Smith
Quote (C.J.O'Brien @ Oct. 31 2007,18:38)
Note also, that in a strict and very real sense these are not "simulations of evolution."

GA's like these we are speaking of are instantiations of real, no-kidding, actual Darwinian processes.

Therein lies the difference.  "Darwinian processes", when coupled with strict selection criteria (which conform to a specific goal), can take any random sequence and eventually meet that goal.

Real Darwinian evolution however, has no goal.  Reproductive fitness is seen as a valid section criteria, but it cannot be the reason for the variety of lifeforms we see.  If reproductive fitness was the goal, nothing beyond bacteria would have ever evolved - since they are probably the fittest reproducers on the planet.

So, if you want to postulate a mechanism for evolution, you must show one that is capable of producing vast complexity without a goal.

Therein lies the conundrum for your theory.

Date: 2007/11/01 19:29:10, Link
Author: Daniel Smith
Quote (JAM @ Oct. 31 2007,19:17)
It's biology. You delete a gene with an essential function. You replace it with random sequence. You go through cycles of genetic variation (random wrt fitness) and selection (only reproduction).

You end up with a functional sequence that is nothing like the designed/evolved one that it replaced.

How do you explain that?

Be more specific.  Show me the paper that describes this experiment.  I will no longer answer your questions unless you provide complete explanations with references.

Date: 2007/11/01 19:48:19, Link
Author: Daniel Smith
Quote (JAM @ Oct. 31 2007,19:26)
 
Quote (Daniel Smith @ Oct. 31 2007,19:08)
More confirmation:

Of what?

Did you read this?

Yes I did.
 
Quote

   
Quote
By combining chromatin immunoprecipitation and high-density oligonucleotide arrays interrogating the [bold]nonrepeat[/bold] genomic sequences of chromosomes 21 and 22 at 35 base pair (bp) resolution (Kapranov et al., 2002), the positions of binding for three human transcription factors (TFs), cMyc, Sp1, and p53, were determined within two cell lines (cMyc and Sp1 in Jurkat, p53 in HCT1116).


What does "nonrepeat" mean, Daniel?
Just what it says.  
Quote
What proportion of "junk" is repeat, and what proportion is nonrepeat (unique)?
There is no junk  
Quote


   
Quote
So not only is the myth of "junk DNA" being systematically shattered, but they are also finding evidence that coding and non-coding sequences not only overlap each other, but also share regulatory factors.


How much DNA was reclassified as something other than the provisional classification of "junk" in this case?
They didn't specifically mention "junk".  
Quote


What proportion of the genome? Be precise and systematic.
Since they didn't refer to any portion of the genome as junk, I cannot answer that.  
Quote

What proportion of the genome did they throw out when they only looked at "nonrepeat" sequences? Be precise and systematic.
I could not find that information in the paper.   Are you equating repeat sequences with "junk"?  
Quote


You lie like a rug, Daniel. The fact that you're lying to yourself doesn't excuse your behavior.

I know: "Liar, liar - pants on fire!"
What are we - in 3rd grade here?
You may be a smart, educated guy - but you're socially retarded.

Date: 2007/11/01 19:50:50, Link
Author: Daniel Smith
Quote (JAM @ Nov. 01 2007,19:37)
 
Quote (Daniel Smith @ Nov. 01 2007,19:29)
   
Quote (JAM @ Oct. 31 2007,19:17)
It's biology. You delete a gene with an essential function. You replace it with random sequence. You go through cycles of genetic variation (random wrt fitness) and selection (only reproduction).

You end up with a functional sequence that is nothing like the designed/evolved one that it replaced.

How do you explain that?

Be more specific.  Show me the paper that describes this experiment.  I will no longer answer your questions unless you provide complete explanations with references.

Your petulant demand is pretty damn funny, coming from a guy who claims that a paper in which the authors explicitly told him that they weren't looking at repeated sequences has something global to say about junk DNA. Moreover, you don't have the integrity to address that problem when I pointed it out to you.

OK, I'll give in to your whining, but you have to answer a question first.

What level reduction do you consider to represent lack of function? For example, if your heart rate was reduced a million-fold, to ~1 beat every 10 days, you'd be dead. Would you agree that your heart failed to function--that it was not meeting design criteria, so to speak?

No more games.  Show me the paper.

Date: 2007/11/03 16:05:03, Link
Author: Daniel Smith
Quote (JAM @ Nov. 02 2007,20:24)
Quote (W. Kevin Vicklund @ Nov. 02 2007,11:43)
I believe I know of the paper JAM is referring to - it came up last month (hint: 10^6 is not the same as six-fold).  I haven't read it myself, though.

I think we can safely assume that Daniel will maintain that even a million-fold reduction in function is still functional.

Yup. Even if it's his heart.

Still waiting...

Date: 2007/11/03 16:47:30, Link
Author: Daniel Smith
Meanwhile, here's a graphic description of the overwhelming complexity within the multi-layered encoding within genomes:

   
Quote
Figure 2. Transcriptional complexity of a gene. Hypothetical gene cluster with detailed zoom-in for highlighted gene demonstrates that a single gene can have multiple transcriptional start sites (TSSs) as well as many interleaved coding and noncoding transcripts. Exons are shown as red boxes and TSSs are green right-angled arrows. Known short RNAs such as snoRNAs and miRNAs can be processed from intronic sequences and novel species of short RNAs that cluster around the beginning and ends of genes have recently been discovered (see text).


From the paper Origin of phenotypes: Genes and transcripts.

Although this illustration is hypothetical, it represents what the author expects to find and indeed what the ENCODE scientists did find, in their recent groundbreaking research.  This prompted the author to make this statement:  
Quote
Thus, in light of this overlapping interleaved network of protein-coding and noncoding transcripts, it seems appropriate to reconsider the concept of gene in describing the relationship of a portion of a genome to a phenotype.

Date: 2007/11/04 12:50:42, Link
Author: Daniel Smith
Quote (Assassinator @ Nov. 04 2007,04:34)
Sorry to break in guys, i'm just new here, but i've got a few questions for Daniel.
First of all, what do you want Daniel? I don't get it, are you interested in reality of are you interested in confirming you're own thoughts? Because if it is the latter, that's not what science is about. I also read you were more interested in the scientists who were shunned by the scientific world, the one's who were laughed at etc etc. But also, that's not where it is about, it's pure about evidence. Hell, it doesn't matter if correct statements are brought by a light-blue, Satan worshipping fairy with daisy's sprouting out of it's head: evidence is evidence, no matter who brought it up. Persons do not matter, and so does your own thoughts about this subject. If you want to learn, let those things go. I don't have the idea you want to learn, but only want to confirm you're own thoughts, that there must be some form of design, designer or end-goal. I think you have emotionally attached yourself to your own idea about reality, i wonder why.
This may be a lot for me to ask, because i'm new, but maybe you could give a little summary about what you think Daniel. Maybe this would help the discussion in general, it's getting a little out of hand because people start ignoring important parts of posts from eachother.

First of all, we all have preconceived ideas we are hoping to verify.  Many here have a preconceived notion that there is no God.  They are not even willing to consider that option.  In fact many will say that such an option is outside the realm of science.  So even if there really is a God, they are forced to find another explanation - no matter how ridiculous.  Is that "seeking the truth"?
I think I've laid out my thoughts and goals pretty straightforwardly throughout the 18 pages of this thread.  I'm willing to let go of anything I believe - provided the evidence against it is convincing.  So far, I've seen nothing convincing here.  The fossil record and the molecular evidence are both consistent with a belief that God designed and implemented life on this planet.
The fossil record shows "explosions" of lifeforms suddenly appearing and then diversifying.
The molecular evidence shows an extremely complex, sophisticated, multi-layered coding system that defies any unguided evolutionary explanation.  If you notice, most of the more recent papers don't even bother to speculate anymore as to how such a system evolved.  It's beyond explanation.
In fact, the more I learn, the more convinced I am of the infinite intelligence of the designing God.
Now, I could take your questions and turn them around and ask them of you:  What is your goal?  What are your preconceived ideas?  Are you willing to let them go and consider the possibility of a designing God?

Date: 2007/11/04 13:05:20, Link
Author: Daniel Smith
Quote (Assassinator @ Nov. 04 2007,04:34)
I also read you were more interested in the scientists who were shunned by the scientific world, the one's who were laughed at etc etc. But also, that's not where it is about, it's pure about evidence. Hell, it doesn't matter if correct statements are brought by a light-blue, Satan worshipping fairy with daisy's sprouting out of it's head: evidence is evidence, no matter who brought it up.

Let me also add; these scientists have theories that have never been falsified.
Their ideas were ridiculed - because they did not fit the current paradigm, but I've seen no convincing evidence against them.  The Prescribed Evolutionary Hypothesis (PEH) of Dr. John Davison is a good example. (link) Many here and elsewhere have ridiculed Dr. Davison for his personal habits, grumpiness, lack of civility, etc., or they have ridiculed his hypothesis from afar, but how many have systematically and thoroughly reviewed it and presented convincing evidence against it?  I've not seen any.
The same can be said about the theories of Berg and Schindewolf I've presented (albeit limitedly) here.  No one has presented any evidence against them.  Most of it was just preconceived suppositions that they must somehow be wrong because they didn't fit the current paradigm!  In fact there's been an almost complete lack of willingness to discuss their ideas - with some frantic subject-changing going on.
So... Yes... I do look for those on the fringes who have presented differing ideas.  If their ideas have been shown wrong, I don't give them much weight, but if it's just that they were made fun of, that doesn't hold much sway with me.

Date: 2007/11/04 13:36:22, Link
Author: Daniel Smith
Quote (Assassinator @ Nov. 04 2007,13:05)
I agree that lots of people also have preconcieved ideas about a god. But there is also something else, it looks like you're emotionally attached to your preconcieved ideas. Note that the word "God" doesn't mean anything by itself, it's rather a coat rack (i hope i translate that correctly) on wich people put there own image of the word "God". The word "God" is thus worthless to science. Science can only work with certain images of the word "God". It's so easy to modify that image. Not even that long ago, and even today, people still beleive that God created and designed everything around us, but not in the way you would beleive it. The role of God has changed, it's like the God of the Gaps.
         
Quote
The fossil record and the molecular evidence are both consistent with a belief that God designed and implemented life on this planet.

Explain yourself. Because i don't see why. I'm only seeing a certain interpretation of the available evidence so the evidence fits in your beleifs. But is that interpretation in agreement with reality? Ofcourse, you can ask the same with other interpretations.
         
Quote
The fossil record shows "explosions" of lifeforms suddenly appearing and then diversifying.

You shouldn't take the world "explosion" too literally. It still took several millions of years, and that's VERY long and LOTS of generations fit into that.
         
Quote
The molecular evidence shows an extremely complex, sophisticated, multi-layered coding system that defies any unguided evolutionary explanation.

No, it does not. It's complex in your eyes, nothing more. Hell, we may meet aliens who laugh at our simple planet with our simple lifeforms. It's simply not an argument to say it's complex compared what we can do. The fact that we don't get it, is no argument for design, it's only an argument for our limited knowledge.
         
Quote
Now, I could take your questions and turn them around and ask them of you:  What is your goal?  What are your preconceived ideas?  Are you willing to let them go and consider the possibility of a designing God?

My goal? To learn more about reality. My preconcieved ideas? No idea, i don't give a ratsass if our planet was made by a God, erupted out of natural laws or made by aliens from starsystems thousands of lightyears away for an experiment. I just care about what's true. Ofcourse i consider the possibility of a designing God, but as i sad before there is no evidence or objective sign for such a being.

You are right. I am emotionally attached to my preconceived ideas - and I will only let go of them when convinced otherwise.
And (I've said this before), I am not advocating a "god of the gaps", I am advocating a "God of all that is".  I give him credit for everything - even those things that man thinks he has explained.  Just because we can explain something doesn't mean we have eliminated design from the argument.  I can explain many of the systems at work within my car, does that mean it wasn't designed?  Obviously not.  It only means I have gained an understanding of the designer's systems.
So... my definition of God is that of an eternal, infinitely intelligent, cognitive agent that exists in a parallel dimension to our own.
Thus, he is a being not bound by time and capable of doing anything.  Now, I realize that that last part seems like a cop-out, since someone who can do anything also explains everything, but let me also point out that - if life were created by a being of infinite intelligence - we would expect to find certain things within life.
Let's use your aliens as an example.  If we were to find an object that we believed to be created by an alien race more intelligent than our own, we would expect to find technology superior to our own within that object.
The fact that we find technology superior to our own within the mechanisms of life can be used as an argument that the designer of life was at least orders of magnitude more intelligent than us.
Now some will argue that the molecular mechanisms - in all their sophistication - are the result of natural processes, but then isn't it up to them to show that these natural processes can create such sophistication and elegance?
So far, I've seen no convincing evidence that natural processes can produce complex, functional systems such as we have in life.  None.

Date: 2007/11/04 13:40:57, Link
Author: Daniel Smith
Quote (Erasmus @ FCD,Nov. 04 2007,13:25)
Schindewolf's theories were devastated by particulate inheritance and the mathematical synthesis.  
Yes, please provide links to those papers and please elaborate as to how these things "devastated" Schindewolf's theory.
Quote
it makes no sense whatsoever to have reserve genetic material, in advance of adaptive radiations, sitting around in the genome.
It makes perfect sense from a front-loading perspective.
Quote

unless we now have a function for noncoding DNA?  not seen that advanced but it would still be a greatly different take from schindewolf.
I have no idea what this sentence means.

Date: 2007/11/04 20:08:55, Link
Author: Daniel Smith
Quote (Richard Simons @ Nov. 04 2007,15:30)
       
Quote
Yes, please provide links to those papers and please elaborate as to how these things "devastated" Schindewolf's theory.

When I asked you about some aspects of Schindewolf's theory your response was

         
Quote (Daniel Smith @ Oct. 25 2007,13:50)
         
Quote (Richard Simons @ Oct. 25 2007,00:00)
Back to Schindewolf! I am not sure why a hypothesis that has been essentially dead for 50 years holds so much fascination for you. However, given that it does perhaps you could explain how the information to constrain an organism's evolutionary pathway is held. What conceivable mechanism could stop evolution from taking place, or enable parts to evolve before they became useful?

I am also curious about the saltational events. Do you see these as creating a new genus, order, phylum or what? What actually occurs during a saltational event? How does the DNA get changed and how does it know what to become, as I gather it is preparing for the next few million years of evolution and changing conditions? When did the last saltational event take place? I don't even know if the proposal is that one day a dinosaur chick hatched that had feathers and wings or if the process was spread over many generations, which might make it little different from the rapid evolution phase of punctuated equilibrium.

I'm looking forward to your answers.

I don't know.

How do you expect us to respond when you can't even tell us some of the basics of the theory?

Schindewolf didn't cover many of the questions you asked.  His theory was based on the fossil record - not genetics.  If you had asked me what evidence exists in the fossil record to support his threefold theory of typogenesis, typostasis and typolysis, I could answer you.

I will say this: Davison's PEH does attempt to answer many of your questions.
     
Quote
perhaps you could explain how the information to constrain an organism's evolutionary pathway is held.
It is contained in the first individual of a new type, and is maintained by sexual reproduction and/or selection.      
Quote
What conceivable mechanism could stop evolution from taking place
Sexual reproduction, selection, extinction...      
Quote
or enable parts to evolve before they became useful?
Semi-meiotic reproduction.      
Quote
I am also curious about the saltational events. Do you see these as creating a new genus, order, phylum or what?
Schindewolf called them "types".  I have no idea what current category that conforms to.    
Quote
What actually occurs during a saltational event?
According to Davison's semi-meiotic hypothesis, the structural reordering of genetic information within the chromosomes.      
Quote
How does the DNA get changed and how does it know what to become, as I gather it is preparing for the next few million years of evolution and changing conditions?
See above.      
Quote
When did the last saltational event take place?
Again, according to Davison - the evolution of humans was the last saltational event.

Now, I have to restate the fact that I don't know the answers to any of your questions, and Schindewolf did not address most of them, so I was not "lying", nor was I unsupportive of Schindewolf's theory.

Date: 2007/11/06 13:58:55, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Nov. 05 2007,02:48)
I can propose anything I like, I don't expect the world to jump on it and disprove it. It's up to me to provide positive proof in the first instance.

Davison cites experimental evidence showing that semi-meiotic reproduction is possible even amongst sexually reproductive animals.

But where is the "positive proof" (you say) you require for the assumed mechanisms of gradual evolution?

Date: 2007/11/09 13:51:18, Link
Author: Daniel Smith
Quote (JAM @ Nov. 07 2007,09:10)
Quote (Daniel Smith @ Nov. 06 2007,13:58)
 
Quote (oldmanintheskydidntdoit @ Nov. 05 2007,02:48)
I can propose anything I like, I don't expect the world to jump on it and disprove it. It's up to me to provide positive proof in the first instance.

Davison cites experimental evidence showing that semi-meiotic reproduction is possible even amongst sexually reproductive animals.

But where is the "positive proof" (you say) you require for the assumed mechanisms of gradual evolution?

Daniel, I take issue with omitsddi's use of the term "proof," but plenty of positive evidence is available from VISTA. That's why you felt compelled to lie and claim that noncoding regions in genes (introns and 5' and 3' UTRs) were "coding regions."

Again, get this through your thick head. It's not about CITING evidence. It's about PRODUCING NEW EVIDENCE by TESTING YOUR OWN HYPOTHESIS.

Surely you're not so stupid that you can't see the immense difference between those criteria. Are you so dishonest that you cant acknowledge it?

I'm still waiting for a paper from you.

Date: 2007/11/09 22:05:36, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Nov. 06 2007,14:14)
 
Quote (Daniel Smith @ Nov. 06 2007,13:58)
   
Quote (oldmanintheskydidntdoit @ Nov. 05 2007,02:48)
I can propose anything I like, I don't expect the world to jump on it and disprove it. It's up to me to provide positive proof in the first instance.

Davison cites experimental evidence showing that semi-meiotic reproduction is possible even amongst sexually reproductive animals.

But where is the "positive proof" (you say) you require for the assumed mechanisms of gradual evolution?

   
Quote
Allen MacNeill
Sources of Heritable Variation (both genotypic and phenotypic) Among Individuals in Populations

Gene Structure (in DNA)
• single point mutations
• deletion and insertion (“frame shift”) mutations
• inversion and translocation mutations
Gene Expression in Prokaryotes
• changes in promoter or terminator sequences (increasing or decreasing binding)
• changes in repressor binding (in prokaryotes); increasing or decreasing binding to operator sites
• changes in repressor binding (in prokaryotes); increasing or decreasing binding to inducers
• changes in repressor binding (in prokaryotes); increasing or decreasing binding to corepressors
Gene Expression in Eukaryotes
• changes in activation factor function in eukaryotes (increasing or decreasing binding to promoters)
• changes in intron length, location, and/or editing by changes in specificity of SNRPs
• changes in interference/antisense RNA regulation (increasing or decreasing binding to sense RNAs)
Gene Interactions
• changes in substrates or products of biochemical pathways
• addition or removal of gene products (especially enzymes) from biochemical pathways
• splitting or combining of biochemical pathways
• addition or alteration of pleiotropic effects, especially in response to changes in other genes/traits
Eukaryotic Chromosome Structure
• gene duplication within chromosomes
• gene duplication in multiple chromosomes
• inversions involving one or more genes in one chromosome
• translocations involving one or more genes between two or more chromosomes
• deletion/insertion of one or more genes via transposons
• fusion of two or more chromosomes or chromosome fragments
• fission of one chromosome into two or more fragments
• changes in chromosome number via nondisjunction (aneuploidy)
• changes in chromosome number via autopolyploidy (especially in plants)
• changes in chromosome number via allopolyploidy (especially in plants)
Eukaryotic Chromosome Function
• changes in regulation of multiple genes in a chromosome as a result of the foregoing structural changes
• changes in gene expression as result of DNA methylation
• changes in gene expression as result of changes in DNA-histone binding
Genetic Recombination
• the exchange of non-identical genetic material between two or more individuals (i.e. sex)
• lateral gene transfer via plasmids and episomes (especially in prokaryotes)
• crossing-over (reciprocal and non-reciprocal) between sister chromatids in meiosis
• crossing-over (non-reciprocal) between sister chromatids in mitosis
• Mendelian independent assortment during meiosis
• hybridization
Genome Structure and Function
• genome reorganization and/or reintegration
• partial or complete genome duplication
• partial or complete genome fusion
Development (among multicellular eukaryotes, especially animals)
• changes in tempo and timing of gene regulation, especially in eukaryotes
• changes in homeotic gene regulation in eukaryotes
• genetic imprinting, especially via hormone-mediated DNA methylation
Symbiosis
• partial or complete endosymbiosis
• partial or complete incorporation of unrelated organisms as part of developmental pathways (especially larval forms)
• changes in presence or absence of mutualists, commensals, and/or parasites
Behavior/Neurobiology
• changes in behavioral anatomy, histology, and/or physiology in response to changes in biotic community
• changes in behavioral anatomy, histology, and/or physiology in response to changes in abiotic environment
• learning (including effects of use and disuse)
Physiological Ecology
• changes in anatomy, histology, and/or physiology in response to changes in biotic community
• changes in anatomy, histology, and/or physiology in response to changes in abiotic environment


Which particular assumed mechanism are you interested in?

I don't care.  Pick one and lets look at the experimental evidence showing it's capabilities towards creating complex functional systems.

Date: 2007/11/09 23:32:33, Link
Author: Daniel Smith
OK, only because you're going to keep acting as if I'm the one who's stalling the discussion, I'll attempt to answer your questions.              
Quote (JAM @ Nov. 09 2007,15:03)
How do you explain the fact that starting with a random sequence, we can use mutation and selection to evolve a function in real time?

I don't know.  I don't know that it is possible.  I'd predict that it isn't.  But first, don't we have to agree what a "function" is?                  
Quote
What level reduction do you consider to represent lack of function? For example, if your heart rate was reduced a million-fold, to ~1 beat every 10 days, you'd be dead. Would you agree that your heart failed to function--that it was not meeting design criteria, so to speak?

This is silly.  Are you asking for a general level for "lack of function"?  Or are you just concerned about the heart?  I would agree that a heart that beats once every ten days would be considered "non-functional" for a human - or any other known animal.  What does that have to do with the paper you refuse to show me?                  
Quote
In addition, why aren't these discoveries being made by ID proponents...like, um, at the Discovery Institute?

I don't know.                  
Quote
Why aren't discoveries like these motivating people like you to start careers in science?

I don't know.  I can't speak for "people like me".  I can only speak for myself.  Science for me, is a hobby.  I already have a career.                  
Quote
What do any of the data have to do with the genetic code, which really isn't very complex?

What's so complex about coding for 20 amino acids, start, and stop in 64 codons?

Or were you just using "genetic code" in a profoundly ignorant way?

Apparently I was.  You are right, the code is simple, what it codes for isn't.                  
Quote
...would you mind commenting on the intelligence of having the same codon that starts protein synthesis also encoding the amino acid methionine?

Is this a problem?                  
Quote
I ask because it seems really, really stupid to me; I can improve the design with my measly human intelligence.

Then why don't you?                    
Quote
Does that therefore make me smarter than God?

No.                  
Quote

Why would one want to worship an unintelligent God?

One wouldn't.                  
Quote
Do you see how the ID movement is bad theology slathered onto nonexistent science?

No.                  
Quote
Here's another question: how long does it take to evolve multiple, different, incredibly specific, functional, new protein-protein binding sites, using nothing but genetic variation and selection?

I don't know.                  
Quote
What does "nonrepeat" mean, Daniel?

I would guess it means "doesn't consist of repeating sequences".                  
Quote

What proportion of "junk" is repeat, and what proportion is nonrepeat (unique)?

How much DNA was reclassified as something other than the provisional classification of "junk" in this case? What proportion of the genome? Be precise and systematic.

What proportion of the genome did they throw out when they only looked at "nonrepeat" sequences? Be precise and systematic.

So how can introns be both coding sequences and junk sequences?

How does studying nonrepeat sequences within and near genes reclassify "junk" DNA?

Since you've never given me a definition for "junk" DNA, I had to do a google search.  I found this here (at the first page I looked at):
 
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#  Less than 2% of the genome codes for proteins.
# Repeated sequences that do not code for proteins ("junk DNA") make up at least 50% of the human genome.


Do you agree with this definition: "Repeated sequences that do not code for proteins = junk DNA"?

If that's the "provisional definition" of junk DNA, then studying non-repeat sequences doesn't have anything to do with junk (as so defined) and I was wrong to argue that it did.

I guess the answer to the other question would be that they "threw out" 50% of the genome when they didn't look at repeat sequences.

I'm curious though, when I asked; "Are you equating repeat sequences with "junk"?", you replied "No, obviously, I'm not.".  So, I'm guessing that this isn't exactly your definition of junk.  Why don't you just tell me what your definition is?
           
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For example, if God designed your body, He clearly understands the concept of plumbing. Why is there nothing analogous within cells?

You mean like pumps?                  
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Why do cells use a system analogous to throwing lipid water balloons full of food and sewage around (allowing them to fuse and ripping them apart) instead of having simple plumbing?

I don't know.  It seems to work just fine though.                  
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According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?

I don't have a specific number.  Did you have one before you found out the actual number?

Now, will you show me the paper?

Date: 2007/11/09 23:42:43, Link
Author: Daniel Smith
Quote (Jim_Wynne @ Nov. 09 2007,22:22)
 
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Pick one and lets look at the experimental evidence showing it's capabilities towards creating complex functional systems.

Define "complex" and tell us how we can identify it, and what the delimiter is between complex and not-complex.  While you're at it, you might also want to tell us what you think a "functional system" is.

Suggested reading.

Date: 2007/11/10 10:45:43, Link
Author: Daniel Smith
Quote (JAM @ Nov. 10 2007,01:05)
http://www.springerlink.com/content/hhcx0pur3545x7v3/

Thank you.

I was not able to read the entire paper, but only the abstract:
 
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Abstract

To explore the possibility that an arbitrary sequence can evolve towards acquiring functional role when fused with other pre-existing protein modules, we replaced the D2 domain of the fd-tet phage genome with the soluble random polypeptide RP3-42. The replacement yielded an fd-RP defective phage that is six-order magnitude lower infectivity than the wild-type fd-tet phage. The evolvability of RP3-42 was investigated through iterative mutation and selection. Each generation consists of a maximum of ten arbitrarily chosen clones, whereby the clone with highest infectivity was selected to be the parent clone of the generation that followed. The experimental evolution attested that, from an initial single random sequence, there will be selectable variation in a property of interest and that the property in question was able to improve over several generations. fd-7, the clone with highest infectivity at the end of the experimental evolution, showed a 240-fold increase in infectivity as compared to its origin, fd-RP. Analysis by phage ELISA using anti-M13 antibody and anti-T7 antibody revealed that about 37-fold increase in the infectivity of fd-7 was attributed to the changes in the molecular property of the single polypeptide that replaced the D2 domain of the g3p protein. This study therefore exemplifies the process of a random polypeptide generating a functional role in rejuvenating the infectivity of a defective bacteriophage when fused to some preexisting protein modules, indicating that an arbitrary sequence can evolve toward acquiring a functional role. Overall, this study could herald the conception of new perspective regarding primordial polypeptides in the field of molecular evolution.

This is an interesting experiment.  I have a couple questions:
1.  Why did they use artificial selection as opposed to natural selection?
2.  My math isn't the greatest so when they say that the replacement phage had "six-order magnitude lower infectivity" than the original phage, and the newly evolved phage "showed a 240-fold increase in infectivity as compared to its origin, fd-RP", they're talking about 0.00024 less infectivity than the original wild phage - correct?

Date: 2007/11/10 11:05:15, Link
Author: Daniel Smith
Quote (JAM @ Nov. 10 2007,01:07)
 
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Here's another question: how long does it take to evolve multiple, different, incredibly specific, functional, new protein-protein binding sites, using nothing but genetic variation and selection?

I don't know.

Two weeks.
Is this information in the paper you linked to?  
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Since you've never given me a definition for "junk" DNA, I had to do a google search.

But you're the one that brought it up! Why would I be responsible for defining it?
       
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#  Less than 2% of the genome codes for proteins.
# Repeated sequences that do not code for proteins ("junk DNA") make up at least 50% of the human genome.

Do you agree with this definition: "Repeated sequences that do not code for proteins = junk DNA"?

Not at all, primarily because I can point you to repeated sequences that do not code for proteins that have a known function and that no one considers to be junk: ribosomal RNA genes.

Junk is mostly repeated and some nonrepeated DNA that has no known function and is very polymorphic. The classification, being negative, is clearly provisional.
My expectation then is that the provisional definition of "junk DNA" will continually evolve until it no longer includes any portion of the genome.  
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If that's the "provisional definition" of junk DNA,...

No, the definition isn't provisional, the classification of a certain sequence as junk is. There's a huge difference.
       
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then studying non-repeat sequences doesn't have anything to do with junk (as so defined) and I was wrong to argue that it did.

Your conclusion is correct, even though the definition wasn't.
       
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I guess the answer to the other question would be that they "threw out" 50% of the genome when they didn't look at repeat sequences.

More like 90-95%.
Are you saying that 90-95% of the human genome is repeats?  
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For example, if God designed your body, He clearly understands the concept of plumbing. Why is there nothing analogous within cells?

You mean like pumps?

Yes, but more like pipes and valves that separate dirty from clean water.
   
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Why do cells use a system analogous to throwing lipid water balloons full of food and sewage around (allowing them to fuse and ripping them apart) instead of having simple plumbing?

I don't know.  It seems to work just fine though.

That all depends on your definition of "just fine." It's laughable as an example of intelligent design. Why not just put structures that serve as pipes and valves in there?
I don't know why most designers do what they do - that is not an argument against design.  It might be an effective argument against the competency of the designer, provided you can come up with a better workable system.  
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According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?

I don't have a specific number.  Did you have one before you found out the actual number?

A range will do: thousands, hundreds, dozens, or <10?

My prediction was too high.
I have no idea.  My hypothesis doesn't really work that way.  What I mean is; since I view each of the multitude of evolutionary events between mouse and man as saltational, there's no way to predict the number of orthologs.  

My main contention is that the genomic sequences of organisms will be found to be fully functional and evolutionarily constrained within species - leaving the only possible mechanisms for the true evolution of new species saltational ones.  
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BTW, I did an experiment today that had a really exciting result. My prediction was wrong.
     
So a wrong prediction is not "lying" then I take it?  ;)

Date: 2007/11/10 11:26:13, Link
Author: Daniel Smith
Quote (JAM @ Nov. 10 2007,01:06)

     
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...would you mind commenting on the intelligence of having the same codon that starts protein synthesis also encoding the amino acid methionine?

Is this a problem?

Wouldn't you agree that not combining the stop signal with an amino acid is an intelligent move, given that functional proteins end in all sorts of different aa residues?

Now, since functional proteins BEGIN with many different residues, what does that say about the intelligence of combining start with methionine?

It's really not a difficult question. There's a perfect control to demonstrate the alleged intelligence of the designer!

Not necessarily.  Many genomic sequences are multi-functional - containing overlapping coding and non-coding functional sequences.  Perhaps we just don't know the functional advantage for combining the codon that starts protein synthesis and methionine.    
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I ask because it seems really, really stupid to me; I can improve the design with my measly human intelligence.

Then why don't you?

Huh?
Why don't you engineer a better design and show it to the world?    
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Does that therefore make me smarter than God?

No.                    

Why not?
It just means you think you're smarter than God.  You have to make a workable system to actually show yourself smarter than God.    
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Why would one want to worship an unintelligent God?

One wouldn't.

I agree. So why do creationists attribute biological design to God, since so much of it is so obviously unintelligent?
So now that you have mastered all the various elements of biological design, you are prepared to say that anyone who was able to design it all would have to be unintelligent and that you could have come up with a better design?  That's a mighty big boast.  Good luck in your new venture (creating an alternate (and improved) form of life)!    
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Do you see how the ID movement is bad theology slathered onto nonexistent science?

No.

Have you considered opening your eyes to the NATURE of biological complexity, and avoiding the dishonest arguments about its presence and extent?
I am attempting to "open my eyes" to anything and everything. Please explain (or link to) anything that will help me better understand "the NATURE of biological complexity".

Date: 2007/11/10 11:29:18, Link
Author: Daniel Smith
I have a question for anyone who wants to take a shot at it:

In the human genome, what percentage of genomic sequence would you say is likely to be transcribed as nuclear primary transcripts?

Date: 2007/11/10 11:40:54, Link
Author: Daniel Smith
Quote (Jim_Wynne @ Nov. 10 2007,10:04)
Unless you're willing to define your terms in your own words, we have no way of knowing what you're talking about, and you are free to move the goalposts at will. So I'll ask again:
1) What do you mean by "complex," how do you identify it, and what are the empirical delimiters between "complex" and not-complex?
2) How do you define "functional system"?

Fair enough.

"Complex" means "composed of many interconnected parts".
As a general rule: more parts = more complex.

"Functional system" means "an assemblage of parts which work together towards the same purpose or function"

Date: 2007/11/10 12:30:37, Link
Author: Daniel Smith
Quote (JAM @ Nov. 05 2007,00:37)
     
Quote (Daniel Smith @ Nov. 04 2007,13:05)
Let me also add; these scientists have theories that have never been falsified.

Let me add that whether they've been falsified is irrelevant, when they have never been TESTED.

Schindewolf based his theory on the observed fossil record as well as observed biological evidence.  His theory was an attempt to explain all the evidence.

Berg based his theory on years and years of his own observations in the field, as well as the documented observations of countless others.

Both of these men were scientists of the highest regard in their respective fields who based their theories on observed, documented phenomena.

Davison took their work and expanded upon it - suggesting a workable mechanism.  This mechanism (semi-meiotic reproduction) has been experimentally verified possible here,
here,
and here.

   
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Gynogenetic reproduction, employing the inhibtion of meiosis I1 and yielding diploid rather than triploid progeny, can be used to map G-K distances as well as
to develop “inbred” strains*. This mode of reproduction is known in several natural populations of invertebrates and vertebrates (SUOMALAINEN 1950; WHITE 1948, 1970; OLSEN 1962; CARSON 1967) and has been produced experimentally in vertebrates when the appropriate meiotic events are altered (TYLER 1955; BEATTY 1967; GRAHAM 1970; TARKOWSKI, WITKOWSKA, and NOWICKA 1970).
(Emphasis mine)


A search for the terms parthenogenesis, gynogenesis, and hybridogenesis reveals more data in this area.

I have no idea why these scientists are ignored, but my guess is that their views don't fit the paradigm, and - based on my own observations - scientists whose ideas don't fit are generally ostracized, lose funding, and eventually relegated to the sidelines.

No one wants to lose their position over such things, so they stick to the paradigm.

That's my guess.

Date: 2007/11/10 15:51:55, Link
Author: Daniel Smith
Quote (mitschlag @ Nov. 10 2007,13:06)
     
Quote (Daniel Smith @ Nov. 10 2007,12:30)
Davison took their work and expanded upon it - suggesting a workable mechanism.  This mechanism (semi-meiotic reproduction) has been experimentally verified possible here,
here,
and here.

                   
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Gynogenetic reproduction, employing the inhibtion of meiosis I1 and yielding diploid rather than triploid progeny, can be used to map G-K distances as well as
to develop “inbred” strains*. This mode of reproduction is known in several natural populations of invertebrates and vertebrates (SUOMALAINEN 1950; WHITE 1948, 1970; OLSEN 1962; CARSON 1967) and has been produced experimentally in vertebrates when the appropriate meiotic events are altered (TYLER 1955; BEATTY 1967; GRAHAM 1970; TARKOWSKI, WITKOWSKA, and NOWICKA 1970).
(Emphasis mine)


A search for the terms parthenogenesis, gynogenesis, and hybridogenesis reveals more data in this area.

That's not the issue.  The issue is not whether semi-meiotic reproduction can occur.  The issue is whether that is the driving mechanism of evolution, as Davison claims.

Furthermore, let's assume that Davison is correct in that claim.  How would that logically entail "front-loading"?
These saltational events are too extensive to be random.  This is what implies front-loading.    
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I have no idea why these scientists are ignored, but my guess is that their views don't fit the paradigm, and - based on my own observations - scientists whose ideas don't fit are generally ostracized, lose funding, and eventually relegated to the sidelines.

No one wants to lose their position over such things, so they stick to the paradigm.

That's my guess.

My guess is that their findings (not their "views," whatever they may be, not having been expressed in the papers you cited), are not RELEVANT to the paradigm.  It's survival of the fittest out there.  (Your case is not strengthened by such gratuitous ad hominems.)

I wasn't aware that I was using "gratuitous ad hominems".  I based my statements on observed incidents such as this one; where a proponent of ID decides to sever his ties (at least publicly) to the movement because he was accepted into a graduate program at Johns Hopkins University.  This after being advised that he "may expect possible complications" for his public involvement with ID.

Dr. Davison suffered extensive repurcusions at the University of Vermont.

What I'm describing here is not imaginary, but a real palpable fear of losing that for which you've worked all your life if you don't embrace the currently held theory.

Date: 2007/11/11 12:36:52, Link
Author: Daniel Smith
Quote (Jim_Wynne @ Nov. 10 2007,17:39)
   
Quote (Daniel Smith @ Nov. 10 2007,11:40)
     
Quote (Jim_Wynne @ Nov. 10 2007,10:04)
Unless you're willing to define your terms in your own words, we have no way of knowing what you're talking about, and you are free to move the goalposts at will. So I'll ask again:
1) What do you mean by "complex," how do you identify it, and what are the empirical delimiters between "complex" and not-complex?
2) How do you define "functional system"?

Fair enough.

"Complex" means "composed of many interconnected parts".
As a general rule: more parts = more complex.

"Functional system" means "an assemblage of parts which work together towards the same purpose or function"

Please reread the first question, and try again. What about boundaries? You need to be able to describe (with more rigor than "I know it when I see it") the difference between complex and not-complex.

You can count can't you?

What part of "more parts = more complex" doesn't make sense?

Complexity is a matter of degree - the only boundary is that it requires more than 1 part.

After that it's not, "this is complex and that isn't"; it's, "this is more complex than that".

Remember we're talking about biological systems here.  If you can point to one that you'd say is not a "complex functional system", go ahead and eliminate that one from the discussion.

I'd like to see some experimental evidence that any one of the myriads of suggested mechanisms for evolution can produce systems that are at least as complex and functional as known biological systems.

Here, I'll make it easy for you:  I'll give you on of the most basic biological system in life; one on which all life depends:  Protein Synthesis.

Now, take any of the mechanisms you like (or any combination of them) and show me experimental evidence that a product very much like protein synthesis can be constructed utilizing those mechanisms.

Date: 2007/11/11 12:52:55, Link
Author: Daniel Smith
Quote (mitschlag @ Nov. 10 2007,17:08)
     
Quote (Daniel Smith @ Nov. 10 2007,15:51)
These saltational events are too extensive to be random.  This is what implies front-loading.

I've read Davison's Evolutionary Manifesto

Please quote where in that document he makes that point.

And please state the criteria that would distinguish "too extensive" from "random," citing data upon which you base your claim.

He doesn't make that point in the Manifesto.  He does make it in his many postings on the web since that time.  The only place in his manifesto where he hints at it is here:
     
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While it is true that the existence of a Creator, while a logical necessity, has never been rigorously proved and perhaps never can be, it is also true that neither has been the spontaneous generation of life. (emphasis mine)

If one reads the various works on which he builds his hypothesis: the writings of William Bateson, Leo S. Berg, Robert Broom, Richard B. Goldschmidt, Pierre Grassé, and Otto Schindewolf, (of which I've only read one work apiece for Berg and Schindewolf, and just started one from Bateson), you find that this need for front-loading (or some type of divine guidance) is necessary (or at least implied) for evolution of the saltational type they espouse to happen.

So, as to the data on which I base my claim, I'll just point you to the Vista Genome Browser, where you can compare the genomes of like organisms and see the multitude of differences for yourself.  If these differences are the result of a small number of saltational events, they could not be random and still produce working, living organisms.

Date: 2007/11/11 12:55:37, Link
Author: Daniel Smith
Quote (Wesley R. Elsberry @ Nov. 10 2007,17:12)
 
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What I'm describing here is not imaginary, but a real palpable fear of losing that for which you've worked all your life if you don't embrace the currently held theory.


Scientific advancement is, broadly speaking, based on merit.

How does one distinguish between simple incompetence that is fully deserving of worsening one's standing in science, and exploration of alternative theories in a competent fashion, which should not be penalized?

Bear in mind that we have plenty of examples of both sorts that we can check your answer against.

I would say one would distinguish between these two types of individuals by careful analysis of their claims via the scientific method.

Date: 2007/11/11 13:38:23, Link
Author: Daniel Smith
Quote (Erasmus @ FCD,Nov. 11 2007,12:16)
indeed if we look at the progression of any body of theory at the basal branches you will find a plurality of alternative theories (see S Naeem Ecology 2006 or 2007 paper for a discussion of this dialectical progression in ecology).  the reasons for the trimming of the branches are varied, but ultimately empirical support is the criterion.

and there is no theoretical nor empirical support for your ideas Martin, and this is the same as for Daniel.  saltational orthogenetical views must deny heredity.  if you believe that speciation is independent of phylogenesis or the arisal of new forms, you must have another mechanism.  i've not read all of davison's manifesto yet so i'll withhold judgment about his proposed mechanisms, but it suffices to say that the discovery and advent of DNA based phylogenetics destroyed any possibility that schindewolf et al could be right because it showed the mechanism for divergence between populations and a workable theoretical framework for constructing hypotheses about nested hierarchies.

schindewolf was right about some things, namely the effects of canalization as a constraint.  but there is no support for the idea of reservoirs of variation, unless you are going to follow daniels lead and claim that this is what non-coding DNA is.  JAM is doing a much better job than I could with refuting that view, so I will simply ask:  do you have a new mechanism?  do you have a testable theory?


Definition of phylogenesis:
     
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phylogenesis - (biology) the sequence of events involved in the evolutionary development of a species or taxonomic group of organisms

Saltational evolution is not "independent of phylogenesis or the arisal of new forms", nor does it "deny heredity" (as in inheritance) ; it is just another explanation for these things.  One more fully supported by the fossil record (especially the many observed gaps followed by intense adaptive radiations).

While "the mechanism for divergence between populations and a workable theoretical framework for constructing hypotheses about nested hierarchies" may be sufficient to explain variations within species, it has never (to my knowledge) been shown a capable mechanism for the arisal of new forms, or unique new biological systems.

Saltational evolution is just an attempt to better explain the observed progression of organisms in the fossil record.

If "the mechanism for divergence between populations" was the mechanism that created new forms, families, orders, etc., we'd surely see a much more diverse and continuous progression in the fossil record than we do.

Date: 2007/11/11 13:50:29, Link
Author: Daniel Smith
Quote (Erasmus @ FCD,Nov. 11 2007,13:07)
Daniel may I recommend a book to you?  it's short.  


book

you might get a broader perspective of galton bateson and devries and why their ideas were wrong.  it has something to do with mendel.

I'll tell you what, after I'm done reading Bateson, I'll let you tell me everything that's wrong with him.  I'd rather read his works myself first if you don't mind.

Date: 2007/11/11 13:54:45, Link
Author: Daniel Smith
Quote (JAM @ Nov. 11 2007,13:05)
 
Quote (Daniel Smith @ Nov. 10 2007,10:45)

This is an interesting experiment.  I have a couple questions:
1.  Why did they use artificial selection as opposed to natural selection?

So that they could analyze the phage after each generation. You're desperately looking for a reason to discount this; how predictable.
Not at all.  I will never discount experimental evidence, but I was curious whether natural selection would have made the same choices they did.  That's all.
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2.  My math isn't the greatest so when they say that the replacement phage had "six-order magnitude lower infectivity" than the original phage, and the newly evolved phage "showed a 240-fold increase in infectivity as compared to its origin, fd-RP", they're talking about 0.00024 less infectivity than the original wild phage - correct?

But that increase was obtained in just seven generations, so that doesn't work as a justification for discounting the data.
I'm not discounting it, I was only asking if my math was right.  Now that I have the full paper, I should be able to answer these questions for myself.  Thanks.

Date: 2007/11/11 14:58:56, Link
Author: Daniel Smith
Quote (JAM @ Nov. 11 2007,13:25)
             
Quote (Daniel Smith @ Nov. 10 2007,11:05)
                   
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Here's another question: how long does it take to evolve multiple, different, incredibly specific, functional, new protein-protein binding sites, using nothing but genetic variation and selection?

I don't know.

Two weeks.
Is this information in the paper you linked to?

No. It's a completely different case.
               
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My expectation then is that the provisional definition of "junk DNA" will continually evolve until it no longer includes any portion of the genome.

Junk isn't a provisional DEFINITION, it is a provisional CLASSIFICATION. Let's take one of the most prevalent types of junk in our genomes: LINE repeats. Just to be clear, you're claiming that if you have 9 LINE repeats and I have 10 at a particular genomic position, you are predicting that the difference will have functional relevance, correct?
Yes.  I have no idea what the functional difference will be.  Line repeats may just be placeholders - similar to the spaces between words in a sentence, so the functional difference may be small, but I expect there to be one.            
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Are you saying that 90-95% of the human genome is repeats?

Don't ask me, look at VISTA. That multicolored line shows the major (not all) families of repeats.  See the legend at lower left.
What percentage of these repeats are thought to be functional?            
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I don't know why most designers do what they do - that is not an argument against design.

Baloney. It demolishes any human's claim that life LOOKS designed, exposing it as dishonest cherry-picking.
I call "Baloney" on that one.  Virtually all evolutionary scientists will tell you that they are trying to explain the apparent design of life.  If it doesn't look designed, what are they talking about?            
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It might be an effective argument against the competency of the designer, provided you can come up with a better workable system.      

It's the same designer that understands the value of plumbing. The point is that you can't recognize design in the cell's "plumbing" at all.
I don't know enough about it to give an answer "Yes" or "No".  My expectation though, is that I will recognize much more design in it than you give credit for.            
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According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?

...I have no idea.  My hypothesis doesn't really work that way.  What I mean is; since I view each of the multitude of evolutionary events between mouse and man as saltational, there's no way to predict the number of orthologs.

So, in your hypothesis, saltational events have nothing whatsoever to do with new genes and proteins?
They do, but only the necessary genes are retained, while others are reordered.  What's retained is retained.  You'd have to know the function of each gene in order to answer your question.  You'd also have to know how many saltational events took place between mouse and man.  I don't have that knowledge.  Maybe it can be answered - I don't know - I know I can't answer it.            
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My main contention is that the genomic sequences of organisms will be found to be fully functional and evolutionarily constrained within species - leaving the only possible mechanisms for the true evolution of new species saltational ones.      

So why wouldn't such mechanisms involve new proteins and genes encoding them? I'm not following your exclusion of the fundamental nuts & bolts of biology.
I'm not excluding them, just saying that I don't know how one (at least with my knowledge) could predict them.            
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So a wrong prediction is not "lying" then I take it?  ;)

Not as long as one admits it. Responding to a question about testing a hypothesis with a long list of things that don't constitute testing is, IMO. ;-)

You know, I began this discussion expecting to talk about Schindewolf, Berg, and the fossil record.  I was almost immediately sidetracked with molecular arguments - so I took the bait and waded right in - figuring that design would show in that arena as well.  

I began that discussion with a severely limited knowledge of genetics - only knowing that there were genes (which I assumed to be regions that only coded for proteins) and non-coding regions between them (which I assumed to be what-is-commonly-referred-to-as "junk DNA").  With this limited knowledge, I made several predictions indicating what I'd expect to find molecularly - including increasing complexity and overlapping and embedded codes.

As I delved in, I found all this and more.  While my view of genes as solely protein coding regions was wrong, as well as my definition of "junk", my expectations as to the complexity of the genome was confirmed many times over.  I learned that many, many transcriptions (both coding and non-coding) overlap each other - with differing reading frames on the same strand, overlapping transcriptions on opposite strands, and overlapping transcriptions in opposite directions on either the same strand or the opposite strand.  

Such things as sense and anti-sense transcriptions, ribosomal {r}RNAs, transfer (t)RNAs, small nuclear (sn)RNAs, small nucleolar (sno)RNAs, microRNAs (miRNAs) and exogenous small interfering RNAs (siRNAs), were all unheard of for me.  Couple that with the newly minted classification "Transcripts of unknown function" (TUFs), and you're talking about a world of complexity I'd never dreamed of when I made those predictions.

Now, maybe you feel that all these things are easily explained by the suggested mechanisms of evolution and that my wonder at it all is just a matter of my own ignorance.  You might be right - I don't know - (I was definitely ignorant coming into this molecular discussion!), but, I feel vindicated in my own mind by what I've found.

I will probably never convince you or anyone else on this board of design, but I'm more fully convinced now than I was when I came here.

Date: 2007/11/11 15:09:14, Link
Author: Daniel Smith
Quote (JAM @ Nov. 11 2007,13:57)
Quote (Daniel Smith @ Nov. 11 2007,12:55)
I would say one would distinguish between these two types of individuals by careful analysis of their claims via the scientific method.

In real science, we don't analyze the claims (hypotheses) of others. We are responsible for analyzing our own claims (testing our hypotheses) and disseminating the data generated by our efforts.

Has any one of your heroes produced a single new datum after advancing the hypotheses with which you agree?

I'm not sure what you mean by "produced a single new datum", but you can look up the papers written by Berg and Schindewolf on Google Scholar for yourself and see if any of it meets your criteria.
Unfortunately most of Schindewolf's papers are in German.

Date: 2007/11/12 21:25:40, Link
Author: Daniel Smith
Quote (JAM @ Nov. 11 2007,13:57)
In real science, we don't analyze the claims (hypotheses) of others. We are responsible for analyzing our own claims (testing our hypotheses) and disseminating the data generated by our efforts.

So only Darwin can test his theory?

Date: 2007/11/12 22:15:59, Link
Author: Daniel Smith
Quote (JAM @ Nov. 11 2007,16:32)
         
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You know, I began this discussion expecting to talk about Schindewolf, Berg, and the fossil record.  I was almost immediately sidetracked with molecular arguments - so I took the bait and waded right in - figuring that design would show in that arena as well.

It wasn't bait; the molecular evidence is much more massive.
More massive than the millions and millions of fossils collected over several hundred years?          
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With this limited knowledge, I made several predictions indicating what I'd expect to find molecularly - including increasing complexity and overlapping and embedded codes.

No, that wasn't your original prediction, and it's not even remotely scientific.
Why not?          
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Your original prediction was wrong, and you lied and claimed that introns were coding to save it.
Did not. (Que the obligatory 3rd grade "Did too!" retort machine)        
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As I delved in, I found all this and more.  While my view of genes as solely protein coding regions was wrong,...

That's only an issue relating to your lack of honesty. What you've strategically omitted are your actual predictions:

"My hypothesis does not predict a flat line - except within a lineage."
There was no flat line, even within what you defined as a lineage.
I don't remember defining Rat and Mouse as a lineage.  I think you did that for me.        
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"My hypothesis predicts that there is no buildup of random mutations within the genome - even in non-coding sites."
Yet the data showed you that there was much higher divergence in noncoding regions.
How do you know this "divergence" is the result of a buildup of random mutations?          
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"My prediction is that the coding and non-coding sequences (basically all sequences) will show an equal amount of evolutionary constraint."
VISTA showed that within or outside what you define as a "lineage," this was utterly false. Yet your hypothesis didn't change!
First, I have no idea what VISTA's parameters are or how it does what it does.  You say it proves me wrong, fine.  I'll defer to you that VISTA proves me wrong as far as you understand my hypothesis.  I just would rather find out for myself if you don't mind.          
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"I believe that most (if not all) sequences in a genome are functional and therefore resistive to mutation (constrained).  This means there are no neutral sites that are accumulating mutations."
Utterly wrong, yet your confidence is increased? How can that be?
I still don't understand how VISTA shows that the mechanism for the differences between genomes was an accumulation of random mutations.  Will you please explain how you know this?          
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"I also believe that macroevolution (when it happens) is not the result of accumulating mutations but is rather; saltational - that is - it creates new types that may have sequences that are radically different from the sequences from which they diverged (hence my earlier prediction)."
So assuming at least one saltational event between mouse and man, how many orthologs of 30K would you predict to be missing or "radically different"?
I can only make a rough guess, but obviously all the genes that make for mammals would be retained, as well as the placental ones, then you'd have the genes for two eyes, two ears, one mouth, four limbs, etc. - How many is that?  
As for differences; obviously the genes that control intelligence, speech, opposing thumbs, walking upright, shape of the skull, lack of a tail, etc. -  How many is that?        
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"I'd say that anything that is transcribed would qualify as functional - since the cellular machinery is going through the trouble of transcribing it."
How does this one stand?
I've been systematically reading through several of the ENCODE consortium's papers, and I feel very confident of that one.   I'll also predict that soon it will be found that pseudogenes are much more functional than previously thought.  My guess is that they are used as a sort of redundant blueprint for regulation of their true gene counterpart.  I'd also not be the least bit surprised if repeat sequences were found to be functional - would you be?      
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as well as my definition of "junk", my expectations as to the complexity of the genome was confirmed many times over.

Evolutionary mechanisms are great at producing complexity. The existence of complexity has nothing to do with inferring intelligent design.
I'm not talking about random complexity, I'm talking about overlapping codes, running in opposite directions on both strands of DNA.  Does your theory predict that?  (If so, point me to the paper where the prediction was made before such things were discovered.)          
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Now, maybe you feel that all these things are easily explained by the suggested mechanisms of evolution and that my wonder at it all is just a matter of my own ignorance.

No, I think that I can speak for the others and say that we share your wonder. What we don't share is your lack of curiosity, and your insistence that you understand it all already, even when you get caught in blatant falsehoods.

I've never claimed that I understand it all.  Talk about blatant falsehoods!

Date: 2007/11/12 22:35:31, Link
Author: Daniel Smith
Quote (mitschlag @ Nov. 11 2007,16:28)
One more time: At what point, quantitatively, does a "small number of saltational events" equal "could not be random"?

First, the number of saltational events doesn't have anything to do with it.  

Second, I think "saltational evolution", by definition, excludes random causes - in that there are two many successful changes all at once.  Maybe I'm wrong.

Date: 2007/11/12 22:59:11, Link
Author: Daniel Smith
Quote (mitschlag @ Nov. 12 2007,14:07)
The evolution of the horse:

No gradualism here, nossir.  All saltational, yessir.

Fig. 4 from Davison's Manifesto.

The horse is used as an example of evolution in a determined direction - not as an example of saltational change.  The caption reads: "Phyletic size increase in the horse". and is used in the section entitled "Are there laws governing evolution?"
Davison (and Schindewolf before him) saw evolution of new types as a saltational event. What followed was a series of constrained variations within that type which usually resulted in over-specialization and extinction.  Oversized organisms were often a sign of this last stage.
Did the fact that this illustration was Schindewolf's own - from his book "Basic Questions in Paleontology" - escape you?

Date: 2007/11/15 15:39:59, Link
Author: Daniel Smith
Quote (JAM @ Nov. 13 2007,11:00)
 
Quote (Daniel Smith @ Nov. 11 2007,14:58)
I began that discussion with a severely limited knowledge of genetics - only knowing that there were genes (which I assumed to be regions that only coded for proteins) and non-coding regions between them (which I assumed to be what-is-commonly-referred-to-as "junk DNA").  With this limited knowledge, I made several predictions indicating what I'd expect to find molecularly - including increasing complexity and overlapping and embedded codes.

I don't see how the fact that you didn't know that introns were within genes and are non-coding preserves your hypothesis against the inescapable fact that introns, whether one looks within species, between races, between species within a genus, between genuses within a family (which met YOUR definition of "within a lineage"), or between phyla, diverge more than exons.

It seems to me that your saltational hypothesis still makes an utterly false prediction.
     
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...I feel vindicated in my own mind by what I've found.

I will probably never convince you or anyone else on this board of design, but I'm more fully convinced now than I was when I came here.

Good! Then you'll have no problem explaining how your hypothesis treats non-coding regions within genes completely differently from non-coding regions outside genes.

Let me just say this:

I am still not convinced that the evidence you showed me from VISTA contradicts my hypothesis.  Until I know what VISTA does and how it does it, I'll have to reserve judgment on it.

You are convinced (based on VISTA) that I am wrong.  That's fine - I very well may be wrong!  After all, I'm trying to guess what God was thinking when he designed life.  I'll probably be wrong more than I'm right.

All I'm saying is, I'm not seeing what you're seeing (yet at least).  I have a lot less knowledge in this area than you so I'm not able to just look at a chart of colors and immediately know what they all represent and how they confirm or falsify my predictions.  Please be patient with me and please stop accusing me of lying whenever I make ignorant statements!

Thank you.

Date: 2007/11/15 15:52:27, Link
Author: Daniel Smith
Meanwhile, I just found out about an hypothesis that another code exists of which it is said, it "considerably
extends the information potential of the genetic code".
Evidence supporting this "histone code" was also recently found here:  
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The identification of these characteristic signatures associated with active regulatory elements, particularly promoters, suggests that there is a strong correlation between the histone modifications and biological activity. This lends support to the idea that there is a histone code associated with the activity of these elements, although perhaps not a completely deterministic one.

I have not read the first paper yet.  I found out about it by reading the second paper - so this post is just an FYI.

Date: 2007/11/16 18:50:17, Link
Author: Daniel Smith
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the ENCODE project.

These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.  (I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

They also show quite clearly that most of the human genome is transcribed and functional.

These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?

Date: 2007/11/16 19:01:18, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Nov. 16 2007,18:55)
Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the ENCODE project.

These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.  (I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

They also show quite clearly that most of the human genome is transcribed and functional.

These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?

yeah yeah, we know, god did it. what further is there to discuss?

No, the "ENCyclopedia Of DNA Elements Consortium" did it.

Have you read any of it?

Date: 2007/11/18 15:08:36, Link
Author: Daniel Smith
Quote (JAM @ Nov. 17 2007,10:30)
1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.

As far as I can see, the only thing messy or fuzzy about our genome is our understanding of it.

Date: 2007/11/18 15:10:03, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Nov. 17 2007,19:10)
 
Quote (Daniel Smith @ Nov. 16 2007,18:50)

No, the "ENCyclopedia Of DNA Elements Consortium" did it.

Have you read any of it?

all of it.

All 29 papers?

Date: 2007/11/18 18:35:18, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Nov. 18 2007,10:46)
   
Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the ENCODE project.

These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.  (I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

They also show quite clearly that most of the human genome is transcribed and functional.

These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

I'll ask again:  When did any of your various theories or hypotheses predict such a complex interwoven tapestry within our genome (or any other)?
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?

Very well Daniel. We can't have you thinking that "darwinists" are scared of your layman point of view. I'm a lay person here too.

And as such, here are my questions (conditions, if you like, for further discussion to take place. I'm not a moderator here but I won't bother to engage  again if you don't make a reasonable attempt to answer. Most other people it seems have stopped bothering already).

1) Could you please show me the specific prediction that "darwinism" makes that specifies that multi-layered, overlapping, multi-directional "coding" schemes within the human genome should not exist?

2) Could you please show me the specific prediction that "darwinism" makes that  most of the human genome should not be transcribed and functional.

3) Could you please show me the specific prediction that "darwinism" makes that predicts such a complex interwoven tapestry within our genome (or any other) cannot exist?

     
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Is that why none of you want to talk about it?  Does it cause difficulties for you?


I suspect you are confusing "scientists were surprised at what they found" with "scientists found something that they  predicted was impossible" or suchlike.

What is it exactly that you want to talk about? So what if scientists are suggesting redefining the gene. How does that in any what whatsoever support the idea that a deity was necessary at any stage along the way. In fact, lets make that question four.

4) How does redefining the gene suggest a supernatural intervention was required? Specifically?

First, I'm not aware of any predictions "darwinism" has made about these types of things so I'll have to give you my take on what "darwinism" might predict:

If I understand it correctly, the modern evolutionary theory hypothesizes that morphological change has occurred as a result of millions of years of accumulated mutations within the genomes of organisms.  These random mutations mostly accumulate in non-coding / non-functional areas within the genome.  They will thus eventually create a new genetic sequence or modify an existing functional sequence to the point that a new or improved feature is developed.  That feature then becomes fixed in the genome due to selection.  Of course, there's a whole lot more to it than that, and many others here will no doubt chime in with their take on the mechanisms of evolution, but that's my "nutshell" version.

Now, if that's the case, then we should see some evidence in every genome of millions of years of these accumulated random mutations in non-functional (and functional) areas of the genome.  

What would you expect to see and how does it compare to what we do see?

Of course, if there are no (or very few) non-functional areas in the genome (as I believe), then there would be no place for random mutations to accumulate.  I think what we are actually observing and discovering about genomes is more in line with this approach.

Which brings me to your last question:
At some point; after we realize that whole genomes are functional; after we've discovered bewildering complexity within them; and after we've pretty much eliminated random causes for such things; we have to explore the possibility that intelligence was involved in the design of such a system.  I predict science will some day soon arrive at that point.

Date: 2007/11/18 18:43:39, Link
Author: Daniel Smith
Quote (VMartin @ Nov. 18 2007,12:47)
JAM

       
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So if one is intelligently designing a spacing mechanism, why in heaven's name (literally) would one use tandem repeats, which expand and contract (via recombination) at ridiculously high frequencies? Wouldn't unique sequence be the far more intelligent choice?


As a layman I dont know what you and Daniel are meaning by "tandem repeats". Are those repeats  "tandem duplication" or pure "repeated sequences"?

In the second case I don't see how how the difference in the structure of repeated sequences between different species proves Daniel theory by saltus as wrong. It may  have been induced by some unknown mechanism during John Davison's chromosome rearrangements, no? As far as I know repeated sequences by two sisters species are sometimes very different. But they are also different from those of the ancestor species.

This phenomenon is very hard to explain without special mechanism that after speciation causes parallel differentiation of repeated sequences in all locuses of genome. There must be obviously also some process of homogenization of repeated sequences. These repeated sequences are often identical in new species and have sometimes hundered thousands copies.  

So there must be process of  differentiation of repeated sequences in daughter species from mother species and at the same time homogenization of all these repeated sequences to new ones.

Wouldn't be it more simple to assume that such  repeated sequences are for each new species created de novo by saltus?

If the phenomenon is to be explained by molecular drive as I have read elsewhere it would mean that by such process (molecular drive) would be affected many individuals of population simultaneously. It would assume some kind of synchronized evolution of repeated sequences.

Generalizing molecular drive to all genome we are dealing with synchronized evolution, something proposed by Leo Berg (with which John Davison disagree btw).

Very astute observations Martin.  

I've often wondered "Why repeats?", "Why not random 'gibberish'?"

It seems to me that millions of years of accumulated random mutations in non-functional areas would have to result in random base pairs - as opposed to repeat sequences.

But then again, I don't understand the logic behind the theory of evolution anywhere near as well as the rest of them say they do.

Date: 2007/11/18 19:19:51, Link
Author: Daniel Smith
Quote (JAM @ Nov. 18 2007,15:30)
           
Quote (Daniel Smith @ Nov. 18 2007,15:08)
             
Quote (JAM @ Nov. 17 2007,10:30)
1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.

As far as I can see, the only thing messy or fuzzy about our genome is our understanding of it.

Mine's a helluvalot less fuzzy than yours. May I take it that you conceded all of the other points in choosing a one-liner?

No.            
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I'm particularly interested in your answers to these questions:

A) Do you predict that whales will be missing a hind-leg gene?
Not necessarily - though I predict it will be suppressed as to it's full development.  IOW, the non-coding "support cast" for that gene will be markedly different from animals that have fully developed hind legs.            
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Do you predict that monkeys have a tail gene that humans lack?
No.  I predict that their "tail gene(s)" (at least the protein coding parts) may be similar to ours, but all their various regulatory and support elements will be markedly different from ours.  Theirs will have much more activity and development in these non-coding areas - possibly evidenced by a markedly higher level of histone activity.  Ours will be suppressed.      
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Both of these stream from your guess as to what God was thinking when he designed, but you are afraid to pursue it, because you have no real faith (Note that this relates to the fuzziness that you lack the integrity to address).
Why does every response from you have to be so peppered with accusations?  It gets tiring after awhile.  I feel like I'm answering you not so much because I have to defend my positions, but rather because I have to defend my character.        
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B) I have a gene, and both mice and humans homozygous for the null allele die shortly after birth (with essentially the same phenotype). Since according to you, transcription implies function, when I look at transcription of that gene, will it be turned on:
1) right before the age of death in the null mutants,
2) right before or at the time at which mutants can be distinguished from wild-type individuals, or
3) more than a month before 1 or 2?
I'm not sure what you mean by "when I look at transcription of that gene, will it be turned on".  Do you mean "will transcription of that gene be turned on", or will "the gene itself be turned on"?  
Because I think transcription of the gene will always be happening,  but as to when exactly the gene gets turned on, I have no clue.      
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C) Why is it that you are so breathtakingly arrogant that you believe that God causes millions of children to suffer and die as a lesson to people like you, but getting you to make predictions is like pulling teeth?

The suffering of these children (and everything else that happens in life) is a lesson for us all - not just for "people like me".

Date: 2007/11/20 18:58:57, Link
Author: Daniel Smith
Quote (Richard Simons @ Nov. 19 2007,08:17)
 
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The suffering of these children (and everything else that happens in life) is a lesson for us all - not just for "people like me".

Only if you are aware of it. In which case, wouldn't it be more instructive if it happened in the developed world where communications are so much better, rather than in Third World villages where TV cameras rarely penetrate?

You know, my wife just lost her mother after years and years of progressive debilitation due to complications of diabetes.  We watched a healthy, beautiful woman disintegrate before our eyes.  When she died, at the young age of 65, she looked like she was 90.  This happened in the most developed nation on earth, with the best medical care available.  Suffering is not restricted to 3rd world countries - nor is it restricted to children.  We all see it.

Date: 2007/11/20 19:20:50, Link
Author: Daniel Smith
Quote (mitschlag @ Nov. 17 2007,07:25)
One thing I find interesting is that when he can't provide answers to standing questions, Daniel changes the subject.

Some of you get on me for not answering every question thrown at me here.  You make it out that, if I don't answer your questions, it's because I'm "running away", or "avoiding real questions", or "changing the subject", (even though I'm only one man and there are many of you, firing many questions at me).

I started out talking about the fossil record, Schindewolf, Berg and natural selection, yet most of you wanted to "change the subject" to molecular evidence.

I asked about the multi-layered complexity of the human genome and most of you dismissed it with a shrug of the shoulders as if it was "old news".

I brought up the "histone code" but - no comments.

And, no one even tried to answer this question I posted:        
Quote (Daniel Smith @ Nov. 10 2007,11:29)

In the human genome, what percentage of genomic sequence would you say is likely to be transcribed as nuclear primary transcripts?


So.  Are you all running away? (Or does that only apply to me?)

Date: 2007/11/21 22:44:32, Link
Author: Daniel Smith
Quote (JAM @ Nov. 17 2007,10:30)
         
Quote (Daniel Smith @ Nov. 16 2007,18:50)
One thing I find interesting here is that most of you have shown no interest in any of the various papers I've cited from the ENCODE project.
These papers clearly show a multi-layered, overlapping, multi-directional "coding" scheme within the human genome.

Why would the human genome be so different from the Drosophila genome?
     
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1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.
2) As for any other, similar phenomena were shown in the Drosophila bithorax complex FIVE YEARS AGO. Therefore, we predicted similar complexity in the human genome.
     
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It doesn't address any of your predictions--it's just the same ol' post hoc spin to try and conceal the fact that you are dishonest, because you won't change or abandon your hypothesis when its predictions are shown to be false.

I hope you don't misinterpret this as "accusing" you of something, but...

How is the complexity of the human genome a prediction of your theory - when you are "predicting" it based on the complexity of the Drosophila genome?  

So both genomes are complex--how does that confirm or falsify the mechanisms of your theory?  

What specific mechanism of the MET is tested by this "prediction"?

And how does this "prediction" differ from what you call, "post hoc spin"?

Date: 2007/11/22 09:35:36, Link
Author: Daniel Smith
Quote (IanBrown_101 @ Nov. 22 2007,07:18)
"
What specific mechanism of the MET is tested by this "prediction"?

And how does this "prediction" differ from what you call, "post hoc spin"?"

It's testing the idea of descent with modification, since if they were totally different then it would be a little....hard to explain, shall we say.

It isn't post hoc because, shockingly, it wasn't developed post hoc, and actually relied on a prediction made before the results were found.

You DO understand what post hoc means, don't you?

My hypothesis embraces "descent with modification" as well.  It just suggests that the modifications are constrained and directed.  So I could just as easily have made the same prediction.  So this prediction says nothing about the actual mechanism that produces these modifications.

Let me give you an example:
Lets say I have an hypothesis that says my house was built by aliens.  I examine my house and find that it contains many complex wall structures - including "rooms within rooms" (closets, bathrooms).  I then predict that my neighbor's house will be also contain rooms within rooms.  I examine his house and find that it does contain rooms within rooms.  I declare my hypothesis verified.

Now, you can see that the prediction had nothing to do with how my house came to contain rooms within rooms.  You could have virtually any hypothesis as to the mechanism - since the observations of rooms within rooms are not relevant to the cause.

So the post hoc part was that the prediction was made after complex genome structure was already discovered in Drosophila.  It says nothing about how genomes get complex in the first place and therefore says nothing about the mechanisms of evolution.

Date: 2007/11/22 09:59:05, Link
Author: Daniel Smith
Quote (JAM @ Nov. 21 2007,11:05)
Also, please convey my deepest sympathies to your wife on the loss of her mother, but let's realize that her death is not relevant to your theologically twisted claim that God is causing children to be poor and dying of malaria just to teach people like you and me a lesson.

Do you not realize that your position implicitly claims that you are much more important in God's sight than those millions of children? If God's goal was to teach you a lesson (because you are so special), wouldn't the lesson be far more effective if he caused YOUR OWN child (or wife or mother) to die of malaria?

Thank you for your sympathy.  I don't think that anyone on this planet is "better" than anyone else.  I certainly don't think that God's goal is to teach me a lesson through the suffering of others because I am "so special" (as you put it).  I think that (and have already given an example from close to home) that anyone can experience suffering and death.  We've all witnessed it.  It doesn't only happen in far away places.  I am of the opinion that those of us who are not currently suffering can learn form the suffering of others because it could very easily happen to us!.  It is not a matter of God killing children in a poverty stricken country so that the fortunate ones in a rich land can get an object lesson in life.  It's a matter of the fact that suffering and death are common to us all and we all can learn from it.  I have learned that death is not the end.  In fact, it is only the beginning. If you can grasp the concept of eternity, and see our place in it, suffering and death becomes less frightening.

I've also learned that suffering and death do not negate the fact that God is good and merciful.  Don't forget that (according to Christian theology) God himself is familiar with suffering and death.  The bible says that God has a special place in his heart for the poor and suffering (remember the parable of Lazarus and the rich man?), and that there is a special place for them in the kingdom of heaven.  It's those of us who haven't suffered, and who aren't poor that have more to worry about eternally.

Date: 2007/11/22 10:21:39, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Nov. 22 2007,09:47)
       
Quote (Daniel Smith @ Nov. 22 2007,09:35)
My hypothesis embraces "descent with modification" as well.  It just suggests that the modifications are constrained and directed.

Unless your "hypothesis" defines how the modifications are directed it's simply worthless.

Daniel, what mechanism does your god use to poke at DNA? Magic sticks? Gluon storms? Quark Storms? Quantum probability manipulation? Zero-point energy?

I don't know.  Based on recent readings, I'd say perhaps histone with intricately designed tails.      
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My hypothesis embraces "descent with modification" as well.


So your contention is as follows, correct me if i'm wrong.

"Evolution is 100% correct, except mutations are not random but directed"

Is that it?

Correct, and natural selection has little to nothing to do with it.  Evolution is based on internal mechanisms, is constrained along certain paths (convergent), and is directed (as in prescribed).  The creation of new types is saltational (happens all at once), is most likely the result of chromosome reordering and is also prescribed in advance.  This view is consistent with the fossil record, (as Schindewolf so eloquently documented), observations in the wild (see Berg's Nomogenesis), and genetics (See virtually any recent paper describing the molecular workings within genomes) and has a workable, testable mechanism (See Davison's Semi-meiotic hypothesis).

In short, I don't see any evidence that random mutations coupled with natural selection can produce complex genomes and all the other elegant complexities within life.  I don't see a fossil record consistent with that, nor do I see that nature works that way in real time.  So, I have embraced instead the evolutionary theories that don't rely on that mechanism.

Date: 2007/11/22 10:57:57, Link
Author: Daniel Smith
Quote (JAM @ Nov. 22 2007,10:08)
         
Quote (Daniel Smith @ Nov. 21 2007,22:44)
             
Quote (JAM @ Nov. 17 2007,10:30)
1) MET makes clear, testable predictions about the mechanisms by which the messy, fuzzy nature of our genome came about.

Daniel, please reread this and explain how your questions below are anything but straw men.
             
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2) As for any other, similar phenomena were shown in the Drosophila bithorax complex FIVE YEARS AGO. Therefore, we predicted similar complexity in the human genome.
                     
Quote
It doesn't address any of your predictions--it's just the same ol' post hoc spin to try and conceal the fact that you are dishonest, because you won't change or abandon your hypothesis when its predictions are shown to be false.

I hope you don't misinterpret this as "accusing" you of something, but...

How is the complexity of the human genome a prediction of your theory - when you are "predicting" it based on the complexity of the Drosophila genome?

It's predicting the phenomena based on common descent with modification.

How does your theory predict the NATURE of the complexity we observe in life--similar, but not identical components performing PARTIALLY-overlapping functions?
If the mechanisms for the production of new types is the reordering of the chromosomal structure of existing types, then we'd expect to see modifications of old types within the new.  I fully expect (as I've stated in the past) to see similar components in organisms.  You seem to be arguing against de-novo creationism more than my stated views.          
Quote


             
Quote
So both genomes are complex--how does that confirm or falsify the mechanisms of your theory?

It's about the mechanisms that generate the complexity (mutational mechanisms, natural selection and drift), not the mere existence of complexity. Do you realize how intellectually shallow your behavior is when you keep ranting about complexity, but run away from any discussions of its nature?
I'm perfectly willing to discuss the nature of complexity.  I am wide open for your explanations as to how mutational mechanisms, natural selection and drift create such things.  Do you have any specific cases you want to discuss?  I'm trying to steer you toward the wealth of papers produced by the ENCODE consortium with the hope that maybe we can get specific and you can explain to me how mutational mechanisms, natural selection and drift produced the systems found within our genome.          
Quote

             
Quote
What specific mechanism of the MET is tested by this "prediction"?

Combinations of natural selection and drift, particularly the utter disgregard for efficiency (the antithesis of intelligent design) when the lack thereof doesn't affect fitness.
Is "the utter disgregard for efficiency" the mechanism tested in the experiment you cited earlier?
Because I seem to remember the selection criteria being based on the efficiency of infectivity:
   
Quote
Each generation consists of a maximum of ten arbitrarily chosen clones, whereby the clone with highest infectivity was selected to be the parent clone of the generation that followed.
"Can an Arbitrary Sequence Evolve Towards Acquiring a Biological Function" J Mol Evol (2003) 56:162–168 (emphasis mine)
       
Quote

             
Quote
And how does this "prediction" differ from what you call, "post hoc spin"?

Because it was made pre, not post. Do you not comprehend this important distinction and its relevance to intellectual honesty?

It was not made preDrosophila.  If you could show me where interwoven, sense, anti-sense, overlapping, and embedded "coding" was predicted before it was actually discovered, I'd call that a prediction.  This was made afterwards and is thus a postdiction.  All you've shown by this is that the same mechanism is responsible for both the Drosophila genome and the human genome.  That's it.  You have not made a prediction that tests a certain mechanism.

Date: 2007/11/23 13:41:55, Link
Author: Daniel Smith
Quote (mitschlag @ Nov. 22 2007,11:53)
A quote from Schindewolf, by Daniel,  here:
     
Quote
"And these are by no means just isolated occurrences; these strange new forms are usually also represented by large numbers of individuals.  Nonetheless, there is no connecting link with the stock from which they derived.  The continuity of the other species gives us no reason to suspect interruptions in the deposition of the layers, or subsequent destruction of layers already deposited, which, furthermore, would be revealed by other geological criteria.  Nothing is missing here, and even drastic changes in living conditions are excluded, for the facies remain the same.

Further, when we see this situation repeated in all stratigraphic sequences of the same time period all over the world... we cannot resort to attributing this phenomenon to immigration of the new type from areas not yet investigated, where perhaps a gradual, slowly progressing evolution had taken place. What we have here must be primary discontinuities, natural evolutionary leaps, and not circumstantial accidents of discovery and gaps in the fossil record"

ibid. pp 104-105 (emphasis his)

How so?  (How does his belief make it so?)

Schindewolf based his theory on some of the most abundant fossils that appear in the fossil record - cephalopods and stony corals.  These fossils are so abundant they are used as index fossils.  He extensively documented the changes within lineages among these organisms.  He came to his conclusions based on this evidence.  His belief has nothing to do with it.  

So when he says something like this (from your quote above (emphasis mine)):
"The continuity of the other species gives us no reason to suspect interruptions in the deposition of the layers, or subsequent destruction of layers already deposited, which, furthermore, would be revealed by other geological criteria. Nothing is missing here, and even drastic changes in living conditions are excluded, for the facies remain the same."
... he's making a case for the continuity of the fossil record within which these "leaps" between types are found.

Again, it has nothing whatsoever to do with "belief", it is an observation - made by one of Europe's leading Paleontologists.

Date: 2007/11/23 13:47:54, Link
Author: Daniel Smith
Quote (JAM @ Nov. 22 2007,18:21)
...

1) Does your hypothesis predict that there will be anything that we humans could reasonably call a "hind-leg gene" based on analogies with our own intelligent designs?

2) Does your hypothesis predict that there will be anything that we humans could reasonably call a "tail gene" based on analogies with our own intelligent designs?

3) What do you mean by "histone activity"?

4) Why would you think that transcription of a particular gene is always happening? WTF do transcription factors do?

5) Wouldn't an intelligent designer design genes so that their transcription was turned on ONLY when (and where) the presence of the gene product is necessary?

6) an you find a single instance of a scientist referring to the design of endocytic (intracellular plumbing) pathways?

7) Explain the intelligence in the design of endocytic pathways, particularly their superiority to more conventional plumbing, as observed from the very same designer in our very own bodies. Be sure to explain the rationale behind the choice of so many similar, closely-related components with partially-overlapping (neither separate nor redundant) pathways.

8) According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?

I'll do my best to answer your questions if you'll do your best to answer this question:
In the human genome, what percentage of genomic sequence would you predict is likely to be transcribed as nuclear primary transcripts?

I think it's only fair that you put your hypothesis on the line as well.  Besides, I'd be interested to know what your answer is.  (No one else has been willing to touch it!)

Date: 2007/11/23 14:29:39, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Nov. 22 2007,10:26)
     
Quote
In short, I don't see any evidence that random mutations coupled with natural selection can produce complex genomes and all the other elegant complexities within life.  I don't see a fossil record consistent with that, nor do I see that nature works that way in real time.  So, I have embraced instead the evolutionary theories that don't rely on that mechanism.


And your contention is that these "alternate theory's" are better supported by physical evidence then "standard evolution" ? Please list such evidence. If it exists.

OK.

Among Cephalopods (from Schindewolf):
1. The "explosion" of Nautiloid types in the lower Ordovician.
2. The  "explosion" of the Goniatitacea in the lower Carboniferous.
3. The  "explosion" of the Ammonitacea in the lower Carboniferous.

Convergent evolution (from Schindewolf and Berg):
1. Multiple instances among marsupial and placental mammals - most notably the wolf.
2. Spermatozoa and parasitic flagellates.
3. Among insects.
4. Between vertebrates and invertebrates.
5. Among amphioxus, lampreys and fishes.
6. Between dinosaurs, crocodiles and birds.
7. Among theromorpha.
8. Between lemurs and apes.
9. Among the ratitae or "keel-less birds
10. Between monocotyledons and dicotyledons.

That's a small portion of the evidence brought forth in the two books I've read.  The list goes on and on, but I'm not going to list it all here - since the books are available.
   
Quote

Tell me Daniel, is there *any* evidence that random mutations coupled with natural selection *cannot* produce complex genomes and all the other elegant complexities within life?

Links please.

Since almost anything is possible, I don't see how anyone can prove that negative.  I would say though that the lack of experimental evidence that random mutations coupled with natural selection can produce complex genomes and all the other elegant complexities within life, is a strong case against such a mechanism.

Date: 2007/11/24 11:13:19, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Nov. 23 2007,17:49)
   
Quote
all the other elegant complexities within life

These words mean nothing. Are worn out knees elegant? Please define elegant complexities so that it means something tangible. Do you think that what initially appears to us to be inelegant, will on further examination (possibly from a ID point of view) turn out to be elegant after all? Otherwise it seems to me a single example of "inelegant" design falsifies your theory.

The phrase "all the other elegant complexities within life" is - yours!  I just copied and pasted it directly from your original question.
Permalink
When you're done digesting the delicious irony of the situation, get back to me!

Date: 2007/11/24 11:19:22, Link
Author: Daniel Smith
Quote (mitschlag @ Nov. 23 2007,16:44)
 
Quote (Daniel Smith @ Nov. 23 2007,13:41)
Schindewolf based his theory on some of the most abundant fossils that appear in the fossil record - cephalopods and stony corals.  These fossils are so abundant they are used as index fossils.  He extensively documented the changes within lineages among these organisms.  He came to his conclusions based on this evidence.  His belief has nothing to do with it.  

So when he says something like this (from your quote above (emphasis mine)):
"The continuity of the other species gives us no reason to suspect interruptions in the deposition of the layers, or subsequent destruction of layers already deposited, which, furthermore, would be revealed by other geological criteria. Nothing is missing here, and even drastic changes in living conditions are excluded, for the facies remain the same."
... he's making a case for the continuity of the fossil record within which these "leaps" between types are found.

Again, it has nothing whatsoever to do with "belief", it is an observation - made by one of Europe's leading Paleontologists.

Schindewolf's theory and conclusions are not equivalent to observation or evidence.  Theory and conclusions may or may not be based on evidence.  If you can't distinguish fundamental categories, you'll continue to be confused.  And your arguments will be futile.

Appeals to authority are also futile: Schindewolf's eminence in paleontology is long gone and was limited to the special circumstances existing at the time (50 years ago!) in German academia.  Outside of Germany, his theory had no traction and it is now a minor footnote in the history of paleontology.

OK.  Because you said so, I'll abandon my affinity for Schindewolf's theory.  This in spite of the fact that you have provided no evidence or observations to contradict it.  

I am abandoning it because you said, "Appeals to authority are also futile".  

That convinced me!

Date: 2007/11/24 11:25:17, Link
Author: Daniel Smith
Quote (Assassinator @ Nov. 23 2007,16:46)
Have you got any idea how long those "explosions" took?
Furthermore, convergent evolution isn't a piece of evidence for directed evolution. It's simply an unsupported interpretation of it. I'll simply quote the Wiki about convergent evolution:
 
Quote
In evolutionary biology, convergent evolution is the process whereby organisms not closely related (not monophyletic), independently evolve similar traits as a result of having to adapt to similar environments or ecological niches[1]. It is the opposite of divergent evolution, where related species evolve different traits.

OK, via Occam's razor, the simplest explanation for convergent evolution is that evolution is constrained by laws down similar paths.  Postulating that random mutations coupled with natural selection can produce the same happy accident numerous times is a much more complicated explanation.

Date: 2007/11/25 12:56:42, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Nov. 25 2007,05:35)
The most amusing aspect of this for me is it illustrates the level and quality of research that Daniel is capable of.

If you click the "all" button then every page in the thread is loaded at once. If I was going to crow over somebody's "mistake" I'd be certain to make sure I'd checked the "all" page to see where the first appearance of the "mistake" was. In this case, as RB points out, the original usage of the words was in the message from Daniel that I quoted! So no need to even search the entire thread. And yet it was missed.

Daniel, Daniel, Daniel. I think you've just blown your chance at tenure.  :D

I'm embarrassed now.  ???

Date: 2007/11/25 13:18:37, Link
Author: Daniel Smith
Quote (mitschlag @ Nov. 24 2007,12:51)
   
Quote (Daniel Smith @ Nov. 24 2007,11:19)
OK.  Because you said so, I'll abandon my affinity for Schindewolf's theory.  This in spite of the fact that you have provided no evidence or observations to contradict it.  

I am abandoning it because you said, "Appeals to authority are also futile".  

That convinced me!

This charming outburst is not reasonable or logical, so I take it as sarcasm.

I intended no offense.  My admittedly sharp remark about argumentum ad verecundiam was directed at your statement:  "Again, it has nothing whatsoever to do with "belief", it is an observation - made by one of Europe's leading Paleontologists."

Do you not agree that it's the quality of Schindewolf's argument that is at issue, not his credentials?

That he was an expert in the paleontology of cephalopods and stony corals is not at issue.  His work in those areas may well have stood the test of time.  The current issue is, I believe, whether his ideas about saltation and orthogenesis are valid.

Since Schindewolf's ideas about saltation and orthogenesis are interpretations of the evidence, they can only be challenged by alternative interpretations, as provided in the modern synthesis.  

But let's assume for fun that saltation and orthogenesis are valid.  Is there any compelling reason to assert that these supposed mechanisms are not "natural"?  Is there any compelling reason to think that a supernatural agency had to bring them about?

The same goes for Davison's semi-meiosis, by the way.

Actually Schindewolf saw these mechanisms as 100% natural - not supernatural in any way.

It's me who sees the supernatural mind behind it all.

It's a matter of perspective.  I approach the evidence from a theological perspective - something most of you have probably never done.  If you approach the evidence from a purely naturalist perspective - not allowing for the possibility of the supernatural - it forces you to seek purely natural explanations for everything.  Sometimes this works, sometimes it doesn't.  For instance, no one can give me a detailed theoretical pathway for the initial creation of even the simplest, most fundamental molecular machinery - protein synthesis - via a purely natural pathway.  Now maybe that's because we just don't know enough.  But there's also the possibility that it just can't be done.

As a believer, I expect to see intricate designs in life - because I believe life came from God.  I am not surprised to find overlapping, multi-directional coding within genomes - I fully expect such things.  I can't explain how such things came to be either - but I'm not surprised by them.

So what am I saying?  Am I suggesting we cancel all research, throw in the towel and just say "goddidit"?  Not at all.  I think we should delve into these mysteries and try to solve them.  No matter what perspective we begin from, there is still much to discover - a never ending (infinite) supply.  Some of us will see such marvels as technology of the highest order - a glimpse inside the mind of God if you will.  Others will see it as the product of natural causes.  Either way, the research should continue.

Date: 2007/11/26 13:56:34, Link
Author: Daniel Smith
Quote (Steverino @ Nov. 25 2007,14:58)
Daniel,

"...Now maybe that's because we just don't know enough.  But there's also the possibility that it just can't be done."

This is basis of your, ID's and Creationists argument. Boiled down it's the standard "God of the Gaps" argument.

When one gap is explained you abandon that point like rats leaving the sinking ship and move on to the next gap.  You (IDiots/Creationists) never admit that it was you that was wrong in your thinking.

It's disingenuous at best because no matter how much Science proves, there will always be a gap for you and yours to hide in.

I've already answered your "god of the gaps" objection once - don't you remember?
Let me just nutshell it for you:
Even though man can explain certain things, it doesn't mean they weren't designed.  I can explain many of the systems at work within my car.  Does that mean they weren't designed?

Date: 2007/11/26 19:15:55, Link
Author: Daniel Smith
Quote (JAM @ Nov. 19 2007,00:38)

Sit down and take a deep breath. Think, as a Christian, for a moment about what YOU are accusing me and the other scientists of doing here. YOU are accusing US of gross incompetence, and in direct contradiction of clear Biblical guidance, you have made this accusation on the basis of nothing but hearsay.

Put yourself in my shoes, Dan. I've spent most of my life doing biology, and you come along. Would you describe your claims as humble ones?

What sort of character makes grandiose claims without evidence, and then discounts the evidence?

These statements have been the cause of much reflection and trouble for me lately.  Am I really accusing you (and the other real scientists here) of something?  If so - what?  And what are my motives?

I think I've come to a bit of a realization here.  What I've realized is that my interest in biology is purely theological.  I look at the inner workings of life as a way to learn more about God.  I'm not interested in biology for biology's sake.  These are my motivations.

So from a theological perspective, when I look at the inner workings of the genome, I expect to find complexity and function.  It has nothing whatsoever to do with my knowledge of biology.  This is my realization.  I have no right to accuse anyone of anything - especially not someone who has devoted their life to the study of biology.  So for that - for that arrogance - I apologize.  I should have prefaced everything with "From my theological perspective...".  Then perhaps my arrogant points would have been seen in their true context.

I've been reading the ENCODE paper on pseudogenes.  This paper, and my reaction to it, clearly illustrate (for me) my motives.  The consensus position on pseudogenes seems to be that they are "dead" copies of once-active genes.  From a theological perspective, I can't believe that God would have "dead wood" in the genome, so I find myself shrugging off their conclusions and latching onto the few statements that hint at pseudogenes being more functional than previously thought.  Again, from a purely theological perspective, I'm expecting that pseudogenes will be found to be functional in some as-of-yet unseen way.  This expectation has nothing whatsoever to do with my knowledge of biology.  Neither do any of my predictions.  My knowledge is of God and his ways - not of science.

With that said, I must say this:  From a theological perspective, I do see much that encourages my beliefs when I look at biology.  I don't see any reason to abandon my core beliefs at all.  The recent discoveries of the inner workings of DNA, RNA, and their chromosomal packaging have me excited to see what scientists will discover next!  I feel encouraged in my beliefs by such things.  I feel in awe of the mind that (I believe) created such things.  I feel I am just that much closer to finding out what actually happened and I am trying to formulate a coherent picture in my mind.

So, my beliefs as to what happened are by no means set in stone.  I study biology as a way to learn what God did - a kind of bio-theology if you will.

So JAM, from the perspective of a life-long biologist, you predict that most of the genome will be found non-functional; and I - from a purely theological perspective - predict that most of the genome will be found to be functional.  We shall see who's right.

I hope this clears things up.

Date: 2007/11/26 19:20:03, Link
Author: Daniel Smith
Quote (Steverino @ Nov. 26 2007,16:36)
 
Quote (Daniel Smith @ Nov. 26 2007,13:56)
   
Quote (Steverino @ Nov. 25 2007,14:58)
Daniel,

"...Now maybe that's because we just don't know enough.  But there's also the possibility that it just can't be done."

This is basis of your, ID's and Creationists argument. Boiled down it's the standard "God of the Gaps" argument.

When one gap is explained you abandon that point like rats leaving the sinking ship and move on to the next gap.  You (IDiots/Creationists) never admit that it was you that was wrong in your thinking.

It's disingenuous at best because no matter how much Science proves, there will always be a gap for you and yours to hide in.

I've already answered your "god of the gaps" objection once - don't you remember?
Let me just nutshell it for you:
Even though man can explain certain things, it doesn't mean they weren't designed.  I can explain many of the systems at work within my car.  Does that mean they weren't designed?

"Let me just nutshell it for you:
Even though man can explain certain things, it doesn't mean they weren't designed...."


Now that argument is called "moving the goal posts".

So, at Dumbfvck U, DI/Creationist Institute of Higher Edumacation, everything is and was designed....until proven otherwise.

"...I can explain many of the systems at work within my car.  Does that mean they weren't designed?"

I'm gonna have to call a non sequitur the play.  Does your car reproduce?

Where is the proof that the appearance of design, proves design?

Steverino,

I see everything as designed - even lightning.  It doesn't matter to me if man can explain it.  I don't see that as an issue - for the reasons I specified.  I'm not advocating "god of the gaps", I'm advocating "God over all".

I'm hoping you can see the difference.

Date: 2007/11/27 13:39:59, Link
Author: Daniel Smith
Quote (Steverino @ Nov. 26 2007,19:36)
I can, and that is not science.

You start with an assumption that skews your research, your interpretation of evidence and your results.  You have identified your goal and cherry pick or distort the evidence that supports your hypothesis. That's not science.

Now, you might wish to argue that evolutionary biologists do the same.  The difference is, their methodology is based on something that has been proven, something that has successful applications in other scientific fields and something that has been validated over and over....and they don't discard evidence that alters their path.

What you are arguing for is not Science.

And I'm not a scientist.  So what's the beef?

Date: 2007/11/27 13:46:57, Link
Author: Daniel Smith
Quote (JAM @ Nov. 26 2007,23:29)
You are lying, Dan. Your interest is purely political.

But you don't look at any inner workings, Dan, you only look long enough to concoct a lie that supports your political positions.

I'm curious; how do you get "political" out of anything I've said here?

Date: 2007/11/28 13:56:25, Link
Author: Daniel Smith
Quote (JAM @ Nov. 27 2007,13:50)
 
Quote (Daniel Smith @ Nov. 27 2007,13:46)
 
Quote (JAM @ Nov. 26 2007,23:29)
You are lying, Dan. Your interest is purely political.

But you don't look at any inner workings, Dan, you only look long enough to concoct a lie that supports your political positions.

I'm curious; how do you get "political" out of anything I've said here?

Because if you were practicing a Christian theology, you wouldn't disregard the Ninth Commandment and the Biblical warnings about hearsay.

Your position is entirely political; it mocks the fundamental teachings of Jesus Christ.

According to... ?

Date: 2007/11/29 20:47:44, Link
Author: Daniel Smith
Quote (Steverino @ Nov. 27 2007,14:32)
 
Quote (Daniel Smith @ Nov. 27 2007,13:39)
   
Quote (Steverino @ Nov. 26 2007,19:36)
I can, and that is not science.

You start with an assumption that skews your research, your interpretation of evidence and your results.  You have identified your goal and cherry pick or distort the evidence that supports your hypothesis. That's not science.

Now, you might wish to argue that evolutionary biologists do the same.  The difference is, their methodology is based on something that has been proven, something that has successful applications in other scientific fields and something that has been validated over and over....and they don't discard evidence that alters their path.

What you are arguing for is not Science.

And I'm not a scientist.  So what's the beef?

No, and that's fine.  Then don't get all tweaked when you want to argue your belief scientifically and are told you cannot because your methodology is not scientifically based.

Case closed.

Maybe my methodology isn't scientifically based, but Schindewolf's, Berg's, and Davison's methodologies are.  The fact that I am co-opting their theories to suit my own needs does not in any way discredit their work.  No one here has taken a serious stab at rebutting those scientists' methodologies or theories.

Date: 2007/11/29 21:06:59, Link
Author: Daniel Smith
Quote (JAM @ Nov. 26 2007,23:29)

Incompetence and dishonesty.
 
Ego.
 
You are lying, Dan.

Your interest is purely political.

If you'll disregard the Ninth Commandment and the Bible's advice to avoid hearsay, you've thrown the baby out with the bathwater.

...Dan, you only look long enough to concoct a lie that supports your political positions.

You're simply not interested in biology for any sake at all.

So why do you keep lying...?

You don't have any significant knowledge of biology, and if any of it threatens your political stance, you'll throw it in the garbage and substitute a lie that pleases you.

Because you'll just lie about the data that don't fit your beliefs?

But you don't study at all, Dan!

   
Quote (swbarnes2 @ Nov. 27 2007,12:10)

This statement of yours is simply a bald-faced lie.

But we all know that that was false, and your lame answers confirmed it.  

It shows that you are a liar.  

Aren't you embarassed to keep showing off our own ignorance and dishonesty time and time again?


After awhile, these endless strings of hollow accusations will say more about your character than mine.

Date: 2007/11/29 21:25:46, Link
Author: Daniel Smith
[quote=JAM,Nov. 26 2007,23:29]        
Quote (Daniel Smith @ Nov. 26 2007,19:15)

         
Quote
The consensus position on pseudogenes seems to be that they are "dead" copies of once-active genes.

Which they generally are, EVEN WHEN THEY ARE TRANSCRIBED.
         
Quote
From a theological perspective, I can't believe that God would have "dead wood" in the genome, so I find myself shrugging off their conclusions and latching onto the few statements that hint at pseudogenes being more functional than previously thought.

Like which statements?

Like these ones:
         
Quote
However, a few pseudogenes have been indicated to have potential biological roles (Ota and Nei 1995; Korneev et al. 1999; Mighell et al. 2000; Balakirev and Ayala 2003). Whether these are anecdotal cases or pseudogenes do play cellular roles is still a matter of debate at this point, simply because not enough studies have been conducted with pseudogenes as the primary subjects. To be clear, in this study the nonfunctionality of a pseudogene is strictly interpreted as a sequence’s lacking protein coding potential, regardless of whether it can produce a (functional or nonfunctional) RNA transcript.
Quote
We believe that the data obtained by RACE experiments or by sequencing analyses (CAGE, PET, EST, and mRNA) provide unambiguous evidence for pseudogene transcription. Altogether, these data indicate that 38 (19% of 201, 20 nonprocessed and 18 processed) pseudogenes are the sources of novel RNA transcripts. This may well represent a low-bound estimate and does not include the ambiguous and possibly inconclusive cases supported only by transfrags. We should emphasize that most cases of pseudogene transcription were only detected in one or a few experiments (manifested by small overlaps between data from different evidence) (Table 1), and thus the example in Figure 3 is not typical. This indicates that pseudogene transcription is quite tissue-specific, as RACEfrags, CAGE, PET, and transfrags were obtained from different cell lines or tissues (see Methods). On the other hand, such a pattern of tissue- (or cell line)-specific transcription was a common characteristic of novel non-coding transcripts (Cheng et al. 2005).
Quote
Although transcription of a pseudogene is not sufficient to indicate whether it has a meaningful biological function, our data showed that pseudogene transcription often occurred at a low level and with a pattern of tissue or cell line specificity. These are similar to the transcriptional characteristics that have been observed for antisense RNA (Dahary et al. 2005; Katayama et al. 2005) and many intronic and intergenic transcripts whose biochemical functions are yet to be unraveled (Bertone et al. 2004; Cheng et al. 2005; Johnson et al. 2005; Willingham and Gingeras 2006). It would not, therefore, be surprising if pseudogenes proved to be one source of novel, functional non-coding RNAs.
Quote
However, these results do not exclude the possibility that some transcribed pseudogenes play biological roles, since it has been found that many experimentally determined functional elements (e.g., promoters) are not significantly conserved either (The ENCODE Project Consortium 2007).

Remember now, I'm not saying that these statements show pseudogenes to be functional.  My statement was that these are "the few statements that hint at pseudogenes being more functional than previously thought."

Date: 2007/11/29 21:38:31, Link
Author: Daniel Smith
Quote (IanBrown_101 @ Nov. 29 2007,20:56)

Davison states that all things are front loaded to end up how they are now, kind of like how a foetus becomes a baby, right?

How the bloody hell do you test that?

You should be able to test it the same way you test the MET - by looking at fossil, molecular and phylogenetic evidence and seeing if it supports the hypothesis.

It would seem you could make predictions based on his hypothesis and then test them to see if they were valid.

I believe Davison also suggested some experiments that could be done to test the semi-meiotic reproductive mechanism, but I don't know the details.

Date: 2007/11/29 22:14:52, Link
Author: Daniel Smith
Quote (JAM @ Nov. 29 2007,12:36)
 
1) Does your hypothesis predict that there will be anything that we humans could reasonably call a "hind-leg gene" based on analogies with our own intelligent designs?
Not a single gene.  More likely "hind leg" development would be controlled by a region containing many genes.        
Quote

2) Does your hypothesis predict that there will be anything that we humans could reasonably call a "tail gene" based on analogies with our own intelligent designs?
Same        
Quote

3) What do you mean by "histone activity"?
I mean the affect specific histones have on the transcription, packaging, expression and suppression of DNA sequences.        
Quote

4) Why would you think that transcription of a particular gene is always happening? WTF do transcription factors do?
Well, I'm unsure of this now.  I think transcription is probably very cell specific - so it would depend on the cell type.  I believe (theologically) that the entire genome is used somewhere and sometime, but not "always" - as I stated.        
Quote

5) Wouldn't an intelligent designer design genes so that their transcription was turned on ONLY when (and where) the presence of the gene product is necessary?
Probably.  That makes more sense than what I originally said.        
Quote

6) an you find a single instance of a scientist referring to the design of endocytic (intracellular plumbing) pathways?
Does this qualify?        
Quote

7) Explain the intelligence in the design of endocytic pathways, particularly their superiority to more conventional plumbing, as observed from the very same designer in our very own bodies. Be sure to explain the rationale behind the choice of so many similar, closely-related components with partially-overlapping (neither separate nor redundant) pathways.
I don't know enough about endocytic pathways to answer this.        
Quote

8) According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?

No idea.  Such things seem completely irrelevant to me.  But, just to hazard a guess, I'd say humans and mice have probably 30-50% similar genes        
Quote

           
Quote
In the human genome, what percentage of genomic sequence would you predict is likely to be transcribed as nuclear primary transcripts?

Among unique sequence, most (70-90%). Among repeats, less, and I'd predict that the probability of transcription increases with proximity to genes for both repeats and nonrepeats.

Of course, you aren't being upfront about your unsupported belief that transcription implies function. I predict that no function will be found for the vast majority of those transcripts. The next largest class will be those in which the transcript has no function, but the transcription does (can you grasp this important distinction?).
I'm not sure what the difference is.        
Quote
Again, the probability that a transcript or transcription serves some function will be highly correlated with proximity to genes.
No doubt that's the safest bet.  I'm still expecting scientists to be "surprised" by functional elements found further and further from genes (again based on my theological beliefs - as are all these answers).

Date: 2007/11/29 22:21:46, Link
Author: Daniel Smith
Quote (JAM @ Nov. 29 2007,21:45)
   
Quote (Daniel Smith @ Nov. 29 2007,21:06)
   
Quote (JAM @ Nov. 26 2007,23:29)

Incompetence and dishonesty.
 
Ego.
 
You are lying, Dan.

Your interest is purely political.

If you'll disregard the Ninth Commandment and the Bible's advice to avoid hearsay, you've thrown the baby out with the bathwater.

...Dan, you only look long enough to concoct a lie that supports your political positions.

You're simply not interested in biology for any sake at all.

So why do you keep lying...?

You don't have any significant knowledge of biology, and if any of it threatens your political stance, you'll throw it in the garbage and substitute a lie that pleases you.

Because you'll just lie about the data that don't fit your beliefs?

But you don't study at all, Dan!

         
Quote (swbarnes2 @ Nov. 27 2007,12:10)

This statement of yours is simply a bald-faced lie.

But we all know that that was false, and your lame answers confirmed it.  

It shows that you are a liar.  

Aren't you embarassed to keep showing off our own ignorance and dishonesty time and time again?


After awhile, these endless strings of hollow accusations will say more about your character than mine.

What's hollow about them, Dan?

They're "hollow" because I've never purposefully lied during this discussion.  I may have said things which I thought to be true at the time, and later found they weren't (in which case I've retracted them), but I've never ever lied.
The fact that you and a few others here seem obsessed with calling me a "liar" says more about you than it does me.

Date: 2007/11/29 22:31:11, Link
Author: Daniel Smith
Quote (IanBrown_101 @ Nov. 29 2007,22:07)
   
Quote (Daniel Smith @ Nov. 30 2007,03:38)
   
Quote (IanBrown_101 @ Nov. 29 2007,20:56)

Davison states that all things are front loaded to end up how they are now, kind of like how a foetus becomes a baby, right?

How the bloody hell do you test that?

You should be able to test it the same way you test the MET - by looking at fossil, molecular and phylogenetic evidence and seeing if it supports the hypothesis.

It would seem you could make predictions based on his hypothesis and then test them to see if they were valid.

I believe Davison also suggested some experiments that could be done to test the semi-meiotic reproductive mechanism, but I don't know the details.

But you CAN'T do that. How the heck are we supposed to tell from fossils if things were MEANT to turn out how they did?

If you flip a coin 5 times and it comes out heads each time, I could say it was predestined. How the hell can you test that idea?

What if it comes out heads 1,000,000,000 times?

Date: 2007/11/30 18:04:06, Link
Author: Daniel Smith
Quote (JAM @ Nov. 30 2007,00:30)
   
Quote (Daniel Smith @ Nov. 29 2007,22:14)

Does this qualify?              

Not even close, because they aren't talking about endocytosis, they attribute any design to evolution, and they point out the stupidity of the process:
             
Quote
The resulting terrestrial mammalian kidney is enor-
mously inefficient and energy-consuming, illustrating the tink-
ering premise. Smith (17) famously stated, “What engineer,
wishing to regulate the composition of the internal environ-
ment of the body on which the function of every bone, gland,
muscle, and nerve depends, would devise a scheme that oper-
ated by throwing the whole thing out 16 times a day and rely
on grabbing from it, as it fell to earth, only those precious
elements which he wanted to keep?”

So if God designed your kidneys, He is stupid. Who would worship such a god?

Interesting then how man cannot improve on such a "flawed" design.  Dialysis is no where near as effective as the natural kidney - in spite of all it's supposed flaws.

Date: 2007/11/30 18:50:13, Link
Author: Daniel Smith
Quote (Richard Simons @ Nov. 30 2007,00:27)
   
Quote (Daniel Smith @ Nov. 29 2007,20:47)
Maybe my methodology isn't scientifically based, but Schindewolf's, Berg's, and Davison's methodologies are.  The fact that I am co-opting their theories to suit my own needs does not in any way discredit their work.  No one here has taken a serious stab at rebutting those scientists' methodologies or theories.

My questions about the 'frontloading' were serious, but you've probably discounted them because they were unanswerable.

       
Quote (Richard Simons @ Nov. 22 2007,16:36)
But you have still not suggested any possible internal mechanism that could constrain evolution or direct it, or any mechanism by which the organism could foresee the future and know what adaptations it will need. As far as I can tell, Schindewolf and Davison are just as barren of ideas for this as you are. The semi-meiotic hypothesis has nothing to do with how the path of evolution is constrained or pre-ordained. Whether evolution procedes by saltation or continuously is a different issue from the mechanism for storing and imposing the constraints.

Until these problems are fixed, as far as I am concerned there is no point in attempting a rebuttal.

I think your questions are probably answerable.  I'm not sure of the mechanism, but something along the lines of a genetic "switch" - which responds to environmental queues would seem a likely candidate.

It would seem to me that the way to test such a mechanism would be to subject natural organisms to specific conditions and see if their adaptations always follow a certain direction.

Berg cites numerous examples of such adaptations in chapters 6 and 7 of "Nomogenesis".  Among his examples are the coloration, number and size of scales, number of rays in the fins, variation in body length and number of vertebrae of fishes of the same genus living in different regions.
He says:
   
Quote
It appears that several groups of species, living in approximately identical conditions, are subject to parallel variations. ibid. pg. 269

He also cites examples where transplanted species almost immediately (often within a single generation) begin to exhibit variations parallel to other species in that region.  Although he does not propose a specific mechanism, his examples are nonetheless food for thought.

Date: 2007/11/30 19:06:49, Link
Author: Daniel Smith
Quote (IanBrown_101 @ Nov. 29 2007,22:48)
           
Quote (Daniel Smith @ Nov. 30 2007,04:31)
             
Quote (IanBrown_101 @ Nov. 29 2007,22:07)
If you flip a coin 5 times and it comes out heads each time, I could say it was predestined. How the hell can you test that idea?

What if it comes out heads 1,000,000,000 times?
 
Then that's what happens.

It implies there might be a cause to it, but it might just as easily be a fluke. There would need to be some evidence that it COULDN'T happen by luck alone, otherwise you could attribute absolutely anything to intelligence.

A coin flip that produces a billion heads in a row makes you think "there might be a cause to it, but it might just as easily be a fluke (my emphasis)"?
Just as easily?  Astounding!  Do you realize what the odds are against such a thing happening?  At some point you have to admit that such a feat is impossible in a fair coin toss.
Pardon me for saying this, but I don't see how any rational person would not conclude that the fix was in.
On the other hand, I think I understand the rationale behind your denial:  If you ascribe a "cut off point" - where something is beyond the realm of chance - you run the risk of negating the mechanism behind the MET.
Maybe I'm wrong - I'm sure pretty much everyone here will say that I am - but that's what I think.

Date: 2007/11/30 19:15:58, Link
Author: Daniel Smith
Quote (swbarnes2 @ Nov. 30 2007,19:05)
 
Quote (Daniel Smith @ Nov. 29 2007,21:06)
     
After awhile, these endless strings of hollow accusations will say more about your character than mine.I may have said things which I thought to be true at the time, and later found they weren't (in which case I've retracted them), but I've never ever lied.


You made a prediction about the results of a hypothetical bacteria experiment.  Then you lied about what your prediction had been.

You claimed that the VISTA data supported your hypothesis.  Then, you claimed that you didn't understand the VISTA data well enough to draw any conclusions from it.  That makes your first statement a lie.

You claimed that you look to nature to tell you about God.

Then you said that what you already knew about god told you what you should see in nature, and that if the two didn't agree, what you were seeing was wrong.  That makes you a liar too.

Sorry, but everything I listed are lies. So spare us your underlined outrage.  The evidence is plain.

If you had a reputation for being honest, people would accept an occasional slip up.  But do you think that a person who's done just the few examples I listed above deserves the benefit of the doubt?

If you really want to claim that these are not lies, that what is happening is that you are tripping over your own arguments desperate attempt to appear reasonable, when your postion is anything but, then say so clearly.  Because the only alternative to you being a bald-faced liar is that you are completely ignorant about your own motivations and beliefs, to the point where strangers on a message boards know more about your thinking than you do.

I have never lied.  I stand by that.  What you perceive as lies are statements made as the result of my own ignorance, and statements where I did not adequately explain my intended meaning  - nothing more - nothing less.
If you want to believe that I'm a liar - go ahead.  I really could care less what you believe.  I will probably just start ignoring your posts - as these endless accusations get old after awhile.  If you want to talk about ideas and issues, that's fine.  If you want to make me the subject - forget it.  I didn't come here for character assassination.

Date: 2007/12/02 19:49:35, Link
Author: Daniel Smith
Quote (Erasmus @ FCD,Nov. 30 2007,19:18)
Daniel what examples of introduced species with parallel adaptations native species in a single or few generations are there?  i'm skeptical of that claim, but not having read Berg or ever having even seen the book I have no way to address this.

He gives many examples, I'll list a few.

Among cattle:
 
Quote
Neumayr, (1889, p. 128, note), following Wilckens, relates that Swiss Cattle, on being removed to Hungary, acquire certain features of the local Hungarian cattle, namely, long horns and legs.
Leo S. Berg, Nomogenesis, p. 280
 
Quote
Shorthorns, bred in Uruguay (Artigas), assume the outward appearance of the native cattle, the so-called "criollos."  
Ibid, p.  281
 
Quote
Simmental cows, purely bred in Hesse (Vogelsberg), in three generations became indistinguishable from the native Vogelsberg cattle (Kronacher, l.c., pp. 128, 129).
Ibid, p.  281


Among fishes, he cites "the observations of J. Schmidt (1920) on the viviparous fish Zoarces viviparus... caried out in Danish waters", in which transplanted fish varied in the number of vertebrae varied according to location.  He quotes Schmidt as saying:  
Quote
"It is therefore evident that the external conditions, altered through the transplantation, have decidedly raised the number of vertebrae in the population" (p. 184)
Ibid, p.  282


He cites another case of a moth, "Saturnia luna (or Actias Luna)", transplanted from Texas to Switzerland, in 1870 by "J. Boll":  
Quote
In America, the catepillar of this species feeds on the leaves of the hickory (Carya) and the black walnut tree (Juglans nigra).  In May, 1871, from the cocoons that had hibernated in Switzerland, emerged moths that were indistinguishable from the American typical form.  Some of these moths laid eggs, and the catepillars of this European generation fed on the leaves of the European walnut (Juglans regia).  They became pupae in the end of June, which early in August produced 35 moths.  These latter most unexpectedly exhibited so many points of difference from their maternal American form that they were described as a new species Saturnia bolli.  They differed in form, as well as pattern and coloration: the body and wings were larger and heavier, the antennae narrower, the longitudinal carmine stripe on the abdomen had disappeared, and the moth became lemon-yellow, instead of yellowish-green.  The carmine marginal stripe on the anterior wings had quite disappeared. (M. Wagner, 1889, pp. 307 - 310.)
Ibid, p.  283
These are just a few of the examples he cites.  I don't have time to list any more right now.  I'd recommend looking for his book - used - on Amazon.com.  That's where I got my copy.

Date: 2007/12/02 19:56:37, Link
Author: Daniel Smith
Quote (IanBrown_101 @ Dec. 02 2007,00:00)
 
Quote (Daniel Smith @ Dec. 01 2007,01:06)
 
Quote (IanBrown_101 @ Nov. 29 2007,22:48)
               
Quote (Daniel Smith @ Nov. 30 2007,04:31)
                 
Quote (IanBrown_101 @ Nov. 29 2007,22:07)
If you flip a coin 5 times and it comes out heads each time, I could say it was predestined. How the hell can you test that idea?

What if it comes out heads 1,000,000,000 times?
 
Then that's what happens.

It implies there might be a cause to it, but it might just as easily be a fluke. There would need to be some evidence that it COULDN'T happen by luck alone, otherwise you could attribute absolutely anything to intelligence.

A coin flip that produces a billion heads in a row makes you think "there might be a cause to it, but it might just as easily be a fluke (my emphasis)"?
Just as easily?  Astounding!  Do you realize what the odds are against such a thing happening?  At some point you have to admit that such a feat is impossible in a fair coin toss.

Why?

 
Quote

Pardon me for saying this, but I don't see how any rational person would not conclude that the fix was in.
On the other hand, I think I understand the rationale behind your denial:  If you ascribe a "cut off point" - where something is beyond the realm of chance - you run the risk of negating the mechanism behind the MET.
Maybe I'm wrong - I'm sure pretty much everyone here will say that I am - but that's what I think.


Then you are wrong. Just because something is unlikely doesn't mean it is impossible. It's unlikely to get a hole in one in golf on the same hole a number of times in a row, does that mean god made the ball go in?

You have to provide a theory we can DISPROVE (to within the limits of "proof").

Aren't there whole theories of probability designed to determining the "unlikelihood" of something?  It's not like one thing is just as unlikely as another.  I seriously doubt that getting several holes in one on the same hole is just as unlikely as getting a billion heads in a row in a fair coin toss.  I may be wrong though.

Date: 2007/12/02 22:57:00, Link
Author: Daniel Smith
Quote (IanBrown_101 @ Dec. 02 2007,22:00)
Quote (Daniel Smith @ Dec. 03 2007,01:56)
 
Quote (IanBrown_101 @ Dec. 02 2007,00:00)
   
Quote (Daniel Smith @ Dec. 01 2007,01:06)
     
Quote (IanBrown_101 @ Nov. 29 2007,22:48)
                   
Quote (Daniel Smith @ Nov. 30 2007,04:31)
                   
Quote (IanBrown_101 @ Nov. 29 2007,22:07)
If you flip a coin 5 times and it comes out heads each time, I could say it was predestined. How the hell can you test that idea?

What if it comes out heads 1,000,000,000 times?
 
Then that's what happens.

It implies there might be a cause to it, but it might just as easily be a fluke. There would need to be some evidence that it COULDN'T happen by luck alone, otherwise you could attribute absolutely anything to intelligence.

A coin flip that produces a billion heads in a row makes you think "there might be a cause to it, but it might just as easily be a fluke (my emphasis)"?
Just as easily?  Astounding!  Do you realize what the odds are against such a thing happening?  At some point you have to admit that such a feat is impossible in a fair coin toss.

Why?

     
Quote

Pardon me for saying this, but I don't see how any rational person would not conclude that the fix was in.
On the other hand, I think I understand the rationale behind your denial:  If you ascribe a "cut off point" - where something is beyond the realm of chance - you run the risk of negating the mechanism behind the MET.
Maybe I'm wrong - I'm sure pretty much everyone here will say that I am - but that's what I think.


Then you are wrong. Just because something is unlikely doesn't mean it is impossible. It's unlikely to get a hole in one in golf on the same hole a number of times in a row, does that mean god made the ball go in?

You have to provide a theory we can DISPROVE (to within the limits of "proof").

Aren't there whole theories of probability designed to determining the "unlikelihood" of something?  It's not like one thing is just as unlikely as another.  I seriously doubt that getting several holes in one on the same hole is just as unlikely as getting a billion heads in a row in a fair coin toss.  I may be wrong though.

The point is it doesn't matter how unlikely it is, but it happened.

Like JAM said, if you filter the coin toss with selection, then it's not even remotely as odd.

Ah, but what kind of selection?
Intelligent selection - yes.
Natural selection?  Not so sure about that one.  You'd have to explain how natural selection could cause a billion in a row without intelligent input.

Date: 2007/12/04 18:54:40, Link
Author: Daniel Smith
Quote (VMartin @ Dec. 03 2007,11:58)
I skimmed the links but I am not wise from them. The misunderestanding rests on my opinion on the concept of gene itself. We should perhaps use alleles instead genes (Dawkins "Selfish gene" is a nonsense, the book should have been titled "Selfish allele").

As Henry noticed:

         
Quote

Having corresponding genes doesn't mean having the same alleles for those genes.


So let say we have a gene for coloration of Iris. Let say human have 5 alleles of this gene and mice also 5 alleles. The average difference between human alleles is let say 15 base pairs and for mice the average difference is also 15 base pairs.

I do't know which alleles of humans and mice are compared on those genes comparisions. Because you can hit on "blue alleles"  in mice and human and such comparision could show a small synonymous difference, or no difference at all.

But you can hit on red allele of mice  having no counterpart in human genome. What will you do? Will you compare this red mice allele with brown human allele?

Obviously difference in pair bases would be much more greater in this case. Consequently it could be inferred that both species diverged sooner as they did.

So I am not expert but I suppose there must exist something like average human allele and average mouse allele or what when we are comparing their genes. Or am I wrong?

The second question (closely connected) is if I give you an allele from mice  would you be able to tell it apart from human alleles because it is more different than are different human alleles of the same gene from each other?

Hi Martin,

I've often wondered the same thing.

How do they settle on a "genome" when there can be much variation within species?

I know of one example in mtDNA where a single species was found to have 8% sequence divergence.

Date: 2007/12/09 13:19:21, Link
Author: Daniel Smith
Quote (JAM @ Dec. 04 2007,21:12)
 
Quote (Daniel Smith @ Dec. 04 2007,18:54)
How do they settle on a "genome" when there can be much variation within species?

I know of one example in mtDNA where a single species was found to have 8% sequence divergence.

How much divergence do you think there is between alleles of the genes contained in and haplotypes of the Major Histocompatibility Complex, Dan?

How much divergence among V genes for immunglobulins and T-cell receptors? Hint: "V" is for variable.
I don't know.  I'm not knowledgeable enough about such matters to answer your endless barrage of technical questions - and you know that.  
Quote


Would you mind directing me to your post in which you retracted and apologized for your ridiculously false claim that Atlantic and Pacific humpback whales have been reproductively isolated from each other for millions of years, when Tierra del Fuego is a prime place for watching them?

Consider it retracted.  That claim was based on my misunderstanding of a sentence I'd read.  When I went back to check my source, I realized my mistake.

Date: 2007/12/09 13:29:01, Link
Author: Daniel Smith
Quote (JAM @ Dec. 08 2007,20:49)
Molecular clocks are based on sequences that are not under selection. Inbreeding is the most intense artificial selection around, so your question is meaningless. We know where the strains came from:


No. Inbreeding reduces and eventually eliminates polymorphisms within a strain, so that the only ones one observes are caused by new mutations. Since the lab strains are closely related to each other to begin with, they are not representative of wild populations.

I'm confused.

Are the mouse genomes used for comparison to other genomes artificially "purified", (eliminating polymorphisms), by inbreeding?

Date: 2007/12/09 15:02:29, Link
Author: Daniel Smith
Quote (IanBrown_101 @ Dec. 09 2007,13:23)
                 
Quote
I don't know.  I'm not knowledgeable enough about such matters to answer your endless barrage of technical questions - and you know that.


So why do you think you can make claims or predictions about this kind of thing?

In hindsight, I probably should have stated that I wasn't knowledgeable enough in the beginning and kept the discussion on Schindewolf, and Berg rather than attempt to delve into the molecular aspect.

But I can't undo what I've done.

My predictions were based on my expectations of God, not on my knowledge of biology.  Some of them were way off base, but some of them have not been.  Since I in no way claim to fully understand God or his mechanisms, this does not surprise me.

The main contention I have with the currently held theory is that of it's mechanism - Variation + Natural Selection - specifically Natural Selection.

We all know that variation happens.  But what does Natural Selection do with that variation?  That's the BIG question. Does it really build better machines out of it?  Or does it maintain the status quo?

I believe the power of Natural Selection is taken for granted - without any real experimental verification.  It is made out to be almost "godlike" in its creativity - but what is really known about it?  

Most evolutionary experiments use artificial selection - so they do not actually test the proposed mechanism.  The true test of Natural Selection is whether a variant can survive in the wild - not in a lab.

This is the crux of the arguments Schindewolf and Berg made.  Based on their observations, Natural Selection had nothing to do with creative evolution.  

Berg cites an almost endless list of examples in chapters with such titles as: "Facts from comparative morphology", "Facts from palaeontology", "Ontogeny", "Convergence and homology", "Phylogenetic atavism", "Parallelism in heterogeneous variations (mutations) and anomalies", "The geographical landscape as an agency in the production of organic forms", "Mimicry and convergence", and "Polyphyletic origin of similar forms".

Schindewolf also makes a solid case based on his extensive study of some of the most abundant fossils known to man.  His arguments are extensively documented in such chapters as: "Discontinuities between structural designs", "Gaps in the material studied by paleontology and neontology", "Patterns in evolution", "The unfolding of the cephalopods", "The unfolding of the stony corals", "The absence of gradual transitions", "The dovetailing of some types", The irreversibility of evolution", "The phases of evolution", "Examples of major cycles", "The origin of the types", "Proterogenic evolution", "Orthogenesis", "Parallel evolution", and "An imaginary picture of an organic world shaped by mutation and selection".

Their observations of real world examples led both of these scientists to the conclusion that evolution is not a matter of random variations filtered through natural selection, but is rather a result of evolution according to law.  Both of them reject Natural Selection as a creative agent.  As a believer in God, I'm much more inclined to embrace their conclusions.

Now, I came here at the invitation of Alan Fox for the express purpose of debating the works of these scientists and their challenges to the theory of evolution.  To date, no one has shown that their claims do not have scientific merit.  In fact there seems to be a reluctance here to talk about them.  Now what conclusion am I supposed to draw from that?

Date: 2007/12/09 15:23:02, Link
Author: Daniel Smith
Quote (JAM @ Dec. 09 2007,14:54)
     
Quote (Daniel Smith @ Dec. 09 2007,13:29)
         
Quote (JAM @ Dec. 08 2007,20:49)
Molecular clocks are based on sequences that are not under selection. Inbreeding is the most intense artificial selection around, so your question is meaningless. We know where the strains came from:


No. Inbreeding reduces and eventually eliminates polymorphisms within a strain, so that the only ones one observes are caused by new mutations. Since the lab strains are closely related to each other to begin with, they are not representative of wild populations.

I'm confused.

I'll say! I'll second Ian's question: what makes you think that you can make sweeping claims when you can't answer simple questions? If you're going to babble on about 8% sequence divergence as having some significance, you have no business claiming ignorance.

Do you realize that natural selection can INCREASE polymorphism?

I know I shouldn't do this but...
Apparently natural selection can also decrease polymorphism - since one of the species in the same study had a sequence divergence of 0.1% - also due to natural selection.  So what does that prove?

       
Quote
     
Quote
Are the mouse genomes used for comparison to other genomes artificially "purified", (eliminating polymorphisms), by inbreeding?

We have all kinds. The initial genomes have been from inbred lab strains, but we have loads of sequence (AFAIK not whole genomes yet) from quasi-different species like Mus spretus and Mus castaneus. I say "quasi-" because both species will interbreed with the house and lab mouse, Mus domesticus.
As will all mice I assume.      
Quote


If you think the inbreeding will justify ignoring the data, what do you predict will be seen in alignments between the mouse species?

Well, since they can all interbreed, they are all the same species (just like all the inbred variations of dogs).  So what we have here is variation within a species.  The differences and similarities within this one species shows us the amount of variation that exists (or can exist) within that species.  I predict therefore that there will be equal evolutionary constraint among all sequences - coding and non-coding - within the mouse species.  But then again, I have no knowledge whatsoever to back up this claim - it's based entirely on my preconceived idea of God.  I therefore welcome correction.

Date: 2007/12/09 15:53:42, Link
Author: Daniel Smith
Quote (Lou FCD @ Dec. 05 2007,06:38)
 
Quote (VMartin @ Dec. 05 2007,01:07)
And last but not at least. Comparing differences between genome of brother and the genome of his sister there are changes let say in 100 genes having (different alleles of it). But those differences are not caused by "random mutation" purified by natural selection but only due "frontloading".


So your alternative hypothesis to modern evolutionary theory is "In the beginning, God did it"?  Please ask whoever is feeding you your lines to explain what sort of predictions you would make from that, and how you would go about testing those predictions.

Also, when next you speak to your "Intelligent" Designer guy, let him know I'd like a refund or exchange on my spinal column, it seems to be defective and I'm frequently in some serious pain.  And it's deteriorating.  While we're on the subject of piss-poor coding, designing, and manufacturing, I'd also like to get refunds and exchanges for the following:

My wife's gall bladder, appendix, large (I think it was the large - whichever one anchors the appendix) intestine, and the whole of her internal girly parts.  They've all had to be removed (well the intestine was a partial) due to manufacturing defects at the frontloading factory.

My son's ankle.  It's a wreck and really should have held up more than 13 years.  You'd think the All Powerful Frontloader would have done a better job with that.  Fortunately, it's still under warranty (although aren't major manufacturing defects an exception to the warranty laws here in the U.S.?).

Also, I'd like to see the code for my Pop.  Is that open-source?  He's having issues of dizziness and fainting, etc., and the doctors don't seem to be able to pin it down.  If they could see the actual code, perhaps they could find the bug and fix it.

Just leave me a message here (or just post the code, I'm sure he won't mind), I have to go back to the hospital to visit my Pop and will be in and out all day.

Thanks.

Lou

P.S. If your "Intelligent" Frontloader needs to make a little extra Christmas money, let him know that I heard that Microsoft was hiring half-assed code writers as temps to work on Vista.  He could look into that.

So you only accept Perfection as evidence for intelligent design?

Show me something then that meets your criteria for an intelligently designed object.

Date: 2007/12/11 19:46:56, Link
Author: Daniel Smith
Quote (Lou FCD @ Dec. 10 2007,05:25)
             
Quote (JAM @ Dec. 09 2007,17:46)
             
Quote (Daniel Smith @ Dec. 09 2007,15:53)
So you only accept Perfection as evidence for intelligent design?

Straw man. He accepts intelligence as evidence for intelligent design.

Well said, thank you.

The end product is a bug ridden, defective hack-job of spare parts and afterthoughts that worked at the time of implementation.

It ain't pretty, it ain't elegant, it ain't intelligent, it just works or it doesn't.

Hogwash.  Pure and simple hogwash.  The "end product" is the most complex, elegant, sophisticated machinery known to man.  

"It ain't pretty"?  Those of us with a preference for the female of the species will beg to differ.  

"it ain't elegant"?  Tell me the human hand is not one of the most elegant structures imaginable.  

"it ain't intelligent"?  The human brain puts our banks of computers to shame with it's processing power.

What is it that blinds you to all this?  Is it your distaste for God?  Do you do this because it's his creation?

I don't understand it; I don't understand how intelligent people can look at such mind-boggling sophistication and deny it even exists!  Within our bodies there are literally billions of working systems - intertwined in complex networks - working together to allow us to do things like laughing and crying, reading and speaking.  All these systems work together so we can cradle a baby, smell a flower, enjoy a sunset, or compose or enjoy music.  They allow us to do the very things we are doing right now.  You can't explain that with "variation and selection".  There's just no way.  There is an "elephant in the room" and I think you know who it is.

Date: 2007/12/11 19:53:43, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Dec. 09 2007,15:46)
 
Quote (Daniel Smith @ Dec. 09 2007,15:23)
Well, since they can all interbreed, they are all the same species (just like all the inbred variations of dogs).  So what we have here is variation within a species.  The differences and similarities within this one species shows us the amount of variation that exists (or can exist) within that species.  I predict therefore that there will be equal evolutionary constraint among all sequences - coding and non-coding - within the mouse species.  But then again, I have no knowledge whatsoever to back up this claim - it's based entirely on my preconceived idea of God.  I therefore welcome correction.

Ring species
From Wikipedia, the free encyclopedia
       
Quote
The coloured bar to the right shows a number of natural populations, each population represented by a different colour, varying along a cline (a gradual change in conditions which gives rise to slightly different characteristics predominating in the organisms that live along it). Such variation may occur in a straight line (for example, up a mountain slope) as is shown in A, or may bend right around (for example, around the shores of a lake), as is shown in B.

In the case where the cline bends around, populations next to each other on the cline can interbreed, but at the point that the beginning meets the end again, as is shown in C, the genetic differences that have accumulated along the cline are great enough to prevent interbreeding (represented by the gap between pink and green on the diagram). The interbreeding populations in this circular breeding group are then collectively referred to as a ring species.


Problem of definition
       
Quote

The problem, then, is whether to quantify the whole ring as a single species (despite the fact that not all individuals can interbreed) or to classify each population as a distinct species (despite the fact that it can interbreed with its near neighbours). Ring species illustrate that the species concept is not as clear-cut as it is often understood to be.

Fasinating stuff. And it's not so simple as "since they can all interbreed, they are all the same species"
http://en.wikipedia.org/wiki/Ring_species

From the page you quoted:  
Quote
A classic example of ring species is the Larus gulls circumpolar species "ring". The range of these gulls forms a ring around the North Pole. The Herring Gull, which lives primarily in Great Britain, can hybridize with the American Herring Gull (living in North America), which can also interbreed with the Vega or East Siberian Herring Gull, the western subspecies of which, Birula's Gull, can hybridize with Heuglin's gull, which in turn can interbreed with the Siberian Lesser Black-backed Gull (all four of these live across the north of Siberia). The last is the eastern representative of the Lesser Black-backed Gulls back in north-western Europe, including Great Britain. However, the Lesser Black-backed Gulls and Herring Gull are sufficiently different that they do not normally interbreed; thus the group of gulls forms a continuum except in Europe where the two lineages meet. A recent genetic study has shown that this example is far more complicated than presented here (Liebers et al, 2004). This example only speaks of classical Herring Gull - Lesser Black-Backed Gull complex and does not include several other taxonomically unclear examples which belong in the same superspecies complex, such as Yellow-Legged Gull, Glaucous Gull and Caspian Gull.
(My emphasis)


The terms "do not normally interbreed" and "cannot interbreed" are not equivalent terms.

Date: 2007/12/15 12:24:40, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Dec. 12 2007,09:27)
 
Quote (Arden Chatfield @ Dec. 12 2007,09:25)
   
Quote (stevestory @ Dec. 12 2007,08:15)
When I saw Daniel's "they can interbreed so they're the same species" the first thing I thought of was ring species. So kudos to Arden.

Credit where it's due, oldmanintheskydidntdoit is the one who posted the info on ring species. I just posted the smartassy rejoinder to Daniel's "no forest here, just trees" response.

So maybe I deserve one kudo at most, or perhaps half a kudo.

Triple kudos all round!

I guess amidst all the kudos and congratulatory back-slapping, you guys missed my response to the ring species argument.

Date: 2007/12/15 12:59:24, Link
Author: Daniel Smith
Quote (JAM @ Dec. 12 2007,11:25)
     
Quote (Daniel Smith @ Dec. 11 2007,19:46)
elegant,

Now you're lying again. You haven't looked, and you haven't offered a single example of elegance. In fact, the nature of biological complexity is usually profoundly and utterly inelegant. "Elegantly simple" is not an oxymoron.
Now you're just lying.  I can look at virtually any biological system and immediately see its elegance and sophistication of design.  Take protein synthesis for example.  Not only is this an incredibly efficient machine - made up of an intricate web of cooperating smaller molecular machines - but it also self-replicates.  You can't explain the origin of even this most basic foundational element of life via the mechanisms of your theory.  You can't improve upon it either.  Why don't you tell me exactly what's "profoundly and utterly inelegant" about protein synthesis?  Your constant bloviating on these points is just hollow bravado that masks your inabilities to comprehend even the simplest of God's works.
       
Quote
   
Quote
"it ain't elegant"?  Tell me the human hand is not one of the most elegant structures imaginable.

I can imagine an infinite number of more elegant structures, beginning with obvious improvements on the existing design.

How about a list?

Date: 2007/12/16 15:15:32, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Dec. 15 2007,14:25)
 
Quote (Daniel Smith @ Dec. 15 2007,12:24)
 
Quote (oldmanintheskydidntdoit @ Dec. 12 2007,09:27)
     
Quote (Arden Chatfield @ Dec. 12 2007,09:25)
       
Quote (stevestory @ Dec. 12 2007,08:15)
When I saw Daniel's "they can interbreed so they're the same species" the first thing I thought of was ring species. So kudos to Arden.

Credit where it's due, oldmanintheskydidntdoit is the one who posted the info on ring species. I just posted the smartassy rejoinder to Daniel's "no forest here, just trees" response.

So maybe I deserve one kudo at most, or perhaps half a kudo.

Triple kudos all round!

I guess amidst all the kudos and congratulatory back-slapping, you guys missed my response to the ring species argument.

You said
 
Quote
The terms "do not normally interbreed" and "cannot interbreed" are not equivalent terms.

Perhaps you could elaborate?

Sure.  Your contention that the sub-species at the ends of these "ring-species" are not the same species is only valid if the hybrid is infertile.  If the sub-species hybrid is fertile, they're still the same species - in spite of their inhibition to mate with each other.
Therefore the terms "do not normally interbreed" and "cannot interbreed" are not equivalent terms.

Date: 2007/12/16 15:44:16, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Dec. 15 2007,17:02)
   
Quote (Daniel Smith @ Dec. 15 2007,12:59)
Now you're just lying.  I can look at virtually any biological system and immediately see its elegance and sophistication of design.

     
Quote
the recurrent pharyngeal nerve, which in all mammals (if
I'm not mistaken) loops around the aorta in order to get from the
brain to the larynx.  In the giraffe, this nerve is thus ~15 feet
long, whereas the larynx is ~1 foot from the brain.  


A quote from TO there, I also found a great site while searching for info.
http://darwinstories.blogspot.com/2007....ck.html
Funny!
Daniel, whats elegant about the pharyngeal nerve in the giraffe then?

The reason the nerve passes between the internal and external carotid arteries is because the giraffe evolved from a short-necked ancestor.  The giraffe most likely represents the over-specialized typolysis phase of Schindewolf's theory.

My guess is that the giraffe will exhibit low genetic variability when compared with other mammals also.

You have to remember that creation took place a long time ago, and lots of evolution and variation has happened since then.  The fact that so much of what remains is still functional is a testament to the brilliance of the Creator.

Date: 2007/12/16 21:15:00, Link
Author: Daniel Smith
Quote (Richard Simons @ Dec. 16 2007,16:40)
   
Quote (Daniel Smith @ Dec. 16 2007,15:44)
The reason the nerve passes between the internal and external carotid arteries is because the giraffe evolved from a short-necked ancestor.  The giraffe most likely represents the over-specialized typolysis phase of Schindewolf's theory.

I just don't understand what causes this facination with what was a passing fad amongst some biologists 70 years ago, and that lasted for even shorter than the streamlined steam locomotives of the same era. It is pure fancy, with no evidence to support it and not even a postulated mechanism.

I'm assuming you have not read Schindewolf's Basic Questions in Paleontology.  If you had, you'd know that Schindewolf endorsed Richard Goldschmidt's theory of Systemmutation, or the "repatterning" of the chromosomes, as a mechanism:    
Quote
This repatterning or Systemmutation, is attributed to cytologically provable breaks in the chromosomes, which evoke inversions, duplications, and translocations.  A single modification of an embryonic character produced in this way would then regulate a whole series of related ontogenetic processes, leading to a completely new developmental type.
Basic Questions in Paleontology, pg. 352, footnote (emphasis his)

That this mechanism has merit has been spelled out in this discussion by the contention that mice and men share "100%" of their genes, yet their chromosomes show complete restructuring in relation to each other.

Date: 2007/12/16 21:25:44, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Dec. 16 2007,17:02)
 
Quote (Daniel Smith @ Dec. 16 2007,15:44)
The giraffe most likely represents the over-specialized typolysis phase of Schindewolf's theory.

Why?

Mainly because he uses it as an example of over-specialization on pg. 287 of his book:
Quote
The Recent giraffe is overspecialized in the extreme lengthening of the neck and forelimbs, which is usually assumed to be a special adaptation for browsing on the leaves and twigs of tall trees.  The excessive length of the legs is compensated for only very incompletely by the neck, upsetting normal proportions; the giraffe can no longer reach the ground or the surface of a water hole with its mouth when standing in a normal position but must instead spread its forelegs wide apart (fig. 3.126).  In addition, the long slender neck makes impossible the development of extensive weapons on the forehead, as are seen, for example, in the related, relatively short-necked Pliocene Sivatherium.  For reasons of weight, only short ossicones could develop.
Basic Questions in Paleontology, pg. 287 (his italics)

Date: 2007/12/16 21:27:57, Link
Author: Daniel Smith
Quote (Steverino @ Dec. 16 2007,07:40)
Denial,

Where is your proof that apperance of design, proves design?

Leap of faith is not proof.

Are you admitting life shows the appearance of design?
Or is this a trick question?

Date: 2007/12/16 21:37:00, Link
Author: Daniel Smith
Quote (JAM @ Dec. 15 2007,17:52)
     
Quote (Daniel Smith @ Dec. 15 2007,12:59)
Take protein synthesis for example.

Since I already did and you ran away from my question, which one of us is lying, Dan?
       
Quote
Not only is this an incredibly efficient machine - made up of an intricate web of cooperating smaller molecular machines

You are incoherent. Intricacy is not a measure of efficiency. You haven't looked at efficiency, have you?
       
Quote
- but it also self-replicates.

Really? How does the protein synthetic machinery self-replicate? What substance makes up the enzymatic core of the ribosome, Dan? Is it synthesized by the protein synthetic machinery?

I predict that you don't know, and you will evade my attempts to get you to look, supporting my claim that you haven't looked.
       
Quote
You can't explain the origin of even this most basic foundational element of life via the mechanisms of your theory.

Can you explain it?
       
Quote
You can't improve upon it either.

You're lying again. It is trivially easy to improve upon it. That's the very point I was making when I asked you this question, from which you ran away, because in your soul, you know that your arguments are fraudulent (i.e., you have no real faith):

         
Quote (JAM @ Dec. 09 2007,16:46)
         
Quote (Daniel Smith @ Dec. 09 2007,15:53)
So you only accept Perfection as evidence for intelligent design?

Straw man. He accepts intelligence as evidence for intelligent design.

Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.

I predict that you will avoid the question.


Why didn't you answer, Dan? Are you deluded, dishonest, or (my choice) both?

Does this feature of protein synthesis demonstrate intelligent design, elegant design, or both?

       
Quote
Why don't you tell me exactly what's "profoundly and utterly inelegant" about protein synthesis?

I will--exactly--when you answer my question. Otherwise, you'll move the goal posts.
       
Quote
Your constant bloviating on these points is just hollow bravado that masks your inabilities to comprehend even the simplest of God's works.

I ask questions, you run away from them while bloviating, and you accuse me of bloviating? What did Jesus say about hypocrisy?

I take these non-answers as admission that your theory cannot explain the origin of even the most basic building blocks of life.  

Also, your contention that you could improve upon the process of protein synthesis is just posturing, IMO.  If you really can, there's a Nobel prize with your name on it, just waiting for you to come pick it up.

Date: 2007/12/17 18:04:27, Link
Author: Daniel Smith
Quote (Richard Simons @ Dec. 17 2007,10:00)
   
Quote (Daniel Smith @ Dec. 16 2007,21:15)
I'm assuming you have not read Schindewolf's Basic Questions in Paleontology.  If you had, you'd know that Schindewolf endorsed Richard Goldschmidt's theory of Systemmutation, or the "repatterning" of the chromosomes, as a mechanism:            
Quote
This repatterning or Systemmutation, is attributed to cytologically provable breaks in the chromosomes, which evoke inversions, duplications, and translocations.  A single modification of an embryonic character produced in this way would then regulate a whole series of related ontogenetic processes, leading to a completely new developmental type.
Basic Questions in Paleontology, pg. 352, footnote (emphasis his)

That this mechanism has merit has been spelled out in this discussion by the contention that mice and men share "100%" of their genes, yet their chromosomes show complete restructuring in relation to each other.

Even if this were correct, it does not answer the problems of how organisms know what information they will need for the future, how this information is stored without being corrupted and how it is turned on at the 'correct' time.

How do organisms or organs "know" anything?
How does the eye "know" to rotate in it's socket when you tilt your head?
How do the ears "know" how to hear?
How do the sex cells "know" they have to cut their number of chromosomes in half?
How do cells "know" during ontogeny what types of cells to differentiate into?

The fact that Life is still here after all these eons is testament to the ingenuity of the designer.  Think about it:  The "god" of the atheist - Natural Selection - has no stake in the matter.  It could care less if genomes get corrupted and unravel.  What does Natural Selection care if life ceases to exist?  Why does every epoch throughout history show an incredible balance of lifeforms - in spite of all variations of environmental conditions? Natural Selection could care less about this.  Again, it has no stake in the matter.  If the earth were to become a dead, uninhabitable planet, Natural Selection would not know the difference.  No, there's something else in play here.  Something is keeping this balance we see.  Something much greater than you and me.

So, to answer both our questions:  It's not that organisms "know" anything, it's that there was someone behind them that knows everything.  God programmed life to live and die, to flourish and become extinct, to evolve and devolve.  It is God who keeps all these things going - for whatever his unknown purposes are.

Date: 2007/12/17 18:52:17, Link
Author: Daniel Smith
Quote (Erasmus @ FCD,Dec. 17 2007,00:01)
Daniel your argument relies upon the empirical content of the proposition that 'Living things are just like non-living things'.  In other words, if we knew enough about physics and chemistry, saith the reductive absurdist who is attempting a muppet mimicry of modern biology, we could derive the rules that govern the origin and maintenance of biological diversity.  Since we can't, Jesus did it.  

The problem lies in the fact that you have been unable to give a first principle defense of why your teleological view should even be considered.  parsimony is a bitch.  

No biologist who is seriously thinking about the issue is willing to go to the plate for that proposition 'living things are reducible to non-living things' (note that this position is an absurd strawman derived from a hard-line formulation of what you call 'materialism'), namely an atomistic determined best of all possible worlds nonsensical hypothesis.  I imagine you will find a wide common ground with modern biology if you express skepticism that living things are reducible to non-living things, but you must do more than say "un-unhhh".  Case studies and examples do nothing to support your thesis, which must ultimately derive some testable first principles of it's own instead of merely denying other theories.  Ask Bob O'Hare why the notion of 'laws' governing biology or ecology has been an unfruitful concept.  It has a lot to do with the fact that no distillable generalizations are available at the level of your analysis, only many examples and counter examples.

I'll add this again, a wise redneck indian once told me something that I consider as hard and fast a biological law that ever could be:

Shit varies.  It matters.  Sometimes.

The teleological view could provide some testable predictions.  relying on schindewolf and goldschmidt means that you are relying on the simple assertions of those who never derived any test of their hypotheses.  Simpson showed that Schindewolf's view of telic horse evolution was at odds with empirical evidence (you should read Tempo and
Mode, there is a chapter devoted to deconstructing Schindewolf that is particularly salient to this discussion).  you should think about some predictions that would distinguish your telic view from an atelic view.  I doubt that this is possible, since we have no a priori notion of what such a teleology would involve (unless of course you are just looking at nature to confirm theological beliefs that you have already held, per your previous comments).  

So here we go:  Life is not reducible to non-living elements (I'll buy this for the sake of discussion, and this has no bearing on whether I personally accept this hypothesis).  If this is true, you have no data from which to evaluate teleology.  If you can tell me 'What is the purpose of living things' then we will have a place to start here.  Otherwise you are just mumbling in the dark.  The sad part about that is I believe you are interested in empiricism.  Your approach, however, is at odds with it.

Edited to add:  Michelob may have something to do with the length of this post.

Michael Denton, in his book Nature's Destiny makes the case for teleological origins much better than I ever could.  While he doesn't really get into empirical tests for design, he does explore its falsification:        
Quote
The strength of any teleological argument is basically accumulative.  It does not lie with any one individual piece of evidence alone but with a whole series of coincidences, all of which point irresistibly to one conclusion.  It is the same here.  Neither the thermal properties of water, nor the chemical properties of carbon dioxide, nor the exceptional complexity of living things, nor the difficu;ties this leads to when attempting to give plausible explanations in Darwinian terms--none of these individually counts for much.  Rather it lies in the summation of all the evidence, in the whole long chain of coincidences which leads so convincingly toward the unique end of life, in the fact that all the independent lines of evidence fit together into a beautiful self-consistent teleological whole...

But the design hypothesis can, of course, be refuted by far less dramatic evidence...  For example, the discovery of an alternative liquid as fit as water for carbon based life, or of a superior means of constructing a genetic tape, better than the double helix, of alternatives superior to oxidation, superior to proteins, superior to the bilayer lipid membrane, to the cell system, to bicarbonate, to phosphates, and so on...  Just one clear case where a constituent of life or a law of nature is evidently not unique or ideally adapted for life, and the design hypothesis collapses.

Nature's Destiny, pp. 384, 386


I should add that Denton's view is that the ultimate purpose of life on this earth was to bring about homo sapiens.  I'd add to that -- "so that mankind can ultimately find God".  Denton cites the unique properties of fire, and man's unique ability to harness it that led to our ability to explore and learn about not only this planet, but the cosmos.  I'd say that the more man learns about life, the more God will become a necessary explanation - as opposed to the commonly held belief that the more we learn, the less God is required.

That's the test I guess.  If the farther we delve into it, the more complicated and amazing it gets, the more likely it's a product of supreme intelligence.  If, on the other hand, the deeper we delve, the simpler it becomes, we can safely assume random causes.

Personally, with what I've learned about the properties of DNA; with all the different transcriptional methods which allow for the transcription of multiple types of RNA from opposing strands, in opposing directions, while often overlapping protein coding DNA; I'd say we're past that point.  But I already believe in God.  You might have a much higher threshold.

Date: 2007/12/17 18:57:40, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Dec. 17 2007,06:12)
 
Quote
I take these non-answers as admission that your theory cannot explain the origin of even the most basic building blocks of life.  


Why not show us how much better your theory is and please describe for us all the origin of even the most basic building blocks of life under your theory. Can you do it without using the world "miracle"? I doubt it.

It was built out of atomic components by a being capable of building such things.  It was intelligently designed to read the programming tape of life and construct proteins from it.
Mankind has done similar things with his limited technology and abilities, so it's not what you'd call a miracle - although to our puny minds it seems so.

Date: 2007/12/18 18:00:43, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Dec. 18 2007,05:58)
So Daniel. Simple question. Who designed the designer? If we're now approaching the level of technology and understanding you claim is required for the "intelligent designer"          
Quote
Mankind has done similar things with his limited technology and abilities
then it seems much more likely that the "intelligent designer" is simply another race of beings about as advanced as we are now. So hardly proof for your gods existence? I simply don't see how you can see it that way.

If mankind can "intelligently design" in a similar way to the "designer" you claim invented life then why does it automatically have to be supernatural? If we can do it..

Daniel, who designed the designer?
I think your view of man is inflated.  We are not even close to being intelligent enough to design life - especially the act of designing self-replicating, evolving systems that can adapt to a multitude of environments - all the while keeping their "programming" intact enough through countless cell divisions and generations to continue giving life to still more generations.

We're nowhere near that level.  When I say man has designed "similar" systems, I'm talking about his tape readers, computers and CD/DVD players which use read-heads and associated circuitry to transfer/translate data from one form to another.

But, if you want to get into first causes, you really only have two choices:  Either the first cause is nothing, or the first cause is eternal.
If you vote for nothing, then you must accept that you can get something from nothing.
Therefore the only logical answer is that the first cause is eternal.

Date: 2007/12/18 18:04:09, Link
Author: Daniel Smith
Quote (Steverino @ Dec. 18 2007,06:58)
I'm no scientist, but even I can see the logical flaw in his position.

Why are we even engaging this twit:

"So, to answer both our questions:  It's not that organisms "know" anything, it's that there was someone behind them that knows everything.  God programmed life to live and die, to flourish and become extinct, to evolve and devolve.  It is God who keeps all these things going - for whatever his unknown purposes are."

There is no proof to back that statement up and he knows it.  It’s an argument that cannot be proven on way or the other, so he clings to it because is leaves the door open for God.

You cannot argue/debate science once someone invokes the God card like this because it’s jut another form of moving the goal posts and at that point it becomes useless.

Do you just trot out the standard "anti-creationist bag of arguments" - no matter who you're debating?  Because you obviously haven't been paying very close attention to what I've been saying.  I've been claiming "God did it" from the beginning.  Where have you been?

Date: 2007/12/18 18:14:47, Link
Author: Daniel Smith
Quote (JAM @ Dec. 17 2007,00:54)
Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.

It's a simple question, and you'd have the integrity to answer it if you really thought that I was just posturing.

You need to answer it beforehand because we both know that you are dishonest when it comes to critically evaluating your own position, and you'll move the goal posts.

You define intelligent design operationally in this case, and I'll show an unequivocal improvement on the "design" USING YOUR CRITERIA. Any knowledgeable biologist can propose reams of obvious improvements.

You don't have any real faith in your position, Dan.

To be honest JAM, I do ignore most of your questions because they seem intentionally deflective - as if you're trying to steer me down a hundred rabbit trails.

This one I don't even understand:  
Quote
Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.

How can a stop codon "[not] encode an amino acid residue" and "allow proteins to have any of the 20 residues" at the same time?
You'll have to make the question less cryptic for me to be able to answer it.

Date: 2007/12/18 18:27:32, Link
Author: Daniel Smith
Quote (JAM @ Dec. 12 2007,11:25)
We're the ones who study His creation, Dan,

Do you really consider it "His creation"?
   
Quote (JAM @ Dec. 09 2007,16:43)
Why not read His book of nature with an open mind instead of a closed one?

I am willing.  What exactly is it that God is trying to teach me?  Give me lesson #1.  Tell me what you've learned about God through "His book of nature".

Date: 2007/12/18 18:40:33, Link
Author: Daniel Smith
Quote (George @ Dec. 18 2007,08:09)
I've not posted on this thread since near the beginning as I'm no gene jockey and not as patient as others.  But I found this an interesting argument:

     
Quote
The fact that Life is still here after all these eons is testament to the ingenuity of the designer.  Think about it:  The "god" of the atheist - Natural Selection - has no stake in the matter.  It could care less if genomes get corrupted and unravel.  What does Natural Selection care if life ceases to exist?  Why does every epoch throughout history show an incredible balance of lifeforms - in spite of all variations of environmental conditions? Natural Selection could care less about this.  Again, it has no stake in the matter.  If the earth were to become a dead, uninhabitable planet, Natural Selection would not know the difference.  No, there's something else in play here.  Something is keeping this balance we see.  Something much greater than you and me.


This is exactly the argument that bolsters climate change deniers - the feeling that someone trustworthy is in charge and that everything will be ok.  But this argument is entirely unfounded.

Daniel:  I've news.  There is no Balance of Nature.  The only people who believe in it anymore are those who write really bad dialogue for nature documentaries.  There is a flux of nature.  Everything changes, nothing stays the same.  Populations of organisms increase, decrease and move around the place.  In the northern hemisphere we're still recovering from the last glaciation.  Sometimes there's variation around a mean population size, but often not.  Many years of ecological research have shown that.

All those variations in environmental conditions you refer to resulted in extinctions.  Lots of them.  Who was looking out for those plants and animals?  Three mass extinctions in geological history, and Homo sapiens are causing the fourth.  These should suggest to you that Natural Selection is in charge of life on this planet and that if a really big, friendly comet comes along or if we banjax the climate, no one is coming to our rescue.

A "balance of nature" is not an argument for teleology, because it doesn't exist.

And by the way, I'm also a Christian and I do science just fine without needing a Designer tugging the strings.  It's bad religion, too.

</rant>

There's a difference between balance and stasis.  It's true that there is no stasis in nature.  There is balance however.  If there weren't we'd be overrun by cockroaches by now.  Extinctions are a part of that balance.  When climate conditions change radically, species that once thrived die out and new ones take their place - all the while maintaining the balance that sustains this planet for life.

Date: 2007/12/18 18:42:35, Link
Author: Daniel Smith
Quote (swbarnes2 @ Dec. 18 2007,18:40)
So your point was not to demonstrate that your conclusion is justified by the facts, your point was to keep making the the same unjustified claim over and over again?

And you think that we will find this an intelligent rebuttal?

Point me to "the facts" that don't justify my conclusion.

Date: 2007/12/20 18:26:34, Link
Author: Daniel Smith
Quote (George @ Dec. 18 2007,18:47)
   
Quote (Daniel Smith @ Dec. 18 2007,18:40)

There's a difference between balance and stasis.  It's true that there is no stasis in nature.  There is balance however.  If there weren't we'd be overrun by cockroaches by now.  Extinctions are a part of that balance.  When climate conditions change radically, species that once thrived die out and new ones take their place - all the while maintaining the balance that sustains this planet for life.

Then please explain to me what you mean by "balance".  And how it relates to cockroaches.  I don't know what you're getting at.

I mean that the world always has exactly the right mixture of species to keep life going (even though the players are in a constant state of flux).  

There's no reason - from an unthinking, uncaring natural selection standpoint - for it to be thus.  If it truly is "the survival of the fittest", cockroaches would win out, take over the world, then die out too when their food sources ran out.  The planet would then be dead - like every other planet we know of.  (Of course, this is just an imaginary scenario where cockroaches just happen to win - you can substitute any "fit", rapidly reproducing species - it doesn't matter, one species should overtake all the others if there's no balance in nature).

That's what I mean by balance.

Date: 2007/12/20 18:46:29, Link
Author: Daniel Smith
Quote (swbarnes2 @ Dec. 18 2007,19:13)
   
Quote (Daniel Smith @ Dec. 18 2007,18:42)

Point me to "the facts" that don't justify my conclusion.

All the facts support the notion that evolution is a purely natural process.  No intelligence required.

Almost every single time you used your theology to predict what biology would look like, you were totally wrong.  Conservation of DNA.  Mouse/human orthologs.  Results of bacterial selection experiments.  I'm sure everyone on this board can name more.  Everywhere we used evolution to predict what we would see, we were right.

Those are the facts.


On the issue of mouse/human orthologs I was way off - yes.  

On the issue of the conservation of DNA, I'm still in the running - since even members of the same species have widely different DNA conservation percentages - anywhere from 0.1% to 8%.

On the results of bacterial selection experiments - none have been done that actually test my prediction (to my knowledge).

So there's actually only one out of the three you listed that would qualify as "totally wrong".

Date: 2007/12/20 19:07:08, Link
Author: Daniel Smith
Quote (JAM @ Dec. 18 2007,18:49)
     
Quote (Daniel Smith @ Dec. 18 2007,18:14)
This one I don't even understand:          
Quote
Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.

How can a stop codon "[not] encode an amino acid residue" and "allow proteins to have any of the 20 residues" at the same time?

The stop codons are TAA, TAG, and TGA. They do not code for aa residues. I didn't write that it allowed them to HAVE any of the residues, I wrote that this allowed them to END in any one of them (i.e., carboxy terminus). Does that make more sense now? Is that an intelligent and/or elegant design?

I'm still a bit unclear because I don't know what's wrong with having stop codons the way they are.  Are you saying it would be better if they did code for amino acids?  

It might help if you could give me an analogy to better illustrate what's going on.

Let me try a language analogy on you and you can correct it where it's wrong:
In my analogy, amino acids would be like the letters of the alphabet and stop codons like sentence ending punctuation ( . ? and !).  So proteins in my analogy would be like sentences.

Is this anywhere near close?

If so, could you use my analogy (or yours - if you have a better one) to show me what's wrong with stop codons?

Date: 2007/12/20 19:25:11, Link
Author: Daniel Smith
Quote (BWE @ Dec. 18 2007,23:46)
       
Quote (Daniel Smith @ Dec. 18 2007,18:00)
But, if you want to get into first causes, you really only have two choices:  Either the first cause is nothing, or the first cause is eternal.
If you vote for nothing, then you must accept that you can get something from nothing.
Therefore the only logical answer is that the first cause is eternal.

Sure, fine. How do you get from there (eternal) to over there-----> where you are talking about this guy with angels licking his feet and demanding servitude of people who have no reliable way to even detect his existence? People who have to believe other people just to find out what he has done?

I mean, hello... Doesn't this strike you as rather... um... like suckering a mark?

The question is not how did I get from here to there, but how did you get, "this guy with angels licking his feet and demanding servitude of people who have no reliable way to even detect his existence", from anything I've said?

When have I ever characterized God in that way?  That sounds more like bitterness talking.  

I've often wondered why some who profess not to believe in God seem to actively hate him.

How can you hate something you believe doesn't exist?

Date: 2007/12/20 19:31:50, Link
Author: Daniel Smith
Quote (JAM @ Dec. 20 2007,19:14)
 
Quote (Daniel Smith @ Dec. 20 2007,19:07)
   
Quote (JAM @ Dec. 18 2007,18:49)
         
Quote (Daniel Smith @ Dec. 18 2007,18:14)
This one I don't even understand:                
Quote
Does having a separate codon(s) for stopping translation (that don't encode an amino acid residue) represent an intelligent design? This allows proteins to have any of the 20 residues at the carboxy terminus.

How can a stop codon "[not] encode an amino acid residue" and "allow proteins to have any of the 20 residues" at the same time?

The stop codons are TAA, TAG, and TGA. They do not code for aa residues. I didn't write that it allowed them to HAVE any of the residues, I wrote that this allowed them to END in any one of them (i.e., carboxy terminus). Does that make more sense now? Is that an intelligent and/or elegant design?

I'm still a bit unclear because I don't know what's wrong with having stop codons the way they are.  Are you saying it would be better if they did code for amino acids?

No, I'm asking for your characterization. Was it an intelligent design decision to use separate codons for stop, instead of combining one or more of those "signals" with a signal to add an amino acid?
 
Quote
It might help if you could give me an analogy to better illustrate what's going on.

I don't think so.
 
Quote
Let me try a language analogy on you and you can correct it where it's wrong:
In my analogy, amino acids would be like the letters of the alphabet and stop codons like sentence ending punctuation ( . ? and !).  So proteins in my analogy would be like sentences.

Is this anywhere near close?

Yes. Is it more intelligent to have separate letters and punctuation marks, or is it more intelligent to always end each sentence with the same letter?
I'd say it's better to differentiate the letters from the punctuation marks.
Quote

 
Quote
If so, could you use my analogy (or yours - if you have a better one) to show me what's wrong with stop codons?

I'm not saying that there's anything wrong with them. I'm asking for your judgment.

If my analogy is correct, then I'd say stop codons should be separate from coding codons (if that's the correct term).

Date: 2007/12/20 19:44:35, Link
Author: Daniel Smith
Quote (JAM @ Dec. 20 2007,19:15)
     
Quote (Daniel Smith @ Dec. 20 2007,18:46)
On the issue of the conservation of DNA, I'm still in the running - since even members of the same species have widely different DNA conservation percentages - anywhere from 0.1% to 8%.

No, you were wrong in every case. You are using fallacies of equivocation to pretend that you're still in the running.

You know that I'm wrong - fine - but I'm not sure how you arrived at that conclusion.  You've pointed me to VISTA and said that the white areas prove me wrong - with very little in the way of explanation.  I'm still not sure I understand exactly how this proves me wrong - since there would be (I'm guessing) white areas if you were to compare your genome to mine.  Maybe I'm wrong about that as well.

I don't have any problem with being wrong.  I only have a problem when someone declares me wrong without showing me, in a way I can understand, exactly how I am wrong.

Date: 2007/12/20 19:45:33, Link
Author: Daniel Smith
Quote (JAM @ Dec. 20 2007,19:15)
       
Quote (Daniel Smith @ Dec. 20 2007,18:46)
On the issue of the conservation of DNA, I'm still in the running - since even members of the same species have widely different DNA conservation percentages - anywhere from 0.1% to 8%.

No, you were wrong in every case. You are using fallacies of equivocation to pretend that you're still in the running.

You know that I'm wrong - fine - but I'm not sure how you arrived at that conclusion.  You've pointed me to VISTA and said that the white areas prove me wrong - with very little in the way of explanation.  I'm still not sure I understand exactly how this proves me wrong - since there would be (I'm guessing) white areas if you were to compare your genome to mine.  Maybe I'm wrong about that as well.

I don't have any problem with being wrong.  I only have a problem when someone declares me wrong without showing me, in a way I can understand, exactly how I am wrong.

Date: 2007/12/20 19:46:32, Link
Author: Daniel Smith
Oops!  Sorry about the double post.

Date: 2007/12/22 18:13:02, Link
Author: Daniel Smith
Quote (JAM @ Dec. 20 2007,23:47)
 
Quote (Daniel Smith @ Dec. 20 2007,19:31)

If my analogy is correct, then I'd say stop codons should be separate from coding codons (if that's the correct term).

And the same goes for start codons, right?

Most likely - yes.  But then again I have no idea what God was thinking when he designed start and stop codons.  The fact that there even are such things; and that they stop and start the encoding of amino acids; which then somehow "know" to join together and fold into proteins; which then "know" exactly where to go and what to do when they get there, is mind-boggling enough.  Now you want me to critique such a system?  It's way over my head.  My analogy of simple letters and punctuation probably comes nowhere near the actual intricacies involved in God's system. But, yes, if stop and start codons are anything like punctuation marks, they should probably be different from amino acid coding codons.

Date: 2007/12/22 18:23:00, Link
Author: Daniel Smith
Quote (George @ Dec. 21 2007,01:25)
   
Quote (Daniel Smith @ Dec. 20 2007,18:26)
   
Quote (George @ Dec. 18 2007,18:47)
         
Quote (Daniel Smith @ Dec. 18 2007,18:40)

There's a difference between balance and stasis.  It's true that there is no stasis in nature.  There is balance however.  If there weren't we'd be overrun by cockroaches by now.  Extinctions are a part of that balance.  When climate conditions change radically, species that once thrived die out and new ones take their place - all the while maintaining the balance that sustains this planet for life.

Then please explain to me what you mean by "balance".  And how it relates to cockroaches.  I don't know what you're getting at.

I mean that the world always has exactly the right mixture of species to keep life going (even though the players are in a constant state of flux).  

There's no reason - from an unthinking, uncaring natural selection standpoint - for it to be thus.  If it truly is "the survival of the fittest", cockroaches would win out, take over the world, then die out too when their food sources ran out.  The planet would then be dead - like every other planet we know of.  (Of course, this is just an imaginary scenario where cockroaches just happen to win - you can substitute any "fit", rapidly reproducing species - it doesn't matter, one species should overtake all the others if there's no balance in nature).

That's what I mean by balance.

Ok.  Now I've three more questions for you, if you'll be so kind, to make sure I know where you're coming from:

Do you think God actively tweaks or toggles the various ecological mechanisms that keep population sizes in check?
Perhaps.  I don't know.  Maybe there's no such thing as natural selection - maybe God does the selecting.  
Quote
 Or is it more of a case that the mechanisms have been set up ahead of time to ensure that no one species can outcompete all others?
Also a possibility.  Or it could be a combination of both.  
Quote


What do you mean by "fit" species?  Could you explain what characteristics they have?  Or maybe give some examples of fit species that perhaps should take over the world but don't?
I already gave the example of cockroaches.  There are probably several insects that could do it - locusts for example, could strip the worlds vegetation bare and completely knock it's ecosystem for a loop.  A resilient virus could wipe out life as we know it and then die out itself for lack of hosts.  There are lots of possibilities.  
Quote


Have you ever thought that we are the cockroaches in your example above, and that since we've taken over the world and are now making a huge mess of it, our downfall is at hand?  Didn't think so.
Yes, I have - in fact that is entirely consistent with the biblical doctrine of the fall.  If you remove man from the world, nature would be much better off.  We are the one organism that's out of sync on this planet.

Date: 2007/12/22 18:25:33, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Dec. 21 2007,05:31)
 
Quote (Daniel Smith @ Dec. 20 2007,19:25)

The question is not how did I get from here to there, but how did you get, "this guy with angels licking his feet and demanding servitude of people who have no reliable way to even detect his existence", from anything I've said?

When have I ever characterized God in that way?  That sounds more like bitterness talking.  

I've often wondered why some who profess not to believe in God seem to actively hate him.

How can you hate something you believe doesn't exist?

It's not god that deserves the hate. As you say, it's illogical to  hate something you don't believe exists.

It's the people that claim that god is whispering in their ear and telling them how other people should live their lives that's the problem. They deserve the hate. Believe whatever you want Daniel, I've no problem with that. There are plenty of theists on this board FYI.

It's when you try and tell me that
a) Action X is a sin because "god said so" and hold up a holy book as proof.
b) Item Y was designed because "I said so" and therefore that proves god exists and evolution is untrue and therefore lets teach it to children as fact.
c) Person Z is unclean because "god said so".

I never told you any of those things.

Date: 2007/12/22 18:27:39, Link
Author: Daniel Smith
Quote (IanBrown_101 @ Dec. 22 2007,18:16)
 
Quote (Daniel Smith @ Dec. 23 2007,00:13)
 
Quote (JAM @ Dec. 20 2007,23:47)
     
Quote (Daniel Smith @ Dec. 20 2007,19:31)

If my analogy is correct, then I'd say stop codons should be separate from coding codons (if that's the correct term).

And the same goes for start codons, right?

Most likely - yes.  But then again I have no idea what God was thinking when he designed start and stop codons.  The fact that there even are such things; and that they stop and start the encoding of amino acids; which then somehow "know" to join together and fold into proteins; which then "know" exactly where to go and what to do when they get there, is mind-boggling enough.  Now you want me to critique such a system?  It's way over my head.  My analogy of simple letters and punctuation probably comes nowhere near the actual intricacies involved in God's system. But, yes, if stop and start codons are anything like punctuation marks, they should probably be different from amino acid coding codons.

My analogy may be wrong (god knows I'm no scientist, but then, neither are you) but I think your claim they "know" to do these things is like saying a light switch "knows" to turn on (or off) a light when pressed.

In fact, a better analogy would be that litmus paper "knows" to turn red when acid is put on it. It doesn't "know" thats just what happens.

They act like they know what to do - which is why I put "know" in quotes.

Date: 2007/12/22 18:33:00, Link
Author: Daniel Smith
Quote (VMartin @ Dec. 21 2007,10:35)
Hi Daniel,

somebody at EvC gave the link to the article written by Professor Richard C. Strohman, Uni California : "Epigenesis and Complexity: The Coming Revolution in Biology"

http://www.thecomplementarynature.com/TCN%20A....ics.pdf

If you have time check it. It is very interesting. I hope such voices will be more common in the future.


According professor Zdenek Neubauer (Charles Uni Prague) modern biology is under strong influence of "fachidiots". You know, some people don't know how to tell apart tiger and lion  but they study, analyze and compare their DNA making bold predictions of evolution of that species .

You don't have to worry about JAM arguments. His concept of many basic bilological words are wrong.    

Epigenesis, epistatic interactions or pleitropic effects of genes play obviously significant role in development of an organism. According Strohman real, genetic disease acount for less than 2% of total disease load.  

Strohman quoted also Feynman who should have said:
"Mind must be a sort of dynamical pattern,not so much founded in a neurological substrate as floating above it, independent above it". But you know, Feynmann is an expert on quantum mechanics and maybe he should more discuss his opinions with evolutionary biologists (JAM etc...).

Thanks for the link Martin.  I'm in the process of reading the article now.  I followed some of the comments made about it over at the bathroom wall.  How much do you want to bet that none of them read the article?  None of their objections reference anything actually stated in the article so I'm guessing that's a safe bet.  But I could be wrong (I often am).

Date: 2007/12/22 18:43:06, Link
Author: Daniel Smith
Quote (Assassinator @ Dec. 22 2007,18:29)
They just act, it happens, that it's. That happening is an action, and is also a reaction from an action that caused that happening. Again, you're think too much in human terms. Trying to fit the normal human perspective onto non-human things.

You're right - it's way beyond human comprehension how "they just act" exactly the way they need to in order to keep an immense, intricate network of embedded systems functioning.

"They just act" explains everything - kind of like "godidit" but in the opposite direction.  It's the kind of explanation that uses the thing that needs explaining as the explanation for the thing that needs explaining.  Makes perfect sense in a kind of blind, mind numbing acceptance of "Nature as Nature's cause" kind of way.

Date: 2007/12/22 18:46:52, Link
Author: Daniel Smith
Quote (IanBrown_101 @ Dec. 22 2007,18:37)
   
Quote (Daniel Smith @ Dec. 23 2007,00:27)

They act like they know what to do - which is why I put "know" in quotes.

So what you're saying is, the fact that chemical reactions occur boggles your mind.

That is in fact, exactly what you are saying, it may not be what you mean, but it's what you said.

And that's terrible (I reckon noone else will get this joke).

No, what I'm saying is that it boggles the mind that exactly the right chemical reactions occur at exactly the right time and exactly the right place.  

Life is not just "chemical reactions".  If it were, you could just measure out all the chemicals in an organism, throw them together in a beaker, and make life.

You're too smart to think that's all that's involved here.

Date: 2007/12/22 18:48:20, Link
Author: Daniel Smith
Quote (IanBrown_101 @ Dec. 22 2007,18:46)
 
Quote (Daniel Smith @ Dec. 23 2007,00:43)
 
Quote (Assassinator @ Dec. 22 2007,18:29)
They just act, it happens, that it's. That happening is an action, and is also a reaction from an action that caused that happening. Again, you're think too much in human terms. Trying to fit the normal human perspective onto non-human things.

You're right - it's way beyond human comprehension how "they just act" exactly the way they need to in order to keep an immense, intricate network of embedded systems functioning.

I hate to sy it, but you really aren't the world Dan.

I'm sorry I had to break it to you....but well, you really aren't. There are other people. Millions of them (billions if you use the incorrect definition of the word).

Sorry man, but...you don't speak for all of us.

Hey I was agreeing with him!
(Well kinda anyway).

Date: 2007/12/22 19:00:44, Link
Author: Daniel Smith
Quote (IanBrown_101 @ Dec. 22 2007,18:48)
   
Quote (Daniel Smith @ Dec. 23 2007,00:46)
     
Quote (IanBrown_101 @ Dec. 22 2007,18:37)
         
Quote (Daniel Smith @ Dec. 23 2007,00:27)

They act like they know what to do - which is why I put "know" in quotes.

So what you're saying is, the fact that chemical reactions occur boggles your mind.

That is in fact, exactly what you are saying, it may not be what you mean, but it's what you said.

And that's terrible (I reckon noone else will get this joke).

No, what I'm saying is that it boggles the mind that exactly the right chemical reactions occur at exactly the right time and exactly the right place.  

Life is not just "chemical reactions".  If it were, you could just measure out all the chemicals in an organism, throw them together in a beaker, and make life.

You're too smart to think that's all that's involved here.

No, that IS what you're saying. Just because they occur at certain times doesn't indicate intelligence, it indicates a working system.

Saying chemical reactions, happening at exactly the right time, in exactly the right proportion, "indicates a working system", is a case of using that which needs explaining as an explanation.  It's pure circular reasoning.    
Quote
Oh, and are you seriously saying that only stupid people think there isn't more to life than what we can see? Chemical reactions and such like?

How did you get that from what i said?

Date: 2007/12/22 19:07:33, Link
Author: Daniel Smith
Quote (Assassinator @ Dec. 22 2007,18:54)
 
Quote
No, what I'm saying is that it boggles the mind that exactly the right chemical reactions occur at exactly the right time and exactly the right place.

Biochemistry is not chance, so the word "exactly" does not mean anything. It happens, that's it, that's just what it does. Nothing more, just happening.
   
Quote
Oh, and are you seriously saying that only stupid people think there isn't more to life than what we can see? Chemical reactions and such like?

Yeap, that's earthern life: chemistry. Bad thing is, we don't know what the exact circumstances were when life first arouse on earth, so we can't.

I agree.  There's not much chance involved.  The question is:  How did we get from "chemicals" to "living, breathing organisms" - if not by chance?

Date: 2007/12/23 10:56:07, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Dec. 23 2007,05:32)
Daniel,
Does god make 2+2=4?
There's your answer then to "why" chemicals behave as they do. 2+2=4.

I sent you a link about populations. No god required. No comment? Coward.

I thought you weren't talking to me.

Date: 2007/12/26 10:56:30, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Dec. 23 2007,11:52)
Quote (Daniel Smith @ Dec. 23 2007,10:56)
 
Quote (oldmanintheskydidntdoit @ Dec. 23 2007,05:32)
Daniel,
Does god make 2+2=4?
There's your answer then to "why" chemicals behave as they do. 2+2=4.

I sent you a link about populations. No god required. No comment? Coward.

I thought you weren't talking to me.

True.

Still, foxes and rabbits, I remember learning that as a child at the science museum. Never heard of them?

Yeah, don't they kind of "balance" each other out?

Date: 2007/12/26 11:07:48, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Dec. 21 2007,05:07)
This information may dispel some of your ignorance Daniel.


Have a good read
http://comptlsci.anu.edu.au/Module-ODEs/ode-overview-notes.html
And let us know if god is still required to maintain population levels.

You do realize that their equations were entirely based on theoretical populations and behavior don't you?

Still, they do illustrate how multiple variables in nature contribute to its overall balance - which was my point in the first place.

Date: 2007/12/26 11:19:54, Link
Author: Daniel Smith
Quote (Erasmus @ FCD,Dec. 22 2007,20:38)
Daniel, the null is 'they act that way'.  It is certainly your burden to show that this is worthy of a design inference.  if they didn't 'act that way', but acted 'another way', and we still had life as it is now, then you would still be claiming a design inference.  it's the kind of crap presupposition that you bring to the table with you.  It has no explanatory value, it has no empirical basis, it is completely a Panglossian jesus loves me the world is perfectly crafted kind of eight year old awe and wonder about the universe.

you're not interested in science and you never have been.  this is all about providing you with an apologetic.  

don't get me wrong.  I'm not saying life is 'just' chemicals.  I'm saying, what is it and how do you know?  Because I smell bullshit.

Well, "the null" doesn't explain very much does it?  "They act that way" does not tell us anything about how chemicals become chromosomes.  As far as I know though, that's all you've got.  There are no other explanations but "the null" for you - if you exclude design.
You ask me what life is...  Well it's an array of simple compounds organized in such a matter as to create working, self replicating systems.
I say that that organization cannot be explained via natural causes and therefore requires design.  But that's just me.

Date: 2007/12/26 18:37:23, Link
Author: Daniel Smith
Quote (Erasmus @ FCD,Dec. 26 2007,11:28)
It is just you (well, and a few other misinformed folks).  

The organization of my little boy has been designed?  I've been present since his conception, and we have no evidence of any designer meddling around with him.  Maybe we can't detect infinite wavelength radiation though.

The null can tell you how chemicals become chromosomes.  Look up biochemistry and cellular biology.  They aren't made of magical powder you know.  They are material.  As unpalatable as that may seem.

What you desire is an ontological explanation.  We've been over this.
No, I do not desire an ontological explanation.  What I desire is an explanation that actually explains something!  "That's the way it is."; or "It just happened"; are no explanations at all.
Sure, you can explain the nuts and bolts of chromosome formation (within a working system that regularly produces chromosomes), but no one has any explanation for the origin of chromosomes.      
Quote


Your assertion that this organization requires supernatural intervention is just that.  An assertion.  In particular, a bland assertion that is predicated solely upon what you don't know.  

The more parsimonious route is:  It may be that supernatural intervention is required for, say, my little boy to grow teeth or his balls to drop.  It may be that it is not.

If you phrase it that way, and then are honest with yourself about what 'supernatural' might mean, and how you would determine such a thing, then you'll drop the foolishness about putting gods in every gap.

Again, how would you know?

I fell the wool being pulled over my eyes here.  You act as if the requirement for explaining the origin of a system is to explain how it works.  These are two separate things.  You can show me how things work all day long, but what you can't show me is how any living system originated.  Now, you take a subtle twist on that line and point to your son.  But that doesn't explain anything.  It just shows me that reproduction happens (again amongst living systems that already reproduce regularly) - it does not explain anything about the origin of even one novel biological system.

This is what frustrates me:  In spite of all the smug answers - no one can explain to me how even the simplest living systems originated via natural causes.  At some point, when no natural explanation is forthcoming, you have to begin looking outside nature for an explanation.

Date: 2007/12/26 19:04:01, Link
Author: Daniel Smith
Quote (Richard Simons @ Dec. 17 2007,10:00)
It still does not answer the question 'Why the fascination with a defunct theory?'

The "fascination" continues for me because this "defunct theory" (as you call it) actually explains the fossil record better than the currently held theory.

For instance: The fossil record shows clear evidence of smooth, gradual evolution amongst the cephalopods.  This evolution is well documented, consisting of millions of fossils, across multiple continents and ages.  In fact these fossils are so numerous and so universal, they are regularly used as index fossils.  

Which brings me to my point:  It's not the smooth, gradual evolution amongst the cephalopods that are used as demarcation for indexing - it's the breaks between these periods.  You see, these breaks are also well documented, and universal.  They are always followed by new forms and types - for which there is no clear, smooth, gradual link to the past - always.  That's why they can be used for index fossils.

So there are periods of "formation of new types"; there are periods of smooth, gradual variation; and there are periods of extinction.  Then the cycle repeats.

All these things are well documented among the cephalopods.  The currently held theory only explains two of them.  Schindewolf's "defunct" theory explains them all - and I find that fascinating.

Date: 2007/12/26 19:29:28, Link
Author: Daniel Smith
Quote (VMartin @ Dec. 21 2007,10:35)
Hi Daniel,

somebody at EvC gave the link to the article written by Professor Richard C. Strohman, Uni California : "Epigenesis and Complexity: The Coming Revolution in Biology"

http://www.thecomplementarynature.com/TCN%20A....ics.pdf

If you have time check it. It is very interesting. I hope such voices will be more common in the future.


According professor Zdenek Neubauer (Charles Uni Prague) modern biology is under strong influence of "fachidiots". You know, some people don't know how to tell apart tiger and lion  but they study, analyze and compare their DNA making bold predictions of evolution of that species .

You don't have to worry about JAM arguments. His concept of many basic bilological words are wrong.    

Epigenesis, epistatic interactions or pleitropic effects of genes play obviously significant role in development of an organism. According Strohman real, genetic disease acount for less than 2% of total disease load.  

Strohman quoted also Feynman who should have said:
"Mind must be a sort of dynamical pattern,not so much founded in a neurological substrate as floating above it, independent above it". But you know, Feynmann is an expert on quantum mechanics and maybe he should more discuss his opinions with evolutionary biologists (JAM etc...).

Martin,

I finally finished that paper.  I must say, the science of epigenetics is fascinating.  Here's another article confirming that there's more to life than genes and DNA.  
Abstract:    
Quote
Chromatin, the physiological template of all eukaryotic genetic information, is subject to a diverse array of posttranslational modifications that largely impinge on histone amino termini, thereby regulating access to the underlying DNA. Distinct histone amino-terminal modifications can generate synergistic or antagonistic interaction affinities for chromatin-associated proteins, which in turn dictate dynamic transitions between transcriptionally active or transcriptionally silent chromatin states. The combinatorial nature of histone amino-terminal modifications thus reveals a "histone code" that considerably extends the information potential of the genetic code. We propose that this epigenetic marking system represents a fundamental regulatory mechanism that has an impact on most, if not all, chromatin-templated processes, with far-reaching consequences for cell fate decisions and both normal and pathological development.


I think it's only obvious that genetic determinism is an incomplete explanation.  Genes are only the beginning.  Cells are where the action is!  It blows my mind how cells act as both feedback and control devices for, and within, a multitude of systems - including DNA - to which they can provide limited or unlimited access, based on many as-yet-unknown factors.

Oh, the mind of God!

Date: 2007/12/31 13:46:37, Link
Author: Daniel Smith
Quote (Richard Simons @ Dec. 28 2007,22:03)
 
Quote (Daniel Smith @ Dec. 26 2007,19:04)
     
Quote (Richard Simons @ Dec. 17 2007,10:00)
It still does not answer the question 'Why the fascination with a defunct theory?'

The "fascination" continues for me because this "defunct theory" (as you call it) actually explains the fossil record better than the currently held theory.

For instance: The fossil record shows clear evidence of smooth, gradual evolution amongst the cephalopods.  This evolution is well documented, consisting of millions of fossils, across multiple continents and ages.  In fact these fossils are so numerous and so universal, they are regularly used as index fossils.  

Which brings me to my point:  It's not the smooth, gradual evolution amongst the cephalopods that are used as demarcation for indexing - it's the breaks between these periods.  You see, these breaks are also well documented, and universal.  They are always followed by new forms and types - for which there is no clear, smooth, gradual link to the past - always.  That's why they can be used for index fossils.

So there are periods of "formation of new types"; there are periods of smooth, gradual variation; and there are periods of extinction.  Then the cycle repeats.

All these things are well documented among the cephalopods.  The currently held theory only explains two of them.  Schindewolf's "defunct" theory explains them all - and I find that fascinating.

Schindewolf's musing has holes large enough to drive a truck through. His theory has no plausible (or even implausible) mechanism for anticipating, storing and implementing the required changes. Without those the theory is completely, utterly useless, explaining nothing, which is why the vast majority of biologists have regarded it as having no more than historical interest.

Have you read Schindewolf's book?  You describe his carefully laid out theory as his "musing" - as if he's just kinda guessing about some vague ideas he has.  In fact, his book is full of evidence for his theory.  I'm guessing that you have not (and probably will not) read it.

Date: 2007/12/31 14:48:39, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Dec. 27 2007,04:22)
                         
Quote (Daniel Smith @ Dec. 26 2007,18:37)
This is what frustrates me:  In spite of all the smug answers - no one can explain to me how even the simplest living systems originated via natural causes.  At some point, when no natural explanation is forthcoming, you have to begin looking outside nature for an explanation.

Then it's odd how you are not frustrated with your belief in god then. After all, no explanations of how even the simplest living systems originated via god are available apart from "poof".

It's odd how you addressed other points but avoid this one.

It's not nice to admit you've been misled, I know, but you've no alternative here.

Whatever the shortcomings of natural explanations for biological systems then are better then nothing. And nothing is what you are offering. Nothing, nada, zip.

The funny thing is Daniel, and this is why you are an entertainment rather then a worry, is that the people doing the research (you know, with lab coats and all that) don't agree at all with you when you say:
                         
Quote
At some point, when no natural explanation is forthcoming, you have to begin looking outside nature for an explanation.

No, they don't. They'll keep on working inside of a natural framework. Your frustration  only matters if you are funding a team to look into those issues. Daniel, this is a messageboard, not a lab,  and your opinions are irrelevant in the place it matters, the lab.  

You and your new buddy can back slap all you want but it won't make a whit of difference unless you can put your money where your overlarge mouth is and produce some results

Goddit is the best you've got? They've had that for thousands of years already. I guess your ignorance also extends to history.

I am of the opinion that a careful, honest assessment of the evidence will show that;
A) There are no plausible natural explanations for the origin of any of life's systems;
And
B) These systems are so intricate, so complex and specific, they require a designer with a mind of infinite intelligence as their source.

It is therefore my prediction that the study of genetics and cellular functions will lead scientists down such a dizzying array of complex, intertwined chemical reactions, that they'll be forced to admit (at least privately) that there are no possible natural explanations for the formation of such systems and their mechanisms.

Statements such as this will become more and more common:
                         
Quote
The mechanisms by which around 2 m of DNA is packaged into the cell nucleus while remaining functional border on the miraculous and are still poorly understood.
Bryan M. Turner, Cellular Memory and the Histone Code, Cell, Vol. 111, 285–291, November 1, 2002, (Emphasis mine)

And from the same article:
                       
Quote
Studies on the rapid transcriptional upregulation of inducible genes provide evidence for a “cascade” of events, each dependent on the one preceding it and each involving specific histone tail modifications (Agalioti et al., 2002; Daujat et al., 2002, and references therein). The final pattern of modifications will represent the end result of this cascade and thus may have no significance in itself.
Ibid, (Emphasis mine)

In essence, cellular life and genetics are just like the earth's ecological system where 'everything affects something else' and where 'everything is dependent on something else'.  Such cascading systems don't just happen.  Perhaps a simple system could beat the odds and 'just happen', but it could never sustain itself for a protracted length of time without another system (its perfect complement no less) coming along behind it.  Now multiply such 'just happens' by trillions of times and you can theoretically explain life via natural causes.  Do you see the dilemma?

Systems such as those on the scale we see in life, could never 'just happen', and also 'just happen to sustain themselves', and that for millions of years!  No, for something such as this; on the scale we see; from the most minute particles to the entire universe itself; all supremely tailored for the sustenance of carbon-based life on this planet; it would require an infinite mind as the source.  No other explanation will suffice.

That is how I address your objections.

Now does that mean scientists should give up?  That they should throw up their hands and say "God did it. what more can we learn?"?

Obviously not.

If we were to find an ancient artifact that exhibited a technological knowledge far beyond that of any known civilization, would we refuse to study it?  Of course not.  We would pour over it in an effort to learn that technology and to learn of that civilization.  

Well such is life.  Life is an artifact of supreme technology laid in our lap by God so that we can learn of it and of him.

We should definitely continue its study.

Date: 2008/01/01 18:21:14, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Jan. 01 2008,06:29)
 
Quote (Daniel Smith @ Dec. 31 2007,13:46)
Have you read Schindewolf's book?  You describe his carefully laid out theory as his "musing" - as if he's just kinda guessing about some vague ideas he has.  In fact, his book is full of evidence for his theory.  I'm guessing that you have not (and probably will not) read it.

   
Quote
In the American vernacular, "theory" often means "imperfect fact"--part of a hierarchy of confidence running downhill from fact to theory to hypothesis to guess. Thus creationists can (and do) argue: evolution is "only" a theory, and intense debate now rages about many aspects of the theory. If evolution is less than a fact, and scientists can't even make up their minds about the theory, then what confidence can we have in it? Indeed, President Reagan echoed this argument before an evangelical group in Dallas when he said (in what I devoutly hope was campaign rhetoric): "Well, it is a theory. It is a scientific theory only, and it has in recent years been challenged in the world of science--that is, not believed in the scientific community to be as infallible as it once was."

Well, evolution is a theory. It is also a fact. And facts and theories are different things, not rungs in a hierarchy of increasing certainty. Facts are the world's data. Theories are structures of ideas that explain and interpret facts. Facts do not go away when scientists debate rival theories to explain them. Einstein's theory of gravitation replaced Newton's, but apples did not suspend themselves in mid-air, pending the outcome. And humans evolved from apelike ancestors whether they did so by Darwin's proposed mechanism or by some other, yet to be discovered.

Moreover, "fact" does not mean "absolute certainty." The final proofs of logic and mathematics flow deductively from stated premises and achieve certainty only because they are not about the empirical world. Evolutionists make no claim for perpetual truth, though creationists often do (and then attack us for a style of argument that they themselves favor). In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms.

Stephen Jay Gould, written for Discover magazine in 1981 via
http://scienceblogs.com/dispatc....hp#more
Now, Daniel, care to re-phrase that?

What, in the passage you quoted, would give me any reason to rephrase my statement?

Date: 2008/01/01 18:53:02, Link
Author: Daniel Smith
Quote (JAM @ Dec. 31 2007,16:11)
     
Quote (Daniel Smith @ Dec. 31 2007,13:46)
Have you read Schindewolf's book?  You describe his carefully laid out theory as his "musing" - as if he's just kinda guessing about some vague ideas he has.

Dan,
Your misrepresentations continue. A hypothesis does not get promoted to a theory unless it has a long record of successful predictions. Schindewolf produced no data from testing his predictions, so there's really no point in considering his musings seriously--he obviously didn't himself, if he couldn't be bothered to test predictions.

Schindewolf was a paleontologist.  His "data" is the fossil record.  He introduced his theory in a paper in 1943 - 7 years before he published Basic Questions in Paleontology in 1950.  He tested his predictions as any paleontologist would - by excavating and sifting through fossils.  He produced much data himself during this period and continued his pursuit of fossils until his death in 1971.  As of this date, I am not aware of anything found in the fossil record that falsifies his theory.  Are you?      
Quote

       
Quote
In fact, his book is full of evidence for his theory.  I'm guessing that you have not (and probably will not) read it.

But what about the evidence that doesn't support his vague notions? Your incredible ignorance about biology doesn't leave you in a position to make any credible claims.

What "vague notions" are you talking about?  What evidence does not support his theory?  Do you even know what his theory is?  If you're relying on my characterization of it, you're cheating yourself - as I am ill prepared to do it justice.

Date: 2008/01/02 18:21:55, Link
Author: Daniel Smith
Quote (JAM @ Dec. 31 2007,16:29)
Why are stop codons separate from amino acid codons, but start codons aren't? Give me a plausible reason from a design perspective instead of running away.
...
So, why would an infinitely intelligent designer separate stop from aa incorporation, but fail to separate start from aa incorporation?

Well, if we can continue our written language analogy (which you agreed was valid), the "start codons" (if you will) of written language are capital letters - which are not separate in meaning from other letters, (being only distinguished by capitalization); whereas the "stop codons" (punctuation marks) are completely separate.  Now, by your  standards, written language should have to either start and stop every sentence with a capital letter, or with punctuation marks.  Any combination of the two (by your standards) would disqualify written language as an intelligent design.
This will of course, come as quite a shock to the thousands of grammarians, linguists and syntacticians who have so diligently shaped our written language rules for centuries.
So, from a design perspective, there seems to be plausible reasons for utilizing different types of start and stop signals in the coding of information.

Date: 2008/01/02 18:44:42, Link
Author: Daniel Smith
Quote (JAM @ Jan. 01 2008,20:33)
SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS...
SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS...
SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS...
SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS...
SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF THE HYPOTHESIS WITH WHICH YOU ARE ENAMORED...

HOW DO YOU KNOW THAT?  
HAVE YOU READ ALL OF SCHINDEWOLF'S PAPERS?  
DO YOU READ GERMAN?

(WHY ARE WE YELLING?)

     
Quote
I know and am not relying on your falsehoods, particularly the one that you pretend that his hypothesis doesn't make predictions about molecular and developmental biology. BTW, there are thousands of fossil discoveries that do not support his hypothesis.

Then you should be able to provide some good examples and explain how they do not support his theory.

BTW, I will continue to call it a "theory" - since Stephen J. Gould has labeled it as such in his forward to Schindewolf's book:
   
Quote
Schindewolf relied on two major theories: (1) The cyclical theory of typostrophism... [and] (2) The ontogenetic theory of proterogenesis...

Stephen Jay Gould, pg. xiii, Forward, Basic Questions in Paleontology (emphasis mine)

Date: 2008/01/03 17:56:18, Link
Author: Daniel Smith
Quote (JAM @ Jan. 02 2008,22:30)
Oh, but Dan, there is only one start codon.
...
Plural. There is only one start codon. Therefore, using the language analogy (or any other), the design of the genetic code is profoundly unintelligent.
...
There's only one start codon. Therefore, using the language analogy, every sentence must start with the same letter, which would be incredibly stupid.
...
In the analogy, every sentence must start not with "a capital letter," but a SINGLE capital letter, M.
...
I don't see anyone proposing that all sentences should start with the same letter, do you?
...
But there's no plausible reason to use a SINGLE start signal.

OK, so we've established that genetic coding is not exactly the same as written language - although both use different start-stop signals.  You seem to be suggesting there's something wrong with the way life is coded for.  It seems to work pretty well to me.
Did you ever stop to ponder the fact that there even is such a thing as a code for life?  It seems profoundly arrogant for a man to call such a thing "stupid".  I guess you'll have to take that up with God when you meet him face to face.

Now, how about all that fossil evidence you promised me?

Date: 2008/01/03 18:17:59, Link
Author: Daniel Smith
Quote (Erasmus @ FCD,Jan. 01 2008,19:55)
Daniel, Simpson destroys Schindewolf's misunderstanding of horse evolution in the 1944 book Tempo and Mode in Evolution.  I suggest giving it a read.

First, Schindewolf did not base his theory on horse evolution - he cites horse evolution as clear evidence of gradual, continuous evolution.  His theory was based on the fossils of ammonites and corals (he believed fossil evidence of mammalian evolution too sporadic to base a theory on).

Second, Schindewolf's book was written in 1950 (6 years after Simpson's).

Third, Schindewolf cites Simpson extensively in his book - mentioning him a total of 9 times - sometimes favorably, sometimes not.  

In light of this, I highly doubt Schindewolf felt threatened (or destroyed) by Simpson.

Date: 2008/01/03 18:23:17, Link
Author: Daniel Smith
Quote (Daniel Smith @ Jan. 02 2008,18:44)
BTW, I will continue to call it a "theory" - since Stephen J. Gould has labeled it as such in his forward to Schindewolf's book:
         
Quote
Schindewolf relied on two major theories: (1) The cyclical theory of typostrophism... [and] (2) The ontogenetic theory of proterogenesis...

Stephen Jay Gould, pg. xiii, Forward, Basic Questions in Paleontology (emphasis mine)

Since I am not allowed to edit my own posts, I'll just point out that I should have said "foreword" rather than "forward".

Date: 2008/01/03 18:33:16, Link
Author: Daniel Smith
Quote (Richard Simons @ Dec. 31 2007,23:13)
Is JAM correct in saying that Schindewolf lacked the courage of his convictions and never used his ideas to make testable predictions?

I've never heard that about Schindewolf anywhere else but here - if that tells you anything.  The main problem is that Schindewolf's writings are all in German, so most of us have no idea what predictions he made.  Certainly though, in the one book that was translated into English, he felt confident enough to lay out a theory that makes some bold predictions about what will be found in the fossil record.  He described definite patterns in evolution that he fully expected to be confirmed with increasing fossil evidence.  I'd say that shows the "courage of his convictions", wouldn't you?

Date: 2008/01/04 22:52:22, Link
Author: Daniel Smith
Quote (IanBrown_101 @ Jan. 03 2008,18:47)
 
Quote (Daniel Smith @ Jan. 03 2008,23:56)
It seems to work pretty well to me.
Did you ever stop to ponder the fact that there even is such a thing as a code for life?  It seems profoundly arrogant for a man to call such a thing "stupid".

Jesus H Christ man, what is your problem?

Just because something just about works doesn't mean it isn't stupid.

Iron lungs are pretty damn stupid, and boy are they oddly designed, but hell, they still work.

And they are still designed aren't they?

Date: 2008/01/04 23:13:10, Link
Author: Daniel Smith
Quote (JAM @ Jan. 04 2008,00:03)

We've established that we agree that the "design" of translational initiation is profoundly unintelligent.
...
Dan, you're a weasel. I've shown that by YOUR standard, the designer made an obviously unintelligent choice.

See, this is why I hate debating with you.  You ask me loaded questions, then twist my answers around to make out like I meant something you know I didn't really mean.  It's a completely dishonest tactic and has nothing to do with the actual debate.  It's all about "winning" (or seeming to) for you isn't it?
       
Quote
Selection does that,
Almighty Selection.  Yes I know, It (capitalized) designed the genetic code.  It's amazing how well this unintelligent, uncaring, unguided, directionless "force" was able to create such complex interleaved systems.  THAT you'll believe, but mention God and it's "liar, liar pants on fire!".
     
Quote

but how would you possibly know, since you're lying about your fascination with life? However, we weren't discussing whether it "works pretty well," we were discussing whether intelligent design choices were made, and by the criterion YOU stipulated, they weren't. This makes perfect sense as a product of evolution, though.
Since it seems to work pretty well to you, maybe you can comment on the number of different N-terminal modifications that proteins are known to undergo as a result of this unintelligent design.
Not again you don't.  Save your "I know more than you do" attitude and your loaded questions for someone else.      
Quote

       
Quote
Did you ever stop to ponder the fact that there even is such a thing as a code for life?

There isn't a "code for life." It's a figure of speech. Do you realize that there's nothing symbolic about it? It only looks like a code when we organize it into a table for you.
Since when does a code have to be symbolic?  Can't I speak to you in a coded language?  All that is necessary is that both of us agree what the code is.  It's the same with the genetic code.    
Quote

       
Quote
It seems profoundly arrogant for a man to call such a thing "stupid".

You agreed that the design choice made on the back end was more intelligent than the one made for the front end. Therefore, the design itself could not have come from a perfect being.
Why not?  Did I ever say the design itself was perfect?  How did you get that from what I said?  That's a complete strawman.      
Quote

       
Quote
I guess you'll have to take that up with God when you meet him face to face.

Don't you mean Him?
Do you?
       
Quote
   
Quote
Now, how about all that fossil evidence you promised me?

So you can tell lies about that, too?

       
Quote
Korn, Dieter (2003):
Typostrophism in Palaeozoic Ammonoids?.
Palaeontologische Zeitschrift, Band 77, Heft 2 . p. 445-470, 20 fig.

Die antidarwinistische ,Typostrophentheorie" von O.H. Schindewolf wird mit den Ammonoiden-Beipielen getestet, auf welchen sie begründet worden ist. Es kann gezeigt werden dass keines der drei theoretischen Elemente der Theorie (Saltationismus, Internalismus und Zyklismus) durch empirische Befunde gestützt werden kann. Vermeintliche Saltationen (,Typogenese") werden durch das Fehlen von Zwischenformen vorgetäuscht. Internalistische und orthogenetische Entwicklung (,Typostase") kann nur postuliert werden, wenn mögliche Funktionen abgelehnt werden. Vorprogrammiertes Aussterben von ,degenerierten" Entwicklungslinien (,Typolyse") kann ausgeschlossen werden, wenn Ammonoideen-Morphologien frei von anthropozentrischen Ansichten betrachtet werden. Auf Grund der Studie von paläozoischen Ammonoideen gibt es keinen Grund, die ,Typostrophenlehre" oder einige der sie aufbauenden Elemente, wie das ,Typus-Konzept" und ,Proterogenese", dem darwinistischen Evolutionsmodell vorzuziehen.

The anti-Darwinian ,Typostrophe Theory" of O.H. Schindewolf can be put to the test by revisiting the ammonoid examples on which this macroevolutionary model was founded. It is shown that none of the three theoretical elements saltationism, internalism, and cyclism can be supported by empirical data obtained from ammonoid research. Putative saltations (,Typogenesis") were feigned because of the lack of knowledge of intermediate forms. Internalistic and orthogenetic development (,Typostasis") can only be favoured by neglecting possible functions of morphological characters. Preprogrammed extinction of ,degenerated" clades (,Typolysis") is unlikely when ruling out anthropocentric views regarding ammonoid morphology. In terms of evolution of Palaeozoic ammonoids, there is no basis for the preference of the ,Typostrophe Theory" or some of its composing elements, including the ,Type Concept" and ,Proterogenesis", over the Darwinian evolutionary model and the Modern Synthesis.

Someone once told me that opinions do not equal evidence.  This is pure opinion.  I asked for fossil evidence and an explanation of exactly how it falsifies Schindewolf's theory.  You provided neither.

Date: 2008/01/04 23:15:36, Link
Author: Daniel Smith
Quote (JAM @ Jan. 04 2008,12:14)
Keeping to that is what makes science so much more honest than religion.

You must be profoundly religious then.

Date: 2008/01/05 13:11:33, Link
Author: Daniel Smith
Quote (JAM @ Jan. 04 2008,12:14)
Whether he expected them to be confirmed is best measured by the extent of his efforts to confirm AND FALSIFY them.

How hard have you tried to falsify "Selection" as a mechanism?
You seem perfectly willing to believe "Selection does that", but how do you know that?  Explain how Selection produced protein synthesis, or chromosomes, or sexual reproduction, or cell division, or... any fundamental biological system.
Give me a plausible pathway from the state that existed before to the state that existed after.  Remember, Selection cannot select for potential so you must be able to show an immediate advantage for every intermediate step in the creation of these systems.
Do you have a viable, plausible pathway for even one?

Date: 2008/01/05 13:25:52, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Jan. 05 2008,06:00)
     
Quote (Daniel Smith @ Jan. 04 2008,22:52)
     
Quote (IanBrown_101 @ Jan. 03 2008,18:47)
         
Quote (Daniel Smith @ Jan. 03 2008,23:56)
It seems to work pretty well to me.
Did you ever stop to ponder the fact that there even is such a thing as a code for life?  It seems profoundly arrogant for a man to call such a thing "stupid".

Jesus H Christ man, what is your problem?

Just because something just about works doesn't mean it isn't stupid.

Iron lungs are pretty damn stupid, and boy are they oddly designed, but hell, they still work.

And they are still designed aren't they?

Yes, they are designed, yes they are stupid solutions to problems that we've not managed to find better solutions for.

So are you saying your designer is stupid? Your designer makes stupid things? Your designer makes stupid mistakes?
Your designer does things that are so stupid a child can point out the mistakes.

Yet you think that terrible design is a indicator of some supreme intelligence behind it all.

Daniel, what's HIV for?

First, you are going to have to convince me that any of life's systems qualify as "stupid".
Just because JAM says they're stupid does not make them so.  Does he dictate your opinions on the matter?
Besides "stupid" is a subjective term in this argument.  What's "stupid" to you may be "brilliance" to another.
I've always said, if you think it's stupid, improve upon it--design a better working system, (like we did with the iron lung).
Most arguments seem to fall by the wayside at that point.
At least we both agree now that the property "stupid" does not negate the property "designed".  There are lots of (subjectively) "stupid designs".  They all remain designs however.
Now, why don't you tell me what's really "stupid" about the start and stop codons in life's code?
Oh and HIV is a disease.  God introduced disease as a consequence of the fall.  It's all there in black and white if you want to read about it.  A designer can make things however he wishes.  God chose to allow humans (and everything else) to die.  It's a fact of life.  Are you only willing to accept a God that makes a perfect world for you to live in?

Date: 2008/01/06 13:36:52, Link
Author: Daniel Smith
Quote (Assassinator @ Jan. 05 2008,13:54)
Daniel, let me ask you a simple question (and thanks for that Kristine): What do you see in life what makes you say it's designed?

I don't know where I got it or who wrote it, but I think this quote fairly sums up my reason for viewing life as designed:  
Quote
Biology is full of problems that are solved, including the problems of
how to harness the sun's energy and how to obtain nutrients.  The
solutions to numerous problems are present throughout biology, and the
solutions involve extraordinarily-complicated and interdependent
organs, structures, and biochemical processes.  The incredibly-complex
solutions strongly exhibit the appearance of having been established/
put together by a problem-solving being(s).

Date: 2008/01/06 13:49:57, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Jan. 05 2008,05:28)
 
Quote (Daniel Smith @ Jan. 04 2008,23:13)
Since when does a code have to be symbolic?  Can't I speak to you in a coded language?  All that is necessary is that both of us agree what the code is.  It's the same with the genetic code.

Then if it's "the same" with the genetic code who is the "both of us".

If I speak to you in a "coded language" then the "both of us" is you and me.

If genetic code speaks in a "coded language" then who are the "both of us" then?

There are many actually - else how does the RNA polymerase "know" to separate DNA strands and produce mRNA from it?

How does mRNA "know" what is an exon and what is an intron during the splicing process?

How does the ribosome "know" to bind to the mRNA at the start codon?

How does the tRNA "know" which amino acids to link to during the translation process?

How does the release factor "know" to bind to the stop codon - thus terminating translation and releasing the polypeptide?

And finally, what's "stupid" about any of the above?

Date: 2008/01/06 14:21:54, Link
Author: Daniel Smith
Quote (VMartin @ Jan. 05 2008,17:12)
I've never read anything from Otto Schindewolf but as far as I can judge he pointed something very paradoxical. In one side there was darwinian gradualism and on the other side there was a biostratigraphy (which focuses on correlating and assigning relative ages of rock strata by using the fossil assemblages). The basic rule of the biostratigraphy was in direct contradction with gradual evolution. Biostratographic always knew there were some species in given rock strata that didn't change continually - otherwise he couldn't have work.  
Because biostratigraphy do not often see in fossil records (there are sometimes exceptions) what gradualists insisted they should have see there, some   tensions arose - with outcomes like "punctuated equilibria" etc..

That's correct Martin.
Schindewolf pointed out "striking contrasts" between biostratigraphic ages.  But it wasn't the species that did not change which formed the boundaries - it was the sudden appearances and rapid evolution of new forms that delineated the boundaries between ages.  This evolution would then slow down and usually (but not always) become the gradual evolution Darwin speculated about, (although Schindewolf attributed it to constrained, internal factors), thus indicating the middle of the age.  This gradual evolution would usually follow a pattern that trended towards overspecialization and mass extinctions - thus delineating the end of that age.  Then the process would repeat - either with new forms bursting upon the scene, or with one lineage from the previous age, that had not overspecialized, then becoming the "root" species for another explosion of forms.

Of course this (as I've presented it), is an oversimplified view of this since there were numerous fossil types upon which these ages were marked.  I'm sure this stuff is all common knowledge amongst paleontologists and geologists.

Date: 2008/01/07 10:54:20, Link
Author: Daniel Smith
Quote (JAM @ Jan. 06 2008,15:59)
BTW, the humble path (the one you didn't take) would have been to question your own ability to judge the intelligence of the "design" of a biological mechanism, but I knew that your ego wouldn't let you do that.

You mean like this?

Date: 2008/01/07 17:55:40, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Jan. 07 2008,11:05)
       
Quote (Daniel Smith @ Jan. 07 2008,10:54)
         
Quote (JAM @ Jan. 06 2008,15:59)
BTW, the humble path (the one you didn't take) would have been to question your own ability to judge the intelligence of the "design" of a biological mechanism, but I knew that your ego wouldn't let you do that.

You mean like this?

Yeah, but you kinda blow it when you say things like
         
Quote
First, you are going to have to convince me that any of life's systems qualify as "stupid".

y'know!

So you can judge the "design" of a biological mechanism after all, insofar as you simply *know* it's not stupid. So don't come all meek now Daniel.

But you're the one calling it "stupid"!  Shouldn't it be up to you to provide the convincing evidence?

 
Quote
And Daniel, what's HIV for? Not why does it exist, but for what purpose did god/jesus create it?

I don't know.  I can't read God's mind.  I only know what he's spelled out in black and white.

Date: 2008/01/07 18:24:37, Link
Author: Daniel Smith
Quote (Assassinator @ Jan. 05 2008,13:54)
Daniel, let me ask you a simple question (and thanks for that Kristine): What do you see in life what makes you say it's designed?

       
Quote
God introduced disease as a consequence of the fall.

You DO know that's completly awfull? It was there first mistake, instead of giving Adam and Eve another chance and talk about what they did (God was so forgiving right?) He gave them the deathpenalty (made them mortal) and forced them into incest (how the hell do you make a population of 2 billion from 2 in 6000 years?) and forced the whole of humanity to suffer horrible from ONE dammed mistake. Sounds good doesn't it? Really sounds like someone I would want to worship...

Do you know how long an eternity is? (Hint: it is actually not "long" at all - since time will not be reckoned there).
The crux of Christianity is that this world, and this life, is not the end but is just a "mist" in the light of eternity.  Therefore, whatever the pain and suffering mankind suffers in this life (including death) will be long forgotten in contrast to the eternal life God is willing to give us freely.
So all that you count as "awful", and "horrible", is only a blink.

I'm sure you'll characterize this as awful and escapist as well.  But that's Christianity.  Millions of people take great comfort in that knowledge.        
Quote
     
Quote
It's all there in black and white if you want to read about it.

O really? And who says the writers wanted those texts to be interpreted so literally as you do it?

You're right, many interpretations are possible.  But that does not change the fact of what the text says (in black and white).  Which is what I meant by that.      
Quote
Why are YOU right and for example Hindus not? You have any idea how many creation stories are out there completly different from yours? What's so special and good about yours that makes it right?

The main attraction for me is the man, Jesus.  His words struck a chord within me.  That's all I can say.  Maybe I am wrong (it won't be the first time), but I'll take my chances.

Date: 2008/01/07 18:30:06, Link
Author: Daniel Smith
Quote (Assassinator @ Jan. 06 2008,14:54)
 
Quote (Daniel Smith @ Jan. 06 2008,13:36)
   
Quote (Assassinator @ Jan. 05 2008,13:54)
Daniel, let me ask you a simple question (and thanks for that Kristine): What do you see in life what makes you say it's designed?

I don't know where I got it or who wrote it, but I think this quote fairly sums up my reason for viewing life as designed:        
Quote
Biology is full of problems that are solved, including the problems of
how to harness the sun's energy and how to obtain nutrients.  The
solutions to numerous problems are present throughout biology, and the
solutions involve extraordinarily-complicated and interdependent
organs, structures, and biochemical processes.  The incredibly-complex
solutions strongly exhibit the appearance of having been established/
put together by a problem-solving being(s).

E.a, because it's so complex from your point of view, it must be designed. I can understand that life looks designed, but you have to make a difference between your own point of view and opinion, and reality. The fact that it looks designed in your eyes, says 0.00 about reality. You do understand that, right?

Yes, of course I do.  That is why I've said numerous times that science will never find a plausible explanation for the origin of any of life's most basic biological systems.  This is a prediction that anyone can falsify.  So it's not just me, and it's not just opinion.
You understand that don't you?

Date: 2008/01/07 19:34:45, Link
Author: Daniel Smith
Quote (JAM @ Jan. 06 2008,16:12)
   
Quote (Daniel Smith @ Jan. 05 2008,13:11)
       
Quote (JAM @ Jan. 04 2008,12:14)
Whether he expected them to be confirmed is best measured by the extent of his efforts to confirm AND FALSIFY them.

How hard have you tried to falsify "Selection" as a mechanism?

In what context? Are you so blinded by your arrogance that you think that I must be an evolutionary biologist?
       
Quote
You seem perfectly willing to believe "Selection does that", but how do you know that?

Because it's been shown to do similar things in real time.
       
Quote
Explain how Selection produced protein synthesis, or chromosomes, or sexual reproduction, or cell division, or... any fundamental biological system.

Let's go with the immune system. How long does it take to produce a new, unique, incredibly specific protein-protein interaction using nothing but genetic variation (random wrt fitness) and selection?
Note that this is a response to your arrogant, ignorant skepticism about the power of selection.
       
Quote
Give me a plausible pathway from the state that existed before to the state that existed after.

Why? You'll just ignore or misrepresent it, as you do all of the other evidence. It's better to be Socratic and present it in a historical context, so there's a slim chance that you might be able to see how real scientists work. It also shows that you're anything but fascinated by biology.

Why does your immune system react so massively to an allogeneic stimulus?

Does your immune system initially recognize any foreign antigen as an independent entity? If not, how does it initially recognize foreign antigens?

Making an honest effort to answer these questions will make the evolutionary origin of your immune system pretty damn obvious. If I just tell you, you'll blow it off.

Remember, I'm claiming that your claim to be fascinated by the complexity of biology was a lie, so you're boxed in. ;-)
     
Quote
Remember, Selection cannot select for potential so you must be able to show an immediate advantage for every intermediate step in the creation of these systems.

We don't know what every intermediate step was (nor do you), so your creationist demand is both preposterous and dishonest. We can, however, show how the main intermediates that had to have existed were selected for.
   
Quote
Do you have a viable, plausible pathway for even one?

Yes. Let's start with the acquired immune system. So do you have a viable, plausible pathway for design of the immune system or anything else?

Do you realize that you're missing the entire mechanism of science here? The way it really works is that if we hypothesize that mammalian system Z evolved from protochordate system X via intermediate Y, we test the hypothesis by making predictions about what mechanisms will exist in other organisms that branched off at critical times.

That's powerful evidence, which is why you completely ignore it in favor of ignorant creationist demands.


No more questions.  Quit dancing around the issues and asking questions in the hope of trapping me with my own words.  If you have a position - just state it.  I'm not playing this game with you anymore.  If you believe you can show me the evolutionary origin of the immune system - step by step - from whatever existed before there were immune systems, then go for it.

Date: 2008/01/07 19:36:29, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Jan. 07 2008,18:17)
a) it's stupid to have the pipe you suck air down combined with the pipe you suck food down. Care to make a case for the elegance of that?

What has that to do with start/stop codons and the genetic code?  Remember, you said that was "all" stupid.

Date: 2008/01/07 19:40:00, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Jan. 07 2008,18:27)
 
Quote (Daniel Smith @ Jan. 07 2008,18:24)
The main attraction for me is the man, Jesus.  His words struck a chord within me.  That's all I can say.  Maybe I am wrong (it won't be the first time), but I'll take my chances.

Fine, witness away, great. Just don't claim life is "designed" or that it can be proved that life was created.

I never claimed it can be "proved".  As for claiming life was designed - why not?  You claim it wasn't.

Date: 2008/01/08 18:27:37, Link
Author: Daniel Smith
Quote (Ideaforager @ Jan. 07 2008,19:45)
Daniel,
I've been holding out way too long!
   
Quote
But that does not change the fact of what the text says (in black and white).

How do you distinguish the amount of honesty contained in two opposing texts?

I don't hold to the belief that the bible is the literal, inerrant word of God.  I believe it is inspired by God - and that it is the spirit of it, not the letter - that reveals God to us.  So, I don't get hung up on the contradictions in the bible (yes there are many), rather I view it as an historical document written by ancient peoples who all had a relationship with the same God I do.  I want to know the reality of God and of this world he created.  I think the truth is in the bible and in the creation.  I want to know what it is.

Date: 2008/01/08 18:38:58, Link
Author: Daniel Smith
Quote (JAM @ Jan. 07 2008,23:52)
Dan,

Science isn't about showing an arrogant twit like Daniel Smith anything because he throws a hissy fit after his blatant lies about being fascinated by biological complexity are exposed.

Science is about making and testing predictions. It's not dancing and it's not trapping.

If you are fascinated by the complexity of biology, go for it yourself.

You won't, because you're afraid of what you might find. Better to make stupid demands.

I am 'going for it myself' - thank you.  I was hoping to learn something from you along the way, but there's just too much baggage that goes along with your "lessons" for me to continue.
So, I'll continue to talk to the others here, but not to you anymore.
I wish you well in your pursuit of biology.  I'd appreciate a link to your next published paper - if it's not too much trouble - or to any of your published papers for that matter.
I think that would be a far better way for me to understand where you're coming from than this forum has been.

Date: 2008/01/08 18:44:41, Link
Author: Daniel Smith
Quote (Erasmus @ FCD,Jan. 08 2008,00:21)
well as much as i have enjoyed this thread (Daniel you have received quite a spanking and also been an absolutely great sport about it) I am tempted to go concern trolling here.

JAM:  Daniel is a creationist.  pure and simple.  no amount of data will change his mind, he brought it with him.

daniel:  we value evidence.  cartesian empirical equivalencies is mental masturbation.  yes we may be brains in vats.  this does not further your argument, which boils down to the awe and wonder that you feel when experiencing 'creation'.  We all feel that, or we wouldn't be biologists or interested in science in general.  You simply fail to discern the appropriate distinction between your emotionally valuable presuppositions and the realities imposed by objective evidence*.

I am sympathetic, on some level, to these orthogenetic notions.  Simply because I think there is something about individual organisms (agency, identity, blah blah imprecise blah) that defies the mereological reductionism that is at least the caricature of evolutionary biology.  Where and what these entities and processes exist and exercise is the question.

the IDC movement conveniently stands on the shoulders of these monumental questions in biology and philosophy in general and proclaims them answered, and you will find those answers in black and white in the ancient handed-down texts of a particular clan of nomadic coprophagic** numerologists.

Pardon the rest of us, me included, if we don't fall for your martyrdom.

*  objective is as objective does.  but i'll be less likely to believe you when you run around yammering about front-loaded this or omphalos that.  you know.

**  see Ezekiel Bread.  True Christians, TM, use cows dung for mans dung.  I have it on as good an authority as you do that the earth was created by yahweh or whatever your sect calls it.

Erasmus,

You say, "we value evidence".  Please define "evidence" for me.  Tell me exactly what kind of evidence you value.

Date: 2008/01/08 18:58:46, Link
Author: Daniel Smith
Quote (Assassinator @ Jan. 08 2008,03:10)
     
Quote
The main attraction for me is the man, Jesus.

Jesus has nothing to do with the origins of life, earth and the universe. If he existed he was a man with a message, a message of love wich has nothing to do with science.

I'm sorry, I misread your question.  I thought you were asking what made my beliefs (i.e. Christianity) right, I see now that you were asking what makes my creation story right.

Sorry.

As for creation stories, I think they all have an element of truth to them.

(BTW, the bible claims that Jesus did have something to do with "origins of life, earth and the universe", FYI.)
     
Quote
   
Quote
Yes, of course I do.  That is why I've said numerous times that science will never find a plausible explanation for the origin of any of life's most basic biological systems.  This is a prediction that anyone can falsify.  So it's not just me, and it's not just opinion.
You understand that don't you?

No, I do not. The fact that your opinion is not equal to reality, has nothing to do with science. Explain yourself.

Uh, I think your going to have to explain yourself on that one.  I have no idea what you meant by that - nor do I know what you want me to explain.

Date: 2008/01/08 19:36:55, Link
Author: Daniel Smith
Quote (VMartin @ Jan. 08 2008,13:51)
   
Quote (Daniel Smith @ Jan. 06 2008,14:21)
         
Quote (VMartin @ Jan. 05 2008,17:12)
I've never read anything from Otto Schindewolf but as far as I can judge he pointed something very paradoxical. In one side there was darwinian gradualism and on the other side there was a biostratigraphy (which focuses on correlating and assigning relative ages of rock strata by using the fossil assemblages). The basic rule of the biostratigraphy was in direct contradction with gradual evolution. Biostratographic always knew there were some species in given rock strata that didn't change continually - otherwise he couldn't have work.  
Because biostratigraphy do not often see in fossil records (there are sometimes exceptions) what gradualists insisted they should have see there, some   tensions arose - with outcomes like "punctuated equilibria" etc..

That's correct Martin.
Schindewolf pointed out "striking contrasts" between biostratigraphic ages.  But it wasn't the species that did not change which formed the boundaries - it was the sudden appearances and rapid evolution of new forms that delineated the boundaries between ages.  This evolution would then slow down and usually (but not always) become the gradual evolution Darwin speculated about, (although Schindewolf attributed it to constrained, internal factors), thus indicating the middle of the age.  This gradual evolution would usually follow a pattern that trended towards overspecialization and mass extinctions - thus delineating the end of that age.  Then the process would repeat - either with new forms bursting upon the scene, or with one lineage from the previous age, that had not overspecialized, then becoming the "root" species for another explosion of forms.

Of course this (as I've presented it), is an oversimplified view of this since there were numerous fossil types upon which these ages were marked.  I'm sure this stuff is all common knowledge amongst paleontologists and geologists.

That's very interesting Daniel. It's a pity you have to waste time here with people who do not care a bit what is the crux of Schindewolf's theory. Discussion about it would be more instructive.

I hit on the problem of biostartgraphy in the following text-book which is unfortunately in Czech. But the author is no way darwinist I dare say.

http://www.mprinstitute.org/vaclav/Kapitol2.htm

The autor has written on my opinion extraordinary good essay "British metaphysics as reflected in Robert Broom's evolutionary theory" available in English here:

http://www.mprinstitute.org/vaclav/Broom.htm

I was surprised with all that memory capacity of Robert Broom and the mentioned article about autism, it can be found also inet - unbelievable what all is hidden in human brains. One would say Plato was right.

Thanks so much for that Martin.  I'm also interested in the works of Goldschmidt and Grasse.  I found Goldschmidt's A Material Basis for Evolution for about $50 on Amazon, but they want almost $150 for Grasse's Evolution of Living Organisms!  Too much for me right now.

Another modern skeptic of Darwinism you might want to check out is Michael Denton.
 
Here's a couple of his recent papers:

Physical law not natural selection as the major determinant of biological complexity in the subcellular realm: new support for the pre-Darwinian conception of evolution by natural law

The Protein Folds as Platonic Forms: New Support for the Pre-Darwinian Conception of Evolution by Natural Law

He also wrote the books Evolution: A Theory in Crisis and Nature's Destiny.

Date: 2008/01/09 18:24:20, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Jan. 09 2008,05:15)
Hey Daniel,
Seeing as things have taken a turn for the off-topic, perhaps you could answer a few simple questions that'll allow the lurkers to decide if you are sincere?

a) How old is the earth?
b) How old is the solar system?
c) How old is the universe?

I don't know.  I haven't really studied both sides of the whole "age of the earth" debate, so I'm not prepared to give an answer on those.
   
Quote
d) Did man and dinosaur share the planet at the same time?

It's possible, but again I don't know.
   
Quote
e) Did every human but 8 die in a global flood?

I believe in the flood, but only because I haven't seen the evidence against it.  My main reason for believing it (other than the bible), is that the landscape looks like the aftermath of massive flood runoff when viewed from the air.  Not very scientific, I know but that's where I'm at.  (insert joke here)
   
Quote
f) Does the "designer" actively "interfere" with the day to day running of the universe?
g) If "yes" to f) then how come we've not noticed?

Again it's possible, although it is equally possible that he planned everything out in advance, and it is just unfolding accordingly.
I definitely don't have all the answers and my opinions are in a constant state of flux.

Date: 2008/01/09 18:35:21, Link
Author: Daniel Smith
Quote (Ideaforager @ Jan. 08 2008,20:57)
Daniel,      
Quote
I don't hold to the belief that the bible is the literal, inerrant word of God.
Good, but how do you distinguish        
Quote
there in black and white
from the gray?        
Quote
I believe it is inspired by God - and that it is the spirit of it, not the letter - that reveals God to us.
Again is that spirit            
Quote
there in black and white
or gray?

There's a lot more gray than there is black and white.  As to how to distinguish this:  I think it can only come through a sincere desire to know God and the truth.  It is only then that you will let everything go; everything you've ever been taught, everything that is orthodox, and be open to correction from God himself - whether it's through a new understanding of scripture or a new understanding of life, the cosmos, or man's place in it.
 
Quote
 
Quote
So, I don't get hung up on the contradictions in the bible (yes there are many), rather I view it as an historical document written by ancient peoples who all had a relationship with the same God I do.
How do you know this? Could the writers have had other more immediate/practical motives?

Perhaps.  I think God has had a say in the matter however.          
Quote
 
Quote
I want to know the reality of God and of this world he created.
That is extremely similar to the sentiments expressed by the greatest scientists. Hopefully, your own foraging efforts are rewarded.          
Quote
I think the truth is in the bible and in the creation. I want to know what it is.

That's good, the key is that you keep on your course and never abandon your individual thinking/analysis.
Welcome to the club.

Thanks.

Date: 2008/01/09 18:43:08, Link
Author: Daniel Smith
Quote (oldmanintheskydidntdoit @ Jan. 09 2008,07:52)
I've asked Daniel *why* HIV was created, but as yet no answer, apart from "I can't read the mind of god".

Funny that, seems when it's convenient people can tell you what god meant when he did all sorts of things in general, but get down to specifics and it all goes quiet.

Daniel, speculate based on your knowledge *why* HIV was created please.

Does the word "punish" come into it at all? As that's where I've been trying to lead you to you see. If you say it, you lose whatever credibility you have left.

Well, now I've said it. Lets see what he says.

I don't know the "why" for almost anything God created.  I don't know why he made horses, flies, starfish, HIV, or man.
I'm not just avoiding the question when it come to HIV.
I can speculate: he made horses for us to ride, flies for us to swat, starfish for us to look at, HIV to kill us, and man so that we could ask "why?" for all this.  My speculations are just that though - speculations.  They mean nothing and have no basis in reality (and they are not even my real speculations).  So why do you ask?

Date: 2008/01/09 18:55:33, Link
Author: Daniel Smith
Quote (Assassinator @ Jan. 09 2008,11:35)
 
Quote
Sorry.

As for creation stories, I think they all have an element of truth to them.

Because of what? Why would they?

They all (to my knowledge) point to life as being designed/created by an intelligent being of some sort.
   
Quote
 
Quote
(BTW, the bible claims that Jesus did have something to do with "origins of life, earth and the universe", FYI.)

What I ment that, even if Jesus existed, it says nothing about the origin of life etc etc.
   
Quote
Uh, I think your going to have to explain yourself on that one.  I have no idea what you meant by that - nor do I know what you want me to explain.

I've asked if you understood that your view that life looks designed says nothing about if it's actually designed. Then you say that science will never find a plausible explanation, huh?

But that is one of the tests for design.  If there is no plausible chance/random/natural explanation, we can infer that something happened as the result of the actions of intelligent beings.  This is the method coroners use to determine whether a death was the result of natural causes or human intervention.

If man were to discover an ancient artifact that exhibited a technology far superior to that of ancient (or modern) man, could he infer that perhaps an alien race had visited this planet from that artifact?  Of course he could.  In fact, that would be the first inclination in such a discovery.  The only way to falsify that theory would be to provide another plausible explanation.

Biological systems represent just such an advanced technology in my opinion.  Until you provide me with a plausible explanation as to their origin, I'll continue to hold that they were designed by a supreme intelligence.  That's my position.
 
Quote
Besides, what do you know about this subject Daniel? Have you got any education on these subjects whatsoever?

Completely self taught, with gaping holes in my knowledge.

Date: 2008/01/10 10:47:55, Link
Author: Daniel Smith
Quote (Erasmus @ FCD,Jan. 09 2008,18:36)
 
Quote
I believe in the flood, but only because I haven't seen the evidence against it.  My main reason for believing it (other than the bible), is that the landscape looks like the aftermath of massive flood runoff when viewed from the air.  Not very scientific, I know but that's where I'm at.  (insert joke here)
 


Are you kidding?  Where in the hell does it look like that?

That isn't even worth making a joke about.  You need some help dude.

Next time you're up in an airplane -- look down.

Date: 2008/01/12 08:23:39, Link
Author: Daniel Smith
Quote (Henry J @ Jan. 10 2008,22:41)
 
Quote
I believe in the flood, but only because I haven't seen the evidence against it.


Ice caps, one with more than 100,000 annual layers.

Over a million species presently living (a handful of survivors would take a long time to diversify that much).

Lots of genetic diversity within those living species (i.e., lots of species that don't show signs of recent extreme inbreeding, including our own).

Lots of unique ecosystems on continents and islands and other geographically isolated regions (those don't form overnight).

At least two civilizations that were keeping records through the period in question (unless the usual estimates for the date are way wrong).

Continuity in geological record from before the presumed dates of the event and after (i.e., no sudden world wide change in what lived where).

Absence of identifiable layer of debris in geological record around the estimated time.

Henry

I'm really not interested at all right now in debating the flood issue.  As I said, I really haven't researched it much at all and I don't want to get into another debate where I am unprepared to defend my position.  I have seen the evidence you've listed and it is food for thought.  I will consider it, I won't just ignore it - I promise you.  But right now this is a rabbit trail I'm not prepared to go down.  I hope you all can respect that.

I'd really like to get back to talking about Schindewolf, Berg, and their theories of constrained evolution and evolution by law.

Date: 2008/01/12 14:16:02, Link
Author: Daniel Smith
I'll just say this and be done with it:
I'm perfectly content with a 4.5 billion year old earth, and I wouldn't cry if it turned out to be only 10,000 years old either.  IOW, it's not really an issue for me.

It's not how old things are; it's their chronological order that matters.

Date: 2008/01/12 19:11:05, Link
Author: Daniel Smith
Quote (Assassinator @ Jan. 12 2008,14:50)
Then what's your problem with the chronological order? We know that life arose step by step, in a certain order (the very first steps of life are unknown, then we've got the theorised RNA-world, DNA-organisms, recognisable microbial life, multi-cellular sea life, multi-cellular land life etc etc). Then what's your problem?

I think you must've missed the first 30 or so pages of this discussion.  I came here to discuss the theories of  Schindewolf and Berg.  Both of them believe in evolution.  The only difference is that they deny "Selection" as the mechanism by which evolution progresses from type to type.  Both favor nomogenesis (evolution by law) instead.  In fact, that's the title of Berg's book.  While Berg did not propose a mechanism for his theory (other than physical law), Schindewolf proposed Goldschmidt's "systemmutation" of chromosomal re-ordering, which has been refined today by Davison as the semi-meiotic hypothesis.

Recent findings that suggest protein folds are more a product of natural law than selection would seem to vindicate these long neglected scientists:            
Quote
Consider the case of the protein folds. Although entirely counter intuitive, the complex spatial arrangements of the amino acid chains in the 1000 protein folds are as natural and necessary as the arrangements of subatomic particles in atoms or atoms in molecules (Denton and Marshall, 2001). This is now the inescapable conclusion of the past 30 years of research into protein structure and folding which have shown that the protein folds used by life on earth represent a set of about 1000 natural and immutable forms, which like atoms or crystals arise from the natural intrinsic self-organizing properties of their constituents, in this case—amino acid polymers (Ptitsyn and Finkelstein, 1980; Chothia and Finkelstein, 1990; Banavar and Maritan, 2003). Moreover, a number of organization rules, ‘laws of form,’ which govern the local interactions between the main structural submotifs have been identified, and these restrict the spatial arrangement of amino acid polymers to a tiny set of about 1000 allowable higher-order architectures (Ptitsyn and Finkelstein, 1980; Chothia and Finkelstein, 1990). These rules are analogous to the laws of chemistry or rules of crystallography which determine the form of molecules and crystals or the rules of grammar which determine the form of meaningful letter and word strings in a language. These are nothing more nor less than a set of ‘laws of form’ like those sought after by pre-Darwinian biology to account lawfully for the diversity of form in the organic world. It is not, as is commonly supposed, the amino acid sequences which specify the three-dimensional form of a protein fold, but rather the abstract laws of protein form. Each of the 1000 allowable folds represents a preferred arrangement of matter which corresponds to an energy minimum (Ptitsyn and Finkelstein, 1980; Banavar and Maritan, 2003). This acts as a pre-existing mold or attractor, drawing the amino acid sequence from its initially disordered structure to its final and predetermined native conformation. So the forms of the folds are given by physics and matter is drawn by a process of free energy minimization into the complex form of the native conformation...
...It is now clear that many different amino acid sequences can fold into the same three-dimensional form (Brandon and Tooze, 1999) and sometimes the same sequence can fold into two different folds (Cordes et al., 2000). Evidently, the rules of fold form are highly restrictive at the level of three-dimensional structure, permitting only 1000 atomic patterns, but highly permissive in terms of sequence—a high proportion of sequences can fold into one or another fold. By analogy with language, we might think of the rules of syntax (fold architecture) as being very strict but the rules of spelling (fold sequence) very lax. Consequently, although the folds are immutable and discontinuosly distributed in fold space they can still be easily found (spelt) in sequence space and utilized by the cell.
Physical law not natural selection as the major determinant of biological complexity in the subcellular realm: new support for the pre-Darwinian conception of evolution by natural law, BioSystems 71 (2003) pp. 297–303, Michael J. Denton, Peter K. Dearden, Stephen J. Sowerby, Biochemistry Department, University of Otago, P.O. Box 56, Dunedin, New Zealand Global Technologies, Dunedin, New Zealand, Received 26 February 2003; received in revised form 16 May 2003; accepted 22 May 2003

And it is not only protein folds that behave this way, it is also RNA folds, the bipolar aster, tensegrity structures in the cell, even cell forms (though less is known about all of these).
So these findings would seem to vindicate both Schindewolf and Berg who knew that evolution must've happened lawfully, but just didn't know how.

Date: 2008/01/12 19:15:05, Link
Author: Daniel Smith
Quote (Erasmus @ FCD,Jan. 12 2008,09:24)
Daniel fair enough we can deal with flood and young earth nonsense at a later date.

If I may be so bold as to offer a summary of Berg Schindewolf Broom etc, the outcome of evolutionary processes are determined by natural law.  In other words, it could not have been any other way.

Post synthesis thought has recognized that there are many constraints imposed on the landscape of what 'could be' (hint, this makes Dembski's NFL a stinky steam-pile), while emphasizing the role of contingency and (for lack of a better word) 'chance'.  

Now, my point is that if there were 'laws' governing evolution, don't you think some of these would have emerged from the millions of statistical analyses performed on biological data since Fisher and Wright?  There is no single distillable biological principle, formulable at any level of detail*, that is held without exception.  There are 'No Laws' (you should chat with Bob O'H about that'un).

See here and here please.

Date: 2008/01/13 17:51:42, Link
Author: Daniel Smith
Responses such as these...
 
Quote (Richard Simons @ Jan. 12 2008,09:05)
It is similar with Schindewolf's ideas. 'Here is an explanation for different organisms apparently following the same evolutionary path.' - 'How was it implemented?' - 'Hush. We don't talk about that.'

   
Quote (Henry J @ Jan. 12 2008,21:58)
That's quite interesting. But near as I can tell, it's not talking about evolution of the DNA for that protein, it's talking about what the protein does after it's been synthesized.

   
Quote (Assassinator @ Jan. 13 2008,07:06)
As far as I can see, you're talking about protein folding, we know why that happens. It's biochemistry.

   
Quote (Albatrossity2 @ Jan. 13 2008,08:19)
(---odious tard by another IDiot deleted-------)

...lead me to believe that none of you have bothered to read any of the material I've presented thus far.

Let me ask this:  Has anyone here read anything by Schindewolf or Berg?  Did any of you read the Denton papers I linked to?  How about any of the ENCODE consortium papers I cited?

And if not, why not?

Date: 2008/01/13 18:11:47, Link
Author: Daniel Smith
Quote (Albatrossity2 @ Jan. 13 2008,08:19)
     
Quote (Daniel Smith @ Jan. 12 2008,19:11)
           
Quote (Assassinator @ Jan. 12 2008,14:50)
Then what's your problem with the chronological order? We know that life arose step by step, in a certain order (the very first steps of life are unknown, then we've got the theorised RNA-world, DNA-organisms, recognisable microbial life, multi-cellular sea life, multi-cellular land life etc etc). Then what's your problem?

I think you must've missed the first 30 or so pages of this discussion.  I came here to discuss the theories of  Schindewolf and Berg.  Both of them believe in evolution.  The only difference is that they deny "Selection" as the mechanism by which evolution progresses from type to type.  Both favor nomogenesis (evolution by law) instead.  In fact, that's the title of Berg's book.  While Berg did not propose a mechanism for his theory (other than physical law), Schindewolf proposed Goldschmidt's "systemmutation" of chromosomal re-ordering, which has been refined today by Davison as the semi-meiotic hypothesis.

Recent findings that suggest protein folds are more a product of natural law than selection would seem to vindicate these long neglected scientists:  

(---odious tard by another IDiot deleted-------)

So these findings would seem to vindicate both Schindewolf and Berg who knew that evolution must've happened lawfully, but just didn't know how.

I was trying to stay out of this conversation, because it is abundantly clear that Daniel has no clues about recent advances in biology or biochemistry. But this post is just way too stupid to ignore.

I'll let JAM handle the gory details, but it needs to be pointed out that the notion that "protein folds are more a product of natural law than selection" is a strawman. If it is not a strawman, Daniel, please document where any reputable scientist claims that natural selection governs the molecular processes involved in protein folding.

I've been searching through the various papers that cite the Denton papers for negative comments about his hypothesis but have yet to find any.
This leads me to believe that the reputable scientists that actually work in his field don't hold his views in contempt like the posters on this board do.  If you can point me to a published paper where the authors take a stance against Denton's hypothesis, please do.
     
Quote
This sort of argument bespeaks not only a profound misunderstanding of evolutionary theory (which Daniel has already demonstrated abundantly), but a profound ignorance about the molecular processes that occur within cells.

Here's a clue, Daniel. It would be a huge surprise if the laws of chemistry and physics did NOT govern the folding of proteins and other biological macromolecules. To claim that these obvious and experimentally determined facts are vindication of Schindewolf and Berg's half-baked notions is profoundly ignorant.

So you're saying that a limited number of protein folds, given an infinite number of potential amino acid sequences available for selection, is a prediction of the MET?
Why then do so many of these scientists use words like "surprising", when referring to the discovery that there are only a finite number of protein folds?

Date: 2008/01/14 10:50:13, Link
Author: Daniel Smith
Quote (Albatrossity2 @ Jan. 14 2008,06:50)
What Daniel is doing, however, is pretending that evolutionary theory has some predictions about how evolutionary processes govern this subcellular realm. Strawman, pure and simple.

If selection does not act at the subcellular level, why then is it said to "constrain" DNA sequences?  The MET surely has a lot to say about DNA sequences - does selection "skip a level" and not act upon protein folds?

Date: 2008/01/14 10:52:27, Link
Author: Daniel Smith
Denton (with others) wrote several papers on this subject - each being cited numerous times, none AFAIK, have been cited unfavorably.

Date: 2008/01/14 11:03:54, Link
Author: Daniel Smith
Quote (Wesley R. Elsberry @ Jan. 13 2008,11:56)
I take it Mark didn't bother to read Dawkins' critique of "weasel"'s "distant ideal target". That puts him in the company of just about every other antievolution advocate.

Dawkins' attempt to illustrate RM+NS with his "Methinks it is a Weasel." example seems more like an example of constrained evolution to me.
The fact that the goal was predetermined, and functional sentences would have to be selected against if they were not on a path towards "Methinks it is a Weasel.", completely destroys the NS part of it IMO.
It is "goal oriented", predetermined selection he illustrates - and which he shows works very well thank you.

Date: 2008/01/14 18:27:18, Link
Author: Daniel Smith
Quote (Albatrossity2 @ Jan. 14 2008,11:43)
     
Quote (oldmanintheskydidntdoit @ Jan. 14 2008,11:20)
           
Quote (Daniel Smith @ Jan. 14 2008,10:52)
Denton (with others) wrote several papers on this subject - each being cited numerous times, none AFAIK, have been cited unfavorably.

List them.

Daniel is right about this narrow but irrelevant point. For example, a paper by Denton et al. in the Journal of Theoretical Biology was cited in passing in that PNAS paper that I noted in an earlier comment.

BUT here's the rub.

1) Denton is careful to say nothing about ID, nomogenesis, or any other woo in those papers. He is addressing theoretical aspects of abiogenesis (hence the use of the term "pre-Darwinian" rather than "anti-Darwinian).

2) These are all theoretical papers, in journals that accept theoretical papers. AFAIK, he has produced no experimental papers.

3) As pointed out before, he is saying nothing that is surprising or earth-shattering. Physical and chemical laws govern protein folding. Big deal. His papers are merely verbose statements about the flaming obvious, which is perfectly consistent with the low citation rate he enjoys.

If Denton did mention this stuff as support for ID, or did act as if he was overthrowing the strawman of natural selection somehow being a direct determinant of protein folding, I suspect that his citation count would go higher, but none of the citations would be very favorable!

So Daniel is right about this. Unfortunately for him, however, it's completely irrelevant to his points about nomogenesis, etc. Another red herring for the steaming pile that has accumulated on this thread already.

I think you are wrong about this.  Denton makes it very clear what "pre-Darwinian biology" means - and it's not abiogenesis:  
Quote
Before Darwin, the majority of leading biologists adhered to a Platonic model of nature, referred to by Owen (1849) in his classic monograph On the Nature of Limbs as ‘‘the Platonic cosmogony.’’ According to this conception, all the basic recurrent forms of the organic world, such as the pentadactyl design of the vertebrate limb, the body plans of the major phyla, the forms of leaves and so forth, as well as the recurrent forms of the inorganic realm, such as atoms, crystals, etc., represent the material manifestations of a finite set of immutable immaterial archetypes or ‘‘ideas’’ termed by Owen (1849) ‘‘predetermined or primal patterns.’’ These pre-existing abstract types or ideas are materialized, or to cite Owen (1849) again, ‘‘clothed in material garb,’’ by the agency of natural law, or more precisely in the case of organic forms by a special class of natural laws which applied uniquely to the vital realm--the celebrated ‘‘Laws of Form.’’

Denton et al, The Protein Folds as Platonic Forms: New Support for the Pre-Darwinian Conception of Evolution by Natural Law, (emphasis mine)

So how exactly does the term "pre-Darwinian biology" come to mean "abiogenesis" in your eyes?  I mean, look at the title of the paper for goodness sake!

Date: 2008/01/14 19:26:37, Link
Author: Daniel Smith
Here's my critique of the "GA as support for biological evolution via RM+NS" argument.

From the talk-origins page:
         
Quote
The GA then evaluates each candidate according to the fitness function. In a pool of randomly generated candidates, of course, most will not work at all, and these will be deleted. However, purely by chance, a few may hold promise - they may show activity, even if only weak and imperfect activity, toward solving the problem.

Here's the first problem in my eyes:  Natural selection does not select for "promise".   Also, reproductive fitness is not considered - since all non-eliminated candidates will reproduce equally for the duration of the GA.      
Quote
These promising candidates are kept and allowed to reproduce. Multiple copies are made of them, but the copies are not perfect; random changes are introduced during the copying process. These digital offspring then go on to the next generation, forming a new pool of candidate solutions, and are subjected to a second round of fitness evaluation. Those candidate solutions which were worsened, or made no better, by the changes to their code are again deleted;

OK, another problem: the candidates that were "made no better" are deleted.  They were good enough to be selected before, but now they are selected against.  While this is the correct way to improve a design, it surely doesn't imitate natural selection - which tends to stabilize populations by maintaining the status quo rather than eliminating all organisms that are not making progress toward a goal.          
Quote
but again, purely by chance, the random variations introduced into the population may have improved some individuals, making them into better, more complete or more efficient solutions to the problem at hand. Again these winning individuals are selected and copied over into the next generation with random changes, and the process repeats. The expectation is that the average fitness of the population will increase each round, and so by repeating this process for hundreds or thousands of rounds, very good solutions to the problem can be discovered.

The selection criteria rewards "promise", does not have anything to do with reproductive fitness, is unrealistic in regard to competition and has to do with the goal oriented solving of a problem. I have no doubt that these types of algorithms will work very well, but they don't mimic biological evolution (via RM+NS) IMO.

Date: 2008/01/15 19:03:59, Link
Author: Daniel Smith
Quote (Albatrossity2 @ Jan. 14 2008,19:51)
         
Quote (Daniel Smith @ Jan. 14 2008,18:27)
I think you are wrong about this.  Denton makes it very clear what "pre-Darwinian biology" means - and it's not abiogenesis:                  
Quote
Before Darwin, the majority of leading biologists adhered to a Platonic model of nature, referred to by Owen (1849) in his classic monograph On the Nature of Limbs as ‘‘the Platonic cosmogony.’’ According to this conception, all the basic recurrent forms of the organic world, such as the pentadactyl design of the vertebrate limb, the body plans of the major phyla, the forms of leaves and so forth, as well as the recurrent forms of the inorganic realm, such as atoms, crystals, etc., represent the material manifestations of a finite set of immutable immaterial archetypes or ‘‘ideas’’ termed by Owen (1849) ‘‘predetermined or primal patterns.’’ These pre-existing abstract types or ideas are materialized, or to cite Owen (1849) again, ‘‘clothed in material garb,’’ by the agency of natural law, or more precisely in the case of organic forms by a special class of natural laws which applied uniquely to the vital realm--the celebrated ‘‘Laws of Form.’’

Denton et al, The Protein Folds as Platonic Forms: New Support for the Pre-Darwinian Conception of Evolution by Natural Law, (emphasis mine)

So how exactly does the term "pre-Darwinian biology" come to mean "abiogenesis" in your eyes?  I mean, look at the title of the paper for goodness sake!

Daniel

Are you really this thick naturally, or are you simply stringing this red herring out so that you hope that I will forget that you haven't answered my questions yet? If the latter, don't count on it. I'd appreciate, greatly, an answer, especially since I have answered all of yours so far, and will now answer the latest one. Your debt is building up...

I haven't read that 2003 Biosystems paper that you originally cited; interlibrary loan hasn't delivered it yet.

I linked to a .pdf copy of the paper when I cited it.  (The entire title was the link). Here it is again.    
Quote
But I can tell you what he said in that  2002 J. Theor. Biol. paper (Denton, M.J., Marshall, C.J., Legge, M., 2002. The protein folds as Platonic forms: new support for the pre-Darwinian conception of evolution by natural laws. J. theor. Biol. 219, 325–342.)
               
Quote
‘‘the lawful nature of the folds together with the intriguing fact that many of the 20 protogenic  amino acids—out of which the folds are constructed—are amongst the most common amino acids found in meteorites and the easiest amino acids to generate in pre-biotic syntheses is surely of considerable significance, consistent with and supporting a deterministic theory of the origin of life

FYI, the "origin of life" = abiogenesis.

FYI, "pre-biotic" = prior to the development of biological life.

FYI, pre-Darwinian also means, in this context, metabolic and chemical processes PRIOR to the development of a system of inheritance.

FYI, a system of inheritance is required for the mechanisms of Darwinian evolution to be effective.

So, despite your notion that "pre-Darwinian" might have a solely philosophical meaning, I think it is clear that Denton's focus is abiogenesis. These papers were published in biology journals, not philosophy journals. My interpretation is confirmed by my reading of all four (4) papers that cite this 2003 Biosystems paper; all the citations cite it in a context that is discussing abiogenesis.

I will report back on my reading of the 2003 Biosystems paper when I get my hands on it. In the meantime, I'm sticking with my interpretation of "pre-Darwinian".

I'm sorry to say this, but you are just dead wrong in your assessment of what Denton means by "pre-Darwinian".
Here is every passage where he uses the term "pre-Darwinian" in the paper:
Quote
the Pre-Darwinian Conception of Evolution by Natural Law ...
The folds are evidently determined by natural law, not natural selection, and are ‘‘lawful forms’’ in the Platonic and  pre-Darwinian sense of the word ...
pre-Darwinian biologists hoped to provide a rational and lawful account of the diversity of organic forms via the ‘‘Laws of Biological Form’’ ...
The fundamental goal of biologists in the pre-Darwinian era to seek rational and lawful explanations for biological form is reflected in Goeffroy St Hillaire’s attempt to derive all the
basic body plans of the major biological types from a basic fundamental plan by a system of simple natural transformations ...
The widespread belief that organic forms are lawful ‘‘givens of nature’’ explains why it was that throughout the pre-Darwinian period from the naturphilosophie of the late 18th century, right up to the period just before the publication of the Origin, although it was universally
accepted that organisms exhibited functional adaptations, for Goethe, Carus Goeffroy and Owen, it was always form which was of primary concern. ...
Holding organic forms to be the result of a set of natural laws which applied uniquely to the organic realm, nearly all the leading biologists of the pre-Darwinian era might be described as ‘‘vitalists,’’ ...
the pre-Darwinian conception of organic forms as intrinsic features of the natural order was never completely laid to rest after 1859. It survived well into the 20th century
particularly on the continent of Europe ...
the pre-Darwinian concept of organic forms as ‘‘built-in’’ intrinsic features of nature determined by natural law provides a more powerful explanatory framework than its selectionist successor ...
They self evidently represent a set of ‘‘Laws of Biological Form’’ of precisely the kind sought after by Geoffroy, Carus and many other Platonic biologists of the pre-Darwinian era. ...
Moreover even the extreme Platonic position of some of the pre-Darwinian biologists, such as Goethe--that form directly determines function, without any or only minimal selective modification--may also be true in certain cases. ...
In their book Biochemical Predestination, the authors Kenyon & Steinman (1969) echoing the early 19th
century views of Owen and Schwann, conclude with sentiments consistent with the pre-Darwinian concept of evolution by natural law and the viewpoint defended in this paper ...
On the contrary, they are wonderful exemplars of the pre-Darwinian and Platonic conception of organic forms as abstract, lawful and rational features of the eternal world order, which will occur throughout the cosmos wherever the same 20 protogenic amino acids are used to make proteins. ...
For the folds represent the first case in the history of biology where a set of complex organic forms can be shown to be unambiguously lawful natural forms in the classic pre-Darwinian sense. ...
turned out to be such perfect exemplars of the pre-Darwinian Platonic cosmogony, and the idea of natural law as the major determinant of organic form and evolution ...
Whether or not there are other sets of lawful organic forms, there is no doubt that the universe of protein folds represents a Platonic universe of precisely the kind sought after by pre-Darwinian biology. ....
For it holds out the prospect that the study of organic form, might eventually become as the pre-Darwinian biologists such as Goethe, Goeffroy and Owen had always hoped, a fully rational and predictive science, and that biology may in the end be unified with physics in Plato’s timeless realm of the gods
 
From these passages it is quite evident that he is using the term "pre-Darwinian" to describe the scientific philosophy that was the paradigm prior to Darwin's publication of The Origin.  "Pre-Darwinian Conception", "pre-Darwinian sense", "the pre-Darwinian era", etc., etc.. are not synonyms for "metabolic and chemical processes PRIOR to the development of a system of inheritance".

And, what - by your concept of his meaning - are "pre-Darwinian biologists" exactly?

Are "biologists in the pre-Darwinian era", biologists who were around for abiogenesis?

Sorry, but this time, you're just plain wrong.

Date: 2008/01/15 19:17:21, Link
Author: Daniel Smith
Quote (Richard Simons @ Jan. 15 2008,18:14)
     
Quote (Albatrossity2 @ Jan. 15 2008,09:30)
It does take time (often years) and effort to become conversant in some of these areas. When you couple that with the fact that many of these folks are barely conversant with biology at the intellectual level that we teach in junior high, it is frankly insulting to read a comment like Mark's last one.

I recently pointed out (can't remember where) that the difference in the time and effort spent gaining information and honing their skills between a newly-independent researcher and someone who has high-school biology is comparable with that between a professional hockey player and 6-year-olds playing street-hockey.

It seems to me (and I'm not trying to be insulting) that you educated guys have a lot of trouble explaining why you're right.  You seem to be much better at telling us uneducated saps how ignorant we are and leaving it at that.  
If you say you're right, but give--as the only reason--the fact that we are not educated, you didn't really tell us what's right about your position.  All you're doing is the equivalent of name calling.  This is just an observation.

Date: 2008/01/17 19:11:14, Link
Author: Daniel Smith
Quote (Albatrossity2 @ Jan. 15 2008,20:32)
     
Quote (Daniel Smith @ Jan. 15 2008,19:03)
Sorry, but this time, you're just plain wrong.

Maybe, but that doesn't explain why EVERY paper that cites that article cites it in a context of abiogenesis. If I'm wrong, I have company, at least.

But even if we agree to disagree on this diversion, let's get back to the original reason why you cited this article. You stated, as if it was surprising, that "protein folds are more a product of natural law than selection". I pointed out  then that this is a strawman. I asked you          
Quote
If it is not a strawman, Daniel, please document where any reputable scientist claims that natural selection governs the molecular processes involved in protein folding. This sort of argument bespeaks not only a profound misunderstanding of evolutionary theory (which Daniel has already demonstrated abundantly), but a profound ignorance about the molecular processes that occur within cells.


They don't (to my knowledge) claim that selection governs the molecular processes that specifically control protein folding.  They do claim however, that selection governs the amino acid sequences that make up these proteins.
Denton (if my reading of him is correct) is arguing that the sequences are not governed by selection because the same folds can be arrived at by several routes (sequences) and the same sequence can yield different folds.
That's what I get out of it anyway.

Also, in regard to whether or not this supports Schindewolf and Berg:  While Denton does not mention them by name, he does say this:      
Quote
However the pre-Darwinian conception of organic forms as intrinsic features of the natural order was never completely laid to rest after 1859. It survived well into the 20th century particularly on the continent of Europe (Gould & Lewontin, 1979).
(Emphasis mine)

So -- A) Denton is making a case for evolution by natural law.  B) He describes that philosophy as "pre-Darwinian" science.  C) He then mentions that this pre-Darwinian concept "survived" the Darwinian revolution in Europe.

That, to me, would include Schindewolf, Berg, Grasse, Bateson and even Goldschmidt -- who all advocated evolution by some sort of natural law.

So - maybe you disagree with that - fine, that's OK, I just think we'll have to disagree on that.

Date: 2008/01/17 19:56:47, Link
Author: Daniel Smith
Quote (Wesley R. Elsberry @ Jan. 17 2008,07:51)
I suspect Mark said "80%" because, IIRC, that's the number Bill Dembski pulled out of his butt for the same purpose in "No Free Lunch" in his argument concerning the Gettysburg Address.

There is actually peer-reviewed literature about the subject of predictability of messages in English. Dembski certainly did not cite it (it wouldn't support the high value he apparently wanted), and I doubt Mark is familiar with the work.

Of course, I think the whole notion Mark is hinging his argument upon is silly. It depends critically upon arguing over what analogy supposedly applies to evolutionary computation that manipulates character strings. When I posed the problem of evolutionary computation for Dembski's arguments to Dembski back in 1997, I certainly didn't put my example in terms of changes in characters in strings to match arbitrary targets; I posed the problem in terms of a genetic algorithm to provide a near-optimal solution to the "traveling salesman problem". Here, the issue is simply how long a tour a candidate solution represents and there is no question about thresholds. The TSP is biologically relevant because movement costs metabolic energy, and organisms that minimize movement in a closed path thus have an advantage.

Dembski has, so far as I can tell, *never* since even had a try at a response that addresses evolutionary computation's successful approach to finding near-optimal solutions to TSP type problems. He has gone on at length about toy evolutionary computation examples, such as Dawkins' "weasel".

If I might.

I think you're all missing one thing.

No matter what, natural selection is not perfect.  

If an unborn bird has a genetic mutation that will turn it into a super-bird -- impervious to all predators -- yet, while still in the egg, gets eaten by a fox, that "solution" is gone.  It was selected against because it did not confer an advantage that was relevant to that particular stage of the bird's development.

If the same bird makes it through to adulthood, yet is killed in an oil spill before it can breed, again that solution is lost -- not because it didn't have the solution to the predator problem -- but because it didn't have the correct solution to another problem (oil).

What if the super-bird is sterile?  What if it is shunned and cannot mate?  What if its 'super-allele' is recessive and its progeny are all wiped out without passing it on?  Etc.

Real life requires multiple solutions to multiple problems (and a lot of times just dumb luck) for survival (selection).  Genetic algorithms are (I'm guessing) much more narrowly fixated than that.

So, unless a genetic algorithm periodically wipes out promising solutions randomly, or throws other unrelated problems into the mix suddenly and removes the bad solutions to those problems as well, it is not a realistic model for natural selection.

Artificial selection, on the other hand, works differently.  It narrows the focus, and essentially (attempts to at least) shield organisms from natural selection.  Dog breeders selectively breed only those dogs with the specific traits they want.  In this way, they can narrow the path genetically and arrive at the correct solution for the much simplified problem.

This is what (I would think) good genetic algorithms, (those that are being actively used to look for solutions), should do as well.

That's my uneducated opinion.

Date: 2008/01/19 09:56:57, Link
Author: Daniel Smith
Quote (Albatrossity2 @ Jan. 18 2008,07:24)
           
Quote (Daniel Smith @ Jan. 17 2008,19:11)
               
Quote (Albatrossity2 @ Jan. 15 2008,20:32)
                       
Quote (Daniel Smith @ Jan. 15 2008,19:03)
Sorry, but this time, you're just plain wrong.

Maybe, but that doesn't explain why EVERY paper that cites that article cites it in a context of abiogenesis. If I'm wrong, I have company, at least.

But even if we agree to disagree on this diversion, let's get back to the original reason why you cited this article. You stated, as if it was surprising, that "protein folds are more a product of natural law than selection". I pointed out  then that this is a strawman. I asked you                            
Quote
If it is not a strawman, Daniel, please document where any reputable scientist claims that natural selection governs the molecular processes involved in protein folding. This sort of argument bespeaks not only a profound misunderstanding of evolutionary theory (which Daniel has already demonstrated abundantly), but a profound ignorance about the molecular processes that occur within cells.


They don't (to my knowledge) claim that selection governs the molecular processes that specifically control protein folding.  They do claim however, that selection governs the amino acid sequences that make up these proteins.
Denton (if my reading of him is correct) is arguing that the sequences are not governed by selection because the same folds can be arrived at by several routes (sequences) and the same sequence can yield different folds.
That's what I get out of it anyway.

Sigh.

Selection operates on biological FUNCTIONS, carried out by macromolecules within organisms, but it acts at the level of the organism. Moving the goalposts to say that scientists claim that "selection governs the amino acid sequences that make up these proteins" is still wrong. Indeed, once you have a new amino acid sequence that generates a new function, selection can operate to favor or disfavor that FUNCTION. But if another amino acid sequence generates the same 3-d structure that also gives rise to the same function, selection had no hand in the molecular processes governing any of that. Selection operates AFTER all of that. It is still a strawman to pretend that reputable scientists ascribe these properties to natural selection.

Daniel, do you understand that different sequences giving rise to the same 3-d structure is exactly what you would expect if selection for the FUNCTION of the sequence, rather than the sequence itself, is operating?

As noted before, Denton is saying nothing surprising from a biochemical or evolutionary point of view. Why you see this as support for your notions is a mystery to me as well.

I'm not as dumb as I may appear.  I actually do realize how selection is supposed to work.  I know it cannot work at any other level below the level of the organism.  In a way, you're making my point for me.  In order to produce a function at the organism level, mutations are filtered through the bottleneck of protein folding - which we agree is constrained by natural law.  Therefore, evolution is constrained by natural law (at least in this one basic area).  Denton's hypothesis (which is spelled out in the two papers we've discussed, as well as a third which appeared in Nature), is that there may be other areas in which evolution is also constrained.  Did you read any of these papers?  Because he very meticulously lays out his case; beginning with a history of the theory of evolution by natural law:      
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that the whole pattern of evolution was itself in a sense already pre-determined or pre-specified by natural law---being the material manifestation of a pre-existing and eternal plan.
pg 327 of the J. Theor. Biol. paper
continuing with an overview of how protein folding is governed by said law; and concluding that this is the first vindication for the theory of evolution by natural law:      
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The subcellular world is thus the first important realm of biology in which the early 19th century idea of evolution by natural law discarded as archaic by most biologists since Darwin, is being finally vindicated.
pg. 302 of the Biosystems paper
 
If he is "saying nothing surprising... from a[n] ... evolutionary point of view", then you must be in agreement with his assessment?

Date: 2008/01/19 10:31:58, Link
Author: Daniel Smith
Quote (Wesley R. Elsberry @ Jan. 17 2008,05:51)
When I posed the problem of evolutionary computation for Dembski's arguments to Dembski back in 1997, I certainly didn't put my example in terms of changes in characters in strings to match arbitrary targets; I posed the problem in terms of a genetic algorithm to provide a near-optimal solution to the "traveling salesman problem". Here, the issue is simply how long a tour a candidate solution represents and there is no question about thresholds. The TSP is biologically relevant because movement costs metabolic energy, and organisms that minimize movement in a closed path thus have an advantage.

So I am no longer accused of avoiding the issue...

My problem with the TSP -- and indeed any GA -- is that the selection mechanism always selects the best solution.  This is not a realistic simulation of how natural selection works in real life (for the reasons I've already stated).  

GAs, at best, simulate artificial selection -- and even then unrealistically -- since even artificial selection (in real life), cannot negate such things as natural disasters, diseases, sterility, chance and coincidence.

To illustrate:  Recently a local breeder of prize dogs had nearly her entire kennel wiped out in a flash flood.  Neither natural selection nor artificial selection could stop that.  These dogs were selected against because they were not ducks!

Show me a GA that can realistically simulate that and you'll have something.

Date: 2008/01/19 11:37:40, Link
Author: Daniel Smith
Quote (Albatrossity2 @ Jan. 19 2008,08:30)
if you don't understand why your notion that scientists are saying that selection governs protein folding is a strawman, I have exhausted my abilities to explain, and will conclude that either you are being purposefully obtuse, or you are indeed as dumb as you seem to be.

I didn't mean to imply that scientists were still saying that.  Scientists are not saying "selection governs protein folding", because the discoveries of recent years have proven otherwise.  I don't know whether they used to think that or not, but from the gist of Denton's papers, I get the impression that they did at one time expect protein folding to be the product of selection from an infinite number of possibilities as opposed to a finite set of about 1000 folds:
           
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By the late 1960s several other proteins had been determined including hemoglobin and lysozyme. Despite these early successes the lack of any apparent regularity in protein structures, and the great dissimilarity among those that had been determined, provided no basis for a rational classification (Ptitsyn & Finkelstein, 1980; Richardson, 1981). The picture was still in those early days compatible with the Lego model---that the folds in living organisms on earth might be individual members of a near infinite set of contingent material assemblages put together by natural selection over millions of years of evolution.
It was only during the 1970s, as the number of 3D structures began to grow significantly, that it first became apparent that there might not be an unlimited number of protein folds---that the folds might not belong to a potentially infinite set of artifactual Lego-like constructs.
pg 330, J. Theor. Biol. paper (my emphasis)


I've also often seen scientists refer to amino acid sequences as "evolutionarily constrained", implying that these sequences are so important for function, they do not tolerate mutations.  Denton takes a different view:
         
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It is not, as is commonly supposed, the amino acid sequences which specify the three-dimensional form of a protein fold, but rather the abstract laws of protein form...
The biological fitness of the folds is greatly enhanced by their accessibility in sequence space. It is now clear that many different amino acid sequences can fold into the same three-dimensional form (Brandon and Tooze, 1999) and sometimes the same sequence can fold into two different folds (Cordes et al., 2000). Evidently, the rules of fold form are highly restrictive at the level of three-dimensional structure, permitting only 1000 atomic patterns, but highly permissive in terms of sequence—a high proportion of sequences can fold into one or another fold. By analogy with language, we might think of the rules of syntax (fold architecture) as being