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Date: 2007/07/12 13:58:58, Link
Author: JAM
Quote (Hermagoras @ July 11 2007,18:03)
DaveScot  
Quote

JAM is no longer with us.


Well now.  That took longer than I thought.


I thought my longevity might have been due to my refusal to engage DaveTard.

Date: 2007/07/12 14:10:56, Link
Author: JAM
Quote (Zachriel @ July 11 2007,20:14)
 
Quote (stevestory @ July 11 2007,19:35)
Wow. The One-Comment Double Ban.

I heard rumors, but I thought it was just an urban legend.

:D

JAM "I make my living designing mutations that enable proteins to utilize new substrates that aren’t found in nature." didn't stand a chance.

scordova        
Quote
You’re persistent, JAM, and dialogue with you has been good practice at rhetoric.

As any student of rhetoric will tell you, banning wins every argument.


Speaking of rhetoric, what did you folks think of my rhetorical tactic in the form of taunting Jehu with that animal-rights lie of omission about polio research, telling him that it is brazenly dishonest, and challenging him to find the flaw?

Of course, I realize that nothing will work to convince Jehu, but what about for those who might be a few miles closer to the cusp of reason?

Date: 2007/07/12 14:13:06, Link
Author: JAM
Quote (Richardthughes @ July 12 2007,14:01)
WELCOME JAM!

Your patience is astounding..

Nah...it's just displacement activity. I'm chained to my computer, with 3 manuscripts to crank out.

Date: 2007/07/12 14:28:01, Link
Author: JAM
Quote (Arden Chatfield @ July 12 2007,12:07)
If there's one thing UD hates, it's real scientists with real credentials.

I like to hold back with my credentials and later, just for spice, mention that I have them without divulging my identity. Then, when I'm challenged to produce my credentials, I demand a wager first. They always back down.

It didn't get a response on the Behe thread on UD, but in other forums, I've managed to induce meltdowns.

The thing that fascinates me about the ID/creationism/animal-rights/ pseudoscientists is their amazing ability to revert to reality when it comes to risking money or careers.

IOW, why are there no pharma firms run on the "theory" of ID?
Why aren't there any creationist fossil hunters?
Why aren't there any pharma firms run by animal-rights wackos, in which all the cell culture is vegan (no bovine serum) and all the drug trials begin with human subjects?

Should we exploit this angle more than we do? Is it effective for those in the Muddled Middle?

Date: 2007/07/12 14:56:26, Link
Author: JAM
Quote (Patrick Caldon @ July 11 2007,21:53)
Here's the last post that didn't make it:
 
Quote

DaveScot, as an aside with your calculation, I think you?²ve neglected that if a nucleotide mutates into itself that?²s no mutation at all, i.e. A -> A is not a mutation by definition.

It's a real shame actually, I read JAM's posts carefully and I learned quite a bit; getting to grips with this kind of stuff almost makes me regret being a CS major.


Patrick, thanks for the compliments.

If I may offer some advice, that last shot at DaveTard was 10x too direct, and in general, you writing is too coherent.  ;-)

At the beginning, you should try to bumble a bit and be less direct (never editing helps), so that the ever-hopeful will initially miss your points, while thinking that you may be an ideal victim. Making a mistake and admitting it forthrightly also keeps the fish on the line a lot longer. Although the mistake I made was not deliberate, did you notice how Sal jumped all over it, then disappeared for more than a day after I responded?

Date: 2007/07/12 14:58:15, Link
Author: JAM
Quote (JohnW @ July 12 2007,14:39)
Quote (JAM @ July 12 2007,14:28)
IOW, why are there no pharma firms run on the "theory" of ID?
Why aren't there any creationist fossil hunters?
Why aren't there any pharma firms run by animal-rights wackos, in which all the cell culture is vegan (no bovine serum) and all the drug trials begin with human subjects?

Do we fail to exploit this? Is it effective for those in the Muddled Middle?

If you have a spare seven or eight days with nothing better to do, you might want to peruse the "afdave" threads from a few months ago.  He was repeatedly asked whether any corporations were using the young-earth/global flood premise to do geological work, e.g. oil exploration.

The silence was long and total.

Yeah, but did it change his mind (whether he admitted it or not) or anyone else's?

Date: 2007/07/12 15:06:34, Link
Author: JAM
Quote (Arden Chatfield @ July 12 2007,15:01)
Of course not, Jesus was watching.

Jokes aside, I'd like to know your impressions without having to wade through the sewage of another mind so soon after my UD marathon with Sal and Jehu.

Do you think we could be disciplined enough to test these rhetorical approaches experimentally?

Date: 2007/07/12 15:20:30, Link
Author: JAM
Quote (JohnW @ July 12 2007,15:08)
Quote (JAM @ July 12 2007,14:58)
Yeah, but did it change his mind (whether he admitted it or not) or anyone else's?

Guess I'll have to break the news
That I got no mind to lose

- Ramones

I wanna be sedated...

Date: 2007/07/14 14:33:35, Link
Author: JAM
Quote (Zachriel @ July 14 2007,11:36)
Someone is whispering in the wind to Denyse.        
Quote
Dog breeding is NOT random. Contra Dawkins that matters very much indeed.” O’Leary

Dawkins does not claim that dog breeding is random, sinse artificial selection is a non-random process just as natural selection is a non-random process.

What he is saying is that the mutations, such as the one that produces the very small dog such as the terrier is random with reference to the desired trait.

Do you have any evidence that the mutations that produce the different dog types were non-random?

O'Leary responds,    
Quote
whisper in the wind, the mutations that produce the different dog types are the outcome of restricting the breeding of bitches to approved sires (non-random) and then protecting the offspring from life outside a human community (no natural selection).

Um, no. Whispering in the wind didn't ask about non-random mating or non-random selection, but about evidence that genetic mutation in dogs was non-random with respect to the desired traits.

O'Leary is so ignorant that she can't distinguish between a mutation and a phenotype.

For how many years has she been ranting about evolutionary biology, and she still doesn't get high-school genetics?



Date: 2007/07/14 14:59:36, Link
Author: JAM
[quote=VMartin,July 13 2007,23:57]
Quote

   
Quote
Dawkins:
Or a heavyset, thick-coated wolf, strong enough to carry a cask of brandy, that thrives in Alpine passes and might be named after one of them, the St. Bernard? Behe has to predict that you'd wait till hell freezes over, but the necessary mutations would not be forthcoming.

The facts are these:
 
Quote

As for the barrel on the collar, it first appeared in a painting by artist Edwin Landseer called “Alpine Mastiffs Reanimating a Distressed Traveler” in 1820; Landseer was only 17 at the time. The cask was thought to contain brandy and quickly caught on in the public imagination, though the monks and their dogs never actually used such a thing. (Alcohol, after all, could hasten dehydration—not a good treatment for a snowbound traveler.)

VMartin,

Your reading skillz aren't that great.

If they were better, you'd have noticed a relevant fact: Dawkins didn't write that they actually carried casks of brandy, but merely that they are strong enough to do so.

So are you disagreeing with what Dawkins actually wrote, or just with what you wish he had written?

Date: 2007/07/14 15:30:57, Link
Author: JAM
Quote (VMartin @ July 13 2007,17:41)
Dawkins picked up dogs to show that random mutation is responsible for their diversity. I would like to see if Dawkins is able to domesticate also lizards or tigers, hehe. Obviously in those species is random mutation somehow frozen.

VMartin,

Would you mind explaining the mental processes that lead you to believe that your first sentence is accurate, and that your second sentence has any logical relationship to the first?

Dogs show more variation than other species because artificial selection was intense and taken in multiple directions.

The underlying source of genetic variation is the same (mutations), but more of it is evident in dogs because we did the selection.

Therefore, Behe is a dishonest twit because he tries to pass off limited diversity caused by reversing selection pressures (Plasmodium) as a low mutation rate, and you're a twit for believing him. If you disagree, answer these questions:

1) Why did Behe extrapolate from Plasmodium to humans instead of using mutation rates measured in humans?

2) Why do people who don't believe that humans and Plasmodium share a common ancestor defend Behe's extrapolations?

Date: 2007/07/14 16:49:50, Link
Author: JAM
Let's not forget the perfect asymmetry in the banning:

I didn't respond to DT's moronic math, therefore DT banned me.

DT didn't respond to Patrick Caldon's correction of his moronic math, so DT banned Patrick Caldon.

Date: 2007/07/14 17:16:32, Link
Author: JAM
Back to the subject of finding the most tard-proof arguments, I had what I think was very good luck with a HC creationist.

I emailed based on a his post on ARN, had a back-and-forth by Email, and finally I offered to spend an hour walking him (by phone) through BLASTing a random sequence and looking at the new tree feature in the results.

He seemed genuinely impressed, at least while he was on the phone with me. Convinced? I don't know.

Date: 2007/07/15 01:43:06, Link
Author: JAM
Quote (Hermagoras @ July 14 2007,19:30)
I actually agree with Patrick, because I think this all needs to be explained to someone with a lay understanding of the issues. However, my way of doing this would differ from what he hopes for.  Clearly, nobody at UD got the picture.  In particular, I don't think anybody over at UD got how Behe's confusion was related to the differences between molecular biology and population genetics.  I get that (and I also think, IIRC, that such confusions are present among mainstream molecular biologists, as well) but I don't have the tools to walk someone through it.  (If someone more expert wrote it up -- along the lines of "why don't IDers understand the flaws in Behe's math?" -- I'd be willing to help with the translation.)


What do you want to know? To boil it down to simple terms:

1) Behe was cherry-picking; he intended to deceive his audience. He needed a really small mutation frequency (= mutation rate) to argue that mutation frequencies are too small to drive evolution (one can't say this at UD). There's no real flaw in his math, the sophistry here is that the number isn't a quantitation of what he says it is.

2) The best way to measure mutation frequency is to measure the rate at a position that changes fitness from 1 to 0, or blue bacterial colonies to white, or vice versa. The key is absolute selection.

3) The mutation frequency has been measured in this way for P. falciparum. It is ~2.5 x 10E-9/nucleotide/cell division, right there with just about everyone else.

4) The idea that anyone would need to extrapolate from P. falciparum to humans is preposterous, because mutation rates in humans have been measured in a similar way--in the form of rates of sporadic (not inherited from parents) cases of dominant inherited diseases. You get a similar rate as in #3.

5) Behe found a number 100 billion-fold lower in a review of the chloroquine resistance (CQR) literature for the frequency with which CQR arises in populations in the real world. The author of the review gave many reasons why this is the case, but the most obvious IMO is the fact that the fitness of the CQR mutants is higher than wild-type in a human treated with CQ, but lower in a human not treated with CQ, of which there are many. Some other, less intuitive reasons are sexual reproduction (occurs in the mosquito without CQ) and immune surveillance.

6) The essence is that Behe is arguing that mutation fails to deliver sufficient variation to natural selection, but the reality in this case is that Behe is cherry-picking a case in which selection is flipping back and forth.

7) The cherry on top of Behe's cherry-picking is that once--just once--his expert, White, mislabeled this frequency as a “per-parasite resistance mutation frequency.” In every other case, he labeled it correctly as the product of complex selection.

I tried several ways to attack this, including avoiding the technical discussion and pointing out that Behe was quoting a review instead of citing the primary literature, and offering a completely dishonest argument from the animal-rights movement that used parallel deceptions. I thought that the latter strategy worked better.

Finally, I'd note that I agree that we're never going to change the minds of UD commenters. It's about the lurkers.

Date: 2007/07/17 11:28:25, Link
Author: JAM
Quote (slpage @ July 16 2007,15:12)
Quote (JAM @ July 14 2007,16:49)
Let's not forget the perfect asymmetry in the banning:

I didn't respond to DT's moronic math, therefore DT banned me.

DT didn't respond to Patrick Caldon's correction of his moronic math, so DT banned Patrick Caldon.

But... but.... IDists are OPEN MINDED and ENCOURAGE dialogue, unlike the hideous atheistic cult of Darwinism...

Yep, and I've just been banned again from Telic Thoughts for pointing out that no IDiot has the courage to risk effort or money when it comes down to testing hypotheses.

The amazingly irrational Joy just claimed that pointing this out meant that I was trying to silence IDiots.

Date: 2007/07/17 11:34:25, Link
Author: JAM
Quote (Robert O'Brien @ May 13 2007,14:47)
Refusing to grant tenure to Guillermo Gonzalez is clearly ideologically/politically motivated. He has at least 55 publications in his field according to ISI Web of Knowledge, which is more than his most vociferous critics have accomplished.

But how many of those were from his time at Iowa State? A lot of pubs before the first independent position and very few after taking that position is damning.

And how much did he bring in in grants? More to the point, how much indirect?

Date: 2007/07/17 11:53:18, Link
Author: JAM
Quote (VMartin @ July 16 2007,14:54)

JAM: Would you mind explaining the mental processes that lead you to believe that your first sentence is accurate, and that your second sentence has any logical relationship to the first?

The problem of domestication is very important.

There's no "problem of domestication" here--Dawkins is trashing Behe's lie that there's not enough variation to support natural selection.
     
Quote
Dawkins avoided the main problem - why we have domesticated only few species? Many species we can't domesticate - they simply die.

Dawkins wasn't avoiding anything--he was directly rebutting the thesis of Behe's sad little book.
     
Quote
Of course Dawkins conclusion is unfounded that random mutation is behind all variety of dogs races . It's only hypothesis that all alleles aroused via random mutation.

Why do we see new alleles appearing all the time? And why are you so dense that you don't realize that "random" only applies to fitness?  
       
Quote
   
Quote
JAM: Dogs show more variation than other species because artificial selection was intense and taken in multiple directions.
The underlying source of genetic variation is the same (mutations), but more of it is evident in dogs because we did the selection.

Underlying source of genetic variation is not the same. It is greater in Jaguars, Leopards and Pumas than in dogs. Heterozygosity in dogs is also lower than in lynx.

Of course heterozygosity in dogs is lower than it is in any wild animal that is not threatened with extinction--we have inbred dogs.

Lab mice are completely inbred--does that say a damn thing about heterozygosity in wild mice?
   
Quote
Consequetly artificial selection should be there as successful as in dogs.  

No. Besides, you'd have to compare heterozygosity in wolves 40000 years ago with heterozygosity in the other species today.
 
Quote
 
Quote

Therefore, Behe is a dishonest twit because he tries to pass off limited diversity caused by reversing selection pressures (Plasmodium) as a low mutation rate, and you're a twit for believing him.

You have no idea what are you babbling about but you have still enough audacity to call Behe dishonest twit.


I've published infinitely more papers in the subjects Behe misleads on in this book (some in retrovirology, microbiology, and mutagenesis) than Behe has (0 for 3).
Quote

But on the other hand I am almost sure that Plasmodium and humans don't share common ancestors.

Then we agree that Behe is a twit, but for different reasons.
Quote
Anyway criticising Dawkin's stories about dogs doesn't mean defending Behe's book, you know.

I know. I also know that you either don't understand, or are pretending not to understand, why Dawkins brought up dogs in a review of Behe's book.

Date: 2007/07/18 00:24:24, Link
Author: JAM
Quote (VMartin @ July 17 2007,12:48)
Jam
   
Quote

Why do we see new alleles appearing all the time? And why are you so dense that you don't realize that "random" only applies to fitness?


Can you give me an example of some new allele that appeared suddenly by random mutation


Many of them. Are you denying that such events have ever occurred? If so, how much are you willing to bet on your certainty?

Get this through your thick skull--"random" is only wrt fitness. Your incoherent use of the adjective makes you look stupid.
Quote
and it wasn't consequently present in the gene pool before?

Huh? If it is new, how could it have possibly been present in the gene pool before?

Should we call you the Master of Redundancy?
Quote
I mean something that is not degeneration of previously existed functional allele.

I do too. Your retarded view of biology certainly is degenerate!
Quote
I know. I also know that you either don't understand, or are pretending not to understand, why Dawkins brought up dogs in a review of Behe's book.

Quote
You are right.

I know.
Quote
I don't know why Dawkins brought it up (with those example of St.Bernadine bearing cask of brandy).

Perhaps you should read Behe's book before making a fool of yourself. Also, we already disposed of your lie that Dawkins claimed that St. Bernards actually did carry brandy; he just noted that they are capable of doing so. Why do you continue to lie about that?
Quote
Dogs are good example of the fact that evolution has nothing to do with natural selection.

Dogs are a good example of the extent of genetic variation that can be brought out by artificial selection.

If you weren't as dumb as a post, you'd know that Behe's thesis is that there is insufficient genetic variation to drive natural selection. Behe's book is not an attack on natural selection. Therefore, the variation we have in dogs is a perfect rebuttal to Behe's stupidity and dishonesty.
Quote
You can breed dogs however you like (diversity in dogs are greatest in mammals) they still remain dogs.

Yes, we call them dogs to reflect their common origin.
Quote
The strongest artificial selection  couldn't change the fact.

It's easily strong enough to bifurcate dogs to completely prevent them from interbreeding.

If you dumped 100 St. Bernards and 100 Chihuahuas on a large island with no other canids, would they ever interbreed? Could they interbreed?

Haven't we already met the major criterion for speciation?
Quote
That's probably the reason no one observed selection as creative force of evolution before Darwin. It also prove the fact that the process is almost fully reversible -dogs  left for themselves would return after some generation to their former state.

So try it with the two breeds I specified and see if it works.  
Quote
Dogs prove the fact that most species are unable to evolve...

Dogs have undergone incredibly rapid evolution, and their diversity shows that natural, existing genetic variation is more than enough to allow natural selection.

It looks to me as though you don't even understand the meaning of the word "evolution."

Date: 2007/07/18 00:26:22, Link
Author: JAM
Quote (Albatrossity2 @ July 17 2007,11:45)
Quote (JAM @ July 17 2007,11:34)
And how much did he bring in in grants? More to the point, how much indirect?

Well, now you're talking over the heads of the whiners, discussing indirect costs. Maybe we should ask Dr. Dr. D. how much IDC he gets with his funding from the DI, just to see if he understands the concept.

Well, to give you an idea of the pervasiveness of administrators' concern with indirect costs, at my last institution, applying for a grant with <15% IDC required the prior approval of the president.

I suspect that the DI pays 0% overhead.

Maybe that's a way that Lehigh can get Behe to leave...

Date: 2007/07/18 16:46:13, Link
Author: JAM
Quote (Paul Nelson @ July 18 2007,07:37)
Funny thing about the reptile-mammal illustration comparison, which Afarensis and other find puzzling and irrelevant.  Several people who did not know that the fossils were being scaled (without their knowledge), to make the morphological transition appear smoother, have told me they regard this practice as objectionable.

Why weren't we shown just how different in size these groups were? they ask.

Because changes in size aren't a big deal genetically:

http://www.sciencemag.org/cgi/content/abstract/316/5821/112

Do you have some data that suggest that size changes are a big deal?

Oh, I forgot--you produce no data, because you're lack sufficient faith to test your hypotheses. Instead, you just spin the data of others.

Date: 2007/07/18 17:02:44, Link
Author: JAM
Quote (VMartin @ July 18 2007,14:47)
Jam
   
Quote

Many of them. Are you denying that such events have ever occurred? If so, how much are you willing to bet on your certainty?

Get this through your thick skull--"random" is only wrt fitness. Your incoherent use of the adjective makes you look stupid.

If anyone here looks stupid it's you. Random mutation is random whatever effect it has on fitness.

Mutations don't occur at random locations or in random directions.

Why are you afraid to bet? 
 
Quote
No. Our ancestors called them dogs and they knew nothing about "common ancestor". We call them dogs because they are the same species. It is very simple.

Very simply, our ancestors had dogs long before the English language existed.
 
Quote
 
Quote
JAM: If you dumped 100 St. Bernards and 100 Chihuahuas on a large island with no other canids, would they ever interbreed? Could they interbreed?

Haven't we already met the major criterion for speciation?

Do you  mean that St. Bernards on a large island
with no other canids will be the same race  St.Bernards also after 200 generation?

No, I asked if they would interbreed. Do you not understand what the word means? If so, just ask, instead of stupidly pretending that I had asked you a completely different question.

Date: 2007/07/18 17:40:41, Link
Author: JAM
Quote (Paul Nelson @ July 18 2007,07:42)
By "actual size," I mean on the same relative scale.

That's not what "actual size" means at all.

If you're going to write your posts in English, "actual size" means "actual size," not "on the same scale."

Writing "on the same relative scale" is mind-numbingly redundant. What do you think "scale" means?

If you can't master these simple terms, why are you writing a textbook? If you're a Christian, why can't you simply admit that you were wrong?

"The process of teaching science requires a precise, unambiguous use of language ... "

Do you remember where that quote is printed, Paul?

Date: 2007/07/18 18:21:50, Link
Author: JAM
Re quotation #24,

The second and third quotations aren't in the cited paper. In fact, this very cool paper supports a hypothesis that provides an explanation for the rapid evolution of the turtle's shell, directly contradicting the apparently manufactured quote:

"The recognition of a simple developmental mechanism, namely an epithelial-mesenchymal interaction, at the initiation of carapace development provides a basis for hypotheses about the rapid evolution of this body plan (Burke 1989b).

Burke, A. C. 1989b. Development of the turtle carapace: implications for
the evolution of a novel bauplan. J. Morphol. 199: 363–378.

Note also that the authors hypothesize which proteins are involved, which inductive relationships between tissues are involved, etc.

Clearly, this is another lie by omission, possibly compounded by lies of commission.

Date: 2007/07/19 16:41:41, Link
Author: JAM
Quote (stevestory @ July 18 2007,23:48)
I'm always on the lookout for new creationists to entice here, so I took a look at that Jason guy from The Sci Phi Show. But he's such a dumbass that I'm not inviting him here.

I've corresponded with him by Email. He's got a veneer of civility about him, but underneath, it's same ol' same ol'. He claimed that programming languages fit in a single nested hierarchy, and then tried to move the goalposts and pretend that the challenge was merely to show some designed things that had evolved. It's pretty sad when a computer jock has to pretend that he doesn't understand the meaning of "nested."
 
Quote
I don't want another FtK. I'm trying to find some creationists with brains. We need a good workout. Semi-conscious punching bags aren't very useful.

May I suggest a non-creationist, then?

Date: 2007/07/20 17:20:16, Link
Author: JAM
Quote (Paul Nelson @ July 20 2007,09:54)
The accurate representation of data is important, especially when most students will never see the actual fossils in question.

JAM, can you say which quotes from the box "Coming Out of Their Shell?" you find objectionable, and why?

All of them. Quoting instead of presenting the data is inherently dishonest, and you know it. How can anyone be so dishonest as to not see the hypocritical contrast between your statement to Afarensis, immediately followed by your attempt to defend your avoidance of representation of data in favor of quotes?

Is quoting an "accurate representation of data," Paul? Why is it that real scientists don't generally do it, and you fake scientists do it all the time?
     
Quote
Also, Burke's data were interpreted by Rieppel (2001) as disproving the "correlated progression" model for turtle evolution, advanced by Kemp and others.

So what? The bottom line is the accurate representation of the data, and you run away from that in the most cowardly way. Your intent is clearly to deceive.
     
Quote
Rieppel writes:

Why not show the students the data, Paul? The  Alcian-blue and Alizarin-red pictures from Figure 3 alone would demolish any doubt that the shell was derived from existing structures.
     
Quote
For his part, Kemp responds:

Selective quoting is inherently dishonest. Show the students the data. What are you afraid of?
     
Quote
[Correlated progression] stands in contrast to an alternative view of the origin of turtles, expressed most recently by Rieppel (2001 [citing Burke]), that the rib-vertebrae-carapace-limb complex is too radically different from the ancestral amniote condition to have evolved gradually, but must have resulted from a macromutational event caused by a radical change in early development.  The difficulty with Rieppel's hypothesis is that it must account for how this sudden developmental change also caused what must have been simultaneous, but functionally integrated

Wow. "Functionally integrated" is definitely not a term I'd use to describe a turtle!
   
Quote
... shifts in many other traits, notably the musculature, limb function, central neural control of locomotion, ventilation mechanism, dietary shift away from faunivory and so on: it is unrealistic in the extreme that any single macromutation could have such a comprehensive effect.

I don't find it unrealistic at all, but then, I've seen some pretty comprehensive effects of single mutations on skeletal morphogenesis. Have you looked at any of those data? Why don't you quote the predictions of which morphogenetically-important proteins will be involved from the Burke paper? Is it because you're too chicken to make a testable prediction yourself?

I know that you are renowned for your avoidance of simple questions, so here's another: why do real scientists cite data, but you choose to quote bits and pieces of interpretation? What would your target audience think if they saw Figure 3 of the Burke paper instead of your chosen quotes?

If you think my questions are unfair, what proportion of my own publications would you bet contain quotations?

Can I get the same bet as Lenny proposed?

Date: 2007/07/20 20:32:11, Link
Author: JAM
Quote (ck1 @ July 20 2007,20:05)
Quote (Hermagoras @ July 20 2007,17:59)
Many of my undergraduate students were trained to cite in Freshman English classes, usually taught in English departments, where the rule is to cite via quotation.  This is a humanities model that is actually disabling in scientific education.  Students in scientific writing classes have to learn that scientists almost never quote (a few exceptions are almost always found in complex and anomalous articles such as, say, Gould and Lewontin's "Spandrel's" essay).  

Yes.  It is actually jarring to come across a direct quote in a technical paper, so rarely is this device used.

It's just as jarring to come across this device in a textbook.

Quote-mining also is a favorite of the equally corrupt animal-rights movement.

Date: 2007/07/23 16:34:02, Link
Author: JAM
Quote (JAM @ July 18 2007,18:21)
Re quotation #24,

The second and third quotations aren't in the cited paper. In fact, this very cool paper supports a hypothesis that provides an explanation for the rapid evolution of the turtle's shell, directly contradicting the apparently manufactured quote:

"The recognition of a simple developmental mechanism, namely an epithelial-mesenchymal interaction, at the initiation of carapace development provides a basis for hypotheses about the rapid evolution of this body plan (Burke 1989b).

Burke, A. C. 1989b. Development of the turtle carapace: implications for
the evolution of a novel bauplan. J. Morphol. 199: 363–378.

Note also that the authors hypothesize which proteins are involved, which inductive relationships between tissues are involved, etc.

Clearly, this is another lie by omission, possibly compounded by lies of commission.

Wesley,

You should update your description of the turtle quotations from page 24, because it doesn't include the second paper that they quote-mined:

How the Turtle Forms its Shell: A Paracrine
Hypothesis of Carapace Formation
JUDITH CEBRA-THOMAS et al.
JOURNAL OF EXPERIMENTAL ZOOLOGY (MOL DEV EVOL) 304B:558–569 (2005)

They are still being completely dishonest, however. Here are the partial quotes from that second paper:
 
Quote
Because "the distinctive morphology of the turtle appears to have arisen suddenly," Gilbert and his colleagues argue that evolution needs "to explain the rapid origin of the turtle carapace [shell]."


The first in context:
 
Quote
This reptile [Proganochelys] had the characteristic derived trunk morphology now associated with turtles. Thus, the distinctive morphology of the turtle appears to have arisen suddenly. We can propose a hypothesis that may explain at least part of how this might happen. The key innovation is to getting the ribs into the dermis. Once there,
variation in the population might enable some individuals to use this heterotopic placement of ribs to form a shell. If they could form a positive feedback loop between the rib and the CR (e.g., through Fgf10 and Fgf8), they could co-ordinate rib and carapace growth. When the ribs undergo normal endochodral ossification, the BMPs would induce the costal bones that form the plate of the carapace. (This may involve overpowering natural inhibitors of BMPs that are secreted by the dermis.) This mechanism, wherein the displacement of a tissue allows it to induce structures at new locations, has been proposed by Brylski and Hall (’88) to account for the rapid emergence of the fur-lined cheek pouches of pocket gophers. The compatibility of our findings with those of the
turtle fossil record has been noted by paleontologists (Rieppel, ’01).


The second in context:
 
Quote
These observations indicate that the ribs act as initiation centers for the dermal ossification of costal bones. The ossifying regions of the dermis extend towards one another to eventually fuse. The data reported in the present report confirm and extend these observations and permit us to frame a hypothesis to explain the rapid origin of the turtle carapace.


There's nothing resembling the context added by Paul and his lying colleagues, and omitting the detailed explanations offered is completely dishonest and deceptive.

Date: 2007/07/23 17:01:22, Link
Author: JAM
Quote (Paul Nelson @ July 23 2007,14:57)
One quick reply, about the use of quotations in scientific writing.  I agree that quoted material occurs very rarely in primary research publications.  Quotes occur frequently in science books, however: take a look, for instance, at Gould's The Structure of Evolutionary Theory, or Dawkins's The Ancestor's Tale.

Are they used in lieu of evidence, as you use them in your textbook? As Albatrossity noted, you are obfuscating when you use the category "science books," because the only relevant category is textbooks.

Quote
P.S. to Lenny and JAM: if you can specify terms, with a dollar cap of $1,000 and some practical way to set up an escrow account where both parties' money will be on deposit, your bet sounds very attractive.  But let's see precise terms.

Set away, Paul. Lenny and I clearly are at least $100 ahead, because the turtle box in EE is a retread of the deception marketed here:

http://www.discovery.org/scripts....id=1127

Contrast the DI lie below with the quotes from the papers above, which at least one of you had to have read to have quoted.
 
Quote
(Neither Rieppel nor Gilbert and colleagues, however, provide a detailed model of this rapid evolutionary transition, but rather refer to the need for further research.)

Date: 2007/07/23 18:05:03, Link
Author: JAM
Quote (Wesley R. Elsberry @ July 23 2007,17:21)
Quote

You should update your description of the turtle quotations from page 24, because it doesn't include the second paper that they quote-mined


I didn't include that reference because they didn't actually offer anything that was supposed to be a quote from it. At least, I didn't see anything quoted as if representing that paper.

Sorry for not being more clear. The asterisks in EE indicate which paper is being quote-mined. The second and third quotations are from the second paper cited.

You should edit the page you wrote--if you'd like, I'll do it.

Date: 2007/07/24 13:14:41, Link
Author: JAM
Wesley,

I think that it would be more clear if each item in your list started with:

*Misrepresentation by...

instead of "misquotation."

Date: 2007/07/24 14:47:04, Link
Author: JAM
Quote (Wesley R. Elsberry @ July 24 2007,14:24)
Those would be good things to track. I think two so far also have been in the TOA QMP.

Lenny,

Who's your favorite yacht dealer?

Date: 2007/07/25 00:45:52, Link
Author: JAM
Quote (RedDot @ July 24 2007,22:25)
Proteins, as they are used in living cells, cannot form from simple amino acids (without help from a skilled organic chemist).

So this is all a fraud?
http://www.sigmaaldrich.com/Brands....is.html

Quote
An amino acid: (1) is at a lower energy state than even a polypeptide (2) has water that must be removed carefully (it just can't be "boiled" off)

I'm sure that Sigma doesn't do that in their syntheses. Boiling is very bad for every protein but ribonuclease.
Quote
and (3) when actually joined together in simple polypeptides, do not have the correct shape (tertiary structure) which would allow it to do anything useful. These facts are not in debate in any Organic Chemistry class.

No, because most of your "facts" are dead wrong.
Quote
There have been several experimental attempts to create proteins from amino acids.

Sigma-Aldrich synthesizes proteins to spec thousands of times, not just "several" times.
Quote
Most add energy in the way of UV or electromagnetic discharge, and then attempt to remove water through a process of drying in between clay "sheets".

Most do neither. Most use solid-phase synthesis in the opposite order from the ones living things use.
Quote
All fail miserably. Nothing but useless, random, polypeptide chains.

If you are correct, why do all these companies synthesize specific sequences and guarantee the results?
http://tinyurl.com/2ydohy

Date: 2007/07/25 16:30:25, Link
Author: JAM
There's some semi-articulate ones here:

http://www.amazon.com/tag....sDetail

and here:

http://www.amazon.com/tag....sDetail

and a wacko who blames "Social Darwinism" on Darwin here:

http://www.amazon.com/tag....sDetail

Date: 2007/07/25 17:25:40, Link
Author: JAM
stephen, ask questions. It's more fun that way.

Date: 2007/07/25 18:54:40, Link
Author: JAM
Quote ("Rev Dr" Lenny Flank @ July 25 2007,17:27)
The typical UDers like Joey are, of course, utterly oblivious, and simply can't shut their mouths.

And that, of course, is why ID will never win in court.

Do you mean Joe G or the far more articulate Joey Campana?

Has anyone invited Campana over here?

Date: 2007/07/26 16:17:08, Link
Author: JAM
Quote (Erasmus @ FCD,July 26 2007,15:37)
[excuses self from room]

To do what, exactly? Wait...I don't want to hear the answer.

Date: 2007/07/28 14:19:02, Link
Author: JAM
Quote (Hermagoras @ July 28 2007,11:13)
If Dembksi does play piano, it's hard to imagine him as a bluesman.  I tend to think ID's engineering/math/piano/chess software personality profile is classical in a tightly wound, mildly autistic sort of way.  For Dembski to play blues piano he'd have to embrace at least some elements of an improvisational tradition, which would open him up to (gasp!) chance.  So I don't see that happening.

As someone who loves to play the blues, I'm not sure you're being fair. First, the bobbing and weaving required to promote ID requires considerable improvisational skills, and ID itself is a wild improvisation only loosely based on science.

Second, the blues, despite involving improvisation, is otherwise one of the most highly structured musical genres.

I see Dembski playing a lousy, original blues lick for 36 bars straight while the crowd (if any) groans in pain, while he desperately hopes that repetition will make them embrace his creation.

Date: 2007/07/29 01:25:24, Link
Author: JAM
Quote (Hermagoras @ July 28 2007,15:30)
Woke up early this morning / and it occurred to me
Yes, woke up bright and early / and it occurred to me
Ain't nobody can define / specified complexity

I got followers by the dozen / O we're a tight-knit bunch
Ban the mockers when I find them / or when Springer has a hunch
They buy my books and feed me / at least I get a free lunch

I like it, but I to make it work, you need to sing it as far behind the beat as you can stand, and then some.

Can I get some songwriting credit if I add the chords?  :D

Date: 2007/08/01 09:33:53, Link
Author: JAM
If things fall apart at Sal's place, I think I've got a live one here:

http://triablogue.blogspot.com/2007/07/in-search-of-evolution.html

Date: 2007/08/01 12:46:50, Link
Author: JAM
Quote (J-Dog @ Aug. 01 2007,10:43)
 
Quote (JAM @ Aug. 01 2007,09:33)
If things fall apart at Sal's place, I think I've got a live one here:

http://triablogue.blogspot.com/2007/07/in-search-of-evolution.html

JAM - Excellent catch - How and where did you find these nuts?  Did you just google "nut-jobs"?

Inquiring minds want to know!

I found it because Bradford of TT linked to it on his own blog. This guy is hysterically funny, yet articulate--check out his justification for using the term "female drones."

It's a special brand of tard.

Date: 2007/08/01 14:22:53, Link
Author: JAM
Quote (Rob @ Aug. 01 2007,13:12)
In his debate with Professor Olofsson, kairosfocus comes across as much more knowledgeable than most of Dembski's defenders, but he still manages to fall for Dembski's specious rhetoric... It would be interesting to talk with him outside of the UD cloister.

Really?

Try reading 3 of his comments and see if you're feeling as charitable. Sitting next to kairosfocus on a transcontinental flight would unquestionably lead to severe nausea, if not self-perforation of my eardrums with one of those plastic airline knives.

Date: 2007/08/01 14:47:39, Link
Author: JAM
OK, Rob, but you had me worried there.

Date: 2007/08/02 01:00:57, Link
Author: JAM
Quote (RedDot @ Aug. 01 2007,22:36)
The ToE demands that proteins can form naturally and spontaneously.

No it doesn't. Modern evolutionary theories have nothing to do with your "tornado in a junkyard" BS, and the current best hypothesis for abiogenesis doesn't either.
 
Quote
Your post does nothing but prove my point.  It takes very skilled biochemists, energy, and equipment to build these molecules, they will not just spring out of a petri dish.

You don't know what you're talking about. It only takes equipment. I suspect that my requested sequence goes right from the Web form into the synthesizer without human interaction. The person running the synthesizer doesn't need to be a "very skilled biochemist" at all.
 
Quote
BTW, how many of Sigm-Aldrich's products are actual functional proteins (not merely peptides or enzymes)?

I'll presume that you just mean the peptide synthesis group, as S-A makes thousands of chemicals.

That being said, your question makes no sense at all, as virtually all enzymes are actual functional proteins. Would you mind rephrasing it in understandable language?
 
Quote
How many of their products use only L-isomers of amino acids?
Virtually all of their peptides do. I suspect that including D-isomers would cost extra. Are you aware that some peptides made by living things contain D isomers?
 
Quote
That's why I put "boiled" in quotation marks.  I'm aiming for the cheap seats so do not make the mistake of assuming I am uninformed when I use rough analogies.

Don't bother aiming for the cheap seats. Arguments by analogy are nearly always vapid, while in the real world, we scientists use analogies merely as explanatory devices.

And I don't have to assume that you are uninformed, because you proved that you were when you claimed that evolutionary theory requires proteins first.

Date: 2007/08/02 09:57:36, Link
Author: JAM
Quote (k.e @ Aug. 02 2007,08:18)
Quote (djmullen @ Aug. 02 2007,08:59)
Freudian Slip Department:

http://www.uncommondescent.com/intelli....-128712

kairosfocus

07/22/2007

6:25 am
PPS: I think Mr O’Leary’s take here will also be helpful.

Well that would explain why kairosfocus is so OCD fastidious on irrelevant detail and still thinks he's the ducks nuts. He’s gay.

edit added.....hmmmm could he be GOP?

I'm pretty sure he's a Bajan.

Date: 2007/08/03 12:00:57, Link
Author: JAM
Quote (Erasmus, FCD @ Aug. 03 2007,10:54)
Is it just me or does Colbert seem to know the fallacy behind the mousetrap analogy?  It's hard to tell with his character and what-all but he seemed more non-plussed than usual.

Colbert clearly knows. He spewed Behe's talking points in a way that made them look ridiculous.

Date: 2007/08/06 09:20:38, Link
Author: JAM
Quote (RedDot @ Aug. 06 2007,00:06)
These are typical results found in the lab.

If those are typical results, why didn't you simply cite some real results instead of writing half a page of gobbledygook?

Date: 2007/08/06 09:23:37, Link
Author: JAM
Quote (RedDot @ Aug. 05 2007,21:52)
Mix amino acids in a test tube, add some heat, or light, or electricity, spin it, dry it, and pretty much the only thing that you will have in your test tube at the end of the day is useless goo.

Um, RD, if you'd ever done anything with amino acids or proteins, you'd know that proteins are gooey, while amino acids aren't.

Date: 2007/08/06 13:52:03, Link
Author: JAM
Quote (RedDot @ Aug. 05 2007,21:16)
I know of no mutation that can occur in multi-cellular organisms, which is capable of adding novel information which can be passed down to future generations.

Yet Lenny just asked you to explain such a case. We know the significance of the information encoded by the major histocompatibility complex, and as Lenny pointed out, given your assumptions, most of those alleles had to have arisen since the flood.
Quote
Certainly no single-point mutation can do this.

How can you possibly be certain if you can't address Lenny's point at all?
Quote
To be sure, they can provide genomic changes in a population,

Genomic changes occur in genomes, not populations.
Quote
... most either deleterious or neutral, but no new structures.

MHC alleles don't code for proteins with different structures? How are differences in the products of the MHC recognized, then? Isn't there an entire friggin' field of study associated with this, and you're going to claim that it's all wrong because it contradicts your wishful thinking? Do you even know what field I'm talking about wrt the MHC and its huge medical importance?
Quote
The single-point mutations which have conferred some measure of improvement when faced with a particular environmental pressure always seem to turn out to be deleterious when the environmental pressure is removed (blind cave fish for example).

A simple note about intellectual honesty, RD. A single example NEVER supports a claim of "always."
Quote
Gene duplication does not add novel information, and is also usually bad for the organism (Huntington's desease is a good example).

RD, Huntington's has NOTHING to do with gene duplications. Its underlying mechanism is CAG triplet expansion.
Quote
Insertion mutations (from say a virus), phase shifts, or gene migration are the only way a chunk of new (to the organism) information can enter a genome, but so far as I know, that happens in single celled organisms or some parasites.

My God, RD, why can't you just muster the integrity to admit you don't know about something? Cancer biology, in both humans and other animals, is filled with such events. They are documented to occur in real time.
Quote
I believe that some insects have had experiments done on them which forced phase shifts, but I can't put my hand on that paper right now for the details.

Of course you can't--you've never read the primary scientific literature.
Quote
I'm also fairly sure that when insertion mutations, or gene migrations happen in a single-celled organism, other information is discarded, resulting in at least a zero-sum gain to the overall base pair count.  However, these experiments are ongoing, so I could be wrong there.

You are utterly, completely wrong. You don't need to look at model systems, as these things are studied in humans.
Quote
To answer your question in a nutshell, I do not believe that Darwinian mechanisms can produce novel genetic information in a macroscopic organism which can be passed down to the next generation.

The real answer is that you will be aggressively ignorant and even fabricate data to support your preconceptions. Is that how the Bible teaches Christians to judge others? What does your Bible say about using hearsay to judge?

Date: 2007/08/06 13:54:22, Link
Author: JAM
Quote (RedDot @ Aug. 06 2007,11:22)
Quote (JAM @ Aug. 06 2007,09:23)
 
Quote (RedDot @ Aug. 05 2007,21:52)
Mix amino acids in a test tube, add some heat, or light, or electricity, spin it, dry it, and pretty much the only thing that you will have in your test tube at the end of the day is useless goo.

Um, RD, if you'd ever done anything with amino acids or proteins, you'd know that proteins are gooey, while amino acids aren't.

So are polypeptides...which is my point.

No, that wasn't your point. Besides, all proteins are polypeptides.

Answer me this: if you can't identify 10 biological proteins that are soluble in physiological saline, do you conclude that protein-protein interactions are rare or unavoidable?

Date: 2007/08/06 13:59:37, Link
Author: JAM
Quote (RedDot @ Aug. 05 2007,21:52)

Proteins and enzymes are not simply polymers of amino acids - that is only half the story.  They are highly specialized, massively built, and precisely folded polymers of amino acids.

Two points:

1) How much real confidence do you have in your grasp of the basics? How much are you willing to bet that ALL enzymes (catalytic macromolecules) are proteins? I'll bet my house. And you?

2) ID/creation folk are fond of claiming that functional protein sequences are rare in "sequence space." Do you agree?

Date: 2007/08/06 14:06:24, Link
Author: JAM
Quote (RedDot @ Aug. 06 2007,11:48)
Creation scientists have alot of catching up to do, and since govenment grants are hard to come by for Creation Research, that means we all need second jobs.

You're bearing false witness. There are plenty of real scientists who produce real data from grants that don't come from the government. There are plenty of rich fundies around to give money. The DI has plenty of money. 

Quote
It's a numbers game gentlemen, you outnumber us by at least 100 to 1.

In science, that doesn't matter if you're right. What matters is if you produce new data, and in that respect our data are infinitely more than yours, as you have produced zero. Having second jobs and not having govt grants is no excuse for ZERO scientific productivity, especially given the mountains of apologetics and PR produced by your movement.

You're not willing to do science at all. You're afraid to do real science, because in whatever dank place you call your "soul," you lack the faith to put a single ID or creationist hypothesis to the test. That means producing real data from real predictions, not spinning anyone else's data.

Date: 2007/08/15 12:37:18, Link
Author: JAM
To make it more accurate:

ID

1) Someone else found X
2) Claim that ID predicted X
3) Refuse to offer any real predictions about anything else

Date: 2007/08/22 15:55:59, Link
Author: JAM
If you're in the mood for a massive helping of cognitive dissonance, there's some great tard from Willy Bradford up at Telic Thoughts.

Date: 2007/08/22 16:29:09, Link
Author: JAM
Quote (Richardthughes @ Aug. 22 2007,16:16)
?We?re not saying that the designer is God, just someone with the same skill-set.? - Jon Stewart.

Say, did Dembski ever explain how the scrotum is intelligently designed? That, IMHO, was Stewart's best question to him.

Date: 2007/08/24 18:28:41, Link
Author: JAM
A thick slab of tard from one of the UD commenters (Charles Foljambe) from that thread here:

He's all over any comments, too:

This could be fun!

Date: 2007/08/27 15:33:28, Link
Author: JAM
Quote (carlsonjok @ Aug. 27 2007,15:24)
Quote (Hermagoras @ Aug. 27 2007,15:16)
Quote (blipey @ Aug. 27 2007,15:08)
Joe is the Maytag Man. ?The Frigidaire Biologist. ?The Astrophysicist of the Deep Freeze. ?The Kitchen Muslim....

Really? ? He's a repairman? ?Fantastic.

Well, sure, in a manner. He works for General Electric, which does makes consumer appliances. ?They also make jet engines, railroad locomotives, medical imaging equipment, and desalination plants to name a few.

Has Joe actually stated what he does service?

I'm guessing the plumbing in the restrooms.

Date: 2007/08/30 15:47:33, Link
Author: JAM
Quote (Richardthughes @ Aug. 30 2007,15:44)
"Lit bluffing" seems to come from Dover where they dropped umpteen articles about evolution of the immune system on a table and asked "expert" behe if he'd read them..

http://www.talkorigins.org/faqs/dover/day12pm.html

Of course, one would actually have to have read the literature before knowing whether someone else citing it was bluffing...

Date: 2007/09/04 01:12:19, Link
Author: JAM
Quote (Bob O'H @ Sep. 04 2007,00:47)
One for those in academia:

...For those of you stuck in the real world, a post-doc is someone who has just got their PhD, and is still considered junior - they can't officially supervise PhD students for example. ?A senior research scientist is at least one step above in the ladder.

I was initially amused that Dembski was prepared to take a demotion, but it looks as if he wasn't, even if administratively that's what was happening.

I don't know that it's above in the ladder, more like different ladders. A postdoc is a trainee with a fellowship and stipend who is expected to move on in 2-5 years, but a senior research scientist is generally an employee with a salary and no term limit.

Date: 2007/09/07 09:09:08, Link
Author: JAM
There's some great new tard from PaV at ERV's blog. He's now retreated to claiming that there's some huge difference in the difficulty of evolving heteromultimers that doesn't apply to homomultimers.

Date: 2007/09/10 13:45:16, Link
Author: JAM
Quote (Rob @ Sep. 10 2007,12:27)
 
Quote (slpage @ Sep. 09 2007,14:49)
A coward at heart.

Here's another tale of Brave Sir Joe:

...Joe's responded with, "BTW I would love to bet you but I can only wager with honest people."


Wagers are the key. They demonstrate that on some cognitive level below the telencephalon, all of these people know that they are lying, and have nothing resembling faith in their position.

We all should use this technique more often.

Date: 2007/09/20 17:43:43, Link
Author: JAM
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?

Date: 2007/09/22 19:09:32, Link
Author: JAM
Quote (stevestory @ Sep. 22 2007,17:22)
I haven't read much Telic Thoughts. The contributors there seem pretty diverse. So far, all I can tell is Mike Gene has at least some brains, and Bradford is an idiot.

And Joy is insane.

Date: 2007/09/22 21:05:38, Link
Author: JAM
Quote (Daniel Smith @ Sep. 22 2007,04:11)
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.

Yes, really. In the first book, he treats the reader to such dishonest misrepresentations as a "purely random process of natural selection," as well as the somewhat more sublime idiocy of his failure to understand basic taxonomic relationships, as well as the idea that conserved amino-acid residues represent functional constraints, in his laughable centerpiece of cytochrome sequences.
Quote
In the second book, he starts to give us his own alternative: a designed universe and directed evolution.

I see no conflict.

That's predictable. Do you see any evidence? I'm struck by the mind-boggling conflict between your claim to be interested in evidence, while simultaneously conflating evidence with opinion.

Have you ever read a paper from the primary biological literature--you know, those ones that have new data in them?

Has Denton ever published any data? If not, why not?

Date: 2007/09/23 10:19:17, Link
Author: JAM
Quote (J. O'Donnell @ Sep. 23 2007,04:33)
It's completely unfair to compare TT to UD, as TT has intelligent discussions on their site, doesn't suppress comments from those who disagree with them...

You are incorrect on that count.

Date: 2007/09/23 10:23:32, Link
Author: JAM
Quote (Thought Provoker @ Sep. 22 2007,23:34)
Hi Jam,

You wrote...
     
Quote
And Joy is insane.


Is that a problem for you? :D


It's simply an observation. Joy routinely makes false claims to support her positions, and when her claims have been shown to be false, claims her positions to be supported anyway.

Quote
Joy is the reason I have stuck around for a year.


You have my sympathies.

Quote
She is very knowledgable and provides substantial, thought-provoking challenges.


She is not knowledgable at all in the field of biology, TP.

Quote
You might also find her political leanings surprising.  (let's just say she has never been a big fan of our current president).

Not at all. That doesn't mean that she's not insane. Her support of the lies of the animal-rights movement is not surprising, either.

Date: 2007/09/23 10:31:06, Link
Author: JAM
Quote (Daniel Smith @ Sep. 23 2007,04:14)
Quote (JAM @ Sep. 22 2007,21:05)
Has Denton ever published any data?


Have a look.


No data that pertain to his two books. Why is that, Daniel? If he has any real passion about the subject(s) of his two books, why not test their assumptions, such as his idiotic assumption that conservation of a residue represents a functional constraint?

Quote
Have you?

Of course, and in better journals to boot. More pertinently, I've published more data relevnt to Denton's assumptions than he has. Why is that?

Date: 2007/09/23 10:37:50, Link
Author: JAM
Quote (Daniel Smith @ Sep. 22 2007,22:04)
 
Quote (Wesley R. Elsberry @ Sep. 22 2007,17:13)
...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".  

But that's a book, not the primary literature. Were you deliberately misleading us when you claimed to be interested in evidence?
Quote
I'm pretty sure Schindewolf qualifies as an "actual paleontologist".

But the opinions of an actual paleontologist aren't actual evidence.  
Quote
Did you read the quotes I supplied from that book in any of my posts so far?

But quotes aren't evidence, either.

You didn't answer my other pointed question: have you ever read a paper from the PRIMARY literature? I mean those papers with actual, new data in them--we real scientists often read them by looking at the figures and tables, because unlike you, we value evidence over opinion.

Date: 2007/09/23 10:43:21, Link
Author: JAM
Quote (Daniel Smith @ Sep. 23 2007,04:22)
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.

Then you have no basis for claiming that the incomplete nature of the fossil record represents a problem for modern evolutionary theory. 

I suggest that you look for the relevant evidence. Here's a place to start: passenger pigeons used to be common, now they are extinct. Has anyone ever found a fossilized one?

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

You'd have to know the answer, as well as the answer to oldman's question, to come to the conclusion you've already asserted.

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

Are they more "resistant"? How would the concept of "resistance" work anyway, since the issue is one of sampling?

Date: 2007/09/23 11:26:27, Link
Author: JAM
Quote (Thought Provoker @ Sep. 23 2007,10:20)
MikeGene's rabbit threads are available to open discussions.

False.
 
Quote
If someone wants to ask her something, there is a recent rabbit thread available that anyone can use.

False again.
 
Quote
from the peer reviewed paper  Orchestrated Objective Reduction of Quantum Coherence in Brain Microtubules: The "Orch OR" Model for Consciousness

Tell me, TP, what is the factual basis for your confident assertion that this paper was peer-reviewed?

Date: 2007/09/23 11:33:58, Link
Author: JAM
Quote (Thought Provoker @ Sep. 23 2007,10:46)

I agree, Joy's expertise appears to be more in understanding physics as opposed to biology.

With the emphasis on "appears." Given her rank dishonesty about biological subjects, I suspect that she's just as dishonest and/or deluded about physics.
Quote
What she brings to the table is the thought that it may be time to quit treating the different scientific disciplines as separate.  Biologists can't continue to ignore General Relativity and Quantum Mechanics.

Can you offer any evidence that would allow me to conclude that biologists do ignore these subjects? I certainly don't consider them separate.
Quote
This concept is what drives Sir Rodger Penrose.

1) How would you know what drives him?
2) If it doesn't drive him to test hypotheses, he's not very driven.
Quote
Combining General Relativity and Quantum Mechanics results in some interesting conclusions.

Science is about testing hypotheses, not about generating interesting conclusions.
Quote
While many people don't like the implications, Penrose's OR quantum interpretation is testable and is being tested.

Then point me to the data instead of his speculations.
Quote
Its implications to the study of consciousness is potentially very profound.

Potentially, yes. Probably, not at all.
Quote
Joy claims to be a “professional fool”.  Sometimes listening to fools allows you to think outside artificial barriers of thinking (“outside the box”).

Sometimes, but not this time.

Date: 2007/09/23 11:36:59, Link
Author: JAM
Quote (stevestory @ Sep. 23 2007,11:31)
JAM, have you been censored at TT? If so, under what conditions?

Severely. I've been banned three times, but TP keeps persisting in his fantasy that the folks at TT are tolerant.

Primarily, I've been banned for pointing out obvious ways to test their hypotheses. Most recently, I was banned for arguing with Sal about malaria.

Date: 2007/09/23 11:54:37, Link
Author: JAM
Quote (Thought Provoker @ Sep. 23 2007,10:20)
from the peer reviewed paper  Orchestrated Objective Reduction of Quantum Coherence in Brain Microtubules: The "Orch OR" Model for Consciousness

TP, let me explain some of the silliness in this paper:

   
Quote
Several types of studies suggest cytoskeletal involvement in cognition.

What Penrose omits is the fact that the evidence supporting the involvement of the ACTIN cytoskeleton is an order of magnitude greater than the evidence supporting the involvement of the MICROTUBULE cytoskeleton.

This alone trashes Penrose's credibility in my eyes.

   
Quote
For example long term potentiation (LTP) is a form of synaptic plasticity that serves as a model for learning and memory in mammalian hippocampal cortex. LTP requires MAP-2, a dendrite-specific, MT-crosslinking MAP which is dephosphorylated as a result of synaptic membrane receptor activation (e.g. Halpain and Greengard, 1990).

But what else does it require? Penrose doesn't say, and you aren't reading carefully enough to be skeptical.
   
Quote
In cat visual cortex, MAP-2 is dephosphorylated when visual stimulation occurs (Aoki and Siekevitz, 1985).

Is that a cause or an effect, TP? Is this provoking any thought in your head?
   
Quote
Auditory Pavlovian conditioning elevates temporal cortex MAP-2 activity in rats (Woolf et al, 1994). Phosphorylation/ dephosphorylation of MAP-2 accounts for a large proportion of brain biochemical energy consumption (e.g. Theurkauf and Vallee, 1983) and is involved in functions which include strengthening specific networks, such as potentiating excitatory synaptic pathways in rat hippocampus (Montoro et al, 1993).

This is trivial relative to the known roles of CaM kinase II, receptor phosphorylation, and receptor trafficking in LTP. Only the last of these (one of the things we study) is known to have any dependence on MTs, and the role of MTs and MAPs may still be constituitive.
Quote
The mechanism for regulating synaptic function appears related to rearrangement of MAP-2 connections on MTs (Bigot and Hunt, 1990; Friedrich, 1990)

Think, TP. "Appears related...," is sufficiently convincing to someone who has the audacity to call himself "Thought Provoker"?

I suggest that you read some LTP reviews from folks in the LTP field and look at the primary literature cited. Very little of it has to do with MTs or MAPs.

Date: 2007/09/23 12:48:49, Link
Author: JAM
Quote (Thought Provoker @ Sep. 23 2007,12:39)
Hi JAM,
You asked...
 
Quote

Tell me, TP, what is the factual basis for your confident assertion that this paper was peer-reviewed?

I may be wrong about this.  But this was included in the acknowledgement...
Quote
Citations to "This Volume"refer to Toward a Science of Consciousness, (1996) S Hameroff, A Kaszniak, A Scott (eds), MIT Press, Cambridge.

Also published in Mathematics and Computer Simulation 40:453-480, 1996

So what? Neither of those suggest that the paper was peer-reviewed.
Quote
And the paper has been very much reviewed, and criticized, by the likes of Tegmark, Grush and Churchland.

Oh, come on! That's not what "peer-reviewed" means, and you know it. "Peer-reviewed" means that it is reviewed by peers BEFORE publication, not after.
Quote
But like I said, I may be wrong.

You probably are. My question is, why would you make such a claim without evidence?
Quote
Maybe MIT Press and Mathematics and Computer Simulation are less particular than I gave them credit for.

That's just pathetic, TP. The point is that contributions to the secondary literature are rarely peer-reviewed, while those to the primary literature almost always are. I know that none of the reviews I have published were peer-reviewed.

Date: 2007/09/23 14:23:06, Link
Author: JAM
Quote (Thought Provoker @ Sep. 23 2007,13:55)
Hi JAM,

Dr. Hameroff provides an explanation for how the ACTIN in needed to support quantum isolation in microtubules.

Explanations aren't enough. Let's do real science, shall we?
 
Quote
I would be very interested in seeing a hypothesis on how actin can be a SOURCE of consciousness.

You won't get one from me, because it would still be silly, just less silly than hypothesizing that MTs are the source.

Perhaps I'm not being clear. I'm trying to explain to you that attributing the emergent property of consciousness to something as distinct as MTs is laughable.

Since the motile response of a single fibroblast to extracellular cues is an emergent property in which the roles of the actin and MT cytoskeletons are hopelessly intertwined, what reasonable person would assume that consciousness woud be so much simpler?

 
Quote
The time order of cause and effects gets very interesting when dealing with quantum mechanics.  Retrocausality is practically a given.

But dephosphorylation is not quantum mechanics, so you have no point. My point is that Penrose is pointing to things happening in the realm of MTs, while ignoring the much larger number of events that don't involve them. That's why the paper is a crock. You're trying to pretend that they are thinking on a less reductionist plane than I am, when the reality is that they are far more reductionist!
 
Quote
Libet's observation of the readiness potential for conscious actions brings provides support in considering consciousness is a retrocausual superposition of quantum states.

But none of that is relevant to an observation of dephosphorylation of a MAP.
 
Quote
Putting them together with the study of consciousness provides a lot of explanatory power for scientific observations like Libet's.

Reducing all these things to MTs is just laughable.
 
Quote
As to direct experimental results...  I recently found this...      
Quote
“In recent times the interest for quantum models of brain activity has rapidly grown. The Penrose-Hameroff model assumes that microtubules inside neurons are responsible for quantum computation inside brain. Several experiments seem to indicate that EPR-like correlations are possible at the biological level. In the past year , a very intensive experimental work about this subject has been done at DiBit Labs in Milan, Italy by our research group. Our experimental set-up is made by two separated and completely shielded basins where two parts of a common human DNA neuronal culture are monitored by EEG. Our main experimental result is that, under stimulation of one culture by means of a 630 nm laser beam at 300 ms, the cross-correlation between the two cultures grows up at maximum levels. Despite at this level of understanding it is impossible to tell if the origin of this non-locality is a genuine quantum effect, our experimental data seem to strongly suggest that biological systems present non-local properties not explainable by classical models."

The experiment has nothing at all to do with microtubules, TP. Therefore it doesn't even come close to testing a microtubule hypothesis.

Date: 2007/09/23 15:34:37, Link
Author: JAM
Quote (Zachriel @ Sep. 23 2007,15:31)
I never did find out why.

For pointing to data and offering ways to test hypotheses.

Date: 2007/09/23 22:19:29, Link
Author: JAM
Quote (Zachriel @ Sep. 23 2007,18:33)
Quote (Joy @ Sep. 23 2007,17:17)
JAM was banned from TT for bad behavior once over a year ago, and every time since then for deception.

Could you point to his original banning?

One would think that if I had been banned for bad behavior, the simplest way to demonstrate it would be to point the reader to my comment(s) that represented this behavior.

Date: 2007/09/24 10:58:47, Link
Author: JAM
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.

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.


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?

 
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.

 
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.

 
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?

Date: 2007/09/24 11:04:52, Link
Author: JAM
Quote (Art @ Sep. 23 2007,22:12)
But there's no reason to question her honesty - she really believes the stories she tells.

Art,

1) The hypothesis that she really believes that I was banned for "bad behavior" predicts that she will point to evidence of the behavior that she judged to be bad. We may not agree with her conclusion, but she shouldn't be reticent.

2) The hypothesis that she doesn't really believe that I was banned for "bad behavior" predicts that she won't point to any evidence, and continue to make vague accusations.

Date: 2007/09/24 13:14:01, Link
Author: JAM
Quote (Thought Provoker @ Sep. 24 2007,11:13)
Hi JAM,

I suggest the burdon of proof in this situation is yours.

I disagree.
Quote
Joy and MikeGene aren't any more capable of finding the comment(s) that caused the problem than you are.

Why not?
Quote
You indicated that you were banned three times.  MikeGene and Joy have offered explaination as to why they automatically enforced the ban on your two aliases.

But the ban wasn't enforced automatically, and their justification is entirely dependent on there being valid reasons for the first banning.
Quote
If you want to continue to try and make a case, then it is up to you to make it.  I already asked you once to provide a link to the first instance so I could judge for myself.  You have yet to do that.

I have no idea when or what that first instance was, TP, except that it occurred before I was banned. Can we agree that TT is not nearly as tolerant as you have repeatedly claimed them to be?

And what about microtubules? Are you grasping the absurdity of the extent of Penrose's reductionism? How can consciousness be reduced to microtubules, if a fibroblast's "decision" about which way to turn resists such reduction?

Why microtubules and not the actin cytoskeleton?

Do you realize how ridiculous a mention of "cytoskeletal microtubules" appears to anyone with the most rudimentary education in cell biology? Can you name an instance of non-cytoskeletal microtubules?

Date: 2007/09/24 15:15:26, Link
Author: JAM
Quote (Thought Provoker @ Sep. 24 2007,14:16)
Hi JAM,

I will deal with the politics first and then with the science in another comment.

You wrote...
   
Quote
I have no idea when or what that first instance was, TP, except that it occurred before I was banned. Can we agree that TT is not nearly as tolerant as you have repeatedly claimed them to be?

Actually, I have loudly questioned MikeGene about whether or not Telic Thoughts lives up to its About Us declaration multiple times.

Yes, but elsewhere, you have touted TT as tolerant.
 
Quote
I have even pointed out the biased treatment of the Smokey verses Bradford discussions.  I felt you two were opposite sides of the same coin.

What sort of coin?
 
Quote
Jam, it is obvious that you have a biased opinion of Telic Thoughts.  Based on your actions here, I would have to agree it would not be in Telic Thoughts best interest to reinstate your privileges.

So what? That seems obvious, since they seem to be far more interested in shield-bashing than in discussing science.
 
Quote
If you actually wanted to come back, you missed an opportunity.

What makes you think I wanted to come back?
 
Quote
It would have been relatively easy to convince me that you were unfairly treated if you tried.

What makes you think that I was trying to convince you?
 
Quote
Had you done that, I would have tried to make the case that Telic Thoughts could use more balanced discussions. Besides, I liked "Smokey".  I might have had a chance, but now, with the way you chose to approach this, I don't see how it would be remotely possible.

I don't think you would have had a chance.
 
Quote
As it is, it looks like the shield bashing games will continue.  After the Bar Closes will be smug in their presumption that ID proponents are arrogant and unreasonable.

It's not a presumption.
 
Quote
Oh well, I tried.

I'm not willing to be as obsequious as you are to the TT crowd. Let's do science!

Or do you have too much invested in this microtubule hypothesis to discuss it with someone who knows something about the neuronal cytoskeleton?

Date: 2007/09/24 16:02:54, Link
Author: JAM
Quote (Daniel Smith @ Sep. 24 2007,14:54)
It wasn't my quote so how could I be "mining" it?

Very easily.
 
Quote
 
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.

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.

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

Which is why you employ it as a straw man.
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.
Quote
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.
Quote
None.

Why not construct some trees, then, unless you weren't being truthful about your interest in evidence?
Quote
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?
Quote
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?
Quote
And I'm happy to discuss any evidence you want to discuss.

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.
Quote
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.
Quote
Quote
What part of this don't you understand?
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.
Quote
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?

Date: 2007/09/24 16:58:46, Link
Author: JAM
Quote (jeannot @ Sep. 24 2007,16:38)
Quote
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".

That's what I'm trying to do with the cannabinoid receptor paper.
Quote
For instance, why do all primates share a non-functional copy of a gene normally involved in the production of vitamin C? And why do the phylogeny of this useless pseudo-gene reflects phylogenies of coding regions?

That might be too complex, as well as getting into Daniel's likely misconceptions about pseudogenes and "junk" DNA.

Date: 2007/09/24 21:05:07, Link
Author: JAM
Quote (Thought Provoker @ Sep. 24 2007,20:23)
Hi Jam,

You asked...
     
Quote
Do you realize how ridiculous a mention of "cytoskeletal microtubules" appears to anyone with the most rudimentary education in cell biology? Can you name an instance of non-cytoskeletal microtubules?

Here is one of many hits I found using the term "cytoskeletal microtubules" in a google search.

It was from The Journal of Cell Biology where they were distinguishing cytoskeletal microtubules from flagellar microtubules.

In that context it is a meaningful distinction. However, neurons lack flagella, cilia, and mitotic spindles (the last of which is still the cytoskeleton IMO).

Are you trying to claim that Penrose was distinguishing anything from flagellar, ciliary, or spindle microtubules, or was he just adding extra polysyllabic words to his tome?

IMO, it's just part of an attempt to obfuscate his sloppy equivocation between the cytoskeleton and the microtubule cytoskeleton.

Again, changes in the actin cytoskeleton have been implicated in neuronal plasticity to a far greater degree than the microtubule cytoskeleton (including the transport of mRNAs encoding beta-actin and actin-binding proteins), yet Penrose ignores it. It seems to me as though he heard about MTs first and can't be bothered with anything more holistic, even though emergent properties involving both are involved in a fibroblast moving 5 microns on a plastic dish.

If that can't be reduced, how sensible is it to believe that consciousness can be reduced so much further?

Date: 2007/09/24 23:51:19, Link
Author: JAM
Quote (Thought Provoker @ Sep. 24 2007,22:05)
Hi Jam,

You ask...
   
Quote
Are you trying to claim that Penrose was distinguishing anything from flagellar, ciliary, or spindle microtubules, or was he just adding extra polysyllabic words to his tome?

IMO, it's just part of an attempt to obfuscate his sloppy equivocation between the cytoskeleton and the microtubule cytoskeleton.

It has been suggested that I am wasting my time here.  That may be true in your case, but on the chance that others are listening in I will continue.


What you quote only confirms the sloppy reductionism of both Hameroff and Penrose.
Quote
Disruption of intra-neuronal cytoskeletal structures impairs cognition, such as tangling of the tau MAP linking MTs in Alzheimer’s disease (Matsuyama and Jarvik, 1989, Iqbal and Grundke-Iqbal 2004).

This is an irresponsible case of stating hypothesis as fact. It's not yet known whether the plaques and NFTs of AD cause cognitive impairment or are the effects of a more subtle mechanism that causes cognitive problems. It's one of the major issues in AD research, and claiming that it is already solved is ludicrous.

Quote
Wherever cellular organization and intelligence are required, MTs are present and involved.

No quarrel there. You seem to have trouble understanding that presence and involvement don't justify reducing consciousness to MTs, just as knowing that MTs are involved in fibroblast motility doesn't justify a similar reduction.
Quote
Since Sherrington’s observation in 1957, the idea that the cytoskeleton—MTs in particular—may act as a cellular nervous system has occurred to many scientists.

I take issue with "in particular."
Quote
Here is a diagram and video showing microtubules appearing to actively orchestrate a cell dividing.

No, TP. MTs are involved and essential, but there's no evidence of orchestration. The movement is caused by motors.
Quote
Here is a video that makes a mockery of thinking of microtubles as passive cytoskeletal components.

Straw man, TP. I had hoped that you were more thoughtful than that. I'm not claiming that they are passive. I'm pointing out that there's no evidence to support the reductionist notion that it all (or even mostly) boils down to MTs.

TP, If I keep asking you this question:

If that [fibroblast motility] can't be reduced, how sensible is it to believe that consciousness can be reduced so much further?

...and you don't answer it, grossly misrepresenting my position instead, are you thinking about what I'm writing at all?

Date: 2007/09/25 00:07:50, Link
Author: JAM
Quote (Thought Provoker @ Sep. 24 2007,22:43)
Hi creeky belly,
YOU SCREWED UP!  LOOK AT THE LINK I PROVIDED.

Do you see the "m" in the first equation under the words "de Broglie relations"?

"m" stands for MASS!

...A tubulin dimer is 8 nm by 4 nm by 5 nm and weighs 55,000 daltons.

You and Hameroff screwed up. The Dalton (always capitalized) is a unit of mass, not weight.

Date: 2007/09/25 09:09:25, Link
Author: JAM
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.

Date: 2007/09/25 10:58:16, Link
Author: JAM
D: Big deal.  Things that are alike are built alike - even at the molecular level.

JAM: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.

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.
[quote][quote]Oh, and Daniel, no set of designed objects has these characteristics, so please save your lying for ignorant lay people.[/quote]
Lots of designed objects fit into nested hierarchies.[/quote]
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.
         
Quote
One could make a nested hierarchy for automobiles - starting with horse drawn carriages and branching out.

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.                            
Quote
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?

Probably because you have the appealing quality of massive arrogance, made even more appealing by massive ignorance.
Quote
Quote
Quote
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?

The ladder part. It's stupid. The equidistance is predicted.
Quote
Denton's last book supports directed evolution.

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

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.
Quote
Quote
Quote
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?

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?
                       
Quote
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.
 
Quote
 
Quote
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.
 
Quote
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. What do you conclude from these relationships? If CB2 was designed, when was it designed?
 
Quote
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?
                           
Quote
But I've reached no firm conclusion as of yet.

Read all the conclusions you advanced above.
 
Quote
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.

Date: 2007/09/26 09:45:44, Link
Author: JAM
[quote]   [quote]Please explain how Darwin was wrong when he predicted nested hierarchies, then.[/quote]
Can you supply that quote from Darwin?[/quote]
Already done. Please explain how his prediction was wrong.
       [quote]  [quote]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.
[/quote]
That's not true.[/quote]
     
Quote
 Most components can also be organized into nested hierarchies.

No, very few can. As Richard pointed out, many will be identical and others will be outsourced to other companies. We don't see either of those things in biology. We get (allowing for systematic and experimental errors) a single, identically-branching nested hierarchy when we look independently at either functional or nonfunctional differences.
       
Quote
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.

Then show us the data.
       
Quote
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.

Yes, but that isn't remotely close to showing that they and their components will fit into a single NH.
             
Quote
     
Quote

The ladder part. It's stupid. The equidistance is predicted.

Where did Denton assume a ladder?  I don't remember that part.

http://www.talkorigins.org/faqs/denton.html
Read the last half of part III.
     
Quote
Like I said, I'm willing to look at any and all evidence.  I'm less interested in opinions though.

Then why have you offered nothing but opinions?
     
Quote
     
Quote
 
Quote
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,    
Quote
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.
[quote]    
Quote
 
Quote
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

Then why do you go back on that below?
   
Quote
   
Quote

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.

Fossils aren't needed for this. This provides much more detail than fossils. And you can do both design and implementation. Just give me a date that explains the relationships between these sequences. MET explains this beautifully.
   
Quote
   
Quote
   
Quote

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.

My conclusions don't matter--what matters is whether your hypothesis can explain this evidence and make predictions about evidence you haven't seen yet.
   
Quote
I need to see the evidence for myself - I won't just take your word for it.

I'm showing you evidence and you are denying that it is evidence.     
   
Quote
The tree is theoretical in that it is just a graphic representation of a proposed relationship.

Daniel, now you're just lying. There is nothing theoretical about that tree; it simply shows the mathematical relationships between the sequences. It is evidence. So, my question is, what hypothesis do YOU advance that explains these relationships and predicts the relationship of other data to these data?
   
Quote
How do you know these genes are not convergent?

If they had converged, they wouldn't be predicted to have this mathematical relationship with each other. However, for you to understand that, you'd have to grasp the concept of NESTED hierarchy, and you clearly don't.

Again, MET explains this relationship and makes predictions about where new sequences will be placed--before we have them.

Your job is to propose a hypothesis. Instead, I predict that you will continue to falsely claim that these trees are theoretical.

Date: 2007/09/26 09:47:42, Link
Author: JAM
Quote (Wesley R. Elsberry @ Sep. 26 2007,09:44)
Quote

Common Design would predict that lungfish and trout would be closer to each other than to humans.


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

That's a much more lucid explanation than the TO page to which I pointed Daniel, thanks.

Date: 2007/09/26 15:52:35, Link
Author: JAM
Quote (Tracy P. Hamilton @ Sep. 26 2007,15:02)
Make a nested hierarchy of

Vega (1971, 1977)...
Be sure to tell us what it is based on:
safety equipment, engine design, number of doors, etc.

As a former owner of a '74, I would group the Vega with fecal matter in an evolutionary hierarchy based on a number of common characteristics. Of course, nothing can be grouped with the aluminum engine's legendary oil consumption. I still remember what I said after it was T-boned at an intersection: "God, I hope this thing is totaled."

Date: 2007/09/26 16:11:51, Link
Author: JAM
Quote (Thought Provoker @ Sep. 26 2007,15:22)
The point is that according to the Dembski's definitions what I have proposed is a "design" in the sense meant for purposes of considering it an ID hypothesis.

Also, according to his definition of "intelligence," natural selection is intelligent.

Date: 2007/09/26 16:16:38, Link
Author: JAM
Quote (Thought Provoker @ Sep. 26 2007,16:01)
I consider MikeGene to be an earnest ID Scientist even though he feels that ID isn’t yet qualified to be called “science.”

Baloney.

"Mike Gene" is scared to death of doing anything that remotely resembles the testing of a hypothesis, probably because it might ruin his book sales.

Earnest scientists set out to find the most stringent tests of their hypotheses, and then do them. If their hypotheses are wrong, new data are still generated.

Date: 2007/09/26 16:52:46, Link
Author: JAM
Quote (Thought Provoker @ Sep. 25 2007,09:55)
However, this has caused this thread to steer significantly off-topic (which, of course, happens all the time).

Hi TP,

Over on TT you claimed:
Quote
I can defend the Penrose-Hamerof hypothesis, in detail.


Then defend in detail, using actual data and citing the primary literature, their attribution of consciousness to microtubule properties instead of those of actin filaments.

Date: 2007/09/28 07:58:11, Link
Author: JAM
Quote (Daniel Smith @ Sep. 28 2007,02:38)
 
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.

The ones that survive and reproduce (survival isn't sufficient) will tend to be the ones that are less inbred, making the "gene pool" deeper. Your arrow is in the wrong direction.
 
Quote
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.

The loss of the more inbred breeds would enrich the gene pool, not deplete it.
 
Quote
Natural selection is a cold mistress.  It works by killing.

No, it works just as well be preventing reproduction. You can live to 150, but if you leave no children, your fitness is zero.
Quote
As Schindewolf said, "Selection is only a negative principle, an eliminator, and as such is trivial." (pg. 360)

You've forgotten yet again that quotes aren't evidence. Why not admit that you were lying when you claimed an interest in evidence? Look at how you've run away from discussing the massive sequence evidence that makes fossils unnecessary, after you realized that you have no hypothesis that explains the data. BTW, Schindewolf is wrong. Look at how your body normally prevents antibodies that recognize your own antigens from being produced.

Date: 2007/09/28 10:20:33, Link
Author: JAM
Quote (Thought Provoker @ Sep. 27 2007,15:39)  
Quote
Labels aren't important, ideas are.

But making predictions and testing them is far more important. Limiting yourself to retrodictions is scientific mendacity.
Quote
Thank you for your comment and thank you for providing the link.  As you pointed out, MikeGene said...
"A working hypothesis has been that the first cells (uni-cellular life forms) were front-loaded with information that would facilitate the evolution of multi-cellular life." (emphasis mine)

I'm curious--in what way is this a "working" hypothesis, if neither Mike nor you are willing to put it to work to make predictions about future observations, while falling over yourselves to claim that data from others fit the hypothesis?

That ain't science.
Quote
I have noticed MikeGene is pretty careful with his words.

I have noticed that he is pretty careful to avoid making predictions.

Date: 2007/09/28 17:37:33, Link
Author: JAM
bornagain77:
Quote
So trying the best I could, in my own way, to cheer him up, I then started to sing, dance and clown around, trying to cheer my friend up. I was singing, dancing and clowning around to the children’s song “What makes that little old ant think he can move that rubber tree plant …. He’s got high hopes, He’s got high apple pie in the sky hopes….” “Well”, my friend said, after I was all done with my clowning around, “I still don’t feel any different”.

Damn, his friend must have been really depressed. Any normal person would feel very different after being subjected to that--and it probably was sandwiched between a couple of 2000-word sentences, too.

Date: 2007/09/29 12:42:51, Link
Author: JAM
Quote (Thought Provoker @ Sep. 29 2007,11:19)
Hopefully, you will understand how I might view this as an unnecessary contrivance if, in fact, life's awareness (consciousness) can be traced to quantum effects that are interconnected over time.

No one who is interested in real science would blow off massive amounts of data as an "unnecessary contrivance" when he has nothing but a house-of-cards hypothesis.

Whatever happened to "Let's do science," TP?

Date: 2007/09/29 14:17:22, Link
Author: JAM
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?

Just to clarify, horses don't (yet) have single-toed hooves. Bones (metacarpal/metatarsal) from the two flanking (2 and 4) digits still remain. They serve no useful purpose (they often become inflamed or broken), while the tops of the front ones still form part of a joint:

http://www.omafra.gov.on.ca/english/livestock/horses/facts/89-093.htm

If they suggest design, their designer was an idiot. Maybe Daniel can explain the elegance of their design if he disagrees.

Date: 2007/09/29 14:20:15, Link
Author: JAM
Other--ID belongs in either pseudoscience or abnormal psychology courses.

Date: 2007/10/01 09:35:50, Link
Author: JAM
Quote (C Gieschen @ Oct. 01 2007,09:19)
Dear Jim Wynne,

By the same token, if you believe in evolution because of Darwin, Miller, Gould, etc. I have the same bridge up for sale.  I take it you have not examined his evidence.

Christopher,

I don't know about Jim, but I've actually PRODUCED evidence that tests predictions made by modern evolutionary theory. At first, my evidence didn't clearly fit any nested hierarchy, but as others produced evidence from other organisms, everything fit beautifully.

Let me guess--when you "examine evidence," you're not anywhere close to examining the actual evidence. You just swallow what someone says about the evidence.

Am I right?

Date: 2007/10/01 12:33:57, Link
Author: JAM
Quote (C Gieschen @ Oct. 01 2007,10:17)
To JAM,

What was the evidence?

Sequence evidence. For the record, I'm not an evolutionary biologist, so please save your misrepresentations about conformism, etc.
Quote
 And most teachers of evolution just swallow what they have been told also, so what is your point?

My point is that you were bearing false witness when you claimed to be examining evidence. If "most teachers of evolution just swallow what they have been told," that doesn't justify your false claim of examining evidence.

Have you ever examined any sequence evidence--not someone else's interpretation of it--for yourself, or are you afraid that you can't make it fit your worldview?

Why do people on our side produce evidence, while people on your side run away from evidence, and project this pathological fear onto us?

Date: 2007/10/01 16:57:07, Link
Author: JAM
Quote (C Gieschen @ Oct. 01 2007,14:33)
Jim,

I was under the impression when you said that you have produced evidence, that you did an experiment or something.

I have--many of them.

 
Quote
I think you meant that you can show your evidence for millions of years based upon stratagraphic layers.

No, I meant that I can show my evidence, as well as evidence from thousands of others, that is easier to interpret than fossils and geology. I bet that you're afraid to examine any evidence for which you can't regurgitate a creationist explanation, and I bet that you're afraid to make predictions about evidence that will be found in the future.
Quote
1. Dr. Berthalt's work which shows laminations can result that appear to suggest individual layering of a horizontal event one at a time.

The laminations would be evidence, but what they suggest is interpretation. What predictions do you make?
Quote
2. Dougals Erwin's quote from Geotimes Feb. 1991, "Resolving many evolutionary...problems... assumes that the stratigraphic order of fossils bears some relationship to their choronological order."  The deleted words do nothing to influence the main point he is making.

Quotes aren't evidence.
Quote
3. Polystrate fossils which have been explained by your side, but that does not mean the explanation is correct.

Explanations aren't evidence. Only the evidence is evidence. Why do you so dishonestly conflate evidence with its interpretation, Chris?

I'll ask again:
Have you ever examined any sequence evidence--not someone else's interpretation of it--for yourself, or are you afraid that you can't make it fit your worldview?

Why do people on our side produce evidence, while people on your side run away from evidence, and project this pathological fear onto us?

Date: 2007/10/01 17:46:52, Link
Author: JAM
Quote (Thought Provoker @ Sep. 30 2007,11:44)
Hi K.E.,

You wrote...
   
Quote
You seem to be arguing that our brains are quantum computers. For that to be true the processing power available from such a device of that size would be orders of magnitude larger than Deep blue.


Maybe you haven't understood the magnitude of woo being presented here.  This isn’t just human brains.  Microtubules are present in practically everything we think of as living.  If Hameroff is right, quantum computers in microtubules explains why life appears to be aware if its surroundings.  From this Hameroff paper (essay?)….

To gauge how single neuron functions may exceed simple input-output activities, consider the single cell organism paramecium. Such cells swim about gracefully, avoid obstacles and predators, find food and engage in sex with partner paramecia. They can also learn; if placed in capillary tubes they escape, and when placed back in the capillary tubes escape more quickly. As single cells with no synaptic connections, how do they do it? Pondering the seemingly intelligent activities of such single cell organisms, famed neuroscientist C.S. Sherrington (1957) conjectured: “of nerve there is no trace, but the cytoskeleton might serve”. If the cytoskeleton is the nervous system of protozoa, what might it do for neurons?

TP,

I suggest that you update your knowledge from 1957 speculations. IIRC, the nervous system of Paramecium works very analogously, but more simply, than the "nervous system" of an individual neuron--by membrane depolarization.

When a Paramecium bumps into something, the bump causes a calcium ion influx via mechanosensitive channels. Increased calcium causes a reversal of direction of ciliary beating, primarily through cyclic nucleotides and protein phosphorylation.

AFAIK, there's no evidence that microtubules, despite conferring rigidity to the cilia, play any computational role in integrating stimuli; the same goes for neurons.

You're pretending that the sophistication of quantum mechanics somehow cancels out the sophomoric reductionism of the neurobiological hypothesis.

There is, however, a lot of mechanistic data demonstrating the far greater importance of the actin cytoskeleton in neuronal plasticity, like this:

http://jcs.biologists.org/cgi/content/full/120/2/205

Date: 2007/10/01 18:00:09, Link
Author: JAM
Quote (Jim_Wynne @ Oct. 01 2007,17:27)
Quote (C Gieschen @ Oct. 01 2007,14:33)
If you don't accept Mr. Strobel's evidence, then what about Mr. Josh Mc Dowell?

I'm not familiar with McDowell's lies evidence. Is it substantially different from the garden variety ignorance and dishonesty apologetics?

Jim, we also should note that real scientists describe the evidence instead of quoting the interpreter of the evidence.

Chris, appeals to authority are always fallacious in science, but they are simply dishonest when such appeals come from someone who pretends to be interested in examining actual evidence. I suspect that you are incapable of resisting your impulse to appeal to authority.

If you disagree, try filling out this form with only evidence and predicted evidence, and without using a single name, quote, or opinion:

1) Evidence supporting an old Earth:
2) Evidence supporting a young Earth:
3) Predictions of an old Earth hypothesis:
4) Predictions of a young Earth hypothesis:

Date: 2007/10/02 01:01:06, Link
Author: JAM
Quote (Jim_Wynne @ Oct. 01 2007,19:54)
Quote (JAM @ Oct. 01 2007,18:00)
Quote (Jim_Wynne @ Oct. 01 2007,17:27)
 
Quote (C Gieschen @ Oct. 01 2007,14:33)
If you don't accept Mr. Strobel's evidence, then what about Mr. Josh Mc Dowell?

I'm not familiar with McDowell's lies evidence. Is it substantially different from the garden variety ignorance and dishonesty apologetics?

Jim, we also should note that real scientists describe the evidence instead of quoting the interpreter of the evidence.

I understand, but The junk that Chris is referring to doesn't amount to anything approaching evidence at any level.  The primary literature for Chris is the King James version.

Oh, I know that. What I find amazing is that no matter how many times we point out that opinions aren't evidence, Chris and his ilk will try to maliciously conflate the two, because in their hearts, they know that real evidence won't support their position.

Date: 2007/10/02 01:27:54, Link
Author: JAM
Quote (Thought Provoker @ Oct. 01 2007,22:47)
Hi all,

For example, Dr. Hameroff explains what he sees as the role of actin and dendrites in papers (essays?) like this one.

My ability to cut through the medical babble to think in laymans terms is limited.

This is not medical babble, it is biological babble. At least we agree that it is babble!

 
Quote
So when Dr. Hameroff says...

...When actin polymerizes into a dense meshwork, the cell interior converts from an aqueous solution (sol state) to a quasi-solid, gelatinous (gel) state.

I think that he doesn't know what he is talking about, as I don't know of any cells in which the cell interior converts from a sol to a gel state. In every cell I do know about, this conversion is going in different directions in different parts of the same cell--even opposite ends of the same filament.

Hameroff is babbling, TP.

 
Quote
In the gel state, actin, MTs and other cytoskeletal structures form a negatively-charged matrix on which polar cell water molecules are bound and ordered (Pollack 2001). Glutamate binding to NMDA and AMPA receptors triggers gel states in actin spines (Fischer et al 2000).

They are dendritic spines, not actin spines, and what happens is at least 10x more complicated than that. That's why it's so ridiculous to pretend that consciousness boils down to MTs, with or without quantum mechanics.
 
Quote
Neuronal MTs self-assemble,...

Twaddle. All MTs do.
 
Quote
... and with cooperation of actin enable growth of axons and dendrites. Motor proteins transport materials along MTs to maintain and regulate synapses. The direction and guidance of motor proteins and synaptic components (e.g. from cell body through branching dendrites) depends on conformational states of MT subunits (Krebs et al 2004).

This is incredibly misleading, because it depends on much more than that. Do you realize that when we look at individual vesicles, they go back and forth from MTs to actin in real time?
Quote
Thus MTs are not merely passive tracks but appear to actively guide transport. Among neuronal cytoskeletal components, MTs are the most stable and appear best suited for information processing Wherever cellular organization and intelligence are required, MTs are present and involved.</b>

Gee, TP, do you realize how ridiculous this is? Take a wild-assed guess as to where in the neuron MTs [b]are not present!
 
Quote
It is going to take a lot of effort on my part to understand the fundamental differences between the two.

Then perhaps you should do so before becoming so enthusiastic about MTs.
 
Quote
The logical implication of Penrose's understanding is that awareness/consciousness is directly tied to quantum effects.  Call it a prediction.

Erm...no, that's a hypothesis, not a prediction. You're quacking just like Bradford, TP.

Date: 2007/10/02 13:11:31, Link
Author: JAM
Quote (Thought Provoker @ Oct. 02 2007,07:28)
Hi JAM,

Dr. Hameroff is...
Professor Emeritus, Departments of Anesthesiology and Psychology,
Director, Center for Consciousness Studies
The University of Arizona, Tucson, Arizona

None of which remotely suggests that he is an authority on the neuronal cytoskeleton.
 
Quote
This has been is the focus of his professional life.

What is the antecedent of "this"?
 
Quote
He is 60 years old.  He is joined by other professionals like Scott Hagan,

Scott Hagan's publications are anything but impressive.
 
Quote
Jack Tuszynski

I've presented my work at a meeting he organized. They were inviting experts to Alberta to learn from us.
 
Quote
and Nancy J. Woolf in his hypothesis concerning the role of microtubules for consciousness.

She hasn't published any data relevant to the hypothesis since 2001.
 
Quote
As an engineer, I approach this pretty as Penrose did as a physicist.

As a scientist, I expect other scientists to be enthusiastic about testing their own hypotheses. Do you see any such enthusiasm here?
Quote
 It makes too much sense to see consciousness connected to quantum effects.

You continue to desperately and deliberately misrepresent my position, just like Bradford. Read carefully, TP, and see if it sinks in this time: I have no objection whatsoever to hypothesizing that consciousness involves quantum mechanics. What I object to is the simplistic idea that consciousness can be reduced to quantum mechanics of microtubules.
Please attempt to address this point. I realize that you are too embarrassed to do so publicly, because misrepresenting my position is so much easier than dealing with my real position.
 
Quote
Why should I accept your "trust me" bombastic babble when Dr. Hameroff takes the time to try and explain it in layman's terms?

I have never engaged in anything resembling "trust me," and you know it, TP.
Quote
Even Max Tegmark explains his objections in layman's terms.

I've explained it plenty of times in lay terms. Since the decision of a fibroblast requires microtubules, but is too complex to be reduced to microtubules, the idea that consciousness can be reduced to microtubules--no matter how magical you believe them to be--is preposterous.

And here's another clear objection: simply reread Hameroff's twaddle and guess which part of the neuron excludes microtubules. If you think that it is sufficiently erudite to quote it, you should have no problem reading it.
Quote
You have made your counter argument.  I will continue my affirmative argument.  We can let the debate judges decide for themselves.

Scientific disagreements are decided by evidence, not by debate judges.

Should I start calling you Bradford-in-drag?

Date: 2007/10/02 15:08:49, Link
Author: JAM
Quote (Thought Provoker @ Oct. 02 2007,13:47)
Hi JAM,

You wrote...
     
Quote
I have no objection whatsoever to hypothesizing that consciousness involves quantum mechanics. What I object to is the simplistic idea that consciousness can be reduced to quantum mechanics of microtubules.

And if it isn't obvious by now, let me state it clearly.  I don't have enough biological knowledge to know whether quantum computation comes from microtubules, actin or pixie dust.

Nor do your heroes.
 
Quote
Dr. Hameroff provides a good-sounding mechanistic model for microtubules.

It sounds ridiculous. Contrast this:
Actin is the main component of dendritic spines and also exists throughout the rest of the neuronal interior in various forms depending on actin-binding proteins, calcium etc...Glutamate binding to NMDA and AMPA receptors triggers gel states in actin spines (Fischer et al 2000).
with this:
Wherever cellular organization and intelligence are required, MTs are present and involved.
Now, hypothesize that Hameroff is self-contradictory and full of hooey. What part of the neuron does that predict will fail to contain microtubules?
 
Quote
If you could provide a mechanistic explanation for quantum computation via actin I would have no qualms about considering it too.  In fact, I would welcome it.

It would be only slightly less ridiculous to claim that it could be reduced to actin.
 
Quote
I suspect any quantum computation requires both actin and microtubules.

And I am extremely confident that no quantum computation can be reduced to either system.
 
Quote
Sure, in the future Dr. Hameroff's attempts may be considered as bumbling and crude as you are making them out to be.

They are considered to be bumbling and crude today. More importantly, they can't be bothered to generate new data by testing this hypothesis. If you bothered to read their more recent, less crude essays, even they are walking back from it.

Date: 2007/10/03 11:37:25, Link
Author: JAM
Quote (Daniel Smith @ Oct. 03 2007,02:52)
   
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!

Daniel,

Scientific arguments aren't about quoting. They are about evidence. If you can't describe the hypothesis, its predictions, and the observations in your own words, you clearly haven't thought it through.

   
Quote
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.

This shows your lack of reading comprehension, because I disagreed with your assumption and provided evidence.

Nested hierarchies of designed objects and their components are different. Nested hierarchies of organisms and their components must be superimposable. You simply disagreed with me without explaining why after I patiently explained to you, "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."

Even worse, you failed to grasp this after I offered a perfect example:

http://www.biolbull.org/cgi/content-nw/full/202/2/104/F2

Do you now see how human and mouse appear in multiple groupings within that tree, and in each clade, the *relative* distances are the same as for the relationships between the whole organisms? For example, look at the CB1 clade--rats and mice are very close, humans and rodents are closer to each other than they are to cats (carnivores). We can add sequences to that and predict where they will branch off, and common design makes no such predictions.
 
Quote
I haven't seen how they all line up.

I was trying to show you that, but predictably, you ran away from discussing evidence. That's because in your very soul, you know that your view won't be supported by the evidence. That's why you desperately quote in lieu of examining the evidence for yourself.

Date: 2007/10/03 15:08:11, Link
Author: JAM
Quote (Thought Provoker @ Oct. 02 2007,15:25)
BTW, instead of asking me leading questions like "What part of the neuron does that predict will fail to contain microtubules?" please tell me what you are saying.

I was being Socratic because earlier, you complained:
Quote
Why should I accept your "trust me" bombastic babble when Dr. Hameroff takes the time to try and explain it in layman's terms?

Do you see an inconsistency between those positions?

Date: 2007/10/03 15:16:19, Link
Author: JAM
Quote (Thought Provoker @ Oct. 03 2007,12:18)
Hi All,

In response to JAM's discussions, I have been trying to understand other points of views of the general idea of the brain using quantum computations.  In this effort, I ran across Walter J Freeman...."With his background as an anaesthesiologist, Hameroff suggested to consider microtubules as an option..."

TP, sit back, take a deep breath, and read this passage carefully. As someone who works in cell biology, it immediately brings to mind Lewis Black's famous joke,

"If it weren't for my horse, I wouldn't have spent that year in college."

WTF does being an anesthesiologist have to do with microtubules? I can see why an erudite oncologist is likely to know something about microtubules, given that oncologists pump people full of taxol, but an anesthesiologist?

Date: 2007/10/03 16:24:28, Link
Author: JAM
Quote (Thought Provoker @ Oct. 03 2007,15:40)
Hi JAM,

You asked...
     
Quote
WTF does being an anesthesiologist have to do with microtubules?

Here is Dr. Hameroff's answer...
"...As it turned out, the same microtubules running the show in mitosis were running the show in neurons and other cells all the time.

But when it comes to LTP, there aren't MTs in the dendritic spines, where most of the LTP show is presented.
Quote
"He told me "If you want to know what consciousness is, study the mechanism of anesthetics." He also gave me a paper suggesting anesthetics depolymerized microtubules,..."

Ah, suggesting. Did that turn out to be correct, TP?
Quote
And here we are ten years after that.

Has Hameroff published any new data about MTs in those ten years?
Quote
BTW, here is a link on my blog showing microtubules in action during cell division.

Your point being? Are the microtubules the only thing in action? What mediates cytokinesis?

Date: 2007/10/03 19:58:41, Link
Author: JAM
Quote (Thought Provoker @ Oct. 03 2007,17:09)
Hi JAM,

Hi, TP. My question was about data.
 
Quote
S. Hagan, S.R. Hameroff and J.A. Tuszynski:
Quantum Computation in Brain Microtubules: Decoherence and Biological Feasibility. Physical Review E 65, 61901:1-10 (2002).

No data there! BTW, it's now 2007, not 2002.
 
Quote
S. Hameroff, A. Nip, M. Porter and J.A. Tuszynski:
Conduction pathways in microtubules, biological quantum computation, and consciousness. BioSystems 64, 149-168 (2002).

None there either!

TP, simple question: has this hypothesis been tested in a way that produces data?
 
Quote
Here is a link to over 50 papers (essays?) written by Tuszynski and various other people on this subject.

Do any of them contain data? I wasted my time looking at the first two, and you either misunderstood me or were misleading me when you offered those.
 
Quote
Here is a 2005 paper Hameroff wrote where he discusses microtubule's role in mitosis and possible role in cancer.

TP, I asked for data, not a discussion. Do you not know the difference?
 
Quote
A lot of other information (presentations, interviews, etc) can be found at www.hameroff.com.

Any DATA, TP? How about a measly datum?

Science produces predictions and data. Whatever happened to, "Let's do science," TP?

Date: 2007/10/03 21:24:13, Link
Author: JAM
Quote (Thought Provoker @ Oct. 03 2007,20:56)
Hi JAM,

From your reaction I am presuming that you do not consider consolidating various observations and running simulations to present results in a coordinated fashion as "publishing new data".

Never and maybe, respectively.
Quote
"In recent times the interest for quantum models of brain activity has rapidly grown. The Penrose-Hameroff model assumes that microtubules inside neurons are responsible for quantum computation inside brain. Several experiments seem to indicate that EPR-like correlations are possible at the biological level. In the past year , a very intensive experimental work about this subject has been done at DiBit Labs in Milan, Italy by our research group. Our experimental set-up is made by..."
link

TP, that experiment has nothing at all to do with microtubules.
Quote
While I am sure you will have an objection to this 2004 experiment too.  The point is that a reasonable number of people are taking this seriously.

No, they aren't taking the microtubule hypothesis seriously unless they are using it to generate new data.
Quote
I don't begrudge Dr. Hameroff for focusing on coordinating and encouraging other’s efforts by publishing overall analyses and lecturing, obviously you do.

I have yet to see a single effort from anyone to use this hypothesis to learn about microtubules, and it appears that you haven't seen one either.
Quote
If you want to suggest an alternative, fine.

The alternative would be to test the hypothesis about microtubules.
Quote
I will listen.  Meanwhile, I am presuming these other people might be on to something.

If they were on to something with the microtubule hypothesis, wouldn't they be doing experiments that involved microtubules?

Date: 2007/10/04 14:25:35, Link
Author: JAM
Quote (Ftk @ Oct. 04 2007,13:39)
Honestly, I think you're all loopy that you don't understand that scientists have not figured out how the immune system evolved.  They've broken down different parts of the system and have offered various senarios as to how it "may" have evolved, but no one can possibly suggest that there is empirical evidence to support the notion that the immune system as a whole has evolved through NS&RM.

Huh? There are mountains of evidence consistent with that.

FTK, do you realize that if your acquired immune system was designed, that God designed the basic mechanism by which it produces a new, unique specific binding site in a protein in ONLY TWO WEEKS--what Behe stupidly claims is "the edge of evolution"?

Do you realize that the mechanism that God chose is random (with respect to fitness) genetic variation + selection?

If variation + selection is unable to produce diversity, why did God choose it in this case?

Date: 2007/10/04 16:56:36, Link
Author: JAM
Quote (Ftk @ Oct. 04 2007,15:37)
...Your students have no cause to question what you teach in class because it's based on microevolutionary facts.

Why not go to his class and learn the truth?
 
Quote
You can extrapolate that evidence as much as you like, but it is far, far, from "fact".  Many aspects of evolution are based on historical science, which I'm not sure even belongs in the science classroom.

The best evidence is the sequence evidence, which is not historical evidence. I'll bet that you're afraid to examine the sequence evidence. Am I right?
Quote
There is no way to test or repeat macroevolutionary assumptions.

Wrong. The sequence evidence can be used to test macroevolutionary predictions, EVEN RELATIONSHIPS BETWEEN PHYLA. Is the phylum level macro enough for you?
Quote
We have never witnessed macroevolutionary changes, so it seems insane to present them as "fact" in the science room.

I suspect that like the rest of us (and unlike Behe), he is careful to present facts as facts, hypotheses as hypotheses, and theories as theories. I also suspect that you couldn't keep those three classes straight if your children's lives depended on it.

Date: 2007/10/04 17:01:24, Link
Author: JAM
Quote (Ftk @ Oct. 04 2007,16:31)
What I should have said was that you evos have been trying to find something, *anything* that you can claim is an example of a macroevolutionary change taking place in nature...something we can empirically detect with our own eyes...it doesn't exist.

Gee, when I was a postdoc, I did my own sequencing and empirically read the sequences with my very own eyes. Nowadays, I send DNA off for sequencing, but I can still read the trace files that are emailed back to me.

How can you babble about seeing things with our own eyes when yours are firmly closed to looking at any real evidence?

Date: 2007/10/04 17:42:22, Link
Author: JAM
Quote (Thought Provoker @ Oct. 04 2007,16:06)
...I have plenty of experience with PhD types providing lists of why a proposed design won't work.

We're not saying it won't work, we're asking why no one is using it to produce any work (new data). If you, Penrose, Hameroff, et al. thought that this hypothesis would work, you'd be producing data with it.
 
Quote
However, when they refuse to offer an alternative we have to go with the best we got.

TP, you're delusional. You're not going with it, and no one else is either.
 
Quote
The funny part is when the project is successfully completed, the PhD types still maintain they were right and provide plenty or reasons why.

Um...we're the ones asking why you and those who love this hypothesis have yet to start a project, much less complete one successfully. We're the doers, and you're just a talker.
 
Quote
The Penrose-Hameroff Orch OR model is a fall out of this.  Consciousness has to be tied to interconnected quantum effects.  Consciousness can't be purely algorithmic.

How would you know? You can't tell the difference between a paper that contains new data and one that doesn't.
 
Quote
Dr. Hameroff takes this a provides a detailed model of how this could work.

Then why hasn't he tested it by manipulating microtubules?
 
Quote
I understand it well enough to go with its basic concept.  Do you have an alternative model?

LTP + a lot of stuff we don't understand yet. Folks (including me) are testing predictions.
 
Quote
...I am suggesting an enhancement that might explain why living organisms like Vernanimalcula guizhouena are more complex than expected.

But does it make any predictions?
 
Quote
While I hesitate to speak for MikeGene, I think it is safe to say he has a similar position.  Front Loading is an enhancement, not a challenge.

Science is about predicting more than explaining. Einstein was famous because he offered testable predictions.

Do you have any? If not, you and the cowardly Mike Gene are avoiding science, not doing it.

Date: 2007/10/04 18:25:28, Link
Author: JAM
Quote (Ftk @ Oct. 04 2007,18:07)
Dave again...
   
Quote
An objective reader might come to the conclusion that I was, as per my job description, trying to educate them. Not convert them, not stop them, not condemn them to eternal damnation, but EDUCATE them. Read the words, please.


Again, the religious angle and the arrogance factor.  Everyone who questions the extent to which the mechanisms of evolution are indeed capable of reaching are in need of you to educate them.

No, the antecedent of "them" is "students," not "everyone." It's his job to educate students, isn't it? Do you really think that you are fooling anyone but yourself when you engage in such blatant dishonesty?
Quote
I, personally, believe that the gaping holes in the theory are too numerous to dismiss, and the fact that Darwinists are working SOOOOO hard at keeping ID at bay has thrown up red flags all over the place for me.

Do you believe that Darwinists have kept the ID journal from publishing an issue in the last two years?
 
Quote
When I mentioned “researching deeper” I was referring to throwing themselves into this debate...

That's not what research is. Scientific debates are decided by data. Your side produces none.
 
Quote
...and listening to all the arguments from both sides

Science isn't about arguments. It's about the evidence, and you're afraid of evidence.
 
Quote
... and actually learning about creation science or ID from someone who advocates the theories.

They aren't theories because they don't have a record of successful predictions. They are notions.
 
Quote
Why would they ever even consider contemplating other theories or working for a creationist when they are told by their professors that creation scientists and IDists are “liars”.

"Work" in science means producing data. Theories aren't contemplated, they are tested, producing work (new data). When you try to portray science as nothing but apologetics, you are lying, ftk. 
 
Quote
This bit about calling us “liars” on a consistent basis tells me that you really have no clue what you are talking about.  Your extreme hostility toward IDists is obviously because you believe them to be filthy "liars"....and, obviously you feel that way about me as well.

For starters, why don't you explain how ID can be touted as a theory when it has yet to make a single prediction?

How can anyone be silencing ID when they haven't published THEIR OWN JOURNAL in nearly two years?

Date: 2007/10/05 00:57:14, Link
Author: JAM
Quote (Ftk @ Oct. 04 2007,18:37)
 
Quote
No, the antecedent of "them" is "students," not "everyone." It's his job to educate students, isn't it? Do you really think that you are fooling anyone but yourself when you engage in such blatant dishonesty?

I'M NOT BEING DISHONEST.  He's told me several times that his job is to educate and he's not only talking about his students.  He's also talking about the general public in regard to these debate issues.

YOU ARE BEING DISHONEST.

Here's the paragraph:
Quote
1) Where in my post did I mention that I thought of my students as "damn religious freaks trying to put a stop to science"? An objective reader might come to the conclusion that I was, as per my job description, trying to educate them. Not convert them, not stop them, not condemn them to eternal damnation, but EDUCATE them. Read the words, please.

You were dishonest because you left out the first two sentences containing the antecedent "my students," and pretended that he was talking about everyone:
Quote
Again, the religious angle and the arrogance factor.  Everyone who questions the extent to which the mechanisms of evolution are indeed capable of reaching are in need of you to educate them.

You were utterly dishonest, FTK.
Quote
It's not that I don't appreciate his effort to educate...it's just that he is targeting the wrong issues.  He's convinced that Christians who question how far evolution can be considered "fact" are "LIARS"

No, FTK. Only Christians who reflexively lie are liars. Like those who, after having the definition of "theory" explained to them, persist in claiming that "ID theory" exists. Or those who conflate data with apologetics after the difference has been explained.
Quote
... and out to deceive and convert the public to Christianity as well as lead them to believe that science = atheism...as if every realm of science relies on the "fact" that Darwinian evolution is true.

Every realm of science? No. Every realm of BIOLOGY relies on modern evolutionary theory, much of which is non-Darwinian.

Date: 2007/10/05 10:05:22, Link
Author: JAM
Quote (Daniel Smith @ Oct. 05 2007,03:24)
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.

Yep, creationism requires rank dishonesty.  
 
Quote
I do admit that I don't have a real good grasp of the subject, and need to learn more.

That doesn't explain why you ran away from my offer to explain it to you using the evidence.
 
Quote
Really my main objection to the current theory of evolution is in regards to mechanism.

I don't think so.
 
Quote
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.

What would be inconsistent with designed descent, Daniel?
 
Quote
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
How do you explain artificial evolution of random sequences, then?  
Quote
- especially as genomes are found to contain more embedded, overlapping codes.

You're completely misusing the term "code."
 
Quote
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).

How can he be a "Darwinist" if much of his book discusses drift, which is non-Darwinian?
 
Quote
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.

If you were being honest, you'd address the evidence, not a book.
 
Quote
...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.

That would be the evolution we observe in sequences, but that's not true of the evolution of the functions of the proteins they encode.
 
Quote
He goes on to say that convergent evolution is an issue for both molecular and morphological theory to explain.

I see a strategic omission on your part here.
 
Quote
He gives the morphological example of the placental and marsupial wolves and gives analogous gene sequences as the molecular example.

Convergent sequences won't fit into a superimposable nested hierarchy. Issue addressed!
Quote
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?

Convergent sequences won't fit into a superimposable nested hierarchy.     
Quote
How also can we tell the distance between analogous sequences - since they are so alike?

Easily--they aren't identical.
 
Quote
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)?

Daniel, this is a creationist/ID LIE, pure and simple. Showing that 0.01% of the genome has a function does not tell us that 98% of the genome has a function.
 
Quote
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?

Why do you think that it is likely? Why not grow some balls and make a prediction instead of hiding from the evidence and making assertions?

Date: 2007/10/06 18:32:46, Link
Author: JAM
Quote (Ftk @ Oct. 06 2007,17:06)
Okay, let's start with the first five and see how many questions are immediately thrown back...        
Quote
5.  How does Behe know what is in a group of books without ever having read the books?

!!! This question is ridiculous.  Obviously, he wouldn't, and I'd have to ask Behe if he was every allowed to go through every book and article one by one and make two separate piles of what he had and had not read.

It doesn't help in Behe's defense. Here's Behe's testimony, under oath:

 
Quote
Q. We'll return to that in a little while. Let's turn back to Darwin's Black Box and continue discussing the immune system. If you could turn to page 138? Matt, if you could highlight the second full paragraph on page 138? What you say is, "We can look high or we can look low in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system." That's what you wrote, correct?

A. And in the context that means that the scientific literature has no detailed testable answers to the question of how the immune system could have arisen by random mutation and natural selection.


There are two very important things here:
1) Behe made the claim, and to make such a claim ethically, he must ALREADY be familiar with ALL the relevant literature. The fact that he's not makes his claim a profoundly dishonest one.
2) Note how Behe moved the goalposts. In his book, he simply wrote "no answers," but he knows that it was a lie, so he adds the qualifications "detailed" and "testable." Then, after that, he moves the goalposts again, to "Not only would I need a step-by-step, mutation by mutation analysis, I would also want to see relevant information such as what is the population size of the organism in which these mutations are occurring, what is the selective value for the mutation, are there any detrimental effects of the mutation, and many other such questions."

Michael Behe is an incredibly dishonest man.

 
Quote
But, I tried desperately to explain in an earlier discussion that just because we have theories about how something *may have* occurred, that does not mean that all the questions have been answered nor should they be regarded as "fact".


That's irrelevant wrt Behe, because he plainly stated, under oath, that his criterion is how it "COULD have arisen by random mutation and natural selection."

"Is there a book or article somewhere that I can read that tells me from start to finish how the immune system evolved through evolutionary mechanisms?[/quote]
No, the subject would fill many books. Just look at these titles:



Note that the evolutionary history of the major histocompatibility complex (a chromosomal region that encodes the incredibly polymorphic proteins that the immune system uses both as self-identification and as a scaffold for recognizing foreign proteins) fills an entire book by itself.

Does the fact that MHC proteins have this dual role suggest any eminently testable hypotheses about the evolutionary origin of the adaptive immune system, FTK?
 
Quote
And, do you believe that this article or book can supply us with enough facts to safely say that the answers in regard to the evolutionary pathways that led to the evolution of the immune system is no longer in question?

No single book could do so because of the complexity involved, and Behe knows it. That's why his challenge is obviously dishonest to any of us who know anything about immunology.
 
Quote
Is it safe to say that the immune system, in fact, slowly evolved over millions of years from the initial starting point of a mere lonely, simple microbe?

When we discuss the immune system, we discuss its origin from a system that was not involved in ridding the organism of infectious microbes. 
Quote
Okay, 5 questions answered, and I'll be counting how many are thrown back at me.

Following up, or pointing out inadvertent or deliberate misrepresentations, is "following up," not "throwing back."

Date: 2007/10/06 19:27:47, Link
Author: JAM
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.

Date: 2007/10/06 20:52:04, Link
Author: JAM
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?
 
Quote
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?

Date: 2007/10/07 13:27:23, Link
Author: JAM
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.
Quote
When I say "functional sequences" I mean functional as in "used within the cell".

That works for me.
Quote
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.
Quote
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?
Quote
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?

What sequences are used for forensic DNA analysis?
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.

Date: 2007/10/07 15:58:37, Link
Author: JAM
Quote (Thought Provoker @ Oct. 07 2007,08:22)
Hi Keiths,

You wrote..
         
Quote
...Human reaction times are well below 500 ms.  Your use of the Libet delay as a cutoff is therefore invalid and would result in false positives.
Libet's observation is that the "reaction time" for a conscious decision is 500ms.  This appears wrong on its face because things like hitting a fastball and playing professional tennis require reaction times faster than that.

http://www.exploratorium.edu/baseball/reactiontime.html

I get reaction times of 210-230 ms in this test, so Libet's observation doesn't merely appear to be wrong.
Quote
However, Libet's scientific observation has withstood challenge.

So you say. Where are the data?
Quote
 Those studying consciousness have had to reevaluate their thinking to explain Libet's observation.

Are you sure, or is that merely what someone else claims?

Date: 2007/10/07 19:21:41, Link
Author: JAM
Quote (keiths @ Oct. 07 2007,16:45)
Quote (JAM @ Oct. 07 2007,15:58)
http://www.exploratorium.edu/baseball/reactiontime.html

I get reaction times of 210-230 ms in this test, so Libet's observation doesn't merely appear to be wrong.

Hi JAM,

Libet's results do hold up under scrutiny.  It's TP's explanation of them that is wanting.

Contra TP, Libet's delay is not a reaction time.

Follow this link for a nice description of Libet's findings.

Thanks. I should've known.

Date: 2007/10/08 13:01:09, Link
Author: JAM
[quote=Daniel Smith,Oct. 08 2007,02:18]     [quote=JAM,Oct. 07 2007,13:27]                   [quote=Daniel Smith,Oct. 07 2007,05:46]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.[/quote]
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.[/quote]
Then this is what we need to test.[/quote]
OK, what do you propose? How about "knocking out" regions using the technology whose developers won the Nobel Prize today?
 [quote]    
Quote
 
Quote
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.[/quote]
That's only true for hypotheses that have a track record. Yours doesn't. I've trashed many hypotheses that I've endorsed in previous publications, for example.
 
Quote
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).

It's your ethical responsibility to state the results that would completely shoot it out of the water.
 
Quote
 
Quote
 
Quote
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?

Easily and empirically. We know the mutation rate in the absence of selection. If the rate of change over time is the same as the mutation rate, the only rational inference is the absence of selection. If it is less than the mutation rate, we infer selection.
[quote]
Quote
We must first determine that these sites are truly neutral and are actually accumulating mutations.
                     
Quote


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.

I'm not asking for the "best answer," I'm simply asking for an answer. Certain sequences are used for forensic DNA analysis. What are their characteristics? How polymorphic are they?
Quote
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.

Good. Please define "lineage" for starters. Are mice and humans in the same or in different lineages?
Quote
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.

And the evidence shows that you are wrong.
Quote
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).

Interesting. Of the ~30,000 protein-encoding genes in the mouse and human genomes, how many do you believe/predict are absent in mouse and present in human, and vice versa?

Quote
Therefore, this is what I expect:

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

I need a rigorous definition of "lineage" before pursuing this one.

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

This is trivially easy to do online. Are you interested or afraid to do so?
Quote
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.

a) How does that relate to today's Nobel Prize?

b) How about classical genetics--do any homozygous normal inversions exist? If so, doesn't that mean that the sequences disrupted by both breakpoints have no function?

Quote
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.

We know a lot about that, Daniel. In fact, it's what I've been working on for the last 16 years, since mouse genetics dumped me into the field.

I'll give you a taste--nothing about the mechanisms involved suggests intelligent design.

Quote
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.

Except for your definition of "lineage," yes. As an introduction to how proteins "know" where to go, you might want to Google "signal sequence" and "nuclear import."

Those are the simple signals intrinsic to the protein. What I study is an order of magnitude or two more complex, fluid, and fuzzy.

Date: 2007/10/08 23:06:46, Link
Author: JAM
Quote (Ftk @ Oct. 08 2007,22:38)
He has provided predictions in regard to future empirical findings...he predicts they “won’t be fruitful” (lol!).

The joke's on you. If the empirical findings supported his hypothesis, they clearly would be fruitful. Behe simply lacks the faith to put his own hypothesis to the test.
 
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Kidding aside, it seems to me that the man has broken down the flagellum in every way imaginable and he’s saying, hey, NS just ain’t gonna ‘splain it.

Behe has done absolutely nothing to break down the flagellum.  
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...I would certainly be guessing, but chances are quite high that Behe would eventually be involved in this type of research in some capacity if it every gets off the ground.

You would certainly be guessing. How much are you willing to bet? I'll bet you $500 that Behe will never do an experiment that is designed to falsify his hypothesis, because in his soul, he knows that he's selling pure snake oil.  
 
Quote
But, again, I believe that this must take place within mainstream science...not in the basement of the Discovery Institute, or it will never be considered anything other than pseudoscience.  If Darwinists continue to censor this type of research the way they have in the past, the public will become more and more skeptical about evolution.

That's a complete fabrication, FTK. Darwinists have never censored this type of research. ID proponents have produced zero research that tests an ID hypothesis. Hell, I've personally done more to test an ID hypothesis than everyone in the ID movement combined--it's that easy.

And BTW, the public will continue to be "skeptical" as a result of the millions of dollars invested in deception by the ID movement.

Date: 2007/10/09 16:20:31, Link
Author: JAM
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

I don't understand it either.

Date: 2007/10/09 18:19:02, Link
Author: JAM
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.

Date: 2007/10/10 10:40:59, Link
Author: JAM
Quote (Daniel Smith @ Oct. 10 2007,02:30)
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.

By "coding," do you mean more than protein-coding sequences, including things like promoters, enhancers, splicing signals, etc.?

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?

Date: 2007/10/10 11:00:59, Link
Author: JAM
Quote (Daniel Smith @ Oct. 10 2007,03:17)
 
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.


1) Descriptions aren't evidence. Why not just be honest and admit that you avoid the actual evidence?
2) My descriptions do not imply that these systems are either "haphazard" or "random." I am accurately describing them as extremely fuzzy, with components that are related to each other with partially-overlapping functions. Therefore, they are in no way analogous to systems designed by humans, which was your preposterously ignorant claim.
 
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In fact I find the opposite to be true.

But you depend on descriptions, not evidence.  
 
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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).

Then show me the evidence you've examined for the cell's recycling systems and I'll show you how you are mistaken. What we real biologists find when examining the real evidence is Rube Goldberg-like, partially-overlapping complexity, with everything borrowed from something else. While this is both incredibly complex and amazing, it is in no way analogous to systems designed by humans.
 
Quote
Take the process of protein synthesis for example.

OK, but you need to explain why you are running away from the examples you initially chose.
 
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Please explain how that process is just a hodgepodge of cobbled together mish-mash that somehow, almost by accident, gets the job done.

First, you are grossly misrepresenting my position by attributing "almost by accident" to me. This is a fundamentally dishonest way to discuss anything.

Second, it is a cobbled-together mish-mash, given the following evidence.

1) Please explain why ribosomal RNA is at the center of the enzymatic active site, when RNA is so much less stable than protein. Since the "RNA World" hypothesis explains this beautifully, explain how a design hypothesis explains this better.

2) Please explain third-base "wobble" and the viability of bacteria carrying amber, ochre, and opal suppressor mutations.

 
Quote
Or explain how the brain is just a random lucky accident,...

You are being dishonest. I am not claiming that the brain is "just a random lucky accident." I am claiming that the brain is not analogous to a designed mechanism.
 
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... 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.

As for details, let's use the cell's waste management system. The details show that there is no single pure membranous compartment anywhere in the cell. Even the proteins that help to specify what we call separate compartments overlap with each other.

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

They are. You're just completely wrong about the qualities because you've not bothered to look at real evidence.

Your need to grossly misrepresent my position speaks volumes about your confidence in your own position, too.
 
Quote
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?

Then tell me about the qualities of the cell's recycling system that lead you to believe that it was designed. You have to go to the primary data, not anyone's interpretation of them.
 
Quote
Are the qualities of "the thing that needs explaining" and analogies excluded also from random or naturalistic explanations?

Analogies are explanatory devices. They are not evidence.
 
Quote
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?

Mostly, it's homology, not analogy.
 
Quote
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.

We don't like the fact that you are ignoring the actual evidence and promoting fake analogies.

Date: 2007/10/11 11:00:09, Link
Author: JAM
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?

Date: 2007/10/11 15:22:49, Link
Author: JAM
Quote (Ftk @ Oct. 11 2007,13:12)
Quote (oldmanintheskydidntdoit @ Oct. 11 2007,08:41)
Quote (Louis @ Oct. 11 2007,08:38)
Simpler analogy for FTK:

FTK: It is impossible for you to get to the end of the street from your house. It's too far and you cannot jump that far.

Me: Ah yes but I could walk there step by step, here are a selection of routes that I could take, all involving walking and all of which get me to the end of the street from my house.

FTK: But those are only POSSIBLE routes you haven't proven that you have taken them so it's STILL impossible for you to get to the end of your street from your house.

Me: Do you understand that the claim that something is impossible is refuted by demonstrating that it is in fact possible?

FTK: No. Understanding is an evil Darwinianatheistmaterialist conspiracy and I want no part of it. I am moving the goalposts and now saying that because you didn't describe each step in detail I still claim that you getting from your house to the end of the road is impossible. Especially by walking. STOP BEING MEAN WAAAAAAAAAAAAAAAAAAAAAH.

Me: Oh, erm, is that the time, I have an appointment with sane people.

Louis

It's that simple FTK.

Yeah, unless Louis has a broken leg, no cast, and no crutches.  He could have someone give him a ride, but that would be another entirely different scenario.  And, in the car scenario, they might have a wreck before they arrive to their final destination.  

:p  :p  :p

You're missing the point (I suspect deliberately). All he has to do is offer a single way to demonstrate that it is possible.

Supporting a negative claim requires massive amounts of evidence, and Behe can't be bothered to do anything but cherry-pick (often from reviews instead of the primary literature, a profoundly lazy and/or dishonest practice).

Demolishing a negative is pretty easy. Behe's entire thesis from DBB is simply wrong, which explains why he avoids actually producing anything from his lab.

Date: 2007/10/12 12:25:31, Link
Author: JAM
Quote (Thought Provoker @ Oct. 12 2007,12:12)
Hi OldMan.

I tried to post the following but I haven't bought anything from Amazon under this name.  I suggest this wouldn't be a recycled argument and might provide for putting Behe in an interesting position to answer.  If anyone wants to copy and paste (or put it in your own words) be my guest....


Dr. Behe,

Taking advantage of the ability to comment here, I wish to publicly ask you something that has bothered me.  You have focused on the microscopic level to suggest that randomness is insufficient to explain observations.  It is obvious that you are dealing at a level of detail that involves quantum mechanical effects.  Experiments have shown quantum effects aren't random.  Why was there so little discussion of quantum physics in your book Edge of Evolution when many scientists have been linking quantum physics to life processes.  For example, Stapp, Patel and those at Berkeley lab who, this year, demonstrated photosynthesis is a quantum mechanical mechanism.

Both you and Abbie Smith could be correct.  Her observations could be correct and your analysis visa-vie randomness could also be correct.  Random Mutation would turn out to be impotent if, in fact, non-random quantum effects are fundamental to life at the microscopic level.

I would have thought you and CSC fellow, Henry F. Schaefer III, would have discussed something like this.

TP,

That's gibberish. You don't even get Behe's thesis right. He's claiming that mutation rates aren't sufficient, not that randomness isn't sufficient. Moreover, virtually every time he uses the term "random," he does so to obfuscate, not to illuminate.

Behe's lies and obfuscations about HIV have no connection to quantum mechanics.

Date: 2007/10/12 16:43:01, Link
Author: JAM
Quote (Ftk @ Oct. 12 2007,16:19)
...when contemplating the IMMENSE COMPLEXITY of nature that we continue to uncover over the years, you'd have to be a LOON to support Darwinism.

FTK, when you're contemplating that immense complexity, you might want to note that *we* continue to uncover it, not *you*.

You might want to contemplate the nature of that immense complexity, because the nature of it doesn't suggest design at all.

You know, the maddening complexity of related components with only partially-overlapping functions, as well as the fact that huge protein superfamilies fit into nested hierarchies, taking us all the way back to our common ancestor with yeast.

Date: 2007/10/13 13:49:45, Link
Author: JAM
Quote (Daniel Smith @ Oct. 13 2007,13:22)
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.

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.

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).

Date: 2007/10/13 17:14:12, Link
Author: JAM
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:

--------------
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.
Quote
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.
Quote
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.

Date: 2007/10/13 17:22:33, Link
Author: JAM
Quote (Daniel Smith @ Oct. 13 2007,14:58)
   
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?

No, I'm pointing out that the analogy you're offering as evidence is simply wrong.    
Quote
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.

I suggest clicking the "Go" button to begin.
 
Quote
BTW, you are generally mean - but I'm still here.
Your meanness has nothing to do with your rightness.

Good for you.

I have to admit, though, that I tend to be more mean when I'm right, particularly when dumping evidence on someone as arrogant as you, who pretends to have a better understanding of my life's work than I do. Or someone who claims to have examined evidence, but moves the goalposts to someone else's "descriptions" when challenged.

Do you get a feeling for my perspective?

Date: 2007/10/13 17:33:35, Link
Author: JAM
Daniel,

Here's a good VISTA example:

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

This is mouse against human, dog, rat, and chicken in graphs 1-4 respectively.

Date: 2007/10/14 00:01:57, Link
Author: JAM
Quote (Daniel Smith @ Oct. 13 2007,23:32)
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.

I already gave you a URL for such a pair--rat vs. mouse. You, predictably, completely ignored the data.
   
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?
     
Quote
Isn't it my hypothesis we're testing?    

We're testing both at once.
     
Quote
What demands?      
Quote
You must show me that the evidence supports this assumed buildup of random mutations first, then we can move on from there.

That's a petulant demand.
     
Quote
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?

Not quite. Your hypothesis predicts that identity will be no different in coding vs. noncoding sites. Predictions are made about observable data, but we both know that you're desperate to avoid that.

You really oughta figure out that "random" only refers to fitness before going on these rants.
 
Quote
Speaking of predictions, I have another one for you:
It's my prediction that random mutations are only neutral or deleterious - never advantageous.

That's not a prediction, it's a hypothesis. Come on, man, this isn't that difficult. Predictions are made ABOUT DIRECTLY OBSERVABLE THINGS.

Let's see if you can grasp this at the second-grade level:
1) The hypothesis that my dog understands the meaning of the word "sit" predicts that that my dog WON'T sit when I say "fit" or "tit" or "sib" or "hit" in the same tone of voice and with the same body language.
2) The hypothesis that my dog does not understand the meaning of the word "sit" predicts that that my dog WILL sit when I say "fit" or "tit" or "sib" or "hit" in the same tone of voice and with the same body language.

Do you get it yet? The prediction is about what you directly observe--whether the dog sits or not.
 
Quote
All advantageous mutations are non-random and are therefore experimentally repeatable.

"Non-random"=/="experimentally repeatable," Daniel. If one does sufficient trials, the random becomes not only repeatable, but predicted. Maybe you should read a primer on the Poisson distribution.
 
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."

That's meaningless without numbers, but that's probably what you were aiming for.

Date: 2007/10/14 10:53:20, Link
Author: JAM
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?

Better, but you still need numbers. Specifically, "rapidly" is not meaningful, because mutation rates are calculated per individual per generation.

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

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?

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

Date: 2007/10/14 11:25:45, Link
Author: JAM
Quote (Daniel Smith @ Oct. 14 2007,10:37)
 
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.

I told you that you were looking at mouse vs. rat in line 3, but you ignored me.
 
Quote
What I want to see is the rat and mouse genome side by side, sequence by sequence.

That's exactly what I showed you in line 3.
 
Quote
That program appears to pick pieces out of the genome and line them up independently of their position in the chromosome.

Utterly, totally false. As I plainly explained to you, this lines up orthologous regions only. If you're going to call me a liar, Daniel, at least have the integrity to do so plainly.
Quote
Basically, I want to start at chromosome 1, bp 1, and see the rat and mouse side by side.  Is that possible?

Absolutely, as long as you're not resistant to basic education.
 
Quote
Quote
 
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.

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"?

Date: 2007/10/14 14:48:24, Link
Author: JAM
Quote (Daniel Smith @ Oct. 14 2007,14:26)
 
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?

"Genes" should be "alleles." Do you understand the difference? It's essential for understanding the concept.
 
Quote
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'd rephrase what Wesley said and point out that your hypothesis predicts that linkage disequilibrium shouldn't be found at all.
 
Quote
I guess I'm not understanding the connection.

It's interesting that you implicitly claim to understand biology sufficiently to claim that you understand it better than we biologists do, but every time someone points to major problems in reconciling it with the data, you become incredibly modest about your intellect.

Do you not see an inconsistency there?

Date: 2007/10/14 14:59:09, Link
Author: JAM
Quote (Daniel Smith @ Oct. 14 2007,14:34)
First, I'm trimming the accusations that I somehow called you a liar because I don't fully understand how VISTA works.
 
You were implying that I wasn't honest despite the fact that I explicitly explained to you that line 3 represented mouse vs. rat, and you complained that "What I want to see is the rat and mouse genome side by side, sequence by sequence." That was precisely what I was showing you. Now, I'm asking if you want to see it.
     
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"?

 
Quote
The designed descent hypothesis accepts that some genetic regions are passed on intact -

Hypotheses don't "accept" things, people do. Hypotheses predict. What percentage of the genome do you mean by "some," Daniel?
 
Quote
... while others are changed during the saltational phase of evolution.  I'm not sure how your objection applies.

I didn't offer an objection. I asked you questions that you are evading. Let's try again. Synteny refers to intact gene orders, not intact sequences.

See if you can answer two questions straight up:

1) When considering man/mouse synteny, what proportion of the genome will retain gene orders?

2) Again, with man vs. mouse (but not synteny), each has ~30,000 genes. According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?

Honest answers will be in numerical form.

Date: 2007/10/14 15:43:18, Link
Author: JAM
Quote (jeannot @ Oct. 14 2007,15:40)
Quote (JAM @ Oct. 14 2007,14:48)
I'd rephrase what Wesley said and point out that your hypothesis predicts that linkage disequilibrium shouldn't be found at all.

I don't see how Daniel's hypothesis contradicts linkage disequilibrium.

He's not implying that a locus undergoes the same selective pressure whatever its genomic background, he's implying that non-coding regions and genes are subject to the same level of selection, on average. Is that right, Daniel?

That all depends on whether "on average" is a part of it, I'd say.

Date: 2007/10/15 14:49:30, Link
Author: JAM
Quote (Thought Provoker @ Oct. 15 2007,13:51)
Hi qetzal,

Thank you for your comment.  You provided some very good points that will take some time for me to respond to.

You correctly pointed out that a tubulin dimer is made up of two tubulin monomers.  This makes for a total mass of 110K amu.

I am adjusting my thinking accordingly.

I think you're missing the much bigger point.

Date: 2007/10/16 15:07:00, Link
Author: JAM
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?

 
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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?

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?

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

Date: 2007/10/16 17:09:50, Link
Author: JAM
Quote (C Gieschen @ Oct. 16 2007,15:26)
John W

The spider part was yours, not blipey's.  My error.  I looked at the aricles and the "tree" is arranged by some appearrance/trait criterion with no relationship to their supposed evolutionary history.

Aren't those the criteria by which we infer their evolutionary history?
 
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All trees are man-made devices and do not prove anything except that we can arrange items in a series.

Trees aren't series, and for sequences, we let computers calculate the trees. Evolutionary theory predicts that with the exception of experimental and systematic errors, THERE WILL BE ONLY ONE TREE THAT FITS THE DATA. If you had bothered to read such papers, you might have noticed that p values are often supplied, and they are tiny.

That's why your objection is not only wrong, but would be irrelevant if it were right.
 
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I will have to find another source.  But do you believe that we have always had AIDS or that it is a recent addition?

When we apply modern evolutionary biology to AIDS, the best hypothesis is that its ancestor moved from chimps to humans in the first half of the 20th century. What's your hypothesis, and what data support it?
 
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Can you prove to me that there were more STDs other than syph. and gon. in decades past?

Yes, but since you made the claim, it's your responsibility to support it.

And if your opinion is that they are new, where did they come from?

Date: 2007/10/16 21:44:35, Link
Author: JAM
Quote (Daniel Smith @ Oct. 16 2007,18:44)
   
Quote (JAM @ Oct. 16 2007,15:07)
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?

Because this has already been done!
 
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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.

Wrong! Completely different, nonhomologous gene. Would you like to see the data?          
 
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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.
     
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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.
     
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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.
     
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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?
     
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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
     
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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.
   
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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?

Date: 2007/10/17 11:50:42, Link
Author: JAM
"I do not accept that mutations of brain cell DNA can result in a creature knowing what to do with structures that have happened to have "evolved" at the same time by coincidence."

Chris, with some exceptions (brain cells NOT among them), all your cells have the same DNA. Any mutations (spontaneous or done by a Designer) that changed our brains would have occurred in the germline, not the brain.

This is elementary high school-level biology, and you clearly don't know it. You're a teacher?

Date: 2007/10/17 19:47:57, Link
Author: JAM
Quote (C Gieschen @ Oct. 17 2007,11:40)
Junk DNA has been found to be not so.

This is false, Chris.

"Junk DNA" is a provisional term. The people who have discovered function for a TINY FRACTION of "junk" DNA are not creationists. We real scientists predicted that SOME "junk" DNA would turn out to be functional.

The vast majority of "junk" DNA still has no known function.

Tell me: what sort of idiot and/or liar would pretend that because a function was found for SOME "junk" DNA, that we should conclude that the entire "junk" category no longer existed?

Note that I'm not accusing you of idiocy or lying, just being laughably gullible. What does your Bible say about bearing false witness?

Date: 2007/10/17 20:35:55, Link
Author: JAM
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.
 
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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?
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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?
 
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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?
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Or does it only compare genes?

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

Date: 2007/10/17 21:03:26, Link
Author: JAM
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
 
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What is "contig"?      

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

Date: 2007/10/18 15:51:13, Link
Author: JAM
Quote (Wesley R. Elsberry @ Oct. 10 2007,09:34)
The real problem is the shortcut epistemology that underlies certain varieties of Christian belief. I'll try to capture this in a shorthand fashion:

1. Christians are commanded to tell the truth.

C1. If another Christian tells you something, you are warranted in taking it as true.

C2. If a non-Christian tells you something, you are warranted in doubting it.

Maybe we can force them to watch the Star Trek episode "I, Mudd."

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Captain Kirk: Harry lied to you, Norman. Everything Harry says is a lie. Remember that, Norman. *Everything* he says is a lie.

Harcourt Fenton Mudd: Now I want you to listen to me very carefully, Norman. I'm... lying.

Norman: You say you are lying, but if everything you say is a lie, then you are telling the truth, but you cannot tell the truth because you always lie... illogical! Illogical! Please explain! You are human; only humans can explain! Illogical!

Date: 2007/10/19 18:21:07, Link
Author: JAM
Quote (Mister DNA @ Oct. 19 2007,18:10)
Quote (Richardthughes @ Oct. 19 2007,17:33)
No "Friday-meltdown" from Dembski.  ???  :angry:

Dembski's busy this weekend. I heard he borrowed DT's pickup truck so that he could move all that lab equipment from Baylor to EIL's new facility.

I thought that he had used a backpack.

Date: 2007/10/19 18:30:37, Link
Author: JAM
Quote (Richardthughes @ Oct. 19 2007,16:07)
 
Quote (oldmanintheskydidntdoit @ Oct. 19 2007,15:58)
 
Quote (Richardthughes @ Oct. 19 2007,14:57)
Okay - we now have IntelligentDesignNews.org

Put up a links page to positive (i.e not dependent on criticizing some aspect of "Darwinism") evidence for ID.#

To keep out the loony fringe (aka BA77) better make it peer reviewed only.

here's my thoughts:

Main page is a variant of the above press release where the date changes each day automatically.

I like that.
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An 'about page' says why the website exists, how it parodies evolution news, discussion on positive evidence, link to talk origins, etc.

I'd omit the first two. How about setting it up in two columns, contrasting "New evidence from the ID movement" with "New evidence from the evolutionists"? You could note new apologetics and quote-mining produced at the bottom.

How about daily rows, with previous days' data being links? The ID ones would link to the daily message on a separate page.
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I also want a "mail me" function so I can post Fundie Screeds here.

You'll get thicker tard if you write it as someone who fervently believes in ID and is desperately waiting for the evidence to be produced by his heroes.

Date: 2007/10/19 20:00:49, Link
Author: JAM
There's some truly awesome tard from ba77. He conflated "six orders of magnitude" with "six-fold."

Date: 2007/10/20 01:00:23, Link
Author: JAM
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.

Second, frameshifts happen to individual genes. The term "frame-shifted bacteria" is gibberish.

 
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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. Moreover, your prediction was based on a false assumption, because more than one enzyme is involved. 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.

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.

Date: 2007/10/20 13:24:21, Link
Author: JAM
Quote (Daniel Smith @ Oct. 20 2007,11:43)
Where specifically did I make this "false assumption"?    

When you assumed that only one gene and one mutation was involved.
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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?  

Because your hypothesis predicts that the same mutation will occur in the same gene. It's not limited to frameshifts or a single species. Your hypothesis is about living things in general.
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How do you know the mutation was random?

Because it was different than the initial one, and in an entirely different gene. Your hypothesis predicts that the same mutations will occur every time. You can't honestly weasel out of it by claiming that it only applies to one species and one gene.

Date: 2007/10/20 13:25:30, Link
Author: JAM
Quote (Daniel Smith @ Oct. 19 2007,18:34)
What's the difference between those two predictions?

One says that the same thing will happen EVERY time, while the other says that the same thing will happen SOME of the time.

Date: 2007/10/20 13:27:58, Link
Author: JAM
Quote (Daniel Smith @ Oct. 19 2007,18:54)
I'm not interested in comparing genes.

BLAST works for the sequences between genes, too, so your evasion doesn't work. That explanation is probably a holdover from the olden days, in which people were more interested in studying individual genes than they were in genomes. Most people still are more interested in the former, btw, you just wouldn't know it from the lay press.

Date: 2007/10/20 14:14:09, Link
Author: JAM
Quote (Daniel Smith @ Oct. 19 2007,18:14)
 
                   
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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.

Interesting. How could you possibly know, since you claim below that you still don't understand what the VISTA graphs mean?          
       
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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 how could you honestly claim that your hypothesis is not in bad shape, Daniel? I don't see how you can flip from certainty to ignorance and retain a shred of credibility.
       
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then I have to know what the parameters of VISTA are (does it ignore the non-coding sites? etc.),

No, it does not ignore non-coding sites. In fact, you were looking at almost entirely non-coding sequences. How's your hypothesis doing?
       
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...and finally I have to interpret these results in the light of designed descent.

No, Daniel, that's utterly dishonest. You make your prediction BEFORE you interpret the data. Remember, you're trying to prevent yourself from fooling yourself.
       
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If, after careful examination, it appears your evidence falsifies my hypothesis, I'll surely admit it.

I don't believe you. Every prediction, explicit and implicit, from your hypotheses has been shown to be wrong, but you claim that it all supports your position.
   
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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.

Yes, there are data--the sequences themselves come up in the browser. What were you thinking they represented?
       
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The only thing I have to go on is your insistence that they falsify my hypothesis.

My only insistence is that you examine the evidence, which you are desperately trying to avoid. Is there some reason why you can't read and/or comprehend the legend in the lower left corner? 
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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?

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
 
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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.
     
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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.

Date: 2007/10/20 14:29:49, Link
Author: JAM
Quote (Daniel Smith @ Oct. 19 2007,18:30)
Thank you.  Once again I'm amazed at the forethought of God!

Umm...then why did you assume that no telomeres were present, that you could just go in at base pair 1 with VISTA?
 
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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.

Yet your perspective predicted that they didn't exist. Can you name a part of the aging process in which telomeres don't work normally?
 
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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.

How do you figure? Contigs and overlapping sequences merely describe the assembly of sequences by humans.

You'll say anything to avoid testing your own hypotheses against the evidence, won't you?    
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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.

How can you be confident when you've predicted the polar opposite in all these cases?

Date: 2007/10/20 23:51:50, Link
Author: JAM
Quote (Daniel Smith @ Oct. 20 2007,18:35)
From Wikipedia:
 
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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.

That passage is bullshit, Daniel. "Junk" DNA is in no way homogeneous, and real scientists don't classify introns as "junk."

The ID approach to "junk" DNA is profoundly dishonest; it ALWAYS depends on equivocating between a tiny fraction of junk and all of the junk.

Every time any IDer talks about it, that dishonesty is displayed. Are you being dishonest or gullible in this case?

Date: 2007/10/20 23:59:32, Link
Author: JAM
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?
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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:
 
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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.

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?

Date: 2007/10/21 00:11:57, Link
Author: JAM
Quote (Daniel Smith @ Oct. 20 2007,19:09)
First, thanks for making it a bit clearer.

You're welcome. Why don't you reread your hypothesis and prediction before replying?
 
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Second, if the protein coding regions are dark blue and UTRs are light blue, what are the pink (CNS) regions?
Are these non-coding?

Yes. 
 
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If so, why are they also so highly conserved between rat and mouse?

By definition. The regions between those regions aren't conserved at all, which falsifies your hypothesis. QED.
 
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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.

God's a cheating kid now? What's His motivation?
 
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BTW, giving credit to "selection" without showing the steps that were selected for is only an assumption and is not grounded in the evidence.    

Assuming that there isn't evidence is dishonest, given your inability to grapple with the evidence that's been served up to you.

Daniel, we have observed inversions and translocations in plants, animals, and people, in real time, and we understand how they can survive. In fact, their mere existence falsifies your hypothesis, because they demolish anything functional at the breakpoints.
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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?

No. For example, we use VISTA to design mouse knock-in constructs (the technology leaves small insertions behind, and we place them in between the pink areas). It makes predictions that we then test, in the process of achieving a different goal.

Date: 2007/10/21 00:19:56, Link
Author: JAM
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.

Date: 2007/10/21 16:45:55, Link
Author: JAM
Quote (Daniel Smith @ Oct. 21 2007,12:53)
 
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?
       
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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:
         
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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.

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.

Daniel, this is utterly, totally, completely, spectacularly false.

"Genes" are in no way synonymous with "coding sequences." Only the exons (blue) are coding sequences. Not only that, but I clearly explained that the introns also were marked on the gene arrows as hash marks.

The introns are NONCODING SEQUENCES.
 
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If you look at the gene markers at the top, you'll see they often extend over white spaces. Like this.

Yes, those are all the noncoding parts of the genes (introns). Your hypothesis is wrong.
 
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As I see it, there is significant constraint amongst coding and noncoding sequences - as well as significant changes.

Your view has no basis in reality.
 
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Nothing here contradicts my hypothesis.

Your confidence and lack of humility is profoundly un-Christian, given your lack of basic knowledge.

Your hypothesis is dead meat.

Date: 2007/10/21 16:57:31, Link
Author: JAM
Quote (Daniel Smith @ Oct. 21 2007,12:55)
 
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

Daniel, any constraint at all gives you a pink area, so according to your hypothesis, everything should be well above that 50% level. That's why I very pointedly asked you the question about why the bottom of the scale is at 50%--to see if you were thinking at all. You weren't. Your hypothesis makes clear predictions.
 
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- 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.

Date: 2007/10/22 20:26:23, Link
Author: JAM
Daniel Smith,Oct. 22 2007,19:26:  "- not that all of it will be conserved. I never said that!"

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."

JAM: What exactly does basically all sequences mean, then?

Here's a question for you. Why didn't you answer that question? You even italicized "all" for emphasis. Now, you didn't mean "all"?
Quote (Daniel Smith @ Oct. 19 2007,18:14)
If, after careful examination, it appears your evidence falsifies my hypothesis, I'll surely admit it.

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

No, first, the evidence falsified your hypothesis and you said that you would admit it.

Instead, your un-Christian pride and your inability to be objective led you to make a patently false claim--that everything within a gene was coding sequence.

                   
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.

Not a problem. We have loads of sequences from mice that can be crossed with each other, despite the fact that they have been classified as different species, and we have inbred strains of house mice, which have been artificially, and completely, inbred for a century. Take your pick.
   
Quote
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.

Yes, and noting that, I asked you to make a simple prediction in response to a simple question:
     
Quote (JAM @ Oct. 14 2007,14:59)
2) Again, with man vs. mouse (but not synteny), each has ~30,000 genes. According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?

You can make predictions for:
race vs. race
strain vs. strain
mouse vs. man
chimp vs. man, etc.

Your hypothesis makes clear predictions in all those cases, doesn't it? Why did you run away from my simple question?
[quote]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.

Yes, and you've just seen that your hypothesis is dead wrong.
   
Quote
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.

We can do the same thing for mouse strains, or mouse "species" that interbreed to yield fertile offspring. It's just not as easy as it is with VISTA, where you had to change basic facts, falsifying your promise to admit that your hypothesis was incorrect.
   
Quote
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.

No, only if you are comparing/contrasting coding and noncoding sequences. You're fudging your hypothesis in addition to the facts now.
   
Quote
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).

False. That was THE HYPOTHESIS BEING TESTED, for Christ's sake.
   
Quote
 A study by Brian Bowen and John Avise (abstract)

Why would you only read/link to the abstract, when the whole paper is freely available?
   
Quote
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.

The BS is getting deep.
1) They looked at RFLPs in mitochondrial DNA. That's coding. Do you know what is special about mtDNA, Daniel?
2) Breeding in this species occurs offshore, so "never been observed" is nothing but pure BS to feed your ego. The authors note this clearly.
   
Quote
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.

So what? The males aren't tagged.
   
Quote
Another example is a study done by Scott Baker (from the abstracts on Google Scholar, I was unsure which one corresponds to this study)

Abstracts aren't evidence. You need to look at the DATA, not your misrepresentations of abstracts.

   
Quote
between Atlantic and Pacific humpback whales - which have been geographically isolated for 3 million years (since the isthmus of Panama separated the two oceans).

I'm sorry, Daniel, but that is just a desperate fabrication:
Humpbacks hang out in Tierra del Fuego. Can you be more blatantly dishonest than that?
   
Quote
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.

It did, eh? The scientists weren't forced to do anything.
   
Quote
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.

False on both counts.
   
Quote
My hypothesis accommodates the known 60-80 million year isolation of the turtles...

Daniel, that is a hypothesis, it is not known.
   
Quote
and the known 3 million year isolation of the humpbacks with no extra speculations added to make the data fit!

And that's just a lie. How can humpbacks be isolated given that they are common in Tierra del Fuego?
   
Quote
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.

Your limb was gone with the VISTA data. You've proven that you'll fabricate rather than test your hypothesis, Daniel.

Date: 2007/10/23 10:38:41, Link
Author: JAM
Quote (blipey @ Oct. 23 2007,09:38)
Quote
So, you can keep badgering me about it, or you can help me understand.  It would help if you try to teach me something rather than keep asking questions or telling me I simply don't understand.  For the moment, I'll allow you to explain it to me as you would a junior high student.  Good enough?


First of all, Ftk, I would like to offer a small commendation to you for appearing interested in the topic of Behe's refutation.  Very nice.  More recently in this thread you seem to fall off the wagon again, but maybe not forever.  I do not say this because you appear to still support Behe's IC argument.  I say this because you are still having trouble addressing the argument and making coherent, logical argument.

I also don't believe that this is your fault.  I don't believe you ever learned to do so; it often is not addressed in American schools.  I would like to offer up my opinion as to why this still seems to be an obstacle for you.  It is because of the bolded portion of your quote above.

You have never seemed to grasp the relationship between knowledge and questions.  Questions are the key to understanding; insight often comes not from out of the blue but rather because you stumbled upon asking yourself the right question.  I don't think you're stupid, I think you often  act stupidly--different things.  I believe you are not interested (or don't realize the importance of) in finding the right questions.

While I think that oldman's and other's comments here are excellent, I don't believe they will have any impact on you until you can change your sentence above to:

Ask me another question; I'll find the answer.

Excellent points.

Science is the process of formulating and addressing questions, not about memorizing facts. More importantly, it's about addressing questions in a way that prevents you from fooling yourself.

In that spirit, I'd suggest that ftk change her response to:

Ask me another question; I'll think of ways in which we could find the answer.

Of course, the ID/creationist movement is all about avoiding attempts to answer questions, because the followers claim to already have the answer. Do they avoid answering questions because they are unable to, or because they are afraid of the answers? I think the latter is more prevalent than the former.

Date: 2007/10/23 21:06:43, Link
Author: JAM
Quote (Richardthughes @ Oct. 23 2007,19:31)
WND IS AWESOME:

http://www.healthresources.net/eoc/landing9.aspx?SC=HEF1549

ALL SCIENCE SO FAR!

"BIG MEDICINE" DOESNT WANT YOU TO KNOW.

Fuck me, is Davetard credulous.

This is the guy I want to be like:

Date: 2007/10/24 11:15:21, Link
Author: JAM
Quote (W. Kevin Vicklund @ Oct. 24 2007,10:10)
 
Quote
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.


I'm going to call shenanigans on this one.  In a 1993 paper, Baker et al. took samples from three major population groups of humpbacked whales.  Geographically, these are located in the North Atlantic, the North Pacific, and the southern oceans.  The results: there was a 3.808% difference in mitochondrial DNA between the North Atlantic and North Pacific populations, which would be the populations affected by the forming of the isthmus.  That's more than 1% per million years, well within the tolerance limit of the very rough 2%/my rule of thumb.  The paper, "Abundant mitochondrial DNA variation and world-wide population structure in humpback whales," can be found at PubMedCentral.  Please note: there's a lot of information there which I didn't bother to communicate, but needless to say, it doesn't uphold Daniel's numbers.

My guess is that Daniel found a paper that dealt solely with the southern oceans population, which is sub-divided into 6 groups.  These 6 groups are not geographically isolated, as others have noted.

We don't even have to read the paper. All we need to do is look at a globe to see the idiocy of Daniel's claim that the isthmus of Panama separated the two oceans. The fact that humpback whales are prevalent at the junction between them (somewhat south of Panama) is a bonus.

Date: 2007/10/28 16:58:12, Link
Author: JAM
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.


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.

So your predictions, in addition to being horseshit because they aren't about anything in particular, have no ability to distinguish between evolutionary theory and whatever it is you think.

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? If not, would you mind commenting on the intelligence of having the same codon that starts protein synthesis also encoding the amino acid methionine?

I ask because it seems really, really stupid to me; I can improve the design with my measly human intelligence. Does that therefore make me smarter than God? Why would one want to worship an unintelligent God? Do you see how the ID movement is bad theology slathered onto nonexistent science?

Since your hypothesis about noncoding DNA was dead wrong, what's your revised hypothesis?

Date: 2007/10/29 00:10:23, Link
Author: JAM
Quote (Mark Iosim @ Oct. 28 2007,18:35)
I am puzzled with random mutation, because it reminds me the protein folding paradox that states: if a protein were to fold by randomly sampling of all possible conformations, it would take about 10E10 years to finish folding.

Can any body help me to find a source of information that explains how random mutation able to produce adaptive changes. What kind of statistical calculations supports this theory?

Thanks

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?

Also, the amount of time it takes a protein to fold is irrelevant to your question, as is the computational time required to predict it. It folds.

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?

Date: 2007/10/30 15:05:02, Link
Author: JAM
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?

Date: 2007/10/31 19:09:02, Link
Author: JAM
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.

Hope that clears up your misunderstanding of JAM's post.

Actually, I wasn't talking about computers at all, but real biology.

Date: 2007/10/31 19:17:36, Link
Author: JAM
Quote (Daniel Smith @ Oct. 31 2007,18:35)
 
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.

You have to do that, otherwise you might have to give up your fantasies for the truth.
Quote
If you want specific, detailed answers, why don't you try starting with a specific example - rather than a vague question?

Because there are many such cases. I'm asking for your explanation, and you came back with nothing but false suppositions.

Quote
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?

Not at all! I can see why you would assume that I wasn't talking about actual biology, though. ;-)

Why wouldn't you ask before spouting nonsense?
Quote
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.

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?

Quote
If you're not willing to give any more info, then be satisfied with general answers.

You didn't give any answers, just false suppositions. You're afraid of the truth.

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?

Date: 2007/10/31 19:26:00, Link
Author: JAM
Quote (Daniel Smith @ Oct. 31 2007,19:08)
More confirmation:

Of what?

Did you read this?

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? What proportion of "junk" is repeat, and what proportion is nonrepeat (unique)?

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?

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.

You lie like a rug, Daniel. The fact that you're lying to yourself doesn't excuse your behavior.

Date: 2007/10/31 21:43:38, Link
Author: JAM
Quote (swbarnes2 @ Oct. 31 2007,20:05)
Quote (Daniel Smith @ Oct. 31 2007,19:08)
So not only is the myth of "junk DNA" being systematically shattered,


I'm curious...do you honestly think that the authors who wrote this paper think that they have shattered major parts of the theory of evolution, as you think this paper has?

If not, why do you think that we should take your grossly ignorant opnion over theirs?

In addition, why aren't these discoveries being made by ID proponents...like, um, at the Discovery Institute?

Why aren't discoveries like these motivating people like you to start careers in science?

You know you're desperately spinning this, and you don't even believe your own spin.

Date: 2007/11/01 19:37:57, Link
Author: JAM
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?

Date: 2007/11/01 19:43:49, Link
Author: JAM
Quote (JohnW @ Oct. 31 2007,15:35)
Today's steaming pile from FTK (my emphasis):

Quote
The oldest known fossil of a 500 million-year-old jellyfish was found in Utah. Wow...looks just like the modern jellyfish on the right. It's interesting that jellyfish have pretty much always looked like jellyfish, birds have pretty much always looked like birds, etc., etc.. Yet, we're also supposed to *imagine* that dinosaurs also evolved from birds. Crazy stuff.


Crazy stuff indeed.

FTK,

Birds evolved from dinosaurs. In fact, they are dinosaurs.

Would you like to look at some nested hierarchies that show that part of the reptiles (the ones that are more related to dinosaurs) are closer to birds than they are to another large group of reptiles? IOW, reptiles are no longer considered to be a separate group from birds?

Nah, you'd just take the illustration that real scientists revise their conclusions based on evidence as an admission that everything must be wrong.

Date: 2007/11/01 20:02:25, Link
Author: JAM
Quote (Daniel Smith @ Nov. 01 2007,19:48)
   
Quote (JAM @ Oct. 31 2007,19:26)
 What proportion of "junk" is repeat, and what proportion is nonrepeat (unique)?
There is no junk

I'm sorry, but I don't understand your sentence fragment.
 
Quote
 
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".

Of course not! YOU did, and you said that THIS PAPER was the evidence. Which one of us is the tard here?
 
Quote
 
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.

The answer isn't in the paper. You'd have to know the answer before concluding that this was evidence supporting your claim that "junk DNA" was:

1) a myth, and
2) being "systematically shattered."

You're just lying, Daniel. Hell, the VISTA output showed you what proportion is made up of repeats, so you've already been shown the relevant evidence in detail, but as usual, you ignore it in favor of wishful thinking and rank dishonesty.
    
 
Quote
 
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.

I didn't say it was in the paper. Having that information is a prerequisite for your claim, though, if you thought that this was evidence supporting it.

Wishful thinking doesn't excuse lying.
 
Quote
Are you equating repeat sequences with "junk"?

No, obviously, I'm not. This paper explicitly dealt with nonrepeat sequences. If I ask you the simple question, "How much of what is classified as "junk DNA" is made up of repeats?" it's pretty damn obvious to anyone who isn't socially retarded that I am very well aware that some is made up of repeats, and some isn't. For you to use this as evidence for your fantasy hypothesis, you need to know the proportions. Not only don't you know, you are afraid to learn.   
 
Quote
 
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!"

No, you already falsely accused me of namecalling. I am accusing you of specific lies. For all I know, you might be a paragon of honesty, but I doubt it.

What does the Bible say about bearing false witness? What does it say about judging on the basis of mere hearsay?
 
Quote
What are we - in 3rd grade here?

No, I'd say you're at about 6th grade in terms of biology.
 
Quote
You may be a smart, educated guy - but you're socially retarded.

Does that make you feel better? How would it excuse your relentless lying?

Date: 2007/11/01 20:08:14, Link
Author: JAM
Quote (Daniel Smith @ Nov. 01 2007,19:50)
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.

I'm not playing games. I'm anticipating your predictably dishonest and cowardly game, Daniel.

Date: 2007/11/02 20:24:57, Link
Author: JAM
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.

Date: 2007/11/03 01:17:45, Link
Author: JAM
Quote (Art @ Nov. 02 2007,22:05)
Behe passes off ubiquitin-mediated degradation as gumming things up.  Apparently, he is not impressed with, um, sex determination, photomorphogenesis, neurogenesis, eye development, meiosis, root development, etc., etc., etc.  (These and more all involve Ub-mediated protein turnover.) I wonder if he has written Stockholm, demanding that the 2004 Nobel Prize in Chemistry be revoked.

I'm amazed at how much biology he has to shove under the rug, just to save his book.

That's might be a good stiletto, Art. Have you ever tried it on any lay subjects? They at least get the idea of the Nobel in Chemistry.

From my dealings with the Tard, it seems to draw a lot of its force from the idea that those of us who argue against it study only evolution.

Date: 2007/11/03 01:21:31, Link
Author: JAM
Quote (Jim_Wynne @ Nov. 02 2007,21:49)
My demise came about as I stuck a needle into one of DT's known soft spots, that being randomness and probability. Unfortunately, I was unable to respond to this gem from Kairosfocus, which came just before the button was pushed:
 
Quote
What we deal with on scientific knowledge is revisable inference to best explanation, and the objection that something utterly improbable just may happen by accident is not the prudent way to bet in such an explanation, once it has crossed the explanatory filters two-pronged test. [The probabilities we are dealing with are comparable to or lower than those that every oxygen molecule in your room could at random rush to one end, causing you to asphyxiate; something you don’t usually worry about I suspect, and BTW, on pretty much the same statistical mechanical grounds, as I discuss in the appendix A, in the always linked. In a nutshell, the statistical weight of the mixed macrostate is so much higher than that of the clumped one, that we would not expect that to happen just once at random in the history of the observed cosmos.]


"...something utterly improbable just may happen by accident..."  Tard at its finest.

He wrote something that short?

Date: 2007/11/03 11:20:10, Link
Author: JAM
Quote (Louis @ Nov. 03 2007,04:51)
I don't see why my knowing a reasonable amount about a subject before I discuss it is somehow a point AGAINST me.

There's your problem right there!

You need to see it through a cultural lens that treats a guy who was:

1) born in Connecticut
2) to an incredibly wealthy family
3) who never worked an honest day in his life
4) who was a mediocre student at Yale and Harvard
5) a deserter during the Vietnam war
6) a cokehead and alcoholic
7) a cheerleader at an exclusive prep school

...as a down-home Texan and real man you'd like to have a beer with.

Date: 2007/11/03 20:17:40, Link
Author: JAM
Quote (Daniel Smith @ Nov. 03 2007,16:05)
 
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...

Yes, I am too. Did you notice that Kevin predicted your weaseling perfectly?

Quote
Meanwhile, here's a graphic description of the overwhelming complexity within the multi-layered encoding within genomes:

In what way is it "overwhelming" if it can be so concisely described? Is it more overwhelming than the fluidity and fuzziness of endocytic pathways, for example?
Quote
Quote
Figure 2. Transcriptional complexity of a gene.

And how is that more overwhelming than the complexity of the multitude of functions of the product of that gene? What about alternative splicing?

And why were you lying and claiming that this says anything about junk DNA?
Quote
Although this illustration is hypothetical, it represents what the author expects to find...

But the author isn't a creationist. Why didn't you find what YOU predicted you'd find? Why did you go off searching for something else to cherry-pick and misrepresent instead of revising or discarding your hypothesis about coding vs. noncoding conservation?
Quote
... and indeed what the ENCODE scientists did find, in their recent groundbreaking research.

But none of those scientists are creationists either, and no creationist or ID proponent predicted this, so your attempt to spin it after the fact is just plain dishonest. If you aren't predicting, it ain't science.
Quote
This prompted the author to make this statement:

Quotes aren't data. You struck out when we dragged you kicking and screaming to the actual data.
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.

We've already reconsidered it (successfully) several times in my lifetime, every time in an evolutionary context, so I don't see this as helping you out. Can you offer more than platitudes about how overwhelming it is to you?

Date: 2007/11/04 01:18:39, Link
Author: JAM
Quote (jupiter @ Nov. 03 2007,21:41)
Quote (carlsonjok @ Nov. 03 2007,13:52)
 
Quote (JAM @ Nov. 03 2007,11:20)
 
Quote (Louis @ Nov. 03 2007,04:51)
I don't see why my knowing a reasonable amount about a subject before I discuss it is somehow a point AGAINST me.

There's your problem right there!

You need to see it through a cultural lens that treats a guy who was:

1) born in Connecticut
2) to an incredibly wealthy family
3) who never worked an honest day in his life
4) who was a mediocre student at Yale and Harvard
5) a deserter during the Vietnam war
6) a cokehead and alcoholic
7) a cheerleader at an exclusive prep school

...as a down-home Texan and real man you'd like to have a beer with.

You forgot:

8. Owns a multi-thousand acre ranch without a single horse in residence.

Just saying.......

I am most reluctantly offering this defense of GWB. He is not, in fact, owner of a "multi-thousand acre ranch" in Texas.  The "ranch" is a mere 1,500 acres. Which is plenty big enough, in that part of the state. The multi-thousand acre spreads (e.g., King Ranch) cover land so arid that you need several acres to support a single head of cattle.

Not that GWB runs any cows, either. They might get in the way of his brush-clearing.

And—here's your moment, carlsonjok—GWB has no horses there because he's askeered of 'em.

I forgot about that--but you forgot that it's not really a ranch. Before he bought it and called it a ranch, it was a pig farm.

Date: 2007/11/04 15:00:41, Link
Author: JAM
Quote (Daniel Smith @ Nov. 04 2007,12:50)
First of all, we all have preconceived ideas we are hoping to verify.

But scientists TEST their preconceived ideas. They try to falsify them. You don't do that.
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Many here have a preconceived notion that there is no God.

I'd say that NO ONE here had such a preconceived notion. More accurately, some here have decided that, AFTER looking at the evidence.

BTW, I don't have that notion, so if you are referring to me, you're once again showing your utter contempt for the Ninth Commandment.
Quote
So even if there really is a God, they are forced to find another explanation - no matter how ridiculous.  Is that "seeking the truth"?

Why don't you look in the mirror?

To falsely claim that you've seen no evidence to refute your preconceptions, you've blatantly lied about the classification of noncoding sequences within genes (primarily introns). Not only that, but your lies contradict each other!

1) When looking at VISTA, you lied and claimed that noncoding sequences within genes were coding regions.

2) Just above, you lied again, claiming that noncoding sequences within genes were classified as "junk."

3) In reality, noncoding sequences within genes (promoters, 5' and 3' UTRs, and introns have NEVER been classified as "junk."

Now, even if you refuse to believe #3, #1 and #2 are complete contradictions.

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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.

That's a lie. You've chosen to lie about the evidence instead.
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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.

So how can introns be both coding sequences and junk sequences in your addled mind?
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The molecular evidence shows an extremely complex, sophisticated, multi-layered coding system that defies any unguided evolutionary explanation.

You're lying again.
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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.

And again.
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In fact, the more I learn, the more convinced I am of the infinite intelligence of the designing God.

How does studying nonrepeat sequences within and near genes reclassify "junk" DNA, then?
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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?

Absolutely. But I've looked at and produced far more evidence than you have, and the NATURE of the complexity (particularly related, but nonidentical parts with partially-overlapping functions) I see and grapple with every day doesn't even remotely suggest intelligent design.

And, unlike you, I'm honest about the evidence.

For example, if God designed your body, He clearly understands the concept of plumbing. Why is there nothing analogous within cells, then? 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? Is your God stupid? Mine sure isn't.

Date: 2007/11/05 00:37:20, Link
Author: JAM
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.

Therefore, you were bearing false witness (check that Ninth Commandment!) when you called them "theories." Theories are hypotheses that have a long track record of withstanding tests designed to falsify them. None of your heroes are willing to do that.
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Their ideas were ridiculed - because they did not fit the current paradigm,

The fact that they are ridiculed doesn't make them right. If they are being ridiculed, they should get to work testing their hypotheses.

Virologists ridiculed Stan Prusiner and his prion hypothesis in the early '80s, too. Did Prusiner blog or write books aimed at lay people? No, he tested his hypothesis inside and out. In 1997, he won the Nobel.
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but I've seen no convincing evidence against them.

We've seen how you can ignore blatant evidence when it's right in front of your face, Daniel. Your credibility is zero.
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...how many have systematically and thoroughly reviewed it and presented convincing evidence against it?  I've not seen any.

It's not our responsibility to "present convincing evidence" against anything, you goof. It's DAVISON'S responsibility to TEST his hypothesis, but he won't. That's the main reason why real scientists ridicule Davison and Behe.
Quote
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.

Again, you can't be bothered to look at the evidence after you make a prediction. You see just what you want to see, and you tell blatant lies. Make a prediction. Do an experiment. Make an observation. Produce new data.

Date: 2007/11/07 09:10:40, Link
Author: JAM
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?

Date: 2007/11/09 15:03:16, Link
Author: JAM
Quote (Daniel Smith @ Nov. 09 2007,13:51)
     
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.

I'm still waiting for you to answer some questions, starting with your predictions for the paper:
------------
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?

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?

------------
And some others:
-------
In addition, why aren't these discoveries being made by ID proponents...like, um, at the Discovery Institute?

Why aren't discoveries like these motivating people like you to start careers in science?

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?

...would you mind commenting on the intelligence of having the same codon that starts protein synthesis also encoding the amino acid methionine?

I ask because it seems really, really stupid to me; I can improve the design with my measly human intelligence. Does that therefore make me smarter than God? Why would one want to worship an unintelligent God? Do you see how the ID movement is bad theology slathered onto nonexistent science?

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?

What does "nonrepeat" mean, Daniel? 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?

For example, if God designed your body, He clearly understands the concept of plumbing. Why is there nothing analogous within cells?

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?

According to your hypothesis, how many human genes won't have a mouse ortholog and vice versa?

You can start with the bolded ones.

Date: 2007/11/10 01:05:12, Link
Author: JAM
Quote (Daniel Smith @ Nov. 09 2007,23:32)
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?

In this case, protein-protein binding.
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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.

Yes, the standard creationist response to this paper is profoundly silly, which is why I'm asking ahead of time.
Quote
Are you asking for a general level for "lack of function"?

No, I'm just asking if a million-fold reduction crosses the line for you.
Quote
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.

Good.
Quote
What does that have to do with the paper you refuse to show me?

I'm not refusing to show you; I'm just heading off an evasive, dishonest response.

http://www.springerlink.com/content/hhcx0pur3545x7v3/

Date: 2007/11/10 01:06:09, Link
Author: JAM
Quote
Quote
In addition, why aren't these discoveries being made by ID proponents...like, um, at the Discovery Institute?

I don't know.

My hypothesis is a lack of faith.
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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.

People change careers all the time, and I think that I can confidently say that science is not a hobby for you.
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Apparently I was.  You are right, the code is simple, what it codes for isn't.

Thanks for admitting that. I'm impressed.
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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!

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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?

Huh?
 
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Does that therefore make me smarter than God?

No.                    

Why not?
 
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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?
 
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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?

Date: 2007/11/10 01:07:57, Link
Author: JAM
Quote
   
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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.
   
Quote
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.
   
Quote
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%.
   
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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.
Quote
   
Quote
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?
   
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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.

BTW, I did an experiment today that had a really exciting result. My prediction was wrong.
   
Quote
Now, will you show me the paper?

See the link to the abstract above.

Date: 2007/11/11 13:05:32, Link
Author: JAM
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.
Quote
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.

Date: 2007/11/11 13:25:25, Link
Author: JAM
Quote (Daniel Smith @ Nov. 10 2007,11:05)
   
Quote (JAM @ Nov. 10 2007,01:07)
 
Quote
 
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.

Two weeks.
Is this information in the paper you linked to?

No. It's a completely different case.
 
Quote
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?
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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.
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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.
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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.
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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? WTF do these saltational events involve, then?  
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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.
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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. ;-)

Date: 2007/11/11 13:44:36, Link
Author: JAM
Quote (Daniel Smith @ Nov. 10 2007,11:26)
 
Quote (JAM @ Nov. 10 2007,01:06)
...would you mind commenting on the intelligence of having the same codon that starts protein synthesis also encoding the amino acid methionine? ...

Not necessarily.  Many genomic sequences are multi-functional - containing overlapping coding and non-coding functional sequences.

That has absolutely nothing to do with my question, and I suspect that you know it.
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Perhaps we just don't know the functional advantage for combining the codon that starts protein synthesis and methionine.      

So you aren't capable of recognizing intelligent design?
       
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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?[/quote]Why don't you engineer a better design and show it to the world?      [/quote]
Switch one of the present serine codons to "start." That provides huge efficiency and energy savings.
         
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Does that therefore make me smarter than God?

No.                    

Why not?[/quote]It just means you think you're smarter than God.[/quote]
That's completely dishonest of you, given that I don't claim that God designed protein synthetic machinery. YOU claim that life was intelligently designed. I don't.
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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?

Again, your argumentative tactics are completely dishonest. YOU claim to be able to recognize intelligent design in biology. I don't. I'm pointing you to a well-controlled example in which one aspect of design is unequivocally unintelligent RELATIVE to another aspect within the SAME mechanism.
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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".

Similar, but not identical, components with partially-overlapping functions.

Name a designed object that has those characteristics.

Date: 2007/11/11 13:53:13, Link
Author: JAM
Quote (Daniel Smith @ Nov. 10 2007,12:30)
 
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.

First, you're not familiar with all the evidence, so you can't make such a claim in good faith. Second, attempting to explain all the evidence isn't enough; it's about making and testing predictions. That's what "testing a hypothesis" means.
 
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Berg based his theory on years and years of his own observations in the field, as well as the documented observations of countless others.

Why not just admit that he never tested his hypothesis?
 
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Both of these men were scientists of the highest regard in their respective fields who based their theories on observed, documented phenomena.

You're lying again. It's not a theory unless it's been tested many, many times, and they are definitely not held in high regard if they don't test their own hypotheses. This is the very essence of science, Dan, and you reject it.
 
Quote
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.

None of those things verifies his mechanism. He hasn't tested it, which means that it isn't science at all.
 
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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.

Baloney. They are ignored because they don't test their hypotheses.
 
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No one wants to lose their position over such things, so they stick to the paradigm.

That's simply a lie, as the way to become famous in science is to overturn dogma. One needs data to do that, though.
 
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That's my guess.

No, it isn't. That's disregard for the truth coupled with wishful thinking.

Date: 2007/11/11 13:57:49, Link
Author: JAM
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?

Date: 2007/11/11 16:11:48, Link
Author: JAM
[quote=Daniel Smith,Nov. 11 2007,14:58]      
Quote

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.[/quote]
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?
   
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What percentage of these repeats are thought to be functional?  

As families, zero. However, evolutionary theory predicts that copies near/inside genes will be coopted.
   
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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.

Virtually all evolutionary scientists? Quote ten of them. The reality is that the ones who say things like that tend not to study evolution.
   
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If it doesn't look designed, what are they talking about?

They are talking about the parts that are apparently designed. Can you find a single instance of a scientist referring to the design of endocytic (plumbing) pathways?
   
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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".

Then how can you have any confidence if you've only been exposed to creationist spoonfeeding of quote mines?

And above, you tried to weasel with "provided you can come up with a better workable system." The problem is that I can point to the fact that the SAME DESIGNER (according to you) came up with a much more intelligently-designed system. I don't have to; I only need to point out the contrasts.

   
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My expectation though, is that I will recognize much more design in it than you give credit for.                

Then go for it. 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.
   
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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.

And what's lost/discarded is lost/discarded. So what's the ratio of the two classes after a typical saltational event?
 
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You'd have to know the function of each gene in order to answer your question.

Not at all. You're weaseling because you have no faith in your position.
 
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You'd also have to know how many saltational events took place between mouse and man.

For grins, let's say just one. How many genes?
 
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I don't have that knowledge.  Maybe it can be answered - I don't know - I know I can't answer it.                  

I'm not expecting you to ANSWER, I'm expecting you to PREDICT. There's a world of difference that you can't bring yourself to acknowledge.
 
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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.

You don't need knowledge--you have a hypothesis that makes predictions. Let it go and do science! It's the most reliable way to gain useful knowledge about the world.

Date: 2007/11/11 16:32:16, Link
Author: JAM
[quote=Daniel Smith,Nov. 11 2007,14:58][quote=JAM,Nov. 11 2007,13:25]               [quote=Daniel Smith,Nov. 10 2007,11:05]                     [quote=JAM,Nov. 10 2007,01:07]                   [quote]                    
Quote

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. 
Quote
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.

No, that wasn't your original prediction, and it's not even remotely scientific. Your original prediction was wrong, and you lied and claimed that introns were coding to save it.
Quote
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.

"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.

"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!

"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 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'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?
Quote
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.
Quote
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.

Date: 2007/11/11 16:42:12, Link
Author: JAM
Quote (Daniel Smith @ Nov. 11 2007,15:09)
 
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",

What don't you understand about it? Prusiner tested his prion hypothesis and generated hundreds of papers worth of data. I've tested my own hypotheses, often found them to be wrong, and still published plenty of papers with new data. Hypotheses only have value when they are tested, and they retain this value even when they are wrong. Those who aren't willing to test their hypotheses are frauds and cranks.
 
Quote
...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.

I didn't see any with data that corresponded with what you were citing.
 
Quote
Unfortunately most of Schindewolf's papers are in German.

Not a problem, as the data are almost always in tables and figures. Why not just come clean and admit that none of your heroes have sufficient faith to test their hypotheses?

Date: 2007/11/11 16:43:39, Link
Author: JAM
Quote (VMartin @ Nov. 11 2007,11:38)
Did anyone of you published so young in the Nature (if you have ever published there something)  that entitles you to dismiss your antidarwinian adersaries who  published there as "confused"?

Yes, yes, and yes, too.

And you?

Date: 2007/11/13 01:19:34, Link
Author: JAM
Quote (Daniel Smith @ Nov. 12 2007,22:15)
[the molecular evidence is] More massive than the millions and millions of fossils collected over several hundred years?            

Yes! That's why dishonest IDers/creationists want to talk about fossils instead. It's easier to obfuscate.
   
Quote
   
Quote
"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.        

You're being incredibly dishonest, Dan.

YOU defined a lineage as containing both African and Asian elephants, two different genuses within the same family. Rats and mice have the same relationship, so you've got no wriggle room.
   
Quote
First, I have no idea what VISTA's parameters are or how it does what it does.

So you were lying when you claimed that what you saw on VISTA supported your hypothesis. I'm glad we cleared that up!
   
Quote
   
Quote
"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.

Your prediction is all about which regions accumulate mutations. You're frantically invoking the Big Creationist Lie of randomness. Do you even have a clue that the "random" in "random mutation" is extremely limited? That mutations don't occur at random places? That they are only random wrt fitness, not truly random in any other way?
   
Quote
   
Quote
"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?

You tell me. Do you realize that you've stumbled into making an easily testable prediction?
   
Quote
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?        

You tell me! You're the one predicting that such genes even exist. Let's get to a more specific prediction: do you predict that whales are lacking "hind leg genes"? What sort of "hind leg genes" or "opposing thumbs genes" do you predict will exist?
 
Quote
I've been systematically reading through several of the ENCODE consortium's papers, and I feel very confident of that one ["anything that is transcribed would qualify as functional"].

Good! Let's take that into a more specific case. I have a gene, and both mice and humans homozygous for the null allele die shortly after birth. 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?
[quote]  
Quote
I'll also predict that soon it will be found that pseudogenes are much more functional than previously thought.

Again, "much more functional than previously thought" is not a scientific prediction. Scientific predictions are not dependent on anyone's opinion, they must be predictions about what is actually observed.
Quote
My guess is that they are used as a sort of redundant blueprint for regulation of their true gene counterpart.

Great! Are you willing to bet your house on it?
Quote
I'd also not be the least bit surprised if repeat sequences were found to be functional - would you be?        

I think only someone who is dishonest, an idiot, or both would ask such a question, as I JUST TOLD YOU OF A CLASS OF FUNCTIONAL REPEATS--rRNA genes. Are you drunk, Dan?

I wouldn't be so arrogant and stupid as to lump all classes of repeats together, and I also just told you which repeats MET predicts will be functional.

Now, why would an intelligent designer use repeats as spacers, when repeats expand and contract all the time because of unequal crossing over? An intelligent designer would use unique sequence as a spacer.

Date: 2007/11/13 01:26:01, Link
Author: JAM
Quote (Daniel Smith @ Nov. 12 2007,21:25)
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?

No. Is this the best you can do? How does "Darwin is responsible for testing his own hypothesis" imply "only Darwin can test his hypothesis"? Do you not see the utter cowardice of expecting others to present evidence to refute your hypothesis when you are too lazy to use it to make and test its predictions yourself?

Do you realize that it wasn't a theory when Darwin proposed it (accompanied by more new data than have been produced by the entire ID movement by testing their own hypotheses in the 150 years since)?

Date: 2007/11/13 11:00:59, Link
Author: JAM
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.
 
Quote
...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.

Date: 2007/11/17 10:30:20, Link
Author: JAM
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?

And if it's a scheme, why don't you understand it? And if it supports your hypothesis, why didn't you predict it?


Quote
(I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

You don't know what you're talking about. Given that, how can you ethically reach the conclusion that we don't know what we are talking about?
Quote
They also show quite clearly that most of the human genome is transcribed and functional.

Now you're just lying. You haven't shown that transcription necessarily implies function. I already asked you to make a prediction about the relationship between the time transcription of an essential gene begins and the time at which the null mutant has a phenotype, but you ran away.
Quote
These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

So what? That does absolutely nothing to support a design hypothesis.
Quote
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)?

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.
Quote
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?

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.

Bearing false witness is a sin in my Bible, Daniel.

Date: 2007/11/17 13:31:49, Link
Author: JAM
Quote (Daniel Smith @ Nov. 15 2007,15:39)
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.
       
Quote
...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.

What should convince you, assuming that you were an honest person, was that your prediction was dead wrong. This is why we have the scientific method.
Quote
Until I know what VISTA does and how it does it, I'll have to reserve judgment on it.

It takes you right down to the sequences themselves, Dan. What more is there to know?
Quote
You are convinced (based on VISTA) that I am wrong.

No, I know from decades of professional experience that you are wrong. I merely chose VISTA as a way to present the evidence.
Quote
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.

You already know that you are wrong. That's why you are afraid to pursue the predictions you made in your last response to me.

Do you predict that whales will be missing a hind-leg gene? Do you predict that monkeys have a tail gene that humans lack? 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. This is why ID is first and foremost bad theology.
Quote
All I'm saying is, I'm not seeing what you're seeing (yet at least).
Have you considered opening your eyes to what God Himself has written in the book of nature?
Quote
 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.
 
So how do you explain why you believe your bottom line more than mine, given your lack of knowledge?
Quote
Please be patient with me and please stop accusing me of lying whenever I make ignorant statements!

Then please don't pretend to know things that you don't know. That's lying.

Date: 2007/11/18 15:30:45, Link
Author: JAM
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? I'm particularly interested in your answers to these questions:

A) Do you predict that whales will be missing a hind-leg gene? Do you predict that monkeys have a tail gene that humans lack? 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).

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?

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?

Date: 2007/11/19 00:38:46, Link
Author: JAM
[quote=Daniel Smith,Nov. 18 2007,19:19]  [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?[/quote]
No.[/quote]
Then maybe you should respond.
Quote
Quote
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.

Genes don't "develop." Organisms and organs do.
Please define "it" in this context. Does your hypothesis predict that there will be anything that we humans could call a "hind-leg gene" based on analogies with our own designs?
Quote
IOW, the non-coding "support cast" for that gene will be markedly different from animals that have fully developed hind legs.

Please define "markedly" in this context. It's important.
Quote
Quote
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.

Does your hypothesis predict that there will be anything that we humans could call a "tail gene" based on analogies with our own designs?  
Quote
Theirs will have much more activity and development

Again, the term "development" is gibberish in this context, and "activity" means transcriptional activity in this context. Is that what you mean?
Quote
in these non-coding areas - possibly evidenced by a markedly higher level of histone activity.

What do you mean by "histone activity"? Again, it's important.
Quote
Ours will be suppressed.

Our what, exactly? It has to be measurable. Please provide units.
Quote
Quote
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?

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.
Quote
It gets tiring after awhile.

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?
Quote
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.

What sort of character makes grandiose claims without evidence, and then discounts the evidence?
Quote
Quote
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"?

The former.
Quote
Because I think transcription of the gene will always be happening,

Why would you think that? WTF do transcription factors do?
 
Quote
 but as to when exactly the gene gets turned on, I have no clue.

Why not? Wouldn't an intelligent designer design it so transcription was turned on when (and where) it was needed, and not before or in other tissues?
Quote
Quote
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".

I'm sorry, but I don't see what the children who suffer and die are learning. Why shouldn't you and your children be suffering and dying?

Date: 2007/11/21 11:05:18, Link
Author: JAM
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?

And if it's a scheme, why don't you understand it? And if it supports your hypothesis, why didn't you predict it?


 
Quote
(I put "coding" in quotes since most of the genome "codes" for things other than proteins and so is currently classified as "non-coding").

You don't know what you're talking about. Given that, how can you ethically reach the conclusion that we don't know what we are talking about?
 
Quote
They also show quite clearly that most of the human genome is transcribed and functional.

Now you're just lying. You haven't shown that transcription necessarily implies function. I already asked you to make a prediction about the relationship between the time transcription of an essential gene begins and the time at which the null mutant has a phenotype, but you ran away.
 
Quote
These scientists are suggesting that a re-defining of the most basic term in genetics - the gene - is necessary.

So what? That does absolutely nothing to support a design hypothesis.
 
Quote
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)?

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.
 
Quote
And...
Is that why none of you want to talk about it?  Does it cause difficulties for you?

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.

Bearing false witness is a sin in my Bible, Daniel.

Daniel, by what twisted logic do you describe this post as running away?

YOU are the one running away.

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?

Date: 2007/11/22 10:08:13, Link
Author: JAM
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.
 
Quote
 
Quote
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? Your failure to address this important point demonstrates why fondness for ID correlates so highly with ignorance about biology. It also illustrates the hypocrisy of abandoning analogies when they don't support your predetermined conclusion.

 
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?
 
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.
 
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?

Date: 2007/11/22 18:21:06, Link
Author: JAM
Quote (Daniel Smith @ Nov. 22 2007,10:57)
If the mechanisms for the production of new types is the reordering of the chromosomal structure of existing types,

Daniel, AFAIK, there is ZERO evidence that the reordering of chunks of chromosomes by inversions, translocations, etc. had anything to do with the "production of new types," whatever the hell "types" means in this context. We know that heterozygosity for inversions and translocations is selected against (leading to rapid fixation), but there's not a lick of evidence that any of the inversions or translocations increased fitness when homozygous.

You grossly underestimate the complexity of the genome. Do you not see any irony in that?

 
Quote
... 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.

Then you also would predict that they have functional significance. Where's your evidence?
     
Quote
You seem to be arguing against de-novo creationism more than my stated views.          

Daniel, you really need to reduce your misrepresentations of the views of others (as well as your far more egregious misrepresentations of the evidence itself) before accusing others.
     
Quote
     
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.

ORLY?
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?

   
Quote
D: ...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.

J: So, in your hypothesis, saltational events have nothing whatsoever to do with new genes and proteins?

D: They do, but only the necessary genes are retained, while others are reordered.  What's retained is retained.

J: And what's lost/discarded is lost/discarded. So what's the ratio of the two classes after a typical saltational event?


Get busy, Dan. ALL of these questions relate DIRECTLY to the NATURE of the complexity you claim to be so convincing, yet you've dodged them.
   
Quote
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?

See above.
   
Quote
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.            

The ENCODE data are pretty nonspecific so far.
 
Quote
 
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)
 

Yes, Dan. Reread the sentence you are pretending to challenge. See the word "drift"? What does it mean? The paper I sent you was about the power of selection to produce function from a random sequence.
   
Quote
   
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.

Why did Rob and Ed choose to do what they did in Drosophila, then, if they weren't testing a hypothesis? What do you hypothesize that the intragenic RNAs code for?

Do you see your hypocrisy here? Your IDers claim to have made all these predictions, but are afraid to invest time, effort and money to test any of them, while when biologists invest time, effort, and money to test a prediction, and you deny, from a position of aggressive, utter ignorance, that they weren't testing a hypothesis. Sheesh.
 
Quote
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.

No, I haven't. You are so far from understanding the data that it isn't even funny.
 
Quote
 That's it.  You have not made a prediction that tests a certain mechanism.

They predicted a certain mechanism, and AFAIK, their data are consistent with it. That mechanism isn't a part of your hypothesis nor your ridiculously vague predictions.

Date: 2007/11/23 13:02:21, Link
Author: JAM
Quote (VMartin @ Nov. 18 2007,12:47)
JAM  
Quote

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"?

It's a purely descriptive term. It simply means that the repeats read in the same direction, in contrast to inverted repeats, in which they read in opposite directions.
 
Quote
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?

We can't distinguish between your alternatives, because we know that tandem repeats expand and contract at very high frequencies, IN REAL TIME, by unequal crossing-over during both mitosis and meiosis. IOW, tandem repeats aren't very stable, so it would be stupid to employ them as spacers if one is designing a genome.

Date: 2007/11/26 13:18:15, Link
Author: JAM
Quote (Daniel Smith @ Nov. 23 2007,13:47)
 
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:

I have trouble buying that, as those are questions that I have already asked you, but what the hey:
 
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?). Again, the probability that a transcript or transcription serves some function will be highly correlated with proximity to genes.

Date: 2007/11/26 16:07:03, Link
Author: JAM
Quote (Assassinator @ Nov. 26 2007,13:22)
Quote
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.

At biology class we calculated that about 1.7% of the whole human genome is for coding. Is that correct?

Yes, but that would be a minimum.

Note that Daniel is making a mammoth error in assuming that transcription implies function.

I think that he is beginning to realize that, too.

Date: 2007/11/26 23:13:34, Link
Author: JAM
Quote (Frostman @ Nov. 26 2007,21:37)
This post is to document my recent banning at Telic Thoughts (telicthoughts.com).  Like here, my username there is Frostman.

...Therein lies the tale of Frostman's adventure with Telic Thoughts.  If I were to speculate, I would cite the various times in which Bradford was cornered by my direct questions.  For example, in one thread, I asked the same question eight times and he would not respond, as the question clearly indicated he made a mistake in reasoning.  He eventually responded by warning me that I was trolling.

Bradford is incredibly stupid, incredibly ignorant, and incredibly dishonest. The three qualities have a delightful synergy.
Quote
I must say Bradford's meltdown was interesting to watch.  He threw the Telic Thoughts deletion policy out the window while behaving quite dishonorably.

That's the norm at TT, not the exception.
Quote
Apparently the motivation was to avoid losing face at all costs.  The light at the end of the tunnel is the cognitive dissonance he will feel as a result.  As all that dissonance adds up, he may eventually question those things he holds dear about himself.

There's not a chance in hell of that happening.

Date: 2007/11/26 23:29:22, Link
Author: JAM
[quote=Daniel Smith,Nov. 26 2007,19:15]
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.[/quote]
Obviously, you haven't reflected enough.
Quote
Am I really accusing you (and the other real scientists here) of something?  If so - what?

Incompetence and dishonesty.
Quote
 And what are my motives?

Ego.
Quote
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.

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.
Quote
I look at the inner workings of life as a way to learn more about God.

But you don't look at any inner workings, Dan, you only look long enough to concoct a lie that supports your political positions.
Quote
I'm not interested in biology for biology's sake.  These are my motivations.

You're simply not interested in biology for any sake at all.
Quote
So from a theological perspective, when I look at the inner workings of the genome, I expect to find complexity and function.

So why do you keep lying and claiming that transcription of a DNA sequence is sufficient to conclude that it is functional?

Why wouldn't you expect elegance in something designed by God?

Why aren't you answering the questions you said you'd answer?
Quote
It has nothing whatsoever to do with my knowledge of biology.

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.
Quote
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.

Accepted.
Quote
I should have prefaced everything with "From my theological perspective...".  Then perhaps my arrogant points would have been seen in their true context.

Your perspective isn't theological, either. As my minister said, "Creationism and ID aren't merely bad science, they are bad theology."
Quote
I've been reading the ENCODE paper on pseudogenes.  This paper, and my reaction to it, clearly illustrate (for me) my motives.

Indeed.
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?
Quote
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.

I don't see that you have very much knowledge of God, as one of "his ways" is evolution, which you clearly reject completely.
Quote
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.

That's because you're not really looking at biology.
Quote
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.

Why? Because you'll just lie about the data that don't fit your beliefs?
Quote
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.

I feel that you are afraid of finding out what actually happened and you are desperately trying to formulate a coherent picture in your mind BY IGNORING MOST OF THE DATA.
Quote
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.

But you don't study at all, Dan!
Quote
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.

So are we betting our houses, Dan, or do you lack real faith in your "purely theological perspective"?

I say it's a political perspective, and you have no real faith.
Quote
I hope this clears things up.

It does, but you need to quit conflating your political position with an untenable theological one.

Date: 2007/11/27 13:48:23, Link
Author: JAM
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?

The practice of science is not limited to those labeled "scientists:"

http://www.ucmp.berkeley.edu/fosrec/Lipps.html

Beyond that red herring, the beef is that you claimed to be interested in biology, and you're not.

Date: 2007/11/27 13:50:27, Link
Author: JAM
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.

Date: 2007/11/27 18:03:43, Link
Author: JAM
Quote (Guts @ Nov. 27 2007,17:16)
I normally don't feel like any website has to explain themselves with respect to banning. TT has always welcomed critics, but if you cross the line, you're gone.

What line, Nelson? Suggesting ID predictions that Mike Gene might test instead of writing books? Pointing out one of the many times that the feckless Bradford contradicts himself?
Quote
...However, this had nothing to do with any dishonesty.

Riiiight. So why is there nothing in the thread at TT to indicate that?

Date: 2007/11/27 18:26:18, Link
Author: JAM
Quote (Guts @ Nov. 27 2007,18:19)
lol JAM, you're delusional, as always.

Your avoidance of two simple questions makes me delusional?

That's pretty funny, coming from someone who claims that "Intelligent agents today build motors that look like the motors in bacteria."

They build nanometer-scale motors out of proteins? Who's done that?

Date: 2007/11/27 18:39:55, Link
Author: JAM
[Graffiti moved to Bathroom Wall. -Admin]

Quote (Guts @ Nov. 27 2007,18:29)
No you're delusional because you think you were banned for that reason. Most people who get banned develop a martydom complex.

No marty here. We're laughing at you, and not merely for your bad spelling of "martyrdom." There are now multiple questions that you can't answer:

They build nanometer-scale motors out of proteins?

Who's done that?

What line, Nelson?

So why is there nothing in the thread at TT to indicate your alleged errors?

Date: 2007/11/27 18:41:41, Link
Author: JAM
Quote (Guts @ Nov. 27 2007,17:16)
I normally don't feel like any website has to explain themselves with respect to banning. TT has always welcomed critics, but if you cross the line, you're gone. Thats just the way life is, and it's true for any blog/website (I was banned from an anti-ID forum myself once).

With that said, I feel that the situation with Frostman was the result of a huge misunderstanding that was completely my fault. I am also their technical support. The Memory Hole function simply did not work, and this was noted on the blog long before this situation snowballed, although it should've been made more explicitely. I specifically instructed TT bloggers to save a copy of the offending comment in their thread and delete it. After which they can send it to me , and I would manually insert it in the database (the memory hole).

This, unfortunately, gave the impression that comments were just being deleted, which is against TT policy. I am more than willing to have Frostman back if he truly respects understands the purpose of the memory hole, and why it exists, and respects the decisions of TT bloggers.

However, this had nothing to do with any dishonesty.

If it was a misunderstanding, why was Frostman banned, Nelson?

Date: 2007/11/27 21:04:29, Link
Author: JAM
Quote (Guts @ Nov. 27 2007,18:54)
Well, at least I demonstrated the point.

What point?

Date: 2007/11/28 14:59:29, Link
Author: JAM
Quote (Daniel Smith @ Nov. 28 2007,13:56)
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... ?

Jesus Christ.

Date: 2007/11/29 12:36:35, Link
Author: JAM
Quote (JAM @ Nov. 26 2007,13:18)
Quote (Daniel Smith @ Nov. 23 2007,13:47)
 
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:

I have trouble buying that, as those are questions that I have already asked you, but what the hey:
 
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?). Again, the probability that a transcript or transcription serves some function will be highly correlated with proximity to genes.

Still waiting...

Date: 2007/11/29 18:48:40, Link
Author: JAM
Quote (JAM @ Nov. 26 2007,16:07)
Quote (Assassinator @ Nov. 26 2007,13:22)
Quote
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.

At biology class we calculated that about 1.7% of the whole human genome is for coding. Is that correct?

Yes, but that would be a minimum.

Note that Daniel is making a mammoth error in assuming that transcription implies function.

I think that he is beginning to realize that, too.

I did answer it.

Date: 2007/11/29 21:45:54, Link
Author: JAM
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?

Date: 2007/11/30 00:00:26, Link
Author: JAM
Quote (Daniel Smith @ Nov. 29 2007,22:21)
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,

No, you've said many, many things that you merely WISHED were true. Those are lies.
Quote
...and later found they weren't (in which case I've retracted them), but I've never ever lied.

ORLY? When did you retract your false claim about introns being coding sequences?
Quote
The fact that you and a few others here seem obsessed with calling me a "liar"

How can I be obsessed with doing something I've never done? I've called some of your statements lies, but I've never gone the ad hominem route and called you a liar.

Date: 2007/11/30 00:30:01, Link
Author: JAM
[quote=Daniel Smith,Nov. 29 2007,22:14][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?
[/quote]Not a single gene.  More likely "hind leg" development would be controlled by a region containing many genes.         [/quote]
You are completely, utterly wrong; apparently you don't understand God's design at all. That won't change your claim that what you've learned supports your position, though, will it?
[quote]  [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?
[/quote]Same[/quote]
You're wrong again, Ofer.
      [quote]        
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]
How are any of those four characteristics separate from each other? What do you mean by "specific histones"?       
       
Quote
       
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.

Yes, and even though you were sure that this was the way that God did it before, you'll still claim to understand Him better than the rest of us do.
     
Quote
I think transcription is probably very cell specific - so it would depend on the cell type.

I, OTOH, KNOW that sometimes it is, but very often it isn't, so your answer is meaningless.
       
Quote
I believe (theologically) that the entire genome is used somewhere and sometime, but not "always" - as I stated.        

That's nice, but both experimentally and ecologically, you're completely wrong.
       
Quote
       
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.        

I agree. But in reality, that prediction of ID is laughably false.
   
Quote
       
Quote
6) an you find a single instance of a scientist referring to the design of endocytic (intracellular plumbing) pathways?
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?
       
Quote
       
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.        

How convenient. But assume I'm correct about the overlap and explain it in terms of intelligent design.
     
Quote
 
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

Dead wrong. Mice and humans share 100.0% of their genes. The number present in one and lacking in the other is in the single digits. There goes your hypothesis...
       
Quote
   
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.

You'd have to think about it. Wouldn't it be important if one is testing a design hypothesis?
       
Quote
       
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.

It's a prediction.
       
Quote
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).

So far, your theology has been worse than worthless. Why not read from the book of Nature, if you believe that God wrote it?[/quote]

Date: 2007/11/30 12:23:36, Link
Author: JAM
Quote (Louis @ Nov. 30 2007,05:15)
Dear All,

The only controversial topic I can think of is the issue of tactics. How do we deal with denialists?

Challenge them to bet real money on their claims. In my experience, they always back down.

That is very strong evidence that they know that what they spout is hooey.

Date: 2007/12/01 15:10:46, Link
Author: JAM
Quote (Daniel Smith @ Nov. 30 2007,19:06)
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.

Your analogy is false, and you're regurgitating the Primary Creationist Lie.

It's easy to get a billion heads in a row if you filter the coin tosses with selection.

Why do you persist with the lie of claiming that because mutation is random only wrt fitness, that therefore all of evolution is random?

Why is defending your political position so much more important than obeying the Ninth Commandment, one of the ones that Jesus Christ reiterated?

Date: 2007/12/01 15:13:30, Link
Author: JAM
Quote (Tracy P. Hamilton @ Dec. 01 2007,09:40)
Quote (VMartin @ Dec. 01 2007,09:12)
My latest post has been deleted, so I 'll try it this way:

Jam
     
Quote

Dead wrong. Mice and humans share 100.0% of their genes. The number present in one and lacking in the other is in the single digits. There goes your hypothesis...


If they share 100,0% genes then it back ups frontloading very well I would say. It would mean that also regulatory genes are the same and it was only due to rearrangements of pre-existing genes in DNA that led to the difference between mice and  human in the distant past.

(In that case the possible explanation could be also different composition of cytosole in gametes and zygotes of both species and consequently the difference between man and  mice could be only epigenetical. But is sounds too "German", neglecting the role of DNA in ontogenesis,  doesn't it?)


--------
Hold on, Daniel.

It would appear that VMartin is "mistaken".

Anybody wishing to see how similar the house mouse and human genomes are just need to go to

http://www.ensembl.org/Mus_musculus/index.html

and

http://www.ensembl.org/Homo_sapiens/index.html

Perhaps VMartin thinks novel genes are those that have fiction books written about them.

Tracy, your post was unclear. Are you disputing that the number of orthologs present in humans but absent in mice (and vice versa) is tiny? Remember, I'm not talking about sequence identity. The question I'm answering is, "In how many cases do mice lack an ortholog of human gene XXX?"

Date: 2007/12/01 15:38:06, Link
Author: JAM
Quote (Daniel Smith @ Nov. 30 2007,19:15)
   
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,

That's not what you did, though. You stated things that you merely WISHED were true as fact, and when you learned that they weren't true you didn't admit that you were wrong. That is lying.
 
Quote
 
Quote
   
Quote
and later found they weren't (in which case I've retracted them), but I've never ever lied.

You have not come anywhere close to retracting all of the false claims you've made.
  [quote]    
Quote (swbarnes2 @ Nov. 30 2007,19:05)
...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.

swbarnes, didn't you miss an additional flipflop on this one? Didn't Dan claim that all the evidence he had seen still confirmed his hypothesis?

Here's another lie:
   
Quote (Daniel Smith @ Nov. 10 2007 @ 11:26)
I am attempting to "open my eyes" to anything and everything.

Every time I've tried to get you to open your eyes to the NATURE of biological complexity, you've run away, so that clearly was a lie.
Quote
I have never lied.  I stand by that.

Then explain why you claimed that Atlantic and Pacific humpbacks have been reproductively separated for millions of years.
Quote
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.

Then you should have retracted your false statements. Where did you retract your idiotic claim about the humpback whales, Dan?

BTW, what about your lie that Atlantic and Pacific populations of humpback whales have been separated for millions of years, when in reality, they hang out in Tierra del Fuego?

Do you know where that is?

Where did you retract that incredibly stupid false claim?

Date: 2007/12/02 10:23:32, Link
Author: JAM
Quote (Louis @ Dec. 02 2007,06:13)
Quote (oldmanintheskydidntdoit @ Dec. 02 2007,11:41)
Quote (Louis @ Dec. 02 2007,04:28)
What amazes me is thast people like FTK and Skeptic don't seem to realise that they are being dishonest.

Is there a known psychological condition that explains this rather gross lack of self examination?

Louis

I suspect introspection is not something that is valued highly in the FTK household.

I'm not sure about that, but what I'm curious to know (for I definitely don't know of this) is if there is a pathology that is behind such extreme denialism. Is it possible that there is a genuine mental illness at work?

My guess is there isn't, and that such denialism falls into the normal range of human behaviours, but I am curious to know if this guess is accurate.

http://www.amazon.com/Why-Lie....&sr=8-1

Date: 2007/12/03 01:25:18, Link
Author: JAM
Quote (Daniel Smith @ Nov. 30 2007,18:04)
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.

Really?

Kidneys filter the blood 24/7. How much time does a dialysis patient spend hooked up?

Besides, we're discussing intelligent design, not its implementation. Why are you trying to change the subject?

Date: 2007/12/03 18:05:04, Link
Author: JAM
Quote (Joy @ Dec. 03 2007,17:03)
...Mark wasn't upset about that action and didn't whine to high heaven about some non-existent "right" to have his typing etched into net-stone...

Ah, a fake quote from the deluded Joy.

If you didn't have the reading comprehension of a seven-year-old, you would have noted that Frostman was stunned by the hypocrisy and dishonesty at TT. He made no claim of any "right."

What he doesn't realize is that your reflexive dishonesty is the norm, not the exception.

Date: 2007/12/04 21:08:12, Link
Author: JAM
Quote (Arden Chatfield @ Dec. 04 2007,20:12)
Actually, I have no idea when he converted, but it appears that a few years into his career at Iowa,...

HEY! Please don't refer to GG's employer as "Iowa," as it suggests that you are talking about the University of Iowa, not Iowa State (aka Moo U).

Date: 2007/12/04 21:12:42, Link
Author: JAM
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.

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?

Date: 2007/12/05 12:54:25, Link
Author: JAM
Quote (VMartin @ Dec. 05 2007,12:50)
You didn't answer my previuos questions. Or using another point of view:

1) how great is an average difference between coding regions of  two different  human haplotypes choosen by random

2) how great is an average difference between the coding regions of two different mice haplotypes choosen by random
 
3) how great is an average difference between coding regions of a mouse and human haplotypes choosen by random.

I suppose the questions are very simple, aren't they?

No, they aren't. Do you know what the term "haplotype" means? If not, why are you using it?

Date: 2007/12/05 14:50:40, Link
Author: JAM
Quote (VMartin @ Dec. 05 2007,14:12)
Jam

Quote

No, they aren't. Do you know what the term "haplotype" means? If not, why are you using it?


I mean all alleles in a haploid cell. In human it is sex cell.

That's not even close to what the term means.

If you want people to answer your questions, you have to speak their language--even if you disagree with their conclusions.

Date: 2007/12/05 19:04:47, Link
Author: JAM
Quote (VMartin @ Dec. 05 2007,15:17)
 
Quote (JAM @ Dec. 05 2007,14:50)
   
Quote (VMartin @ Dec. 05 2007,14:12)
Jam

     
Quote

No, they aren't. Do you know what the term "haplotype" means? If not, why are you using it?


I mean all alleles in a haploid cell. In human it is sex cell.

That's not even close to what the term means.

If you want people to answer your questions, you have to speak their language--even if you disagree with their conclusions.

There are more approaches how a haplotype could be defined. Obviously you have never heard yet about this definition:

"Another way to think about it is that a haplotype is half of a genotype."

http://www.everythingbio.com/glos/definition.php?word=haplotype



That page provides the proper definition I'm using:
"A haplotype, a contraction of the phrase "haploid genotype", is a set of closely linked genetic markers present on one chromosome which tend to be inherited together (not easily separable by recombination)."

Can't you read? That definition does not even suggest "...all alleles in a haploid cell. In human it is sex cell."

Date: 2007/12/05 23:10:12, Link
Author: JAM
http://www.uncommondescent.com/the-des....-153641
Quote
Hard evidence is hard evidence no matter what the evolutionists/materialists try to say.

I'd call it material evidence, myself. If one rejects materialism, how can one jump up and down while squealing about the material evidence?

I would've thought that bs77 would have avoided the adjective "hard" from his past experience with the nanny filter, but he may possibly have an incredibly insensitive, but still functional, irony meter.

Date: 2007/12/07 18:22:01, Link
Author: JAM
Quote (VMartin @ Dec. 06 2007,03:34)
JAM

         
Quote

Can't you read? That definition does not even suggest "...all alleles in a haploid cell. In human it is sex cell."

I can read. I can read also this:

In the case of diploid organisms such as humans, a genome-wide haplotype comprises one member of the pair of alleles for each locus (that is, half of a diploid genome).

But I didn't use the adjective "genome-wide," so it should be obvious to anyone who can read that I didn't mean that.
Quote
But I don't want to dispute with you which definition is correct. I have no problem accept yours as better for scientists and formulate my questions without using "haplotype".I would like to know your opinion about average genetic difference between  mice and human.

First you have written that 100% genes are same.

That's not what I wrote.
 
Quote
I have found this:


This is what was actually determined: 99% of mouse genes have homologues in man (the actual protein similarity is much less than 99%....

That's not supported by the numbers on that page. 118/30000 = ~100%, not 99%. The author also uses "homologues" when he means "orthologs." There's a big difference, but there's little hope for you being able to understand it.


http://www.evolutionpages.com/Mouse%20genome%20genes.htm
 
Quote
What do they mean using "the best match"? Exactly or synonymous mutation or what?

Orthologs.
 
Quote
If scientists speak about genes I am not very wise from it. I would like to know how many different alleles there are between mice and human actually and how great that difference is in let say in  base-pairs.

Your question makes no sense. We only use the term "alleles" WITHIN a species.

Date: 2007/12/08 16:01:28, Link
Author: JAM
Quote (Assassinator @ Dec. 08 2007,15:55)
Slap me and call me a donkey, but I alwayse thought evidence and proof were 2 synonyms. Before I want to use that in that discussion, can you explain a bit more about the difference between those 2?
(It's almost astonishing how much you can learn on the internet ;))

In science, every conclusion is provisional, and no conclusion is considered to be proven. We say that a hypothesis is or is not supported by evidence.

The most powerful part of science is to use one's hypothesis to correctly predict the evidence before it is in hand, something that has never been done by a creationist/IDer.

Date: 2007/12/08 20:49:07, Link
Author: JAM
Quote (VMartin @ Dec. 08 2007,08:56)
   
Quote

That's not supported by the numbers on that page. 118/30000 = ~100%, not 99%. The author also uses "homologues" when he means "orthologs." There's a big difference, but there's little hope for you being able to understand it.

Alec MacAndrew writes evolutionary articles.

Never heard of him. Clearly, he can't do percentages.
 
Quote
Perhaps he don't know what's the difference between "homologues" and "orthologs" and "paralogs", I don't know. But believe me I know what orthologs mean.

If you really did, you would realize that MacAndrew does not know.
Quote
 You are not the only person in the world who knows it.

I never made such a claim.
 
Quote
 
The researchers compared human alleles with mouse and found that the mouse gene is identical to the major (most common) human allele in 67% of cases (similar to the 70% amino acids which are identical between mouse and man proteins).
You omitted the context, VM. That was preceded by this sentence:
"Further evidence for common ancestry comes SNPs (Single Nucleotide Polymorphisms) – differences in genomes that exist in different humans where the variation is a single base pair substitution and the alleles co-exist in the population."

SNPs aren't genes. You're hopeless.

http://www.evolutionpages.com/Mouse%20genome%20proteins.htm

 
Quote
These words nitpicking is interesting but my questions remain unanswered. Comparing alleles of two genomes of different mouse strains after 20 generation of imbreeding what would be the result as to their last common ancestor using molecular clocks?

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:

http://www.informatics.jax.org/morsebook/figures/figure16-1.shtml
 
Quote
If the polymorphism of mouse genes is 35% wouldn't be the result several million years?=

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.

Again, you're hopeless.

Date: 2007/12/09 14:54:25, Link
Author: JAM
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?

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.

If you think the inbreeding will justify ignoring the data, what do you predict will be seen in alignments between the mouse species?

I predict a dodge.

Date: 2007/12/09 16:43:04, Link
Author: JAM
Quote (Daniel Smith @ Dec. 09 2007,15:02)
 
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.

There's so much more molecular evidence, and as you've learned, it's much harder to spin when you haven't been preprogrammed by propaganda.
Quote
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.

Then why make predictions based on your expectations of Him? Why not read His book of nature with an open mind instead of a closed one?
Quote
The main contention I have with the currently held theory is that of it's mechanism - Variation + Natural Selection - specifically Natural Selection.

There are many more mechanisms. How can you be so contentious about something you aren't willing to understand?
Quote
We all know that variation happens.  But what does Natural Selection do with that variation?

It has to do something, as living things generally don't live to ripe old ages.
Quote
That's the BIG question.

So why avoid it?
Quote
Does it really build better machines out of it?

Metaphorically, yes. The biggest clue is the relationships between radically different "machines"--it is in no way consistent with intelligent design.
Quote
Or does it maintain the status quo?

It does that too.
Quote
I believe the power of Natural Selection is taken for granted - without any real experimental verification.

That is simply a lie. When we tested your hypothesis against the data, NONE of what you took for granted turned out to be true.
Quote
It is made out to be almost "godlike" in its creativity - but what is really known about it?

The passive voice is weaselly, Dan--the point is that when you look at the relationships between the components of life, it clearly is NOT "godlike in its creativity." It modifies existing parts, which is anything but creative. The complexity comes from the long spans of time and the cumulative properties of evolution.  
Quote
Most evolutionary experiments use artificial selection - so they do not actually test the proposed mechanism.

False. You haven't even looked. There are plenty of experiments that use artificial variation with natural selection.
Quote
The true test of Natural Selection is whether a variant can survive in the wild - not in a lab.

We find new variants in the wild all the time.
Quote
...Berg cites an almost endless list of examples...

But Dan, how would someone as ignorant as you know whether they are examples or not? Examples are representative.
Quote
...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".

The fact that you prefer to quote titles instead of making predictions about evidence you haven't seen yet proves your dishonest approach to the matter.
Quote
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".

Titles aren't evidence. You're afraid of evidence.
Quote
Their observations of real world examples

Again, you have insufficient expertise to know whether they are examples or not. For example, is ID's favorite structure--the eubacterial flagellum (any IDer who omits the adjective is being dishonest)--an example of what appears to be design in biology, or is it an outlier?
Quote
...As a believer in God, I'm much more inclined to embrace their conclusions.

I don't see how the second clause follows the first.
Quote
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.

So where are the new data they produced?
Quote
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?

IIRC, I asked you to direct me to the new data they had produced by testing their hypotheses. You couldn't find any. That means that you can't credibly claim that their hypotheses have any scientific merit at all.

Where are the predictions? Where are the new data produced by testing them?

Date: 2007/12/09 16:46:56, Link
Author: JAM
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.

Date: 2007/12/09 16:56:02, Link
Author: JAM
Quote (Daniel Smith @ Oct. 22 2007,19:26)
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).


 
Quote (JAM @ Dec. 04 2007,21:12)
 
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?

   
Quote (Daniel Smith @ Dec. 04 2007,18:54)

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.


Hallelujah! You finally got around to retracting a spectacularly stupid statement that you made SIX WEEKS AGO.

Where do you think that pegs your credibility on our meters, Dan? BTW, what sentence did you misunderstand? I'm fascinated by the way your mind works.

And since you made a false assumption, shouldn't you be retracting the conclusion you derived from it as well?

Date: 2007/12/09 17:13:14, Link
Author: JAM
Quote (Daniel Smith @ Dec. 09 2007,15:23)
 
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?

Nothing is considered to be proven in science. What it shows is the nature of the selection pressure(s). That makes testable predictions.

           
Quote
   
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.  

You assume incorrectly. For example, deer mice don't interbreed with house mice.

       
Quote


If you think the inbreeding will justify ignoring the data, what do you predict will be seen in alignments between the mouse species?

 
Quote
 Well, since they can all interbreed, they are all the same species (just like all the inbred variations of dogs).

Not quite. They CAN interbreed in the lab, but they DON'T interbreed in the wild AFAIK. Inconsistent with your hypothesis, "species" doesn't represent a bright white line. These are members of the same genus.  
 
Quote
 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.

You are utterly wrong.
http://www.jstor.org/view/00222372/ap050331/05a00030/0
Note that in this case, the PCR primers used to amplify the introns were in the highly-conserved exons.

http://genomebiology.com/2007/8/5/R80

http://www.springerlink.com/content/ur1r657751t80262/
Quote
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.

You're wrong. I predict that this will have no effect on your view of God.

Date: 2007/12/12 11:25:36, Link
Author: JAM
Quote (Daniel Smith @ Dec. 11 2007,19:46)
 
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"

What's the "end product," Dan? Humans? If so, there are plenty of aspects of nonhumans that are far more complex, elegant, and/or sophisticated than the homologous aspect of human biology.
Quote
... is the most complex,

Complexity does not imply design.
Quote
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.
Quote
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.

Why are some females more pretty than others? Experimental psychology tells us that we choose on the basis of symmetry and averageness.
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.  
Quote
"it ain't intelligent"?  The human brain puts our banks of computers to shame with it's processing power.

Your ignorance makes you look foolish. The problem with this claim is that the connections that provide our brains' processing power are acquired, not designed. The "design" is one of reiteration, the common theme of biology.
Quote
What is it that blinds you to all this?  Is it your distaste for God?  Do you do this because it's his creation?

We're the ones who study His creation, Dan, you're the one who avoids studying life itself and resorts to quote mining. You are intentionally blind to the realities of biology. What are you afraid of?
Quote
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 -

Yes, as are nonworking ones. Time and iteration produce both the working and nonworking ones, while the existence of the latter class is inconsistent with not only design, but intelligent design.
Quote
intertwined in complex networks - working together to allow us to do things like laughing and crying, reading and speaking.

But not all of us can do those things. You can't explain that.
Quote
All these systems work together so we can cradle a baby, smell a flower, enjoy a sunset, or compose or enjoy music.

But not all of us can do those things. This is why you are a deeply dishonest man, Dan.
Quote
They allow us to do the very things we are doing right now.

Why did God design you to remain in denial about your incuriosity, Dan?
Quote
You can't explain that with "variation and selection".  There's just no way.

Sure we can, just as we can explain why those systems break.
Quote
There is an "elephant in the room" and I think you know who it is.

The elephant in the room is your fear of reality.

Date: 2007/12/13 15:22:52, Link
Author: JAM
[Graffiti moved to Bathroom Wall. -Admin]

Quote (VMartin @ Dec. 13 2007,13:19)
 
Quote

So atheism = Natural Selection?


That's the question!

But I am waiting for JAM's answers to my post where I disclosed his his evasive - and sometimes even wrong I hope - sentences.

JAM could also explain us how those genes he asked Daniel about survived. I mean hind-legs genes in whales.

I was asking whether hind-leg genes exist to begin with. A designer would design them.
Quote
There are still some hind legs bones inside whales as far as I know. But the evolution of whales finished some 40 millions years ago.

Evolution doesn't stop.
Quote
I don't see a selective pressure for those genes to make their job so long.

What genes in particular? Do you think that God designed hind limb development in an organized, hierarchical way?
Quote
They should have acquired deleterios mutations you know.

Only if they exist, and their function is limited to the hind limbs. Do any such genes exist, Marty? Please give their names.
Quote
Not being under selective pressure they should have been destroyed by deleterious mutation.

Can you even name a SINGLE gene whose function is limited to hind limbs? Development or function?
Quote
It was your argument against frontloading, that genes could not survive if they are not under selective (purifying) pressure. But this hind-legs whales genes seems to me contradict such theorizing.

Actually, you and Dan have implicitly predicted that such genes exist, based on your understanding of intelligent design.

We're testing an ID hypothesis, Marty! What fun!

Date: 2007/12/13 18:22:30, Link
Author: JAM
The parallels are scary.

'73 Gibson SG
'76 Mesa Boogie (the knob labels in back are Dymos)
Ovation 6 and 12
'74 Fender Jazz Bass

Date: 2007/12/14 00:37:40, Link
Author: JAM
[Graffiti moved to Bathroom Wall. -Admin]

Quote (VMartin @ Dec. 14 2007,00:23)
JAM
     
Quote

Only if they exist, and their function is limited to the hind limbs. Do any such genes exist, Marty? Please give their names.


Do you think such genes do not exist?

I don't know of a single gene that has its only function(s) during hindlimb development. Do you?
Quote
That's very interesting. So those bones of hind legs are atavism which are no coded in DNA?

That's not what I'm saying at all, Marty.

Why are you evading my question? If you believe that there is even a single gene that only does hindlimb development AND NOTHING ELSE, why don't you name one?

Do you see how you've made an implicit prediction that the mechanisms underlying hindlimb development were designed de novo, and not co-opted?
Quote
Your reasoning has been always very inspiring.

When you don't know what you're talking about, attempting sarcasm only makes you look even more ignorant. It's hard to do in your case, but you've never failed yet!

   
Quote
 
Quote

We're testing an ID hypothesis, Marty! What fun!

I was testing darwinian hypothesis actually.

Actually, Marty, there was nothing Darwinian at all about assuming that there are genes devoted to hindlimb development and nothing else. Modern evolutionary theory predicts the polar opposite: gobs of overlapping, co-opted functions.
Quote
Difference of alleles in polymorphic loci between mice strains and comparing different alleles of human vs mice. In one case the difference serve nothing in the second case the difference should prove evolution and divergence from  something called as common ancestor.

You're incoherent.

Date: 2007/12/14 11:14:36, Link
Author: JAM
[Graffiti moved to Bathroom Wall. -Admin]

Quote (VMartin @ Dec. 14 2007,10:29)
LOU
         
Quote

There was a day when we had nothing to do for some reason (I don't recall the circumstance) and so the old guy who was my mentor took me to this big room where they had a computer much more like a modern one - CRT (green text on black of course), tower, keyboard, blah blah.
.
.
.
Talking to that computer was a lot like talking to Marty.



Maybe you were using  IBM with COmmon Business Oriented Language (At least I have heard it was used in the army, also for the navigation of missiles). But I suppose your knowledge about computers are as limited as your knowledge about secrets of evolution. Have you ever heard that in this language is written the majority programming lines in the world even today? 80% of businness in USA is running under it. I suppose programmers still use those "green text on black" on IBM using TSO, ISPF and so on. You know ISPF is used in 90% of companies in FORBES 500. (check it.)

Maybe my orthogenetic opinions are not so outdated as you would like to believe.

Why are you evading my questions?

If you believe that there is even a single gene that only does hindlimb development AND NOTHING ELSE, why don't you name one?

Do you see how you've made an implicit prediction that the mechanisms underlying hindlimb development were designed de novo, and not co-opted?

Date: 2007/12/15 17:42:19, Link
Author: JAM
Quote (Daniel Smith @ Dec. 15 2007,12:24)
I guess amidst all the kudos and congratulatory back-slapping, you guys missed my response to the ring species argument.

That wasn't a response.

Date: 2007/12/15 17:52:46, Link
Author: JAM
Quote (Daniel Smith @ Dec. 15 2007,12:59)

Now you're just lying.

No, I'm not, and you support my claim to boot:
 
Quote
 I can look at virtually any biological system and immediately see its elegance and sophistication of design.

"I can look at" does not falsify "have not looked at." You haven't really looked; you run away at the slightest challenge.
 
Quote
 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?

Date: 2007/12/15 17:56:26, Link
Author: JAM
Quote (Lou FCD @ Dec. 15 2007,17:53)
And should we even go into the playpen/sewage disposal thing?

The funny thing is that it's even worse on the intracellular level. Dan ran away from explaining the elegance of that too.

Date: 2007/12/17 00:54:48, Link
Author: JAM
Quote (Daniel Smith @ Dec. 16 2007,21:37)
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.

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.

Date: 2007/12/17 00:59:07, Link
Author: JAM
Quote (Daniel Smith @ Dec. 16 2007,21:15)
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.

You're lying again, or perhaps profoundly stupid.

Their chromosomes do NOT show "complete restructuring in relation to each other." There are vast regions in which gene order has been perfectly preserved (synteny), falsifying your desperate claim.

Or are you being so idiotically ignorant that you are implicitly claiming that the chromosomes were numbered on the basis of homology, instead of the single, simple criterion of length?

Date: 2007/12/17 22:26:11, Link
Author: JAM
Quote (Daniel Smith @ Dec. 17 2007,18:52)
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,...

Dan, this is just absurd. You haven't learned much about the properties of DNA if you don't even realize that its strands are antiparallel. Therefore, transcription on opposing strands can only occur in opposite directions.

High-school students know this, while you're so arrogant that you claim to understand complexity better than practicing scientists while lacking the knowledge of a ninth-grader.

Most of the things you claimed to have learned turned out to be fabrications, like your false claim that introns are coding sequences.

You're afraid to confront and discuss the NATURE of biological complexity.

Date: 2007/12/18 14:09:59, Link
Author: JAM
Quote (VMartin @ Dec. 18 2007,13:51)
JAM 14.dec.
 
Quote

If you believe that there is even a single gene that only does hindlimb development AND NOTHING ELSE, why don't you name one?

Do you see how you've made an implicit prediction that the mechanisms underlying hindlimb development were designed de novo, and not co-opted?

There are only some remnants of bones of hind-legs of whales.

True. We're talking about the implicit prediction you made about the genes involved in their morphogenesis.
Quote
I don't see a reason why such complicated structures as joints etc are not preserved, but only part adjacent to femura etc.. If there are not single gene why some of them are expressed for 40 million years but some of them not?

Because it's several orders of magnitude more complicated than you think it is. Simply name a gene that functions ONLY in hindlimb morphogenesis and nothing else. Remember, you claimed that there were multiple genes that met this criterion!
Quote
We can go into details which some hind leg bones of whales are found and which not.

We could, but it wouldn't be relevant. You've made a prediction about the nature of the design, so you need to test it against reality.
Quote
I would say that if some useless bones must be expressed due evolutionary constraints but some needn't is nothing else as an ad hoc explanation without any evidence.

That has nothing to do with my challenge to you, Marty. You predicted that "hindlimb genes" would accumulate harmful mutations, but that prediction requires the assumption that there exist "hindlimb genes" that function in no other way.

Why are you afraid to test your assumption against reality, Marty?

Date: 2007/12/18 18:49:40, Link
Author: JAM
Quote (Daniel Smith @ Dec. 18 2007,18:14)
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.

I'm trying to steer you into the light of reality. Do you realize that you just completely contradicted your claim that I was "posturing"?
Quote
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?

Date: 2007/12/19 11:24:32, Link
Author: JAM
Quote (VMartin @ Dec. 18 2007,23:47)
JAM

 
Quote

That has nothing to do with my challenge to you, Marty. You predicted that "hindlimb genes" would accumulate harmful mutations, but that prediction requires the assumption that there exist "hindlimb genes" that function in no other way.

Why are you afraid to test your assumption against reality, Marty?

Obviously there are genes which are only responsible  for creation of metatarsus.

If it's so damn obvious, why don't you name them?
Quote
This group of "metatarsus genes" are not expressed anymore in hindlimbs of whales.

Name them, Marty. How can they be obvious if you can't name them?
Quote
There are also genes which are responsible for creation of tarsus and other small bones. This group of "tarsus genes" are not expressed anymore in hindlimb of whales either.

Marty, eye on the ball now. We're discussing your idiotic assumption that genes exist that ONLY function in the development of the hindlimb.
Quote
But group of genes responsible for creatrion of tibia and femura are expressed. These bones are protracting from bodies of terrestrial mammals. In whales they are buried inside their bodies.

They are expressed 40 million of years without any obvious function.

The point is not if "hind-limbes" genes have other function or not.

Yes, that is the point, because you claimed that they would be accumulating harmful mutations. I am challenging the profoundly stupid assumption underlying your claim.
Quote
Or do you think that tibia genes have other functions and metatarsus genes do not have?

I think that you can't name a single gene involved in hindlimb development that does not function elsewhere, because your view of the design of developmental pathways has zero foundation in reality.

Date: 2007/12/20 19:14:14, Link
Author: JAM
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?
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.

Date: 2007/12/20 19:15:11, Link
Author: JAM
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.

Date: 2007/12/20 23:47:07, Link
Author: JAM
Quote (Daniel Smith @ Dec. 20 2007,19:31)
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).

And the same goes for start codons, right?

Date: 2007/12/31 16:11:45, Link
Author: JAM
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.
 
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.

Date: 2007/12/31 16:29:16, Link
Author: JAM
Quote (Daniel Smith @ Dec. 31 2007,14:48)
I am of the opinion that a careful, honest assessment of the evidence

You've been neither careful nor honest, so your assessment doesn't count. I'm still waiting for your explanation of how you honestly misread anything that would allow you to conclude that Atlantic and Pacific humpback populations have been isolated from each other for millions of years when in fact, they frolic at the junction between those oceans.
Quote
will show that;
A) There are no plausible natural explanations for the origin of any of life's systems;

We already have them. Your claim that they are implausible is based on aggressive ignorance.

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.
Quote
And
B) These systems are so intricate, so complex and specific,

Again, you are simply being dishonest. The complexity comes from the iterative nature of evolution. The specificity is an illusion, which you'd realize if you had the smidgen of integrity required to take me up on my challenge to look at the NATURE of biological complexity.

For example, how do you explain the LACK of specificity in receptors and second-messenger pathways? That lack would be trivially easy to avoid in design.
Quote
they require a designer with a mind of infinite intelligence as their source.

So, why would an infinitely intelligent designer separate stop from aa incorporation, but fail to separate start from aa incorporation?
Quote
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.

Evolution explains their complexity and intertwining quite easily. It also explains their lack of specificity, which you don't have a hope in hell of explaining.
Quote
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)

Statements aren't evidence.
Quote
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'.

But intelligent designs tend to prevent such interactions.
Quote
Such cascading systems don't just happen.  Perhaps a simple system could beat the odds and 'just happen',

You're lying, Dan. Evolution doesn't "just happen."
Quote
but it could never sustain itself for a protracted length of time without another system (its perfect complement no less) coming along behind it.

You're lying. Your claim of perfect complementation is a complete fabrication.
Quote
Now multiply such 'just happens' by trillions of times and you can theoretically explain life via natural causes.  Do you see the dilemma?

No, since evolution doesn't work that way.
Quote
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!

How would you know? You can't even bring yourself to examine the evidence in any detail without throwing up your hands and lying about it.
Quote
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.

Explain what is "supremely tailored" about endocytosis, when the "sewage" keeps getting mixed up with the "drinking water."

Quote
That is how I address your objections.

You haven't addressed any of them. You've misrepresented them.
Quote
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.

So what's YOUR explanation for reality, in which every single ID proponent in the world has done exactly that?
Quote
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.

But you don't learn. You run away and pretend that you understand it better than those of us who jump into its study.
Quote
We should definitely continue its study.

But you don't study. You take a preposterously superficial approach and pronounce yourself superior to the people who study life in depth.

Date: 2008/01/01 20:33:25, Link
Author: JAM
Quote (Daniel Smith @ Jan. 01 2008,18:53)
 
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.

I know, twit. That does not falsify the fact that SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS. Quit lying, and stop calling it a theory.
 
Quote
 His "data" is the fossil record.

That does not falsify the fact that SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS.
 
Quote
He introduced his theory in a paper in 1943 - 7 years before he published Basic Questions in Paleontology in 1950.

You continue to lie. It was a mere hypothesis, and SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS.
 
Quote
He tested his predictions as any paleontologist would - by excavating and sifting through fossils.

Dan, you lie like a rug. The way that paleontologists test predictions of their hypotheses is by predicting the locations, time of deposition, and morphologies of fossils BEFORE THEY FIND THEM, not after. Tiktaalik is a fine example of this sort of prediction.

SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF HIS HYPOTHESIS. Do the caps help?
 
Quote
He produced much data himself during this period and continued his pursuit of fossils until his death in 1971.

You are a deeply dishonest man, Dan. I didn't claim that Schindewolf produced no data, I pointed out that SCHINDEWOLF PRODUCED NO DATA FROM TESTING THE PREDICTIONS OF THE HYPOTHESIS WITH WHICH YOU ARE ENAMORED.

Can't you read?
 
Quote
As of this date, I am not aware of anything found in the fossil record that falsifies his theory.  Are you?

You are blatantly dishonest, Dan, as Schindewolf's hypothesis makes clear predictions about the molecular evidence, and what we know about molecular and developmental biology falsifies his hypothesis.

For example,

1) What magnitude of genetic change is required to change the number of vertebrae in a vertebrate?
2) What magnitude of genetic change is required to change the IDENTITY of a vertebra in a vertebrate?

         
Quote

What "vague notions" are you talking about?

His hypothesis that you dishonestly describe as a theory!
 
Quote
What evidence does not support his theory?

His hypothesis, you mean. Can you carry on a conversation without using such a blatant lie?
 
Quote
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.

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.

Date: 2008/01/02 22:30:13, Link
Author: JAM
Quote (Daniel Smith @ Jan. 02 2008,18:21)
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)

Oh, but Dan, there is only one start codon.
Quote
of written language are capital letters

Plural. There is only one start codon. Therefore, using the language analogy (or any other), the design of the genetic code is profoundly unintelligent.
Quote
...- which are not separate in meaning from other letters,

There's only one start codon. Therefore, using the language analogy, every sentence must start with the same letter, which would be incredibly stupid.
Quote
(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,

You're lying again, Dan. In the analogy, every sentence must start not with "a capital letter," but a SINGLE capital letter, M.
Quote
... or with punctuation marks.  Any combination of the two (by your standards) would disqualify written language as an intelligent design.

You're lying again.
Quote
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.

I don't see anyone proposing that all sentences should start with the same letter, do you?

BTW, do all functional proteins end up having methionine at their N-termini?
Quote
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.

But there's no plausible reason to use a SINGLE start signal. You lie like a rug.

Date: 2008/01/04 00:03:55, Link
Author: JAM
Quote (Daniel Smith @ Jan. 03 2008,17:56)
 
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.

We've established that we agree that the "design" of translational initiation is profoundly unintelligent.
Quote
You seem to be suggesting there's something wrong with the way life is coded for.

Dan, you're a weasel. I've shown that by YOUR standard, the designer made an obviously unintelligent choice.
Quote
It seems to work pretty well to me.

Selection does that, 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.
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.
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.
Quote
I guess you'll have to take that up with God when you meet him face to face.

Don't you mean Him?
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.

Date: 2008/01/04 12:14:55, Link
Author: JAM
Quote (Daniel Smith @ Jan. 03 2008,18:33)
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.

Stop weaseling, Dan. The issue is not whether he made predictions in his writings, but whether he tested the predictions of his hypothesis(es). If a hypothesis is properly formulated to be useful, there simply is no debate about its predictions.
Quote
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.

BS. The measure of confidence and boldness is whether he (or for that matter, you) seeks to test the predictions, particularly those that have the potential to falsify the hypothesis.
Quote
He described definite patterns in evolution that he fully expected to be confirmed with increasing fossil evidence.

"Patterns in evolution" is the hypothesis, not the prediction. Whether he expected them to be confirmed is best measured by the extent of his efforts to confirm AND FALSIFY them. Predictions are about what will be found, not their interpretation. Keeping to that is what makes science so much more honest than religion.
Quote
I'd say that shows the "courage of his convictions", wouldn't you?

Not at all.

Date: 2008/01/06 15:59:53, Link
Author: JAM
Quote (Daniel Smith @ Jan. 04 2008,23:13)
   
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.

No, you hate debating with me because your predictions are always dead wrong, and you try to deny that with falsehoods.
   
Quote
You ask me loaded questions, then twist my answers around to make out like I meant something you know I didn't really mean.

My questions were not loaded, and I did not twist your answers. You explicitly agreed that separating stop from aa "signals" was an intelligent choice. Therefore, it is inescapable that we also agree that not separating start from aa signals is an unintelligent choice, unless you can explain why there should be different criteria for starting and stopping translation. I can easily explain this huge difference in evolutionary terms.
   
Quote
It's a completely dishonest tactic and has nothing to do with the actual debate.
 There's nothing dishonest at all about what I did. I was merely preventing you from being dishonest and moving the goalposts, which we both know you would have done.
   
Quote
It's all about "winning" (or seeming to) for you isn't it?

No, it's about honesty and your lack of it. I am perfectly willing to admit when I don't understand something.

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.


           
Quote
   
Quote
Selection does that,
Almighty Selection.  Yes I know, It (capitalized) designed the genetic code.

Not by itself. The explanation for the huge difference between the "design" of starting and that of stopping translation has a lot to do with variation, too.
   
Quote
It's amazing how well this unintelligent, uncaring, unguided, directionless "force" was able to create such complex interleaved systems.

Let's look at the interleaving, shall we? The evidence eliminating design is very prominent there.
   
Quote
THAT you'll believe, but mention God and it's "liar, liar pants on fire!".

Quote an example of me doing that. Your lies have been about the evidence and your feigned interest in it.
           
Quote
   
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.

See, you aren't interested in the NATURE of biological complexity at all. The simple fact is that I know much more about this than you do, because it's my life's work. You're trying to project your massive arrogance onto me, and THAT'S dishonest!
           
Quote
 
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?

Every time.
   
Quote
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.

If we agree what the code is, then it is symbolic. It's nothing like the "genetic code."

         
Quote
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.

That's pretty funny, since I wrote that the design could not have come from a perfect being and you misrepresented that as a claim that the design was perfect.[/quote]
   
Quote
Someone once told me that opinions do not equal evidence.  This is pure opinion.

How is pointing out the existence of intermediates "pure opinion," Dan?

Date: 2008/01/06 16:02:09, Link
Author: JAM
Quote (Mark Iosim @ Jan. 05 2008,07:55)
Opps! The previous reply was due to “fat fingers” error.

JAM
You mentioned before that "Selection does that...".
You probably realize, that Selection cannot create, but only chouse from what was already created.

Yes, I do.
Quote
So I am going back to the question I asked before. If a chance (mutation) is a creator, do you think that it is a scientist’s obligation to demonstrate that the probability of this chance is in agreement with statistical analysis? Do you know anything about this issue?

A lot, given my training in genetics. It's been demonstrated over and over. Have you considered looking at the data?

Date: 2008/01/06 16:12:36, Link
Author: JAM
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.

Date: 2008/01/07 20:01:24, Link
Author: JAM
Quote (Daniel Smith @ Jan. 07 2008,18:30)
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.

It's not science, Dan, because scientific predictions are about what will be observed, not one's interpretation of it, not one's explanation.

Scientifically, you're still a total fraud.
Quote
So it's not just me, and it's not just opinion.

You're lying, because you inserted the adjective "plausible." That makes it entirely subjective opinion.
Quote
You understand that don't you?

Yes, I understand that you are a deeply dishonest person.

Date: 2008/01/07 23:52:06, Link
Author: JAM
Quote (Daniel Smith @ Jan. 07 2008,19:34)
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.

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.

Date: 2008/01/08 00:35:57, Link
Author: JAM
Quote (Erasmus @ FCD,Jan. 08 2008,00:21)
JAM:  Daniel is a creationist.  pure and simple.

I'm well aware of that, thanks.
Quote
 no amount of data will change his mind, he brought it with him.

I know. The only thing maintaining my interest in this thread has been that Dan didn't know this about himself until we dragged him, kicking and screaming, to look at the data. There was a bit of sincerity wrapped up in all of his arrogance.

Since then, he's become the standard dishonest creationist and I'm losing interest.

Date: 2008/01/08 00:38:53, Link
Author: JAM
Quote (Mark Iosim @ Jan. 06 2008,22:25)
I am looking for the relevant studies, but didn’t find them yet? Apparently, you have plenty of evidences. Can you refer me to any sort of statistical analysis that in your opinion demonstrates that random mutations could be responsible for adaptive changes in biological systems?

Why would you want a "statistical analysis" instead of the evidence itself?

Do you realize that statistical analysis is something a scientist does WITH the evidence?

Date: 2008/01/10 14:39:48, Link
Author: JAM
Quote (dheddle @ Jan. 10 2008,13:09)
...The bottom line is that while I am only semi-serious it is true, as we all know, that arguing from correlation is fraught with peril.

You're flipping things. It's the Christianists who are claiming a correlation.

Correlations are weak evidence for causation.

The fact here is that there is a lack of correlation, which is extremely strong evidence against causation.

Quote
You must have a handle on all variables before you can make definitive statements. For example, maybe (I have no idea if it is true) theists in the south are on the average more impoverished, and the increase in crime is due in part to poverty.

Have you seen the surveys of prisoners?

Date: 2008/01/13 18:24:33, Link
Author: JAM
Quote (Daniel Smith @ Jan. 13 2008,18:11)
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.

You're pathetic. Biology isn't rhetoric.

If you think Denton's hypothesis is so wonderful, why don't you and/or Denton test it and publish data instead of rhetoric?
Quote
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.

Has anyone who actually works in Denton's field tested his hypothesis?

Precisely what IS Denton's field, Dan? Your criterion is blatantly dishonest.
Quote
If you can point me to a published paper where the authors take a stance against Denton's hypothesis, please do.

Biology isn't about taking stances. It's about TESTING hypotheses and publishing the data, not crap like Denton's repetitive musings.
Quote
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?

No, moron, it's a prediction of physical biochemistry.
Quote
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?

"Surprising" doesn't even suggest that "the pseudoscientists who could never be bothered to test their hypotheses were correct."

Date: 2008/01/14 17:12:01, Link
Author: JAM
Quote (Daniel Smith @ Jan. 14 2008,10:50)
 
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?

You're delusional. If you recall your false prediction, selection only acts on DNA sequences when they affect fitness at the organismal level.
Quote
The MET surely has a lot to say about DNA sequences - does selection "skip a level" and not act upon protein folds?

Selection doesn't "skip a level." You just don't know enough biology (less than a smart 8th-grader) to understand what informed people are saying, making you vulnerable to making ridiculously hasty generalizations in your desperate attempt to defend your bad theology.

Date: 2008/01/15 19:50:23, Link
Author: JAM
Quote (Daniel Smith @ Jan. 15 2008,19:17)
 
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.

In science, it's not a matter of explaining things to a dilettante's satisfaction. Science is about making and testing predictions. You are egotistically ignoring the fact that every prediction you made here is false.
Quote
You seem to be much better at telling us uneducated saps how ignorant we are and leaving it at that.

That's a lie, Dan. We got you to make predictions and we showed you that you were wrong. Then you metaphorically closed your eyes and claimed that you haven't seen anything inconsistent with your hypotheses.
Quote
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.

But we did, Dan. We led you by the hand through the process of making and testing predictions. Yours were uniformly wrong.
Quote
All you're doing is the equivalent of name calling.  This is just an observation.

No, it's a self-serving lie. Prodding you into making predictions and showing you that they were wrong is in no way equivalent to name calling.

Date: 2008/01/18 18:26:20, Link
Author: JAM
Quote (Mark Iosim @ Jan. 18 2008,07:28)
I also looked back over resent posts, but couldn’t find the post where JAM calling, Daniel moron. However you can find plenty (every other) of JAM’s posts are filled with accusation that Daniel is “deeply dishonest person”, lier,...

He sure is, at least in the realm of biology. How would you describe someone who made patently false predictions, but revises that in his mind to claim that we have offered nothing but arguments from authority?

Honest?
Quote
and that his arguments are stupid.

Would you mind pointing me to that one? Dan's hypotheses are wrong because the predictions they make have no basis in reality.
Quote
Daniel is a very bright person...

I don't see any evidence for that.
Quote
...and if his arguments some time get fuzzy it is because he tried to defend his convictions...

But if we're to approach this scientifically, we're supposed to attack our own convictions. If I had racist convictions, would you admire me for defending them?
Quote
... and we all have the same problem, as was demonstrated in the recent discussion.

I don't see how we all have the same problem. I see that you're not credible when you claim to have an open mind.
Quote
My whole reason to follow up this forum was to see how Daniel withstanding a heat and I was impressed with his intelligence, ability to learn quickly and with his dignity.

How is it dignified to pretend that God is killing children with malaria to teach a lesson to white-bread folks in the US? That's theologically obscene.
Quote
In the same time I was irritated by some folks and especially by JAM who was trashing Daniel in manner not acceptable for scientifically inclined discussion (at least not in my book)

Daniel rejects the scientific method. What book have you written?
Quote
and by bragging his knowledge.

More than Dan was discounting my knowledge?
Quote
Eventually, I decided to participate just to have an opportunity to tell JAM that having Curriculum Vita instead of Resume doesn’t make him a scientist yet.

Haha, funny. What makes me a scientist is that I publish papers with new data that come from testing my own hypotheses, something no creationist or ID proponent has ever done. How do you explain that massive deficiency?

Date: 2008/01/20 14:06:13, Link
Author: JAM
Quote (Daniel Smith @ Jan. 20 2008,13:32)
Quote (Wesley R. Elsberry @ Jan. 19 2008,08:45)
...Of course, I suppose it is way out of line to ask Daniel that he learn something about the stuff he feels compelled to criticize.

I don't pretend to be an expert on this subject by any means Wesley.

You claim to understand it better than the experts, which is an implicit claim of expertise. The reality is that you are avoiding learning about it. God is screaming at you with evidence. Why do you cover your ears?
Quote
I'm sure your knowledge on this subject exceeds mine by light years.  I barely know the basics and thus am only able to critique these things at there most basic and fundamental level.

No, Dan, you don't even barely know the basics. You repeatedly bear false witness, demonstrating your contempt for one of the central rules of Christianity. Therefore, you shouldn't be critiquing anything that you can't describe accurately.
Quote
So that said...

My objection was that selection algorithms always select the best solution.  By this I mean, of course, the best available solution.

I don't see how you got that "of course," because of course, "the best solution" doesn't mean "the best available solution."
Quote
If all the solutions degrade at some point during the process---which seems likely since bad solutions will always outnumber good ones when the mechanism for generation is random---then that still does not address my objection, since the best available solutions are still always selected for.

That's not true at all.
Quote
Selection in real life cannot afford such low fitness levels however.

How would you know?
Quote
Another objection I will raise here concerns the pool of potential solutions from which GAs can select.  Are these pools infinite?  Or are they constrained?

They are incredibly constrained, which is why it is both stupid and arrogant to claim that life's "solutions" were intelligently designed by an omnipotent God.
Quote
Real life selection does not have an infinite pool of solutions to select from -- as we have been discussing with protein folding

You haven't been discussing selection wrt protein folding. We've been trying to explain to you that you are using a straw man fallacy.
Quote
-- the pool is limited for real life selection.  This is also evidenced by the many, many known instances of convergent and parallel evolution where the same solution is arrived at via different pathways.

The pool is limited, but that's not the evidence. The evidence is common descent of both organisms and their components, a phenomenon for which every one of your predictions has been WRONG.
Quote
This phenomenon can be interpreted to represent a limited number of lawful solutions for life's problems from which nature has to select.

Your insertion of the unnecessary qualifier "lawful" is pure sophistry, and you know it.
Quote
As Leo S. Berg said...

If you were a seeker of God's handiwork, you would look at the handiwork (the data) instead of what lowly humans write about it.

Intellectually, you are a fraud, Dan. God has put the evidence on display for you, and all you do is run to politically-motivated misrepresentations of it to defend your ego and your political motivations.

Date: 2008/01/23 11:07:24, Link
Author: JAM
Quote (oldmanintheskydidntdoit @ Jan. 23 2008,03:07)
Daniel, do what I suggested earlier. Learn to program. Write some GA's. Do something, anything, rather then leech off other peoples work and claim it supports your case when you don't even understand it in the first place.

Or, look directly at (according to you) God's designs for yourself.

If you had any real faith, you wouldn't need to resort to decades-old hearsay from people who lacked the courage/faith to put their own hypotheses to the test.

Dontcha just love the irony?

Date: 2008/01/24 10:59:18, Link
Author: JAM
Quote (mitschlag @ Jan. 24 2008,04:53)
Quote (Daniel Smith @ Jan. 23 2008,18:32)
I get the distinct impression that no one here has read anything these men have published.  I also get the impression no one here wants to.

Please give citations to PEER-REVIEWED papers.

Not just "peer-reviewed," but PRIMARY literature--that is, papers that contain new data from testing the hypotheses you have decided must be true, Dan.

For example, Denton actually publishes in the primary literature, albeit descriptive, relatively minor clinical genetics papers. Ask yourself why he lacks the faith to:

1) Make an unequivocal prediction about future data
2) Go looking for such data himself.

Don't you see the irony in your obvious lack of faith? Why do you have more faith in unsupported musings than you do in the actual evidence (according to you, the very stuff designed by God Himself)?

Why do you need filtration?

Date: 2008/01/24 11:10:12, Link
Author: JAM
Quote (Daniel Smith @ Jan. 24 2008,11:05)
Quote (mitschlag @ Jan. 24 2008,02:53)
 
Quote (Daniel Smith @ Jan. 23 2008,18:32)
I get the distinct impression that no one here has read anything these men have published.  I also get the impression no one here wants to.

Please give citations to PEER-REVIEWED papers.

Like Darwin's?

Please....

Darwin's books are primary literature, because they contained new data, unlike the musings you desperately want to believe.

Science is about predicting, not spinning the existing data.

Schindewolf's gaps have been filled, falsifying his hypothesis, even for his speciality, ammonites.

Date: 2008/01/24 15:42:49, Link
Author: JAM
Quote (Ftk @ Jan. 24 2008,14:21)
Daniel,

I certainly hope there are lurkers reading this thread who are interested in getting at the truth with regard to what the mechanisms of evolution can actually accomplish, because you are doing a marvelous job of asking the right questions and pointing out the Darwinian fallacies...

What "Darwinian fallacies" has he pointed out, FTK?

Date: 2008/01/25 00:40:28, Link
Author: JAM
Quote (Daniel Smith @ Jan. 24 2008,17:50)
Quote (JAM @ Jan. 24 2008,09:10)
Darwin's books are primary literature, because they contained new data, unlike the musings you desperately want to believe.

Science is about predicting, not spinning the existing data.

Schindewolf's gaps have been filled, falsifying his hypothesis, even for his speciality, ammonites.

I'm breaking my silence towards you this one time because this cannot go ignored.  

You know nothing of Schindewolf, you've never read his books - so how can you possibly know if his book contains new data or existing data?  Are you just guessing?  (I think you are.)

As for his "gaps" being filled, I'm calling you on that.  Show me from the primary literature where the specific gaps he pointed to (of which you're blissfully unaware) have been filled.

CALLOMON, J. H.  1985.
The evolution of the  Jurassic  ammonite family Cardioceratidae.
Special Papers in Palaeontology. 33, 49-90.

DONOVAN,  D.  T. et al.  1981.
Classification of the Jurassic Ammonitina.
In: HOUSE. M. R. & SENIOR, J. R. (eds)
The Ammonoidea. Systematics Association Special Volumes. 18, Academic Press,  London, 101-155.

Oh, and while you're gagging on those, would you mind summarizing the modern evidence supporting Schindewolf's assertion that ammonites, ichthyosaurs, and terrestrial dinosaurs went synchronously extinct at the very end of the cretaceous?

The most hypocritical thing about you is that you are afraid to look at the designs (according to you) of God himself, frantically hand-waving about what people say.

What does your Bible say about the reliability of hearsay as evidence, Dan?

And why didn't you answer my earlier questions: how many bases must change in the human genome to cause an extra vertebra? How many to change the identity of a vertebra?

Have you found a "hind leg gene" yet, or was that just a lie?

Date: 2008/01/25 00:41:27, Link
Author: JAM
Quote (Daniel Smith @ Jan. 24 2008,17:53)
I've cited peer-reviewed papers plenty of times in this thread.

Are you claiming that the Denton papers you cited were peer-reviewed, Dan?

Date: 2008/01/25 09:02:22, Link
Author: JAM
One more for you not to read, Daniel:

Cladistic analysis of the Middle Jurassic ammonite radiation
S. MOYNE and P. NEIGE
Geological Magazine, Volume 141, Issue 02, Mar 2004, pp 115-123

Date: 2008/01/26 14:25:16, Link
Author: JAM
Quote (Daniel Smith @ Jan. 26 2008,10:25)
   
Quote (JAM @ Jan. 24 2008,22:40)
             
Quote (Daniel Smith @ Jan. 24 2008,17:50)
             
Quote (JAM @ Jan. 24 2008,09:10)
Darwin's books are primary literature, because they contained new data, unlike the musings you desperately want to believe.

Science is about predicting, not spinning the existing data.

Schindewolf's gaps have been filled, falsifying his hypothesis, even for his speciality, ammonites.

I'm breaking my silence towards you this one time because this cannot go ignored.

But you are ignoring the evidence, proving unequivocally that you lied when you claimed to be interested in evidence.
 
Quote
 
Quote
 
Quote
You know nothing of Schindewolf,

This is yet another lie from you, Dan. You are a reflexive, pathological liar when it comes to evolution and evidence.
 
Quote
 
Quote
   
Quote
... you've never read his books - so how can you possibly know if his book contains new data or existing data?  Are you just guessing?  (I think you are.)

As for his "gaps" being filled, I'm calling you on that.  Show me from the primary literature where the specific gaps he pointed to (of which you're blissfully unaware) have been filled.

CALLOMON, J. H.  1985.
The evolution of the  Jurassic  ammonite family Cardioceratidae.
Special Papers in Palaeontology. 33, 49-90.

DONOVAN,  D.  T. et al.  1981.
Classification of the Jurassic Ammonitina.
In: HOUSE. M. R. & SENIOR, J. R. (eds)
The Ammonoidea. Systematics Association Special Volumes. 18, Academic Press,  London, 101-155.
 
These two papers only show up as citations in Google Scholar.  That doesn't help me much.

I long since gave up trying to help you. You demanded that I show you "from the primary literature where the specific gaps he pointed to (of which you're blissfully unaware) have been filled."

Leaving aside your bald-faced lie about my being blissfully unaware, that's precisely what I did. You didn't ask me to help you, you demanded that I show you where the evidence is.

Then, of course, you lied and claimed that I provided "dead links," when what I provided was citations from the primary literature that rebut Schindewolf's claims.

Why can't you keep yourself from lying, Dan?

   
Quote
       
Quote (JAM @ Jan. 25 2008,07:02)
One more for you not to read, Daniel:

Cladistic analysis of the Middle Jurassic ammonite radiation
S. MOYNE and P. NEIGE
Geological Magazine, Volume 141, Issue 02, Mar 2004, pp 115-123

I actually found this paper.  I find nothing is this paper which falsifies Schindewolf's theory in any way.

That's not surprising, since you found nothing in the sequence evidence that falsified your patently false prediction about noncoding sequences. Have you considered looking at the evidence? Not what ANYONE writes about the evidence, but the ACTUAL EVIDENCE?  
   
Quote
 They do mention him once:...

My God, you are breathtakingly dishonest. No one has to bother with explicitly stating that Schindewolf was wrong any more, because everyone who looks at the evidence knows that he was.

My claim was about evidence, not rhetoric. Yet again, you prove that you were deliberately lying when you showed up here and claimed to be interested in evidence.
   
Quote
I fail to see how this would lead anyone to conclude that "Schindewolf's gaps have been filled, falsifying his hypothesis".

That's because you are a reflexive liar who places rhetoric above evidence while claiming the polar opposite.
   
Quote
They mention two hypotheses...

What they mention is irrelevant. I'm citing their evidence. Can't you get that simple point through your lying, pseudo-Christian skull?
   
Quote
If you somehow misconstrue this as falsifying his entire theory, I fail to see it.

Quit lying. Their evidence falsifies his CLAIM ABOUT THE EVIDENCE: "The gaps that exist in the continuity of forms, which we always encounter at those very points, are not to be blamed on the fossil record; they are not illusions, but the expression of a natural, primary absence of transitional forms. [italics in the translation]
   
Quote
The authors make no claim otherwise.

It's about evidence, not claims. Does their evidence fill a gap that Schindewolf claimed would not be filled?
   
Quote
The authors make no claim otherwise.

Again, our dispute is about evidence, and again, you prove that you were lying when you claimed to be interested in evidence.
     
Quote
   
Quote
Oh, and while you're gagging on those, would you mind summarizing the modern evidence supporting Schindewolf's assertion that ammonites, ichthyosaurs, and terrestrial dinosaurs went synchronously extinct at the very end of the cretaceous?
That view is not expressed in his book.

I didn't claim that it was, liar.
   
Quote
You'll have to provide the direct quotation.

Why? You haven't bothered to name a single "hind leg gene," even though you clearly claimed that more than one such gene exists.

Date: 2008/01/28 01:23:50, Link
Author: JAM
Quote (Daniel Smith @ Jan. 27 2008,13:41)
<Snip of typical JAM accusations>

Why? They're all true. You're afraid of evidence.
 
Quote
       
Quote (JAM @ Jan. 26 2008,12:25)
It's about evidence, not claims. Does their evidence fill a gap that Schindewolf claimed would not be filled?

No it does not.

You're lying. Read what that arrogant ass Schindewolf wrote on p. 105-106.  
Quote
Explain to me specifically, a) which "gap" Schindewolf claimed would never be filled, and b) how their evidence fills it.

Schindewolf's arrogant, false claim was GLOBAL, fool, so no specific explanation is needed.

You are an intellectual (and theological) fraud, Dan. You asked for evidence, I pointed you to it, and you moved the goalposts. You never even looked at any of the evidence in that paper. You simply searched for the word "Schindewolf," and made a complete ass of yourself yet again.

I just submitted a manuscript describing multiple tests of a competitor's hypothesis, smashing it to smithereens. His name is not anywhere to be found in the text (I did cite his lab's data, so his papers are cited) so your test (and your utterly dishonest, yet predictable, avoidance of actual evidence) is bogus.

Quote
<Snip of more typical JAM accusations>

They're all true. You started lying in your first post here when you claimed to be interested in evidence, and you've continued to lie at a frantic pace. This is all about your ego, because your fear of evidence shows that you have no faith.

Date: 2008/01/28 22:14:32, Link
Author: JAM
Quote (Daniel Smith @ Jan. 28 2008,19:29)
 
Quote (JAM @ Jan. 27 2008,23:23)
       
Quote
                 
Quote (JAM @ Jan. 26 2008,12:25)
It's about evidence, not claims. Does their evidence fill a gap that Schindewolf claimed would not be filled?

No it does not.

You're lying. Read what that arrogant ass Schindewolf wrote on p. 105-106.  
         
Quote
Explain to me specifically, a) which "gap" Schindewolf claimed would never be filled, and b) how their evidence fills it.

Schindewolf's arrogant, false claim was GLOBAL, fool, so no specific explanation is needed.

Schindewolf's claim was global, but it wasn't universal.  It doesn't apply to every phase of every lineage.  It only applies to the very beginnings of types - his typogenesis phase.

You're lying again. His claim applies to gaps. He does not limit his claim.
Quote
I hope you can appreciate the difference.

I appreciate your predictable dishonesty.
Quote
Quote
You asked for evidence, I pointed you to it, and you moved the goalposts. You never even looked at any of the evidence in that paper. You simply searched for the word "Schindewolf," and made a complete ass of yourself yet again.

You're wrong about that.  I looked through the entire paper for the evidence you spoke of.  I did not find it.

That's not what you wrote. Your argument was that the authors didn't MENTION Schindewolf in such a context. You didn't look at the evidence.
Quote
The crux of the paper was that the authors believed the evidence supported the "two-lineage" hypothesis over the "one lineage".

No, this is not lit crit. The crux of the paper was that the authors SHOWED that the evidence supported two lineages. The salient point in our little disagreement is that they had much more evidence to work with--IOW, they had evidence that Schindewolf claimed would never be obtained.

Schindewolf's dependence on suture morphology is another matter that makes his conclusion even more suspect.
Quote
Schindewolf sided with the "one-lineage" hypothesis,

You're doing lit crit again. Schindewolf claimed that the evidence supported one lineage rather than two. That's not what we're disagreeing about. My point is that Schindewolf claimed that the evidence in his possession was complete. He was wrong.
Quote
... but made no claim that this represented one of the unbridgeable gaps of his theory.

The gaps aren't really part of his theory. He claimed that the gaps in continuity of the fossils he had in hand represented gaps in evolution. His hypothesis utterly depended on his assumption that the evidence was complete, BUT HIS ASSUMPTION WAS WRONG.
Quote
I thought I already explained that to you?

No, you didn't. You can't even distinguish between predictions and hypotheses or between evidence and opinion.

When are you going to test your inadvertent prediction that "hind limb genes" exist, Dan? If they don't exist, doesn't that completely trash your hypothesis about the hierarchical nature of God's design of limb development?
Quote
I think, if you're going to critique Schindewolf, you should maybe follow the advice you gave me a while back and read what he actually said first - instead of quote-mining.

I'm not quote mining anything. I'm pointing out that his fundamental assumption about the evidence is spectacularly false. His hypothesis depends on that assumption.

Date: 2008/01/28 22:23:12, Link
Author: JAM
Quote (Daniel Smith @ Jan. 28 2008,19:10)
 
Quote (Wesley R. Elsberry @ Jan. 27 2008,13:14)
Another interesting bit comes from the Foreword to Schindewolf's book by Stephen Jay Gould, where he notes that Schindewolf's forcefulness of character inhibited expression of critical views in Germany for many years:  

       
Quote

Reif ends: "Finally, as late as the 1970s young authors risked censure by their superiors if they discussed typostrophism [Schindewolf's main concept] critically. Under the influence of Schindewolf's authority, evolution was no topic for the would-be paleontologist." I believe I sense some legitimate bitterness in Reif's words.


So it seems that when he was at his prime, Schindewolf encouraged stifling dissent from typostrophism and failed to be a role model for any sort of "strengths and weaknesses" blather.


I'm sure many scientists won't win personality contests.  I also don't see where that's an issue except only peripherally - since Schindewolf's 'reign of terror' could only extend as far as his university in Germany.

Your reflexive mendacity is amazing. So, if Schindewolf's influence was confined entirely to his own university as you claim, you must have evidence that he:

1) Never reviewed any manuscripts from authors at other universities.
2) Never was asked for a tenure recommendation letter from tenure committees at any other universities.
3) Never wrote a letter of recommendation for a student or colleague to any university but his own.

Since all of those are negatives, you must have done an exhaustive search before (ethically) making such a grand claim.

Do you have any evidence that any of the above conditions existed, or were you simply talking out of your pompous hind end again?

Date: 2008/01/29 15:01:32, Link
Author: JAM
Quote (mitschlag @ Jan. 29 2008,07:10)
Quote (JAM @ Jan. 28 2008,22:23)
Your reflexive mendacity is amazing. So, if Schindewolf's influence was confined entirely to his own university as you claim, you must have evidence that he:

1) Never reviewed any manuscripts from authors at other universities.
2) Never was asked for a tenure recommendation letter from tenure committees at any other universities.
3) Never wrote a letter of recommendation for a student or colleague to any university but his own.

Since all of those are negatives, you must have done an exhaustive search before (ethically) making such a grand claim.

Do you have any evidence that any of the above conditions existed, or were you simply talking out of your pompous hind end again?

Not necessarily pompous.

All the evidence points to it, though.

As Wes pointed out, Daniel is perfectly willing to denigrate the life's work of thousands of people, while rationalizing Schindewolf's misrepresentation of Darwin, only because Schindewolf's hypothesis appeals to his particularly offensive twisting of Christian theology.
Quote
Inexperienced and uninformed, more likely.

Absolutely, but I've found that those two qualities tend to be highly associated with pomposity.

Date: 2008/01/31 11:21:39, Link
Author: JAM
Quote (mitschlag @ Jan. 31 2008,09:53)
It's all moot, anyway, being unsupported by the evidence:

Daniel doesn't do evidence, despite his claim on arrival that he was interested in evidence.

Only opinions that support his prejudices are elevated in his narrow mind.

Date: 2008/01/31 21:48:24, Link
Author: JAM
Quote (Daniel Smith @ Jan. 29 2008,18:53)

And for you JAM:
         
Quote
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"
ibid, pp 102-103

The only "gaps" Schindewolf was concerned with were at the beginning of a "structural type".  He makes that abundantly clear throughout the book.  Furthermore, since Schindewolf had already mapped out a line of descent for the hammatoceratins, this cannot constitute one of his "gaps".

Sure it does. The additional evidence (which, remember, Schindewolf claimed would never be found because it did not exist) supporting two lineages over one eliminates at least two of his vaunted gaps.

Date: 2008/01/31 22:11:01, Link
Author: JAM
Quote (Daniel Smith @ Jan. 31 2008,19:06)

I don't see anything in this graph or in its description that contradicts Schindewolf.

Yeah, just like you saw introns as coding sequences for no valid reason, and when you were corrected, you retreated to the lie of not seeing anything that contradicted your perverted theological views, which are so important to you that you will justify violating the Commandment against bearing false witness.
Quote
In fact, all the older species (until 25MY ago) were "mostly browsers" - just like Schindewolf said.  And, since the reduction in toes began then, Schindewolf is again proved correct by modern evidence.

Um, Dan, Schindewolf's claim was about the EARLY Tertiary. 25MY ago was not in the early Tertiary. The early Tertiary was 65MY ago.

You'll fudge anything, won't you?

Date: 2008/02/01 15:25:47, Link
Author: JAM
Great tard from Joy at Telic Brain Farts:

Quote
We eat meat (well, some of us do) because it's an 'easy' food for nutritional purposes - our cells don't have to do the hard work of constructing complete proteins from raw ingredients, since we can get them pre-synthesized from animal sources whose cells did the work.


http://telicthoughts.com/news-in....-174682

Date: 2008/02/01 23:41:08, Link
Author: JAM
Quote (Daniel Smith @ Feb. 01 2008,19:02)

I'm sorry to have to do this to you JAM, but it appears I was wrong when I said Schindewolf held to the 'one lineage' hypothesis.

You've been wrong about virtually everything so far, so that's not surprising.

What you can't seem to get through your thick head is that we are trying to point out to you that Schindewolf's claim about the EVIDENCE (that the gaps would not be filled) is wrong, so you can't win by arguing one vs. two lineages.

The point is that the papers I cited contain evidence (not words) that Schindewolf claimed did not exist.
 
Quote
A more careful reading reveals that Schindewolf believed the hammatoceratins to be a superfamily that could be divided into two separate lineages.

Are they the same lineages indicated by the newer evidence? You'd have to examine the evidence to tell, and we both know that you categorically reject examining evidence in favor of lit crit.
 
Quote
It's a little hard to follow the author's descriptions...

The descriptions don't matter. The evidence is what matters, and you ignore evidence.
 
Quote
So what did the authors conclude?

It's not really relevant, because my point is about evidence. Can you grasp the simple fact that opinion is not evidence, Dan?
Quote
 
Quote
The principal result of the cladistic analysis presented here is that the ammonites under study form two groups, each including members of the hammatoceratins root group and their late Aalenian descendants. This confirms that the hammatoceratins group is in fact an association of two lineages (‘Hammatoceras group’ and ‘Erycites group’) that diverged early on, during the Toarcian stage, in the history of the emerging clade as suggested by Rulleau, Elmi & Thevenard (2001).

Do you notice that they aren't citing Schindewolf's evidence here? Why would more recent evidence be more informative than your master's?
 
Quote
Thus, much to your chagrin I'd suppose, the paper you cited to undermine Schindewolf actually ends up supporting him!

No, Dan, it doesn't, because it contains evidence (you ignore evidence) that Schindewolf claimed didn't exist. It's that simple.
 
Quote
Ya gotta love science!

But science is about evidence, not your frantic quote mining.

Date: 2008/02/01 23:45:03, Link
Author: JAM
Quote (Daniel Smith @ Feb. 01 2008,19:08)

This is why Schindewolf based his theory on cephalopods and stony corals - as opposed to mammals, reptiles and the like.

Hmmm...let's see...octopi have no bones, while birds do. I don't see your point.
Quote
He (as far as I can tell) only looked to the latter to see if the patterns he saw in the former abundantly fossilized lineages

I hate to break it to you, Dan, but not all cephalopods are abundantly fossilized, and italicizing your lie only makes you look silly.
Quote
...He found nothing that contradicted those patterns.

But plenty of others have found the evidence he claimed didn't exist in the decades since.

Date: 2008/02/01 23:51:33, Link
Author: JAM
[quote=Daniel Smith,Feb. 01 2008,19:18]  
Quote (mitschlag @ Feb. 01 2008,06:15)

At issue is Schindewolf's claim:                    
Quote
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...

Schindewolf did not claim that the one toed foot came about before the plains,

Yes, he did.
Quote
he claimed that the reduction of digits began before there was any advantage for it.

You should reread the text you are so desperately trying to promote.
Quote
You have confirmed his words by pointing out that by the time grasslands were becoming abundant, the horse's ancestors were already down to three toes!

You're lying, Dan. You left out one of Schindewolf's words. The "rest of the lateral toes" refers to the transition from 3 to 1 toe, not from 5 to 3.

Once again, you bold or italicize your dishonesty, as though emphasizing it somehow magically compensates for its falsehood.

Date: 2008/02/06 11:30:33, Link
Author: JAM
Quote (Daniel Smith @ Feb. 04 2008,19:04)
 
Quote (JAM @ Feb. 01 2008,21:45)
                 
Quote (Daniel Smith @ Feb. 01 2008,19:08)
...He found nothing that contradicted those patterns.

But plenty of others have found the evidence he claimed didn't exist in the decades since.

JAM,

It didn't take long for me, from the time you first entered this discussion, to lose my respect for you as a human being.

Why? Because by making you look at the sequence evidence, your initial proclamation of interest in evidence was shown to be a bald-faced lie?

Look above. I'm arguing evidence, you're ignoring evidence and going for the ad hominem attack.

How many times do you have to hear "opinions aren't evidence" before this essential distinction gets through your head?

Do you realize that a real scientist (or anyone else interested in actual evidence) looks at the tables and figures long before she/he consults the text?

Quote
Anyone with common courtesy or decency can read back through and immediately see why.

I don't see why. I see us calling you on your initial lies:
Quote (Daniel Smith @ Sep. 22 2007,04:48)
My main problem is that I want to see unbiased and unadulterated evidence; not evidence that is made-to-fit the observers viewpoint....I decided what I needed was just to see the evidence for myself.

You're scared to death of actual evidence.
Quote
I still, though, maintained a grudging respect for you as a scientist.

Why, given your utter contempt for the scientific method?
Quote
In fact, I'm beginning to have doubts that you really are a scientist.

Cool. How many $K do you wanna bet? 
Quote
Nevertheless, I think I'll go back to ignoring you now.  You obviously have nothing of substance to contribute to this conversation.

Evidence is the substance of science, not opinion. Thanks for demonstrating again that you were lying when you claimed to be interested in evidence.

Date: 2008/02/06 16:27:06, Link
Author: JAM
Quote (Daniel Smith @ Feb. 06 2008,13:58)
 
Quote (JAM @ Feb. 06 2008,09:30)
Evidence is the substance of science, not opinion. Thanks for demonstrating again that you were lying when you claimed to be interested in evidence.

Where, specifically, is the evidence...

In the figures and tables, Dan.

Why did you search for "Schindewolf" in the text instead of looking at the evidence presented in those papers?
Quote
[you thought was] in that paper [you never read]

There were three papers, remember? You got caught lying when you claimed that two of them were "dead links," when I provided citations, not links.
Quote
... that [supposedly] destroys Schindewolf's theory?

Wow. Your mendacity is astounding. I was very, very specific about what these papers showed:
Quote (JAM @ Jan. 24 2008,11:10)
Schindewolf's gaps have been filled, falsifying his hypothesis, even for his speciality, ammonites.

Dan, can you ever muster sufficient integrity to simply portray your opponents' positions accurately?

Aren't you bearing false witness every time you misrepresent anyone's position?

How can anyone claiming to follow the teachings of Jesus Christ (who said nothing about evolution, but a lot about the evils of hypocrisy) do what you do with impunity?

Date: 2008/02/06 16:32:34, Link
Author: JAM
Quote (Daniel Smith @ Feb. 06 2008,13:54)
My post was never meant to be a defense of my level of knowledge.  It was a defense of my level of effort in learning about ideas that don't jibe with my current views.

Ah, but on your arrival here, you claimed to be interested in EVIDENCE. That was a lie. You have frantically evaded the consideration of evidence in favor of quoting opinions. That's pseudoscience in a nutshell.
Quote
It was in the context of comparison with the amount of effort spent by others on this board in learning more about Schindewolf and Berg.

Why should we learn more about PEOPLE'S OPINIONS when you claimed to be interested in EVIDENCE?

Why weren't you interested in the evidence that's been acquired since Schindewolf offered his hypothesis, which depends utterly on the veracity of his assumption that gaps would not be filled?

Date: 2008/02/06 16:36:40, Link
Author: JAM
Quote (Daniel Smith @ Feb. 06 2008,14:03)
No, I think that people are afraid of being ridiculed for wanting to test a saltational theory - so they dismiss it out of hand.

But you don't dismiss it, so why are you afraid of offering predictions and testing them? If you're so sure you're right, you have nothing but fame ahead of you. I can only conclude that you are lying about your faith in your position.

Also, aren't IDers and creationists ridiculed because they REFUSE to test any of their own hypotheses?

Isn't that refusal the very reason why they (and you) are pseudoscientific frauds?

Date: 2008/02/06 20:58:08, Link
Author: JAM
Quote (Daniel Smith @ Feb. 06 2008,17:42)
 
Quote (JAM @ Feb. 06 2008,14:27)
           
Quote (Daniel Smith @ Feb. 06 2008,13:58)
 
Where, specifically, is the evidence...

In the figures and tables, Dan.


Which figure, and which table, and what exactly do they show that falsifies (but apparently doesn't destroy) Schindewolf's theory?


I was not referring to what you call "Schindewolf's theory." I was referring to the hypothesis (more of an assumption) on which it utterly depends:

"The gaps that exist in the continuity of forms, which we always encounter at those very points, are not to be blamed on the fossil record; they are not illusions, but the expression of a natural, primary absence of transitional forms."

I've already explained this to you. Why are you lying and pretending that the evidence is about anything but this assumption/hypothesis?
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Try to be specific about how the data in "the figures and tables" falsifies Schindewolf.

Why should I bother with someone as mendacious as you?
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If you say "it fills his gaps" - explain which gaps you are talking about and cite the quotation where Schindewolf made the claim that those specific gaps would never be filled.

I already did. You have dishonestly tried to pretend that I did not. Moreover, Schindewolf made a general, not a specific, claim.
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Remember JAM, you're all about the evidence!

And you lied when you claimed that you were!
 
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Why did you search for "Schindewolf" in the text instead of looking at the evidence presented in those papers?

I searched for Schindewolf's name before I read the paper just to see if they mentioned him, then I read the paper.

Did everyone see that goalpost move? I asked why he didn't look at the evidence, then Dan dodges my question completely, pretending I was asking whether he had read the paper or not.
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I did this before I responded to you the first time.

But you didn't look at the evidence--in fact, you still haven't.
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You accused me of searching for his name without reading the paper.

No, Dan, I accused you of searching for his name INSTEAD OF LOOKING AT THE EVIDENCE.
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That was an untrue accusation on your part JAM.

It is an untrue accusation, which is why you deliberately and dishonestly decided to falsely attribute it to me.
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You do understand that an accusation doesn't make something true -- don't you JAM?

I do. Do you realize that falsely attributing an accusation to someone doesn't mean that he made the accusation, Dan? Do you realize that it's a blatant violation of a Commandment?
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Then, after responding to you, I read it again.  So I've read it twice (so far).

But you have yet to look at the evidence. That's the big difference between the primary scientific literature and what you choose to quote-mine.
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Have you read it once yet?

Yes. More importantly, primarily I examined the evidence presented in the papers, which exists independently of my, your, Schindewolf's, or the authors' opinions, which is all you read and quoted.

Have you grasped the essential distinction between evidence and opinion, and do you have the integrity to admit that you lack both the desire and curiosity to examine the evidence for yourself, which means that you opened up here with a laughably bald-faced lie?

Date: 2008/02/08 09:21:03, Link
Author: JAM
Quote (Daniel Smith @ Feb. 07 2008,18:39)

What's so "hilarious" about it.  I've been poring over the tables and figures in this paper and can find nothing that contradicts anything Schindewolf said.

Let's not forget that you frantically moved the goalposts, when this paper is about contradicting his assumption, on which his "theory" depends:
"The gaps that exist in the continuity of forms, which we always encounter at those very points, are not to be blamed on the fossil record; they are not illusions, but the expression of a natural, primary absence of transitional forms."
 
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Nothing.

So, Dan, in the context of Schindewolf's claim above, tell me where in the nested hierarchy Schindewolf classified Riccardiceras.
 
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Are you going to tell me there's evidence here that I can't see?

I'm telling you that you are afraid of evidence.

I'm telling you that you fabricate evidence when your political positions are threatened by real evidence, as you did when you claimed that the isthmus of Panama isolated Atlantic and Pacific humpback whale populations, a claim that an 8-year-old can see is false by glancing at a globe.

You also fabricated evidence when you made the inadvertent prediction (based on your hypothesis of how our bodies were designed by God) that "hind limb genes" even existed, a dishonest claim that you lack the integrity to either support or retract.
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One thing I will tell you:  Schindewolf extensively utilized shell suture lines in his classifications of ammonites - something these authors -- because of the scope of their study -- were unable to do:        
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Suture line characters are not used in this analysis because of their high variability between the different species of each genus. Moreover, using suture line characters for such different taxa would involve establishing clear homologies between the different sutural elements via an ontogenetic approach. The wide scope of the present study precludes this.
ibid. pg. 117

Dan, you twist the most obvious things to fit your sick political views so that they are unrecognizable.

Schindewolf's reliance on suture lines is the reason I keep asking you (and you keep ducking, because you know you are being dishonest) these questions:
1) How many nucleotide changes are required to change the number of mammalian vertebrae in an individual?
2) How many nucleotide changes are required to change the identity of a mammalian vertebra?

Surely we can agree that the genetic complexity involved in constructing the different vertebral morphologies is far, far greater than the genetic complexity of a suture line in an ammonite's shell.

 
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Schindewolf, on the other hand, extensively documented suture line evolution into the early ontogenetic stages.  You must realize that this was Schindewolf's area of expertise!

I realize that. I also realize that EVEN LIMITING CONSIDERATION TO SUTURE LINES, Schindewolf's gaps have been filled: