RSS 2.0 Feed

» Welcome Guest Log In :: Register

Pages: (12) < [1] 2 3 4 5 6 ... >   
  Topic: The best fact that falsifies Darwinism, DNA homology disproves the dogma< Next Oldest | Next Newest >  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 04 2006,17:17   

Almost all facts that appear to falsify Darwinism have been explained away by invoking ad hoc hypothesis. I have recently found a fact that can falsify Darwinism. To my knowledge, this fact has never been previously recognized as odd by either the creationists or Darwinists. No one seem to have paid attention to it. But that is not surprising because none of the present ideas will lead people to it. I came to it from a novel perspective which I will share with the public in the future. This fact is the only one you need to use to falsify Darwinism because no Darwinists that I have met had any clue.

This conspicuous fact that falsifies the Darwinian hypothesis is that no genes have shown signs of having reached the maximum divergence between any two species. The Darwinian idea suggests that a new species splits from an older species with nearly identical genes in the beginning and thereafter gradually accumulates sequence divergence in a time dependent manner. Accordingly, given enough time, a gene may diverge between two species from a beginning near 100% identity to a lowest identity point that still retains gene function. This point may be anywhere below 100% identity, depending on genes. If 500 million years is enough time for gene X to reach its maximum degree of divergence between species A and B, then X of species A would show the lowest possible identity to species B if A diverged from B 500 million years ago. Furthermore, if species A diverged from C much earlier than B, say 800 million years ago, the identity in gene X between A and C would be the same as that between A and B. But such a gene X has never been found and it is not because life on earth has not been given enough time to mutate or diversify. While different genes may require different amount of time to diverge from 100% identity to the lowest possible, 500 million years are certainly enough time for a large number of genes to do so. There are many genes that show border-line homology around 15-20% between human and sea urchin that diverged about 500 million years ago. Since unicellular eukaryotes diverged from multicellular eukaryotes at least 500 million years ago, we would expect that many genes from higher animals would have diverged from yeast to the lowest possible identity. These genes would then also show the same identity to bacteria. However, despite nearly a half century of gene sequence analysis, not a single animal gene has been found that shows equal identity to its homologous versions in yeast and bacteria.

Anyone has any idea on how to explain this fact?  It is not what Darwinism would predict.

  
stevestory



Posts: 10127
Joined: Oct. 2005

(Permalink) Posted: Mar. 04 2006,17:18   

hey Shi, check out www.fixedearth.com . That guy falsifies heliocentrism with the same brilliant level of logic with which you falsified uh ‘Darwinism’.

   
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 05 2006,13:10   

Ok, it's my turn to post the answer I posted on PT:

The maximum level of divergence between two gene sequences is 75 %, which is the average divergence between two random sequences.
Of course natural selection can impose constraints to mutations and the maximum level of divergence between two sequences may be lower, but I’m not certain of that.
Gene sequence comparisons between distant taxa are almost exclusively used in phylogenetic studies, AFAIK. A gene that has reached its maximum level of divergence between different given taxa is useless for the phylogenetic inference regarding these taxa. That explains why you never saw a phylogeny that puts mammals, bacteria, and yeats at the same distance, in what we call a “rake” (not sure whether the translation from French “rateau” applies here).
Lots of genes do not qualify for large scale phylogenetic studies, some of them do not even exist in all taxa and others have reached their maximum level of divergence (75% or less).

  
Bob O'H



Posts: 2132
Joined: Oct. 2005

(Permalink) Posted: Mar. 05 2006,18:50   

Quote
That explains why you never saw a phylogeny that puts mammals, bacteria, and yeats at the same distance, in what we call a “rake” (not sure whether the translation from French “rateau” applies here).


Are you looking for a "star phylogeny"?  It's the same thing, but a different shape.  :-)

To get far too technical, evidence of long branch attraction (i.e. the Felsenstein zone) in a pair of sequences would falsify the falsification quite nicely.  Anyone have a reference handy?

Bob

--------------
It is fun to dip into the various threads to watch cluelessness at work in the hands of the confident exponent. - Soapy Sam (so say we all)

   
Sheikh Mahandi



Posts: 47
Joined: May 2005

(Permalink) Posted: Mar. 06 2006,01:24   

Quote
That explains why you never saw a phylogeny that puts mammals, bacteria, and yeats at the same distance......


I hope you mean yeasts and are not making reference to my family.   :D

--------------
"Love is in the air, everywhere I look around,.....Love is in the air, every sight and every sound,......"

  
Henry J



Posts: 4565
Joined: Mar. 2005

(Permalink) Posted: Mar. 06 2006,05:26   

I'm glad somebody answered the question that started this thread, since I didn't know if the prediction was (1) a prediction that wasn't actually predicted by the current theory, (2) already confirmed by researchers, or (3) not yet investigated.

Apparently it was case 2.

Henry

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 06 2006,06:48   

Quote (jeannot @ Mar. 05 2006,19:10)
A gene that has reached its maximum level of divergence between different given taxa is useless for the phylogenetic inference regarding these taxa.
Lots of genes do not qualify for large scale phylogenetic studies, some of them do not even exist in all taxa and others have reached their maximum level of divergence (75% or less).

My message is clear enough to most experts in the field.  But for the benefit of non-experts, I will explain it in more detail.  First, I mean protein sequence homology not DNA.  The border-line identity between two proteins is 15-20%, beyond which the two may not be eaisly recognized as homologous.  

Second, The beauty of the fact that I am presenting is that it both supports and falsifies Darwinism, which makes it impossible for Darwinists to escape the falsification.  It supports Dariwinism because there exist genes like cytochrome C.  Human cyto C is identical to monkeys, less so to birds, still less to frogs, still less to fish, still less to yeast, and least similar to bacteria.  Cyto C is thought to have a slow mutation rate and is obviously not showing signs of having reached maximum divergence.  On the other hand, there are many genes that mutate faster.  If A splited from B 100 myr ago, from C, 200 myr ago, from D 300 myr, from E, 400 myr,from F, 500 myr ago, and from G, 700 myr ago, there are many genes that show this pattern:  identity between AB 90%, between AC, 70%, between AD 50%, between AE, 30%, between AF, 15-20%, between AG, no recognizable relationship.  This pattern supports Darwinism and nearly all proteins show that type of pattern.  However, if Darwinism is true, another pattern must exist for some genes X.  Gene X would show identity between AB 90%, between AC 60%, between AD 30%, between AE 20%, between AF 20%, between AG, 20%.  In this case, 20% is the lowest possible identity for gene X to retain similar function.  But no genes like gene X has been found.  

Darwinists can refute my logic by doing two things, 1, find a gene like X, 2, claim that Darwinism does not predict the pattern of gene X.  No expert evolution biologists that I have contacted have been able to do those two things.  

I hope this is now clear to everyone.  If there are still some who do not get it, they should consult with an expert.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 06 2006,07:02   

Quote
However, if Darwinism is true, another pattern must exist for some genes X...

I hope this is now clear to everyone.  If there are still some who do not get it, they should consult with an expert.
It's not clear what you mean by "Darwinism", and I doubt that contacting an expert is going to clear that up. I take it there's some particular aspect of either common descent or natural selection that entails the prediction you describe. Can you be more specific?

--------------
Must... not... scratch... mosquito bite.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 06 2006,07:11   

The one I am referring to is What ever version of Darwinism that is being claimed to have been supported by the protein homology facts such as the pattern displayed by cyto C.

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: Mar. 06 2006,07:44   

I dont know how many times I have to say this to ID supporters, you can't just come up with a hypothesis and then say that it is right until someone else proves it wrong, you need evidence to back up your claim. Which particular evolutionary biologists have you contacted and what were their responses?

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 06 2006,07:45   

Quote (shi @ Mar. 06 2006,12:48)
My message is clear enough to most experts in the field. ... First, I mean protein sequence homology not DNA.

Well, your message wasn't clear enough even for experts because you were talking about genes, not proteins.


Anyway, I don't see the difference. I suppose that lots of proteins are not suitable for large scale phylogenies based on amino acid sequences, because they evolve too fast and have reached their maximum divergence between distant lineages. Cyt b and COI maybe...?

But you raised an interesting point, it could be very instructive to compare the maximum level of divergence (if there is any) for several proteins found in almost all living beings.

However, "Darwinism" does not predict a minimum level of identity between too homologous proteins since a protein doesn't have keep the same function forever.

  
edmund



Posts: 37
Joined: Jan. 2006

(Permalink) Posted: Mar. 06 2006,08:30   

Hi Shi,

Can you tell me where you are getting your data from? Without knowing that, it's difficult to evaluate this pattern that you say you're finding. Thanks.

It seems to me that there a couple of possible problems with this approach. The first is this: once the similarity between two amino-acid sequences drops below a certain level, it becomes very difficult to recognize them as homologous, even if they were descended from the same ancestral sequence. You suggest that we ought to be finding mammal genes that are equally (maximally) distant from the homologous yeast and bacterial genes. But if they're so distant that the sequences have essentially "saturated" with changes, how can we tell that they're homologous in the first place?

The second possible problem: Your argument seems to assume that some minimum number of amino acids in the sequence will be conserved even after the rest of the sequence "saturates" with replacement mutations. For example, you suggest that for gene X, 20% of the sequence will be conserved no matter what. Is there evidence that this happens? Is there evidence that this minimum amount is large enough that homologous sequences can be recognized as such?

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 06 2006,08:38   

ATP generation is a function that every life form needs to have here on earth.  the proteins involved in that process need to function the same no matter how long evolution has or will take place.  the original function of cyto C will never be changed regardless of time of evolution.  Cyto C may gain some extra functions as evolution progresses, such as apoptosis, but its bare bone function that is essential for every cell must stay unchanged.  By the same logic, a bare bone sequence needs to be maintained regardless evolution.  Cyto C has an well estimated mutation rate of 1% amino acid change per 20 myr and this rate is supposed to be constant.  human cyto C showes 35% identity with bacteria and 60% identity with yeast.  Based on the cyto C mutation rate and Darwinism, we would predict in 400 myr, (400/20 x 1% =20%) human cyto C will show 15% identity to bacteria and 45% identity to yeast.  In 800 myr, human will show 0 or -5% identity to bacteria and 25% to yeast.  In 1200 myr, human will show 0 or -25% identity to bacteria and 5% to yeast.  Our decendents will have to assume then that despite 0%-5% identity, human cyto C has a functional homolog in bacteria and yeast.  If they take that position, then sequence identity is meaningless in inferring homologous relationships.  They will not be able to conclude there exist any protein in humans that does not have a homolog in bacteria.  The common fact is that when two proteins share less than 10% identity, it is pretty safe to conclude that they are totally different proteins with distinct functions.  It is far more likely that cyto C cannot diverge beyond a certain identity before it loses its bare-bone function.  Let's assume it is 15%.  We would predict then that in 400 myr, human will be 15% identical to bacteria and 45% to yeast.  In 800 myr, human will be still 15% idetical to bacteria (any lower would lose function) but will be 25% to yeast.  In 1200 myr, human will be 15% to bacteria and 15% to yeast.  In 1600 myr, 15% will still hold and will stay forever.  If this picture is what is consistent with Darwinism and could occur in 1200 myr in the future, there is no reason that it has not occured in the past 3000 myr for some gene X that is indispensible for life but has a faster mutation rate of 1% change per 40 or 80 myr.  The only reason that it has not occured in the past is that the Darwinism interpretation of nature may not be a complete and precise one.

  
J. G. Cox



Posts: 38
Joined: Dec. 2005

(Permalink) Posted: Mar. 06 2006,09:23   

I don't have much time to respond, so you get bullet points. In short, if shi actually did propose this idea to a real evolutionary biologist, shi did not get a response because the biologist took one look at it and realized that shi had no idea what he/she was talking about. ####, I'm in ecology and I can see that it's bunk.

-as jeannot meantioned, gene products can change functions over time, so shi's argument fails to apply to such situations. Let's assume that we're talking about proteins with retained functions, however.
-shi implies that the original protein sequence is not mutating; we know this to be untrue, and this (on average) inflate sequence divergence over time
-shi implies a step function for the protein. In other words, it either functions perfectly or not at all at some critical value of sequence divergence. Again, this is for all practical purposes never true. The ability of proteins to perform their functions and the rates at which they do such or respond to control proteins are practically continuous functions that depend on folding patterns, binding site affinities, etc. Such functional responses affect the effects of natural selection both on the protein in question and other proteins which take part in other steps of the associated process. Shi essentially proposed a neutral mutation model which is extremely unlikely, especially for old genes like cyt c.
-shi assumes that the original protein configuration was optimal, and that subsequent mutations must eventually serve to cripple it. This assumption is wholly unjustified. Gradual or punctuated improvements in function could be mirrored in rewrites of substantial portions of a protein, or even the whole thing
-the ability of a protein to serve its function depends not only on its own configuration, but that of the proteins and other molecules with which it interacts. Thus, a mutant protein could easily serve the same 'function' in an organism if one or more of the other proteins also mutates into an appropriate configuration. This also invalidates shi's step function model of protein function, and is I beleive the most important of my criticisms.
-shi needs to take into account back mutation, which in his model would establish equilibrial divergences independent of his minimum identity needed to retain function

Thus, the reason that shi probably has not received a response is that shi's prediction is not biologically valid.

As an aside, your math is wrong shi. I'll give you a hint: it resulted in your calculating negative % 'identities.'

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 06 2006,09:30   

Quote
In 1200 myr, human will show 0 or -25% identity to bacteria
Well, yes. If there's a version of "Darwinism" that predicts homology falls at a linear rate indefinitely - eventually producing negative % identity between two genes, that version is in trouble. Just like the version of physics that says that, if my phone battery is losing 0.05 volts per hour, it will eventually reverse polarity.

--------------
Must... not... scratch... mosquito bite.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 06 2006,09:54   

Shi,

Cyt C transfers electrons from complex n° 3 to complex n° 4 in the microchondrium internal membrane, IIRC. That's its function.
So cyt c co-evolves with these two protein complexes (at least) and these complexes also co-evlove with other proteins.

I don't see the reason why there should be a minimal level of identity for homologous cytochromes C just because ATP is produced at the end of the reaction chain.

EDIT: thank you Mr Cox, that was a better answer than I could ever give in English (or even in French after all ;)).

EDIT 2: Shi, phylogenetic inferences are not based on sequence identities anymore (phenetics). We identify precisely all the mutations that occured in each lineage, regardless of the distance between sequences (cladistics).

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 06 2006,10:04   

That the cyto C data is used today to support Darwin is precisely because of neutral mutation theory.  Without the assumption of neutral mutation, there is no molecular clock idea and no evidence of protein homology being evidence of evolution.  So, Cox needs to do some homework before taking part in a discussion outside his field.  He should pay attention also that most things in nature (the fundametal ones) stay unchanged once created.  The pentadactyl design of vertibrate limb is one example.  The hair of a mammal is another.  There is only one ATP generation process.  There is only ATP as energy source.  Why should not some fundamental genes or functional domains stay unchanged once created, just like countless other things that stay unchanged in nature?  

To Russel, if no version of Darwinism predicts infinite mutation, then show me a version that predicts that at some point mutation should stop.

  
sir_toejam



Posts: 846
Joined: April 2005

(Permalink) Posted: Mar. 06 2006,10:16   

Quote
...stay unchanged once created


I predict that continued discussion with shi will be unproductive.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 06 2006,10:21   

Shi, the neutral theory of molecular evolution only applies for neutral mutations. If you think that all amino acid substitutions in Cyt C are neutral, you are plain wrong. Therefore I suggest that you read some books or papers on protein evolution before arguing with Mr Cox who knows far more than you do on this topic.

The theory of evolution does not rely on the molecular clock (which does not very well apply to amino acid sequences). I fail to understand why you think it should. The mutation rate of cyt C is just an average between lineages.
And you seem to confuse genetic distance with mutations.

[BTW, the neutral theory is NOT Darwinism (= evolution by natural selection).]

  
Flint



Posts: 478
Joined: Jan. 2006

(Permalink) Posted: Mar. 06 2006,10:43   

I think Sir Toejam has identified the problem here - the inherent stability of created kinds is not a biological theory.

  
tiredofthesos



Posts: 59
Joined: Jan. 2006

(Permalink) Posted: Mar. 06 2006,11:11   

If "shi" is actually a practicing scientist with a revolutionary criticism of current evolutionary theory, why the **** is he/she posting it on the chatsite of a layman's forum?  This doesn't have to be a rhetorical question: I will accept answers.

 Of course, anyone who uses the expression "darwinist" to attack the current ToE has already revealed their real motivation in making any statement.  
 What always feels even more insulting to me is the clear indication the people of the "shi" type don't really have any interest in their own explanations, or in the education of others: conversion and indoctrination are the only goals, making them no more than half-living carriers of creationist mental viruses.

  
J. G. Cox



Posts: 38
Joined: Dec. 2005

(Permalink) Posted: Mar. 06 2006,11:30   

Quote
Without the assumption of neutral mutation, there is no molecular clock idea and no evidence of protein homology being evidence of evolution.


Neutral mutation theory is very useful in evolutionary studies, but only when examining neutral mutations. That is why molecular 'clocks' are usually based off on non-coding regions of DNA, not on extremely important genes like cyt c. Shi has assumed a very large range (>80% in examples) of neutral mutation and a tiny field of non-neutral mutation (the function disabling minimal identity); this is not a valid assumption for most genes or gene products. The use of protein homologies as evidence for common descent in no way requires that changes between proteins be due to neutral mutation.

Quote
So, Cox needs to do some homework before taking part in a discussion outside his field.

I wrote that I am not an expert in evolutionary biology; unlike ID 'experts,' I do not claim false expertise. I do, however, make use of evolutionary theory in my work, and so am perhaps a smidgen more qualified to discuss evolutionary theory than, say, a lawyer or an engineer. If you wish to engage in credential combat, shi, may I ask what constitutes your expertise in evolutionary biology?

Quote
He should pay attention also that most things in nature (the fundametal ones) stay unchanged once created.

Really? Most things do not stay unchanged. To be fair, shi claims that "fundamental" things stay unchanged. However, since we identify how fundamental traits are by how resistant they are to evolutionary change, this seems tautological to me. Shi's example of the pentadactyl limb reveals exactly this: there is nothing functionally 'fundamental' about pentadactyly; it just appears to be developmentally hard to mess with because it has been generally conserved. In fact, how would we even know if a trait that we observe in the fossil record was 'fundamental' or not except by whether or not it was still present in some form today?
I suppose that "Fundamental" genes could be thought of as those which are much more likely to induce very large reductions in fitness when mutated. Evolutionary theory predicts relatively slow mutation rates for such genes, but not immunity to mutation at some arbitrary '% identity.' It's informally referred to as phylogenetic inertia. I see it as somewhat analogous to cultural inertia, which is the primary force sustaining creationist and ID junk.
Anyway, doesn't claiming that traits like ATP generation processes should remain unchanged through time undermine the entire premise of the idea which you orinigally proposed, shi?

Quote
There is only one ATP generation process.

Not true. However, the Krebs cycle is by far the more efficient and thus (in concordance with evolutionary theory) more widespread. Only a few Archaea still do it the old way, if I remember correctly.


@jeannot
As for rakes, don't hesitate to say unresolved polytomy. We're not afraid of big words here.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 06 2006,11:39   

Quote (J. G. Cox @ Mar. 06 2006,17:30)
@jeannot
As for rakes, don't hesitate to say unresolved polytomy. We're not afraid of big words here.

Polytomy ?
I didn't even know that word.  ???  In French we use "topologie" (=topology?).

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 06 2006,11:45   

Here is another attempt to illustrate the problem with the Darwinian idea.  For the sake of argument, let us assume the position of some peoples here that a protein like cyto C can be mutated beyond recognition (lower than 15% identity) while can still retain the same function. Use my calculation above, in 800 myr, humans will not be able to recognize a cyto C homolog in bacteria.  Given that Cyto C is among the most conserved genes, we would predict at some point in the future (1200 myr), not a single human proteins will have a recognizalbe homolog in bacteria.  At this point, there will be no sequence data that suggests we come from bacteria.  Now, at this point, we can still find some genes of humans have homologs in yeast. So we can still say we come from yeast.  But suppose in 1600 myr, it happens that not a single human gene can be recognized to have a homolog in yeast, we would have to conclude that we did not come from yeast.  At that point, human will conclude that human is equally dis-related (or related) to yeast and bacteria.  So, the rational used to support common decent today could be used against common decent in the future.  The rational today is that we share common ancestor because we share sequence homology.  It implies that if we do not share sequence homology, we do not share a common ancestor.  So in 1600 myr, human will find that they do not share sequence homology with yeast or bacteria, so they will conclude that their ancestor is neither yeast nor bacteria but is something more advanced such as fish.  But by the same logical progression, in 2000 myr, human will find them equally dis-related to fish, yeast, and bacteria. Finally, in 4000 myr, humans will find them equally dis-related to chimpanzees, chicken, frogs, fish, yeast, and bacteria.  There will be no sequence evidence to show that human has shared a common ancestor with any species.  The evidence of evolution today will evaporate in the future.  If the future humans have no access to today's knowledge, they would conclude from their own sequence analysis that there is no evolution going from bacteria to yeast to fish to humans.  A theory that claims to explain evolution is then explained away or eliminated by time and evolution itself.  Time is the best test of any theory and Darwinism will be doomed in time, as is apparent by a simple thought experiment.

  
J. G. Cox



Posts: 38
Joined: Dec. 2005

(Permalink) Posted: Mar. 06 2006,11:47   

A polytomy is a node in a phylogenetic tree that has more than 2 descendant lines branching off from it; i.e. it looks like a rake instead of a 2-prong fork. They are called 'unresolved' becaue the chance that multiple lines actually did diverge simultaneously is almost zero, therefore we can safely assume that the apparent polytomy is simply due to the fact that our data are not good enough to resolve the polytomy into multiple nodes.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 06 2006,12:01   

Shi, our homologies with species X doesn't imply that X is our ancestor.
This is one very basic principle in evolutionary biology. So your condescending remarks regarding our knowledge on the subject are not welcome here.
And I don't get your logic. Even if, in several billions of years, the distances between humans, yeasts and bacteria are too high to infer evolutionnary relationships, why would this mean that common descent is wrong?

EDIT, thanks for the explanation Mr Cox. I knew the definition of a polytomy (what I called a rake), I had just forgotten the correct term.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 06 2006,12:28   

Quote
To Russel, if no version of Darwinism predicts infinite mutation, then show me a version that predicts that at some point mutation should stop.
If you read the responses above, and have the ability, you will understand why mutation rate does not equal rate of change in homology. If you don't, I have more educable people I need to attend to.

--------------
Must... not... scratch... mosquito bite.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 06 2006,12:33   

Quote (tiredofthesos @ Mar. 06 2006,17:11)
If "shi" is actually a practicing scientist with a revolutionary criticism of current evolutionary theory, why the **** is he/she posting it on the chatsite of a layman's forum?  This doesn't have to be a rhetorical question: I will accept answers.

 

I am a male scientist in genetics.  I do not have any work in the field of evolution per se but I am interested in studying the theory by critical thinking.  There are clearly rooms for improvement for the theory.  After all, no body debates 1+1=2 or a Newtonian theory.  If Darwinism is as goods as it is presented by its believers, we would not have any debate going on.  

As I said earlier, I came to my fact only recently from a novel perspective.  I am in the process of writing up my perspective for publication in a science journal.  In it I will present the fact and my explaination for it.  At this point, I am just asking people if I have indeed raised an issue that have been overlooked in the past.  I am doing it to both experts and laymen.  I have asked several experts by private email but have received no response, even though the same experts have nicely and quickly replyed to me before on a more conventional issue that they are more familiar with.  

If you think you can publish major challenges to dogma without providing a new theory to explain the challenges better, you are being naive about the science profession.  So, I am not going even to try to publish it until I have an explanation ready.  But it is fun to see how other people may explain it.  The sad situation today is that the experts are finding problems all over the place with Darwinism but they are not being open with the laymen.  The laymen is led to believe that everything is fine with Darwinism.  The laymen then participate in forums like this as if they know evolution.  I am here to allert people that there are things that you dont know and nobody knows.  There are so many holes with the theory that the only reason it still dominates is the present lack of a better theory.  The forum here could only be productive if it serves to spark new ideas for new theories.

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: Mar. 06 2006,12:36   

Yes im having trouble working out your point shi, so assuming what you say is true what is your explanation for the phenomenon? It is now possible to detect homology between proteins that have incredibly low sequence identity, and I can only assume that methods will get progressively better, unless teaching evolution is banned of course :).

Quote
The sad situation today is that the experts are finding problems all over the place with Darwinism but they are not being open with the laymen.  The laymen is led to believe that everything is fine with Darwinism.
May I ask how you came by this information then if you are not an evolutionary biologist?

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 06 2006,13:11   

So after Shi revolutionizes biology, we'll all stop being "Darwinists" and become... "Shi-ites"?

(Sorry. I just can't read this thread any more except for laughs.)

--------------
Must... not... scratch... mosquito bite.

  
J. G. Cox



Posts: 38
Joined: Dec. 2005

(Permalink) Posted: Mar. 06 2006,14:01   

If you are in fact a scientist, then you should get an evolutionary biologist to co-author your paper with you. If you make grossly mistaken statements like the following
Quote
Now, at this point, we can still find some genes of humans have homologs in yeast. So we can still say we come from yeast

then your paper won't even make it out to review. Having a real evolutionary biologist co-author will help you, er, avoid such mistakes. If you do publish such a paper, please post the reference here, because I would be very much interested in reading it.

However, I do not think that you are a scientist for the following reasons:
1. your gross mathematical errors in your hypothesis (negative % similarity??? it must range from 0% to 100%)
2. your assertion that the evolutionary biologists know that there are serious and growing problems with evolutionary theory but are just not telling anyone. Any real scientist knows that scientists do not work in this way and that the accusation is absurd.
3. you stated that forums such as this are places in which new biological theories are "sparked"

Therefore, I think that you are either an interested layperson or, perhaps, a research technician in a lab that does genetics research. If you are a scientist, prove that I am wrong by posting references to papers that you have authored and state which author you are. Don't worry if they are in non-English journals (as English does not appear to be your first language); I have broad journal access.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 06 2006,14:18   

Quote
If you do publish such a paper, please post the reference here, because I would be very much interested in reading it.
I guess I won't be so much interested in reading it, as in finding out what journal's review process such a paper had survived - and checking to see if one R. v. Sternberg was maybe on the editorial board.

--------------
Must... not... scratch... mosquito bite.

  
sir_toejam



Posts: 846
Joined: April 2005

(Permalink) Posted: Mar. 06 2006,15:25   

Quote
If you think you can publish major challenges to dogma without providing a new theory to explain the challenges better, you are being naive about the science profession.


ridiculous.

I see critiques of hypotheses (even well accepted ones) all the time;  they're usually published as notes.

pick up ANY scientific periodical and i can guarantee that about 80% of the time or more, you will find published notes that contain dissenting opinions.

you're a joke, shi.

  
Henry J



Posts: 4565
Joined: Mar. 2005

(Permalink) Posted: Mar. 06 2006,15:59   

Re "There are so many holes with the theory that the only reason it still dominates is the present lack of a better theory."

If by "holes" you mean that there are questions that haven't been answered, well of course there are - that's what keeps biology researchers employed.

But the existence of unanswered questions is not by itself an argument against the accuracy of the conclusions that have been reached by scientists.

Henry

  
thordaddy



Posts: 486
Joined: Jan. 2006

(Permalink) Posted: Mar. 08 2006,09:29   

Shi's point seems simple enough now that he has raised it.  A theory based on common descent should show a lack of descent in certain biological entities due to the inevitability of mutations radically altering those same entities over time to the point that a commonality in descent can no longer be established.  The biological entity should have evolved to such a degree that it can no longer be said to be related to the original.

Common descent should show two patterns emerging and yet it does not?  Why?  Not enough time?  Wrong theory?  Let's find out.

  
Lou FCD



Posts: 5402
Joined: Jan. 2006

(Permalink) Posted: Mar. 08 2006,09:55   

J.G. suggested that  "Having a real evolutionary biologist co-author will help you, er, avoid such mistakes."

So will a big stick to knock some sense in.

--------------
Lou FCD is still in school, so we should only count him as a baby biologist. -carlsonjok -deprecated
I think I might love you. Don't tell Deadman -Wolfhound

Work-friendly photography
NSFW photography

   
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: Mar. 08 2006,09:59   

Quote
The biological entity should have evolved to such a degree that it can no longer be said to be related to the original.
Please define 'can no longer be said to be related to the origional'.

  
Faid



Posts: 1143
Joined: Mar. 2006

(Permalink) Posted: Mar. 08 2006,10:05   

Hmm. Interesting, thordaddy. So, you seem to say that all the evidence for common descent actually speak against common descent; only if we had some evidence against common descent we could succesfully establish common descent.


...


MUAHAHAHAHAHAHAHAHA
Oh man, You just made my week.

--------------
A look into DAVE HAWKINS' sense of honesty:

"The truth is that ALL mutations REDUCE information"

"...mutations can add information to a genome.  And remember, I have never said that this is not possible."

  
tiredofthesos



Posts: 59
Joined: Jan. 2006

(Permalink) Posted: Mar. 08 2006,11:08   

Hey, Thordaddy!

 Do you want a literal interpretation of the (Christian) Bible to be used to modify and/or replace the Constitution?

 If you are honest <ha!> the answer will be some sort of mealy-mouthed equvication or refusal to answer, or a proud "Yes!"

 Except for a very few, and completely sidelined, cranks and kooks, EVERY "anti-Darwinist" I have come into contact with over the past decade of following this issue has very little real interest of ToE -- and not even a simple layperson's understanding, but an absolute obsession with seeing the destruction ("cleansing" and "renewal" are their words of course: like the Taliban or OBL) of the freedoms our nation was founded upon.

 Also, far too often to be the individual's quirk, this obsession proves to be accompanied by a xenophobia and racism of the most classic type, though rationalised and sanitised so that the carrier him/herself can, like the YEX, deny it.

 C'mon!  Cough up the basic POLITICAL views that lead you to profess believing in such obvious bullshit!

  
thordaddy



Posts: 486
Joined: Jan. 2006

(Permalink) Posted: Mar. 08 2006,14:53   

Chris Hyland,

What I mean is that at a certain point a biological entity will have evolved to such an extent that it has no recognizable commonality to its original ancestor.  Shi's point seems to say that we have had enough time to see this break in common descent.  What common descent seems to imply is that there is an unevolvable commonality amongst biological entities that enables us to forever link humans to this most fundamental biological formation.

Faid,

I think the point being made is that common descent should produce 2 patterns in evolution with one showing common descent and one showing no evidence of common descent.  

tiredofthesos,

You make a silly mistake in believing that those that question current scientific theory to be religious fundamentalists.  You actually weaken scientific credibility because such an assumption leaves one blind to the vast array of other opinion with no religious basis.  I'm neither religious nor anti-Darwinist.  

I'm just actually someone stunned by the arrogance and blinkered view of many so "scientists."

  
sir_toejam



Posts: 846
Joined: April 2005

(Permalink) Posted: Mar. 08 2006,15:27   

Quote
I'm neither religious nor anti-Darwinist


nope.  just your run-of-the-mill idiot.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 08 2006,15:38   

Quote
I'm just actually someone stunned by the arrogance and blinkered view of many so "scientists."
Oh, please, do go on! I mean specifically: what's arrogant? what views are being "blinkered"?
Or is this just the generic, "those fools at the university" rant?  

If Shi's ideas are an example of what you think is unfairly dismissed, let me just say this:

Dismissed? - yes. Unfairly? - no.

Really, the flaws in the logic are high school level. If you can't see that, I'm afraid that your opinions, too, will have to be dismissed. Fairly.

--------------
Must... not... scratch... mosquito bite.

  
Henry J



Posts: 4565
Joined: Mar. 2005

(Permalink) Posted: Mar. 08 2006,15:38   

Re "A theory based on common descent should show a lack of descent in certain biological entities due to the inevitability of mutations radically altering those same entities over time to the point that a commonality in descent can no longer be established."

That doesn't appear to make sense. For the relationship to become totally unrecognizable, all the most fundamental functions would have to be replaced by entirely new but equivalent functions. Seems highly unlikely that anything in the current theory actually implies that this would be expected in 4 billion years of evolution. (And a prediction of what might happen in 5 to 8 billion years doesn't seem overly relevant in understanding the current evidence.)

Henry

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 08 2006,16:44   

The challenge that Shi failed to address, and that I'm waiting for Thordude to address, is this: do you understand that a constant mutation rate does not translate into a linear decrease in homology over time?

--------------
Must... not... scratch... mosquito bite.

  
thordaddy



Posts: 486
Joined: Jan. 2006

(Permalink) Posted: Mar. 08 2006,17:16   

Russell,

That sounds like an argument for irreducible complexity?

  
thordaddy



Posts: 486
Joined: Jan. 2006

(Permalink) Posted: Mar. 08 2006,17:36   

Henry J opines,

That doesn't appear to make sense. For the relationship to become totally unrecognizable, all the most fundamental functions would have to be replaced by entirely new but equivalent functions.

These "equivalent functions" would still seem to be fundamental and therefore unworthy of the idea that they are "entirely new."  They are not "new," but seemingly evolved to a point where the original function and the evolved function have no recognizable commonality.  

To state that the original fundamental function can be "recognized" in the evolved function is to say that the fundamental function has not evolved.

This sounds like an argument for irreducible complexity.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 09 2006,04:05   

Quote
That sounds like an argument for irreducible complexity?
Nope. It has nothing to do with "IC".

Now, let me just throw this out for your consideration. Could it be that what you perceive as "arrogance and blinkered views" of scientists might, in fact, be limited patience with people who don't realize the limits of their own knowledge and understanding of science, but feel qualified to question not only the competence of others - not just individuals, but entire professions - who have spent decades studying it, but also their motives, character and integrity? Do you think that might be possible?

--------------
Must... not... scratch... mosquito bite.

  
J. G. Cox



Posts: 38
Joined: Dec. 2005

(Permalink) Posted: Mar. 09 2006,04:30   

Quote
at a certain point a biological entity will have evolved to such an extent that it has no recognizable commonality to its original ancestor


 This was shi's second idea. Notice that it is at odds with his first idea (that proteins should diverge until a maximal, function-retaining distance). The first idea I think is flawed. The second idea, however, has some merit. As some point, eventually, different descendent lines of some ancient ancestor should be unrecognizable as being related. One could quibble about at what point that is; when they only share 1% of genes in common? When one no longer uses DNA/RNA? When one is composed of cells without billayer membranes? When one is no longer built primarily of carbon and water?

 However, shi simply asserted that enough time has passed so that we should observe this phenomenon. He/she has provided no support for this nor any way of estimating the average amount of time it would take for this phenomenon to occur. Simply, even if we assume that the basic constraints on evolution are not so strict as to prevent this extreme divergence (e.g., imagine how unlikely it would be to evolve an information-storage system to replace DNA), we have no way of knowing if it would, on average, happen in 5 million years, in 5 billion, 5 trillion, or  not before the universe collapses on itself again (or whatever the physicists believe our fate to be at the moment). Thus, though shi's idea may be a valid prediction from evolutionary theory, the assertion that it is a failed prediction is wholly unwarranted.

Quote
This sounds like an argument for irreducible complexity.

 I would disagree with this statement. Doesn't IC assert that evolution cannot mess with the parts without destroying function? Therefore, a protein that retains function while wholly re-formatting itself cannot be said to be IC.

Quote
do you understand that a constant mutation rate does not translate into a linear decrease in homology over time?

This was the math error I alluded to. This is another reason that I do not think that shi is a biologist, let alone a geneticist. Let's assume that shi is simply bad at math (and I know many biologists that are). Even in this case, shi should have recognized his/her model as the same as those neutral mutation models he/she should have had in undergraduate courses, and thus expected an identity function which asymptotes on zero, not one that goes negative. That doesn't even account for back mutation, which would pull that asymptote away from zero.

  
Dizzy



Posts: 3
Joined: Mar. 2006

(Permalink) Posted: Mar. 09 2006,06:42   

Quote (shi @ Mar. 06 2006,18:33)
There are clearly rooms for improvement for the theory.  After all, no body debates 1+1=2 or a Newtonian theory.  If Darwinism is as goods as it is presented by its believers, we would not have any debate going on.  


Erm, which "Newtonian Theory" are you referring to?

If you're talking about gravitation or a host of other related ideas, you're wrong.  There was a debate, Newtonian gravitation was found (scientifically) to be incomplete or wrong, and General Relativity took over.

If you mean "religous wackos don't challenge teaching Newtonian gravitation in high school - even though it's demonstrably incongruent with empirical observation - because it doesn't conflict with their beliefs," that would be an accurate depiction of the difference between ToE and "a Newtonian theory."

If your last sentence above were changed to "If Darwinism didn't appear threatening to a bunch of ignorant, bible-thumping wingnuts, we would not have any debate going on," that would be accurate.

  
thordaddy



Posts: 486
Joined: Jan. 2006

(Permalink) Posted: Mar. 09 2006,09:37   

Russell,

What so hard to understand about science?  It's a method of interpreting empirical evidence and giving meaning to that interpretation.  That's all science can do. Or, I guess we can say science is what that judge said it is?  LOL!

The problem of course lies in the definition of empirical evidence and the meanings given to the interpretations.

I think one said that science was an "evolving method."  I think such an admission would put an ear to ear grin on those that are currently outside of the scientific clique.  

You seem to be saying that the meanings given to the empirical evidence are meaningless to the vast majority of people.  Why is this?  Why do scientists have such a hard time conveying their findings in language that can be understood by a majority of people?  Are we just too darn ignorant or are the scientists to slick for their own good?

I think Shi's argument forces the scientist to make a claim of an unevolvable fundamental function.  How else could one make the assumption of a common descent unless this fundamental function was easily recognizable in ALL biological organisms back to the origin?  If this fundamental function is unrecognizable in some biological entity then it is merely an assumption that it is a product of common descent.

  
Henry J



Posts: 4565
Joined: Mar. 2005

(Permalink) Posted: Mar. 09 2006,10:01   

Re "If this fundamental function is unrecognizable in some biological entity then it is merely an assumption that it is a product of common descent."

Yeah, if a species is found to not share the stuff that's fundamental to eukaryotes , it might then be logical to think it might be of a separate origin. But as I understand it even bacteria and archaea share the same fundamentals as eukaryotes. So finding an apparently unrelated species wouldn't affect the relationships among the previously known ones.

Henry

  
MidnightVoice



Posts: 380
Joined: Aug. 2005

(Permalink) Posted: Mar. 09 2006,10:26   

Quote (thordaddy @ Mar. 09 2006,15:37)
 Why do scientists have such a hard time conveying their findings in language that can be understood by a majority of people?  Are we just too darn ignorant or are the scientists to slick for their own good?

It is not ignorant in the pejorative sense, merely not cognizant of the background knowledge to fully comprehend.  Just as I have trouble with fully understanding string theory, even though I am a biochemist, so do non-scientists have trouble understanding biology in general.

And we also get back to the fact that in MOST cases, these people seem only object to those portions of science that seem to contradict their particular version of the bible, at one particular point in time (flat earth, sun going round the earth, evolution etc).  They are quite happy to accept the rest is just peachy.

On another board I was fascinated to reads the posts of someone who admitted his last science class was in 10th grade, and happily admitted he understood almost no chemistry, physics or math, yet still believed he understood biology well enough to know that it was fine except for evolution, which was wrong.  Now THAT is arrogant.

--------------
If I fly the coop some time
And take nothing but a grip
With the few good books that really count
It's a necessary trip

I'll be gone with the girl in the gold silk jacket
The girl with the pearl-driller's hands

  
tiredofthesos



Posts: 59
Joined: Jan. 2006

(Permalink) Posted: Mar. 09 2006,10:54   

Thor,

 You are a hollow, ignorant fake. You are a pompous, evasive jerk-off, and no one really needed more proof of what a lying shit you and your kind are, but you are always ready to serve it up.
  What a pathetic, ugly life you must lead, and deservedly.

 A last communication: ANY challenge of science, through research and/or disinterested discussion is welcome.  You and your closet fascism (not at all an exaggeration), and your open dishonesty and incompetence are not.

 I'll let others with vast amounts of free tiime waste it engaging losers/cranks like GoP, Larry of the 10,000 names, etc., etc. etc.  You are all unworthy of reading, much less rebuttal, especially by your intellectual and moral superiors -- pretty much half the world's population.  I'll just relieve some of my disgust before leaving:

 <spit>

 It's time for me to move on, dressing down only the cracks and shits like you I can meet face-to-face, where they have something at stake.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 09 2006,11:20   

Well, I really don't know what Thordudy is on about, but it's pretty clear he's not addressing any of the questions put to him. So, I think I'll just join Tiredofthesos in regarding him as not worth my time.

--------------
Must... not... scratch... mosquito bite.

  
thordaddy



Posts: 486
Joined: Jan. 2006

(Permalink) Posted: Mar. 09 2006,18:47   

Henry J opines,

But as I understand it even bacteria and archaea share the same fundamentals as eukaryotes.

Here in lies the problem.  If these three share the same fundamental then this fundamental has either not evolved (remained exactly the same and therefore indentifiable in all three) or evolved in the exact same manner in all three (so as to stay easily identifiable).  

I don't see how else one could claim that they share this same fundamental unless such fundamental was easily identifiable in all three either by virtue of no change or the exact same change over time?  The former stays true to the definition of fundamental while the latter leaves one baffled as to how exact fundamental change leads to highly different results?

PS I appreciate your responses.

  
Jay Ray



Posts: 92
Joined: Feb. 2006

(Permalink) Posted: Mar. 10 2006,01:10   

I should keep my yap shut and let the real biologists respond here, but as an interested layman, I think I can muster something up to start with.


Quote
I don't see how else one could claim that they share this same fundamental unless such fundamental was easily identifiable in all three either by virtue of no change or the exact same change over time?  The former stays true to the definition of fundamental while the latter leaves one baffled as to how exact fundamental change leads to highly different results?



You're defining a black and white and claiming neither works, when the reality is quite colorful and adequate to the task.

Its by no means obvious to me that identifying common structures is all that easy.  Lots of these similiarities become noticable only with an impressive collective effort:  hundreds of hours of poring over data, which itself took thousands of man-hours to compile.  I've taken a gander at the end results of this work.  In the many diagrams comparing limb bones or genetic sequences and the like, the precise similarities don't exactly jump out at me.  It could be that I'm especially dense, but I'm grateful for the captions for explaining the point of the diagrams.

Next, I challenge your use of this phrase:  "by virtue of no change or the exact same change over time".  Here again, its by no means obvious to me that a fundamental structure can't retain its function while also undergoing variation.  A bonafide biologist with some specific examples could make this point better than I can, but here goes.

- genes can vary in their specific code and yet still produce the same results.  For example, in a fundamental HOX type gene, a variation like this could breed true, as it were.  Incidentally, tracking these changes is a very good way of identifying points of divergence.

- proteins themselves can be made of slightly different amino acids and yet still serve the same function

- The ID mascot itself (yes, the bacterial flagella) comes in many different flavors.  This always makes me chuckle.  

So these examples are just off the top of my head, but they should help to clarify and answer your question, Thor.  If indeed you were seeking clarity and answers, perhaps this helps...

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 10 2006,03:13   

Quote
I should keep my yap shut and let the real biologists respond here, but as an interested layman, ...
No, you shouldn't. Your perspective, once again, is spot on.  And I,  speaking as one "real biologist", have lost the will to try to get through to Thorguy.

--------------
Must... not... scratch... mosquito bite.

  
Henry J



Posts: 4565
Joined: Mar. 2005

(Permalink) Posted: Mar. 10 2006,07:25   

Re "Here in lies the problem.  If these three share the same fundamental then this fundamental has either not evolved (remained exactly the same and therefore indentifiable in all three)"

Critical parts of the DNA are going to be way more conserved than less critical DNA. They might eventually change some, but I see no reason to expect all the critical functions to change in any particular amount of time (like say 4 billion years).

Of course, some important functions probably have evolved. Whether any of those have done so to an extent to make them appear non-homologous (is that the right word?), maybe a biologist can jump in to answer.

Henry

  
thordaddy



Posts: 486
Joined: Jan. 2006

(Permalink) Posted: Mar. 10 2006,10:46   

Jay Ray opines,

Its by no means obvious to me that identifying common structures is all that easy.

Why not, if they are common structures?  Doesn't commonality require easiness in identifiability?

Here again, its by no means obvious to me that a fundamental structure can't retain its function while also undergoing variation.

Well, then the fundamental function hasn't changed.  The only thing that has changed is apparently the structure.  The fundamental function does not evolve.  In order to claim common descent this fundamental function must be identified, but it seems silly to say it's identified by variations in structure.  

genes can vary in their specific code and yet still produce the same results.

So we get common RESULTS from VARYING SPECIFIC code?  I don't get this.  How does one vary THEIR SPECIFIC code?  And if the results are common then why vary the specific code  (if that can really be done)?  What's the point?  The specific code DOES NOTHING to the fundamental function.  It stay the same.

- proteins themselves can be made of slightly different amino acids and yet still serve the same function

Again, the fundamental function doesn't change.  Only the structure changes.  How can this change in structure be evidence of a fundamental function common to all biological entities?

Henry J says,

Critical parts of the DNA are going to be way more conserved than less critical DNA. They might eventually change some, but I see no reason to expect all the critical functions to change in any particular amount of time (like say 4 billion years).

But isn't there a function more critical than the rest?  The fundamental function?  This fundamental function representing the commonality that underpins common descent?  All this biological structural variation represents the argument against common descent.  It is only with this fundamental function common to all biological entities that one could claim common descent.  Either this fundamental function remains unchanged or changes exactly the same in all biological entities.  How else could one claim common descent?

  
Stephen Elliott



Posts: 1754
Joined: Oct. 2005

(Permalink) Posted: Mar. 10 2006,10:59   

ThorDaddy,
What do you believe?
Can a virus evolve? Is the worry about bird flu evolving so as to make humans susceptible all non-sense? Or will the designer do it?

If germs and virus are designed by our designer, does it make medical doctors/researchers evil?

  
stevestory



Posts: 10127
Joined: Oct. 2005

(Permalink) Posted: Mar. 10 2006,10:59   

Quote
Russell said:



No, you shouldn't. Your perspective, once again, is spot on.  And I,  speaking as one "real biologist", have lost the will to try to get through to Thorguy.
I lost that will years ago. Now I just point and laugh.

   
Henry J



Posts: 4565
Joined: Mar. 2005

(Permalink) Posted: Mar. 10 2006,11:19   

Re "It is only with this fundamental function common to all biological entities that one could claim common descent.  Either this fundamental function remains unchanged or changes exactly the same in all biological entities.  How else could one claim common descent?"

What? The more critical a function is, the more likely a change is to break it. Therefore changes to the more critical parts of the DNA don't get passed to later generations as often as do changes to less critical parts of the DNA.

afaik, common descent can be claimed based on various types of evidence: (1) when a large enough portion of the DNA shows more similarities than would be expected if the two types had separate origins, (2) mostly similar anatomy (and/or biochemistry) with only minor differences, or (3) where fossils of predecessors of the two types converge (as one goes from more recent to older) on a single predecessor for both. (And there might be other ways I haven't thought of.)

(Note that chimp-human relationship can be claimed based on all three of those.)

Henry

  
thordaddy



Posts: 486
Joined: Jan. 2006

(Permalink) Posted: Mar. 10 2006,13:15   

Henry J,

Let's go back to what I believe was Shi's original point and that is a theory of common descent should show 2 patterns: both common descent and that "break" in common descent.  There should be or will be a biological entity that shows no commonality to the original entity.

In order to claim that all biological entities were derived from an original entity (either in function or structure or both) such entities must share an easily identifiable commonality.  But what is this commonality?  The best we can say is it's a fundamental function that DOESN'T change.  You say as much when you state:

Therefore changes to the more critical parts of the DNA don't get passed to later generations as often as do changes to less critical parts of the DNA.

Unless of course you are saying that the fundamental function does change and so it seems we should see this "break" in common descent in some biological entities in which the fundamental function has evolved.

Then you state,

afaik, common descent can be claimed based on various types of evidence: (1) when a large enough portion of the DNA shows more similarities than would be expected if the two types had separate origins, (2) mostly similar anatomy (and/or biochemistry) with only minor differences, or (3) where fossils of predecessors of the two types converge (as one goes from more recent to older) on a single predecessor for both. (And there might be other ways I haven't thought of.)

Why would one need VARIOUS types of evidence to explain commonality?  Shouldn't the commonality be the evidence ITSELF...  The only evidence needed?  Remember, common descent is claimed to be an evolutionary FACT yet this FACT requires a myriad of explanations, conjectures and sub-theories.

PS I appreciate this exhange.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 10 2006,13:46   

The following is to summarize my response to many constructive comments so far.

If species A diverged from B 100 myr ago
C 200 myr ago
D 400 myr ago
E 500 myr ago
F 700 myr ago
G 1000 mry ago (yeast and bacteria split)

Facts:  

1. A gene from species A shows amino acid identity between AB 90%, AC         80%, AD 50%, AE 15%, AF no recognizable relationship, AG no recognizable relationship.  Most human genes show this pattern.  This pattern is consistent with Darwinian theory if we assume all proteins can be substituted to beyond recognition while still retain same function, a big if.  The assumption is valid for some proteins but is not for the majority of proteins.  A gene with the above pattern may seem to have reached a maximal divergence between AE at 15% but we do not know for certain.  It could go lower than 15% but we will not be able to say they are homologous.  So, this pattern does not suggest that a gene has shown signs of maximum divergence.  

2. A gene from A shows amino acid identity between AB 95%, AC 85%, AD 70%, AE 60%, AF 50%, AG 35%.  Most human genes that have bacteria homologs show this pattern, such as cyto C.  This pattern is also consistent with Darwinian theory.  It does not show signs of maximum divergence.  

3. Is limit on maximum divergence expected based on what we know about protein structure function relationship?  Yes.  Old fundamental genes are more conserved and show slow amino acid substitution rates.  This is because most substitutions are incompatible with survival.  This suggests that certain proteins or domains will not tolerate any substitutions or will allow very few substitutions.  So the fact that there exist conserved proteins and domains suggests that there should exist some fundamental proteins or domains that will not tolerate any mutations or will allow very few substitutions.  Such proteins or domains cannot diverge beyond a minimal identity while still retain minimal function or confer survival advantage.  Such minimal identity could vary depending on proteins, some may be 35%, some 25%, or some 10%.  If 500 myr is enough time for AE divergence to minimal identity of 15%, than AF and AG should also show 15% identity.  In short, some conserved genes should show this pattern, AB 90%, AC 75%, AD 40%, AE 15%, AF 15%, AG 15%.  This is the only pattern that shows signs of maximum divergence.  This pattern is what is predicted by Darwinism based on what is known about conserved proteins or domains.  But the fact is that no genes show this kind of pattern.  Is time not enough the explanation for fact 2?  But fact 1 suggest that time is enough for most genes. If time is enough for genes with pattern of fact 1, why no signs of maximum divergence?

Darwinian explanation 1: time is not enough and there is no limit on minimal identity.
If we assume that all proteins can be substituted to beyond recognition, like the pattern in fact 1, we would predict that human would gradually lose any recognizable homology with bacteria, in turn yeast, in turn fish, in turn chicken, in turn rodents, in turn chimpanzees.  If this picture can happen in the future, the question is why it has not already happened. Bacteria is known to have existed on earth for more than 3000 myr.  If bacteria A diverged from bacteria B 3000 myr ago, then the identity in cyto C (1% amino acid change per 20 myr) for today's descendents of A and B would be 0%.  However, despite the genome sequencing of many species of bacteria, all known bacteria species show recognizable sequence identity.  The fact proves that the assumptions of unlimited substitution and not enough time are false.  The phenomenon of conserved domains also invalidates such assumption.  So, the reason that the pattern in paragraph 3 has not been observed is not because time is not long enough or because of no limit on minimal identity.  

Darwinian explanation 2: proteins in advanced species gain extra functions
Even if time is enough and there are limits to diversity, Darwinism can try the following explanation.  The reason that human shows 35% identity in cyto C with bacteria but not any lower is because 35% is the minimal identity allowed and will stay unchanged forever once reached.  The reason that human shows 60% identity in cyto C with yeast but not any lower is the same.  If this is true, Darwinism must assume that a protein in yeast has gained some extra functions compared with its homolog in bacteria.  So more portions of the protein are resistant to change.  This may be true for some proteins.  But it is hard to believe that all proteins in yeast have gained extra functions compared with their homologs in bacteria.  This explanation requires us to believe in an ad hoc hypothesis that is unlikely to be true.

The alternative:
One possible alternative interpretation of all the facts is that maximum species divergence is set up at the beginning and stay unchanged during evolution.  The 35% identity between bacteria and eukaryotes in cyto C was established already 1000 myr ago and stayed largely unchanged during evolution and will remain unchanged in the future.  The 60% identity between yeast and multicelluar eukaryotes in cyto C was established in the beginning.  The more recent the species split, the less diverged versions are used.  We may yet to have a mechanism for how this may occur. But there exist many facts at the level of phenotypes that show that maximum phenotype distance is established at the beginning of species split and remains unchanged during evolution. The lack of intermediate transition species in the fossil record and the persistence of the same fossil structure over millions of years are examples of maximum distance at the beginning that stays unchanged through evolution.  The 5 finger pattern of land vertebrates has stayed unchanged for 400 myr since its arrival on earth.  The distance between land vertebrates and fish in the 5 finger design has remained at the same level since the design appeared and is likely to remain unchanged forever in the future.  It is only logical to conclude that the genetic distance responsible for such phenotype distance has also remained the same since the appearance of the 5 finger design and its related genes.

A self-destructive flaw:
The simple thought experiment on protein homology reveals a self-destructive flaw with the present theory. Both change and no-change or stability are fundamental facts of past life history on earth.  If change/mutation explains both sides of the coin, i.e., change and no-change in phenotype, it explains neither.  A living fossil has remained phenotypically unchanged for millions of years. But Darwinism plus its ad hoc hypothesis the neutral theory requires us to believe (without any facts) that its genotype has changed dramatically.  The theory has no way to explain how phenotype stability is maintained by changes in genes.  If change in phenotype is explained by changes in genes, the same theory is self-destructive to say that no-change in phenotype is also explained by changes in genes.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 11 2006,08:15   

double post.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 11 2006,08:19   

Quote

Darwinian explanation 1: time is not enough and there is no limit on minimal identity.
...
The phenomenon of conserved domains also invalidates such assumption.  So, the reason that the pattern in paragraph 3 has not been observed is not because time is not long enough or because of no limit on minimal identity.  
Well, we don't know if the bacterian lineages we have today diverged 3 billions years ago. Most of them are probably extinct. But if you compare bacteria with archea, their level divergence appears pretty huge. Wich proves that only two very ancient prokaryote lineages have survived.
Quote

Darwinian explanation 2: proteins in advanced species gain extra functions
(The concept of "advanced species" is not supported by any objective fact.) This hypothesis should apply to a very limited set of proteins. We told you that proteins can evolve through co-evolution with other proteins. I don't see any extra functions here.
Quote

Even if time is enough and there are limits to diversity, Darwinism can try the following explanation.  The reason that human shows 35% identity in cyto C with bacteria but not any lower is because 35% is the minimal identity allowed and will stay unchanged forever once reached.  The reason that human shows 60% identity in cyto C with yeast but not any lower is the same.  
Why do you think it should be the same reason?
Quote

If this is true, Darwinism must assume that a protein in yeast has gained some extra functions compared with its homolog in bacteria.  So more portions of the protein are resistant to change.  This may be true for some proteins.  But it is hard to believe that all proteins in yeast have gained extra functions compared with their homologs in bacteria.  This explanation requires us to believe in an ad hoc hypothesis that is unlikely to be true.
I don't quite follow you. You say that yeasts proteins should have gained extra functions because they show higher identities with ours?
Anyway, your two hypothesis are not mutually exclusive. If you compare DNA sequences (I don't know why you stick to amino acids sequences since DNA is the material of heredity, not proteins), you will notice that non-coding sequences reach the maximal level of divergence (75%) very fast in their evolution so that we can detect homologies anymore. That is your first hypothesis. Genes show different levels of divergence, depending on their function. Fundamental genes such as 16 S rDNA can be used to build the tree of life. Cyt b cannot because its level of divergence between lineages increases too fast. So maybe there is a minimum level of identity for 16s rDNAs, but we don't know it for sure and we don't know when lineages will reach it.
Quote

The alternative:
One possible alternative interpretation of all the facts is that maximum species divergence is set up at the beginning and stay unchanged during evolution.  The 35% identity between bacteria and eukaryotes in cyto C was established already 1000 myr ago and stayed largely unchanged during evolution and will remain unchanged in the future.  The 60% identity between yeast and multicelluar eukaryotes in cyto C was established in the beginning.  The more recent the species split, the less diverged versions are used.  We may yet to have a mechanism for how this may occur.
Indeed, you have to. Since you refer to Cyt C, should this mechanism take the theory of endosymbiosis into account?
Quote

But there exist many facts at the level of phenotypes that show that maximum phenotype distance is established at the beginning of species split and remains unchanged during evolution. The lack of intermediate transition species in the fossil record and the persistence of the same fossil structure over millions of years are examples of maximum distance at the beginning that stays unchanged through evolution.  
You should also learn more on fossilization. I recommend you to check talkorigins.org
Quote

The 5 finger pattern of land vertebrates has stayed unchanged for 400 myr since its arrival on earth.
And I didn't know that birds and cetartiodactyles had 5 fingers. Anyway what's your point? Does this disprove Neodarwinism?
Quote

The distance between land vertebrates and fish in the 5 finger design has remained at the same level since the design appeared...
Sorry I don't get your point.
Quote
...and is likely to remain unchanged forever in the future.
Why?
Quote

It is only logical to conclude that the genetic distance responsible for such phenotype distance has also remained the same since the appearance of the 5 finger design and its related genes.
The probleme is: what mutations in what genes are required to modify the number of fingers? We don't expect a single gene controling the number of fingers with one allele for each number.  
Quote

A self-destructive flaw:
The simple thought experiment on protein homology reveals a self-destructive flaw with the present theory. Both change and no-change or stability are fundamental facts of past life history on earth.  If change/mutation explains both sides of the coin, i.e., change and no-change in phenotype, it explains neither.  A living fossil has remained phenotypically unchanged for millions of years. But Darwinism plus its ad hoc hypothesis the neutral theory...
The neutral theory have been confirmed by many experiments and studies (which also involve micro-evolution that IDers can't deny anymore). You should read more about it.
Quote

... requires us to believe (without any facts) that its genotype has changed dramatically. The theory has no way to explain how phenotype stability is maintained by changes in genes.  If change in phenotype is explained by changes in genes, the same theory is self-destructive to say that no-change in phenotype is also explained by changes in genes.

If you've found a link between 16 S rDNA or Cyt C and morphology, you should publish, indeed.

  
Apesnake



Posts: 7
Joined: Feb. 2006

(Permalink) Posted: Mar. 11 2006,12:20   

I know this has been explained in other posts but it might be easier for Shi and those who might think he is on to something to understand this way:

Quote
Shi said:
"Cyto C has an well estimated mutation rate of 1% amino acid change per 20 myr and this rate is supposed to be constant."

Then:
Quote
"It is far more likely that cyto C cannot diverge beyond a certain identity before it loses its bare-bone function."


When an organism possesses a gene that is needed for survival and it looses its bare-bones function it will die.

Quote
"If this picture is what is consistent with Darwinism and could occur in 1200 myr in the future, there is no reason that it has not occurred in the past 3000 myr for some gene X that is indispensable for life but has a faster mutation rate of 1% change per 40 or 80 myr."


It has occurred. The organisms that had it happen in them died (natural selection). Mutations occurr in one organism at a time. Really bad ones do not spread into the entire population.

Quote
"let us assume the position of some peoples here that a protein like cyto C can be mutated beyond recognition (lower than 15% identity) while can still retain the same function"


Uh, why? It seems like an unsupported assumption. Even if it is true you said that 15% was needed to to identify two proteins as being homologous. How can you say it is a fault of "Darwinism" for not being able to provide examples of something that is undetectable?

Quote
"The rational today is that we share common ancestor because we share sequence homology.  It implies that if we do not share sequence homology, we do not share a common ancestor."


WOW. I think I may have found the flaw in your reasoning. A shadow provides evidence of an object's presence. If the sun goes behind a cloud, the shadow disappears. What happens to the object? Footsteps in the snow show someone went by. Does history change when the wind blows? If descent is harder to see a billion years from now because mutations have blurred homologous relationships it is not a challenge for common ancestry. If genomic records are kept over a billion years one would be able to trace any homologous relationships that were not visible by comparing the end products.

Maybe the reason these experts are not responding to you is that they suspect that you hold beliefs which no logic or evidence will dislodge from you, and so, feel that correspondence is pointless.

Sorry to bring this post back to the top but I just felt I needed to make some points in a different manner.

  
Apesnake



Posts: 7
Joined: Feb. 2006

(Permalink) Posted: Mar. 11 2006,14:29   

Quote
Why would one need VARIOUS types of evidence to explain commonality?  Shouldn't the commonality be the evidence ITSELF...  The only evidence needed?  Remember, common descent is claimed to be an evolutionary FACT yet this FACT requires a myriad of explanations, conjectures and sub-theories.


The various types of evidence is not to explain commonality but to support common descent. How is having too many separate lines of evidence a weakness? What kind of world are we living in?

  
sir_toejam



Posts: 846
Joined: April 2005

(Permalink) Posted: Mar. 11 2006,16:23   

Quote
What kind of world are we living in?


You post here and you don't know the answer to that?

we of course live in a world where Larry Farfarfromsane is the norm, rather than the aberration, and the scientists are the minority.

the only real question is whether any of us care whether we are the minority or not.

  
Jay Ray



Posts: 92
Joined: Feb. 2006

(Permalink) Posted: Mar. 11 2006,20:54   

well, let's try this again.

Quote
Why not, if they are common structures?  Doesn't commonality require easiness in identifiability?


Commonality.  I'm not sure how you are using this term, but I'm going with a sort of common sense version that simply means, "pretty much the same thing."

The answer to this question is not a simple yes or no.  It really depends on what you are referring to.  Asking someone to identify the commonality between twins is a different thing than asking someone to identify the commonality between second cousins, thrice removed.  Or more difficult still, what is the commonality between PMS, weed killer, and twinkies?



Quote
Well, then the fundamental function hasn't changed.  The only thing that has changed is apparently the structure.  The fundamental function does not evolve.


Very good!  

Although I can imagine successful mutations going on at this level, the host organism's chance of survival will likely be a product of the fundamentalilty of the fuction, the severity of the mutation.  That is, the more fundamental the function, and the greater the mutation, the worse for the host.  In all, probably not very great in the best of cases these days.

Quote
In order to claim common descent this fundamental function must be identified...


Erm.  There are many ways to verify common descent, and this is one of them.  The more sources of verification, the more confident we are of the link.

Quote
but it seems silly to say it's identified by variations in structure.


That wasn't my point, brother.  I guess I should have been more clear.

This isn't as complicated as it will take words to explain, but what the heck.  I hope this makes sense.


Say you've got organisms A B X Y and Z.

Every critter but A is known to be alive today, and all the rest are strongly suspected or confirmed through other means as being descendants of A.  

B is the critter that is most like A.  We suspect that he diverged from A before all the other critters.  

X Y and Z diverged later, in the same order as their designations.

Well, to confirm our suspicions of common descent, we could do a gene sequence analysis.  Technically, I reckon we could do this with any homologous gene, but let us say its some "fundamental function" type gene.   And why not?  This might be an especially good place to look, because we also suspect that a gene of this type should undergo the least amount of changes, so as you pointed out, any changes should be easy to see.

My main point is this.  By comparing sequences among the surviving species, we can tally the changes and see which changes carry over.  

Our hypothesis would be that sequence X should be a little bit different from sequence B.  Sequence Y should be different from X, but it should also show evidence of the earlier changes between B and X.  Z should be more different still from the others, but it should show evidence of the changes from both.  In this way, you can tell in which order they diverged, confirming or disputing the original hypothesis.

See what I mean?  I'd draw pictures for you, but I'm lazy.  You don't identify the "fundamental function" by changes in its structures.  But once you've identified it, you can compare it to the same gene in other species.  Through a comparison study, you can tell a lot of things about the relationships between them.

EDIT:  fixed up critter letters.. *smacks forehead*

  
Jay Ray



Posts: 92
Joined: Feb. 2006

(Permalink) Posted: Mar. 11 2006,21:31   

Quote
So we get common RESULTS from VARYING SPECIFIC code?  I don't get this.  How does one vary THEIR SPECIFIC code?


My apologies if you already know what I'm about to say, but it seems like its worth the telling.  I won't go into major detail, but the short story is like this.  

A couple years ago, I took a biology course which explained how DNA codes for amino acids.  It was very cool.  

DNA is made up of 4 different nucleotides all strung out in a long line.  You've surely seen pictures of this.
Amino acids are the pieces of proteins that make up the stuff in our bodies.  There are 20 different amino acids.

Each amino acid takes a sequence of three nucleotides to make.  But there are 64 different combinations of 3 nucleotides.   We call each of those a "codon."  Three of those 64 codons don't code for an amino acid.  They say either "start making a protein here" or "stop!".  That leaves 61 codons to make 20 different amino acids.  Well, here is the kicker: a lot of amino acids can be made by more than one codon.

So.  Back to the original point.  Many mutations don't do anything at all.  If the mutation changes a letter in a codon, there is a fair to good chance that the codon will still make the same amino acid.  

This is how we get common RESULTS from VARYING SPECIFIC code.  Are we good?

Quote
And if the results are common then why vary the specific code  (if that can really be done)?  What's the point?


It does happen. If you don't believe me, take a biology course which covers DNA / RNA / AMINO ACIDS / PROTEINS.  At my college, this was bio 102.  Or google it.  You shouldn't have too much trouble finding a good link.

What's the point?   Heck if I know.  Why do stars shine?  Why does gravity attract?  Why does there have to be a point at all?

Quote
Again, the fundamental function doesn't change.  Only the structure changes.  How can this change in structure be evidence of a fundamental function common to all biological entities?


To say again, the changes are more evidence of points of divergence between the species.  Evidence of common function *could* be gathered from here, I guess, but from other sources as well.

  
Henry J



Posts: 4565
Joined: Mar. 2005

(Permalink) Posted: Mar. 13 2006,04:38   

And, it's not just the base pair changes that still put the same amino acid in that position. As I understand it, some positions in the protein aren't directly involved in either the function or the folding of the thing into the right shape. Also,
some amino acids are fairly similar to each other.

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: Mar. 13 2006,06:41   

There seems to be a confusion between the lower limit of sequence identity at which we can reasonably infer homology, and the lower limit at which it is possible for the protein to retain its original function. The second of these, in many cases at least, is lower than the first. Up until recently, we couldn't reliably detect homolgy below about 20-30% identity, but it is now much lower than that in many cases, due to more sophisticated methods.

If we have a protein structure, we can perhaps estimate the amount of change it can tolerate before it ceases to function. These estimates ussually rely on changing a number of amino acids simultaneously, this is obviously different to changing them individually, as each change will produce a protein with a slightly different structure, which has a different set of mutations that it will tolerate. We can perhaps say that there are several essential amino acids that perform the activity of the protein, and they cannot be changed, but beyond that we cant really give good lower limits. I have seen several proteins that appear to be homologous and have similar active site structures that have well below 15% sequnce identity.

Quote
In short, some conserved genes should show this pattern, AB 90%, AC 75%, AD 40%, AE 15%, AF 15%, AG 15%.
Can we have evidence that this hasn't occured please, I am also still waiting for this information that evolutionary biologists are aware of (apart from the dozens that I have spoken to apparently) that shows problems with evolution that they are not telling the public about.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 13 2006,07:16   

Quote (Chris Hyland @ Mar. 13 2006,12:41)
Quote
In short, some conserved genes should show this pattern, AB 90%, AC 75%, AD 40%, AE 15%, AF 15%, AG 15%.
Can we have evidence that this hasn't occured please, I am also still waiting for this information that evolutionary biologists are aware of (apart from the dozens that I have spoken to apparently) that shows problems with evolution that they are not telling the public about.

If the pattern you quoted has occured, you would have heard about it by now.  Some evolution biologists would be screaming that humans are equally related (or disrelated) to yeast and bacteria.  But all we hear today is that humans are eqaully related to two types of bacteria, eu and archea.  

You want an example of specialists not being open with the layman.  Here is one.  I am sure you are familiar with the neutral theory and molecular clock.  You can open any biology textbooks and you will find the molecular clock concept.  The booklet Science and Creationism by the national academy of sciences also teaches molecular clock.  All textbooks intended for the layman teach the clock hypotheisis as if it is well proven and accepted.  But is it?  It is clearly not among the specialists.  Let me give you an example of a paper by no-less an authority on evolution, the NAS member Dr. Francisco Ayala, who chaired the NAS committee that wrote the evolution booklet Science and Creationism.  In his 1999 paper (BioEssays, 21:71-75) titled "Molecular Clock Mirages", he expressed strong criticisms on the clock idea, as is apparent from the paper's title.  He wrote:'Whither the molecular clock?  Should it be abandoned altogether?  The theoretical foundation originally proposed for the clock, namely the neutrality theory of molecular evolution, is untenable.  The vagaries of molecular rates of evolution have contributed much to invalidating the theory.'

Now remember, without the neutral theory, no one will be able to explain the protein homology pattern shown by cyto C within the paradigm of Darwinism.  It then logically goes that if the neutral theory is untenable the cyto C pattern would be inexplicable by Darwinism.  Rather than supporting Darwinism as the laymen are taught by textbooks, the cyto C pattern actually falsifies it.

The alternative interpretation I proposed eariler for the cyto C pattern is morely likely to be correct.  At least it has no factual contradictions.  The maximum genetic divergence between any two species is set up at the beginning of species split, just like what we know about phenotype divergence.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 13 2006,07:38   

Quote (shi @ Mar. 13 2006,13:16)
Quote (Chris Hyland @ Mar. 13 2006,12:41)
Quote
In short, some conserved genes should show this pattern, AB 90%, AC 75%, AD 40%, AE 15%, AF 15%, AG 15%.
Can we have evidence that this hasn't occured please, I am also still waiting for this information that evolutionary biologists are aware of (apart from the dozens that I have spoken to apparently) that shows problems with evolution that they are not telling the public about.

If the pattern you quoted has occured, you would have heard about it by now.  Some evolution biologists would be screaming that humans are equally related (or disrelated) to yeast and bacteria.  But all we hear today is that humans are eqaully related to two types of bacteria, eu and archea.  

Shi,
Depending on the genetic sequence you use, you can easily show the same distance between humans, yeasts and bacteria.
This is nothing new and scientists just interpret it as a useless sequence for their phyologenetic analysis. That's why you won't find any article about it.

In fact, only a few genes can be use to build a phylogeny regrouping mammals an bacteria.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 13 2006,07:47   

Quote (jeannot @ Mar. 13 2006,13:38)
Shi,
Depending on the genetic sequence you use, you can easily show the same distance between humans, yeasts and bacteria.
This is nothing new and scientists just interpret it as a useless sequence for their phyologenetic analysis. That's why you won't find any article about it.

jeannot, show me one sequence then.  I am confident that you stated what you did without any factual support.  I challenge you, like I did with other experts, to find one animal gene sequence that shows equal distance with yeast and bacteria.  Now of course you and I can find many animal genes that show no discernible relationship with yeast or bacteria.  These genes may be what you meant by not good for phylogenetic analysis.  But if you understand my point, you would know what I am looking for and what is lacking is an animal gene that has obvious homologs in yeast and bacteria and is equally related to these homologs.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 13 2006,08:00   

Quote (jeannot @ Mar. 13 2006,13:38)
In fact, only a few genes can be use to build a phylogeny regrouping mammals an bacteria.

Here is a parodox for you.  Let us follow your logic, that some genes are good and some are bad for phylogenetic analysis.  Let us say the bad one shows that humans are equally related to yeast and bacteria.  Now who are you or we to say or judge which genes better serve our idiology or actually reflect reality?  Indeed, if both types of genes exist, Darwinism would be in trouble.  We will have specialists divided into two camps, one saying that we are more closely related to yeast and the other saying that we are equally close to yeast and bacteria.  In such a case, gene homology would be useless in phyologenetic inference.

  
Shirley Knott



Posts: 148
Joined: Feb. 2006

(Permalink) Posted: Mar. 13 2006,08:03   

Shi, we have at least one major problem.
This discussion has dithered back and forth trying to discern what your particular issue is.
So far, you have not adequately laid out whether your assertion is with respect to genes or with respect to proteins.
Until that is cleared up, the discussion is doomed to go nowhere.
Personally, I believe there has been more than enough here to undercut your 'arguments' regardless of which branch you choose to take -- but you MUST take a branch, clearly and unequivocally, so that others know which argument you are presenting, and can keep their replies relevent to your actual claims.

hugs,
Shirley Knott

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 13 2006,08:12   

Shirley,
what is the meaning of a gene if it does not mean or encode a protein?  I dont see an issue here but if you insist, I will take the protein branch.  After all, cyto C PROTEIN homology is what is taught in textbooks as molecular evidence of evolution.  

IF you think the commonts I have received here had already explained away my case, you dont have a clue.  The experts I contacted knew better, which is why they were silent.  They would not want to give explanations that would only make them look less knowledgeable.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 13 2006,08:13   

Shi, you should get familiar with phylogenetics, particularly with the term "homoplasy". Otherwise, like Shirley said, this thread will go nowhere. ???

  
Shirley Knott



Posts: 148
Joined: Feb. 2006

(Permalink) Posted: Mar. 13 2006,08:23   

Shi, if you don't see an issue here, you're not even reading the responses.
Note that the relationship between genes and proteins is not so simply one-to-one as you would like to imply.
This has been explained in this thread.
Note that you have failed to establish a minimum or maximum divergence of either genes or proteins, under any scenario you have listed.
This has been explained in this thread.
Note that you have frequently, and always fatally, omitted context from your scenarios, such that you invariably omit the environmental factors which can be assumed to apply.
This has been explained in this thread.
Your frequent recourse to "but if you're right and I'm not, why didn't my experts say so?" is pretty weak.
What experts?  What *specifically* did you ask?
Is it possible that the lack of response was due more to the incoherency of your question than any "gee, I'm stumped" feeling on the part of the questioned.
Gee, ya think?
This has been explained in this thread.
Your scenario as you continue to lay it out is incoherent and, given your radically incomplete exposition, unsupported in key essentials.
This has been explained in this thread.
And thus you can, and should, be ignored until you fill in the missing pieces.

hugs,
Shirley Knott

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: Mar. 13 2006,08:29   

Quote
But if you understand my point, you would know what I am looking for and what is lacking is an animal gene that has obvious homologs in yeast and bacteria and is equally related to these homologs.
What do you mean by obvious homologues? I assume you mean a reasonable level of sequence identity, why would you expect this to be the case?

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 13 2006,08:50   

Quote (Chris Hyland @ Mar. 13 2006,14:29)
Quote
But if you understand my point, you would know what I am looking for and what is lacking is an animal gene that has obvious homologs in yeast and bacteria and is equally related to these homologs.
What do you mean by obvious homologues? I assume you mean a reasonable level of sequence identity, why would you expect this to be the case?

anything above 15% identity is suggestive of a homologous relationship.  The question is why human cyto C should show 35% identity with bacteria and 60% identity with yeast.  The present theory says that with time the identity with yeast will decrease.  But I predict that the identity has been at 60% all along and will will stay the same in the future.  

For Shirley to imply that there should exist a minimal diversity criterio for proteins just shows her lack of knowledge.  Some proteins can share 7% identity and be still homologous in sequence and function.  Some may need to be 35% identitical in order to stay homologous in sequence and function.  It is all protein dependent.  

Much of Shirley's other charges indicated the same.  They are irrelevant to the main point here and worthy of no further comments.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 13 2006,08:55   

Shi, we all fail to get your point.

"Darwinism" makes NO prediction about any minimal level of identity between nucleotids or amino acid sequences in genes or proteins (above the typical 1/4 and 1/20 respectively).
As we told you, a protein may change its function, gain new ones or co-evolve with other proteins while remaining functional. Anything is possible as long as it doesn't alter its organism's fitness.
If you think that some proteins should have some minimal level of identity across distant lineages (maybe this is true in some cases, I'm not a expert in protein evolution) it's your concern, not ours, because it as nothing to see with the falsification of common descent.
You can go to NCBI or genebank, get some proteins sequences and perform all the distance comparisons you like. Maybe you'll find some interesting things that confirm or contradict your thoughts.
Good luck.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 13 2006,09:18   

Quote (jeannot @ Mar. 13 2006,14:55)
Shi, we all fail to get your point.

jeannot.  

you know as well as I that what you said is false.  remember the dadey guy?  

I think Einstein said it, a problem cannot be solved by the same mind set that created it.  What is needed is a change of perspective.  If you are too indoxicated by one theory, it is no surprise that you will fail to see anything else.  

If we must dump the neutral theory, we will need a brand new perspective to explain the protein homology data across species.  If you want to stick with what you are stuck with, regardless of factual contradictions, it is sign of narrow mindedness, not conductive at all to scientific progress.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 13 2006,09:28   

Well, goodby Shi... until you have some clear arguments.

  
Shirley Knott



Posts: 148
Joined: Feb. 2006

(Permalink) Posted: Mar. 13 2006,09:32   

Shi, we begin to believe you HAVE no point.

Do please consider
"anything above 15% identity is suggestive of a homologous relationship."
Error number one.  You are not arguing that relationships are homologous, but rather that two proteins are homologus.  And you equivocate frequently on the homology you are addressing -- is this structural, functional, or what?
Is it YOUR claim that 15% identity [of what, determined how?  please specify] is suggestive of homology?
Or is it an expert opinion, in which, a cite please.

"  The question is why human cyto C should show 35% identity with bacteria and 60% identity with yeast. "

From whence do those numbers come?  Please cite the relevent studies.
Also, please justify the assertion that cyto C "should" [according to whom?  according to what principle? ]
show 35% percent identity [identity of what precisely?]
with bacteria and 60% with yeast?
Who asserts this?
What theory predicts this?
If you think the modern synthesis ("neo-darwinian evolutionary theory") predicts this, why do you think so?
Show your work, that is to say, do not assert it, show the premises, the intermediate steps, and the conclusion.

" The present theory says that with time the identity with yeast will decrease."
Wanna bet?
Where is that stated in the modern synthesis?
Or is this self-referential to the "theory" [sic] you are attempting to lay out?

" But I predict that the identity has been at 60% all along and will will stay the same in the future.  "
This is utter nonsense.
If the homology is measured at 35%, it is not at 60%
Or is your math as bad as your biology?

"For Shirley to imply that there should exist a minimal diversity criterio for proteins just shows her lack of knowledge. "
Hardly.
And your response trumpets your ignorance to the heavens.
The minimal diversity criterion for any two proteins is 0 -- two identical proteins are identical.
Two proteins that structurally diverge by some amount > 0 may or may not have identical function.  And other two proteins that structurally diverge by the same amount as the first two referenced in the previous sentence might or might not have identical function to each other.  Note well that the divergence in the first case is, by itself, insufficeint ground for asserting that identical amount of divergence elsewhere will have the same impact on function.

"Some proteins can share 7% identity and be still homologous in sequence and function.  Some may need to be 35% identitical in order to stay homologous in sequence and function.  It is all protein dependent.  "
And again, this is incoherent.  Were it not, I'd suspect you have a clue as to what my previous paragraph is about.
If 2 proteins are some percent identical in some specific respect, they are some percent homologous *in that respect*.  Which, as noted above, DOES NOT SPEAK to whether the will be similarly homologous in some other respect.

Reduce the level of incoherency, equivocation, imprecision, and misdirection and you might get closer to conveying something both meaningful and useful.

But I doubt it.

hugs,
Shirley Knott

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 13 2006,09:38   

I dont have time to educate you about the theory that you claim to know but obviously dont.

  
Shirley Knott



Posts: 148
Joined: Feb. 2006

(Permalink) Posted: Mar. 13 2006,09:45   

IOW, you give up.

Thank you for acknowleging defeat, Shi deary.
Go crawl back under the rock you oozed from beneath.

pfeh.  I spit in your general direction.
It is clear you do not understand theory in general, let alone the modern synthesis.
If you did, you'd be able to speak more coherently on the subject, not make elementary errors of ascription (homologous relationships?  please...), and more clearly lay out what you see to be a problem, and why you believe it is a problem of the theory.
Clearly, you cannot.
I spit again in your general direction, and recommend your children consider retroactive abortions to erase the stain of their descent from you.


hugs,
Shirley Knott

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 13 2006,09:49   

I hope I have made my case clear with the above example of clock and DR. Ayala that what you learned in textbooks on evolution is less than truthful.  So if your knowledge of evolution is not much beyond the textbooks, you are much better off to stay open-minded and learn more before letting the world know that you are less than informed.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 13 2006,09:55   

Quote (shi @ Mar. 13 2006,15:38)
I dont have time to educate you about the theory that you claim to know but obviously dont.

Yeah, like confusing mutation rates with genetic distances, homology with ancestry, applying neutral theory to non-neutral mutations, connecting the identity in the "5 fingers design" with Cyt C...

(It's hard to resist responding sometimes... :p )

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 13 2006,09:55   

Quote (Shirley Knott @ Mar. 13 2006,15:45)
I spit again in your general direction, and recommend your children consider retroactive abortions to erase the stain of their descent from you.


hugs,
Shirley Knott

Wow, that is agreesive and uncalled for.  Very classy.  It shows perfectly well why you and your arguments should be ignored.

  
Alan Fox



Posts: 1391
Joined: Aug. 2005

(Permalink) Posted: Mar. 13 2006,10:05   

Shi

You could avoid being abused by taking your theory elsewhere. Why not compare notes with Professor Davison; I'm sure you will find a more sympathetic ear there. (Unless you are Shi Huang, in which case, you didn't get very far there either.)

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 13 2006,10:11   

Alan, I thought you were in rehab regarding your addiction to JAD's blog.  ;)

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: Mar. 13 2006,10:11   

Can you at least cite evidence which says that all the cytochrome c's should stop at exactly 15% sequnce identity to each other.

  
Alan Fox



Posts: 1391
Joined: Aug. 2005

(Permalink) Posted: Mar. 13 2006,10:20   

Jeannot

I had a lapse but I'm back on the wagon  ;)

  
Shirley Knott



Posts: 148
Joined: Feb. 2006

(Permalink) Posted: Mar. 13 2006,10:39   

Uncalled for?

Your ignorant arrogant rants are sufficient warrant for whatever verbal abuse anyone chooses to fling in your general direction.

It is abundantly clear that you know neither logic nor genetics, neither evolution nor philosophy.  We may doubt your awareness of physics and chemistry as well.
Why, then, should anyone bother with you and the nonsense which springs from your confusion?

hugs,
Shirley Knott

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 13 2006,12:46   

Quote (Chris Hyland @ Mar. 13 2006,16:11)
Can you at least cite evidence which says that all the cytochrome c's should stop at exactly 15% sequnce identity to each other.

I never claimed what you asked.  Maybe 35% is more likely (the identity between human and bacteria).  Anything lower would perhaps inactivate cyto C but I dont know if any one has such information.

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: Mar. 13 2006,13:36   

Fair enough, but then Im not sure I understand, your claim seems to be that there is a limit for how much the sequence of a protein can change and still retain its function, and for essential proteins therefore they will essentaily settle at the same level of divergence for all species. The problem I see is that if you have a protein, with a list of mutations that it will tolerate, as soon as you make a mutation the list changes, to a degree depending on the mutation, maybe mutations that would have been tolerated before now will disrupt function, and vice-versa. It is currently impossible to predict what this limit may be, and there is no reason to suspect that proteins will all reach the same level of maximum divergence over time. Assuming that they do however, you have provided no evidence that this hasn't happened.

  
edmund



Posts: 37
Joined: Jan. 2006

(Permalink) Posted: Mar. 13 2006,17:47   

Hi Shi,

The pattern that you're talking about is called "saturation". It's a very well-understood phenomenon-- biologists know that if you're using genetic divergence data to work out very deep evolutionary relationships, you can't use rapidly-evolving genes, because the sequences will have approached a maximum divergence from one another a long time ago. Saturation is usually discussed with respect to neutral genetic differences, but the idea's really the same for the protein-level differences that you're discussing.

Saturation does not present any sort of problem for evolutionary theory. Yes, if the saturated sequences were all the evidence available for reconstructing evolutionary relationships, saturation would make it impossible to figure out those relationships. But since we have lots of sequences that are not saturated, it doesn't matter at all.

You seem to suggest that the divergences between lineages were "added" to their DNA at the moment that the two lineages diverged. I'm afraid that the data we have overwhelmingly supports the hypothesis that lineages diverge gradually over time by the accumulation of random mutations, which may be eliminated or kept by selection. For example, if you understand the difference between synonymous and nonsynonymous substitutions, you should understand why the former would logically accumulate faster than the latter. And that's exactly what we see when we compare DNA sequences. We can observe the mutation process on the small scale and deduce what we should see if that process were going on for long periods of time. Over and over again, such predictions have been confirmed.

If you really want to understand these processes and predictions, you could try Googling "molecular clock saturation". But don't expect other people to do your work for you. And don't get emotionally attached to your ideas. Frankly, I haven't been impressed with what you've had to say on this thread-- I'm not sure that you clearly understand your own arguments, and I'm not sure that you're ready to put in any hard work to learn the stuff you don't know. But if you prove me wrong about that I'll be overjoyed to apologize.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 14 2006,05:27   

Quote
Frankly, I haven't been impressed with what you've had to say on this thread-- I'm not sure that you clearly understand your own arguments, and I'm not sure that you're ready to put in any hard work to learn the stuff you don't know
That's my take as well.

But I was inspired to take a peek a the sequences in question (cytochrome C) and I'm curious to know where this "35%" homology between human and bacterial sequences comes from.

--------------
Must... not... scratch... mosquito bite.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 14 2006,08:38   

Edmond,

Proteins or DNAs can be divided into conserved and non-conserved sequences.  Just like phenotypes: the nucleus of all eukaryotic cells is a conserved phenotype speicific to eukaryotes.  The five finger pattern is conserved.  The eye is less conserved because there are many different kinds of eye designs.  

For non-conserved sequences, saturation is a well known phenomenon.  Saturation here means that a sequence has been changed into a totally different sequence.  The mitochondrial control region is one such example, where human show 90% identity with chimps, 33% to orangutans, and no recognizable relationship to dogs and beyond. So for this sequence, saturation occured within 20 myr.  Now for some medium level conserved sequences, saturation may take 500 myr.  Now the question that interests me is that do we always expect saturation regardless of how conserved the sequence is.  There are two predictions.  The first is that even for the most conserved sequences, saturation will occur though it may take longer time such as 2-3 billion years.  This prediction is what is given by the present theory. It has not been proven to be true since there exist conserved sequences that show recognizale identity between two species seperated 2-3 billion years ago.  The second is that the most conserved sequences cannot be mutated to beyond a minimal functional level; regardless of time and mutation rate, one should still find enough sequence identity.  If human cyto C shows the same identity with yeast and bacteria at 35%, we would conclude that cyto C cannot be mutated to below 35%.  The second prediction is more consistent with what we know about nature.  A conserved function or phenotype are very stable and stay unchanged during evolution.  We dont expect to see the eukaryotes to lose their nucleus some day.  We dont expect our five fingers be mutated into a totally different design in the future.  But despite all our expectations of a conserved sequence that should show signs of stability at a recognizable identity (such as 35%), we have found none.  This may indicate that the present theory of gradual divergence may be incorrect.  The present theory and the data we have require us to accept the first prediction to be true even though it has no factual support.  So cyto C would one day be mutated to saturation so that it can no longer be recognized as cyto C.  But somehow the totally changed cyto C can still function the same.  The first prediction is not consistent with common sense and what we know about the stability of conserved functions and phenotypes.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 14 2006,09:01   

Again - where does this 35% identity number come from? What bacteria are we talking about?

AND, doesn't the fact that you're comparing a mitochondrial enzyme (yeast, human) to bacterial enzymes render your argument moot? I would expect the minimal basic function of an enzyme that has to operate as a soluble enzyme in a mitochondrial environment to be rather different from the minimal basic function of what I believe is generally a membrane bound enzyme in the huge range of environments lumped together under the heading "bacterial cytoplasm".

No?

--------------
Must... not... scratch... mosquito bite.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 14 2006,09:26   

Russell

mgdvekgkki fimkcsqcht vekggkhktg pnlhglfgrk tgqapgysyt aanknkgiiw
      61 gedtlmeyle npkkyipgtk mifvgikkke eradliaylk katne

here is the human cyto C protein.  do a blastp with it against bacteria and find out for yourself.

One can argue whether cyto C is a good example or not.  but there are many other proteins or sequences that is shared among yeast bacteria and humans.

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: Mar. 14 2006,09:40   

Quote
expectations of a conserved sequence that should show signs of stability at a recognizable identity (such as 35%)

Can you provide a source for this, I see no reason to expect that if proteins do stop evolving at some maximum level, all homologues will show the same level of sequence identity.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 14 2006,10:13   

Quote (edmund @ Mar. 13 2006,23:47)
You seem to suggest that the divergences between lineages were "added" to their DNA at the moment that the two lineages diverged. I'm afraid that the data we have overwhelmingly supports the hypothesis that lineages diverge gradually over time by the accumulation of random mutations, which may be eliminated or kept by selection. For example, if you understand the difference between synonymous and nonsynonymous substitutions, you should understand why the former would logically accumulate faster than the latter. And that's exactly what we see when we compare DNA sequences. We can observe the mutation process on the small scale and deduce what we should see if that process were going on for long periods of time. Over and over again, such predictions have been confirmed.

For any given facts, there may be more than one explanation.  The present theory merely represents one of the possible interpretations of the sequence homology data.  It is based on the neutral theory, which is well invalidated according to some experts such as Dr. Ayala.  My interpretation of fact represents a new one.  It explains all that has been accounted for by the present theory but also explains much more.  Given that evolution cannot be reproduced or tested, the best evidence for a correct theory is its explanatory power. how many facts can it explain? does it have factual contradictions?  

If you are familiar with Gould's PuncEqu, you would know that new structures or phenotypes of new species appear suddenly and stay unchanged for millions of years.  What is the genetic basis for such sudden appearance of new phenotypes?  I suggest that the new phenotypes should be correlated with new genotypes which stay largely unchanged during evolution.  But the present theory says that the new species, depite having drastically different phenotypes, differs very little in genotypes from its ancestor species when they first splited.  Then subsequently, the genotype of the new species keeps mutating/changing during evolution, all the while the phenotype stays unchanged.  It does not seem to make any sense.  As I said earlier, the theory is self destructive or self contradictory when it says that changes in phenotypes is associated with mutations while it also says that no change in phenotype is also associated with mutations.

Small amout of mutation do occur within a species.  But there is no direct evidence that genotype difference between species is caused by accumulation of variations within species.  Humans can try to mutate bacteria randomly for however long time and they will not be able to make a eukaryote out of a bacteria.  Bottem line, there is limit to everything.  Against such common sense, the present theory requires us to believe the fiction that there is no limit to what random mutation can do.  The many examples of stabilities of structure and phenotypes prove that random mutations can do very little.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 14 2006,10:28   

Quote
here is the human cyto C protein.  do a blastp with it against bacteria and find out for yourself.
Right. And when I do that, I see a large range of "hits" covering a large range of % identities, and including various size and various numbers of gaps introduced to align the sequences. (I don't know how you want to calculate the impact of gaps on your % identities, but obviously you can't just ignore them). The % identity dips well below 35%, if you recognize that BLAST only reports the % identity of that part of the sequence it can align. Also, you'll notice that there are a lot of bacteria in which no cytochrome C homolog is seen.

So... so if you still have a point, in light of all that, I've lost track of what it is.

--------------
Must... not... scratch... mosquito bite.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 14 2006,10:40   

It is true that some bacteria has no cyto c homolog.  But they also do not have a cyto c equivalent function.  They have slightly different ways of ATP production that does not use a cyto C equivalent function.  

As someone commented in this thread, my point is rather simple. Apparently it is only simple to people who got it.

  
Arden Chatfield



Posts: 6657
Joined: Jan. 2006

(Permalink) Posted: Mar. 14 2006,10:43   

Quote (shi @ Mar. 14 2006,16:40)
As someone commented in this thread, my point is rather simple. Apparently it is only simple to people who got it.

It's your job to be coherent. It's not our job to understand you no matter how you explain yourself.

--------------
"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 14 2006,10:55   

Quote
As someone commented in this thread, my point is rather simple. Apparently it is only simple to people who got it.
Apparently.

So far as I can tell, no one here thinks you have a point, at least not a point that makes any sense. But I only speak for myself.

No, wait! There was "Thordudy" - does he count?

Anyone else following this: do any of you see a point that makes any sense? Or am I just not simple enough?

--------------
Must... not... scratch... mosquito bite.

  
improvius



Posts: 807
Joined: Jan. 2006

(Permalink) Posted: Mar. 14 2006,11:03   

[quote=Russell,Mar. 14 2006,16:55]
Quote
Anyone else following this: do any of you see a point that makes any sense? Or am I just not simple enough?

As far as I can tell, it just seems to be a rehash of the "limits of biological change" argument.  Nothing new to see here...

--------------
Quote (afdave @ Oct. 02 2006,18:37)
Many Jews were in comfortable oblivion about Hitler ... until it was too late.
Many scientists will persist in comfortable oblivion about their Creator ... until it is too late.

  
C.J.O'Brien



Posts: 395
Joined: Aug. 2005

(Permalink) Posted: Mar. 14 2006,11:12   

Quote
If you are familiar with Gould's PuncEqu, you would know that new structures or phenotypes of new species appear suddenly and stay unchanged for millions of years.  What is the genetic basis for such sudden appearance of new phenotypes?  I suggest that the new phenotypes should be correlated with new genotypes which stay largely unchanged during evolution.  But the present theory says that the new species, depite having drastically different phenotypes, differs very little in genotypes from its ancestor species when they first splited.  Then subsequently, the genotype of the new species keeps mutating/changing during evolution, all the while the phenotype stays unchanged.  It does not seem to make any sense.  As I said earlier, the theory is self destructive or self contradictory when it says that changes in phenotypes is associated with mutations while it also says that no change in phenotype is also associated with mutations.


You're conflating "phenotype" with "gross morphology" here. Gross morphology is what fossilizes. Phenotype, while inclusive of gross morphology, is not synonymous with it, encompassing as it does all expressed products of gene differences, most of which will be invisible to the paleontologist. So no contradiction. Also, like many before you, you overstate the import of PunkEek. PE is a hypothesis about the fossil record more than it is about the actual history of life represented by it in its fragmentary fashion. Until you understand that, refrain from drawing grand conclusions from the idea.

Quote
Small amout of mutation do occur within a species.  But there is no direct evidence that genotype difference between species is caused by accumulation of variations within species.  Humans can try to mutate bacteria randomly for however long time and they will not be able to make a eukaryote out of a bacteria.  Bottem line, there is limit to everything.  Against such common sense, the present theory requires us to believe the fiction that there is no limit to what random mutation can do.  The many examples of stabilities of structure and phenotypes prove that random mutations can do very little.


Eukaryotes arose via endosymbiosis. Really, as you make your ideas more clear, I realize that this is not much more sophisticated than "we see dogs, we see cats, but nobody's ever seen a 'dat.'" And why not go ahead and use the terms "macroevolution" and "microevolution"? All the cool creationists are doing it.

--------------
The is the beauty of being me- anything that any man does I can understand.
--Joe G

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 14 2006,11:17   

Quote (shi @ Mar. 14 2006,16:13)
Small amout of mutation do occur within a species.  But there is no direct evidence that genotype difference between species is caused by accumulation of variations within species.

Have you heard of "ring species"?

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 14 2006,11:41   

Quote (C.J.O'Brien @ Mar. 14 2006,17:12)
You're conflating "phenotype" with "gross morphology" here. Gross morphology is what fossilizes. Phenotype, while inclusive of gross morphology, is not synonymous with it, encompassing as it does all expressed products of gene differences, most of which will be invisible to the paleontologist. So no contradiction.

Even if we only limit our phenotypes to fossilized morphology, the same issue remains with the present theory.  Beginning in the species split, dramatic morphology change is associated with very few changes in genotypes.  Several hundred million years later, the same morphology is now correlated with vastly changed genotypes.  I hope you are not suggesting non-random directed mutations, which knows to leave the gross morphology untouched while knows to change only genes involved with phenotypes invisible to the paleontologist.

  
C.J.O'Brien



Posts: 395
Joined: Aug. 2005

(Permalink) Posted: Mar. 14 2006,11:53   

Quote
Beginning in the species split, dramatic morphology change is associated with very few changes in genotypes.

Incorrect. The current theory does not predict dramatic differences of any kind between populations undergoing a speciation event. In fact, it reveals that such events can only be aprehended as such with the benefit of hindsight.
And I am certainly not suggesting anything of the "directed" sort. I cannot imagine what would give you that idea.

--------------
The is the beauty of being me- anything that any man does I can understand.
--Joe G

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 14 2006,12:01   

Quote (C.J.O'Brien @ Mar. 14 2006,17:53)
The current theory does not predict dramatic differences of any kind between populations undergoing a speciation event.

Of course it does not.  That is why it is inconsistent with facts.  That is why it is falsified by facts.  It predicts gradual transition.  But where are the transition speices?

  
C.J.O'Brien



Posts: 395
Joined: Aug. 2005

(Permalink) Posted: Mar. 14 2006,12:05   

I s there a lineage in particular that you find lacking?

--------------
The is the beauty of being me- anything that any man does I can understand.
--Joe G

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 14 2006,12:08   

lack of transistion species has been a well known phenomenon since Darwin.  It remains so today.  If this is news to you, I just give up.

  
improvius



Posts: 807
Joined: Jan. 2006

(Permalink) Posted: Mar. 14 2006,12:14   

I think you just gave up.

--------------
Quote (afdave @ Oct. 02 2006,18:37)
Many Jews were in comfortable oblivion about Hitler ... until it was too late.
Many scientists will persist in comfortable oblivion about their Creator ... until it is too late.

  
C.J.O'Brien



Posts: 395
Joined: Aug. 2005

(Permalink) Posted: Mar. 14 2006,12:19   

"Lack" is not a very precise term. While I will agree that there are "gaps," they are not nearly as pronounced after a hundred and fifty years of evolution-informed paleontology as they were in Darwin's day. Dawkins has made the point that we are lucky the fossil record isn't "complete," for the proliferation of finely-graded specimens across multiple morphological markers would make the task of nomenclature a farce. We have the transitionals we need to have a high degree of confidence in the theory, which is also supported by other lines of evidence. And more are discovered all the time. You don't hear so much about the cetacean lineage so much anymore, for instance.

I'm sorry you are frustrated, but, quite frankly, since the obfuscatory sheen of your argument tarnished, you seem to be engaged in the aping of long-ago refuted creationist boilerplate.

Let's look at it from this angle: If this "lack" (of transitional fossils) is so well-understood, and it poses such a big problem for the neo-Darwinian account, what exactly is wrong with the paleontologists and evolutionary biologists of the world? Are they a) stupid, b) dishonest, or c) confused?

It would seem you need one or more of those to be true, across the board. Seems a little unlikely to me.

--------------
The is the beauty of being me- anything that any man does I can understand.
--Joe G

  
Louis



Posts: 6436
Joined: Jan. 2006

(Permalink) Posted: Mar. 14 2006,12:21   

Shi, as Jeannot said:

RING SPECIES.

Really, look them up. Then realise that ALL species are ring species, some rings (sadly most of them) are discontinuous at the present time because of "breaks" in the ring. The breaks are not caused by saltations, but by extinctions etc.

Fascinating topic ring species.

--------------
Bye.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 14 2006,12:28   

Quote
I just give up.
Well, don't let us discourage you. Go ahead and make the most tightly reasoned argument you can, and try to get it published.

Just don't automatically blame closed-minded dogmatic Darwinists if Nature declines to publish it. Consider the possibility that - clear though your argument appears to be to you - it doesn't make any sense to anybody else*.

*(Except, of course, to creationists who wave their pom-poms for anything and everything that purports to challenge evolution, no matter how inconsistent with reality, logic, or even their other anti-evolution arguments.)

--------------
Must... not... scratch... mosquito bite.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 14 2006,12:34   

Quote (shi @ Mar. 14 2006,17:41)
Beginning in the species split, dramatic morphology change is associated with very few changes in genotypes.  Several hundred million years later, the same morphology is now correlated with vastly changed genotypes.

Could you give us a precise example supported by some data: the two species involved in a speciation event, the "few changes" in genes that control their dramatically different morphologies (unless you wan't to explain morphology by changes in genes like Cyt C)?
Then, could you give us some evidence of the vastly changed genotypes, at the same loci of course, without new change in their morphologies?
Lastly, could you comment this example regarding the predictions of your theory?

Thanks in advance.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 14 2006,12:40   

Quote (C.J.O'Brien @ Mar. 14 2006,18:19)
Let's look at it from this angle: If this "lack" (of transitional fossils) is so well-understood, and it poses such a big problem for the neo-Darwinian account, what exactly is wrong with the paleontologists and evolutionary biologists of the world? Are they a) stupid, b) dishonest, or c) confused?

It would seem you need one or more of those to be true, across the board. Seems a little unlikely to me.

Glad you raised an interesting point.  As Gould himself once said, a theory is overthrown by rival theories.  Implication, a theory cannot be overthrown by factual contradictions.  And he is absolutely right.  It is nothing surprising to find scientists to be a, b, and c, as you listed.  After all human beings are capable of those and scientists are only human and need to earn a living.  When seeking truth compromizes self interest (grants, salary to feed family, career), self interest takes over, at least for most sane people.  

The present theory has so many factual contradictions that it reqires many ad hoc hypotheses to get by.  The molecular clock is one.  This is just like the Ptolemaic astronomy with its fanciful epicycles.  I am sure you would not hesitate now with hindsight to call those scientists of the 19 th century a, b, and c, who defended Ptolemaic astronomy with a zeal and creativity comparable to how today's scientists are defending the present evolution theory.

  
improvius



Posts: 807
Joined: Jan. 2006

(Permalink) Posted: Mar. 14 2006,12:48   

So I guess you could say that you're something of a modern-day Galileo, and that the scientific community is conspiring against you (and others like you) to prevent the world from finding out what a sham the present "science" really is.  Does that sound about right?

--------------
Quote (afdave @ Oct. 02 2006,18:37)
Many Jews were in comfortable oblivion about Hitler ... until it was too late.
Many scientists will persist in comfortable oblivion about their Creator ... until it is too late.

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: Mar. 14 2006,12:54   

Quote
When seeking truth compromizes self interest (grants, salary to feed family, career), self interest takes over, at least for most sane people.
So imagine if the goverment suddenly announces funding for ID, and it is acceptable to believe and research in either, you think evolutionary biologists are all going to turn round and say they didn't believe in 'Darwinism' all along?

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 14 2006,12:56   

Quote (improvius @ Mar. 14 2006,18:48)
So I guess you could say that you're something of a modern-day Galileo, and that the scientific community is conspiring against you (and others like you) to prevent the world from finding out what a sham the present "science" really is.  Does that sound about right?

while many insane people may think the way as you just described, the truth of the matter is that there will be future Galileos.  That is just how nature works.  That is evolution.  Human has evolved for 5000-10000 years and has 4 billion years to go.  Kuhn's paradigm scheme of scientific progress is, like it or not, prety to the point.

  
C.J.O'Brien



Posts: 395
Joined: Aug. 2005

(Permalink) Posted: Mar. 14 2006,12:59   

self interest takes over
And I'm glad you raise an interesting point. The best way to earn a lasting name in the sciences is to conclusively overthrow an existing "self-evident" belief.

So why is it that it's just creationists sniping from the wings who see evolution the way you're describing? You don't think there would be at least a few scientists out there who are neither a, b, or c, just itching for their moment of fame?

You verge pretty close to conspiracy theory, and I have no patience for that.

--------------
The is the beauty of being me- anything that any man does I can understand.
--Joe G

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 14 2006,13:01   

Quote (Chris Hyland @ Mar. 14 2006,18:54)
Quote
When seeking truth compromizes self interest (grants, salary to feed family, career), self interest takes over, at least for most sane people.
So imagine if the goverment suddenly announces funding for ID, and it is acceptable to believe and research in either, you think evolutionary biologists are all going to turn round and say they didn't believe in 'Darwinism' all along?

You dont think so.  Are you from outer space or just naive?

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 14 2006,13:09   

Quote (C.J.O'Brien @ Mar. 14 2006,18:59)
self interest takes over
And I'm glad you raise an interesting point. The best way to earn a lasting name in the sciences is to conclusively overthrow an existing "self-evident" belief.

So why is it that it's just creationists sniping from the wings who see evolution the way you're describing? You don't think there would be at least a few scientists out there who are neither a, b, or c, just itching for their moment of fame?

You verge pretty close to conspiracy theory, and I have no patience for that.

Yes indeed, scientist would do anything to make a name.  But to find a contradiction to a popular theory is not going to be the way to do it.  It never worked in history.  The only way to do it is to create a better theory that explains more facts better.  That, as you probably know, is not so easy.  If it is, it would have been done by now.  But the present lack of a better theory is no evidence for the truthfullness of the present theory.  It just means time is not ripe yet.  Knowledge evolves, just like nature.  And evolution needs time.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 14 2006,13:20   

Quote
The present theory has so many factual contradictions that it reqires many ad hoc hypotheses to get by.  The molecular clock is one
This is the kind of vacuous generality that most anti-evolution rhetoric boils down to.

So far, your attempts to point out any "factual contradictions"  have been, well, let's just say uncompelling.

"The" molecular clock? The idea that you can use the accumulation of mutations to say something about the relative antiquity of various phylogenetic  branchings seems pretty uncontroversial. The fact that there are limitations to that also fails to surprise me. If there's something basic to evolutionary theory that demands that every gene in every organism diverge at a constant rate, I missed that lecture.

Quote
Human has evolved for 5000-10000 years and has 4 billion years to go.
Now there's a doubly remarkable sentence. We've only been evolving for 10000 years? That will certainly constitute a "paradigm shift" for every anthropologist and paleontologist I've ever known. And we have 4 billion years to go? Not if we're like 99% of every species that have come before.

Quote
But the present lack of a better theory is no evidence for the truthfullness of the present theory.  It just means time is not ripe yet.
No, actually it means nothing at all. But the time is as at least as ripe as ever. How much of what we teach as evolution would Darwin even recognize? Genes, alleles, DNA... You think the theory of evolution is waiting for insights like yours to "evolve"? You may have delusions of significance.

--------------
Must... not... scratch... mosquito bite.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 14 2006,13:34   

Quote (Russell @ Mar. 14 2006,19:20)
If there's something basic to evolutionary theory that demands that every gene in every organism diverge at a constant rate, I missed that lecture.
You think the theory of evolution is waiting for insights like yours to "evolve"? You may have delusions of significance.

Indeed you missed.  Yeast and human cyto C show equal identity with bacteria. The present explanation of this so-called molecular equidistance is to say that cyto C in yeast has undergone the same rate of mutation as the lineage leading humans.  Pretty fanciful stuff.

At least with people like me, we have a chance, no matter how slim, to evolve the theory into a better shape.  But with people like you, the theory has nothing new to gain and no future.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 14 2006,14:01   

Quote
The present explanation of this so-called molecular equidistance is to say that cyto C in yeast has undergone the same rate of mutation as the lineage leading humans.
Can you point to anything, anywhere that states this "explanation"? You're trying to explain a nonexistent phenomenon.

Quote
At least with people like me, we have a chance, no matter how slim, to evolve the theory into a better shape.  But with people like you, the theory has nothing new to gain and no future.
Oh, don't worry about me. I just sort of use the theory of evolution in my work. I don't assume responsibility for improving it. Do let us know when your ground-breaking, paradigm-shifting theory is published. Or at least when anyone more credible than Thordude thinks you have a point.

--------------
Must... not... scratch... mosquito bite.

  
Arden Chatfield



Posts: 6657
Joined: Jan. 2006

(Permalink) Posted: Mar. 14 2006,14:13   

I'm surprised no one called Shi on this:

Quote
So imagine if the goverment suddenly announces funding for ID, and it is acceptable to believe and research in either, you think evolutionary biologists are all going to turn round and say they didn't believe in 'Darwinism' all along?

You dont think so.  Are you from outer space or just naive?


So, Shi, your assumption must be either:

a) all those scientists don't really believe in evolution, they only claim to because of peer pressure,

or,

b) Once it becomes (more) profitable to do ID research, all the current scientists are going to LIE and claim to believe in ID just to get grants.

Which is it? Since if it's (a) you're quite delusional, and if it's (b), we might have just gotten an interesting glimpse into your view of what scientists are like ethically. Which is a good indication that you aren't one yourself.

Personally, I'm waiting for Shi to come up with the old fave "if humans are descended from apes, why do we still have apes?" argument any minute now...

--------------
"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 14 2006,14:14   

Quote (Russell @ Mar. 14 2006,20:01)
Quote
The present explanation of this so-called molecular equidistance is to say that cyto C in yeast has undergone the same rate of mutation as the lineage leading humans.
Can you point to anything, anywhere that states this "explanation"? You're trying to explain a nonexistent phenomenon.

[

I am really surprised by your lack of information.  Go to the paper by Elsbery and find out for yourself at http://www.antievolution.org/people/wre/evc/argresp/sequence.html

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 14 2006,14:25   

Russell,

You could also read Michael Denton's book Evolution: a theory in crisis.  He made some good points but I am not suggesting that I agree with all his points.

Here is a challenge for you. If you find out what I stated about molecular equidistance is ture, would that change you a bit in your believe in your theory?  I would be overjoyed if you do.  But I highly doubt it.  My doubt has nothing personal about you.  It is just a consistent pattern with human beings.  When people believed in a theory, they would not give it up no matter how many contradictory facts exist.  They only give it up when they are told a new theory that explains the facts better.

  
Arden Chatfield



Posts: 6657
Joined: Jan. 2006

(Permalink) Posted: Mar. 14 2006,14:35   

Shi, if you want to be taken seriously, and if you have any thought of publishing what you're working up, I strongly urge you to read up on ring species and to consider their implications for what you're saying. Otherwise, you're going to look a lot like just another crackpot ID/C advocate who repeats discredited talking points and ignores any evidence that causes problems for his theory. I hope you don't want to end up that way.

--------------
"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: Mar. 14 2006,14:55   

Quote
So imagine if the goverment suddenly announces funding for ID, and it is acceptable to believe and research in either, you think evolutionary biologists are all going to turn round and say they didn't believe in 'Darwinism' all along?

You dont think so.  Are you from outer space or just naive?
I speak to evolutionary biologists fairly regularly, and none of them have expressed doubts about evolution, from grad students to well known professors. Are you saying:

a) I am lying now, and I don't believe in evolution.

b) They are lying to me.

c) The evolutionary biologists I have spoken to belive in evolution, but the rest don't.

Ill give you a clue, it's definately not a).

I'm still not sure how any fact you've stated so far refutes evolution, could you restate the one fact you think does this, with links to the relevant evidence.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,00:44   

Quote (shi @ Mar. 14 2006,20:14)
Quote
The present explanation of this so-called molecular equidistance is to say that cyto C in yeast has undergone the same rate of mutation as the lineage leading humans.[quote=Russell,Mar. 14 2006,20<!--emo&:0]Can you point to anything, anywhere that states this "explanation"? You're trying to explain a nonexistent phenomenon.

I am really surprised by your lack of information.  Go to the paper by Elsbery and find out for yourself at http://www.antievolution.org/people/wre/evc/argresp/sequence.html

In your link, Wesley also explains why the same distance found between different animals (mostly vertebrates) and bacteria unsing Cyt C is not a problem for the theory of evolution, which was Denton's argument


Anyway, your link doesn't refer to the distance between animal, yeasts and bacteria, that you've been talking about.
Do you have a link stating that these three lineages have accumulated the same number of mutations since their divergence (naive question)?

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 15 2006,05:18   

Quote
I am really surprised by your lack of information.  Go to the paper by Elsbery and find out for yourself at ...
As I said before, within limits, I buy the concept of the "molecular clock". But my big problem with your idea is that it goes way beyond those limits. The reference you gave deals only with actual cytochrome C, by definition a mitochondrial enzyme. The constraints on its evolution - its rate of accumulation of differences after lineage splits - are at least comparable. When you talk about the bacterial homologs, all bets are off.

Fortunately, this very discussion board is Elsberry's baby, so he can explain to you whether or not his essay justifies the conclusions you draw from it. Wesley?

Quote
You could also read Michael Denton's book Evolution: a theory in crisis.  He made some good points but I am not suggesting that I agree with all his points.
Yeah, I have read it. I think Denton was wise to abandon this argument in his followup book, Nature's Destiny.

--------------
Must... not... scratch... mosquito bite.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 15 2006,06:43   

Quote (Chris Hyland @ Mar. 14 2006,20:55)
Are you saying:

a) I am lying now, and I don't believe in evolution.

b) They are lying to me.

c) The evolutionary biologists I have spoken to belive in evolution, but the rest don't.

Ill give you a clue, it's definately not a).

I'm still not sure how any fact you've stated so far refutes evolution, could you restate the one fact you think does this, with links to the relevant evidence.

Few people lie on purpose.  I am not accusing anyone that.  But people honestly fool themselves and others all the time due to ignorance and self interest.  Most people including most biologists, except a few specialists, believe in evolution not because they have studied it carefully.  They do so because the experts told them so. The experts have a lot of self interests to defend, fame, career, funding, which may not have much to do with seeking truth.  

You want one fact that refute the theory.  You got one handy.  The protein/DNA homology fact refutes Darwinian selection theory.  To save the theory, peolpe invented the ad hoc molecular clock idea and neutral theroy.  But as I showed you before with the paper by Dr. Ayala, the neutral theory is now invalidated.  But people forgot that we still have an explanation job to do.  Presently we dont have any sound theory to explain the protein/DNA homology fact.  When the fact cannot be explained by any present theory, it is pretty clear that the fact falsifies all those theories.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 15 2006,06:49   

Quote (jeannot @ Mar. 15 2006,06:44)
Anyway, your link doesn't refer to the distance between animal, yeasts and bacteria, that you've been talking about.
Do you have a link stating that these three lineages have accumulated the same number of mutations since their divergence (naive question)?

read Michael Denton's book Evolution: a theory in crisis.

  
The Ghost of Paley



Posts: 1703
Joined: Oct. 2005

(Permalink) Posted: Mar. 15 2006,06:56   

Russell wrote:
Quote
As I said before, within limits, I buy the concept of the "molecular clock". But my big problem with your idea is that it goes way beyond those limits. The reference you gave deals only with actual cytochrome C, by definition a mitochondrial enzyme. The constraints on its evolution - its rate of accumulation of differences after lineage splits - are at least comparable. When you talk about the bacterial homologs, all bets are off.

You might find the first footnote to this essay interesting:
Quote
As an aside, Camp has misplaced the above Denton quote. To be fair, Denton made that remark in response to the controversial "molecular clock" hypothesis, which is related though distinctly different from the observation of equal molecular divergences between species. From his later comments, Camp evidently does not understand this difference. The molecular clock hypothesis is the idea that rates of evolution are constant throughout time. Rates could be extremely variable yet result in equal genetic distance between two species serendipitously. Conversely, rates could be very constant in specific lineages, yet result in unequal genetic distances (if the rates are unequal between lineages). Regardless, Denton is still confused on the subject, as he uncritically assumes that absolute background mutation rates in yeast should be "100,000 times greater than in a tree or a mammal ..." (Denton 1998, p. 291-292). This would only be true if DNA replication errors were the primary source of mutations. However, there is currently little data supporting this directly. Recent studies have indicated that other sources of mutation are more important (Huttely et al. 2000; Bohossian et al. 2000; Kumar and Subramanian 2002). All else equal, we expect that absolute background mutation rates should be equivalent between species, and that is roughly what is observed. Even if DNA replication errors are the primary cause of mutations, from the most basic conclusions of neutral theory there are other reasons (beyond the scope of this rebuttal) for why rates of protein evolution should be relatively equal between organisms with very short or very long generation times (see Ohta 1993 and references therein -- this article gives the consensus explanation which Denton claims does not exist, and it demonstrates that the evidence supports this explanation).

Shi's point may be valid, but there are better ways to establish it than relying on out-of-date books. Just my opinion, of course.

--------------
Dey can't 'andle my riddim.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,07:00   

Sorry Shi I don't have the time to read Denton's book. But I suppose his claims are based on research articles, aren't they? If you have his book, could you paste some references here?

  
Arden Chatfield



Posts: 6657
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,07:11   

Quote (shi @ Mar. 15 2006,12:43)
Few people lie on purpose.  I am not accusing anyone that.  But people honestly fool themselves and others all the time due to ignorance and self interest.  Most people including most biologists, except a few specialists, believe in evolution not because they have studied it carefully.  They do so because the experts told them so. The experts have a lot of self interests to defend, fame, career, funding, which may not have much to do with seeking truth.  

How remarkably arrogant you are to know what the motives of all scientists are, and to be so sure you know what they're thinking better than they do.

You quite sure that YOU don't "fool yourself and others all the time due to ignorance and self interest"? May I ask if you have religious beliefs that enter into this?

--------------
"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
stevestory



Posts: 10127
Joined: Oct. 2005

(Permalink) Posted: Mar. 15 2006,07:20   

Quote
Most people including most biologists, except a few specialists, believe in evolution not because they have studied it carefully.  They do so because the experts told them so.
It just doesn't get any better than this.

Except maybe at Uncommonly Dense.

   
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 15 2006,07:24   

Quote (Russell @ Mar. 15 2006,11:18)
The constraints on its evolution - its rate of accumulation of differences after lineage splits - are at least comparable. When you talk about the bacterial homologs, all bets are off.

Okay. But you still need to explain why human, plant, insects, and fish all show equal identity (equal distance) to yeast in cytoC.  The present explanation, as examplified by the Elsberry paper, is the molecular clock idea.  That is that all these vastly different species share the same constant mutation rate in cyto C.  This is pure fancy.  As I said earlier in this thread, the clock is proven invalid now.  So, essentially, we dont presently have any explanation for the equal distance phenomenon, which plainly means that the present theory is inadequate.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 15 2006,07:39   

Quote (Arden Chatfield @ Mar. 15 2006,13:11)
How remarkably arrogant you are to know what the motives of all scientists are, and to be so sure you know what they're thinking better than they do.

You quite sure that YOU don't "fool yourself and others all the time due to ignorance and self interest"? May I ask if you have religious beliefs that enter into this?

Human nature and motifs are not that tough to figure out.  When we see someone behave not the way we expected them to, we call them insane.  

For your infor, now that you asked, I am not religious in anyway.  I would rather keep an independent mind.  If faith in something we dont know, like God, is religion, it is equally a religion to have faith in random mutation as our creator, since we know absolutely nothing about how random events can create order and life.

  
Arden Chatfield



Posts: 6657
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,07:50   

Quote
Human nature and motifs are not that tough to figure out.
 

Oh really? Maybe they are, since you claim to have all scientists figured out, and somehow the scientists can't see this fact which is so self-evident to you.

Quote
When we see someone behave not the way we expected them to, we call them insane.


That is your definition of 'insane'?? Quite a revealing statement from you. (Seems to contradict your previous statement as well.) Hope you don't go into the mental health field.

Quote
If faith in something we dont know, like God, is religion, it is equally a religion to have faith in random mutation as our creator, since we know absolutely nothing about how random events can create order and life.


Now, you see, Shi, when you say tangibly false things like that and ignore people's counterevidence for your claims, it makes you look not so much like any kind of scientist, but more like another ID apologist or crackpot full of conspiracy theories about wicked cabals of dishonest scientists covering up the truth out of self-interest. If you don't want to end up like those people at UD, you do need to try harder than that.

--------------
"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
stevestory



Posts: 10127
Joined: Oct. 2005

(Permalink) Posted: Mar. 15 2006,07:56   

Shi, English isn't your first language, is it?

   
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 15 2006,08:15   

Quote (Arden Chatfield @ Mar. 15 2006,13:50)
Now, you see, Shi, when you say tangibly false things like that and ignore people's counterevidence for your claims, it makes you look not so much like any kind of scientist, but more like another ID apologist or crackpot full of conspiracy theories about wicked cabals of dishonest scientists covering up the truth out of self-interest. If you don't want to end up like those people at UD, you do need to try harder than that.

Frankly, I am not that impressed with your lot of so-called scientists here in this forum.  You understand little about your faith.  You often do and say things that could only be characterised as uncivilized.  Such as freely insulting  and calling people names like crackpots.  Such as prefer to spit rather than to speak.  

Just because there are some crazy guys associated with ID, it does not mean that all ID people are crazy.  By the same token, just because scientists have a reputation to be rational and civilized, it does not mean that all people who call themselves scientists are rational and civilized.  

Please learn to appreciate the value of all people, regardless of their faith.  You are only making yourself foolish when you abuse people.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,08:18   

Quote (shi @ Mar. 15 2006,13:24)

Quote
[quote=Russell,Mar. 15 2006,11:18]The constraints on its evolution - its rate of accumulation of differences after lineage splits - are at least comparable. When you talk about the bacterial homologs, all bets are off.

Okay. But you still need to explain why human, plant, insects, and fish all show equal identity (equal distance) to yeast in cytoC.  The present explanation, as examplified by the Elsberry paper, is the molecular clock idea.  That is that all these vastly different species share the same constant mutation rate in cyto C.  This is pure fancy.  As I said earlier in this thread, the clock is proven invalid now.  So, essentially, we dont presently have any explanation for the equal distance phenomenon, which plainly means that the present theory is inadequate.

Plants and animals show equal distance to yeasts in Cyt C? I doubt it, though I may be wrong.
And why do you think insects, fishes and human should have different distances to yeasts in this protein? What are your arguments?
If you can explain this observation with another hypothesis, can you share your insight with us? You were talking about a distance not increasing between lineages but set from the beginning. Could you be more precise?

You state that the molecular clock has been proved wrong, in a sense I agree. The molecular clock is not applicable in lots of cases (conserved domains in proteins come immediately to mind), but this doesn't imply that it's not applicable to neutral susbstitutions.

  
Arden Chatfield



Posts: 6657
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,08:21   

Quote (shi @ Mar. 15 2006,14:15)
[quote=Arden Chatfield,Mar. 15 2006,13:50]Now, you see, Shi, when you say tangibly false things like that and ignore people's counterevidence for your claims, it makes you look not so much like any kind of scientist, but more like another ID apologist or crackpot full of conspiracy theories about wicked cabals of dishonest scientists covering up the truth out of self-interest. If you don't want to end up like those people at UD, you do need to try harder than that.

Quote
Frankly, I am not that impressed with your lot of so-called scientists here in this forum.  You understand little about your faith.  You often do and say things that could only be characterised as uncivilized.  Such as freely insulting  and calling people names like crackpots.  Such as prefer to spit rather than to speak.  

Just because there are some crazy guys associated with ID, it does not mean that all ID people are crazy.  By the same token, just because scientists have a reputation to be rational and civilized, it does not mean that all people who call themselves scientists are rational and civilized.  

Please learn to appreciate the value of all people, regardless of their faith.  You are only making yourself foolish when you abuse people.

Oh, so you're a scientist? Really.

'Foolish' to me is ignoring what others tell you, and calling it 'insane' when others act in a way you don't expect. 'Insane' is blaming your frustrations on conspiracies.

As for 'civilized', it helps if you don't say one thing then deny it five minutes later.

Quote
You understand little about your faith.


'Faith'? Um, Shi, do you actually know what that word means?

--------------
"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
Henry J



Posts: 4565
Joined: Mar. 2005

(Permalink) Posted: Mar. 15 2006,08:26   

Re "explain why human, plant, insects, and fish all show equal identity (equal distance) to yeast in cytoC. "

Plant? Insects and vertebrates have had the same amount of time since divergence from fungi, but plants have had somewhat longer than that.

Henry

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,08:29   

That's what I was thinking too, Henry.

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 15 2006,08:56   

Quote
Okay. But you still need to explain why human, plant, insects, and fish all show equal identity (equal distance) to yeast in cytoC.  The present explanation, as examplified by the Elsberry paper, is the molecular clock idea.  That is that all these vastly different species share the same constant mutation rate in cyto C
Now that we're just talking about mitochondrial CytC, the picture is a little clearer. Within metazoa, say, I think the molecular clock works reasonably well. And - except for plants - we think all the creatures you mentioned diverged from yeast at the same time, no? So, isn't (approximately) equal levels of homology exactly what we'd expect?

However, Elsberry's paper suggested that the clock idea works for neutral differences. When you're talking about the difference between yeast and mammals, I would guess that the level of homology you see reflects just about the minimum you can expect for a functional CytC.

Also, there are important differences between yeast and mammals in terms of the functional demands on the molecule (range of temperature, range of oxygen tension) that may make that comparison unuseful.

--------------
Must... not... scratch... mosquito bite.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 15 2006,09:19   

Quote (Russell @ Mar. 15 2006,14:56)
And - except for plants - we think all the creatures you mentioned diverged from yeast at the same time, no? So, isn't (approximately) equal levels of homology exactly what we'd expect?

Yes, it is exactly what you would expect if the neutral clock theory is valid.  But as I have said repeatedly (but you fail to get the point repeadly), in Dr. Ayala's own words, the theory 'is untenable'.

The job now for you and all of us is how to explain the fact without assuming the fancy of an already falsified neutral clock.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,09:41   

Shi, what mechanism is supposed to prevent a comparable number of mutations in different lineages after an evolutionary branching?

(not that I'm expecting an answer, after all the unanswered questions I've asked you. :( )

  
Henry J



Posts: 4565
Joined: Mar. 2005

(Permalink) Posted: Mar. 15 2006,09:46   

Well, I can think of a couple of things that could throw off the "clock": (1) a different average mutation rate per copy per base pair, or (2) a different average number of generations per year.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 15 2006,09:50   

Quote (Henry J @ Mar. 15 2006,15:46)
Well, I can think of a couple of things that could throw off the "clock": (1) a different average mutation rate per copy per base pair, or (2) a different average number of generations per year.

Henry, thanks for answering it for me.  Sorry, jeannot, I simplly do not have time to take all the questions.  I have a day job to do.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,09:52   

Quote (Henry J @ Mar. 15 2006,15:46)
Well, I can think of a couple of things that could throw off the "clock": (1) a different average mutation rate per copy per base pair, or (2) a different average number of generations per year.

Of course Henry, but that wasn't my question. I didn't make myself clear.

Shi appears to have a problem regarding the same amount of mutations accumulating in Cyt c for different lineages.
I wanted to know why he thinks it is *impossible* in that particular case, why he thinks that some lineages *must* (not could) have accumulated more mutations than others.

Can you answer me, Shi?

BTW, your comment on Henry's last post leads me to the conclusion that you agree with darwinism. :0

  
Russell



Posts: 1082
Joined: April 2005

(Permalink) Posted: Mar. 15 2006,10:00   

Quote
Yes, it is exactly what you would expect if the neutral clock theory is valid.  But as I have said repeatedly (but you fail to get the point repeadly), in Dr. Ayala's own words, the theory 'is untenable'.
No, I didn't fail to get the point. I just don't think Ayala's objections to "the theory" apply to this kind of example. I'll have to take a look at what Ayala actually wrote - in context - but I find it hard to believe that he is discrediting the common sense aspects of evolution that apply here.

--------------
Must... not... scratch... mosquito bite.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 15 2006,10:02   

Quote (jeannot @ Mar. 15 2006,15:52)
I wanted to know why he thinks it is not possible in that particular case, why he thinks that some lineages *must* (not could) have accumulated more mutations than others.

I can give simple answers.  It is a proven fact, not an assumption.  that 'some lineages *must* (not could) have accumulated more mutations than others.'  Dont believe me? go read the paper by Ayala that I posted earlier.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,10:08   

Quote (shi @ Mar. 15 2006,16:10)
Quote
[quote=jeannot,Mar. 15 2006,15:52]I wanted to know why he thinks it is not possible in that particular case, why he thinks that some lineages *must* (not could) have accumulated more mutations than others.

I can give simple answers.  It is a proven fact, not an assumption.  that 'some lineages *must* (not could) have accumulated more mutations than others.'  Dont believe me? go read the paper by Ayala that I posted earlier.

Ok Shi, since different lineages could not possibly accumulate the same number of mutations (note that you haven't told me why), how do you explain the observed pattern in Cyt c? (a pattern that has not yet convinced me since we cannot really align human Cyt C with the bacterial equivalent)

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 15 2006,10:31   

Quote (jeannot @ Mar. 15 2006,16:08)
Ok Shi, since different lineages could not possibly accumulate the same number of mutations (note that you haven't told me why), how do you explain the pattern observed in Cyt c? (a claim that has not yet convinced me since we cannot really align human Cyt C whith the bacterial equivalent)

that is exactly what I am working on.  I hope you will do too.  If my posts here have caused people like you to know that there are  facts that refute the present theory, I would be more than satisfied.  I hope an alternative and more correct explanation of the facts will come out soon in the form of a published paper.  I do have some ideas in the broad outline that I posted earlier, which you have noticed.  But I am not ready to go into details in a forum like this.  Suffice to say, Darwinism is not the only game in town.  

Facts do not care if we are Darwin people or ID people.  If neither can explain the facts, neither is entitled to intimidate the other.  Humility is in order here, especially for the scientists since they freely call others less intelligent, crackpots etc etc.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,11:01   

Well, I'm afraid you have not convinced me (yet), Shi.

You haven't provided any clair evidence of a comparable identity between human-yeasts and bacteria (which was the ground of your argumentation). You have not adressed Russel's critiques on your argument.
And even if true, you know, Shi, that the divergence between eubacteria and mitochondria began long before the separation between fungi and animals. Not to mention the divergence between protostomia (insects, molluscs...) and deuterostomia (vertebrates...), that you were taking as example, which is even more recent. Think about it and realize that most of the difference between human-yeasts and bacteria in cyt C accumulated in the common ancestors of animals and fungi, not in their two lineages separately. Moreover, this is considering our lineage only because, we don't know (AFAIK) the amount of mutations that accumulated between the common ancestor of bacteria-mitochondria, and modern bacteria in Cyt C. Maybe it's huge, maybe not. Maybe the ancestor was closer to our mitochondria, maybe it was closer to E. coli.

You know that the molecular clock does not apply in lots of cases, therefore it is not used for phylogenetic analysis anymore. The good old UPGMA is obsolete. We don't use distance matrix to build phylogenetic trees anymore.

Then you lead me to an article (the PNAS papper I suppose) where the evolution rate of different genes is discussed. (Note that I took the time to read the summary.) So you believe it rules out the molecular clock hypothesis for all genes? The molecular clock is not a requirement of Neodarwinism anyway...
So you assert that the molecular clock hypothesis is wrong in all possible cases--without telling us why--whereas your haven't provided any coherent explanation of the pattern you described in Cyt C.

Shi, if you can produce an alternative scientific theory for evolution, we sure like to hear about it. But for know, your arguments against the current theory are rather unclear, to say the least.

(EDIT: various translation mistakes  :( )

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,11:12   

So your point is that the molecular clock hypothesis does not always hold, and some lineages diverge faster than others, how does this refute 'Darwinism' exactly. Like jeannot said, modern phylogenetic techniques do not use it, and they have turned out to be more accurate. Can I confirm that by 'Darwinism' you mean 'current evolutionary theory'?

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 15 2006,11:21   

Quote (jeannot @ Mar. 15 2006,17:01)
Well, I'm afraid you have not convinced me (yet), Shi.
But for know, your arguments against the current theory are rather unclear.

I am not bothered by that a bit.  That is why, as I said earlier, no one can make a name for himself by exposing contradictory facts to popular theories.  I am doing it here just for the fun of it, while working on my own idea.  In the absence of a replacement, most peolpe cannot see things in a clear way because they are partially blinded by the existing paradigm.  That is why few people are convinced of a need for a replacement and activly working to find one.  But when one day, the replacement is offered to the public, they would all say, gee, that is so simple, how come I did not think of that.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 15 2006,11:33   

Quote (Chris Hyland @ Mar. 15 2006,17:12)
So your point is that the molecular clock hypothesis does not always hold, and some lineages diverge faster than others, how does this refute 'Darwinism' exactly. Like jeannot said, modern phylogenetic techniques do not use it, and they have turned out to be more accurate. Can I confirm that by 'Darwinism' you mean 'current evolutionary theory'?

I am afraid you have got some major homework to do and sorry I cannot do it for you in light of time.

no matter which theory you have in mind, the current one is still a Darwinism.

  
argystokes



Posts: 766
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,11:35   

Shi slides on in here and declares:

Quote
Almost all facts that appear to falsify Darwinism have been explained away by invoking ad hoc hypothesis. I have recently found a fact that can falsify Darwinism. To my knowledge, this fact has never been previously recognized as odd by either the creationists or Darwinists. No one seem to have paid attention to it. But that is not surprising because none of the present ideas will lead people to it. I came to it from a novel perspective which I will share with the public in the future. This fact is the only one you need to use to falsify Darwinism because no Darwinists that I have met had any clue.


... and is now preaching to scientists about humility?  Holy macirony!

--------------
"Why waste time learning, when ignorance is instantaneous?" -Calvin

  
Reluctant Cannibal



Posts: 36
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,12:04   

Hello Shi,

Could you clarify for us which aspects of "Darwinism" you feel that you have falsified:

1) Common descent (universal or otherwise).
2) Random mutations (as the source of the raw material of diversity) + natural selection (as the source of adaptive change).
3) Both
4) Neither
5) Something else

A clear answer to this would be a big help in understanding your arguments.

Thanks,

RC.

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,12:04   

Quote
no matter which theory you have in mind, the current one is still a Darwinism.
I don't think I have heard Darwinism referred to as a noun before. I am just trying to get you to state which particular fact you think refutes evolution, along with evidence. Is it that some genes should have diverged to equal sequnce identity due to reaching functional limits, or that animal cytochrome c proteins are equally distant from yeast but shouldnt be due to differing mutation rates.

  
Arden Chatfield



Posts: 6657
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,12:27   

:04-->
Quote (Chris Hyland @ Mar. 15 2006,18:04)
Quote
no matter which theory you have in mind, the current one is still a Darwinism.
I don't think I have heard Darwinism referred to as a noun before. I am just trying to get you to state which particular fact you think refutes evolution, along with evidence. Is it that some genes should have diverged to equal sequnce identity due to reaching functional limits, or that animal cytochrome c proteins are equally distant from yeast but shouldnt be due to differing mutation rates.

Actually, 'Darwinism' is always a noun, it's just that Shi is mistakenly using it as a count noun rather than a mass noun, which is what it actually is. Presumably an ESL problem.

(I'll just be on my way, said the linguistics nerd...)

--------------
"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,12:33   

Apparently I need to do some english homework as well as biology homework. :p

  
Arden Chatfield



Posts: 6657
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,12:34   

Quote (shi @ Mar. 15 2006,16:31)
I hope an alternative and more correct explanation of the facts will come out soon in the form of a published paper.

What journal do you intend to publish this in?

Quote
But when one day, the replacement is offered to the public, they would all say, gee, that is so simple, how come I did not think of that.


You're certainly modest, I'll give you that. What's more, you've figured out how corrupt and dishonest most scientists are, as well. No mean feat.

Just send us the reference when it comes out.

--------------
"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 15 2006,12:42   

Quote (Reluctant Cannibal @ Mar. 15 2006,18:04)
Hello Shi,

Could you clarify for us which aspects of "Darwinism" you feel that you have falsified:

1) Common descent (universal or otherwise).
2) Random mutations (as the source of the raw material of diversity) + natural selection (as the source of adaptive change).
3) Both
4) Neither
5) Something else

A clear answer to this would be a big help in understanding your arguments.

Thanks,

RC.

The molecular homology data is claimed to support common decent.  I am Okay with that but the data did not and cannot rule out a supernatural intervention in converting chimps to humans.  I am not saying there is a supernatural, neither do I rule it out.  For the current paradigm to rule it out is baseless without any sound jusitification whatsoever.  It is purely from self interest: so government funding would not be diverged from so-called science to invesitigating possible existence of a supernatural or the cause of religion.  To rule somthing out without any justification is not in the spirit of true science or seeking truth.  

The sequence homology data contradicts the second Darwinian thesis of natural selection of random fitting mutations.  That is why there is a need for the ad hoc idea of molecular clock and neutral theory.  If you dont follow this, you need to do some homework.  Since we have yet to have a theory to replace the clock idea, to make sense of the sequence homology data within the paradigm of Darwinism absolutely requires the neutral clock idea to be true.  But the clock idea has now been proven wrong and untenable.  So here you go, without the clock, no one has any clue to explain the homology data.  So the falsification of Darwin's second thesis stays well established.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 15 2006,13:14   

Quote (Arden Chatfield @ Mar. 15 2006,18:34)
you've figured out how corrupt and dishonest most scientists are, as well. No mean feat.

Please do not misrepresent me.  To make the record clear, I believe most people (scientist, ID people, religious people, Darwin people) are honest human beings.  But all it takes is one single individual to cause the majority of the society to think in one way or the other.  If that individual is an honest truth seeker, we have a major advance in knowledge, as illustrated by countless individuals in history.  On the other hand, if we have an influential individual that is honestly fooling himself and the society, we will have the majority of the society repeating together with him what he is telling us.  In such a case, I would not accuse the majority of people being dishonest.  Rather, I would call that influential individual a fool if he is honest and a liar if he is dishonest.  

To give you an example, most people here in the forum honestly believe in evolution without knowing much details about it or its problems.  That is abundantly clear based on what I read here.  Do you think they come to their conclusion by first hand research like Darwin did?  Of course not.  They mostly got it second hand through things like textbooks.  All you need is one dishonest textbook author to make millions of people looking like dishonest liars or honest fools.

  
Arden Chatfield



Posts: 6657
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,13:57   

Quote
Please do not misrepresent me.  To make the record clear, I believe most people (scientist, ID people, religious people, Darwin people) are honest human beings.  But all it takes is one single individual to cause the majority of the society to think in one way or the other.  If that individual is an honest truth seeker, we have a major advance in knowledge, as illustrated by countless individuals in history.  On the other hand, if we have an influential individual that is honestly fooling himself and the society, we will have the majority of the society repeating together with him what he is telling us.  In such a case, I would not accuse the majority of people being dishonest.  Rather, I would call that influential individual a fool if he is honest and a liar if he is dishonest.  

To give you an example, most people here in the forum honestly believe in evolution without knowing much details about it or its problems.  That is abundantly clear based on what I read here.  Do you think they come to their conclusion by first hand research like Darwin did?  Of course not.  They mostly got it second hand through things like textbooks.  All you need is one dishonest textbook author to make millions of people looking like dishonest liars or honest fools.


That doesn't really jibe with what you said earlier:

Quote
Few people lie on purpose.  I am not accusing anyone that.  But people honestly fool themselves and others all the time due to ignorance and self interest.  Most people including most biologists, except a few specialists, believe in evolution not because they have studied it carefully.  They do so because the experts told them so. The experts have a lot of self interests to defend, fame, career, funding, which may not have much to do with seeking truth.  


This makes it sound like you're convinced most biologists -- not just people on this board, but biologists -- are ignorant and only believe in evolution because of peer pressure; and, that the rest of them are a handful of phony experts who only believe in evolution because it helps their career -- essentially, people who are dishonest.

In other words, you are saying only stupid people and a small handful of dishonest people disagree with you. That certainly no one honest and intelligent could really disgree with you.

I personally believe this is a quite egomaniacal position for you to take (tho it's quite common among intelligent design types), but let me take a different tack: what is your evidence for this conspiracy? Thousands of biologists, actual working scientists, claim to take evolution as a given in their work. What is your evidence that these people are simply ignorant, or lying to protect their jobs? It seems to me that burden of proof is on YOU to show us how terribly smart you are and how terribly foolish everyone else is.

Like I said, compete like everyone else and get your work published in a real journal. Compete in the meritocracy, and quit complaining about conspiracies. Because until then, what I'm hearing sounds an awful lot like one of those angry cranks who's convinced the scientific establishment is corrupt and wrong about everything, and who knows better than all of them, yet who dodges all the difficult questions anyone asks. ID has too many of them as it is.

--------------
"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
argystokes



Posts: 766
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,14:05   

Quote (shi @ Mar. 15 2006,19:14)

Please do not misrepresent me.  To make the record clear, I believe most people (scientist, ID people, religious people, Darwin people) are honest human beings.  But all it takes is one single individual to cause the majority of the society to think in one way or the other.  If that individual is an honest truth seeker, we have a major advance in knowledge, as illustrated by countless individuals in history.  On the other hand, if we have an influential individual that is honestly fooling himself and the society, we will have the majority of the society repeating together with him what he is telling us.  In such a case, I would not accuse the majority of people being dishonest.  Rather, I would call that influential individual a fool if he is honest and a liar if he is dishonest.


It's really too bad that science doesn't have some sort of method of review by scientific peers to make sure this doesn't happen.

Also, for what reason would you doubt the common ancestry of chimps and hunams?  The molecular and paleontological evidence is certainly striking.  What other origin for chimps would you suggest, if they are not closely related to the other great apes such as humans and gorillas?

--------------
"Why waste time learning, when ignorance is instantaneous?" -Calvin

  
stevestory



Posts: 10127
Joined: Oct. 2005

(Permalink) Posted: Mar. 15 2006,14:06   

Shi, which Asian country are you from?

   
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 15 2006,14:31   

Arden,

All I am saying is that most people including most biologists believe in evolution in a casual fashion.  Whatever the specialists tell them, they would respond, okay, I am with you.  It has got nothing to do with their life or work. They dont conspire anything except to making an honest living. If evolution theory claim its correctness by to touting its number of believers among scientists, it is not a sign of strength.  A theory is not won by popular votes. Have not we learned anything from history?  It takes only one individual to overthrown a popular theory.

It is no secret that religion and evolution theory are competing for public attetion and funds.  Without the threat of religion, the holes of evolution theory will be much more openly discussed.  This is unfortunate but that is okay.  And I am not worried about that at all.  I am not accusing anyone who disagrees with me of anything.  Truth will come out regardless, given enough time.  In the mean time, the best advice for you is to take an open mind and enjoy the ride.

  
Arden Chatfield



Posts: 6657
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,15:01   

Quote (shi @ Mar. 15 2006,20:31)
All I am saying is that most people including most biologists believe in evolution in a casual fashion.  Whatever the specialists tell them, they would respond, okay, I am with you.  It has got nothing to do with their life or work. They dont conspire anything except to making an honest living.

May I ask how you know that biologists have such a shallow understanding of evolution?

--------------
"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
Henry J



Posts: 4565
Joined: Mar. 2005

(Permalink) Posted: Mar. 15 2006,16:44   

Re "Do you think they come to their conclusion by first hand research like Darwin did?  Of course not."

Certainly amateurs aren't likely to take a voyage to the Galapagos. My acceptance of the theory comes largely from the lack of convincing arguments presented against it, even from the people who claim that such arguments exist.

For one thing, a counter argument needs to be aimed at a particular premise of the theory, not at something vaguely called "Darwinism". Does the proposed argument try to show that some species don't have ancestors? That two species with lots of common features came from lines that had separate abiogenesis events? Or does it just question details about some specific lineages?

Exactly which premise of evolution theory is supposed to be impacted by this molecular clock argument? (Btw, isn't the molecular clock concept intended for neutral dna anyway? A critical gene is hardly neutral territory.)

Re "A theory is not won by popular votes."

Course not - its "won" by whether the experts in the relevant fields regard it as supported by the evidence, not by whether or not they like it or its conclusions, which is generally what a popularity contest would try to measure.

Re "All you need is one dishonest textbook author to make millions of people looking like dishonest liars or honest fools."

Wow - could somebody use that as a straight line if they wanted to...

Henry

  
edmund



Posts: 37
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,18:02   

Quote
The sequence homology data contradicts the second Darwinian thesis of natural selection of random fitting mutations.  That is why there is a need for the ad hoc idea of molecular clock and neutral theory.  If you dont follow this, you need to do some homework.  Since we have yet to have a theory to replace the clock idea, to make sense of the sequence homology data within the paradigm of Darwinism absolutely requires the neutral clock idea to be true.  But the clock idea has now been proven wrong and untenable.  So here you go, without the clock, no one has any clue to explain the homology data.  So the falsification of Darwin's second thesis stays well established.

Hi Shi,

I don't think you realize this, but the things that you're writing make you sound very arrogant. Some of the folks you're talking to are professional biologists, and they know a *lot* about the "molecular clock" and neutral theory.

For example, you keep insisting that the molecular clock is "untenable". In support of this claim-- and it's not a small claim-- you've presented a single quote from a single article from BioEssays.

On the strength of this one quote, as far as I can tell, you are insisting that the idea of the molecular clock is completely empty and valueless. I can tell you that no working biologists agree with your interpretation. The molecular clock is not universal-- different genes and different lineages evolve at different rates. We do not understand a lot of the reasons for the variations. But the phenomenon of the "molecular clock" is real, and reliable, in many contexts. You can find dozens or hundreds of articles on the topic in the professional literature, if you aren't averse to "doing some homework", as you put it.

Neither the neutral theory nor the molecular clock are "ad hoc" hypotheses, as you are claiming. Both are phenomena which we can study in real time in evolving populations of bacteria or viruses in culture. For both, there are instances where they do not apply, but both concepts are well-supported by data.

When you tell professionals that you know more about their field of study than they do, you are insulting them, whether you intend to or not. You also make yourself look bad. If you have the "humility" that you are accusing us of lacking, please try listening harder to what we're saying. There are some very useful suggestions being made, and sincere questions being asked, that you're overlooking.

  
Reluctant Cannibal



Posts: 36
Joined: Jan. 2006

(Permalink) Posted: Mar. 15 2006,22:49   

Quote

The sequence homology data contradicts the second Darwinian thesis of natural selection of random fitting mutations.  That is why there is a need for the ad hoc idea of molecular clock and neutral theory.  If you dont follow this, you need to do some homework.  Since we have yet to have a theory to replace the clock idea, to make sense of the sequence homology data within the paradigm of Darwinism absolutely requires the neutral clock idea to be true.  But the clock idea has now been proven wrong and untenable.  So here you go, without the clock, no one has any clue to explain the homology data.  So the falsification of Darwin's second thesis stays well established.


Hello Shi,

Perhaps I do "need to do some homework" (like everyone else here, and perhaps the biological science community in general). Or perhaps you have not yet managed to articulate precisely what your thesis, and the evidence for it, is. Or perhaps you are simply wrong, but have enough cunning to avoid committing yourself to any concrete claims.

So I'll take your response to mean that you do accept common descent (with the reservation that magic might have been involved, in the case of humans and chimps).

What is missing from your thesis is any explanation of why "The sequence homology data contradicts the second Darwinian thesis of natural selection of random fitting mutations." The molecular clock and neutral theory are simply consequences of the way that genomes work. The molecular clock idea does not explain the data, it is a tool for inferring absolute and relative ages of branching within phylogenies. It is one thing to say that the molecular clock is inaccurate (which it is). It is quite another thing to say that the phenomenon which it measures does not occur. That is the only way I can interpret this: "... to make sense of the sequence homology data within the paradigm of Darwinism absolutely requires the neutral clock idea to be true.".

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 16 2006,07:55   

Quote (Reluctant Cannibal @ Mar. 16 2006,04:49)
What is missing from your thesis is any explanation of why "The sequence homology data contradicts the second Darwinian thesis of natural selection of random fitting mutations."

I thought that anyone who is more than a casual believer would know this but I was wrong.  Ardon, it just proves my point that most biologists know very little about evolution, especially its problems.  When you only know what the specialists allowed you to know, you are a casual believer.  The limited selective presentation of all relevant facts is shamelessly done in the name of not to confuse the non-specialists.  

I think Edmond, russell, jennot may be able to answer your question.

Let me put the answer in this way.  Before people know any sequence data in the 1940s, do you know what was the experts' expectation or prediction of what the sequence data would show?  Are the data we today have confirmed their prediction or falsified it?  If the data falsified their prediction, I hope you would agree that it also logically falsified the theory that is the basis for their prediction.  Well the fact is that the data falsified their prediction.  But somehow the neoDarwinian theory stays unscrached to this day.  Odd?  It just shows that in the absence of a better replacement, people will do all kinds of creative things, like the clock, to make do with their emotionally attached baby.  

Well to save you the trouble to dig into history books, here is what the experts' prediction and how today's experts views their prediction.  I cite from a paper by the new age evodevo expert Sean Carroll, <http://www.naturalhistorymag.com/).>http://www.naturalhistorymag.com/). see Sean Carroll’s article, “The Origins of Form,”

In this paper Carroll says:  'But Mayr's view is incorrect.  The architects of the modern synthesis expected the genomes of vastly different species to differ vastly.'  

I hope you know who Mayr is and what is the rational for his expectation.  If you dont, some experts here in this forum should have no trouble to help with that.  Indeed, the fact is that vastly different species shares nearly identical DNA sequence whereas similar species differs vastly in DNA sequences.  Thus, a major prediction of the survival of fittest selection of random mutations is proven false by facts.  According to the selection theory, a change in genotypes or mutations would not be fixed in a population without selection.  When two species are similar in phenotypes, they must have experienced similar selections and therefore should show similar sequences.  This is simply what the second thesis of Darwinism would predict.  I have said too much.

  
stevestory



Posts: 10127
Joined: Oct. 2005

(Permalink) Posted: Mar. 16 2006,07:58   

Quote
new age evodevo expert Sean Carroll
LOL

   
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 16 2006,08:37   

Quote (edmund @ Mar. 16 2006,00:02)
I don't think you realize this, but the things that you're writing make you sound very arrogant. Some of the folks you're talking to are professional biologists, and they know a *lot* about the "molecular clock" and neutral theory.

For example, you keep insisting that the molecular clock is "untenable". In support of this claim-- and it's not a small claim-- you've presented a single quote from a single article from BioEssays.

On the strength of this one quote, as far as I can tell, you are insisting that the idea of the molecular clock is completely empty and valueless. I can tell you that no working biologists agree with your interpretation. The molecular clock is not universal-- different genes and different lineages evolve at different rates. We do not understand a lot of the reasons for the variations. But the phenomenon of the "molecular clock" is real, and reliable, in many contexts.

Neither the neutral theory nor the molecular clock are "ad hoc" hypotheses, as you are claiming. Both are phenomena which we can study in real time in evolving populations of bacteria or viruses in culture. For both, there are instances where they do not apply, but both concepts are well-supported by data.

When you tell professionals that you know more about their field of study than they do, you are insulting them, whether you intend to or not. You also make yourself look bad. If you have the "humility" that you are accusing us of lacking, please try listening harder to what we're saying. There are some very useful suggestions being made, and sincere questions being asked, that you're overlooking.

Edmond,  

Your point is well taken.  I have no intention to be arrogant or insulting.  I may commit the sin without realizing it in my single-minded zeal to express my point.  But at least I have not freely called anyone names like some so-called scientists here in PT often do to anyone who disagrees with them like the ID people.  But if you look at things from my perspective, which may be totally different from everyone else, you may realize that my perspective requires the clock to be a sham, regardless how little I know about the clock.  That may look insulting to the clock specialists but it really is not.  It is a matter of perspectives.  You observe the mountain from the east side and I from the west side and we can see very different things.  If your view from your side represents more truth about the mountain than the view from my side, you have my congratulations.  

From my perspective, the current situation with the clock idea is like the following.  Among thousands of genes, people found two types of genes.  One type turns out to be a good clock and the other not so good.  In fact, the vast majority is not good.  This plainly means to them that the clock idea works for some genes while not for others.  It never occurs to them that maybe the clock is a 'mirage'.  Even if the clock idea is completely false, we would still find, by chance, that some genes may behave like a clock.  This simply means that the fact of some good clock genes is no evidence at all that there is a clock.  There may exist a totally different theory to account for the behaviors of all genes.  In that new perspective, some genes may still appear to be a clock but that is really a mirage.

There are much more evidence for suspecting the clock idea to be a sham.  One only needs to observe how absurd the field has become in terms of the many different versions of the clock, each with its complicated mathematical formulas.  It has simply become impossible to follow for a non-specialist.  When a field becomes that complicated, it is a sign of weakness not strength.  It is time for a new perspective.  Beauty is simplicity and truth.  When a field lacks beauty and simplicity, it most likely has very little truth to it.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 16 2006,09:35   

:01-->
Quote (Arden Chatfield @ Mar. 15 2006,21:01)
[quote=shi,Mar. 15 2006,20:31]All I am saying is that most people including most biologists believe in evolution in a casual fashion.  Whatever the specialists tell them, they would respond, okay, I am with you.  It has got nothing to do with their life or work. They dont conspire anything except to making an honest living.

May I ask how you know that biologists have such a shallow understanding of evolution?[/quote]
I know because it is plain clear that the specialists have not taught the non-specialists (including most biologists and me included) all the things they know.  Their presentation of their theory is highly selective, omitting most contradictory facts shamelessly all in the name of not confusing the non-specialists.

To take just one example.  The sequence homology data is touted in most textbooks as evidence for common decent.  The same data however has two presentations.  One is that human gene is nearly identical to chimps, less identical to monkeys, still less to rats, still less to frogs, to fish etc and least similar to bacteria.  Now this is what is being touted by the textbooks to support common decent.  This is fine.  But have you wondered why no textbook is saying anything about the second thesis of Darwin being also vindicated by the sequence data.  The second presentation of the same data set is the molecular equidistance phenomenon: human, rat, frogs, and fish are all equally related to yeast.  You will not find this presentation in any mainstream textbooks.  Why the omission?  I have studied biology for 25 years and know nothing about this equidistance until I recently discovered it independently.  Out of curiosity, I asked many people including many biologists about the equidistance but none knows anything about it.  

You can do the test your self.  Ask people to answer a simple question such as: given orangutan being the common ancestor of both human and chimp, which is more related to orangutan, human or chimp, or are they equally related?  Most people would say chimp is more related to orangutan because they look more similar.  But they are wrong, human and chimp are equally related to orangutan.  You can also ask them, is frog more related to fish than human is?  They would say yes and be wrong.  Human and frog are equally related to fish.

If you do such a test, I believe 99% of non-specialists would fail the test.  It is also clear from this thread.  People like Russell seems to know a lot about evolution and is clearly a biologist but in fact knows little about the equidistance phenomenon.  

This is what I mean that most biologists are casual believers of evolution (including myself for 25 years before I decided to truly know something about evolution).  They only know the story that is selectively presented to them by the specialists.  To truly know something, you need to know both the plus and minus side of it.  You need to know that while the specialists are touting the clock in books for the layman, the same specialists are calling the clock a mirage in specialist journals.

  
Reluctant Cannibal



Posts: 36
Joined: Jan. 2006

(Permalink) Posted: Mar. 16 2006,09:40   

Quote

Shi:

ME: What is missing from your thesis is any explanation of why "The sequence homology data contradicts the second Darwinian thesis of natural selection of random fitting mutations."

I thought that anyone who is more than a casual believer would know this but I was wrong.


There you go again,Shi. I can't "know" something that is clearly false. If I were to tell you that there is a hollow world full of dinosaurs inside this one, and that you didn't know this because your knowledge of geophysics was lacking, you would (I hope) want a detailed explanation.

Quote

Shi:
When you only know what the specialists allowed you to know, you are a casual believer.  The limited selective presentation of all relevant facts is shamelessly done in the name of not to confuse the non-specialists.  

More dark hints about the conspiracy of the scientific establishment against the gullible public, eh?

Quote

Shi:
I hope you know who Mayr is and what is the rational for his expectation.  If you dont,some experts here in this forum should have no trouble to help with that.

Of course I've heard of Mayr, please keep the condescension down to a dull roar. Carroll's comment goes to the state of understanding of how the genome worked at the time. Given our current understanding of genetic processes, can you demonstrate your claim with mathematics and data, rather than selective quoting from the literature?

Quote

Shi:
Indeed, the fact is that vastly different species shares nearly identical DNA sequence whereas similar species differs vastly in DNA sequences.


Oh yeah? This looks like a pretty strong claim at first sight, but it's not very meaningful without a clear way to quantify both genetic and phenotypic similarity. Sequence matching and cladistic analysis come to mind. Can you name two living species which are "vastly different" phenotypically, and "nearly identical" genetically?

My apologies for the dodgy quoting. Could somebody spare me a clue?

  
Henry J



Posts: 4565
Joined: Mar. 2005

(Permalink) Posted: Mar. 16 2006,09:49   

Re "The second presentation of the same data set is the molecular equidistance phenomenon: human, rat, frogs, and fish are all equally related to yeast. "

What about that point that somebody made upthread - vertebrates diverged from yeast long before they diverged from each other. So most of that "distance" may have come from a time when "vertebrate" was one evolving species.

Henry

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 16 2006,10:11   

Quote (shi @ Mar. 16 2006,15:35)
... 
But have you wondered why no textbook is saying anything about the second thesis of Darwin being also vindicated by the sequence data.  The second presentation of the same data set is the molecular equidistance phenomenon: human, rat, frogs, and fish are all equally related to yeast.  You will not find this presentation in any mainstream textbooks.  

You can do the test your self.  Ask people to answer a simple question such as: given orangutan being the common ancestor of both human and chimp, which is more related to orangutan, human or chimp, or are they equally related?  Most people would say chimp is more related to orangutan because they look more similar.  But they are wrong, human and chimp are equally related to orangutan.  You can also ask them, is frog more related to fish than human is?  They would say yes and be wrong.  Human and frog are equally related to fish.

If you do such a test, I believe 99% of non-specialists would fail the test.  It is also clear from this thread.  People like Russell seems to know a lot about evolution and is clearly a biologist but in fact knows little about the equidistance phenomenon.  

This is what I mean that most biologists are casual believers of evolution (including myself for 25 years before I decided to truly know something about evolution).  They only know the story that is selectively presented to them by the specialists.  To truly know something, you need to know both the plus and minus side of it.  You need to know that while the specialists are touting the clock in books for the layman, the same specialists are calling the clock a mirage in specialist journals.

(Shi, we told you that distance is not used to infer phylogenies anymore.)

Of course human, rats, frogs, and fishes are all equally related to yeasts, these animals all have the same common ancestor with fungi. You find it in any book about phylogeny.

And your last examples are just wrong. Orangutan is the ancestor of nothing, human and chimp are not equally related to orangutan (in fact, chimps are closer to us than they are to gorillas). You are wrong again regarding frogs and fishes.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 16 2006,10:16   

Quote (Reluctant Cannibal @ Mar. 16 2006,15:40)
Can you name two living species which are "vastly different" phenotypically, and "nearly identical" genetically?

I have given my best try to explain things to you.  And if you don't get it, I doubt you ever will.  I leave your question for others on this thread to deal.  (hint, if you think you are just a regular monkey, no one will blame you if you only mean yourself but not other intelligent homo sapiens)

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 16 2006,10:21   

Quote (jeannot @ Mar. 16 2006,16:11)
And your last examples are just wrong. Orangutan is the ancestor of nothing, human and chimp are not equally related to orangutan (in fact, chimps are closer to us than they are to gorillas). You are wrong again regarding frogs and fishes.

From your earlier posts, you know little about the equidistance before I made an issue of it here.  Now all of sudden you become an expert and is accusing the teacher being wrong.  I have lost patience with you.  Suffice to say, you have more to learn with the facts.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 16 2006,10:21   

Quote (Reluctant Cannibal @ Mar. 16 2006,15:40)
Quote

Shi:
Indeed, the fact is that vastly different species shares nearly identical DNA sequence whereas similar species differs vastly in DNA sequences.


Oh yeah? This looks like a pretty strong claim at first sight, but it's not very meaningful without a clear way to quantify both genetic and phenotypic similarity. Sequence matching and cladistic analysis come to mind. Can you name two living species which are "vastly different" phenotypically, and "nearly identical" genetically?

My apologies for the dodgy quoting. Could somebody spare me a clue?

Well, his claim could be true, since most genes used in phylogenetic studies don't control morphology.
Anyway, I don't see how it contradicts the theory of evolution.
It would tend to rule out the current models of gene expression (traduction in proteins and so on). Thus it could as well contradict common design or prescribed evolution.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 16 2006,10:29   

Quote (shi @ Mar. 16 2006,16:21)
Quote
[quote=jeannot,Mar. 16 2006,16:11]And your last examples are just wrong. Orangutan is the ancestor of nothing, human and chimp are not equally related to orangutan (in fact, chimps are closer to us than they are to gorillas). You are wrong again regarding frogs and fishes.

From your earlier posts, you know little about the equidistance before I made an issue of it here.  Now all of sudden you become an expert and is accusing the teacher being wrong.  I have lost patience with you.  Suffice to say, you have more to learn with the facts.

Oops, I didn't read your post correclty. Yes human and chimps are equally related to orangutan (but chimps are closer to us of course). I thought you were saying that the distance between chimps, orangutan and humans was the same. Strange because I didn't make this mistake when I read your claim about yeast and animals. :0 (keep in mind that English is not my first language.)

However, I don't understand what's your problem with that.

PS: You're still wrong on orangutan being the common ancestor of humans and chimps. Where did you get that from? Or was it just an random example you gave to prove your point?

  
edmund



Posts: 37
Joined: Jan. 2006

(Permalink) Posted: Mar. 16 2006,10:32   

Quote
It never occurs to them that maybe the clock is a 'mirage'.  Even if the clock idea is completely false, we would still find, by chance, that some genes may behave like a clock.

No, we would not. If the clock idea is completely false, the odds of getting a "clocklike" pattern are essentially zero.

Quote
Before people know any sequence data in the 1940s, do you know what was the experts' expectation or prediction of what the sequence data would show?  Are the data we today have confirmed their prediction or falsified it?

Hypothesis testing in a complex field like biology is not as straightforward as you think it is. Before genetic sequencing, biologists thought that all DNA changes would have an effect on phenotype, and that DNA sequences would therefore be largely the outcome of selection. When DNA sequences did not match their expectations, there were multiple possible explanations. Here are two of them:

1) They were wrong about the evolutionary history of organisms on Earth, or:

2) DNA sequences were not driven only by selection.

By now, we have abundant evidence that most DNA does not affect phenotype and is therefore free to drift under a *neutral* model rather than a *selectionist* model-- in other words, we know that 2) is correct.

If you recognize that most changes at the DNA level are neutral, then the patterns of similarity and difference among living organisms do not contradict what we thought we knew about the evolutionary history of organisms. Instead, those patterns confirm what we thought we knew.

Quote
But if you look at things from my perspective, which may be totally different from everyone else, you may realize that my perspective requires the clock to be a sham, regardless how little I know about the clock.  That may look insulting to the clock specialists but it really is not.  It is a matter of perspectives.

But science is not a matter of perspectives. That's why it's reliable. You have a right to your own opinion, as the saying goes, but you don't have a right to your own facts. The clock phenomenon either exists or it does not exist; it does not depend on your perspective.

Quote
The same data however has two presentations.  One is that human gene is nearly identical to chimps, less identical to monkeys, still less to rats, still less to frogs, to fish etc and least similar to bacteria.... The second presentation of the same data set is the molecular equidistance phenomenon: human, rat, frogs, and fish are all equally related to yeast.  You will not find this presentation in any mainstream textbooks.

This is incorrect. I have taught students about the molecular clock and about molecular equidistance at the undergraduate level, and I'm holding an undergraduate text-- a mainstream text, Futuyma's "Evolutionary Biology" (3rd edition)-- that explains the phenomenon as well as discussing when the "molecular clock" is and is not useful.

Quote
You need to know that while the specialists are touting the clock in books for the layman, the same specialists are calling the clock a mirage in specialist journals.

Shi, several people have asked you where you are getting this information. You need to answer those questions. What "specialist journals" have you looked at? How many articles have you read?

To understand why people are so frustrated with you, Shi, consider this: there are lots of people out there who come onto Panda's Thumb insisting that they have some special insight into biology despite the fact that they have not read more than a handful of articles by specialists. Unless you can demonstrate that you've studied the molecular clock and molecular equidistance in detail, why should we assume that you know more than any of these other ID folks? In other words: if you want our respect, prove to us that you've done your homework!

  
Reluctant Cannibal



Posts: 36
Joined: Jan. 2006

(Permalink) Posted: Mar. 16 2006,11:08   

Quote (Shi @ Mar. 16 2006,16:16)

Me: Can you name two living species which are "vastly different" phenotypically, and "nearly identical" genetically?
I have given my best try to explain things to you.  And if you don't get it, I doubt you ever will.  I leave your question for others on this thread to deal.  (hint, if you think you are just a regular monkey, no one will blame you if you only mean yourself but not other intelligent homo sapiens)

I didn't think you would be able to substantiate this absurd claim. Do you really expect anyone else to answer the question when you are the only person who believes it?

Anyway, enough of the technical stuff -- we are clearly not going to have a meeting of minds. I would rather hear more of your views about the pro-evolution conspiracy.

Basically, you have a select cadre of leading scientists who know the truth and actively suppress it. Then you have a second tier of postgrad students who believe the dogma, or doubt it but want a piece of that lucrative government funding, and fear for their careers.

Then right at the bottom, you have poor deluded laymen such as myself, trapped in the web of deception.

Is that about right? Could you supply more detail? Maybe suggest some names of the inner circle?

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 16 2006,11:24   

Edmund,

You have no basis for asserting the odds of something you know nothing to be zero.  Do you suppose the odds of a God is also zero?  If you do, that is just your assumption, not science or mathematics.  

Fact is fact, theory or interpretation of facts is not fact but is perspectives.  A gene that shows diversity pattern that correlated with lineage history is a fact.  But the theory, the clock, is not a fact.  There are other theories or perspectives that could also account for the same clock-looking fact.  The truth that you only know about clock but nothing else is no basis for asserting the clock to be the only perspective to explain the fact.  Most scientific theories are provisionally ones, ready to be replaced or modified by future ones.  They are not reliable in many ways.  We have been fooled by them countless times in history.  Remember ether?  

I have looked through 5 major biology textbooks and also the booklet by NAS Science and Creationism that is supposed to be a guideline for how to teach evolution.  None of these books teach the molecular equidistance, although all mentioned the clocks.  If you think the Futuyama book teaches the equidistance, quote me a few sentences from the book so I can be convinced.  

I think I have posted a paper called 'molecular clock mirages'.  If you somehow missed it, it is easy enough to go back find it.

The mentality of your so-called scientists is incorrect.  I am not here to convince anyone I know more about their subject than they do.  You seem to think that if someone does not know as much as a specialist about the specialist's subject, that someone is not in a position to say anything about the subject.  I am sure you know that Einstein does not know as much as about the ether subject than the creators of the ether idea.  But nonetheless he destroyed that idea.  You see, knowing too much about a flawed theory could only hinder creative imagination.  As Einstein put it, imagination is more important than knowledge.  For your own good, please refrain from accusing ID people not knowing enough about your so-called evolution theory-fact.  Yours is one provisional perspective and ID is another one.  The jury is still out and we have 4 billion years to go to see who laughs the last.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 16 2006,11:28   

If I understand correctly, Shi, we have the same problem.
You regret that a simplistic vision of evolution is still dominant among believers in the theory, even biologists. Most of them only see living beings as more 'primitive' or more 'evolved', which leads them to wrong conceptions: the primitive should be closely related to each others, and the evolved 'advanced' species should belong to different groups.
Well, it's our job to change this old vision of life, but we'll rely on the current theory of evolution for that.

  
Arden Chatfield



Posts: 6657
Joined: Jan. 2006

(Permalink) Posted: Mar. 16 2006,11:30   

Uh oh. Shi's comparing himself to Einstein. Not a good sign.

I suspect Shi has no proof of this grand conspiracy, but he knows it must be real, because this could be the only reason why scientists disagree with him.

Go ahead, shake the world of biology down to its foundations, Shi! Get yourself published in a real journal and blow us all away! Show us all how dimwitted we really are!

--------------
"Rich is just mad because he thought all titties had fur on them until last week when a shorn transvestite ruined his childhood dreams by jumping out of a spider man cake and man boobing him in the face lips." - Erasmus

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 16 2006,11:46   

Quote (Reluctant Cannibal @ Mar. 16 2006,17:08)
Anyway, enough of the technical stuff -- we are clearly not going to have a meeting of minds. I would rather hear more of your views about the pro-evolution conspiracy.

Sir Fred Hoyle puts it, 'It is a mistake to suppose that science is an unswerving pursuit of objective truth.  Partially it is, but only to the extent that the truth does not turn out to contradict what has already been taught in the educational process'.  

The lawyer Edward Sisson put it, 'acceptance by the public of the truth of unintelligent evolution gives to scientists a kind of power, prestige, and income'.

I am not interested in conspiracy as much as you.  Even if there is , it cannot be changed.  So why bother.  Better focus your energy to be creative.  As Kuhn noted, science evolves in paradigms.  It is only natural for leaders of an existing paradigm to resist the force of a new paradigm. If you want to label that conspiracy, then it is.  But really it is just human nature and it is just how things work.  As all things, it has its merits as well as its flaws.  But no matter, paradigms will keep coming and going.  Evolution happens, and no one or any group of individuals can alter the path of evolution, not for long.

  
Seven Popes



Posts: 190
Joined: Mar. 2006

(Permalink) Posted: Mar. 16 2006,11:53   

Shi:
Quote
The mentality of your so-called scientists is incorrect.  I am not here to convince anyone I know more about their subject than they do.  You seem to think that if someone does not know as much as a specialist about the specialist's subject, that someone is not in a position to say anything about the subject.

My little brother liked to hover behind me while I fixed his motorcycle.  He constantly pestered me, asking me if I had tourqed everything down tightly enough, if I was sure I had adjusted everything correctly, if i had sealed up everything carefully.  It's not that I had made any mistakes, He was just worried.  I got tired of all the unwarranted second guessing, so one day when his bike needed a repair, I told him "since you're the expert, you fix it".
  Shi, since you're the expert, you prove it.

P.S.
Quote
The mentality of your so-called scientists is incorrect
So called?  why do you say this?

--------------
Cave ab homine unius libri - Beware of anyone who has just one book.

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: Mar. 16 2006,11:58   

Quote
The truth that you only know about clock but nothing else is no basis for asserting the clock to be the only perspective to explain the fact.
It has been pointed outto you that scientists are well aware with the problems with the molecular clock theory, and as edmund points out, this is taught to undergraduates(at least in my university anyway), and modern phylogentic methods do not use it. The paper you mention has been cited many times and is in a general biology journal so you can hardly say evolutionary biologists hide the truth from the rest of us. I am not sure that the difference between genotypes and phenotypes falsifies evolution: organisms with similar phenotypes but different genotypes are the result of neutral non-selectable mutations, and similar genotypes but very different phenotypes are the result of the effects we are starting to learn about from fields such as evodevo. I dont see how these are ad-hoc hypothesis, yes many people have been wrong about things over the years, but please tell us how any of this refutes unguided common descent (my ad-hoc definition of Darwinism).

  
Reluctant Cannibal



Posts: 36
Joined: Jan. 2006

(Permalink) Posted: Mar. 16 2006,12:47   

Quote (jeannot @ Mar. 16 2006,15:40)

Well, his claim could be true, since most genes used in phylogenetic studies don't control morphology.
Anyway, I don't see how it contradicts the theory of evolution.
It would tend to rule out the current models of gene expression (traduction in proteins and so on). Thus it could as well contradict common design or prescribed evolution.

Of course gross phenotype differences may arise from a tiny number of genetic differences -- it really comes down to how one defines "vastly different". I was trying to pick my words carefully (which is why I mentioned cladistics), but I had in mind differences of the kind that led biologists to assign animals to different taxonomic categories before the modern synthesis.

But this is an interesting point, because I think it is at the root of Shi's misconception. He thinks that it does contradict evolution, and that is why he objects so strongly to the actual explanations.

  
edmund



Posts: 37
Joined: Jan. 2006

(Permalink) Posted: Mar. 16 2006,13:46   

Quote
You have no basis for asserting the odds of something you know nothing to be zero.

molecular clock
Actually, it's possible to calculate the odds quite precisely. If there is no inherent correlation between molecular divergence between two species and the time since they split (as inferred from the fossil record), you'd expect no pattern in the graph I linked to above. I don't have the raw data, but I'd guess that the p-value associated with that graph is less than 0.0001. That's the odds of that occurring "by chance", as you put it. Essentially zero.

Quote
There are other theories or perspectives that could also account for the same clock-looking fact.  The truth that you only know about clock but nothing else is no basis for asserting the clock to be the only perspective to explain the fact.

Perhaps, but "chance" isn't one of them. Nor have I heard of any other theories to explain that pattern that are remotely convincing. Evidence of roughly "clocklike" divergence between taxa has piled up to the point where it's no longer realistic, in my opinion, to expect the idea of the "molecular clock" to be completely overturned. Will it be modified? Of course. But you don't have any reason to think that there will even be any major modifications. At least, if you do, you haven't presented them yet.

Quote
If you think the Futuyama book teaches the equidistance, quote me a few sentences from the book so I can be convinced.

That's a fair request. Here's a bit from page 121: "The time that has elapsed from any branch point, or node (i.e., common ancestor), on a phylogenetic tree to each of the living species derived from that ancestor is exactly the same. If lineages have diverged at a constant rate (i.e., substitutions/time), then the number of changes should be about the same along any path between living descendants and their common ancestor (Figure 5.32)." (The emphasis is in the original.) Futuyma goes on from here to discuss the "relative rate test" and when the "molecular clock" is and is not reliable.

Quote
The mentality of your so-called scientists is incorrect.  I am not here to convince anyone I know more about their subject than they do.  You seem to think that if someone does not know as much as a specialist about the specialist's subject, that someone is not in a position to say anything about the subject.

No, my stance is that someone knows what they've studied, and if they haven't studied it, they can't expect to know it. If you haven't studied the molecular clock and molecular equidistance, you can't expect to know the full story. And if you don't know the full story, you can't know that the full story is wrong.

That's why I continue to ask-- and I'm sorry, but I'm trying to ask politely-- exactly what you've read and whether or not you can back up your claims with references to facts.

Quote
As Einstein put it, imagination is more important than knowledge.

That does not imply that one can do science in the absence of knowledge.

If you believe that science can be done with imagination alone, I urge you to start small. Try fixing your car with imagination (but no knowledge). Try repairing your plumbing with imagination (but no knowledge). Try baking a cake with imagination (but no knowledge). You will find that imagination and "provisional perspectives" are of limited value when they have to generate practical results. And that's what science is about-- results with practical value, results that can survive being tested against the objective world.

If knowledge without imagination is a headless body, imagination without knowledge is a bodiless head. Neither is going very far.

Quote
Do you suppose the odds of a God is also zero?  If you do, that is just your assumption, not science or mathematics.

The odds of God are beyond my ability to calculate. If you really want to know, I'm fiercely religious, but my faith isn't based on calculations. It's a wager based on hope.

I'm aware that there are countless questions that science can't address. I'm aware that there are countless possibilities that agree with what we already know about this world.

But I'm also aware that hypotheses that ignore what we know, or contradict what we know, about this world are not likely to be valuable in science.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 16 2006,14:28   

Quote (Reluctant Cannibal @ Mar. 16 2006,18:47)
But this is an interesting point, because I think it is at the root of Shi's misconception. He thinks that it does contradict evolution, and that is why he objects so strongly to the actual explanations.

I can see my work here is pretty worthless in terms converting anyone to my side.  But I have enjoyed it and it gave me first hand experience in understanding the mind set of believers of evolution.  Don't get me wrong, I believe in evolution as a fact too.  Evolution is a fact but the current theory is not.  The theory is only a partial truth.  I accept all that is good and proven by scientific papers in the field of evolution.  But it is only the speculative extrapolation part I found non-convincing.  What happens and what we can see within populations of a species may or may not be what happens, which we cannot see, for one species to give rise to a vastly different species.  The theory says that the same law applies in the so called micro evo and macro evo.  But that is, at this point in time at least, baseless and wishful thinking.  It is perfectly Okay for a scientist to accept the theroy that works for micro evo but in the mean time rejects its application in macro evo.  

From a neutral perspective, if a person from outer space is observing the conflict between evolution theory and ID, he should not be able to pick an obvious winning side.  There are highly intelligent peoples on both sides.  For the so-called scientists here on PT, they must ponder why intelligent people disagree with them so strongly.  There are several possible reasons,

1, the theory is inadequate, it is only a partial truth.
2, ID people has other motifs beyond seeking truth, such as religion
3, ID people are not real scientists and are incapable of seeking truth.
4, ID is not a theory

I think 1) and 4) are the most rational reason.  Reason 2) may be true for some ID people but cannot be all.  Besides, the same reason could apply to scientists who clearly have other motifs such as funding, career, and fame.  The kind of real or ideal scientists is an extreme minority today.  Until scientists can be totally set free from economic pressure, the ID people can always rightly charge that scientists have non-scientific motifs in protecting their babe theory.  Reason 3 is false because scientists are not the only intelligent people on earth who can make major discoveries.  Philosophers, artists, free thinkers/mathematicians do it all the time.  Einstein made his discovery by free thought experiment as a patent clerk, not a scientist.  Reason 4 is also valid.  ID lacks a credible theory that must incoporate the merits of Darwinism in micro evo while at the mean time explain the macro evo.  The ID people are presently not good enough to do that yet.  All they are doing is to point out what is inadequate with Darwinism.  But, to be fair, they do make some good points that deserve to be taken seriously by the evolution biologists.  

If we assume that most people are intelligent and honest, we must give our babe theory a second thought if 90% of the US population is not accepting it.  Blame others as non-intelligent and religious are signs of foolishness and weakness.

  
Alan Fox



Posts: 1391
Joined: Aug. 2005

(Permalink) Posted: Mar. 16 2006,21:01   

Shi says:

Quote
ID lacks a credible theory that must incoporate the merits of Darwinism in micro evo while at the mean time explain the macro evo.  The ID people are presently not good enough to do that yet.  All they are doing is to point out what is inadequate with Darwinism.


Exactly what you seem to have been doing. Pleased to see that you now realise that Behe's IC and Dembski's "No Free Lunch" etc. are only attempts at claiming flaws in evolutionary theory. Neither they nor anyone else have proposed a positive hypothesis which offers an alternative explanation for the diversity of life on earth, other than "poof", "Goddidit" or "Big front loaderdidit".

  
Chris Hyland



Posts: 705
Joined: Jan. 2006

(Permalink) Posted: Mar. 16 2006,23:10   

Quote
The theory is only a partial truth.
Quote
1, the theory is inadequate, it is only a partial truth.
Scientists are not saying that it is known exactly how a species evolve into a new species, that doesn't mean the current theory is wrong. I think the main problem is understanding, when a scientist says 'microevolution extends to macroevolution', a layperson might take that to mean 'accumulations of mutations in protein sequences is adequate to create new species', which is almost certainly wrong. New evidence from evodevo, systems biology etc are letting us know more and more about how species evolve, the point is that all this evidence suggests that our current ideas are on the right path. When trying to explain this of course it gets very complicated when we don't know the whole story yet. ID proponents do mainly bring up problems with evolutionary theory and some of them might be worthy of discussion; the problem is that most of them aren't, a lot of them are obvious untruths, plus they claim to show empirical evidence of design. As far as scientists go, do you think that a lot of them suspect design or think the current theory is completely wrong, or just have one or two problems with current parts. I seriously doubt the former.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 17 2006,06:26   

Edmund,
The clock idea is based on the assumption that two species split with nearly identical sequences and accumulate mutations gradually.  Based on this assumption, the whole field of clock is built. Under such assumptions, the odds of no clock may be zero, as you may calculate.  But what if this assumption is wrong?  If someone has prove that this assumption is wrong, he would not need to know any of the specialists' fancy models in order to say that the whole field is a mirage.  From the new assumption, such as two species split with maximum genetic difference and the more recent the split the less diverged versions of genes are used, the chance of a gene showing a clock pattern is pretty high.  

I congratulate Futuyama for doing a more accurate job in presenting facts of evolution.  But unfortunately he represents a minority.  So is Mick Denton who presented the equidistance in his book.  But the majority is not doing it.  It is only logical for intelligent people to ask why.

You seem to always want proves of my knowledge.  That is really pointless.  It proves nothing.  That is why I say it is pointless to accuse other people not knowing enough.  You should be able to judge if a person knows or not what he is talking about based on what he said, not what he read.  If you have no such abilities, why would other people take you seriously?

Who ever said imagination alone is what needed for creative work?  A baby has no knowledge but full of imagination, and do we expect him to create anything?  When Einstein said what he said, do you think he meant what you think he meant?  That is only your wishful thinking, a silly argument solely raised for the sake of argument.

I am glad you believe in some sort of God.  I am not religious but the possibility of God must be taken seriously before one can rule him out.  The current theory is based on no God.  What you and I should be working on is an alternative hypotheses that does not “ignore what we know, or contradict what we know, about this world'.  No one has proven that a hypothesis based on God will necessarily ignore 'what we know, or contradict what we know, about this world'.  

The current theory ignores or contradicts a lot what we know about this world.  If you don't know what these are, you must assume that the ID people are all stupid.  If you do that, who are you to say you are smarter.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 17 2006,08:00   

Quote (shi @ Mar. 17 2006,12:26)
Edmund,
The clock idea is based on the assumption that two species split with nearly identical sequences and accumulate mutations gradually.  Based on this assumption, the whole field of clock is built. Under such assumptions, the odds of no clock may be zero, as you may calculate.  But what if this assumption is wrong?

It's not wrong, from the evidence we have.
See in a recent article in Nature: two fish species (Amphilophus citrinellus and A. zaoliosus) recently diverged in a crater lake (Lake apoyo). Basically, the genetic distance between both species in the lake is less than the distance they show with populations of A. citrinellus living outside the lake.
I assume you know how to interpret a haplotype tree.
 
You have a comparable genetic situation in the polar bear and the brown bear.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 17 2006,08:33   

jeannot,

Thanks for the effort.  But you misunderstood me.  In my persepective, when I talked about maximum genetic difference being setup at the beginning of two MAJOR speceis split, I still allow minor diversities within populations of a species to follow the clock idea.  Varieties within a major species may also follow the clock.  Two slightly different subspecies of fish represents varieties of a species.  They are not really comparable to converting a chimp to a human, or a fish to a frog, the so called macro evo.  All the evidence of evolution presented in scientific papers are merely cases of micro evo.  This is not controversial.

  
edmund



Posts: 37
Joined: Jan. 2006

(Permalink) Posted: Mar. 17 2006,11:36   

Quote
The clock idea is based on the assumption that two species split with nearly identical sequences and accumulate mutations gradually.  Based on this assumption, the whole field of clock is built. Under such assumptions, the odds of no clock may be zero, as you may calculate.  But what if this assumption is wrong?

We do not simply "assume" these things about diverging species-- we can test those assumptions. We can look at diverging lineages of bacteria in the lab and watch them accumulate mutations gradually. And we can correlate divergence times from the fossil record with genetic divergences. As I showed you last time, there is a striking correlation. That correlation is not an assumption.

Quote
From the new assumption, such as two species split with maximum genetic difference and the more recent the split the less diverged versions of genes are used, the chance of a gene showing a clock pattern is pretty high.

But why were less diverged genes used in more recent splits? Who or what accomplished this? How was it engineered? Is there a mechanism that *just happens* to give exactly the same result as a "molecular clock"?

A few posts back, you said that simplicity and elegance are the hallmarks of a good scientific theory. We are faced with two choices. Either genes appear to evolve in a clocklike fashion because they really do evolve in a clocklike fashion, or some remarkably complex unknown mechanism just happens to counterfeit a "molecular clock". I am sorry, but there is a great deal of evidence supporting reasonably clocklike evolution, and no evidence supporting any alternative mechanism. Until new evidence comes along, it is not good science to prefer the second explanation.

Quote
You seem to always want proves of my knowledge.  That is really pointless.  It proves nothing.

Quite to the contrary-- it is extremely important. Biology is not like theoretical physics; thought experiments won't get you very far. To build a solid theory, you need to build it on the facts, and if you don't know what the facts are, you're helplessly adrift. That's why I keep insisting that imagination alone won't allow you to do good science.

There are a couple of reasons why I keep asking you to explain how much you've studied and where you're getting these ideas from. For one thing, I know that a lot of what's written about evolution is wrong. Michael Denton's "A Theory in Crisis", for example, may be where you're getting some of your ideas-- you've mentioned it a couple of times. Denton's book is seriously flawed and very misleading. If that's where you're getting these misconceptions, maybe I can help you understand why everyone on Panda's Thumb disagrees with Denton.

Second, frankly, there are people who come through here who think they can overthrow the theory of evolution without doing any homework. If you're one of those people, I can't help you, and I shouldn't try.

Do you have a reason for refusing to explain what you've read and how much you've studied? It was not intended to be a threatening question. If you find it threatening, that is a problem.

Quote
The current theory ignores or contradicts a lot what we know about this world.

As far as I know, that statement is completely false. That is why I keep asking you where you're getting your ideas about "what we know about this world". Because I suspect that you are not as well-informed as you think you are.

  
shi



Posts: 80
Joined: Mar. 2006

(Permalink) Posted: Mar. 17 2006,13:36   

The clock when applied in micro evo is not an assumption and is perhaps even a fact.  But to apply it in macro evo is a big assumption.  Your assertion to the contrary just shows a common pattern with you: you frequently mix up facts and fancy.  And it is in macro evo, the clock idea encounters many contradictions.  There are some good correlations and there are also many bad ones.  Besides, correlation does not prove or indicate a cause and effect relationship.  

My perspective is intended to open your mind, so you will not get hang up with just one idea.  Perhaps we will find a mechanism and rational for my perspective someday.  Before that happens, it is fair for you to stick with the clock idea for now.  But the many widely known problems with the clock idea should at least cause you to be cautious and less certain about its value.  Refrain from applying it too freely in macro evo.  You may be fooling yourself and others when you pick one gene or a few as good clocks while ignore other genes that contradict your chosen clocks.  Remember, all the evidence against the clock idea could be evidence for an alternative perspective.  When an idea has factual contradictions, it is always wise to look for alternatives that will have less or no contradictions.  

You may have some major delusions.  Delusion 1, there is only one correct way of doing biology and thought experiment is not it.  Knowing certain facts and some current provisional ideas are indeed important.  But if the current ideas are fundamentally flawed due to wrong assumptions, a change in assumption will rebuild the whole enterprise.  In that case knowing too much of what have been built based on a wrong assumption is not going to be very useful.  

Delusion 2, the current theory has no factual contradictions.  Well there are a lot of people who disagree with you.  Who are the stupid ones here?  At least the people who disagree with you are not saying that the present theory is all wrong.  They at least give your intelligence credit for believing a partial truth.  But you are essentially insulting their intelligence when you insist that what they have to say is complete rubbish.  That is really not the behavior of intelligent people.  One can ask you the same question that you asked me, have you learned enough about the problems of the present theory?  Most people, you know, know very little.  Perhaps you are like them also, I suspect, not as well informed as you think you are.

  
jeannot



Posts: 1200
Joined: Jan. 2006

(Permalink) Posted: Mar. 17 2006,14:25   

Shi,

The example I provided involves two true species, not varieties or subspecies. In fact, all the studied models of speciation show a high genetic identity between the new species (in gene sequences) according to the molecular clock, and rely on random mutations, drift and selection.

However, you suggest that sometimes, a major instant split creating very different species could occure.
Your hypothesis would rely on unknown mechanisms (genetic remodeling...). I have a few questions about it.
When should this process take place? When two genera split ? Or two families, orders, classes, phyla, reigns? Would this process have different magnitudes depending on the phenotypic changes that are needed in order to create a new phyla vs a new genus?
For example, do you think that birds or mammals originated in a single major mutational event, or several?
You also imply that humans were... designed by this unknown process. Could you be more precise regarding the species involved: do you think all human species (H. habilis, erectus, ergaster, neanderthalensis, sapiens) and pre-humans (Saelanthropus, Ausrtalopithecus...) appeared this way, or did some of them appear through the known speciation process? You know that the difference between H. neanderthalensis and H. sapiens is more subtle than the difference between the two fishes above.

  
Chris Hyland



Posts: 705
Joined: Jan. 2006