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: 13407 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: 1201 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: 2561 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.   -------------- "Love is in the air, everywhere I look around,.....Love is in the air, every sight and every sound,......"

Henry J Posts: 5760 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: 1201 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: 1201 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: 1201 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: 1201 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: 1201 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: 5760 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: 5452 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. -------------- “Why do creationists have such a hard time with commas? Linky“. ~ Steve Story, Legend

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: 5760 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: 5760 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: 5760 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: 1776 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: 13407 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: 5760 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: 1201 Joined: Jan. 2006 (Permalink) Posted: Mar. 11 2006,08:15    double post.

jeannot Posts: 1201 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: 5760 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: 1201 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: 1201 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: 1201 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: 1201 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: 1201 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... )

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: 1552 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: 1201 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: 1552 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: 1201 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: 1201 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.