Darwin in the Genome

dear Paul,Originally posted by peter borger:
[B]Dear Paul,
[Edited irrelevant stuff]PK: Peter, (B) so far you have not explained your argument at all. YOu just contnue to make assertions without support.PB: That is because you are new here. I've explained my stance over and over and over in several threads on this board. Before Dr Caporale posted her link to her book 'Darwin in the Genome' (with exactly the same conclusion I've been repeating for months now: nonrandom mutations) several evolutionists on this board (in particular dr Page is very rude ) kicked my but, scoffed, mocked... well, the usual childish behaviour. So, I recommend to get acquianted to what I have contributed to this board over the last six months.PK2 : Peter if you cannot give references to your arguments then it would seem necessary to at least repeat sufficient information to explain what you are talking about. If you do not wish to repeat your arguments provide links to the relevant messages or better collect your arguments on a web page where it will be easier to make sense of them.PB2: Look here for all relevant references:http://EvC Forum: molecular genetic proof against random mutation (1)andhttp://EvC Forum: molecular genetic evidence for a multipurpose genomeandhttp://EvC Forum: Dr Page's best example of common descent easily --and better-- explained by the GUToBandhttp://EvC Forum: More non-random evolutionandhttp://EvC Forum: scientific end of evolution theory (2)PK: You have not explained how redundancy is related to how easy the genes are to knock out,...PB: the more redundant the gene, the easier lost through inactivating mutationsPK2 : It seems that you still do not want to explain your argument. I begin to suspect thaty you have none.PB2: see the other threads.PK: ...nor do you supply any reasoning as to how your "GuToB" would explain the mechanisms if they were redundant (indeed so far as I can tell your GuToB renders these mechanisms not only unnecesary but a potentital liabilility so it is highly questionable if their very existence is compatible with your views).PB: This sounds interesting, so could you please expand. I am aware that the GUToB requires some tiny aesthetic additions, so please elaborate.PK2 : the sloppy polymerases seem to contradict your view since they represent a very different strategy to the elusive "adaptive mutation". Rather than delivering precisely targetted mutations they take more of a "shotgun" approach - increasing the mutation rate.PB2: How do you think this works according to molecular evolutionism? The initial copy of the polymerase has to duplicate (non-traceable I presume). After duplication the gene is redundant since there is no constraint on the second copy. So it gets easily lost through inactivating mutations or is expelled from the genome through recombination to get rid of this energy consuming embellishment. Or, according to evolutionism it starts to change randomly (mutations, you know). By the way, which one? (genetic uncertainty, you know). Until the error prone polymerase has evolved. Now what is the constraint to keep this new error prone stable in the genome? Since it is only induced upon stress. So evolutionism must predict that these error prone polymerases should change with a higher rate than the essential polymerase. I predict it doesn't, for genetic redundancies do not mutate faster than essential genes.
So, I foresee another false prediction. (Hay, evolutionism is a false prophet! )PK: Nor do you even say how the other mechanisms from _Darwin in the Genoome_ fit inot your views.PB: I will fit them in. The are part of the GUToB and will find their place in the MPG. Dr Caporale's work is very timely.PK: As for your final paragraph to the best of my knowledge neither Darwin nor Wallace worked with your mechanisms at all and certainly they did not have the knowledge of molecular biology required to investigate those from _Darwin in the Genome_. Nor does the book validate your other assertions.PB: What D and W really observed was the MPG in action. Their extrapolation was entirely unwarranted. They observed an active mechanism already present in the genome (of course you are right they didn't kow about that) that generates variation over time.PK2 : This doesn't seem to really have much to do with the actual observations of Darwin and Wallace. They were certainly not extrapolating a mechanism of variation because they had non....PB2: they've postulated the evolution theory from microbe to man. Probably from one or a few initial bio-forms (sounds like GUToB, isn't it). I will look up what Darwin postulated exactly, a quote.PK2: ...Indeed I would suggest that their work could be better termed an interpolation because it starts with an overarching view of taxonomy, biogeography and the fossil record and seek to explain the pevasive patterns observed in terms of what is observed at the level of individual animals and populations over relatively restricted geographic and temporal ranges.PB2: ....and which can also be interpolated differently. The GUToB can explain this equally well.PB (CONT): Now, the elucidation of the underlying mechanisms demonstrate the extrapolation of evolution from microbe to man to be a nonsequitur. We are looking at two unequal phenomena here. The one that has been demontrated to operate in the genome to induce variation CANNOT be taken to demonstrate evolution from micobe to man. If you propose to do that than you have also to propose that evolution from microbe to man is mechanistically determined. That's creation.PK2 : This simply demonstrates your failure to understand the actual arguments for evolution. As I have stated above it is more of an interpolation than an extrapolation....PB2: No, it is an extrapolation from the finches he encountered on Galapagos and from some fossils known to science.PK2: ...The overall view of evolution is an inference from other data entirely - and scientists, quite properly, attempt to explain how it happened by extrapolating known mechanisms. But that extrapolation is HOW it happened - not that it DID happen which is based on other lines of evidence entirely.PB2: It happened through the MPG present in created archetypes. That's what can be inferred from contemporary biology.PK: The lack of discussion seems to be due to your preference for "just so stories".PB: I've explained my position over and over on this board; NONRANDOM mutations with repect to position and nucleotide are found in TH 1G5 gene, mtDNA and the ZFY region. All I got: denial and ignorance, so you can imagine that I am very glad with this new thread. And it confirms my opinion on evolutionism: unfair and outdated.PK2 : As has been shown on this thread your own knowledge of evolution seems to be very weak - to the point that you were claiming a refutation of evolution based on an obvious error.PB2: I've been defending nonrandom mutations for six months against evolutionist's attacks. You --as an obvious evolutionist-- will always claim that I am in error. It is the Dr Page style. Listen, Mr Paul, I know what the data holds and what they indicate. It is you and the evolutionists that have been hit by blindness, and that explains why you don't see your error. (140 years of wasted time is hard to swallow. Well, not completely wasted: at least we know now how it did NOT happen).
In the meantime I was not hindered by blindness, and I've set up an alternative to evolution that explains what we observe on this planet. That should be sufficient. (What do we need a theory for that tries to explain the never-observed? It is gratuitous.)
Also, my knowledge on molecular evolution is excellent. The problem is that evolutionism isn't explanatory since the paradigm is wrong. It is NOT common descent from one/few living single cell by random mutations and selection. It is common descent from archetypes geared with MPG's through nonrandom mutations, shuffling/rearrangement and duplication of preexisting DNA elements and loss of genes.
Nowadays, evolutionists have to twist and turn facts to try to fit them in their paradigm. Fortunately, adaptive --and non-random-- mutations, and genetic redundancies are the end of the story. At last, in 2003 science can make a fresh start. We've all been deluded for about 140 years.PK: As you could have found out from a very famous popular book written in 1986. Talk about outdated.PB: You mean the work by my favorite author R.D.? (Not to be confused with the other excellent story teller R.D: Roald Dahl).
By the way it was published almost 20 years ago. THAT is outdated.See: http://EvC Forum: Richard Dawkins lack of knowledge on DNA exposedPK: Certainly you do not seem willoing to go into the necessary details to back up your claims nor do you seem willing to discuss the refutation of your original claims that the "non-random" mechanisms refuted NDT (an error based on your failure to understand the very point of the theory you vlaim to have been falsified!).PB: I already did that and I am getting a bit tired of reiteraing the details over and over. They can be found on this board. However, I am very glad with the publication of Dr Caporale's book; it saves me a lot of time finishing my own.PK2 : So far I have seen no significant connection between Dr. Caporale's book and your assertions. How, for instance does Huntington's disease fit into your views ? It is caused by one of the mechanisms discussed by Dr. Caporale and it is not only detrimental but additional mutations based on the same mechanism have a tendancy to reduce the age at which the condition appears. It is certainly not an adaptive mutation.PB2: No, it is degeneracy. It is the GUToB.Best wishes,
Peter

Dear Percy,Percy: The significant issue is the causative agent of NRM. Dr. Caporale argues it fits within a Darwinian framework,PB: Yes, let's discuss this. I bet it is more in accord with the GUToB than with NDT. And of course one can claim that it still is Darwinism. That selection is involved doesn't mean it is Darwinism, the GUToB also includes selection, but holds that selection is predominantly a mechanism to get rid of degenerate genomes.PB: I wouldn't mind discussing this with Dr Caporale. However, and not unimportantly, if one is to say that molecular genetics is not in accord with NDT in public, it would be --to speak with Dr Page's words-- 'career ending nonsense'. Apparently, it is better to watch your words in the evo community. Since I am not looking for a career in evolutionism (I don't like keeping up appearances), I don't mind.Furthermore, I really start to believe that evo's don't understand their own theory. And I am not surprised since the paradigm it rests on has been demonstrated over and over to be completely, entirely wrong.Percy: ...while you, other than repeating your initial premise, have suddenly clammed up. Why are you replying to me and not Dr. Caporale?PB: Dr Caporale is free to respond to my vision, isn't it? I already had a little communication with Dr Caporale, and she agrees with me on implications for phylogentics (although my stance is probably much more rigorous) and I have the feeling that she doesn't advocate NDT either. So, let's wait for her reply to this mail.Best wishes,
Peter

Page: What is not surprising is that despite the fact the she clarified her position and the evidence for it, Borger still maintains that her book supoorts essentially the opposite of what it does.PB: You read the book, I presume? Anyway, you still dont get it Page. Let me explain to you once more. The mechanisms described by Dr Caporale have been observed over and over on the organism level, for instance by Darwin and Wallace: variation within species. Now, 144 years after Darwin, we know that the mechanism for variation are preexisting in the genomes of organisms. So, you can NOT take Darwin's observations to extrapolate evolution from microbe to man, since if you do so than you have to also concur that evolution from microbe to man is mechanistically determined.Best wishes,
Peter

Dear Paul,In response to:
The mechanisms described by Dr Caporale have been observed over and over on the organism level, for instance by Darwin and Wallace: variation within species. Now, 144 years after Darwin, we know that the mechanism for variation are preexisting in the genomes of organisms. So, you can NOT take Darwin's observations to extrapolate evolution from microbe to man, since if you do so than you have to also concur that evolution from microbe to man is mechanistically determined.Paul says:
I note that Peter Borger is still continuing his misrepresentations fo evolutionary theory.
The fact is that the observations of Darwin and Wallace remain relevant and remain strong evidence for common descent. _Darwin in the Genome_ makes no change to that at all. What it does do is add to our knowledge of how the variation required by Darwinian and neo-Darwinian theory is generated.PB says:
Now Paul has a nice opportunity to show where my claim quoted above is wrong. If you think that we are allowed to extrapolate the observations on the genome to evolution from microbe to man, please explain in detail. I am very curious. Thanks in advance.Best wishes,
Peter

Dear PaulPlease expand.Let's see where logic leads you.Best wishes,
Peter

Page says:"And when the evidence is repeatedly ignored or twisted?"Borger says:"Exactly my point, Page. At last you get it" best wishes,
Peter

[copy deleted][This message has been edited by peter borger, 01-31-2003]

Dear Paul, thanks for your revealing mail.PaulK: I don't see any need to expand further.PB: I am always so impressed by the way evolutionists are able to debate and discuss in a contemporary scientific way on a topic that supposed to be their own. Remember my little discussion with Page? He made a nice caricature of himself and -in effect- the whole evo- community. At least we now know how evolutionary 'science' keeps up the appearance.PK: Your repeated erros on quite basci matters - as well as your extreme reisistance to correcting those errors speak for themselves.PB: I've demonstrated that your socalled 'basic matters' are in error and founded on poor science.PK: But then what can we expect from somebody who cannot comprehend the idea that the author of a science book might be a trustworthy authority on the meaning of that book ?PB: Well, I was expecting an interesting discussion. My expectations were too high, I guess. Anyway, why did you think she wrote the book? Because orthodox evo's do not understand a single letter (A, T, C, G) of genomes. (As demonstrated in my exchange with Page).Best wishes,
Peter

dear Paul,PK: You have NOT answered the points I have raised against your basic errors you simply repeat the errors. Your claim to the contrary is an outright and intentional falsehood.PB: Please explain the errors, so that everybody is able to understand what the 'errors' are. Then I will respond.Simply claiming that someone is in error is non-scientific. Back it up, please. Thanks in advance.Best wishes,
Peter

Dear Paul,Paul: From ypour answer it seems that you admit by implication at least that your claim to have refuted the theory of evolution is not scientiifc. That is an advance.PB: The evo's inability to draw proper conclusions is amazing.Paul: As for your errors can we start with your claim that Neo-Darwinian Theory requires mutations to be random in some sense that is contradicted by such observed mutatiosn as the removal of hairpin loops of DNA.PB: Why don't you read my mails first and also try to understand the content and implications of Caporale's book. All you do is present me a straw man. My claim is that due to contemporay biology we know that all DNA elements that are required for evolutionary OBSERVATION are preexisting in the genome, and cannot be extrapolated to evolution from microbe to man. That is what I like to discuss here. Not your irrelavancies. I am familiar with all the evolutionary debating tactics, since I discussed a lot with evo's.Paul: Are you prepared to explain in what sense NDT requires mutations to be random and to support it with actual referecnes to relevant literature ? Or will you continue to evade the issue ?PB: Ever read something about NDT? The NDTers were unwilling to accept environmental influence [as Darwin had suggested in 'The Origin' (although he never addressed THE origin)] as a cause of variation, and the NDTers could not think of a mechanism that triggered genetic changes (speaking of outdated theories!). Therefore, they chose randomness as the source of variation.And you didn't really understand why Dr Caporale wrote her book, did you?To demonstrate that NDT is wrong, of course.Best wishes,
Peter

Dear PK,PK: I see that you cannot answer the key point which requires explaining the alleged error in NDT. Since you are unable or unwiling to do so your claim to have refuted NDT is cleearly unscientific by your own criterion.PB: If you think so, why don't you -as an evolutionary expert- start explaining:"3) You don't really know what you are talking about. Your rejection of Dawkins' points sbout randomness on the grounds of age ignores the fact that Dawkins is expressing a view that is stll the mainstream - as explained in the book that this thread is about and which you claim to have read!"[From: http://EvC Forum: Darwin in the Genome -->EvC Forum: Darwin in the Genome]PB: Dawkins? Don’t let me laugh. His outdated non-sense that he is still able to propagate? Listen PK, it is Dr Caporale who attacks outdated visions like Dawkins’ Junk DNA (for a reference don’t hesitate to ask, but of course you won’t ask). However, to stick to your own words, you were also talking about mainstream opinion, so now you have an excellent opportunity to explain to the audience what mainstream evolutionists hold. Please explain and I will immediately demonstrate it to be false.DB: Therefore your statement "PB: The evo's inability to draw proper conclusions is amazing." is not do to an error of reasoning on my part - but your objection to the conclusion.PB: I am perfectly able to draw conclusions myself. As demonstrated for the ZFY region. It was easy to overthrow the completely, entirely stupid explanations of dear evo-fellow Dr Page. Better get used to the idea that molecular biology doesn’t support the current concept of evolutionism.PK: I can only repeat that since Dr. Caporale was quite content with my summing up of her book on this point that there is no problem with my understanding there.PB: Repeats = Mantras. I don’t buy anything for mantras. Dr Caporale does not oversee the implication for her book, I presume. [I know what you gonna say, but I can also point out a couple of shortcomings in her book, and at least one wrong assertion. Did you really read her book?]. Dr Caporale also concurred that NRM has important implications for phylogeny, a vision that I share. But I am more extreme.PK: As for your attempt to divert the discussion by calling my point a strawman - well it is not since you were the one who cliamed that non-random mutations refuted NDT. You asked me to talk about your errors, so I chose to start with that one since it is so glaring. So this "debating tactic" is forthrightly giving an answer you demanded. Whereas we see your debating tactics in your attempt to change the subject.PB: As mentioned you now have an excellent opportunity to demonstrate what mainstream evo’s hold with respect to NRM.PK: Your own statements indicate that - according to you "randomness" weas not a key part of the theory at all but just an assumption made when there was no evidence of anything else. And one made before DNA was evne known to be the carrier of genetic information. So it is not an essential part of the theory at all ! So why don't you just admit that you were wrong ?PB: When a position is not tenable I will admit that. Something I haven’t seen in evolutionists on this board. Keep up the appearance any time, also when scientific evidence demonstrates the opposite. Just invent another story: non-science.PK: And no, you clearly do NOT know why Dr. Caporale wrote her book which only adds to the suspicion that you have not read it at all.PB: Don’t challenge me on this. I have an email from Dr Caporale here in my computer that implies that she is addressing orthodox evolutionists’ visions. And your suspicion is ludicrous.Best wishes,
Peter

Dear PK,PK2: I am not afraid to challenge your false assertions.PB: Well, do it.PK2:
Dr Caporale intended to add to and enrich evolutionary theory, not overthrow it as you falsely asserted.PB:
You don't read my mails, that's obvious.
Dr Caporale's book demonstrates NDT to be wrong (you don't want the references from her book, I guess?), and it also demonstrates that Darwin's extrapolations are completely, entirely unwarranted. That is the point here. That you don't address these points is tale telling evolutionary strategy. You have aexcellent opportunity to defend your theory, here. You don't let your pet theory drop without any defence, do you?So my claim that NDT and Darwinism RIP, still stands.Let me reiterate my point:All genetic elements for variation are preexistent in the genome (=multipurpose genome) and can be activated nonrandomly (as demonstrated by contemporary biology). Darwin was the first to discover the MPG, but his extrapolation of microbe to man evolution is completely, entirely unwarranted because the mechanism are unequal. (Unless you assume an uncommited MPG of the original microbe we all evolved from). You don't have to be a rocket scientist to understand that.(More soon)Best wishes,
Peter

dear Paul,Paul:
You don't have to be a rocket scientist to work out what the NDT requires in the way of "random" mutations. It was even mentioned in this thread, but it still seems to be beyond you.PB: I invited you to explain it to the board. This is another nonanswer.Paul:
If you were REALLY any sort of scientidt at all - or even had a PhD it wouldn;t be difficult for you to discuss such a simple basic point. So either you know full well that you are wrong and are just evading the issue or you are misrepresenting your qualfications.PB: The mocking and scoffing starts here, I guess. Not impressive.Paul:
You don;t have to be that bright to notice that I did deal with your point about Darwins alleged extrapolations by pointing out that it was false.PB: No, you didn't such thing. If so, make a link. Proof your claims.Paul: It doesn't take much brain to say that your reference to "Darwinian tale telling" is simply a random insult with no reference to the actual discussion.PB: I offered you to demonstrate the references, you didn't respond. For obviousl reasons.Paul: And you have no references from _Darwin in the Genome_ that demonstrate NDT to be wrong. We both know that..PB: I will spell out the references later, haven't the book here.PK: We both know that Dr. Caporales findings are a bigger problem for your views than for NDT.PB: I explained why they are a bigger problem for DNT and evolutionism in general. Now YOU are going to explain. Simply claiming is all you do. EXPLAIN PLEASE. IN DETAIL, like I do all the time.Paul: Your assertions about the MPG are not supported by the evidence.PB: Get real, PK. That all the info for variation is in the genome is what Caporale demonstrated. That is the MPG I have been discussing for ages, now. Close your eyes, put your fingers in your ears and hummmmmmmmmmmm.Paul: And misrepresentign Darwin's reasoning - as you so repeatedly do here is just a contemptible debate tactic.PB: Okay, another excellent opportunity to explain how Dawrin got his dangerous idea. (Next, I will obliterate it.)Paul: But keep on evading and backpedalling, Peter. It shows that your view doesn't have a leg to stand on.PB: The Page attitude?Best wishes,
PeterWell, if this is all evo's can put forward I consider evolutionism RIP. Long live the GUToB!![This message has been edited by peter borger, 02-10-2003]

Dear Paul,Thanks for your non-answers. Since you seem to hold scientific truth let's try again to start up a scientific debate on the topic. These are the points I have made and are still unsolved.1) Non-Random Mutations type 1 (NRM1). This type of NRM introduces mutations on the same positions and the position where they are introduced depends on the flanking DNA regions. NRM1 are also known as ‘positional NRM’. NRM1 have been also observed in the ZFY region and in mtDNA. NRM1 has been observed in T4 by Lynn Ripley and was described in Caporale’s book (page 37, 38).
Implications: NRM1 will line up and give the illusion of common descent in phylogenetic analysis. Since phylo-geneticists cannot exclude NRM1, this type of mutations invalidates the evolutionary conclusions that the alignment of genes and shared mutations is proof for common descent.2) Non-Random Mutations type 2 (NRM2). This type of NRM is mediated by protein and/or RNA driven mechanism that translocate preexisting DNA elements, or vary nucleotides in genes in a similar fashion as observed for immunoglobulins. NRM2 also plays a pivotal role in parasite-host interactions, and are likely to be abundant in other interactions between organisms where ‘evolutionary armsrace’ is ongoing. They have been demonstrated beyond any doubt for the 1G5 gene in Drosophila.
Implications: Alignment of mutations (‘shared mutations’) in related MPGs. Variation is preexisting.3) NRM1 and NRM2 explain observed biological variation. It tells us that the mechanisms for biological variation are already preexistent in the genomes of organisms (=multipurpose genome) and can be activated upon the right triggers. Darwin was the first to discover the MPG, but his extrapolation of microbe-to-man evolution is completely, entirely unwarranted because the phenomena are unequal. (Unless you assume an uncommitted MPG of the original microbe we all evolved from). That Darwin’s extrapolation on variation in Galapagos finches to support ‘microbe-to-man-evolution’ is unwarranted is also demonstrated by observations that ‘his’ finches are still able to interbreed (Science, 26 April 2001). Thus, they are still the same MPG.Your comments, please.Best wishes,
Peter[This message has been edited by peter borger, 02-11-2003]

Dear paul,In response to:PB:
Thanks for your non-answers. Since you seem to hold scientific truth let's try again to start up a scientific debate on the topic. These are the points I have made and are still unsolved.PK says:
If you want a scientific discussion we can start with your explanation of how non-random mutations actually refute NDT - after all refusing to explain your criticisms is non-scientific as you said. But it seems that you do not want to discuss that.
I also notice that providing the link to prove my claim - as you demanded seems to be considered a "non-answer".PB2: Your link is a non-answer for I already rebutted mail #47 in mail #48. And, since you keep repeating that I have to demonstrate NRM to refute NDT (what I did months ago, but apparently you don't read my mails) let's find out what Dr Caporale has to say about this in her excellent book that is a big thorn in the eye of the orthodox evolutionists. From Darwin in the Genome:"Once we learned about DNA, we saw that mistakes in copying generate mutations and so we've assumed that random mutation followed by selection underlies evolution. However, I have come to the conclusion
that using our current knowledge to expand on Darwin's insights does not require that all mutations be random with respect to their potential effects on biological function". (page 42)."So, E coli cannot randomly try every possible change and then wait for selection to capture the very best one". (page72)."Randomly trying out mutations in each copy of each of many thousands of gene families could mean eons spent wandering lost through the broad mutation landscape, in spite of the fact that information could be could be available to help guide the journey. Still, most people assume that mutaions happen randomly throughout the duplicated genes, and that natural selection picks those that lead to a useful new function". (page 129)."New levels of interaction and regulation rarely arise through letter by letter random mutations of random DNA sequences". (page 144)."The genomic landscape is huge. Random wandering through the landscape of possible mutations is no the most efficient strategy for long term survival. In our own case, random mutation would mean that any one of the more than 3 billion spots in our genome had the same probablity of each kind of change." (page 185)."Current evolutionary theory states that variation results from genetic changes that remain forever random, and that selection operates upon the results of this random genetic variation. It is time to incorporate the observations described in this book into evolutionary biology". (page 192).I completely agree and I already mentioned this in a mail in May 2002: NDT RIP. Then, it was firmly denied and now here we have Dr Caporale with exactly the same claim. You can of course deny her, too.PK (cont): As is my list of examples which show that _Darwin in the Genome_ refutes your claim that information is never added to the genome (proving my point that the book is a greater problem for your views than for NDT).PB: Apparently you didn't read the book properly. The mechanisms described are included in GUToB.PK (cont): In short your idea of a "scientific" discussion means dropping the discussion because your errors are being revealed.PB: What a humbug. I've never dropped a discussion. As a matter of fact, I have won all my discussions with evo's. (Till now, Dr Douglas Theobald from the Talk-origin was the best defender of evolutionism, but not good enough. He couldn't defend the IL-1 beta incongruence).In response to:PB: 1) Non-Random Mutations type 1 (NRM1). This type of NRM introduces mutations on the same positions and the position where they are introduced depends on the flanking DNA regions. NRM1 are also known as ‘positional NRM’. NRM1 have been also observed in the ZFY region and in mtDNA. NRM1 has been observed in T4 by Lynn Ripley and was described in Caporale’s book (page 37, 38).
Implications: NRM1 will line up and give the illusion of common descent in phylogenetic analysis. Since phylo-geneticists cannot exclude NRM1, this type of mutations invalidates the evolutionary conclusions that the alignment of genes and shared mutations is proof for common descent.PK says:
Anyway to deal with your assertions.
1) p37-38 deal with the "hairpin" model. Since such models require that the existing sequence is similar they can only upset phylogenetic analysis at fine resolutions- which you apparently accept, unless you wish to claim each species is a seperate creation (which would then pose the question of why the sequences are similar enough to see such mutations). It poses no threat to the larger scale phylogenies which you seem to object to.PB2:
At present, the hairpin model is able to explain specific NRM in T4. There is no reason to assume that additional mechanism are not operative in the genome. As mentioned several times before, since you cannot exclude NRM, evidence of common descent based upon shared mutations is a non scientific conclusion. You have to exclude NRM in the assessed sequence. I have demonstrated NRM for the ZFY region and mtDNA on this board and that should have far reaching consequences for evolutionism (if it is science).In response to:
PB: 2) Non-Random Mutations type 2 (NRM2). This type of NRM is mediated by protein and/or RNA driven mechanism that translocate preexisting DNA elements, or vary nucleotides in genes in a similar fashion as observed for immunoglobulins. NRM2 also plays a pivotal role in parasite-host interactions, and are likely to be abundant in other interactions between organisms where ‘evolutionary armsrace’ is ongoing. They have been demonstrated beyond any doubt for the 1G5 gene in Drosophila.
Implications: Alignment of mutations (‘shared mutations’) in related MPGs. Variation is preexisting.PK says:
2) Translocations - since these require that the material to be translocated is already present in the genome it would seem that your "related MPGs" are related by common descent. I thought your assertion was that MPGs were NOT related in that way.PB2: Correct, there is only common descent within MPGs. Related MPGs have been created. Why would the Creator reinvent the wheel? It is illogic. A gene encoding cytochrome in chimp works as good as it works in human. So, if it mutates nonrandomly in human, also in chimp. What you observe is the illusion of common descent. I have provided evidence for this view in the ZFY region in primates.PK (cont): It seems to me that again translocations can only interfere with phylogenies at the fine resolution of individual branch points and can only do so because large scale evolution is correct.PB: Tranlocation of genetic elements may affect gene expression and thus induce variation within the MPG. That was my claim, not that they affect the illusion of common descent. It probably depends on the DNA sequences (docking sites, recognition sites) where the elements translocate to. If the MPG is similar probably such nonrandom translocation of DNA elements also line up. "Expect the unexpected"In response to:
3) NRM1 and NRM2 explain observed biological variation. It tells us that the mechanisms for biological variation are already preexistent in the genomes of organisms (=multipurpose genome) and can be activated upon the right triggers. Darwin was the first to discover the MPG, but his extrapolation of microbe-to-man evolution is completely, entirely unwarranted because the phenomena are unequal. (Unless you assume an uncommitted MPG of the original microbe we all evolved from). That Darwin’s extrapolation on variation in Galapagos finches to support ‘microbe-to-man-evolution’ is unwarranted is also demonstrated by observations that ‘his’ finches are still able to interbreed (Science, 26 April 2001). Thus, they are still the same MPG.PK says:
3) Your list is hardly exhaustive and so to suggest that these two factors alone account for all variation would be an obvious error. However unless you make that error your assertion is clearly unproven.PB: Of course there are many more preexisting/preprogrammed mechanism to induce variation in the MPG, but where does help that help you? Why would it unprove my assertion?PK (cont): I also note that you insist on repeating your false claim about Darwin, despite the fact that you know it to be untrue. The former is unscientific, the unscientific and dishonest.PB: None of these remarks relates to my claim that Darwin made an unwarranted extrapolation. Maybe you could point it out. I mean how is your answer related to my claim? I almost have to believe that you agree with me on Darwin's unwarranted extrapolation.Since you were unable to rebut my claims, evolutionism still stands refuted. But at least you gave it a try.Finally, I owe you the Dr Caporales vision on Junk DNA:"Now that our genome is available, we will be able to connect these slippery DNA regions to their-fine tuning-knob role, if they have one. But we will be able to do this only if we look into our genome with some respect, seeking to learn. We will not find them if we dismiss boring repetitive sequences as junk DNA". (page 69)."Transposons are found among the many repetitive sequences in the genome that have been called 'junk DNA'. They are by no stretch of imagination useless junk, however." (page 149).PB: Dawkins is out.Best wishes,
Peter[This message has been edited by peter borger, 02-12-2003][This message has been edited by peter borger, 02-12-2003]