Darwin in the Genome

Dear Caporale,C: In doing a search on another topic, I came across the thread on this forum regarding molecular evolution. I have just written a book on this topic, discussing the effect of natural selection on the mechanisms that generate genome variation [which is affected by a whole range og biochemical activities, from polymerases to proofreading to mismatch and other repair, to the sizes of nucleotide pools, to recombination].I have come to the conclusion that through natural selection, many mutations move away from being completely random.PB: Could you please be so kind to share with us briefly how you arrived at this conclusion.C: It is important to note that it was not Darwin who suggested that variation was generated by completely random changes in DNA, and, in fact, the concept that the mechanisms that generate genome variation fall under natural selection not only is consistent with the Darwinian framework, but also gives us a deeper sense of the potential power of natural selection.For those interested in more detail, there is a links page at http://www.DarwinGenome.info that includes other writing on this subject, including the conference volume "Molecular Strategies in Biological Evolution". There also will be a review in the 2003 volume of Annual Reviews of Microbiology.PB: Could you please be so kind to provide the issue number.Best wishes,
Peter

Dear Primordial,
Essentially, Neodarwinian theory holds that evolution = random mutation plus natural selection. If these pillars cannot hold than the theory of evolution has no foundation, and all explanations that rely on it are invalid.Now NON-RANDOM mutations have been scientifically proven the NDT is false. In another thread I also demonstrated that natural selection is highly doubtful for the evolution and maintenance of genetic redundancies. So, both pillars of NDT are invalid at the molecular level. It explains a lot.Best wishes,
Peter[This message has been edited by peter borger, 01-09-2003]

Dear Lynn,LC: Just to clarify an important point: Darwin and Wallace proposed that evolution takes place by selection acting on variation. They did not know the mechanisms that generate variation. Therefore, that some mutations may become more likely than others would not at all violate Darwin and Wallace's framework, but rather illustrate that variations in the mechanisms that generate variation can fall under natural selection, much as variations in wings and beaks can.PB: I agree, Darwin and Wallace discovered the multipurpose genome.Best wishes,
Peter

Dear Andaya,AP: Say, Dr Borger, does your theory acknowledge common descent? If not, how do you explain the fossil record and the taxonomic hierarchy in nature?PB: Common descent from archetypes? Yes.Best wishes,
Peter

Dear PE,I read Dr Caporale's book. I know what it holds and I know what it implicates,Best wishes,
Peter

Dear paul,PK: In the end I think that this book both makes things easier and more difficult for evolution in the public arena. The mechanisms discovered make evolution more plausible because they improve the odds of getting useful mutations. But the origins of these mechanisms will need ot be explained - a big research project.PB: For adaptive mutations in bacteria it has already been observed that they are mediated by alternative stress induced error prone polymerases. I predict that such polymerases can be readily knocked out and thus are genetic redundancies. If such redundant polymerases are equally stable as essential polymerases the question you have is easily solved.Best wishes,
Peter

dear Andya,AP: [example] Termites, my animals, evolved from wood-eating semisocial cockroaches, within Arthropoda; and insects & arachnids (spiders) evolved from the arthropod archetype. The archetype was specially created some time around the Ediacaran age/before the Cambrian explosion.PB: There is 'nothing' before the Cambrian explosion. It will soon be confirmed at the molecular level.best wishes,
Peter

Dear paul,PK: If you had read the book you would know that the polymerases you are talking about do not specifically produce adaptive mutations - they are simply more error-prone. However your ideas about redundancy have no bearing on what I stated nor do they make a coherent argument.PB: You only make a couple of statements. Please expand. Let's have another close look how contemporary biology obliterates NDT.Best wishes,
Peter

Dear Primordial,PE: and are you able to share this knowledge? I'm sure Dr Caporale would be interested.PB: I discussed the consequences of non-random mutations for over six months now. All info can be found on this board. I've contacted Dr Caporale, and she concurs that such mutations indeed have implications for phylogenetics.
I already spelled out on this board in a letter to Dr Page how non-random mutations invalidate molecular evidence of common descent. It used to be the best evidence of molecular evolution, but due to the existence of non-random mutations not any more. For instance, the ZFY region is better exlained by NRM.
Not only Dr Caporale, but the entire evolutionary community should be interested.Best wishes,
Peter"Evolution? NO, GUToB!"[This message has been edited by peter borger, 01-13-2003]

dear lynn,LC: When you say it will be confirmed at the molecular level soon:...PB: The data are already present. A reanalysis of molecular data demonstrates that the cambrian explosion is real.LC: ...what kind of data at the molecular level would confirm your theory, and what kind of data would make it less likely to be true?PB: The kind of data that are demonstrated in the fossil record and now these reanalysis of molecular data that confirm the cambrian explosion. As soon as the current edition of UNINEWS (univerity of Sydney publications) is online I will make a link to this prepublication.For an overview of the predictions and falsification of my theory see my thread: molecular evidence for the multipurpose genome.Best wishes,
Peter[This message has been edited by peter borger, 01-12-2003]

Dear Paul,quote:
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Originally posted by peter borger:
Dear paul,
PK: If you had read the book you would know that the polymerases you are talking about do not specifically produce adaptive mutations - they are simply more error-prone. However your ideas about redundancy have no bearing on what I stated nor do they make a coherent argument.PB: You only make a couple of statements. Please expand. Let's have another close look how contemporary biology obliterates NDT.Best wishes,
Peter
--------------------------------------------------------------------------------PK: As I pointed out in my first post too this thread the mechanisms described in the book represent only a modification to the theory. You did not dispute that. Instead you made assertions without even a coherent argument that were not even clearly related to my comments.PB: You where claiming that the origin of such mechanism would involve a big research project. But that remains to be seen. If the error-prone polymerases are redundant --as I predict from GUToB-- the answer to your question is readily found. So, in contrast to what you stated I adressed your specific remark.PK: As for this response, if you have read the book there is no need for me to elaborate on the first sentence and the second is a request for you to fill in the holes in your post, so there is no need to elaborate there.PB: I've read the book and I am aware of all the work that has been caried out over the past years on the topic of error prone polymerases, and other observations that proof non-random mutations (for instance in human mtDNA, in D. mel's 1G5 gene, in the human ZFY region).PK: As my original point refutes your claim that NDT has been "obliterated" by the evidence in _Darwin in the Genome_ and you have not responded to that it seems that there is no discussion - and no "obliteration" to take a look at - closely or otherwise.PB: Lister, Mr Paul, the observations Darwin and Wallace did were on these mechanism. These mechanism perfectly explain what they observed: the multipurpose genome. At last we find out --through work described in Dr Caporale's and my threads on this board-- that their other claims on evolution from microbe to man are nothing but unwarranted extrapolations.And of course there is no discussion, only just-so-stories.Best wishes,
Peter

Dear Andya,AP: I'll play by your rules. Okay, so the arthropod archetype existed sometime in the early Cambrian, then it evolved into the ancestors of insects, crustaceans, arachnids, etc. The ancestor of insects branched off into many orders, one became the cockroaches, and then among the cockroaches, one took the step to become termites.
Does that scenario follow your theory?PB: Your scenario probably is an oversymplification. However, it can be conjectured that the MPG is subject to directed, non-gradual evolution through NRM. The extreme version of the MPG could hold that all the information of the orders was present in the ancestor and branched of through the rules dictated by GUToB, i.e. selective but irreversible loss of (redundant) genes, the transfer and/or hopping around of genetic (regulatory) elements, etc.best wishes,
Peter[This message has been edited by peter borger, 01-13-2003]

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.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 mutationsPK: ...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.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. Now, the elucidaation 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.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.PK: 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.Best wishes,
Peter[This message has been edited by peter borger, 01-14-2003]

Dear PE,quote:
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Originally posted by peter borger:
Dear Primordial,
PE: and are you able to share this knowledge? I'm sure Dr Caporale would be interested.PB: I discussed the consequences of non-random mutations for over six months now. All info can be found on this board. I've contacted Dr Caporale, and she concurs that such mutations indeed have implications for phylogenetics.
I already spelled out on this board in a letter to Dr Page how non-random mutations invalidate molecular evidence of common descent. It used to be the best evidence of molecular evolution, but due to the existence of non-random mutations not any more. For instance, the ZFY region is better exlained by NRM.
Not only Dr Caporale, but the entire evolutionary community should be interested.Best wishes,
Peter"Evolution? NO, GUToB!"[This message has been edited by peter borger, 01-13-2003]--------------------------------------------------------------------------------PE: This is a very childish response, given that I would have expected you to be more than willing to post your conjecture as many times as possible, if you genuinely believed it had any value...something about the action of "creatons" on a "morphogenetic field" wasn't it?PB: I think childish is not the right term, but anyway. If you are interested I will make the links. It has nothing in common with creatons and morphogenetic fields, that's what some evo's on this board made of it, so they had a straw man. The GUToB I referred to is about non-random mutations in a multipurpose genome. Here you can find a brief summary of the GUToB:http://EvC Forum: molecular genetic evidence for a multipurpose genome -->EvC Forum: molecular genetic evidence for a multipurpose genomePE: Given your obvious reluctance to describe your conjecture or subject it to any sort of scrutiny, your trite responses ("I have read the book and I know what it contains"), your dishonest and specious arguments on this thread, your persistent misunderstandings of the concepts you try to refute and your continual trolling, its very difficult to avoid the conclusion that you are simply seeking attention ("my theory's the best! my theory's the best!") without any kind of supporting argument or evidence. In short, you have no cogent theory which will revolutionise biology.PB: I postulated an alternative to evolutionism, that’s all I did. Is that a crime? Everybody objective scientist knows that evolutionism is NOT explanatory. So we need something else: the GUToB. And since we are not able to scientifically explain the origin of genes from scratch (and due to ‘genetic uncertainty’) the GUToB does not address it. Although creatons and morphogenetic fields could be introduced to explain the origin, I’d rather not use these concepts for obvious reasons (=straw man attack).PE: My own opinion of your motives is that if you repeat this often enough, you're fervently hoping that it may get noticed by one of the less honourable creation science research foundations in the US who might give you a fat funding cheque for your "research" - if so, I don't know whether to wish you luck or not.PB: My motifs are NOT materialistic (I already have a very satisfying job). I simple demonstrated scientifically the validity of my theory. That’s not prohibited, is it? And the book of Dr Caporale confirms what I and others have been thinking about the genome.Best wishes,
Peter

Dear Percy,--------------------------------------------------------------------------------
I must confess this isn't the direction I hoped this thread would take. I expected that PB and Dr. Caporale would engage in a longer dialogue. Dr. Caporale said that non-random mutations fit within a Darwinian framework, thereby disagreeing with PB's views on their origins. PB has ignored this but keeps painting a picture that attempts to make it seem like Dr. Caporale supports his views, like mentioning areas of inconsequential agreement such as the impact on phylogenetics and expressing support for her book. I would have liked to see a discussion about the origins of non-random mutations, which is the primary area of disagreement that evolutionists here have had with PB.PB: My problem was the blindness of NDT and atheistic nihilism (as mentioned on this board, so it should be known), not Darwin or Wallace. They were the first to discover the MPG in action. They simply made some false 19th century deductions. Now NRM is scientifically proven, the GUToB is complete. The debate creation versus evolutionism can be concluded: creation.Best wishes,
Peter[This message has been edited by peter borger, 01-14-2003]