Darwin in the Genome

It is good to see the author of a book appear in the discussion. I hope that if I get something wrong I will be corrected.So far as "random mutations" go the idea important to the theory is usually summed up as "random with regard to fitness". Dawkins discusses this in _The Blind Watchmaker (chapter 11) although he doesn't use that phrase. So this isn't new.The mechanisms in _Darwin in the Genome_ do mean modifying this view a bit. They do bias the mutations that happen in favour of mutations which MIGHT be useful. Although they can also produce mutations which are clearly detrimental like Huntington's disease. However, in a more important sense the mutations are STILL random with respect to fitness. By this I mean that the probability that a particular mutation will happen remains the same whether or not it would, in fact, be useful in the current environment.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.For scientists however, this must be a very exciting set of findings. New understanding of how mutations occur as well as a big challenging research project to consider. One possibility that might be worth investigating is the relationship, if any, between the development of these mechanisms and the Cambrian "Explosion".

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Originally posted by peter borger:
Dear paul,

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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.

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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.

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Best wishes,
Peter

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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.

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Originally posted by peter borger:
Dear paul,

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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.

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PB: You only make a couple of statements. Please expand. Let's have another close look how contemporary biology obliterates NDT.

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Best wishes,
Peter

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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.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.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.

Dr Caporale, thank you for your response, I'm glad to know that I am on track.It will be interesting to see where things go from here.

Peter, (B) so far you have not explained your argument at all. YOu just contnue to make assertions without support.You have not explained how redundancy is related to how easy the genes are to knock out, 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).
Nor do you even say how the other mechanisms from _Darwin in the Genoome_ fit inot your views.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.The lack of discussion seems to be due to your preference for "just so stories". 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!).

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 bettter collect your arguments on a web page where it will be easier to make sense of them.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.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.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 none. 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.PB (CONT) 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.PK2 : This simply demonstrates your failure to understand the actual arguments for evolution. As I have stated above it ismore of an interpolation than an extrapolation. 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 liens of evidence entirely.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. As you could have found out from a vey famous popular book written in 1986. Talk about 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.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.

So if I sum up your position.
1) In your opinion your GuToB explains the evidence as well as evolution. Since your GuToB relies on mechanisms that have not been observed it should be rejected in favour of evolution even if your opinion is correct2) If anyone points out errors in your claims it is because they are prejudiced against you. no matter what the truth is. Rejecting points out of hand without discussion is hardly the stuff of rational debate3) 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 !As to your assertions that the experts are blind because they do not share your view such views are common to cranks. When such a claim is made as an excuse to avoid admitting to the existence of your errors - well, everythingAnd no, provided links to the heads of long theads is still not an adequate reference. One of these threads is at least 19 pages long!One of the shorter threads ("More Non-Random Evolution") does not seem to have much in the way of substance. Indeed so far as I can tell it outright rejects many of the mechanisms mentioned by Dr. Caporale in favour of some unspecified mechanism of "directed mutation" which supposedly always produces exactly the same mutations. It also repeats the same misunderstanding of "random" as it applies in mainstream evolutionary theory that you still insist on. This only reinforces my negative view of your claims and your tactics in advancing those claims.

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.

Peter, YOU have just proved my point. You continually repeat falsehoods despite being corrected.The observations of Darwin and Wallace that support microbes to man evolution do not involve an extrapolation Nor do they rest on mechanisms to generate variation. I pointed that out long ago, you have offered nothing to dispute it.

I don't see any need to expand further. Your repeated erros on quite basci matters - as well as your extreme reisistance to correcting those errors speak for themselves.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 ?

I have sent you no mail.The commentary on your posts is not a scientific argument. That you think it is only revealy your lack of knowledge.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.You have not given any references to ANY evolutionary work which uses YOUR understanding of "random" mutations. Nor have you produced any evidecen that Darwin or Wallace based the idea of common descent as an extrapolation of natural selection rather than proposing natural selection to explain common descent.The reason the book was written was to inform the public of new knowledge in genetics and how it adds to our understanding of evolution. Apparently our own knowledge of genetics is so weak that yoou fail to see how the mechanisms Dr Caporale describes fit into evolutionary theory and contradict your weird ideas.All you can do is bluster in the face of the facts.

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.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. 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 ?

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.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.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.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.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 ?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.

PK: I see that you cannot answer the key point which requires explaining the alleged error in NDT. Since you are unableor unwiling to do so your claim to have refuted NDT is clearly 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.PK2 : S. Dr Caporale also concurred that NRM has important implications for phylogeny, a vision that I share. But I am more extreme.PK2: Obviously you feel the need to find an excuse to dismiss my point. But calling a fact a "mantra" as an excuse to disregard it ! Such an argument demonstrates only the weakness of your position.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.PK2: But I ALSO have an opportunity to - yet again - point out that your repeated evasion of this point shows that you did not bother to even find out what mainstream evolutionary theory actually claimed before asserting that you hasd a refutation.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.PK2: Since your position on this point clearly is untenable - and has been since the start of this thread it is obvious that you will NOT admit it even when it is obvious even to you. Why else the repeated evasion ?PK: And no, you clearly do NOT know why Dr. Caporale wrote her book which only adds to the suspicion that you havenot 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.PK2: I am not afraid to challenge your false assertions. Dr Caporale intended to add to and enrich evolutionary theory, not overthrow it as you falsely asserted.

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.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.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.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.And you have no references from _Darwin in the Genome_ that demonstrate NDT to be wrong. We both know that.. We both know that Dr. Caporales findings are a bigger problem for your views than for NDT.Your assertions about the MPG are not supported by the evidence. And misrepresentign Darwin's reasoning - as you so repeatedly do here is just a contemptible debate tactic.But keep on evading and backpedalling, Peter. It shows that your view doesn't have a leg to stand on.