Darwin in the Genome

PaulK:
You have summarized the issues very well.
I agree with the concept that a biochemical innovation in the mechanisms that generate genome variation could lead to a great expansion, such as the Cambrian---the following example, on a less comprehensive scale than the Cambrian expansion, is discussed in the book:Cone snails appear to have evolved an efficient mechanism for exploring new toxin sequences [which they use eg to kill prey], facilitating the access to a wide range of food sources for diverse species of snail.

Archetypes. I see... In your exchanges with Dr Page & others your problem with common descent seem to be limited in the evolution of phyla. So I assume that you don't have any problems with evolution within phyla?[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.Does that follow from your theory?

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

Peter-
When you say it will be confirmed at the molecular level soon: 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?
Lynn

quote:

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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.

​

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

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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.

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]

Hi Peter-
Since you referred to our email exchange, I thought I'd include here my response to your question about implications for phylogenetic analysis to share with the others:
You are absolutely right that there are implications for phylogenetic analysis-- Lynn Ripley emphasized this to me when she was preparing her talk for the NYAS conference.
There has been some necessary work to incorporate recombination A Bayesian model for detecting past recombination events in DNA multiple alignments - PubMed
and variable mutation rates
The effects of variable mutation rates across sites on the phylogenetic estimation of effective population size or mutation rate of DNA sequences - PubMed
into phylogenetic analysis
Lynn

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]

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

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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.

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?

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.

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]