stilllll waiting, Peter B...

Borger had written:"ACCORDING TO EVOLUTIONARY BIOLOGISTS, GENE TREES HAVE TO BE IN AGREEMENT WITH SPECIES TREES. "I provided a quote from an evolutionary biologist that contradicts this. Borger has yet to provide any support for this claim of his.I know why that is.Does anyone else?

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Originally posted by peter borger:
Dear Dr page,

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If I were as childish as you, I would have opened a new thread that I am still waiting for your apology.

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As matter of fact, I mailed you a reference on this topic, and the contence demonstrates that certain genes have to be reconsiled, e.g. IL-1beta, LDH, etcetera. I asked you in a previous letter "if it doesn't matter that gene trees are not in accord with species trees why is there a discipline in evolutionary biology that reconsiles the trees in an utterly speculative manner by the addition and/or deletion of putative gene duplications?" Since you are the PhD evo-biologist --not me-- I expected that this is not such a difficult question. But, apparently it is a tough question for you, since you keep avoiding it.

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best wishes,
Peter

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I am very childish, this is true.However, you are merely trying to pull a bait and switch type thing here.YOU claimed that evolutionary biologists say all gene trees must be congruent. I provide a quote form an evolutionary biologt that contradicts this. You have STILL to propvide any such support for your original contention.I have avoided nothing - your question/claim are false and vacuous.There IS NO discipline whose sole purpose is to 'reconcile' gene trees and species trees.Now, please provide documentation supportive of:1. your claim re: evolutionary biologists believing that all gene trees and species trees must be congruent2. your claim that there is a discipline whose purpose is to reconcile gene trees and species treesAs for this gibberish about an apology - I already admitted that I was in error, that I did not realize that you were referring to Rod Page.Now, how about some apologies for misrepresenting my colleagues and their work?Yes Peter B, I might be childish, but as yet, I am not purposely deceptive.You are engaging in a campaign of disinformation. That, or you are competely ignorant of the entire field. I vote a little of each.

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Originally posted by peter borger:

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YOU ALSO WRITE:
However, you are merely trying to pull a bait and switch type thing here.

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YOU claimed that evolutionary biologists say all gene trees must be congruent. I provide a quote form an evolutionary biologt that contradicts this. You have STILL to propvide any such support for your original contention.

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MY RESPONSE:
Quote from chapter 8.2 Gene trees and species trees, p286, Molecular Evolution, A Phylogenetic Approach by R Page and EC Holmes, isbn nr:0-86542-889-1.

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"The implicit assumption made when we use molecular phylogenies to infer organismal relationships (section 8.1) is that GENE TREES ARE ISOMORPHIC WITH SPECIES TREES (caps are mine, PB) -- the former can be converted into the latter merely by substituting the name of the sequence with the name of the organism form which the sequence was obtained. As sequence data have accumulated it has become increasingly clear that the relationship between gene trees and species trees may be more complex than a simple one-to-one correspondence."

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AND from chapter 8.2.1:

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"One of the first attempts to deal with this PROBLEM (caps are mine, PB) is the concept of RECONSILED TREES, first introduced by Morris Goodman and colleagues in 1979..... etcetera"

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That still does not support your earlier claim. A few key words:implicit assumptionUnderstanding that English is not your first language might account for some of the issues here. The assumption that gene trees and species trees would/should be congruent is basically an intuitive one. As is pointed out in your quote, NEW INFORMATION has shown that such is not always tenable. The quote I provided form Futuyma is one of many on the subject - there is no 'rule' that gene trees and species trees (or all gene trees) [si]should[/i] be congruent. Of course, the incongruencies - the creationists beloved anomolies - are typically of very small scale.
The fact that Goomdna et al. looked at this issue does not support your claim that there is a discipline devoted to reconciling trees. I know Goodman was not involved in such a discipline.So, basically, I am still waiting for: 1) Evidence that evolutionary biologists believe that gene trees and species trees must be congruent and 2) that there is a scientific discipline devoted to reconciling trees

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You say:
I have avoided nothing - your question/claim are false and vacuous.

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I say:
Apparently, may claim is supported by the reference above.

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Actually, it is not.

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YOU SAY:
There IS NO discipline whose sole purpose is to 'reconcile' gene trees and species trees.

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I SAY:
Apparently, you didn'r read Dr R. Page's work.

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No, i did not. But having read it, it doesn't appear that you got much out of it. That some looked into ways of reconciling trees is not the same thing as there being a scientific discipline devoted to such an endeavor as per your original claim. Of course, it does not seem to me tha you actually understand what the 'reconciliation' involves. Do you think that performing sequence analyses on non-homologous paralogous genes that havbe undergone conversion should yield the same results as analyses of non-paralogous genes? Your answer to this will provide great deal of insight into whether or noyt you understand what the 'reconciliation' consists of.

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YOU SAY:
Now, please provide documentation supportive of:

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1. your claim re: evolutionary biologists believing that all gene trees and species trees must be congruent

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I SAY:
See my reference above.

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Saw it, red herring.

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You say:
2. your claim that there is a discipline whose purpose is to reconcile gene trees and species trees

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I SAY:
Apparently, it is a (sub)discipline of molecular phylogeny.

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Actually, it is not. It was just an attempt by a creationist to make it oook as though there are big troubles in evolutionary systematics ...

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YOU SAY:
Now, how about some apologies for misrepresenting my colleagues and their work?

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I SAY:
No, as demonstrated above I was right.

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No, you did not, but that will not stop the creationist from insisting otherwise. It never does.

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YOU SAY:
Yes Peter B, I might be childish, but as yet, I am not purposely deceptive.

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I SAY:
Purposely deceptive? If I were you I wouldn't use such words in a discussion. I could demand for another apology. For that you accuse me of deception. Luckily, I am not childish.

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No, just deceptive. Or deluded. How else could one take evidence counter to their position and claim that it actually supports it?

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YOU SAY:
You are engaging in a campaign of disinformation. That, or you are competely ignorant of the entire field. I vote a little of each.

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I SAY:
All information I reported here was backed up by literature. And, please, mind your words.

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I am minding them, and your's as well, and sadly, no, you did not support your claims.

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Originally posted by peter borger:
Dear Dr Page,

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Maybe you didn't get it but ISOMORPHIC is greek and means SAME FORM. Thus according to these phylogeneticists the form of the gene tree has to be the same form as the species tree. So, I proved my point. Now, all you can do is distort my words or back track.

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Best wishes,
Peter

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I know what ISOMORPHIC means. I also know what IMPLICIT ASSUMPTION means.Do you?Do you understand what reconciliation means?It seems not.I suggest you read R. Page's book again, and this time for reasons other than finding a few key quotes that you can spin.As you have been unable to substantiate your claims re: 'discipline' devoted to 'reconsiling' trees and evolutionary biologists needing gene trees and species trees to be the same, I will conclude that you cannot.Bye.

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Originally posted by mark24:

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Originally posted by monkenstick:
i'm an undergrad, and the topic recently in "genetics, biodiversity and evolution" has actually been phylogenetic trees. The lecturer specifically stated that gene trees are not synonymous with species trees and that it was incorrect to automatically assume that any data used in phylogenetic tree building would give you a 100 percent accurate species tree

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The book Peter B quotes concurs, I don't know why he thinks it doesn't.

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Chapter 8. 8.2 Gene trees & species trees.

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Mark

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I know why.Like most internet creationists, Borger has tripped himself up again, and as with biblical apologists, the creationist cannot allow a mistake to be noticed, l est the observer will have doubts about their other claims.This is moot, as practically everyone here recognizes Borger's desperation, unorthodox 'interpretive' skills, unwarranted assumptions and conmclusions, etc., so admitting hyperbole would be the least of his problems.However, it would be an admission, and the hyperconfident cannot have that.I proved my point, I'm done with this issue.

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Originally posted by Mammuthus:
I actually went through Page and Holmes this weekend and also an older Mol Evol book of John Avise and they both explicitly state that it would be naive to assume that gene trees are always identical to species trees....how did this supposed "controversy" start in the first place in this thread?

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cheers,
M

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Borger had claimed that "evolutionary biologists" expect gene trees and species trees to be congruent, and the fact that he found a couple incongrencies in the literature lead him to the 'conclusion' that therefore evolution did not happen.
He also claimed that becasue of these incongruencies, evolutionists set in place a 'discipline' whose sole role was to 'reconsile'[sic] this incongruence. The implication is that this 'reconciliation' is to smooth over the 'rough spots' for the poor evos. Unfortunately, it is not how Borger implies (as usual).

[QUOTE]Originally posted by peter borger:
Your solutions sounds like Dr Page's explanation of genes in human not present in primates: random deletion in all primates but man.[QUOTE] 1. Please provide the quote in which I stated that.2. Please find out what a Primate is.

[QUOTE]Originally posted by peter borger:
YOU SAY: [QUOTE]Originally posted by peter borger:
Your solutions sounds like Dr Page's explanation of genes in human not present in primates: random deletion in all primates but man.

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1. Please provide the quote in which I stated that.

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MY RESPONSE:
You are of particular short memory. In your mailing #170 (thread molecular evidence against random mutation)

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Oh yeah - just after I demonstrated that you had misrepresented Kimura and that you were backtracking on a number of emphatic laims you had previously made...

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you gave this brilliant evolutionary explanation for the gene in the human LCR16a region not present in apes

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Hmmm.... The only reference I found to LCR16a in the literature in fact indicates that not only do apes have the region, but so do Old World monkeys:********************************
J Hered 2001 Nov-Dec;92(6):462-8Divergent origins and concerted expansion of two segmental duplications on chromosome 16.Eichler EE, Johnson ME, Alkan C, Tuzun E, Sahinalp C, Misceo D, Archidiacono N, Rocchi M."Within the human genome, at least 70% of the LCR16u copies were duplicated in concert with the LCR16a duplication. In contrast, only 30% of the chimpanzee loci show an association between LCR16a and LCR16u duplications. The data suggest that the two copies of genomic sequence were brought together during the chimpanzee/human divergence and were subsequently duplicated as a larger cassette specifically within the human lineage..."****************************
more later...

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Originally posted by peter borger:
Dear Dr Page,

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It was about the GENE present in human not present in apes. Not about the LCR16a region alone.

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Best wishes,
Peter

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[This message has been edited by peter borger, 10-23-2002]

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Which GENE is that? Ref please. I searched this site and got no hits, and I searched Medline for LCR16a and got the single hit I cited.