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Author | Topic: stilllll waiting, Peter B... | |||||||||||||||||||
derwood Member (Idle past 1876 days) Posts: 1457 Joined: |
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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peter borger Member (Idle past 7665 days) Posts: 965 From: australia Joined: |
Dear Dr page,
If I were as childish as you, I would have opened a new thread that I am still waiting for your apology. 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. best wishes,Peter
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derwood Member (Idle past 1876 days) Posts: 1457 Joined: |
quote: 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 congruent 2. your claim that there is a discipline whose purpose is to reconcile gene trees and species trees As 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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peter borger Member (Idle past 7665 days) Posts: 965 From: australia Joined: |
Dear Dr Page,
YOU WRITE: quote:-------------------------------------------------------------------------------- Originally posted by peter borger: Dear Dr page, If I were as childish as you, I would have opened a new thread that I am still waiting for your apology. As matter of fact, I mailed you a reference on this topic, and the content 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. best wishes,Peter -------------------------------------------------------------------------------- I am very childish, this is true. MY RESPONSE:Yeah, it was obvious. YOU ALSO WRITE: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. 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. "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." AND from chapter 8.2.1: "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" You say:I have avoided nothing - your question/claim are false and vacuous. I say:Apparently, may claim is supported by the reference above. YOU SAY:There IS NO discipline whose sole purpose is to 'reconcile' gene trees and species trees. I SAY:Apparently, you didn'r read Dr R. Page's work. YOU SAY:Now, please provide documentation supportive of: 1. your claim re: evolutionary biologists believing that all gene trees and species trees must be congruent I SAY:See my reference above. You say:2. your claim that there is a discipline whose purpose is to reconcile gene trees and species trees I SAY:Apparently, it is a (sub)discipline of molecular phylogeny. AND YOU SAY:As 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. I SAY:Admitting you were wrong is a good start. YOU SAY:Now, how about some apologies for misrepresenting my colleagues and their work? I SAY:No, as demonstrated above I was right. YOU SAY:Yes Peter B, I might be childish, but as yet, I am not purposely deceptive. 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. 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. I SAY:All information I reported here was backed up by literature. And, please, mind your words. Best wishes,Peter [This message has been edited by peter borger, 10-15-2002]
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derwood Member (Idle past 1876 days) Posts: 1457 Joined: |
quote: That still does not support your earlier claim. A few key words: implicit assumption Understanding 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 quote: Actually, it is not. quote: 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. quote: Saw it, red herring.quote: 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 ...quote: No, you did not, but that will not stop the creationist from insisting otherwise. It never does.quote: No, just deceptive. Or deluded. How else could one take evidence counter to their position and claim that it actually supports it?quote: I am minding them, and your's as well, and sadly, no, you did not support your claims.
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peter borger Member (Idle past 7665 days) Posts: 965 From: australia Joined: |
Dear Dr Page,
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. Best wishes,Peter
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derwood Member (Idle past 1876 days) Posts: 1457 Joined: |
quote: 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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peter borger Member (Idle past 7665 days) Posts: 965 From: australia Joined: |
Dear Dr Page,
You write: I know what ISOMORPHIC means. I also know what IMPLICIT ASSUMPTION means. Do you? MY RESPONSE:My dictionary says: Implicit, 1) implied though not plainly expressed; 2) virtually contained; 3) absolute, unquestioning, unreserved. Which one do you prefer? My disctionary also says: Assumption, 1) the act or an instance of assuming; 2) the act of an instance of accepting without proof, 3) arrogance; 4) the reception of the Virgin Mary bodily in heaven, according to the Roman Catholic Doctrine. Which one do you prefer? Not #4, I guess YOU SAY:Do you understand what reconciliation means? It seems not. MY RESPONSE:My dictionary says: Reconcile = harmonise; make compatible. YOU SAY: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. MY RESPONSE:Actually I have it right here on my desk, and I rather like his work. YOU SAY: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. MY RESPONSE:According to the meaning of the words (see above), I substantiated my claim and you are in denial. However, if gene trees do not have to be in accord with species trees, what is all this fuss about? And also, what is the reconciliation good for? Please explain, so I can understand it. Thanks in advance, Best wishes,Peter
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Mammuthus Member (Idle past 6475 days) Posts: 3085 From: Munich, Germany Joined: |
quote: ************************** If I can jump in briefly as you and SLPx slug it out, there is no reason to expect all gene trees to be identical to species trees. Horizontal transfer precludes the transferred genes from matching a species tree...in fact this is how I look for transfer events. i.e.the Bov-B elements present in snakes are shared almost identically by some but not all ungulates such as cows. The sequence divergence is not very pronounced. This is not true of other genes in snakes and cows. The Bov-B element is a retrotransposon which can jump from species to to species. Thus, no expectation that this genetic element when analyzed would give an identical gene and species tree.
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monkenstick Inactive Member |
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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mark24 Member (Idle past 5195 days) Posts: 3857 From: UK Joined: |
quote: The book Peter B quotes concurs, I don't know why he thinks it doesn't. Chapter 8. 8.2 Gene trees & species trees. Mark ------------------Occam's razor is not for shaving with.
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derwood Member (Idle past 1876 days) Posts: 1457 Joined: |
quote: 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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Mammuthus Member (Idle past 6475 days) Posts: 3085 From: Munich, Germany Joined: |
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?
cheers,M
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derwood Member (Idle past 1876 days) Posts: 1457 Joined: |
quote: 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).
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Mammuthus Member (Idle past 6475 days) Posts: 3085 From: Munich, Germany Joined: |
quote: ****************************** I get it now. Thanks. This is akin to his "Dawkin's has no right to talk about evolution since he is a zoologist" post. Or the "you cannot run a gel in a tube" blunder
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