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Author
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Topic: Peter Borger: Shared mutations: Common descent or common mechanism?
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John A. Davison
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Member # 1425
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posted 28. June 2006 17:59
Peter
Doesn't the achodroplasia gene occurring in distantly related organisms actually support a common descent? I can't follow your reasoning here. Do you believe that dogs and humans do not have a common ancestor? If so why? Do you believe in reproductive continuity or do you not?
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peter borger
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posted 29. June 2006 03:34
John,
I think molecular biology shows common descent is seriously in trouble. Like selection hypothesis. Like random mutations.
peebee
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John A. Davison
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posted 29. June 2006 22:19
Nothing at present seriously challeneges either common descent or reproductive continuity - absolutely nothing.
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Charles M Byrne
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posted 30. June 2006 18:49
Achondroplasia is a spontaneous mutation in humans in 85% of the cases (OMIM 100800). The site is a CpG dinucleotide. Also, the occurence is significantly higher than the known CpG bias would account for. That alone seems to support the common mechanism hypothesis.
The fixation in Dachsunds would be due to artificial selection by human breeders. (Do they all have the funny legs?)
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John A. Davison
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posted 30. June 2006 22:55
Not only are loci for mutation non random so are the loci at which chromosomes are most likely to break and recombine. There is no place for randomness anywhere in either ontogeny or phylogeny. It was all "prescribed" if I may use that word.
"Neither in the one nor in the other is there room for chance."
Leo Berg, Nomogenesis, page 134
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Mesk
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Member # 630
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posted 01. July 2006 01:33
quote:
Mesk:
As for the predictions from standard theory: 95-99% of sites should be able to map unambiguously onto the standard phylogeny, with no incongruencies. This is a high-risk prediction; if common descent is false, the odds of this proportion of the sites being congruent is minuscule.
Scott:
Is this really a prediction though? What if they don't map with that high a level of congruence? Wouldn't that just be taken as evidence of a separate evolutionary history rather than as a denial of common descent?
Sorry about the delayed reply. Basically, the common descent of two organisms implies the common descent of all of their genes (except in unicellular organisms, where genes can be transferred independently of normal vertical inheritance). In other words, if there is a specific pattern of relationship between a group of organisms, all of the genes you look at should display that pattern of relationship. You can't simply dismiss incongruency in a subset of genes as "evidence of a separate evolutionary history", as that would imply that this subset of genes had somehow followed a different evolutionary trajectory to the organisms that carried them - which is impossible in most multicellular organisms.
Of course, things can get complicated when you try to determine the pattern of relationship from gene sequence data. If a gene has a very high mutation rate, then within a comparatively short period of time the "signal" of relationship will be eroded by recurrent mutations over-writing the phylogenetic information in the gene. In contrast, if a gene has a very low mutation rate, then it may not experience enough mutations to be able to generate a phylogenetic tree (in an extreme case, a gene with no mutations at all clearly cannot be used to generate a tree - there is nothing to delineate the branches). Informative genes sit in between these two extremes.
So basically, all genes sitting within the informative range of mutation rates should provide congruent trees. There will be some incongruent sites, as there are only a limited number of sites within a gene so occasionally some will be hit by a double mutation or a reversion; but in most cases this number should be low (it will increase in proportion to the mutation rate of a gene and the evolutionary distance between two organisms). In some cases there will be particular sites within a gene that have an unusually high mutation rate due to their sequence context (as I mentioned above, it is common for a CG to mutate into a TG or a CA due to DNA methylation), and these will present "hotspots" that more likely to be incongruent - this is what can be observed in Peter's GULO data.
quote:
Btw, where do these numbers come from?
To be honest, 95-99% is just a rule of thumb I use in my own research. I suspect it is largely valid for phylogenies involving only vertebrates, but the number would decrease if you started adding organisms from other evolutionary branches (increasing the evolutionary distance spanned by the tree will increase the probability of recurrent mutations and reversions, and thus the number of incongruent sites).
Mesk.
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peter borger
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posted 10. July 2006 04:25
quote:
(as I mentioned above, it is common for a CG to mutate into a TG or a CA due to DNA methylation),
Studying the GULO "hotspots" we only see three CpG dinucleotides involved. The major part of the NRM is of unknown character. Here is a excelent challenge to the scientific community concerned with alignment of mutations to figure out the mechanism(s).
peebee
[ 10. July 2006, 04:41: Message edited by: peter borger ]
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Jehu
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posted 12. July 2006 13:39
Mesk,
quote:
Basically, the common descent of two organisms implies the common descent of all of their genes (except in unicellular organisms, where genes can be transferred independently of normal vertical inheritance). In other words, if there is a specific pattern of relationship between a group of organisms, all of the genes you look at should display that pattern of relationship. You can't simply dismiss incongruency in a subset of genes as "evidence of a separate evolutionary history", as that would imply that this subset of genes had somehow followed a different evolutionary trajectory to the organisms that carried them - which is impossible in most multicellular organisms. ...
So basically, all genes sitting within the informative range of mutation rates should provide congruent trees.
No. When this does not occur Darwinism has an explanation for it. Take for example the Chimp and Human Genom where the genes do not display a uniform distance of separation but rather deviate by millions of years. The present theory is that certain genes "followed a different evolutionary trajectory" and then were imported into the human genome at a later date through a hybrid species.
[ 12. July 2006, 14:31: Message edited by: Jehu ]
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Jehu
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posted 12. July 2006 13:42
Peter,
Sorry, you lost me. Looking at the genes detailed in your paper. Isn't it true that even if we allow for hotspots, the remaining mutations that do not occur at hotspots still follow a predicted pattern of common descent?
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John A. Davison
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posted 12. July 2006 19:07
To deny common descent is to deny evolution. To deny organic continuity is unthinkable.
"A past evolution is undeniable, a present evolution undemonstrable."
John A. Davison
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peter borger
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posted 13. July 2006 03:14
quote:
Sorry, you lost me. Looking at the genes detailed in your paper. Isn't it true that even if we allow for hotspots, the remaining mutations that do not occur at hotspots still follow a predicted pattern of common descent?
How do you know that the shared mutations in the primate sequences which are not found in guinea pig are NOT the hotspots in these multipurpose genomes?
You simply cannot know, because we are unable to distinguish between mutations that are due to a common mechanism or the result of common descent.
May claim is that what we see as alignments in primate phylogeny is the result of a common mechanism as well. This is because the primates do not reproduce together and as such there is no reason to believe they ever did so in a common ancestor. I have come to believe the whole evolutionary story with common descent of all organisms is a pure human invention, devoid of any scientific evidence, in particular now I have shown that the alignment of mutations can as well be understood as the result of a common mechanims operating in similar genomes.
As a matter of fact the sequences presented show that most likely the shared mutations in primates are the result of a common mechanism. Position 55 and 131 made me originally propose (in 2002) that the aligment is the result of a common mechanims. My proposition was confirmed in 2003 by the Japanese group.
Remarkably, most phylogenetic analysis I have seen have wobbly positions such as 55 and 131 in the GULO gene. My claim therefore is: all alignments in phylogenetic studies that give an illusion of common descent are in actuality due to a common mechanism.
The ball is now in the court of the common descent advocates to dispell my proposition. In other words, provide the scientific evidence that I am wrong.
peebee
[ 13. July 2006, 05:15: Message edited by: peter borger ]
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peter borger
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posted 13. July 2006 03:31
quote:
To deny common descent is to deny evolution. To deny organic continuity is unthinkable.
This is merely an assertion. Common descent can be demonstrated to be false on the molecualr level and so there is no common descent. I do also see no evidence of common descent in the fossil record. Maybe you do. If so, could you please be so kind to point it out.
In your manifesto you argue against continuity of germ plasma, as well, implying discontinuity of reproduction, and thus against common descent of all organisms.
Peebee
[ 13. July 2006, 03:32: Message edited by: peter borger ]
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Jehu
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posted 13. July 2006 04:07
Peter,
You said, quote:
The ball is now in the court of the common descent advocates to dispell my proposition. In other words, provide the scientific evidence that I am wrong.
I am sorry but that is unrealistic. Common descent is the accepted consensus and when you are trying to break with consensus you carry a heavy burden of perusasion
You also said, quote:
Position 55 and 131 made me originally propose (in 2002) that the aligment is the result of a common mechanims.
You may have a point with those two positions, I would add 76, 97, and 156 as well.
Also, it seems to me that positions 1, 22, 31, 58, 78, 79, 109, and 157 could easily be explained as a result of a mutation in the rat gene rather than a mutation with common descent in the chimp, human, and Orangutan.
However, if we eliminate those mutations the remaining mutations are consistent with common descent. Positions 75, 85, and 95 seem particularly consistent with common descent and since each of these mutations appear in only 2 of the 4 species it doesn't appear that one can make a strong argument that they are NRM.
[ 13. July 2006, 04:34: Message edited by: Jehu ]
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John A. Davison
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posted 13. July 2006 05:17
Peter
I never argued against common descent in my Manifesto or anywhere else. That is a cheap shot. Quite the contrary, I suggested that the original source of the germ cells was the germinal epitheliun of the gonad and that source had been "independently replaced" by extragonadal sources. I also said that sex-determining devices had "independently evolved." There is not a word in my Manifesto that denies reproductive continuity and none in any of my other papers. The only thing I have suggested is that life may have been created and/or front-loaded more than once and quite frankly I don't see how anyone can ever deny that possibility. I know of absolutely no evidence that demands special creation of man or any other organism, plant or animal. Furthermore, it is counterproductive to claim special creation. All it does is inflame the Darwinians and foment more meaningless rhetoric.
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peter borger
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posted 13. July 2006 05:36
quote:
However, if we eliminate those mutations the remaining mutations are consistent with common descent. Positions 75, 85, and 95 seem particularly consistent with common descent and since each of these mutations appear in only 2 of the 4 species it doesn't appear that one can make a strong argument that they are NRM.
Any homologous sequence is consistent with common descent. As is any homologous characteristic. That is not the issue. The issue is that we are unable to discriminate between a mechanism of non-random mutations that gives an illusion of common descnet and common descent. That is my point. My proposal of common mechanims is the alternative to common descent. Isn't that obvious. I am not a chimpanzee, and I do not want to be one.
peebee
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