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Topic: Implications of Behe and Snoke paper
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Jules
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Member # 181
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posted 09. July 2006 17:16
Michael Behe and David Snoke wrote a paper a while back, in which they tried to calculate the probability of single point neutral mutations resulting in a new, functional gene:
http://www.proteinscience.org/cgi/content/abstract/ps.04802904v1
During testimony at the Dover trial, Behe admitted that a ton of earth contained enough bacteria, that a new gene could be produced this way in about 20,000 years (I'll try to find the exact page of the transcript and enter it in the next post).
Given that bacteria have been around a few billion years, the question arises: Couldn't this method of making new genes have resulted in the genes that produce the bacterial flagellum?
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Jules
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posted 09. July 2006 17:39
Well, I guess Behe didn't say a new gene. What he did say in the transcript:
quote:
The fact that very large population sizes, 10 to 9th or greater, are required to build even a minimal MR feature requiring two nucleotide alterations within 10 to the 8th generations by the processes described in our model, and that enormous population sizes are required for more complex features or shorter times, seems to indicate that the mechanism of gene duplication and point mutation alone would be ineffective, at least for multicellular diploid species, because few multicellular species reach the required population sizes.
"An MR feature requiring two nucleotide alterations...." Is that a new gene?
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Jules
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posted 10. July 2006 17:32
OK, so far nobody has tried to enlighten me. So I've gone back to Behe's article. I don't know how to copy the graph, but it's the last one in the article. It shows that the more mutations needed, the larger the population size required, or the more generations required. By the time one gets to 10 mutations, the population size required is 10<30>, and the number of generations is ... was it 10<14>? I'll have to go back and check.
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Jules
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posted 10. July 2006 17:35
No, merely 10<12> generations. Now I'll have to go back to the transcript. I think Behe explained how many bacteria there are (or have been?).
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Jules
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posted 10. July 2006 17:46
From the transcript:
quote:
10 to the 30th, that is quite a lot, right?
A. Yes. That's roughly what is calculated to be the bacterial population of the Earth in any one year. And so over the course of the billion year, 4 billion year history of the Earth, there would probably be a total of roughly 10 to the 40th.
So if we needed 10 neutral mutations to a duplicated gene, before we had a new selectable trait, that would require 200 billion years, if my calculations are correct.
But what if we only needed 2 neutral mutations per duplicated gene, but we needed 5 additional genes ? Would we still require 200 billion years, or would the calculations be different?
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Zachriel
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posted 11. July 2006 08:13
Jules: ""An MR feature requiring two nucleotide alterations...." Is that a new gene?"
Yes.
There are many, many problems with Behe & Snoke's paper. They choose a rather difficult example from protein evolution, but no matter. They assume that the duplicate gene has fixed in a population and deactivated along the way. The reasonably correct model is that a duplication starts in a single individual, then evolves from there. They assume that every mutation that doesn't reach the teleological goal are deleterious. This is not the case, and flies in the face of modern protein biology which finds that most genes are very tolerant of amino acid substitutions. They then assume that these intermediaries are not subject to selection. In fact, a substantial portion of the intermediate products will be subject to positive selection and fixation. For the same reason, the original unduplicated gene in the population may already have many of the features of the teleological goal.
As Behe admitted this teleological goal could be reached in 20,000 years, it would seem this does not present a problem for the standard evolutionary model of population genetics.
Specialists indicate that Behe and Snoke's estimate is far too long. Behe additionally admits that his model doesn't include many of the salient processes of actual evolution. In his reply to Lynch's criticism he even confuses beneficial selection of reduced function with deleterious selection.
You might actually read Lynch's paper on this. Publication in a peer journal is just the first step of the scientific review process.
M. Lynch
Simple evolutionary pathways to complex proteins
Protein Sci., September 1, 2005; 14(9): 2217 - 2225.
http://protsci.highwire.org/cgi/content/abstract/14/9/2217
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Jules
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posted 11. July 2006 15:52
Thanks Zach, for the information. If you and others don't mind, I think I would like to reserve this current thread for comments on the implications of the Behe and Snoke paper, assuming it is correct, accurate, "true", or valid.
What if we start another thread, where we ask the question, Is the Behe and Snoke paper correct, accurate, true, or valid? If the moderator doesn't mind, and if you don't mind, I think I'll start one now, and put your comment first.
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Jules
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posted 11. July 2006 16:20
Whoops! I said 200 billion years, and I believe I should have said 200 million years. If 10<8> generations of bacteria is 20,000 years, then I believe 10<12> generations would be 200 million years. So it would take a bacteria population of 10<30> (the amount of bacteria estimated to be on the earth at any one time) 10<12> generations, or 200 million years, to produce a new protein with 10 new amino acid residues, using single point neutral mutations in a duplicated gene.
If I got that right (who knows?), what are the implications?
It seems that bacteria had plenty of time to produce the proteins needed to make a bacterial flagellum. However, I think we still haven't answered the question of whether each protein provides a selectable advantage for the organisms, until all the proteins are "in place" to produce the flagellum. We could say that the TTSS came first. But there is still a wide gap from whatever would have preceded the TTSS, and there is still a wide gap from the TTSS to the flagellum. What are the proteins "doing" while waiting until all the proteins needed for the TTSS or the flagellum are present?
At this point, regardless of the accuracy of the Behe/Snoke paper, it looks to me like we are still in need of a detailed Darwinian scenario to explain how the bacterial flagellum came to be.
But then, Behe and Snoke seem to think the significance of their paper wasn't that it caused problems for evolution among bacteria. They think it caused problems for evolution of systems among eukaryotes, especially multicellular organisms. Maybe I'll try to "tackle" (HA!) that next.
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Jehu
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Member # 1981
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posted 12. July 2006 13:29
Behe and Snokes replied to Lynch in the same journal. Lynch made a strawman argument and his comments were little more than high sounding statements devoid of relevance but intending to satisfy those who are convinced by such things.
"MR feature" stands for multiresidue feature. Behe says that populations of 10 to the 9th or greater are needed to mutate even a minimal MR feature (two amino acids) within 10 to the 8th generations. Understand that this is not some kind of damaging admission against his argument, this is the sort of calculation Behe and Snokes took for granted before writing their paper. Constructing the flagellum is not an simply an issue of minimal MR features.
Also, please explain to me where you get 20,000 years from 10 to the 8th generations. I must be missing something. Or you are.
[ 12. July 2006, 13:31: Message edited by: Jehu ]
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Jules
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posted 12. July 2006 17:15
Jehu wrote: quote:
Also, please explain to me where you get 20,000 years from 10 to the 8th generations. I must be missing something. Or you are.
Sorry, Jehu, I should have just quoted from the transcript:
quote:
Q. Okay. So 10 to the 8th generation, that's 100 million generations?
A. That's correct.
Q. And yesterday, you explained about bacteria, that 10,000 generations would take about two years in the laboratory, correct?
A. Yes.
Q. So 100 million generations, that would take about 20,000 years?
A. I'm sorry?
Q. 100 million generations, which is what you calculated here, that would take about 20,000 years?
A. Okay, yes.
Jehu also wrote: quote:
Constructing the flagellum is not an simply an issue of minimal MR features.
Understood. I'm assuming, for the sake of argument, that one might believe that the flagellum could have evolved by neutral mutations of duplicated genes. And it seems that there is enough time available for that to happen. Of course, I'm also assuming that we would never need more than 10 new amino acids in our new proteins. Other problems probably remain. If I knew more science, I might know what they are. The one that seems obvious to me is that a bacteria that has produced a new protein, that folds and has new binding sites, needs a function for that protein, or there's no need to make it. So we need a scenario that explains what the new proteins were doing before all of them needed to construct a flagellum were present.
Jehu started out by writing: quote:
Behe and Snokes replied to Lynch in the same journal. Lynch made a strawman argument and his comments were little more than high sounding statements devoid of relevance but intending to satisfy those who are convinced by such things.
Yes. I haven't looked at Zach's link, yet. Are Behe and Snoke's comments there, as well? If not, could you provide a link to them? And would you mind posting it at the other thread (Is Behe/Snoke paper true...)?
[ 12. July 2006, 17:24: Message edited by: Jules ]
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Jules
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posted 12. July 2006 17:28
So before I try to find out generation times for eukaryotes, does anybody already know what they are? Starting with the "simplest" unicellular eukaryotes?
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Jehu
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posted 12. July 2006 18:55
I don't have a copy of Behe's response but here is an excerpt:
Lynch’s and our models are not mutually exclusive. Some evolutionary pathways might involve both deleterious and neutral mutations. Lynch writes in the section “The Model” that we “imply that all amino acid changes lead to nonfunctionalization.” We imply no such thing. Although we assumed that intermediate mutations required for a new feature decreased function, we wrote, “it can be calculated that on average a given position will tolerate about six amino acid residues and still maintain function.” Our estimation of explicitly takes into account the tolerance of sites for substitution.
In “The Model,” Lynch writes, “As in Behe and Snoke (2004), this adaptation is assumed to be acquired at the expense of an essential function of the ancestral protein…” We made no such assumption. In our model, the final mutation might restore and enhance the original function.
http://www.uncommondescent.com/index.php/archives/1283
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Zachriel
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posted 12. July 2006 20:28
Jehu: "Lynch made a strawman argument and his comments were little more than high sounding statements devoid of relevance but intending to satisfy those who are convinced by such things."
Lynch is a widely cited professional biologist who is making an argument concerning the applicability of the assumptions made by Behe and Snoke. They are considerable objections. The sensitivity of the calculation to p (the average number of mutations required to inactivate a gene) is one such problem. I mentioned others previously.
Jehu: "Behe says that populations of 10 to the 9th or greater are needed to mutate even a minimal MR feature (two amino acids) within 10 to the 8th generations."
Bacterial generations can be measured in hours, so 10^8 generations is not such a long period of time. As there are ~10^14 prokaryotes in the average human gut, and ~10^30 in the world at any one time, that means that the evolution of the posited genes occurs thousands of times a second — according to Behe & Snoke's calculations. And they admit to have only considered one very limited type of evolutionary process.
Behe and Snoke have "proved" that evolution of new genes is an inevitability.
[ 12. July 2006, 20:31: Message edited by: Zachriel ]
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