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Author | Topic: Does Neo-Darwinian evolution require change ? | |||||||||||||||||||||||||||||||||||||||||||
PaulK Member Posts: 17828 Joined: Member Rating: 2.3 |
quote: Is that really true ? I'd have thought that the discovery of fewer genes than expected by the Human Genome Project would have cut the amount of functional DNA, and I very much doubt that the relatively small number of regulatory sequences etc. discovered makes up the difference. So is the figure really 30% ? Do you have any evidence ?
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RAZD Member (Idle past 1433 days) Posts: 20714 From: the other end of the sidewalk Joined:
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Hi slevesque.
But this is statistically very unrealistic. If a generation moved away from the peak by 50 mutations, in a genome of 3 billion, it is extrememly improbable that the next generation will move back towards the peak on not simply farther away. Why? Draw a circle around the original individual and then draw the same size circles around a point on the circumference of that circle. The first circle represents the range of possible mutations away from the position of the parent individual, the second is the possible range of mutations away from one of the outermost the offspring -- how much of that outer offspring circle is inside the parent circle? I get 39.1%, which I do not count as extremely improbable, and that is the worst case. You could have second generation individuals slightly away from center such that >90% of their offspring would be within the parent circle. With neutral drift there could be a slight tendency to move subsequent offspring gradually away from the parent center, but when selection is included, the portions inside are differentially selected from the portions outside, thus weighting the proportion within the parent circle higher than the proportion outside the circle. If sexual selection is involved there would be a strong selection for individuals at the center to reproduce more, to the disadvantage of outer individuals, where some may be left entirely out of the picture for the next generation. If we disregard sexual selection, there can still be significant selection pressure. Just because the population appears to be in stasis, this does not mean that there is no selection pressure in the population: if the population has expanded to consume the limits of the ecology (which is normal in a stable ecology), and reproduction produces many more offspring than needed to replace the losses, then competition for limited resources can produce high survival selection, such that any second generation individuals within the circle could reproduce significantly more than those outside, thus moving the offspring back towards the center. You can also envisage fitness topologies around the peak, and the further away an individual is, the more of their offspring circle is inside the topology line, and the stronger would be the selection pressure to benefit those inside versus those outside the topological boundary. It becomes very easy, imho, to see that most of the population would always be near the peak, that the trend for the offspring of the outer individuals would be towards the center, overcoming any slow trend of the offspring of central individuals away from the center, thus generating oscillations in the lineages where movement away in one generation is balanced by movement back towards the center in other generations. Enjoy. (2/3-(3)0.5/2π) = 0.391 Edited by RAZD, : clrty by our ability to understand Rebel American Zen Deist ... to learn ... to think ... to live ... to laugh ... to share. Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)
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dwise1 Member Posts: 5952 Joined: Member Rating: 5.2 |
Two rather influential graphics early in my studies were both from the circa-1980 article in either Science or Nature which covered the introduction of Punc Eq -- I have a xerox copy of that article stored away in a box somewhere. One graphic illustrated that highly specialized species that are finely tuned to their environments tend to be very short-lived, going extinct when that environment changes to rapidly for them to adapt, whereas less-specialized species tend to be much longer-lived, being better able to weather changes in their environments as well as a wider range of environmental conditions, such that they would appear in the fossil record as being in stasis.
The other graphic is the one that's more apropos here. It illustrated a period of "rapid" change by a slanted line between two conditions of stasis. Over that line was a long parade of bell curves representing individual generations. Each generation's bell curve overlapped the bell curves of the neighboring generations. Over the years, I have arrived at the opinion that there really isn't any such thing as actual "evolutionary processes." Rather, evolution is mainly just the end result of life doing what life does, of populations of plants, animals, and protista surviving-or-not and reproducing-or-not. What we describe as evolution and evolutionary processes is our observation of and analysis of the cumulative and aggregate effects of life. Nothing magical about it. And the only way for evolution to violate the laws of thermodynamics would be if life itself were to violate those laws, which it does not. And the only way for evolution to be impossible would if life itself were impossible. Just throwing that out there, in part to see how much fire it will draw. But I do have one question about these graphing models of the individuals of a population clustering and oscillating about local adaptive peaks. Instead of graphing their genomes about those adaptive peaks, shouldn't we be graphing their phenotypes? Because selection does not directly select for or against the genotypes, but rather for or against the phenotypes that those genotypes would express. Edited by dwise1, : just throwing that out there, ...
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AZPaul3 Member Posts: 8563 From: Phoenix Joined: Member Rating: 4.7 |
Yes, but even taking those in the population closer, their babies will be farther then there parents because of the high mutation rates. The mutations will always force a population to drift away from the optimal peak ... Really? Based on what? First, why do you assume mutation moves the individual away from the optimum? Why do you assume mutation moves the offspring further away than is the parent? Is it possible for the offspring to have a mix of beneficial mutations for some attributes, mildly dilitarious for others, neutral for most and have the kid wind up at the same point or better then the parent. Second, those with dilitarious mutations have the least effect on the population, especially larger populations. Do you understand why? And those closer to the optimum have a better chance of having offspring with beneficial mutations. Do you understand why?
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Dr Adequate Member (Idle past 313 days) Posts: 16113 Joined: |
Of course, and the most deletirious mutations will be wiped out of each generation without any problem. But some individuals most survive and reproduce, and what I'm sayign is that the high mutation rates imply that those individuals will have inherited lots of mutations, and although they may have the least deleterious set of mutations to have appeared in that generation, doesn't mean they still don't have those mutations. So we'll get neutral drift, which is technically evolution but not in the interesting sense of the word, and which needn't show up in the fossil record.
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sfs Member (Idle past 2562 days) Posts: 464 From: Cambridge, MA USA Joined:
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slevesque writes:
I assume you're talking about the human genome. The estimates for the functional fraction of the human genome that I'm familiar with started around 100%, dropped to 20%, dropped to "at least 5%", and are now hovering in the range of 6 - 10%. I'm not aware of any secular trend in this estimate.
Ok I think I got misunderstood there. What I was saying was: The % of functioning genome has been ever increasing in the past few years, as I'm sure you know. quote:Well, you can safely say it in the sense that no one will throw a brick through your window for doing so, but I don't know of any geneticists who think that. quote:Yeah, but the entire genome almost certainly isn't functional, and even their estimates for the transcribed fraction were probably much too high (at least if what the people who do that sort of thing have told me is correct). quote:Geneticists keep finding functional bits of noncoding DNA, and the bits they keep finding constitute only tiny fractions of the genome. Meanwhile, vast swathes of the genome look and act exactly like junk: transposons, pseudogenes, and the like, almost all showing no sign of selective constraint. The fact that a single experiment, using rather dubious methodology, concluded that much of the genome is transcribed shouldn't weight very heavy in your thinking.
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sfs Member (Idle past 2562 days) Posts: 464 From: Cambridge, MA USA Joined: |
quote:I haven't been following the argument here, but this analogy is not a good one. Mutations are, to a first approximation, orthogonal to one another, so you should be working in a much higher dimensional space. Imagine the 50 mutations to be fifty unit steps in 50 of perhaps a million dimensions. The next 50 mutations will be in another 50 random dimensions. The probability of heading back toward the peak (neglecting selection) is tiny.
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slevesque Member (Idle past 4669 days) Posts: 1456 Joined: |
For example:
quote: Junk DNA Guides Embryo Formation – SciScoop Scitext ChemSpy I think that we are starting to see a paradigm shift in this field. The paradigm was that, DNa was mostly junk, and so it was a waste of time to try searching for it's use. Once more and more parts are being unravelled and found to have a use, I think an avalanche of discoveries in that field will come. But, as prof. John Mattick said:
quote:
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slevesque Member (Idle past 4669 days) Posts: 1456 Joined: |
Really? Based on what? First, why do you assume mutation moves the individual away from the optimum? Why do you assume mutation moves the offspring further away than is the parent? Is it possible for the offspring to have a mix of beneficial mutations for some attributes, mildly dilitarious for others, neutral for most and have the kid wind up at the same point or better then the parent. The most conservative estimate of the deleterious-to-beneficial ratio of mutations was 50 to 1. I've seen some suggest perhaps as high as a million to 1. But even with the 50-1 ratio, it's still pretty obvious that the high mutations rates will push the next generation farther away from the peak then their parents from the optimal peak.
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slevesque Member (Idle past 4669 days) Posts: 1456 Joined: |
So we'll get neutral drift, which is technically evolution but not in the interesting sense of the word, and which needn't show up in the fossil record. Kimura's ''neutral evolution'' only works if the vast majority of the genome has no function. Even if only 5% of it were functional, a mutation rate of 40mpipg would result in two mutations falling into the functional part of it. And all that I have said would still hold. Of course, this problem becomes increasingly more difficult the more functional the genome turns out to be.
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slevesque Member (Idle past 4669 days) Posts: 1456 Joined: |
This is about exactly what I was going to say.
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PaulK Member Posts: 17828 Joined: Member Rating: 2.3 |
quote: So all you've got is speculation ? I'd have thought that things would have moved on a bit since 2004. So much for your claim that practically all geneticists would agree with your 30% figure.
quote: Wake up. The truth is that the existence of regulatory sequences has been known for a long time. And the search for function in non-coding sequences has been going on for quite a time too - where do you think all the results you use to try to "prove" that so much of the genome has a function come from ?
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AZPaul3 Member Posts: 8563 From: Phoenix Joined: Member Rating: 4.7 |
Look
Look Look The most conservative estimate of the deleterious-to-beneficial ratio of mutations was 50 to 1. I've seen some suggest perhaps as high as a million to 1. But even with the 50-1 ratio, it's still pretty obvious that the high mutations rates will push the next generation farther away from the peak then their parents from the optimal peak. BS. Your numbers are either very wrong or very purposefully skewed. [ABE] No, I do not mean by you, but by your sources. Which are where, btw? Edited by AZPaul3, : No reason given.
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Wounded King Member Posts: 4149 From: Cincinnati, Ohio, USA Joined: |
Kimura's ''neutral evolution'' only works if the vast majority of the genome has no function. Oh really? Do you have any clue what you are talking about? Kimura was principally talking about protein evolution, i.e. that portion of the genome that is already accepted as having biologically relevant function. Once again you conflate transcriptional activity with biologically relevant function, exactly the same thing half a dozen people just called you out on and you made wounded noises about having been misunderstood over. Have you never heard of synonymous mutations? Do you not understand third base wobble? Even going by just this one phenomenon you can mutate ~30% of a protein coding gene without changing a single amino acid in the resultant protein. That is before you even touch upon the fact that many amino acids can functionally substitute for one another and that in many instances almost any amino acid will do as long as it has the correct level of hydrophobicity. What you say just highlights, once again, that you don't understand what you are talking about. TTFN, WK
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RAZD Member (Idle past 1433 days) Posts: 20714 From: the other end of the sidewalk Joined: |
Hi sfs, thanks,
I haven't been following the argument here, but this analogy is not a good one. If you haven't followed the argument, then how do you know the analogy is not a good one?
Mutations are, to a first approximation, orthogonal to one another, so you should be working in a much higher dimensional space. Imagine the 50 mutations to be fifty unit steps in 50 of perhaps a million dimensions. The next 50 mutations will be in another 50 random dimensions. The probability of heading back toward the peak (neglecting selection) is tiny. What was being discussed was the relation of the individual to a fitness map, with a peak of fitness for the population in a static ecology. You can correlate all your 50 dimensional mutations into direction to or away or orthogonal to fitness and from that derive a radius for each individual relative to the parent.
(neglecting selection) And we definitely are not neglecting selection. Enjoy. by our ability to understand Rebel American Zen Deist ... to learn ... to think ... to live ... to laugh ... to share. Join the effort to solve medical problems, AIDS/HIV, Cancer and more with Team EvC! (click)
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