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Author | Topic: Do you really understand the mathematics of evolution? | |||||||||||||||||||
PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
And quite enlightening it is, although hardly surprising, especially in light of the previous thread.
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PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
From the Wikipedia article Models of DNA Evolution
The models described on this page describe the evolution of a single site within a set of sequences. They are often used for analyzing the evolution of an entire locus by making the simplifying assumption that different sites evolve independently and are identically distributed. This assumption may be justifiable if the sites can be assumed to be evolving neutrally. If the primary effect of natural selection on the evolution of the sequences is to constrain some sites, then models of among-site rate-heterogeneity can be used. Let us note that there will be selection constraining some sites in a Kishony experiment.
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PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
quote: I don’t think that is going to last.
quote: No, it really isn’t a problem. These are models of neutral evolution. They are used to estimate divergence times between species. Since neutral evolution dominates and since it is not practical to identify which loci were selected in the distant past - except by divergence from these models - that’s obviously a sensible thing.
quote: I think you will find that neutral evolution would. The fact that the models don’t describe selection is not an error at all. It’s an intentional feature. Edited by PaulK, : Fixed tag
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PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
quote: No, I think you’ll be unhappy because I am thinking and because I do have a good idea of how DNA evolution works.
quote: Many bases will be varying neutrally. So a model of neutral evolution will give a reasonable estimate.
quote: No, of course not. But do you think the majority of bases are under selective constraint in the Kishony experiment? It’s only a few that are under selection for antibiotic resistance. Others will be under stabilising selection, but hardly the entire genome.
quote: Because many bases will be evolving neutrally. Really it’s not so hard. Of course, looking for bases that change more slowly also helps - neutral change can be too fast.
quote: And there is another bizarre assertion. The equilibrium would be roughly equal proportions of each base in a single genome.
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PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
quote: A small portion, certainly not, you’d want a number of genes to get a robust result,
quote: Oh dear, oh dear, oh dear. This is not at all a rational argument. In fact it is a complete non-sequitur. There are bases which can freely change without deleterious or beneficial effect.
quote: The distribution of the bases in an interbreeding population wouldn’t be random. So how could you apply the probabilities across individuals? Anyway, until you recognise that DNA evolution is driven by neutral drift, you do not understand the mathematics of DNA evolution.
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PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
quote: Applying the model to multiple sites is hardly a difficult idea to grasp. Indeed it’s implicit in the part I quoted for you earlier,
quote: You’re only showing that you’re bananas.
quote: Apparently I know how DNA evolution works better than you. You do realise that the DNA sequences found in the population are not independent?
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PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
quote: And you still have no idea. Look, if you can’t understand how these models are used, just admit it rather than inventing silly straw we.
quote: It’s the correct math when selection is tightly constraining the viable outcomes at that site, but that’s hardly the normal case for DNA evolution.
quote: Well you’re wrong because it mostly doesn’t.
quote: Since you don’t know how DNA evolution works, your arguments are worthless.
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PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
quote: Then why are you misrepresenting it?
quote: The models aren’t meant to predict the results of those experiments.So the mistake is all yours.
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PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
quote: Yes you did. You tried to pretend that phylogenetic analysis was derived from the figures for a single base. Either you know that’s not true or you don’t know how the models are used.
quote: It is not an error, but since you don’t understand DNA evolution or how the models are used you can’t see that. Too bad for you.
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PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
quote: More proof that you don’t understand DNA evolution and refuse to learn.
quote: Do you really think that making things up like this is useful or constructive?
quote: I don’t think that making a fool of yourself on an obscure Internet forum helps them much either.
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PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
quote: As I keep telling you that DNA evolution is predominantly neutral. Until you grasp that point you will continue to blunder. You cannot make an accurate model until you understand what you are modelling.
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PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
quote: Fixation of alleles does. But that can include a degree of polymorphism With regard to individual bases however I think it will come down to the numbers. How long does it take to reach equilibrium? The mere fact that it would eventually is insufficient. The values seen within a population are not independent. The distant descendants of an individual may be divided between two or more populations - indeed that is exactly the case that phylogenetic analysis is looking for. Further, for more distant relatives sites that freely vary are not useful because they change too quickly. So it appears that the models are accurate on that score.
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PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
quote: Obviously not. But if you are concerned with phenotypic change the distinction is important.
quote: I am saying that it is possible for the site to be in equilibrium - with all four bases roughly equally represented - among the distant descendants. But at the same time the site is fixed in some or all of the populations existing at that time.
quote: Both. At the same time. As explained above. Fixed in some populations but not in equilibrium over all the descendants.
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PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
quote: Fixation occurs within a population and populations are outside the scope of the model. It’s a model of DNA evolution, not population genetics.
quote: No, you’ve done that to yourself. I really don’t know how you make up this stuff. The equilibrium state is reached in the distant descendants who are divided amongst a number of populations. The base may be fixed in some populations but it is not fixed over all the populations combined.
quote: Why would they need to? That isn’t what these models are about.
quote: For the purposes of this discussion that doesn’t matter at all. The models don’t deal with populations and don’t need to.
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PaulK Member Posts: 17822 Joined: Member Rating: 2.2 |
quote: If you think you can get population level information out of a model which doesn’t deal with the concept of populations at all, you are the one that is confused. Population genetics deals with the dynamics of evolution within populations, so that is obviously more appropriate,
quote: Oh dear, you are deeply confused. I‘m not claiming anything different at all. I’m just trying to interpret the probabilities produced by the models in terms of the genes we might find, taking into account simple facts like the fact that genes are inherited and that individual bases have a low mutation rate so that closely related individuals will tend to have very similar genes (especially in your favourite haploid populations)
quote: It don’t believe that it matters, not for the actual applications of the models. Why should it ? If you want to interpret the probabilities as frequencies among descendants, go ahead. But the model won’t give you the distribution. Even you should be able to see that. I guess I should leave the task of educating you to better teachers, with great patience (which you will no doubt sorely try).
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