tag:blogger.com,1999:blog-37148773.post2598473538604608192..comments2024-03-19T00:24:23.577-04:00Comments on <center>Sandwalk</center>: A philosopher's view of random genetic driftLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger38125tag:blogger.com,1999:blog-37148773.post-49503266413701399852016-09-29T17:40:32.572-04:002016-09-29T17:40:32.572-04:00Off topic: "Canadian medical journals hijacke...Off topic: "Canadian medical journals hijacked for junk science"<br /><br />This should interest you Larry and maybe few more. There is going to be more "junk science out there as if there wasn't enough already...<br /><br />https://www.thestar.com/news/world/2016/09/29/canadian-medical-journals-hijacked-for-junk-science.htmlJmachttps://www.blogger.com/profile/04392421995310271733noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-4510203537501808112016-09-29T17:22:35.134-04:002016-09-29T17:22:35.134-04:00I don't think that's helpful. I mean, we c...I don't think that's helpful. I mean, we can distinguish between the neutral case, where s~0 and the case when s is significantly different from 0. But there simply isn't a way to remove the effect of selection from some other type of sampling. The normal way of doing this is just what Joe discusses above, it splits a random variable into an expected value and a centered term (in the diffusion approximation that centered term then undergoes a CLT approximation, which you can't perform on a non-centered RV, so there is a reason for splitting it up as you go from something like Fisher-Wright to diffusion, but I don't think we should read that much into a mathematical operation).<br />I think that pretty much any discussion that contrasts selection and drift would be much clearer if we were talking about the magnitude of s instead.Anonymoushttps://www.blogger.com/profile/04521153536420798640noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-21992566206125881112016-09-29T13:19:09.034-04:002016-09-29T13:19:09.034-04:00Simon - Sorry about the elementary level of the qu...Simon - Sorry about the elementary level of the question, but I'm a layperson.<br /><br />- Do you think it is helpful conceptually to distinguish sampling of the population due to a less than infinite effective population size from sampling due to factors that could be lumped under the heading of "selection" (e.g., predation and avoidance of it, access to food sources, etc.)?judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-51165481164136048162016-09-29T12:04:53.733-04:002016-09-29T12:04:53.733-04:00@Joe: I do not think that they would have to act a...@Joe: I do not think that they would have to act additively in the sense that you could superimpose the neutral case and an infinite population model. But I argue that by making the distinction we give students the impression that they do. I'm pretty sure if you polled professional biologists, even evolutionary biologists, if their research was not primarily concerned with mathematical modeling, a majority would get that wrong. As I said above, this is a didactic point - thinking of drift and selection as separate processes or forces is more likely to hinder somebodies understanding than to help it.<br /><br />Now, regarding the KFE and KBE I think the first thing to note is that the drift term explicitly depends on s. Sure it goes to 0 as N->inf, but the effect of differential fitness which s records, bleeds into your drift term in all other cases. The same holds in other models - your drift term always depends on s. It's worth noting that in each case we are dealing with random processes and thus have sequences of random variables. We can of course (and it's easy to exclude RVs for which this doesn't work from consideration, since gene frequencies are not negative and have an upper bound at 1) rewrite these RVs as X=(X-E(X))+E(X). But that alone is no reason to call E(X) and (X-E(X)) different processes. We could say that a fair die with 6 sides has a probability of 1/6 for each number in {1,2,3,4,5,6}. We could also claim that a fair die is subject to two processes, one which always gives 3.5 and one which produces a number from {-2.5,-1.5,-.5,.5,1.5,2.5} with probability 1/6 each. Does this aid our understanding of die rolling?<br />Anonymoushttps://www.blogger.com/profile/04521153536420798640noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-17017954460283617822016-09-29T03:58:52.477-04:002016-09-29T03:58:52.477-04:00@ Joe Felsenstein
I fully agree, but I am also sy...@ Joe Felsenstein<br /><br />I fully agree, but I am also sympathetic to Simon's argument that separating selection from genetic drift is like separating the bias from a biased coin toss. You can do it, for example by assuming infinite populations, but it does feel artificial and it doesn't reallly occur anywhere in nature.<br /><br />Now if you could show that the coin you are using has a centre of gravity that is off-centre, then you know what is causing your bias. But this is something you never will learn from your model (I believe this was Rich's point). So nothing is gained from treating selection and drift as separate "forces".Corneelhttps://www.blogger.com/profile/02884855837357720225noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-84026079442865592202016-09-28T15:41:36.856-04:002016-09-28T15:41:36.856-04:00Larry wrote: "However, it does not cause adap...Larry wrote: "However, it does not cause adaptation and many biologists think that adaptation is the only important mechanism of evolution."<br /><br />I suspect that he meant to write something like "many biologists think that adaptation is the only important *consequence* of evolution."Jim Menegayhttps://www.blogger.com/profile/06217224823822142530noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-55973876221318095352016-09-28T15:35:59.743-04:002016-09-28T15:35:59.743-04:00@Corneel: I think that the philosopher made somewh...@Corneel: I think that the philosopher made somewhat heavy weather of the distinctions, but was basically correct.<br /><br />I do not think, as @Simon seems to, that making a distinction between selection and drift means that they have to act additively, and that we have to be able to calculate for any gene frequency change how much of it was due to the one and how much due to the other. Actually the Kolmogorov Forward Equation and the Kolmogorov Backward Equation for gene frequencies have two terms on their right-hand side. The first has all the deterministic forces in it, the second the genetic drift. As the population size rises, the second term is reduced toward zero. The forces of drift and selection can be distinguished, in the sense that it is not a hopeless task to detect selection.<br />Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-14678666843548543252016-09-28T09:22:43.395-04:002016-09-28T09:22:43.395-04:00Cruglers says:
"Almost anything is possible i...Cruglers says:<br />"Almost anything is possible if you preset computers with Darwinian bias."<br /><br />How very interesting you say this, because you are right. If you let computers use biological aka Darwinian selection rules, the computer all of a sudden can solve stuff human engineers can't. It's called <a href="https://en.wikipedia.org/wiki/Evolutionary_algorithm" rel="nofollow">Evolutionary algorithm</a> . <br />Edhttps://www.blogger.com/profile/15924368353226400878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-69308532644469742162016-09-28T09:17:44.361-04:002016-09-28T09:17:44.361-04:00Cruglers says:
"I can make a pretty good argu...Cruglers says:<br />"I can make a pretty good argument that Darwinian anti ID propaganda is bs. "<br />Well, go ahead. But 'pretty good' ain't gonna hack it, you'll need convincing evidence.<br /><br />Edhttps://www.blogger.com/profile/15924368353226400878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-84230635153489132282016-09-28T08:50:05.948-04:002016-09-28T08:50:05.948-04:00"Almost anything is possible if you preset co...<i>"Almost anything is possible if you preset computers with Darwinian bias. "</i><br /><br />That's cute. First you ask for proof, then when you get what you asked for you claim it's due to "Darwinian bias". <br /><br />Prove that there is such a flaw in their research. <br /><br />Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-81654082464967073382016-09-28T04:11:26.406-04:002016-09-28T04:11:26.406-04:00@ Joe Felsenstein
Since Simon himself joined in, ...@ Joe Felsenstein<br /><br />Since Simon himself joined in, I will leave it to him to clarify his position. He is much better at it.<br /><br />To make my position clear: In the OP Larry was somewhat dismissive of the contribution of philosophers to our understanding of drift and selection, and I got the impression that you supported his view. I just wanted to point out that there have been quite basic discussions about selection and drift here on Sandwalk, that could have benefit from the distinctions made in the article.Corneelhttps://www.blogger.com/profile/02884855837357720225noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-22058650957657755872016-09-27T22:07:31.747-04:002016-09-27T22:07:31.747-04:00I'm moving somethings I had typed above here, ...I'm moving somethings I had typed above here, hoping it doesn't get too confusing.<br /><br />@Rich Lawler: <i>But such a covariance could also occur just via drift, due to random reproduction.</i><br />Not if fitness is (as it should be) defined as the expected number of offspring (or half the expected number of offspring in the case of sexual reproduction).<br /><br />To (hopefully) clarify my position, there are 3 arguments to not treat selection and drift as fundamentally different. One of them is historic, one is didactic and the final one is based on the notion of parsimony.<br /><br />The historic argument is that in their joint presentation both Darwin and Wallace define selection as a sampling process, noting that fitness is given by an expected number as above and that in finite populations sampling error has relevant effects. This is also the view presented in the origin. The earlier publications in the modern synthesis also did not draw a distinction, but it is worth noting that selection was always understood first as the resampling of a finite population. As simpler infinite population models were produced, the term drift was introduced as a descriptor for the error of the simplified models. Only later - starting AFAIK with Dobzhansky - was drift reified. This is an amathematical view of mathematical models. If you look at the Fisher-Wright model, you have a rather elegant description of evolution. If one was to write it in a form that would contain drift and selection as additive components, it stops being anywhere near that elegance.<br /><br />The didactic argument is that the idea that selection and drift are conceptually different encourages students to think of them as additive effects. If we introduce them to these with the special cases N->inf and s=0 they will tend to superimpose them for other cases. It's worth noting that the s=0 case leads to additional confusion as students (but not only students!) confuse drift and neutrality. Reading the Stanford entry, that appears to be precisely what gives philosophers pause, with some arguing that drift is to be defined as strict neutrality and others arguing that it occurs when s!=0 as well.<br /><br />The final argument is parsimony. As I've already noted, we do have very elegant descriptions of evolution in the form of models that are drift+selection. From Fisher-Wright, through Moran to Kimura. All of these get less elegant if one is to split them into drift and selection slices. And it's also worth noting that we do not do this for other things. We could for instance easily split selection into an allelic selection component and a dominance-related error term. Another way to put this is the following example. Let's say we have a population of 5 cats (Alvin, Bertha, Clodwig, Dustin and Erwin). There is a probability distribution for which of these 5 cats is the next to die, say p(A)=.06, p(B)=.12, p(C)=.37, p(D)=.41 and p(E)=.04. On the death of a cat we get this:<br />Through selection .06 of Alvin, .12 of Bertha, .37 of Clodwig, .41 of Dustin and .04 of Erwin died.<br />Through drift .96 of Erwin, -.06 of Alvin, -.12 of Bertha, -.37 of Clodwig and -.41 of Dustin died.<br />We could also just say "Erwin is dead". Now, I like maths. I like them a lot. But anybody who prefers a description that includes the death of negative real values of cats to one that says that from time to time a cat dies should at least have to have a very strong argument on how this is helpful.Anonymoushttps://www.blogger.com/profile/04521153536420798640noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-79868758744888052072016-09-27T10:06:08.778-04:002016-09-27T10:06:08.778-04:00I certainly agree in the case of infinite populati...I certainly agree in the case of infinite population size. I'm more thinking of something we measured out in nature, like a selection gradient, then having to make the call as to whether the pattern is due to random reproduction or fitness differences. <br /><br />And to be clear, I'm not even trying to be argumentative or dogmatic, just pointing out that *sometimes* the pattern produced by selection versus drift is difficult to disentangle. rich lawlerhttps://www.blogger.com/profile/13353965284524429553noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-79819351540752849262016-09-27T09:49:28.842-04:002016-09-27T09:49:28.842-04:00This is a brilliant analogy! This is a brilliant analogy! My Username Is Inigo Montoyahttps://www.blogger.com/profile/05644342904907896852noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-69654236434498641932016-09-27T08:49:53.438-04:002016-09-27T08:49:53.438-04:00@rich and @Corneels: If we consider the same case...@rich and @Corneels: If we consider the same case, with the same genotypes having the same fitnesses, but the fitnesses of different genotypes being different, and now we make one change in the case: the population is made to be infinite. Then there is no genetic drift, but the genotype frequencies do change. So selection is still present, but genetic drift is not present. That makes them conceptually distinct. And the gene frequency change observed in that case is causally related to the differences in fitness between the genotypes.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-8641631344870004262016-09-27T07:54:36.641-04:002016-09-27T07:54:36.641-04:00@Joe...I see what you're saying, and would gen...@Joe...I see what you're saying, and would generally agree, but (I think!) there is nothing in the actual math that includes causation. Instead, in your case, we see a pattern and causally assign this result to selection, not drift. In my comment I was thinking of the case where we conceptualize selection as a non-zero covariance between fitness and phenotype (as in the Price equation). But such a covariance could also occur just via drift, due to random reproduction. Hence, when using the Price equation, we would need to decide if a non-zero covariance was causally due to differential fitness or non-causally due to random reproduction. The causation is assigned after the fact and not embodied in the actual math (even though the fitness terms are included in the math). <br /><br />I guess I am convinced by Sean Rice's argument that he made in Chapter 6 of his book. [And I'm also certainly biased since he was one of my teachers in grad school].rich lawlerhttps://www.blogger.com/profile/13353965284524429553noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-18208825191099683052016-09-26T17:53:20.792-04:002016-09-26T17:53:20.792-04:00Manning
I can make a pretty good argument that Da...Manning<br /><br />I can make a pretty good argument that Darwinian anti ID propaganda is bs. <br />I can also make more than one pretty good argument that for evolution to fit a scientific theory there are just too many dead ends on the way. I like speculations but scientific theory has to have some evidence and not faith based bs. Jmachttps://www.blogger.com/profile/04392421995310271733noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-57071486931761135722016-09-26T17:43:00.402-04:002016-09-26T17:43:00.402-04:00Mikkel,
Almost anything is possible if you prese...Mikkel, <br /><br />Almost anything is possible if you preset computers with Darwinian bias. Just because you want it to be true doesn't necessarily make it so... Jmachttps://www.blogger.com/profile/04392421995310271733noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-14110704855198880932016-09-26T17:17:19.487-04:002016-09-26T17:17:19.487-04:00@ Joe Felsenstein
Yes, I think he would agree that...@ Joe Felsenstein<br />Yes, I think he would agree that selection can be detected but I believe he took issue with viewing selection and drift as conceptually different processes.Corneelhttps://www.blogger.com/profile/02884855837357720225noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-26937005143933082016-09-26T13:52:01.660-04:002016-09-26T13:52:01.660-04:00@Corneel: Simon Gunkel's argument is that par...@Corneel: Simon Gunkel's argument is that particular changes cannot be dissected into selection parts and parts due to random genetic drift. The distribution of outcomes is affected by both selection and drift, and if we remove the selection part, that distribution will change. So there is then statistical information enabling us to infer whether or not the selection part is present. How much information depends on the exact situation. But it is <i>not</i> true that there is no information enabling us to infer whether selection is present. I doubt that Simon Gunkel would disagree with me on this.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-28473135525027031072016-09-26T08:51:10.896-04:002016-09-26T08:51:10.896-04:00What makes a Dunning-Krugerite blog troll an exper...What makes a Dunning-Krugerite blog troll an expert on evoution or ID?nmanninghttps://www.blogger.com/profile/14767343547942014627noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-56329383415123265442016-09-26T04:45:28.763-04:002016-09-26T04:45:28.763-04:00AND I also remember Simon Gunkel arguing on this b...AND I also remember Simon Gunkel arguing on this blog that selection and drift cannot be disentangled as a process either. e.g. <a href="http://sandwalk.blogspot.nl/2014/12/how-to-think-about-evolution.html?showComment=1419139552086#c1668518642432182835" rel="nofollow">here</a> Corneelhttps://www.blogger.com/profile/02884855837357720225noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-10012795404440050602016-09-26T04:20:32.841-04:002016-09-26T04:20:32.841-04:00@Joe Felsenstein
Well, I remember a discussion on...@Joe Felsenstein<br /><br />Well, I remember a discussion on this blog where it was argued that <a href="http://sandwalk.blogspot.nl/2013/11/natural-selection-may-not-lead-to.html" rel="nofollow"> natural selection does not necessarily produce a change in allele frequency</a>, for example without any heritable variation present. I think a distinction between process and outcome is something biologists tend to be very sloppy about indeed.Corneelhttps://www.blogger.com/profile/02884855837357720225noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-12378981179212372922016-09-26T00:46:44.465-04:002016-09-26T00:46:44.465-04:00@Rich: A unified body of math covers both selecti...@Rich: A unified body of math covers both selection and drift, but I would think that the outcomes of two differ at least probabilistically. I am confused by the implication of your comment that they cannot be distinguished even probabilistically. If we have a population of 1,000,000 fruit flies and see change of an allele frequency from 0.5 to 0.55 and then to 0.60 in three generations, that's very unlikely to be the result of drift -- though it could be but it would be a very unlikely outcome.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-13791165862832422872016-09-25T18:20:08.113-04:002016-09-25T18:20:08.113-04:00"..mathematically proving that say...evolutio...<i>"..mathematically proving that say...evolution is possible in time available?"</i><br /><br /><a href="http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003818" rel="nofollow">That's already been done. </a>Mikkel Rumraket Rasmussenhttps://www.blogger.com/profile/07670550711237457368noreply@blogger.com