tag:blogger.com,1999:blog-4989966954446423670.post5044926830565157546..comments2024-03-02T00:44:55.128-08:00Comments on Pleiotropy: Can we predict evolution?Bjørn Østmanhttp://www.blogger.com/profile/08859177313382114917noreply@blogger.comBlogger19125tag:blogger.com,1999:blog-4989966954446423670.post-30804377780009718382014-05-16T10:02:42.883-07:002014-05-16T10:02:42.883-07:00No. It is a claim that I make (e.g., in Østman &am...No. It is a claim that I make (e.g., in Østman & Adami, 2013). It is also an inference one can partially make from my work in the NK landscape (Østman et al, 2012), if one understands the question "how the population will evolve" as whether they get stuck on a local peak or reach the global peak. There is more to it than just that, of course. From some of these <a href="https://www.msu.edu/~ostman/landscapes.html" rel="nofollow">videos of populations evolving</a> in 2-dimensional phenotype-fitness landscapes and multi-dimensional genotype-fitness landscapes, it is also clear that just by looking at the topology, one can predict where a population will end up in some cases.Bjørn Østmanhttps://www.blogger.com/profile/08859177313382114917noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-59150579937944320832014-05-16T08:21:02.130-07:002014-05-16T08:21:02.130-07:00Fitness Landscape
.... If the fitness landscape is...<b>Fitness Landscape</b><br />.... If the fitness landscape is known, then the effect of every mutation is known, and it can be predicted statistically how the population will evolve. <br /><br />Do you have the reference abot that fact?Unknownhttps://www.blogger.com/profile/13254070286989130411noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-27186657442042597412013-04-18T06:58:37.666-07:002013-04-18T06:58:37.666-07:00Yes, I totally agree that knowing everything about...Yes, I totally agree that knowing everything about the fitness landscape is practically impossible. When we make and measure landscapes in biology, we are not including events like gene duplication that will expand the dimensionality of the genotype/phenotype. Hopefully there are systems regular enough that they are somewhat predictable.Bjørn Østmanhttps://www.blogger.com/profile/08859177313382114917noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-88076041945481086962013-04-18T01:43:10.141-07:002013-04-18T01:43:10.141-07:00Thinking about it, I guess you are right and I was...Thinking about it, I guess you are right and I was wrong, if "knowing the fitness landscape" means knowing every possible genotype and all its fitness consequences (plus the other assumptions mentioned in your post).<br /><br />But: "Knowing every genotype" would also mean to take into account innovation and novelty, such as those caused by gene duplication and subfunctionalization. <br />In practice, evolutionary innovations are - almost by definition - a source of endless surprises, and you'd be stretched to make predictions with all those unknown unknowns. Anonymoushttps://www.blogger.com/profile/11961913804829923287noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-27425311658905555412013-04-17T09:30:34.234-07:002013-04-17T09:30:34.234-07:00Constraints limit which genotypes are connected, a...Constraints limit which genotypes are connected, and that is part of the fitness landscape. If you don't think this is an adequate view, can you elaborate?Bjørn Østmanhttps://www.blogger.com/profile/08859177313382114917noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-40602785016448697282013-04-17T05:02:52.260-07:002013-04-17T05:02:52.260-07:00I don't think that the constraints I have in m...I don't think that the constraints I have in mind are built into the fitness landscape - and that's because fitness landscapes deal with selection coefficients, but that's not what people mean when talking about "developmental constraints" . These constraints exist irrespective of selection and to predict "possible creatures" you would have to somehow include a model of how developmental pathways can change. It's as if certain peaks in your fitness landscape are cordoned off by wire fencing, whereas others have cable car access.<br /><br />That said, I just discovered an interesting article in eLife - experimental evolution of multicellularity in yeast:<br />http://elife.elifesciences.org/content/2/e00367<br /> Under these controlled conditions, it was indeed possible to predict what would happen to yeast populations under low sucrose conditions, based on biochemical and genetic knowledge. Although evolution provided some surprise solutions too, overall the expected outcome was observed. So I guess, I agree with you, whether or not evolution is predictable depends on what kind of system you have in mind, and what time scales you are looking at. <br /><br /> Anonymoushttps://www.blogger.com/profile/11961913804829923287noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-26529703092728780722013-04-16T14:50:51.553-07:002013-04-16T14:50:51.553-07:00Hans, I don't disagree with the importance of ...Hans, I don't disagree with the importance of constraints. However, those constraints are already built into the fitness landscape. I repeat that getting comprehensive knowledge of a large area of the fitness landscape is a daunting task (practically impossible in many instances), but in principle it does contain all the necessary information, including genetic constraints.Bjørn Østmanhttps://www.blogger.com/profile/08859177313382114917noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-16205624984938948922013-04-16T13:27:55.267-07:002013-04-16T13:27:55.267-07:00Great post, but I disagree with your conclusion. E...Great post, but I disagree with your conclusion. Even if we know population size, mutation rate, and the fitness landscape, evolution will usually not be predictable, in my opinion. You concentrated on external factors, and thereby you somehow treat the phenotype as a kind of dough that can be formed into every imaginable shape, and will always find a way to the peaks of the fitness landscape. <br />Internal factors, i.e. developmental constraints, make-up of genetic networks etc. are also crucial, and here the outcome of evolution is impossible to predict, in my opinion. The evolutionary trajectory may take dramatically different turns depending on which kind of genes are "hit" first by mutation, creating very different types of mutually exclusive phenotypes that may all be more or less equally favored by selection. <br /><br />To give a hypothetical example: Let's say an animal species on a small island faces extinction due to slowly rising water levels, over thousands of years.<br />One way to get your gene pool out of this threat is the emergence of wings, another would be to turn aquatic. But once a trend towards "becoming fish-like" is set in motion by the first random mutations, the other path is virtually blocked, and vice versa. <br />The example is a bit silly, but these kinds of things also happen at the molecular level. Anonymoushttps://www.blogger.com/profile/11961913804829923287noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-66661324217020267602013-04-16T12:49:56.740-07:002013-04-16T12:49:56.740-07:00Ok, got it. But no, µ is simply the rate at which ...Ok, got it. But no, µ is simply the rate at which new mutations occur, irrespective of it's effect, s.Bjørn Østmanhttps://www.blogger.com/profile/08859177313382114917noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-45438740313562418222013-04-16T10:25:00.562-07:002013-04-16T10:25:00.562-07:00Just to clarify: My genetics professor at the univ...Just to clarify: My genetics professor at the university (I'm an undergrad student) calls what I mentioned mutation rate and represents it by the same symbol you used. But I've noticed that it looked like it wasn't the same thing. Anonymoushttps://www.blogger.com/profile/14647952761619665724noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-86777268961594837262013-04-16T10:09:43.243-07:002013-04-16T10:09:43.243-07:00S - selection coefficient
q^2 - frequency (affec...S - selection coefficient <br /><br />q^2 - frequency (affected proportion of the population)Anonymoushttps://www.blogger.com/profile/14647952761619665724noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-71791453396646988122013-04-16T09:02:00.973-07:002013-04-16T09:02:00.973-07:00No, I am talking about the per-site mutation rate....No, I am talking about the per-site mutation rate. Mainly in haploids, so traits are neither dominant or recessive. What is sq^2?Bjørn Østmanhttps://www.blogger.com/profile/08859177313382114917noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-76144607397379090822013-04-16T02:33:20.493-07:002013-04-16T02:33:20.493-07:00Hi. Are you refering to that mutation rate that is...Hi. Are you refering to that mutation rate that is, for instance, in the case of an autosomal recessive trait = sq^2 ?Anonymoushttps://www.blogger.com/profile/14647952761619665724noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-68463471282899147172013-04-14T12:02:20.530-07:002013-04-14T12:02:20.530-07:00Yes, incorporating all details will be impossible....Yes, incorporating all details will be impossible. My point here is then to reduce the problem to something we can solve and go from there.Bjørn Østmanhttps://www.blogger.com/profile/08859177313382114917noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-86330457264780938312013-04-14T11:38:37.716-07:002013-04-14T11:38:37.716-07:00Ouch, slapped with semantics! Good thing I am in s...Ouch, slapped with semantics! Good thing I am in science and not philosophy.<br /><br />I don't know. How much fraud in science is caused by these students? News to me, frankly.Bjørn Østmanhttps://www.blogger.com/profile/08859177313382114917noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-84225666539295884262013-04-14T11:35:49.391-07:002013-04-14T11:35:49.391-07:00Artem, I didn't mean to say that no work is do...Artem, I didn't mean to say that no work is done on dynamic fitness landscapes at all. You're right that systems with frequency-dependent selection are studied using game theoretical approaches in simulation (in fact, I'm in a <a href="http://adamilab.msu.edu/" rel="nofollow">lab</a> where this has been done extensively). To what extent is this used to predict evolution, do you think?<br /><br />Endpoints of evolution here refers exclusively to the final state in a static fitness landscape. If this is indeed not a single genotype, like you highlight, then I don't see any problems incorporating that into the entropy measure. Just include several solutions and weigh them accordingly. Agree?<br /><br />And you might be right that this approach is not possible in chaotic systems. But, gotta start somewhere.Bjørn Østmanhttps://www.blogger.com/profile/08859177313382114917noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-38002211366376247192013-04-14T03:03:15.197-07:002013-04-14T03:03:15.197-07:00In philosophy of science, AFAIK, prediction means ...In philosophy of science, AFAIK, prediction means a deduction from general laws like the law of gravitation or of ideal gases. What you call "prediction" is not based on such laws but on a huge amount of observations about population size, mutation rates and fitness landscapes. Therefore, it is not a proper prediction. If you thought about your knowledge of population size, mutation rates and fitness landscapes as observations, you could regard the whole exercise as an induction (that's what Darwin thought of his conclusion about natural selection). If you thought of them as premises, you could consider the exercise a deduction of hypotheses. None comes with the same high claims to truth the way predictions do. <br /><br />P.S.: I consider the obsession of scientists with "prediction" a vice. How much fraud in science is due to students believing they really have predictive powers?Joachim Dagghttps://www.blogger.com/profile/00985198925581721229noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-69068779576241044712013-04-13T23:12:55.095-07:002013-04-13T23:12:55.095-07:00Nice summary, however I disagree with:
> There...Nice summary, however I disagree with:<br /><br />> There is very little research done on such dynamic fitness landscapes and how they affect evolutionary dynamics.<br /><br />Evolutionary game theory studies fitness landscapes that are completely frequency-dependent and thus the fitness landscape the population sees varies at the same rate as the population. This is the polar opposite of a fixed fitness landscape and is extensively studied. See Nowak's Evolutionary Dynamics for a quick intro, or Hofbauer & Sigmund's Evolutionary Games and Population Dynamics for a more dated (1998) but technical introduction.<br /><br />I am also very skeptical whenever someone talks about an "end-point" of evolution. For convenience, mathematical models tend to consider compact genotypes spaces and so by Brouwer's fixed-point theorem these models have equilibria. However, it is not obvious to me that these sort of models should always be used, because they are prone to inviting a very teleological account of evolution that I think most biologist would inherently be opposed, too. But even in these models, it is not clear to me that we are always justified in assuming that the population will converge to an equilibrium. You might have limit cycles (for instance for replicator dynamics with 3 or more strategies), or even chaotic attractors (replicator dynamics with 4 or more strategies). Even when you don't have this constant feedback between population and fitness landscape, it still seems that one should be cautious to assume that the population can reach an equilibrium in a reasonable (non-exponential in size of genome) time.<br /><br />Finally, the possibility of chaotic dynamics (as mentioned in the previous paragraph) inherently makes the system unpredictable except over very short timescales. Physicists face the same problem when they study their (in your words) "simple" systems, for instance you can't predict the dynamics of a double pendulum very well without unreasonably (even for physics) accurate measurements of initial conditions.Artem Kaznatcheevhttps://www.blogger.com/profile/10862186635014217785noreply@blogger.comtag:blogger.com,1999:blog-4989966954446423670.post-34660580039224034982013-04-13T16:59:39.477-07:002013-04-13T16:59:39.477-07:00Great post.
I guess that when it is said that evol...Great post.<br />I guess that when it is said that evolution is not predictable people refer to the immense difficulty of knowing how the fitness landscape is going to vary in time in the long term. Maybe also the impossibility of ever reconstructing a multidimensional landscape that is so variable and dependent of so many genome sites.<br />Sergio,Sergio A. Muñoz-Gómezhttps://www.blogger.com/profile/16871487193128538778noreply@blogger.com