tag:blogger.com,1999:blog-37148773.post4442847415140641909..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: On the difference between Neutral Theory and random genetic driftLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger53125tag:blogger.com,1999:blog-37148773.post-59704849262906207822014-03-03T22:43:03.863-05:002014-03-03T22:43:03.863-05:00on another note: My IB Y2s are almost into review ...on another note: My IB Y2s are almost into review and I'm going to have them read this post AND comments [probably the the older post you had on neutral, maybe PZ's] and have them synthesize the argument. Its a great teaching tool. :) Linzelhttps://www.blogger.com/profile/01514267602859699974noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-5702204921015672842014-03-03T22:41:23.647-05:002014-03-03T22:41:23.647-05:00As a high school AP and IB teacher [and future gra...As a high school AP and IB teacher [and future grade 10 life science NGSS teacher], and you probably know this, we have a HUGE set of content and skills we are expected to teach - effectively. It should not be surprising that natural selection has the advantage to be a more easily observable and appreciated aspect of evolution. Drift and neutral theory are more abstract and require more depth of thought, knowledge and effort to TEACH and APPRECIATE [teacher and student]. The amount of time in the IB dedicated to evolution are maybe 10 hours. Often the depth of understanding is relegated to memorization of the ideas rather than application of concept to a distinct situation. I think I'll stop here.....the challenge to teach this WELL is large. Linzelhttps://www.blogger.com/profile/01514267602859699974noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-80333321407678776662014-02-26T10:32:55.747-05:002014-02-26T10:32:55.747-05:00Well, the formula is for diploid species... :-)
(...Well, the formula is for diploid species... :-)<br /><br />(ok, trolling)Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-17990141975159190802014-02-25T13:15:38.758-05:002014-02-25T13:15:38.758-05:00@ Joe - thank you for that explanation. I remain ...@ Joe - thank you for that explanation. I remain in your debt!<br /><br />BTW - I am still scratching my head over what I percieve here as a non-debate. <br /><br /> Please correct me if I a wrong, but hasn't PZ Myers merely rediscovered the Luria–Delbrück distribution?<br /><br />I must be missing something - what?<br /><br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-73235499835020763812014-02-21T21:21:49.745-05:002014-02-21T21:21:49.745-05:00OK, close enough. OK, close enough. John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-72807817124028323192014-02-21T17:50:13.964-05:002014-02-21T17:50:13.964-05:00Kimura's 1962 formula, which is damn-near exac...Kimura's 1962 formula, which is damn-near exact, is that the fixation probability for a new mutant present in a single copy in a population of N individuals, is<br /><br />(1 - exp(-2s)) / (1 - exp( -4Ns))<br /><br />so you can check this yourself. For example when s = 0.1, and N = 1,000,000, Kimura's probability is 0.18126, while 2s would be 0.2. For s= 0.01, the fixation probability from Kimura's formula in 0.01980133 instead of 0.02.Joe Felsensteinhttps://www.blogger.com/profile/06359126552631140000noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-73460105718944441402014-02-21T17:08:52.191-05:002014-02-21T17:08:52.191-05:00Hey, isn't 2S a good approximation only when S...Hey, isn't 2S a good approximation only when S is very small?John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-9577496407586734222014-02-21T06:39:12.447-05:002014-02-21T06:39:12.447-05:00If everyone here would just read Coyne & Orr&#...<i>If everyone here would just read Coyne & Orr's Speciation, much would be simpler.</i><br /><br />Would be nice if it came out for Kindle.judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-33075934728039876092014-02-20T11:21:00.936-05:002014-02-20T11:21:00.936-05:00If everyone here would just read Coyne & Orr&#...If everyone here would just read Coyne & Orr's <i>Speciation</i>, much would be simpler.<br /><br />Larry: <i>Jerry Coyne believes that most, but not all, of the differences that lead to reproductive isolation are due to natural selection acting on one of the species to make breeding with the other population impossible.</i><br /><br />Not quite. First, speciation doesn't require that breeding be impossible, only infrequent and with selection against hybrid offspring. Second, he doesn't think that the differences are selected for the purpose of isolation, but that isolation is a byproduct of selection acting for other reasons, usually in allopatry where there is no possibility of selection for isolation. (Though reinforcement in later sympatry may contribute too, but only after isolation is well on its way.)<br /><br /><i>I think there are many evolutionary biologists who think that the development of reproductive isolation is usually due to random genetic drfit. I think their view is more likely to be correct.</i><br /><br />Why? Coyn & Orr give a good argument to my mind: drift acts much more slowly than selection, requiring both a much longer period of allopatry and the absence of selection during that period.<br /><br /><i>But, as you note, most "species" are recognized by other phenotypic differences that distinguish them long before reproductive isolation evolves.</i><br /><br />I noted no such thing. I don't think it's true, either.<br />John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-32570023288525199242014-02-20T10:24:28.395-05:002014-02-20T10:24:28.395-05:00OK OK… where does this leave us so far?
First o...OK OK… where does this leave us so far? <br /><br />First of all – this discussion really does not have a handle on what exactly is meant by the terms “species” or "speciation".<br /><br />Second of all – this discussion also needs to define its terms regarding “neutral” vs. ”subject to selection” especially considering disruptive selection ( I hope I am not begging the question)<br /><br />I like to think of Bmp4 and morphological Variation of beaks in Darwin's Finches as random genetic events<br /><br />http://www.sciencemag.org/content/305/5689/1462<br /><br />What is random as well? …any genetic mechanisms for reproductive isolation separating the populations of finches adapted to their particular ecological niches.<br /><br />At one point – Galapagoes finches were no different than Przewalski’s and domestic horses. However, the game-changer occurred when hybrids suffered any disadvantage. At that point (by tautological definition) Natural Selection kicks in and becomes more important than Genetic Drift.<br /><br />I explain to my students that actually this is not at all surprising but expected. Consider Ring Species such as Larus Gulls (OK – that may now turn out to be a bad example, but moving on…)<br /><br />One simplified way to explain the Bateson-Dobzhansky-Muller Model of speciation is along the following. http://en.wikipedia.org/wiki/Bateson-Dobzhansky-Muller_Model<br /><br />At least two major genetic changes are required to cause hybrid incompatibility and eventual speciation.<br /><br />A first major genetic change distinguishes population A from population B. Interbreeding between A & B is possible, albeit with reduced viability.<br />A second major genetic change distinguishes population B from population C. Interbreeding between B & C is possible, albeit with reduced viability.<br /><br />Interbreeding between A & C is now impossible.<br /><br />Otherwise speciation would be impossible! Consider, the lone mutation event that distinguishes the first B individual form the A population. With whom will B now breed other than within the original A population? The A population provides the gene pool for the new B variant to spread. <br /><br /> Otherwise, the B lineage would perish.<br /><br />(aside to Piotr – everything I discuss above is in fact discussed in greater detail on the ENSI site)<br /><br />I am becoming unclear on what exactly we really are debating here? <br /><br />I have this nagging suspicion that the hard done by “hard” interpretation of the “modern synthesis” is really just another “strawman”. Can speciation occur by genetic drift – sure why not – check out paradigm textbook examples such as Squirrels on either side of the Grand Canyon<br /><br />Here is a common site used by high school teachers and university profs.<br />http://evolution.berkeley.edu/evolibrary/article/_0_0/speciationmodes_01<br /><br />Please note the IMPORTANT caveat:<br /><br />[This change might evolve by natural selection OR genetic drift.]<br /><br />But, as I explained in my opening above, I am easily confused and I could be missing something.<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-14473328305462152442014-02-20T10:17:44.428-05:002014-02-20T10:17:44.428-05:00Larry – forgive me, but I am getting too old for t...Larry – forgive me, but I am getting too old for this sort of thing. My brain is no longer as agile as when I was younger.<br /><br />I am wondering out loud if some present (myself definitely included) occasionally fall in the trap of conflating two completely separate notions.<br />“Random Genetic Events” vs. “Random Genetic Drift”… the two are not equivalent.<br /><br />I remember enrolling in an Evolutionary Genetics undergraduate course in university. Our prof was most emphatic back then – species and populations within species manifest much variability and the majority of this variability is frankly an accumulation of genetic bric-a-brac – neither useful nor deleterious – his example was hair colour. That was 30+ years ago!<br /><br />OK – let’s not get bogged down with the relative benefits of differential melanin deposition vis-à-vis Vitamin D deficiency vs. susceptibility to melanoma.<br /><br />My take home message back then was that the majority of genetic variability was simply unimportant – i.e. neutral<br /><br />But – and this is the important bit - As soon as formerly unimportant variability does indeed become important, then ipso facto, that very variability becomes subject to Natural Selection and is no longer neutral!<br /><br />My favorite mammal is the Przewalski’s Horse which provided me the aha moment to finally comprehend exactly how reproductive isolation paces speciation.<br /><br />SOMETIMES, species that have a different number of chromosomes can’t breed and create viable offspring. For example, domestic horses have 64 pairs of chromosomes and donkeys have 62. When they breed and give birth to a mule, with 63 chromosome pairs, it is usually sterile. <br /><br />The Przewalski’s horse has 66 chromosomes. When a P-horse and a domestic horse breed, their offspring are born with 65 chromosomes. And get this - those offspring are usually viable.<br /><br />So are domestic horses and Przewalski’s horses different species? According to most textbooks – the answer is yes.<br /><br />Things that make you go hmmm… Consider many perfectly healthy populations of house mice, for example, which can be distinguished from each by examining their karyotypes for fused chromosomes? Are different populations of mouse now different species? What about Polar Bears and Grizzly Bears?<br /><br />Moving on…<br /><br />So why aren’t P horses and domestic horses reproductively isolated? … maybe it is just too early in the evolutionary game? … but then on the other hand, maybe because reproductive isolation was unnecessary – i.e. unimportant – i.e not subject to Natural Selection. <br /><br />I notice that a great number of illuminati get very confused on such subtleties. I cite PZ Myers’ errors regarding so-called “chromosome incompatibilities”: http://scienceblogs.com/pharyngula/2013/07/02/the-mfap-hypothesis-for-the-origins-of-homo-sapiens/<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-62058152636857260182014-02-20T05:20:50.252-05:002014-02-20T05:20:50.252-05:00Sorry I am not read up on these matters nor deeply...Sorry I am not read up on these matters nor deeply familiar with evolution theory, so the following might be too full of misunderstanding for anyone to comment on: but what is the basis for suggesting that reproductive incompatibility is largely due to selection? Surely there would not be direct selection for mutations that lead to a biochemical basis for reproductive incompatibility, would there? Is it rather a case of linkage to other alleles that are subject to selection? Or are we simply talking about the physical tendency or ability to interbreed upon phenotypic divergence? <br />Otherwise it would seem, regardless of how phenotypically different two groups become upon, say, geographical isolation, that the eventual random fixation of neutral or nearly neutral alleles would be the most likely explanation for a true biochemical inability to reproduce.SRMhttps://www.blogger.com/profile/07299706694667706149noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-69824691890760155232014-02-20T02:06:25.477-05:002014-02-20T02:06:25.477-05:00Jerry Coyne believes that most, but not all, of th...Jerry Coyne believes that most, but not all, of the differences that lead to reproductive isolation are due to natural selection acting on one of the species to make breeding with the other population impossible. There are very few examples that are well-supported. Jerry has published some of them.<br /><br />I think there are many evolutionary biologists who think that the development of reproductive isolation is usually due to random genetic drfit. I think their view is more likely to be correct.<br /><br />But, as you note, most "species" are recognized by other phenotypic differences that distinguish them long before reproductive isolation evolves. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-46389584870642402132014-02-19T10:04:39.446-05:002014-02-19T10:04:39.446-05:00Jerry would agree with this much: that those diffe...Jerry would agree with this much: that those differences that result in reproductive isolation between closely related species are mostly due to selection. Whehter those particular differences constitute the majority of differences may not be clear, but it's certainly suggestive.John Harshmanhttps://www.blogger.com/profile/06705501480675917237noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-20634515640112091502014-02-19T08:57:32.119-05:002014-02-19T08:57:32.119-05:00Chas Peterson says,
Please at least admit that yo...Chas Peterson says,<br /><br /><i>Please at least admit that your "thought" is not supported by any data.</i><br /><br />Not a problem ... as long as YOU admit that no other explanation is supported by any data. Deal?<br /><br />BTW, Jerry Coyne would not disagree. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-8866410318136472652014-02-18T23:01:21.589-05:002014-02-18T23:01:21.589-05:00"I think that, as a general rule, most of the..."<i>I think that, as a general rule, most of the [phenotypic] differences between closely related species are due to drift and not selection.</i>"<br /><br />Please at least admit that your "thought" is not supported by any data. And that people who study speciation (Coyne, for one) would, in general, disagree.Chas Petersonhttps://www.blogger.com/profile/12014964778727329625noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-66668233896452030522014-02-18T18:25:00.798-05:002014-02-18T18:25:00.798-05:00They have things like "A HARDY-WEINBERG EXCEL...They have things like "A <b>HARDY-WEINBERG</b> EXCELL SPREADSHEET FOR GENE FREQUENCY CHANGES <b>DUE TO SELECTION</b>" there (bold type added). They do mention the word "drift" but do you think they understand what the Hardy-Weinberg equilibrium is?Piotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-43724631903453689882014-02-18T17:37:27.058-05:002014-02-18T17:37:27.058-05:00oops and I almost forgot
http://tinyurl.com/jwtjd...oops and I almost forgot<br /><br />http://tinyurl.com/jwtjdm6Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-9430524490606903702014-02-18T17:36:03.858-05:002014-02-18T17:36:03.858-05:00Hi Piotr
I find the ensi site is difficult to sea...Hi Piotr<br /><br />I find the ensi site is difficult to search... but a first quick aproximation to answer your question<br /><br />http://tinyurl.com/kbjowcm<br /><br />http://tinyurl.com/m5kww2rTom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-72498861677908577242014-02-18T16:33:16.260-05:002014-02-18T16:33:16.260-05:00Hmm... Where do they mention mechanisms other than...Hmm... Where do they mention mechanisms other than natural selection producing adaptations?<br /><br />http://www.indiana.edu/~ensiweb/evol.fs.htmlPiotr Gąsiorowskihttps://www.blogger.com/profile/06339278493073512102noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-15343800836785489862014-02-18T16:19:10.707-05:002014-02-18T16:19:10.707-05:00@ Ben
Point well taken - I think I may need to re...@ Ben<br /><br />Point well taken - I think I may need to re-examine "emphasis" as well and make sure none of the trees get lost in the forest.<br />Tom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-36890868479418040612014-02-18T16:10:05.228-05:002014-02-18T16:10:05.228-05:00Hi Larry – you raise an interesting point of conte...Hi Larry – you raise an interesting point of contention.<br /><br />Very interesting – I think I now understand where you are coming from. <br /><br /> For example, I am exasperated that students can often walk away from 1st year University Genetics courses with an even worse understanding of Genetics than before. I applaud and employ PZ Myers' clarifications such as <br /><br />http://scienceblogs.com/pharyngula/2011/12/19/steve-pinkers-hair-and-the-mus/<br /><br />My students understand that Mendel is the exception that proves the rule and not the rule!<br /><br />Forgive my presumption, I hope my efforts on evolution in class can pass muster. Regarding any pop quiz - here is a SAMPLE of some of the questions (cut and pasted word for word) from my evolution test for Biology 12 students NOT enrolled in AP.<br /><br />Actually – I have an ulterior motive here. I would love feedback and suggestions for improvement from any and all. I hope it passes muster – remember this is only a selection of questions – not the entire test. (eg – pseudogenes and endogenous retroviral insertions are also discussed)<br /><br />Test sample from a regular high school evolution test:<br /><br />Someone tells a Biologist that the “missing link” has never been discovered so Evolution is only just a “theory”! How would a Biologist respond? (hint: there are at least two parts to the answer) <br /><br />This diagram [of different anteaters on different continents] describes typical observations that Darwin made during his five year voyage on the Beagle. This phenomenon is called: _____________________<br /><br />Why would these different kinds of anteaters support Darwin’s theory of evolution as opposed to a religious belief called “special creation”? (hint: only one is a marsupial)<br /><br />What exactly is the “theory of evolution”? Simply that…<br /> <br />List and describe six lines of evidence that support the Theory of Evolution (some have already been mentioned on this test)<br /><br />Do chromosomal rearrangements guarantee reproductive isolation? Explain with examples…<br /><br />Can reproductive isolation occur without chromosomal rearrangements? Explain with examples…<br /><br />[a photo of Ardi together with a diagram of hominid pylogeny is provided] Some scientists have suggested Ardipithecus ramidus (Ardi) is “the missing link” between humans and apes. Others disagree. What is/are the problem(s) here? We have the fossil, so why can’t we all agree? [I am hoping students recognize that speciation cannot be determined by morphology alone and recognizing that “missing link” is a loaded term often pregnant with misconception]<br /><br />Darwin was the first to concede that Natural Selection was not the only explanation for Evolution<br /> <br />Describe in detail TWO other mechanisms.<br /><br />Describe two classes of genes whose mutations would allow for very sudden evolutionary changes: <br /><br />Give an example (of such a sudden evolutionary change) we studied in an earlier unit: (hint – it was on a worksheet in the earlier DNA unit)<br /><br />Last question to Larry:<br /><br />Larry - I am but a humble high school Biology teacher. I hope that my former students would do well on any of your pop quizzes.<br /><br />ITMT – trust me, this is boiler-plate for AP teachers, nothing at all remarkable. Check out the NEW AP curriculum framework again. Hopefully the newer batch of students coming up the the pipeline will be more to your liking.<br /><br />In any case, I know I am not alone. Check out this site: http://www.indiana.edu/~ensiweb/lessons/ws.extensions.htmlTom Muellerhttps://www.blogger.com/profile/09829281784362177069noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-2171591307365152112014-02-18T14:20:53.984-05:002014-02-18T14:20:53.984-05:00I agree with Tom Mueller that every single text I&...I agree with Tom Mueller that every single text I've seen that discusses evolution (including human genetics books for nonmajors) prominently addresses drift. <br /><br />I've also found that questioning undergraduates about evolution (in cell biology and microbiology classes) regularly elicits natural selection as its essence. A little questioning and discussion, though, regularly shows that they have been exposed to drift and seem to grasp it.<br /><br />I confess that Larry's uh.. emphasis on this issue has caused me to sharpen my focus on it in the above-mentioned classes over the years.<br /><br />Ben MurrayAnonymoushttps://www.blogger.com/profile/00950268920091952819noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-13762472548831114612014-02-18T13:41:13.040-05:002014-02-18T13:41:13.040-05:00Tom Mueller says,
The fact remains that you may b...Tom Mueller says,<br /><br /><i>The fact remains that you may be exaggerating and guilty of incorrect extrapolation.</i><br /><br />No, Tom, I'm not. I've been studying this for 25 years and there's absolutely no doubt at all about the conclusion. Adaptationism is alive and thriving among the general public and even among university science students. There may be a few good AP Biology teachers out there who are teaching about drift and Neutral Theory but there aren't having much of an impact.<br /><br />For the past seven years I've been handing out a questionnaire to second year biology students on the first day of class. They all took an evolution course the previous year. Only about 20% of them are able to identify random genetic drift as a mechanism of evolution. When asked to DEFINE evolution, typically 75% of them define it in terms of selection, adaptation, or natural selection. <br /><br />Why don't you spring a surprise quiz on your own students and ask them to write as sentence of two that DEFINES evolution? I'm willing to bet that most of them will equate evolution with natural selection in spite of what you think you're teaching. Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-29113158441959672442014-02-18T13:23:39.773-05:002014-02-18T13:23:39.773-05:00Read the Wikipedia article on the Modern Synthesis...Read the Wikipedia article on the <a href="http://en.wikipedia.org/wiki/Modern_evolutionary_synthesis" rel="nofollow">Modern Synthesis</a>. I think it fairly represents the consensus view. The emphasis is on natural selection and the role of drift is suspect. <br /><br />Also read <a href="http://sandwalk.blogspot.com/2013/12/is-modern-synthesis-effectively-dead.html" rel="nofollow">Is the "Modern Synthesis" effectively dead?</a> and leave comments there if you disagree with the consensus understanding of what the "Modern Synthesis" actually means.<br /><br />Joe is upset about all the modern kinky ideas that are supposed to be overthrowing evolutionary theory and I agree with him that this is silly. However, almost all those "revolutionaries" seem to be completely ignorant of random genetic drift and Neutral Theory. In other words, they missed the real revolution.Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.com