tag:blogger.com,1999:blog-37148773.post3732377853569476124..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: You MUST read this paper if you are interested in evolutionLarry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger54125tag:blogger.com,1999:blog-37148773.post-83597451912710201322017-01-11T13:08:54.373-05:002017-01-11T13:08:54.373-05:00I’m suggesting one assumes the drift hypothesis, o...I’m suggesting one assumes the drift hypothesis, one would never ‘prove’ the drift hypothesis, but one could disprove the hypothesis. This is a normal situation in science, as Einstein pointed out, (to paraphrase) 'no test could prove general relativity is true, but one could disprove it.'<br /><br />By ‘advantage’ what I mean is ‘more likely to reproduce’. So if one can prove an organism with a particular sequence is more likely to reproduce than one without, then one has a case for selection.<br />It would be at that point one would try to find a trait associated with the sequence that would ‘explain’ the selection.<br /><br />This avoids the ‘just so story’ which we humans seem so good at producing and buying without any evidence beyond the cleverness of the story that explains the ‘just so’.Anonymoushttps://www.blogger.com/profile/01987183007523742829noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-15556535459180958402017-01-10T15:44:13.754-05:002017-01-10T15:44:13.754-05:00@Jarle Kotsbak
I would suggest actually searching...@Jarle Kotsbak<br /><br />I would suggest actually searching the journal's website. Searching for "genetic drift" produces results from more than 4,500 articles (link here: https://goo.gl/MqpkEX). A similar search for "neutral theory" produces results from more than 2,500 articles (https://goo.gl/tGTewI).<br /><br />In any case, I read articles in MBE regularly, and neutral theory is discussed both explicitly and used implicitly as an assumption or null model on a pretty consistent basis. The results of selection will always, I think, be sexier to a majority of researchers, but that doesn't necessarily mean that neutrality is always neglected.Dave Carlsonhttps://www.blogger.com/profile/18110718908216269032noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-88441125141198150892017-01-10T15:06:35.184-05:002017-01-10T15:06:35.184-05:00@Dave
I made a search in Pubmed on articles in tha...@Dave<br />I made a search in Pubmed on articles in that journal. I found for "neutral theory" 36, for "genetic drift" 104, for "selection" 1716 and for "natural selection" 273. The results are better than with a general search, which gave 446, 4592, 407592 and 10249 respectively. My impression when reading articles is that results are much more often checked against selection than against neutral theory. And the numbers support this impression.Misconceptions in evolution theorieshttps://www.blogger.com/profile/02221854011348738166noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-23595369330547267182017-01-10T12:30:57.638-05:002017-01-10T12:30:57.638-05:00@Marleen
what percentage of the evolutionary proce...@Marleen<br /><i>what percentage of the evolutionary process was directed by drift and what by selection</i>.<br /><br />This question may of cause be answered if you mean what percentage of the genome is conserved due to natural selection compared to all the rest, which changes freely due to genetic drift. In the human genome much less than 1% of the genome is protected from drift by selection. We can say that the constancy is directed by selection and the changes are directed by drift. But whether or not this is a good answer depends what you mean by "evolutionary process". If you mean something active, i.e. changes, then the percentage that is directed by selection is very close to zero. Misconceptions in evolution theorieshttps://www.blogger.com/profile/02221854011348738166noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-82142468758605034592017-01-10T12:07:44.574-05:002017-01-10T12:07:44.574-05:00@judmarc
Yes, neutral changes, or what is usually ...@judmarc<br />Yes, neutral changes, or what is usually called mutations. There is a lot of redundancy in most functional sequences. The third bp in codons, that bwilson mentioned is only one example. Such changes are often silent, i.e. produce the same amino aced sequence. But a lot of amino acid sequences could change almost freely with no consequence. There are a few examples of proteins with little room for changes, e.g. the histones. Histones from non-related species therefore have very similar amino acid sequences. Misconceptions in evolution theorieshttps://www.blogger.com/profile/02221854011348738166noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-72229270066070436392017-01-10T11:32:35.077-05:002017-01-10T11:32:35.077-05:00bwilson - So we are talking about neutral *changes...bwilson - So we are talking about neutral *changes* within functional *sequences*?judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-41450770962291870462017-01-10T10:53:57.806-05:002017-01-10T10:53:57.806-05:00All organisms? Including organisms that do have ve...All organisms? Including organisms that do have very large effective population sizes, like microorganisms?<br /><br />Two different concepts causing confusion here, I think. Bacteria with very high effective population sizes loose (nearly) all their junk DNA because it is mildly harmful and in huge populations even very small selection coefficients can have effects. On the other hand, truly neutral changes (e.g. many third bp changes in codons and DNA sequences in bits of DNA needed as spacers only) would continue to change by drift.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-71113733752098698852017-01-10T09:08:18.735-05:002017-01-10T09:08:18.735-05:00@judmarc
"All organisms? Including organisms ...@judmarc<br />"All organisms? Including organisms that do have very large effective population sizes, like microorganisms?"<br /><br />Yes, all organisms. Neutral changes are independent of selection. Their probability of fixation is independent of population size. Therefore they are used as molecular clocks. The only difference between small and large populations are that fixation takes longer time in large populations. This was shown by Motoo Kimura fifty years ago. Misconceptions in evolution theorieshttps://www.blogger.com/profile/02221854011348738166noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-41430370624628890512017-01-10T06:57:11.752-05:002017-01-10T06:57:11.752-05:00because absolutely neutral changes are also fixed,...<i>because absolutely neutral changes are also fixed, and they are actually totally dominating in all organisms.</i><br /><br />All organisms? Including organisms that do have very large effective population sizes, like microorganisms?judmarchttps://www.blogger.com/profile/03111006189037693272noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-57850913521654710622017-01-10T04:47:10.599-05:002017-01-10T04:47:10.599-05:00@Marleen
"How can we tell that a sequence or ...@Marleen<br />"How can we tell that a sequence or trait is advantageous,.."<br />As it is almost impossible to tell in advance whether or not a sequence is advantageous, there has been a common misunderstanding that it is possible in retrospect to tell this based upon the reproductive success of the possessor. In that way one makes no room for drift. Many researchers like to assume that the population size is so large that they can disregard drift as a cause. They still have a problem, because absolutely neutral changes are also fixed, and they are actually totally dominating in all organisms. So the best answer to your question, seen in retrospect, is that the best and maybe the only way to identify a sequence as advantageous is that it does not change. All base pairs that are not critical change very readily, so a sequence comparison to related and not so related species directly identifies the critical and therefore advantageous parts of the sequence. <br /><br />I answered your question based on your term "evolution of one particular organism or trait". That indicates you are talking about evolution including creation of novelty and not just adaptation of allele frequencies in a population, which some researchers has also called "evolution". But when you say: "..what percentage of the evolutionary process was directed by drift and what by selection.", then I would say that the question is impossible for evolution. For adaptation it is also difficult to answer, but at least it has a meaning. <br /><br />I am much more interested in evolution than adaptation, and I am writing a book based on my understanding of how drift and selection works together creating new features and improving old features. My theory, which I have called "contra-Darwinism", explains how both drift and selection are absolutely necessary in creating or improving features.Misconceptions in evolution theorieshttps://www.blogger.com/profile/02221854011348738166noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-89693163259432071512017-01-09T23:06:45.261-05:002017-01-09T23:06:45.261-05:00How can you tell there is an advantage to (‘having...How can you tell there is an advantage to (‘having’ or carrying) a sequence. First of all you need to determine what this advantage is, in what it consists. There exists already a problem in my opinion: as soon as you assign a possible advantage to a trait or sequence you claim to know what the advantage of this trait is.<br /><br />You say that if you assume the ‘drift’ hypothesis and are able to demonstrate there is an ‘advantage’ you may claim selection. Also in this case however you might overlook the possibility of other advantages, hence you may overlook any advantage. Therefore you can never claim the ‘drift’ hypothesis.Marleenhttps://www.blogger.com/profile/01404234060103026188noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-77428936685378575482017-01-09T22:47:26.523-05:002017-01-09T22:47:26.523-05:00@Jarle Kotsbak
Strictly spoken your are right: si...@Jarle Kotsbak<br /><br />Strictly spoken your are right: since we know nothing about the origin of introns and exons we may speculate whatever we want. It seems to me however that the current hypothesis is that eukaryotes evolved from prokaryotes (alfa-proteobacterie was engulfed by an archaeon). Therefore, it seems reasonable to consider exons (the protein-coding part of a gene) as the descendant of the intron-free genes of prokaryotes. Hence the necessity of the evolution of a spliceosome to get rid of this novelty, the introns.<br /><br />I am not sure that neutral theory and drift should be ‘promoted’. Why should they, if most if not all evolutionary biologist agree that these theories have an important role in evolution.<br /><br />May I ask you something? How can we tell that a sequence or trait is advantageous, how can we determine the importance of genetic drift with respect to natural selection in the evolution of one particular organism or trait. We do agree that natural selection is important, so what percentage of the evolutionary process was directed by drift and what by selection. Personally I have no idea about how we can determine this.<br /><br />Marleenhttps://www.blogger.com/profile/01404234060103026188noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-76454949814740134132017-01-09T16:35:04.034-05:002017-01-09T16:35:04.034-05:00@Jarle Kotsbak
"That is very good. But why ar...@Jarle Kotsbak<br />"That is very good. But why are so few authors writing about it or using it in their research? My impression is that in nearly all microbiological or molecular research articles, when it is discussed how their results relate to evolution, then it is "committee evolution" (ref. Mayr, Dobzhansky et al) based on selection it is referred to. Who except Masatoshi Nei, Arlin Stoltzfus and Koonin are today promoting the neutral theory? "<br /><br />Molecular Biology and Evolution is the most highly cited journal in evolutionary biology (I think this is largely due to the publication of papers describing certain widely used bioinformatics programs, but let's leave that aside for the moment). If you do a keyword search for neutral theory or genetic drift in that journal, you will see that the topics come up extremely frequently in research articles. Dave Carlsonhttps://www.blogger.com/profile/18110718908216269032noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-12279275262682611512017-01-09T15:20:58.044-05:002017-01-09T15:20:58.044-05:00@Marleen
"If one looks up "genetic drift...@Marleen<br />"If one looks up "genetic drift" or "random drift" in one of the handbooks of evolution (p.e. Barton’s “Evolution” 2007) there is a substantial chapter (chapter 15) that treats genetic drift." <br /><br />That is very good. But why are so few authors writing about it or using it in their research? My impression is that in nearly all microbiological or molecular research articles, when it is discussed how their results relate to evolution, then it is "committee evolution" (ref. Mayr, Dobzhansky et al) based on selection it is referred to. Who except Masatoshi Nei, Arlin Stoltzfus and Koonin are today promoting the neutral theory? There was not too many in the twentieth century either. Motoo Kimura opened up my eyes for what evolution really is with his neutral theory in 1968. Before that I thought evolution was all about selection. <br /><br />"I agree very much with the comments of S Johnson" <br /><br />That is interesting. Can you tell me what really is the essence of his comments? Misconceptions in evolution theorieshttps://www.blogger.com/profile/02221854011348738166noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35561037144551304852017-01-09T05:19:23.652-05:002017-01-09T05:19:23.652-05:00"Since we do not know why the ‘highly efficie..."Since we do not know why the ‘highly efficient and precise splicing machinery’ and the nucleus evolved, it seems to me an adaptionist view to assign them this particular role and function,"<br /><br />"It is possible however to speculate that there has been a co-evolution between the appearance of introns in genes and the formation of a splicing machinery."<br /><br />That is true. But it is also possible to speculate that the splicing machinery is older than the exons. We do not know the origins of introns or the splicing machinery, and we do not know the origin of the nucleus. Thereby we cannot know much about their early evolution. But we can know about their more recent evolution. Regarding their origin, we have to also consider the possibility that introns were the original, and exons the novelty. In that case the splice machinery was needed to pick out the introns and to use them as different sorts of RNA. The spiced waste was only useful as mRNA after invention of the translation machinery. <br /><br />Regarding the nucleus, it may have been the original, and cytosol may have been the novelty. It was only needed as a place for the translated RNA, i.e. proteins to operate.Misconceptions in evolution theorieshttps://www.blogger.com/profile/02221854011348738166noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-7057038268867455952017-01-06T20:42:15.030-05:002017-01-06T20:42:15.030-05:00Very good, Pauline. You've explained why the ...Very good, Pauline. You've explained why the premise of the creationist "chicken and egg" arguments often made here is false. I'm glad you seem to understand where I'm coming from. Maybe you could try explain this to your creationist buddies like Steve and txpiper, so they could stop embarrassing themselves and setting such a bad examples for religious believers.<br /><br />And, of course, since you're so clever you clearly only intended your question to "evolutionists" as an illustrative example of the kind of moronic questions creationists less enlightened than yourself are prone to asking, and don't really need anyone else to explain to you why it's such a stupid question.<br /><br />Right?<br />Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34364648902205584122017-01-06T20:17:19.740-05:002017-01-06T20:17:19.740-05:00Here is a "no one has even given it a try&quo...Here is a "no one has even given it a try" reply lutesuite: An analogy: "Every artist we know who paints pictures is a painter. So who painted the Bayeux tapestry?" Well the premise that the Bayeux tapestry was "painted" is wrong. So the question cannot be answered.<br />So your question presupposes that every 'designer' is a living being. God is not a "living being" in the set of living beings that you describe. Christians believe that God is outside of creation. <br /><br />A common question from Atheists is "If God create the world, then who created God?" This presupposes God was "created", but christians believe that God existed before time began and was not created (ignore the fact that we as humans cannot understand this - why should we?) <br />Now let's turn this on evolutionists - if all theories work on existing life (eg natural selection, survival of the fittest) then how did the first life 'evolve' from non life?<br /><br />I look forward to your reply<br />Paulinehttps://www.blogger.com/profile/10942276886899973371noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-82521660986196105152017-01-06T11:30:42.675-05:002017-01-06T11:30:42.675-05:00@Simon, yes Koonin is mistaken about "determi...@Simon, yes Koonin is mistaken about "deterministically eliminated or fixed by selection". The statement should be "deterministically eliminated by selection or stochastically fixed (with p ~ 2s)". There is a widespread misconception that the probability of fixation relates in some strong way to population size. Instead it is almost entirely a matter of how close the number of alleles is to 0, not how far it is from 2N. Arlinhttps://www.blogger.com/profile/03243864308260498878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-57535522105111855502017-01-06T11:20:45.707-05:002017-01-06T11:20:45.707-05:00@Marleen, you may be right that students today lea...@Marleen, you may be right that students today learning about drift, but Larry went to a conference of *old people*, the sort who attend conferences about the state of evolutionary theory. If you are over 50, then when you went to university, "molecular evolution" (including the neutral theory) was a specialty topic. Arlinhttps://www.blogger.com/profile/03243864308260498878noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-45623088760031395352017-01-06T03:02:47.160-05:002017-01-06T03:02:47.160-05:00Trying to play the moderator here. IT is true that...Trying to play the moderator here. IT is true that those studying molecular evolution typically involve NT in their work, as this has always been the bedrock of the field. But in the more Ecology/Animal Evolution world, I would propose you will have a hard time finding examples of neutral mechanisms being the null. And fun stories of mammalian “X probably evolved for Y” are the non-specialists day-to-day familiarity with Evolutionary Biology.<br /><br />And underlying the ENCODE phenomenon - we have an entire discipline of "Molecular Biologists" out there now from various disciples who have had no real formal training in modern evolutionary thinking. They remember Darwin, Origin of Species and the "Survival of the Fittest" from intro biology classes and move forward as though their understanding is complete. I see this daily in my field, and in the intro lectures I give in a course here. The students are stunned at the implications of the classic simulations like the <a href="http://www.biology.arizona.edu/evolution/act/drift/frame.html" rel="nofollow"> Driftworm simulation </a> . They have just never thought about it, having only heard the “why a zebra has stipes” stories. <br /><br /> Setting aside the semantics of the ENCODE debate, this underlying assumption they have the whole evolution thing worked out leads them to the sorts of claims you see in the "headline" ENCODE papers. And I think this is unique to evolution. I would never dare to write a about how my molecular-genetics work solves great mysteries of Developmental Biology. But somehow, everyone with a half-hour intro to evolution under their belt is quite willing to make grand proclamations about their RNA-Seq data and the implication of this for Evolutionary Theory. <br />TheOtherJimhttps://www.blogger.com/profile/01727633779107067250noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-18967201852220709472017-01-05T11:39:56.985-05:002017-01-05T11:39:56.985-05:00I believe this is convincing argument for the ‘neu...I believe this is convincing argument for the ‘neutral’ hypothesis as the default assumption:<br /><br />If one assumes the ‘drift’ hypothesis, then one can test to see if there is an actual advantage to the sequence or not. If one can find an unequivocal advantage, then one can claim ‘selection’.<br /><br />If one assumes there must be an advantage to the sequence (selection hypothesis), then one can never falsify this hypothesis (there could always be some other ‘advantage’ we haven’t thought of yet).<br /><br />Therefore in order to have a testable, falsifiable hypothesis, we should stick with the ‘neutral’ hypothesis regarding genetic sequences.Anonymoushttps://www.blogger.com/profile/01987183007523742829noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-34447927829847048672017-01-05T06:29:24.856-05:002017-01-05T06:29:24.856-05:00Hey there, Steve. Would you care to try answer a ...Hey there, Steve. Would you care to try answer a question I have posed to several other of your fellow proponents of the idea that life was created by a "designer"? So far, no one has even given it a try.<br /><br />Every "designer" we know of is a living being. Therefore, all available evidence suggests that life has to exist before a "designer" can. So how is it possible for life to have been created by a "designer", if designers only arise after life already has?<br /><br />I look forward to your reply. Faizal Alihttps://www.blogger.com/profile/00937075798809265805noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-2250935365942942222017-01-05T04:05:48.835-05:002017-01-05T04:05:48.835-05:00It really doesnt matter if one leans toward neutra...It really doesnt matter if one leans toward neutral theory, adaptation, natural selection, yada yada.<br /><br />any theory of evolution can only ride on the coattails of design.<br /><br />I have not come across one person (including the IDiot slayer Moran) who can logically articulate how the first simple organism could possibly evolve considering any of the above explanations without design at its core.<br /><br />Will Moran be the first?<br /><br />Now that Larry will retire soon, maybe he'll have the time to take a crack at a narrative that describes logically sound scenarios that can explain the complexification of organism without any bells and whistles to work with.<br /><br />Anyway, dont get me wrong. Im fine with design deniers slugging it out to see who becomes king of the 1%ers.<br /><br />Stevehttps://www.blogger.com/profile/15246115342112568778noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54406398715532855732017-01-04T15:57:45.005-05:002017-01-04T15:57:45.005-05:00Deleted response with typo! Corrected version foll...Deleted response with typo! Corrected version follows.<br /><br /><br />The sentence refusing to be parsed was referring to Coyne's attack on Gould, and his citation of a refutation. <br /><br />Coyne wrote: "Steve Gould and Niles Eldredge, with their theory of punctuated equilibrium proposed in the Seventies, essentially made the extreme non-Darwinian claim that big evolutionary changes happens when small populations somehow lose their 'genetic equilibrium' (how wasn’t specified), and, further, that species selection was responsible for trends in the fossil record as well as adaptations themselves." (Original at https://whyevolutionistrue.wordpress.com/page/6/)<br /><br />I had thought what punctuated equilibria, as demonstrated in the fossil record, was the stabilizing role of natural selection as the general rule, which is why natural selection as the main driver of optimal adaptations seemed to me to be, well, not quite obvious. But since I do not understand it after all, as you tell me, then the refutation made so long ago must be entirely correct. That is at https://wp.biota.utoronto.ca/theseedsofscience/files/2015/05/Charlesowrth-1982.pdf<br /><br />Multiplication of species is what most lay people are primarily interested in when thinking about evolution. Most accept on authority natural selection has pervasively perfected traits. <br /><br />As to personal opinions of Coyne, since I do not understand punctuated equilibrium I must agree with you and Coyne. "I [Coyne] wanted to add one additional reason why evolution is liable to such critiques: scientists are always out to make a name for themselves, as our currency of achievement is not money but reputation. You don’t get well known by just adding another brick to the evolutionary edifice, but you can do by pushing the wall over. That’s how Steve Gould made his name, flawed as his theories were. With all its messiness, poorly understood phenomena (what are females choosing during sexual selection?) and historical contingency, you can always assemble a list of phenomena that you can claim show severe deficiencies in evolution. But as with theological arguments, a lack of explanation doesn’t mean that we have to resort to drastic conclusions." <br /><br />Lastly the date 1982 was not a reference to any papers by Gould, Eldredge or Lewontin, but to the conclusive refutation so unjustly overlooked by Gould's fans for these many decades. I thought I was being ironic but plainly the jokes on me.<br />S Johnsonhttps://www.blogger.com/profile/11610068751705809284noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-572352877324354562017-01-04T15:47:53.864-05:002017-01-04T15:47:53.864-05:00Simon, I am not defending what he said, only tryin...Simon, I am not defending what he said, only trying to work out what he was trying to say. Sometimes authors say one thing in words, and another in maths, and leave it as a puzzle for the reader to decide whether to work forwards from the words to correct the maths, or backwards from the maths to correct the words. (I think you know this all too well, but others may be reading.)<br /><br />I wouldn't discount mutations. That would be weird.<br /><br />As to whether there has been time for stationarity to be reached, it will be different for different cases, and I think it's an interesting set of questions that are too complicated to answer here.<br /><br />Graham Joneshttps://www.blogger.com/profile/09212540504498321504noreply@blogger.com