Two paradigms underlying human evolution have crumbled?

_{Denyse O'Leary

July 20, 2012

Human evolution, News}

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In the last few years, two paradigms underlying human evolution have crumbled. Modern humans have not totally replaced previous hominins without any admixture, and the expected signatures of adaptations to new environments are surprisingly lacking at the genomic level. Here we review current evidence about archaic admixture and lack of strong selective sweeps in humans. We underline the need to properly model differential admixture in various populations to correctly reconstruct past demography. We also stress the importance of taking into account the spatial dimension of human evolution, which proceeded by a series of range expansions that could have promoted both the introgression of archaic genes and background selection.

– Alves I, Šrámková Hanulová A, Foll M, Excoffier L (2012) Genomic Data Reveal a Complex Making of Humans. PLoS Genet 8(7): e1002837. doi:10.1371/journal.pgen.1002837

Actually, the loudest crumble has been the fact that it is now okay, apparently, to admit this.

Comments

wd400: I asked for an answer. And I asked for a reference. I don't see a reference; and I think I see your answer. Your answer seems to be: "it's a process, not an event" coupled to "I tend to think of pop. gen as mainly being about netural evolution, with selection an extension of those models," which is the formula most evolutionary biologists are comfortable with these days. This, to me (IMO), is no more than "hand-waving." There is no reference that I know of where a plausible "process" has been mathematically explicated. It doesn't exist. So, you've given me no reference (as I thought). The fact is, that Fred Hoyle, in his population genetics from 'scratch' book, "The Mathematics of Evolution," comes to the conclusion that the authors of this study seem to come to: namely, that NS functions primarily as a means of eliminating deleterious mutations. From the above quoted study: ". . . suggesting that the diversity trough in genic regions is not due to positive selection acting on amino-acid changing mutations, but better fits a model of background selection, which eliminates strongly deleterious mutations in functional regions." Mathematics is not friendly to Darwinism. (I love to point out that R.A. Fisher's "fundamental equation of natural selection", the term he uses IIRC, is based on equating differentiated equations that come from actuarial tables! Wow!) Now, as a clue to the thinking lying behind your 'answer', you do mention the 50 million SNP's which would have fixed in the six million year time period. I suppose that sounds impressive to you, and perhaps others. and I suppose this is to mean that RV is all over the place, ready to be utilized by NS. But, wait a second, we're talking about "neutral" fixations. If they are "neutral" mutations, then, by definition, they have no phenotypic effect. So, where does this get you? I see it as getting you nowhere. (My imagination will only allow me to go so far.) Now, I've already mentioned that in the last 100,000 years (833,000 mutations would have fixed in this time per your calculation) our human forebears had to endure multiple ice ages, and had to contend with drastically changing fauna and flora. By even "neutral theorist" standards, this should have elicited all kinds of "adaptations" to the environment. And what do we see? Humans are still like humans. So much so that the authors of this study have to invoke Neanderthals to explain any kind of variation we see. Neutral mutations seem to remain just that: neutral. Now maybe when you go to sleep at night you are honestly convinced that "neutral drift" and "positive selection" can, together, form a "process" that leads to speciation (thank you, BTW, for the helpful distinction between anagenesis [I'll look that up later] and speciation. It helps to make needed distinctions], but from all I can tell, it's but wishful thinking. Fault Michael Behe all you want, but he nevertheless is trying to take a realistic look at what evolution can do. And it doesn't seem like RV+NS gets you very far---even over large spans of time. And this study buttresses that opinion.PaV_{July 25, 2012
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wd400:
6 million years does seem so short a time to me = we’d expect about 50 million single nucleotide differences to fix over that time without selection.
Yeah in imagination-land. However there still isn't any evidence that any amount of genetic change can transform a knuckle-walker into an upright biped.Joe_{July 25, 2012
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Think this exhange has probably served its purpose... You confuse speciation with anagenesis (or just evolutionary change if you want). The thing that made chimps and humans different is not speciation, that's just makes our evolutionary trajectories separate. The change that followed was a process, not an event. The rest of your gish gallop is... weird. Positive selection is hardly the sine qua non of pop. gen. (I tend to think of pop. gen as mainly being about netural evolution, with selection an extension of those models), there is ample evidence for recent selection in humans, it's just that it's not the major process on display in modern genomes. Roberstoninan transolacations are not large changes, they just change how genes are packaged up and have little phenotypic effect. Of course dark skinned humans are humans - skin colour being one example of the among-population differences that arise from selection over the last 100 000 years or so. I don't get the point here? 6 million years does seem so short a time to me = we'd expect about 50 million single nucleotide differences to fix over that time without selection. It's not clear how many changes that seperate us from chimps would need to fixed by selection (in on or other lineage), but when me measure selection in the field forces can be very strong indeed. Finally, I can't imagine the relevence of the Chesterton quote, I have provided topics for you to read on every time you'v made a mistake here.wd400_{July 24, 2012
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Here's an interesting quote from G.K. Chesterton taken from another post: God condescended to argue with Job, but the last Darwinian will not condescend to argue with you. He will inform you of your ignorance; he will not enlighten your ignorance.PaV_{July 24, 2012
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My use of "large speciation event" was an effort to avoid the way in which "speciation" is used when talking about small amounts of variation within various lineages. Evolutionists routinely call this 'changed' lineage a new species. Perhaps, phenotypically, there is a change. But does this make it a "new species"? In your example above, you cite "Robertsonian translocations". This is quite a big change; and yet you say: "They look like humans to me." Which is exactly my point: are dark-skinned humans a different "species" than white humans? And what about brown-skinned, etc., etc.? Thus, the use of the phrase "large speciation event" was simply an effort to prescind the usual trivial kind of events that evolutionists want to define as "speciation." No more. I am not a full-time biologists, although I have a degree in it from a long time ago---and I hated genetics when I took it. Nevertheless, I've read my share of population genetics books---with one goal in mind: to find some kind of plausible means of Darwinian evolution. I have found none. Neo-Darwinian mechanisms move too slowly to even come close to explaining what we see in fossil record. My initial comment here merely underlined this slowness: 100,000 years, complete changes in temperature and flora and fuana, and yet humans show no sign of positive selection, the sine qua non of population genetics. What will it take to falsify neo-Darwinism? How much evidence do you need? Now, I'm sure you're eminently educated in the area of population genetics. But education sometimes, inadvertently, becomes indoctrination. Max Planck said that new theories didn't win out based on the merits; rather, the people holding onto the older view simply died off to be replaced by those familiar with the new view of things. However, in our current educational model, one generation of true believers in Darwinism is simply replaced by a new one. Why? Because if you don't view things the "right way", then you're showed the door. The 60's had a word for this: "reactionary." So, in the end, here's my question for you: how did apes become humans in so short a period of geological time as six million years? What neo-Darwinian processes were at work? Do you have an answer? Do you have a reference?PaV_{July 24, 2012
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I'm sorry PaV, I don't think anyone who thinks "Large speication event" is meaningful phrase can understand much about population genetics. If you think fusion of acrocentric chromosomes is a saltation then you might want to meet some of the ~1/1000 people walking around with Robertsonian translocations. They look like humans to me. You don't need any special pop. gen. to deal with these rearrangements, they have mutation rates you can measure their fitness effects and away you go.wd400_{July 23, 2012
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wd400: I think I understood them quite well. And, I understood all of the very little things that evolution can do via population models. And it's not much. And Michael Behe has successfully point out these limitations, and continues to do so. Yet, right here at UD we're talking about human chromosome 2. Darwinists tell us that this comes from a fusion of two chimp chromosomes. Tell me, wd400, what theory of population genetics covers this kind of chromosomal rearrangement? Do we just say: "Oh, well, you know, it's kind of like cross-linking"? __________________ Do you know who talked about chromosomal rearrangements as the source of biological speciation? Yes, Richard Goldschmidt, author of the "Material Basis of Natural Selection." You know, "hopeful monsters". Darwinism is based on "gradualism." Darwin absolutely insisted upon this. "Hopeful monsters" throw out Darwinian theory---which should have been done a long time ago. The problem with every evolutionary model I've seen is that it takes too much time. It's too gradual. It can't explain anything much bigger than a handful of protein changes. This gets you nowhere.PaV_{July 23, 2012
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"Large speciation events"! Ha, that's awesome. I don't think you understood those books...wd400_{July 23, 2012
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I've read a whole host of books on population genetics. Nowhere have I seen anything that comes remotely close to a viable mechanism for large speciation events. Yes, using certain assumptions, you can assume a certain linkage between various lineages and such. I suspect there's some validity, and, hence, utility to such methods---but probably more limited that evolutionary biologists would think. But nowhere do you find any feasible, plausible way of introducing significant species' change. This study simply underlines the limitations inherent in the putative methods population geneticists employ. Belief is not proof. That's the point. Another day; another bad day for Darwinism.PaV_{July 23, 2012
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Umm... evolutionary biologists can detect selection, we don't just invoke it for every change we see. Read up about Ks/Ks ratios and reduced heterozygosity. And there _have_ been sweeps in recent histroy, lactase persistance probably being the fastest, it's just that positive selection isn't the main force shaping genomeswd400_{July 23, 2012
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wd400: You say this: On the other hand, when we compare our genome to those of other apes there is abundant evidence for positive selection. This statement 'presumes' "positive selection." IOW, what we really see are distinct differences in various parts of the human genome and in other primates. Yet, it is this difference that is in need of explanation. You're simply assuming that RV+NS has brought this about. Now, hopefully, you can see my argument: IF, over, as you say 100,000 years, given all the changes of climate and space, of fauna and flora, that have occurred during this time, why then (if "environmental changes" are the trigger for evolutionary change) have we not seen ANY positive sweeps take place? If you want to argue that it is because no 'speciation event' has taken place; well, that's fine and good. But if 100,000 years of environmental change (how many "ice ages" does this time span cover? What about Sabre-tooth tigers and woolly mammoths once existed?), then what, perforce, brought about the change between apes and humans? IOW, we see "stasis", not change. This, of course, is the problem with evolution: it can't turn a cat into a dog (or even a rabbit). [BTW, I haven't mentioned here another disturbing fact: Kimura invented his "Neutral Theory" because of the very large number of polymorphisms found in various genomes. The problem with invoking "positive selection" is that for every polymorphism, some kind of selection is taking place. If there are a huge number of sites in the genome where this is taking place, this puts a tremendous "genetic load" on the population. This motivated Kimura's thinking. So, really we're dealing with a: "heads I win, tails you lose" proposition. Either way, Darwinism fails.]PaV_{July 23, 2012
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PaV, I really have no idea what you're talking about. The article says drift and background selection are sufficient to explain most of the differences among human populations, although "soft sweep" selection could mask recent positive selection. That's it. On the other hand, when we compare our genome to those of other apes there is abundant evidence for positive selection. You're not really arguing that because positive selection hasn't been the major force driving changes over the last ~100 thousand years that it can't have played a role in the last 6 million are you?wd400_{July 21, 2012
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wd400: Please get off your high horse! When they say that there is no evidence (or very little) for positive selection, then Darwinism is dead, kaput. It's as simple as that, no matter how much you what to get worked up about it. The party is over. RV+NS that has nothing to do with "positive selection" is a toothless form of "evolution." This is like taking a Doberman Pincher and breeding it with a Labrador Retriever. Obviously "bits of the genome" will show up as polymorphisms, but you're still dealing with some type of dog. There is no new "species." Applied to "human evolution," yes, the claim of 'admixture' can be resorted to as a way of explaining why there are differences among humans in the absence of evidence for positive selection. But this gives absolutely no explanation for how this "information" (and they use this very word in the paper!) came about. As an evolutionist, you're simply looking at the evidence that way. You're viewing it in terms of how humans moved genetically forward in time. OTOH, I'm viewing it as moving back in time. IOW, if humans show no signs of 'positive selection,' and no signs of selective 'sweeps' when confronted with 'different environments', then what possible RV+NS explanations are there for the transition from apes to human kind? How do you explain it? Without positive selection, you have nothing. Period. Nothing is left to you except the mantra: "Evolution is a fact. Evolution is a fact. Evolution is a fact...." Another day; another bad day for Darwinism.PaV_{July 21, 2012
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PaV. What are you talking about? "Among-population polymorphism" just means bits of the genome in which populations are distinct (or somewhat distinct). The evidence is that very few of these differences are the result of selection driving different populations in different directions (but some are). There is abundant evidence for selection in our genome, it's just we all share the products of most of it.wd400_{July 21, 2012
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wd400: PaV, the paper is talking about among-population polymorphism within modern humans. The point is not that we haven’t had any positive selection in the last 6 million years, but that for the most part the differences between say, Asian and Polynesian genomes aren’t the result of selection. The paper talks about "among-population polymorphism" precisely because no evidence exists for "positive selection." IOW, 'we have to throw RV+NS out; but, don't get discouraged, we still have "among-population polymorphisms."' But, when positive selection is thrown out, so, too, is Darwinism. In the paper they talk about the transfer of information. You see, they can't explain the origin of information. As jstanley01 humorously points out, it's time to play "taps" for Darwinism. It's all over except for the shouting. Finis. Over and out. Sayonara.PaV_{July 21, 2012
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So here we have humans, showing the most divergence with all of the remainder of nature in our upright posture, our speech, our consciousness, and all of this happening in the least amount of time——and……without the aid of positive selection.
The article is discussing the differences between humans, not the differences between humans and other animals. I didn't think anyone was under the impression that most of the various differences among human populations was due to adaptation. I've always heard that most such differences as likely being a result of genetic drift.goodusername_{July 20, 2012
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PaV, the paper is talking about among-population polymorphism within modern humans. The point is not that we haven't had any positive selection in the last 6 million years, but that for the most part the differences between say, Asian and Polynesian genomes aren't the result of selection. (Of course some differences, like skin colour or lacatse persitance will be the result of selection).wd400_{July 20, 2012
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http://www.youtube.com/watch?v=S-Xrlf3taEojstanley01_{July 20, 2012
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I should have highlighted this sentence as well: Evidence is thus building that background selection can explain most aspects of observed patterns of polymorphism. Another day; another bad day for Darwinism.PaV_{July 20, 2012
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Here's a quote from the article: Three recent observations have further shaken the paradigm of positive selection. First, it has been realized that regions showing high levels of differentiation between continents (high FST) were not associated with large levels of linkage disequilibrium, suggesting that allele frequency shifts occurred long ago and not because of recent adaptive events [3], [9]. Second, it was shown that the reduction in diversity is practically identical around non-synonymous or synonymous sites [2], suggesting that the diversity trough in genic regions is not due to positive selection acting on amino-acid changing mutations, but better fits a model of background selection, which eliminates strongly deleterious mutations in functional regions (see e.g., [42], [43] for recent reviews on background selection). Finally, models with selective sweeps have been shown to lead to an overly strong negative correlation between levels of synonymous polymorphism and non-synonymous divergence [8], whereas models of background selection fit the observed correlation. Evidence is thus building that background selection can explain most aspects of observed patterns of polymorphism. Without positive selection, Darwinists are left with Neutral Drift. But, of course, neutral drift moves too slowly. So here we have humans, showing the most divergence with all of the remainder of nature in our upright posture, our speech, our consciousness, and all of this happening in the least amount of time------and......without the aid of positive selection. It appears, in fact, that the conclusion reached by almost everyone who has ever studied Natural Selection, is confirmed by this study: NS eliminates deleterious mutations. It has almost NO ability to bring about positive changes (in conformity with Michael Behe's latest peer-reviewed article last year.) So much for Darwinism. May we be soon rid of its foolishness.PaV_{July 20, 2012
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Actually, admixture vs replacement has been a subject of debate since the 1930's.grannyape92_{July 20, 2012
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