Hybridization as a Challenge to Common Descent?

_{September 30, 2011

Intelligent Design}

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Here’s an article from New Scientist that will be open for the next seven days to registered viewers. It’s about the “metamorphosis” of species from larval to adult stages, and brings in the views of Donald Williamson.

Here’s a link to his 2006 paper, and the entire abstract (it’s worth it!):

Examples of animal development that pose problems for Darwinian evolution by ‘descent with modification’ but are consistent with ‘larval transfer’ are discussed. Larval transfer claims that genes that prescribe larval forms originated in adults in other taxa, and have been transferred by hybridization. I now suggest that not only larvae but also components of animals have been transferred by hybridization. The ontogeny of some Cambrian metazoans without true larvae is discussed. The probable sequence of acquisition of larvae by hemichordates and echinoderms is presented. I contend (1) that there were no true larvae until after the establishment of classes in the respective phyla, (2) that early animals hybridized to produce chimeras of parts of dissimilar species, (3) that the Cambrian explosion resulted from many such hybridizations, and (4) that modern animal phyla and classes were produced by such early hybridizations, rather than by the gradual accumulation of specific differences.

Another day; another bad day for Darwinism!

Comments

1- "Beneficial" is a relative word meaning what is beneficial for one generation in one specific environment isn't necessarily going to be beneficial for the next generation in a slightly different environemnt. 2- Competing "beneficial" mutations- your scenario doesn't account for them. I guess that is why it is imaginary. 3- Your scenario also doesn't account for sexual reproduction 4- So I think your example is totally bogus.Joseph_{October 3, 2011
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What point was that? What ever point you were trying to make. As I say, I don't understand it, so it's really up to you to make it.wd400_{October 3, 2011
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Even very beneficial mutations are unlikely to be fixed. So, how likely is that the mutation I talked about, that gives the tiny rise in fitness I talked about, gets fixed? What do you think? 1%? 0.1%?wd400_{October 3, 2011
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Imagine a population of 10 000 fixed for an allele we’ll call “-”.
Exactly- your position relies on imagination not science.
Given that you think beneficial mutations can’t be fixed...
I didn't say nor think that. I said: Even very beneficial mutations are unlikely to be fixed. Sexual reproduction sees to that. So you seem to have issues with reading what I post. Oh well.
(and if you don’t think common descent predicts everyone in a population contributes tot he next generation, then I really can’t understand you point about recombination)
What point was that?Joseph_{October 3, 2011
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Ok. Imagine a population of 10 000 fixed for an allele we'll call "-". A new mutation pops up making the allele "+", and the finesses are "-/-" : 0.98 "+/-" : 0.99 "+/+" : 1.0 That's hardly "very beneficial". Given that you think beneficial mutations can't be fixed I guess you think there is no chance that "+" will be in this scenario? (and if you don't think common descent predicts everyone in a population contributes tot he next generation, then I really can't understand you point about recombination)wd400_{October 3, 2011
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Nice non-response- I never claimed that common descent = every indidual in a population contributing to future generations- never.
If you mean weakly benifical mutations are unlikely to be fixed well… that’s call the nearly neutral theory and it’s been around for more than 30 years.
Even very beneficial mutations are unlikely to be fixed.
What amazes me is how little of evolution those that oppose the theory have bothered to learn.
Nice unsupported nonsense...Joseph_{October 3, 2011
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Excuse me, but how is it possible for none of one parent's genes to get passed on? Has that ever been documented in humans?Joseph_{October 3, 2011
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Kindly note, tilt the head up . . .kairosfocus_{October 3, 2011
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points 10 - 13 ffkairosfocus_{October 3, 2011
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Kindly cf here.kairosfocus_{October 3, 2011
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You did not follow basic instructions, to tilt it up so it would try to burn the already burned wood. Yet another distraction.kairosfocus_{October 3, 2011
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Assertion, not evidence. And, not of causeless beginnings, nor of a fourth causal factor, but of ART being reducible to chance plus necessity. Kindly demonstrate it, empirically; without imposing materialistic a prioris that end up begging the question. And, along the way, please show that key empirical signs of design acting by art, are empirically shown to originate from chance plus necessity. Otherwise, we are simply looking at question-begging materialist a prioris censoring thought. As happened so blatantly with Lewontin, Sagan, Coyne et al.kairosfocus_{October 3, 2011
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Well, I'd argue that "chance" and "necessity" (which I don't think are separate, in fact) underlie "art", and what is necessary (but not sufficient) for "art" is feedback between output and input.Elizabeth Liddle_{October 3, 2011
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What is the half-burned match exercise?Elizabeth Liddle_{October 3, 2011
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Irrelevant. If you are objecting to analysing causal factors as mechanical necessity and/or chance and/or art, then show either things that begin to exist with NO -- including no logically necessary causal factors -- causal factors, or a fourth factor. Otherwise, you are simply making a verbal objection to be selectively hyperskeptical. I have said nothing against causal factors for a given outcome not being composite, just that -- per massive experience -- they will be analysable on chance and/or mechanical necessity and/or art. In that analysis, I further hold that we can often isolate factors responsible for aspects of many phenomena based on tested, reliable signs. let us know how the match exercise turns out. GEM of TKIkairosfocus_{October 3, 2011
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"PS: Dr Liddle, please do the half-burned match exercise and discuss your proposals in its light. Note especially the point that a necessary causal factor is a causal factor." My match burned my fingers when I turned it upside down. What lesson was I supposed to learn?DrREC_{October 3, 2011
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Nothing has a single causal factor, kf, and causes can usually be considered on many levels, proximal and distal. Some events have proximal intentional causes, some distal intentional causes. Some events do not have intentional causes at all. And intentions fall on an continuum. Does a plant that moves a stone as it grows intend to do so? Does a worm? Or an ant? Or a person? As I see it, "intention" involves the creation of a forward model, the output of which is fed back into the decision-making process as input. Humans do this. Worms possibly do, at a very crude level. Plants probably don't.Elizabeth Liddle_{October 3, 2011
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PS: Dr Liddle, please do the half-burned match exercise and discuss your proposals in its light. Note especially the point that a necessary causal factor is a causal factor.kairosfocus_{October 3, 2011
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Dr Liddle: Kindly show us a process that has a beginning and cannot be described as one or more of these factors in action, i.e. it traces to a fourth factor, or else to no causal factor [including no necessary factors; cf here]. Failing a credible empirical counter example, we are simply dealing with selectively hyperskeptical verbal objections unconnected to empirical reality. GEM of TKIkairosfocus_{October 3, 2011
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Well.... you comment is utterly informed. No one calims common descent = every indidual in a population contributing to future generations so why would anyone bother with your odd claim? If you mean weakly benifical mutations are unlikely to be fixed well... that's call the nearly neutral theory and it's been around for more than 30 years. What amazes me is how little of evolution those that oppose the theory have bothered to learn.wd400_{October 3, 2011
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Well, UD seems to have spammed my reply. But to find what people think of Williamson read Hart and Grosberg (2009) PNAS who use the phrase "astonishing and unfounded". Or Giribert (2009) in the same journal who went with "Why did the author ignore the weight of phylogenetic evidence that utterly falsifies his claim?". On blogs you'll fine "worst paper of the year" and a "preposterous hypothesis"wd400_{October 3, 2011
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Joseph, We could use the computer code methphor, if I know that some notable atheists share among each other, notably, that their father died before the horse. There is nothing exciting to do with it? I was, as you think chemistry knows, whither it is taking place in a movie Woody Allen complained about the alphabet and, most importantly, about information semantics, i.e. what is the best explanation? And that calculation is only for one single gene could do so much. Oops! It turns out that neither Darwin nor subsequent biologists have ever assumed that point mutations has been known since before 1950 and has been rigidly looked at, and a chemical soup with zero functional bits – zero to 130 bits and you must explain how it happens. “Intelligent” selection monitors on or two dimensions. Why should biology be an exception? Formally, for information, very good paper by Abel which explains very well the concept of targets and goals, you would like to point out that neither Darwin nor subsequent biologists have ever assumed that point mutations are neutral or neutral alleles. I find most interesting about autistic savants, is the same: spontaneous generation of information not only does one have to sneer at everything? As for me, for a minimal replicator of 130 bits and you must show that it puts the cart before the genes were knocked out! In fact at one time in one word.kellyhomes_{October 3, 2011
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Elizabeth, What I find disconcerting is that nobody seems to know what on earth the TOE should really exactly mean. That is a very bad sign suggesting that perhaps the whole concept is fuzzy and untenable. Many a biologist tacitly admit this, in the presence of strong evidence of its implausibility. I don't know what you, Elizabeth, mean by the TOE, but I mean exactly what Darwin did as per the "Origin of Species". I am quite ignorant as to the latest "additions and not refutations" as regards the theory, as you put it. As a layman in biology, I can only say that there are very few people who are willing to fight to the end at the side of the classical Darwinism (or neo-Darwinism). Perhaps, now it's only Dawkins. What I find unhealthy about the contemporary variant of the TOE is that no matter what evidence against it is produced, this evidence gets built into the theory. As a result the "unshakable" theory gets another crutch and on it stumbles.Eugene S_{October 3, 2011
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Actually, Joseph, the parent's contribution can be eliminated in one generation. It is an average of 1/2 the genes that are passed on. It is possible (although extraordinarily improbable) that none of one parent's genes are passed on. The chances of none of a parent's genes making it through two generations are also incredibly small - although slightly larger. However, none of this is relevant because the majority of both parent's genes will be the same and will be part of common gene pool belonging to the species.markf_{October 3, 2011
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Hi, gpuccio! A few comments, as Chris Doyle pointed me to your post:
I think you certainly understand the point, but still I would like to specify, for tyhe benefit of all, that the fact that events have the same probability of happening is in no way a requisite of a random system. That is a property of a very special probability distribution, the uniform distribution. So, even if genetic variation were made of events having different probabilities, it could well be a completely random system.
Hmmm. You are of course right that "random" events need not have a uniform probability distribution, and most don't (the direction of Brownian motion being a nice example of one that does!) But I still think the term "random" is misleading, because it has so many meanings in common English. If something has a 999/1000 probability of happening, you don't usually call the result "random", and "certainty" is approached asymptotically! For that reason I think "stochastic" is a better term, and then we are not tempted to apply the meaning "not on purpose". We can intend events that are nonetheless stochastic. Drawing a bingo number is a deliberate act, done "on purpose" but it makes use of a stochastic process. So I think it's really important to tease apart the concept of something being been drawn from a probability distribution from the concept of something being done on purpose.
The only part of the darwinian algorithm that is not random is NS, that is the expansion of those random events that confer a reproductiove advantage.
I disagree. Natural selection is just as much a stochastic process as mutation. However, it refers to a systematic bias in the direction of reproductive success. Mutations are not biased in the same sense (but then the concepts are not analogous either), although they are much more likely to have no effect on the reproductive success of de novo beaerr than to be deleterious or advantageous. So they are "biased" in favour of neutrality. But I'd say it is better to describe both systems as simply stochastic, where mutation has probability distribution with a peak around neutral, and breeding successfully has a probability distribution with a peak around mutations that confer some survival advantage to the phenotype in the current environment.
That said, I agree with you that the probability of events in RV at the biological level is not necessarily completely uniform. First of all, if we are talking the transition from one protein to a new, unrelated one, variations near the original protein are certainly more likely, given that the most common tool of variation is probably point mutation.
I think duplication and insertion, and, in the case of sexually reproducing species, recombination within an existing gene, are probably more common.
That’s why we describe genetic transitions as a “random walk”, which is not exactly like tossing a coin, even if the probabilistic consequences are not so different. That said, I believe however that a uniform distribution for nucletides (and therefore for aminoacids) is still the best approximation of the system for big transitions, because nucleotides (and aminoaxcids) have really a rather independent chance of being reprersented in the random variation events, even taking into account some asimmetries.
I don't see how this belief is justified at all! In fact, I don't even find it coherent. Are you suggesting that "big transitions" (not even sure what you mean by this - all transitions are achieved by means of incremental genotypic changes, even if occasionally, the phenotypic change may be fairly substantial) involve some kind of radical shuffling of the genome? If not, what do you mean?
Even events like inversion, hybridization and similar, which are more “macroscopic” than point mutations, in the end cannot create real differences, if we consider that any random inversion, or hybridization, is in principle possible. Applying combinatorics may not be easy, but I think it can be done.
Well, "hybridization", which is simply mating between individuals with markedly different genomes, as opposed to mating between individuals with much more similar genomes, as generally happens, just means that radically novel alleles are more likely to arise by recombination. But as radical novelty in sequences is much more likely to be disastrous than slight novelty, I doubt it plays much role in adaptation.
Obviosuly, there can be some biochemical necessity mechanisms that can alter the simmetries and make the distribution somewhat non uniform (but random all the same), but that’s where your second point is pertinent. However, almost all biologists would say the variation is mostly (with the exception of some evidence of Larmarckism) not directed towards any end and in particular it is not directed towards increasing the fitness of the organism.
Well, epigenetic variation probably serves an important function, possibly at population-selection level. But epigenetic changes don't alter the genome.
That’s the really important point. Whatever the probability distribution, or even the contribution of some necessity aspects from biochemical laws (except for NS), the point is that none of that can possibly favor the kind of functional information we observe in proteins, because neither RV nor biochemical laws have any pertinent information about the sequence of functional proteins.
What do you mean by this? In what sense could "RV" have "information"? What has "information" is the genome itself, and that information is the information laid down over generations as to what leads to survival in each environment through which the population has persisted. And every "RV" is a "probe" if you like, into the current environment, to "see" if there is anything that might come in useful, or even do no current harm, but might come in handy later. And yes, I'm using anthropomorphic metaphors, but then so are you :)
So, to sum up: a) RV is always random, whatever the form or the probability distribution. It can in no way overcome the “probability barrier” of a random walk towards functional complexity. It doesn’t matter if the variation mechanism is point mutation, inversion, duplication, hybridization, or whatever. The system remains random. The results remain random.
But it isn't a random walk! You are forgetting that there is not one "walker" but millions, and only those that randomly take a step in a useful direction get to make the next step! "RV" is simply that - random variation. It doesn't "walk" anywhere. What "walks" are the RVs that prove to be neutral, advantageous, or only slightly deleterious. So the "walk" is not "random" in your sense at all (though it is stochastic) but that is because the "walk" is the natural selection part, not the variation part!
b) The only non random mechanism in darwinian theory (and, I believe, in any non design theory) is NS. I will not repeat here the arguments against its “creative” powers. The only point I want to make here is: NS is not random, it is a necessity principle, and it is the only pertinent necessity principle that can change something (but not much) in an explanation of protein information. But, as all necesiity mechanisms, it must be explicitly understood, and its real import must be explicitly evaluated, before it can be accepted as relevant to an explanation.
I think you have some good points, but they are awfully muddled! "NS" isn't really a process at all, it's simply a consequence of heritable variation in reproductive success. That heritable variation is, indeed "random" with respect to reproductive success, in that a de novo mutation that is confers increased reproductive success in the current environment is no more probable, and indeed less - than one that is neutral or slightly deleterious. However because the vast majority of de novo mutations make virtually no difference to reproductive success in the current environment, they drift through the population by means of what you could legitimately call a "random walk". However, to the extent that some variants do turn out, at some point, to confer reproductive advantage, that "walk" is biased in favour of those variants that happen to confer advantage in the current environment, and it is those variants that then stand a greater chance than the others of being the ones in whom the next potentially de novo mutation happens.Elizabeth Liddle_{October 3, 2011
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I don't you know what you mean by "all this equivocation over neo-Darwinism" - it's precisely to avoid equivocation that I want you to say exactly what you mean by the term! But Darwin's basic principle that heritable variance in reproductive success leads to adaptation is certainly simple enough to be taught to primary school kids. Indeed, sunflower growing competitions are a great way to illustrate the point! Also, so is the principle of common descent, and can be readily illustrated. Most primary kids are delighted to recognise bird skeletons as miniature T Rex fossils, and to point out to less-well-informed adults that dinosaurs aren't actually extinct. And I don't actually agree with gpuccio's post, though s/he makes some good points. I'll comment there, though :)Elizabeth Liddle_{October 3, 2011
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Well Elizabeth, perhaps YOU can post what biologists mean when they say the mutations are random. I was taught over and over again that the accumulation of random mutations led to evolutionary change — led to new species.-Dr Lynn Margulis I say they use the word to mean “entirely by chance; just happened for no purpose” IOW they use it just as dictionies define it.
Well, "entirely by chance" doesn't really help you - it just passes the buck to the word "chance". If you mean "happened for no purpose" then that probably is what biologists mean, but "happened for no purpose" isn't the same as "happened for no reason" or "was not caused by anything". There are several causes of mutations, and while biologists would argue that they "happen for no purpose" (i.e. no-one intended them to happen) they certainly don't "happen for no reason", and what Shapiro and Margulis argue, persuasively, is that the reason that organisms mutate in the way that they do is that optimal mutation types and frequences are themselves selected at population level. Just as heritable variance in reproductive success at the level of the individual organism results in adaptation of the population, so heritable variance in adaptive success at the population level results in adaptation at the population-of-populations level. As I said, this is readily demonstrable by computer modelling.Elizabeth Liddle_{October 3, 2011
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Colleagues, Given that so many evidence based objections to the theory of evolution turn out to be actually its valuable additions and not refutations, is it possible to suggest at least anything that would be falsification enough for the TOE?
Well, it depends what you mean by "the TOE". If you mean the principle that populations adapt by means of heritable variance in reproductive success, possibly not, as it's virtually a syllogism - i.e. is self-evidently true. You could falsify its application to biology by showing either that reproductive success is not heritable, but we know that it is! If you mean something else - perhaps that all heritable traits are genetic, then yes, that's falisfiable, and has been falsified. It isn't true. Possibly you meant neither of these things - if so, what do you mean by "the ToE"? In other words, what claim is it that you think should be falsifiable but may not be?Elizabeth Liddle_{October 3, 2011
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Yep, so it turns out that Lamarckism is the new Darwinism… wait a minute, wasn’t Darwin a Lamarckist?
Well, no, Lamarckism isn't "the new Darwinism". And yes, Darwin did consider it possible that variance was generated by Lamarck's proposed mechanism (inasmuch as it was a mechanism - it was more a postulate). Lamarck wasn't right, but he wasn't completely wrong either. There are mechanisms by which the behaviour in one generation affects what the next inherits, one being via natural selection (the behaviour of other members of the population forms part of the environment to which subsequent generations adapt), the other being epigenetics, although that doesn't produce mutations.Elizabeth Liddle_{October 3, 2011
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Colleagues, Given that so many evidence based objections to the theory of evolution turn out to be actually its valuable additions and not refutations, is it possible to suggest at least anything that would be falsification enough for the TOE?Eugene S_{October 3, 2011
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