Mud-to-Mozart Atheology (Or, Who are the real skeptics?)

_{Gil Dodgen

October 22, 2011

Intelligent Design}

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I find the “skeptic” claim on the part of Darwinian materialists very interesting and equally illuminating. Darwinists exhibit no skepticism whatsoever about the thesis that physical stuff turned into Mozart by chance. (Don’t try to deny this, Darwinists, that is the essence of your claim. You can try to obfuscate with legion “peer-reviewed scientific papers,” but you’re not going to fool me and many others about what you are actually promoting and advocating.)

I choose Mozart not just because I am a classical concert pianist, but because his existence epitomizes everything that Darwinian theory is totally powerless to explain.

Darwinists, claiming to be skeptics, actually exhibit the antithesis of skepticism — making transparently ludicrous claims and providing a never-ending stream of unsupported extrapolations, based only on wildly imaginative speculation with no empirical support.

How is it that Darwinian atheists are the only ones who get to declare themselves legitimate skeptics? Is mud-to-Mozart-by-chance philosophy the only worldview immune to skeptical inquiry?

Comments

DrBot: First of all, thank you for your detailed answer. This is exactly the kind of explicit and detailed response I am looking for, and I appreciate it. I allows discussion to grow. I will try to address your points. You say: You appear to be treating drift as a type of search No. What I said is: "if we must consider the probabilities of a random walk from A to B (unrelated), all the states have similar probabilities of being reached, both with or without drift." I am not "treating drift as a type of search". I am only saying that in a random walk of the kind I have proposed as a model (from an existing basic protein domain A to a new, unrelated protein domain B) the probabilities of reaching B remain the same, either drift is part of the scenario or not. Please, note that genetic drift is not the same as the existence of neutral mutations, as you seem to argue in your examples. Drift is a very specific kind of random amplification of some neutral trit, in sexual reproduction. From Wikipedia: "Genetic drift or allelic drift is the change in the frequency of a gene variant (allele) in a population due to random sampling" In all your post, you give no discussion of genetic drift, only of simple neutral variation. But that is not important. My point, that I maintain fully, is that neither neutral variation not genetic drift in its proper sense change the probabilities of a random walk in the model we are discussing. Let's go on. Why are you talking about random walks and neutral mutations? Neutral drift is not a random walk. A random walk will take you in any direction and can result in a change if reproductive potential (selection can act). A neutral mutation is just those steps that do not result in a change of fitness. I am talking about random wlaks because that's exactly what a transition as I have described is. Unless NS acts. I will be more clear. What we are discussing is the emergence of B (a new unrelated basic protein domain, with a new function and structure) from A (an existing functional protein domain). OK? Well, as the "engine" of the transition is RV (in all its forms), and as the searach space has to be traversed by definition (the two states are unrelated, and therefore distant in the search space), it is a random walk. Each variation event is random. They may have different probabilities (IOWs, the probability distribution of the events need not be uniform), but the events are random all the same. Another aspect of the problem, hoever, is what happens after a variation event. As we are talking of a reproducing population in an environment, NS can and does act. So, while with regard to pure RV the random walk is a purely random system, as soon as we take into account NS the system becomes "modulated" by the effect of NS. But what are those effects, and when does NS act? Here, we have to make distinctions, and be analytic. Recurring to poetic phrases like "differential reproduction of inherited traits". We must ubderstand well how things work. So, the variation event can be characterized according to two parameters: a) is it local or not? b) what are its effects on reproductive potential? About a) you seem to assume that all variation events are local. That is not really true. Some forms of variation are not local, as I have already pointed out. A single framshift event, for example, is not local, and determines a sudden random "jump" in the search space. But,as my point is that both local and non local events have in the end similar probabilities of reaching B, I will stick in the discussion to local events, like SN mutations. About b), you will agree that they can be classified in three sets: a) Those that have no effect on reproduction b) Those that have a detectable negative effect c) Those that have a detectable positive effect Let's make another assumption: that protein A is importnat for successful reproduction, and therefore significant loss of its funtion will result in b). Now, is NS acting? In the beginning, the only function available is the function of A. The main effect of NS on an existing functional protein, well documented, is to act as negative selection: the variations that strongly affect function will be eliminated because of reduced, or absent, reproduction. The main effect of that is that a protein can change to a point its sequence while retaining its structure and function. That's why the same protein is usually more different in distant species, while its function remains the same. Let's call that process "traversing the functional island". It is possible that local variations give an increase of the function of A, but that is much more difficult, and anyway it could bring only to the "tweaking" of the existing function, or at most to the emergence of a new function with a different active site in the same family. For the moment, we will not discuss that, because it is not relevant to the discussion of how to reach B. Unless you can show that a more functional A is a step towards the sequence of B. Because, you see, we are talking very specific objects here: proteins, with specific biochemical roles integrated in the general scenario. And we must always be consistent with this premises. So, the detectable effect of neutral variation plus negative selection on an existing functional protein will be the "traversing of the fucntional island" in the course of naturla hisotry. the function remain the same, the sequence changes to a point. Is that a random wlak towards B? Absolutely not. B will be never reached that way. Because, to reach B, we have to traverse the genral search space, that is we have to go beyond the local sequence space, and dive in the sea of unrelated states. The way darwinists usually try to solve the problem is through the model of "duplication". A is duplicated and becomes non translated, or however non functional. The original A maiontains the existing functionality. So, the new A, let's call it A', can change without the limitations imposed by negative NS. OK? Now, that makes practically any variation of A' "neutral", except for those variation that implement some new useful function, luckily associated with persisting translation. IOWs, any variation is neutral, until we reach B. Or B00, or B0 (some functional, selectable precursor of B). At that point, the remaining problem would be the transition form B00 to B. But now it is perfectly true that the search space can be freely traversed by NS, because there is no more the limit of negative selection, defending the functional island of A. It is true, as you say, that the initial variation will remain local, but as neutral variation accumulates, we are diving into the sea of unrelated states. And we can, now, reach B. But the probabilities are exactly those deriving from the total dFSCI of B. Or of the functional internediate, if and when it exists. So, you see, you model of GA has really nothing to do with the real biological scenario. The reason is simple: it is a bad model. In no way it has the form of what it pretends to model. I could comment on it further, but why? It is completely non relevant. I will stop here, for the moment. There are many other things that should be said, but I am interested in your comments about these first ideas.gpuccio_{October 29, 2011
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For dFSCI computation, you need a purely random system
So when you are wrong about something, you simply make up something, like protein domains being poofed into existence. 150 bits. Poof. Rather than look to known and observed phenomena like cousin extinction, you assert that you know the true history of isolated lineages.Petrushka_{October 29, 2011
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Basically you have lines where the cousins have gone extinct and lines where they haven't. Cousin extinction is speciation. What you refer to as the origin of protein domains is an example of speciation. That's why your argument is a gaps argument.Petrushka_{October 29, 2011
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We known that language evolves, because we have written records documenting the emergence of languages like English. and yet we have languages like Basque, for which there is not know precursor. Is that evidence of a miracle, or intervention? It is always possible for cousin lines to become extinct.Petrushka_{October 29, 2011
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I must say, that, having run out of patience long ago, I’ve decided to “bang [their] head[s] against the wall”. It’s a lot more fun that way. :)
I can't say I agree that subjecting people who's arguments you disagree with, or don't understand, to physical violence is ever justified - and I certainly don't view violence as 'fun' like you do.DrBot_{October 29, 2011
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I had already addressed those points in my post #50 (to you).
well, not really, otherwise we wouldn't be where we are
.. neutral mutations in no way change the probabilities of a random walk, and neither does genetic drift, because it is a purely random event, and therefore does not change anything.
That just reads as incoherent to me - but I'm starting to see the problem ...
IOWs, if we must consider the pobabilities of a random walk from A to B (unrelated), all the states have similar probabilities of being reached, both with or without drift. That’s why I always say that drift is irrelevant to the computation of probabilities, and favours no specific configuration, least of all a functional one.
You appear to be treating drift as a type of search ...
any time you reach an unrelated state through a random walk, by neutral mutations, drift, frameshift mutation, inversion, translocation, ot whatever, the probabilities that such a state is functional are 1:10^140.
Why are you talking about random walks and neutral mutations? Neutral drift is not a random walk. A random walk will take you in any direction and can result in a change if reproductive potential (selection can act). A neutral mutation is just those steps that do not result in a change of fitness. Neutrality is a feature of the evolutionary search space - it is defined in the context of fitness, of which heritable elements are subject to selection, so it cannot be treated as something different, it cannot be ignored in your calculations.
a) the search is not local. It is a random walk that has to necessarily traverse the space
Ok, you got several things wrong here. First, neutral drift is not a random walk, it is not the exploration of the whole search space, it is just a local move within the search space that does not affect fitness. Second, and only incidentally, a random walk is, by definition, a local search because it proceeds by moving in small steps across the search space - with each iteration there can only be movement in the immediate locality. By comparison a random search is one where the search space is sampled at random - with each iteration there can be movement to any other location in search space. Both of these can navigate the whole search space, its just that the random walk can only search the local space from one iteration to the next.
Not good, eh?
No. I think the best way to explain where you are going wrong is with a direct, if simplistic, example designed to illustrate how neutrality influences evolutionary search dynamics. We have a 'genome' (deliberately in scare quotes) that consists of two finite integer values - so our search space is two dimensional - and we have a fitness value at each location (fixed, rather than dynamic for the sake of simplicity) The grid of values below explicitly defines the fitness landscape (the x axis is one 'gene' and the Y axis is the other) and the value in each cell is the fitness at that (x,y) point. With each step (generation) a mutation can occur on only one axis (gene) and to a magnitude of +/- 1.0 in other words, in each step a mutation can only move us in ONE of these four directions: North, South, East or West. Here is the fitness landscape (hopefully formatted correctly because this ASCII art works best with a fixed width font! ) Directions: N E W S Landscape: 00000000000 01111111110 01222222210 01233333210 01234443210 01234543210 00123432100 00123432100 00123432100 00123432100 0012x432100 00012321000 00001210000 00000100000 00000000000 For the sake of argument, lets start at the position marked with an x (where you have a fitness of 3). From here there are four possible directions a mutation can take you: N, S, E, W. So, for sake of argument again, a mutation takes you E -> you now have a fitness of 4 (consequently selected for by NS because you are fitter - you have climbed up the fitness hill) Now, again, you have four possible directions that mutation can take you. N results in fitness of 4, all other directions will result in a fitness of 3. N therefore is neutral (no change in fitness) but all other mutations are deleterious - NS selects against mutations that are deleterious - ones that take you S,E or W. From here there is no way up, no way to increase fitness through a single mutation, BUT any mutation that takes you North is not selected against because it does not reduce your fitness. The ONLY way you can move is North WITHOUT reducing fitness and consequently subjecting yourself to the filtering effect of NS. ANY mutation except a northward one is deleterious and selection will act - your reproductive success is reduced by these mutations. Drift is any movement north - any movement that does not invoke selection, that does not affect your reproductive success. In this situation you are on a fitness ridge - a flat path across the landscape with lower fitness areas on each side. Any move off this ridge will be punished by NS so the effect of mutations over time will be that you drift forwards and backwards along this ridge because natural selection acts to keep you in this neutral zone. If you drift far enough north you end up on the side of a fitness peak and then a further northward mutation will actually increase your fitness. Now compare the previous fitness landscape to this one: 00000000000 01111111110 01222222210 01233333210 01234443210 01234543210 00123432100 00123332100 00001210000 00123332100 0012x432100 00012321000 00001210000 00000100000 00000000000 The landscape is identical except that the neutral ridge is missing. So, start again - you start at X and mutate East - to a fitness peak of 4 - now a mutation in any direction will reduce your fitness, and be selected against. Now do the math: What is the probability of reaching a fitness of 5, from the starting point x, within this landscape compared to the previous landscape, using an evolutionary search? One important thing to take note of is that both landscapes have neutrality - for example a mutation that takes you around the side of a fitness hill rather than up or down is neutral. The difference is the ridge, these types of search space features are sometimes referred to as neutral networks - networks of neutral ridges connecting areas of the search space. They are a feature of the search space and represent degrees of freedom with respect to selection. It is a relatively easy task to turn the the examples above into a simple computational model and do some tests. If you explicitly define some different landscapes, with and without neutrality, seed a population to low fitness areas and apply a super simple GA, you can see the effect of neutrality on the evolutionary process. This should make it perfectly clear why the degree of neutrality, and the existence of neutral networks within a fitness landscape has an important effect on the evolutionary process.
It’s nonsense. It’s wrong. Try to motivate it, or remain silent. Anyway, I will not explain the same things for the nth time.
Nor will I. The example above should be more than enough for you to understand where you are going wrong - I would encourage you to work through the two examples, they are similar to, and pitched at the same level as, introductory lectures for year 1 CS students studying evolutionary algorithms. If you calculate probabilities about neutrality as if it is a random walk across the entire search space then you are not calculating the probabilities of evolutionary mechanisms finding a solution, or the effect of neutral networks on the search. This is what Elizabeth what trying to explain when she pointed out that you cannot carve neutrality off from selection - because it is defined by selection, and it is not a random walk. In order to calculate the probabilities you actually need to know how much neutrality there is in the landscape - how many sequences link one protein to another via a series of single steps that do not significantly affect fitness. IF a near neutral ridge like this exists then natural selection can act to 'walk' the sequence along this ridge.DrBot_{October 29, 2011
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Petrushka: That is just a hidden version of why are there no intermediates among contemporary organisms. Why should there be? A simple question, a simple answer. Let's say that a transition from one basic domain to another, at some point of natural history, "helped" by NS, is of the form: A - A1 - A2 - B00 - B0 - B With "A1 - A2 - B00 - B0" all being naturally selectable intermediates, each of them giving a reproductive advantage, xand therefore selected, expanded and fixed. In the modern proteome, we have A. We have B. But we have no trace of A1 - A2 - B00 - B0. Not in some particular case, but in the general case. I would say without exception. Why? Now, don't come and say that what we are observing are the modern proteins, and similar nonsense. I have shown you, with examples, how those "modern proteins" show amazing homologies even between the bacterial and the human form (that I would take as the two extremes of observable evolution). I hope you may agree that the only meaning of that is that they still have amazing homology to their very old precursor in LUCA, more than 3 billion years ago. So, we can see in the proteome the very clear traces of what existed in the old times. We do see them all the time. If, for a whole supposedly rcih category of molecules (the "bridging intermediates") we can find no trace in the proteome, what is the only reasonable explanation? I supppose a three year old baby is already answering: they never existed.gpuccio_{October 28, 2011
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PaV: Thank you for the psychological support :) It's beautiful to know that at least someone cares about my poor head...gpuccio_{October 28, 2011
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gpuccio: We here in the US say that "it's like banging your head against the wall" when referring to a situation where the person your speaking with just doesn't want to, or just doesn't understand, what you're trying to tell them. I think you've "bang[ed] your head against the wall" for the nth time. You better stop. Advil only helps so much! ;) I must say, that, having run out of patience long ago, I've decided to "bang [their] head[s] against the wall". It's a lot more fun that way. :)PaV_{October 28, 2011
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gpuccio: I think what is obvious to you, is not obvious to EL and DrBOT. When it comes to neutral drift, you have clearly, and correctly, said that this amounts to no more than a "random walk". And the implication, then, is clearly that: "In that case, the system is acting randomly, there is no selection, no amplification," which, of course, means that almost nothing can happen given the known improbabilities for dFSCI. They're missing this point entirely. Instead of blind faith in NS+RV, it's blind faith in RV. Once faith is blind, what's the difference?PaV_{October 28, 2011
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Lizzie: I'll assume you'll look at my response at 47.2.1.1.7 (Sorry, I got it in the wrong spot the first time around)PaV_{October 28, 2011
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Lizzie: I'll assume you'll look at my response at 47.2.1.1.7 above.PaV_{October 28, 2011
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Lizzie: Sorry for taking so long to reply. I must admit that with this new format, and with the sheer number of posts taking place each day, it's very hard to keep track of where I've left an entry. (Hope somebody's taking note) But, I'v also been away from a computer for a couple of days. Now,
I don’t know what you call it, PaV, and I don’t care very much; the important thing is that it’s a key part of modern evolutionary theory.
Certainly neutral drift is part of "modern evolutionary theory"; however, it has serious problems---which you seem to deny for whatever reason. But let's move on.
What we now know is that the vast majority of new variants are near-neutral, which means that any given population at any given time represents a pool of phenotypic variants of which some variants may prove more successful than others in surviving when the enviroment changes.
This is probably true---given enough time for drift to work. But, is the mere 'presence' of such 'successful variants' sufficient. Obviously the 'presence' of these putative 'successful variants' is necessary. But is it also sufficient for macroevolution to take place? We continue . . . .
This means that when we set up Darwinian computer models, we find, to our surprise, that complex functions evolve more readily than perhaps Darwin might have anticipated because necessary but neutral precursor variants are already likely to be there in the population.
Is this true? Do 'Darwinian computer models' actually show this? Behe and Snoke set up what they considered to be a 'Darwinian computer model' and they got no such result---in fact, it showed even NS, let alone neutral drift, was rather impotent to bring about meaningful changes. But let's say that what you say is true. Well, what you're saying is that the "necessary" neutral precursor (variant) is already likely there. Okay. But, as I said above, the variants are necessary, but are they sufficient to explain evolutionary change? This is where the whole idea of "fixation" comes in. You're simply assuming that because this 'beneficial' (I know, 'beneficial' relative to the 'current' environment) is there, the rest automatically takes care of itself. But this is where, IMHO, you're going wrong. The next step---which is 'necessary' and 'sufficient'---is for this 'beneficial variant' to become fixed, wherein, every member of the population shares this variant. This is because, let's say, a little kitten, born with a 'variant' that allows it to sniff out potential prey better than any of the other cats around, has a likely reproductive advantage over its litter mates as an adult. And so, too, would its offspring. But what if, one day, while still a kitten, it became distracted while crossing the street, and was run over. What, then, of this 'beneficial variant'? What becomes of it? ANS: Nothing. It's lost to the population. This is a random event, and this randomness---that is, the potential for a single member of the population to be accidently lost, or, for whatever reason, not be able to furnish offspring; or for the offspring themselves to be killed off or reduced in number---all these random kind of events need to be overcome by the population. And that's why population geneticists calculate such things as "fixation" times. Once a variant is incorporated into the entire population, it's very likely not to be lost very easily. And now the population, as a whole, can work on acquiring---and fixing!---the next variant. But how long does this take? Well, Kimura did the calculations, and it turns out to be 1/4N_eff. And, hence, in 49.1 below, I include a sample calculation from Kimura's magnus opus, "The Neutral Theory of Molecular Evolution". It turns out that this is a very slow process. So......the mere appearance of a 'beneficial variant', though 'necessary', is not sufficient. Fixation is also a necessary, and somewhat sufficient condition for macroevolution to occur. The problem though is that this "fixation" process works way too slowly to account for the fossil record. This is only more so the problem when considering chimp---human differences (only 4 million years for all these "fixations" to occur!)
But what it does mean is that the old cliche that mutations are random and natural selection isn’t, is pretty well meaningless (and I wish people, especially Dawkins, would stop saying it!)
Dawkins is the leading apologist for the Darwinian cause. His entire argument falls apart if NS is considered to be 'random'. Per your view, his arguments fall apart. So that leaves Darwinism with no leading apologist. So now what?PaV_{October 28, 2011
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Petrushka,
That is just a hidden version of why are there no intermediates among contemporary organisms.
Wow. The lack of evidence to support one speculation provides an explanation of the lack of evidence to support yet another. Evidence is evidence, and no evidence demonstrates consistency with other cases in which there is no evidence. You've got all the bases covered. This can never be wrong.ScottAndrews2_{October 28, 2011
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No trace of any intermediate sequence “bridging” basic protein domains is found in the proteome.
That is just a hidden version of why are there no intermediates among contemporary organisms. why should there be?Petrushka_{October 28, 2011
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Elizabeth: Just another note: drift does not "enrich" anything. If a neutral mutation es expanded by drift, other neutral mutations are lost in that expansion. There is no enrichment. Drift is absolutely useless, or at least it does nothing different from what other kinds of RV do: it randomly changes the existing sequences. We cannot even say that drifts accelerates the rate of variation. First of all it is a rare event. Other forms of variation are much more common. Secondly, we know well that too much variation is worse than too little. That is well known, I believe, in population genetics. You cannot increase your chances of reaching new functional targets only by increasing the rate of variation, be it by drift, or by any other means. Just an example of how drift can be in the same way useful or deleterious, so that its global effect is nil. Let's say that to reach B you need serine at position 126. Well, you get lucky enough and get that mutation in A. It is not amlified, but luckily it is neutral, so it is not lost too. It is there, ready to contribute to the final result (provided that other lucky events accumulate). Now, if by further luch that neutral mutation is expanded by drift, we will certainly be nearer to the goal. But in the population there are many other neutral mutations. After all, as you say, neutral mutations don't tend to favour what works better. Now, let's say that for once you are not lucky, and the neutral mutation that is expanded by drift is one, in another individual, that has glycine at position 126. Now, that is a neutral mutation for A, but it is not neutral at all for the future target, B. Indeed, let's say that with glycine at 126, B will never be functional. Now, if the neutral glycine is expanded by drift, instead of the neutral serine (they have the same probability, after all), what has happened? You have lost the favourable neutral mutation that had already accumulated. That is the truth for neutral mutations and genetic drift. They don't change the explanatory scenario. The only place where they are "useful" are the wrong arguments of darwinists.gpuccio_{October 28, 2011
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Elizabeth: So, let's sum up, another time: a) Neutral mutations are not in any way tending to a new function (your words: "I am not saying that variant-producing mechanisms are biased in favour of what works better," b) They must be neutral, not to be exposed to negative selection, in which case they would reproduce worse (your words: "merely in favour of what works about as well as the parent genotype." c) And yet, new biological functions appear all the time in the course of natural history, under the form of new basic protein domains that accomplish new things. e) How do we explain that? If we invoke NS, then we are no more relying on neutral mutations only. But against a significant role of NS there are at least two big empirical facts: e1) The complex biochemical functions of basic protein domains are not decontructable into simpler progressive steps with naturally selectable functions, not even in one case, least of all in the general case. e2) No trace of any intermediate sequence "bridging" basic protein domains is found in the proteome. I have explained in detail, many times, why neither e1 nor e2 can be answered from a NS point of view. Nobody has given any concrete counter argument, only evasion, usually again in the direction of neutral selection and drift, which are not pertinent in this specific discussion (remember, this is point "e)" that starts with "If we invoke NS, then we are no more relying on neutral mutations only." f) If, instead, we leave alone NS, or at least drastically redefine its role to solve our problems in e), then we are faced by another problem: probabilities. g) You know very well that RV favours local searches. You have said that yourself, suggesting that that would be a reason not to rely on a uniform distribution in the computation of probabilities. But that is simply worng. Local searches are not useful here. Local searches can, at best, tweak an existing domain, or slightly change an active site. But to produce a new domain, unrelated, at the sequence level, to anything that already exists, we have to abandon the local. The local is the set os sequences with high homology to what exists. h) Once we abandon the local, and dive into the sea of unrelated states, the distribution of probabilities becomes practically uniform: each unrelated state has more or less the same probabilities to be reached by a random walk. i) The sea of unrelated states is extremely huge for most (almost all, indeed) known functional protein domains (see the discussions on dFSCI and the Durston paper). l) As a consequence, functional basic protein domains are the perfect objects to infer design: they exhibit lots of dFSCI, their origin by a pure random system (neutral mutations and genetic drift) is practically impossible, and the only explicit mixed algorithm (RV + NS, the neodarwinian algorithm) is falsified by existing evidence (see points e1 and e2). That's my reasoning. I have made it as simple and schematic as possible. Now, please, don't argue again that I should not talk of NS and RV, but rather of differential reproduction of inheritable traits, or whatever. Don't insult my intelligence, and especially yours. If you have objections, please take my points, my terms, and my reasoning, and say explicitly where and why they are wrong.gpuccio_{October 28, 2011
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Still going to extract myself for a bit, but on reflection, I'll try and respond to posts addressed to me! I just try not to be distracted by new shiny things! No, I don't mean "current". A "current" would be analogous to something that is biased towards or away from propagation, because it promotes or undermines reproductive success. "Drift" is the name we give to what happens to variants that are neutral in the current (no pun intended) environment, and are therefore as likely to be slightly less prevalent as slightly more prevalent in each successive generation. A random walk in other words. And "drift" doesn't "do" anything, other than be the word we give the phenomenon by which populations are continually enriched with neutral variance. The reason that is important is that if the environment changes, that neutral variance can be potentially beneficial, and by "environment", I mean not only the external environment, which includes the population itself, and its ever-changing allele frequencies (gene *environment interactions), but also the "genetic environment" - a variant that is entirely neutral in one genotype may be beneficial in another (gene * gene interactions) So I hope it is now clearer what I mean by drift. Like "selection" it isn't an agent, it's just an observed phenomenon, but it's important, because it means that genetic diversity, which enables populations to adapt to changing environments, consists of a gene pool of variants including those that were originally neutral, not merely variants that were beneficial from the get go.Elizabeth Liddle_{October 28, 2011
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Elizabeth (emphasis added):
But what it does mean is that the old cliche that mutations are random and natural selection isn’t, is pretty well meaningless (and I wish people, especially Dawkins, would stop saying it!) Mutations and differential reproduction are stochastic process that are strongly biased in favour of what works. In that sense, they aren’t even “blind” or “undirected”. But I’m not going to argue about labels, because what matters is what the theory actually is, not the descriptive words we use to describe it.
I admittedly do not understand your argument here, specifically the bold part. How can natural mutations be biased in favor of what works? If you mean that they originate in a biased manner, I see how that applies to a natural modern synthesis. If you mean that they propogate in a biased manner, to me that means that natural selection behaves in a biased manner. Either way, I don’t understand your point or why you feel it is important to state it. Further explanation?
OK, apologies, let me try to make it clearer what I mean: By "mutations" I mean novel sequences in the genome (sequences present in neither parent). Near-neutral mutations are far commoner than strongly beneficial or strongly deleterious mutations, and include mutations that have no phenotypic effect at all, as well as those that have a phenotypic effect that makes no difference at all to reproductive success. In that sense, even before we consider the filtering effect of differential reproduction, the actual generation of variants is biased in favour of what works, i.e. something that is similar to the sequence present in what is by definition a viable parent. This in itself is a potential outcome of Darwinian processes, in that organisms with reasonably hi-fidelity reproduction mechanisms will tend to leave more copies of their genome around than organisms with low-fidelity reproduction mechanisms. I am not saying that variant-producing mechanisms are biased in favour of what works better, merely in favour of what works about as well as the parent genotype. It's a highly non-flat probability distribution, in other words, with a peak around neutral. Hope that makes a little more sense :) Will drop by again to check.Elizabeth Liddle_{October 28, 2011
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DrBot: I had already addressed those points in my post #50 (to you). I quote myself: "DrBot: Let’s try some order. Look at my post 38.1.1: “And it is well obvious, even if the dumb logic of darwinists will never recognize it, that neutral mutations in no way change the probabilities of a random walk, and neither does genetic drift, because it is a purely random event, and therefore does not change anything. The term “RV” includes all forms of possible random variations, including neutral mutations and genetic drift. And all RV is accounted for and evaluated in the ID model.” and my post 47 (in response to you): “IOWs, the point is: a) We have a domain that appears for the first time (B). b) To explain that by neodarwinian mechanisms, we need some precursor (A), previously existing, that by RV and NS gave the result of the appearance of B. The only alternative would be that the transition from A to B was merely by RV, that is neutral mutations and drift and similar. But, as both A and B are unrelated long molecules, that is practically impossible: the probabilities are completely against that, and any good neodarwinist knows that.” And so on. ... Some more reflections on the reason why drift is non relevant in the computation of probabilistic resources. ... Now, let’s say that in the same population we have a number of possible neutral mutations in a certain time. And let’s say that in that time one drift event will expand one of those neutral mutations. Obviously, if one of the neutral mutations is “favorable” to the final result, and it is expanded by drift, in that case the probabilities of the final result will increase. But how likely is that scenario? Exactly as likely as a similar scenario for each of the other neutral mutations, that in no way contribute to the final result, or even make it impossible. IOWs, if we must consider the pobabilities of a random walk from A to B (unrelated), all the states have similar probabilities of being reached, both with or without drift. That’s why I always say that drift is irrelevant to the computation of probabilities, and favours no specific configuration, least of all a functional one." So, let's sum up (maybe for the fifth time to you): The propblem with the transition from one to another complex unrelated state (unrelated means that they share no significant sequence homology, like all basic protein domains), then: a) the search is not local. It is a random walk that has to necessarily traverse the space b) it is perfectly possible to traverse the space, thorugh neutral mutations and other kinds of variation (some of which, like frameshift mutations, can provide immediate jumps). But the probabilities of reaching a specific unrelated state through RV are extremely low, if the search space if big. IOWs, if there are 10^150 unrelated non functional states, and only 10^10 unrelated functional states, the probability of reaching an unrelated functional state if 1:10^140. That means that, any time you reach an unrelated state through a random walk, by neutral mutations, drift, frameshift mutation, inversion, translocation, ot whatever, the probabilities that such a state is functional are 1:10^140. Not good, eh? Genetic drift, or the possibility you siggest that neutral m utation are expanded "together with" a selected mutation, do not alter this situation at all. The rate between functional and non functional unrelated states remains the same. Therefore, I don't understand for what sirt of mental hypnosis you go on stating, with admirable stubborness, that neutral mutations and drift and so on change the probabilites. It's nonsense. It's wrong. Try to motivate it, or remain silent. Anyway, I will not explain the same things for the nth time.gpuccio_{October 28, 2011
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Elizabeth (emphasis added):
But what it does mean is that the old cliche that mutations are random and natural selection isn’t, is pretty well meaningless (and I wish people, especially Dawkins, would stop saying it!) Mutations, and differential reproduction are stochastic process that are strongly biased in favour of what works. In that sense, they aren’t even “blind” or “undirected”. But I’m not going to argue about labels, because what matters is what the theory actually is, not the descriptive words we use to describe it.
I admittedly do not understand your argument here, specifically the bold part. How can natural mutations be biased in favor of what works? If you mean that they originate in a biased manner, I see how that applies to a natural modern synthesis. If you mean that they propogate in a biased manner, to me that means that natural selection behaves in a biased manner. Either way, I don't understand your point or why you feel it is important to state it. Further explanation?uoflcard_{October 28, 2011
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DrBot: "So in one case you have a thing that eternally exists, and causes the universe to exist, and in the other case you have a thing that eternally exists, and causes the universe to exist. But in one of those two cases there is an absurdity of an infinite regress of causes … Can you explain why?" Sorry for the late response. Yes. I'm going to assume that you are familiar with what is meant by an infinite regress of causes. It becomes an absurdity only if we are dealing with causes that require material existence. It is not an absurdity if the first cause of all that contingently exists is outside of material reality. Something or someone could have caused everything that began to exist. That something or someone could not itself or him/herself be a part of that which was caused, because then he/she/it would enter into the realm of the absurdity. Actual infinites in space and time are logically untenable. There's more on why this is so, but for the sake of brevity I'll leave that one alone for now.CannuckianYankee_{October 28, 2011
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The problem is, if the systen is only random, or mainly random, the probabilities are those relative to the whole dFSCI of each protein.
Evolutionary search is not the same as random search, it only searches locally. Drift is a part of that search - that's why it is called drift and not random jumping - genotypes drift along neutral parts of the landscape. From the perspective of proteins, drifting can involve ANY gene sequence, not just protein coding ones, just so long as it has a near neutral effect on the phenotype. When you look at the probabilities you have to take into account potential pathways across the whole gene space - any route that is viable can potentially be taken - and consequently intermediates between different protein domains can potentially be any type of gene that does not have a detrimental effect on the phenotype.DrBot_{October 28, 2011
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Again with neutral mutations. I have explained. If you don’t understand, what can I do?
Listen and try and understand - perhaps read some textbooks on evolutionary theory ;)
OK, it’s fine for me. You are the first darwinist I know who believes in evolution by RV alone.
Clearly you haven't been reading my posts for comprehension.
Congratulations: you have just refuted the neo darwinian model, cancelled NS form the scenario, and proposed the most blatantly absurd explanatory theory for the origin of protein domains.
Again, making up a ridiculous position, claiming that I hold that position, then knocking it down with sarcasm is not really very impressive.
My reasoning was simple: if NS helped in the formation of new domains, we should have expanded (selected) functional intermediaries. And it seems that strangely all of them have disappeared.
NS acts on the phenotype - if an organism is born with one genotypic trait that gives a reproductive advantage, and one or more traits that diverge from the parent(s) but do not influence reproductive succes then those neutral traits are, in a sense, being selected for, because they contribute to a phenotype that is sucesful.
Well, I am not saying that “intermediates have to be selected for”. I an saying that, if they are nor selected for (they are neutral or quasi neutral), they are of no special utility to the explanation of the result.
Well see my response above - your mistake seems to be in considering genes in isolation and not in the contect of the genotype and phenotype. Neutrality increases the effectiveness of search in large dimensional search spaces - there is a lot of literature out there on neutrality and fitness landscapes - if you ignore, or fail to understand the effects then your probability calculations will always be wrong.
If, instead, intermediates are functional, and are selected for and amplified, then the algorithm is surely much more powerful, and many probabilistic walls can be overcome. But we should find the intermediates, ot at least some of them.
Yes, if there is a path up a fitness landscape from A to B then it is the easiest route to find. Fitness landscapes that have lots of neutrality provide many routes from A to B, not just up hill ones. I agree that there should be some intermediates - what would they look like? Psuedogenes, non-coding regions ... ?
“how are you computing that probability?” Whow! Must I start all the discussion about dFSCI and the design inference again?
You could start by explaining why you discount from your probability calculations things that affects the probability?DrBot_{October 28, 2011
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Elizabeth, I'll reply anyway. When you say "drift," you seem to mean "current." Why does your idea of drift work like a current? Why would drift, which doesn't even pretend to act systematically, incline toward greater and greater unneeded capability? If this is what drift does, even occasionally, then where are the other examples besides human intellect? Where are the cheetahs that can run 100mpg but never do because their prey never runs that fast? Where are the birds that can ascend out of the atmosphere but never do because there's no reason to go there? How can you use drift to explain the "normal" variation and also use it to explain the bizarre anomaly? Is there anything that drift can't do?ScottAndrews2_{October 27, 2011
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No, it isn't, because of drift effects. Scott, it's been nice talking to you, but I think it's time I left you guys to yourselves :)] If you want to get in touch, I'm here: http://theskepticalzone.com/wp/ and you, and everyone else, are very welcome to drop by. The idea behind the site is that it is a place where people with very different views can debate with as little rancour as possible. At least, that's the idea :) Hope to see you around. LizzieElizabeth Liddle_{October 27, 2011
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Elizabeth: But... Have you followed the discussion between me and DrBot? It's DrBot, not me, that refuses NS in the reasoning. My reasoning was simple: if NS helped in the formation of new domains, we should have expanded (selected) functional intermediaries. And it seems that strangely all of them have disappeared. Simple, isn't it? But no, nothing is simple with darwinists. So DrBot objects: "The problem is you are assuming that intermediates have to be selected for. They don’t, they can just be near neutral. This, I would argue, is a fundamental misunderstanding you have of evolutionary processes." ???? I have never "assumed that intermediates have to be selected for". I am assuming nothing. I am saying: a) If intermediates are not functional, and are not selected, they don't help in comparison to simple random variation. In that case, the system is acting randomly, there is no selection, no amplification. Accidenmtal amplification may occur by drift, but, as already discussed, that cannot favour any functional result, and is still pure random variation. Well, I am not saying that "intermediates have to be selected for". I an saying that, if they are nor selected for (they are neutral or quasi neutral), they are of no special utility to the explanation of the result. It's not the same thing. b) If, instead, intermediates are functional, and are selected for and amplified, then the algorithm is surely much more powerful, and many probabilistic walls can be overcome. But we should find the intermediates, ot at least some of them. You ask: Is your argument that precursor sequences of new protein domains must be neutral, and there must be too many of them to be probable? No, as you can see. My argument is that according to what we observe, the best explanation is that those functional precursors did not exist. Because otherwise we would have trace of them. So, for purely empirical reasons, we should get rid of the hygpothesis that there were many functional precursors, selected and then erased. It just does not work. It is falsified by what we can observe. Obviously, it is always possible that domains evolved by neitral evolution, and in that case it is less suprising that the precursors are not found (well, if they were amplified by drift, we should find them just the same, but whatever...). The problem is, if the systen is only random, or mainly random, the probabilities are those relative to the whole dFSCI of each protein. So, just to reason according to the results of the Durston paper, mosat protein families are well beyond the threshold of "credibility" I have suggested (150 bits). Well, many of them are also beyond Dembski's UPB of 500 bits. You ask: "how are you computing that probability?" Whow! Must I start all the discussion about dFSCI and the design inference again?gpuccio_{October 27, 2011
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Elizabeth, I should have included one more word: Evolutionary theory predicts that living things should possess only features or behaviors that are necessary for their survival or reproduction, or were at some point necessary for the survival or reproduction of their ancestors. For example, if giant peacock feathers are explained as a result of reproductive selection, then for the sake of argument, fine. But you should never find a predator that can run 100mph for ten minutes if the fastest prey animal can run 20mph for 1 minute. With the addition of "only," should that not be a prediction of evolution? I assert that it must be.ScottAndrews2_{October 27, 2011
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It's scarcely a prediction, ScottAndrews - we know that they do. It's what requires explanation. Evolutionary theory is one explanation. A prediction of evolutionary theory is that we should see incremental adaptations in the direction of an optimum along each lineage.Elizabeth Liddle_{October 27, 2011
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gpuccio, I have to say that from where I'm standing it really does look as though you are misunderstanding what DrBot and I are saying. Please consider that your separation of "RV" "NS" and "neutral drift" are not very useful way of parsing evolutionary theory! Neither of us think that "RV alone" produces evolution. "RV alone" is a pretty useless concept. What do you mean by "RV alone"? Variants with no phenotypic effects at all? Or variants with completely neutral phenotypic effects under all environmental conditions? Is your argument that precursor sequences of new protein domains must be neutral, and there must be too many of them to be probable? In which case, how are you computing that probability?Elizabeth Liddle_{October 27, 2011
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