Random Mutations: vjtorley

vjtorley, at UD, writes a post entitled It’s time for scientists to come clean with the public about evolution and the origin of life that includes this:

Edward Frenkel, a professor of mathematics at the University of California, Berkeley, recently reviewed a book titled, Probably Approximately Correct: Nature’s Algorithms for Learning and Prospering in a Complex World (Basic Books, 2013) by computer scientist Leslie Valiant, in a report for the New York Times (Evolution, Speeded by Computation, September 30, 2013). The following excerpt conveys the gist of Dr. Valiant’s conclusions:

The evolution of species, as Darwin taught us, relies on natural selection. But Dr. Valiant argues that if all the mutations that drive evolution were simply random and equally distributed, it would proceed at an impossibly slow and inefficient pace.

Darwin’s theory “has the gaping gap that it can make no quantitative predictions as far as the number of generations needed for the evolution of a behavior of a certain complexity,” he writes. “We need to explain how evolution is possible at all, how we got from no life, or from very simple life, to life as complex as we find it on earth today. This is the BIG question.”

Dr. Valiant proposes that natural selection is supplemented by ecorithms, which enable organisms to learn and adapt more efficiently. Not all mutations are realized with equal probability; those that are more beneficial are more likely to occur. In other words, evolution is accelerated by computation.

The criticisms being made here of the Darwinian theory of evolution are pretty devastating: not only is it far too slow to generate life in all its diversity, but it’s also utterly incapable of making quantitative predictions about the time required for a structure of known complexity to evolve, by natural selection. And there’s no reason to believe that the “nearly neutral theory of evolution” espoused by biologists such as Professor Larry Moran would fare any better, in this regard.

 

Dr Torley is a scholar and a gentleman and someone for whom I have a great deal of personal respect. In fact I owe him more than one debt of personal kindness.  But that does not mean that I think his ideas are correct, and I submit he is profoundly wrong here in an extremely useful way.  Unusually, the passage he cites is very specific about the kind of randomness that cannot be the kind of randomness that would produce Darwinian evolution: equally distributed.

Leslie Valiant is absolutely correct: equally distributed mutations (any mutation as probable as any other) could not possibly result in Darwinian evolution.  And Darwin (who to my knowledge did not even use the word “random” nevertheless “equally distributed”) proposed nothing resembling such a thing.  And nor has any neo-Darwinian either.

In other words, “random equally distributed mutations” is a straw man of epic build.  The unusual thing about Dr Torley’s quotation is that it is explicit.  The “equally distributed” part is more usually taken as read into the meaning of “random” when “random” is held up for ridicule as an important factor in the evolution of complex life, as we can tell from the persistent avoidance of tackling the eleP(T|H)ant in the room.  Even though Dembski tells IDists to use “the relevant chance hypothesis” all calculations for the alphabet soup of FIASCOs that I have seen, including Durston et al, assume blind draw from a distribution that may or may not consist of an equiprobable distribution of bases, but does consist of an draw from an unordered bag of the things, a process that will make any drawn sequence of given length as likely as any other.

And of course, the way that mutations occur is nothing like that. A mutation is most likely to be extremely similar to the sequence from which it mutated, slightly less likely to be a little more different, and extremely unlikely to be very different.  Moreoever, as, by definition, the parent sequence belongs to a cell or organism capable of reproducing, i.e. is part of a viable genome, any mutation is far more likely to be viable than not. In other words, mutations, far from being “random, equally distributed” variants, are colossally biased in favour of viability.  Which means (and it is what we observe) that the vast majority will be neutral or near-neutral with respect to reproductive success, with some being slightly better, and, at least in a well-adapted population with a genomes that are already near-optimal, probably slightly more being slightly worse.

Even more importantly, the fact that the vast majority of mutations will be near neutral with respect to reproductive success means that most populations will be extremely rich in variants with more or less equal, and near optimal, viability in the current environment.  This in turn means that the population is extremely well-equipped to face any change in that environment – which has a rich pool of variance to sample from in order to move the population to a new optimum.

And this is why both drift (the generation of a rich pool of near-neutral variants) and Darwin’s process (heritable variation in reproductive success aka natural selection) are such a powerful pair of factors (not that they are really separate factors; we can regard biased sampling, i.e, as special case of random sampling, just as the distribution of throws of an eccentrically weighted die is a variant on the distribution of throws from a centrally weighted die, but still “random”) in accounting for adaptive evolution, and why, contrary even to Darwin’s prognosis, adaptive evolution is so rapid, as the Grants discovered with Darwin’s own finches in the Galapagos.

Valiant is correct – if mutations were “random, equally distributed”, Darwinian evolution would be impossibly slow.  But they aren’t, and so Darwinian evolution is impressively rapid.  The limitation on its net movement (as opposed to its ability to keep finch populations optimised under changing environmental conditions) is not due to the mutations being “equally distributed”, but, ironically, because they are not – because of the strong bias in favour of what works in the current environment, the distribution of variants is necessarily limited, and too rapid an environmental change will tend to deplete the pool of the very range of variation that will confer robustness in the face of further change.  Which is why, of course, that rapid habitat loss causes extinctions, rather than successful adaptation.  But as long as environmental change is slow enough that the pool of neutral variants can continue to be enriched, and there is a reasonable spread of viable variation round the optimum, adaptive evolution can and must occur, and, indeed, can be observed doing so in real time.

60 thoughts on “Random Mutations: vjtorley

  1. Dr Torley is a scholar and a gentleman …

    I’m not so sure about that. Torley’s title is “It’s time for scientists to come clean with the public about evolution and the origin of life.” There’s a clear insinuation in that choice of “come clean”, that evolution is a massive conspiracy and that scientists have been deliberately telling lies.

    Nobody who is a scholar and a gentleman would make such an insinuation.

    And what does Torley argue? In effect, he is saying that a computer scientist (Leslie Valiant) understands biology better than the biologists. A real scholar would at least be suspicious that the computer scientist might have misunderstood the theory that he was criticizing. And, of course, that is what has happened. The mistake is glaringly obvious — that part about “equally distributed” is clearly wrong. I am not aware of any biologist who claims that.

  2. Oh, I think he really thinks that scientists are being either inadvertently or deliberately dishonest, and given that, I think it is a perfectly fair challenge.

    And I’m not sure that Valiant is even making the point that Dr Torley thinks he is – I’d like to read the book to check. There are lots of ways of construing reality, and not all of them are incompatible. But on the surface, Valiant does seem to have started with one heck of a straw man. His alternative may well boil down to what evolutionary theory effectively says anyway, and I’d like to see how a computer scientist expresses it.

  3. Torley spends another 2000 words arguing that design gives recognizably different patterns than a fair coin. Design recognition is possible in part because of finite human memory and limited human information.

    Why is it that humans can recognize the designs of other humans even for token objects like a system of 500 fair coins? Why does life resemble designs? Answer: designs frequently conform to simple organizing principles rather than explicit patterns.

    He mentions “simple organizing principles” but does not lay them out explicitly. This ought to give you some pause: Designers are finicky. What is simple to one designer is not necessarily simple to another. Torley’s post contains one great example of that.

    As another example, if I knew another human had memorized a 500-bit pattern like this:

    [a random-looking sequence of 500 bits follows].

    I could put out that pattern on a table using uniquely numbered fair coins (where Heads =1, Tails =0), and he ought to recognize it as designed. As pointed out in the essay To recognize design is to recognize products of a like-minded process, Part I, the real probability in the question of design recognition isn’t the probability of a given sequence, but the probability that a sequence conforms to recognizable patterns special to the observers.

    Great. This is an example of a pattern that was most likely generated by an RNG but the touch of a human magically made it designed! We can take any sequence and declare it special. This is literally drawing a bullseye after shooting an arrow.

    Great scholarship, that.

  4. Lizzie:
    And I’m not sure that Valiant is even making the point that Dr Torley thinks he is – I’d like to read the book to check.

    I have read the book and Dr. Torley misrepresents it, possibly due to an imprecise characterization of what Valiant is trying to do in Frankel’s review.

    Very roughly: Valiant is not saying evolutionary theory is wrong, but rather than it could be improved by a quantification of evolutionary speed. He suggests this be done by considering evolution as a learning process which is exploring the fitness landscape and trying to learn which genotypes best match some ideal for that fitness landscape. A common idea which Valliant tries to make more specific by applying machine learning algorithms and an idealization of the way the genotype is matched to an optimum in the fitness landscape.

    The quote from Frankel’s review regarding equally probable is Frankel, not Valiant. I have access to an electronic copy of the book, and I could not find anything similar in it in some quick searches. Instead, what Frankel may be referring to is this passage:

    A simple hypothesis, at least for asexual species, would be that each based pair in the DNA sequence will randomly flip to one of the other three possibilities, with the same small probability. There is no evidence, however, that this simple derivation mechanism is what occurs. Equally importantly, there is no evidence this this simple mechanism can lead to evolution at the pace at which is has occurred in biology. Treating Darwinian evolution as a learning mechanism provides a way forward. This approach enables use to consider not just one possible variation mechanism, such as this one, but many, and to explore the ultimate limitations on all such mechanisms.

    As I read it, Valiant is proposing simplifying assumptions as a way of testing the model he is proposing.

  5. The following excerpt conveys the gist of Dr. Valiant’s conclusions:

    Misspelled Gish.

  6. I’m all for regarding evolutionary processes as learning processes – I’ve been saying this for years! In fact, it’s what DaveScot gave me my first UD banning for!

    In fact, it is that similarity – beyond similarity, I’d say – that makes the product of evolution look so much like the product of human designers . Both are the result of learning by experiment.

    The main difference between human designers and evolution is that human designers are much faster – they can take shortcuts, because they can mentally simulate the effects of various options before executing one, whereas evolutionary processes can’t – they have to “try” every “idea” that “pops into” their virtual head, no matter how doomed, although, and this is the point I’m trying to make in my OP, they preferentially “try” ideas similar to those that have previously worked, and actually take fewer leaps, as a result, than human designers.

    The payoff, however, is that they sample possibility space a great deal more thoroughly than we do, pursuing what would seem to us fruitless paths that ultimately lead to spectacular successes, and which humans wouldn’t bother to try.

    Which, of course, is why human designers increasingly use evolutionary methods to solve intractable problems! Their very blindness is an asset – they don’t look beyond the next step, and thus are not deterred by an apparently unpromising path.

    And that, of course, is why life looks like the product of evolution, not human design – it has all the thoroughness we need to look to evolutionary algorithms for, but also the stupidity that goes along with that thoroughness – it cannot apply a solution in one lineage to another, and it can only retrofit, it cannot go “back to basics” and start again.

  7. So will the regulars at UD pounce on VJ for relying on a review rather than buying and reading the book?

  8. Dr. Torley is a scholar and a gentleman…

    I also disagree, unless you are only comparing him to the other regulars at UD.

    Back in my Mathgrrl days, Torley (to his credit) was the only intelligent design creationist to even attempt to calculate CSI by Dembski’s definition. He came to the conclusion that:

    I note that for the duplicated genome, the specified complexity Chi is much greater than 1, so Dembski’s logic seems to imply that any instance of gene duplication is the result of intelligent agency and not chance.

    Rather than admit that Dembski’s CSI does not, in fact, work as claimed, he immediately began squirming:

    I therefore conclude that CSI is not a useful way to compare the complexity of a genome containing a duplicated gene to the original genome, because the extra bases are added in a single copying event, which is governed by a process (duplication) which takes place in an orderly fashion, when it occurs.

    He followed this up with Why there’s no such thing as a CSI scanner where he claims it is unreasonable to take Dembski at his word, as documented in Specification: The pattern that signifies intelligence.

    Finally, Torley was the one who took great pleasure in outing Mathgrrl. The failure of pseudonymity was clearly my fault, but the choice to out rather than address the points being raised shows that he values the approval of the other intelligent design creationists at UD more than searching for the truth.

  9. BruceS: Very roughly: Valiant is not saying evolutionary theory is wrong, but rather than it could be improved by a quantification of evolutionary speed. He suggests this be done by considering evolution as a learning process which is exploring the fitness landscape and trying to learn which genotypes best match some ideal for that fitness landscape. A common idea which Valliant tries to make more specific by applying machine learning algorithms and an idealization of the way the genotype is matched to an optimum in the fitness landscape.

    Thanks. That, at least, makes more sense.

    Personally, I do look at evolution as a learning system, though not in terms of “machine learning” algorithms.

  10. A key quote from Valiant’s book:

    Another way of stating the extreme possibilities is the following. One view of the variation process behind evolution is that it is simply the result of errors occurring in the basic genetic processes. Thus errors in copying the DNA during reproduction could be the main mechanism for producing the variant genomes of the next generation. An opposite viewpoint is that the process of producing the variants is highly complex and clever, as it may well be if it has undergone extensive evolution itself.

  11. Which seems entirely plausible. There is no good reason to suppose that Darwin’s principle can’t apply at the level of the population, and optimal rates and kinds of mutational processes would be highly selectable at that level.

  12. Excellent discussion, folks.

    When I saw the Frenkel / Valiant quotes at UD, I could not see what they were talking about. A mutational process in which individual mutations are random changes in one base of the sequence is what we use in models of molecular evolution. That is, changes that take a randomly chosen position in the sequence and change its base. And of course such a process gives sequences very close to the parent sequence.

    But you have clarified that this is not what Frenkel was talking about. He was describing a mutation process that comes up with a completely new, randomly chosen sequence each time. That sounds strangely familiar — people objecting to evolution have repeatedly come up with this as their model of the mutational process:

    1. It was the process imagined by the mathematicians and physicists in the infamous 1967 symposium Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution. (Sewall Wright, who was present, answered these objections at the time, but the biologists present did not press the point — they did not foresee that the volume would be kept in print for decades by creationists citing it and buying it).

    2. It is the mutational process implicit in William Dembski’s No Free Lunch argument. Dembski did not assume that mutation was to all bases in the sequence at the same time, but his use of Wolpert and McReady’s NFL Theorem implied that fitnesses were randomly assigned to sequences. So a single mutation carried the genome to a sequence that was no better than a randomly chosen new sequence.

    3. It keeps getting dredged up by creationists.

    It is a model that imagines a process that mutates every site in your genome all at once. The result is a dead organism.

    As you have all noted, it’s a silly model of mutation. I suspect that Frenkel himself is not intending to refute evolution but has just mistaken what Valiant was saying.

    I don’t have Valiant’s book but found a PDF online summarizing his argument. I have not gotten through all the math but the Discussion section certainly sounds as if Valiant does not himself think that he has refuted evolutionary theory. Here it is.

  13. ,,, and here is the published version of Valiant’s technical article on Evolvability, which apparently appeared in the Journal of the ACM in 2009.

    The difficulty with doing general mathematical models of this sort is that one doesn’t know what to assume about how smooth the fitness surfaces are. If they are infinitely jaggy then evolution will stall out quickly. To model how smooth they are is to make a great many decisions about how biological systems work.

    There was a wonderful computer simulation by the population genetic theoretician Lee Altenberg. He used Stuart Kauffman’s NK model, which is a model that has a tunable parameter (K) that controls how smooth the fitness surface is. When K=1 we are in Richard Dawkins’s Weasel situation, when K=N-1 we are in the infinitely jaggy “white noise” case. He found that, starting with modest values of K and allowing K to differ from genome to genome, K actually evolved downwards. In his simulation the biology simplified itself and made the fitness surface smoother.

  14. One additional comment. Having the mutational process evolve to be very sophisticated is harder that you might think. The problem is that a mutation that changes the mutational process is selected by the success or failure of the mutants that are created by that mutational process. And in genomes that have outcrossing and recombination (i.e. “sex”) the resulting mutants quickly get separated from the context in which they occurred. So their deaths do not have much impact on the frequency of the modifier alleles that changed the mutational process.

  15. might I add that there appears to be no way of predicting the consequences of a mutation. At least not positive consequences.

  16. petrushka:
    might I add that there appears to be no way of predicting the consequences of a mutation. At least not positive consequences.

    This is a terribly important point.

  17. Leslie Valiant is absolutely correct: equally distributed mutations (any mutation as probable as any other) could not possibly result in Darwinian evolution.

    Afraid I don’t see this. Mutations aren’t equally likely base by base, as it happens, but even if they were, I don’t see how evolution should stall if it were. As long as there is an input of better-than-neutral mutations, ‘Darwinian evolution’ (by which I presume adaptation) should tootle along at some rate, even if it would never be fast enough to satisfy the ardent IDist.

  18. Allan Miller: Afraid I don’t see this. Mutations aren’t equally likely base by base, as it happens, but even if they were, I don’t see how evolution should stall if it were. As long as there is an input of better-than-neutral mutations, ‘Darwinian evolution’ (by which I presume adaptation) should tootle along at some rate, even if it would never be fast enough to satisfy the ardent IDist.

    Ah. Well, it depends what he meant by “equally distributed”. I thought he meant: “one mutation as likely as any other”. That could mean several things, I agree, but I can’t see a sense in which it is true – small mutations are more likely than large; mutations that result in a similar phenotype are more likely than mutations that result in a very different one; mutations that result in a phenotype with a similar degree of reproductive success are more likely than mutations that result in a phenotype with a greatly different degree of reproductive success; some sequences are much more likely to be mutated than others; some kinds of mutation are more likely than others; mutations affecting the phenotype are less likely than ones that don’t.

    And if any of those things were not true, evolution would be much slower, and might not occur at all. And if any mutation were really as common any any other mutation – if novel genomes were randomly drawn from all possible genomes, “self-replication” would be a misnomer.

  19. I’m sure it’s been mentioned before but it’s worth repeating. Evolution doesn’t explore all possible search space because it doesn’t have to. In each generation evolution only explores the search space immediately around a known good configuration. It then keeps the new finds only if they’re better or neutral.

  20. Lizzie,

    if novel genomes were randomly drawn from all possible genomes, “self-replication” would be a misnomer.

    Yes indeed – the background state of a successful genome is a comfy perch from which to probe nearby space.

  21. thorton:
    I’m sure it’s been mentioned before but it’s worth repeating.Evolution doesn’t explore all possible search space because it doesn’t have to. In each generation evolution only explores the search space immediately around a known good configuration.It then keeps the new finds only if they’re better or neutral.

    Exactly. Which is why all the nonsense about FSCSI and the impossibly vast search space of theoretical proteins (Durston etc) is, well, nonsense.

  22. Joe Felsenstein: The difficulty with doing general mathematical models of this sort is that one doesn’t know what to assume about how smooth the fitness surfaces are. If they are infinitely jaggy then evolution will stall out quickly. To model how smooth they are is to make a great many decisions about how biological systems work.

    The problem comes down to physics and chemistry. The probability of a molecular configuration changing to another state – i.e., a mutation, (and ignoring for the moment energetically induced transitions by x-rays or cosmic rays) – is proportional to exp(-φ/kT), where φ is the potential energy barrier to a nearby state.

    But herein lays the big problem with any complex molecule sitting within a complex environment; what is the distribution of potential energy barriers to nearby states? This depends entirely on the current structure of the molecule and its current environment.

    What other factors contribute to a transition; bending of the molecule, temperature variations, the introduction of other chemicals from the environment?

    Under what specific circumstances can a transition take place in this particular distribution of potential energy barriers in this particular molecular environment?

    ID/creationists want us to make such calculations under the presumption that all transitions are equally probable; and they want an atom-by-atom, molecule-by-molecule account of the changes. And they want us to assume that atoms and molecules are inert things like Scrabble letters.

    Well, that’s not going to happen any time soon. We can’t account for any one transition let alone thousands going on at the same time.

    Instead, we look at the phenomenological results of all these transitions as determined by the number of offspring left by the parents and the subsequent distribution of phenotypes in the resulting populations.

  23. Joe Felsenstein: There was a wonderful computer simulation by the population genetic theoretician Lee Altenberg. He used Stuart Kauffman’s NK model, which is a model that has a tunable parameter (K) that controls how smooth the fitness surface is. When K=1 we are in Richard Dawkins’s Weasel situation, when K=N-1 we are in the infinitely jaggy “white noise” case. He found that, starting with modest values of K and allowing K to differ from genome to genome, K actually evolved downwards. In his simulation the biology simplified itself and made the fitness surface smoother.

    That’s fascinating, and is something I’ve wondered about.

    I’m wondering also whether it’s important to distinguish between the smoothness of a landscape and its degree of dimensionality.

    Both a smooth landscape and a high-dimensioned landscape will facilitate adaptive evolution, but a smooth landscape isn’t necessarily high-dimensioned, and a high-dimensioned landscape isn’t necessarily smooth.

    To what extent are these features of the landscape themselves evolvable i.e. properties of organisms or populations of organisms, and how much constrained by relative immovables, like the non-biological environment, and physics and chemistry?

    Candidates for the former would seem to me to be: degree of fidelity of self-replication; the tightness of the coupling between genotype and phenotype; the degree to which similar genotypes result in similar phenotypes. Are there some others? Are some of these wrong?

  24. Allan Miller: Afraid I don’t see this. Mutations aren’t equally likely base by base, as it happens, but even if they were, I don’t see how evolution should stall if it were. As long as there is an input of better-than-neutral mutations, ‘Darwinian evolution’ (by which I presume adaptation) should tootle along at some rate,

    Valiant is not saying Darwinian evolution is wrong, only that it is incomplete because it does not yet have a quantitative theory of the evolution rate. That claimed “gap” (so to speak) is what the quote from the book is referring to.

    Whether such a gap exists and whether Valiant’s approach is a useful way to try to fill it are questions I would leave to the experts in the group.

    I enjoyed the book itself for what it is: a short (less than 200 page) popularization of machine learning with some speculations about how it might apply to scientific theories in general, to evolution, to human learning, and to why artificial intelligence has failed in its grandest goals. The evolution chapter is about 25 pages from the whole book.

    Off topic: Frankel is a respected mathematician whose mathematical autobiography I also enjoyed, although his attempt to popularize the contents of his field of study in the same book is less successful, IMHO. I have no idea why he seems to have mis-characterized what Valiant says about mutations. A charitable reading would be that Frankel meant “realization” and “occur” to mean “persist”, but this seems to be stretching it.

  25. For all the concentration on mutation as the heart of evolutionary novelty, I always think it worth mentioning endosymbiosis and homologous recombination. Prokaryotes bimbled along for 2 billion years armed with mutation and LGT-style recombination, and very little happened.

    Then came the eukaryotes, internal mitochondria greatly increasing the surface area available for energy conversion and freeing the outer membrane to engulf food. In better-nourished luxury much larger genomes, assisted by multiple origins of replication, became possible, and new niches opened up accessible to the larger and the more complex.

    Then came sex, and the bizarre process we have of reciprocal exchange between diploid chromosomes. This introduced a massive rate change and the possibility of ‘distributed processing’, the characters of an organism capable of quasi-independent tuning. It also provided a rationale for the co-ordination of multicellular diploid somas, permitting a substantial increase in complexity.

  26. Joe Felsenstein,

    ‘Mutation control’ genes in general seem to be subject to reflexive issues. If you increase the mutation rate, you increase the likelihood that your mutation-rate-enhancing capacity will itself be damaged. If you reduce the mutation rate, there is a limit to how successful you can be, since the only available source of further enhancement is mutation, which you are busily squeezing the life out of, with the result that mutation rate reduction is ultimately self-limiting, even if the optimum is zero.

  27. Lizzie:

    that cannot be the kind of randomness that would produce Darwinian evolution: equally distributed.

    So what kind of probability distribution do evolutionists envisage?

    This in turn means that the population is extremely well-equipped to face any change in that environment – which has a rich pool of variance to sample from in order to move the population to a new optimum

    How would a organism know which of those mutation to ‘select’ in order to survive in the changed environment? Wouldn’t the organism have to try out all the combinations before it manages to ‘select’ which is better? Aren’t you advocating ID here by implying the organism ‘knows'(information) which mutation to select?

  28. coldcoffee: How would a organism know which of those mutation to ‘select’ in order to survive in the changed environment?

    The organism doesn’t select the mutations. they happen randomly, some are good, some are bad (even fatal) and most are neutral. The (Changed) environment then selects. The organism must adapt to the environment, if it can.

  29. I think the word “select” is confusing you. It doesn’t mean “make a conscious choice”, but it acts as a filter (along with luck). If you were a rodent that had a gene that made you more hairy, would you be less at risk from the cold? If the environment got colder, would your odds be better?

  30. Dr Liddle said:

    There is no good reason to suppose that Darwin’s principle can’t apply at the level of the population, and optimal rates and kinds of mutational processes would be highly selectable at that level.

    How does your idea differ from the theory of group selection?

  31. coldcoffee:

    How would a organism know which of those mutation to ‘select ’in order to survive in the changed environment? Wouldn’t the organism have to try out all the combinations before it manages to ‘select’ which is better? Aren’t you advocating ID hereby implying the organism ‘knows’(information) which mutation to select?

    Populations evolve, not individual organisms. In the entire population there are many many different mutation ‘trials’ by individuals The members of the population with the best results (on average) get to reproduce and produce the next generation population with the beneficial changes.

    CC I have to admit I had a good laugh when you quote-mined my comments about Meyer’s stupidity and *twice* posted that whiny diatribe over at UD. What were you hoping to accomplish? I challenge you to post my questions about Meyer’s idiocy here over at UD and see what the answers are. Do you have the spine to do so?

  32. Richardthughes: I think the word “select” is confusing you. It doesn’t mean “make a conscious choice”, but it acts as a filter (along with luck). If you were a rodent that had a gene that made you more hairy, would you be less at risk from the cold? If the environment got colder, would your odds be better?

    Thanks for the clarification , so now I have ‘Filter’ which means random climate change + random Natural calamities + random Predator/prey ratio ?

    Wouldn’t it mean that Evolution is a random process- even the ‘selection/Filter’- whose components are nothing but a set of random process? Since no one knows the probability distribution of these random events and Evolutionists don’t want to use uniform distribution,how would you know evolution was NOT ‘ far too slow to generate life’ (vjtorley) and that the evolution hypothesis is true?

  33. thorton: CC I have to admit I had a good laugh when you quote-mined my comments about Meyer’s stupidity and *twice* posted that whiny diatribe over at UD. What were you hoping to accomplish? I challenge you to post my questions about Meyer’s idiocy here over at UD and see what the answers are. Do you have the spine to do so?

    -and become a laughing stock of UD like Dr. Matzke?. ‘News’ confirms that insulting is Darwinist evolutionary trait:

    Coldcoffee: they win principally by frightening Johnny-goes-home-at-five and Jerry Jesusholler into avoiding any critical questions:Thomas Nagel: “The intelligentsia was so furious [at him] that it formed a lunch mob”
    http://www.uncommondescent.com/intelligent-design/thomas-nagel-the-intelligentsia-was-so-furious-at-him-that-it-formed-a-lynch-mob/

    Having said that, I have replied to your questions at the other thread. I would still insist you read ‘Darwins doubt’ and raise questions at UD or ‘Discovery’ site or ‘Evolution’ site

  34. coldcoffee: Thanks for the clarification , so now I have ‘Filter’ which means random climate change + random Natural calamities + random Predator/prey ratio ?

    No.
    We can’t help you if you don’t want to understand.

  35. timothya:
    DrLiddlesaid:

    Howdoesyourideadifferfromthetheoryofgroupselection?

    It doesn’t – it’s another way of saying the same thing.

    We know that 99% of lineages go extinct. That suggests the possibility that the 1% that don’t are lineages in which members have some property that makes their lineage more robust. This could include more optimal mutation rates (not too many; not too few), possibly because of genes that tend to repair copying errors. It could also include some aspect of reproduction in which certain kinds of genomic variants are favoured, for instance, recombination of two viable genomes, as in sexual reproduction, or some other process of gene-exchange, as between lineages in bacteria.

    Or the capacity for language in groups that have developed a language in comparison to the same capacity in groups that haven’t. That would be a kind of neo-Lamarckian group selection.

    You can probably think of other possible examples.

  36. Lizzie,

    We know that 99% of lineages go extinct. That suggests the possibility that the 1% that don’t are lineages in which members have some property that makes their lineage more robust.

    It’s possible to generate very realistic-looking patterns of extinction and lineage survival using completely .. um … ‘random’ programs. It’s not necessarily the case that the survivors had something special. The ‘null’ would be, effectively, Drift on the grand scale.

  37. coldcoffee:

    thorton: CC I have to admit I had a good laugh when you quote-mined my comments about Meyer’s stupidity and *twice* posted that whiny diatribe over at UD. What were you hoping to accomplish? I challenge you to post my questions about Meyer’s idiocy here over at UD and see what the answers are. Do you have the spine to do so?

    -and become a laughing stock of UD like Dr. Matzke?. ‘News’ confirms that insulting is Darwinist evolutionary trait:

    Coldcoffee: they win principally by frightening Johnny-goes-home-at-five and Jerry Jesusholler into avoiding any critical questions:Thomas Nagel: “The intelligentsia was so furious [at him] that it formed a lunch mob”
    http://www.uncommondescent.com/intelligent-design/thomas-nagel-the-intelligentsia-was-so-furious-at-him-that-it-formed-a-lynch-mob/

    Having said that, I have replied to your questions at the other thread. I would still insist you read ‘Darwins doubt’ and raise questions at UD or ‘Discovery’ site or ‘Evolution’ site

    coldcoffee, I have read Darwin’s Doubt. I have also read Nick Matzke’s review. Matzke is a much more informed reader than I am, and nothing in his review indicated to me that he had not read the book. It’s not a difficult read, not least because it is so glib, and so short on any kind of detail.

    And insulting is not the prerogative of “Darwinists” – here is a rather extreme example, but there are many others at UD – not least of Matzke.

    News’s report on Nagel is absurd – embarassing – hyperbole. Yes, Nagel’s book got a lot of flack,but (and again, I’ve read it) I’d say that that is due to the fact that it is an extremely flawed book. It’s an interesting book but based on a ludicrously flawed premise, and it is a pretty damning indictment of Nagel that he made so little effort to investigate whether his premise was well-founded before writing an entire book based upon it.

    That said, it remains an interesting and thoughtful book, as many reviewers, including those who, like me, thought it fatally flawed, said.

    So not only is news’ “lynch mob” metaphor obscene (real lynch mobs were all too common, and, although it is largely irrelevant, still worth noting, consisted of at least nominal Christians – the symbols burned by the KKK weren’t crosses by coincidence), it’s not even apt metaphorically.

    When people write bad, or even controversial books, people write scathing reviews. It’s not violence, or anything like; rather it’s the process by which ideas are exchanged, evaluated, and propagated. If nobody ever disagreed, mankind would make no progress.

    That we mostly disagree these days by pen rather than sword is a tribute to our progress, and it’s as much to do with the advance of evidence-based reasoning as anything else. Certainly religion hasn’t had a particularly conspicuous role to play in replacing violence by verbal arguments. People used to be burned at the stake for writing the “wrong” thing. Wouldn’t you rather people simply wrote rebuttals?

  38. A disconcerting comment by gpuccio on the UD thread, addressed to Mark Frank:

    I was not saying that you should not come here to criticize ID. I was only reflecting on the meaning of the fact that most critics of ID here, like you, rely on philosophical arguments, rather than scientific ones, and that they criticize ID without really supporting the alternative explanations. Just a reflection.

    The reason I set up this site was because I was intrigued by the symmetry (not total, however) between the way ID proponents see “evolutionists” and the way “evolutionists” see ID proponents. This is a classic.

    From my PoV it seems blindingly apparent that most ID critics of evolution “rely on philosophical arguments, rather than scientific ones”, and that it is ID proponents who criticize evolution “without really supporting the alternative explanations”, not the other way round.

    What would a visiting Martian think?

    I can’t help thinking that, without evaluating the arguments themselves, the “evolutionists” would win on points. Which “side” provides the vast bulk of actual empirical findings? Evolutionists. Which “side” brings theology into the argument? ID proponents. Which “side” brings moral philosphy into the argument? ID. Which side’s academic output is largely theoretical modelling and review articles about general principles, with a tiny proportion of empirical studies? ID. Which side actually presents testable alternatives? Evolution. Which side actively rejects the very idea that its core putative causative agent should itself be subject to empirical investigation? ID.

    So why would an ID supporter, albeit one who, to his credit, is himself an emprical scientist, or at least a practitioner in an empirical field, think the balance so strongly tilted the other way?

    I can only conclude that it is the very wealth of empirical studies in evolution that undermines its credibility amongst those that seek a single solution – evolution must seem messy and ad hoc as compared to the simplicity of “It was intelligently designed”.

    What gpuccio misses, however, is that at the core of “it was intelligently designed” is pure metaphysics, not empirical science. It might look superficially parsimonious, but only because the additional entity it invokes is so mind-bogglingly able (omnipotent, omniscient) that far from being parsimonious, as in entia non sunt multiplicanda praeter necessitatem, it masks an infinite number of additional entities – entities capable of interfering with electomagnetic, gravitational, quantum and other forces according to rules so complex that they are literally unrecoverable (because if they were, they would become, simply “science”).

    This is why I think ID is fundamentally, to use Feynman’s phrase, “cargo cult science”. It looks superficially like science, it looks more like “hard science” such as physics, based on a fundamental principle or four, rather than messy “soft science” like biology, and it has a few of the trappings – the odd lab, math, jargon, reasoning.

    But it’s not connected to the grid. The principle isn’t “simple” at all – it’s just a portmanteau for “we can’t explain this”. The empirical science is based on an irrelevant null. The mathematical models don’t model the actual world, and aren’t tested on actual data. The reluctance to investigate the putative causal agent isn’t based on any scientific principle, but an apparent reluctance to put what must be (in Dembski’s own words) a theological concept – a deity – to the test.

  39. coldcoffee:-and become a laughing stock of UD like Dr. Matzke?.

    Having a professional evolutionary scientist be a laughing stock at UD is like having Dr. Martin Luther King be a laughing stock of the KKK, or having Neil Armstrong be a laughing stock of the Moon-Landings-Were-A-Hoax society. It doesn’t carry the gravitas you think it does.

    ‘News’ confirms that insulting is Darwinist evolutionary trait:

    LOL! Denise “News” O’Dreary says so so it must be true!

    Having said that, I have replied to your questions at the other thread. I would still insist you read ‘Darwins doubt’ and raise questions at UD or ‘Discovery’ site or ‘Evolution’ site

    I can’t. I’m one of the very many who UD has banned for posting pro-science data. Neither UD nor the DI’s sites allow open discussion. Instead it is heavy handed censorship all the time. That should tell you something but it probably won’t.

  40. I was banned several times at UD. The first time fo asking a question. The second time for suggesting KF was wrong about a spcific point regarding the history of science. The third time I was banned for refusing to recite Arrington’s catechism on quantum uncertainty.

    When a forum bans people merely for presenting their arguments, the forum is not worth paying attention to.

  41. thorton: I can’t. I’m one of the very many who UD has banned

    Personally I wouldn’t ban people from forums unless they spam, but I don’t really know UD rules – I haven’t read the rules!

  42. petrushka: I was banned several times at UD

    so you were allowed after a brief ban period every time? Personally I wouldn’t ban people from forums unless they spam, but I don’t really know UD rules – I haven’t read the rules!

  43. There are some rules at UD, I think, but they basically boil down to – don’t do anything the blog owner finds boring or objectionable. At least that was what it was in Dembski’s day. Barry seems more tolerant of “boring” but is just as “random” as far as I can see when it comes to anything else.

    Without wishing (well, OK, perhaps wishing) to blow my own blog-trumpet here, I will say that the entire point of this blog is to encourage people from both sides of the ID divide to talk as constructively as they can, and I truly appreciate that people who come over from UD do so. I do realise that they will be in the minority here, but that is not simply because I myself think that the ID arguments are fundamentally flawed, but because at UD, and most other ID sites, comments are either not allowed or heavily censored, and bannings frequent.

    I do occasionally ban people here (well, I did once) but only if they post something that members really wouldn’t want to link to or have on their computers (basically malware or porn), or something that would make me legally liable for something criminal. I do “censor” in the sense that there are rules, and if they are broken I and the other admins will, with a fairly light touch, move them to “guano”, but they are not deleted, or even edited, except for malicious links, and people can still read them, and even link to them. And of course they can repost the same thing, in rule-conforming ways. There is no (legal) opinion I would censor, no matter how I might abhor it. I am a fervent believer (hey, does that make me an ideologue?) in the idea that the best way of addressing a view you disagree with is to argue with the holder – and occasionally you might even find yourself changing your own views. Hence the title and strapline of this blog, which does NOT only refer to people with whom I (think I) disagree!

    And I think that says quite a lot about the position I and others hold – we are not frightened of debate, of questions, even of criticism. In fact, we seek it out. My only problem as blog owner is to try to keep rancour from discussion as much as possible without having to wield too big a stick. That’s why the mod team is so small.

    But that is not true at UD, or at most ID sites (Corny Hunter’s was an exception, but even he has clamped down now). “Evolutionist” sites may be rude to creationists or IDists, and that in itself can be a form of censorship to the non-rhino-skinned, which is why I have quite strict rules here.

    They are not moral principles – simply game rules that govern this particular blog. Although I do happen to think that mutual respect is a good thing, and I have personally found over my sixty plus years of life that almost everyone is worth listening to, and it’s worth listening even to the odd person who doesn’t seem to be, in case they turn out to be one of the vast majority who are 🙂

  44. Neil Rickert: To be fair to News, she (or he) got that wording from David Gelernter’s rant on “Commentary”.

    No, that’s not being “fair” to News, that’s giving them a undeserved pass for their immorality. It’s immoral for the editors at News to repeat that disgusting lie about lynch mobs and then get to claim innocence because they were copying what someone else said … “Don’t blame me, I just repeated what the other guy said. I didn’t say I agreed with him ” …

    Yeah, but they repeated it approvingly, they didn’t offer any objection, and they never take into account the damage that repeating such vicious a propaganda-phrase does to the lives of actual humans who end up reading it or hearing about it.

    That makes them immoral creeps and it’s only fair to call them on that.

    They are without excuse. As is the douchey David Gelernter to begin with. And he really should know better!

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