Evolution’s Search Problem

Tom English: (If Mung does not know that authors at Evolution News and Views often disagree with one another, but never point out their disagreements, then I’ve given him way too much credit. For instance, Dembski told us that “evolutionary search” really does search for targets. But Meyer and Axe have both gone out of their ways to explain that “evolutionary search” actually does not search.)

Did Tom ever reveal his sources?

New article up at Evolution News and Views:

Douglas Axe on Evolution’s Search Problem

Are they flat out lying?

299 thoughts on “Evolution’s Search Problem

  1. Allan Miller,

    I really don’t see how the extensive molecular phylogenies that support common descent can be so airily dismissed, and replaced by something that has no associated rationale for its capacity to be analysed as if it were a signal of phylogeny when it isn’t.

    UCD is an inference argument IMHO. There are mounds of data that support a connection across life. The difficult problem is how does animal DNA sequence A turn into animal DNA sequence B. There are lots of proposed mechanisms like endosymbiosis, SNPs HGT insertions deletions etc. The theory says that this occurs because of isolation of populations of the same specie. How are functional sequences created out of these mechanisms? I do not have any confidence in stochastic mechanisms forming complex sequences and I think I am far from alone with this opinion even outside creationist circles.

  2. colewd:
    Allan Miller,

    UCD is an inference argument IMHO.There are mounds of data that support a connection across life.The difficult problem is how does animal DNA sequence A turn into animal DNA sequence B.There are lots of proposed mechanisms like endosymbiosis, SNPs HGT insertions deletions etc. The theory says that this occurs because of isolation of populations of the same specie.How are functional sequences created out of these mechanisms?I do not have any confidence in stochastic mechanisms forming complex sequences and I think I am far from alone with this opinion even outside creationist circles.

    FML, not again. Do you suffer from short-term memory loss or what? Can you make no new memories?

  3. colewd: The difficult problem is how does animal DNA sequence A turn into animal DNA sequence B. There are lots of proposed mechanisms like endosymbiosis

    … wat? Endosymbiosis is not an explanation for how sequences change over time.

    colewd: SNPs HGT insertions deletions etc.

    SNPs are single nucleotide changes (A -> C, G -> T and so on), so yes that would be one of the contributing mechanisms. ¨

    HGT doesn’t explain how a sequence changes, it merely explains how it is a sequence can move from one organism into another outside of reproduction.

    Insertions and deletions is another contributing factor to how sequences change over time yes.

    Now, why is insertions, deletions, frameshifts, fusions and point mutations NOT enough to explain how sequences change over time? Why?

    colewd: The theory says that this occurs because of isolation of populations of the same specie.

    What the actual fuck are you on about?

    No, the theory doesn’t say sequences change because of reproductive isolation. Sequences change when there is an adaptive value to that change (positive selection on new adaptive mutations), or when there is an absence of purifying selection.

    colewd: How are functional sequences created out of these mechanisms?

    Usually like this:

    Step 1: Gene is duplicated.
    It can now change, while the original is kept as it was due to purifying selection.
    Step 2: Mutations accumulate in one of the two versions of the gene. It changes by a few point mutations here and there. Then a fragment of another gene gets inserted (a fusion) and so on and so forth.

    Why is this not enough?

    colewd: I do not have any confidence in stochastic mechanisms forming complex sequences

    What merits this lack of confidence? Why do you not have “any confidence” in the various types of mutations being able to change a sequence? What, other than your utterly worthless intuitions, is this based on?

    Please SHOW that the above is not enough.

    colewd: and I think I am far from alone with this opinion even outside creationist circles.

    Yeah, there’s like 3 other “non-creationist” guys out there who share that opinion. The rest are creationists and ID-proponents. Regardless, it is entirely possible you’re not the only insane person in the world. So this kind of appeal to popularity is of literally zero value or consequence.

    For every guy you can find who shares that belief and has a degree in plumming, I can one named some variation of Steve with actual degrees in biology-related fields.

    So now that the appeals to authority and popularity have been dealt with, we are back to step one: You SHOWING why the common evolutionary mechanisms are not enough rather than just throwing unsupported opinions around as if they mattered.

  4. Allan Miller:
    phoodoo,

    I’m not talking about any other posters, I am talking about you. (Though, you obviously missed WJM’s meltdown!).

    You chide me for a bit of snark, while being one of the more obnoxious of your breed.

    That’s sort of my point Allan. First you blame me for your snarky posts. Then you say you don’t care that every other poster on your side of the ledger is rude, your job is to just point out that you don’t like if I give it back.

    Kind of shows your incredibly biased blind spot now doesn’t it? When will you have the integrity to call out posters who are wrong, but have the worldview you like?

  5. phoodoo,

    I don’t blame you for anything. The subject matter is beyond you, and your religious convictions drive you.

    Besides, I love having you as an advert for ID.

  6. That’s the thing about much of Colewd’s writings. It’s nonsensical. He throws a lot of words around he just doesn’t really know what mean. Probably, his writing reflects his understanding, which implies his understanding is extremely muddled and confused. He has this vague idea idea that things like common descent, speciation and sequence evolution is all related, he just doesn’t know how and constantly missteps because he doesn’t understand the relations.

    And then there’s just the technical jargon aspect. Those words where he has almost no clue at all what they mean, they are just words he has some sort of vague idea what kind of subject they can be associated with. But they sound impressive and technical, so if he can put them in a sentence he might appear competent. It’s really sad and funny at the same time

    Like when he blathers “the fact that the genome is a sequence, it’s the largest mathematical space in the universe and any theory that says you can mutate through it is total nonsense”. I can’t facepalm enough at that sentence. What the hell does this fucknuttery even mean?

  7. Tom English: I insist that you explain to us what computer scientists mean by algorithm.

    Did I pass or fail? Do you need more? Do you agree that algorithms are designed to solve problems?

  8. Rumraket: He has this vague idea idea that things like common descent, speciation and sequence evolution is all related, he just doesn’t know how and constantly missteps because he doesn’t understand the relations.

    Why would you bother to learn and understand something you know is wrong?

  9. Mung: Did I pass or fail? Do you need more? Do you agree that algorithms are designed to solve problems?

    No, I’m afraid not. Some of the authors you quoted said outright that the explanations were rough/provisional.

    The biggest problem, in present context, is that you’re saying nothing about halting. A definition I heard often when I was in school was “a definite procedure that halts in a finite number of steps on all valid inputs.” That’s not entirely satisfactory (what’s valid?), but it gets you closer to what’s correct than what you’ve quoted.

    Does an evolutionary process halt? I think you know the answer: only on extinction. There’s nothing “evolutionary” about the halting of an evolutionary algorithm. You can actually decompose an evolutionary algorithm into an evolutionary process that continues indefinitely and another process that observes the evolutionary process, halting in finite time. The halting “observer” process corresponds to nothing in biological evolution.

    I was making good headway with an illustration that makes it obvious that an evolutionary process tuned to minimize the expected number of generations to hit the target does nothing like search for the target. But then Barry came along. Tell you what… I’m genuinely trying to reach you more than anyone else with this. And I’ve put a fucking lot of work into it. Here’s a sneak preview of an animation of two evolutionary processes — David Glass’s weasel-on-steroids (with crossover, you may recall). One has a randomly initialized population of 500 strings (sentences). The other is initialized with 500 copies of the target string. There is no other difference. The mutation rate is tuned to make the randomly initialized population hit the target as fast as possible. What you’ll see is the two processes settling into statistical equilibrium (identical for both). There is nothing pathological in what I’m showing you. It shocked even me, when I first saw it. (And don’t give me your glib “testing” bullshit. I’ve subjected the system to tests you would never consider. And I’ve replicated Glass’s results.) Click the link below to watch.
    ___________________________________________________

    Animation 1. Populations in runs of the Glass model (orange) and the modified Glass model (blue) are depicted as bar charts. The height of a bar indicates how many of the individuals in a population have the corresponding fitness. Each of the populations contains 500 strings (sequences of letters and spaces) of length 50. The fitness of a string is the number of positions in which it matches the target string. The mutation rate is tuned to make the Glass model “hit the target” fast. The first occurrence of fitness 50 in an orange population is at time 1:15 (generation 1836 among 2000).

  10. Tom English: A definition I heard often when I was in school was “a definite procedure that halts in a finite number of steps on all valid inputs.”

    Computable Function:

    According to the Church–Turing thesis, computable functions are exactly the functions that can be calculated using a mechanical calculation device given unlimited amounts of time and storage space. Equivalently, this thesis states that any function which has an algorithm is computable and vice versa. Note that an algorithm in this sense is understood to be a sequence of steps a person with unlimited time and an infinite supply of pen and paper could follow.

    So is it your point that EA’s are not EA’s unless they halt, or is it your point that evolution is not algorithmic because it does not halt?

    But species do go extinct.

    I read your post and watched the animation, but I have not grasped what it is I am supposed to take away. What view do I hold that I ought to modify in some way?

    ETA: Evolutionary algorithm is a misnomer?

  11. Mung: Note that an algorithm in this sense is understood to be a sequence of steps a person with unlimited time and an infinite supply of pen and paper could follow.

    Pretty much nothing like what is claimed of evolution then.

  12. So Tom, your point seems to be that if you do not halt the program when a maximum fitness string is identified in the population the maximum fitness string will disappear from subsequent populations and never re-appear and therefore this cannot be thought to be a search algorithm. Is that it?

  13. Richardthughes: How do you know you’ve reached the maximum?

    You look at the bar. On the right you can see it starting out at the maximum and on the left you can see it hit the maximum very quickly.

  14. phoodoo: Pretty much nothing like what is claimed of evolution then.

    Perhaps all our models of evolution are wrong. Then where would ID theory be?

  15. Tom English: I sent Mung a PM, alerting him to my last comment. He’s since commented on other threads.

    It’s not about progressing a shared understanding of reality. It’s about winning some particular point.

  16. Mung: You look at the bar. On the right you can see it starting out at the maximum and on the left you can see it hit the maximum very quickly.

    But in say a complicated Steiner tree (minimum length = maximum fitness, unknown before hand) – how do you know when you’ve hit maximum fitness vs. a local maxima?

  17. OMagain: It’s not about progressing a shared understanding of reality. It’s about winning some particular point.

    Mung’s main point has always been that TSZ cannot function according to Lizzie’s rules. Establish that, introduce a false dichotomy, and it follows that Banny the Pimp is totally justified in running his one-whore house the way he does.

  18. OMagain: It’s not about progressing a shared understanding of reality. It’s about winning some particular point.

    This is nonsense. Under a shared understanding of reality winning some particular point is progress.

    OMagain: It’s not about progressing a shared understanding of reality. It’s about winning some particular point.

    Are you an atheist? Then we have no shared understanding of reality, and your fantasy of “progressing a shared understanding” is just that, a fantasy.

  19. Tom English: Mung’s main point has always been that TSZ cannot function according to Lizzie’s rules.

    Do you know of anyone here, including Queen Lizzie herself, who parks their priors? Hell, look at the banner to the site and explain to me how Elizabeth has led the way in admitting the possibility she might be mistaken.

  20. Mung: So is it your point that EA’s are not EA’s unless they halt, or is it your point that evolution is not algorithmic because it does not halt?

    Both. Furthermore, even if we were to allow definite procedures to “run forever”, and to impose determinism on evolutionary processes, and to restrict the phase space of evolutionary processes to a finite set, there would be many more processes than procedures. (Actually, I can state that in terms of algorithms, taking an approach that is barely different from Turing’s handling of computable numbers as possibly-infinite sequences of symbols. But you’re not giving me any reason to think it’s worth the trouble.)

  21. Mung: Hell, look at the banner to the site and explain to me how Elizabeth has led the way in admitting the possibility she might be mistaken.

    IMHO, your preoccupation with the covers of books is unhealthy.

  22. Mung: Are you an atheist? Then we have no shared understanding of reality, and your fantasy of “progressing a shared understanding” is just that, a fantasy.

    I’ll chalk that up as a HUGE difference with Douglas Axe, who makes much of the fact that he and Thomas Nagel share quite a bit in their understanding of reality (e.g., objective morality, incapacity of material evolution to generate minds).

  23. So let me see if I understand.

    A Dawkins biomorph program would not be an EA if it just continuously displayed successive images on a screen, because there is nothing inherent in the algorithm itself that would cause the program to halt.

    Is the Glass program you linked to not an EA, or is there some point at which it halts which is not shown in the animation?

  24. Richardthughes: But in say a complicated Steiner tree (minimum length = maximum fitness, unknown before hand) – how do you know when you’ve hit maximum fitness vs. a local maxima?

    I’ve read hundreds of papers on real-world applications of EC, and cannot recall any in which the maximum fitness was known to the practitioner.

  25. Mung:
    So let me see if I understand.

    A Dawkins biomorph program would not be an EA if it just continuously displayed successive images on a screen, because there is nothing inherent in the algorithm itself that would cause the program to halt.

    Is the Glass program you linked to not an EA, or is there some point at which it halts which is not shown in the animation?

    Neither is algorithmic. You can, in principle, keep exploring Biomorphs Land forever. The Glass model is nonalgorithmic for the same reason that Dawkins’s monkey/Shakespeare model of cumulative selection is nonalgorithmic. For all n in {0, 1, 2, …}, the probability of hitting the target in n or fewer generations is less than 1. The process does not terminate surely in a finite number of steps.

  26. Tom English: IMHO, your preoccupation with the covers of books is unhealthy.

    Because they can’t be trusted, or because upon ingestion they produce effects counter to good health. Unhealthy to the body, or unhealthy to the mind?

    If you’re not a materialist, Tom, which immaterial entities exist?

    Still waiting for a link to where Barry called you a materialist and a reason to post at UD saying otherwise, something I am perfectly willing to do.

  27. Mung: If you’re not a materialist, Tom, which immaterial entities exist?

    I have personal knowledge of experience that is ineffable — effing stupid to attempt to convey, and effing-er stupiderer to foist onto the corporate enterprise of science.

  28. Tom English: I have personal knowledge of experience that is ineffable — effing stupid to attempt to convey, and effing-er stupiderer to foist onto the corporate enterprise of science.

    ok. How does it follow from this that you are not a materialist? Do you believe that such an experience can only issue from an immaterial source?

    Let me put this another way. Even if only God can produce in you this experience of the ineffable, how does it follow that you are not a materialist?

    I submit, respectfully, that It is not sufficient to doubt that your experience has a material explanation. You must believe that there is no hope of a material explanation, that there is “something” that transcends the material world, something that physical and psychological theory can never attain to explain, and that this “something” is by it’s nature non-material.

    That you can neither describe nor explain your experience might be reason to believe it originated from a non-material being, but do you believe it issued from a non-material source? Do you believe that at least one non-material entity, an entity which is not the product of the mind of man, but which rather is the end of the mind of man, exists?

  29. Mung: Tom, what do the Glass models tell us about biological evolution?

    IIRC, Glass went with the title “Parameter Dependence in Cumulative Selection.” He acknowledges that the prespecified target is biologically unrealistic, and says, more or less, “Well, Dawkins did it.”

    I’ve told you before that the monkey/Shakespeare model of cumulative selection eliminates just one of two errors in a classic argument from improbability. It retains the prespecified target, and replaces what Dawkins calls single-step selection with what Dawkins calls cumulative selection. The objective is to illustrate what a huge difference one of the two errors makes. Dembski (joined by Marks) has always used slick rhetoric to make it seem as though Dawkins tried to “take back” the example after he gave it. No one bothering to read The Blind Watchmaker would get that impression.

    Mung: Why did you find them shocking?

    When the processes are at statistical equilibrium, only 1 in 295 generations contains an individual of maximum fitness. I had no idea that tuning the mutation rate to make the randomly initialized process hit the target fast would make the processes hit the target so rarely.

    All I’m doing here is to look at the Glass model much as Joe Felsenstein looked at the Weasel in “Wright, Fisher, and the Weasel.” I do not have the sort of mathematical analysis that Joe provided. It would be difficult, and it would not be worth the bother. Glass’s recombination of strings (I misspoke above, when I called it crossover) is idiosyncratic. The reason I’m willing to use his model as an example is that when I replace his recombination operator with conventional uniform crossover, the impact on the behavior of the model is quantitative, not qualitative. And I’m hoping that Intelligent Dismissers will be less dismissive when the model comes not from me, but instead from a Christian apologist who is trying to show that there’s a problem with cumulative selection. I assure you that I would not exploit an idiosyncrasy in his model.

    ______________________________________

    Figure 1. Average populations for the Glass model (orange) and the modified Glass model (blue) in 998 thousand generations following those of Animation 1. The mean and standard deviation of the fitnesses are 39.5 and 2.84, respectively, for both models. The average frequencies of fitness 50 in the populations are 0.00338 (Glass) and 0.00345 (modified Glass).

  30. Mung: If you’re not a materialist, Tom, which immaterial entities exist?

    Tom English: I have personal knowledge of experience that is ineffable — effing stupid to attempt to convey, and effing-er stupiderer to foist onto the corporate enterprise of science.

    Mung June 21, 2015 at 9:02 pm:

    Materialism is the philosophy of the subject who forgets to take account of himself.

    – Arthur Schopenhauer

    Is consciousness also a dormitive principle?

    The experience I refer to is purely subjective. I am anything but a subject who has forgotten to take account of the subject (the self is perhaps illusory). You prompt me to respond in terms of the categories material and immaterial. But those categories contain objects, not the subject.

    Schopenhauer is, among Western philosophers, the one who writes what is most relevant to me. However, the inescapable fact of the matter is that I was born on the wrong side of the world. No, I did not delve into Eastern philosophy in my youth. I did my own exploration, and went my own way. I felt increasingly as though I belonged on another planet — a planet I could not name. It was several years before I learned anything about Eastern philosophy. I have never studied philosophy to acquire beliefs. I do it to straighten out my own beliefs. (Actually, what I do most often is let go of beliefs. There’s a great deal on which others pronounce, and on which I remain silent.) Unlike the trained philosophers here, I cannot give a good account of what X said about Y. The reason is that I really do not care. What matters is how I live my own life. I’ve read enough about Eastern philosophy to know that no one needs to hear my personal philosophy. There’s nothing I have to say that hasn’t been said before, and said much better. And I don’t know that there’s much value in the saying of it, anyway.

    The principal concerns in science are not ontological, in my (perhaps insufficiently considered) opinion. They are epistemological, beginning with the fact that science is a corporate, not individual, account. What I regard as consciousness is intrinsically private and empirically inaccessible. I have no sense at all of it as a cause of phenomena.

    I am not trying to deflect this comment of yours, which I recognize as remarkably thoughtful, articulate, and kind. In all honesty, I cannot respond in the terms you establish. I’m also not going to talk about this stuff anymore. You should recognize, at least, that I don’t quack at all like a materialist when addressing my self (two words).

  31. Tom English: In all honesty, I cannot respond in the terms you establish.

    My offer stands to state at UD that you are not a materialist and that you object to being called a materialist and to provide a link to this comment. Can you direct me to the thread in which you were labelled a materialist. I’m not playing games, I haven’t been keeping up with the latest threads there lately, so I really don’t know where the comment took place.

    Tom English: You should recognize, at least, that I don’t quack at all like a materialist when addressing my self (two words).

    I shall do my utmost best to keep that in mind. If I at some point falter please forgive me and offer a gentle reminder.

    Thank you

  32. Mung: My offer stands to state at UD that you are not a materialist and that you object to being called a materialist and to provide a link to this comment.

    Don’t bother. I was jousting with you rhetorically — little substance to it, I confess. I’m trying to compose a response to Barry. I can’t find anything I’ve said about the construct of intelligence that derives from materialism. What’s important is not that Barry mischaracterized me, but instead that it is too easy for ID proponents to dismiss challenges by branding them materialism.

  33. Tom English,

    And yet you brand everyone who doesn’t buy evolution nonsense as a creationist, or better still an ID’iot.

    I personally take no offense whatsoever from your pejoratives.

  34. Tom English: Don’t bother. I was jousting with you rhetorically — little substance to it, I confess.

    That’s fine. I’m sure you’ve noticed my penchant for doing the same thing.

    I always rather admired hotshoe_ for her willingness to straight up ask me where I stood on some point if I wasn’t being clear enough for her and her willingness to believe me that I was being serious when I responded to such a request.

    I’m sure you and I will be able to work something out. 🙂

  35. Just dropping in to inform you that that post I promised to post will come along soon(tm). Not that it took this long to write it, I just found better (as in more fun) stuff to do with my time. Like play world of warcraft 😛

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