Genetic Algorithms: When Drift Overcomes Selection

I often encounter posters here at TSZ who claim that Genetic Algorithms (GAs) either model or simulate evolution. They are never quite clear which it is, nor do they say what it means to model or simulate evolution (what would be required) and how GAs qualify as either one or the other. My position is that GAs neither model nor simulate evolution. In addition to other reasons I’ve given in the past I’d like to present the following argument.

GAs are often used to demonstrate “the power of cumulative selection.” Given small population sizes drift ought to dominate yet in GAs drift does not dominate. Why not?

Three questions:

  1. How do we determine the effective population size for a GA?
  2. How do we calculate the value of the selection coefficient?
  3. How do we determine when genetic drift will overcome the effects of selection?

In a GA written by keiths (a version of the WEASEL program) the default population size is 200.

#define POPULATION_SIZE 200 // total population size

Effective population size is the number of individuals in a population who contribute offspring to the next generation.

Even though the population size is 200, only one is selected to contribute offspring to the next generation.

#define NUM_SURVIVORS 1 // number of survivors per generation (must be less than POP_SIZE)

Given an effective population size of one, drift ought to dominate, but it doesn’t.

Given an effective population size of one, what must the selection coefficient be for drift to not dominate selection?

I’d truly appreciate any assistance with the concepts or the math.

In any event, there is no way that this GA (the keiths WEASEL program) either models or simulates evolution.

Reference:

Neutral Theory: The Null Hypothesis of Molecular Evolution

535 thoughts on “Genetic Algorithms: When Drift Overcomes Selection

  1. Allan Miller,

    And not trying to make evolution look inadequate? I don’t see the relevance of the total permutations of a mechanism that no-one proposes to come up with a sequence no-one thinks is the sole possible functional sequence.

    My point was that when you are looking to search proteins by trial and error the task is monumental.

    And not trying to make evolution look inadequate?

    Something seems broken here.

  2. colewd: My point was that when you are looking to search proteins by trial and error the task is monumental.

    Can you describe that process a little? What is doing what to what and how many times a second?

    You say “trial and error” but what does that actually mean?

  3. Flint: I wonder if your toss missed its target. I don’t fully understand the structuralism argument, but my hazy understanding is that it claims structures are constrained by environments.

    Okay, I have asked several times for some clarification from Denton supporters, and haven’t seen an answer.

    I’ve seen a reference to archetypes, but that doesn’t really make sense. It’s just word magic.

    My understanding of structuralism is that biological forms are something like snowflakes. They grow out of some natural tendency embedded in the design of nature. Soft crystals.

    I guess the payoff for Denton can be found in his phrase, Nature’s Destiny.

    All the forms of living things were planned.

    That’s my take on Denton. I’ve read some of his stuff, but not the latest book.

  4. JoeCoder:
    Patrick,

    I’ve moderated r/creation for two years.But having never visited there yourself you somehow know much more about it than I do?

    How would I? You prevent people from viewing it.

    The majority of text I type in r/creation comments is debating our ID critics there.The next largest category is debating against ideas from other creation/ID people I disagree with.If you think it’s an echo chamber and do not trust me I would again invite you to contact our resident skeptics I linked above.

    Why don’t you change the settings to allow people to at least view the comments without registering?

    We used to be a public sub and ID critics outnumbered ID proponents about 10 to 1.We have around 1000 subscribers and reddit’s r/atheism has 2 million subscribers and our own posts would sometimes be crossposted there.It’s simply impossible to have a good discussion when so severely outnumbered–especially when the “lol skyfairy” crowd leads the parade.

    That’s one possibility. The other is that your arguments are poor and you have no evidence for your position, so you shut out the reality-based commenters.

    Besides, I do regularly debate outside r/creation (and outside reddit) and so do many of our other members.Sal regularly invites our members to discuss here, and it was through one of his posts in r/creation that I found this thread.

    I hope you invite all of /r/creation here. You might want to warn them that all creationist arguments have been refuted for years as documented on the Talk Origins Archive, so they may want to be able to address those rebuttals before joining an open forum.

  5. OMagain,

    I mean random mutation natural selection neutral mutation random drift. Trial and error is random change and selection for fitness or drift. In the product development it means making a change and measuring if you got the result you wanted.

  6. Rumraket,

    The size of the search space is very large for an average protein 4^1500. The debate is whether there is an almost equally large fitness landscape. The absence of the fitness landscape is why Hoyle’s argument falls short. There is limited data on this but I will attach an evolutionary biologists Art Hunts debate with ID proponent Doug Axe.
    http://aghunt.wordpress.com/

  7. The actual “search space” is always just one mutational step from whatever the sequence is now.

    We know from experimentation that a modest sized population can try all the possible sequence variations. Lenski’s bugs accomplished this.

    Douglas Axe could be asking whether there are any genes that cannot be varied. I suspect he doesn’t ask this obvious question because he already knows the answer.

    What Wagner’s book adds (and this is widely known, but not popularized befor Wagner) is the fact that once you have a variant or allele, different variations at different positions become possible.

    The WEASEL equivalent would be the word ladder game, in which a change to one letter makes it possible to change another letter and still have a word.

  8. colewd:
    Rumraket,

    The size of the search space is very large for an average protein 4^1500.The debate is whether there is an almost equally large fitness landscape. The absence of the fitness landscape is why Hoyle’s argument falls short. There is limited data on this but I will attach an evolutionary biologists Art Hunts debate with ID proponent Doug Axe.
    http://aghunt.wordpress.com/

    Consider that you can drive your car almost anywhere, yet nearly everyone drives exclusively on roads that comprise only a very small percentage of the “search space”. These roads are the fitness space. So are we witnessing a miracle, or a violation of enormous odds, or are we seeing the results of selection?

    To phrase it differently, you are focusing on the size of the search and fitness spaces, when you would better to focus on the search mechanism, and notice that it stays always within the fitness space. And then you might reflect that the roads will take you almost anywhere you wish to go.

    (And Doug Axe is notorious for attempting to answer silly questions no biologist would see any sense in asking.)

  9. colewd: I mean random mutation natural selection neutral mutation random drift. Trial and error is random change and selection for fitness or drift

    No, I mean what physical process is happening, specifically?

  10. colewd:
    Flint,

    The search mechanism is random change of the genome.Are you talking about natural selection as a search mechanism?

    We may have a terminology problem here. Random change, by itself, isn’t a search mechanism. You need some element of a search mechanism that’s able to recognize when it has found something of value.

    So around we go again. A drunkard’s walk isn’t likely to get you from point A to point B. But if our drunk gets put back where he was every time he takes a step moving him east, he will move west despite himself.

  11. Patrick wrote: “Why don’t you change the settings to allow people to at least view the comments without registering?”

    Because reddit doesn’t have a setting to allow doing this. As Petruska said, we already grant read access to everyone who asks politely.

    Patrick wrote: “That’s one possibility. The other is that your arguments are poor and you have no evidence for your position, so you shut out the reality-based commenters.”

    I had a chuckle at this one. In my first reply to you I already provided you ample attestation from our resident ID skeptics that this is not the case. Did you contact any of those people? And now you now make the accusation–without evidence and contrary to the evidence I provided–that I don’t deal in evidence?

    I have no interest in fending off baseless accusations so I think I’m done here. I can tell that some of the commenters here are very intelligent. Maybe if there were better moderation I’d spend more time here.

  12. colewd,

    My point was that when you are looking to search proteins by trial and error the task is monumental.

    And my point was that the figure of 20^141 is irrelevant to this ‘search’.

    Me: And not trying to make evolution look inadequate?

    colewd: Something seems broken here.

    Could you be a little less gnomic? When someone trots out something looking very similar to Hoyle’s argument, I have a knee-jerk reaction to it. I treat it as Hoyle’s argument, that Life is vastly improbable, or proteins unchangeably islanded, because of the size of the search space containing every single example of a n-bit polymer of v monomers: v^n. It’s a naive and bogus argument against evolution. Do you agree?

  13. JoeCoder: I have no interest in fending off baseless accusations

    And we presume a “baseless accusation” is that the “sky-fairy” crowd is ill equipped to handle the “lol sky fairy” crowd. We are not surprised. We see it here in nearly every thread.

    so I think I’m done here.I can tell that some of the commenters here are very intelligent.Maybe if there were better moderation I’d spend more time here.

    How marvelously creationist. I can’t answer, but I can run away in a cloud of self-serving insults. Moderation that lets everyone post is lousy moderation. Disagreement with us “sky fairy” advocates must be carefully controlled. Where do we keep seeing this?

    I might mention that to counter Patrick’s general characterization of his forum, he…yes, he quote mined his own forum to extract a few exceptions, which he then represents as typical. Which, of course, were plucked out of the forum’s context AFTER the mass banning.

  14. colewd,

    I will read the book and comment after.

    Good.

    Hopefully then I will better understand your analogy.

    And hopefully you will then understand why we roll our eyes at the ASSS (the Argument from the Size of Sequence Space).

  15. colewd: Do you mean physical changes to the genome like SNP’s?

    No.

    My point was that when you are looking to search proteins by trial and error the task is monumental.

    What I’m asking is what space is being searched. And I’m asking how it’s searched. If randomly, what does that mean? Is a random protein generated and tried out? Or is one step away from an existing one explored? The difference between the two would seem to shift the task from monumental to not-monumental, would you not agree?

    What Allan said basically…

  16. Hi JoeCoder.

    I think the argument that ID is embryonic / in need of protection is passed its sell-by date. Dover was a decade ago, there has been plenty of opportunity for scientific progress.

    This forum is open, honest, frank and direct (Hi Frank!). If your ideas are good, you’ll do fine. If you need a “safe space”, you’re probably better off at UD.

  17. JoeCoder:
    Patrick wrote:“That’s one possibility. The other is that your arguments are poor and you have no evidence for your position, so you shut out the reality-based commenters.”

    I had a chuckle at this one.In my first reply to you I already provided you ample attestation from our resident ID skeptics that this is not the case.Did you contact any of those people?And now you now make the accusation–without evidence and contrary to the evidence I provided–that I don’t deal in evidence?

    The evidence is that there are no good arguments nor any evidence to support creationist claims, including those of the intelligent design variant. If creationists had either, they’d be shouting it from the rooftops. You’ve got faith in the face of evidence and the lack of shame required to vote based on your willful ignorance.

    I have no interest in fending off baseless accusations so I think I’m done here. I can tell that some of the commenters here are very intelligent. Maybe if there were better moderation I’d spend more time here.

    The minimal moderation allows good ideas to be demonstrated and encourages those insisting on holding bad ideas to run away with their tails between their legs.

  18. It’s funny, but I never had a problem with being in the minority at UD or with fending off attacks from the “lol chance worshippers” crowd.

    I had confidence in the ideas I was defending and in my ability to defend them.

    I didn’t need the protection of the moderator. I needed protection from the moderator, who is notoriously frightened of open discussion and freely bans those who embarrass him.

  19. OMagain,

    Got it sorry. Yes, I think that the way it works is a good protein is copied then it may morf into another protein and I agree that natural selection could find another protein of similar function. For example two enzymes with like active sights. But then it gets a little foggier as you need to integrate the new function so you need transcription sights activated etc. How does the transcription timing fit? etc. I want to read the book Keith’s and Petrushka recommended and see if it makes any of these issues clearer.

  20. Colewd is using Hoyle’s tornado-in-a-junkyard argument. They may not realize they’re using it, but any “mainstream evolution is doing it wrong! wrong, I say!! wrong!!!” argument which is centered around the BIGSCARYNUMBER of the total search space is, fundamentally, a tornado-in-a-junkyard argument. This argument has an underlying presumption which colewd, in common with most (if not all) of the people who use said argument, do not acknowledge: Namely, that the particular sequences-of-interest they’re talking about are evenly distributed throughout the entirety of that BIGSCARYNUMBER total search space, with no clustering at all.

    This presumption is bullshit.

    Many amino acids are coded for by more than one codon. Therefore, as far as the notional “sequence space” is concerned, any functional nucleotide sequence is surrounded by a dense cloud of equally functional sequences which are 1 (one) point mutation away from the original sequence—and yield exactly the same sequence of amino acids as the original sequence does.

    Moving ‘up’ the scale, from nucleotides to amino acids: The functions of proteins and enzymes are, in large part, determined by the physical shape of their molecules—the particular manner in which they fold. There’s a comparatively small number of distinct “fold maneuvers” which go into the actual folding of any given molecule of biological interest, and it turns out that for any given “fold maneuver”, there are a number of alternative animo acid sequences that will yield that particular “fold maneuver”.

    Any argument which is built on the presumption that biologically-interesting nucleotide sequences are evenly distributed thruout the notional space of all possible nucleotide sequences, is bullshit. Colewd has not seen this, and if past performance is any indication, they will continue not to see this even after it’s pointed out to them. C’est la vie.

  21. cubist,

    True that.
    It still cracks me up that despite all we know about protein structure, if somebody wants to make an avid ligand, they still resort to using random-with-respect-to-function mutation and differential replication, whether using Phylos technology (hint for colewd: Lipovsek) or, more often, just raising a frigging antibody…
    Protein design is limited to making changes to make one protein more like another known protein (humanizing an antibody or doing a helix-swap a la Hollis and Valenzuela) or simple shit like “make an amphipathic helix” or make a better tryptic cleavage site.
    RM + NS still kicks ass.

  22. keiths: I didn’t need the protection of the moderator.

    So? Here at TSZ you enjoy the protection of the moderators. Don’t think it goes unnoticed.

  23. Patrick: The evidence is that there are no good arguments nor any evidence to support creationist claims, including those of the intelligent design variant.

    Intelligent design is not a variant of creationism. That’s a myth adopted and spread by people why want to be able to dismiss ID not based on science but on some out-dated court ruling.

    Scared people. People who can’t defend their ideas in public debate because they are massively outnumbered by people who disagree with them. Hypocritical people, because they are no different than the Creationists they love to hate.

    TSZ is an aberration. It’s not the norm. Get over it.

  24. Flint: We may have a terminology problem here. Random change, by itself, isn’t a search mechanism. You need some element of a search mechanism that’s able to recognize when it has found something of value.

    Do you mean a target or targets?

    Value? Which of the laws of physics and chemistry define value?

  25. Richardthughes: This forum is open, honest, frank and direct (Hi Frank!). If your ideas are good, you’ll do fine. If you need a “safe space”, you’re probably better off at UD.

    As long as you don’t question this forum. For that you get your threads censored.

    Open, honest, frank, direct, except when it isn’t. A new motto for TSZ.

  26. petrushka: My understanding of structuralism is that biological forms are something like snowflakes. They grow out of some natural tendency embedded in the design of nature.

    From whence do you obtain the idea that structuralism says that natural tendencies are embedded in nature by design?

  27. Patrick: The minimal moderation allows good ideas to be demonstrated and encourages those insisting on holding bad ideas to run away with their tails between their legs.

    What is thought to be a good idea ought not be determined by the moderators.

  28. Mung: What is thought to be a good idea ought not be determined by the moderators.

    Yes! I thought you didn’t understand. CoderJoe, as moderator, is determining what is a good idea, and whether those who don’t share it should be permitted in his forum. Here, moderation is extremely light – nobody is banned except for the worst sins (posting porn, posting viruses, posting spam). Here, good ideas get to be put out there to take on all comers.

  29. Mung: Do you mean a target or targets?

    Value? Which of the laws of physics and chemistry define value?

    Survival to replicate, in Real World biology, is the only value. If you wish to regard biological survival as a target, then of course there is a target.

  30. Mung: Intelligent design is not a variant of creationism.

    It is correctly regarded as IDC, creationism all dressed up but nowhere to go. Intelligent design is as much a variant of creationism as a beagle is a variant of a dog.

    Seriously, do you really think everyone else is an idiot?

  31. Mung,

    What is thought to be a good idea ought not be determined by the moderators.

    Exactly! That’s why you are allowed to post bogus attacks on Weasel, for example — including this very thread — despite not knowing what you are talking about.

  32. Mung: Which of the laws of physics and chemistry define value?

    Do you have a complete list? If so, provide it and I will be happy to point it out.

  33. Mung,

    The evidence is that there are no good arguments nor any evidence to support creationist claims, including those of the intelligent design variant.

    Intelligent design is not a variant of creationism. That’s a myth adopted and spread by people why want to be able to dismiss ID not based on science but on some out-dated court ruling.

    You should read that court ruling. It demonstrates the religious nature of intelligent design creationism quite clearly.

    In particular, note the testimony of Dr. Barbara Forrest. She and the NCSE reviewed thousands of pages of draft copies of the book “Of Pandas and People”. Immediately following the 1987 Supreme Court ruling in Edwards v. Aguillard where the Court found the teaching of “creation science” unconstitutional, the text of Of Pandas and People was dramatically modified.

    Without change to the rest of the book, the term “creationist” was replaced with “intelligent design proponent.” The evolution from creationism to Intelligent Design did, however, leave a fossil record. On page 3-41 of the 1987 version is the sentence “Evolutionists think the former is correct, cdesign proponentsists accept the latter view.”

    When you can replace those terms without changing the meaning of an entire book, it is clear that they are synonyms. Intelligent design is creationism.

  34. I might believe ID is non religious if I saw a month go by without seeing IDists mentioning the word atheist or the word materialist or without promoting non material minds, and so forth.

    Deism is compatible with evolution. Do we have any deistic IDists around?

  35. If one considers OoL impossible without intervention, and the Intervener some kind of deity, then one must surely be a creationist, even if not a herds-of-zebras-going-pop kind. But it is possible to be a non-creationist ID-er, I suppose. Just rare.

    Funny how we like to push each others buttons with this kind of thing, though. I recall a poster insisting only yesterday that atheism is a religion.

  36. I think there is a religious temperament, and I think it is possible for a atheist to engage in apologetics.

    The real problem with calling scientism a religion is that the methods of science get results that are independent of race, religion, politics, ann sex. Even when attempts are made to suppress findings.

    Science is like the internet. It can be blocked and damaged, but it works around blockages and heals damage.

  37. keiths: And if that’s your concern, then please read Arrival of the Fittest by Andreas Wagner. The research he presents shows that the structure of sequence space is very friendly to evolution.

    It’s bad news for ID.

    Another case of fine-tuning is not “bad news” for ID.

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