Weasel Wars – Directed Evolution

This is just an effort to help keep Joe’s thread focused and to help keep it from being derailed. People can use it or not. I hope they will.

CharlieM: Can someone explain to me, why is all of this not just a model of directed evolution? Surely it is set up to be directed towards a target?

Allan Miller: It gets towards the target by means of variation and selection of genotypes in the current population. The programmer does not direct it towards the target. Indeed, there would be no point in writing GAs for problem solution if it were simply a matter of specifying a target and directing the program to find it.

Consider a small modification – instead of distance from target, evaluate fitness by adding up the ASCII bits. Those with the greater sum are fitter than those with a lesser. There is no mention of a distant target – although it is clear that the program will converge on a string of all Zs, the program doesn’t know this. It is not drawn by, nor directed towards, that target. It is simply doing generational evaluation of fitter and less fit genotypes in the current population.

Discuss.

340 thoughts on “Weasel Wars – Directed Evolution”

  1. MungMung Post author

    keiths: The snark and lame jokes would be much more tolerable if Mung were actually contributing intelligently and interestingly to the discussions here.

    Given that I am always wrong, I think I do actually contribute intelligently and interestingly to the discussions here. Or do you think I’m always wrong just by pure accident?

  2. MungMung Post author

    Alan Fox: Assuming other commenters state of mind or motive is against the rules.

    Yea Flint. Why are you acting like a complete keiths?

  3. MungMung Post author

    Allan Miller: 1) If there were two phrases against which fitness was evaluated (2/S targets), would this be an example of directed evolution?

    Yes.

    2) If the answer to the above is yes, what ‘target’ proportion of the string space do you regard as a cutoff between directed and undirected?

    You may not realize this, but that’s a question I asked to which I received no answer. I think it was dazz who was claiming that Weasel is not a GA because it has a single target. I wanted to know how many targets there needed to be for it to qualify as a GA.

    I don’t think the number of targets is relevant. I think it’s the means used to locate the target or targets. If there are no targets then it’s difficult to argue that it’s a directed search.

    If there are no targets in evolution then evolution can’t be a directed search.

    Speaking of Tom:

    With five minutes of googling, I found a paper from 8 years ago that gives an exact analysis that allows for the target to drift due to mutation: Stefan Droste, “On the Analysis of the (1+1) EA for a Dynamically Changing ONEMAX.” Obviously a fixed target is a special case.

    here

  4. Allan Miller

    Mung,

    I think it was dazz who was claiming that Weasel is not a GA because it has a single target. I wanted to know how many targets there needed to be for it to qualify as a GA.

    I don’t think the number of targets is relevant. I think it’s the means used to locate the target or targets. If there are no targets then it’s difficult to argue that it’s a directed search.

    Well, I agree the number of targets is irrelevant – or, indeed, whether you call the subset of sequence space reached a ‘target’ at all. What qualifies an algorithm as a GA is, in my opinion, the implementation of biological concepts such as populations, inheritance, mutation, crossover and selection. Of those, all but ‘population’ and ‘inheritance’ are optional. Depends what you’re doing it for, but all GAs operate on populations of strings (I disagree with Joe F on the technicality that single Weaselly survivors mean that the ‘population’ is 1. 1 is the effective population size if measured at the moment of breeding, but not if measured immediately after).

    If there are no targets in evolution then evolution can’t be a directed search.

    One can easily write a GA with no target(s), hence my gibbering about ultilising a simple numeric operator. This is closer to evolution, which merely rewards fitter genotypes that exist in the population. Of course that’s all Weasel does too, but it does so by reference to a single, currently non-existent genome that eventually comes to exist.

  5. John HarshmanJohn Harshman

    CharlieM: I don’t notice but you obviously do. So what are the differences?

    They’re molecular differences: DNA sequences, different proteins, and metabolic pathways. Bacteria have enormous diversity.

    Why are animals categorised into separate classes? It is because they contain features in common not shared by those outside the group. Extant amphibians are recognised by the same features as extinct amphibians, that is how we determine which class a fossil belongs to.

    You are locked into a framework abandoned by biologists 50 years ago. What you think of as fossil amphibians are mostly primitive tetrapods. Modern amphibians preserve some of their characteristics and have altered others, and so have modern mammals. And the diversity within amphibians (a clade) is immense.

    Now do you agree that the line leading to birds once contained amphibians but the line leading to amphibians did not contain birds?

    No, I don’t agree. The common ancestor was not an amphibian. It had some of the characteristics of amphibians, but so do you.

  6. dazzdazz

    Mung: I think it was dazz who was claiming that Weasel is not a GA because it has a single target

    And it was probably the wrong thing to say. So what? What I meant when I said that, and I clarified this a number of times, is that GAs used to solve problems in real life don’t have explicit target solutions in it’s implementation. The fact that there’s a single solution is irrelevant to whether something is a GA or not, true, it’s just that the fitness landscape has this particular shape with a single peak.

    It’s always the same crap with you, semantics and more semantics, always playing your stupid gotcha game with all your equivocations and all.

    If you claim that GAs are directed, and they are an example of directed evolution, it’s on you to define what you mean by that. You refuse to. You also refuse to answer any questions like:

    If GAs have targets, how do you know you’ve reached one?
    If GAs have targets, why do they follow erratic paths?
    If GAs have targets, why do they “find” different solutions every time they’re run?
    If only the potential (or a local) maximum fitness “solution” is a target (as you once claimed), what about all the intermediate solutions? Are those not “solutions” at all? If you run a GA and it reaches a local maxima at f=10 and then in another run you get f=15, are 10 and 15 solutions but solutions with f=11, 12, 13 and 14 not solutions even if they’re fitter than f=10 and why?

    When you consider what that means in evolutionary terms, and with some basic understanding of it and GAs, it’s obvious that any solution is potentially a viable one but none of them are targets in pretty much any sense of the word, although I’ll leave it to you to play your useless semantic games

  7. CharlieMCharlieM

    John Harshman:

    Ah, so humans are not just the most highly evolved. We’re the reason for the whole thing, and everything else is just our support system. Do you have any evidence for this interesting hypothesis?

    Earthly life evolves to the point where consciousness appears and then consciousness develops to the stage where it is now. If you think there are organisms that have a greater awareness of reality than humans, which ones are they? If these organisms have a greater grasp of reality than that gained by human science then what is the point of that science?

    Time to quote Mark Twain again: “Man has been here 32,000 years. That it took a hundred million years to prepare the world for him is proof that that is what it was done for. I suppose it is. I dunno. If the Eiffel tower were now representing the world’s age, the skin of paint on the pinnacle-knob at its summit would represent man’s share of that age; and anybody would perceive that that skin what what the tower was built for. I reckon they would, I dunno.”

    The above quote highlights the difference between a reductionist view of reality and a holistic one. To know the human form in its complete reality it has to be considered in past, present and future and not just as a static snapshot from the present. Did Mark Twain and do you think that humans just appeared 32 000 years ago with no previous history?

    The problem with that analogy is that you haven’t shown any reason to suppose it bears a relationship to the evolution of life. The other species on this planet are not part of any mission other than their own. You are not an astronaut, and fleas and malaria are not part of your support crew.

    Its an analogy. The problem with all analogies is that they break down if they are pushed too far.

  8. Allan Miller

    CharlieM,

    The problem with all analogies is that they break down if they are pushed too far.

    The problem with analogies is identifying the point at which that happens.

  9. John HarshmanJohn Harshman

    CharlieM: Earthly life evolves to the point where consciousness appears and then consciousness develops to the stage where it is now. If you think there are organisms that have a greater awareness of reality than humans, which ones are they? If these organisms have a greater grasp of reality than that gained by human science then what is the point of that science?

    Do you have any evidence for the contention in your first sentence, that the entire history of life has been building up to pushing one species into sentience? There are clearly organisms that have a greater awareness of reality than you do; me, for instance. But I don’t understand the point you’re trying to make, unless you are once again supposing that Charlie is the measure of all things, and that “grasp of reality” is the goal of evolution. I’ll add that to the other goals you have mentioned, all of which are designed solely to put humans on top.

    The above quote [Mark Twain] highlights the difference between a reductionist view of reality and a holistic one. To know the human form in its complete reality it has to be considered in past, present and future and not just as a static snapshot from the present. Did Mark Twain and do you think that humans just appeared 32 000 years ago with no previous history?

    I have no idea what that is supposed to mean. Note that Twain’s “32,000” was a 19th Century estimate, and we would increase both his numbers by around an order of magnitude, which leaves the analogy still nicely in proportion. How does our having a history reduce the force of his quote? The paint on the Eiffel Tower has hundreds of feet of steel beneath it; does that mean the purpose of the steel is to allow us to know the paint in its complete reality?

    Its an analogy. The problem with all analogies is that they break down if they are pushed too far.

    Yes, and some analogies are pushed too far as soon as they are mentioned, like yours. Good analogies are meant to clarify, like Twain’s; yours are meant to obfuscate, or at least do have that effect.

  10. MungMung Post author

    dazz: It’s always the same crap with you, semantics and more semantics, always playing your stupid gotcha game with all your equivocations and all.

    It’s not my fault that in your haste to disagree with everything I write you say stupid stuff.

  11. dazzdazz

    Mung: It’s not my fault that in your haste to disagree with everything I write you say stupid stuff.

    And more hand-waiving. Pathetic Mung

  12. hotshoe_

    CharlieM: Earthly life evolves to the point where consciousness appears and then consciousness develops to the stage where it is now. If you think there are organisms that have a greater awareness of reality than humans, which ones are they? If these organisms have a greater grasp of reality than that gained by human science then what is the point of that science?

    Nothing except unwarranted human pride says that consciousness is acme of evolution of life. Sure, it’s interesting and important to us but peacocks’ tails are interesting and important to them, and you’re not holding them up as the desired endpoint which all of life has been reaching for. Why not?

    Why exalt humans for their fragile metabolically-expensive and ultimately destructive self-consciousness?

    Well, I figure that you have to exalt humans for something, but not for their useful wings, nor for their gliding scales, nor for their exquisitely accurate sense of smell, nor for their ability to colonize any environment without aid of artifice. Seems pretty likely that you have to exalt humans for “awareness of reality” because otherwise you couldn’t maintain your belief that you personally are something special, something above the rest, something standing on the highest step of the ladder leading from the beasts to the angels and god itself.

    Yeah, well, whatever makes you happy. As long as you don’t have to trample on any actual animals to maintain your imaginary standing as the superior creature, feel free …

  13. CharlieMCharlieM

    John Harshman: They’re molecular differences: DNA sequences, different proteins, and metabolic pathways. Bacteria have enormous diversity.

    Yes bacteria have enormous diversity but far less diversity than that shown by the individual cells of multi-cellular life.

    You are locked into a framework abandoned by biologists 50 years ago. What you think of as fossil amphibians are mostly primitive tetrapods. Modern amphibians preserve some of their characteristics and have altered others, and so have modern mammals. And the diversity within amphibians (a clade) is immense.

    Yes but the defining features of amphibia such as ectothermy, the requirement of external water bodies in which to breed, are features that human forebears also once possessed but have moved beyond. Unless of course you are going to argue that humans have descended from a line that was always endothermic and so have not moved from a state of ectothermy to one of endothermy.

    No, I don’t agree. The common ancestor was not an amphibian. It had some of the characteristics of amphibians, but so do you.

    Yes and that is my point. If you think about the common ancestor between us and amphibians, it is the latter that have retained the most similarity to the putative common ancestor. Do you disagree that the common ancestor between us and amphibians was thought to be amphibian like? Some major difference between us and the common ancestor are that we are large brained , amniotes with hair and bipedalism who educate our young. Can you list the major differences between present day amphibians and the common ancestor?

  14. CharlieMCharlieM

    John Harshman: Do you have any evidence for the contention in your first sentence, that the entire history of life has been building up to pushing one species into sentience? There are clearly organisms that have a greater awareness of reality than you do; me, for instance.

    But it isn’t just one species that has sentience. Every animal that possesses a nervous system has sentience in some degree.

    You say you have a greater awareness of reality than me, that could be true. What about other lifeforms? Do you think that you have a greater awareness of reality than a newt?

  15. CharlieMCharlieM

    John Harshman:
    The paint on the Eiffel Tower has hundreds of feet of steel beneath it; does that mean the purpose of the steel is to allow us to know the paint in its complete reality?

    Yes, and some analogies are pushed too far as soon as they are mentioned, like yours. Good analogies are meant to clarify, like Twain’s; yours are meant to obfuscate, or at least do have that effect.

    You say that Twain’s analogy is a good one. I say it is a poor one in the context of what we are discussing. The paint does not grow out of the metal below, but humanity has developed out of the past life of the planet.

    Maybe you think that humanity is a separate entity placed on the top of all other life like paint spread on top of the bare metal of the Eiffel Tower..

  16. CharlieMCharlieM

    hotshoe_: Nothing except unwarranted human pride says that consciousness is acme of evolution of life.Sure, it’s interesting and important to us but peacocks’ tails are interesting and important to them, and you’re not holding them up as the desired endpoint which all of life has been reaching for.Why not?

    You are equating the tail of a peacock with consciousness. Look around, which of the two has had the most effect on the planet? Human consciousness is not just important to us, it is having dramatic planet-wide consequences which affects all other life. On the other hand, apart from helping the peacock to get laid, what has its tail ever done for the planet?

    Why exalt humans for their fragile metabolically-expensive and ultimately destructive self-consciousness?

    I am just making observations.

    Your question leads back to Sal’s Rube Goldberg thread. Why would evolution persist with a fragile metabolically-expensive system such as consciousness? Bacteria are very successful and they have no need for it.

  17. John HarshmanJohn Harshman

    CharlieM: Yes bacteria have enormous diversity but far less diversity than that shown by the individual cells of multi-cellular life.

    That turns out not to be true. The main diversity of bacteria is metabolic. Eukaryotes do pretty much one thing: glycolysis. For their other major processes, they borrow bacteria.

    Yes but the defining features of amphibia such as ectothermy, the requirement of external water bodies in which to breed, are features that human forebears also once possessed but have moved beyond. Unless of course you are going to argue that humans have descended from a line that was always endothermic and so have not moved from a state of ectothermy to one of endothermy.

    Those aren’t defining features of Amphibia. It’s true that as far as I know all amphibians are ectotherms. But not all of them require external water bodies. The variety of reproductive strategies in frogs alone is amazing, and some of them do not lay eggs in water. Further, though it’s true that the common ancestor shared the characters you mention, again you are just choosing some characters we happen not to retain and ignoring the ones that amphibians don’t.

    If you think about the common ancestor between us and amphibians, it is the latter that have retained the most similarity to the putative common ancestor. Do you disagree that the common ancestor between us and amphibians was thought to be amphibian like? Some major difference between us and the common ancestor are that we are large brained , amniotes with hair and bipedalism who educate our young. Can you list the major differences between present day amphibians and the common ancestor?

    You are comparing incomparable groups; the proper comparison to amphibians as a whole would be to amniotes as a whole, while you’re talking about our one species. I feel free to range similarly. So: loss of a finger, fusion of the axial skeleton, direct development, gliding, etc.

    But it isn’t just one species that has sentience. Every animal that possesses a nervous system has sentience in some degree.

    You say you have a greater awareness of reality than me, that could be true. What about other lifeforms? Do you think that you have a greater awareness of reality than a newt?

    Now you’re just playing with words. You know what I meant by “sentience”; we’ve been talking about human-level intelligence. And aren’t you the one who is now claiming that there’s no general phenomenon, but one in which life pushes one species to the top? Try to keep your story straight.

    I’d say that even you have a greater awareness than a newt (though of course a newt has senses you don’t and is aware of some things you aren’t).

    You say that Twain’s analogy is a good one. I say it is a poor one in the context of what we are discussing. The paint does not grow out of the metal below, but humanity has developed out of the past life of the planet.

    Maybe you think that humanity is a separate entity placed on the top of all other life like paint spread on top of the bare metal of the Eiffel Tower.

    You have pointed out where the analogy breaks down, but I don’t think that has anything to do with the point of the analogy. Which you fail to confront at all. The evidence suggests that our species is not the point of life on earth, and you seem to be arguing the contrary.

  18. CharlieMCharlieM

    John Harshman: CharlieM: Yes bacteria have enormous diversity but far less diversity than that shown by the individual cells of multi-cellular life.

    That turns out not to be true. The main diversity of bacteria is metabolic. Eukaryotes do pretty much one thing: glycolysis. For their other major processes, they borrow bacteria.

    You see no diversity in the various neurons, liver cells, stem cells, blood cells, skin cells, photoreceptors, myocytes, etc, etc, etc?! These are all virtually the same to you?

  19. Flint

    CharlieM:You see no diversity in the various neurons, liver cells, stem cells, blood cells, skin cells, photoreceptors, myocytes, etc, etc, etc?! These are all virtually the same to you?

    You were talking about DEGREE of difference. Just because cats are less different from dogs than they are from cactus, doesn’t mean they are “virtually the same”.

  20. John HarshmanJohn Harshman

    CharlieM:
    You see no diversity in the various neurons, liver cells, stem cells, blood cells, skin cells, photoreceptors, myocytes, etc, etc, etc?! These are all virtually the same to you?

    I see plenty of diversity, though not metabolic diversity. All the cells in your body do glycolysis; almost all of them have formerly bacterial buddies that do respiration for them, and that’s about it on the metabolic front. I’m trying to get you to notice the characteristics that you, given your obsession with a single lineage and the corresponding ladder of life, are not paying attention to. In some ways the cells in your body are more diverse than bacteria; in other ways bacteria are more diverse than your cells.

  21. hotshoe_

    CharlieM: You are equating the tail of a peacock with consciousness. Look around, which of the two has had the most effect on the planet?

    Why is effect on the planet your standard for the acme of evolution?

    And when that’s your standard, why are you ignoring the oxygenating cyanobacteria which overturned the entire atmosphere of the planet? Compared to them, anything humans will do is mere noise (and that includes the human-caused Sixth Great Extinction, and global warming).

    CharlieM: On the other hand, apart from helping the peacock to get laid, what has its tail ever done for the planet?

    This is the fundamental inhumanity of your attitude: that the worth of a thing is measured by “what has [it] ever done for the planet”. Measured by your standard, every human individual would deserve to be immediately disposed of, since all of us are contributing damage to the planet by existing and consuming.

    Fortunately, most of us aren’t as inhumane in our standards as you are.

  22. hotshoe_

    John Harshman: The evidence suggests that our species is not the point of life on earth, and you seem to be arguing the contrary.

    Right. Evidentially, we are not the point of life on Earth, and logically, we could not possibly be. Logically, we aren’t an end point of anything, we’re just one momentary phase of an ongoing or diversification extinction and radiation. Who knows what will appear next, but logically, it will be something other than us.

  23. MungMung Post author

    The first few chapters of this book were confined to simple genetic algorithms – GAs guided largely by the machinations of three operators: reproduction, crossover and mutation. With this focus, we have been able to see both theoretically and empirically, the central role of unnatural selection and randomized, structured recombination in artificial genetic search.

    Goldberg, David E. Genetic Algorithms in Search, Optimization, and Machine Learning

    guided
    unnatural selection
    artificial genetic search
    wet dream

  24. dazzdazz

    Mung: Goldberg, David E. Genetic Algorithms in Search, Optimization, and Machine Learning

    guided
    unnatural selection
    artificial genetic search
    wet dream

    Ahhh, OK. Glad to know reproduction, crossover and mutation “guide” evolution.
    Can we finally agree gods are expendable then?

  25. CharlieMCharlieM

    John Harshman: I see plenty of diversity, though not metabolic diversity. All the cells in your body do glycolysis; almost all of them have formerly bacterial buddies that do respiration for them, and that’s about it on the metabolic front. I’m trying to get you to notice the characteristics that you, given your obsession with a single lineage and the corresponding ladder of life, are not paying attention to. In some ways the cells in your body are more diverse than bacteria; in other ways bacteria are more diverse than your cells.

    You believe that mitochondria have evolved from captured bacteria. Even if this is true it reinforces my position. It means that the cells of multi-cellular life have moved beyond bacterial cells simply because they are made up of these types of cell plus the nucleus, cytoplasm and all the other organelles. they are baceterial cells and more.

    I feel as though I am highjacking this thread and taking it off topic so I probably won’t continue to debate here, although I might open a new thread if I think this line is worth pursuing.

  26. John HarshmanJohn Harshman

    CharlieM: You believe that mitochondria have evolved from captured bacteria.

    On what basis do you doubt the evidence for this?

    Even if this is true it reinforces my position.

    Perhaps this would be a good moment to make a clear statement of just what your position is.

    It means that the cells of multi-cellular life have moved beyond bacterial cells simply because they are made up of these types of cell plus the nucleus, cytoplasm and all the other organelles. they are baceterial cells and more.

    Once again you state a new criterion for evolutionary advancement. Now it’s having more cellular features, specifically some of the ones that once again separate you from some other organisms. Once again Charlie is the measure of all things. I ask again that you just realize you’re doing it.

  27. keithskeiths

    Allan, to Mung:

    I’m afraid you’re going to have to spell out your point a bit more.

    And if history is any indication, Mung is afraid of having to spell it out a bit more.

  28. MungMung Post author

    dazz: Can we finally agree gods are expendable then?

    Who was claiming that gods were guiding the keiths Weasel program?

  29. dazzdazz

    Mung: Who was claiming that gods were guiding the keiths Weasel program?

    Great job with your equivocations once again. Why don’t you quote the entire post so it’s clear it was about evolution and not the weasel?

  30. OMagain

    Mung: Who was claiming that gods were guiding the keiths Weasel program?

    Well, silly, you are of course. Unless, that is, you don’t think your deity is in control of everything that happens?

  31. OMagain

    Mung: Who was claiming that gods were guiding the keiths Weasel program?

    Have you stopped beating your wife yet Mung?

  32. MungMung Post author

    dazz: Great job with your equivocations once again. Why don’t you quote the entire post so it’s clear it was about evolution and not the weasel?

    How many times do I need to say I’m not arguing about whether or not biological evolution is guided or directed? I’m talking about GAs in general and the Weasel program specifically.

  33. dazzdazz

    Mung: How many times do I need to say I’m not arguing about whether or not biological evolution is guided or directed? I’m talking about GAs in general and the Weasel program specifically.

    You’re not arguing about anything. You’re just asserting, deflecting, quote mining and word playing. You also claimed that the weasel was an example of directed evolution
    Everytime I ask you to clarify what you mean by that, what’s directing GA’s, what’s that “directed” evolution that GA’s exemplify, you just fall back to your good all hand-waiving. That’s not arguing, it’s pure, unadulterated bullshitting

  34. ZachrielZachriel

    John Harshman: Modern bacteria are as different from their ancestors as a bird, just in ways you don’t notice.

    CharlieM: I don’t notice but you obviously do.

    The every asian beetle bacterium looks alike school of biology.

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