704 thoughts on “Holding tank for general chatter about GAs”

  1. Joe G: the rest wqas an already existing organism.

    So an” empty cell” stripped of all it’s DNA is an “existing organism” is it?

  2. OM: So an” empty cell” stripped of all it’s DNA is an “existing organism” is it?

    It was NOT an empty cell- it had all of its original contents except the DNA.

    As I said you are just ignorant

  3. Thorton: None of the examples from “Evolving Inventions” had the GAs residing INSIDE the organisms being evolved.

    You need to explain how that works in your scenario, where the internal GAs have no control over external selection pressures.

    Those GAs demonstrate that GAs find solutions to problems. And the computer would be the organism.

    And as I said the internal GA responds to the external pressures.

  4. OM: So I ask again. So what, in addition to matter and energy, was required then?

    So if this mysterious life-force is in the cell itself what happens when the cell is fully synthesised too? Your gaps are shrinking day by day.

    So, presumably, the GA is instantiated via the proteins and lipids etc in the cell. What evidence do you have for that?

    The cell was never fully synthesized.

    Your ignorance betrays you, as usual.

  5. Joe G: Those GAs demonstrate that GAs find solutions to problems. And the computer would be the organism.

    Joe, this is still not even wrong. The computer is not the organism. It plays the role of nature. Organisms live in it.

  6. olegt: Hahahaha!

    Well she seemed to think that I was saying we had to know what the mutations would be in order to have a GA to get them to happen.

    I corrected her on that. Notice how she had nothing to say to me about GAs since yesterday, after I corrected her.

  7. olegt: Joe, this is still not even wrong. The computer is not the organism. It plays the role of nature. Organisms live in it.

    TRY to focus- I am talking about “Evolving Inventions” IOW you are still clueless.

  8. I corrected her on that. Notice how she had nothing to say to me about GAs since yesterday, after I corrected her.

    You don’t suppose that might have anything to do with her actually going to Wales on vacation, do you?

  9. Joe G: Well she seemed to think that I was saying we had to know what the mutations would be in order to have a GA to get them to happen.

    This wouldn’t indicate her lack of knowledge of GAs. It would only indicate that she misunderstood what you were saying.

  10. Joe G: TRY to focus- I am talking about “Evolving Inventions” IOW you are still clueless.

    Genetic algorithms are genetic algorithms. Either you know what they are or you don’t.

  11. Joe G: Umm computers are made from information Elizabeth. Without information we wouldn’t have them. Without information computers would not run.

    I’m not saying otherwise, Joe. I’m saying that the properties of a computer are the properties of a system of material parts. But if you took away all the material parts, you wouldn’t be left with anything over!

    Because the additional “thing” is the system itself. By dismantling it you destroy the system, even though the bits remain completely intact and present.

    In other words, the system – the information – is embodied in the configuration of the material parts. Same with DNA and the rest of biochemistry. There aren’t molecules + programming: the configuration of the molecules themselves are the program. Change the configuration, by perfectly observable biochemical processes, and you change the program.

    If you want to get a GA into a cell, and the GA isn’t part of the cell, where is it? What is the physical substrate for the GA?

  12. ben h: You don’t suppose that might have anything to do with her actually going to Wales on vacation, do you?

    Still here 🙂 Off in a few hours I hope.

  13. Joe G: I read it- I undersatnd GAs and my scenario is in line with the examples from “Evolving Inventions”.

    Elizabeth doesn’t seem to have a clue either.

    I’m certainly not an expert. But I have written them, and also analysed a few in some detail. Is DrBot around? I can’t remember what his/her other names are.

    Joe, I have read that Evolving Inventions piece you linked to, and it seems to have exactly the same notion of GAs that I do – but it doesn’t seem to be closely related to yours. I am genuinely puzzled as to what you mean by a GA. You seem to mean “any problem solving algorithm”. But not all problem solving algorithms are GAs, and not all GAs are designed to solve problems. You can even (and I have done this) randomly adjust the fitness function so that you don’t even pre-decide what problem your population will solve!

    So could you perhaps flesh out what you have in mind for the problem-solver (What I have called the IMG – the Intelligent Mutation Generator) in the cell? What physical means does it use to generate new DNA sequences? How does it shift the nucleotides around? How does receive signals from the environment?

  14. Joe G: Well she seemed to think that I was saying we had to know what the mutations would be in order to have a GA to get them to happen.

    Well, can you tell me how this putative GA works, then? How does the GA get the right ones to happen?

    I corrected her on that. Notice how she had nothing to say to me about GAs since yesterday, after I corrected her.

    I may have missed the correction. Could you link? Sorry, I’ve been busy.

    And I really am off to Wales shortly.

    [Also, moved some more stuff to guano. Sheesh.]

  15. Joe,
    So if your “GA” is in the cell, not the DNA then answer me this.

    Presumably the “GA” does not know that the DNA has been replaced in Craig’s cells. So it’s now issuing instructions to the “wrong” DNA, agreed?

    You’d expect therefore that there would be some differences in behaviour between Craig’s cells and unaltered cells. Yet none, to my knowledge, has been observed.

    How do you explain that?

  16. Joe G: The cell was never fully synthesized.

    I realise that. What I’m saying is that he’s working on it. And at that point, when both are synthesised by a computer there will be nowhere left for you to claim your “more then matter and energy” compinent resides.

  17. Joe G: And as I said the internal GA responds to the external pressures.

    How are these external pressures communicated to the GA?

  18. Allan: (cough) There is no evidence for common descent. It’s all common design and/or convergence. The GAs were reprogrammed at each apparent speciation event. And ID isn’t anti-evolution.

    Joe: You have no idea what “evolution” is.

    Ya see if you have a change in allele frequency over time you have evolution. IOW Common Descent is not required to have evolution.

    Ya see … I think organisms need to have offspring in order for biological evolution to happen. If ID is not anti that, then well done. But that is common descent, among the descendants of such a DNA-copying series.

    If (as you often do) you are talking about evolution happening independently of descent, you are talking about some process of serial creation (with slight modification). Alternatively, you have Creation events more intermittently dispersed, and in between there is a process of descent that includes Directed Mutation and some means of Directed Fixation, mediated by these mysterious GAs. You can call it evolution, and not be against it, but this scenario is not evolution in any sense that makes the plaint “ID is not anti-evolution” meaningful. ID is, in fact, pure Creationism, in your version, and we end up with the oxymoronic “Creationism is not anti-evolution”.

  19. Joe G: And as I said the internal GA responds to the external pressures.

    Still waiting for you to explain what these GAs do when external selection pressure drives them AWAY from their pre-specified targets.

  20. Thorton: Still waiting for you to explain what these GAs do when external selection pressure drives them AWAY from their pre-specified targets.

    They communicate with the designer and get the environment reset!

    ID sure is easy…

  21. We can certainly choose to model the patterns of the state of the RAM chips using information theory, but the computer as a system is operating based on its configuration and well understood electronic and mechanical principles.

    So, getting back to the original question, please provide any objective, empirical evidence you have for anything other than physics and chemistry being used by living organisms (or computers, for that matter). Where, exactly, is this élan vital you seem to be asserting?

    Again computers require INFORMATION to run and to be manufatured.

    You seem to be using the word “information” as a synonym for élan vital. There are literally dozens of different definitions for “information” in a biological context, but I’m not familiar with any that align with your usage.

    Let me step back so that I can try to better understand your claims. I joined this conversation by responding to one of your posts about the source of mutations. I said:

    There is no empirical evidence that suggests that particular mutations are induced by any external entity. The rate of mutation can certainly be influenced, but not the specific changes that occur.

    If you have any objective, empirical evidence that suggests otherwise, please present it. Otherwise, your speculation is no different from the idea that tiny, undetectable gremlins are weaving DNA for their own unknowable purposes while carefully making their changes look consistent with known natural processes.

    Your response was:

    The only reason to say that all mutations are do to blind and undirected chemical processes is if living organisms are reducible to matter, energy, necessity and chance.

    Upon my request for clarification, you added:

    ID claims that living organisms are not reducible to matter, energy, necessity and chance- ie that there is more to be a living organism that physics and chemistry.

    So your argument as you’ve presented it thus far seems to be:

    Claim 1: Mutations are not (solely) the product of physics and chemistry

    Claim 2: “Information” is required, in addition to and separate from physics and chemistry, for life.

    This leads to a number of questions, but I’ll start with just three:

    1. Is my statement of your second claim, particularly the phrase “and separate from”, accurate?

    2. What objective, empirical evidence do you have for your first claim?

    3. What is your definition of “information” as you use it in this context?

  22. Joe G: Thorton, walk us through the mutations taht allowed a knuckle-walker to “evolve” into an upright biped- you know that natural GA

    Note that you’re proposing a series of mutations from some unspecified ancestor too. And while we have information about the genetic change between humans and our common ancestors with other modern apes (you were shown a paper about humans and chimps in a previous thread), and we can and do work on improving that knowledge, your hands are completely empty. And we have explicit models to explain those changes, but your “GA” is completely unknown. But somehow, you know that your “GA” works, and we all should trust you.

  23. Elizabeth: Well, can you tell me how this putative GA works, then?How does the GA get the right ones to happen?

    I may have missed the correction.Could you link?Sorry, I’ve been busy.

    And I really am off to Wales shortly.

    [Also, moved some more stuff to guano.Sheesh.]

    Liz- i told you how it works- you really need to erad my responses to your posts.

    If you are not going to read them then why even bother with this blog?

  24. Elizabeth: I’m certainly not an expert.But I have written them, and also analysed a few in some detail.Is DrBot around?I can’t remember what his/her other names are.

    Joe, I have read that Evolving Inventions piece you linked to, and it seems to have exactly the same notion of GAs that I do – but it doesn’t seem to be closely related to yours.I am genuinely puzzled as to what you mean by a GA.You seem to mean “any problem solving algorithm”. But not all problem solving algorithms are GAs, and not all GAs are designed to solve problems.You can even (and I have done this) randomly adjust the fitness function so that you don’t even pre-decide what problem your population will solve!

    So could you perhaps flesh out what you have in mind for the problem-solver (What I have called the IMG – the Intelligent Mutation Generator) in the cell?What physical means does it use to generate new DNA sequences?How does it shift the nucleotides around?How does receive signals from the environment?

    Elizabeth,

    My scenario is exactly that of “Evolving Inventions”- solving a problem- as I said i have already explained this- you need to read my responses to your posts.

  25. Elizabeth: I’m not saying otherwise, Joe.I’m saying that the properties of a computer are the properties of a system of material parts.But if you took away all the material parts, you wouldn’t be left with anything over!

    Because the additional “thing” is the system itself.By dismantling it you destroy the system, even though the bits remain completely intact and present.

    In other words, the system – the information – is embodied in the configuration of the material parts.Same with DNA and the rest of biochemistry.There aren’t molecules + programming: the configuration of the molecules themselves are the program.Change the configuration, by perfectly observable biochemical processes, and you change the program.


    If you want to get a GA into a cell, and the GA isn’t part of the cell, where is it?What is the physical substrate for the GA?

    That is your position yet you cannot support it. As I said just support your claims and my claims will be refuted.

  26. olegt: Genetic algorithms are genetic algorithms. Either you know what they are or you don’t.

    Yes I know what they are.

    OTOH you cannot make a case against me.

    Go figure…

  27. OM: I realise that. What I’m saying is that he’s working on it. And at that point, when both are synthesised by a computer there will be nowhere left for you to claim your “more then matter and energy” compinent resides.

    IF that ever happens I will address it then.

    My bet is it will never happen.

  28. Thorton: Still waiting for you to explain what these GAs do when external selection pressure drives them AWAY from their pre-specified targets.

    Keep fishing- it is entertaining.

  29. OM:
    Joe,
    So if your “GA” is in the cell, not the DNA then answer me this.

    Presumably the “GA” does not know that the DNA has been replaced in Craig’s cells. So it’s now issuing instructions to the “wrong” DNA, agreed?

    You’d expect therefore that there would be some differences in behaviour between Craig’s cells and unaltered cells. Yet none, to my knowledge, has been observed.

    How do you explain that?

    Keep fishing- it is entertaining.

  30. Joe:

    “you really need to erad my responses to your posts.”

    Read or erase? please clarify. If you could explain better, perhaps we’d understand more?

  31. Joe G: Keep fishing- it is entertaining.

    That’s not fair. He’s asking direct, relevant questions. Don’t bluff – engage.

  33. Joe G: My bet is it will never happen.

    Why? Presumable you would have said that about DNA, before he started printing it out.

    Joe, here is a list of chapter headings regarding the contents of a cell:

    10. Membrane Structure
    11. Membrane Transport of Small Molecules and the Electrical Properties of Membranes
    12. Intracellular Compartments and Protein Sorting
    13. Intracellular Vesicular Traffic
    14. Energy Conversion: Mitochondria and Chloroplasts
    15. Mechanisms of Cell Communication
    16. The Cytoskeleton
    17. The Cell Cycle
    18. Apoptosis

    From here: http://en.wikipedia.org/wiki/Molecular_Biology_of_the_Cell_(textbook)

    Which of those things contain this “GA” you claim exists? If none of the above, then what?

  34. Geoxus: Note that you’re proposing a series of mutations from some unspecified ancestor too. And while we have information about the genetic change between humans and our common ancestors with other modern apes (you were shown a paper about humans and chimps in a previous thread), and we can and do work on improving that knowledge, your hands are completely empty. And we have explicit models to explain those changes, but your “GA” is completely unknown. But somehow, you know that your “GA” works, and we all should trust you.

    You are just wrong- no one has done a complete side-by-side genome comparison between humans and chimps and no one even knows if any amount of change to the genome can account for all the morphological changes required.

  36. OM: Why? Presumable you would have said that about DNA, before he started printing it out.

    Joe, here is a list of chapter headings regarding the contents of a cell:

    10. Membrane Structure
    11. Membrane Transport of Small Molecules and the Electrical Properties of Membranes
    12. Intracellular Compartments and Protein Sorting
    13. Intracellular Vesicular Traffic
    14. Energy Conversion: Mitochondria and Chloroplasts
    15. Mechanisms of Cell Communication
    16. The Cytoskeleton
    17. The Cell Cycle
    18. Apoptosis

    From here: http://en.wikipedia.org/wiki/Molecular_Biology_of_the_Cell_(textbook)

    Which of those things contain this “GA” you claim exists? If none of the above, then what?

    Wrong again- DNA is inert and I never doubted that it could be synthesized.

    And again you are a moron for thinking that I need all the answers NOW when your position doesn’t have any answers for anything.

  37. Joe G: Keep fishing- it is entertaining.

    It’s a question that you yourself should have thought of, if you’d have spent even a minute thinking about your own claims.

    If the GA is in the cell but not the DNA why can you replace the DNA and have no ill effects?

  38. OM: It’s a question that you yourself should have thought of, if you’d have spent even a minute thinking about your own claims.

    If the GA is in the cell but not the DNA why can you replace the DNA and have no ill effects?

    Well you can’t just replace it with any ole DNA sequence.

    If you would have known that you would have known something, but you didn’t.

  39. Joe G: I don’t care what you say Rich- and all you do is bluff and falsely accuse people.IOW you are sick.

    I’m not bothered what you think of me, Joe. And here’s not the place for it – come and moan at me at AtBC if you feel the need. The fact remains that good, honest questions need answering about claims you’ve made.

  40. Joe G: Wrong again- DNA is inert and I never doubted that it could be synthesized.

    So, are you willing to bet that the cell cannot be synthesized also?

  41. Joe G: Well you can’t just replace it with any ole DNA sequence.

    So there are rules regarding what DNA your GA would be able to work with?

    What are they? How do you know about them?

  42. OM: So, are you willing to bet that the cell cannot be synthesized also?

    The cell isn’t inert.

    As I said keep fishing

  43. Joe G: DNA is inert and I never doubted that it could be synthesized.

    So only inert things can be synthesized?

    Interesting….

  47. Rich: I’m not bothered what you think of me, Joe. And here’s not the place for it – come and moan at me at AtBC if you feel the need. The fact remains that good, honest questions need answering about claims you’ve made.

    Well when you evotards start answering my questions I may take a look at yours.

    However it is obvious that evotards are intellectual cowards.

  48. Joe G: non-sequitur

    I don’t think you understand what that means Joe. My question directly follows from your specific claims. If you don’t know, you don’t know. No big deal. Just say it is all.

  49. OM: I don’t think you understand what that means Joe. My question directly follows from your specific claims. If you don’t know, you don’t know. No big deal. Just say it is all.

    Nope YOU just wrongly think they follow

  50. Joe G: Venter had a pre-specification in hand- the DNA has to be able to code for proteins…

    And? As far as your GA is concerned it’s still guiding the development of the original organism.

    It would be like dropping the engine from one car into another and reconnecting the wires randomly and expecting it to work.

    Joe, so when the DNA is changed out for other DNA how does the GA know this and adapt?

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