Pharyngula

How to evolve a watch

Here’s an interesting thought and modeling experiment: how to evolve a watch, literally.

As an example, it’s nice, but there are also real biological examples of organisms evolving clocks — evolution of the period gene, for instance, which also shows evidence of being calibrated to day lengths by natural processes, or the somitic clock. Most organisms on the planet seem to have multiple clocks built right into them, and they’ve all evolved.

(via No More Mr. Nice Guy!)

Comments

  1. #1 BicycleRepairMan
    October 29, 2007

    I posted this over at the excellent site VideoSift a few months ago (VS is a “best of youtube site, I did NOT make the video)(http://www.videosift.com/video/Evolution-IS-a-Blind-Watchmaker) I had to do my best to defend evolution over there :) (even if most sifters are evolutionists), but its highly interesting what you say about organic clocks, thanks!

    By the way, this’d be my first comment on here.. is there any way to login, so I dont have to type in my email each time?

  2. #2 Paholaisen Asianajaja
    October 29, 2007

    As a watchmaker I can safely say: an excellent video. The simulation could also feature the changing shapes of gears’ teeth. That alone could alter the selection pressures for other components.

  3. #3 tiny
    October 29, 2007

    the code for this clock evolution thing requires a PROGRAMMER or a DESIGNER.
    damn you intelligent design!

  4. #4 Flaky
    October 29, 2007

    @archgoon: I took a look at the code linked by Masklinn. According to the comments in the code (clocktest.m), the clocks are ranked so that first the program looks to see if there is a functional pendulum (apparently a minimum requirement for any clock in the simulation), do the gears lock up, are there hands? If there are hands, do the hands trace specific intervals of time (hours,seconds,minutes, etc.). A score is computed from these. I didn’t get what the springs are for though.

  5. #5 David Marjanovi?, OM
    October 29, 2007

    By the way, this’d be my first comment on here.. is there any way to login, so I dont have to type in my email each time?

    Your computer remembers it anyway. Unless you jump through a few hoops to stop that.

    It took well over 3 billion years to get a single celled organism

    Erm, no. It took well over 3 Ga from the first (single-celled) organism to the diversity seen in the Cambrian.

    Speaking of clocks, don’t forget to set yours back an hour next weekend if you’re one of those living in a area with Daylight Savings Time.

    …in the USA, I suppose. In the EU it was yesterday.

  6. #6 David Marjanovi?, OM
    October 29, 2007

    By the way, this’d be my first comment on here.. is there any way to login, so I dont have to type in my email each time?

    Your computer remembers it anyway. Unless you jump through a few hoops to stop that.

    It took well over 3 billion years to get a single celled organism

    Erm, no. It took well over 3 Ga from the first (single-celled) organism to the diversity seen in the Cambrian.

    Speaking of clocks, don’t forget to set yours back an hour next weekend if you’re one of those living in a area with Daylight Savings Time.

    …in the USA, I suppose. In the EU it was yesterday.

  7. #7 Doddy
    October 29, 2007

    Aww…didn’t do abiogenesis. That’s the best bit!

  8. #8 Brendan S
    October 29, 2007

    Can someone stick the code elsewhere?

    file-upload.com is being upgraded, and I’d like to take a look at the code.

  9. #9 Julian
    October 29, 2007

    Wow; what an amazing vid. Nice music for it too.

    Doug: What really amazes me about there reliance on that specific tautology is that religionists have been making it for literally 3000 years now; Its the same exact reasoning you find in Plato’s Republic regarding reality and the Ideal. How anyone could find an argument like, “I can imagine a better chair than that, therefore all chairs, by their nature, must be descended from an ideal perfect chair,” convincing is quite the stumper.

  10. #10 T_U_T
    October 29, 2007

    a few years ago I stumbled upon an IT engineer turned creationist who posted a peculiar challenge on the web.
    He demanded to show evolution of a kind of hypercycle which switches between alternate paths on an arbitrary external signal.
    That’s easy, I thought, and spend an evening writing it. After I sent it to him he simply moved the goalposts and wanted ti to be a real chemical reaction. Oh man, i said and started searching a suitable oscillating reaction (there are a legion of them ), But he attached the goalposts to a FTL drive and demanded that the reaction should appear without any human interference, not even setting up the experiment is allowed and he wanted it to produce a viable protobiont.
    So he essentially asked to be transported to a planet where abeiogenesis is happening right now, being given a magical device that allows him to see chemical reactions with his own eyes, and a time machine alowing him to see milions of years from first chemicals to the first true cell.

  11. #11 jfatz
    October 29, 2007

    Seriously. Watch ALL of cdk007’s videos. Heck, then watch his Favorites! ‘sall good, ‘sall good.

  12. #12 cm
    October 29, 2007

    Well done, but I wish he hadn’t ended on “Because clocks are not alive”. “Alive” in this context can be interpreted by many non-scientists as suggesting a vitalist view of things, as if “aliveness” is some fundamental property, the “life force” type of thinking.

    The list he gives in the beginning of the biological features which allow evolution (molecular affinities, mutation, inheritance, selective pressure, etc.) is a much better to describe the difference between clocks and biota. Less punchy, sure, but more correct.

  13. #13 Brownian
    October 29, 2007

    Does anybody understand Dembski’s or Behe’s formulae for detecting design? I’d love to run them against the simulation’s results and see what they score.

  14. #14 MartinM
    October 29, 2007

    Does anybody understand Dembski’s or Behe’s formulae for detecting design?

    1) Pick a poorly-understood* complex system.
    2) Wow! It’s really complex!
    3) Therefore, design.

    *by you, anyway.

  15. #15 Doug
    October 29, 2007

    Does anybody understand Dembski’s or Behe’s formulae for detecting design? I’d love to run them against the simulation’s results and see what they score.

    LOL! That’s a good one. Formulae? Snicker.

    You make it sound as if they have an actual hypothesis for design.

  16. #16 woozy
    October 29, 2007

    #10

    I took a look at the code linked by Masklinn. According to the comments in the code (clocktest.m), the clocks are ranked so that first the program looks to see if there is a functional pendulum (apparently a minimum requirement for any clock in the simulation), do the gears lock up, are there hands? If there are hands, do the hands trace specific intervals of time (hours,seconds,minutes, etc.). A score is computed from these. I didn’t get what the springs are for though.

    #12

    Isn’t it obvious that these watches are evolving towards gods perfect watch?

    Brilliant as this video was, I think the process of artificial selection was its least convincing aspect. If resemblence to a preconcieved idea of a clock is the criterion for survival it’s more analogous to dog-breeding then evolution. (Although Dog-breeding is pretty cool and in some ways is even more fascinating than natural selection.)

    It *does* counter the “irreduciably complex” argument of ID nicely though.

    Maybe if the program’s criteria involved whether organisms moved at all (initially only a pendulum would move???) and to what degree the movement coincided with with periodocity of a 24 hour day? Maybe the code does that.

    So let’s see:
    i) we call the hypothesis that organisms mutate randomly are selected on the basis of survival in an environment “natural selection”
    ii) we call the hypothesis that organisms don’t mutate randomly but are jiggered with to survive an environment “Intelligent Design”
    iii) what do people call the hypothesis that organisms mutate randomly but are selected and judged on an ideal (e.g. “God’s watch”)?

  17. #17 Brendan S
    October 29, 2007

    Maybe if the program’s criteria involved whether organisms moved at all (initially only a pendulum would move???) and to what degree the movement coincided with with periodocity of a 24 hour day? Maybe the code does that.

    This is exactly what the code does. First, any clocks without a pendulum are assigned a score of ‘0’ (I think) Then movement is tested. Then once the clocks move, then the gears are matches against how well they produce seconds, minutes, hours, etc. This is a relative score. Then any clock which makes a hand turn at the appropriate rate is scored MUCH higher then the gear that turns at the correct rate.

  18. #18 grasshopper
    October 29, 2007

    PZ said

    … As an example, it’s nice, but there are also real biological examples of organisms evolving clocks — evolution of the period gene, for instance, which also shows evidence of being calibrated to day lengths by natural processes …

    Here is another sort of biological clock that relies on moonlight.
    From ‘The Science Show’ on ABC Radio (Australia)

    There are 400 species of corals and hundreds of invertebrates on the Great Barrier Reef. Many spawn in mass over a couple of nights after the full moon in October or November. So how do they all know to do it together? It seems that corals can detect moonlight. Ove Hoegh-Guldberg explains how a class of proteins has been discovered which tune circadian rhythms. They are produced by a particular gene. So despite the faintness of moonlight, organisms can detect it and time their spawning to maximise the chance of reproduction.

    Ove Hoegh-Guldberg is Professor of Marine Science at the University of Queensland.

    Transcript and podcast are here

  19. #20 Russell
    October 29, 2007

    Mooser writes:

    Yes that’s all very cute and all, but do not confuse technical progress and the process of improved products we call the “evolution” of technology. That way lies “intelligent design”!

    Economic and technological progress under capitalism has an interesting analogy to evolution, because it depends to a large degree on selection over which there is no purposeful control. Every business principle thinks they are managing their enterprise well, and expects to succeed. Most are wrong, and will seen their enterprises fail. The next generation incorporates the successful processes and hard-won lessons from the previous generation of mostly failed businesses.

    Unlike the molecular machinery of biological evolution, the actors in this are conscious. It’s interesting, though, to wonder how much such progress depends on the performance of the actors, and how much is built into the dynamics of the system. Historically, the rate of progress we see in business and technology is concurrent with the practice of capitalism, which features the merciless destruction of non-competitive businesses and technologies, and the easy reproduction of a next generation of businesses recombining qualities from the previous. The core mechanics of capitalism — market determination of product success, corporate structure, equity markets, venture capital, etc. — all focus on precisely the kinds of things that are needed to competitively evaluate, kill off, and regenerate businesses. These processes were less salient in earlier economic systems, and are muted in socialist systems. (Labor and capital must be separable for these mechanisms to work.)

    So, no, economic and technological evolution are not identical with biological evolution. But, in capitalist economies, they share some important mechanisms.

  20. #21 frog
    October 29, 2007

    Moretti: “Where it falls down, of course, is that hardline Creationist “thinking” is incredibly concrete, and they cannot appreciate the subtleties of analogy.”

    That needs to be put in bold. We’re talking about people who, when they think to themselves, assume that it must be an external voice talking to them. When they imagine a scene, they believe it really is happening in some kind of alternate reality. When they read a book, they can’t distinguish between fantasy, metaphor and literal description.

    And that’s not exactly stupidity. They are simply very bad at partitioning different aspects of their thoughts, which is very common (and unnecessary) in small scale societies. If you live in a village, you can safely assume that your ideas about the world are coterminous with the world itself: if you “hear” someone’s thoughts, it’s likely that they were actually thinking that (because they’re your first cousins raised in almost identical conditions); if you believe that gophers bring the rain, it’s likely that it actually does reflect some sort correlation recognized over the centuries (even if the causation is wrong).

    And there’s the problem: a large percentage of humans will be literal thinkers because that kind of thinking has not been selected against for most of human existence – and it may have been selected for as a conservative variety. It is unlikely to change any time soon – even if in the last few centuries or millenia conditions have changed with widespread urbanization, we’re talking about the whole scale elimination of a major neurological phenotype that may have some co-adaptations tied to it. No amount of “logic” will eliminate it in that case.

    The problems may even become worse with widespread democratization – at least under an elitist system humans with certain psychological/neurological traits gained power, some of which may have been associated with a well-structured personality. But now that everybody’s “opinions” are “equal” regardless of their objective reality, regardless of their basis in empirical evidence… What’s not to drive society to simply fulfilling the fantasies of those who are the most disturbed by complexity’s demands for highly structured and disjoint personalities?

  21. #22 Michael X
    October 30, 2007

    I don’t know about the rest of you guys, but I haven’t heard the “smash up watch and put it in a box…” creationist ploy before. Not that it diminishes the impact of the video. Though it seems to be a variation on a theme so I guess I shouldn’t be too surprised. I can’t hear all the crap arguments. Which is probably a good thing.

    Also, Coldplays song “Clocks” playing throughout was not lost on me. A fun touch.

  22. #23 zobi
    October 30, 2007

    The springs are also present:
    if ~isempty(gr)
    %This is the gear the spring connects to

  23. #24 ostap
    October 30, 2007

    Amazing. I happened to have found an article on a simular object but discribing it in much greater detail. Here’s the link if you want it http://www.quazen.com/Science/Biology/The-Genetic-Code.53412

  24. #25 tomcpp
    October 30, 2007

    I’m not arguing for creationism but to say this “proves” evolution … is a shitty argument, and a fallacy.

    It shows that this “evolutionary” algorithm can guess (literally) how your test works and match it (that’s why you get 4 handed clocks), because you test directly for clocks. It does not show the clocks are somehow “new” principles, being created here.

    This is just something rewriting your “fitness” test into something that tests “the most” positive.

    Why not use this to design a “better” clock. One that is more energy efficient. Or what is the minimum amount of gears. Or design a clock that uses pendulums, but can be rotated without distorting it. Or or or …

    Remember … how ready are you to accept evolution yourself ? You basically know that if you have children, they will either kill off the rest of humanity or get killed off at some point in the future. (distant ? good question, as can be seen on your graphs, it all happens quite sudden)

    Or how ready are you to accept more controversial observations of science ? Such that every non-dogmatic system is necessarily wrong (second incompleteness theorem). So “not thinking in dogma” will never, ever produce a correct theory. Are you ready to accept that ?

    Or how about psychology. That we (all, except for a TINY minority, certainly no more than 0.2%) are racists who will kill our best friends for the mere approval of others ? (stanford prison experiment)

    Or how about economics, the difference between nash balance and why a nash balance is not pareto efficient, and what that means. Because it predicts that a society that does not accept the “golden rule” of christianity as an imposed law will implode ?

    You profess to believe science. But the truth is simpler : you believe in nothing. If not, let’s see you confirm the above points first. Especially the last one, which could be interpreted as “perhaps Christianity is wrong, but if too many people leave the Christian faith, America will collapse”. In any case if Christianity were to disappear, something quite similar would have to take it’s place, or it will fall (to say this more exact, it would evolve into a nash equilibrium, only the law of the jungle would apply). And its true meaning is not too far from that. Islamic nations for example, that do not accept that rule, are doomed to collapse. Atheist societies … the same. It can take a while, but it cannot be avoided.

    As you people like to say so much … you cannot have it both ways. Either you follow science, and indeed the assertion that a rational society will fall, and so atheism is wrong, or at the very least will have disastrous consequences, or you don’t. If you’re wondering what it means for a society to fall, you don’t want to know. Especially not with 6 billion people on the planet.

  25. #26 Keith Douglas
    October 30, 2007

    Brownian: IMO, their equations are utter crap, so that won’t work.

  26. #27 woozy (Um, am I coherent? One never knows.....)
    October 31, 2007

    I’m not arguing for creationism but to say this “proves” evolution … is a shitty argument, and a fallacy.

    No one is claiming this proves evolution. Just that the “broken watch in a box” counter-argument to evolution is false.

    Also it shows that 1) given reproducing organisms that pass traits 2) and given random mutations and C) given forces favoring time-telling, watches will evolve. It may not prove evolution but I’ve yet to see a situation were given 1) and 2) and someother favoring force D) doesn’t result in a complex efficient system.

    It shows that this “evolutionary” algorithm can guess (literally) how your test works and match it (that’s why you get 4 handed clocks), because you test directly for clocks. It does not show the clocks are somehow “new” principles, being created here.

    This is darn near incoherant. Not sure what your point is. Mutating organisms guess how environmental stresses work and match it. That’s why you get finches with beaks suited to their diets, because the available food source is testing directly for apropriate shaped beaks. What does new principles being created have to do with anything?

    This is just something rewriting your “fitness” test into something that tests “the most” positive.

    Yeah? And…?

    Why not use this to design a “better” clock. One that is more energy efficient. Or what is the minimum amount of gears. Or design a clock that uses pendulums, but can be rotated without distorting it. Or or or …

    And…? Sure. If we “tested” for scarcity of gears, or energy efficiency, I’d be pretty sure we could “evolve” such.

    Remember … how ready are you to accept evolution yourself ? You basically know that if you have children, they will either kill off the rest of humanity or get killed off at some point in the future. (distant ? good question, as can be seen on your graphs, it all happens quite sudden)

    Now you are not darn near incoherant. You are totally incoherent. What the heck are you talking about?

    Or how ready are you to accept more controversial observations of science ? Such that every non-dogmatic system is necessarily wrong (second incompleteness theorem). So “not thinking in dogma” will never, ever produce a correct theory. Are you ready to accept that ?

    Uh, not familiar with 2nd incomplete theorem that says dogma *can* produce a correct theory… The first theorem says consistant and complete systems are impossible so *no* theorem is “correct*”, and, yes, I *do* accept that.

    (* if “correct” can only exist in a consistant and complete system…)

    Or how about psychology. That we (all, except for a TINY minority, certainly no more than 0.2%) are racists who will kill our best friends for the mere approval of others ? (stanford prison experiment)

    Uh, yeah… So what? It’s unpleasant but believable.

    Or how about economics, the difference between nash balance and why a nash balance is not pareto efficient, and what that means. Because it predicts that a society that does not accept the “golden rule” of christianity as an imposed law will implode ?

    Not familiar with that one and not sure I believe it. But I’m certainly willing to believe that without stabilizing beliefs a society will collapse. I personally like the “golden rule” altruism as a “good” stabilizing belief but I believe other beliefs (totalitarianism, slavery, etc.) could be equally stabilizing. They’ve certainly passed the tests many times.

    You profess to believe science. But the truth is simpler : you believe in nothing. If not, let’s see you confirm the above points first.

    Well, I think you need to state them better but, sure, I’ve got nothing against accepting those “points” might conceivably be true.

    Especially the last one, which could be interpreted as “perhaps Christianity is wrong, but if too many people leave the Christian faith, America will collapse”.

    Not even close! Altruism is *not* the sole provision of Christianity and never has been. Animal societies, probably as a result of your very same “points”, display altruism. I’ve yet to see a Christian Elephant. (yes, Babar went to church once or twice but that was only to humor the old woman. When he enforced a societal ethic he based it upon elephants rather than humanity and replaced the bloody primate on sticks with floating cherubic pachyderms.)

    In any case if Christianity were to disappear, something quite similar would have to take it’s place, or it will fall (to say this more exact, it would evolve into a nash equilibrium, only the law of the jungle would apply).

    Um. It’s altruism you are talking about; not Christianity. We’ve replaced it with ideals of liberty and freedom and good ol’ americanisms. In fact, despite all my critical thinking and cynacism, I find myself almost incapible of questioning my belief in free-speech and equality. The way we are going though, we could probably replace it with facism. Abject fear does pretty well keeping a society in line.

    And its true meaning is not too far from that. Islamic nations for example, that do not accept that rule, are doomed to collapse. Atheist societies … the same. It can take a while, but it cannot be avoided.

    Um, what nations *aren’t* doomed to collapse? I know of no society that hasn’t collapsed. Well, maybe the Kalahari Bushmen… It seems a bit naive to think any Christian society *won’t* collapse. I don’t think any Christian society is over 500 years old right now. Even if you wish to believe the Christian society of Roman occupied Judea is the same as our current society it’s only lasted 2000 years. Egypt and imperial China and Sumeria and oodles of others have far outlasted that.

    As you people like to say so much … you cannot have it both ways.

    Um, what are the “both ways” again? You were being incoherent when you brought them up so I never understood what you were getting at.

    Either you follow science, and indeed the assertion that a rational society will fall, and so atheism is wrong,

    Huh? How does that make atheism wrong?

    … or at the very least will have disastrous consequences,

    Oh, right. Rejecting altruism causes a society to fall and, somehow, you are assuming causing a society to fall to be the equivalent of being wrong.

    1) Altruism does not equal christianity and atheism *is* compatible with altruism. and
    2) Not liking results doesn’t make *anything* wrong. If I die, it will be disastrous and horrible. That doesn’t mean I’m not going to die. I will. And it *will* be disastrous and horrible. Unfortunately (for me) that’s not enough to make my death false. Even if by some twisted logic that atheism will kill us all, doesn’t mean it’s not true.

  27. #28 bertok86
    October 31, 2007

    Quick, everybody point and laugh at tomcpp! The funnient bit had to be the Golden Rule of “Christianity” schtick. I wonder how the Zoastrians* would have felt (do feel?) about what is arguably their rule being appropriated by those new fangled Xtian types? In any case, it’s hardly a Christian idea.

    *Google (and perhaps a library) is your friend

  28. #29 Brian Macker
    November 3, 2007

    #43 frog,
    “we’re talking about the whole scale elimination of a major neurological phenotype that may have some co-adaptations tied to it.”

    Since when did anyone discover such purported phenotypes? Sounds like you are just speculating. Why can’t these differences in belief be purely cultural in orgin? You know passed down from parent to child via a decision to enroll the kid in a particular religious school.

  29. #30 Brian Macker
    November 3, 2007

    Dave,

    Immortality due to superiority is not a “flaw”. It is not important to the point he’s making.

    Besides you are only right about their immortality if the perfect clock has evolved and his algorithm doesn’t pick at random in the case of ties. Surely the perfect clock is occasionally going to have some offspring just as fit. Does it matter which survives since no offspring could be better? What does it matter to the point of the program that this happens, nothing. His point was to show that you can evolve precise clocks and not to simulate every aspect of biological evolution.

  30. #31 truth machine
    November 6, 2007

    If resemblence to a preconcieved idea of a clock is the criterion for survival it’s more analogous to dog-breeding then evolution.

    Dog breeding is evolution — a fitness function is a fitness function. And go read Darwin on the subject of breeding. Sheesh, such ignorance and conceptual blindness. The complaint that there’s a predefined goal is incredibly stupid — it’s inherent in the claim that he’s refuting; since the creationists name something specific — a clock — that can’t evolve, they have already set the goal. The video shows that their claim is wrong, and why. But, as the video notes, there are no limitations on the design; the parts can connect up any which way, it is only the function that determines fitness — just like in the natural biological world.

  31. #32 truth machine
    November 6, 2007

    I’m not arguing for creationism but to say this “proves” evolution … is a shitty argument, and a fallacy.

    No one claimed it “proves evolution”, moron, it refutes a specific creationist claim. As for shitty arguments and fallacies, this is the carbon-encrusted kettle calling the shiny aluminum pot black.

  32. #33 truth machine
    November 6, 2007

    It shows that this “evolutionary” algorithm can guess (literally) how your test works and match it (that’s why you get 4 handed clocks), because you test directly for clocks.

    The algorithm “matches” the test by evolving collections of parts, idiot. The test is for keeping time — that’s a functional test. The algorithm “guesses” how to keep time by … evolving mechanisms that keep time; duh. Keeping time is an environmental constraint in the simulation just as, say, avoiding being consumed before reproducing is an environmental constraint for biological organisms.

    every non-dogmatic system is necessarily wrong (second incompleteness theorem)

    Gödel’s second incompleteness theorem: For any formal recursively enumerable (i.e. effectively generated) theory T including basic arithmetical truths and also certain truths about formal provability, T includes a statement of its own consistency if and only if T is inconsistent.

    If one takes “wrong” to be “inconsistent” and “dogmatic” to be insisting that one is right, that would mean that every dogmatic system is necessarily wrong.

    Does being Christian lead to being ignorant, stupid, and dishonest, or does being ignorant, stupid, and dishonest lead to being Christian? Or perhaps there’s some common underlying cause. But the correlation is unmistakable.

  33. #34 FlyinGreaseMonkey
    November 13, 2007

    This simulation is built on a faulty premise; this fellow has miss-defined intelligent design. The majority of the Christian community accepts evolution, they know things change. Intelligent design isn’t just creation, it’s steering evolution by giving it purpose. For instance, the first result of this simulation is the formation of a pendulum, then the pendulum starts to swing. How does the pendulum know it can swing, how does the pendulum then know how to swing, and how does the pendulum know that it should swing rather than stay at rest. It knows because the creator formed it that way. For this simulation to be true, it needs to evolve its own purpose and then trough evolution achieve it. The heart of this watch is a spring operated engine, it became a watch because thats what the creator told it that it was; it couldn’t be happy as an engine ready to do something else.

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