Creating CSI with NS

Imagine a coin-tossing game.  On each turn, players toss a fair coin 500 times.  As they do so, they record all runs of heads, so that if they toss H T T H H H T H T T H H H H T T T, they will record: 1, 3, 1, 4, representing the number of heads in each run.

At the end of each round, each player computes the product of their runs-of-heads.  The person with the highest product wins.

In addition, there is a House jackpot.  Any person whose product exceeds 1060 wins the House jackpot.

There are 2500 possible runs of coin-tosses.  However, I’m not sure exactly how many of that vast number of possible series would give a product exceeding 1060. However, if some bright mathematician can work it out for me, we can work out whether a series whose product exceeds 1060 has CSI.  My ballpark estimate says it has.

That means, clearly, that if we randomly generate many series of 500 coin-tosses, it is exceedingly unlikely, in the history of the universe, that we will get a product that exceeds 1060.

However, starting with a randomly generated population of, say 100 series, I propose to subject them to random point mutations and natural selection, whereby I will cull the 50 series with the lowest products, and produce “offspring”, with random point mutations from each of the survivors, and repeat this over many generations.

I’ve already reliably got to products exceeding 1058, but it’s possible that I may have got stuck in a local maximum.

However, before I go further: would an ID proponent like to tell me whether, if I succeed in hitting the jackpot, I have satisfactorily refuted Dembski’s case? And would a mathematician like to check the jackpot?

I’ve done it in MatLab, and will post the script below.  Sorry I don’t speak anything more geek-friendly than MatLab (well, a little Java, but MatLab is way easier for this).

529 thoughts on “Creating CSI with NS

  1. Elizabeth: Good luck. Elizabeth is convinced that evolutionary algorithms create something from nothing, the informational equivalent of perpetual motion. Incidentally, I’m not sure why she is still trying to demonstrate this, given the passionate arguments made that evolutionary algorithms such as Avida have already demonstrated this. Or maybe she finally realized they haven’t demonstrated any such thing.
    Well, no, Eric. I’m trying to do two things: …

    A few years ago, when the crowd at UD couldn’t make such a program work, I wrote one for my HP50G graphing calculator just to be contrary. And it has a few extra features as well.

    Big programs and fancy platforms are not needed for these demonstrations.

  2. sorry. guilty as charged. feel free to move to WJM’s topic, or the sandbox, or wherever you feel appropriate.

  3. Elizabeth is convinced that evolutionary algorithms create something from nothing, the informational equivalent of perpetual motion.

    If my wife said something like this I’d say, “Yes, dear. I was wrong.”

    Coming up on my 42 anniversary.

  4. who considers that the universe itself was designed, ab initio, with the capacity to produce these patterns.,

    Count me in the second group. It’s ol’ fashioned Catholic theology.

    The current scientific debate about the mechanisms at work in evolution requires theological comment insofar as it sometimes implies a misunderstanding of the nature of divine causality. Many neo-Darwinian scientists, as well as some of their critics, have concluded that, if evolution is a radically contingent materialistic process driven by natural selection and random genetic variation, then there can be no place in it for divine providential causality. A growing body of scientific critics of neo-Darwinism point to evidence of design (e.g., biological structures that exhibit specified complexity) that, in their view, cannot be explained in terms of a purely contingent process and that neo-Darwinians have ignored or misinterpreted. The nub of this currently lively disagreement involves scientific observation and generalization concerning whether the available data support inferences of design or chance, and cannot be settled by theology. But it is important to note that, according to the Catholic understanding of divine causality, true contingency in the created order is not incompatible with a purposeful divine providence. Divine causality and created causality radically differ in kind and not only in degree. Thus, even the outcome of a truly contingent natural process can nonetheless fall within God’s providential plan for creation.

  5. I’ve implemented the following (1+1)-ES (I think it’s called), which means that competition is between just one parent and one offspring per generation. It’s in (hopefully portable) C, with a mutation rate of .004 and tie goes to the offspring. The latter is crucial — it seems that neutral mutations are important for balancing out the runs of heads. For example, if you have an unbalanced sequence like:
    THHHTHHHHTHHHHHT
    a neutral mutation can get you to
    THHHHTHHHTHHHHHT
    which can then get you to
    THHHHTHHHHTHHHHT

    It takes between 1 million and 3 million generations, which should take a minute or less on a normal PC.

    Here‘s the code.

  6. Chrome helpfully offers to translate this into English.

    Fortunately C is my second language. And my favorite.

  7. I’ve been bit too busy to come up with several examples for which this little program could be a model; but I should point out that my initial comment that the products of the numbers of heads in each partition could represent energy accumulation was not correct. Energy adds; not multiplies. (I knew that.)

    But the series of heads and tails could represent a two state system in which each head could represent an energetic state and each tail could represent a ground state. They could be two-state atoms or spin states. If there are, say, N atoms each capable of holding a unit of energy, then the number of accessible states for a total of E units of energy is just the number of combinations of N things taken E at a time or,

    Ω = N!/((N – E)! E!).

    The entropy, S, is the natural log of Ω multiplied by Planck’s constant, which we can set to 1 for purposes of illustration (its value is an accident of the independent histories of the temperature and energy scales anyway).

    The reciprocal of the temperature is the rate of change of entropy with respect to the corresponding change in energy. So if we take N to be large, and each unit of energy to be 1, then the change in entropy with respect to energy, or reciprocal of the temperature, is just the discrete derivative of S with respect to E,

    1/T = ln((N-E)/(E+1)),

    where E goes from 0 to N-1 units.

    For those interested, try looking at the temperature as a function of E. You may find it interesting.

    Also note that the entropy goes from 0 when all atoms are in the ground state, through a maximum when half the atoms are in an excited state, and back to zero again when all atoms are in the excited state. This is while energy is being added. And it behaves the same way when energy is drained out of the system.

    So this little system that Elizabeth is using could be something like an array of two state atoms embedded in a crystalline lattice in which every 5th atom is attached to another atom or molecule that inhibits the transition of that two-state atom to an excited state.

    However, that product of the numbers of heads (numbers of excitations) would have to be a feature of interest (“information?”) to someone not particularly concerned with the physics.

  8. I am utterly lost as to what the point of this exercise is, or how it relates to Dembski’s jabberwockies. I do understand that we have here a point mutation exercise coupled with animal husbandry and herd management from a vindictive deity that slays all the ‘wrong’ children. Without fail, and at every harvest season. And that we’re trying to get over 1 in a chi squared test of… no idea how many independent variables.

    Which shouldn’t seem to matter much given that evolutionary processes are defined as being non-independent tests.

    So here’s the question: How much of the hash that headlines this is from Dembski’s examples and how much is just a misunderstanding of GAs and their relation to biology?

  9. madbat089,

    3) maximizes the product of H-runs = fitness function
    4) liz’s coin toss string = maximizes the product of H-runs

    // 3 and 4 are both true if, liz’s coin toss string = fitness function. The pattern of {H,T} is not the fitness function (it is the result), so 3 is accurate not 4.
    For 2) we can recover the sequence by referring to the function, and identify the function by referring to the sequence, but we can’t recover liz’s sequence with, “maximizes the product of H”. The only specifications are {1 & 2}. {3} is an accurate description, but it is not specified, as there are many possible fitness functions that will maximize H. 4) is simply false.

  10. junkdnaforlife:

    2) specific dna sequence = interacts with the glucocorticoid receptor,
    3) maximizes the product of H-runs = fitness function
    4) liz’s coint toss string =maximizes the product of H-runs

    // 3 and 4 are both true if, liz’s coin toss string = fitness function. The pattern of {H,T} is not the fitness function (it is the result), so 3 is accurate not 4.

    Did you understand anything I wrote? (2) and (3) are in no sense equivalent, whereas (2) and (4) are equivalent, where the description after *=* is a property of the entity described in front of *=*. Furthermore, if *=* is taken to mean *results in* (which is a ready and widespread meaning of *=*), both (2) and (4) have meaning, are true, and are equivalent.

    For 2) we can recover the sequence by referring to the function, and identify the function by referring to the sequence,

    Woah. False. We cannot assign a DNA sequence by knowing the function of the corresponding protein. Neither can we identify the function of a string of DNA by knowing its sequence. Scientists really really wish they could….

    {3}is an accurate description, but it is not specified, as there are many possible fitness functions that will maximize H.

    Sorry, I don’t understand what you are saying here. *maximizes the product of H-runs* is the fitness-relevant trait. The trait is specified, according to Dembski, when only a tiny subset of your possible population of strings exhibits this function. That is given for this trait. That’s why Liz chose it.

    Also, there is an unknown number of possible DNA sequences that code for the function *interacts with the glucocorticoid receptor*.

  11. madbat089,

    Hand this list to a scientist, and ask them to recover the sequence:

    1) 10 1′s
    2) regulate filament length mice
    3) maximizes the product of H-runs

    [A]

    1) 1111111111
    2) KYTSPVDMLGVVLAKKC QALVSDADYRNYLHQW TCLPDQNDVIQAK KVYELQSENMYKSD
    3) …

  12. Joe G: How did you determine all mutations and recombinations are random in some sense of the word. By what method?

    Also the designer just had to design the correct genetic programming/ genetic algorithm and the software does the rest- you don’t need a computer program sitting at your computer, programming as you type, do you?

    Can you show any evidence that verifies that ‘the designer’ actually did “design the correct genetic programming/ genetic algorithm and the software does the rest”? What happened to side loading/intervention?

    “No intervention required if the right program was written. But then the question would be- can such a program be written?”

    Since you and other IDists claim that a program was written, it’s up to you to verify it.

    “And BTW, right now we are saying that materialism’s science claims are meaningless.”

    No matter how much you say that, you won’t get anywhere with science unless you show convincing, positive, testable evidence of whichever version of immaterial ID you’re promoting.

    Are you saying that the universe, or living things, are computers?

  13. Maus:
    I am utterly lost as to what the point of this exercise is, or how it relates to Dembski’s jabberwockies.I do understand that we have here a point mutation exercise coupled with animal husbandry and herd management from a vindictive deity that slays all the ‘wrong’ children.Without fail, and at every harvest season.And that we’re trying to get over 1 in a chi squared test of…no idea how many independent variables.

    Specification: the Pattern that Signifies Intelligence, in which he gives a formula for computing a value “chi” from a pattern, that if the chi of a pattern exceeds unity, then we must infer “Intelligence”, not “chance”. My point is that Natural Selection is also a candidate generator of such a pattern, and that Dembski’s chi>1 indicates is some kind of selection process, which could include “intelligence” but which also includes, for example, natural selection.

    Dembski’s “chi” is not the “chi” of “chi square”.

    You could regard my exercises as an analogy for of “animal husbandry” in which a farmer only breeds from the virtual organisms with the largest product, just as children have sunflower growing competitions and only plant seeds from the largest sunflowers. Or, as an analogy for a vindictive deity. But Darwin’s point was that “selection” also occures “naturally” – i.e. it does not require an intentional culler. The environment itself will do the job. So, equally, you can regard my exercise as an analogy for a population of critters trying to thrive on limited resources, in which those best at accessing those resources will be the ones most likely to raise viable offspring. The point is that there is no difference between the selection mechanisms in the three cases – only the intention differs, and the intention merely affects the criterion used to select, not the fact of selection itself.

    Which shouldn’t seem to matter much given that evolutionary processes are defined as being non-independent tests.

    Could you explain what you mean by this?

    So here’s the question: How much of the hash that headlines this is from Dembski’s examples and how much is just a misunderstanding of GAs and their relation to biology?

    I don’t know what “the hash that headlines this” means. In that piece by Dembski he does not refer to biology explicitly, but attempts to make a general probabilistic claim about the origin of patterns. My point is that, given a system of self-replicators that replicate with variance, and some criterion that means that some variance have a better chance of replicating than others, the patterns that emerge will reliable exhibit chi>1.

    That does not, of course, refute the the claim that only an Intelligent Agent could have produced self-replicators, but that is not the claim Dembski is making. Elsewhere he specifically claims that Darwinian mechanisms (for whic self-replication with variance is a prerequisite) cannot generate Specified Complexity in which chi>1. I have shown that starting with patterns in which chi is well below 1 (by definition, as my starting patterns are indeed randomly generated by a virtual coin-tosser), Natural selection can reliably lift them to chi>1.

    Now, Dembski is aware of this kind of rebuttal, as it has been made many times. His response is not (that I am aware of) that we are assuming self-replication which itself requires intelligence, but that all selection systems involve the “smuggling in” of information in the form of a fitness function.

    My response is that no “smuggling” is required. As I say above, sure, a fitness function can be provided by an intelligent agent, me, in this case, a sunflower-growing child in another. But an intelligent agent is not necessary – limited resources will do the trick.

    Now, ID proponents might argue that an Intelligent agent was required to create a world with limited resources. Fine. But that wouldn’t distinguish ID from TE, and many ID proponents, including Dembski, are extremely opposed to TE!

    And in any case, it is not true that I have provided the solution to the problem. I have not “smuggled in” the optimum answer to the “problem” I set my virtual organism. I merely gave them the problem. The evolving population has to find a tiny subset of optimal answers. Interestingly, it has difficulty finding the optimum answer, because it turns out that, given only point mutations, that optimum answer is quite “IC”. In other words, the fitness space is really quite unconnected at the top end – the tiny subset of answers in which chi>1 are quite widely separated in “search space”.

    No matter. The population can find answers within it, given Natural Selection. Without Natural selection, my program could run on until the End Times and never get there.

  14. He’s desperately trying to ignore your demonstration and tell himself you made it up out of whole clothe

  15. William J. Murray: Ultimately, science doesn’t resolve anything anyway, IMO.

    (fixed)

    Creodont: Then why do you rely on what science provides in your everyday life?

    Would it not be more apposite to ask: How is it that science can provide what we rely on in our everyday life?

  16. Mike Elzinga: I’ve been bit too busy to come up with several examples for which this little program could be a model; but I should point out that my initial comment that the products of the numbers of heads in each partition could represent energy accumulation was not correct. Energy adds; not multiplies. (I knew that.)

    That’s not a problem, Mike. Take the logarithm of the product of the number of heads in each run and you’ve got an additive energy. A head run with n heads adds energy −log(n). We can use base-10 logs for an easier comparison with Elizabeth’s original definition.

    States with lowest energy have lone tails separated by head runs. The lowest energy states found by DiEb (4 3-runs and 97 4-runs) have E = −4 log 3 −97 log 4 = −60.3. Their entropy is S = ln[101!/(4!97!)] = 15.2.

    One can do calculations along these lines to estimate the temperature in the target space.

  17. Let’s stick with DiEb‘s sequences containing mostly 4-runs and a few 3-runs. These dominate the states of lowest energy.

    14 3-runs and 89 4-runs:
    E = −14 log 3 −89 log 4 = −60.263.
    S = ln[103!/(89!14!)] = 38.77.

    19 3-runs and 85 4-runs:
    E = −14 log 3 −89 log 4 = −60.240.
    S = ln[104!/(85!19!)] = 47.15

    So replacing 4 4-runs with 5 3-runs increases energy by ΔE = 4 log 4 – 5 log 3 = 0.0023 and entropy by ΔS = ln[104(89!/85!)(15!/19!)] = 8.38. From these we obtain the temperature:
    T = ΔES = 2.7×10^{−4}.

    Single-coin mutations are going to be rather ineffective at this temperature. For instance, when a 5-run is converted into two 2-runs (by changing the middle H into a T), the energy rises by log 5 − 2 log 2 = 0.097. The probability of acceptance of this move is exp(−ΔE/T) = exp(−359) = 10^{−156}.

  18. What do any of your posts have to do with the topic of this thread?

    What does the topic of this thread have to do with anything ID claims?

  19. William J. Murray: William J. Murray on March 16, 2012 at 10:14 pm said: Edit

    I think I”ve already told you what I think about your efforts as per this thread, but that shouldn’t stop you from celebrating :) What’s important is that you believe you’ve proven Dembski wrong.

    No, what is important is whether I have in fact proven Dembski wrong.

    This is verifiable independently of what I believe, because it is a matter of logic, something you yourself regard as a valid arbiter.

    If you do not consider I have proven Dembski wrong, can you please point to the flaw in my logic. I you think that all that matters is what we happen to believe, then I disagree :) I don’t think postmodernism applies to science or math.

  20. Well perhaps you should take it up with Dembski- and I have exposed the flaw in your logic.

    I have also tried to get others involved but they already understand that trying to correct you is not worth the effort.

    So all I have left to say is you need to take it up with Dembski. I know if I was as sure as you are I wouldn’t hesitate.

  21. One more thing:

    “I beseech you, in the bowels of Christ, think it possible that you may be mistaken.”

    Which may be meaningless as “Christ” doesn’t mean a thing to either one of us… ;)

  22. junkdnaforlife:

    Hand this list to a scientist, and ask them to recover the sequence:

    1) 10 1′s
    2) regulate filament length mice
    3) maximizes the product of H-runs

    [A]

    1) 1111111111
    2) KYTSPVDMLGVVLAKKC QALVSDADYRNYLHQW TCLPDQNDVIQAK KVYELQSENMYKSD
    3) …

    I am sorry. I am a scientist, and I don’t even understand the meaning of your new #2?

  23. Joe G : “Well perhaps you should take it up with Dembski- and I have exposed the flaw in your logic.”

    In a few short sentences, expose the flaw in the logic.

    I’ll then try if I can, to explain to you why you’re wrong.

  24. Indeed. And so does Dembski. But I have provided my math, and my script, and you can check it.

  25. junkdnaforlife:

    We are clearly talking past each other. Let’s try this from a different angle:

    According to Dembski, we cannot conclude that just because a pattern is one of a vast number of possible patterns that it was designed; to conclude design, it has to be one of a small subset of those patterns that conforms to some kind of *specification*. As a vast pool of possible patterns, Dembski chooses strings of coin tosses. As a specification that will only be a property of a very small subset, he chooses *compressibility* (ease of description). If, according to the relationship between the number of patterns exhibiting the specification and the number of possible patterns in the pool, the number of opportunities for them to happen at least once in the history of the universe is too low (=falls below Dembski’s probability threshold), he claims that we can reject non-design.

    In other words, Dembski chose *compressibility* because it is one of the properties that coin toss strings can have that conform to his criterion for specification.

    Lizzie uses, equivalent to Dembski, a string of coin tosses. She then chooses a property (*product of H-runs above a specific threshold*) that only a very small subset of the vast number of possible patterns exhibits. By Dembski’s criterion for a specification (according to the relationship between the number of patterns exhibiting the specification and the number of possible patterns in the pool, the number of opportunities for them to happen falls below Dembski’s threshold), that’s a specification. Thus, Lizzie’s simulation is valid, adequate test of Dembski’s claim.

  26. Joe G:
    Well perhaps you should take it up with Dembski- and I have exposed the flaw in your logic.

    I have also tried to get others involved but they already understand that trying to correct you is not worth the effort.

    So all I have left to say is you need to take it up with Dembski. I know if I was as sure as you are I wouldn’t hesitate.

    The other interpretation of the silence of the “others” is, of course, that they can see that Elizabeth is right! – as she transparently is.There is no flaw in her logic.

    Not that they’ll ever admit it, even to themselves…

  27. What is strange is Dembski’s claim that Darwinian processes are inadequate to account for CSI.

    If he was claiming that Darwinian processes must be initiated by an intelligent agent, that would be a different argument (readily rebutted, but my demonstration would not be a rebuttal).

    For a less artificial example of specificational resources in action, imagine a dictionary of 100,000 (= 105) basic concepts. There are then 10^5 1-level concepts, 10^10 2-level concepts, 10^15 3- level concepts, and so on. If “bidirectional,” “rotary,” “motor-driven,” and “propeller” are basic concepts, then the molecular machine known as the bacterial flagellum can be characterized as a 4-level concept of the form “bidirectional rotary motor-driven propeller.” Now, there are approximately N = 10^20 concepts of level 4 or less, which therefore constitute the specificational resources relevant to characterizing the bacterial flagellum. Next, define p = P(T|H) as the probability for the chance formation for the bacterial flagellum. T, here, is conceived not as a pattern but as the evolutionary event/pathway that brings about that pattern (i.e., the bacterial flagellar structure). Moreover, H, here, is the relevant chance hypothesis that takes into account Darwinian and other material mechanisms. We may therefore think of the specificational resources as allowing as many as N = 10^20 possible targets for the chance formation of the bacterial flagellum, where the probability of hitting each target is not more than p. Factoring in these N specificational resources then amounts to checking whether the probability of hitting any of these targets by chance is small, which in turn amounts to showing that the product Np is small.

    So here, he actually gives, as the specification the “evolutionary pathway that brings about the pattern”: “a bacterial flagellum”. Mine is defined as: “a sequence of coin-tosses in which the product of the runs-of-heads is very large”. And we’ve calculated the search space for such sequences above a certain threshold, and confirmed that the “probabilistic resources”. I don’t know why he thinks that his H “takes into account Darwinian and other material mechanisms”, but he does. However, it is clear, from my example, that “Darwinian and other material mechanisms” are capable of hitting the target pattern. And it is also clear, from the fitness plots, that some of the intermediate patterns in the evolutionary pathway in my example are “IC” – they are not reached by consistently advantageous steps and frequently involve deleterious steps. The AVIDA examples show the same thing.

    Dembski is simply wrong in his claim. His only defense, that I am aware of, is this story about “smuggling in” information via the fitness function.

    If any ID proponents would like to discuss this, I’d be delighted to hear from them :)

  28. Elizabeth: Dembski is simply wrong in his claim. His only defense, that I am aware of, is this story about “smuggling in” information via the fitness function.

    This reminds me of an old joke in which God tells scientists “No, no, no. You go get your own dirt!”

    Seriously, Dembski’s argument that information is smuggled through the fitness function is trivially true. The information content cannot increase if the fitness landscape is entirely flat (turning an evolutionary search into a purely random walk) or extremely rugged (algorithm trapped at a local minimum). So evolutionary theory begins with an assumption that fitness landscapes are neither too flat nor too rugged. At that point, Dembski says, roughly, “OK, but where did the smooth landscape come from?” This, in a nutshell, is what makes ID unscientific.

    Like any scientific theory, evolutionary biology is concerned with a narrow set of questions. It does not have a goal of finding the ultimate answer to life, the Universe, and everything. Creationism, on the other hand, is interested in finding God in the gaps of scientific knowledge. Once you explain how CSI emerges through mutation and natural selection, creationists move the goal posts to the origin of fitness landscapes. They could not care less about CSI. Ho hum.

  29. Liz,
    I really like the product-of-runs-of-heads problem as an easily understood example of optimization. Did you come up with it yourself, or did you learn it from somewhere?

  30. R0b:
    Liz,
    I really like the product-of-runs-of-heads problem as an easily understood example of optimization.Did you come up with it yourself, or did you learn it from somewhere?

    I came up with it myself :) Someone else may have come up with it independently though, I don’t know. I was trying to think of something like DNA, but with two “nucleotides” rather than four (to be more analogous to coin-tossing, and thus directly comparable to Dembski’s coin-toss examples) and in which the sequence would “code” for something, as a sequence of codons does in DNA. And which was numeric so it could be easily implemented!

    I thought of it on my bike. I get all my best ideas on my bike. It’s one of the reasons I cycle to work (it’s also a lovely route – along a riverbank, by a wooded escarpment full of interesting wildlife).

  31. olegt: That’s not a problem, Mike. Take the logarithm of the product of the number of heads in each run and you’ve got an additive energy. A head run with n heads adds energy −log(n). We can use base-10 logs for an easier comparison with Elizabeth’s original definition.
    States with lowest energy have lone tails separated by head runs. The lowest energy states found by DiEb (4 3-runs and 97 4-runs) have E = −4 log 3 −97 log 4 = −60.3. Their entropy is S = ln[101!/(4!97!)] = 15.2.
    One can do calculations along these lines to estimate the temperature in the target space.

    This is not too far from another line I was thinking about, namely a set of N Einstein oscillators.

    In this case Ω = (N-1+E)!/((N-1)!E!)).

    We get this because, for N oscillators, there are N-1 partitions distributed among E units of energy so we want the number of combinations of N-1+E things taken E at a time.

    This is an interesting contrast to the two-state system because

    ΔS/ΔE = ln((N+E)/(E+1)), where E goes from 0 to infinity.

    i.e., with a plus sign in the numerator instead of a minus.

    However this can’t apply to Elizabeth’s model because the number of oscillators is changing depending on how the energies are distributed and how many partitions are adjacent. The reason for this is because of the fixed number of heads and tales. That is a weird constraint.

    The counting is a little funnier because we arbitrarily don’t multiply the zero-energy states along with the nonzero-energy states. And of course, the logarithm of a zero-energy state is negative infinity. I suppose we could count a single head as a zero energy state (log(1) = 0), but zero heads is a tail, and for every additional adjacent tail, we loose an oscillator. And we have to find all combinations consistent with a given total energy. So the counting gets pretty messy.

    At first I was thinking about a set of “four-state” oscillators, but every string of tails just eliminates oscillators. So with the moving around of partitions, and with many adjacent partitions, not only do the number of oscillators keep changing, but for any given energy, we have to find all possible combinations of states consistent with that energy. And we do that for a changing number of oscillators as well as counting all combinations that produce the same total energy. And we have to allow for the fact that the energy saturates at 4 for any particular oscillator.

    That was the part I have not had time to think about (I’m laid up with a nasty virus, had to cancel a cross-country trip, and I have a backlog of tasks piling up).

    I don’t think taking samples from DiEb’s runs is going to give us the actual number of combinations of energy state for a given total energy. That has to be calculated.

    It is not a usual kind of system, but it is certainly not unusual for a system to have microscopic states become available and unavailable as conditions change. It just makes things harder to calculate analytically.

  32. Mike Elzinga: However this can’t apply to Elizabeth’s model because the number of oscillators is changing depending on how the energies are distributed and how many partitions are adjacent. The reason for this is because of the fixed number of heads and tales. That is a weird constraint.

    I don’t think taking samples from DiEb’s runs is going to give us the actual number of combinations of energy state for a given total energy. That has to be calculated.

    It is not a usual kind of system, but it is certainly not unusual for a system to have microscopic states become available and unavailable as conditions change. It just makes things harder to calculate analytically.

    No worries, Mike. Statistical mechanics is sufficiently versatile to cope with constraints. Working with a microcanonical ensemble (constraint of fixed energy) is a pain in the butt, so we switch to a canonical one. Working with a fixed number of particles is also difficult, so we go around that constraint by switching to the grand canonical ensemble and work at a fixed chemical potential instead of a fixed particle number.

    Similar tricks can be used in this problem. The sequence-length constraint can be handled by adding a “tension” term to the energy. The energy of an n-run changes from −log n to −log n + σ(n+1), where σ is a Lagrange multiplier taking care of the length constraint. I’ll see if this program can be pushed all the way. Back-of-the-envelope calculations show that it might work.

  33. Mike Elzinga: I don’t think taking samples from DiEb’s runs is going to give us the actual number of combinations of energy state for a given total energy. That has to be calculated.

    I think DiEb’s estimate is right. 3-runs are the lowest-energy excitations. Here is a quick table of energy costs per excitation, with the length constraint taken into account:
    2-runs: −log 2 + (3/5) log 4 = 0.0602
    3-runs: −log 3 + (4/5) log 4 = 0.0045.
    5-runs: −log 5 + (6/5) log 4 = 0.0235.
    6-runs: −log 5 + (6/5) log 4 = 0.0647.
    3-runs are by far the cheapest and are the only ones at low temperatures. We might have to take into account 5-runs, but they are few and far between. With the ground-state energy of −60.308, you can add at most 0.308 to it before crossing the threshold of −60. That energy window allows for a max number of 68 3-runs and only 13 5-runs. 2 and 6-runs are even more costly and you can add at most 5 of those.

    To get a rough estimate, we can say that any combination of 3 and 4-runs is admissible. There are between 100 and 114 runs in total (depending on the exact number of 3 and 4-runs). There are roughly 2^114 = 2.1×10^34 such states, not far from DiEb’s number.

  34. olegt: 2-runs: −log 2 + (3/5) log 4 = 0.0602
    3-runs: −log 3 + (4/5) log 4 = 0.0045.
    5-runs: −log 5 + (6/5) log 4 = 0.0235.
    6-runs: −log 5 + (6/5) log 4 = 0.0647.

    Although the numerical values are fine, there is a typo in the last line. Should be
    2-runs: −log 2 + (3/5) log 4 = 0.0602
    3-runs: −log 3 + (4/5) log 4 = 0.0045.
    5-runs: −log 5 + (6/5) log 4 = 0.0235.
    6-runs: −log 6 + (7/5) log 4 = 0.0647.
    (Forgot to edit a copied and pasted expression.)

  35. Elizabeth:

    You could regard my exercises as an analogy for … a vindictive deity. … So, equally, you can regard my exercise as an analogy for a population of critters trying to thrive on limited resources, in which those best at accessing those resources will be the ones most likely to raise viable offspring.

    So yes, if by ‘natural selection’ you mean ‘unnatural selection’ then by all means everything is as you say, because you say it. Which is all a bit Humpty Dumpty, but I’ll join it by saying that you’re proven your point. So equally, we can all regard that you did not.

    But if saying anything is to include and mean its opposite as well… Then we’re right back to the notion of non-Contradiction that brought me here in the first place and we’ve made absolutely no progress in the matter. So topically, on point, and with the preferred argumentation presented to me: You failed to refute Dembski. Because you say you did.

    Or we can try working with actual definitions rather than ever-shifting sands of sophistry:

    1. What is ‘unnatural selection’? If your toy-Darwin suffices then my cigarette lighter is natural climate variation.
    2. What is Dembski’s ‘chi’? It is not ‘chi squared’ but almost surely (It’s Dembski) a renamed common concept.

  36. Maus: “But if saying anything is to include and mean its opposite as well…”

    No, what Elizabeth offered you was a choice of “analogies”.

    An analogy is not real. It is an alternate “description” that is generated by a speaker to illustrate the “description” of something unrelated but similar, in the hopes that it will aid in understanding a point made by the speaker.

    In your case, the misunderstanding seems to go deeper as the popular analogy, “The glass is half-empty / The glass is half-full” are not opposites.

  37. Elizabeth said: “You could regard my exercises as an analogy for … a vindictive deity. … So, equally, you can regard my exercise as an analogy for a population of critters trying to thrive on limited resources, in which those best at accessing those resources will be the ones most likely to raise viable offspring.

    Maus:

    So yes, if by ‘natural selection’ you mean ‘unnatural selection’ then by all means everything is as you say, because you say it.Which is all a bit Humpty Dumpty, but I’ll join it by saying that you’re proven your point.So equally, we can all regard that you did not.

    But if saying anything is to include and mean its opposite as well… Then we’re right back to the notion of non-Contradiction that brought me here in the first place and we’ve made absolutely no progress in the matter.So topically, on point, and with the preferred argumentation presented to me:You failed to refute Dembski.Because you say you did.

    Analogy: “resemblance in some particulars between things otherwise unlike”
    - Merriam-Webster

    It seems you fundamentally misunderstood Elizabeth when you thought her saying *x is a good analogy for y, but also for z, because all three of them result in the reproduction of only a certain proportion of the population with a certain distribution of traits* was her saying *y means x, and z means x, too*. In fact, I’ve never even heard of a definition of analogy that would support that kind of interpretation. How did you come up with that?

  38. olegt: No worries, Mike. Statistical mechanics is sufficiently versatile to cope with constraints. Working with a microcanonical ensemble (constraint of fixed energy) is a pain in the butt, so we switch to a canonical one. Working with a fixed number of particles is also difficult, so we go around that constraint by switching to the grand canonical ensemble and work at a fixed chemical potential instead of a fixed particle number.
    Similar tricks can be used in this problem. The sequence-length constraint can be handled by adding a “tension” term to the energy. The energy of an n-run changes from −log n to −log n + σ(n+1), where σ is a Lagrange multiplier taking care of the length constraint. I’ll see if this program can be pushed all the way. Back-of-the-envelope calculations show that it would work.

    Oh I think it shouldn’t be an excruciatingly difficult problem. There might be a partition function that would work. I’m just too wiped out to think about it right now. All I want to do is sleep.

    Give it a shot. I think we’re on the same page.

  39. Maus:
    Elizabeth:

    So yes, if by ‘natural selection’ you mean ‘unnatural selection’ then by all means everything is as you say, because you say it.Which is all a bit Humpty Dumpty, but I’ll join it by saying that you’re proven your point.So equally, we can all regard that you did not.

    No, “natural selection” doesn’t mean “unnatural selection” but both mean selection. Artificial selection is what we call it when the fitness criteria are an “artifice” – ie. decided on by an intelligent agent. Natural selection is when the fitness criteria are simply those implicit in the hazards and resources of the natural world.

    But as far as my exercise goes, it doesn’t matter, because the actual mechanism is the same in both cases.

    But if saying anything is to include and mean its opposite as well… Then we’re right back to the notion of non-Contradiction that brought me here in the first place and we’ve made absolutely no progress in the matter.So topically, on point, and with the preferred argumentation presented to me:You failed to refute Dembski.Because you say you did.

    No, you have misunderstood. A black cat is not the same as a white cat, but if what we are interested in is their cattiness, not their colour, then it doesn’t matter whether we talk about a black one or a white one. What we have in my exercise is a systematic fitness criterion. The fact that it was invented by me doesn’t mean it isn’t analogous to a naturally presented one, for example limited resources.

    Or we can try working with actual definitions rather than ever-shifting sands of sophistry:

    That’s exactly what we are doing, and I have defined what I’m doing with great precision. So has Dembski.

    1. What is ‘unnatural selection’?If your toy-Darwin suffices then my cigarette lighter is natural climate variation.

    My model will serve as an analog for either natural or unnatural selection. Darwin’s insight was to see that both worked in exactly the same way – some environmental criterion determines what features in an organism will promote reproductive success. If that “environmental criterion” is a child who wants to win the tallest sunflower contest, then we call it “artifical selection”; if it is solar gain, then we call it “natural selection”. But the mechanism in both cases – and the result in this case – is the same – selection for taller flowers.

    2. What is Dembski’s ‘chi’?It is not ‘chi squared’ but almost surely (It’s Dembski) a renamed common concept.

    Well, read the paper. He gives the equation and explains its derivation quite clearly. I have used his definition, and plugged in relevant values from my exercise.

  40. It turns out that the number of generations required is non-linearly dependent on the population size. With a population of 1000, I only got to 9.2x10e59 after 300,000 generations. Bumping the population size up to 10,000 reliably generates a solution over 10e60 in around 700 generations. My code and results are available here.

    I do hope the ID proponents appreciate that crossover (SEX!) generates CSI even faster than asexual evolutionary mechanisms.

  41. Patrick:
    It turns out that the number of generations required is non-linearly dependent on the population size.With a population of 1000, I only got to 9.2x10e59 after 300,000 generations.Bumping the population size up to 10,000 reliably generates a solution over 10e60 in around 700 generations.My code and results are available here.

    I do hope the ID proponents appreciate that crossover (SEX!) generates CSI even faster than asexual evolutionary mechanisms.

    And not just CSI either!

    … or so I’m told….

  42. Patrick,

    Patrick you say on your site:

    “That being said, based on Dr. Liddle’s interpretation of Dembski’s paper, this exercise clearly demonstrates that a simple subset of known evolutionary mechanisms is more than capable of generating sequences of bits that exhibit what he seems to be claiming is CSI.”

    // Based on Dr. Liddle’s interpretation indeed. You provide a string, I’ve taken the first two lines of it and included them in the following three examples to examine specificity. (However, clipping a fragment may not be representative of the specificity of a string, as we could toss a coin a billion times and find some clusters of patterns, which if clipped out and isolated would not be representative.) But for the purpose of this, the first two lines of your example seemed to be a fair representation of the string you posted.

    (1) 3 1′s then 3 0′s repeat to 96

    111000 111000 111000 111000 111000 111000 111000 111000 111000 111000 111000 111000 111000 111000 111000 111000

    (2) Regulates thin filament length in mice

    KYTSPVDMLG VVLAKKCQAL VSDADYRNYL HQWTCLPDQN DVIQAKKVYE LQSENMYKSD LEWLRGIGWS PLGSLEAEKN
    KRASEIISEK KYRQPPDRNK FTSIPDAMDI VLAKTNAKNR

    (3) 4 1′s then 0, 3 1′s then 0 twice, 4 1′s then 0 twice, five 1′s, 0 then 4 1′s three times, 0 then 5 1′s, 0 then 3 1′s three times, 0 then four 1′s twice, 0 then five 1′s, 0 then 4 1′s five times

    11110 11101110 1111011110 11111 011110111101111 011111 011101110111 0111101111 011111 0111101111011110111101111

    // I will leave it for the reader to decide which string is Patricks’s, as well as which would be considered examples of analogous specificity.

    // 2 is a fragment of a string length of 1358, and if we wish to complete the string the description will not change. 3 is also a fragment, however if we complete the string the description will increase.

  43. junkdnaforlife:

    madbat said:

    “According to Dembski, we cannot conclude that just because a pattern is one of a vast number of possible patterns that it was designed; to conclude design, it has to be one of a small subset of those patterns that conforms to some kind of *specification*. As a vast pool of possible patterns, Dembski chooses strings of coin tosses. As a specification that will only be a property of a very small subset, he chooses *compressibility* (ease of description). If, according to the relationship between the number of patterns exhibiting the specification and the number of possible patterns in the pool, the number of opportunities for them to happen at least once in the history of the universe is too low (=falls below Dembski’s probability threshold), he claims that we can reject non-design.

    In other words, Dembski chose *compressibility* because it is one of the properties that coin toss strings can have that conform to his criterion for specification.

    Lizzie uses, equivalent to Dembski, a string of coin tosses. She then chooses a property (*product of H-runs above a specific threshold*) that only a very small subset of the vast number of possible patterns exhibits. By Dembski’s criterion for a specification (according to the relationship between the number of patterns exhibiting the specification and the number of possible patterns in the pool, the number of opportunities for them to happen falls below Dembski’s threshold), that’s a specification. Thus, Lizzie’s simulation is valid, adequate test of Dembski’s claim.”

    Would you care to comment on this post of mine? Why do you think Lizzie’s string is not specified in Dembksi’s sense of specification?

  44. junkdnaforlife:

    KYTSPVDMLG VVLAKKCQAL VSDADYRNYL HQWTCLPDQN DVIQAKKVYE LQSENMYKSD LEWLRGIGWS PLGSLEAEKN
    KRASEIISEK KYRQPPDRNK FTSIPDAMDI VLAKTNAKNR

    Could you explain what this is? It’s clearly not a DNA sequence….

  45. madbat089: Could you explain what this is? It’s clearly not a DNA sequence….

    Ok. I figured it out. You moved goalposts. This is no longer a DNA sequence, it is an amino acid sequence. Either way – you are suggesting that this snippet of the amino acid sequence of Nebulin is accurately described by: *Regulates thin filament length in mice*. Are you seriously suggesting this?

  46. Patrick:

    I do hope the ID proponents appreciate that crossover (SEX!) generates CSI even faster than asexual evolutionary mechanisms.

    Hee hee! I knew it would! What is interesting is that here we have what is effectively a single gene, not multi-gene combinations, yet even here recombination explores the space much more efficiently. By combining the front and back of genes whose fitness has already been ‘proven’ (well, they are still in the population), recombination generates novelty in a way that avoids the deleterious load that mutation alone suffers.

    There are numerous other things going on, too, in a recombinant population. Let’s hear it for Recombination! The best idea evolution ever had.

  47. Allan Miller:
    Patrick:

    Hee hee! I knew it would! What is interesting is that here we have what is effectively a single gene, not multi-gene combinations, yet even here recombination explores the space much more efficiently. By combining the front and back of genes whose fitness has already been ‘proven’ (well, they are still in the population), recombination generates novelty in a way that avoids the deleterious load that mutation alone suffers.

    There are numerous other things going on, too, in a recombinant population. Let’s hear it for Recombination! The best idea evolution ever had.

    I always use recombination for anything I really want a solution for. I deliberately eschewed it for this, on the grounds that recombination itself is an evolved capacity.

  48. OK, well, my last run got stuck at a local maximum so I aborted it at 274725 generations, at which point its product was 7.5751e+59.

    The first 500 generations looked like this (Heads white, Tails black):

    And the last 500 generations looked like this:

  49. junkdnaforlife:
    Patrick,

    Patrick you say on your site:

    “That being said, based on Dr. Liddle’s interpretation of Dembski’s paper, this exercise clearly demonstrates that a simple subset of known evolutionary mechanisms is more than capable of generating sequences of bits that exhibit what he seems to be claiming is CSI.”

    // Based on Dr. Liddle’s interpretation indeed. You provide a string, I’ve taken the first two lines of it and included them in the following three examples to examine specificity.

    What exactly do you mean by “examine specificity”? Dr. Liddle has already provided a specification as part of her problem description.

  50. This is sort of fun: as well as point mutations, I’ve now introduced a mutation type in which I randomly select a short sequence (length drawn from a Poisson distribution), delete, it, then insert it randomly elsewhere (to keep the genome the same length).

    That makes the search space much better connected. It’s still running, but in only a few thousand generations (population N=100) I’ve got to within spitting distance of the jackpot:

  51. Take-home message: the connectedness of the search space is a function of the types of mutation possible.

    I never thought of that before.

  52. how very cool – this has been very enlightening – thanks for thinking up this great little experiment, Liz, and sharing it with all of us!!!

  53. Elizabeth: Take-home message: the connectedness of the search space is a function of the types of mutation possible.

    Exactly. To reach the jackpot, a sequence has to get its tails shuffled around so that they become equidistant. Single-bit mutations become deleterious: they introduce extra tails or remove existing ones, decreasing the fitness.

  54. Elizabeth: Take-home message: the connectedness of the search space is a function of the types of mutation possible.
    I never thought of that before.

    Chemists and physicists have known for a long time that transitions from one form of molecule to another form take place with higher probability than what one would expect from just plucking an atom from one location and tacking it on somewhere else.

    In recent years, femtosecond chemistry experiments using lasers have shown the kinds of things that happen that make this possible.

    As it turns out, the process of adding enough energy to break bonds often brings a molecule close to its melting temperature. That then distorts the molecule radically enough to change the shapes of the mutual potential wells connecting the various atoms together.

    The distortions are enough to pull down barriers between otherwise energetically isolated configurations that allow atoms to sort of “slip-slide” into new positions without having to make large jumps in energy as they do so.

    The results are not especially surprising since we often see examples of this occurring macroscopically; such as when we untangle a mess of stuff by giving it a gentle shake.

    But it is nice to see examples from the chemistry of molecular formation that shake us out of the habit of thinking in terms rigid molecular diagrams that are energetically “impossible” to go between.

  55. madbat089:
    how very cool – this has been very enlightening – thanks for thinking up this great little experiment, Liz, and sharing it with all of us!!!

    Well, thanks to all who have contributed their far superior mathematical and coding skills to the project!

  56. Elizabeth:
    What is strange is Dembski’s claim that Darwinian processes are inadequate to account for CSI.

    If he was claiming that Darwinian processes must be initiated by an intelligent agent, that would be a different argument (readily rebutted, but my demonstration would not be a rebuttal).

    So here, he actually gives, as the specification the “evolutionary pathway that brings about the pattern”:”a bacterial flagellum”.Mine is defined as: “a sequence of coin-tosses in which the product of the runs-of-heads is very large”.And we’ve calculated the search space for such sequences above a certain threshold, and confirmed that the “probabilistic resources”.I don’t know why he thinks that his H “takes into account Darwinian and other material mechanisms”, but he does.However, it is clear, from my example, that “Darwinian and other material mechanisms” are capable of hitting the target pattern.And it is also clear, from the fitness plots, that some of the intermediate patterns in the evolutionary pathway in my example are “IC” – they are not reached by consistently advantageous steps and frequently involve deleterious steps.The AVIDA examples show the same thing.

    Dembski is simply wrong in his claim.His only defense, that I am aware of, is this story about “smuggling in” information via the fitness function.

    If any ID proponents would like to discuss this, I’d be delighted to hear from them

    There ya go- just go into a lab and have a flagellum evolve via darwinian processes- heck Behe even supports that:

    In fact, my argument for intelligent design is open to direct experimental rebuttal. Here is a thought experiment that makes the point clear. In Darwin’s Black Box (Behe 1996) I claimed that the bacterial flagellum was irreducibly complex and so required deliberate intelligent design. The flip side of this claim is that the flagellum can’t be produced by natural selection acting on random mutation, or any other unintelligent process. To falsify such a claim, a scientist could go into the laboratory, place a bacterial species lacking a flagellum under some selective pressure (for mobility, say), grow it for ten thousand generations, and see if a flagellum–or any equally complex system–was produced. If that happened, my claims would be neatly disproven.(1)

    How about Professor Coyne’s concern that, if one system were shown to be the result of natural selection, proponents of ID could just claim that some other system was designed? I think the objection has little force. If natural selection were shown to be capable of producing a system of a certain degree of complexity, then the assumption would be that it could produce any other system of an equal or lesser degree of complexity. If Coyne demonstrated that the flagellum (which requires approximately forty gene products) could be produced by selection, I would be rather foolish to then assert that the blood clotting system (which consists of about twenty proteins) required intelligent design.

    Let’s turn the tables and ask, how could one falsify the claim that, say, the bacterial flagellum was produced by Darwinian processes? (Professor Coyne’s remarks about a Precambrian fossil hominid are irrelevant since I dispute the mechanism of natural selection, not common descent. I would no more expect to find a fossil hominid out of sequence than he would.) If a scientist went into the laboratory and grew a flagellum-less bacterial species under selective pressure for many generations and nothing much happened, would Darwinists be convinced that natural selection is incapable of producing a flagellum? I doubt it. It could always be claimed that the selective pressure wasn’t the right one, or that we started with the wrong bacterial species, and so on. Even if the experiment were repeated many times under different conditions and always gave a negative result, I suspect many Darwinists would not conclude that the claim of its Darwinian evolution was falsified. Of complex biochemical systems Coyne himself writes “we may forever be unable to envisage the first proto-pathways. It is not valid, however, to assume that, because one man cannot imagine such pathways, they could not have existed.” (Coyne 1996) If a person accepts Darwinian paths which are not only unseen, but which we may be forever unable to envisage, then it is effectively impossible to make him think he is wrong.

  57. I do hope the ID proponents appreciate that crossover (SEX!) generates CSI even faster than asexual evolutionary mechanisms.

    Great, sexual reproduction requires CSI- you are are great at starting with the very stuff that needs explaining.

    Asexual reproduction is irreducibly complex:

    Peering into Darwin’s Black Box:
    The cell divsion processes required for bacterial life

    So yes, if you start with CSI you can design a program that can do interesting things.

  58. Elizabeth:
    Did you mean to write that sexual reproduction is irreducibly complex?

    No, but sexual reproduction is also IC. Read the article I linked to- it makes the (positive) case for asexual reproduction being irreducibly complex.

  59. Joe G,

    Great, sexual reproduction requires CSI- you are are great at starting with the very stuff that needs explaining.

    Great, intelligence requires CSI – you are great at starting with the very stuff that needs explaining.

  60. dr who:
    Joe G,

    Great, sexual reproduction requires CSI- you are are great at starting with the very stuff that needs explaining.

    Great, intelligence requires CSI

    Right and your position can’t explain either- intelligence nor CSI.

    - you are great at starting with the very stuff that needs explaining.

    We make observations and so far CSI comes from intelligence that also has CSI. And, as per Newton’s First Rule, materialism has all the power because if someone could demonstrate that intelligence and therefor CSI can be produced by matter, energy, necessity and chance, materialism wins.

  61. Joe G: Right and your position can’t explain either- intelligence nor CSI.

    We make observations and so far CSI comes from intelligence that also has CSI. And, as per Newton’s First Rule, materialism has all the power because if someone could demonstrate that intelligence and therefor CSI can be produced by matter, energy, necessity and chance, materialism wins.

    So, where did the ‘intelligent designer’ get its CSI and intelligence?

    It’s not about winning, except to those of you who think it’s only about winning (control). To scientists it’s about exploring and understanding nature.

  62. Joe G:

    We make observations and so far CSI comes from intelligence that also has CSI. And, as per Newton’s First Rule, materialism has all the power because if someone could demonstrate that intelligence and therefor CSI can be produced by matter, energy, necessity and chance, materialism wins.

    Dear Joe. Intelligence certainly can’t be explained by Intelligent design, can it? And as observation tells us that “CSI” is a prerequisite for intelligence, then we should look at the theory of variation and selection of chemical self-replicators that I suggested on the other thread, as it’s in chemical self-replicators that we observe intelligence of all levels, giving it the appearance of a phenomenon that can gradually emerge.

    Veering back to the topic of this thread, you can see illustrations in the models people have made here of how such a process might work to build up CSI.

  63. So, where did the ‘intelligent designer’ get its CSI and intelligence?

    ID is not about the designer. The only way to say anything about the designer is by studying the design and all relevant evidence.

    To scientists it’s about exploring and understanding nature.

    And that is exactly what Intelligent Design is all about.

  64. Intelligence certainly can’t be explained by Intelligent design, can it?

    I never said that. I said that your position can’t explain it and you confirm my claim with every one of your posts. Thank you.

    And as observation tells us that “CSI” is a prerequisite for intelligence, then we should look at the theory of variation and selection of chemical self-replicators that I suggested on the other thread, as it’s in chemical self-replicators that we observe intelligence of all levels, giving it the appearance of a phenomenon that can gradually emerge.

    Your position can’t explain self-replicators nor how self-replicators became living organisms.

    The OP of this thread is a strawman.

  65. Joe G: I never said that. I said that your position can’t explain it and you confirm my claim with every one of your posts. Thank you.

    Your position can’t explain self-replicators nor how self-replicators became living organisms.

    The OP of this thread is a strawman.

    Joe, you are applying double standards here. You insist on limiting ID to the detection of design and not the investigation of the designer. Fine, scientific theories have a limited scope. They focus on one particular aspect of nature. Maxwell’s electromagnetic theory assumed the existence of electric charges without explaining their origin. Newton’s theory of gravitation dealt with the effects of gravity without explaining its origin.

    In the same vein, Elizabeth is investigating whether CSI can arise through natural selection without asking where the fitness landscape came from. I think this is an entirely reasonable approach. For some reason, however, IDers dismiss such studies as trivial. Well, they aren’t.

  66. olegt: Joe, you are applying double standards here. You insist on limiting ID to the detection of design and not the investigation of the designer. Fine, scientific theories have a limited scope. They focus on one particular aspect of nature. Maxwell’s electromagnetic theory assumed the existence of electric charges without explaining their origin. Newton’s theory of gravitation dealt with the effects of gravity without explaining its origin.

    In the same vein, Elizabeth is investigating whether CSI can arise through natural selection without asking where the fitness landscape came from. I think this is an entirely reasonable approach. For some reason, however, IDers dismiss such studies as trivial. Well, they aren’t.

    oleg- if we could study the designer then we wouldn’t have a design inference as design would be a given. And Elizabeth’s example has nothing to do with natural selection. And it has nothing to do with anything Dembski has claimed.

    BTW you are the one applying double-standards as yiou constantly ask of ID what your position can’t produce.

  67. Joe G: I never said that. I said that your position can’t explain it and you confirm my claim with every one of your posts. Thank you.Your position can’t explain self-replicators nor how self-replicators became living organisms.The OP of this thread is a strawman.

    My position? My position for the purposes of this discussion is “non-intelligent design”, just as yours is “intelligent design”.

    My position of non-telic chemistry is clearly the better general explanation for self-replicators, as observation tells us that self-replicators are a prerequisite for all known intelligent designers. Surely you must agree with this observation?

    The fact that we don’t yet know the details of how the first self-replicators came about certainly does not warrant an intelligent designer of the gaps argument. You I.D. guys are hardly in a position to complain about lack of detail, are you?

    Anyway, you informed me on the other thread that I.D. makes no claims about the OOL, so we should have agreement on the best explanation for self-replicators.

  68. My position for the purposes of this discussion is “non-intelligent design”, just as yours is “intelligent design”

    You don’t have any evidence for “non-intellignet design”

    My position of non-telic chemistry is clearly the better general explanation for self-replicators

    What self-replicators?

    as observation tells us that self-replicators are a prerequisite for all known intelligent designers.

    Good luck providing evidence for that.

    The fact that we don’t yet know the details of how the first self-replicators came about certainly does not warrant an intelligent designer of the gaps argument.

    LoL! So because we cannot figure out how nature built Stonehenge we shouldn’t call on the “designer of the gaps”.

    But anyway there was an experiment pertaining to the self-sustained replication of RNAs, but it doesn’t come close to supporting anything you have claimed.

    Anyway, you informed me on the other thread that I.D. makes no claims about the OOL,

    Obvioulsy you misread what I said- ID is all about the OoL

  69. Joe G: oleg- if we could study the designer then we wouldn’t have a design inference as design would be a given. And Elizabeth’s example has nothing to do with natural selection.

    Of course it does. It’s a straightforward demonstration of natural selection, and how, when self-replicating variants differ in their reproductive success, you will get vast increases in CSI, sufficient to breach Dembski’s chi threshold.

    And it has nothing to do with anything Dembski has claimed.

    It’s a direct refutation of his claim in that paper.

  70. Elizabeth:

    I always use recombination for anything I really want a solution for. I deliberately eschewed it for this, on the grounds that recombination itself is an evolved capacity.

    Well … yes. Nonetheless, all the kind of complexity that really impresses us occurs in recombinant sexual species (or their asexually-reverted descendants). OK, some people regard the bacterial flagellum as the acme of design, but there are more things in heaven and earth than dreamt of in their philosophy. Recombination also impacts Behe’s error in the ‘CCC’ in malaria – the chances of a CCC arising are greatly enhanced by recombination, even though it sometimes breaks them apart again.

    Joe characterises asexual reproduction as ‘CSI’, but asexual reproduction simply goes back to the OoL (where we always seem to end up!). A simple replicator is nothing more than an asexually-reproducing species. Sex itself is not irreducibly complex – indeed, it is a classic example of a system asserted to be irreducibly complex that is not. In the modern version with which we are most familiar, we have two sexes and (frequently) multicellular bodies possessed of a division between germ line and soma, and homologous recombiination. But these are derived states – they are not essential for characterising the basic sexual process, which is simply cyclic syngamy and division. Such a cycle must start with syngamy, not division – you have to have a diploid to divide. Anyone who thinks of sex as being irreducible is thinking of genders, and multicellular diploid organisms with recombinant meiosis. But they only exist because of sex, not as a precursor.

    But even recombination is an optional extra in the basic cycle. It’s not there in order to speed up searches, disrupt local maxima, distribute processing in a parallel manner, or any other of the myriad consequences it has for evolution. It just happens to do all those things, and its raison d’etre is likely to be much more prosaic – it stabilises bivalents in meiosis for one thing, and is a potential response to ‘chromosome-killer’ genes for another.

    The same goes for transposition – and, indeed, mutation. They aren’t there in order to make evolutionary ‘searches’ more efficient, they just do. At least, if recombination was the Designer’s idea, it took him 2 billion years to hit upon it.

  71. Joe G: Obvioulsy you misread what I said- ID is all about the OoL

    So why are so many ID proponents so anti-Darwin, then?

  72. Joe G: You don’t have any evidence for “non-intellignet design”What self-replicators?Good luck providing evidence for that.LoL! So because we cannot figure out how nature built Stonehenge we shouldn’t call on the “designer of the gaps”.But anyway there was an experiment pertaining to the self-sustained replication of RNAs, but it doesn’t come close to supporting anything you have claimed.Obvioulsy you misread what I said- ID is all about the OoL

    Stonehenge is not a prerequisite for the existence of intelligent designers. Life, if we follow observations and evidence, is.

  73. Elizabeth: Of course it does.It’s a straightforward demonstration of natural selection, and how, when self-replicating variants differ in their reproductive success, you will get vast increases in CSI, sufficient to breach Dembski’s chi threshold.

    It’s a direct refutation of his claim in that paper.

    You don’t understand natural selection. It is just a result. Also self-replication is a pipe-dream. the current science says that the RNA world did not exist, and that there had to be a ribonucleoprotein world- IOW the stakes have been increased.

    And I say you are misrepresenting the papaer.

  74. Elizabeth: So why are so many ID proponents so anti-Darwin, then?

    As I have told you- Darwinism has nothing to say about evolution if it is silent on the OoL because if the ooL was designed then evolution was designed.

    That and there isn’t any evidence that differential reproduction can construct new, useful multi-protein configurations.

  75. Allan Miller2:
    Elizabeth:Well … yes. Nonetheless, all the kind of complexity that really impresses us occurs in recombinant sexual species (or their asexually-reverted descendants). OK, some people regard the bacterial flagellum as the acme of design, but there are more things in heaven and earth than dreamt of in their philosophy. Recombination also impacts Behe’s error in the ‘CCC’ in malaria – the chances of a CCC arising are greatly enhanced by recombination, even though it sometimes breaks them apart again.

    Joe characterises asexual reproduction as ‘CSI’, but asexual reproduction simply goes back to the OoL (where we always seem to end up!). A simple replicator is nothing more than an asexually-reproducing species. Sex itself is not irreducibly complex – indeed, it is a classic example of a system asserted to be irreducibly complex that is not. In the modern version with which we are most familiar, we have two sexes and (frequently) multicellular bodies possessed of a division between germ line and soma, and homologous recombiination. But these are derived states – they are not essential for characterising the basic sexual process, which is simply cyclic syngamy and division. Such a cycle must start with syngamy, not division – you have to have a diploid to divide. Anyone who thinks of sex as being irreducible is thinking of genders, and multicellular diploid organisms with recombinant meiosis. But they only exist because of sex, not as a precursor.

    But even recombination is an optional extra in the basic cycle. It’s not there in order to speed up searches, disrupt local maxima, distribute processing in a parallel manner, or any other of the myriad consequences it has for evolution. It just happens to do all those things, and its raison d’etre is likely to be much more prosaic – it stabilises bivalents in meiosis for one thing, and is a potential response to ‘chromosome-killer’ genes for another.

    The same goes for transposition – and, indeed, mutation. They aren’t there in order to make evolutionary ‘searches’ more efficient, they just do. At least, if recombination was the Designer’s idea, it took him 2 billion years to hit upon it.

    What simple self-replicator? And unfortunately for you, the evidence says sex is IC and asexual reproduction is IC.

  76. Joe G: ID is not about the designer. The only way to say anything about the designer is by studying the design and all relevant evidence.

    And that is exactly what Intelligent Design is all about.

    Same old same old.

    If it’s not about “the designer”, then what’s the point of studying “the design”? Is it to try to figure out all the parts and processes in nature? Do you really think that scientists aren’t already doing that? What EXACTLY do you think that studying “the design” would change in the way that scientists go about their research into biological evolution? What new equipment would be needed and developed? What new scientific methods would be employed? What new scientifically testable and useful hypotheses and theories would be necessary and developed? How exactly would it positively change anything and exactly what would applying the ID label to biology and evolution and the theory of evolution do that isn’t already being done?

    You say that ID is all about origins (and you IDists don’t all agree on that) but you can’t make up your mind about which origins. It’s the origin of life, or the origin of the universe, or the origin of the Earth, or the origin of CSI, or the origin of IC, or the origin of morals, or the origin of worldviews, or the origin of particular religious beliefs, or the origin of evil, or the origin of philosophies, or the origin of atheism, or the origin of side loaded programming/information, or the origin of humans or other species, or the origin of ‘laws’, or the origin of geological features, or the origin of forces, or the origin of molecules, or the origin of cells, or the origin of intelligence, or whatever origin is convenient at the time, but it’s way out of line for people to question you about the alleged source of the origins, the so-called “intelligent designer”, and the source of the “intelligent designer”. And if ID is all about ultimate origins then why are you attacking the theory of evolution? Science has plenty of other hypotheses and theories about particular origins.

    Oh, and the (biological) theory of evolution isn’t “about” religion, or atheism, or Darwin, or Wallace, or Lewontin, or Alinsky, or Sagan, or Dawkins, or moral grounding, or absolute truths, or the origin of life, or the origin of the universe, or Hitler, or Stalin, or Pol Pot, or politics, or abortions, or evil, or genocide, or a long list of other things that you IDists erroneously combine it with in order to smear it and the people who accept it. You IDists are conveniently nitpicky when it comes to ID but not when it comes to the theory of evolution, except of course that you’re conveniently nitpicky when you’re attacking real or imagined gaps in the theory of evolution.

    And that’s what your arguments are really all about, gaps, whether real or imagined. You only go for the origins claim because you know that science hasn’t (yet) completely figured out the ultimate origins of life, the universe, and some other things. The more that science does figure out about evolution and the history and processes of nature the more you go for the origins argument. It’s your fall back safety net. As the gaps get smaller you IDists get more nitpicky about which gaps you think (and demand) have to be filled. Believe it or not, scientists want to fill all of the real gaps and are working hard to do so. Just because you’re impatient and want to force your religious beliefs into the gaps doesn’t mean that science is ignoring the real gaps or the realities of nature. Real science takes time and work, unlike “God-did-it”.

  77. Joe G: You don’t understand natural selection.

    Yes, I do. Rather well.

    It is just a result.

    Yes it’s the result of differential reproductive success, according to some fitness criterion, as in my demonstration. The result is of those variants that best match the fitness criterion.

    Also self-replication is a pipe-dream. the current science says that the RNA world did not exist,

    No, “the current science” does not say that. We do not yet know how our earliest ancestors got started, but there are some promising ideas generating testable hypotheses.

    and that there had to be a ribonucleoprotein world- IOW the stakes have been increased.

    Yes, there are a number of theories. We don’t know the answer.

    And I say you are misrepresenting the papaer.

    How?

  78. Joe G: As I have told you- Darwinism has nothing to say about evolution if it is silent on the OoL because if the ooL was designed then evolution was designed.

    Joe, this makes no sense. It’s like saying that chemistry has nothing to say about molecules if it is silent on Big Bang. Darwinian evolution is the mechanism postulated to account for the evolution of life from the simplest proto-life forms to now. It is not the mechanism postulated to account for the emergence of teh simplest proto-life forms. If you want to infer an ID from the fact that Darwinian evolution requires a starting population of self-replicators capable of self-replicating with differential reproductive success, fine. But then don’t knock Darwin for his huge insight in understanding how we got from proto-cell to now.

    That and there isn’t any evidence that differential reproduction can construct new, useful multi-protein configurations.

    Well, yes, there is.

  79. From the UD Glossary:

    CSI – Life shows evidence of complex, aperiodic, and specified information in its key functional macromolecules, and the only other example we know of such function-specifying complex information are artifacts designed by intelligent agents. A chance origin of life would exceed the universal probability bound (UPB) set by the scope of the universe; hence design is a factor in the origin and development of life. Contrary to a commonly encountered (and usually dismissive) opinion, this concept is neither original to Dr Dembski nor to the design theory movement. Its first recognized use was by noted Origin of Life researcher, Leslie Orgel, in 1973:

  80. Well, there you go, Joe. You have two references there, except that Dembski specifically addresses the probability of an evolutionary search reaching such a target. He is wrong about that.

  81. Yes it’s the result of differential reproductive success, according to some fitness criterion, as in my demonstration.

    Umm, in the real world, the “fitness critereon” is differential reproduction due to heritable random variation. That is it.

    Point 2- There isn’t any evidence for a “RNA World”, nor is there any evidence for self-replication.

    Point 3- re misrepresentation- you are starting with CSI by starting with replication.

  82. Elizabeth:
    Well, there you go, Joe.You have two references there, except that Dembski specifically addresses the probability of an evolutionary search reaching such a target.He is wrong about that.

    Liz- the reference says origin of life….

  83. As I have told you- Darwinism has nothing to say about evolution if it is silent on the OoL because if the ooL was designed then evolution was designed.

    Joe, this makes no sense.

    maybe not to you. But even dawkins said we would be looking at a totally different type of biology- meaning we would ahve to reconsider the stuff we think we know.

    And again it ain’t darwinian evolution if there are active targets being searched for

    And please support your claim:

    That and there isn’t any evidence that differential reproduction can construct new, useful multi-protein configurations.

    You said there was yet refused to provide it.

  84. It’s like saying that chemistry has nothing to say about molecules if it is silent on Big Bang.

    You have to keep in mind the various and sometimes conflicting agendas within the ID movement.

    There’s the YEC agenda, which is still going strong, although it will never be the public face of ID. It’s still acceptable at UD. We may have been banned for defending quantum theory, but no one will ever be banned from UD for defending biblical literalism. In principle this is the interventionist agenda.

    There’s the No Kin To Monkeys agenda, which has been held by many respectable people. A lite version of it lives in the Catholic church in the form of ensoulment. Noam Chomsky has even toyed with it in the form of the irreducible complexity of human language.

    There’s the OOL agenda that accepts evolution after the origin of life, but not for the origin itself. Front loading could be embedded in OOL.

    There’s the fine tuning agenda, which can be indistinguishable from mainstream science.

    I don’t know that any one person embraces all of these, but no one in the ID movement ever criticizes anyone who defends any of them.

  85. Elizabeth:
    Well, there you go, Joe.You have two references there, except that Dembski specifically addresses the probability of an evolutionary search reaching such a target.He is wrong about that.

    No, dembski was not referring to an evolutionary search- but a search based on blind and undirected processes.

  86. Yes, Joe, and I am not addressing Orgel’s argument, whatever it was, I am addressing Dembski’s.

    Also as far as I know, Orgel coined the term “specified complexity”. I’m not aware that he made Dembski’s argument about the UPB.

    But that’s irrelevant anyway. I am specifically demonstrating that Dembski’s argument that if we observe a specied pattern, whose probability under some null renders it unlikely to have occurred in the history of the universe, then we must infer non-Design.

    It’s a silly argument, and, clearly, wrong, as my example shows. Such a pattern indicates that something like natural selection is going on, not that something intelligent is going on. Now, if you want to make the argument that natural selection requires self-replicators, and they require an intelligent designer, then feel free.

    But that is not Dembski’s argument. If it were, why would he have bothered with No Free Lunch? Why would he even have bothered with any of that math at all, if he could have just said: hey, biological things self-replicate! They must have been designed!

  87. I don’t think people like Szostak think life originated by chance. I think they believe it is inevitable given the laws of chemistry.

  88. <span id="comment-8733-unapproved" class="tc_highlight">Joe G</span>: Umm, in the real world, the “fitness critereon” is differential reproduction due to heritable random variation. That is it.

    No. Heritable random variation may not lead to differential reproduction. When it does, i.e. where something in the environment means that some variants have a better chance of reproducing successfully than others, we call it “natural selection”, and the environmental criterion, when incorporated in a computer algorithm, is called a fitness function.

    Point 2- There isn’t any evidence for a “RNA World”, nor is there any evidence for self-replication.

    I don’t understand your second clause.

    Point 3- re misrepresentation- you are starting with CSI by starting with replication.

    Show me evidence (or argument) that a self-replicator must have a CSI value of chi>1.

  89. Umm, in the real world, the “fitness critereon” is differential reproduction due to heritable random variation. That is it.

    No. Heritable random variation may not lead to differential reproduction.

    Hello? The only way to determine fitness is when heritable random variation leads to differential reproduction.

    When it does, i.e. where something in the environment means that some variants have a better chance of reproducing successfully than others, we call it “natural selection”, and the environmental criterion, when incorporated in a computer algorithm, is called a fitness function.

    Whatever survives to reproduce, ie whatever is “good enough”. And usually a change in behaviour is enough to do the trick, and that is much easier than waiting for some mutation that may never come.

    Show me evidence (or argument) that a self-replicator must have a CSI value of chi>1.

    Show me evidence of a self-replicator. And then show me the evidence that said self-replicator can “evolve” into something more via darwinian processes.

  90. Now, if you want to make the argument that natural selection requires self-replicators, and they require an intelligent designer, then feel free.

    What self-replicators? We make the argument that the OoL requires a designer and therefor evolution is a design mechanism- ie organisms were designed to evolve.

    But that is not Dembski’s argument.

    It is in “No Free Lunch”.

    If it were, why would he have bothered with No Free Lunch?

    You didn’t read the book.

  91. petrushka:
    I don’t think people like Szostakthink life originated by chance. I think they believe it is inevitable given the laws of chemistry.

    Yes, that is what they believe. And if someone actually demonstrates such a thing then ID will be falsfied.

  92. Elizabeth,

    Show me evidence (or argument) that a self-replicator must have a CSI value of chi>1.

    At the same time, Joe could show me evidence that a non-living intelligent designer with a lower CSI value than the simplest possible self-replicator could possibly exist.

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