Intelligent Design

Beware of Question-Begging Computer Simulations

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Begging the question is a logical fallacy in which the proposition to be proved or defended is assumed implicitly or explicitly in one or more of the premises. It is a type of circular reasoning in which the truth of what one is trying to prove is assumed from the outset. One encounters a lot of question-begging arguments in defense of blind-watchmaker evolutionary theory.

Question-begging reasoning can appear in unexpected places…

Since I am a software engineer by vocation, and have developed quite a number of simulation programs, I take particular interest in computer programs that claim to simulate biological evolution. In every case, I have observed that these programs beg the question by incorporating up front (sometimes in a subtle manner) the very things they are meant to demonstrate.

Eric Anderson, who is a very sharp fellow and an excellent writer, has an essay on this topic that I highly recommend: http://www.evolutiondebate.info/BitByte.pdf He doesn’t cover all the deficiencies of these simulation programs (for example, they artificially shelter the replication engine from the effects of mutations), but he covers the circular-reasoning and question-begging deficiencies very effectively. I have read attempts to refute these arguments, and find the attempts about as convincing as the highly imaginative co-option story as a refutation of biological irreducible complexity.

In the process of writing simulation programs one learns very quickly that a single erroneous assumption about the system in question, or a single overlooked variable, can cause the simulation to go down in flames and leave a big smoking hole in the ground, or worse, produce results that appear reasonable but are totally invalid and misleading. Fortunately, in a hard science like aeronautical engineering we can deploy the system and see if it behaves in real life like the simulation says it will — and we are often surprised by the results, despite our best efforts and intentions!

There is no such reality check for computer programs that attempt to simulate biological evolution, and they are so vastly oversimplified and divorced from the biological reality they attempt to imitate that claims made on their behalf should be taken with a shovelful of salt.

As a footnote: I really enjoy Eric Anderson’s prose. Check out “The Little Dinosaur That Could” at
http://www.evolutiondebate.info/Diney%20the%20Amazing%20Dinosaur.htm
Eric tells the real story about how birds evolved from dinosaurs. It will put a smile on your face.

30 Replies to “Beware of Question-Begging Computer Simulations

  1. 1
    dougmoran says:

    Nice post, GilDodgen. I’ve been thinking about evolutionary simulators a lot lately. Has anyone ever designed one that makes sense, especially relative to origins? I don’t expect to see any realistic results published – none exist and none ever will.

  2. 2
    Artist in training says:

    My son designs software and is contantly talking about utilizing “emergent behavior” in pattern software. He showed me this link:
    http://www.cmcrossroads.com/br.....intro.html
    to explain it to me. Have your read the book “Emergence” by Steven Johnson? Imagine thinking that you can simulate evolution with a finite number of variables. Is life able to be boiled down into a computer program? Should it be?

  3. 3
    tb says:

    I have programmed John Conway’s game of Life once 😉 Software Patterns, as I understand them, are inteligently designed algorithms which can be used and reused for a lot of recuring problems in software engineering.

    “Imagine thinking that you can simulate evolution with a finite number of variables.”

    I cannot imagine that. And even if you could, who designed the algorithm? Software engineering does imply ID. Engineering an Evolution Simulation would be a contradiction in itself.

    I want to see a simulation that maybe takes as input a very simple text file say, “01”. Then you simulate with “EvoSim” 4.5 Billion years and a lot of randomness and environmental variation (say heat, cold, power alternation onto the simulation system, water damage… you may be creative here), and somehow, through variations and probability, the text file has evolved into a fully flawless operating system after the simulation. That would be somehow proof for simulating evolution. Yet it would beg the question, who created the text file 🙂

    Enjoyed Diney very much 🙂

    P.S. I don’t see Evolution to be ever simulated since software is desigend and always will be, just as I don’t see artificial conciousness to be brought forth by machines. (I could be wrong on the latter, but that is an entirly different topic).

  4. 4
    John Davison says:

    Life IS a computer program which seems to have run its course. The programmer was the Big Front Loader in the Sky, BFL for short. That is the whole point of the PEH. What remains unknown and doesn’t really matter anyway is how many BFLs there were, when they wrote the programs, where they wrote them or even how they wrote them. All that matters is THAT they wrote them. They no longer exist and don’t need to. Programs once written do not require any further participation by the programmer. The whole thing was endogenous with no role for the environment beyond that of possibly acting as a trigger and even that is debatable. I don’t know if one can set up a simulated program for evolution or development either for that matter. I think it would have to have some goal-seeking properties and most certainly would not be driven solely by chance. I still cannot imagine a creative computer program but I’m no expert. Maybe someone else can. I wouldn’t give you a nickel for Avida which seems to have died on the vine.

    Allelic mutations never had anything to do with creative evolution, although they may have played an indispensible role in extinction. Without extinction there could never have been evolution.

  5. 5
    valerie says:

    Eric Anderson’s essay is fraught with problems. The biggest is that he seems to misunderstand the concept of irreducible complexity as propounded by Michael Behe and William Dembski.

    To Anderson, any system which can be approached by a “cumulative pathway” is not irreducibly complex:
    “Avida was programmed so that a slight, successive cumulative pathway to the ultimate complex function existed. In other words, the researchers assumed that the ultimate complex feature was not irreducibly complex, and wrote their program in such a way as to guarantee that it would not be irreducibly complex, before they even ran the very first simulation.”

    Note that Avida’s “cumulative pathway” to the final EQU function was via precursors having *different* functions. So to Anderson, “irreducibly complex” means “cannot be achieved by ANY gradual cumulative pathway, whether or not the function changes along the way.”

    On the other hand, Behe and Dembski see an IC system as one which loses its *current* function when a part is removed. Dembski makes this clear in the following quote:
    “The problem is that for an irreducibly complex system, its basic function is attained only when all components from the irreducible core are in place simultaneously…Darwinian evolution cannot produce an irreducibly complex system exhibiting a given basic function by having natural selection act on and improve simpler precursors that already display that function.”

    Behe concurs and acknowledges that a “gradual route” to an IC system is possible via systems having functions that differ from that of the final system:
    “Demonstration that a system is irreducibly complex is not a proof that there is absolutely no gradual route to its production. Although an irreducibly complex system can’t be produced directly, one can’t definitively rule out the possibility of an indirect, circuitous route.”

    Thus Anderson is wrong in claiming that the EQU function is not irreducibly complex. It is Anderson’s own understanding of irreducible complexity that is faulty.

    What the Avida experiment provided was an actual example of how an IC system, as defined by Behe and Dembski, could be approached via an “indirect route”, to use Behe’s phrase. Thus “irreducibly complex” cannot be construed as a synonym for “unevolvable.”

    In fairness to Anderson, it should be noted that his version of irreducible complexity is the more interesting one, and does in fact correspond to “unevolvable by gradual means.” The challenge, of course, is to find a system which meets his more stringent definition of IC.

    Computer simulations are just that – simulations. Their results must be tested against reality which is the ultimate judge of the quality of the simulation. As far as Avida goes – wake me up when it can take the rules of chemistry and physics, a plausible environment of some sort where energy and raw materials are available, and through randomized means finds a way to produce from that a simulated self-replicating chemical machine able to evolve by random errors in the replication process. At that point we can take the simulated pathway and attempt to reproduce it in a laboratory, verifying a self-replicating chemical machine capable of further evolution is the result, to make sure the simulation was indeed a valid representation of reality. I won’t be holding my breath waiting for positive results. -ds

  6. 6
    Scott says:

    valerie, it remains established that the IC core of these machines having evolved via indirect Darwinian pathways is so rediculously improbable that it’s effectively impossible. Please take a look at this paper:

    http://www.designinference.com.....isited.pdf

  7. 7
    scordova says:

    Avida is an excellent example of a computer program which offers a tautology as “proof” of what it seeks to demonstrate. It assumes selective forces exist which can make IC systems, and then shows if such forces exist, an IC system will be made. It affixes 100% probability to the existence of such selective forces when 0% might be a closer approximation, and makes no serious consideration to the likelihood such forces existing in physical reality. Video games routinely model things that are physically impossible, Avida does little better. But unfortunately, Avida’s results are passed off as proof of evolution.

    I’m pleased to brag, Avida 1.6 has a bug fix that is attributable to me (an IDist, no less). 🙂 Evan Dorn gave me credit for alerting them to one of their bugs. You can look him up at ARN and his exchage with me. If I had my way, I’d have fixed the entire program, but then their would be nothing much left!

  8. 8
    DonaldM says:

    Amazingly, Lenski et.al. virtually admit to their question begging method in the article published in nature. In the Discussion section they write:

    Our experiments demonstrate the validity of the hypothesis,
    first articulated by Darwin1 and supported today by comparative
    and experimental evidence2–16, that complex features generally
    evolve by modifying existing structures and functions. Some readers
    might suggest that we ‘stacked the deck’ by studying the evolution of
    a complex feature that could be built on simpler functions that were
    also useful. However, that is precisely what evolutionary theory
    requires…

    What evolution “requires” to build a complex system is precisely what is being investigated. How do the researchers know what evolution “requires”? If they had biological examples of what evolution required to build a complex system, all they had to do was point to it. In my mind, this admission invalidates the conclusion of the whole study. It’s little more than a sophisticated version of what we all did in high school chemistry: draw you graph THEN plot your points!! (hey, I could NEVER get those experiments to work the way the lab book said they would!!)

  9. 9
    scordova says:

    Exactly Donald M, Lenski’s supporters offer his circular reasoning as “proof”! The self-imposed blindness is distressing to watch.

    Salvador

  10. 10

    Results need to be validated against real life to see flaws. I would second those insights.

    We have a term for random mutations in computer circles: hardware failure.

  11. 11
    DonaldM says:

    Another side-benefit of the Lenski et.al. Avida study is that it demonstrates conclusively that ID is testable and potentially fasifiable…two qualities ID is often said to lack.
    After all, what is Avida attempting to do but test Behe’s notion of irreducible complexity and attempt to falsify it. Oh, I know the article didn’t say that, but even the title seems to indicate that that is what they’re really doing.

    So, IC as a sub-set of ID is scientific, because thanks to Lenksi et.al., we now know that it is both testable and (potentially) falsifiable. Of course, in this study, for the reasons already given above, IC withstood the test. Nice try, though!

  12. 12
    physicist says:

    Dear scordova

    I don’t know that much about Avida. Would it be possible for you to summarise what in practice are the “selective forces which can make IC systems”? Is there an analogy of what such selective forces would look like in nature, and why you think they are unrealistic?

  13. 13
    avocationist says:

    Having read Valerie’s post a few times, I am now hopelessly confused. If a gradual route, that may include a few stopovers from parts performing different functions, can lead to a system such as the flagellum, then we have no need of the IC concept.

    “Demonstration that a system is irreducibly complex is not a proof that there is absolutely no gradual route to its production. Although an irreducibly complex system can’t be produced directly, one can’t definitively rule out the possibility of an indirect, circuitous route.”

  14. 14
    valerie says:

    avocationist wrote:
    “Having read Valerie’s post a few times, I am now hopelessly confused. If a gradual route, that may include a few stopovers from parts performing different functions, can lead to a system such as the flagellum, then we have no need of the IC concept.”

    avocationist,
    You’re right; the concept of irreducible complexity, as defined by Behe and refined by Dembski, does nothing for us. IC is only interesting if it implies that a system cannot evolve. The Avida study shows that an IC system CAN evolve via random mutation and selection in the “environment” created by the program. Pointing out that a system is IC thus says nothing about its evolvability in principle.

    The question becomes, can a particular system evolve in a particular environment from particular precursors? But this is the question we were asking all along, long before the concept of irreducible complexity was put forward.

    As I mentioned before, the accusations of circularity in Avida fall flat because Anderson uses a definition of IC which is different from those of Behe and Dembski. The latter version of IC is the one addressed by the Avida paper.

    Anderson’s definition of IC is much more interesting, because it rules out ANY gradual path to a system. The problem is that you have to consider all possible indirect paths to prove that the system is IC under Anderson’s definition. This amounts to a tautology, because then you are saying 1) that a system is IC under Anderson’s definition if it cannot evolve, and 2) that a system cannot evolve if it is IC under Anderson’s definition.

  15. 15
    valerie says:

    Scott wrote:
    “…it remains established that the IC core of these machines having evolved via indirect Darwinian pathways is so rediculously improbable that it’s effectively impossible. Please take a look at this paper (Dembski’s “Irreducible Complexity Revisited”).”

    Dembski’s paper simply represents the probability of evolution of an IC system as a multiplicative chain and argues that at least one of the factors must be really small, so that the overall probability is really small.

    The biggest problem with his argument is that it assumes that the exact IC system in question was the “target” of evolution. But evolution has no foresight and does not target specific long-term results. If evolution were rerun, it might take a different path altogether and miss the particular IC system being considered. As Dembski says in another paper, “…exceedingly improbable things happen all the time,” but a *particular* improbable event happens rarely.

  16. 16
    valerie says:

    DonaldM wrote:
    “What evolution “requires” to build a complex system is precisely what is being investigated. How do the researchers know what evolution “requires”? If they had biological examples of what evolution required to build a complex system, all they had to do was point to it. In my mind, this admission invalidates the conclusion of the whole study. It’s little more than a sophisticated version of what we all did in high school chemistry: draw you graph THEN plot your points!!”

    Donald,
    By Behe’s definition, an IC system cannot be approached gradually while maintaining the same function. If so, then obviously the only way that evolution coul approach is via *different* functions. That is all the Avida paper authors are saying that evolution “requires” to build an IC system. They did not “draw the graph first”, because they did not specify in advance the path that Avida would take in reaching the EQU function (in fact, they were suprised by some of the paths taken).

    “Another side-benefit of the Lenski et.al. Avida study is that it demonstrates conclusively that ID is testable and potentially fasifiable…two qualities ID is often said to lack.”

    Irreducible complexity as a barrier to evolution is falsifiable, but ID itself is not falsified simply because IC is. For example, Dembski’s ideas, while incorporating IC, do not depend on it. Dembski will presumably continue to argue for ID even if IC is discredited as a criterion for unevolvability.

    The charge of unfalsifiability applies to ID’s thesis that a designer, who might be God or some other supernatural entity, is responsible for certain features of nature.

  17. 17
    physicist says:

    Dear Valerie,

    Your exposition of certain aspects of the Avida paper and answers to people’s questions here are interesting and very clear.

    I’d certainly be interested in the ID responses to what you have said….

  18. 18
    valerie says:

    Thank you, physicist.

    I too would be interested in hearing some responses, particular from GilDodgen, scordova, and DonaldM, as to whether they still maintain that the Avida authors use “circular reasoning” and “question-begging” methods, and if so, on what basis?

    Valerie

  19. 19
    crandaddy says:

    Hi Valerie,

    I just want to offer some thoughts concerning what you said in comment #15. It’s true that modern evolutionary synthesis (MES) is comprised of processes that are understood to be causally complete without the input of intelligence. Therefore, it goes without saying that any biological structure or system which displays goal orientation can be adequately reduced to effectively unintelligent evolutionary processes if said processes did, in fact, produce the structure or system in question. Still, that goal orientation is an objectively perceivable phenomenon in biology and that it is at least anologous to intelligent design is a fact that cannot be ignored. For me to accept the unintelligent evolution of any biological phenomenon that contributes to an organism’s survival and reproductive fitness (be it real or hypothetical) as valid science, I want to know two things:

    1) That each step in its formation would not have caused so great a deficiency in the organism’s fitness as to cause natural selection to eliminate the transitional form.

    2) Given the first criterion is met, that the phenomenon in question would have had enough time to develope into its final form.

    For your final sentence in that comment, you wrote, “As Dembski says in another paper, ‘…exceedingly improbable things happen all the time,’ but a *particular* improbable event happens rarely.”

    Yes, that’s right. Natural processes are observed to produce highly improbable events all the time, but only intelligent agents are known to produce highly improbable events whereby means are incorporated to achieve ends. Living organisms are unique to all of nature because they alone are known to incorporate matter from their surrounding environment to grow and reproduce themselves. Moreover, they incorporate integrated mechanistic processes to achieve their tasks. As far as I know, MES is the only testable explanation for biological phenomena which does not require intelligent input.

    I know none of this applies to evolution simulation programs, but I thought it was worth saying, nonetheless.

  20. 20
    j says:

    scordova (comment #7): “[Avida] assumes selective forces exist which can make IC systems, and then shows if such forces exist, an IC system will be made. It affixes 100% probability to the existence of such selective forces when 0% might be a closer approximation, and makes no serious consideration to the likelihood such forces existing in physical reality.”

    physicist (comment #12): “I don’t know that much about Avida. Would it be possible for you to summarise what in practice are the “selective forces which can make IC systems”? Is there an analogy of what such selective forces would look like in nature, and why you think they are unrealistic?”

    In the “The Evolutionary Origin of Complex Features,” published in Nature in 2003 by Lenski et al, the selective forces that have 100% probability affixed are those for various simple binary arithmetic functions, which are ultimately used to build the “equals” (EQU) function, and for the EQU function itself. What’s more, the more complex the function, the greater the reward given to the digital organisms for it. There is no analogy for such selective forces in nature. Nature doesn’t care whether something is more or less functionally complex. And what happens when no step-by-step rewards are given for functional complexity? An article on Avida in Discover magazine last year (Feb. 2005) stated, “when the researchers took away rewards for simpler operations, the organisms never evolved an equals program.” By building rewards into the system — ie providing a fitness function — the programmers gave the system a purpose. Hence its creative power:

    “Both the regression and the search bias terms require the transmission function to have ‘knowledge’ about the fitness function. Under random search, the expected value of both these terms would be zero. Some knowledge of the fitness function must be incorporated in the transmission function for the expected value of these terms to be positive. It is this knowledge — whether incorporated explicitly or implicitly — that is the source of power in genetic algorithms.”
    http://www.cs.uml.edu/~giam/91.....g1994a.pdf

    “…evolution has no foresight and does not target specific long-term results” (valerie, comment #15). Avida does. That is why the Avida research is unrealistic. In undirected nature, all increases in functional complexity must, ultimately, be due to chance. Fat chance.

  21. 21
    valerie says:

    crandaddy wrote:
    “Still, that goal orientation is an objectively perceivable phenomenon in biology and that it is at least anologous to intelligent design is a fact that cannot be ignored.”

    Hi Crandaddy,
    I agree, with the proviso that the word “goal” means something very different if the design is apparent vs. real. There is no denying the amazing adaptations we see in nature, and I think all of us on this blog agree that these adaptations cry out for an explanation. We only differ on what the best explanation is.

    “For me to accept the unintelligent evolution of any biological phenomenon that contributes to an organism’s survival and reproductive fitness (be it real or hypothetical) as valid science, I want to know two things:

    1) That each step in its formation would not have caused so great a deficiency in the organism’s fitness as to cause natural selection to eliminate the transitional form.”

    Ideally we would be able to sketch out every evolutionary transition to that level of detail, but I think we will never realistically be able to reach that standard of truth in any historical science. Here’s an analogy: It’s like seeing a backpacker standing on one rim of a rugged, seemingly impassable canyon, then seeing him an hour later on the other rim without watching what he does in between. Some people insist that he climbed down one wall, crossed the raging torrent at the bottom, and climbed up the other wall. Others claim that he would have gotten stuck had he tried to do that, and therefore that he must have been helicoptered across. Hard-core skeptics might demand to see the precise route that he took, so that they could judge whether it was passable. Some might be content to know that others have made the traverse without necessarily following exactly the same route. Still others might be satisfied knowing that other similar canyons had been traversed by other backpackers.

    I suspect you see what I’m driving at: the ones demanding to see the exact route for every backpacker who claims to have crossed the canyon will never be completely satisfied, even if the traversal hypothesis is true.

    “2) Given the first criterion is met, that the phenomenon in question would have had enough time to develope into its final form.”

    I’m not sure what you mean by that. Could you elaborate?

    “For your final sentence in that comment, you wrote, “As Dembski says in another paper, ‘…exceedingly improbable things happen all the time,’ but a *particular* improbable event happens rarely.””

    Sorry if I was unclear. I was just trying to make the point that you would not expect to get exactly the same result if you “reran” RM + NS again. You most likely would not end up with the same IC structure that you got the first time around.

    This means that it is overconservative to calculate the probability of evolving the exact IC system in question, seeing that the probability is minuscule, and concluding that the system could not have evolved. This would be analogous to reading tonight’s winning lottery numbers, observing that the odds of that particular combination are tiny, and concluding that the drawing must have been rigged.

    Valerie

    Your analogy is wrong. It’s like a canyon that no one has ever been seen traversing before and no similar canyon had ever been crossed before. No one has EVER observed RM+NS traversing the canyon that creates novel cell types (like a bacteria crossing the canyon into a nucleated cell), novel tissue types (like a free living cell turning into muscle), organs (like all the tissue types that organize into a 4 valve heart), or body plans (like a reptile turning into a bird). -ds

  22. 22
    John Davison says:

    There are some single cells that contain within them in miniature form “muscles”, “spinal columns,” “esophagi” whole “nervous systems” complete with “circumesophageal connectives” such as occur in annelids and arthropods and other structures ordinarily associated with much higher forms of life. I pictured one such creature, the ciliate protozoan Diplodinium ecaudatum on page 50* of my Manifesto, available on the sidebar. On tbe next page is the extensive key to all its internal structure. Such animals provide living proof that all the necesary information for the production of advanced features were present very early in the evolutionary scenario. They also prove beyond any doubt that cells are not necessarily the units of structural complexity. Enormous morpholocical complexity can be expressed within the confines of a single reproductive unit, in this case a protozoan that inhabits in huge numbers the stomach of cattle.

    It is hard to believe isn’t it? That does not mean it is wrong.

    “Facts can be very stubborn things.”
    anonymous

    * I am sorry the figure is so poorly reproduced. The original is unbelieveably impressive.

  23. 23
    scordova says:

    ‘I too would be interested in hearing some responses, particular from GilDodgen, scordova, and DonaldM, as to whether they still maintain that the Avida authors use “circular reasoning” and “question-begging” methods, and if so, on what basis?

    Valerie

    Avida has no tie to physical reality. It makes no attempt to quantify how likely it is a selective force to create complexity is in the first place. The burden of proof for their claims that such selective forces exist in nature is on their shoulders, not ours. Absent of that, it is little more than wishful thinking.

    Salvador

  24. 24
    valerie says:

    Hi Salvador,

    My question was whether you (and GilDodgen, and DonaldM) still thought the Avida authors used “circular reasoning” and “question-begging” methods, given that Eric Anderson’s criticism was based on a misunderstanding of the definition of irreducible complexity.

    Valerie

  25. 25
    valerie says:

    DaveScot wrote:
    “Your analogy is wrong. It’s like a canyon that no one has ever been seen traversing before and no similar canyon had ever been crossed before.”

    Hi Dave,
    You’re right that he (crandaddy) should ask for evidence that a similar canyon had been crossed before. My point was simply that it was unrealistic to expect the precise route to be mapped out for every crossing that was ever made, which is what his original comment seemed to demand.

    And rephrasing my lottery example in the context of the canyon metaphor, it would be unfairly stringent to say “The probability of crossing by this *exact* path is minuscule; therefore the crossing couldn’t have happened at all.” You’d have to look at all feasible paths, not just the exact one that was purportedly taken.

    There’s been no route mapped for any canyon and no one has ever seen a person on one side subsequently appear on the other side. When the canyon was discovered there were people on both sides and no knows how they got there. As far as anyone knows for sure they were each born on their own side of the canyon. The nut is that they all have identical birthmarks which almost surely indicates they are related to each other.

    This analogy is getting silly. The bottom line remains that no one has ever observed the creation of a novel cell type, tissue type, organ, or body plan. All these things were already there when we emerged from our caves thousands of years ago and started looking around trying to figure out how we got here. -ds

  26. 26
    crandaddy says:

    In comment #19, I said, “2) Given the first criterion is met, that the phenomenon in question would have had enough time to develope into its final form.”

    By this statement, I mean to suggest that given enough time and enough opportunities, any particular extremely improbable event can occur by chance. As the probability of an event’s occurrence decreases, the amount of time and the number of opportunities required for it to occur both increase.

  27. 27
    j says:

    Valerie,

    In the “Bits, Bytes, and Biology,” Anderson wrote, “As used in this essay ‘irreducible complexity’ matches the irreducible complexity initially proposed by Behe and refined by Dembski, meaning that there is no cumulative pathway to such complexity. I have shown in my article ‘Irreducible Complexity Reduced: An Integrated Approach to the Complexity Space,’ (see http://www.evolutiondebate.info) that this is not a logical requirement of the concept of irreducible complexity, and I term Behe’s and Dembski’s approach “per se irreducible complexity.” Avida targets this per se irreducible complexity, and it is sufficient for our present purposes.”

    Now, besides the contextless quote from Behe that you presented above (“one can’t definitively rule out the possibility of an indirect, circuitous route”), Behe makes statements in Darwin’s Black Box (pp. 112-113) that imply that he does not consider such circuitous co-option routes for the evolution of IC to be a serious possibility for any of the real-life examples he proposes: “specialized parts of [a] complex systems [can’t be used] as specialized parts of a second irreducibly complex system unless the parts [are] first extensively modified. Analogous parts playing other roles in other systems cannot relieve the irreducible complexity of a new system; the focus simply shifts from ‘making’ the components to ‘modifying’ them. In either case, there is no new function unless an intelligent agent guides the setup.” (All the potential precursors that he knows of require extensive modification.)

    And from Dr. Dembski’s intro to the book Uncommon Dissent:

    “What about … Richard Lenski et al.’s May 8, 2003 paper in Nature titled “The Evolutionary Origin of Complex Features.” This paper describes a computer simulation and thus contains no actual biology. Go to the discussion section, and you’ll read: “Some readers might suggest that we ‘stacked the deck’ by studying the evolution of a complex feature that could be built on simpler functions that were also useful. However, that is precisely what evolutionary theory requires….” In other words, the computer programmers built into the simulation what they thought evolution needed to make it work. The validity of this study therefore depends on whether the simulation faithfully models biological reality.

    “Unfortunately, the simulation presupposes the very point at issue. It therefore begs the question and doesn’t prove a thing about real-life biological evolution. The Lenski simulation requires that complex systems exhibiting complex functions can always be built up from (or decomposed into) simpler systems exhibiting simpler
    functions. This is a much stronger assumption than merely allowing that complex systems may include functioning subsystems. Just because a complex system can include functioning subsystems doesn’t mean that it decomposes into a collection of subsystems each of which is presently functional or vestigial of past function and thus amenable to shaping by natural selection.

    “The simulation by Lenski et al. assumes that all functioning biological systems are evolutionary kludges of subsystems that presently have function or previously had function. But there’s no evidence that real-life irreducibly complex biochemical machines, for instance, can be decomposed in this way. If there were, the Lenski et al. computer simulation would be unnecessary. And without it, their demonstration is an exercise in irrelevance.”

    Anderson’s understanding of IC as used by Behe and Dembski seems OK, and the Avida research clearly seems to be begging the question.

  28. 28
    valerie says:

    j,

    Anderson’s “question-begging” accusation was that “Avida was programmed so that a slight, successive cumulative pathway to the ultimate complex function existed. In other words, the researchers assumed that the ultimate complex feature was not irreducibly complex…”

    Anderson is therefore claiming that the EQU function is not irreducibly complex. However, if you remove a part, the system no longer performs the EQU function. By Behe’s definition, that means the EQU function is irreducibly complex.

    Anderson says EQU is IC; Behe says it is not. If Anderson’s definition is correct, the argument for the unevolvability of IC systems becomes a tautology, as I pointed out above. Using Behe’s definition of IC, however, Anderson’s accusation of question-begging is clearly false.

    As DaveScot likes to say, “Takes yo pick.”

  29. 29
    j says:

    I takes the latter. Anderson’s understanding of the definition of “irreducible complexity” is faulty. He does confuse “irreducible complexity” with “unevolvable.” I somehow missed that “beer bet” hiding in the text. ( http://www.uncommondescent.com.....chives/825 ) Of course, the question-begging that Dr. Dembski points out still stands.

  30. 30
    valerie says:

    j wrote:
    “I somehow missed that “beer bet” hiding in the text.”

    Good one.

    Regarding Dembski’s criticism, while it’s true that Avida does not mimic real-life biology (and the authors do not deny that), it does show that an IC system can evolve *in some environments* under conditions of replication, variation, and selection.

    This is important, as some ID supporters seem to regard “irreducibly complex” as tantamount to “unevolvable in principle”. If IC systems are not unevolvable in principle, then you have to assess the probability of all indirect pathways in order to rule evolution out.

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