Things That IDers Don’t Understand, Part 2a – Evolution is not stranded on ‘islands of function’

Intelligent design proponents make a negative argument for design.  According to them, the complexity and diversity of life cannot be accounted for by unguided evolution (henceforth referred to simply as ‘evolution’) or any other mindless natural process.  If it can’t be accounted for by evolution, they say, then we must invoke design. (Design, after all, can explain anything.  That makes it easy to invoke, but hard to invoke persuasively.)

Because the ID argument is a negative one, it succeeds only if ID proponents can demonstrate that certain instances of biological complexity are beyond the reach of natural processes, including evolution.  The problem, as even IDers concede, is that the evidence for evolution is too strong to dismiss out of hand. Their strategy has therefore been to concede that evolution can effect small changes (‘microevolution’), but to deny that those small changes can accumulate to produce complex adaptations (‘macroevolution’).

What mysterious barrier do IDers think prevents microevolutionary change from accumulating until it becomes macroevolution?  It’s the deep blue sea, metaphorically speaking.  IDers contend that life occupies ‘islands of function’ separated by seas too broad to be bridged by evolution.

In this post (part 2a) I’ll explain the ‘islands of function’ metaphor and invite commenters to point out its strengths and weaknesses.  In part 2b I’ll explain why the ID interpretation of the metaphor is wrong, and why evolution is not stuck on ‘islands of function’.

Read on for an explanation of the metaphor.

The ‘islands of function’ metaphor

The ‘islands of function’ metaphor is a variation of another metaphor, the ‘fitness landscape’.  If you’re unfamiliar with the concept of fitness landscapes, I encourage you to do some Googling before reading on.

For those who are familiar with fitness landscapes, a brief review. Imagine a three-dimensional landscape, similar to a terrestrial landscape.  There are mountains and depressions, ridges and valleys, plains and plateaus.  An organism occupies a particular spot on the landscape.  Nearby spots represent organisms that are similar, but with slight changes.  As you move further away from the spot, in any direction, the organisms represented become less and less like the original organism.

Evolution can be visualized as a journey across such a landscape.  Individual organisms don’t move, but their offspring may occupy different nearby spots on the landscape.  So too for their offspring’s offspring, and so on.  Thus successive generations trace out a path (or paths) on the fitness landscape as changes accumulate.

Clearly, not all paths are possible.  Many mutations are deleterious, causing their possessors to die young or to otherwise fail to reproduce.  Paths going through such points on the landscape will end abruptly. Other mutations are beneficial, neutral, or only slightly deleterious.  Paths going through those points may continue.

Now let’s bring in the third dimension, height.  The height of a point on the landscape is an indication of the fitness of the corresponding organism, where fitness equates to the organism’s ability to survive and reproduce. Greater heights correspond to higher fitness, lower heights to reduced fitness. Offspring that move downhill from their parent(s) are less fit,  and therefore tend to leave fewer offspring of their own.  Offspring that move uphill from their parent(s) are more fit and tend to leave more offspring.  Over time, then, a population tends to shift in an uphill direction as the offspring become fitter.

Eventually the population may reach the tip of a peak and get stuck there.  From the peak, movement in any direction results in less fitness.  Thus the mutants will tend to die off and the population will remain at the tip of the peak.

So far we’ve been imagining a dry landscape.  Now suppose that it rains for 40 days and 40 nights. The rain fills up our landscape, forming a vast sea.  Only the mountain tops remain above the water as islands – the ‘islands of function’ that IDers are so fond of.

Our populations occupy the islands.  Sea level indicates the minimum fitness at which mutants remain viable. Small changes will create viable descendants at different spots on the island, though the population as a whole will gravitate toward the high spots. Larger changes will put the mutants underwater, where they will die out.

The idea, according to ID proponents, is that populations remain stranded on these islands of function.  Some amount of microevolutionary change is possible, but only if it leaves you high and dry on the same island.  Macroevolution is not possible, because that would require leaping from island to island, and evolution is incapable of such grand leaps.  You’ll end up in the water.

There is some truth to the ‘islands of function’ metaphor, but it also has some glaring shortcomings that ID proponents almost always overlook.  I will mention some of the strengths and  shortcomings in the comments, and I know that my fellow commenters will point out others.

I may add them to the OP as they come up in the comments.  If I do this, I will note that I am doing so and I’ll include a link to the place in the comments where each one is discussed.

Have at it!

338 thoughts on “Things That IDers Don’t Understand, Part 2a – Evolution is not stranded on ‘islands of function’

  1. Pactrick observes: You pay Mung too much of a compliment, Mike. He (or she) may dream of being a thug, but thus far I haven’t seen anything from him (or her) other than bluster that utterly fails at being intimidating.

    🙂

    Not to worry, Patrick. If it shows any new interesting behaviors (extremely unlikely), I’ll just sit back a profile.

    My last attempt at trying to teach a creationist anything was on an earlier thread here with Sal Cordova; and that just convinced me to stick with my policy of studying them without interacting with them.

    This kind of stuff has happened so often that I feel like I’m reliving that scene from the movie “Groundhog Day” where Bill Murray suddenly realizes that he is observing what he has been seeing repeatedly and begins reciting out loud to himself the unfolding of events just seconds before they occur.

    Neil said:I’m going to disagree with that. For one thing, I doubt that UD is well enough organized to be able to “send one of their thugs over here.” I’ll assume that Mung’s decision to participate here was voluntary.

    It was my weak attempt at sarcasm; fell flat. I agree completely with your assessment of UD. That kind of organization requires intelligent design.

    But thuggery is still one of the hallmarks of ID/creationism. From Duane Gish’s antics in Kalamazoo, to the Grablers in Texas, to Don McLeroy in Texas, to the Kansas State Board of Education, to Bill Buckingham at Dover, to the death threats against Judge Jones; stupid, but it’s what they do.

  2. I’ve got to say, though, that the more dimensions you add (and time is one of those dimensions), the “island” metaphor, or even the “Mt. Improbable” metaphor, becomes less and less tenable.  If there’s always a way out, then there’s no real isolation.

    I’m thinking now of a city with hundreds of air, rail, waterway, and highway access routes entering and leaving.  It’s not so much an “island of probability” but a self-sustaining attractor.

  3. Indeed it does.  But the response is not always predictable, and it’s only one more dimension among many that can cause landscape changes.  So, to say that a population is part of its own fitness landscape is correct, but it’s by no means a refutation of the OP — if anything, it’s a statement of support.

  4. There is also the “scaffolding” metaphor that portrays a self-standing, “irreducibly complex” structure as the result the removal of a previous set of events or structures that lead to the one currently being observed.

  5. My interest is to respond specifically to  gpuccio’s claim that major blocks of code — mainly protein domains — are isolated and unreachable. Based on this assumption, gpuccio calculates dFSCI on from the length of the coding string.

    The first major problem is that the paper linked from this thread indicates that raw function is hardly isolated or hard to reach. If you reduce the critical length of a string by 75 percent, you drastically reduce any number based on using that length as an exponent. 

    But there is a more profound problem for any putative designer, and that is that there appear to more dimensions being selected by nature than just raw functionality.  Perhaps synonyms aren’t perfect synonyms.

    I kud, fer eckampal, intrudusce speling errers in to mai post without changing it;s meaning, but there are other factors at work, tending to standardize spelling. Spelling is conserved, even though it isn’t strictly necessary to preserve function.

    We know this because the invention of dictionaries and the standardization of spelling happened in historical times, and we know that spelling varied widely before dictionaries.

    the task of gpuccio’s intelligent selector  is more difficult than just refining a protein function. He must refine the function within the context of a living system without using trial and error.

  6. Mung,

    You mean there is a percentage of posters here at TSZ open to intelligent design?

    I get the impression that there is a audience ready and waiting, ready to patiently listen to anything anyone might say in support of ID then ask searching questions in reply.  

    What more could you ask for? They are open to your ideas and if you can support them or not. What else matters?

  7. The problem with “functionality” is no different than the problems connected with any trait or characteristic of a complex, evolving system.  It is stated after the fact; and it is simply another example of the Lottery Winner Fallacy.

    If some other characteristic behavior or “function” emerged and found a niche in the environment in which the system is immersed, one could argue that such “functionality” cannot be explained by previous steps in an evolutionary chain.

    The organization, behavior, “functional interrelationships,” and coordinated activities take place at finite temperatures. They are permitted, not required, by the current state of the system.  Complex systems behave as they do in a given environment because of what they are and how they interact within themselves and with their surroundings.

    Singling out certain interrelationships or dynamic behaviors and referring to them as “functions” is simply a way of describing the characteristics of the system and its environment.  Function does not imply purpose, which must therefore be accounted for by invoking design.

    As we see repeatedly with ID/creationist definitions of “function,” they are never consistent, and they are bent in arbitrary ways to fit the argument at hand.  Just about any interrelationship and dynamic behavior can be described in terms of “function.”  Gravitation functions to hold solar systems together in a series of elliptical orbits.  Electrical charge has the function of making electrons and protons stick together to form hydrogen.

    Flowing water functions to carve out river valleys and canyons.  The function of the neck is to hold up the head and keep the nose pointed downward so rain can’t drown the individual. Wind functions to keep bodies cooler. How can wind do that if it were not designed to do that?

    These attempts at anthropomorphizing the dynamic characteristics of complex systems go back to pre-scientific superstition in which actions, motion, and other dynamic behaviors were attributed to “life forces,” “inner yearnings,” and purpose.  Earth, water, air, fire, – each seeking its place in the hierarchy of spherical shells surrounding the Earth at the center – are imbued with purposes to be with their kinds. The  function of heavy things is to be at and to hold the center.  The function of fire is to rise toward the outer celestial sphere and illuminate all within.  The universe is in harmony and balance when each element is allowed to fulfill its function according to its nature.

    ID/creationism is a truly medieval world view, gussied up with modern sounding, pseudo-scientific words in order to make it look respectable.

     

  8. ‘Tis true. Many posters here took up a UD login and attempted to defend evolutionary theory to a hostile audience. “Your minds are closed” is not an argument I recall any of them using. They were/are confident enough to make the attempt to reason.

    People on the ‘materialism side’ are naturally skeptical of the capacities of the agents you (Mung) think the evidence points towards. You feel they are not skeptical enough of the ability of the main evolutionary forces – mutation, recombination, selection and drift – to explain Life in its entirety. I guess the question would be: how long does one hold off provisional assent? Evolution has been extensively characterised, and two major discoveries since Darwin’s day – genetics and molecular biology – plus the entire mathematical theory, have provided support in spades. I’m perfectly prepared to be wrong, but for now, I find the evidence for ‘naturalistic’ evolution’s ‘micro-‘ capacity being the source of all higher-order change to be compelling. I am genuinely interested in why other people don’t.

  9. says mung:

    You mean there is a percentage of posters here at TSZ open to intelligent design?

    Yes, there are. And I’m one of them, not least because I am an intelligent designer myself—I design and create stories, art, software, boardgames, user interfaces, and so on. While I freely acknowledge that I haven’t found any existing ID argumentation to be particularly persuasive, I also do not reject such argumentation a priori. Rather, I reject this argumentation when I recognize gaping flaws in it.

    Case in point: Behe’s argument that ‘irreducible complexity’ is unevolvable, hence must necessarily be the work of a Designer. Behe presented this argument in his book Darwin’s Black Box, and it runs somewhat thus: An ‘irreducibly complex’ system is one in which each and every one of its component parts must be present and intact in order for the system to perform its function; therefore, there is no ‘direct Darwinian pathway’ by which such a system can be created; therefore, evolution cannot produce an ‘irreducibly complex’ system; therefore, all ‘irreducibly complex’ systems which exist must necessarily be the product of Design. Well, it’s true that by Behe’s definition of ‘irreducibly complex’, an irreducibly-complex-system-minus-one-part must necessarily be nonfunctional, but that just means that for any irreducibly complex system which may have been produced by a Darwinian process of stepwise modifications, the final step cannot have been ‘add a new piece’.
    The problem for Behe is, a Darwinian process of stepwise modifications has three classes of modifications to choose from. ‘Add a new piece’ is one of those three classes of modifications which are available to a Darwinian process of stepwise modifications; the other two classes are ‘remove an existing piece’ and ‘alter an existing piece’. The immediate precursor of an IC system whose final stepwise modification is ‘add a new piece’ would be the-IC-system-minus-a-part, which is nonfunctional by definition… but for any Darwinian process of stepwise modification whose final step is ‘remove an existing piece’, the IC system’s immediate precursor would be the-iC-system-plus-one-part. For some reason, Behe neglected to demonstrate that an IC system ceases to function when you add a part to it.
    Likewise, for any Darwinian process of stepwise modification whose final step is ‘alter an existing part’, the IC system’s immediate precursor would be the-IC-system-with-one-modified-part. And again, Behe neglected to demonstrate that an IC system ceases to function when one of its component parts is modified.
    So Behe’s argument that ‘irreducible complexity’ is unevolvable, is an argument that crashes and burns.

    Case in point: Dembski’s Explanatory Filter, which purports to detect Design by ruling out all possible non-Design explanations for the Design-candidate thingie of interest… but you can’t rule out an explanation you aren’t aware of. So let’s say there is a specific Design-candidate D, and Design-candidate D is, in fact, not a product of Design. Let’s further say that ID theorist John Doe is aware of Design-candidate D’s non-Design explanation, and ID theorist Richard Roe is not aware of Design-candidate D’s non-Design explanation. When ID theorist Roe applies Dembski’s Filter to Design-candidate D, Roe will not be able to rule out Design-candidate D’s non-Design explanation, and in consequence, Roe will conclude that Design-candidate D is, in fact, the product of Design.
    Meanwhile, ID theorist Doe, who is aware of Design-candidate D’s non-Design explanation, will (as the Explanatory Filter directs) start ruling out possible non-Design explanations for Design-candidate D. Doe will discover that he cannot rule out the non-Design explanation which is Design-candidate D’s non-design explanation, and as a result, Doe will conclude that Design-candidate D is, in fact, not the product of Design.
    Both Doe and Roe are using the same investigatory protocol, that being Dembski’s Explanatory Filter. Both Doe and Roe are using it on the same entity of interest, that being Design-candidate D. But! Doe and Roe differ on the level of background knowledge they bring to the task (Doe is aware of the relevant non-Design explanation, Roe is not), and it is that difference in background knowledge—a quality of, not the Design-candidate of interest, but, rather, the ID theorists who are investigating that Design-candidate—which determines which ID theorist concluded that Design-candidate D was Designed, and which ID theorist concluded that Design-candidate D was not Designed.
    In short: Dembski’s Explanatory Filter is a gauge of the investigator’s level of ignorance. If the investigator does not know of the actual non-Design explanation by which a given Design-candidate was generated, that investigator will necessarily arrive at a false conclusion of Design.
    So Dembski’s Explanatory Filter cannot do the job Dembski wants it to do, because the results of using that Filter are wholly and entirely dependent on its user’s level of knowledge, not on any quality of the entity to which its user is attempting to apply it.

    Case in point: gpuccio’s protocol for detecting CSI. As it happens, I haven’t yet seen any ID-proponent cough up a definition of CSI which is sufficiently clear and unambiguous to be of any practical use by someone who actually does want to detect CSI; Dembski, for instance, is inconsistent in his treatment of CSI, shuffling between a number of incompatible definitions of CSI and not providing any usable guidance for determining which CSI-definition should be applies under what conditions. As a result, I just don’t believe that gpuccio actually does have the CSI-detecting protocol he claims to have.
    Well, fine; maybe I’m just ignorant about the truth of CSI. Maybe there is a definition of CSI which is sufficiently clear and unambiguous to be of any practical use by someone who actually does want to detect CSI, and I just don’t know about that clear, unambiguous, pragmatically-useful definition of CSI. If that’s the case. gpuccio might well have the honest-to-Dembski CSI-detecting protocol he claims to have. But if gpuccio actually does have such a protocol, why is he so reluctant to use the silly thing? For that matter, why hasn’t gpuccio written up his CSI-detecting protocol with a sufficient level of clarity and specificity that anybody, ID-proponent or no, can actually use gpuccio’s CSI-detecting protocol and see for themselves that gpuccio’s CSI-detecting protocol actually does live up to its press releases?
    Right now, there is exactly 1 (one) reason to believe that gpuccio actually does possess the honest-to-Dembski CSI-detecting protocol that gpuccio claims to possess, and that single reason is “gpuccio claims to possess a genuine CSI-detecting protocol”. Unfortunately, gpuccio’s behavior provides ample reason to believe that he does not, in fact, possess the genuine CSI-detecting protocol he claims to possess. Indeed, gpuccio’s behavior provides more than ample reason to believe that gpuccio ain’t got nothing and is just bullshitting everybody when he claims he does have something.
    Nullius in verba: Not just a pretty slogan. Perhaps gpuccio will learn its truth some day.

  10. Case in point: Dembski’s Explanatory Filter, which purports to detect Design by ruling out all possible non-Design explanations for the Design-candidate thingie of interest… but you can’t rule out an explanation you aren’t aware of.

    Dembski’s argument had a theorem, his Law of Conservation of Complex Specified Information (LCCSI) which was supposed to rule out non-Design explanations. It was supposed to show that any deterministic natural process could not get the system more specified than it started out to be.

    Even if one had mechanisms that you had not thought of, this was supposed to rule them out as sources of the Specified Information. 

    The LCCSI has been eliminated from the argument twice over:

    1. Elsberry and Shallit in 2003 pointed out that Dembski’s proof of his Law was flawed: it stated a precondition and then violated it.
    2. I argued (here) that even if his LCCSI was a correct theorem, it could not do the job. It defines the specification of the information differently before and after the transformation. To show that evolution cannot increase specified information one needs to use the same definition of the specification before and after evolution acts. Dembski’s argument does not do that. When you require that the specification remain the same, you can immediately find many processes that violate the LCCSI, so a version for a fixed definition of the specification cannot be true.

    The Design Inference argument relied on the LCCSI. Without it, it simply is a Design-or-Natural-Selection Inference, which isn’t very interesting. It is just an argument that the adaptations in life achieve fitnesses that are far too great to have arisen by pure mutation without natural selection involved. And I think we already knew that.

     

  11. I keep thinking about Behe’sEdge of Evolution. He argues that an adaptation that requires three or more coordinated mutations is ruled out on grounds of improbability. But the number of mutations is irrelevant if each contributes. For example, skin color involves variations in approximately nine separate genes. That’s at least nine mutations within human history.

    Of course Behe would argue that each is separately selected, so it’s not IC.

    The problem is that without knowing the exact history of a system it is impossible to say whether the contributing mutations were separately beneficial or neutral. We do know that in Lenski’s experiment there was a necessary neutral precursor. The only ID response has been to downplay the scope of the adaptation, completely ignoring the process. I find this to be intellectually dishonest and morally repugnant. The kindest description is moving the goalposts.

  12. Suppose some accident of history, some bottleneck in the human population, had resulted in two varieties of humans — those with all nine pigment varients and those wih all nine alternates. Would that look IC?

    That’s how Behe treats the flagellum, despite the fact that nearly all the genes contributing to the flagellum exist in various combinations in non-motile organisms.

  13. The problems with intelligent design theories coming out of the ID/creationist movement is that they all rely on profound ignorance of even the basics of physics, chemistry, and biology.

    If someone wants to postulate design in nature, shouldn’t one at least get the science right first?  Design inferences and “design filters” based on misconceptions about how matter and energy behave in the universe are not going to tell anyone anything about a “designer.”

    The only thing that anyone could conclude from such “calculations” is that one’s own ideas about how nature works can’t explain what one sees and, therefore, it must be explained by design because your own misconceptions didn’t get through the filter of your own making.  It doesn’t tell you that your ideas about science are wrong from the beginning.

    But now you have simply reinforced your belief that science – that is, “science” as you know it – can’t explain what you see, so you double down and keep tinkering with your “math” and with your “filter.”  You become locked in an infinite loop of self-fulfilling expectations simply because you refuse to ask yourself, “Do I really understand what the science says here?  Maybe I should go back and check my understanding; I mean, maybe I should take a few years off from my obsessions and REALLY CHECK.”

    ID/creationist obsessions with sectarian, anthropomorphized designers keep them searching in all the wrong places as they continue to reject REAL scientific evidence that tells them they are wrong.  And the ego trip of being a “guru” of ID/creationism is not going to allow any of the leaders of this movement to admit they got the science wrong all the way back to high school, or that their understandings were, at best, extremely superficial.   Obviously a PhD is not enough; no matter how much they like to wave them around.

  14. Late to the party and welcome to mung.

    @ Neil

    I think we can cut mung a little slack as a new commenter and also well-known to many as having a rather abrasive delivery. I would think moving off-topic comments would be sufficient to keep the thread tidy. I would be unhappy to see any commenter put into moderation without sore provocation and abusive comments can always be dealt with retrospectively.

  15. You become locked in an infinite loop of self-fulfilling expectations simply because you refuse to ask yourself, “Do I really understand what the science says here? Maybe I should go back and check my understanding; I mean, maybe I should take a few years off from my obsessions and REALLY CHECK.”

    I remain convinced that you’re looking at it backwards. These misconceptions don’t result from improper calculations based on a misunderstanding of science. The misconceptions are givens. They ALWAYS come first. Then, when ordinary science implies something very different, of course that science must be reconstructed to fit. What the science DOES say here is irrelevant; what matters is what the science MUST say, whatever it takes.

    If real scientific evidence tells them they are wrong, then it cannot be evidence.  Evidence is what supports TRUTH, which is predetermined and not negotiable.

    Really, all this scientistical pretense is nothing more than an effort to dress up a fixed religious doctrine in the hopes of fooling the public and the courts. You keep trying to show that their conclusions do not follow from their evidence, they keep trying to show that their “evidence” follows from their conclusions. So long as their conclusions are their starting points, and are not subject to change, scientific evidence is really quite meaningless.   

     

  16. A pitfall of the ‘islands of function’ and fitness landscape metaphors is that they encourage people to misapply their knowledge of physical landscapes.

    I’ve already mentioned how IDers’ intuition fails them in dealing with the high dimensionality of actual fitness landscapes versus the three-dimensionality of physical landscapes.

    Another problem is that physical landscapes are constrained and shaped by the laws of physics and the nature of rock, soil, water and air. Fitness landscapes are a mathematical abstraction and are not so constrained. Structures that are not possible in the physical world are quite viable in the mathematical space of fitness landscapes. A wispy tendril connecting two islands might be unusual and evanescent in the physical world, yet common and robust in the world of fitness landscapes. Solid masses may be common in the physical world, whereas spindly latticeworks might be the norm in the space of fitness landscapes.

    The comments I’ve seen from IDers suggest that most of them haven’t even considered this problem, the dimensionality problem, or the problem of dynamic landscapes.

  17. Flint says: I remain convinced that you’re looking at it backwards. These misconceptions don’t result from improper calculations based on a misunderstanding of science. The misconceptions are givens. They ALWAYS come first. Then, when ordinary science implies something very different, of course that science must be reconstructed to fit. What the science DOES say here is irrelevant; what matters is what the science MUST say, whatever it takes.

    Well, yes; that is what I think I have been saying all along. Do I have it backwards? Not in the least.

    Sectarian dogma ALWAYS comes first; and all else is bent and broken to fit. Their “understanding” of science is always of a “science” that comports with sectarian beliefs.

    This is something I have observed on many occasions – taking place in real time – as I have watch these sectarians wrestle science concepts into agreement with their beliefs.

    One can even find written advice – given out by the leaders of this kind of sectarianism – on how to go about the process of shaping and reinforcing one’s doubts about real science. They word-game every qualifier in a scientific textbook into an excuse for complete rejection of a scientific idea. It’s a very deliberate and methodical process.

    But once you are there in the “sectarian zone,” your misconceptions are now a given. They are now your “truths” about science; and they can’t explain nature. So your ID filter now confirms what you already “know” about “science.” It is the loop-closer. It’s all closed-up and airtight; and you never have to question it after that.

    That is the very essence of sectarian thinking. It is complete anti-science masquerading as science for the purposes of enhancing sectarian dogma.

  18. I think we can cut mung a little slack as a new commenter …

    I agree, and have been doing that. He is not in moderation, and thus far I have not moved or removed any of his posts, though I did move a couple of reactions to his posts.

    It rather looks as if he had just one short foray, and might not come back.

  19. A pitfall of the ‘islands of function’ and fitness landscape metaphors is that they encourage people to misapply their knowledge of physical landscapes.

    And landscapes tend to be thought of as fixed, whereas the environment is anything but with intra and inter species competition, fluctuations in weather and climate, catastrophes such as eruptions or meteors etc. etc.

  20. I think communication is failing at a much simpler level. I see no less than three kinds of fitness that should be discussed.

    The first two are determined by chemistry. Sequences can code for specific proteins or catalytic function, or they can code for some regulatory function.

    The third category assumes one or both of the first two, and it would be contextual  function — adaptive function within the living organism and its environment.

    I think that ID proponents cannot get to the third category because they believe that the first two are so rare as to preclude  occurrence by accident.  It would appear that this is a basic error of fact. The 80 or 120 or 500 bit combination lock with a single correct key is simply a myth.

  21. keiths,

    It’s probably unwise to try to speak for ID proponents, considering how little you know about what they actually believe

    But you’re in a much better position to speak for them than I am. That’s your position?

    Intelligent design proponents make a negative argument for design.

    I spent some time looking on the internet for what you could possibly mean by a “negative argument.” I didn’t have much luck.

    One site said the following:

    “A Positive Argument is an argument for your particular position. A Negative Argument is an argument against an opposing position.”

    http://lukenixblog.blogspot.com/2009/05/positive-arguments-vs-negative.html

    Do you agree with that?

    So in what possible way should the word “for” in your first line be taken to mean “against“?

    Another site has an entire article refuting your claim. Apparently it’s a common mistake people make when making a negative argument against ID. At least they don’t confuse “for” with “against.”

    http://www.ideacenter.org/contentmgr/showdetails.php/id/1161

    Is ID just a negative argument against evolution?

    Unfortunately it is a common misperception about intelligent design theory that it is merely a negative argument against evolution. This negative argument usually mischaracterizes intelligent design as follows:

    “Intelligent design theorists argue that evolution cannot produce irreducibly complex structures, therefore they must have been designed (by God).”

    Sound familiar?

  22. Sound familiar?

    Very familiar. Perhaps you could be the first ID advocate to break from this formula.

    You could, perhaps, provide positive evidence for the existence of a designer, some observations of the designer at work, some attributes of the designer, such as capabilities, motives methods of operation.

    These are all things considered by archaeologists when cataloging objects designed by humans.

  23. But you’re in a much better position to speak for them than I am.

    What is ID according to Mung then?
    When did the designer act last?
    How often does the designer act?
    How do you know?
    etcetc

    Or insert questions that illustrate your position re: ID and then answer them.

    I’m intrigued!

    Please, do speak for Mung! 

  24. keiths, among others, spent weeks and weeks debating gpuccio, who put forth a positive argument for design.

    It did not take the form:

    “If it can’t be accounted for by evolution, they say, then we must invoke design.”

    1. It is not the case that the argument for intelligent design takes the form, evolution can’t do it therefore ID. That would be a non sequitur.

    2. It is not the case that there is no positive argument for Intelligent Design.

    It follows that the OP misrepresents ID.

    Because his premises are false, his argument is not sound.

    If keiths wants to set out an argument about what ID proponents actually believe and he truly wants to encourage debate he should avoid the poisoning the well tactics.

    My guess is that he never expected anyone to question his first paragraph.

     

  25. Two concepts are frequently confused by people on both sides: the fitness landscape and the ‘map of function’.

    Each point in a space of strings of a particular length will have a number of parameters, which relate to phenotype. Fitness is one, and ‘function’ another. The two do not necessarily correlate.

    Both landscapes are effectively constructed from the possible genotypes at a locus. If you’re mapping fitness, each genotype is simplistically assumed to have a stable coefficient of selection that represents its ‘intrinsic’ rate of increase against a common genetic background – the mean fitness of carriers of that allele, measured in offspring. Higher coefficients give more elevated points than lower, while closely related genotypes are closer together than more distant cousins.

    This is not a map of function. [and it’s not even a practical tool for fitness in nature]. ‘Function’ is a rather slippery notion, in biology – unless one simply declares it to be ‘that which maximises reproductive output’, ie fitness. But there are so many ways to do that. A protein may catalyse numerous biochemical reactions to some degree. Each point may therefore attract a number of parameters additional to fitness, equating to the degree to which, translated into protein, the genotype is able to achieve sundry biochemical results, regardless of the benefit or detriment of doing so. We could (in our notional exercise) colour these in, and discover what relationship fitness bore to one or other of these reactions, and the extent to which the different colour-coded reactions deepened or faded at fitness peaks. 

    So a locus in a species could at the extreme generate a map that, in fitness terms, has but a single peak – an island, of sorts – and yet is not composed of ‘islands of function’ at all, but actually contains masses of ‘true’ biochemical function. It’s just that none of it is any use!

    A single peak is highly unlikely to be found, either by ‘Darwinian evolution’ or by clever Designers. But there is no reason to suppose that any species has such a locus. We would be saying that there is only one biochemical process that gives an advantage at all, and only one way to achieve that process. If protein spaces typically contain multiple peaks, randomness can more reasonably get us a toe-hold that selection may refine. So what we need is a means of roughly assessing the useful function in a space – that which has the potential to turn biochemical activity into reproductive capital. And this is where the many mass-throughput analyses come in. And for this, I return, with no apology, to this paper: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0015364 . It’s not the only paper on the topic, but I find this one particularly interesting and accessible. 

    The authors wanted proteins that would fold, so they generated a polar-nonpolar repeat pattern (among many they could have tried) that restricted the space of all possible 100-acid peptides massively. I mean massively. So massively that … well, a lot. But to put that into gee-whiz context, I estimate that the total number of possible proteins they were left with would occupy a sphere over 5 AU (5x the earth-sun distance) across. They generated 1.6 million random peptides from that space. This is equivalent to using a discarded E coli cell wall as a scoop and filling it about a tenth full with random proteins from the 5 AU sphere. And in this tiny scoop they found viable replacements for 4 out of 27 native E coli proteins tried. How these proteins fit on a fitness map is another matter. But it’s a fairly safe bet that an NS competition would improve their function, however low they might be in the landscape vs the ‘native’ peptide. And that those 1.6 million peptides contain functional analogues for a damned sight more natural proteins than just those 4 E coli genes. These specific proteins may (for all anyone knows) be inaccessible to ‘Darwinian evolution’ from all historic genomes. But, as a sampling exercise, they certainly point to a protein space rich in function, and not islanded to any degree that need trouble typical population sizes.

  26. keiths to Mung:

    It’s probably unwise to try to speak for ID proponents, considering how little you know about what they actually believe: (Dembski, Upright BiPed, gpuccio).

    Mung:

    But you’re in a much better position to speak for them than I am. That’s your position?

    Yes, because I read and understand what they say, whereas you apparently don’t bother.

    I spent some time looking on the internet for what you could possibly mean by a “negative argument.” I didn’t have much luck.

    It’s spelled out in the first three sentences of my OP, and reiterated in the fifth. Didn’t you make it that far?

    Another site has an entire article refuting your claim.

    Except that it doesn’t refute my claim.

    Look at gpuccio’s dFSCI argument, for example. Suppose we have two functional sequences, A and B, that surpass the dFSI threshold and are both designed. We present them to gpuccio without telling him anything about their origin.

    They’re functional and they exceed the dFSI threshold, so they satisfy the first two requirements for dFSCI. Now suppose that gpuccio is aware of an evolutionary mechanism that can produce A. He is aware of no such mechanism in the case of B.

    He will attribute dFSCI to B, but not to A, which means he will infer design for B, but not for A (A is a false negative, which is fine). What made the difference? Gpuccio doesn’t think B could have evolved, so he infers design. Gpuccio thinks A could have evolved, so he doesn’t infer design.

    It’s a perfect example of a negative argument.

  27. I think communication is failing at a much simpler level. I see no less than three kinds of fitness that should be discussed.

    Trying to understand how the ID maps the concept of recognizably intelligently patterns maps to actual DNA is difficult without a suitable example.

    I assume that the 500 bit threshold specifically referred to 500 sequential nucleobases, but perhaps “bit” refers to each individual pair. Then again, functionality need not come from contiguously coded proteins. Given that ID posits there is little, if any, “junk”, I’m not sure how dFSCI is recognizable from naturally occurring coded proteins.

    Given that the flagellum motor is the prime example of IC, I would like to see an ID analysis of the “bits” involved.

  28. keiths,

    So far we’ve been imagining a dry landscape.  Now suppose that it rains for 40 days and 40 nights. The rain fills up our landscape, forming a vast sea.  Only the mountain tops remain above the water as islands – the ‘islands of function’ that IDers are so fond of.

    Why don’t we just imagine in that the water dries up?

    Do you plan to cite any actual ID sources?

    For example, KF argues that GA’s start on an island of function.

    Let me explain what’s wrong with your metaphor, other than the fact that you’re mixing two different metaphors.

    You have the populations getting to where they are on the landscape, except you’re supposed to be arguing against a position which says they can’t get there. So you’re assuming they can and not addressing the argument that they can’t.

    Then you poof into existence some water and create some islands. But the “mountains” wouldn’t even exist in the first place, so adding water isn’t what creates the islands.

    It seems to me that the argument you’re trying to present as that as the argument of ID is not that organisms can’t get from point A to point B on the landscape, it’s that they can’t get to point A.

    Not that I grant that this is even an ID argument.

    The argument, as I understand what it is you’re trying to argue against, and I could be completely off the wall here since I really have no idea what your sources are, would be not whether things can get from point A to point B, but rather the very nature of the landscape itself.

  29. To expand just briefly on my prior post. Take protein folding.

    An amino acid sequence consisting of a single amino acid probably isn’t going to fold and probably has no function. We can quibble about it if you want to. Given 20 amino acids, that right there is 20 “points” of non-function. It’s not that proteins can’t get there, it’s that there is no there there to get to.

    It’s not a point on a landscape, it’s no landscape.

     

     

  30. I’m not entirely sure what you are saying here. A fitness landscape does not require that the genotypes be translated into protein. Fitness relates to the ability of a genotype to get its bearers replicated. Granted that modern organisms make protein, it is not the essential characteristic of a fitness landscape: replication is. I know it is a popular ID view that replication sans ribosomally-specified protein is impossible, but what the genotype turns into is secondary to the basic fact that, if it is replicated, there must be a landscape of some kind constructible from relatedness (lateral distance) and fitness (height). It might be flat or might wobble like a waterbed in a brothel, but it ‘exists’ (in the way other mathematical representations such as graphs ‘exist’).

    KF is also wrong about GAs, if that’s what he says.

  31. I’m looking for some knowledge of science, particularly some knowledge of the chemistry and physics of complex molecular systems such as amino acids.  Even some knowledge about simpler organic structures would be nice. But so far there is nothing.

    Arguing with metaphors and analogies drawn from models that have no relationship whatsoever to the behaviors of atoms and molecules, and without knowing the science, is not going to get anywhere.  It will just be word-gaming and running in circles.

    Atoms and molecules interact.  Scaling up the energies of interaction at the molecular level to analogs at kilogram and meter sizes produces energies on the order of 1010 megatons of TNT.  Charge-to-mass ratios at the molecular level are not inconsequential.  You don’t model them with letters, marbles, or bits that don’t interact among themselves.

  32. Mung,

    It sounds like you may be under the impression that the fitness landscape is something that evolution builds, rather than something it navigates.

    A point on a fitness landscape represents a possible organism, along with its associated fitness. The point exists even before there is an organism to occupy it. In fact, many points on a landscape will never be occupied at all — that is, there will never be actual organisms of the specified types. That’s what Allan was trying to explain to you in this comment.

    A point on the side of a mountain exists whether or not anyone sets foot there. Likewise, points in a fitness landscape exist whether or not they are occupied by actual organisms.

  33. An amino acid sequence consisting of a single amino acid probably isn’t going to fold and probably has no function.

    You an be sure a single amino acid will not demonstrate protein folding! As to function, amino acids are the building blocks of protein (making up around three quarters of our bodies) as well as intermediates in important metabolic pathways.

    We can quibble about it if you want to.

    See above.

    Given 20 amino acids, that right there is 20 “points” of non-function. It’s not that proteins can’t get there, it’s that there is no there to get to.

    Did you look at the McLaughlin paper?

  34. OK, this starts to get into something that fascinates me. How do the sectarian convictions get implanted? When does it happen, why do similar exposures not have the same effects on everyone, why are some willing to question these convictions later while others cannot. And what is going on inside the brains of those who cannot question even the most flagrant idiocy?

    I understand that once people have taken a public position on something, they have “married” it and (even in academia) will cling to it until death rather than admit error. But what happens in private, when it becomes clear that the sectarian convictions are worse than baseless? What CAUSES a Kurt Wise to decide, in private, that his misinterpretation of scripture MUST trump a reality he understands so thoroughly?

    And do you suppose it is exactly the same tendencies of the brain that lock people into creationism, that make science possible in the first place? That creationism in some is the price of scientific ability in others? What is malleable enough to mold into imagining a cyclotron, is necessarily malleable enough to mold into a mental ball and chain.   

  35. Study shows Proteins Cannot Evolve

    Once again, the details of molecular biology in even a seemingly simple bacterial protein, point towards the creative hand of God.

    It would have been nice if they had explained why.

    I would have to agree this appears to be a case of “not evolution, therefore God.” But I certainly wouldn’t call it an ID argument.

     

     

     

  36. Todd Wood’s blog post on this is hilarious. He conflates ID’ists with Creationists. I’m guessing he’s a Creationist.

    Hey Todd, how about dealing with the ICR article.

    Mutations bad – That’s the stock Creationist line.

     

  37. petrushka, your 4th link doesn’t work

    I have edited that. I think it works now.

    Note: the only change I made was to add </p> at the end of the link.

  38. keiths,

    It sounds like you may be under the impression that the fitness landscape is something that evolution builds, rather than something it navigates.

    I can’t even make sense of that statement.

    A point on a fitness landscape represents a possible organism, along with its associated fitness.

    Perhaps you need to take a second look at what you wrote in your OP. Maybe revise it in light of your new-found understanding.

    If the height is reproductive rate, doesn’t it make sense that some reproductive rates are beyond the capabilities of certain genotypes?

    IOW, certain points can’t be reached. That would make for islands that can’t be reached, wouldn’t it?

    In fact, many points on a landscape will never be occupied at all — that is, there will never be actual organisms of the specified types.

    So what are you arguing against? I thought that’s the point of view you claim is without merit.

     

  39. This thread seems to be in some measure a response to gpuccio’s comments about protein domain superfamilies.

    A superfamily groups together domains which have an evolutionary relationship.

    http://supfam.cs.bris.ac.uk/SUPERFAMILY/

    Inherent in the very concept of a superfamily so-defined, is the idea that the superfamilies themselves do not have an evolutionary relationship. Else there would be a single superfamily.

    So where is the evidence for the evolutionary relationships between superfamilies? What sorts of ad-hoc “explanations” can you come up with for the missing intermediates?

     

     

  40. Well, so far all we are seeing are the usual evasive tactics of someone trying to hide his ignorance of the subjects he pretends to be able to critique.

  41. keiths,

    Real fitness landscapes have hundreds or thousands of dimensions, and the likelihood of getting stuck on a peak diminishes exponentially as the number of dimensions increases.

    So evolution proceeds via wormholes in the dimensional fabric? Cool!

    What’s the difference between a real fitness landscape and the one you were talking about in the OP? Does a real fitness landscape involve real organisms and actual reproductive rates, rather than hypothetical genotypes and hypothetical reproductive rates?

    So if the genotype distance is along the x and y axis and the reproductive rate is the z axis (height), what are all these trillions and trillions of other dimensions?

  42. What sort of ad hoc explanation can you come up with for why your god Designer created proteins in families/superfamilies to begin with?

    Do tell, Mung.   

  43. Well, so far all we are seeing are the usual evasive tactics of someone trying to hide his ignorance of the subjects he pretends to be able to critique.

    I don’t pretend to be able to critique nonsense.

     

     

     

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