James Shapiro: Bill Dembski asks the question we’ve all been dreading …

_{Denyse O'Leary

January 12, 2012

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Is Shapiro really a design theorist but doesn’t want to admit it? (Evolution News & Views, January 12, 2012)

For proponents of intelligent design, James Shapiro’s constant dancing in the DMZ between Darwin and design can be frustrating. On the one hand, Shapiro is as dismissive of Darwinism as any ID proponent. On the other, he constantly gives public notice that he is not on the side of ID. And yet, methinks he protests too much.

Or not enough.

Shapiro is a molecular biologist on faculty at the University of Chicago. When it comes to ID, Shapiro admits that it has identified some legitimate problems, such as Michael Behe’s irreducibly complex biochemical systems (in this he is light years ahead of Richard Dawkins and Kenneth Miller, who deny that any problem exists). Shapiro admits that these are unresolved in Darwinian terms.

Some Darwinism sounds like such nonsense as to cast grave doubt on the intelligence of the persons who utter it.

Fast forward to two days ago, January 8, 2012. In the Huffington Post, Shapiro wrote an insightful article on the mechanisms involved in antibiotic resistance, rejecting the standard Darwinian picture of antibiotic resistance being conferred by the gradual accumulation of slight adaptive modifications. Appealing to lateral gene transfer as a way of bacteria quickly acquiring complex biological structures and functions, and then appealing to natural genetic engineering to adapt those structures to new circumstances of life, Shapiro offers a picture that seems utterly congenial to intelligent design.

And yet, intelligent design is anathema in the circles in which Shapiro moves, so he must utter the mandatory denunciations:

Well, every form of refuge has its price. Some would find that stuff humiliating.

Like, placating the Darwin tenure bore, the Darwin lobbyist, the government Darwin stiff, the reverend who found Jesus n’ Darwin …

There’s a great relief in telling them all to just go to blazes, but we can’t pretend that it translates into interest from TV hair models or Arianna Huffington – once they realize that you must know what you are talking about, and no compromise.

To get anywhere with these problems, you have to be more embedded in this planet than they are.

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Comments

Timaeus : You say, "“learning” is normally associated with an agent who is doing the learning, and the agent is normally conceived of as a subject, an “I,” a mind." and "That certain mathematical models, embodied in computer programs, may illuminate certain aspects of human choosing or selecting, I do not deny. But they do not capture the subjective aspect of choosing or selecting, and from the human point of view (and possibly also from the animal point of view, though it is hard to place ourselves inside the mind of animals), the subjective aspect is central." René Descartes said, "Cogito ergo sum." Indeed, we perceive that which is outside of ourselves in the light of, and uniquely in the light of that which is within. (Forgive me for stating that which is obvious to you, cher Timaeus. To many, it will be novel and/or repugnant.) When we observe structures or patterns that resemble those which allow us to function as human beings, we conclude, "A-ha! A human-like (intelligent) characteristic! Bonnie Bassler's cells really are smart!" Now here's the rub : as a general rule, when we recognize design or teleology, we are correct often enough that our survival is not jeopardized. But we can also be wrong in a non-life-threatening way. (Crocodile or log?) No matter.Survival is all. But is the survival imperative the result of a conscious choice? Does it sometimes appear to be a purposeful choice? To the materialist neo-Darwinist, survival just happens because it accidentally started happening one day and became the frozen chemical accident. (I recently tried that reasoning with the man from the IRS. It didn't work. I had to pay.) Let's face it, if survivability was intelligently designed, in spite of the fact that it appears to be a very hit'n'miss process ("Why is it that every time I look for something I've lost, I always find it in the LAST place I look?) it appears to be successful. Life still continues in spite of plate tectonics, ice ages and Walmart. Is this success a clear sign of intelligent design? Is my capacity to "recognize" and impute intentionality to the vast scheme of things just another survival mechanism? Timaeus, we need you to share more light on these issues. Dawkins says, "Reverse engineering has removed the need for God." Wordsworth said, "We murder to dissect." My postman (a very smart guy who operates a quantum delivery service - both my neighbour AND I receive my mail) said, "Merde!" What I'm saying, Timaeus, in a word, is, "Help!" (PS. I'm a 65 year-old Welshman living in the south of France, and a recent convert to Catholicism. Little, or none, of that will be apparent from my post.)RichardMorgan_{January 17, 2012
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Elizabeth Liddle, May 2011
Well, my position is that IDists have failed to demonstrate that what they consider the signature of intentional design is not also the signature of Darwinian evolutionary processes.
Elizabeth Liddle, June 2011
All I am proposing to demonstrate is that Information (recorded Information, even symbolic information, as I think we now mutually understand it) can arise from a non-intelligent source.
Elizabeth Liddle, July 2011
I made the counter-claim that I could demonstrate that Chance and Necessity could indeed generate information, for any regular English usage of the word information ... So what are candidate definitions? ... Clearly, nobody is making the claim for Shannon entropy ... However, Upright BiPed suggested something that in my view is much more interesting ... This makes a lot more sense to me, as I’ve said ... This definition invokes not only a pattern but some form of transmission protocol ... the mapping has to be achieved via some kind of inert arbitrary intermediary (as is done by tRNA in mapping an RNA codon to an amino acid) ... and so the the ID claim I aim to refute becomes: Chance and Necessity cannot generate information, where information consists of arrangements of something that produce specific functional effects by means of inert intermediary patterns.
Again, there is no misunderstanding between us. All of your protests of me on this thread was nothing more than to gloss over the obvious. Did we have a contentious back and forth? Sure we did. If you were going to simulate a falsification of ID, then I was going to push for it be valid. But, as I have already stated, your issue is with the material evidence, not with me. An IDist "demonstrated what they consider the signature of intentional design" and you were unable to demonstrate that it "is not also the signature of Darwinian evolutionary processes." Which by the way, this statement is one which you were asked repeatedly to retract given the outcome - and yet you have refused to do so, even given that outcome.Upright BiPed_{January 15, 2012
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Good. In that case I misunderstood your last post. We agree then: information is transferred. And we shall probably continue to baffle each other. Peace LizzieElizabeth Liddle_{January 15, 2012
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You invented that out of thin air; completely divorced from anything whatsoever exchanged in our conversation. I have never once suggested (even for a moment) that you don't think information transfer takes place; as the entire challenge was based upon the transfer of information. If you'll remember, it was the transfer of information which was the only operational method of confirming its existence and would validate your simulation (if you should be successful in creating it). I actually had to read your post again just to be certain you used those words in that sentence. It is simply baffling. Such a suggestion would make our entire conversation moot, so I can't even imagine why you would say such a thing, except as a last attempt at grist for the mill.Upright BiPed_{January 15, 2012
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Indeed it will, Upright BiPed. Although I am bemused by your apparent implication that I do not think that information transfer occurs (presumably you mean, within and between organisms). Just goes to show how little we managed to communicate to each other.Elizabeth Liddle_{January 15, 2012
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Well Dr Liddle, there is one thing we can both be certain of; tomorrow the material evidence of information transfer will still be there, as will the documentation on UD of our extended conversation.Upright BiPed_{January 15, 2012
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lastyearon (8.1.1.2): Funny; I feel the same way about discussion with you. But before you go, maybe you could explain to me the syntax of "Your so wrong." And maybe, after taking the time to learn what "vitalism" means, you could concede that you used the term erroneously, and promise never to misuse it again. (I would like to believe that all my efforts weren't completely wasted, and that I taught you at least one thing, however small.) T.Timaeus_{January 15, 2012
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Your so wrong, and so unaware you could be wrong, that any further discussion is hopeless.lastyearon_{January 15, 2012
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As for the rest of your post, which I have now glanced at, it is pure cow squeeze (to use your colourful term).Elizabeth Liddle_{January 15, 2012
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Your strategy of cloaking the issue in a fog has been noted by myself and others.
It may have been "noted", but it that doesn't make those observations accurate. I don't have a "strategy" of "cloaking" anything. On the contrary, my "strategy" is to attempt to make all relevant matters absolutely explicit. Please stop impugning my integrity. As I've said, I will not discuss anything with you unless you are prepared to do me the basic courtesy (which I extend to you) of assuming that I am posting in good faith.Elizabeth Liddle_{January 15, 2012
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Dr Liddle, Your strategy of cloaking the issue in a fog has been noted by myself and others. It is a recurrent theme where you are concerned to cling to “miscommunication” as a defense. I first noticed your use of this tactic in our previous discussions, where we systematically took the issues being discussed one material step at a time over several months. At that time I began repeating back to you quotes from your own posts, showing where you clearly understood the issues at hand. Of course, repeating your words back to you had no effect whatsoever on your use of the tactic, and still doesn't to this day. By “no effect” I mean that the charade is so blatant that you will complain of a “miscommunication”, then I will repeat back your own words indicating you understood completely, and you will then simply (without missing a beat) return to “miscommunication” as a defense. I have often wondered if persons on this board who refuse to interact with you, are not refusing for that specific reason – as it becomes cumulatively frustrating to deal with someone who practices such deception (even when their polite about it, and perhaps even more so). In any case, one would have to believe that when you characterized my definition of information as being “more defensible” than other ID proponents, you were complimenting a definition that you claim you didn't understand. For a scientist, a mature investigator, that just doesn't pass the smell test, let alone the direct quotes to the contrary. I remember back in the 1980s, there was a communicator/psychotherapist named John Bradshaw who wrote several books on human behavior, selling several million copies (as I recall). The Public Broadcasting System even picked up his work and produced several highly-rated multi-part documentaries of his works, which is how I became acquainted with him (being in the media). In one of his books, Bradshaw talked about the meanings of words in different languages, and commented that the English language was somewhat compromised because it only had a single commonly-used word for “shame”, whereas other languages had multiple examples for various meanings. For instance, there is the sense of shame, where a person has done something wrong (crossed a ethical or moral boundary for instance) and is externally shamed as a means of correcting the behavior. Another sense of shame is more of a internal protective emotion, where a person has a healthy sense of shame, and does not jump off buildings while thinking he has the capacity to fly. Other senses of the word follow thereafter. In any case, I bring this up only because when I read your post this morning (even after becoming well acquainted with your tactics) I was simply dumbfounded not only by your sheer lack of shame, but the incredible sense of sincerity you are able to muster in the defense of it. It is not I that impugns your integrity Dr Liddle, your own words do that themselves. This little spat between us is not about two people who have misunderstood each other, its about your position being totally undermined by the physical evidence, and your complete failure as an empiricist to own up to it (as in, alter your perceptions based upon the physical evidence). And you did not “freely concede” that you couldn't demonstrate the rise of information. I cannot even begin motivate the Berlinski-esque level of dismay/contempt appropriate for that statement. Your concession was more akin to pulling every tooth in your mouth with a spoon, as evidenced by your poor choice to portray it otherwise. In the cause of defending yourself, you've entirely lost the real value of the challenge. You see, if you had been able to actually produce the rise of information, that would have had a profound impact on me (and maybe others as well). It would have shown that recorded information really can emerge from unguided material processes, and it would have stood in stark contrast to every other instance of information transfer ever observed, by anyone, anywhere. In other words, the challenge (as in, the competition between two persons) is of little concern – it was the evidence that would have been profound. Yet (as you have very clearly demonstrated) the complete lack of evidence – and more importantly, the physical reasons for it – doesn't effect you in the least. You have no intentions of integrating that knowledge whatsoever. So you cover up this glaring problem with ridiculous comments like this: “We failed to reach a mutual understanding, so I withdrew my challenge” which is nothing but pure unadulterated cow squeeze. You withdrew because the observed physical entailments of information transfer is beyond even a conceptual unguided process, and you know it.Upright BiPed_{January 15, 2012
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Upright BiPed, if you don't intend entering the conversation then don't. If you do enter it, then, if you want a response, please stop impugning my integrity. You are perfectly smart enough to understand that when two people fail to understand each other, it is not necessarily because one of them lacks integrity. I freely conceded that I could not make good on your challenge. My original claim assumed a different definition of information from the one you have asked me to use. I hoped we could clarify it sufficiently to make it possible for me to attempt to rise to it (although I never claimed confidence that I could). We failed to reach a mutual understanding, so I withdrew my challenge. The failure reflects neither lack of integrity on my part nor, necessarily, error on yours. It does reflect failure in communication. I do not see a solution, so there we must leave it.Elizabeth Liddle_{January 15, 2012
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Elizabeth: Here it is: https://uncommondescent.com/intelligent-design/evolutionist-youre-misrepresenting-natural-selection/gpuccio_{January 14, 2012
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I agree johnnyb - if Shapiro's evidence and views are valid, then as Carl Woese said, it's a game changer. Why should the self-organisation not include irreducible complexity? But then, as I've already said, you still have to explain how the ability to exercise "natural purpose" (or I guess you'd have to call it "the illusion of purpose") arose without purpose.Jon Garvey_{January 14, 2012
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"But it is an entirely natural purpose within biological systems." It's not clear what you think Shapiro is denying. But I'm even less clear what "natural purpose" means. Whatver it means, it's not "random with regard to fitness" is it?Jon Garvey_{January 14, 2012
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Wow! How can you ever prove it does and stay scientific?Eugene S_{January 14, 2012
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I think it is useful, following Abel, to distinguish between selection of existing function and selection for potential function. While the first can be done by agents or physicality, selection for potential function is exclusively agent-based. When we have 'automatic' selection by physicality, it is purely eliminative and can therefore lead to nothing genuinely new functionally.Eugene S_{January 14, 2012
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I'm not offended, gpuccio, but I profoundly disagree :) BTW Could I possibly ask you to give me that link again? I've gone and mislaid it.Elizabeth Liddle_{January 14, 2012
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Timaeus: I fully agree with you. Thank you for the clarity about these fundamental points :) The recycling of terms that have always been used to describe fundamental subjective experiences to artificial and very "ad hoc" aspects of objective systems is a widespread "trick" that generates confusion in the discussion about consciousness, function, free will and so on. There is only one simple truth about those points: words like "meaning", "purpose", "intelligence", "function", "motive", "pleasure", "pain", "joy", "suffering", "truth", and many others, cannot be even defined without any reference to subjective experiences to which each of us has direct access in his own conscious experience. They just describe what we experience, and not an objective configuration of objects. If materialists only had the cognitive coherence not to "invent" new and useless "meanings" for words and concepts that have a very definite meaning of themselves, then many intellectual "frauds", like compatibilism, would immediately cease to have any reason to exist. And yes, I have just said that compatibilism is an intellectual fraud, and I repeat it, and whoever wants to take offense is free to take offense.gpuccio_{January 14, 2012
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Elizabeth (4.2.3.2.5): I don't want to extend this conversation very long, as it seems that we are agreeing on the substance and disagreeing mainly over the application of terms. I couldn't find, either in the column above, or in the opinion piece to which it is linked, where Dembski uses the words "choice," "choose," or "intention." You must be getting the definition attributed to Dembski from some other place. However, it seems to me that you are being "dictionaryish" in making a big deal out of the fact that "choose" and "select" can be synonyms. Yes, they can be. But "selection" in Darwinian theory is rather a special case. Darwin chose the metaphor of "selection" because he wanted to parallel the development of new breeds and the development of new species (see Chapters 1 and 2 of the *Origin*). He saw nature as capable of doing over a long period of time what breeders could do over short periods of time. In that sense, nature was like a breeder. So I'm not denying the force of your parallel, or Darwin's. But note that Darwin many times pointed out that the language of selection was anthropomorphic and not to be taken literally; "Nature" was not a personal being who "selected" or "chose" anything, as breeders are and do. And when many critics seized upon the anthropomorphic language in Darwin's evolutionary scheme (see the biography by Desmond and Moore), Darwin saw the advantages of replacing "natural selection" by Spencer's suggestion of "survival of the fittest." The latter phrase captured the truth of natural selection while eliminating any possible misunderstanding that any literal "choosing" was going on. That certain mathematical models, embodied in computer programs, may illuminate certain aspects of human choosing or selecting, I do not deny. But they do not capture the subjective aspect of choosing or selecting, and from the human point of view (and possibly also from the animal point of view, though it is hard to place ourselves inside the mind of animals), the subjective aspect is central. But let's come back to intelligence. The primary use of the word "intelligent" is with reference to people, or to creatures that strike us as in crucial respect like people -- e.g., apes, aliens from science fiction stories, angels, etc. We say that someone is intelligent, or that apes are intelligent, etc. When one says that a system is intelligent, the listener or reader has to adjust, and internally say something to himself such as: "This person does not mean that the system thinks, feels, has a soul, has a mind, has a sense of self, or has a mental quality called "intelligence"; this person means either that the system works as if it were intelligently designed to perform a certain function, or that this system resembles a human being in that it produces results that we would expect of a living creature that is intelligent." And under normal circumstances I would gladly make such an adjustment to a reasonable extension of the meaning of a word. But in the context of the current discussion, the usage of "intelligent" came across as blurring crucial differences between ID and Darwinian notions. And as you know from our discussion of the term "Darwinian" and its (significantly misleading) application to Shapiro and Margulis, I'm always concerned to make sure that crucial distinctions aren't blurred. Notice that I haven't contested the substance of your claim, i.e., that Darwinian mechanisms can mimic intelligence as thoroughly as you (and Dawkins, and most evolutionary biologists) claim that they can. I of course have severe doubts about that. But my point had nothing to do with those doubts. If I thought that pure Darwinian or neo-Darwinian evolution were the complete truth about the origin of species, I still would not speak of evolutionary processes as "choosing" anything, or as "intelligent." I understand the use of such metaphors, but I think it is better for the most part to choose different words. That's all I will say here. T.Timaeus_{January 13, 2012
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Are you ever going to answer my question as to whether your argument concerns the origin of life? Yes or no?Petrushka_{January 13, 2012
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Dr Liddle, As I said, I do not intend on entering this conversation, but your demonstrated lack of integrity forces a clarification. The physical phenomenon of information transfer was coherently described to you. That description was based entirely upon material observations. Over the course of months, and literally tens of thousands of words, you were unable to demonstrate a shortcoming in that description. You remain unable to this very day. Yet, here you are, again, wanting to imply that your failure was somehow tied to the description, when in fact, your issue was with the material evidence - and only the material evidence. You were wrong Elizabeth, flat out wrong. You are free to keep kicking the can down the road, but each time you do, you can do nothing but further demonstrate that material evidence is subservient to your ideology.Upright BiPed_{January 13, 2012
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lastyearon: Here is what I wrote: 'For me, “choosing” involves a combination of intellect and volition which I would never impute to any set of evolutionary processes, any more than I would impute it to any set of chemical or geological or cosmic processes.' First, it was "choosing" (a combination of intellect and volition), not "intelligence" by itself, that I was speaking about here, so you didn't read carefully; but as it happens, I would say the same thing about intelligence, so you're off the hook on that point. Second, there are other natural processes. There are biological processes, many of which aren't connected specifically with evolution. For example, cell division. But of course, I wouldn't grant that most of those involve choice, either. On the other hand, what about a beaver building a dam? There is a biological process, which may very well, for all I know, involve a number of genuine choices -- where and when to build the dam, what lengths of tree to use, etc. There is nothing supernatural about dam-building. So your leap from "intellect and volition" to "supernatural" is unwarranted, on the strength of such examples; but even if I couldn't think of any examples offhand, there is no direct *logical* link between "intellect and volition" and "the supernatural," so it was poor argumentation for you to make the leap without explaining. You shouldn't make your conversation partner do your expository work for you. Regarding "learning": I understand perfectly well the analogy you and Elizabeth are making, and I already said that I saw the parallel. The point is about the usage of words. I'm unwilling to use the word "learn" where the subjective aspect is lacking. Where there is no "I," no "self," there is no learning in the strict sense. You might as well say that a river "learns" not to try to bore through a hard boulder on its way down the mountain to the sea, because that hard boulder won't let it through, and so "learns" to wend around the rock and flow through the soft earth intead. If you choose to use "learn" in such a sense, I cannot stop you; but to make sure I am not misunderstanding you, I am going to have to question you to ask you what you mean. It would be more efficient if you would simply use the word "learn" as it (with its corresponding terms in other lands) has been used in the overwhelming majority of cases in Latin, Greek, French, Italian, German, etc., for thousands of years. Perhaps "adapt" or some other verb would serve to express your meaning without confusing me and others by imputing subjectivity to a process where there is none. On reductionism, I don't know any ID proponent who would say that living things can be reduced to the sum of their parts. Indeed, that is the whole point of ID, that there is something "holistic" about living things -- they originate in a vision of the whole which is greater than the parts used to achieve the whole. Darwinian thinking, on the other hand, explicitly denies that anything greater than the parts is ever necessary to achieve even the most exquisitely complex wholes. Origin-of-life research is the same: its whole point is to reduce the living to the non-living, and to show that the organic can emerge from the inorganic by steps that are wholly mechanical -- entirely in accord with contingent combinations and physical-chemical laws, with zero left over that needs explaining. I suspect that you have read very little ID literature, or you would not be saying such things about what ID people believe. The definition that you got from Wikipedia captures some aspects of reductionism. Where you went wrong was in imputing that definition to me and to ID people. Was it also from Wikipedia that you got the idea that vitalism was a form of reductionism? This is the problem when philosophically untrained people try to make up for years of non-reading of philosophical literature by doing quickie look-ups on the internet. They have no ability to discern between reliable and unreliable information. Indeed, this the problem with internet debating generally; the mass of information out there makes it ever more possible for people to try to fake it, because they can look things up very quickly, and give the impression of massive erudition, but while one can look things up very quickly, one can't understand things very quickly, especially terms like "vitalism" which have a complex history. Those of us who have studied the history of scientific and philosophical concepts for decades get a wee bit irritated when people who invest five minutes learning something are ready to argue about it vigorously, as if they are peers of those who have studied the subject for a thousand times longer. T.Timaeus_{January 13, 2012
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It's rather evident that the neurons in the brain do form a system which behaves intelligently. Organisms in an environment? Yes, if you're talking about people. Organisms in the environment at times appear intelligently arranged. That is not the same as being intelligent, just as the words of a book are intelligently arranged but not themselves intelligent. This is a drawn-out form of question-begging. First show that darwinian evolution has accomplished something that could be compared to intelligence, and then the discussion of what to call it will be more relevant and interesting.ScottAndrews2_{January 13, 2012
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Scott, are you saying that brains are not responsible for intelligence? Or would you not count the brain as a system?Elizabeth Liddle_{January 13, 2012
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LYO, If that were the case I wouldn't split hairs disputing it. But there's no indication of any property of intelligence emerging from them, any more than it emerges from an arrangement of letters, words, and sentences. Let's agree that if darwinian evolution did, in fact, "invent" the frog, then it is intelligent. Or the property of intelligence has emerged from the molecules which formed the cells which formed the frogs. You word it and I'll agree with it. But agreeing on what we could call it if it were true doesn't have any bearing on whether or not it is.ScottAndrews2_{January 13, 2012
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"as it is properly defined" No - as it was defined by you in that context. There is no "proper" definition of words, there are simply usages. That is why operational definitions are so important.Elizabeth Liddle_{January 13, 2012
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In the context of that post, UBP, I am using "CSI" as defined by Dembski in the relevant paper. I should have given the link. Here it is: http://www.arn.org/docs/dembski/wd_idtheory.htmElizabeth Liddle_{January 13, 2012
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Thanks for the reply, Scott,
Rather than using “intelligence” as a verb we might say that the parts of the system behave intelligently or act with intelligence. Then there’s a verb.
But the parts of the system don't act intelligently. They just act, and out of that emerges intelligence. That's why I was referring to intelligence as a verb. Intelligent is an emergent property of things doing things (acting).lastyearon_{January 13, 2012
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I never said anything that was the slightest bit “reductionist.” Either you are misunderstanding what I am saying, or you’re misusing the term “reductionism.”
It seems from your writing that you don't think that intelligence (real intelligence, not mimicry of it) can arise solely from a system consisting of interacting parts. And therefore you cannot see how evolution could be intelligent. So when Elizabeth mentioned that evolution displays intelligence, in that it has the ability to "choose", you said this...
How can a system be “intelligent”? A system can be intelligently designed, but a system, not having a mind, can’t possess an intelligence
This strikes me as reductionist thinking. One of the definitions from Wikipedia:
a philosophical position that a complex system is nothing but the sum of its parts, and that an account of it can be reduced to accounts of individual constituents
I don't believe one can explain the emergence of true intelligence from a system using a reductionist framework, since the system is "just" the sum of its parts.
How did you get from my understanding of “choice” as involving “intellect and volition” to “intelligence is supernatural”? Wouldn’t you say that you’ve missed one or two steps in your exposition?
Because you also said you wouldn't impute intelligence to "any set of chemical or geological or cosmic processes". What other natural processes are there?
My definition of “learning” does not proceed from “lack of imagination” on my part,
Well, just because we normally think of learning as a characteristic of human beings, doesn't mean that other systems can't learn, in much the same sense that we do. That's what I was referring to as your lack of imagination.lastyearon_{January 13, 2012
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