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Doug Axe now replies to James Shapiro: Can we let the science decide?

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Readers will recall James Shapiro, author of Evolution: A View from the 21st Century. Bill Dembski asked him, based on his observations, Why aren’t you a design theorist?

Which, in the context, is somewhat like asking, “Well, if you agree with me about how badly things are run down at City Hall, will you join Citizens for Municipal Reform?”

Well, Shapiro replied, giving his objections, and now Biologic Institute’s Doug Axe has replied to Shapiro here:

I think we all agree that science should be the arbiter here. Naturalism and ID both make testable claims about how things happen in the real world, so it ought to be possible to evaluate these positions by evaluating their respective claims.

If crutches are devices for propping up lame positions, then I completely agree that they should go, but let’s be careful to call a crutch a crutch. As an ID proponent, I’ve put forward the scientific case for thinking that the thousands of distinct structures that enable protein molecules to perform their specific tasks inside cells cannot have arisen in a Darwinian way. Moreover, the facts of this problem seem to preclude any naturalistic solution, Darwinian or not.

Shapiro is looking for a no-Darwin but no-intelligence  solution. Does it exist?

Also, Axe’s senior scientist Ann Gauger offer some thoughts on Dembski’s questions here.

0 to 60 quick, on Shapiro:

Antibiotic resistance: The non-Darwin truth

“Four kinds of rapid, multi-character evolutionary changes Darwin could not have imagined”

“Key non-Darwinian Evolutionary Scientists in the 20th Century”

Follow UD News at Twitter!

Comments
>>>Champignon wrote on 1/18/12: "Darwinism’ doesn’t appeal to the supernatural." That's because it relies on mathematical miracles. Darwinists habitually stare sequence probabilities of 1/10^150 or less without batting an eyelash. If they can go THAT deeply into denial, it makes sense that they don't feel the need to invoke a designing intelligence.WD
June 2, 2012
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Eric: I can't explain, in Elizabeth's case. Her motivations are an enigma shrouded in a mystery etc. She does seem to obsessed with reciting standard population genetics approaches to evolution, however. It's almost as if, when she took up an interest in evolution -- which I suspect was not early in her life, but relatively recently -- she imbibed the standard approach from some textbooks or general books recommended to her, and learned their approach religiously. (Remember, her first two degrees were in music and architecture, so she may never have actually taken an undergraduate biology course, and population genetics wouldn't be on the curriculum for a Ph.D. in cognitive psychology.) If that's the case, she probably tries to make everything she reads about evolution somehow fit into her first understanding. In one of her comments above, she speaks of Shapiro as explaining things in terms of "between-population selection," but in the article she cites, the word "population" occurs exactly once, and the phrase "between-population selection" not at all. And she couldn't have got the idea from Shapiro's book, because at the time she hadn't read it yet. Maybe, in making that remark, she had some other articles by Shapiro in mind, but as far as the cited article goes, the phrase is purely her invention. It's as if she is determined to see Shapiro, and all other evolutionary biologists, through a set of glasses tinted with a certain shade. ID people, on the other hand, read Shapiro, Margulis, etc. in accord with their own stated intentions, which are insurrectionist. Shapiro thinks that much of mainstream evolutionary thought is blatantly wrong. He's shaking the foundations. That is why Coyne is so furious with Shapiro lately, and is insulting him and belittling him in public. If Shapiro were just offering another source of mutational novelty, Coyne wouldn't be so angry. Coyne, who knows evolutionary theory far better than Elizabeth will ever know it, understands that Shapiro isn't just adding another modification, which the mainstream theory can absorb with a little adjustment, but throwing down a gauntlet. All the ID people understand that, and Elizabeth doesn't -- which calls into question the depth of the understanding of evolutionary theory which she has acquired in her autodidactic wanderings through the field.Timaeus
March 5, 2012
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Timaeus, Why is it that true believers keep claiming there are things addressed in papers when the papers don't actually address the things claimed? Is it a problem of reading comprehension? Faulty logic? Wishful thinking? With Nick Matzke I think it is just a literature bombing debate tactic. With Elizabeth it seems to be more of the wishful thinking. Interesting . . .Eric Anderson
March 4, 2012
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Elizabeth Liddle: I don't know if you still read UD, or get responses to threads via some kind of automatic feed, but if either is the case, I have an answer to your last post. I had written: "The question is: how on earth did life first acquire this Swiss Army knife of self-engineering tools? Was it put together by a trial-and-error? Shapiro doesn’t claim to answer that question" You answered: "Well, he gives a theory in that paper I linked to." I just checked the paper you linked to, which was: http://shapiro.bsd.uchicago.edu/Shapiro.2005.Gene.pdf I have now read the article, and I see nowhere where he tries to answer the question which I posed. It thus appears that you have misunderstood either my question or Shapiro's article. It would indeed have been surprising if Shapiro had presented an answer to such a fundamental question in 2004 and then, more than 7 years later, in 2012, denied (as he does, in the passage I quoted) that he had any clue how to answer the question. That is why I doubted from the beginning that you had interpreted the article correctly. And now, having looked at the article, I see that my doubts were quite warranted. He gave no origin for the capacity I identified, back then any more than he does now. He's simply agnostic about it. And really he has to be, because the question cannot be answered without answering the question of the origin of cellular life itself.Timaeus
March 4, 2012
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Elizabeth: I don't perceive that you owe me any apology. I made a joke without thinking that it might be taken less than affectionately. If we were old chums from school days, I think it would have been taken in good part, but given that I had irritated you earlier, I should have known enough not to venture the wisecrack. And I did press you a little hard on your internet persona. You had a right to show irritation, if that's what you felt. Nonetheless, you have to know that irritation can be generated by many things; it can be generated by aggressive manners (which is what you felt from me), or it can be generated by polite manners coupled with an air of certainty about a wide range of scientific and intellectual subjects that no human can encompass in a lifetime, and that's what I've often felt from you (whether you intend it or not). So I guess both of us gave way to irritation, only the reason for my irritation was probably not clearly visible to you and therefore it would have come across to you as ungrounded belligerence. Bad judgment on my part. I don't know what the date of the paper is that you read, or what it was about. I assume that Bill Dembski's quotation of Shapiro from January 2012 would represent Shapiro's current view on the subject we were discussing. That's all about Shapiro for now. T.Timaeus
January 21, 2012
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Well, he gives a theory in that paper I linked to. So we'll have to agree to differ on that for now :) Apologies for the grumpy old lady stuff earlier. Peace. LizzieElizabeth Liddle
January 21, 2012
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Agreed (re John). Thanks for the link.Elizabeth Liddle
January 21, 2012
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Elizabeth: You ask: "What do you think that Shapiro is saying?" I'm confused. I gave you direct quotations from Shapiro. I think he is saying what he is saying there. He is saying that he has no theory about the origin of the self-engineering capacities of the cell. And that's what I said (16.1.2.1) that Shapiro said in the original comment that you objected to (16.1.2.1.1). You expressed doubt that I had interpreted him aright, so I provided direct quotations. If you find his paper unclear, why don't you read his new book? Probably every ID person I know has bought it and has read it or is in the process of reading it. It has technical parts aimed at evolutionary biologists, but parts of it are quite clear to the non-specialist with a basic general knowledge of evolutionary ideas. Here is an example of his writing, not on the point above about the origin of systems, but about the distinction between the new evolutionary biology and the mainstream evolutionary biology of the 20th century: "A shift from thinking about gradual selection of localized random changes to sudden genome restructuring by sensory network-influenced cell systems is a major conceptual change. It replaces the "invisible hands" of geological time and natural selection with cognitive networks and cellular functions for self-modification. The emphasis is systemic rather than atomistic and information-based rather than stochastic." (145-146) I find that a rather elegant summary. He has similar lucid remarks on Darwin and neo-Darwinism on pp. 1-2. (And note that he ties them together, justifying my claim that he is critical of "Darwinian" thought more broadly, not just neo-Darwinism.) He seems to me to be an adequate communicator. I am nowhere near understanding all of his book yet, but his key claims seem to be clear enough. I don't think I've misinterpreted those. I won't discuss Shapiro any further at this point, until I know more about him. In the meantime, if you still disagree with my original statement, "Shapiro doesn’t claim to answer that question" (16.1.2.1 above) there is nothing more I can do about that. I've documented it in his own words. T.Timaeus
January 21, 2012
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Yes, well, old loves often die hard or live again. Agreeing about John's power, though as more than just 'literature.' The specific question was made here: https://uncommondescent.com/intelligent-design/methodological-naturalism-science-enabler-or-science-stopper-a-response-to-dr-elizabeth-liddle/ Question/Section 9.1 It is made as clear as possible.Gregory
January 21, 2012
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Well, I'm not :( I loved my religion. Still do, in a way. And St John's Gospel is still one of my favorite pieces of literature.
Waiting in line for Elizabeth to philosophise about ‘naturalism’ and its alternatives.
Well, you may wait awhile :) Unless you have a specific question? Or have I gone and lost track of one I owe you?Elizabeth Liddle
January 21, 2012
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This is called being 'religiously unmusical' in technical terms, by Max Weber. He claimed the same (temperament) of himself, according to the ideology of 'secularisation,' aka 'disenchantment.' Nowadays, new theorists have arisen that challenge this supposedly 'scientific' thesis. My view is that 'music' is a 'universal,' i.e. not just an 'evolutionary' one but a 'real one, which all human beings share. Religious music is one type, demonstrated in manifold ways (genres). There are of course other types as well, which perhaps Elizabeth is keen to celebrate. Waiting in line for Elizabeth to philosophise about 'naturalism' and its alternatives.Gregory
January 21, 2012
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Yes I saw the smiley face, Timaeus :) Did you not see my harrumph? No, I don't remember the exchange, although I've exchanged musical thoughts with Gil before now. In fact I was playing his lovely Chopin on my computer only half an hour ago. Not that I can play Chopin. I can't play keyboard at all. But I was a leetle bit cross about the continued digs at my (supposed) areas of expertise/lack of expertise. Hence the harrumph. Back to business: Not sure what you are trying to say about Shapiro. Dembski seems keen to point out what Shapiro is not saying. What do you think that Shapiro is saying? I have to say, he's not the best communicator, but this paper is worth wading through, I think: http://shapiro.bsd.uchicago.edu/Shapiro.2005.Gene.pdf Anyway, no hard feelings :) Cheers LizzieElizabeth Liddle
January 21, 2012
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Well, maybe. But I'd be just as happy if s/he'd actually say what s/he means. I can't exactly offer a defence to an allegation like that. Perhaps I do have a tin ear for religion. Dunno. I don't think so.Elizabeth Liddle
January 21, 2012
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Elizabeth: Did you not see the smiley face? And you have obviously forgotten the earlier exchange you had with someone here, which was the basis of the teasing remark. Since my attempt to relieve tension by joking flopped, I'll assume a Puritan seriousness from here on in. T.Timaeus
January 21, 2012
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Timaeus has a tin ear for social interactions. Perhaps some musical training would help.champignon
January 21, 2012
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You are quite rude, Timaeus! What do you mean by my "unmusical thinking about religious matters"? I have no idea. You seem far more interested in putting me into some box of your own making than actually communicating. harrumph. I'll try and respond to content later.Elizabeth Liddle
January 21, 2012
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Elizabeth: On what Shapiro says, I would direct you to the following: http://www.evolutionnews.org/2012/01/is_james_shapir055051.html And particularly to this exchange between Dembski and Shapiro: ************ Dembski: "James, we met the first time at Wheaton College at a symposium in the spring of 1997 featuring principally you and Michael Behe along with Paul Nelson and David Hull. At the time, I asked you about the origin of such "natural genetic engineering" systems. As I recall, you indicated that this was not really the problem you were addressing. Have you thought any more about this problem? Specifically, how do such systems arise that can take over their evolution? And how much complexity do they require? Are you confident that non-teleological mechanisms can account for the rise of natural genetic engineering systems, and if so why?" Dembski (narrating) Shapiro's reply was illuminating for what it failed to say: Shapiro: "I am not sure how to answer your question. All existing living organisms possess natural genetic engineering capabilities. So they must be pretty fundamental. Any self-organizing evolving system has to have the capacity to alter its information store. That's what they do. Where they come from in the first place is not a question we can realistically answer now, any more than we can explain the origin of the first cells." Dembski (narration): Where do the fundamental biological structures that make natural genetic engineering possible come from in the first place? Shapiro punted on this question back then and continues to punt to this day. [Dembski, in his narration, then goes on to say that Shapiro maintains his agnosticism as of January 2012, and provides this:] Shapiro: "How did the first functional envelope-spanning complex originally arise in evolution? Although we can easily reject the supernatural solution ID advocates propose in response to this question, we also have to acknowledge that we still have no clear scientific answer to it." ***************** Elizabeth: It was these statements, and statements like them, that I had in mind. Now do you see that I was not making anything up, and what I meant? As for this comment: "That only matters if bad prototypes are costly. If they are cheap, it doesn’t matter how deleterious most alterations are as long as you a) keep producing the good ones and b) start producing beneficial ones when they come along. This is precisely why engineers need to think like population geneticists." I don't know what distinction you are making between "good" and "beneficial" in a and b above, but anyhow: the engineer would grant the point, but would say that the order of acquisition is important, because islands of functionality must be created between original form A and ultimate form B. Not all orders of acquisition, even of all the right parts, allow for this. If I have a bicycle with three speeds, and it has the capacity to admit the substitution of a five-speed system, I can ride my bicycle with only three speeds, until I acquire a five-speed system. But if someone gives me the chain and gears and other apparatus for a five-speed system, but no bicycle, I cannot ride at all until a bicycle comes along. I have to walk. That is no minor inconvenience. So if you tell me that, given five million years, eventually part A and part B will be found together, and then the creature will have a new function, I am going to ask: what will the creature do for five millions years with only part A, and what with only part B? And then you have to construct a scenario, plausible to the engineering mind, in which at least one order of acquisition (and I'm keeping it unrealistically simple, with only two parts) will give the creature some viable intermediate capability. The engineer does not object if such scenarios are hypothetical, if only they are plausible. Unfortunately, when asked for such detailed scenarios, 99% of population geneticists duck out, claiming that it's utterly unreasonable to demand such a thing before accepting their model. They think the model should be accepted on the basis of their mathematical calculations alone, without any discussion of the physical/engineering problems that might arise when actual forms have to be dealt with. And so the standoff continues. Population genetics math is great -- I don't object to it. But it will never, never convince a Darwin skeptic by itself. It has to be supplemented by a discussion of the structure and function of the hypothetical intermediate organs, systems and organisms which must fall between A and B. And that is what Darwinians, neo-Darwinians, Darwinians + drifters, etc., rarely or never do. Yes, you have mentioned your musical training to us many times. And I think someone here pointed out to you that it does not show up in your unmusical thinking about religious matters. :-) T.Timaeus
January 21, 2012
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Uhm - they all appear to come from the one blog.  They seem to part of a campaign rather than a genuine assessment of the book.  For example, one of the five blog items is dedicated to one line (the An Lushan revolt) in one of Pinker's many tables.  The conclusion is the figure may be wrong.  Pinker says of the same table: These figures cannot of course be taken at face value. Some tendentiously blame the entire death toll of a famine or epidemic on a particular war, rebellion or tyrant. And some come from innumerate cultures that lacked modern techniques for counting and record keeping. The other blog posts are on much the same lines. Take one figure or fact and dispute it. This is a very broad book which includes an absolute mass of data and facts and some important and novel ideas.  If they can only find five items to dispute (and they are obviously trying very hard) then I think he is not in bad shape.  I cannot find anywhere on the blog a proper review of the book.  They don’t even summarise the conclusions – much less say if they agree. The other thing that stands out is they appear to see this as a dispute about religion.  Pinker is an atheist but this book is not about religion.  For example, he emphasises the large role communism had in violent deaths in the 20th century.  He does argue that for a really large body count you need an ideology – but who would dispute that?markf
January 21, 2012
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You are not understanding my meaning.
OK.
The “smart features” of the genome-cell system that I am talking about would have to have existed (in at least a 1.1 version) in the very first living cell, when there was no “population” to derive the features from. I don’t think Shapiro purports to explain the origin of the first cells, the first genomes, the protein-DNA system, etc.
No, he doesn't, but I don't think he shares your premise, either.
As a side remark, I think that you approach evolutionary models from the point of view of population geneticist, and I approach them from the point of view of an engineer, and I think this accounts for a number of confusions between us. We are trying to describe the same entities and processes, but we are using entirely different languages. This, incidentally, is a very old problem; it was present at the Wistar Conference of 1966, where some of the leading physicists and engineers in the world challenged the leading neo-Darwinians regarding the mathematical plausibility of their model, and it continues today, as ID people (who generally think like engineers) challenge current population geneticist types.
Well, I think that's a false distinction, myself. Although I do see it frequently made, here.
I actually find it rather odd that a neuroscientist would think more like a population geneticist than like an engineer, especially a neuroscientist with background in architecture. I would think that such a person would be thinking more in terms of the complex interlocking of parts needed to build organs and systems,
As indeed I do, but that is not incompatible with "thinking like a population geneticist", if indeed that's what I do (I don't think it's a very good description myself). I'm very interested, obviously, in feedback loops, and indeed, in chaotic systems, and the systems I model (systems of neurons, for example) have a substantial family resemblance to evolutionary systems. Perhaps it's time that engineers learned some populations genetics :) As in fact a lot of them have (hence GAs).
and the strict engineering constraints which would make most alterations deleterious, and most of the remaining alterations less efficient than existing arrangements.
That only matters if bad prototypes are costly. If they are cheap, it doesn't matter how deleterious most alterations are as long as you a) keep producing the good ones and b) start producing beneficial ones when they come along. This is precisely why engineers need to think like population geneticists :)
The type of arguments you are offering I would expect to hear from someone who taught genetics and evolution in a standard biology department, not from someone with your unique training. But hey, as it said in the Monty Python film, “WE’RE ALL INDIVIDUALS!”, and a neuroscientist/architect has the right to think like a population geneticist if she wants to, just as a philosopher has a right to think like an engineer if he wants to.
Indeed. And don't forget I have a musical training too :)Elizabeth Liddle
January 21, 2012
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Elizabeth (16.1.2.1.1): You are not understanding my meaning. The "smart features" of the genome-cell system that I am talking about would have to have existed (in at least a 1.1 version) in the very first living cell, when there was no "population" to derive the features from. I don't think Shapiro purports to explain the origin of the first cells, the first genomes, the protein-DNA system, etc. As a side remark, I think that you approach evolutionary models from the point of view of population geneticist, and I approach them from the point of view of an engineer, and I think this accounts for a number of confusions between us. We are trying to describe the same entities and processes, but we are using entirely different languages. This, incidentally, is a very old problem; it was present at the Wistar Conference of 1966, where some of the leading physicists and engineers in the world challenged the leading neo-Darwinians regarding the mathematical plausibility of their model, and it continues today, as ID people (who generally think like engineers) challenge current population geneticist types. I actually find it rather odd that a neuroscientist would think more like a population geneticist than like an engineer, especially a neuroscientist with background in architecture. I would think that such a person would be thinking more in terms of the complex interlocking of parts needed to build organs and systems, and the strict engineering constraints which would make most alterations deleterious, and most of the remaining alterations less efficient than existing arrangements. The type of arguments you are offering I would expect to hear from someone who taught genetics and evolution in a standard biology department, not from someone with your unique training. But hey, as it said in the Monty Python film, "WE'RE ALL INDIVIDUALS!", and a neuroscientist/architect has the right to think like a population geneticist if she wants to, just as a philosopher has a right to think like an engineer if he wants to. T.Timaeus
January 21, 2012
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You are free to believe anything, but it's possible that chemistry can do things you haven't dreamed of. It will be settled in the laboratory, not by philosophy.Petrushka
January 21, 2012
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'Population' in natural-physical (*read impersonal) science-speak Translates into 'Community' or 'Society' in human-social science-speak. The latter is of course Home to choice, decision-making, purpose, plan, teleology, etc. Not the former. (Return to discussion after having pointed out the obvious.)Gregory
January 21, 2012
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Shapiro doesn’t claim to answer that question
Well, my understanding from what I've read of his, he does - explains it by population-level selection. You can disagree, of course, but I think that's his proposal :) Cheers LizzieElizabeth Liddle
January 21, 2012
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Apologies for all capsvelikovskys
January 21, 2012
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blue_savannah
If I.D and creationism were the same, why would there be disagreements???
Do you agree with Old Earth Creationists completely or are there disagreements?
velikovskys
January 21, 2012
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Dr.Rec, I think you need to brush up on your pig Latin , " od-gay" not godnayvelikovskys
January 21, 2012
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Thank you, Elizabeth. I'm glad if I was able to communicate my ideas to you more effectively, even if I achieved it only indirectly in trying to reply to markf. I want to study Shapiro more closely before I make anything beyond the general statements I've already made, so I can't comment properly on your remark about populations in relation to his understanding. You are right that I am focusing on organisms, not populations. Before any genomic change can spread into a population, it has to occur in an individual organism. And I've always found the neo-Darwinian explanation of how useful genomic changes first arise in organisms to be highly suspect. But if Shapiro is right about the two-way interaction, and if such interaction is common rather than rare, then a much less improbable explanation of significant evolutionary change is available. I agree with you about the Swiss Army knife, but of course, Swiss Army knives are designed by intelligent agents who have in mind the broad types of things that soldiers, hikers, campers, travellers, etc. might need to do. The question is: how on earth did life first acquire this Swiss Army knife of self-engineering tools? Was it put together by a trial-and-error? Shapiro doesn't claim to answer that question, and to be sure, he can do his evolutionary theorizing without answering it; but inquiring minds still cannot let that question rest. T.Timaeus
January 21, 2012
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Thanks, markf. I don't deny that some ID proponents, especially those whose main claim to fame is their contribution to blog sites, have misused or ambiguously used the word "Darwinian." They've also sometimes misused the word "evolution" as a synonym for "Darwinian evolution," forgetting (or never aware) that there have been other explications of evolution: Lamarck's, Bergson's, Chardin's, etc. I often have to criticize ID proponents who claim that ID is against "evolution," pointing out to them that Michael Behe is against the Darwinian explanation but not against evolution itself. Most of the time, however, the major ID figures use terms like "Darwinian" and "evolution" fairly consistently, and quite often they explain what they mean by "evolution" or "Darwinian evolution" near the beginning of their books or papers. For myself, I've tried to follow the usage of mainstream writers. The meaning of "Darwinian" that I employ is one I absorbed from reading semipopular science works long before I ever heard of ID, TE, or the New Atheists. And in those books the "Darwinian" formulation of evolution was always: (1) changes -- usually ascribed to "random mutations" -- were filtered by natural selection; (2) over long periods of time, such changes could accumulate to produce new species, families, classes, phyla, etc.; (3) that this process was gradual, with no sudden leaps (say, from fish to reptile, or insectivore to primate), but only very small gradations, often invisible to inexperienced observers; (4) that the whole process was wholly natural, without any intervention, however slight, by supernatural action; (5) that neither the mutations nor the selection process had any end in mind, so that evolution had neither particular goals nor even a destined general direction -- toward man or anything else. It is such a characterization of evolution that I absorbed very early on, as a young person obsessed with natural science who scoured school and public libraries for every book on cosmology, dinosaurs, evolution and other subjects, and who spent his pennies on paperbacks by Ph.D.s-turned science writers like Sagan, Asimov, etc. So when I first came across Behe several years ago (I had barely heard of ID at the time, and of the current edition of TE I as yet knew nothing), and he used the phrase "Darwinian evolution" or "Darwinian mechanisms" or the like, I immediately clicked with his usage, and had no adjustment to make. Similarly, when Denton contrasted his view of evolution with the "Darwinian," the contrast struck me as obvious and justified, and I took it in stride. I'm certainly interested in moral questions, and some day I may give Pinker a look. My reading list is backed up several books at the moment, however. T.Timaeus
January 21, 2012
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Petrushka, That is a tard different kettle of fish. It's strange that you don't see the obvious distinction. I strongly believe that whenever there's code, the coder must have come first. Rules that complex systems - such as biological machinery - obey are not the same as physical laws. Say, I have an electric switch on the wall. It is clear that its existence is not necessitated by the existence of Ohm's law.Eugene S
January 21, 2012
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Obviously the quotes are just tasters
They are indeed. Saying it might still happen by chance is unbeatable. It takes a different kind of mentality to accept that it might not just be by chance. But that of course is a no-no. I am not impressed. Anyway, thanks for the leads.Eugene S
January 21, 2012
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