Why Were So Many Darwin Defenders No-Shows at the World’s Premier Evolutionary Conference?

"This is less about biology than about just plain clear thinking. Someone who can’t see that this preliminary question (*how many* morphological changes, and *which* morphological changes) needs to be answered before the detailed evolutionary explanations can begin, is not a clear thinker." Bingo. Leaving aside the question of neo-Darwinist evolution, the very word 'design' predicates both intelligence and purpose, so that that the simple prefacing of that word, 'design', with the word, 'intelligent', is effectively tautological. Secularists need to coin a new word, which conveys the clear sense of the word, 'design', but a magical provenance from a seemingly endless chain of random coincidences and involving only inanimate matter. Looks really like it's been designed, but it's a whole nother animal. pbecke

GUN: This on dogs etc may be interesting, as will this on Cichlid fish. (Note red deer and elk from US -- rated as different species -- are apparently interfertile in New Zealand; and the same has been happening with finches in the Galapagos.) GEM of TKI kairosfocus

F/N: on all time [ since was it April] pop and hot posts lists, so not quite dead yet Dr Cudworth. However your points are well made on the main subject and on Dr Matzke's attempted intervention. kairosfocus

Dirac, 1928 -- 83 years ago; an expression that implied the existence of antimatter, i.e. a confirmed prediction. Long enough ago that this should be fairly common knowledge. kairosfocus

Petrushka: I have nothing to do with moderation. Take it up with whoever is responsible. As for your questions about quantum theory and so on, all five of them are entirely irrelevant to the point I was making. I do not find fault with physics or chemistry or mathematics for any of the things you mention. But I would find fault with them if their practitioners could not get their lines of argument into logical order. This is what peeves people like Eugenie, that incredibly smart non-biologists like Berlinski force them to state their argument in a logical order, so that an intelligent lay person can understand it and see its potential weaknesses. We can't have the lay people knowing that the Modern Synthesis has any weaknesses, can we? That's why she wants criticism of Darwinian theory banned from the schools. Berlinski is spoiling her party. In neo-Darwinian theory, selection is at the level of the organism, not the genes or the proteins. Specifying plausible morphological intermediates is therefore an absolute requirement. Any theoretical work on Darwinian evolution that tries to bypass this requirement, no matter how sophisticated its genetics and no matter how dazzling its comparison of homologous proteins, is not worth the paper it's written on. It looks like this thread is pretty well dead now. It's obvious that no one is going to answer my question about how many papers the ID critics I discussed have published on evolutionary biology in the past ten years. (I suspect the answer, in most cases, is zero.) And Nick's been soundly thrashed, yet again, for his distortions and misrepresentations of ID, and has retreated, and the other participants seem to have drifted away. So unless Elizabeth jumps back in with answers to my earlier responses to her, I'll make my exit. Thanks for all who made it a great discussion. Thomas Cudworth

William A. Dembski:

But Orr was reviewing my book No Free Lunch, and I carefully avoid tying intelligent design’s critique of Darwinism to the unreasonably high standard of logical impossibility or mathematical certainty (though, granted, I employ mathematics).

Mung

Thanks bornagain77, your words are encouraging :) LivingstoneMorford

In the physical and chemical sciences, you see organization of thought in the theories...

Really? In physics, what formula unites general relativity with quantum theory? How can physicists take either seriously when they contradict each other? In chemistry, how do you pridict the folding of a protein from first principles. How can chemistry be taken seriously if it can't answer such a simple question? How can mathematics be taken seriously if it can't answer a simple yes or no question as to whether a simple and elegant proof of Fermat's Last Theorem is possible? As an aside, it's really difficult to participate when it takes 48 hours to get through moderation. For a mild offence committed a year ago. An offence that didn't even reach the level of name calling or of suggesting another poster is on drugs. Petrushka

TC @ 326: "I’m trying to be gracious to Elizabeth because she is being gracious to us. That’s rare among our critics. We need people like her, who criticize us gently and reasonably." I think you have a strange idea of what both 'graciousness' and 'reasonable' entail. LE refuses to reason ... and she frequently declines to speak certain truths or to acknowledge any truth that falsifies her constantly-changing assertions. But, she's not frothing-at-the-mouth and calling you stupid, directly (though, her "reasoning" indirectly treats any who attempt to reason with her as being stupid) ... so, yeah, that's real 'gracious' and 'reasonable'. Ilion

TC @ 326: "I’m trying to be gracious to Elizabeth because she is being gracious to us. That’s rare among our critics. We need people like her, who criticize us gently and reasonably." I think you have a strange idea of what both 'graciousness' and 'reasonable' entail. LE refuses to reason ... and she frequently declines to speak certain truth or acknowledge truth that falsifies her constantly-changing assertions. But, she's not frothing-at-the-mouth and calling you stupid, directly (though, her "reasoning" indirectly treats any who attempt to reason with her as being stupid) ... so, yeah, that's real 'gracious' and 'reasonable'. Ilion

aw shucks :) Thank you Thomas. And I'll try to keep searching for what common ground I think we have :) Elizabeth Liddle

Mung (308): I'm trying to be gracious to Elizabeth because she is being gracious to us. That's rare among our critics. We need people like her, who criticize us gently and reasonably. In fact, I'm feeling a bit bad about the forcefulness of my earliest comments to Elizabeth. My sense that she was defending Nick and/or the tactics of our other critics got the better of me at times, and I was, if not actually rude, sometimes too aggressive and lecturing in my tone. But she showed great self-control in not getting heated in return, and I thank her for that. (Maybe it's the music in her soul that gives her this composure.) Elizabeth, if you are reading this, I've enjoyed your posts, and I'll work on calming myself down in future replies. Thanks for your patience. Thomas Cudworth

Petrushka (315): "Perhaps it is a mistake to treat the question as ridiculous, but it is also ridiculous to treat the lack of detail[ed] historical knowledge as equivalent evidence discrediting a theory." Berlinski did not do that. He did not say that because she could not give a number, therefore neo-Darwinism was false. He was asking (as his follow-up questions showed) how, if she did not have the slightest idea what the number might be, she could know that neo-Darwinism was true. I suggest you watch the video if you haven't already. There is a difference between saying: "theory X is false" and "theory X is so poorly formulated that it is not yet in good enough intellectual shape for us to tell whether it is true or false." The latter is Berlinski's critique of Darwinism, as one can see also from the interview in *Expelled*. As for genetic changes producing morphological changes out of proportion to their number, two points: (1) that's not classic neo-Darwinism, which postulates a rough one-to-one correspondence between genotype change and phenotype change, and it's classic neo-Darwinism that the ID people are attacking; and (2) that *still* doesn't exempt a biologist from listing the number of morphological changes necessary to turn one creature into another. Regarding (b), if you don't even know what it is that you need to change, you can't even start talking about evo-devo mechanisms as the means of changing it. If I don't know that whales have fins and artiodactyls have hooves, I can't start speculating on how a hoof might turn into a fin. If I don't know the comparative anatomy of the nostrils in whales and artiodactyls, I can't start speculating on where the blowhole came from. If I don't know the anatomy and physiology of marine lactation, I can't begin to speculate on how it might have derived from land lactation. So whether I'm a neo-Darwinist or an evo-devo follower, my first order of business is to list the number of changes that need to be made. This is less about biology than about just plain clear thinking. Someone who can't see that this preliminary question (*how many* morphological changes, and *which* morphological changes) needs to be answered before the detailed evolutionary explanations can begin, is not a clear thinker. In the physical and chemical sciences, you see organization of thought in the theories; a layman can follow the general logic, even if he can't follow all the detailed math. But in neo-Darwinism, you can't even follow the general logic, because its practitioners hardly ever demonstrate any. Berlinski's question, and Eugenie's evasive answer, make the case that some evolutionary theorists would benefit from taking some courses in logic and/or in the history of scientific theorizing, because clearly some of them have trouble presenting a hypothesis in an orderly way. Thomas Cudworth

If you claim to be a whale evolution *specialist* …

Is there such a thing?

Yes. http://scholar.google.co.uk/scholar?hl=en&q=whale+evolution&as_sdt=1%2C5&as_ylo=&as_vis=1 Elizabeth Liddle

Mung:

Elizabeth Liddle:

This, incidentally is the first scientific error Dembski makes – he sets up his hypothesis incorrectly, and so finds himself in a position where no other hypothesis, by definition, can account for the data.

And yet are you not the exact same person who repeatedly argued that the null hypothesis and the alternate hypothesis must be mutually exclusive? Yes, I do believe that was you.

Yes, indeed it was. Is, rather. Elizabeth Liddle

LivingstoneMorford, if they ignore it [you] hopefully it [you] and all the meddling [science] will go away. junkdnaforlife

N.Matzke @ 118

If you aren’t convinced by these works, please come up with a better explanation for the evidence when you write your rebuttal.

There is in this "request" something even more insidious than J.Cassidy discusses @ 316. Ultimately, what Mr Matzke is doing is asserting a faqvoréd ploy of DarwinDefenders when faced with criticism of Darwinism – he is asserting that even if one irrefutably shows that Darwinian “explanations” fail to explain, even if one irrefutably shows that that they are false, and why, that one hasn’t the right to dis-believe them, nor to persuade others to dis-believe them, unless and until one has devised a “better” “explanation” – and Darwinists, of course, get to decide what counts as “better”; and “better” will be something compatible with Darwinism, of that you can be sure. It’s just another gloss on the old, familiar, “Heads I win, tails you lose.” Ilion

"Nick doesn’t understand “agnostic”." And that's OK, really; because he also doesn't understand 'skeptic' and 'skeptical'. Ilion

Nick doesn't understand "agnostic". Mung introduces himself as agnostic, and Nick replies:

If you aren’t convinced by these works, please come up with a better explanation for the evidence when you write your rebuttal.

So if you remain agnostic, you need to have better explanation for what you aren't sure about? Gotcha. If agnostic could possibly have a "better explanation" while maintaining agnosticism, what does that say about the original explanation? jjcassidy

LivingstoneMorford, I want to thank you for the time and effort you have put into this thread. It has been very informative. bornagain77

I note that my discussion on the implausibility of Nick Matzke's pathway was ignored by the Darwinian side, and I also note that my sequence analysis of the idea that FliM was formed by a FliN/CheC fusion was ignored, even after providing the sequences I used. I wonder why that could be. Oh well. LivingstoneMorford

If you claim to be a whale evolution *specialist* ...

Is there such a thing? Mung

not having *any idea* of the number, even the order of magnitude, is inexcusable.

That would be seem true only if you know nothing about evo/devo. Genetic changes can produce morphological changes that seem far out of proportion to their number. A single mutation can change the number of limbs, for example. Perhaps it is a mistake to treat the question as ridiculous, but it is also ridiculous to treat the lack of detail historical knowledge as equivalent evidence discrediting a theory. Is there or is there not a simple proof of Fermat's last theorem, a proof that could fit in on a page or two? A simple yes or no question. Does failure to know the answer demonstrate that there is no correct answer? Petrushka

goodusername: I don't see the problem regarding dogs. A trained dog breeder could easily identify, say, fifty main differences between a jack russell and a labrador retriever -- fur length, fur curliness, coloration, snout length, snout shape, tail length, tail shape, dentition, average body mass, average height, average length, ear shape, pitch of barks and growls, sleep habits, tendency to dig holes, snappy versus calm temperament, etc. And then, to the extent that these differences were genetically determined (though I'm told by some that many of the differences in dog varieties have as much to do with developmental processes as genetic differences), one could try to determine what parts of the genome are responsible for the various differences in dog varieties. Now if someone were to pose as an expert in dog breeding and a master at producing entirely new types of dogs, or dogs with certain desired characteristics, and I asked: "Can you tell me roughly how many major differences there are between a german shepherd and a poodle?" and the "expert" said "That's a ridiculous question! No dog breeder has *any idea* of the number of differences between a german shepherd and a poodle!" -- well that is one "expert" dog breeder that I would certainly never consult on dog matters. My point is that any evolutionary biologist who claims to be certain that a land mammal became a whale by neo-Darwinian mechanisms must *at a minimum* be able to tell me the main differences (anatomical, physiological, etc.) between the land mammal and the whale. If he is not certain whether the number of major differences is 57 or 58, I'm not going to quibble. But if he's not sure whether the number of differences between a primitive deer or hippo and a modern whale is 10 or 1,000, then I'm certainly not going to have any confidence in his ability to give me an evolutionary pathway from the one to the other. All I would have wanted to hear Eugenie say is something like: "I'd say there are between somewhere between 50 and 200 major differences between the primitive artiodactyl and the whale, depending on how "major" is defined." That's all Berlinski was asking for. Thus, her non-answer seems evasive. And if she didn't honestly know the answer, she could have said: "I'm an anthropologist, not a mammalologist, so I don't know offhand how many crucial differences there are between artiodactyls and whales, but if you will allow me to speak in my field, I can tell you how many major morphological differences there are between the most primitive fossil apes and modern human beings, and I can show you how those differences could easily be bridged by neo-Darwinian processes in the time allowed by the fossil record" -- that would have been a reasonable answer to the question. Instead, she conveyed the view that it was ridiculous to expect evolutionary biologists to have even a rough idea of the number of basic differences between the animals they are discussing. And that's just silly. If you claim to be a whale evolution *specialist* and can't enumerate the main differences between whales and hippos, or whales and deer, you shouldn't be in the evolutionary biology business. Not knowing the exact number off the top of your head is understandable; not having *any idea* of the number, even the order of magnitude, is inexcusable. Thomas Cudworth

Dembski: "I will be more clear. Once we infer design, the design can be observed, analyzed and evaluated. ID gives us a way to identify, as much as it is possible with present data, specific deseign inputs (for instance, the emergence of protein superfamilies). There are many aspects, observabble aspects, facts, about design input which are in the range of science." All our inferences are provisional. Indeed all our inferences are hypotheses, that should generate further predictions. So, if we conclude that our hypothesis of Design is supported by our data, then the first thing we should ask is: is there an alternative hypothesis that could generate these data? This, incidentally is the first scientific error Dembski makes – he sets up his hypothesis incorrectly, and so finds himself in a position where no other hypothesis, by definition, can account for the data. This is a false rendering of Dembski's position. There's a reason Dembski talks about "inferring" design - because it's exactly that: An inference. I would like to see where Dembski says that once design is inferred we can be certain that an alternative explanation will never emerge - my guess is that there is no place where he says this. Simply suggesting how we can build upon an inference after we've made it is not sufficient to suggest that Dembski "finds himself in a position where no other hypothesis, by definition, can account for the data". nullasalus

Thomas Cudworth, “goodusername (not!):” :-( “The comparison with dogs is misleading, for dogs, despite many superficial variations, are all of one species” --It isn’t misleading, it’s illustrative of how silly Berlinski’s questions are (or at least how silly it is to it as an argument against darwinism). I purposely chose dog breeds because it’s a change that no one – even the most anti-evolutionary Creationist – would dispute occurred. And yet, if one asked all the same questions about a breed-to-breed transition, one would run into all the same problems. Might the number of morphological differences between one breed and the next be 50k (a number that Berlinski came up with for the evolution to whales) if you looked at every minute morphological detail? Quite possibly. Are we able to list the steps at the molecular or genetic level of how any such change occurred? Not even close. It’s simply well beyond modern science. Some day we MAY be able to put together a* hypothetical* list of changes at the molecular level, but we have ways to go for even that. And yet, as you point out, this is merely a change WITHIN a species. “Note that if Eugenie had answered the question, instead of using up the allotted time in stalling, Berlinski could have used her answer as a springboard to the higher-level theoretical question of evolutionary pathways, as I’ve just done.” --I pretty much agree with you as to how it could have played out. Eugenie Scott could have listed some of the necessary morphological changes for the evolution of whales, and possibly showed how there is a chronological series of intermediate fossils displaying these morphological transitions, and perhaps argued how the DNA evidence agrees with the fossil evidence as to when and from what group of animals whaled evolved, and Berlinski can keep taking the discussion further and start asking about molecular evolutionary pathways and asking questions until we inevitably hit the limits of what science is currently capable of. And that’s fine. Asking such questions is how science progresses. But I do think it silly to use the fact that eventually one hits the limits of current knowledge as an argument against a theory. goodusername

Elizabeth Liddle:

This, incidentally is the first scientific error Dembski makes – he sets up his hypothesis incorrectly, and so finds himself in a position where no other hypothesis, by definition, can account for the data.

And yet are you not the exact same person who repeatedly argued that the null hypothesis and the alternate hypothesis must be mutually exclusive? Yes, I do believe that was you. Mung

Mung: Type "Elizabeth" and "I apologise" into the box below. Elizabeth Liddle

Elizabeth, Type "Dembski" and "monograph" into your favorite search engine. Mung

Thomas, Your posts are so much more civil than mine. But I've enjoyed them immensely in spite of that. Thank you. Mung

goodusername (not!): Your first paragraph shows the same lack of big-picture thinking that Eugenie showed in her reaction to Berlinski's question. With a philosopher as bright as Berlinski you have think about not only the question itself but the trajectory of the question -- where it's going. Yes, of course, he only asked her *directly* for a number. But why do you think he was asking here for a number? Do you think he would have cared if the answer was 327 rather than 328? He wouldn't have cared at all. The significance of asking for the number was twofold. First, he wanted a ballpark figure: are we talking about ten changes, a hundred changes, five thousand changes? The larger the number of changes required, the higher Mt. Improbable becomes. So not the exact number, but the order of magnitude of the number is important for assessing the plausibility of the neo-Darwinian mechanism. If the number were "ten billion", then it would be completely irrational of Eugenie to believe that neo-Darwinian mechanisms could do the job in the allowed time. So her acceptance that neo-Darwinian mechanisms could do the job in the allowed time implies (a) that she had at least a rough number in mind, and that it was sufficiently low; or (b) that she hadn't thought about the number at all. If it's the latter, it would show that her thinking was fundamentally sloppy and unscientific. And if it's the former, she should have been able to give a rough, ballpark figure. (Even Ken Miller, later in the debate, realized the reasonableness of providing a ballpark figure, and tried to do so in a half-baked way.) The second reason for asking for a number is that if one doesn't know roughly how many steps one has to account for, one cannot construct a plausible evolutionary pathway. It is true that there might be many evolutionary pathways from artiodactyl to whale, some of the involving maybe 300 steps, some 325, some 275, etc. But there won't be any that involve 10, or 12, or 20 steps. Without a ballpark figure, you can't even get started. Aside: The comparison with dogs is misleading, for dogs, despite many superficial variations, are all of one species, and the *genetic* (as opposed to superficial phenotypical) differences are much smaller than the genetic differences that have to be crossed from artiodactyl to whale. Regarding your second paragraph, no, I *don't* think it is commonly done. Please give me the names of books and articles where you have seen lists of the necessary morphological changes needed to get from artiodactyl to whale. I'm not talking about alleged fossil intermediate forms here. I'm talking about physically necessary morphological changes. You don't need to know a thing about fossils to enumerate these. A whale has flippers. You have to get from feet to flippers. Is that *one* major change at the molecular/genetic level, or would it require *several* smaller changes, each requiring its own molecular/genetic pathway? What about moving the blowhole on the skull? Is that *one* change, easily accomplished by a so-called "point mutation", or does it requires several independent changes which are not going to happen together? Is the change to marine lactation *one* step, or does it require changes to several bodily systems, each involving one or more genetic changes? If you can't roughly enumerate the basic gross physical changes required, you can't even get started on the list of protein and DNA changes that would be necessary. This point is well made by Sternberg in his whale video, which someone mentioned above. Note that if Eugenie had answered the question, instead of using up the allotted time in stalling, Berlinski could have used her answer as a springboard to the higher-level theoretical question of evolutionary pathways, as I've just done. And this is what ID people find so frustrating with Darwinists; they constantly avoid getting down to nitty-gritty, especially in public debates. It's of course not to their advantage for the public to see how much trickier it is to get neo-Darwinian changes to major organs, systems and body plans than those tidy little tree diagrams in popular science books suggest. Thomas Cudworth

Thomas Cudworth, “However, the theoretical question posed by Berlinski remains: How can one be sure that Darwinian mechanisms could have accomplished X if one cannot spell out even a hypothetical pathway by which they could have done so? Or cannot even state how many morphological changes (let alone genetic changes) would be required?” --She wasn’t asked about a hypothetical pathway (at least in the linked video). She was asked to literally put a NUMBER on how many changes are necessary to go from cows (cows?) to whales. It’s an absurd question. To illustrate how absurd it is, ask yourself how many changes are necessary to go from one breed of dog to another? Almost every anatomical feature is different from one breed to the next. Every bone changes – in multiple ways. The hair, teeth, ears, tail, paws etc all change – sometimes subtlety, sometimes dramatically. To try to ACTUALLY count – literally - the number of changes (does “hair” count as one change or is each hair counted separately?) would be insane. Apparently in the video above Berlinski actually created such a list of the morphological changes from cows to whales and “stopped at 50,000” – I’d love to see the list. I wonder how long a list it would be to go from Doberman to Chihuahua. “If I were on their side, and were working on whale evolution, I would have dozens of diagrams of comparative anatomy of whales and artiodactyls all over my desk and walls, and books of comparative physiology open all over my study, and would, before even beginning to enter on any particular evolutionary speculation, enumerate the major and minor anatomical and physiological differences between the two creatures I was trying to connect, and determine how many things would have to be altered.” --You don’t think this is commonly done?? How do you think those reconstructions of hypothetical intermediates (those things that Creationists endlessly laugh at as imaginary) are constructed? Just something someone doodled out on their lunch break? I’ve seen literally what you mentioned – in person and often on television on programs about whale evolution – of walls and desks covered with drawings (a WHOLE lot more than “dozens") which are years of work reconstructing fossils and proposed links between fossils in the offices of paleontologists. Paleontologists often rely on such reconstructions to get an idea of where to look for intermediates, as such reconstructions can help discern what environment to look in (should we look at the site of an ancient shallow sea? Perhaps the shoreline?) goodusername

Oh boy. I don't know quite how I'd distinguish a monograph from another kind of writing, but I'd put many of Dembski's papers here in the the category of monograph: http://www.designinference.com/ Which wikipedia, for what it's worth, defines as: "A monograph is a work of writing upon a single subject, usually by a single author. It is often a scholarly essay or learned treatise, and may be released in the manner of a book or journal article. It is by definition a single document that forms a complete text in itself. An author may therefore declare his own work to be a monograph by intent, or a reader or critic might define a given text as a monograph for the purpose of analysis. " http://en.wikipedia.org/wiki/Monograph I guess I was using the word in that sense. I know he hasn't published a great deal of peer-reviewed papers, so I guess I used the word "monograph" to indicate the kind of scholarly self-sufficient exposition of a thesis you'd expect from a peer-reviewed paper. As opposed to some more informal writings on that site. I have not read any of his books. Is that clear? I can't imagine that it is important, but if I inadvertently led you to believe that I had read some of his books then I hope I have now put you straight. I have not. I have read a large number of his online "monographs" aka self-sufficient treatments of his ideas, including his application of NFL theorems to evolutionary algorithms that are available on his website, and his 2005 treatment of CSI in which he claims to review, clarify and extend the ideas in No Free Lunch and The Design Inference. Is that clear now? Elizabeth Liddle

Elizabeth, How do you define monograph? How do you define book? Is a monograph a book? How many monographs has Dembski written? There's a couple points that can be made here. Mung

Mung, for goodness sake, what is your point?

Febble (aka Elizabeth Liddle): I have read a fair number of Dr. Dembski’s monographs and writings, although I have not read the book “No Free Lunch”. However, I have read his piece: Intelligent Design as a Theory of Information

Elizabeth Liddle (aka Febble): no I have not read any of Dembski’s books, as I have already said.

Spit it out, man, I can tell it's bugging you. Elizabeth Liddle

lastyearon (297): No, it was not a lie. However, it was an error. My memory betrayed me. I haven't looked at the video in several months. I remembered two things: (1) That Ms. Scott did not answer Berlinski's question, but rather brushed it off; (2) that she was very angry at him for asking it. My memory of the first point was correct. My memory of the anger was clearly wrong, so I apologize to Ms. Scott for misrepresenting her reaction. I have no idea why I remembered anger; perhaps I conflated the memory of that episode with the memory of some other event where Ms. Scott showed anger. In any case, I misreported what happened, and I thank you for correcting this misrepresentation before it spread any further. However, the theoretical question posed by Berlinski remains: How can one be sure that Darwinian mechanisms could have accomplished X if one cannot spell out even a hypothetical pathway by which they could have done so? Or cannot even state how many morphological changes (let alone genetic changes) would be required? I find it astounding that champions of neo-Darwinism do not find this even an interesting question, let alone an essential one. If I were on their side, and were working on whale evolution, I would have dozens of diagrams of comparative anatomy of whales and artiodactyls all over my desk and walls, and books of comparative physiology open all over my study, and would, before even beginning to enter on any particular evolutionary speculation, enumerate the major and minor anatomical and physiological differences between the two creatures I was trying to connect, and determine how many things would have to be altered. Only after I had done that would I move to the genetic level to start trying to explain how Darwinian mechanisms could have done the job. But apparently, by a kind of divination, Darwinian science is allowed to skip this nitty-gritty descriptive and comparative work, intuiting evolutionary pathways invisible to normal intellects and producing beautiful cladistic diagrams linking artiodactyls and whales. Darwinian biology apparently has secret shortcuts that normal empirical sciences do not possess. Whenever they expected me to believe something that was at first sight impossible or improbable, my physics and my chemistry teachers always showed me all the steps. As a result, I knew they were not bluffing, and respected their knowledge, to the point where sometimes I would accept things from them without being shown all the steps. However, the neo-Darwinians *never* show me all the steps; they never even show me a *tenth* of the steps. And they wonder why I do not accord to them the trust that I put in my chemistry and physics teachers. I would think that the answer to that should be quite obvious. Trust has to be earned. Isn't it about time the neo-Darwinians earned it, by producing some full evolutionary pathways for major organs or body plans? Thomas Cudworth

LYO: It is quite clear to me that Ms Scott became flustered, angry and resorted to intemperate, dismissive language. (I also think Dr Berlinsky could perhaps have been gentler in manner and tone.) More importantly, it is clear that -- at the time when whale evo was being touted as the latest headlined icon -- there was no real substance behind the claim. Ms Scott patently had no clue as to the way the body plan level transformation could or did occur, and on what empirical evidence apart from a priori assumptions and the usual just so stories. And, she was not at all pleased to have that publicly exposed, as her manner and language revealed. I suggest you view the video by Sternberg -- a qualified evolutionary biologist -- here. (A significantly older Berlinski takes up the point further here, too; estimating 50,000 transitional forms to make a cow into a whale. if you think him wrong, explain why on empirical data, bearing in mind also Sternberg's observations on pop genetics and evo.) Let's see where the balance of evidence is on the issue of body plan origination and the origin of associated bio-information and its fixing in reasonable pops under reasonable conditions. On the OP topic, this would have been a splendid contribution of Dr Scott et al to the relevant conference. GEM of TKI kairosfocus

Dr Cudworth: I wonder if this 1997 panel debate is the money shot. GEM of TKI kairosfocus

Thomas Cudworth, you said..

When Eugenie Scott, in public debate with David Berlinksi, was asked the question how many morphological changes would be needed to turn a land mammal into a whale, she flew into a rage (literally).

Which is a lie. Here's the link to the video of the debate (go to 00:39 to hear Berlinsky's question) http://www.youtube.com/watch?v=O5aC6RMurkE lastyearon

Elizabeth Liddle (aka Febble):

no I have not read any of Dembski’s books, as I have already said.

Mung

Febble (aka Elizabeth Liddle):

I have read a fair number of Dr. Dembski’s monographs and writings, although I have not read the book “No Free Lunch”. However, I have read his piece: Intelligent Design as a Theory of Information

Mung

In other words, the next step is to apply the codification of design inferences in (2) to natural systems and see whether it properly leads us to infer design.”

And you don't see the difference between that and your original assertion? What they do instead is to say: the pattern of life must, because of these equations, be designed. Mung

Elizabeth Liddle:

What they do instead is to say: the pattern of life must, because of these equations, be designed.

Let's try this again. Who is they and where do they say "the pattern of life must, because of these equations, be designed." What is this "pattern" you're talking about which you've named "the pattern of life?" Where did you get that phrase from? Which ID theorist? Elizabeth Liddle:

Well, Dembski argues that “Specification” is the “pattern that signifies intelligence” and that living things display this pattern, allowing us to infer that they were designed.

Where does Demski say, "the pattern of life must, because of these equations, be designed?" Where does Dembski say "living things display this pattern, allowing us to infer that they were designed?" In particular, where does he say that in his 2005 paper? The remainder of your post is a red herring so yes, I'm going to ignore it. Mung

Well, I was fairly convinced that Nick’s pathway was plausible. What was wrong with it? Nick Matzke's pathway is not plausible. The problem with cooption in this case is that a functional shift from one protein to another often requires several individually non-adaptive mutations, and the higher the number of individually non-adaptive mutations are required for the functional shift to take place, the less likely it is that that scenario is true. Note that, for example, there ~200 amino acid residues in FliF that remains unaccounted for. That is to say that the origin of those ~200 residues which have no homologues is largely a mystery. How did those ~200aa residues in FliF which are not found in YscJ acquire the functional specificity needed for FliF to function? And the origin of FliG offers difficulties, of course. Given that MgtE (FliG's homologue) is only 20% similar in sequence identity to FliG, it is extremely implausible for the modern MgtE to evolve into the modern FliG. Yet there is no reason to suppose than an ancient MgtE could plausibly evolve into an ancient FliG, since that evolution would probably require the crossing of a neutral gap of several individually non-adaptive residues. There are numerous problems with Matzke's scenario, and I've only scratched to surface here. LivingstoneMorford

kairosfocus: It was on Telic Thoughts. I think the heading was "Oldie but Goodie" or "A Blast from the Past". There is a picture of Berlinski on the still video. It's just a segment of a longer debate between a whole mob of participants on both sides, and many people speak; the but the revelatory moment for me was Eugenie's reaction to Berlinski. That reaction perfectly expresses why all the thoughtful neutrals are inclined to think ID people might be more reasonable. The side that shouts down its opposition almost always has some serious weaknesses that it's trying to cover up. Thomas Cudworth

I mean a step-by-step recipe for building a bacterium with a flagellum, out of a bacterium with no flagellum, not even a partial flagellum.

Which of the many flagella and partial flagella do you mean. Why do you exclude "partial flagella" when there are so many sub-components functioning in bacteria that are not motile? Is it not self-evident that if sub-components are found to have functions in real living bacteria, that the concept of irreducibility is flawed, at least in the case of flagella? Petrushka

"We are not communicating. Are you sure that you have read what I wrote? ..." Ah, but you *are* "dialogging"; and for some persons, mouths-in-motion is what gives life its meaning. Ilion

Elizabeth: We are not communicating. Are you sure that you have read what I wrote? Do you realize what I mean by an evolutionary pathway? By an evolutionary pathway to the flagellum, I mean a step-by-step recipe for building a bacterium with a flagellum, out of a bacterium with no flagellum, not even a partial flagellum. I want to see the flagellum going up in stages before my very eyes, as I can watch a skyscraper going up in stories before my eyes. I want a morphological description of the bacterium for each intermediate stage, an explanation of the selection advantage of each stage, and a list of DNA bases that had to be altered to get to that stage, and what the substitutions were, and the exact locations where all this took place along the bacterial genome. And of course that implies I need a count of the number of necessary stages (10? 20? 100?), and also I need a full discussion of mutation rates and the time-frame that is being hypothesized, so that I can see whether wildly optimistic estimates of favorable mutations are being employed, etc. Now, has Nick provided a pathway *in accord with my specifications*? If so, *where*? (It wouldn't be in a journal article, I can tell you that. A 500-page book, minimum, complete with many diagrams of both DNA sections and morphological changes, would be needed to cover the details I've asked for.) Thomas Cudworth

Dr Cudworth: Do you have a link to the vid and/or transcript of the debate? GEM of TKI kairosfocus

Well, I was fairly convinced that Nick's pathway was plausible. What was wrong with it? Elizabeth Liddle

Easy to answer, Elizabeth: "So Nick only needs to posit a plausible stepwise pathway to infirm Behe." Nick has *not* posited a plausible stepwise pathway from bacterium without flagellum to bacterium with flagellum. Nor has any biologist, living or dead. I specified what is needed for a plausible stepwise pathway. Reread it, then tell me the book or article in which such a pathway has been proposed, for the flagellum or for any major organ or body plan. You won't find any such pathways. In fact, Darwinians deny that they should have to provide them. When Eugenie Scott, in public debate with David Berlinksi, was asked the question how many morphological changes would be needed to turn a land mammal into a whale, she flew into a rage (literally). Yet it was a perfectly reasonable question, one which every mammal evolutionist should be daily trying to answer. Her denial that Darwinians need to produce such answers was revelatory of the degree to which adherence to Darwinian mechanisms has become an article of faith, detached from honest empiricism. With a mentor like that, I don't expect Nick to get very far explaining the origin of the flagellum or of anything else. Thomas Cudworth

Why does he, Thomas? I mean, Behe's position is that the flagellum is "Irreducibly Complex" - that there is no plausible stepwise pathway that leads to it. So Nick only needs to posit a plausible stepwise pathway to infirm Behe. I once made the analogy with the Old Man of Hoy. http://www.flickr.com/photos/mountainandshore/4084206511/ If you saw a photograph with people on top, you might say: there is no way they could have climbed that: they must have been dropped from skyhooks. But if Nick or someone were to look carefully, and show that indeed there is a way up, we have no reason to infer a helicopter. They still might have been dropped from skyhooks; they might have climbed but not taken Nick's route. But we can no longer say they must have been lowered by skyhooks, because Nick has shown there is at least one route that is climbable. Moreover, not only is it climbable, but we know that people can climb; we also have no evidence for skyhooks. Elizabeth Liddle

Nick wrote (58): "The most ironic thing about this debate is that all the published work which ID guys cite in favor of “flagellum-first” rely explicitly on phylogenetics results, which only make sense if evolution is accepted. So to make these arguments at all they have to accept common ancestry over billions of years of evolution. Which, again, means they’ve lost the main debate." This is true only for ID proponents who are confused. I think that it is clear that all the leaders of the ID movement are speaking for the sake of argument. That is, *if* Darwinian evolution were true, and *if* the so-called experts are right, the flagellum post-dates the TTSS, and therefore its origin cannot be explained by the TTSS. And this logic is unassailable. So that leaves the Darwinists without the only viable intermediate step they have come up with. We are in complete darkness as to the transitional phases in the phenotype from no-flagellum to full flagellum, if we can't use the TTSS as a bridging form. All we can do is tell Darwinian fairy tales about imaginary organelles or parts that might have served viable functions en route to the flagellum, and later been co-opted, etc. But it's all free invention, until the Darwinians can (a) describe the physiology of each of the transitional organelles or parts that they have in mind; (b) show that the transitional organelles or parts would be selected, and specify the environment in which they would be selected, and show that that enviroment in fact existed in the earth's past; and (c) specify the genomic changes that would have to occur to produce said organelles and parts. The greatest evolutionary biologist on the planet is not even 1% of the way toward providing this sort of account. So if Nick intends to spend his life explaining the evolutionary origin of the flagellum, he's got his work cut out for him. (And then after he's done that, he has to repeat for the avian lung, the bat's sonar, the cardiovascular system, etc.) Thomas Cudworth

Excellent :) Thanks, Thomas. I have found it true of Dembski's scientific articles as well. Elizabeth Liddle

Mung, Elizabeth: The agreement I spoke of was that, in the books Elizabeth has read, she finds the ID writers calm and non-polemical in tone and focused on scientific rather than religious questions in contents. As for article vs. book, I agree with Elizabeth that an article can be judged on its own merits as an article. My point was not to defend any particular article by Dembski, but only to point out that there is important material in his book that is not in his articles, and to make the more general point that when ID writers put so much stress on longer treatments, it is unreasonable to avoid the longer treatments and seek out only online articles. But Elizabeth has since clarified that she has in fact read some ID books (other than Dembski's) and is working on Meyer's book now, so I don't think we are really disagreeing. Thomas Cudworth

Aha: I just found the UD thread in the archives where I first made may case for Dembski's error: https://uncommondesc.wpengine.com/intelligent-design/id-in-the-uk/ And let me take the opportunity to repeat: I appreciate being here and the welcome I have received in my second incarnation :) Elizabeth Liddle

I should like to observe that, in my view, Dr. Liddle invariably posts in good faith, good humor, and with enormous patience and courtesy. The treatment meted out to her on this forum, often by those who would like us to believe they uphold the highest standards of decency, is nothing short of deplorable. For shame! FrogBox

Mung:

Elizabeth Liddle: This, incidentally is the first scientific error Dembski makes – he sets up his hypothesis incorrectly, and so finds himself in a position where no other hypothesis, by definition, can account for the data.

A lie.

Mung, a lie is a deliberate untruth, right? I do not lie. If my statement is untrue, then it is a mistake. Please tell me why you think it is untrue. I think it is true, and I am willing to support my case. Therefore it is not a lie. It would only be a lie if I thought it was true. If I think an untrue statement is true, making it is not a lie but a mistake. Do not tell me again that I am lying. Thank you. Elizabeth Liddle

Mung:

Elizabeth Liddle: What they do instead is to say: the pattern of life must, because of these equations, be designed. Huh? What is “the pattern of life”?

Well, Dembski argues that "Specification" is the "pattern that signifies intelligence" and that living things display this pattern, allowing us to infer that they were designed. If he isn't arguing that, tell me what you think he is arguing here: http://www.designinference.com/documents/2005.06.Specification.pdf

Cite a source please, for an ID theorist, preferably one who is well known, to substantiate your assertion.

I take it that Dembski is well known enough. Let me also cite: "At the heart of my codification of design inferences is the notion of specified complexity, which is a statistical and complexity-theoretic concept. Provided this concept is well-defined and can effectively be applied in practice, the next question is whether specified complexity is exhibited in actual physical systems where no evolved, reified, or embodied intelligence was involved. In other words, the next step is to apply the codification of design inferences in (2) to natural systems and see whether it properly leads us to infer design." http://www.designinference.com/documents/2000.11.ID_coming_clean.htm That seems to me to be saying that if we can detect specificied complexity in physical systems, we can infer design. Obviously these physical systems include living things. Or are you saying that Dembski and other IDists do not think that living things exhibit specified complexity?

I say you just made it up. I say that the most likely response, if we get one, is that: a) you were misunderstood (we didn’t read your whole post!) b) you didn’t really mean wh you wrote, you meant something else.

Well you often don't read my posts, and you often misundertand me, but in this case you seem to have understood perfectly well. So do I take it that you do not think that specified complexity is exhibited by living things? Or that it is, but it doesn't imply design? Or that ID has nothing to do with any of these issues and that Dembski is out to (free) lunch? Elizabeth Liddle

Mung:

Elizabeth Liddle:

If there is key point in his books that he does not make in his articles, then it does not say much for his articles!

Sure, blame your failure to perform due diligence on Dembski. He should have known you would not read his books, but only his online articles.

Yes, he should. What point is there in writing an article that only makes sense if you also read a book? Especially when the article itself claims to review, clarify, and extend the book? How would any paper ever get through peer-review if it did not stand alone? An scientific paper is not a dumbed down precis. Quite the reverse. A scientific paper must provide all the information the reader needs to evaluate the argument. Retreating to: "well she admits she hasn't read the books" is to concede that the papers themselves do not make sense alone. I doubt that is what Dembski would want to claim. There may well be persuasive alternative arguments in his books that I am unaware of. But the ones he presents in his articles I do not find persuasive, and I am willing to go through each one, if you like, and tell you exactly why. Elizabeth Liddle

Mung:

Elizabeth Liddle: no I have not read any of Dembski’s books, as I have already said. not any. not one. none. Surely then, you’re an expert. I am NOT surprised by this “revelation.” Elizabeth Liddle: I have, however, read all, I think, of his online articles, in considerable depth. Please demonstrate when you first published the fact that you had read Dembski’s 2005 article on specification. There’s nothing quite like a “critic” who has not read the relevant source material.

come again? What are you talking about? Are you asking me when I first read Dembski's 2005 article? I can't remember. Why is it important? If you aren't asking me that please explain your request, I don't understand it: "Please demonstrate when you first published the fact that you had read Dembski’s 2005 article on specification." I have no idea when I "first published the fact that [I] had read Dembski's 2005 article on specification". I certainly read it a while back, so I'm sure I've commented on it somewhere. I know I've commented on this one: http://www.designinference.com/documents/2000.11.ID_coming_clean.htm and this one: http://www.arn.org/docs/dembski/wd_idtheory.htm because I actually did so here at UD a few years ago (and was subsequently banned by DaveScot). Elizabeth Liddle

Mung:

Thomas Cudworth: Glad you agree with me about the contents and style of ID books. Dude. She has admittedly never read a single book by Dembski.

I have read all his online papers. I did not make any comment at all about either the the content or style of his books.

Who has she read? Behe? Johnson? Gonzales? Denton? Berlinksi?

Books Behe, Denton, Sanford, now half of Meyer. Articles by Johson, Behe, Dembski.

Her “agreement” about the “content and style of ID books” is based on what, exactly?

Yes, I'd quite like to know that.

Complete utter freaking ignorance? Seriously.

Let me say once again: If I read a scientific paper (by Dembski or anyone) and it contains what I believe are flaws, it is no defense to say that I need to read a book. A scientific paper should stand on its merits. Right? And: My comment concerned the tone of the books and papers I have read. With the exception of Sanford, they have not contained polemic, but have been calmly reasoned. In that sense I agree with Thomas, and I assume that was the sense in which he gave that response. You are picking fights where there are none. It's a bit annoying. Elizabeth Liddle

Thomas Cudworth, I very much enjoyed your exchange with Lizzie (particularly yesterday). Very insightful and plenty of 'keepers' (as Cannuckian Yankee would put it) in your comments. Chris Doyle

Thomas Cudworth:

Glad you agree with me about the contents and style of ID books.

Dude. She has admittedly never read a single book by Dembski. Who has she read? Behe? Johnson? Gonzales? Denton? Berlinksi? Her "agreement" about the "content and style of ID books" is based on what, exactly? Complete utter freaking ignorance? Seriously. Mung

Elizabeth Liddle:

They do not call that Design a miracle./blockquote> We do not call that "Design" Design. What is it, precisely, that you wish to convey through your use of big D Design? And if big D Design is not a miracle, what is it? How is it that you can understand what is meant by miracle but not understand what is meant by supernatural?

Mung

Elizabeth Liddle:

Can I ask what your field is, Thomas? It might help us understand each other. There is no "field" that helps one understand nonsense. There is no "science of handwaving." There is no field of "I want to believe, therefore..."

Mung

Elizabeth Liddle: What they do instead is to say: the pattern of life must, because of these equations, be designed. Huh? What is "the pattern of life"? Cite a source please, for an ID theorist, preferably one who is well known, to substantiate your assertion. I say you just made it up. I say that the most likely response, if we get one, is that: a) you were misunderstood (we didn't read your whole post!) b) you didn't really mean wh you wrote, you meant something else. Mung

Elizabeth Liddle: This, incidentally is the first scientific error Dembski makes – he sets up his hypothesis incorrectly, and so finds himself in a position where no other hypothesis, by definition, can account for the data. A lie. Mung

Elizabeth Liddle:

If there is key point in his books that he does not make in his articles, then it does not say much for his articles!

Sure, blame your failure to perform due diligence on Dembski. He should have known you would not read his books, but only his online articles. Mung

Elizabeth Liddle: no I have not read any of Dembski’s books, as I have already said. not any. not one. none. Surely then, you're an expert. I am NOT surprised by this "revelation." Elizabeth Liddle: I have, however, read all, I think, of his online articles, in considerable depth. Please demonstrate when you first published the fact that you had read Dembski's 2005 article on specification. There's nothing quite like a "critic" who has not read the relevant source material. Mung

Nick Matzke:

Even the mildest forms of ID depend on insertion of miracles into biological history, even if it’s just to tweak the DNA a little bit. It’s still a violation of conservation of mass/energy

lol. how quaint.

Until miracles are abandoned by the ID movement, ID will be just a form of creationism.

likewise. Nick, do you have an actual argument? Mung

Elizabeth: Ah, I see. Well, all I can say is that it's different in the Arts. Articles are important, but the Book (which is often refereed) remains the focus. And that's of course rooted deeply in the Western tradition of the liberal arts. For me, the issue is: when an author chooses a certain format in which to express his thought, he should have a good reason. If he chooses a book rather than an article, it must be because he thinks he can say certain things only in a book, or better in a book. I respect authors. If they write a book on ID, I will read it without wishing that they had written an article instead, just as, were I a mathematician in Newton's day, I would have read his Principia without wishing that he had written an article instead. Arts professors think in terms of reading books. They think of the book as the main medium of communication for all truly important thought. It's a habit of thought that goes back to the books of Plato, of Homer, of Augustine, of Aquinas, etc. And it's a habit I'll never shake. Of course, I do sometimes wish that some books were 20% or 33% shorter, including some ID books! But that has to do with the author's lack of skill in organization or prose editing, not the decision of book vs. article. I would still maintain that the book form was the right choice for Darwin's Black Box, The Edge of Evolution, The Design of Life, Nature's Destiny, etc., as it was the right form for Darwin. When one is trying for scope, for novelty, and for breaking down old prejudices, one needs many examples and much explanation because the audience may be slow to be convinced, and in such cases the book is the right choice. I would argue that the different procedures in the Arts and Sciences have some bearing on the ID debate. I would argue that a lifetime of publishing by scientists under the conditions you outline creates an entirely different strategy of research, writing and reading. And I would argue that it tends to make scientists more conscious of precise minutiae, and less inclined to big picture thinking. Let me give you an example. I've been involved in many internet discussions of ID. And I've been surprised how often people will vehemently and angrily argue something like this: "On Page 16, Behe mistakes 2-glucy-amino-globulin-major for 2-thucy-amino-globulin-major, and only a dense undergrad would make an error like that. Anyone who would make such a blunder does not know even sophomore biochemistry, let alone evolutionary theory, and has no claim on scientific attention." Now in such discussions, various people will ask these scientific critics whether the alleged error is such that it destroys the entire argument of Behe's book, or only weakens one small part of one sub-argument, still leaving the overall structure standing. Usually these critics refuse to answer, or they grumble that this isn't the only error, though they specify few others, and those they specify appear to be of similar moment, affecting usually only a sentence, or paragraph, rarely a whole chapter and never the whole book. One thus gets the very strong impression that what they are professionally and almost morally offended by is *sloppiness*, *even if they know that this sloppiness isn't enough to destroy his thesis*. I wonder if the scientific system of publishing you are describing -- the emphasis on minute technical articles which have no great literary or philosophical or paradigm-changing virtue, and whose *only* value is that their data or their calculations are correct and reliable -- doesn't produce a sort of "tunnel vision", whereby "good science" becomes identified with "good technical craftsmanship" *and nothing more*. Whereas, in Darwin's day, while there were doubtless many errors in the *Origin* (he produced five more corrected editions), you didn't hear people arguing, "Darwin had the wrong Latin name for the skink on page 34, and that proves he is no true naturalist, so we can ignore the rest of his book as unscientific speculative rubbish by an untrained amateur." In those days, the scientific readers were looking at the big picture, what Darwin was trying to do overall. Is it possible that a lot of the carping against ID authors is not so much due to malice, as just to intellectual narrowness, coming from very competent but undistinguished bench scientists whose idea of good science is a very crude notion of correctness? And that ID people's notion of good science involves reconceptualizing a field in light of a bold new insight? So that what we have is two clashing scientific cultures, the big-picture culture (which is more like the Arts culture) versus the detail culture? And that detail men are often very uncomfortable with big broad questions? Certainly it is the case that many of the ID people have a much stronger "Arts" component in their education than most biologists. Dembski has degrees in Psychology and Divinity as well as Math and Logic; Nelson has a Ph.D. in Philosophy to top off his Biology degree; Wells has a Ph.D. in both cell biology and Religious Studies; Richards has a Ph.D. in Philosophy/Theology; Meyer has degrees in Physics and Geology but a Ph.D. in the Philosophy of Science. Is it perhaps that the broad kind of education that ID people bring to the table clashes with the narrow, more craft-oriented education of most working scientists? And that they overreact to small examples of technical sloppiness as a defense mechanism to avoid having to undertake a searching criticism of the standard paradigm, an epistemologically unsettling kind of scientific activity which is not their forte? Just asking. :-) Thomas Cudworth

Thomas: I agree with you about Origin. It is a great book. But I think you have misunderstood the issue of books vs papers for scientists. Scientific books are not really peer-reviewed at all. Publishers commission books because they want them to sell, and they will commission reviews if they think it will help them sell better, or improve the book. There are some very good scientific books, but they don't count much towards grants, tenure, because they are not peer-reviewed. It isn't that scientific papers lack scope or vision - review papers can have huge scope and be very influential. But they are peer-reviewed. Books are not a step above - they are a step sideways, and mostly slightly down. My husband has over 200 peer-reviewed papers, a few book chapters, and one book. It's a very good book. But it's irrelevant to his CV. I don't read articles rather than books because they are nice and short, or because they are free. I read them because they are cast in a scientific format, and have, normally, undergone the rigor of peer-review, and, if not, at least are written in a format that facilitates rigorous review. Elizabeth Liddle

Point. kairosfocus

Elizabeth: "Here, peer-reviewed publication counts in the humanities as well as science – I’m not aware of any field where tenure depends on books as opposed to peer-reviewed papers, although I am aware of fields where books are a reasonable substitute." You write here as if "book" and "peer-reviewed" are mutually exclusive. They aren't. I was speaking not of popular books that an academic might write "on the side," but fully academic books in the academic's special field. These would be in most cases sent out by the publisher for peer review before the manuscript was accepted for publication. That might not be true for some minor or slightly shady academic publishers, but it would be true for the big high-quality ones. There's no formal requirement of book versus article for tenure; a historian *could* get tenure on the strength of a lot of good articles in major journals. But it's a lot more impressive to have a 400-page book on the Black Plague published by Oxford University Press than to have two or three piddly articles in the Journal of Thirteenth-Century French History. To give you an idea of how tough the competition is: I once applied for a tenure-track job. I had two books published. I didn't get interviewed. I found out who did. He had *four* books (and also articles) published. For an entry-level job!!! So if people are getting *hired* with several books, for someone not to have even *one* book yet, four years after being hired (when tenure review would take place) -- that looks really bad. So most Arts profs try for a mix -- a few articles in journals, hopefully at least one in a major journal, and at least one book with a decent academic press. It's my impression that at the early, pre-tenure stage, scientists don't worry about books at all. They go for lots of articles -- joint articles, solo articles, whatever; ten or twenty or twenty-five if they can manage that much in four years; and departments then go by various ratings systems to evaluate the articles, taking into account the quality of the journals, the author's citation index, etc. So the incentive in science is to produce small, quickly doable, tight pieces of research, which though lacking much scope are likely to get cited precisely because they answer a narrow technical question very well when someone needs it. Arts people, on the other hand, are encouraged to be thinking of large-vision pieces from the very start. Thus, they write more books, and review more books, and read more books, than scientists generally do. Articles are still very important in the Arts culture, but books are thought of as showing more integrative power, as requiring more work, and as giving more prestige to the institution. So Arts people just take it for granted that they will be reading a lot of long, hard, theoretical books in their careers; and they often prefer reading books to articles because they are broader and more stimulating. So when someone says, Dembski has written this great book No Free Lunch, as more of an Arts person, it would never even occur to me to ask: "Hey, that's 400 pages! Has he got anything shorter I can check out?" If that's what's being touted as his decisive theoretical work (as it was at one time), then that's what I felt obligated to read. It would be like saying "Origin of Species"? Ugh. 500 pages. Has this Darwin got anything shorter? Of course, in Darwin's day, no one objected to reading a long and thorough treatment of a breakthrough idea. But back then scientists were gentlemen of leisure, and now they are careerist busy beavers, and they often lack the patience for that sort of time investment. They want brevity, a businesslike precis they can file away in the mind as yet another current view. To me this is very sad. I read *The Origin of Species* through lovingly and patiently, and consider it one of the greatest books ever written. The fact that most biologists today won't take the time to read it is really depressing to me. (And it's even more depressing when they say stupid things about Darwin on their authority as biologists, and I know they are wrong because I've actually read the book, while they're going on hearsay.) Thomas Cudworth

PPS: How could I forget, Wikipedia's ID article must come up for special mention, as a LOCKED-in -- look at the locked article icon, as at a few days ago! (you can't make this up . . . ) -- piece of willful deception. Wiki is simply of no credibility on this subject. kairosfocus

PS: This thread is no 1 on daily popular. kairosfocus

Dr Cudworth Sadly, we need to do both. On long observation, I have found that the favourite and most consistent rhetorical tactic of the evolutionary materialist Darwin defenders is to distract attention from a cogent response or point, by dragging a red herring away towards already set up strawmen soaked in ad hominems and ignited by incendiary rhetoric to cloud, poison, polarise and confuse the atmosphere. To win, they plainly need confused, angry people drunk on toxic materialist rhetoric. This of course is exactly what Alinsky espoused in his Rules for Radicals. Especially in the aftermath of having had an attack on my family by way of the mafioso tactic we know you, we know where you are, we know those you care for . . . and other vile and slanderous things I will not summarise; where my family has absolutely nothing to do with the issues I have addressed, e.g. in the foundations series that has a new post here today, but such outing tactic thuggery is going to have an intimidatory and chilling effect on others.

(SIDEBAR: If they had bothered to ponder on what my given name means and why I got it as a Jamaican, they would have learned that they picked the wrong man to try to intimidate or hurt by personal abuse and threats to his family -- just look up "bydand" and the Jamaican national hero of the same name of that regiment to see why -- but this tells me we are dealing with exactly the sort of ruthless amoral materialist thuggery that Plato warned against: "the highest right is might." NOT. Bullies like this only understand the equivalent of a swift bloody nose from an intended victim in the school yard, and those who egg them on or harbour them will only understand seeing that such tactics backfire bigtime and cost them more than they can afford to pay. They are going to have to learn that when they go nuclear like that, they are going to pay a stiff price, one they have only just begun to pay. The first down payment is that these have now totally lost all credibility and respect, and are now known enemies of the civil peace of justice; in the case of one of my would be tormentors, he is trying to hold up the fig leaf that the girl he took dubious pics of is 23 years old, i.e. half his age, and plainly her face says 1/3 his age or so; so when he came out spewing hate over an expose of damage wreaked by cyber porn, that tells me all I need to know. We need to understand this is what we are dealing with and we must understand that the pretence of civility or morality in such mouths is going to be simply a subterfuge. Until there is clear evidence of repentance and transformation of life, we are dealing with those who have crossed the line beyond mere personal insult to being threats to the civil peace of justice. That is, they have become criminal. The Christian duty is to love sinners while dealing firmly with sin and its destructive effects. That implies a right of defense of the innocent and of the civil peace of justice; why the Magistrate bears the sword as God's servant. Starting with the friendly local police. [Updating the technology, SA 85s and MP 5s. Don't forget, Paul accepted protection of the equivalent of a reinforced armoured cav troop.])

So, yes, we have to get the scientific issues right. We have to get our tone right:polite but firm. We have to deal with worldviews and ethics issues right, and correct a lot of fallacies. Yes, where we make mistakes, these jokers will try to pounce. So, if we see errors, let us correct them, making sure we have the vital points right. But, we have to understand that even where we are right we are going to deal with those who will be willfully deceitful and will construct handy strawmen laced with poisonous ad hominems they can ignite. Such as Dr Matzke et al have plainly done for YEARS in the teeth of all corrections on the "ID is creationism in a cheap tuxedo" smear. What we have to do on this one, is that when we see those who are patently dishonest like this, we have to stop simply trying to please and plead with such to be reasonable and civil. "Nay, my sons . . . " does not work. He who insists on poisonous rhetoric like this in the teeth of correction has identified himself as an enemy of the truth and the right, and as an ally of the sort of internet thugs I am dealing with. Such a person -- hard as it is for me to have to say so -- is, by his persistent actions, a slanderer and a willful deceiver. And yes, Dr Matzke, regrettably, by your actions, that means you. And until you amend your ways, it will continue to mean you. So, please amend your ways before it is too late. Those who cross a nuke tripwire by indulging in thuggery or willful slander and willful deception -- refusing all correction -- have to live with the consequences of the path the have insistently taken. Bydand, GEM of TKI kairosfocus

Elizabeth: I explained neo-Darwinism in another post, but you’ve fallen behind on reading them. Why not space out your replies over several days? It would help both of us.

Probably a good idea. I probably won't get much time to post next week.

I meant that no evolutionary biology is taught *as part of the medical school program*. So if a medical student arrives in medical school without any evolutionary biology, he’ll graduate without any.

Well, that's a shame.

Most, but not all, pre-med students major in biology. Some major in biochemistry (where evolution is not taught); some in chemistry (where evolution is not taught); in some more progressive medical schools, they can come in with liberal arts degrees in lieu of science degrees. But even the ones who major in biology don’t necessarily take much evolutionary biology. Oh, of course they will take an undergraduate course in something like “Genetics and Evolution”, which will be more basic genetics than evolution, but beyond that, they may well never take any courses specifically on evolutionary theory again. That’s the full scope of formal evolutionary knowledge that most medical students start out with. And there’s no evidence that if they knew more about whale evolution they would better be able to diagnose illnesses. So the medical schools don’t make them take any more. Quite sensibly. You mention antibiotic resistance. Are you not aware that ID people have answered that 5 million times? That’s pure microevolution. Doesn’t prove a thing relevant to ID. Read Behe’s Edge of Evolution.

So, it's part of evolutionary theory. So, they'd better understand it.

You can understand how rodent and primate brains differ from human brains by empirical means. You don’t need one stitch of evolutionary theory. Dissect them. Stimulate the lobes. Find out what controls what. All that evolutionary theory of mammal brains will give you is theory-derived preconceptions about what you might *expect* to find in rodent or primate brains; but those preconceptions might be wrong (and probably will be wrong, as evolutionary theory is in constant flux and what it predicts about rodent brains ten years from now will be different from what it predicts today) and in the final analysis only the lab results are of demonstrative force. Rodent brains are what they are, and do what they do, no matter how Margulis or Coyne or Matzke thinks they evolved. Trust your experimental work, and forget wildly speculative evolutionary pathways which no biologist on earth can even enumerate, let alone demonstrate. I’m an intellectual jack of all trades, much like yourself, all over the map, winning a science scholarship but then criscrossing boundaries between Arts and Science, leading to a Ph.D. I studied Music, too. (How can anyone love music and be a Darwinian? What a metaphysical mismatch! Unless maybe the music you love is Wagner, or Strindberg.) But more on my biography another time.

Interesting! But gotta run right now. PS: my field is "early music": http://www.google.co.uk/search?q=Elizabeth+Liddle+viol&ie=utf-8&oe=utf-8&aq=t&rls=org.mozilla:en-GB:official&client=firefox-a with a bit of contemporary (I compose). Elizabeth Liddle

gpuccio, Elizabeth: Yes, move it to a new thread. This one is too long now, and it will get buried. Also, we're already off the Contents page (most recent entries), so no one will know abuot it. It needs a fresh title and a fresh start. gpuccio, don't you have writing privileges here? If you do, why not just start a thread of your own? If not, maybe kairosfocus could start a new one for you. In the meantime, people can continue to talk here about the ongoing subjects. Thomas Cudworth

Elizabeth: I explained neo-Darwinism in another post, but you've fallen behind on reading them. Why not space out your replies over several days? It would help both of us. I meant that no evolutionary biology is taught *as part of the medical school program*. So if a medical student arrives in medical school without any evolutionary biology, he'll graduate without any. Most, but not all, pre-med students major in biology. Some major in biochemistry (where evolution is not taught); some in chemistry (where evolution is not taught); in some more progressive medical schools, they can come in with liberal arts degrees in lieu of science degrees. But even the ones who major in biology don't necessarily take much evolutionary biology. Oh, of course they will take an undergraduate course in something like "Genetics and Evolution", which will be more basic genetics than evolution, but beyond that, they may well never take any courses specifically on evolutionary theory again. That's the full scope of formal evolutionary knowledge that most medical students start out with. And there's no evidence that if they knew more about whale evolution they would better be able to diagnose illnesses. So the medical schools don't make them take any more. Quite sensibly. You mention antibiotic resistance. Are you not aware that ID people have answered that 5 million times? That's pure microevolution. Doesn't prove a thing relevant to ID. Read Behe's Edge of Evolution. You can understand how rodent and primate brains differ from human brains by empirical means. You don't need one stitch of evolutionary theory. Dissect them. Stimulate the lobes. Find out what controls what. All that evolutionary theory of mammal brains will give you is theory-derived preconceptions about what you might *expect* to find in rodent or primate brains; but those preconceptions might be wrong (and probably will be wrong, as evolutionary theory is in constant flux and what it predicts about rodent brains ten years from now will be different from what it predicts today) and in the final analysis only the lab results are of demonstrative force. Rodent brains are what they are, and do what they do, no matter how Margulis or Coyne or Matzke thinks they evolved. Trust your experimental work, and forget wildly speculative evolutionary pathways which no biologist on earth can even enumerate, let alone demonstrate. I'm an intellectual jack of all trades, much like yourself, all over the map, winning a science scholarship but then criscrossing boundaries between Arts and Science, leading to a Ph.D. I studied Music, too. (How can anyone love music and be a Darwinian? What a metaphysical mismatch! Unless maybe the music you love is Wagner, or Strindberg.) But more on my biography another time. Thomas Cudworth

gpuccio:

Elizabeth: The ID argument about the design inference is simple, beautiful and consistent. It can be expressed in various ways, and that creates some of the confusion you allude to. I can discuss it with you in very simple and empirical form. The paper by Dembski you allude to is not, IMO, his best, whatever he thinks. We are not tied in any way to what Dembski thinks. You can criticize it, and I would probably agree with you. In no way that means that the concept of design inference and the explanatory filter are lee strong or valid. For some of the basic concepts about functionally specified information (a concept which is not always clear in Dembski, because he sticks to more general mathematic definitions of specification) I would suggets some papers by Abel, like: “Self-organization vs. self-ordering events in life-origin models” http://adsabs.harvard.edu/abs/.....30;3..211A “Three subsets of sequence complexity and their relevance to biopolymeric information” http://www.tbiomed.com/content/2/1/29 “Constraints vs Controls” http://www.benthamscience.com/.....4TOCSJ.pdf Or you can just discuss that point here, now, with me. Why have I the impression that you are eluding that? :)

Probably because, as I've said, I don't want to hijack Thomas's thread, especially as he has specifically asked us not to. I've suggested we adjourn here: https://uncommondesc.wpengine.com/intelligent-design/is-the-csi-concept-well-founded-mathematically-and-can-it-be-applied-to-the-real-world-giving-real-and-useful-numbers/ Elizabeth Liddle

kairosfocus (237): I agree with you. I'm on your side both in the culture war and on the scientific question of design. But I don't think the two should be mixed together in theoretical discussions of biology. So yes, I'm against Dawkins's biology *and* against his shallow and ignorant attacks on religion; I'm against P.Z. Myers's biology *and* against his revolting verbal treatment of other human beings, which disgraces the very position of university professor and in an older and morally healthier world would have cost him his job; I'm against Eugenie Scott's biology *and* against her tyrannical ideas about science education. But if I accidentally make a bad argument regarding education, ethics or religion, I don't want the argument for design in nature to fail because of that. That's why we need to keep them separate. But I think you are right that at the ultimate level the questions of science and culture come together. The Greeks saw that certain metaphysical positions about nature and certain social and political results were connected. They saw much more clearly than modern philosophers do. So I'm attuned to the connection you are making. But we have to limit our arguments to the capacity of our opponents; and when they are unphilosophical people like Myers and Shallit and Dawkins who cannot grasp metaphysics but only a vulgar, positivist conception of science, that's the level we have to argue at. We will never make them thinkers; but we can show the world that they cannot defend their reductionist science even in its own terms. The rest will follow at the appropriate time, in accord with the rational unfolding of the Good. Thomas Cudworth

Thomas:

Elizabeth (247), you are being silly. I never said anything so dumb at that people in the Arts don’t publish articles. I said the big currency for hiring, tenure and promotion was books. In the sciences, someone could have a stellar career publishing almost nothing but articles — rise to the top of the academic heap. In the Arts that is almost impossible. You have to publish books, and the earlier in your career, the better. You almost certainly won’t get tenure if you haven’t published at least one book, in most Arts fields. That’s not true in most sciences.

OK, fair enough. It's not my experience (I have friends across the Arts and Sciences, as you can probably imagine, given my weird CV!), but it may be true in the States. Here, peer-reviewed publication counts in the humanities as well as science - I'm not aware of any field where tenure depends on books as opposed to peer-reviewed papers, although I am aware of fields where books are a reasonable substitute.

Regarding the importance of evolution for biology, it’s pure propaganda that all of modern biology is undergirded by evolutionary theory. It true that all of modern biology is *glossed* by evolutionary theory. But all the really useful advances in gene sequencing, gene function determination, cell physiology, biochemistry, ecology, medicine, etc. can proceed quite well under six-day creationism.

I disagree. Or, only by being parasitical on evolutionary theory, as it were, just as YEC geologists manage to survive in the oil industry, by making old earth assumptions for the purposes of the work. Although I'm still not quite clear which 10% of modern biology you have the problem with. Perhaps you could explain? Do you accept common descent? Microevolution? Differential reproduction? The spontaneous generation of potentially beneficial alleles? Drift? Speciation?

Only where questions of origins become central would the collapse of evolution harm biology. But questions of origins are almost never central. We never need to know where a biological system came from in order to study how it works.

But it still underpins the study, and any predictive hypotheses.

We only need to know where it came from if we are interested in the question where it came from. But there is no need for more than a handful of biologists to occupy themselves with that question. Tell me, do you have to know the evolutionary pathway from the brain of Zinjanthropus to the brain of the Cro-Magnon in order to do a neural scan properly?

No, but without rodent and primate studies, neuroscience would be way behind where it is, and in order to understand how rodent and primate brains differ from human brains, evolutionary theory is highly relevant. Also genetic imaging is virtually impossible to divorce from evolutionary theory. Yes, as with the YEC geologists, I guess it can be done, but only by deliberately cutting yourself of from any but the most proximal questions. Which seems a weird thing for any scientist to do.

Do you have to know whether Margulis’s theory or classic neo-Darwinism is more correct to explain how axons and dendrons work?

As I'm still struggling to know what "classic neo-Darwinism" is, I'm not sure, but Margulis's theory is potentially relevant. But as I say, if you want to stay focussed on the trees without considering the forest, then it's possible. Handicapping, but possible.

Is there anything you do in your profession that you would have to stop doing if the Cambrian rabbit were found tomorrow? Can you name any scientific profession (other than those obviously based on evolution, e.g., paleontology and evolutionary biology) that would have to stop operating in such a case?

Not "stop operating" but undertake a radical rethink, as I explained above.

Not a single medical school in the USA requires doctors to take a course on evolutionary biology. Why is that, if evolution is central to biology and biology is central to medicine?

I hope that medical schools in the USA require biology, and that it includes evolutionary biology. If not, I'm quite shocked. It's important for many aspects of medicine including the understanding of antibiotic resistance. Also epidemiology.

Prediction could carry on just fine without evolution. If I didn’t believe in evolution, I’d probably guess that things were specially created, and then I’d probably predict that most DNA will have function, and not write off most DNA as “junk,” as many “experts” did. So I’d do knockout experiments to test for function. But even if I were agnostic about origins I could still ask how much DNA has function, and test for it, out of sheer natural curiosity. No overarching theory of origins is required at all. In fact, I might *deliberately* put off grand theories of origins until I knew much better how the organic machinery actually worked. That would be a good, healthy, empirical attitude. But of course it would not make as much work for evolutionary biologists.

Can I ask what your field is, Thomas? It might help us understand each other. Elizabeth Liddle

Elizabeth: The ID argument about the design inference is simple, beautiful and consistent. It can be expressed in various ways, and that creates some of the confusion you allude to. I can discuss it with you in very simple and empirical form. The paper by Dembski you allude to is not, IMO, his best, whatever he thinks. We are not tied in any way to what Dembski thinks. You can criticize it, and I would probably agree with you. In no way that means that the concept of design inference and the explanatory filter are lee strong or valid. For some of the basic concepts about functionally specified information (a concept which is not always clear in Dembski, because he sticks to more general mathematic definitions of specification) I would suggets some papers by Abel, like: "Self-organization vs. self-ordering events in life-origin models" http://adsabs.harvard.edu/abs/2006PhLRv...3..211A "Three subsets of sequence complexity and their relevance to biopolymeric information" http://www.tbiomed.com/content/2/1/29 "Constraints vs Controls" http://www.benthamscience.com/open/tocsj/articles/V004/14TOCSJ.pdf Or you can just discuss that point here, now, with me. Why have I the impression that you are eluding that? :) gpuccio

Elizabeth (247), you are being silly. I never said anything so dumb at that people in the Arts don't publish articles. I said the big currency for hiring, tenure and promotion was books. In the sciences, someone could have a stellar career publishing almost nothing but articles -- rise to the top of the academic heap. In the Arts that is almost impossible. You have to publish books, and the earlier in your career, the better. You almost certainly won't get tenure if you haven't published at least one book, in most Arts fields. That's not true in most sciences. Regarding the importance of evolution for biology, it's pure propaganda that all of modern biology is undergirded by evolutionary theory. It true that all of modern biology is *glossed* by evolutionary theory. But all the really useful advances in gene sequencing, gene function determination, cell physiology, biochemistry, ecology, medicine, etc. can proceed quite well under six-day creationism. Only where questions of origins become central would the collapse of evolution harm biology. But questions of origins are almost never central. We never need to know where a biological system came from in order to study how it works. We only need to know where it came from if we are interested in the question where it came from. But there is no need for more than a handful of biologists to occupy themselves with that question. Tell me, do you have to know the evolutionary pathway from the brain of Zinjanthropus to the brain of the Cro-Magnon in order to do a neural scan properly? Do you have to know whether Margulis's theory or classic neo-Darwinism is more correct to explain how axons and dendrons work? Is there anything you do in your profession that you would have to stop doing if the Cambrian rabbit were found tomorrow? Can you name any scientific profession (other than those obviously based on evolution, e.g., paleontology and evolutionary biology) that would have to stop operating in such a case? Not a single medical school in the USA requires doctors to take a course on evolutionary biology. Why is that, if evolution is central to biology and biology is central to medicine? Prediction could carry on just fine without evolution. If I didn't believe in evolution, I'd probably guess that things were specially created, and then I'd probably predict that most DNA will have function, and not write off most DNA as "junk," as many "experts" did. So I'd do knockout experiments to test for function. But even if I were agnostic about origins I could still ask how much DNA has function, and test for it, out of sheer natural curiosity. No overarching theory of origins is required at all. In fact, I might *deliberately* put off grand theories of origins until I knew much better how the organic machinery actually worked. That would be a good, healthy, empirical attitude. But of course it would not make as much work for evolutionary biologists. Thomas Cudworth

kf: yes, that's a good idea - I'll get back to one of those threads. Elizabeth Liddle

Thomas: I understand that you are angry with Nick. I've said that I disagree with him about ID being about miracles. I have no comment to make on any other role he has played, because I don't know (from primary sources!) what it is. I have however, read his scientific papers which I very much admire. And yes, I'd dearly like to see civilised conversations between IDists and others, which is why I'm delighted to be here. But no, I haven't "read many more internet pages about ID's social side than [I] have read about its theoretical side", although I was once banned from here, not for sneering (the sneering was all the other way), but AFAICT for disagreeing with (technically "not understanding") the science. But I do appreciate that UD has moved on, and I think that's extremely healthy. And given that UD has changed, yes, I'd like to see the quality of the conversation improve from both sides of the ID argument, and I've been very appreciative of those who have welcomed me here, including those who have disagreed with me profoundly. Like you, I find sneers utterly irrelevant to most interesting conversations, which is why I mostly ignore them. Elizabeth Liddle

GP & EL: Actually, I have recently put up threads discussing the CSI and related concepts; cf here and here, actually on two successive days within the past two weeks. The Dembski Chi metric can be empirically simplified and reduced by taking up the logs. Clipping the first link just given:

1 –> 10^120 ~ 2^398 2 –> Following Hartley, we can define Information on a probability metric: I = – log(p) . . . eqn n2 3 –> So, we can re-present the Chi-metric: [where, from Dembski, Specification 2005, ? = – log2[10^120 ·?S(T)·P(T|H)] . . . eqn n1] Chi = – log2(2^398 * D2 * p) . . . eqn n3 Chi = Ip – (398 + K2) . . . eqn n4 4 –> That is, the Dembski CSI Chi-metric is a measure of Information for samples from a target zone T on the presumption of a chance-dominated process, beyond a threshold of at least 398 bits, covering 10^120 possibilities. 5 –> Where also, K2 is a further increment to the threshold that naturally peaks at about 100 further bits [that's a reasonable upper limit for the number of PTQS's or our observed cosmos, 10^150; where even the fastest chemical reactions need 10^30 PTQS's] . . . . 6 –> So, the idea of the Dembski metric in the end — debates about peculiarities in derivation notwithstanding — is that if the Hartley-Shannon- derived information measure for items from a hot or target zone in a field of possibilities is beyond 398 – 500 or so bits, it is so deeply isolated that a chance dominated process is maximally unlikely to find it, but of course intelligent agents routinely produce information beyond such a threshold. 7 –> In addition, the only observed cause of information beyond such a threshold is the now proverbial intelligent semiotic agents. 8 –> Even at 398 bits that makes sense as the total number of Planck-time quantum states for the atoms of the solar system [most of which are in the Sun] since its formation does not exceed ~ 10^102, as Abel showed in his 2009 Universal Plausibility Metric paper. The search resources in our solar system just are not there. 9 –> So, we now clearly have a simple but fairly sound context to understand the Dembski result, conceptually and mathematically [cf. more details here]; tracing back to Orgel and onward to Shannon and Hartley . . . . As in (using Chi_500 for VJT’s CSI_lite [UPDATE, July 3: and S for a dummy variable that is 1/0 accordingly as the information in I is empirically or otherwise shown to be specific, i.e. from a narrow target zone T, strongly UNREPRESENTATIVE of the bulk of the distribution of possible configurations, W]): Chi_500 = Ip*S – 500, bits beyond the [solar system resources] threshold . . . eqn n5 Chi_1000 = Ip*S – 1000, bits beyond the observable cosmos, 125 byte/ 143 ASCII character threshold . . . eqn n6 Chi_1024 = Ip*S – 1024, bits beyond a 2^10, 128 byte/147 ASCII character version of the threshold in n6, with a config space of 1.80*10^308 possibilities, not 1.07*10^301 . . . eqn n6a [UPDATE, July 3: So, if we have a string of 1,000 fair coins, and toss at random, we will by overwhelming probability expect to get a near 50-50 distribution typical of the bulk of the 2^1,000 possibilities W. On the Chi-500 metric, I would be high, 1,000 bits, but S would be 0, so the value for Chi_500 would be - 500, i.e. well within the possibilities of chance. However, if we came to the same string later and saw that the coins somehow now had the bit pattern of the ASCII codes for the first 143 or so characters of this post, we would have excellent reason to infer that an intelligent designer, using choice contingency, had intelligently reconfigured the coins. that is because, using the same I = 1,000 capacity value, S is now 1, and so Chi_500 = 500 bits beyond the solar system threshold. If the 10^57 or so atoms of our solar system, for its lifespan, were to be converted into coins and tables etc, and tossed at an impossibly fast rate, it would be impossible to sample enough of the possibilities space W to have confidence that something from so unrepresentative a zone T, could reasonably be explained on chance. So, as long as an intelligent agent capable of choice is possible, choice -- i.e. design -- would be the rational, best explanation on the sign observed, functionally specific, complex information.]

And of course immediately following I have applied straightforwardly to the Durston et al protein family cases. The debates on Dembski's terms are moot. Notice, the key issue is that observed events E from functionally specific complex cases will be in narrow and unrepresentative zones T from the space of possibilities W. Precisely because of the narrowness and unrepresentativeness of T, in the face of the scope of possibilities W, relatively small samples of he space will be maximally unlikely to land on the shores of zones T. In the case of 500 bits, there are ~10^150 possibilities, 10^48 times the number of PTQS's of our solar system to date. Such a small relative sample is most UNlikely to find cases from T, save by intelligent direction. To break this inference, you would have to find a case where either the zone T is typical and a large fraction of cases from the set W, or else where there is some unknown mechanism apart from intelligence that in the face of high contingency directs one to zones T. GA's and the like, START within a narrow zone of function. Their hill climbing is within a narrow unrepresentative zone T, and so they beg the question when presented as though they solve the problem of finding T in W. GEM of TKI kairosfocus

Elizabeth (243): Glad you agree with me about the contents and style of ID books. As for the culture war questions, what would you have me say? Am I happy that *some* ID people, *many* years ago, produced the Wedge Document? No. Am I happy that Of Pandas and People was rewritten using ID language to disguise its character? No. Am I happy that the Dover School Board used ID for its creationist purposes? No. Do I wish that ID people had stuck to nothing but scientific arguments from the start? Yes. But, you know, Elizabeth, it's funny. I became aware, almost as soon as I heard of ID, of charges that it was closet creationism, that it had a theocratic agenda, etc. Within a few months of reading all the charges and defenses, all the blogs on Discovery and hostile sites, I had things pretty well sorted out. It was clear to me that most ID proponents were strongly motivated by religious faith, that some were fundamentalists and creationists, that many of them were as much concerned about the moral and political reform of America as about science. But it was *also* clear to me that the particular arguments they made, against Darwinism and for design, didn't ultimately depend on these motivations. So I immediately decided: the important part of the ID movement, the part that may have lasting impact on science, and indirectly on philosophy and theology, is this whole set of arguments revolving around design vs. chance, information theory, genetic entropy, etc. I decide that this was the only part of the business worth studying in detail. (If I were a sociologist I might have made a different judgment, since sociologically the other stuff is very interesting.) From then on, I simply made separations as needed. "Darwinism is bad science" -- a scientific claim. "We must oppose Darwinism because it led to Hitler" -- a historical and moral claim. One must separate them. So if some ID proponent makes a bad argument that Darwin led to Hitler (and note that I'm being hypothetical here, not taking sides on that question), and that argument were refuted by a historian, that still wouldn't prove that Darwinism is good science. They are separate questions. So I can take in stride a number of weak or even foolish arguments made by ID people about moral, cultural, political and other issues. They have nothing to do with the crucial question, which is whether unguided processes such as random mutation and natural selection can produced complex integrated biological systems. Now I could achieve that separation of issues, that intellectual clarity, after just a few months of getting the lay of the land. Five years later, I know what I'm doing. But I keep having to argue with people who, after five years or sometimes ten or fifteen years of studying ID, still can't (or more likely won't) make these basic separations. They can't or won't see that the sociology, the history, the science, the theology, etc. all need to be argued separately, and that a bad argument in one area doesn't invalidate a good argument in another one. They can't see that a bad policy blunder by Discovery doesn't invalidate the arguments that Discovery fellows make in their books. Such a person is Nick Matzke. He's still arguing about a Thaxton book published nearly 30 years ago, before modern ID or Discovery ever existed. He's still harping on the Pandas book. In the post-Dover world, the focus of ID has been greatly sharpened. It's now more than ever a theory of design detection. Its proponents now hold regular conferences in which heavy-duty science is discussed in serious papers -- evolutionary computer algorithms, genetic entropy, molecular evolution, organism-centered vs. gene-centered evolution, etc. The peer reviewed papers are starting to come out. The books are slowly getting grudging attention from at least a few non-doctrinaire scientists. This is what Nick should b e focused on. Not ID's past, but its present and future. You know, if I were judged by what I was like as a teenager, I would have been condemned by the world before I could get started. I was immature, irregular, finding myself. Sometimes I acted well, and sometimes like a jerk. In the end I overcame many of my negatives and grew up into something moderately positive. Movements, like people, need time to define themselves, achieve a focus, and accomplish something. I'm not going to go back into Nick Matzke's yearbook and say: "Gee, what a stupid witticism you wrote under your photo, Nick; you can't possibly be an intelligent evolutionary biologist if you made a joke like that about Bono." And I'm not going to look at the fact (if for the sake of argument it was a fact) that Nick once belonged to the Youth Libertarian Party, and say, "Gee, Nick, the fact that you were a libertarian explains the roots of your Darwinism and proves that all your science is governed by a philosophical agenda." I'm going to cut Nick some slack, and say: "Nick, if you can write some good, fair, objective science, I will never try to undermine it by referring to your yearbook or your youthful political adventures." But Nick won't cut ID that slack. He won't read the books I've recommended, and limit his commments on ID to the arguments in those books. He insists on dragging up other stuff. And what applies to Nick applies to all the other people I've named -- whose internet and other activity you seem to be barely aware of. They should let Pandas go, and let Dover go, and let Thaxton go, and let the Wedge go, and *meet the arguments posed in the books*. If they cannot make this separation, if they insist on making essentially *ad hominem* arguments against ID, we cannot have a rational discussion. We can only re-enact stupid culture war fights which I and all the more sophisticated ID proponents want to leave behind. So again, I grant you that ID people have done some dumb things and taken some dumb stands. But none of those things touch ID at the theoretical heart. I'm a thinker. I do theory, not culture-war politics. So I'd appreciate if if you would let the culture-war stuff go, and if Nick would be man enough to admit that he has played culture-war politics himself, and that he is every bit as guilty as any Discovery person at doing so. He has deliberately misled the public about Behe and Denton and the main theoretical claims of ID. He should apologize, and desist. But he won't. He will keep sputtering his defenses, keep bringing up ancient history like Thaxton etc. And that tells me that his arguments against ID must be really lousy. If he had good ones, he would be arguing about information theory and genetic entropy, not Thaxton and Pandas. If you bring up ID's social behavior again, Elizabeth, I won't reply. It's irrelevant the questions I'm interested in. And you dwell on it far more than is good for your mind. It's clear that you've read many more internet pages about ID's social side than you have about its theoretical side. I suggest you reverse that proportion. In the future, if ID should prove to have any valid insights at all, that reshape any aspect of biology, what will be remembered is not Dover and Pandas and the NCSE and the Pharyngula; all of that will be footnotes of interest only to dusty historians. What will be remembered is the few key books and articles where the arguments were made. So far, those arguments have been addressed 80% by sneers and ad hominems and only 20% by calm scientific discussion which treats ID authors with dignity. I'd like to see that changed. I hope you would, too. Thomas Cudworth

Thomas:

Elizabeth: By the “Arts” subjects I meant the Humanities and Social Sciences, not the creative arts.

For some reason this made me laugh! But do you think that academics in Humanities and Social Sciencies do not publish papers in peer-reviewed journals? That they only write books? Really?

The place to argue the details of Dembski and Behe is not on this thread. You will have to raise your objections in some other thread on Behe or Dembski when their arguments come up.

I agree. That's why I suggested a different thread.

However, from what you tell me, your undergraduate degree was in Music and your graduate study was in neurology or neurological imaging technology. That does not give me confidence that you have enough knowledge in the field of Probability Theory (in which Dembski holds two Ph.D.s, one from a Philosophy Department, one from a Math Department) or Information Theory (which Dembski has been working on for years now in collaboration with several specialists in that field) to be sure that you have refuted or even fully understood Dembski’s arguments.

And so it should not. You should wait for my refutation, and evaluate it on its merits, not take it on trust, whatever my credentials. But, FWIW, my first bachelors was in Music,and my second in a slightly more quantitive subject (or at least with quantitive parts), architecture. I took various programs in linguistics (an important aspect of information), and my masters was an application of linguistic theory to urban design and semiotics. My PhD was in Cognitive Psychology, and of course required statistical training. I currently work in neuroscience, which is heavily statistical (an fMRI brain image is in fact a statistical map, the result of, usually, a set of General Linear Models). My work also includes writing statistical programs, including bootstrapping/Monte Carlo algorithms, as well as stochastic computational models of cognitive processes. So I do have a bit of expertise, as it happens, in probability theory. But it certainly does not rule out the possiblity that I may have misunderstood Dembski's arguments.

The mere fact that you are a scientist doesn’t make you any more than a layman in scientific specialties that are not close to your own area of research.

Well, it does a little. I can read the equations. And, as I say, I compute probabilities daily. But obviously that does not mean you should take my word for it that I have refuted Dembski.

But in any case, if you do have knowledge enough to refute Dembski, you are free to publish your arguments. Let us know when and where. Until you do produce such a publication, I disregard your claim to have found fatal flaws in any of his work. Claims like this are a dime a dozen on the internet.

Sure, that's why I suggested a thread. But you are probably aware that some refutations have already been published?

By the way, in No Free Lunch Dembski applies his math to Behe’s flagellum example. It is likely that you will find most of your objections to Behe’s discussion of the mousetrap and other things answered by Dembski’s treatment. Another advantage of reading book-length treatments.

Well, I trust Dembski to apply his math correctly. What I dispute is that it's the right math.

“But IDists do not seem to find it necessary to acquaint themselves with the whole of modern biology before deciding it is fundamentally flawed, so why should we do differently with ID?” This is wrong, and I’ve already refuted it another reply to you. ID does not say that the whole of modern biology is fundamentally flawed. ID proponents think that 90% of modern biology is entirely sound. But the evolutionary gloss which is attached to it is in their view unsound.

But modern biology does not have a "evolutionary gloss". Evolutionary theory is fundamental to modern biology.

If a Cambrian rabbit were found tomorrow, 90% of empirical biology would go on as if nothing had happened.

Well, no. Or rather, yes, because that Cambrian rabbit would almost certainly be either a fake, or an extraodinary example of convergent evolution. But the fact is it doesn't exist. But to put your point differently: if it could be shown that some feature (the bacterial flagellum for instance) really is unevolvable - that some features of biology really are not just irreducibly complex (which isn't a problem) but cannot be reached by any incremental pathway that does not involve a fatal intermediate step, then, yes, empirical biology would be fundamentally shaken.

The honorific evolutionary glosses in the last couple of paragraphs of the writeups would simply be dropped from future articles; but those glosses are inessential to scientific progress anyway. Give me a good empirical knockout experiment which determines actual gene function over some hypothetical evolutionary origin story of that gene any day.

You underestimate just how great the debt is that modern biology owes to Darwin. Sure, you could continue to write papers on biochemistry and genetics, and biological functions, but they would no longer make much more than proximal sense. There would now be a huge new force at the heart of biology, the properties of which would be completely unknown, and render predictive hypotheses useless. And without predictive hypotheses, science is impotent. Elizabeth Liddle

Elizabeth: By the "Arts" subjects I meant the Humanities and Social Sciences, not the creative arts. The place to argue the details of Dembski and Behe is not on this thread. You will have to raise your objections in some other thread on Behe or Dembski when their arguments come up. However, from what you tell me, your undergraduate degree was in Music and your graduate study was in neurology or neurological imaging technology. That does not give me confidence that you have enough knowledge in the field of Probability Theory (in which Dembski holds two Ph.D.s, one from a Philosophy Department, one from a Math Department) or Information Theory (which Dembski has been working on for years now in collaboration with several specialists in that field) to be sure that you have refuted or even fully understood Dembski's arguments. The mere fact that you are a scientist doesn't make you any more than a layman in scientific specialties that are not close to your own area of research. But in any case, if you do have knowledge enough to refute Dembski, you are free to publish your arguments. Let us know when and where. Until you do produce such a publication, I disregard your claim to have found fatal flaws in any of his work. Claims like this are a dime a dozen on the internet. By the way, in No Free Lunch Dembski applies his math to Behe's flagellum example. It is likely that you will find most of your objections to Behe's discussion of the mousetrap and other things answered by Dembski's treatment. Another advantage of reading book-length treatments. "But IDists do not seem to find it necessary to acquaint themselves with the whole of modern biology before deciding it is fundamentally flawed, so why should we do differently with ID?" This is wrong, and I've already refuted it another reply to you. ID does not say that the whole of modern biology is fundamentally flawed. ID proponents think that 90% of modern biology is entirely sound. But the evolutionary gloss which is attached to it is in their view unsound. If a Cambrian rabbit were found tomorrow, 90% of empirical biology would go on as if nothing had happened. The honorific evolutionary glosses in the last couple of paragraphs of the writeups would simply be dropped from future articles; but those glosses are inessential to scientific progress anyway. Give me a good empirical knockout experiment which determines actual gene function over some hypothetical evolutionary origin story of that gene any day. Thomas Cudworth

gpuccio:

Elizabeth: Not that paper, please. Many of us have difficulties with it. The fact that it is more recent does not mean that it is the best.

Really? So a paper that Dembski regards as reviewing, extending and clarifying his earlier work, including those of his two books, The Design Inference and No Free Lunch is not his best? Where do you think he goes wrong?

I suggest instead that we discuss the design inference as we have many times presented here (especially with kairosfocus, Stephen B and others), based on a much simpler concept and on more direct biological arguments.

But this is the problem, gpuccio! The goal posts are constantly moving! Nobody seems to agree with anyone else about what Information is, or what even what Design is! And yet people seem sure that ID is a valid inference. To tackle this properly, it seems to me that what we (or you, with or without me!) have to do is to take each argument, individually, and see whether it has merit. Some may, some may not. For example, I think the best ID argument, frankly, is probably Meyer's - it's an application, as I understand it of Behe's concept of Irreducible Complexity to the OOL problem (a much more sensible place to locate it - IMO). It's not an anti Darwinian argument though, it's an anti abiogenesis argument. So it seems to me it would be useful, at least, to establish whether other arguments (e.g. that macroevolution cannot occur by Darwinian means, just microevolution; that random mutations cannot create information; that rm+ns cannot be creative; that GAs involve smuggled information; that the genome must have been frontloaded) have intrinsic merit. My view is that they do not. I think it is readily demonstrable that they do not. However, I think it is less readily demonstrable that an organism capable of Darwinian evolution could emerge from non-self-replicating entities, or that even if it could, that that it could evolve to be as complex as a modern-type cell (with ribosomes). But that would involve being selective (heh) - finding out which ID arguments and theories have merit and which do not. It is my view that many do not. I'm intrigued that one of the most prominent is one you would rather not suject to critique. *evil grin* But can you imagine better evidence for the integrity of the ID movement for a group of ID proponents to subject a key paper to critical scrutiny, and conclude that it does not hold water? Or, even better, conclude that it does, having openly subjected it to intense cross-examination? Because it seems to me that the ID movement suffers from what is called the "faggot fallacy" - that a bunch of weak sticks is as strong as a strong stick (actually it can be, but that's a fault with the metaphor, not with the definition of the fallacy!) In other words, that several weak arguments amount to a strong one. They don't, and they especially don't if they actually contradict each other as IMO many ID arguments do. So a good place to start in restoring the reputation of ID, is not to lambast Nick, but to subject the body of argumentation itself to rigorous debate, throw out what doesn't work, face the truth wherever it may lead (not to atheism - very few arguments lead inescapabley to atheism and certainly not Darwinism), and make it clear that whatever its theological implications, ID is rigorous science not religion. By doing rigorous science. Elizabeth Liddle

Elizabeth: Again, not that paper. We can easily define functional specification empirically, for all that is needed in our scientific debate about ID and evolution. there is no need of other definitions. gpuccio

Thomas, I absolutely agree with you that Dembski, Behe, Meyer and others do not incorporate theological arguments or anti-atheist polemic into their scientific works. I have not said that they do! It was precisely my point to Nick that they do not. However, that does not infirm my other point, regarding some quite extrordinarily own-foot-shootings by IDists when it comes to the culture wars, Pandas being one, the Wedge being another, and Expelled being a third. That is what I mean when I say that IDists bear a large share or responsibility for any misunderstandings about their project. But I must re-emphasise, it seems: I do not fault ID science because it is couched in polemic. Mostly it isn't. In fact, I don't think there's any polemic in any of Dembski's papers that I have read. And Meyer's book (what I have read of it so far) is a model of even-handed clarity. My issue is solely with the argument itself. In the abstract of Specification: The Pattern That Signifies Design, Dembski writes:

Specification denotes the type of pattern that highly improbable events must exhibit before one is entitled to attribute them to intelligence. This paper analyzes the concept of specification and shows how it applies to design detection (i.e., the detection of intelligence on the basis of circumstantial evidence). Always in the background throughout this discussion is the fundamental question of Intelligent Design (ID): Can objects, even if nothing is known about how they arose, exhibit features that reliably signal the action of an intelligent cause? This paper reviews, clarifies, and extends previous work on specification in my books The Design Inference and No Free Lunch.

This seems to me to make it clear that the content of the paper a) addresses "the fundamental question of Intelligent Design" as perceived by Dembski and that b) it covers (indeed, extends and clarifies) the essentials of his two books, The Design Inference and No Free Lunch. And this paper seems to me to be fundamentally flawed. I am happy to discuss it here, or on a purpose-built thread :) Elizabeth Liddle

Elizabeth: Not that paper, please. Many of us have difficulties with it. The fact that it is more recent does not mean that it is the best. I suggest instead that we discuss the design inference as we have many times presented here (especially with kairosfocus, Stephen B and others), based on a much simpler concept and on more direct biological arguments. We can do it here, or kairosfocus could start a new thread. I would willingly start with my empirical definition of the design inference, and the others could give their version. And you are free to debate what we say. gpuccio

Well, how about someone starts a thread about one of Dembski's papers (I suggest this one, as it is relatively recent, and seems to be key: http://www.designinference.com/documents/2005.06.Specification.pdf) and we can have a kind of journal club on it? Obviously the best person to do so would be Dembski, but maybe kf would do it? Elizabeth Liddle

Elizabeth: "The scientific output that I have read, including key papers by Dembski, and Behe’s first book, I find deeply flawed, logically. But that doesn’t make them not-science, it just makes them bad science." Still waiting for the details. gpuccio

Thomas Cudworth - no problem about the misunderstanding. What matters is that we understand each other now :)

Even if you had not identified yourself as a scientist, your remarks about “books vs. articles” would give you away as one. No “Arts” professor would ever utter the words that you did. In the Arts, articles are great, but books are the currency. It’s books, not articles, that get you jobs and tenure in most cases.

Indeed. My first degree was in music, and what got most people tenure was musical composition or performance :) But the entire point of this discussion is not whether ID is good Art, but whether it is good science, isn't it?

Second, I completely disagree with you when you suggest that that you should not expect to find things in Dembski’s books that aren’t in his online articles. This is partly for the reason given above: books are a different thing from articles, something scientists often don’t seem to appreciate. In a book you make a sustained argument that involves the intricate interconnection of many different things; in an article you write up the results of one experiment or criticize one particular idea. Scientists’ bread-and-butter is publishing scores or even hundreds of very focused articles, but you can’t achieve integratation of a broad range of questions at article length.

Oh, sure. But it means that if I find a flaw in the argument when cast as a scientific article, it's not much of a defense to say: "oh, but you need to read the book". The argument should stand alone, right?

That’s why Darwin wrote *The Origin of Species* and not a 15-page journal article. The ID people, in their books, are trying to present a broader synthesis of some previously unrelated ideas, and for that, book-length is often necessary.

Yes, sometimes it is. But it would be perfectly possible to condense the argument in Origins to the length of a scientific article. It is already structured in that way.

So it’s unreasonable to expect that Dembski should accommodate you by making sure that his entire argument in *No Free Lunch* (which I’ve read in its entirety, very carefully) is available in article form. It’s still less reasonable to expect that it should be available in articles that are accessible via the internet! You must be from a younger generation that expects everything to be electronically accessible.

Well, no :) But I do expect that his scientific reasoning should stand alone in his scientific articles, and I also expect that his key argument should be expressible in that format. Indeed, I'd hope it could be expressible in abstract format.

But in fact many of the most important books and even articles are not available online and must be read in the old-fashioned way, between paper covers. Anyone who is serious about learning what ID argues will read the key ID sources that are not available online, as well as those that are.

But what if what is available online contains serious logical flaws? My issue is not with paper versus pixels, it's whether the papers, with titles like "Specification: the pattern that signifies intelligence", which Dembski himself has cited as encapsulating his latest thinking on how Intelligence can be detected, actually survives critical review. And, from this site: "In a broader sense, Intelligent Design is simply the science of design detection — how to recognize patterns arranged by an intelligent cause for a purpose". So why would I not expect to find the essence of the ID argument in a paper,by Dembski, entitled: "Specification: the pattern that signifies intelligence"? Sure, there may be other interesting related matters that would be interesting to read, but if there is a flaw in a paper that purports to answer the very issue at the heart of ID - how to detect intelligence - why should I read further?

Third, you mention only Dembski. I asked you about ID authors generally. Are you saying that the only ID author you have read (as opposed to read about) is Dembski, and even there, only those parts of his work that are available online? If so, you are hardly going to have a good first-hand knowledge of ID thinking.

Fine. If there are ID scientists who make better founded claims, cool. But if one major, highly cited argument bites the dust, highly cited, moreover, by those other authors, then why should I pursue ID further? But FWIW, I've read Behe's Darwin's Black Box, and also found it deeply flawed. I have not read his latest, but I see no evidence that he has addressed the flaws of DBB. Indeed, I was somewhat appalled to see an interview with him, where he went right back to his original "mousetrap" concept, despite at one point having modified it considerably in responses to critiques to include degrees of irreducibility, as though there had never been a problem. There is a limit to the number of chances I will give a theory when everything I've read so far seems to have glaring holes. So let's at least start with what I think are holes - if they aren't, then sure, I'll go further. But IDists do not seem to find it necessary to acquaint themselves with the whole of modern biology before deciding it is fundamentally flawed, so why should we do differently with ID?

And it hardly fits in with this claim: “I am a trained academic, like many here, and I try where possible to go to primary sources for my information.”

Yes, it does.

If the only ID person you have read is Dembski, and only that portion of his works which is available online, you are not behaving “like a trained academic” when you post opinions about ID for all the world to see. A trained academic would have spent a great deal of time in the library (or at the bookstore) acquiring books, essay collections, photocopied articles, etc., before making a judgment about what ID says and what its weaknesses are.

No, you are conflating two different things. If I was claiming to be an expert on ID, I would indeed be expected to have read the vast majority of literature on the subject. However, I am not. I am merely claiming that a large number of arguments made for ID are flawed. I do not accept, as a counter-argument, the excuse that I have not read enough articles. At a journal club, we evaluate papers on their merits. If the paper doesn't make sense, it makes no difference that the authors have published books and other papers that do. The whole format of scientific publishing is that you make a self-sufficient argument. If that argument fails, it fails, it is not compensated for by some book chapter elsewhere that may not.

Fourth, pertinent to this, on another thread you make this comment: “Not only is it bad science, but there has been an extraordinary reluctance on the part of most IDists even to respond to the criticisms of it as science.” Again this makes me wonder how much ID material you have read, even online mateial. For example, we have here at UD an archive of all of Behe’s responses to the scientific critics of *The Edge of Evolution*. They are focused on the science of ID, and Behe answers in detail, often citing science journal literature in his discussions. Have you read any of those responses?

I do concede that I was primarily talking about Dembski's arguments. I'm better qualified to evaluate those than Behe's, as I am not a biochemist.

You will also find numerous responses to alleged scientific criticisms of ID on the Discovery web site, written by many different ID supporters, and in many ID books (by Wells, Dembski, etc.) which are not available online. Behe has refuted Miller regarding the flagellum in many places, including in his essay in the Dembski/Ruse collection (a volume which anyone purporting to offer an informed opinion on ID should have read).

Fair enough. As I said, I was primarily talking about Dembski's thesis, not Behe's. I don't think much of Behe's either (from reading DBB) but I haven't kept up with the discussion about The Edge of Evolution.

Your insinuation that somehow the movie *Expelled* is to be taken as one of ID’s main scientific defenses — when it was made by Ben Stein and some independent filmmakers, not by ID scientists — is ludicrous. That film did not purport to be a work *of* science, but a work about the implications of science and about the politics of science. Whatever its flaws, it doesn’t bear on the question you raise about ID’s scientific defense.

It bears on the question as to why IDists get accused of being all about religion, which was my point. I don't quite know why this is such a difficult point to get across, but I'll try again: I have no problem with the idea that ID is science. The scientific output that I have read, including key papers by Dembski, and Behe's first book, I find deeply flawed, logically. But that doesn't make them not-science, it just makes them bad science. I have also no problem with the idea that people should not condemn ID science on the grounds that it is religion/creationism in disguise. They shouldn't. However: I would lay a heavy burden of responsibility for this unfortunate state of affairs on ID proponents themselves, for tying their science to ideological projects (the Wedge), for trying to write a high school textbook about ID by editing a Creationist one, in places using no more than Find and Replace, and for allying themselves with a movie like Expelled, in which the science of origins and a stance on God are made to appear one and the same.

Be aware, also, that ID people cannot always get their scientific responses published. Some of Behe’s letters to major science journals, rebutting false claims about his work in reviews, have not been published by those journals.

Which is why I did not include formal peer-review as an absolute criterion. If someone can't get a paper published, fortunately the internet allows them to post it online. This is a huge advance in terms of freedom of speech. But that does not mean they will escape peer-review (and formal peer-review is only part of the peer-review process anyway). Ultimately, a scientific argument stands or falls on its merits. My view is that all the scientific arguments for ID that I have read, which clearly is not exhaustive, fall. I will however readily concede that there may be arguments for ID that I have not read, that do not fall. I am currently half way through Meyer's Signature in the Cell. I have some fairly serious issues so far, but will hold off until I see whether he resolves them, as it is a book, not a paper. I think he has a better point than most. But if a stand-alone article does not stand up to scrutiny, and I have found none of Dembski's that do, then it doesn't make me optimistic that I will find a better argument in one of his books. Elizabeth Liddle

Thomas: And I think you agree with me there. Absolutely! :) gpuccio

Dr Cudworth: There is another issue, that has been on the table since Plato in The Laws, Bk X gave a clear warning: evolutionary materialist factionism and its amoral principle that the highest right is might. When I point this issue out and call for a principled defense of our civilisation, I am not being merely hot under the collar, I am pointing to a wider worldviews issue that is credibly a danger to our civilisation, and which motivates some pretty serious willful manipulation and even outright thuggery, internet and otherwise. And while I of course am strongly in favour of focussing on the scientific issues [cf here today], I also have to bear in mind this side. Especially given recent direct threats made against my family by some of those internet thugs, cheered on by all too many of the darwinism defenders. GEM of TKI kairosfocus

Dr Liddle: Pardon, but how many times have we had to go over misreadings of the design filter, the sequence of its nodes, and the point that the inferences are (1) hi/lo contingency then (2) presence/absence of FSCI? GEM of TKI kairosfocus

Elizabeth Liddle re 220: Thank you for correctly representing the ID position regarding miracles to Nick. I am glad to see that you have not *completely* swallowed the propaganda of ID's critics. :-) Nick should know better, as he has been one of the major and vocal ID critics for years. He shouldn't be criticizing ID if he doesn't grasp the basic point you made. You are right that some ID proponents go overboard in *equating* Darwinism with atheism. However, there are strong thematic and historical connections between Darwinian arguments and atheism. Darwin himself was not an atheist (rather, at the end of his life, apparently a muddled agnostic), but there is no doubt that, as Dawkins says, Darwin's uncompromising naturalism, and more important, his uncompromising antiteleology, was a gift to atheists. And if you are predisposed to be an atheist, *something like* Darwinism must be the truth about the origin of species (and *something like* Carl Sagan's molecules to man picture must be the truth about the universe overall). The atheist thus has a very strong reason to endorse Darwinian evolution or some modified version of it. I'm all in favor of examining the science of ID "without ideological priors" as you put it. The difficulty is that the loudest culture-war critics of ID, who have been poisoning the well against ID (with charges of miracles, God of the Gaps, etc.) are loaded with ideological priors. Shallit, Rosenhouse, Chu-Carroll, Myers, Moran, Dawkins, Coyne, Lewontin, Provine, Weinberg, Dennett, Forrest, Eugenie Scott -- the list goes on and on. These people, along with a legion of atheist bloggers who are generally too cowardly to reveal their names as they utter base and vile personal insults to Behe, Dembski, etc., have sought to shape the public image of ID from the beginning, to portray it as religion with little or no scietific content, while themselves explicitly or implicitly pushing a non-neutral, materialistic, antiteleological understanding of nature. If you would read some of the ID books I have asked you to read -- Behe's two books, The Design of Life by Wells and Dembski, No Free Lunch by Dembski, Signature in the Cell by Meyer, Nature's Destiny by Denton, etc. -- you would find that these ID people write with great politeness, great calm, and attempt to base their arguments on scientific data, not on theology or metaphysics. They don't name-call their opponents or fulminate against alleged connections between Darwin or the Holocaust or anything of the sort. I am not saying that the scientific arguments in these books are flawless or beyond criticism. I am saying that they are written in the way that you are calling for, with theoretical detachment. If you compare these books with the anti-ID literature -- Miller's two books, Pennock's book, Gross and Scott's book, etc. -- you will find a huge difference in tone and attitude. The ID books are much closer to the tone and attitude we expect from scientists; the anti-ID books read in many places like fiery tracts. they are loaded with indignation, accusation of bad motives, etc. So I don't accept your conclusion that ID people have brought most of their trouble upon themselves. Yes, some people on ID blog sites such as this one get hot under the collar and rage against atheism and spout Christian holy war against modern materialism and immorality and so on; but if you want to know the heart of ID as theory, read the books I've indicated. You may be pleasantly surprised. Thomas Cudworth

To sum up the people who know the most about ID and Creation know and understand the differences between the two. And teh only people who try to conflate ID with Creation are the people with an agenda. ALL formal definitions of "Creationism" state it relies on the Bible. OTOH if the Bible were falsified today ID would not be phased. Creationism satnds and falls with the Bible. ID stands and falls with the scientific data. But of course Nick Matzke exposes his ignorance of ID when he said:

Even the mildest forms of ID depend on insertion of miracles into biological history, even if it’s just to tweak the DNA a little bit.

Wrong again Nick, as usual. No miracles needed unless you are saying that Dawkins "weasel" program was written by and runs on a miracle. Joseph

gpuccio @ 216: I agree with what you say here, subject to the qualifications you've carefully put in. Yes, ID can probably infer *something* on each of the points you raise. My point was that ID methods (the application of notions such as information and irreducible complexity) do not commit ID from the outset to any decision regarding supernatural vs. natural causes. And I think you agree with me there. Thomas Cudworth

Elizabeth Liddle @ 217: Sorry I misunderstood your intent. Please understand the reason. 99% of the people who have ever referred to the Dembski quotation about the Logos-theology of John have misused it for polemical purposes, i.e., to prove that ID improperly confuses religion with science, or to prove that ID rests on theological arguments. So when I saw it in your post, I jumped to the conclusion that you were doing the same. (Especially when your remarks about the Pandas books and the Dover Trial seemed to indicate that you had been reading the sort of internet sources that regularly draw that conclusion about Dembski.) I agree with you that ID people are more likely to draw explicit theological conclusions from their theory than evolutionary biologists are. As a side point, however, I'd add that this means little; as a point of fact surveys have shown that biologists lean very strongly towards atheism/agnosticism and that "elite" biologists (NAS members) have among the strongest inclinations toward atheism/agnosticism of all elite scientists. (Noticeably higher than, say, elite mathematicians.) And of those who hold full-time positions *specifically in evolutionary biology*, I suspect that the numbers would be 95% or higher atheist/agnostic. Outside of paleontology (Conway Morris and one or two American TEs), I can't think of a full-time evolutionary biologist who is a religious believer. So it's not as if there isn't a religious connection; it's just that the biologists don't openly talk about it as much. The fact that only a small proportion of biologists is loudly and aggressively atheist about evolution doesn't mean that evolution hasn't quietly influenced many more to the same conclusion. Of course, I'm not drawing a necessary logical connection between *any* form of evolution and atheism. But the neo-Darwinian form of evolution has proved very friendly to it. Regarding what you read, a few quick points: Even if you had not identified yourself as a scientist, your remarks about "books vs. articles" would give you away as one. No "Arts" professor would ever utter the words that you did. In the Arts, articles are great, but books are the currency. It's books, not articles, that get you jobs and tenure in most cases. Second, I completely disagree with you when you suggest that that you should not expect to find things in Dembski's books that aren't in his online articles. This is partly for the reason given above: books are a different thing from articles, something scientists often don't seem to appreciate. In a book you make a sustained argument that involves the intricate interconnection of many different things; in an article you write up the results of one experiment or criticize one particular idea. Scientists' bread-and-butter is publishing scores or even hundreds of very focused articles, but you can't achieve integratation of a broad range of questions at article length. That's why Darwin wrote *The Origin of Species* and not a 15-page journal article. The ID people, in their books, are trying to present a broader synthesis of some previously unrelated ideas, and for that, book-length is often necessary. So it's unreasonable to expect that Dembski should accommodate you by making sure that his entire argument in *No Free Lunch* (which I've read in its entirety, very carefully) is available in article form. It's still less reasonable to expect that it should be available in articles that are accessible via the internet! You must be from a younger generation that expects everything to be electronically accessible. But in fact many of the most important books and even articles are not available online and must be read in the old-fashioned way, between paper covers. Anyone who is serious about learning what ID argues will read the key ID sources that are not available online, as well as those that are. Third, you mention only Dembski. I asked you about ID authors generally. Are you saying that the only ID author you have read (as opposed to read about) is Dembski, and even there, only those parts of his work that are available online? If so, you are hardly going to have a good first-hand knowledge of ID thinking. And it hardly fits in with this claim: "I am a trained academic, like many here, and I try where possible to go to primary sources for my information." If the only ID person you have read is Dembski, and only that portion of his works which is available online, you are not behaving "like a trained academic" when you post opinions about ID for all the world to see. A trained academic would have spent a great deal of time in the library (or at the bookstore) acquiring books, essay collections, photocopied articles, etc., before making a judgment about what ID says and what its weaknesses are. Fourth, pertinent to this, on another thread you make this comment: "Not only is it bad science, but there has been an extraordinary reluctance on the part of most IDists even to respond to the criticisms of it as science." Again this makes me wonder how much ID material you have read, even online mateial. For example, we have here at UD an archive of all of Behe's responses to the scientific critics of *The Edge of Evolution*. They are focused on the science of ID, and Behe answers in detail, often citing science journal literature in his discussions. Have you read any of those responses? You will also find numerous responses to alleged scientific criticisms of ID on the Discovery web site, written by many different ID supporters, and in many ID books (by Wells, Dembski, etc.) which are not available online. Behe has refuted Miller regarding the flagellum in many places, including in his essay in the Dembski/Ruse collection (a volume which anyone purporting to offer an informed opinion on ID should have read). Your insinuation that somehow the movie *Expelled* is to be taken as one of ID's main scientific defenses -- when it was made by Ben Stein and some independent filmmakers, not by ID scientists -- is ludicrous. That film did not purport to be a work *of* science, but a work about the implications of science and about the politics of science. Whatever its flaws, it doesn't bear on the question you raise about ID's scientific defense. Be aware, also, that ID people cannot always get their scientific responses published. Some of Behe's letters to major science journals, rebutting false claims about his work in reviews, have not been published by those journals. Thomas Cudworth

kf:

Time and again, you have been taken step by step through the design inference process, and have been forced to say you agree with the corrections. Then, equally repeatedly we see some little while later, the sort of false claims above.

Please show me what corrections I have been forced to say I agree with. Elizabeth Liddle

Elizabeth: You choose where and when (sounds like a duel, doesn't it? :) ) gpuccio

Dr Liddle: I am disappointed:

if we conclude that our hypothesis of Design is supported by our data, then the first thing we should ask is: is there an alternative hypothesis that could generate these data? This, incidentally is the first scientific error Dembski makes – he sets up his hypothesis incorrectly, and so finds himself in a position where no other hypothesis, by definition, can account for the data.

Time and again, you have been taken step by step through the design inference process, and have been forced to say you agree with the corrections. Then, equally repeatedly we see some little while later, the sort of false claims above. In brief summary, with reference to say here at UD and here in my online IOSE draft course. Let us observe: 1: It is long since well established that causal patterns exist and have reliable empirically tested signs. If we see deer tracks and droppings in the snow, whether Osti looking for what he probably did not know would be his last meal [Red Deer, it seems] 5,000 YA, or today, we infer from sign to signified: I:[signs] --> Objective state of affairs O, on a warrant W 2: In particular we routinely observe that causes come in patterns assignable to chance and/or mechanical necessity and/or design. (When an arrow head was found in Osti's corpse, suddenly the nature of his demise was clarified: probable murder.] 3: In the design inference process, the first default is that a given aspect of an event -- and notice the per aspect focus highlighted since a few years ago, we are not back in 1998 here -- is by necessity and so will exhibit low contingency under sufficiently similar initial conditions. 4: If there is high contingency, then chance and/or choice are the credible causal factors for the relevant aspect of an object, phenomenon or process. 5: In that context, if there is a statistically dominated pattern, i.e we are coming from what seems to represent a random variable driven distribution, the obvious conclusion is that chance is at work. 6: But, if on the other hand we see events E coming from an independently describable set T, which is a narrow and UN-representative zone in a set of possibilities W, then that -- as Dembski has argued ever since NFL -- is a strong sign of intelligently directed choice not chance as the material factor. 7: Text in this thread is highly contingent, but obviously distinct from random finger walking on a keyboard:fuiwjsgvbfhlirmsd4ronzsejkv 8: Said text is an observable cluster of events that come from a zone T of remarks in English relevant to a context of discourse, and are sufficiently long [beyond 500 - 1000 bits] that it is utterly unlikely that such would occur by chance dominated processes of trial and error on the gamut of our solar system or observed cosmos. 9: And yet, we intelligent posters have been churning them out routinely. 10: The same holds for DNA etc. The best explanation is the process of design, not chance based random walks, for reasons already gone over in details. So, please, do better next time. Dembski was on teh right track, and by updating to incorporate a per aspect analysis, we have captured the matter adequately. It has even been reduced to a mathematical expression, here on a solar system scope: Chi_500 = I*S - 500, bits beyond the solar system threshold. If you think that chance and necessity without intelligence can beat that threshold, then please provide concrete examples. And if you are doing a simulation, do so in a way that does not raise the question of active information being fed in by the back door, by mistake. GEM of TKI kairosfocus

gpuccio:

But again, I would ask you to express in detail your problem with Dembski. I don’t understand what you mean, and I suppose that I would like to debate a little the design inference with you in more detail.

I'm more than happy to, but possibly on a different thread :) Elizabeth Liddle

of interest: While neo-Darwinian evolution has no evidence that material processes can generate functional prescriptive information, Intelligent Design does have 'proof of principle' that information can 'locally' violate the second law and generate potential energy: Maxwell's demon demonstration turns information into energy - November 2010 Excerpt: Until now, demonstrating the conversion of information to energy has been elusive, but University of Tokyo physicist Masaki Sano and colleagues have succeeded in demonstrating it in a nano-scale experiment. In a paper published in Nature Physics they describe how they coaxed a Brownian particle to travel upwards on a "spiral-staircase-like" potential energy created by an electric field solely on the basis of information on its location. As the particle traveled up the staircase it gained energy from moving to an area of higher potential, and the team was able to measure precisely how much energy had been converted from information. http://www.physorg.com/news/2010-11-maxwell-demon-energy.html bornagain77

Falsification of neo-Darwinism; First, Here is the falsification of local realism (reductive materialism). Here is a clip of a talk in which Alain Aspect talks about the failure of ‘local realism’, or the failure of reductive materialism, to explain reality: The Failure Of Local Realism – Reductive Materialism – Alain Aspect – video http://www.metacafe.com/w/4744145 The falsification for local realism (reductive materialism) was recently greatly strengthened: Physicists close two loopholes while violating local realism – November 2010 Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview. http://www.physorg.com/news/2010-11-physicists-loopholes-violating-local-realism.html Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009 Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables. http://www.sciencedaily.com/releases/2009/07/090722142824.htm (of note: hidden variables were postulated to remove the need for ‘spooky’ forces, as Einstein termed them — forces that act instantaneously at great distances, thereby breaking the most cherished rule of relativity theory, that nothing can travel faster than the speed of light.) And yet, quantum entanglement, which rigorously falsified local realism (reductive materialism) as the complete description of reality, is now found in molecular biology on a massive scale! Quantum Information/Entanglement In DNA & Protein Folding – short video http://www.metacafe.com/watch/5936605/ Quantum entanglement holds together life’s blueprint – 2010 Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours (arxiv.org/abs/1006.4053v1). “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford. http://neshealthblog.wordpress.com/2010/09/15/quantum-entanglement-holds-together-lifes-blueprint/ The relevance of continuous variable entanglement in DNA – July 2010 Excerpt: We consider a chain of harmonic oscillators with dipole-dipole interaction between nearest neighbours resulting in a van der Waals type bonding. The binding energies between entangled and classically correlated states are compared. We apply our model to DNA. By comparing our model with numerical simulations we conclude that entanglement may play a crucial role in explaining the stability of the DNA double helix. http://arxiv.org/abs/1006.4053v1 Quantum Information confirmed in DNA by direct empirical research; DNA Can Discern Between Two Quantum States, Research Shows – June 2011 Excerpt: — DNA — can discern between quantum states known as spin. – The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team’s results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property. http://www.sciencedaily.com/releases/2011/03/110331104014.htm Information and entropy – top-down or bottom-up development in living systems? A.C. McINTOSH Excerpt: This paper highlights the distinctive and non-material nature of information and its relationship with matter, energy and natural forces. It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate. http://journals.witpress.com/paperinfo.asp?pid=420 i.e. It is very interesting to note that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale, for how can the quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy space/time) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own ‘causation’ in the first place? (A. Aspect) Appealing to the probability of various configurations of material particles, as neo-Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the energy/matter particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘specified’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place! ,,,To refute this falsification of neo-Darwinism, one must falsify Alain Aspect, and company’s, falsification of local realism (reductive materialism)! ,,, As well, appealing to ‘non-reductive’ materialism (multiverse or many-worlds) to try to explain quantum non-locality in molecular biology ends up destroying the very possibility of doing science rationally; BRUCE GORDON: Hawking’s irrational arguments – October 2010 Excerpt: For instance, we find multiverse cosmologists debating the “Boltzmann Brain” problem: In the most “reasonable” models for a multiverse, it is immeasurably more likely that our consciousness is associated with a brain that has spontaneously fluctuated into existence in the quantum vacuum than it is that we have parents and exist in an orderly universe with a 13.7 billion-year history. This is absurd. The multiverse hypothesis is therefore falsified because it renders false what we know to be true about ourselves. Clearly, embracing the multiverse idea entails a nihilistic irrationality that destroys the very possibility of science. http://www.washingtontimes.com/news/2010/oct/1/hawking-irrational-arguments/ ,,,Michael Behe has a profound answer to the infinite multiverse (non-reductive materialism) argument in “Edge of Evolution”. If there are infinite universes, then we couldn’t trust our senses, because it would be just as likely that our universe might only consist of a human brain that pops into existence which has the neurons configured just right to only give the appearance of past memories. It would also be just as likely that we are floating brains in a lab, with some scientist feeding us fake experiences. Those scenarios would be just as likely as the one we appear to be in now (one universe with all of our experiences being “real”). Bottom line is, if there really are an infinite number of universes out there, then we can’t trust anything we perceive to be true, which means there is no point in seeking any truth whatsoever. “The multiverse idea rests on assumptions that would be laughed out of town if they came from a religious text.” Gregg Easterbrook ================= Alain Aspect and Anton Zeilinger by Richard Conn Henry – Physics Professor – John Hopkins University Excerpt: Why do people cling with such ferocity to belief in a mind-independent reality? It is surely because if there is no such reality, then ultimately (as far as we can know) mind alone exists. And if mind is not a product of real matter, but rather is the creator of the “illusion” of material reality (which has, in fact, despite the materialists, been known to be the case, since the discovery of quantum mechanics in 1925), then a theistic view of our existence becomes the only rational alternative to solipsism (solipsism is the philosophical idea that only one’s own mind is sure to exist). (Dr. Henry’s referenced experiment and paper – “An experimental test of non-local realism” by S. Gröblacher et. al., Nature 446, 871, April 2007 – “To be or not to be local” by Alain Aspect, Nature 446, 866, April 2007 bornagain77

Nick states: 'Even the mildest forms of ID depend on insertion of miracles into biological history, even if it’s just to tweak the DNA a little bit. It’s still a violation of conservation of mass/energy, and it’s still just inserting God into the gaps in our understanding…' No Nick, a violation of conservation of mass/energy would mean that MORE mass or energy was put into the universe than was already present in the universe, moreover the big bang itself represents the most blatant violation of the conservation of mass/energy that one could have since the entire temporal 'energy/matter' universe was brought into being instantaneously from a transcendent spaceless/timeless realm. In fact the only violation of conservation laws that is going on here is the blatant violation of the conservation of information law that Darwinism requires i.e. evolution of the gaps; LIFE'S CONSERVATION LAW: Why Darwinian Evolution Cannot Create Biological Information William A. Dembski and Robert J. Marks II http://evoinfo.org/publications/lifes-conservation-law/ ,,,Encoded classical information, such as what we find in computer programs, and yes as we find encoded in DNA, is found to be a subset of 'transcendent' quantum information by the following method:,,, This following research provides solid falsification for Rolf Landauer’s contention that information encoded in a computer is merely physical (merely ‘emergent’ from a material basis) since he believed it always required energy to erase it; Quantum knowledge cools computers: New understanding of entropy – June 2011 Excerpt: No heat, even a cooling effect; In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy. Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.” http://www.sciencedaily.com/releases/2011/06/110601134300.htm ,,,And here is the empirical confirmation that quantum information is 'conserved';,,, Quantum no-hiding theorem experimentally confirmed for first time Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment. http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html bornagain77

kf: I agree with you that the relevant distinction is between "natural" and "artificial" when it comes to design question. "Did he fall or was he pushed?" is a classic design question. An "artefact" is one that is made by a living thing (usually a human being, but not always). But that does not mean that the designers themselves (the living things) are not "natural". In other words, there are not two kinds of things: natural things and artificial things. Rather there are two kinds of explanations - one that accounts for a thing in terms of the intentions of another thing, and one that does not. For instance, as you know, I do not think the Intelligent Design hypothesis for living things stands up to scrutiny. However, that is not because I do not countenance explanations in terms of the intentions of living things. My computer is clearly an artifact - it was designed by a living thing. A hollow in a log, with a neighbouring stone, may be an artefact by a chimp, designed for cracking coconuts. A bird's nest is an artefact, made by birds, from twigs, in order to lay their eggs. A caddis fly larva-case is an artefact, made by the larva, from anything to hand, to protect itself. A coral reef is a kind of artefact, made by coral polyps, in which to live. Dental placque is a kind of artefact, made by bacteria, to protect themselves from your toothbrush. Indeed you could argue that living things are artefacts, made by themselves, in order to go on living, as their offspring are artefacts, made by their parents, in order to perpetuate their pattern. So where does "natural" diverge from "artificial"? I'd argue that it doesn't. The really important cleavage IMO is not between natural things and artificial things, or even between explanatory levels, but between intentional processes and unintentional processes. It is my contention that living things are the result of unintentional processes. It is the contention, as I see it, of IDists that living things are the result of intentional processes. Our differences do not lie in my prior commitment to "Naturalism" which you are free of, but in the fit of the model to the data. I do not think there is any evidence that intentional processes gave rise to living things. But I'm perfectly prepared to change my mind if presented with such evidence :) Elizabeth Liddle

PS: Cf my response to Dr Matzke here, which documents what happened several years ago at Telic Thoughts. kairosfocus

Onlookers: Apparently Dr Matzke is not able to see the key issue, in his search for talking points and in his obsession with words that to him are red flags and hooks to hang those talking points on:

In general, our society has answered yes, condoning the expression of naturalism and many of its companion ideas. We are not in conflict with this. We are opposed to the censorship of ideas. But here is the crux of the present problem. Though our U.S. Constitution provides for free expression of ideas — even those diametrically opposed such as naturalism and theism — it seems that the champions of naturalism want to take that Constitutional freedom of expression away from theists instead of allowing the ideas of each view to coexist in an academically free system. [ --> As in cf. Gaskell, Sewell, and many others in recent months and years and so on back.] This is why there is a conflict between naturalism and theism, between evolution and creation in the public schools. It is the intent of a relative few naturalists to supplant theism through the exclusive teaching of evolution in our schools.

Given what I have just had to clip, that tells us a lot. And none of it reflects well on Dr Matzke. To date, Dr Matzke seems unable to accept that many people have thought long and hard on nature, for centuries, from various perspectives, and have made contributions to science and its worldviews analysis context. A significant number of such were design thinkers, and even theists or even Bible-believing creationists. Perhaps it has escaped his notice that among the latter were: Copernicus, Kepler, Galileo and Newton. Men who believed that the strong appearance of design in our world was so for the very good reason that it speaks the truth. Thaxton et al, and those who have followed them over the past generation now, have re-looked at the evidence, starting with the evident fine-tuning of the cosmos, and the evident design of life from its ultimate origin on our planet. In particular by 1984/5, TBO published a major technical monograph that launched a new paradigm and research programme, now known as Intelligent Design. They did so, not by parsing Genesis 1 -2, but by examining on the usual timelines and evidence, the circumstances of a pre-life earth, and the formation of the precursors for life. They then applied not only geological knowledge but chemical kinetics on thermodynamics and polymer chemistry. It was patently obvious that the hoped for prebiotic soup was a myth, as the concentrations of relevant precursors would not work, as well, the hoped for reducing atmosphere was not plausible. So, even the monomers were in question -- a result that has continued to be underscored ever since the mid 1980's. We now see speculations on undersea volcanic vents -- which do not work, and hopes pinned to moons orbiting Jupiter and/or to comets. Those are marks of desperation, a desperation that has led to the two leading schools of thought on OOL coming to mutual destruction, as the exchange between Orgel and Shapiro amply documented a few years ago. TBO took time to grant a generous scenario, then looked at the reaction kinetics on thermodynamics, to see the result if such a prebiotic soup could somehow exist, despite its problems. They came up with a devastating result: a conc of 10^-338 molar is by many orders of magnitude, less than one molecule in our whole observed cosmos of some 10^80 atoms. Prebiotic soup models are simply dead. And it is TBO who put in the knife. That is why they concluded that while the work of what I have called clumping can be accounted for on reasonable reaction kinetics -- i.e tars made of long but uncontrolled chains of molecules form all the time in organic chemistry exercises that go out of control, but that of configuring functionally specific information-rich polymers cannot be so easily accounted for apart from investigator action. While we have updated some to the approaches and the terms used, since those pioneering days, the result is the same: the only empirically credible source of the highly specific configuring work required to make and arrange the molecules of the living cell into a functional whole, is information-controlled, step by step processes. The manufacture of proteins in teh cell in the ribosomes is the classic instance of this, and the precursor tRNA, m-RNA and r-RNAs are likewise produced by step by step informationally controlled processes based on stored coded digital information in DNA. The only empirically warranted source for codes, storage in data structures, algorithms based on use of coded information etc etc, is design, by intelligence. So, as a matter of basic scientific and epistemological integrity, the inference to design is a well warranted player in the discussion on OOL. But plainly Dr Matzke and ilk do not want that to be known, so they have again resorted to trying to brand the design theory movement with the term they and their predecessors have already poisoned, creationism. But it is quite plain that the discussion summarised above does not depend on anyone's worldview for its warrant. Geology, chemistry, thermodynamics and the like are open to all, and the arguments stand on their own merits on a vast body of empirical facts. Nor are these "creationist" facts, they are scientific facts. So, Thaxton et al were right in 1983, and we are right today, to highlight the agenda that seeks to censor our thoughts on science, substituting a radical materialism in the place of science with empirically warranted integrity. So, let us again cite Lewontin's summary of the game that is -- and has long been -- afoot:

. . . To Sagan, as to all but a few other scientists, it is self-evident [[actually, science and its knowledge claims are plainly not immediately and necessarily true on pain of absurdity, to one who understands them; this is another logical error, begging the question , confused for real self-evidence; whereby a claim shows itself not just true but true on pain of patent absurdity if one tries to deny it . . ] that the practices of science provide the surest method of putting us in contact with physical reality, and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test [[i.e. an assertion that tellingly reveals a hostile mindset, not a warranted claim] . . . . It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes [[another major begging of the question . . . ] to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute [[i.e. here we see the fallacious, indoctrinated, ideological, closed mind . . . ], for we cannot allow a Divine Foot in the door. [NYRB, Jan 1997. If you think that the following clip from Beck makes a difference that turns this into quote-mining, kindly read the notes here; they only dig in deeper into the hole of a priori censorship and willfully misguided misrepresentation of alternatives.]

Well did Philip Johnson rebut, in Nov that year in First Things:

For scientific materialists the materialism comes first; the science comes thereafter. [[Emphasis original] We might more accurately term them "materialists employing science." And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) "give the appearance of having been designed for a purpose." . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [[Emphasis added.] [[The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]

At this stage, Dr Matzke owes us all not only a serious explanation, but patently, an apology and retraction for what he and his ilk have done. GEM of TKI kairosfocus

Elizabeth: What should, of course, happen, once you make an inference is that you ask, something like: “If our design inference is indeed correct, what kind of design process would produce the patterns of design that we observe?” – and this is where you and I converge again! But that conditional “if” is vital – we must always be prepared to revisit our earlier inferences. Major paradigm shifts are rare, but they must not be ruled out a priori. I have never thought or said differently. The provisional status of any scientific hypothesis is one of the foundations of my epistemology. When I say: "Once we infer design" I just mean that those who don't agree with the inference will not be motivated to inquire further :) But again, I would ask you to express in detail your problem with Dembski. I don't understand what you mean, and I suppose that I would like to debate a little the design inference with you in more detail. gpuccio

I disagree with Nick (Brits will appreciate the reference....) Nick, you write:

Even the mildest forms of ID depend on insertion of miracles into biological history, even if it’s just to tweak the DNA a little bit. It’s still a violation of conservation of mass/energy, and it’s still just inserting God into the gaps in our understanding...

No, they don't. And that's why they are so angry with you for implying they do. They go to enormous lengths NOT to do precisely what you have alleged they do! What they do instead is to say: the pattern of life must, because of these equations, be designed. No law of Necessity explains it, and for it have happened by chance is so unlikely that the probability is vanishingly small even if we factor in the entire number of events in the history of the universe. And the only alternative is Design. They do not call that Design a miracle. They occasionally even mention aliens, although that is deeply illogical, because, asssuming that the aliens are members of that self-same universe they cannot, clearly, be invoked as the cause of their own existence. So what must be posited instead is a Designer that is beyond our own universe. It need not be miraculous - presumably, one solution is that our universe is merely a construction by intelligent designers within a much larger universe of supra-universal boffins, whose origins may possibly have arisen by Chance, given a much larger number of total events. I just made that up, and I'm sure no IDist here would embrace it, but I give it as an example of a non-miraculous theory that could account for the inferred signature of Design in terrestrial living things. And just as some scientists, faced with evidence of the Big Bang, say: "Therefore, God" while others say: "Therefore existence appears to be a fundamental property of reality", yet both can work happily in the same lab, so the fact that ID people tend to equate the Designer with the Abrahamic God (even the Logos of John) does not imply that that is the only philosophical conclusion. Now, I completely agree with you that they have brought the problem on their own heads, by constantly equating "Darwinism" with atheism, by presenting ID as the restorating of theism into the American worldview, by condemning scientists for ruling out "Design" a priori (which we do not) or "the supernatural" a priori (which is simply a direct consequence of the scientific method), by, as you point out, making a High School textbook an early vehicle for the idea, and moreover, not writing one from scratch, but converting a creationist ready-made, initially, and crassly, by means of a find-and-replace button. So I think their anger is wildly misplaced. Nonetheless, every time someone like you (or me) accuses them of positing miracles to account for data, then it draws the fire back on us, not their own number. And we deserve it, for not listening properly! What is wrong with ID, fundamentally, is not that it is religion, or creationism, or not-science, but that it is bad science. Not only is it bad science, but there has been an extraordinary reluctance on the part of most IDists even to respond to the criticisms of it as science. Instead we see a paranoia, expressed in films like Expelled, in which the claim is made that if anyone dares to question thenaturalist orthodoxy,their careers are doomed. Ben Stein bangs on to Dawkins not about the science of ID, but about God. If, as IDists protest, ID is science, and theology is merely the inevitable conclusion from the science - why accuse scientists of excluding theology from science? Sure we do. That's exactly our point, and now, it's exactly the point Thomas Cudworth is, oddly making - that ID is science, not theology, and should therefore not dismissed as theology-not-science. So this has been a very enlightening thread! If we can take it from henceforth that the merits of ID are entirely those of its science, divorced from any theological implications, then let the accusations that ID is just religion dressed up as science stop, but equally let the accusations that "Darwinism" or "neo-Darwinism" is the expression of an ideological faith in naturalism stop too. Science can do no more than make naturalistic hypotheses. That's how the methodology works. It can lead us to astonishing hypotheses with profound philosophical and even theological implications, but it cannot test those implications. If ID is science, then it should stand or fall on the science. If the data support it, then yes, we may find ourselves faced with some fairly worldview-shattering implications, not least being the possibility that we are merely a kind of Matrix, controlled by a super-universe of perhaps benign, perhaps malign, super-organisms. Another possiblity is God. But first, let's figure out whether the science works, without mutal accusations of ideological priors, because in both cases they are, or should be, irrelevan. That's what makes science so glorious. Elizabeth Liddle

Pardon me, Dr Liddle: I cannot help but notice that we are here dealing with those "few" who control major institutions and are busily trying to redefine the actual meaning of science, turning science itself into applied atheism. I particularly note what the US National Science Teachers Association, for a decade now, is on record (cf the above linked) on:

The principal product of science is knowledge in the form of naturalistic concepts and the laws and theories related to those concepts . . . . [[S]cience, along with its methods, explanations and generalizations, must be the sole focus of instruction in science classes to the exclusion of all non-scientific or pseudoscientific methods, explanations, generalizations and products . . . . Although no single universal step-by-step scientific method captures the complexity of doing science, a number of shared values and perspectives characterize a scientific approach to understanding nature. Among these are a demand for naturalistic explanations supported by empirical evidence that are, at least in principle, testable against the natural world. Other shared elements include observations, rational argument, inference, skepticism, peer review and replicability of work . . . . Science, by definition, is limited to naturalistic methods and explanations and, as such, is precluded from using supernatural elements in the production of scientific knowledge. [[NSTA, Board of Directors, July 2000. ]

That is highly significant. Especially, as ever since Plato in The Laws, Bk X, 2350 years ago, it should have been plain that he relevant contrast is not natural vs supernatural but natural vs artificial. Where the artificial leaves empirically reliable and rouinely used traces that we infer on. So, there is here a willfully misleading caricature of design thought, and there lurks the "creationism in a cheap tuxedo" smear. And, the above is thus highly revealing of an extremely radical and question begging institutionally entrenched atheistical worldviews agenda, which becomes all the more evident when we realise that to such "science" is the gold standard of knowledge. Remember, already our children are being taught this sort of radical and patently unjustifiable redefinition as the "true" definition of science. Sorry, but -- painful as this may sound -- that sounds to me uncommonly like the problem of handing over the administration of the asylum to its inmates. It is time to fix the chaos. GEM of TKI kairosfocus

gpuccio @216: I entirely agree. You write:

As you may know, I have a position which is slightly different. While I agree with you that there are certainly many aspects on the problem of the designer which are of pertinence of philosophy and theology, I b elieve, and have always stated here, that ID must not necessarily stop at the design detection, but has the possibility and the duty, as a scientific paradigm, to go beyond as much as possible.

Exactly. Moreoever, the failure to do so is what brings it into disrepute as science, not its potential theological or philosophical implications. Big Bang theory had huge potential philosophical and theological implications, and yet that didn't stop it being regarded as science, nor of people going on to try to understand it ever more deeply.

I will be more clear. Once we infer design, the design can be observed, analyzed and evaluated. ID gives us a way to identify, as much as it is possible with present data, specific deseign inputs (for instance, the emergence of protein superfamilies). There are many aspects, observabble aspects, facts, about design input which are in the range of science.

Yes, indeed, except for a rather important quibble. you say: "Once we infer design...." That is not how science works. All our inferences are provisional. Indeed all our inferences are hypotheses, that should generate further predictions. So, if we conclude that our hypothesis of Design is supported by our data, then the first thing we should ask is: is there an alternative hypothesis that could generate these data? This, incidentally is the first scientific error Dembski makes - he sets up his hypothesis incorrectly, and so finds himself in a position where no other hypothesis, by definition, can account for the data. What should, of course, happen, once you make an inference is that you ask, something like: "If our design inference is indeed correct, what kind of design process would produce the patterns of design that we observe?" - and this is where you and I converge again! But that conditional "if" is vital - we must always be prepared to revisit our earlier inferences. Major paradigm shifts are rare, but they must not be ruled out a priori.

Those aspects can certainly give at least some information about: a) The nature of the designer b) If only one desiner ot many designers can be reasonably inferred c) The nature, structure, and possibly some of the pusposes of the design (while the whole purpose of biological design is probably a philosophical subject, specific sub purposes and strategies can certainly be inferred form the observed design). d) The modalities of implementation of design in natural history, such as cronological properties (gradual, sudden), and possible implementation strategies (guided mutation, intelligent selection, direct writing, etc.) All these things, and probably others, are IMO perfectly in the range of ID as science.

Absolutely.

It is true that the existing data can shed only a very partial light on these problems, but data are increasing, and our scientific mind must be open and try to build reasonable inferences and explanations whenever possible.

Yes. Bravo! Elizabeth Liddle

Thomas Cudworth:

Elizabeth re 200: Regarding Dembski, you’ve made a logical slip. The fact that Dembski identifies the God of intelligent design with the God of Christianity does not prove that he improperly conflates religion and science.

You have still missed my point. I'm not sayint that the conflation is improper. I'm simply pointing out that the proportion of IDists who make a theological connection with their theory is much higher than the proportion of "evolutionists" who do.

None of his *arguments* for design depend on his belief that the designer is the Logos of John. He merely indicates that science and religion, when each conducted properly according to their own methods, meet at the highest plane. That does not indicate any improper mixing of the subjects at all.

And I did not say that they did.

This is why I asked you if you had actually read any ID books straight through, as opposed to relying on quotes you’ve picked up, out of context, from internet debates. For example, the book in which Dembski made the Logos statement, have you read it straight through, to get the context and qualifying statements? And have you read No Free Lunch straight through, which doesn’t talk about the Logos? If you had, you wouldn’t have made the invalid argument that you did.

Well, first of all you mistook the argument that I was making (which was not even an argument, just an observation, made to balance the observation that a number of vocal atheists are also "evolutionists"). Second: no I have not read any of Dembski's books, as I have already said. I have, however, read all, I think, of his online articles, in considerable depth. If there is key point in his books that he does not make in his articles, then it does not say much for his articles! But I assume that he does, in fact, make his points in his articles. And yes, I am well aware that his science does not depend on his religious stance (which was why I never said that it did - it is rather that his religious stance, in anything, draws sustenance from his science, I assume). Please do not assume that those who disagree with you have merely picked up their knowledge from secondary sources. I am a trained academic, like many here, and I try where possible to go to primary sources for my information. I also, as I said, prefer scientific papers to books, preferably peer-reviewed, but that doesn't matter in itself, what matters is that the argument is laid out in scientifical paper format, namely in such a way that the reader can independently ascertain the validity of the conclusions. Elizabeth Liddle

Thomas: As I’ve argued repeatedly, in its theoretical purity, ID must stop after settling the question of design vs. chance. The next question, how did design get into nature, raises the natural vs. supernatural question. But that question is not about design, and therefore is not part of ID’s mandate. It belongs to philosophy or theology. As you may know, I have a position which is slightly different. While I agree with you that there are certainly many aspects on the problem of the designer which are of pertinence of philosophy and theology, I b elieve, and have always stated here, that ID must not necessarily stop at the design detection, but has the possibility and the duty, as a scientific paradigm, to go beyond as much as possible. I will be more clear. Once we infer design, the design can be observed, analyzed and evaluated. ID gives us a way to identify, as much as it is possible with present data, specific deseign inputs (for instance, the emergence of protein superfamilies). There are many aspects, observabble aspects, facts, about design input which are in the range of science. Those aspects can certainly give at least some information about: a) The nature of the designer b) If only one desiner ot many designers can be reasonably inferred c) The nature, structure, and possibly some of the pusposes of the design (while the whole purpose of biological design is probably a philosophical subject, specific sub purposes and strategies can certainly be inferred form the observed design). d) The modalities of implementation of design in natural history, such as cronological properties (gradual, sudden), and possible implementation strategies (guided mutation, intelligent selection, direct writing, etc.) All these things, and probably others, are IMO perfectly in the range of ID as science. It is true that the existing data can shed only a very partial light on these problems, but data are increasing, and our scientific mind must be open and try to build reasonable inferences and explanations whenever possible. gpuccio

Nick, here's the last: “It’s not lying that motivates me — that’s absurd anyway. What would be the point? It’s knowledge and experience.” The point would be that lying or misrepresenting via exaggeration or strategic omission gives your side a huge advantage in the culture-war situation, and therefore you have a natural motive to do so. If the NCSE had nuanced its attack on ID, and if the ACLU lawyers had nuanced their attack, saying things like “A lot of ID people are really creationists, but there are a few people like Behe who aren’t, and gee, Scott Minnich seems to be doing genuine empirical lab work, knockout experiments, not Biblical exegesis, and a lot of the ID arguments come from Denton who isn’t a creationist, and of course many of their arguments go back to ancient Greek philosophers who couldn’t possibly have been creationists because they’d never read the Bible, etc.” – the Dover Trial would have been a lot harder to conduct, wouldn’t it? Your side -- the lawyers and expert witnesses -- deliberately fed the judge a skewed and distorted vision of ID. They did not tell the judge the whole truth. They felt that a few little white lies and strategic omissions were permissible for the greater good of keeping ID out of the schools. (They also fed the judge a sanitized version of Darwinian theory, failing to mention Darwin’s religious anguish over the implications of his theory -- and Darwin surely knew the implications better than Miler does -- and making sure they didn’t call Dawkins or Coyne or Myers or Provine as witnesses to say what *they* thought were the implications of evolution for religion. But that’s another issue.) The point is that lying, or misrepresenting, or strategically omitting important parts of the truth, has always been advantageous for your side, and so your side has often done it. And by “your side” I don’t just mean the atheists and agnostics, but the TEs; Biologos willfully misrepresents ID people and writings all the time (which is, I suppose, just the sort of thing that Jesus Christ would want them to do.) Thus, your side keeps saying that Behe supplements natural processes with miracles even though he has repeatedly denied that his argument requires that. How many times have you guys shouted "God of the Gaps," knowing full well that Behe denies the charge and that it doesn't apply to Denton? But hey, why spoil a killer argument by putting in those awkward little qualifications? (And *you* complain when people misrepresent Gould. Sheesh.) A genuine philosopher, a genuine scholar, a genuine scientist, always represents his opponent’s argument at its strongest. He doesn't strategically omit. He doesn't impute arguments that people haven't made. He doesn't say "all" when facts support only "most". He separates alleged motives from the substance of arguments. Your side has not done any of this with ID. You have tried to smear ID from the beginning with guilt by association -- the “creationism” charge -- before the argument can even begin. And you personally have not only condoned this behavior but actively participated in it from the beginning. And you were doing it again here on my thread. That’s why I jumped in. If you are going to continue poisoning the well, do it somewhere else. I'll summarize: many ID proponents, the majority of the leaders and probably the majority of the rank and file, are personally creationists. But ID as a theory is not creationism. Its data and its arguments and its methods (probability theory, information theory, engineering concepts like irreducible complexity, etc.) are completely separable from creationism. And its truth or falsity as an explanation for living systems has nothing to do with Dover School Board, the Kansas hearings, Pandas, or any of the other irrelevancies you have brought up on this thread. Thomas Cudworth

Nick, almost done: “Then ID advocates started pushing ID in the state science standards in Kansas and elsewhere.” I wasn’t there. Don’t blame me. And anyhow, since then, Discovery’s policy has been very explicit: No mandated ID in the schools; but teach *more* neo-Darwinian theory, including scientific criticism of neo-Darwinian theory. And no, not non-refereed criticism coming from ID proponents. Criticism coming from *the existing peer-reviewed scientific literature*. There lots of it. There’s Margulis. I’ve read peer-reviewed papers by paleontologists and botanists expressing doubt whether macroevolution can be explained simply by microevolution writ large. There’s the Altenberg group. None of these people are ID proponents, and many of them hate ID, but they are very critical of Darwinian theory. Yet Eugenie and the NCSE have thrown all their money and influence into blocking these proposals. How can it hurt students to hear that maybe, after all, Mayr, Dobzhansky and Gaylord Simpson, whose word was like Gospel 50 years ago, were very wrong on some very major things about evolution? That maybe chance plays a much lesser role, and maybe self-organization a greater one? That maybe evolution can make leaps that the older theory doesn’t allow? That maybe the purely gene-focused theory of evolution is in deep trouble? Why doesn’t Eugenie want students to hear about intra-scientific criticism of the Darwinian model? The motive can’t be anything but political. She wants to present evolutionary theory as a "united front" in order to fend off creationism. But in doing so she falsifies the scientific process, giving the very wrong impression that there is this huge consensus about evolutionary mechanisms and we're just twigging the details a bit to polish things off, and then it will be a done deal. Nothing could be further from the truth. Evolutionary theory is in a major transition period right now, with major tenets up in the air, and it's not doing the students any favor to conceal that from them. But she'd rather present this myth of invincible, unified "science." She wants to protect the students from any doubts about the received wisdom. That's not education, that's propaganda. The current Discovery policy is exactly the right one, if science and not ideology is what we are supposed to be teaching. “And then I started reading more ID literature — not just “Darwin’s Black Box” and the like, but JP Moreland’s “The Creation Hypothesis”, Phillip Johnson’s numerous works which all phrased the debate as supernaturalism vs. naturalism, etc.” I don’t agree with those ID proponents who cast ID as supernaturalism vs. naturalism. It shows category confusion. The question of supernaturalism vs. naturalism is important, but it’s separate from the question of design vs. chance. As I’ve argued repeatedly, in its theoretical purity, ID must stop after settling the question of design vs. chance. The next question, how did design get into nature, raises the natural vs. supernatural question. But that question is not about design, and therefore is not part of ID’s mandate. It belongs to philosophy or theology. Thomas Cudworth

Continuing, Nick: "There are a handful of evolution popularizers, and some of them are atheists and some aren’t. It is regrettable, in my opinion, that some have chosen to try and promote atheism via the science of evolution." But we haven't heard you stressing that very loudly, have we? How often are you on record saying this right in the heart of the atheist territory? "... most importantly, as mentioned above, those who even kinda-sorta accept common ancestry are a tiny minority in the ID movement. It is very widely rejected, by 95% or more of the major figures. You don’t get to portray the tiny minority position as being representative of the movement." First of all, I never did any such thing. I didn't claim that any group within ID represented the "movement" (a vague sociological term). I’m not interested in who represents ID as a “movement.” That's a matter of politics. I'm interested in promoting ID as a theoretical perspective to explain biological systems. And regarding that question, if IDers are only 5% evolutionists -- though that's an underestimate, because the rank and file has a higher percentage that is evolutionist than the leaders -- that makes no difference to me. The ID argument, their core theoretical argument, isn't about evolution, anyway. It's about whether chance (even aided by natural selection) can produce complex integrated organic structures. If chance can't do it, then either you have to have direct creation, or some kind of guided or planned evolutionary process, or a combination ot the two. As to how ID people split up over those possibilities, that's sociologically interesting, but has nothing to do with the chance/design arguments. "Look. Back in the late 1990s I first heard of ID. At the time, it was being advertised as a revolutionary new scientific movement, and definitely not creationism. Reading the ID guys seemed like a refreshing change from the older creationist works, since they did have less Bible and seemingly more science. But once I learned more science, it became clearer and clearer to me that the ID arguments were just the same old creationist arguments but with more science-y sounding technical language covering them up." What “old creationist arguments”? Like, the argument that the formation of a protein-DNA system without intelligent guidance is vanishingly unlikely? How is that a creationist argument? It’s a perfectly good theoretical and empirical argument. It may one day be disproved; but it’s got no special connection with religion. So is Meyer not allowed to use a modern version of that argument, just because Duane Gish used it? That’s ridiculous. If I drive a car that Ken Ham used to own, am I a creationist? If the argument is separable from the creationism assumptions, the fact that creationists used it earlier is irrelevant. Thomas Cudworth

Nick, more comments: "In reality, ID, right now (and in the past) is dominated by conservative evangelicals and a few other types of conservative theists, all of them doing straight-up conservative theist apologetics (again, dominated by conservative evangelicals) and culture-warring in support of their supernaturalist, interventionist view of God. It has a literal handful of people that kinda-sorta don’t meet this description, maybe, although sometimes they deny being IDists (e.g. Berlinski) or have drastically retreated from their former positions (e.g. Denton)." Behe doesn't do apologetics. And when Dembski does them, he does them in books which he identifies as explicitly as books written for Christian purposes. He doesn't do them in No Free Lunch, for example. I don't see apologetics in Meyer's Signature in the Cell. I don't see apologetics in The Design of Life. Whether Meyer and Wells do apologetics in religious settings I don't know. But if they do, it's irrelevant to their claims for detecting design in nature. They've asked to be criticized for their science, not their private religious views. "You are expecting me, the media, society at large, etc., to exhibit extreme gullibility and pretend that the composition of the ID movement is the reverse of the above." NO. I never said that. Never implied it, either. I said that you were wrong to identify ID with creationism, since that implies that all (not most) ID proponents are creationist. I said you were wrong not to specifically exempt all ID proponents whom you knew not to be creationists. I said you were wrong to deliberately leave the public with the impression that all ID people were creationists, and I said that you and the NCSE did this for deliberate tactical reasons even though you knew it was less than the whole truth. I still stand by that judgment. Will you admit that you and your allies have consciously bypassed hundreds of opportunities to "nuance" your statements? And that the repeated use of "ID Creationism" by your camp was deliberately intended to conflate the two in the public mind, against the express wish from the ID camp that the two terms be distinguished? Thomas Cudworth

Continuing interspersed comments, Nick: "It’s still a violation of conservation of mass/energy, and it’s still just inserting God into the gaps in our understanding" No, for reasons given above. "Until miracles are abandoned by the ID movement, ID will be just a form of creationism." There is no need to abandon miracles because miracles are not part of ID. ID detects design. It does not detect the means of insertion of design. It's theoretically neutral between miraculous and non-miraculous means of insertion. And I'm talking about ID as it currently stands at its theoretical purest and best. If Johnson or anyone else 15 years ago said or implied that ID required miracles, that tells us one person's view back then; it's not part of formal ID theory now. ID now speaks of intelligent causes, not supernatural causes; it has ways of testing for intelligent input, but no way of testing for supernatural input. Thomas Cudworth

Nick, more interspersed comments: "Even the mildest forms of ID depend on insertion of miracles into biological history, even if it’s just to tweak the DNA a little bit." False. That is not true of Denton (who is small-id even if you don't call him big-ID). His account of evolution is wholly naturalistic. It is also not true of Behe. You guys keep trying to make out that Behe insists on miracles, but you've been challenged on this on virtually every web site on the planet, and have never been able to show it from his text. You've sloppily inferred it. In fact, whenever he has been asked directly about it, he's said explicitly that while ID is compatible with "tweaking," it doesn't inherently require it. This of course fits in with the rousing endorsement he gave to Denton's second book. Denton's account was wholly naturalistic and Behe knew that. Behe recognizes that "built-in evolution" or "programmed evolution" is one option within an overall ID framework. Is it the one he holds to personally? I don't know. He hasn't said. But we are talking about the definition of ID, what it is as a theory, not which version of it various ID proponents subscribe to personally. And Behe, Dembski, and Meyer all agree that it is conceptually possible that macroevolution could be driven by a built-in design rather than by miraculous interventions. (Whether they think such programming is scientifically feasible or not is another matter. I think that both Meyer and Dembski, at least, might see insurmountable practical problems. But the general concept doesn't violate their understanding of what ID is. And it's the definition of ID, the theoretical essence of ID, that we should be talking about here.) Thomas Cudworth

Nick, comments interspersed. "It was pro-ID people on the thread that brought up Mystery of Life’s Origin, not I! Your argument is with your own side, I’m afraid…" I never brought up that book, or Pandas, and never undertook to defend either book. Don't expect me to argue for others. My point was against your claim that ID was creationism. You didn't say: "ID used to be creationism" or "ID was partly inspired by a creationist book of the early 1980s" or "ID uses some arguments that creationists use" or "Many ID proponents are creationists" or even "Most ID proponents are creationists". You equated ID with creationism without qualification, and wouldn't cede an inch of ground, despite repeated evidence from me that it wasn't. That was the issue between us. "C’mon, even old-earth creationism doesn’t depend on the *literal* truth of Genesis, yet no one has a problem calling old-earth creationism creationism." If you read my original comments, far above (to which you didn't respond), you will see that I provided nuance with "literal or near-literal" and granted the existence of old earth creationism as well, and explained what it was. The point is that both young-earth and old-earth positions reject macroevolution, that both require discrete acts of creation, and that both apply the Bible to set limits to what science is allowed to conclude. That's why they're both forms of creationism. Thomas Cudworth

207: Where is the real Nick Matzke, and what have you done with him? The Nick Matzke ID people know and love responds to any criticism by avoiding the central question and mechanically spewing out pre-rehearsed NCSE talking points. The real Nick would never actually try to respond in a direct and orderly way the substantive criticism. So who is this that I'm talking to? Come to think of it, it doesn't matter. If it's a new and improved Nick, congratulations, Nick. And if it's an impostor, I'll answer the points anyway, and the real Nick can read them from his cyberspace hideaway. I'll split the answer over a few posts. Thomas Cudworth

I’m always amazed that people can get a Ph.D. in the natural sciences, and yet be so dense when it comes to registering simple, everyday reasoning. Let me say this plainly, so you won’t waste more time writing long diatribes about old books: THE THAXTON BOOK IS IRRELEVANT TO THE DEBATE AT HAND. OF PANDAS AND PEOPLE IS IRRELEVANT TO THE DEBATE AT HAND. THE MOTIVES OF THE WRITERS OF THESE BOOKS IS IRRELEVANT TO THE DEBATE AT HAND. ANY BIBLICAL REFERENCES THAT MIGHT BE IN THOSE BOOKS IS IRRELEVANT TO THE DEBATE AT HAND.

But your claim is in stark contradiction to what the leaders of the ID movement say, and even what many pro-ID people on this very thread say! It was pro-ID people on the thread that brought up Mystery of Life's Origin, not I! Your argument is with your own side, I'm afraid...

THE DEBATE AT HAND IS WHETHER *CURRENT* ID THEORY IS CREATIONIST. THAT IS, WHETHER CURRENT ID THEORY DEPENDS ON THE ASSUMPTION OF THE LITERAL TRUTH OF GENESIS, AND INTRUDES RELIGIOUS CONTENTS INTO ITS SCIENTIFIC REASONING.

C'mon, even old-earth creationism doesn't depend on the *literal* truth of Genesis, yet no one has a problem calling old-earth creationism creationism. Even the mildest forms of ID depend on insertion of miracles into biological history, even if it's just to tweak the DNA a little bit. It's still a violation of conservation of mass/energy, and it's still just inserting God into the gaps in our understanding -- or really, more commonly, gaps in the ID movement's understanding, because often biologists know the answers to how X or Y evolved, and the ID folks just haven't done the literature search to find the answers. Until miracles are abandoned by the ID movement, ID will be just a form of creationism.

CURRENT ID THEORY IS FOUND IN THE TECHNICAL OR SEMITECHNICAL, NON-DEVOTIONAL WRITINGS OF DEMBSKI, BEHE, MEYER, WELLS, DENTON, ETC. AND ITS ARGUMENTS DO NOT PRESUPPOSE ANY RELIGIOUS FAITH AT ALL, LET ALONE A LITERAL INTERPRETATION OF THE BIBLE. THEY ARE THEREFORE BY DEFINITION NOT CREATIONIST ARGUMENTS. Are you able to grasp that, Nick? Did your profs in biology train you to read and comprehend English prose on matters pertaining to evolution and design?

Really? Take off the rose-colored glasses. By this argument, "creation science" magically became science as soon as they dropped explicit mention of the Bible and claimed they were arguing that scientific evidence supported "catastrophism" and "sudden emergence." In reality, ID, right now (and in the past) is dominated by conservative evangelicals and a few other types of conservative theists, all of them doing straight-up conservative theist apologetics (again, dominated by conservative evangelicals) and culture-warring in support of their supernaturalist, interventionist view of God. It has a literal handful of people that kinda-sorta don't meet this description, maybe, although sometimes they deny being IDists (e.g. Berlinski) or have drastically retreated from their former positions (e.g. Denton). You are expecting me, the media, society at large, etc., to exhibit extreme gullibility and pretend that the composition of the ID movement is the reverse of the above. And, since you like to bring up the atheism of various evolution popularizers, (a) there are theist popularizers of evolution as well, and (b) much more importantly, evolution is dominated by scientific publishing. There are a handful of evolution popularizers, and some of them are atheists and some aren't. It is regrettable, in my opinion, that some have chosen to try and promote atheism via the science of evolution. But there are, literally, tens of thousands of evolutionary biologists around the world, publishing tens of thousands of articles and books on the science of evolution every year. And there are hundreds of thousands more scientists that use evolution in their work on a day-to-day basis. With ID, we've got the opposite. The movement is dominated by popularizers with culture-warrior and apologetics goals, and the scientific production of ID ranges between tiny and nonexistent, depending on how generous one wants to be.

Do you keep harping on Thaxton and Pandas because you don’t want to admit that you and your friends have been lying to the public for six years (since the Dover Trial) in saying or implying that Behe, Sternberg, Denton and many other ID proponents are creationists when they are in fact evolutionists?

Even if it were true that Behe, Denton, and Sternberg all clearly accepted common ancestry (where's the clear statement from Sternberg? I've never seen one), (a) Denton is pretty much nonexistent in the ID movement, and has given up on all of the "evolution is a theory in crisis" claims that he made in his 1985 book; (b) even Behe has hedged his bets on evolution -- as I co-wrote in 2007:

The denial of common ancestry is unsurprising in creation science, but it is a common misconception that ID advocates accept common ancestry and “macroevolution.” In fact, the vast majority of ID proponents deny the common ancestry of humans and apes. Behe is the only significant exception, although he is much-touted by those who wish to portray ID as a moderate position. Even Behe's support is lukewarm; in 2005, he wrote that “my Intelligent Design colleagues who disagree with me on common descent have greater familiarity with the relevant science than I do” (66). Dembski's position is typical, accepting “some change in the course of natural history,” but believing “that this change has occurred within strict limits and that human beings were specially created” (67). This is the standard position of an ID advocate. In May 2005, ID supporters on the Kansas Board of Education held hearings to support ID-friendly science standards. Mainstream scientists boycotted the hearings, but a series of pro-ID witnesses, mostly teachers and academics (but few professional biologists) testified in support of the standards. During cross-examination, only 2 of 19 witnesses accepted the common ancestry of humans and apes. One was an independent scholar who clarified that although he supported the Kansas standards, he was not an ID advocate; and the other was Behe. The rejection of evolution by the vast majority of ID witnesses at the Kansas hearings parallels the rejection of evolution by ID proponents in general.

and (c) most importantly, as mentioned above, those who even kinda-sorta accept common ancestry are a tiny minority in the ID movement. It is very widely rejected, by 95% or more of the major figures. You don't get to portray the tiny minority position as being representative of the movement. Well, actually you can do whatever you want, but you won't convince any well-informed observers.

Why do you lie, Nick? And how can you live with yourself when you do? You said you weren’t an atheist? Well, whatever your religion is, doesn’t it include an injunction not to lie to people? Not even for the “good end” of keeping ID out of the schools?

Look. Back in the late 1990s I first heard of ID. At the time, it was being advertised as a revolutionary new scientific movement, and definitely not creationism. Reading the ID guys seemed like a refreshing change from the older creationist works, since they did have less Bible and seemingly more science. But once I learned more science, it became clearer and clearer to me that the ID arguments were just the same old creationist arguments but with more science-y sounding technical language covering them up. Then ID advocates started pushing ID in the state science standards in Kansas and elsewhere. And then I started reading more ID literature -- not just "Darwin's Black Box" and the like, but JP Moreland's "The Creation Hypothesis", Phillip Johnson's numerous works which all phrased the debate as supernaturalism vs. naturalism, etc. And I read more about the history of creationism, and it was extremely clear that ID was basically just another expression of the decades-old creationist movement, with the same arguments, same basic tactics, and same goals, just with new terminology. Only years later came the Kitzmiller case and the "smoking guns" proving direct transition of a creationist text into the first ID textbook. It's not lying that motivates me -- that's absurd anyway. What would be the point? It's knowledge and experience. NickMatzke_UD

Nick: I'm always amazed that people can get a Ph.D. in the natural sciences, and yet be so dense when it comes to registering simple, everyday reasoning. Let me say this plainly, so you won't waste more time writing long diatribes about old books: THE THAXTON BOOK IS IRRELEVANT TO THE DEBATE AT HAND. OF PANDAS AND PEOPLE IS IRRELEVANT TO THE DEBATE AT HAND. THE MOTIVES OF THE WRITERS OF THESE BOOKS IS IRRELEVANT TO THE DEBATE AT HAND. ANY BIBLICAL REFERENCES THAT MIGHT BE IN THOSE BOOKS IS IRRELEVANT TO THE DEBATE AT HAND. THE DEBATE AT HAND IS WHETHER *CURRENT* ID THEORY IS CREATIONIST. THAT IS, WHETHER CURRENT ID THEORY DEPENDS ON THE ASSUMPTION OF THE LITERAL TRUTH OF GENESIS, AND INTRUDES RELIGIOUS CONTENTS INTO ITS SCIENTIFIC REASONING. CURRENT ID THEORY IS FOUND IN THE TECHNICAL OR SEMITECHNICAL, NON-DEVOTIONAL WRITINGS OF DEMBSKI, BEHE, MEYER, WELLS, DENTON, ETC. AND ITS ARGUMENTS DO NOT PRESUPPOSE ANY RELIGIOUS FAITH AT ALL, LET ALONE A LITERAL INTERPRETATION OF THE BIBLE. THEY ARE THEREFORE BY DEFINITION NOT CREATIONIST ARGUMENTS. Are you able to grasp that, Nick? Did your profs in biology train you to read and comprehend English prose on matters pertaining to evolution and design? So why do we all have to keep repeating these statements for you? Do you have a reading disability that you've kept hidden from your supervisors? Or is the problem one of honesty? Do you keep harping on Thaxton and Pandas because you don't want to admit that you and your friends have been lying to the public for six years (since the Dover Trial) in saying or implying that Behe, Sternberg, Denton and many other ID proponents are creationists when they are in fact evolutionists? Why do you lie, Nick? And how can you live with yourself when you do? You said you weren't an atheist? Well, whatever your religion is, doesn't it include an injunction not to lie to people? Not even for the "good end" of keeping ID out of the schools? Nick, to paraphrase a book for which you and most of your evolutionary biology friends have contempt: We know thee who thou art. We know that you are lying, and you know that we know that you are lying. Why prolong the agony. Why not either admit you are lying, and leave this thread with a clean conscience, or do what your mentor Eugenie did when she was clearly losing the argument to David Berlinski -- fly into an uncontrollable rage at us for exposing the truth? Either option would produce catharsis. The course of action you've chosen here -- studied evasion -- is just wasting your time and everyone else's. Good-bye, Nick. If you were a true scientist, a true thinker, or an honorable man who could admit a fault, I'd continue debating with you. But you are none of the above. Thomas Cudworth

Elizabeth re 200: Regarding Dembski, you've made a logical slip. The fact that Dembski identifies the God of intelligent design with the God of Christianity does not prove that he improperly conflates religion and science. None of his *arguments* for design depend on his belief that the designer is the Logos of John. He merely indicates that science and religion, when each conducted properly according to their own methods, meet at the highest plane. That does not indicate any improper mixing of the subjects at all. This is why I asked you if you had actually read any ID books straight through, as opposed to relying on quotes you've picked up, out of context, from internet debates. For example, the book in which Dembski made the Logos statement, have you read it straight through, to get the context and qualifying statements? And have you read No Free Lunch straight through, which doesn't talk about the Logos? If you had, you wouldn't have made the invalid argument that you did. Thomas Cudworth

Here's some more history that Mike Gene, Thomas, etc. don't take into account. Again, it's from the actual relevant time period, not retrospective apologetics done with rosy glasses to make ID appear cleaner than it is.

Thaxton, Charles, and Buell, Jon (1983). "Why All the Fuss About Evolution And Creation?" The Foundation Rationale, 1(1), 1st edition, pp. 1-3. Published by the Foundation for Thought and Ethics. THE FOUNDATION RATIONALE Vol. 1, No. 1 © by Foundation for Thought and Ethics, 1983 Price $1.00 [pp. 1-2 have a discussion of morality in the public schools, the Arkansas trial, the alleged metaphysical naturalism of evolution, etc. The conclusion is on pp. 2-3: ] As unpalatable as this Darwinian perspective may be to some of us, it is fair to ask if there isn't room for it to be expressed and taught in public education? In general, our society has answered yes, condoning the expression of naturalism and many of its companion ideas. We are not in conflict with this. We are opposed to the censorship of ideas. But here is the crux of the present problem. Though our U.S. Constitution provides for free expression of ideas -- even those diametrically opposed such as naturalism and theism -- it seems that the champions of naturalism want to take that Constitutional freedom of expression away from theists instead of allowing the ideas of each view to coexist in an academically free system. This is why there is a conflict between naturalism and theism, between evolution and creation in the public schools. It is the intent of a relative few naturalists to supplant theism through the exclusive teaching of evolution in our schools. Most naturalists lend only passive influence -- chiefly by ignoring theism. But many theists have supported the efforts to exclude creationism from the classroom as well. Many theists resist what they consider too narrow a form of creation and some react to individual personalities rather than to the ideas presented. Unfortunately, too little attention is given the end result -- that naturalism has gained a favored status, with the effect that Judeo-Christian moral absolutes are exiled as irrelevant to our time. In a court of law, witnesses are sworn in with the oath "to tell the truth, the whole truth, and nothing but the truth". This wise convention was established in the understanding that often partial truth can masquerade (even if unwittingly) as whole truth. It is our opinion that the exclusive teaching of evolution in the public schools is part of an overall process that removes theistic thought from the public sector. Some have rightly called a world view a "world and life view". This is certainly appropriate, since our actions express our thoughts. Unfortunately, the effects of the shift from theism to naturalism aren't abstract. They burst from the classroom into society as a whole. The new naturalistic consensus translates directly and energetically into people's [page 3] self-images, into how employers and employees respond to one another, into how we try to solve man's problems and specifically into the issues of child abuse, abortion, euthanasia and the many other pressing matters with which parents are concerned. A major problem is that no one has provided a naturalistic ethic with teeth in it; no attempt to logically support a moral lifestyle on an evolutionary base has demonstrated any compelling moral force on the societal level. That's clear from looking at how far civilization has declined in just the last hundred years. Thomas Huxley, the staunch "Darwinian bulldog", agreed: he once asserted that although evolution is true, it leads to bad ethics. Thus if Christians make their peace with the monopolistic teaching of evolution, they cannot justifiably complain that students reject Judeo-Christian values and principles. That's why Christians -- in fact all theists -- must insist that whenever origins are discussed, public schools allow the teaching of the evidence for creation alongside instruction in the naturalistic concept of evolution. If the scientific rationale for both creation and evolution were taught, there would be an equality demanded by the symmetry of the two metaphysical views, theism and naturalism. If both are not taught, it is not just the subject of origins that is affected. The whole of naturalistic thought is given privileged status by the state, with the de facto result that young minds are prepared to reject theistic approaches to morality and religion. At the same time, they are prepared to receive both moral relativism and the various naturalistic religions, such as Unity, Buddhism, Scientology and Religious Humanism. In summary, we discern the primary conflict in the public schools to be in the realm of metaphysics, between theism and naturalism. The concern about origins and moral values should not lose sight of this. The exclusive teaching of evolution is a major force of modern naturalism which, if not checked, will remove every trace of theistic thought from the public sector. Therefore, we should recognize that even if we are not individually interested in the origins question, the creation issue touches us all. The exclusive teaching of evolution ushers in moral relativism and inclines young minds toward naturalistic religions. But a call for censorship is not appropriate. Instead, the emphasis in our efforts to counter the naturalistic indoctrination in the public schools and public sector should be to restore balance in the free expression of ideas. Let us remember that Jesus also told us to be "wise as serpents but innocent as doves". -- Charles Thaxton, Ph. D. -- Jon Buell

NickMatzke_UD

F/N: MikeGene weighs in on the Pandas talking point (HT: Wayback Machine):

...and he completely ignores what was going on legally at that exact time, and which Thaxton, Bradley, etc. were deeply involved in. Why, for the love of the IDer, would someone attempting to start a "revolutionary new scientific movement" make their 2nd book, and their first book using the "intelligent design" terminology, a high school biology textbook? NickMatzke_UD

Mung, why don't you read my posts in their entirety? Immediately before the sentence you just quoted, I wrote: "So let’s make a very simplified model:" I was trying to explain something to you which you seem determined not to understand. I'm not trying to persuade you that evolutionatry theory is true, merely what it is. But if you want to stick with your straw man version, feel free. It's just you'd have more success attacking evolutionary theory if you actually knew what evolutionary theory was. I was trying to help. Elizabeth Liddle

Life starts with a single living cell. That cell divides into two, almost identical cells. Those two divide into two each, making four.

Is that what you really believe? What's your evidence?

So we have a tree that bifurcates with every cell division.

But you're not equivocating, are you. You wouldn't do that. You're assuming what you need in order for your claim to be true. So you're begging the question. You're equivocating over the type of tree that was in the original discussion. You only bring in HGT when you think it can't harm your story, which is completely ad hoc. Do you just type the first thing that you can think of that you think will make the last thing you wrote make you look less foolish? There's a reason people are frustrated with you Lizzie, and it's not because they disagree with you. If you think that's what it is then you're lying to yourself. Mung

gpuccio:

That’s not fair from you! Dembski is a mathematician “and” a theologian. As far as I can say, he keeps the two things strictly separate. I have not found theologic arguments in his scientific books. Are you saying that a scientist cannot have a religious or theologic activity in his life?

Not at all. It was in response to the challenge that lots of evolutionists are vociferous atheists. My point was that the proportion of evolutionists that are vociferous atheists is much smaller than the proportion of IDists who are vociferous theists. And if a theologian isn't a vociferous theist, I'm not sure what a theologian is :) But no, he doesn't keep the two things strictly separate - he has specifically identified his Intelligent Designer with the God of the gospels (IIRC, specifically the God of John I). And nor do people here. Evolutionary theory seems very much less closely entwined with atheism than ID is with theism. I know there are some atheist IDists (well, I know of a couple, I guess) but I know of countless evolutionary scientists who don't have much in the way of a view on religion at all, and a large number of theists who are perfectly happy to accept evolutionary theory. Elizabeth Liddle

How, in the name of Aristotle, did a “true” statement become a false one?

Had me rolling. Mung

And as for the alleged "tree" of life: Charles Darwin's tree of life is 'wrong and misleading', claim scientists:

Dr Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, said: "For a long time the holy grail was to build a tree of life. We have no evidence at all that the tree of life is a reality."

Now what? Joseph

Ooops- Here is the link: Nested hierarchy- see potential falsification Joseph

Elizabeth Liddle @ 177- <a href=http://www.talkorigins.org/faqs/comdesc/section1.html#nested_hierarchyDr Theobald says- in potential falsifications of nested hierarchies:

It would be very problematic if many species were found that combined characteristics of different nested groupings.

and:

A mix and match of characters like this would make it extremely difficult to objectively organize species into nested hierarchies.

That said a mix of characteristics is the very definition of a transitional. Do you understand that? The point being is we may expect a Venn diagram- in which there is overlapping. But a nested hierarchy cannot have any overlapping. Also we do not observe a nested hierarchy for the bulk of the biomass- prokaryotes. Does that mean the theory is falsified? Joseph

H'mm:

Dembski teaches in a seminary!

'E baane expelled -- twicet! G kairosfocus

Mung:

Elizabeth Liddle:

There are a couple of interesting violations, however: one is horizontal gene transfer, which makes bacterial lineages much less of a tree and much more bushy and tangled.

HGT between bacteria is irrelevant Lizzie. Pick a story and stick with it please. Less of a tree? Yet elsewhere you have claimed repeatedly that these organisms don’t speciate at all. So no, not less of a tree, no tree. I thought you were all about being completely honest?

Yes indeed I am Mung, but your skill in placing yourself in positions where the trees obstruct the forest is formidable. Let's unpack: What do we mean by a tree, in phylogenetics? Well, we mean inheritance of traits down a lineage. Right? So let's make a very simplified model: Life starts with a single living cell. That cell divides into two, almost identical cells. Those two divide into two each, making four. So we have a tree that bifurcates with every cell division. Now, let's say that some of the daughter cells of a parent cell are slightly different from the parent cell. Those changes will be inherited downstream from the variant daughter. And so we can simplify our map of the tree, by plotting not every cell division event, but only those cell divison events that result in a daughter cell that differs from the parent. So we might go for, say 20 generations before we find a mutant daughter. Now we have a branching point - a lineage of cells descending from that daughter, and a lineage descending from the rest. Then another mutant daughter occurs, perhaps in the original mutant daughter's lineage, perhaps in another. And so, even in a cloning population we have a tree. We won't call the branches "species" though, because normally that word is reserved for populations that don't interbreed, and our clones don't interbreed anyway. But we still have a tree. However, we also have HGT, apparently. So our tree, at this point starts to look tangled. Let's say we have a clean tree up to the millionth generation, at which point we have, say 50 "twigs" - fifty types of cell, each with their own lineage, and tracing their origin back to a first mutant daughter. Now the first great HGT day dawns: an individual from twig 3 bumps into an individual from twig 29, and gains some genetic material. When the twig 3 individual divides into two daughters, we have another mutant, another branch of the tree. But this branch is no ordinary branch, because if we trace its origins backwards, it does not simply lead to a mutation event at the millionth generation on twig 3; it also leads to some mutation event in the ancestry of twig 29. So while up till now we had "nested hierarchies (namely, a tree) now we have a tangle. Now, fast forward a bit, to the first multicelled organisms, and the beginnings of sex. Sex, of course, is just a very specialised example of HGT (sorry about that), in which the HGT happens regularly between pairs of individuals. Now we need to simplify the tree description still further, in order to see the forest, not by grouping populations by their genetic identity, but by their genetic similarity. Humans are not genetically identical, but they are genetically similar. Now, what defines our bifurcations is lack of between-branch HGT (although this occasionally occurs, and we call it "hybridisation"). But we still have nested hierarchies. Plus of course, our single celled cloning populations are still cloning away, branching away, and doing their HGT thing from time to time. So the "forest" we can now see is: Individual cell spawns a tree lineage where each branch is consists of identical individuals. This tree acquires tangles from time to time as genetic material crosses from branch to branch. One branch becomes multicellular, and continues to clone itself, producing further branched descendent lineages. One of these branches starts to do within-branch HGT more systematically (because ones that do do rather well), between pairs of individuals. This branch produces a branched descendent lineage, in which there is a large amount of HGT within each branch, and very little between branches. Meanwhile, co-existing are cloning unicellular branches of the Big Tree in which the HGT is more haphazard, although it will tend to happen more between neighbouring branches (who occupy the same environment) than more distant branches (who have adapted to very different environments.

And since a nested hierarchy is not predicted for the most basic and fundamental forms of life known, from which forms supposedly all other life arose without speciation, your claim is clearly false.

Yes, a nested hierarchy is predicted for the most basic and fundamental forms of life, it's just that we don't call the branchings "speciation" because they are not defined by the capacity to interbreed, and that HGT means that there are crosslinks of genetic material between branches, which happens only rarely in sexually reproducing populations (leaving aside viruses, of course, but I'm trying get the view of the forest clarified here - and it turns out to be a tree!) Elizabeth Liddle

Elizabeth: Behe doesn’t, much, but Dembski teaches in a seminary! That's not fair from you! Dembski is a mathematician "and" a theologian. As far as I can say, he keeps the two things strictly separate. I have not found theologic arguments in his scientific books. Are you saying that a scientist cannot have a religious or theologic activity in his life? As for me, I have never used any religious argument in my scientific debates here. And never will. Not only that, but unlike, say Shapiro, who thinks about intelligent systems, whenever I ask here about possible design mechanisms I’m told that’s not what ID is about – it’s just about detecting design! I don't agree with you. This is a commonly misunderstood point. Whe we say (including me) that design detection does not need understanding the mechanisms of design, we are saying a very simple truth. That's exactly the way it is. That does not mean, however, that ID cannot make models of possible design mechanisms. It certainly can, as much as current data allow. Some ID proponents will discuss those models, other will not, and will just stick to the design detection point, which is however very important. But the point that design detection does not need understanding of the mechanisms of design is irrenounceable. As for me, I have many times discussed here my idea about possible mechanisms for design of biological information, usually in response to objections like yours. I can do that again, if you are interested. For starters I’d like to know what this “neo Darwinian” part of evolutionary theory is that is supposed to be shaky. Can you tell me? I genuinely want to know. And I genuinely give you my answer: a) Universal common descent is controversial, but IMO reasonable. I I accept it, like many other IDists (Behe, for instance), as a viable hypothesis. Other IDists definitely refute it. I don't agree with them. b) The causal mechanism for the generation of biological information proposed in classical neodarwinism, instead, is completely wrong and unsupportable. It has no empirical support nor logical consistency. I am speaking, obviously, of the concept that a mixed algorithm, including a random part (Random Variation) and a necessity part (Natural Selection) can effectively create complex functionally specified information. c) There are obviously various forms of neo-neo darwinism, attempting alterbative "explanations". IMO, they are worse than classical neo darwinisms. Indeed, classical neo darwinism at least proposes an explanation, although wrong. Many of these "new" forms of theory do not even try to really explain anything at the causal level. As such, they are not even scientific theories. Neutralism is interesting (I do believe that almost all mutations are negative or neutral), but as I have tried to explain it does not add anything at the level of causal explanation. Vague references to ill defined concepts, like self organizing systems and emerging properties, are only confounding and flawed, and have no explanatory power (I am ready to discuss each of these points in detail). Classical neo darwinism has potentially explanatory power: its mechanism of variation (RV) is well defined, and so is its necessity mechanism (NS). The problem is that the RV part, the random part, has not the probabilstic power to generate complex information selectable by the necessity part (NS). I have affrimed many times explixitly, and I repeat it here, that if complex fucntional information were deconstructable into simple selectable steps, the classical neo darwinian model "could" work, at least in principle. But that premise is not true, never has been. There are lots of logical and empirical reasons to be certain of that. In practice, the only viable theory to explain biological information (which is a fact) is the design theory. gpuccio

PS: In a separate thread I have been documenting Dr Matzke's record on what now has to be called a willful side tracking of an issue over the serious -- and patently scientific -- issue of the origin of FSCO/I in biology, through the trifecta fallacy, back to 2007 and beyond to at least 2005. There is some serious explaining to do here on NM's part. kairosfocus

F/N 2: Jekel's review of TMLO when it came out: http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2589926&blobtype=pdf __________ >> THE MYSTERY OF LIFE'S ORIGIN: REASSESSING CURRENT THEORIES. By Charles B. Thaxton, Walter L. Bradley, and Roger L. Olsen. New York, Philosophical Library, Inc., 1984, $14.95. Most non-scientists who read the popular press, and probably even most scientists, believe that recent work demonstrating the production of essential amino acids by the action of energy on gases assumed to be in the primordial atmosphere has solved most of the problems of abiogenesis, the idea that living organisms arose from non-living chemicals by the action of natural laws that can be observed today. In particular, the work of Miller and Urey, using electric spark, and that of Harada and Fox, using thermal synthesis, are well known. Others have used ultraviolet light alone or in combination with heat as the energy sources. To all who share the comfortable assumption that the scientific problems of abiogenesis are mostly resolved, this book will come as a real surprise. The authors have developed a critique of current hypotheses that is a synthesis of the concerns of many working in the field, combined with their own additional contributions. The essence of their critique is that

... in the atmosphere and in the ocean, dilution processes would dominate, making concentrations of essential ingredients too small for chemical evolution to be significant [p. 42].

The dilution processes referred to here include both the diffusion of small created quantities into the vastness of primordial seas and the action of destructive processes on those amino acids that are created. The special problems leading to the conclusion of dilution include: (1) evidence that life appeared very early in the earth's history, providing only a relatively short time for chemical evolution; (2) the fact that destructive processes would tend to dominate over creative processes; (3) the possibility of thermal decay in the oceans, and (4) the presence of various chemical decay processes. The latter include: the hydrolysis of hydrogen cyanide to formic acid, the reaction of carbonyl groups with amino acids, various reactions with the many non-proteinaceous amino acids that would also have been formed, and the termination of growing polypeptides and polynucleotides by reactions with a variety of chemicals or by hydrolysis. The authors say, ". . . survival of proteins in the soup would have been difficult, indeed" (p. 55) and "As with proteins, it is difficult to conceive of a viable nucleic acid existing in the primordial soup for more than a very brief period of time" (pp. 55-56). One of the most striking concepts to this reviewer was the emphasis that most of the proposed creative mechanisms would, in fact, be both creative and destructive to abiogenesis and that the estructive actions would tend to dominate. For example, some theories postulate that ultraviolet light would also have been destructive to many of the early chemicals. If one postulates a different energy source (problematic in itself) and enough oxygen-ozone to prevent ultraviolet-induced chemical decay, there would have been enough oxygen to be destructive to many primordial chemicals through oxidation processes. As a proposed solution to dilution-destruction problems, various concentration mechanisms are proposed, such as small concentrating ponds in areas protected from ultraviolet light with a heat source to speed up evaporation. However, such unlikely settings have problems of their own, and there is, apparently, no geological evidence for an organic prebiotic soup, either generally or locally (although evidence for such localized areas could easily have escaped detection to date). Some of the most fascinating chapters are those on the thermodynamics of abiogenesis, which is probably not surprising, given the fact that the first author's doctorate is in physical chemistry (the other two authors have doctorates in materials science and geochemistry). They state the results of the estimates of the required energy input per mole and conclude, "This trivial yield emphasizes the futility of protein formation under equilibrium conditions" (p. 142). They conclude that open system energy sources might be sufficient ".... for doing the chemical and thermal entropy work, but clearly inadequate to account for the configurational entropy work of coding (not to mention the sorting and selecting work)" (p. 165). They believe there is a need to postulate some sort of a coupling mechanism, or the thermodynamic laws alone would probably rule out abiogenesis along the lines of any of the current theories. The volume as a whole is evastating to a relaxed acceptance of current theories of abiogenesis. It is well written, and, though technical, much of the book is within the reach of the informed on-scientist. The book apparently has been well received by many who are working in the field of abiogenesis, such as Dean Kenyon and Robert Shapiro. The volume, however, has still another surprise for the reader, a philosophical epilogue in which several general theories of origins are considered: new natural laws, panspermia, directed panspermia, special creation by a creator within the cosmos, and special creation by a creator beyond the cosmos. This section was interesting, and provided information new to this reviewer, such as the strong position of Hoyle that ". .. Darwinism has failed to account for the origin of life and the development of terrestrial biology" (p. 196). Whether such a philosophical epilogue is appropriate or not must be left to the reader to decide, but, in any case, the philosophical questions are not introduced into the science portion of the text (which is 187 out of 217 pages). This book is reasonably priced and is strongly recommended to anyone interested in the problem of chemical and biological origins.>> _____________ Plainly, we can see the lines of thought that would come out more and more in the next 15 years emerging. Lines that are also developed at popular level in Pandas, whatever its defects may be. Some rethinking is in order, NM. GEM of TKI kairosfocus

F/N: MikeGene weighs in on the Pandas talking point (HT: Wayback Machine): ___________ >> . . . The pivotal point for ID then came in 1984, when Charles Thaxton, Walter Bradley, and Roger Olsen published their book, The Mystery of Life’s Origins: Reassessing Current Theories. Since the book was not poofed into existence, the ideas contained within must have been developed in the early 80s. Thaxton et al.’s book was significant for many reasons. First, it was not a typical ‘creationist’ book coming from the Institute of Creation Research. On the contrary, the book received praise from Robert Shapiro and Robert Jastrow. Second, the book did not deal with evolution or its mechanism, but instead focused entirely on abiogenesis. Third, the authors were clearly influenced by Yockey: “As was pointed out, Yockey has noted that negative thermodynamic entropy (thermal) has nothing to do with information, and no amount of energy flow through the system and negative thermal entropy generation can produce even a small amount of information.” (p. 183) The Epilogue of Mystery is the most significant, as Thaxton et al. are clearly moving in the direction of ID as a response to abiogenesis. In this chapter, we find the other influence on the birth of ID: “Hoyle and Wickramasinghe argue that the evidence is overwhelming that intelligence provided the information and produced life.” (p. 197) Hoyle’s stuff was published in the late 70s and early 80s. This is a theme Thaxton et al. would repeat several times in the Epilogue:

If an Intelligent Creator produced the first life, then it may well be true that this observed boundary in the laboratory is real, and will persist independent of experimental progress or new discoveries about natural processes. Also an intelligent Creator could conceivably accomplish the quite considerable configurational entropy work necessary to build informational macromolecules and construct true cells. (p. 210)

and

The failure to identify such a contemporary abiotic cause of specified complexity is yet another way to support our conclusions that chemical evolution is an implausible hypothesis. (p. 211)

and

True, our knowledge of intelligence has been restricted to biology-based advanced organisms, but it is currently argued by some that intelligence exists in complex non-biological computer circuitry. If our minds are capable of imagining intelligence freed from biology in this sense, then who not in the sense of an intelligence being before biological life existed?

One year later, an even more influential book was published – Michael Denton’s Evolution: A Theory in Crisis. It’s easy to view Denton’s book as the crucial half-way point between creationism and intelligent design. Like Thaxton et al, Denton was not a member of the ICR. Yet he presented a typological view of life that played extremely well among the creationists. But more significant, in my mind, is another chapter near the end of the book, one entitled, “The Puzzle of Perfection.” In this chapter, Denton turns to the issue of design and includes a section that is almost poetic and inspiring. He writes, “Aside from any quantitative considerations, it seems intuitively impossible that such self-evident brilliance in the execution of design could have ever been the result of chance.” (p. 327) Denton then takes his readers on a walk-through of the cell, writing, “We wonder at the level of control implicit in the movement of so many objects down so many seemingly endless conduits, all in perfect unison. We would see all around is, in every direction we looked, all sorts of robot-like machines….We wonder even more as we watch the strangely purposeful activities of these weird molecular machines, particularly when we realized that, despite all our accumulated knowledge of physics and chemistry, the task of designing one such molecular machine – that is one single functional protein module – would be completely beyond our capacity at present and will probably not be achieved until at least the beginning of the next century.” (p.328-9) [As an aside, I just noticed that it was Denton who introduced the term ‘molecular machine’ in 1985.] Then comes 1986, where Robert Shapiro publishes, Origins: A Skeptic’s Guide to the Creation of Life on Earth. Although this book runs independently of the ID stream, it’s a powerful book that appears to confirm much of Thaxton et al.’s book. Anyway, from here we know that Denton’s book influenced Behe, Thaxton’s book influenced Kenyon, and that Thaxton, Kenyon, and Behe worked on Pandas. So there seems to be a more accurate, although less sensational, explanation for the birth of ID. In the 1950s, researchers such as Sanger, Watson, and Crick brought sequence to the center stage of molecular biology. In the 1960s, the genetic code was worked out and Michael Polanyi began to explore the implications of such things. In the 1970s, Hubert Yockey would consider sequence and begin to make arguments that would resonate among the creationists. Such resonance was then amplified by Fred Hoyle in the late 70s and early 80s. Along came Thaxton et al’s book in 1984, providing a powerful critique of abiogenesis and ends with tantalizing ideas about intelligence, specified complexity, and design. A year later, 1985, Michael Denton puts Darwin in the cross-hairs and ends his book with an inspiring section on design. In 1986, abiogenesis researcher Robert Shapiro gives abiogenesis a stinging criticism. The arguments from Hoyle, Thaxton et al., Denton, and Shapiro were all laid out from 1978-1986 and it’s safe to say that the authors of Pandas, Thaxton and Kenyon, were well immersed in them . . . . So there is no reason to invoke any form of marketing or political conspiracy. The authors of Pandas had begun to sincerely express a new argument, that while loosely fitting within the creationist context, was never dependent on such a context. Since 1987, intelligent design has continued to develop and I have already spelled this out . Both Behe and Dembski have contributed essential steps in developing intelligent design into a serious method to explore nature. And today, as you can see from this blog, there are ID evolutionists [--> Of course, Behe is a leading example]. Who knows what the future may hold? >> ___________ Until this came up in a web search, I did not know the above existed. But, my own reading of TMLO and Denton definitely pointed in this direction as the best historical explanation of the rots of modern ID. Design thought, in general, was by Plato's day, long since a serious option. NM has some serious explaining to do. For, it is a moral duty that when an innocent explanation is accessible and covers the material facts, a decent person will prefer it to an accusatory one. GEM of TKI kairosfocus

"When did it become not true? How recently?" How, in the name of Aristotle, did a "true" statement become a false one? Ilion

Elizabeth Liddle:

There are a couple of interesting violations, however: one is horizontal gene transfer, which makes bacterial lineages much less of a tree and much more bushy and tangled.

HGT between bacteria is irrelevant Lizzie. Pick a story and stick with it please. Less of a tree? Yet elsewhere you have claimed repeatedly that these organisms don't speciate at all. So no, not less of a tree, no tree. I thought you were all about being completely honest? And since a nested hierarchy is not predicted for the most basic and fundamental forms of life known, from which forms supposedly all other life arose without speciation, your claim is clearly false. Mung

Nick Matzke:

For the love of the IDer, that was 152 years ago, it’s illegitimate to quote it without even considering what has happened since then. We’ve discovered rather a lot of transitional fossils since then. The main point of Prothero’s book is that Darwin’s statement back then is no longer true.

When did it become not true? How recently? But now my copy is on it's way. I can only hope that Prothero puts forth an explanation as to how Darwin's claim can in fact be refuted. Hos is it that we can know that Darwin's statement is no longer true? "We've found a lot of intermediates since then" just isn't going to cut it for me. How many intermediates should there be? Why are the ones we've found enough to falsify Darwin's claim? Are you saying that in Darwin's day there were no claimed "intermediates"? Have you read Deep Time by Henry Gee? Mung

Thanks, Elizabeth @ 184. I agree with your tone and some of what you say, but consider the following: 1. It appears that I have read far more than you have of evolutionists (usually of a neo-Darwinian stripe) who are openly atheists and who openly draw connections leading from evolutionary science to atheism (Coyne, Dawkins, Myers, Lewontin, etc.) You do not seem to be aware how many such scientists there are, or how vocal they are, and how much effect they have (or try to have) on middle-class public opinion. As for whether the vocal ones are the majority of evolutionary biologists, I agree they are not, but in America at least, they often claim to speak for evolutionary biology or for biology or for "science" (as if anyone could do that), and they get a lot of press. And when they do so, the "rank and file" of less loud biologists does not "rein them in" by chastising them for mixing atheism and science, but condones their activity by silence. 2. You apparently are not as aware as I am of work the ID people are doing. For example, your man Shapiro has collaborated in the past with ID ally Richard Sternberg. And in the past few years several peer-reviewed papers have been published on mathematical/computer modelling of evolution, evolutionary biochemistry, etc. You will find references to these as they come out, here on UD, at Discovery, or at the Bio-Complexity web site. 3. That Dembski currently teaches at a seminary is irrelevant to the quality of his scientific work, and bringing it up is *ad hominem*. I do not hear you saying the Coyne's work on evolutionary biology is suspect because his blogs and books ally him closely with atheism; I do not hear you saying the Polkinghorne's comments on physics are inadmissible because he is now an Anglican priest. I'm disappointed in your application of a double standard, which indicates a conscious or unconscious prejudice. 4. You misconstrue Denton's first book, which I have read carefully. He stops short of endorsing creationism, or even of saying "evolution is false" in that book. He merely indicates that the data conform more closely in many respects to what one would expect on creationist premises. He was not a religious believer when he wrote that book, and had no motivation to try to persuade people of creationism. As for whether ID people raved about Denton's first book, yes, they did, but get your facts straight. On the UD survey you refer to, Denton's first book got three votes; his second book got six. And Behe wrote a rousing endorsement of the second book. 5. Neo-Darwinism, better named "the Modern Synthesis," makes random mutations plus natural selection the main (not the only, but the main) driver of evolutionary change. It is the view presented by Dawkins and by Ken Miller and by Eugenie Scott; it is held by most of the TEs on Biologos; it is the view criticized by Denton and Sternberg and by ID people. It is odd that I seem to understand more of the basic terminology of evolutionary theory than you do, but then, I have found that oddity repeated across the internet; the champions of "science" seem to do very little reading in the history of evolutionary theory; ID people do *lots*. 6. If you want to stop short of accusing Nick because you don't know the facts of the case, that's fine (though I *do* know the facts of the case, and I know he is willfully misrepresenting); but you are still ducking your obligation as a scientist to endorse, as a general principle: *It is wrong to impute views to people that they have repeatedly and explicitly denied that they hold.* Such behavior is not countenanced at any scientific conference, in any scientific journal, etc. It is "gutter science" and you should explicitly repudiate it. And I can tell that you *do* know enough about ID to know that Behe claims to be an evolutionist, not a creationist, so, even you do not want to name Nick, you should be willing to say: "It is scientifically and academically dishonest to try to portray Behe as a creationist against his explicit protests, and those doing so, whoever they are, should stop." If you will not go that far, I do not believe that you are being either fair or honest about the facts, but are being partisan. 7. Finally, may I be so bold as to ask you which ID books you have read from cover to cover? And if you have read critiques of Behe, have you read his detailed rejoinders to those critiques which are posted on this site? I often find that critics of ID have read far, far less ID than its defenders have. Often as little as a quick read through Darwin's Black Box, and sometimes less than that. Forgive my curiosity. Thomas Cudworth

Onlookers: The above is part of why I specifically, consistently refer to [often, Lewontinian, a priori] evolutionary materialism, from hydrogen to humans on blind chance plus mechanical necessity, acting on only matter and energy in space and time (inclusive of multiverse speculations) held to constitute and delimit reality. This is what, on the specifically biological, macro=evolutionary facet, Philip Johnson aptly rebuked thusly, as "scientific material[ism]":

For scientific materialists the materialism comes first; the science comes thereafter. [[Emphasis original] We might more accurately term them "materialists employing science." And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) "give the appearance of having been designed for a purpose." [Emphasis added, showing the relevant core of the neo-Darwinian synthesis, which still dominates modern evolutionary theory, despite all the pointing to various variants and proposed adjustments] . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [[Emphasis added.] [[The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]

The underlying begged questions that have been institutionalised through so-called methodological naturalism and associated attempts to improperly redefine science itself, and in that pursuit have distorted the actual history and nature of modern science and the relevant views of many major founding and current scientists, and which are what makes darwinist claims sound far better merited than they are on actual empirical evidence, are now exposed before us. GEM of TKI kairosfocus

Thomas: thank you for the references to post numbers. I will try to respond. Meanwhile, in response to your more recent post: Yes, I am aware of Margulis and Shapiro's work. I am a fan of both actually. I guess one problem I have is with this thing called "neo-Darwinian evolutionary theory" that is supposed to be "one of the shakiest parts of modern biology." Which part is it supposed to be? Shapiro and Margulis may be controversial but they are also widely admired. They get work published. They are not denied tenure. Their work is, in other words, sound. But evolutionary biologists are always arguing! There is no "neo-Darwinian" orthodoxy that I am aware of. Another of my own heros is Denis Noble, who directly challenges the notion of The Selfish Gene. Indeed, one of the reasons I come here, and one of the reasons I applauded your earlier post, is that I agree that ID has an important kernel of truth. As a neuroscientist I am interested in intelligent systems, and I think Darwinian systems are intelligent systems. Indeed they are hugely important in models of learning. I just think that IDists have, in large respect, brought the disrespect they receive on themselves, partly by conflating the science with a religious stance, and partly by, well, not doing rigorous science. And when you say that the other side are making religious points too - well, not exactly! Sure there are a bunch of very vocal atheists who support evolutionary theory AND who argue vociferously for atheism, but what propertion are they of the total number of evolutionary biologists! And contrast that with the ratio of ID scientists who align their work with religion to those who don't. Behe doesn't, much, but Dembski teaches in a seminary! As for Denton, he is indeed, now, an "evolutionist" but guess which of the books he wrote made it on to the top ten ID list here - the one he wrote first, when he wasn't :) Not only that, but unlike, say Shapiro, who thinks about intelligent systems, whenever I ask here about possible design mechanisms I'm told that's not what ID is about - it's just about detecting design! What I'm saying to ID, I guess is: get your own house in order. Beef up the science; find out what Shapiro is saying and test his hypotheses; figure out what kind of design process could lead to living things, bearing in mind the really important fact that unlike human designs living things reproduce themselves with variance. However, I must decline your offer to prove my "neutral" credentials. I don't even know if I could claim to be neutral. All I can claim to be (and do) is honest. And I do not know who has acted dishonestly here, and would not presume to, even if I had more facts than I do. Of course people should not deliberately mislead, but in my experience, most accusations of deliberate deception, in the science world, are not. I think there is far too great a tendency for people to think that those with whom they disagree are lying to them. That happens on both sides of any debate, IMO. That, or they accuse the other side of stupidity. I don't do that. I find it deeply counterproductive. If we want to understand each other, we need to find out why the other thinks the way they do, not assume that they are being stupid or dishonest. For starters I'd like to know what this "neo Darwinian" part of evolutionary theory is that is supposed to be shaky. Can you tell me? I genuinely want to know. Elizabeth Liddle

Dr Liddle: As you know, I am a Caribbean person, but have been around while the issues brought into this thread were happening, and have long had scientific and worldviews interests in the matter. A few notes, also observing that I have clipped off some key points elsewhere this morning for those who need to focus: 1: My take on the significance of Pandas is somewhat different than Dr Cudworth's, as I read it in light of the earlier history of TBO's TMLO. 2: From that view, The period across the 1980s was seeing a transitional pattern, with TMLO emerging by 1984/5 as the first technical ID work. 3: You will notice how Dr Matzke cannot answer to the point that he whole frame of argument in TMLO is not Genesis-controlled, but instead is asking what can give rise to what I have descriptively termed -- in part on remarks and citations in TMLO Ch 8, FSCI. 4: Pandas is a more popular level work in that context, and it struggled in the context where the terminology that is now routine was not then identified and accepted. Indeed, Pandas my be where the term (Intelligent Design emerged as a key and wide3ly recognised term for the new -- and yet very old, back to Plato and others -- pattern of thought.) 5: There are indeed points where Pandas used arguments raised by creationists, though there is a distinction to be made between technical arguments that stand on their own empirically anchored merits and a characteristic frame of thought that rests on interpretations of and debates over Genesis. 6: What I find first and foremost inexcusable is the attempt to smear design thought as "creationism," instead of addressing the issues on their merits. 7: In that regard, it is highly material to note, as I have repeatedly pointed out, that Lewontin let the cat out of the bag on the controlling a priori of evolutionary materialism that dominates key centres of power in science, education, legal thought, the media and politics. If you read the linked and read on down, you will see that this is not just one man's idea by any means. 8: In short, this is all about the inherently dishonest rhetoric of turnabout false accusations by evolutionary materialism advocates. Those who live in materialist glass houses should not be throwing stones at even creationists much less design thinkers. 9: Now, in Pandas, some rough drafts were dragged into the trial, and the publishers were willfully locked out of being able to defend their editorial work. This is symptomatic of willful well poisoning, just as how the deceitful film Inherit the Wind was earlier used to poison the well about where creationists were coming from. 10: My response to that is that we are looking at transitional work, in a transitional time, and a case where the people involved were conceptually and terminologically distinguishing themselves from creationist thinking. 11: As Dr Cudworth has noted, this continued, and the new book reflects the matured design thought. 12: Design thought stands on its own merits, as an exercise linked to the key issue of the empirically warranted origin of functionally specific complex organisation and information. 13: The attempt to brand is as deceptively disguised creationism is a turnabout false accusation, intended to poison the well and close minds. 14: That is inexcusable, and those who knowingly are party to this, as Dr Cudworth has highlighted, are being willfully deceptive in the teeth of correction. Sad, but that is the hard reality that we face. GEM of TKI kairosfocus

Elizabeth: The posts to which you didn't reply are 103 and 104 above. Thomas Cudworth

Elizabeth: Thanks for your clarifications. It is good to know that you are in fact a scientist, and a polite one. If you are in neuroscience, you might be interested to know that Dr. Michael Egnor, one of the leading pediatric neurosurgeons in America, is anti-Darwinist and an ID supporter. But that's just an aside. I note, however, that by your own declaration, your field is not evolutionary biology. This doesn't mean that you haven't read up on evolutionary biology, or that you never took a course or two on evolution in your undergraduate days, but it does mean that you aren't going to have the time to keep up on evolutionary biology the way that evolutionary biologists do. I would point out to you that there are many full-time evolutionary biologists who are every bit as critical of neo-Darwinism as ID people are, and often for the same reasons -- scientific reasons. If you do not believe this, read some of the statements of Lynn Margulis and of the Altenberg group -- all infinitely more qualified to talk about evolutionary biology at a high theoretical level than any of the expert witnesses at the Dover Trial. So please don't assume that the criticism that ID people make of Darwinism is mainly of a religious character -- it isn't. Darwinism, both on the "random mutation" and on the "selection" side, has been under attack from various quarters among biologists who are secular and agnostic or atheist, for a few decades now. So you are wrong -- quite wrong -- to say that ID people are attacking the entire edifice of modern biology. ID people accept 95% of the findings of modern biology. They just happen to think that neo-Darwinian evolutionary theory is one of the shakiest parts of modern biology. And they are not alone in thinking this. You say or imply that the religious motivation is more real or more obvious on the ID side than the Darwinist side. Really? Have you read The God Delusion by the arch-Darwinist, Dawkins? Have you read the Brit Peter Atkins? Have you read Coyne's blog? Have you read Myers's blog? Moran's? Shallit's? Rosenhouse's? These are all people with Ph.D.s in some science, who have openly admitted to atheism and who in most cases have confessed that their atheism does indeed affect their scientific conclusions. Most of them in fact rule out design *a priori*, if not formally, then certainly privately and existentially. How can this have escaped your notice? I of course agree with you that the science of evolution should be separated from one's metaphysical prejudices as far as possible. But no one who has read the writings of Carl Sagan, Will Provine, E. O. Wilson, Peter Singer, etc., can possibly believe that these men have completely hived off their metaphysical presumptions from their science. But perhaps you have not spent as many years of your life reading these people as ID proponents have, and perhaps you are not as familiar with the unmistakably metaphysical bias of their writing and thinking. You still avoid my concrete point about Nick's dishonesty, which I'll ask again directly: Behe, Sternberg and Denton are evolutionists, not creationists. Matzke and the NCSE know this. They either will not acknowledge it, or actively try to obfuscate it. (Notice that Nick will not answer me on this point.) I say this is dishonest, and politically, not scientifically, motivated. Am I right or wrong? And if I am right, why will you not join me in condemning all such dishonest tactics from the Darwinist side? If not, you excuse by your refusal to condemn. What I want to hear from you -- if you expect me to believe that you are the "neutral" scientist you affect to be -- is condemnation of deliberate attempts to mislead the public by equating ID with creationism when leading ID figures have openly denied that they are creationists. I have condemned some actions on "my" side. (Though of course creationism is not my side.) It's time for you, and Nick, and Eugenie, and all the others on the Darwinist side, to condemn wrong actions of their own allies. It's time for you to condemn the literal thousands of unscientific *ad hominems* which have been issued by Coyne, Shallit, Moran, and hundreds of anonymous scribes (claiming to represent "science") almost daily for the past several years, in book reviews, on Amazon, on Wikipedia talk pages, on blog sites, at public talks, etc. It's time for people like you to say that these tactics are disreputable, unscientific, unacademic, inexcusable from the lips or pens of tenured professors, and should immediately cease. Will you do this? Will you say that Nick has been wrong? Will you say that the others have been wrong? Will you say that they have greatly and unnecessarily heated up the culture wars and distracted from cool scientific discussion of the origins of biological form? Until you concede these things, it is hard for me to take your pose as a fair, calm, non-partisan person entirely seriously. A Darwinian who was *only* interested in pure science would be just as repelled by the words and actions of the Darwinians as ID people are. Thomas Cudworth

Thank you for your generous response, Thomas, given the response I owe you. I will try to find it - a link would be helpful, as I do not find this site the easiest to navigate. Most of my knowledge of the trial comes from the transcripts, which I followed. Being a Brit, they were the documents I had easiest access to (the trial wasn't covered particularly well in the British Press, or, at any rate, not in the press I read). I accept the points you make, but it still seems to me that by their involvement in the conversion of a creationist book to an ID book, IDists were doing something pretty foolish. I also recall Dembski writing something around that time to the effect that while he himself was not a creationists, that IDist and creationists must consider themselves allies against Darwinism (or words roughly to that effect - I'm sorry I am going from memory, which is, of course, fallible). Moreover, on this site, one of the premier sites for ID discussions (and at least at one time, Dembski's own blog, and host to Behe's) atheism and "Darwinism" are frequently equated. I put Darwinism in scare quotes because what we are really talking about is the entire edifice of modern biology which goes well beyond Darwin's theory. So it seems to me that however distinct ID science may be from religious concerns, IDists see it, and regularly project it, as a coming triumph over the retreating atheist forces of Darwinism. This may be regrettable, but again, it seems that the problem originates with the ID movement, not with Darwinists. If ID wants to be persuasive as science, which it should, then it was absurdly foolish to try to build an ID textbook out of a second hand creationist one; it is also foolish, IMO, to consistently present ID as a threat to atheism. Worse, the people who really come in for the most devastating criticism are Christians who accept evolutionary theory! Is it any wonder, then, that biologists are suspicious of the bona fides of ID qua science? Note that I do not say that the criticism is fair merely that if you hitch your scientific waggon to religion then it's not going to be very surprising that people look askance at the science. Look at Ben Stein in Expelled, going on and on to Dawkins about not science, but God. I find it highly regrettable that those who criticise biological theories from and ID point of view should find themselves struggling to gain tenure - although I'd point out that many prominent ID scientists remain in post (Behe for instance). But again, I have to ask: if ID is constantly promoted as a religious argument (not a creationist argument, I accept that it is not), is it any wonder that it is rejected as a scientific one? It is often stated here that scientists are "biased" and have an "a priori" commitment to "naturalism" and thus against "design". I emphatically dispute this. But what there is, in science, is a methodology that simply does not have the capacity to verify or falsify supernatural claims. However, it most certainly does have the capacity to verify and falsify design hypotheses. And in my view, ID fails, not because it is religious, but because the scientific argument fails. tbh I think it obviously fails (which is not to say that Darwinism is true). And so I suggest (although as a non-American I do not know) that at least some of the struggles faced by ID scientists are not because of prejudice against ID, but because the science simply does not pass muster, does not get through peer-review for perfectly decent reasons, and leaves the scientist in question with a thin CV. And yes, I am a scientist - my field is neuroscience, specifically neuroimaging research into mental disorders. Elizabeth Liddle

(Mr Cudsworth please forgive me) CHA-CHING!! Upright BiPed

Elizabeth Liddle: I'm not sure I should reply to you, since you still owe me a reply to my previous response, but here goes: 1. I've read all the Dover trial transcripts, including the final judgment (the latter several times); I've also read lengthy legal dissections of the judgment by lawyers (not all of which are available online); I believe my understanding of the trial is as good as that of all but a handful of people on the planet. 2. The trial was not *primarily* about the book Of Pandas and People, which was never even taught at Dover, but was only to be purchased to be available in the library for such students as might want an alternate account of origins. The trial was ostensibly about the religious motivations of the school board, of which the Pandas book was one, but only one, indication. It was the religious motivations overall which rendered the policy unconstitutional. 3. Yes, the religious nature of the Pandas book was surely very important in the verdict on motivation, but several other factors, including direct statements of school board members recorded by reporters, and the action of a school board member in burning an evolution mural, etc., were very important as well. 4. But all of that pertained only to the *narrower* legal verdict. If that had been the only issue, the trial could have been a half to a third of the length that it was. 5. The plaintiffs' lawyers made it clear from the beginning that their goal was not merely to put the school board on trial, but to put intelligent design on trial (not just the book Pandas but *everything to do with intelligent design*). This was to be a show trial, exactly as the Scopes trial had been 80 years earlier, with all parties (plaintiff, defendant and judge) willingly co-operating in the "show" aspects of the trial. And just as the purpose of the Scopes Trial -- the deeper purpose -- was not merely to determine whether or not some teacher had violated some State statute, but to challenge the very notion of religious restrictions on science, so the purpose of this trial was to show that *any form* of ID that had ever appeared or ever could possibly appear could not possibly be science and must inevitably be religious and therefore would always and everywhere be unconstitutional. 6. If you did not pick this up, you are not familiar with the American ethos (as you wouldn't be, if you are a Brit) regarding First Amendment cases, and in particular cases to do with evolution. 7. If you want further reading on this, to balance out the spin you've picked up directly or indirectly from The New York Times and the NCSE, try reading *Traipsing into Evolution* by the Discovery Institute Press. Several of the authors are lawyers and political scientists and understand the legal, constitutional and historical ethos of the trial. 8. Thus, most of the "expert witness" testimony had nothing to do with the narrower case; Ken Miller's, Kevin Padian's and Rob Pennock's testimonies, trying to prove that Darwinism was good science and that ID was bad science (or, inconsistently, both bad science and not science at all), were irrelevant. Only the testimony of Alters and Forrest pertained to religious motivation on the Board's part. Why was all the other stuff in there? To poison the well regarding ID for future trials and future school board discussions across the country. 9. Behe's views on the flagellum could be the worst science ever; that wouldn't make his motivation religious. And if the only problem with Behe's view was that it was bad science (which it wasn't), his *scientific* views (as expressed without religious clutter in Darwin's Black Box) could be excluded from biology class by State curriculum decision, without suing any school board. But the goal of the lawyers was not just to prevent the demonstrably religious Pandas book from being used at Dover; it was to tar the demonstrably non-religious *Darwin's Black Box* and *No Free Lunch* and other ID books, written and yet to be written, with the sin of the Pandas book. And they succeeded; the science-challenged, philosophy-challenged, theology-challenged, history-challenged, sociology of science-challenged judge bought into it. 10. Regarding the "ire" you want me to show toward the school board for using ID as a mask for creationism, I've already sufficiently indicated that in several comments here. I condemn that school board utterly. 11. Regarding your take on the rewriting of the Pandas book, you are not being clear whether you are talking about the rewriting that happened before the trial, where creationist language was expunged and ID language put in, or the complete revision of the book years later to the point where it was really a new book. I presume you mean the former. 12. It's clear that you've read only one side of the story, the side people like Nick want you to hear. In fact, while some ID people were involved in writing parts of the Pandas revision -- Behe did the part on the flagellum -- many creationist parts were not changed, and Behe, Dembski, etc. cannot be held responsible for that. They were not in charge of the book, but were more like contributors of chapters. Behe did his part to make his section a true ID, as opposed to creationist, argument. And in court, he explicitly distanced himself from some of the creationist language -- that part of the transcript has been reproduced here recently -- and insisted that his formulation -- the ID formulation -- was much preferable to the creationist one. 13. You say that the Discovery people should have distanced themselves from the book. Well, in a sense, they did. They strongly advised Dover not to proceed with its ID policy; Dover ignored them. And later, when the publisher ordered a *radical* rewrite of the book, Dembski and Wells stripped it of every creationist assumption and argument, and the current "version" of the book (the original is no longer in print) is a pure ID book, not a creationist book at all. So that tells you where major ID people stand today, that they transformed the book not merely to get rid of creationist *language* (which was mostly what the first revision had done), but to get rid of creationist *contents*. But Nick and the NCSE will never point that out to you. 14. By the way, I recommend *The Design of Life* as an excellent introduction to ID; but actually it's even better as a critique of Darwinism and of chemical origin of life theories. It would be an ideal book to have advanced high school students read, as it doesn't really push ID, but focuses on scientific criticisms of the reigning theories. But of course, neither Nick nor the NCSE thinks that scientific criticism of their pet theories should be allowed in American schools. They want a monopoly for Darwinism and accidental chemical origin of life views. They don't believe that science education should be about teaching students how to think critically and to grasp the radical revisability of all scientific theorizing; they think science education should be about feeding students the reigning paradigm on a spoon. This is a repugnant and even anti-American view of education, the sort of view that was held by the Soviets and Communist Chinese for decades. 15. Like Nick, you put far too much emphasis on one book, which has not been in print for years now, and which is not regarded by any leading ID proponent as a serious theoretical exposition of ID. You are completely ignoring the most important thing, which is what the ID people have told you they are about. You are completely ignoring the fact that Behe, Sternberg and Denton *are evolutionists, not creationists*, and that Nick and the NCSE have deliberately and dishonestly obscured that fact. You have completely ignored the fact that I and many other columnists here (including O'Leary and StephenB and others) have repeatedly said that we are fine with evolution -- have no theological objections to the concept -- but just don't believe that there was no intelligence behind it, which all forms of Darwinism (when understood honestly) assert. Both you and Nick suppress or ignore the fact that the lead moderator here for several years, Dave Scot, was an unrepentant agnostic who had no use for creationism, but supported ID. Both you and Nick suppress or ignore the fact that Dembski and Meyer have repeatedly said that, whatever their private beliefs about evolution, ID as a theory is compatible with it (as creationism is not). So whether through design or ignorance, you are following Nick in making a mountain out of a molehill (one creationist book which 99% of the American public would never have heard of had there never been a Dover trial, and whose sales in fact skyrocketed *because* of the free publicity of the Dover trial), and you are diverting attention from what ID has claimed it is about from even before the Dover Trial, and certainly for every waking moment since. Have you asked yourself why you are ignoring the salient facts: (a) ID has defined itself precisely and distinguished itself precisely from creationism; (b) Many leading proponents of ID and many of its followers are evolutionist, not creationists. Have you asked yourself why you don't emphasize these points in your thoughts about ID? have you considered that you might be deliberately blocking them out? And have you asked yourself why you give the dishonest tactics of Nick and his gang a free pass, while dwelling on the alleged sins of the ID side? Have you asked yourself whether you are taking a truly balanced view of the matter, or whether your scientific prejudice in favor of Darwinism might be coloring the way you read the political and cultural side of the debate? 16. I have noticed your comments in several columns here, and your comment that you were writing from Britain. If you are a Brit, that would explain why your criticisms of ID are expressed with greater politeness than are the criticisms of Americans. After all, in general terms, Brits tend to be less brash and more polite than Americans, and they don't have the ugly culture-war history over evolution that America has. However, this very distance seems to prevent you from seeing dimensions of the struggle that a local knows instantly. Your comments on Wikipedia entries on another thread show lack of perception about how the anti-ID factory operates, about how dishonest and malignant it is; and your comments here and elsewhere show a willingness to see manipulative behavior only on the ID side, and a blindness to manipulative behavior on the Darwinist side. Thus, while I respect your scientific comments, which appear knowledgeable, I don't think your gift is for commenting on social, political, cultural and legal matters. I submit that you are too inexperienced in the trenches to have any real insight as to what is going on behind closed doors, and that you are far too trusting of the side whose science you happen to agree with. I am willing to believe that you are an honest scientist (if you are a scientist) who would never willingly prevent a good scientist from getting a job or publishing an article merely because he had ID sympathies; I am willing to believe that you would never deliberately misrepresent the views of your opponent, to make them easier to knock down. But the people you are here supporting have in fact done that regularly -- the NCSE, Nick, Shallit, Moran, Myers, etc. And your scientific expertise will be used by people less honorable than you, who would suppress all criticisms of Darwinian theories and of chemical origin of life theories if they could, keeping them out of lower schools completely and as far as possible even out of universities completely, by denying publications, jobs and tenure to those critics. If you do not understand this, you do not know how the American university works, and you do not know how Darwinists work. I would suggest that you supplement your scientific reading with some political philosophy, starting with the writings of Machiavelli, if you want to understand the real operations of the American culture war over evolution. Best wishes, Elizabeth. Thomas Cudworth

Joseph:

For example Theobald says a nested hierarchy is expected from univewrsal common descent. However the existence of transitionals, by their very definition, means a nested hierarchy would be violated- Theobald even says that in his “potential falsification”.

No, it does not mean that a "nested hierarchy would be violated". Perhaps the term "nested hierarchy" is unclear. A nested hierarchy is a tree structure in which once a bifurcation has occurred, there is no rejoining. It's "nested" because what it means is that features that are unique to one branch at a bifurcation can only be shared by organisms downstream of that bifurcation. But if we follow any one lineage back upstream from a "twig" as it were, back to the main "trunk" we will see continuous transitions. There are a couple of interesting violations, however: one is horizontal gene transfer, which makes bacterial lineages much less of a tree and much more bushy and tangled. The other is that speciation itself can be fairly gradual (by human timescales, anyway) and so incipient bifurcations can, in the early stages, remerge. For instance, there is some evidence that Neanderthals and Sapiens started to diverge - speciate - then re-emerged (with Sapiens as the dominant source of genetic material nonetheless). So the bifurcations aren't totally clean, when looked at at a fine grain scale. But transitional series are certainly predicted by the theory - indeed Darwin specifically predicted, although he didn't hold out much hope of evidence, because of the rarerness of fossilisation. However, he'd probably be delighted by how mean very nice transitional series of fossils have, in fact, been found! Elizabeth Liddle

Welcome. kairosfocus

Thank you for that information kairosfocus. Elizabeth Liddle

Is it this critique? kairosfocus

Joseph: spill,mon, spill. Link? kairosfocus

PPS: Dr Liddle, you should also know that at the time the Discovery Institute Center for Science and Culture and several of its principals counselled the Dover District NOT to do what they insisted on doing. Then and now the CSC's official position on origins science education is that the issues, strengths and limits of established theories are to be taught, not that ID -- an emergent theory -- should be added to the curriculum. You will notice that my own IOSE is specifically intended to serve as a demonstration pilot for what a community based independent effort could look like. Let me cite the actual DI CSC policy declaration:

What does the Discovery Institute's Center for Science and Culture recommend for science education curriculum? As a matter of public policy, Discovery Institute opposes any effort to require the teaching of intelligent design by school districts or state boards of education. Attempts to mandate teaching about intelligent design only politicize the theory and will hinder fair and open discussion of the merits of the theory among scholars and within the scientific community. Furthermore, most teachers at the present time do not know enough about intelligent design to teach about it accurately and objectively. Instead of mandating intelligent design, Discovery Institute seeks to increase the coverage of evolution in textbooks. It believes that evolution should be fully and completely presented to students, and they should learn more about evolutionary theory, including its unresolved issues. In other words, evolution should be taught as a scientific theory that is open to critical scrutiny, not as a sacred dogma that can't be questioned. Discovery Institute believes that a curriculum that aims to provide students with an understanding of the strengths and weaknesses of neo-Darwinian and chemical evolutionary theories (rather than teaching an alternative theory, such as intelligent design) represents a common ground approach that all reasonable citizens can agree on. Seven states (Alabama, Minnesota, Missouri, New Mexico, Pennsylvania, South Carolina and Texas) have science standards that require learning about some of the scientific controversies relating to evolution. Additionally, Louisiana has a statewide law that protects the rights of teachers “to help students understand, analyze, critique, and review scientific theories in an objective manner,” specifically naming evolution as an example. Texas’s science standards require that students “analyze, evaluate and critique scientific explanations … including examining all sides of scientific evidence of those scientific explanations so as to encourage critical thinking.” Texas also requires students to “analyze and evaluate” core evolutionary claims including “common ancestry,” “natural selection,” “mutation,” and the formation of “long complex molecules having information such as the DNA molecule for self-replicating life.” Although Discovery Institute does not advocate requiring the teaching of intelligent design in public schools, it does believe there is nothing unconstitutional about voluntarily discussing the scientific theory of design in the classroom. In addition, the Institute opposes efforts to persecute individual teachers who may wish to discuss the scientific debate over design in an objective and pedagogically appropriate manner. The U.S. Supreme Court in Edwards v. Aguillard strongly affirmed the individual teacher’s right to academic freedom. It also recognized that, while the statute requiring the teaching of creationism in that case was unconstitutional, “…teaching a variety of scientific theories about the origins of humankind to schoolchildren might be validly done with the clear secular intent of enhancing the effectiveness of science instruction.”

Do you see how someone out there is making up a strawman target to attack and smear? Someone with which Dr Matzke has been strongly associated for some years? [I suspect that had what is going on been in a UK or commonwealth jurisdiction, some serious libel and slander suits would long since have been made, and would probably have been won.] kairosfocus

PS: The statement that was to be read (I add a link or two):

The Pennsylvania Academic Standards require students to learn about Darwin’s Theory of Evolution and eventually to take a standardized test of which evolution is a part. Because Darwin’s Theory is a theory, it continues to be tested as new evidence is discovered. The Theory is not a fact. Gaps in the Theory exist for which there is no evidence. A theory is defined as a well-tested explanation that unifies a broad range of observations. Intelligent Design is an explanation of the origin of life that differs from Darwin’s view. The reference book, Of Pandas and People, is available for students who might be interested in gaining an understanding of what Intelligent Design actually involves. With respect to any theory, students are encouraged to keep an open mind. The school leaves the discussion of the Origins of Life to individual students and their families. As a Standards-driven district, class instruction focuses upon preparing students to achieve proficiency on Standards-based assessments.

--> Talk about making a mountain out of a molehill because an ideologically driven a priori materialist agenda holds power in key institutions! --> Science education policy as touching especially origins needs to be seriously revisited in light of what is clearly the de facto establishment of the functional equivalent of a religion. kairosfocus

Dr Liddle, Please read here in my always linked note through my handle at UD, on the Dover story. A disclaimer that in a less polarised era would have been seen as patently essentially innocuous -- it is a LOT less menacing than the mafioso stunt that some Internet thugs have played on my family in the past few days -- was to be read, and students were to be told in it that there was a reference book in the library (bought with independent funds). GEM of TKI [ . . . (links)] kairosfocus

NickMatzke 135:

And, I did give you the link to the huge 29+ Evidences website, which is book-length and discusses all of the issues, fossil, molecular, etc., in more detail, starting from the basics, than you’ll find anywhere else. And it’s free!

It is also nonsense. For example Theobald says a nested hierarchy is expected from univewrsal common descent. However the existence of transitionals, by their very definition, means a nested hierarchy would be violated- Theobald even says that in his "potential falsification". Heck that site is so pathetic a lawyer tore the evidence apart... Joseph

PaV: Pardon, but he is also being willfully deceptive. As Dr Cudworth outlined, he knows or should know that significant design theory advocates such as Dr Behe or Mike Gene [Mr Frontloading] do in fact accept universal common descent, and that the design inference is independent of whether or not common descent is true. In fact, given the information challenge involved in novel body plans, an obvious contender for a reasonable account of origin of that level of biodiveristy, is genetic engineering of ancestral types [viri or the like would be a useful candidate vector, on projection of ideas being discussed, though of course we also need to address epigenetic factors . . . ], setting up ancestral groups of life forms that were designed to radiate thereafter through environmental adaptations. In addition, the likes of a Platypus with its obvious mosaic character and genome level mosaic character, suggest the use of a library of adaptable parts. The recent announcements that kangaroos have in them huge swaths of the human genome sitting there in an animal that is held to be on a 150 MY branch from the line leading to us, is suggestive along the same lines. In short, we can actually make up a synthetic view that has common ancestry, genetic [and epigenetic?] engineering, code reuse and adaptation through a library, AND adaptive mutation by variation and success in niches. So, the issue cannot logically be common descent vs design. Nor is it whodunit. A molecular nanotech lab run by a race operating our solar system as a bio experiment station, and with technologies some generations beyond Craig Venter would be able to do what was just described. Within 50 years, probably, we will be doing it. (H'mm: How about a few hundred million flying locust-scorpion chimerical forms with a self-limiting built in lifespan of several months carrying incapacitating viral diseases -- maybe with genetic manipulation in them too -- as a war-winning weapon? As in, the ultimate locust plague as a military attack. So much for sci fi . . . we hope.) The real question is where did the variations in genetic information and epigenetic organisation come from to make up the new body plans? On the induction from observations, and from needle in a haystack config space search analysis from what we observe for functionally specific information beyond the solar system or cosmological thresholds, we have excellent reason to infer to intelligence. In that context, questions on the age of the earth or of life on it, or of the solar system and cosmos, or geological eras and fossil life forms, or homologies at gross and genomic levels or proteinome levels etc. etc., are simply irrelevant. The decisive issue is that there is a need for advocates of evolutionary materialism to demonstrate analytically and empirically, that information beyond the threshold set by the log reduced Chi metric, can be produced as a practical matter by undirected forces of chance and necessity. Namely: Chi_500 = I*S - 500, bits beyond the threshold. To date, such is conspicuous by absence, active information driven genetic algorithms (it seems the latest misleading icon of evolution promotion) notwithstanding. The only -- and abundantly -- empirically well-warranted source of such FSCO/I is design. Design as that tweredun is thus an empirically and analytically well warranted inference on the sign of FSCO/I. Whodunit or whateverdunit -- let's line up a few suspects:

a: our advanced race of let's call them "angels" or even "gods" or "aeons" or other parties? b: Some other entity or party like an ancient race seeding the cosmos because they were lonely or curious [a la Star Trek]? Or, c: this is all a super-Matrix world? Or d: not least, the same as who on the sign of cosmological fine tuning of a cosmos for C-chemistry, cell based life with a credible beginning at a finite point in the past?

. . . why, can be deferred to a second level issue. As at now, absent an empirically credible chance and necessity explanation for the FSCO/I in an original cell based life form which has metabolism joined to code driven self replication a la von Neumann, and for the FSCO/I in major body plans from kelp to bamboo to toadstools to fish, crabs, worms, birds and us, we have a perfect epistemic RIGHT to hold that the evidence points to design as the most credible explanation for cell based life and its forms. We already have proof of concept in hand thanks to Venter et al, so it is those who wish to hold otherwise who need to provide a good, empirically warranted explanation. A priori imposed materialism, politically correct censorship and career busting joined to smears against those who differ, will not do. GEM of TKI kairosfocus

If any mistakes were made by the Dover Area School District, they pale into insignificance compared to the highly erroneous and suspicious written ruling of Judge Jones. Check out this link for more information on that: http://www.discovery.org/a/3829 Chris Doyle

Thomas Cudworth: I am very glad to read what you wrote above, and I think you make some absolutely key points. Particularly:

I was completely opposed to the action of the Dover school board because its motives were clearly creationist. The trustees wanted the Bible to have veto power over what scientists could conclude. If the judge had simply tossed the school board’s policy out, and made the board pay all legal expenses, I’d have been quite happy.

Yes, indeed. But here I think you are attacking quite the wrong target:

But the judge made a wider verdict, led by the nose by the team of “expert witnesses” put together by your gang, that ID was religion. The judge was wrong.

From my reading of the transcripts this is a faulty summary. IIRC, what was at issue was what had started off as a creationist book, which was being proposed as a school text book by creationists with creationist motives. What ID is, was not the issue. What was at issue was what was being passed off as ID in that textbook. Your indignation, it seems to me, should be at creationists for subverting ID by disguising their own ideas as ID ideas, and attempting to wriggle under the bar by assuming the scientific gravitas of what is a (fatally flawed, IMO, but that's not the point, as you rightly point out) scientific theory, namely ID. What is puzzling still further to me is that the redrafting of Pandas was done by IDists. The result was simply drawing lipstick on a pig. A side effect was that ID got tarred with the creationist brush, instead of creationism being gilded by the ID brush. But those IDists who supported the lipstick-applying project seem to me to have only themselves to blame, and that includes Behe. Not only that, but there were rude noises off here at UD, directed at Dawkins and Jones, inter alia, as I recall, at the judgement, when it would have been more appropriate, IMO, for the noises off to have been directed to the people who tried to pass Pandas off as ID, thus sullying potentially decent science. Pandas contains a definition of ID which is fundamentally different from the definition given on this site, and was adapted, as the draft history tells us, directly from a definition of the word creationism. Who did that? Why aren't they the object of your ire?

He wasn’t qualified to make distinctions between religion, philosophy, science, etc. That’s not the place of a courtroom, that’s the place of a university seminar discussion.

Well, IANAL, and I would agree, but you have to go with what you've got in the US, which is separation of church and state. Pandas clearly had its roots in creationism, as did the motives of those promoting it. IDists should have had nothing to do with that book, and written their own, from scratch.

He should have refused to rule on the wider issue, shut down the school board on the narrower issue, and all would have been well. But because he believed the lies and misrepresentations from your side, he overreached himself, and committed an injustice against both ID and the American people.

And no injustice would have been done to ID if IDists had dissociated themselves from Pandas from the start. Nick's point, surely, is that they did not. You sow what you reap. And yes, while I think that ID as it stands is fatally flawed, it annoys me that the whole ID kerfuffle has directed attention away from the actual scientific argument, which I happen to think contains the kernel of an important idea. But I'm tempted to say: with creationists as friends, who needs enemies? Dover did you a favour, in a way, as does Nick, in enabling you to clarify what the ID scientific argument is, and how it differs from creationism, after the re-drafters of Pandas had muddied the waters with an ugly hybrid that did no favours to either. Elizabeth Liddle

Yes, Nick, I know that in the above quote, you're quoting from Pandas; but you're quoting it in hopes of claiming that ID disbelieves in common descent and therefore is just like "creationism". PaV

Nick Matzke @ 96:

Design proponents have a realistic and more cautious approach to the use of homologies. They regard organisms which show great structural differences, such as starfish and chimpanzees, as having no common ancestry.

Why do you place such importance on the idea of common descent? It's an illogical concept, isn't it? For example, is a fish egg like a bird egg? No, they're very dissimilar. Would you want to argue that a bird egg 'evolved' from fish egg? Well, then, how? What were the stages? Where are the intermediates? And, if there are no intermediates, then how can you talk about common descent when we actually see not a continuous gradation, but rather abrupt changes. If you want to talk about the common descent of sharks, e.g., that is a different matter. That makes some sense. But the whole notion of "common descent" as it applies to all phyla, flies in the face of known facts. It's simply some kind of assumption that's made based on Darwinian/gradualistic thought. But nature doesn't bear it out. PaV

Dr Cudworth: It is sad that you have had to lay out the issue as above, but a review of the exchange and its wider context will show that you are essentially correct. Today's "scientific" atheists and their fellow travellers have committed several travesties against both truth and justice, and do not realise the exceedingly dangerous implications of the rhetorical, administrative and legal matches they are playing with in the courtroom, the hearings room or the seminar room. It has ever been so with those who see themselves as representing a new order of the ages, and who buy into ideologies that boil down to our desired ends "justify" any and all means we perceive as "necessary." Thirty odd years ago, I saw it with the young marxists on my campus and in my society, even as they and their elders were igniting the flames of a low grade civil war; blaming the other all the way along. But then, Alinsky's evil counsel is that one acts decisively only in the perception that the angels are on one side -- yours, of course, and only and all devils lie on the other. So the exaggerated, loaded strawman caricature rhetoric -- willfully deceptive -- soon feeds the power politics of slogan-driven scapegoating, and ruthless factionism so soon thereafter leads to doing things that if one is at all honest (but then, too often the conscience is benumbed until effectively dead), one will regret for life thereafter. A bit over a decade after this horror scarred my homeland for a generation now, I lived to see representatives of the USSR come to my homeland and book a hall to hold a public meeting in which they made a public apology for what they had done. I respect that honesty in the end, though ever so many took no notice; and the event is now largely forgotten. What I am seeing today is ever so reminiscent of those painful days now long past. Especially, the moment when I realised that some zealously self-righteous and hate-filled fanatics have thought it their "right" to dig up personal information and pretend that there is no harm or menacing threat in publishing a cluster of information that boils down to: we know you, we know where you are and we know those you care for. (These have resorted to painting a target on my back and on the backs of my family; regardless of inaccuracies in information, there is more than enough for whichever half-mad rage filled idiot will be willing to take the next step. And ever so many have been cheering this on. Oh, how this reminds me of those who blandly excused their incitements when a close friend of my family, beloved "auntie" and shopkeeper was murdered by some rage-filled idiot pumped up on incendiary rhetoric against "hoarding" in a day when rice was in obviously short supply in the midst of economic crisis. Oh yes, so-called Committee of Women for Progress, I have not forgotten. For shame!) Dr Matzke and others need to take a serious moment to understand that the dominant evolutionary materialism involved at the core of what they are about, as Plato pointed out so long ago now, is inherently, inescapably amoral, promotes ruthless factionism and abuse should such unhinged ideologues gain power. And if they refuse to be corrected in such outrages, we need to mark what is happening, and take due precautions. For, the little bit of classical literature that warns of how great a conflagration a small flame can ignite, comparing this to the destructive power of the evil tongue, speaks truly. And yes, that bit of counsel that needs to be heeded comes from a book of hard-bought wisdom such "bright" people despise. They would also do well to heed what follows that bit of advice:

James 3:12Can a fig tree, my brethren, bear olives, or a grapevine figs? Neither can a salt spring furnish fresh water. 13Who is there among you who is wise and intelligent? Then let him by his noble living show forth his [good] works with the [unobtrusive] humility [which is the proper attribute] of true wisdom. 14But if you have bitter jealousy (envy) and contention (rivalry, selfish ambition) in your hearts, do not pride yourselves on it and thus be in defiance of and false to the Truth. 15This [superficial] wisdom is not such as comes down from above, but is earthly, unspiritual (animal), even devilish (demoniacal). 16For wherever there is jealousy (envy) and contention (rivalry and selfish ambition), there will also be confusion (unrest, disharmony, rebellion) and all sorts of evil and vile practices.

There comes a day when sowing leads to reaping. Dr Matzke and ilk need to think very carefully indeed as to what crops of dragon's teeth they are sowing for our civilisation. GEM of TKI kairosfocus

Nick Matzke: Well, at least I finally got a reply! Nick, I'm old enough to be your father, and I was reading "Creation Science" material before you were born. So I don't need your introduction to that material, any more than I need your introduction to the Beatles or the Vietnam War. Yes, Creation Science (Gish, Morris, etc.) was indeed creationism. Yet the fact that Creation Science used some arguments that are now used by ID people does not make ID Creation Science, any more than the fact that the Democratic Party uses some arguments that Marx used makes the Democratic Party Marxist. You keep trying to hide out in historical trivia in order to avoid the fundamental issue, which is *how the word "creationism" is used in typical American discourse*. And in typical American discourse, a "creationist" is someone whose views on origins are tied up with a literal or near-literal understanding of Genesis, and whose scientific investigations are governed by the need to maintain that literal understanding at all costs. In other words, in creationism, *the literal reading of Genesis has veto power over what scientists are allowed to conclude*. There is no theoretical work currently regarded as "ID" that relies upon a literal reading of Genesis, or allows a literal reading of Genesis any veto power over what scientists may conclude. Period. You can scour the works of ID proponents -- Signature in the Cell, Darwin's Black Box, No Free Lunch, Nature's Destiny -- you will find no place where Genesis is called in to referee a scientific question. You will not even find any places where general Christian theological notions, or even more basic requirements of theistic religion, are called in to referee a scientific question. If you want to say that ID should not be in high school science classes because it is lousy science, then say so. But that is not a *legal* or *constitutional* issue. It's a normal curriculum issue. If it's lousy science, there is no one forcing State educational authorities to put it on the curriculum or in the textbooks, any more than anyone is forcing State educational authorities to promote Holocaust denial as a serious scholarly theory on the history curriculum. But your team is not trying to block ID on the grounds that it is lousy science; your team is trying to block it on the grounds that it's religion. And it isn't. And you know that it isn't. That many ID proponents have religious motivations, no one denies. Most of the people on your team have religious motivations: do you think that Coyne, Shallit, Myers, Forrest, etc. keep their atheism hermetically sealed off from the way they think about nature? C'mon Nick, that's naive. The question is not whether ID proponents have religious motivations. Everyone does. The question is whether ID *arguments* make religious assumptions or require religious faith. And they don't. And you know they don't. And by trying to convey to the public that they do, you are misleading the public. Deliberately, willfully. Because you don't want ID to get a foothold in public thinking. If you don't like an idea, battle it on the plane of ideas; don't try to ban it in the courtrooms of the nation, thus making mockery of the sacred principle of freedom of speech, thought, debate, and discussion. I was completely opposed to the action of the Dover school board because its motives were clearly creationist. The trustees wanted the Bible to have veto power over what scientists could conclude. If the judge had simply tossed the school board's policy out, and made the board pay all legal expenses, I'd have been quite happy. But the judge made a wider verdict, led by the nose by the team of "expert witnesses" put together by your gang, that ID was religion. The judge was wrong. He wasn't qualified to make distinctions between religion, philosophy, science, etc. That's not the place of a courtroom, that's the place of a university seminar discussion. He should have refused to rule on the wider issue, shut down the school board on the narrower issue, and all would have been well. But because he believed the lies and misrepresentations from your side, he overreached himself, and committed an injustice against both ID and the American people. What you guys accomplished at the Dover trial was the establishing of a very evil precedent; that lawyers and judges can call scientists, philosophers, scholars and theologian into a courtroom, ask them inappropriate questions which can't be settled in the confrontational, adversarial atmosphere of a courtroom, and then render judgments on the divisions of knowledge (what counts as science, what counts as religion, etc.) -- epistemological decisions which are *way* beyond the average lawyer or judge's pay grade. This was a dangerous procedure which threatens the ground on which free speech and free debate stand. Yet you guys supported it all the way, because, before any loyalty to free speech, to freedom of scientists and theologians and philosophers to work out their own boundaries in dialogue, your loyalty is to the monopoly of a certain account of origins. That you would use the court system of America to impose that monopoly on American children says a lot about you and your friends. But back to the linguistic point: Every time Eugenie and her gang say "ID creationism," they are creating an association between serious arguments about nature and images of stupid country bumpkins, burning effigies of Darwin and marrying their first cousins in the hills, waving their Bibles around fanatically. And Eugenie does that deliberately and with full calculation of the propaganda advantage of doing so. She knows that urban, educated middle-class people will react in a Pavlovian way against "creationism" in a way that they wouldn't react against an argument about "irreducible complexity," which might catch their attention and seem to have some merit. So she poisons the well right away. It's a tactic demagogues throughout history have learned well, and the NCSE is first and foremost a demagogic organization. Yet Eugenie knows, and *you* know, that Mike Behe is a Catholic, not a Protestant, let alone a fundamentalist, and that he has nothing religious in common with the Bible-thumpers that you and Eugenie are trying to link with ID in the public mind, by using the word "creationism." And Eugenie knows, and *you* know, that Rick Sternberg is a Catholic, and that Mike Denton is a lapsed Christian who no longer accepts the authority of the Bible for anything, etc. And you know that all three of these men accept evolution, which in normal public discourse is the opposite of "creationism". So you know that calling these men "creationists" will create the wrong impression in the public mind; yet you do it anyway. Thus, you stand convicted of willful dishonesty. And if you are dishonest about this, I have no reason to think you will be any more honest in your science. I have no reason to think that in any articles you publish on evolution that you will have gone out of your way to fairly represent the views of biologists who disagree with you. I have no reason to think you won't set up straw men, suppress contrary evidence, etc. If you do it regarding the definition of ID, you might well do it to advance your scientific career. So I would not trust any article you published, even in a scientific journal. I would always assume that you have an axe to grind and an agenda to promote. Finally, you say you are not an atheist. Well, you could have fooled me, since most of your friends and allies are atheists, and you use mostly the same arguments, mostly the same sneers, and mostly the same demagoguery that the atheists do. But if you aren't an atheist, what are you? An agnostic? Then you should be open to design arguments, not closed to them a priori as you have been from the beginning. Or are you a Christian? Then why do you deceive people and willfully misrepresent the position of others? Would a Christian do that? Or are you perhaps a Jew? Then what does Judaism teach about the origin of living things? By all means, Nick, since you so frequently accuse others of religious prejudice, lay out your religious views for us, so we know what your secret prejudices might be. Thomas Cudworth

"FliM isn’t even universally found in flagella, IIRC." Not sure how this is supposed to be relevant. FliM is not universally found in flagella, and nor is FliN, but you will always find one of those proteins in flagella. Incidentally Nick Matzke, are you saying that the entirety of both proteins -- CheC and FliN -- fused or that only certain domains of CheC and FliN fused to form FliM? LivingstoneMorford

Nick Matzke: "I’m pretty sure your analysis is incorrect and/or whatever proteins you pulled out of the database are incomplete or unusual in some way (proteins are sometimes mislabeled by automatic annotation software, particularly when they are homologous to two or more proteins, e.g. FliM can return hits to both CheC and FliN, even though CheC and FliN are not themselves homologous to each other)." Here are the sequences I used, you can check them out for yourself: >sp|P06974|FLIM_ECOLI Flagellar motor switch protein FliM OS=Escherichia coli (strain K12) GN=fliM PE=1 SV=1 MGDSILSQAEIDALLNGDSEVKDEPTASVSGESDIRPYDPNTQRRVVRERLQALEIINER FARHFRMGLFNLLRRSPDITVGAIRIQPYHEFARNLPVPTNLNLIHLKPLRGTGLVVFSP SLVFIAVDNLFGGDGRFPTKVEGREFTHTEQRVINRMLKLALEGYSDAWKAINPLEVEYV RSEMQVKFTNITTSPNDIVVNTPFHVEIGNLTGEFNICLPFSMIEPLRELLVNPPLENSR NEDQNWRDNLVRQVQHSQLELVANFADISLRLSQILKLNPGDVLPIEKPDRIIAHVDGVP VLTSQYGTLNGQYALRIEHLINPILNSLNEEQPK >sp|P15070|FLIN_ECOLI Flagellar motor switch protein FliN OS=Escherichia coli (strain K12) GN=fliN PE=3 SV=1 MSDMNNPADDNNGAMDDLWAEALSEQKSTSSKSAAETVFQQFGGGDVSGTLQDIDLIMDI PVKLTVELGRTRMTIKELLRLTQGSVVALDGLAGEPLDILINGYLIAQGEVVVVADKYGV RITDIITPSERMRRLSR >sp|P40403|CHEC_BACSU CheY-P phosphatase CheC OS=Bacillus subtilis GN=cheC PE=1 SV=1 MSIFNGIKEEQMDILREVGNIGAGHSASAMAQLLNRKIDMEVPFAKLLSFDELVDFFGGA DVPVASIFLRMEGDLTGSMFFIMPFFQAEQFIRELIGNPDFDIEDLGEDHMSSSALHELG NILAGSYLTALADLTKLQLYPSVPEVSLDMFGAVISEGLMELSQVGEHAIVVDTSIFDQS HQQELKAHMFMLPDYDSFEKLFVALGASL LivingstoneMorford

Nick: "but I think you are trying to say that after 50,000 generations E. coli is still E. coli, therefore we shouldn’t think it is possible for humans and chimps to share a common ancestor." Really? Again... "Does the direct evidence of the adapting 50,000 e-coli generations provide us with enough confidence that mut/sel administers sufficient horsepower for a chimp diverge from common ancestor, and from common ancestor to the bi-pedal ardi in the same 50,000+ or so generations?" I'm asking about observed mechanism. junkdnaforlife

More evidence that my statement about FliM = CheC + FliN was correct: 2006 PNAS article: http://www.pnas.org/content/103/32/11886.full

The middle domain of FliM (FliMM, residues 45–242) has low, but detectable, sequence similarity with the CheC/CheX/FliY family of CheY phosphatases (23, 24). The CheC and CheX phosphatases have pseudo-2-fold symmetry that likely arose from gene duplication (24). Well conserved segments of sequence on two long projecting helices (?1 and ?1?) are essential for the dephosphorylation of CheY-P (24). FliM neither conserves these residues nor has phosphatase activity (10, 25, 26). Lastly, FliM also contains a C-terminal domain (FliMC, residues 250–328) that resembles FliN and binds FliN in the overall flagellar assembly (17). T. maritima FliM and FliN form a stable FliM1FliN4 solution complex (17).

NickMatzke_UD

junkdnaforlife -- you aren't being particularly clear about what your argument is, but I think you are trying to say that after 50,000 generations E. coli is still E. coli, therefore we shouldn't think it is possible for humans and chimps to share a common ancestor. The answer: 1. Humans and chimps are connected by about 600,000 generations, not 50,000 (6 million years * 2 lineages / 20 years per generation). 2. Primates are sexual species with large genomes, E. coli is not. Sexual species can maintain a lot more variability and produce beneficial combinations of traits much more quickly than asexual species. 3. Primates have relatively low population size. This means selection is less effective when selection coefficients are very small (whether positive or negative). This also promotes genetic diversity and enhances chances for recombination and evolution of genome complexity. See the work of Michael Lynch. 4. Lab E. coli are kept in a simple, constant selective environment. They have selective pressure to adapt to basically one thing. They will tend to find that optimum and sit there. Humans, on the other hand, evolved in a complex, constantly changing environment. Constantly changing environment = more change than in a simple constant environment. 5. It's a fallacy to equate bacterial taxonomy and primate taxonomy. In many ways, the E. coli "species" is much more different than humans and chimps. E.g., in terms of sequence divergence, genome composition, etc. Some E. coli have 50% more genes than others. And no, you can't just brush this off with "they're all just E. coli." There are huge ecological differences between these strains. E.g. some are helpful gut bacteria, others are deadly specialized diseases. So I think your argument fails on multiple levels. NickMatzke_UD

Nick: I see you’ve turned tail again, refusing to answer my decisive rebuttal regarding the meaning of “creationism”. That’s not surprising. The rhetorical position you and the NCSE have staked out depends on promoting the willful, conscious lie that ID is creationism. You have repeatedly been shown irrefutable evidence that ID is not creationism, and you know in your heart that this is right (i.e., you know that neither Dembski nor Behe nor Meyer ever makes use of any argument in their technical ID works that requires the assumption of Christian faith or the literal truth of Genesis), yet you push the connection, as a propaganda tool.

The "creation scientists" said *exactly* the same thing in the 1980s. They said it in defense of the "creation science" laws. Bradley, Kenyon, etc., said that in defense of the "creation science" laws. Yet you and everyone else now acknowledge that that stuff was creationism. Even the arguments, as far as biology goes, are basically the same then as they are now. Irreducible complexity, random-assembly-is-impossible (never mind that evolution isn't random assembly), etc. And, heck, *you yourself* admitted:

OF PANDAS AND PEOPLE WAS NOT AN ID BOOK. IT WAS A CREATIONIST BOOK. IT HAS NO STATUS, ABSOLUTELY NONE, AMONG SERIOUS ID THEORISTS.

...and yet, the Pandas authors and producers, and Behe (on the stand!), and the DI, and most ID fans today all claim Pandas was totally definitely ID and definitely not no-way creationism. It's not my evil bias that connects ID to creationism, it is hard and undeniable historical facts. Any neutral observer will see it.

Neither you nor Eugenie cares about the true definition of ID in the slightest. Nor are you interested in an impartial investigation into questions of origins (or you would keep all options open, including those that don’t appeal to your religious views). All that you care about is victory for your materialist world view, and any means, fair or foul, will do. You should be ashamed of yourselves. If you don’t agree with ID, fine. But don’t lie about what it is. It isn’t creationism, and you know that it isn’t creationism, and you are willfully dishonest to keep insisting that it is. You’re hardly going to be a model for young scientists if your career starts out with a lie. Why not retract the lie now, and give yourself a clean start? Just say this: “ID is not creationism. I apologize for my willful misrepresentation of ID over the past several years.” If you do that, my respect for you will go up from negative 100 to zero, and then maybe you can start building up some positive credit by doing some real science instead of atheist/materialist ideology.

First, I'm not an atheist. Second, if I started ignoring what I know about the actual history of the ID movement, I would be abandoning my intellectual integrity. I won't do that. You don't get to put on rosy-colored glasses and ignore all the inconvenient parts of the history. NickMatzke_UD

If one aligns FliM with CheC (using Tcoffee) one will find that most of the similar residues between the two sequences are located in the “right half” of FliM (~70% of residues that are similar between FliM and CheC are located in the area around FliM’s C-terminus). Now, if one aligns FliM with FliN, one will find, again, that most of the similar residues between the two sequences are located in the area around FliM’s C-terminus (~60% of residues that are similar between FliM and FliN are located in the “right half” of FliM). This information, by itself, is not very interesting because fusion proteins are not always formed by two whole proteins fusing together (i.e., if FliM is the result of FliN and CheC simply fusing together – say FliN’s C-terminus fusing with CheC’s N-terminus – then we would expect that FliN would share more similar residues in FliM’s N-terminus, while CheC would share more similar residues in FliM’s C-terminus). But it does refute the notion that FliM is the result of a single fusion event of CheC and FliN. So, what evidence do you have that FliM is the result of a fusion of a FliN domain and a CheC domain?

I'm pretty sure your analysis is incorrect and/or whatever proteins you pulled out of the database are incomplete or unusual in some way (proteins are sometimes mislabeled by automatic annotation software, particularly when they are homologous to two or more proteins, e.g. FliM can return hits to both CheC and FliN, even though CheC and FliN are not themselves homologous to each other). This is the standard paper on the FliM/CheC question: Kirby et al. (2001). "CheC is related to the family of flagellar switch proteins and acts independently from CheD to control chemotaxis in Bacillus subtilis." Molecular Microbiology, Volume 42, Issue 3, pages 573–585, November 2001 DOI: 10.1046/j.1365-2958.2001.02581.x http://scholar.google.com/scholar?q=%22CheC+is+related+to+the+family+of+flagellar+switch+proteins+and+acts+independently+from+CheD+to+control+chemotaxis+in+Bacillus+subtilis.%22&hl=en&btnG=Search&as_sdt=1%2C5 See Figure 8. FliM isn't even universally found in flagella, IIRC. As I wrote back in, let's see, 2003:

Explaining the origin of the switch complex, which couples the chemotaxis system to flagellar rotation, requires an examination of the domain structure and interactions of the switch proteins. FliN and FliM, which make up the C-ring, are partially homologous. FliN is homologous to the C-terminal domain of FliM, and as a result the two proteins probably occupy similar positions in the C-ring, perhaps alternating in a 3 FliN:1 FliM pattern, which approximately matches their stoichiometry (Mathews et al., 1998; see also Figure 2, this paper). FliM also has a N-terminal domain with no counterpart in FliN that is the actual CheY-P receptor. CheY-P binds to the receptor domain, increasing the probability of a switch to CW rotation (Eisenbach, 2000) via an unknown mechanism involving interactions between FliM/N and FliG (Mathews et al., 1998). The receptor domain is homologous to the single-domain chemotaxis protein CheC of Bacillus subtilis (Kirby et al., 2001). CheC binds reversibly to the Bacillus C-ring, and is released when it binds to CheY-P. CheC has not been found in E. coli, but homologs are found in many early-branching bacteria, as well as archaea. A cladogram generated for CheC and the FliM CheC-like domain shows that CheC is phylogenetically basal (Kirby et al., 2001). A pre-existing sensory transduction system could be coupled to flagellar rotation in a single step on the hypothesis that a FliN-like protein existed for some nonflagellar cellular response purpose, serving as a receptor for CheC. The exact function of modern CheC is not known, but it appears to interact with CheA, CheD, and McpB, which form a receptor complex (Kirby et al., 2001). CheC may also have a FliM-like function via interaction with the C-ring (Szurmant et al., 2003). The ancestor of FliN might therefore be found among the other proteins that CheC interacts with. On the model, a mutation in this FliN-like protein created a proto-FliN that bound to FliG, slowing or jamming the motor. The reversible binding of CheC to proto-FliN, however, happened to alleviate this effect by changing the conformation of proto-FliN. CheY-P binding to CheC would result in the dephosphorylation of CheY-P and the release of CheC from proto-FliN, resulting in the slowed-rotation behavior. Chemotactic behavior would thereby originate by a single mutation (all other interactions would be inherited), which could then be followed by gradual improvements in the initial crude function. This hypothesis is more economical than supposing that FliN originated for some role in structural support or enhancing export, and was later coopted to a switching function via the binding of CheC, although this remains a possibility as FliN homologs are retained in type III virulence systems for some purpose. The first hypothesis suggests that the homolog of FliN will be found within sensory transduction systems as one of the proteins that CheC or a CheC homolog interacts with; it is difficult to know where to look with the latter hypothesis. The considerable variations in the C-ring of bacteria may yield further hints, as major variations on chemotaxis and the switch complex are known; for example, Aquifex aeolicus lacks the traditional chemotaxis system as well as FliM; Bacillus spp. have FliY (a FliM-FliN fusion protein; Bischoff and Ordal, 1992; Celandroni et al., 2000) rather than FliN. In any case, the fusion of CheC-like and FliN-like proteins would produce the FliM seen in most bacteria.

http://www.talkdesign.org/faqs/flagellum.html#chemo NickMatzke_UD

Nick: "Ah, typical creationist tactics too" What part of "does the mut/sel observed in the 50000+ generations of adapting e-coli show sufficient mechanism? don't you understand. Liz jumped in and created a distraction. My question was to you. Nowhere did I suggests that the e-coli speciate. My question was about observed mut/sel: Again, from the top:

Is this consistent with the observable evidence of mut/sel in the e-coli study of the 50,000+ generations? Does the direct evidence of the adapting 50,000 e-coli generations provide us with enough confidence that mut/sel administers sufficient horsepower for a chimp diverge from common ancestor, and from common ancestor to the bi-pedal ardi in the same 50,000+ or so generations? From Pre-cambriam to Cambrian body plans?

These are yes or no answers. junkdnaforlife

I appreicate Dr Cudworth's thought, but he is spitting in the wind. Nick is not a scientist, he is a culture warrior. He will use Dr Cudworth's appeal only to hit it again. It's simply the nature of his identity. Upright BiPed

I second Dr Cudworth's motion. kairosfocus

Nick: I see you've turned tail again, refusing to answer my decisive rebuttal regarding the meaning of "creationism". That's not surprising. The rhetorical position you and the NCSE have staked out depends on promoting the willful, conscious lie that ID is creationism. You have repeatedly been shown irrefutable evidence that ID is not creationism, and you know in your heart that this is right (i.e., you know that neither Dembski nor Behe nor Meyer ever makes use of any argument in their technical ID works that requires the assumption of Christian faith or the literal truth of Genesis), yet you push the connection, as a propaganda tool. Neither you nor Eugenie cares about the true definition of ID in the slightest. Nor are you interested in an impartial investigation into questions of origins (or you would keep all options open, including those that don't appeal to your religious views). All that you care about is victory for your materialist world view, and any means, fair or foul, will do. You should be ashamed of yourselves. If you don't agree with ID, fine. But don't lie about what it is. It isn't creationism, and you know that it isn't creationism, and you are willfully dishonest to keep insisting that it is. You're hardly going to be a model for young scientists if your career starts out with a lie. Why not retract the lie now, and give yourself a clean start? Just say this: "ID is not creationism. I apologize for my willful misrepresentation of ID over the past several years." If you do that, my respect for you will go up from negative 100 to zero, and then maybe you can start building up some positive credit by doing some real science instead of atheist/materialist ideology. Thomas Cudworth

Nick Matzke: FliM is indeed basically a fusion of a CheC-domain and a FliN domain. A domain? You mean just one FliN domain and one CheC domain fused to form FliM? I think the entirety of those two proteins would be needed to form the number of amino acid residues present in FliM. But that in itself it just a touch irrelevant. Based on a sequence analysis of FliM, FliN, and CheC I have to disagree with the view that FliM is basically a fusion of CheC and FliN. If one aligns FliM with CheC (using Tcoffee) one will find that most of the similar residues between the two sequences are located in the “right half” of FliM (~70% of residues that are similar between FliM and CheC are located in the area around FliM’s C-terminus). Now, if one aligns FliM with FliN, one will find, again, that most of the similar residues between the two sequences are located in the area around FliM’s C-terminus (~60% of residues that are similar between FliM and FliN are located in the “right half” of FliM). This information, by itself, is not very interesting because fusion proteins are not always formed by two whole proteins fusing together (i.e., if FliM is the result of FliN and CheC simply fusing together – say FliN’s C-terminus fusing with CheC’s N-terminus – then we would expect that FliN would share more similar residues in FliM’s N-terminus, while CheC would share more similar residues in FliM’s C-terminus). But it does refute the notion that FliM is the result of a single fusion event of CheC and FliN. So, what evidence do you have that FliM is the result of a fusion of a FliN domain and a CheC domain? But note that once you are arguing about issues like statistical significance of homology matches, ID has basically already lost, because there are a bunch of homology matches that no one doubts, and if homology is conceded, then we have agreed there is direct evidence of evolutionary history between flagellar and nonflagellar proteins. The problem is that Darwinian evolution is not the only explanation for homology. As I said earlier – and just for the record, I don’t think you replied to this – if one, for example, aligns the un-evolved sequences designed by Fisher et al., one will find a very high level of sequence similarity. This is because human designers often take an already-existing protein and then modify the amino acid sequence to produce another protein, but since the original amino acid sequence is rarely modified to an extreme amount, there is often a fairly significant level of sequence similarity between two designed proteins. In other words, homology in itself is not evidence that a given protein system arose via purely mindless processes. LivingstoneMorford

Namecalling, instead of dealing with the merits. What part of bottom up vs top down, and gateway does the above not understand? Methinks, very little. But, it is soooo convenient to shout "creationist in a cheap tuxedo" Utterly telling. kairosfocus

Ah, typical creationist tactics too -- when you lose on PunkEek for reasons of complete misunderstanding, switch to the Cambrian, a completely different issue. This sort of stuff many fool lay audiences, but it will never, ever get credibility with the serious people in academia, and this is why ID will never deserve a place in universities or schools where serious people who know the science firsthand hang out. NickMatzke_UD

PPS: Recall, DNA exhibits codes in accord with linguistic rules, to specify functional proteins sand to regulate how they are given effect in building and operating a body plan. That is going to put you into islands of quite specific function. PPPS: Sternberg of course is an expert in evolutionary biology, and is here making a presentation in light of that expertise. But notice how he points out reasonably easily accessible or check-able facts on whale anatomy, the background knowledge that testes need to be at a proper, lower temp range than the rest of the body [why they hang in those little bags in most mammals . . . ], reasonable or generous scenarios and standard models accessible in textbooks. kairosfocus

PS: Please watch this clip by Sternberg [as was linked earlier], to see the limitations of darwinist mechanisms on pop genetics and mutation fixation in the context of body plan origination. kairosfocus

Dr Liddle: Thanks for the thoughts. I am very aware of the claims. On my physics background, I tend to take the implications of say 10^57 atoms, 5 - 12 BY, 10^45 or so Planck-time quantum states [PTQS] [10^30 of which are needed for the fastest chem reactions] fairly seriously as constraining what can happen on the gamut of our solar system in our galaxy. The above makes 10^102 a reasonable upper bound on number of PTQS events in our solar system. Just 500 bits of functionally specific complex information specifies some 10^150 configurational possibilities. So, the PTQS resources of our solar system -- our practical universe -- could not sample 1 in 10^48 of the space. Now a sample like that will be fine for getting to typical states in the space, but it is going to be way too small to have a reasonable chance of picking up UN-representative needle in the haystack FSCI clusters. A look at this will show that body plan level origin, where the evidence is that starting from a unicellular organism we need 10 - 100 mn bases worth of complex new info [you were shown linked data on that in an earlier thread but IIRC never came back to it], in a context where the embryological development program that gives it effect is KNOWN to be exquisitely vulnerable to breakdown on blind tampering by mutations, will be severely challenged on search space grounds. Such is BTW the same basic analysis that grounds the 2nd LOT. E.g. if all the O2 molecules in a room are seen at one end, that is so utterly unlikely on chance plus necessity that if we say such a room -- say with an asphyxiated dead man at one end and the O2 at the other -- we have prima facie grounds to infer murder, even if we do not have a clue how that was done. Maybe that demon raised in another thread recently dunit. So, as of right now, there is need for those who propose unlimited, smooth variation across body plans to show some direct observational evidence for their claims. There has been a lot of huffing and puffing, smoke, mirrrors and handwaving in front of exhibits that show a lot less than this or even have been in some cases outright frauds. But what has not been done is to actually demonstrate as fact that we observe body plan origination or what can credibly lead up to it. BTW, horizontal gene transfer, drift of near neutral mutations and the like do not answer to the info origination challenge. Giving the reduced form of the Chi equation, we have abundant evidence on observation, that where we directly see the cause, info beyond the FSCI threshold is an excellent index of design as cause: Chi_500 = I*S - 500, bits beyond the solar system threshold. And, if you want to thing at cosmos scale, simply doubling that number of bits to 1,000 puts the challenge way beyond the resources of our observed cosmos. If you believe that chance and necessity are sufficient to generate FSCI, instead of simply being an illustration of how searches that are intelligently designed will in specific cases outperform chance based random walks in the task of finding target zones, within which hill-climbing mechanisms have differential function to work off. GEM of TKI kairosfocus

Liz: junkdnaforlife – remember that bacteria (including e-coli) do not speciate. The oldest known life found in the universe was bacteria or archaea so I was told. From LUCA, rumor has it, that everything from a flagellum motor to the human brain has sprouted. All I am concerned with now is if the 50,000+ generations of adapting e-coli bacteria has shown sufficient mechanism. junkdnaforlife

kf:

The body plan origination and embryological feasibility of mutations required to effect it challenges have of course never been met. Instead, we have been told that macro-evo is simply accumulated micro evo, as though there is not a major informational threshold issue at work.

Couple of points: Yes, that is the issue - "evolutionists" do dispute the existence of a "major informational threshold". So that is probably what we should be talking about. They certainly dispute it as occuring between "macro" and "micro"! Secondly - depends what you mean by macro and micro - if macro means speciation - lateral divergence, then yes, macro isn't simply more micro, there is another ingredient which is population divergence I'd put it this way: micro-evolution is, essentially, adaptation, down any one lineage. And it has no obvious longitudinal limits. Speciation is independent adaptation down two divergent lineages. Again, it has no obvious longitudinal limits, but once the point of hybridisation is passed, there are clear lateral limits - an adaptive innovation in one lineage cannot be transferred to another. Bird lungs will not be transferred to mammals; however, both bird lungs and mammal lungs can continue to adapt down their separate lineages. If there is an unsolved "leap" - an informational threshold, if you like, it's from non-replication to replication - that's abiogenesis. But it isn't relevant to evolution, once started, nor to speciation. Or, at least, I do not see that a convincing case has yet been made that it is :) Elizabeth Liddle

Re Dr Matzke:

using that Gould quote outside of context of what it really means is a classic cheap creation-science trick. There, Gould is talking about species-to-species transitions in the fossil record . . .

Of course, this -- sadly -- is yet another misleading talking point, further poisoned by namecalling; all intended to carry us further and further from the main issue in the thread, while poisoning the atmosphere. All, further revelatory on the underlying rhetorical games that are afoot. What was not acknowledged above is that in the usual darwinist scheme, species to species transitions are held to be the basis for all else, so if these are systematically missing in action -- and they should be the most numerous of all, everything else above in the taxonomic pattern will be problematic. So the attempted deflection actually implies far more problems than is suggested by the smoothly poisonous way it is done. But in fact the fossil transitions problems are much bigger than this. For in fact right from the days of Darwin the three of life has been stood on its head -- top down not bottom up, and with transitions all across the scale notoriously generally missing in action [never mind the rare exceptions that as Gould points out are headlined, in a context where the implied admission of data cutting across the expectations, is a serious challenge to the pretension to be scientific] -- when confronting the evidence of the actual fossils. Meyer's PBSW summary -- which BTW (despite attempts to smear it and expel the editor for in effect being open minded) passed proper peer review by "renowned" scientists -- aptly sums up with the most significant case, right from the top. In so doing Meyer exposes the key issue that is unaccounted for in the Darwinist scheme, which underlies the informational challenge (which thanks to the informational view of thermodynamics is linked directly to thermodynamics issues on the credible source of functionally specific complex information) that design theory has highlighted:

The Cambrian explosion represents a remarkable jump in the specified complexity or "complex specified information" (CSI) of the biological world. For over three billions years, the biological realm included little more than bacteria and algae (Brocks et al. 1999). Then, beginning about 570-565 million years ago (mya), the first complex multicellular organisms appeared in the rock strata, including sponges, cnidarians, and the peculiar Ediacaran biota (Grotzinger et al. 1995). Forty million years later, the Cambrian explosion occurred (Bowring et al. 1993) . . . One way to estimate the amount of new CSI that appeared with the Cambrian animals is to count the number of new cell types that emerged with them (Valentine 1995:91-93) . . . the more complex animals that appeared in the Cambrian (e.g., arthropods) would have required fifty or more cell types . . . New cell types require many new and specialized proteins. New proteins, in turn, require new genetic information. Thus an increase in the number of cell types implies (at a minimum) a considerable increase in the amount of specified genetic information . . . . In order to explain the origin of the Cambrian animals [an issue of origin of dozens of phyla and sub-phyla, not bottom up from speciation but top down from the highest levels of body plan organisation], one must account not only for new proteins and cell types, but also for the origin of new body plans . . . Mutations in genes that are expressed late in the development of an organism will not affect the body plan. Mutations expressed early in development, however, could conceivably produce significant morphological change (Arthur 1997:21) . . . [but] processes of development are tightly integrated spatially and temporally such that changes early in development will require a host of other coordinated changes in separate but functionally interrelated developmental processes downstream. For this reason, mutations will be much more likely to be deadly if they disrupt a functionally deeply-embedded structure such as a spinal column than if they affect more isolated anatomical features such as fingers (Kauffman 1995:200) . . . McDonald notes that genes that are observed to vary within natural populations do not lead to major adaptive changes, while genes that could cause major changes--the very stuff of macroevolution--apparently do not vary. In other words, mutations of the kind that macroevolution doesn't need (namely, viable genetic mutations in DNA expressed late in development) do occur, but those that it does need (namely, beneficial body plan mutations expressed early in development) apparently don't occur.6 [NB: For the open-minded, the video discussion of Cichlid variability patterns here and of origin of the whale body plan in light of pop genetics issues here will be interesting. As will this video that brings out more details on the Cambrian life problem. The problem is much broader and deeper than is usually admitted by evo mat advocates as they make their talking points.]

The body plan origination and embryological feasibility of mutations required to effect it challenges have of course never been met. Instead, we have been told that macro-evo is simply accumulated micro evo, as though there is not a major informational threshold issue at work. And, ironically, what is a species is an unanswered question so that North American Elk and Red Deer are seen as interbreeding in New Zealand, Grizzlies and Polar bears can mate and form similarly fertile offspring, and in the Galapagos, birds have been seen happily breeding across species lines. There is plainly a lot of adaptation and variation within the body plan "island of function" level but that is where the issue just highlighted kicks in: where do body plans come from and how can the huge jump in FSCI to explain that new "wiring diagram" come from given the problem of traversing huge config spaces to find narrow target zones of function that are UNREPRESENTATIVE of the physically possible configs. Chance and necessity without intelligence do not provide a feasible, plausible answer; unless the deck is subtly stacked in favour of a priori Lewontinian materialism. Getting back to the main issue raised by Dr Cudworth, it is plain that a serious double-standard is at work, and there is a selectively hyperskeptical game afoot, centred on fallacies of distraction, distortion and denigration by namecalling. (Notice the creationism in a cheap tuxedo distortion point is simply being reiterated again and again on various talking points, without warrant. FYI Dr Matzke, I am a biological origins deep past reconstruction agnostic, save on the point that it is patent that FSCI has to be properly accounted for and its most credible answer is intelligence, so if the cosmological evidence that there has been deep time and origin in a big bang 13.7 BYA speaks true -- and that has a lot better, less circular empirical warrant -- then it is at minimum a credible option that the cosmos is a work of design, and in that light one of the best candidate explanations of origin of life and body plans is design working with intelligently built in evolutionary adaptation capacity to fill niches based on robust, flexible body plans. Worse, even had my cite above been truly out of context -- and plainly, it was only a gateway pointing to a much broader problem that was in turn being diverted from by atmosphere poisoning tactics, and was not indicative of wider and wider problems as we go, quoting out of context is not a specifically "creationist" problem. So, there is an unwarranted snide inference here. But to tag any and all questioning of the evolutionary materialist agenda as "creationist" where that stands in for "ignorant, stupid, insane or wicked" IS patently a serious problem with the ruthless, amoral evo mat factionism that has been exposed at one level or another since Plato. Cho man, do betta dan dat! [Let me be a bit more explicit: If you continue to try to force-fit me into a handy strawman caricature in the teeth of an explicit summary as above, all that will tell me is that you are more interested in pushing ideology than in truth or fairness. In light of the internet thuggery I have been recently subjected to, to the cheers of too many on your side, that will be utterly revealing on the significance, current relevance and force of Plato's grim warning in The Laws, Bk X.) Surely, there is a better way, to actually teach people about what science is historically (especially in modern times) and what it tries to do, acknowledging the limitations of scientific and broader empirical warrant and especially those of attempts to reconstruct a deep, unobserved past: we were not there and we cannot directly observe the true state of the deep past, so we should not project an unwarranted confidence, especially one driven by ideological imposition of a priori materialism. In that context, the major historic and recent approaches to origins views can be presented on a true and fair view basis [Wikipedia style distortions and trashing will not do], in the context of that history and the strengths and limitations of evidence, inference and reasoning can be assessed, with an eye to the issues of institutional politics and rhetoric. To do less than that -- as we are, sadly, plainly seeing at the hands of the evolutionary materialist establishment -- is to resort to mind closing indoctrination, not sound education. Which would be a failure in duties of care. We can and must do better than that. GEM of TKI kairosfocus

junkdnaforlife - remember that bacteria (including e-coli) do not speciate. Elizabeth Liddle

Nick: "In most theories, small isolated populations are the source of new species, and the process of speciation takes thousands or tens of thousands of years. This amount of time, so long when measured against our lives, is a geological microsecond" Is this consistent with the observable evidence of mut/sel in the e-coli study of the 50,000+ generations? Does the direct evidence of the adapting 50,000 e-coli generations provide us with enough confidence that mut/sel administers sufficient horsepower for a chimp diverge to common ancestor, and from common ancestor to the bi-pedal ardi in the same 50,000 or so generations? From Pre-cambriam to Cambrian body plans? junkdnaforlife

LOL, using that Gould quote outside of context of what it really means is a classic cheap creation-science trick. There, Gould is talking about species-to-species transitions in the fossil record, which is what his "Punctuated Equilibrium" model was about. He is talking about the transitions between *very similar* and *very closely related* species -- things like horses and zebras. At that very fine scale -- differences much smaller than the differences within what creationists usually call "created kinds", which creationists usually put at the genus or family level (or even higher) -- we don't have very many gradual transitions. Punk Eek suggests that this is because speciation is rapid and often takes thousands of years instead of millions (whereas the fossil record usually has a time-resolution of only hundreds-of-thousands or millions of years). Gould could be right or wrong about this, it's still debated. But either way, larger changes than species-to-species transitions, e.g. reptiles to mammals, dinosaurs to birds, etc. have *lots of transitional fossils*. As Gould himself said, specifically to rebut creationist abuse of exactly that quote! Decades ago!! ======== [T]ransitions are often found in the fossil record. Preserved transitions are not common -- and should not be, according to our understanding of evolution (see next section) but they are not entirely wanting, as creationists often claim. [He then discusses two examples: therapsid intermediaries between reptiles and mammals, and the half-dozen human species - found as of 1981 - that appear in an unbroken temporal sequence of progressively more modern features.] Faced with these facts of evolution and the philosophical bankruptcy of their own position, creationists rely upon distortion and innuendo to buttress their rhetorical claim. If I sound sharp or bitter, indeed I am -- for I have become a major target of these practices. I count myself among the evolutionists who argue for a jerky, or episodic, rather than a smoothly gradual, pace of change. In 1972 my colleague Niles Eldredge and I developed the theory of punctuated equilibrium. We argued that two outstanding facts of the fossil record -- geologically "sudden" origin of new species and failure to change thereafter (stasis) -- reflect the predictions of evolutionary theory, not the imperfections of the fossil record. In most theories, small isolated populations are the source of new species, and the process of speciation takes thousands or tens of thousands of years. This amount of time, so long when measured against our lives, is a geological microsecond . . . Since we proposed punctuated equilibria to explain trends, it is infuriating to be quoted again and again by creationists -- whether through design or stupidity, I do not know -- as admitting that the fossil record includes no transitional forms. Transitional forms are generally lacking at the species level, but they are abundant between larger groups. - Gould, Stephen Jay 1983. "Evolution as Fact and Theory" in Hens Teeth and Horse's Toes: Further Reflections in Natural History. New York: W. W. Norton & Co., p. 258-260. ======== http://www.talkorigins.org/faqs/quotes/mine/part3.html This kind of thing is exactly why ID proponents don't get no respect from scientists, and until this kind of thing stops, they won't deserve it. PS: If you think Gould and Prothero -- both famous paleontologists -- are too biased to be believed about transitional fossils, have a look at what YEC paleontologist Kurt Wise says: http://pandasthumb.org/archives/2009/01/honest-creation.html ========== [p. 218] In various macroevolutionary models, stratomorphic intermediates might be expected to be any one or more of several different forms: – (a) inter-specific stratomorphic intermediates; (b) stratomorphic intermediate species; (c} higher-taxon stratomorphic intermediates; and (d) stratomorphic [intermediate] series. As an example (and to provide informal definitions), if predictions from Darwin’s theory were re-stated in these terms, one would expect to find: – (a) numerous stratomorphic intermediates between any ancestor-descendent species pair (numerous interspecific stratomorphic intermediates); (b) species which were stratomorphic intermediates between larger groups (stratomorphic intermediate species); (c} taxonomic groups above the level of species which were stratomorphic intermediates between other pairs of groups (higher-taxon stratomorphic intermediates); and (d) a sequence of species or higher taxa in a sequence where each taxon is a stratomorphic intermediate between the taxa stratigraphically below and above it (stratomorphic series). With this vocabulary as a beginning, the traditional transitional forms issue can be gradually transformed into a non-traditional form, more suitable to the creationist researcher. It is a Very Good Evolutionary Argument Of Darwinism’s four stratomorphic intermediate expectations, that of the commonness of inter-specific stratomorphic intermediates has been the most disappointing for classical Darwinists. The current lack of any certain inter-specific stratomorphic intermediates has, of course, led to the development and increased acceptance of punctuated equilibrium theory. Evidences for Darwin’s second expectation - of stratomorphic intermediate species - include such species as Baragwanathia27 (between rhyniophytes and lycopods), Pikaia28 (between echinoderms and chordates), Purgatorius29 (between the tree shrews and the primates), and Proconsul30 (between the non-hominoid primates and the hominoids). Darwin’s third expectation - of higher-taxon stratomorphic intermediates - has been confirmed by such examples as the mammal-like reptile groups31 between the reptiles and the mammals, and the phenacdontids32 between the horses and their presumed ancestors. Darwin’s fourth expectation - of stratomorphic series - has been confirmed by such examples as the early bird series,33 the tetrapod series,34,35 the whale series,36 the various mammal series of the Cenozoic37 (for example, the horse series, the camel series, the elephant series, the pig series, the titanothere series, etc.), the Cantius and [p. 219] Plesiadapus primate series,38 and the hominid series.39 Evidence for not just one but for all three of the species level and above types of stratomorphic intermediates expected by macroevolutionary theory is surely strong evidence for macroevolutionary theory. Creationists therefore need to accept this fact. It certainly CANNOT said that traditional creation theory expected (predicted) any of these fossil finds. ========== NickMatzke_UD

PS: Mr Roache -- being plainly enamoured of the talking points of objectors who are at minimum careless of facts -- seems unaware of this, on the EF applied to biological objects. He should pay particular attention to the examples as given since April in response to challenges, from the 35 protein families addressed by Durston et al. kairosfocus

Gould's summary of the actual as opposed to headlined state of the fossil evidence, which continues to today after 1/4 million and more fossil species and many millions of fossils:

"The extreme rarity of transitional forms in the fossil record persists as the trade secret of paleontology. The evolutionary trees that adorn our textbooks have data only at the tips and nodes of their branches; the rest is inference, however reasonable, not the evidence of fossils. Yet Darwin was so wedded to gradualism that he wagered his entire theory on a denial of this literal record:

The geological record is extremely imperfect and this fact will to a large extent explain why we do not find intermediate varieties, connecting together all the extinct and existing forms of life by the finest graduated steps [[ . . . . ] He who rejects these views on the nature of the geological record will rightly reject my whole theory.[[Cf. Origin, Ch 10, "Summary of the preceding and present Chapters," also see similar remarks in Chs 6 and 9.]

Darwin's argument still persists as the favored escape of most paleontologists from the embarrassment of a record that seems to show so little of evolution. In exposing its cultural and methodological roots, I wish in no way to impugn the potential validity of gradualism (for all general views have similar roots). I wish only to point out that it was never "seen" in the rocks. Paleontologists have paid an exorbitant price for Darwin's argument. We fancy ourselves as the only true students of life's history, yet to preserve our favored account of evolution by natural selection we view our data as so bad that we never see the very process we profess to study." [[Stephen Jay Gould 'Evolution's erratic pace'. Natural History, vol. LXXXVI95), May 1977, p.14.]

For more at the first level, cf here. Design theory, as Behe -- and even Wallace, co-founder of the theory of evolution -- will point out, is compatible with common descent, up to and including universal common descent. However, it should be noted that there is here a common distortion of the actual overall state of the fossil evidence that tells much, and none of it good for the promoters of Darwinism. kairosfocus

Right. And you said Darwin’s book. And Nick recommended a book on fossils. And Darwin said the fossil record could be urged as a valid objection against his theory.

For the love of the IDer, that was 152 years ago, it's illegitimate to quote it without even considering what has happened since then. We've discovered rather a lot of transitional fossils since then. The main point of Prothero's book is that Darwin's statement back then is no longer true. NickMatzke_UD

128 Mung 07/12/2011 2:05 pm p.s. I was really hoping for more than just fossils though. I meant the big case. All the evidence. Including molecular, etc. The best case for common descent is a book on fossils?

It discusses phylogenetics and some of the other arguments as well. But it has lots of fossils. Lots and lots of *transitional* fossils. I think this is a more direct argument than many of the other arguments, which are more statistical in nature and thus more abstract. And, I did give you the link to the huge 29+ Evidences website, which is book-length and discusses all of the issues, fossil, molecular, etc., in more detail, starting from the basics, than you'll find anywhere else. And it's free! NickMatzke_UD

FliM is indeed basically a fusion of a CheC-domain and a FliN domain. IIRC YscQ and other T3SS FliN homologs have only the region homologous to FliN, so a score based on comparing to FliM is inappropriate. IIRC if you start a standard PSI-BLAST search on FliN you will easily retrieve YscQ and homologs without difficulty and without lots of random sequences. Re: homology -- it is a common mistake to say 2 proteins are "20% homologous". Except in cases like domain shuffling, two proteins are either homologous or not. 20% sequence similarity is evidence that helps us determine which is the case. Typically 25% or more amino acid sequence similarity makes homology a "sure thing", and 10-20% similarity is the "twilight zone" where you can't be sure just from the sequence similarity number. But if the shared similarities are spread out over an alignment, not eliminated by a low-complexity filter, etc., the e-values will still indicate statistically significant similarity well beyond what is expected from random matches in the database. In many, many cases homology has been concluded from this sort of analysis, and has later been supported by linking intermediate sequences, strongly similar structures, etc. Every paper you will read on flagellum/T3SS acknowledges the FliN/YscQ homology, it's one of the classic "10 shared proteins" you always hear about. The FliG/MgtE one is admittedly less certain (although I think it's likely as I get it in PSI-BLAST searches), having been proposed in only 1 paper by Pallen and colleagues. But note that once you are arguing about issues like statistical significance of homology matches, ID has basically already lost, because there are a bunch of homology matches that no one doubts, and if homology is conceded, then we have agreed there is direct evidence of evolutionary history between flagellar and nonflagellar proteins. NickMatzke_UD

You asked for a book that laid out the case for common descent.

Right. And you said Darwin's book. And Nick recommended a book on fossils. And Darwin said the fossil record could be urged as a valid objection against his theory. Mung

Nick Matzke: “In actual fact, phylogenetically we have, as further and further out sister groups…” Two points here: firstly, I don’t think you’ve presented any evidence so far that indicates that “a T3SS-like common ancestor preceded the flagellum and the modern T3SS.” Secondly, you cite several examples of ‘sub-parts’ of the flagellum, and functions that contain some flagellar homologues. However, one of my concerns here is the low level of homology between flagellar proteins and their non-flagellar homologues. For example, last time I checked the flagellar switch complex protein FliG shares only 20% homology with its non-flagellar counterpart, MgtE. And the alignment score that results from a ClustalW alignment of FliM (accession no. P06974) and YscQ (accession no. A9R9I6) is a whopping 7. If one aligns a randomly-generated string of amino acid letters with another randomly-generated string of amino acid letters, the ClustalW score will be somewhere around 6-8. So the homology between FliM and YscQ is unimpressive, to say the least. In the case of the bacterial flagellum, I have never been impressed by the cited homologues, one reason being the fairly low level of homology present. So, where do you think FliM, for example, came from, and what evidence can you cite in favor of your hypothesis? Back in 2003 I believe you argued that a proto-FliN/CheC fusion formed FliM, but I’m not sure if you still hold to that idea. LivingstoneMorford

Re WR: Copying of gross and distorting errors -- in the teeth of direct and undeniable evidence in open court -- is "standard practice" for judges? Bad news, that. kairosfocus

KF

And if Judge Jones’ blind copying of NCSE/ACLU submissions, gross errors and all, is anything to go by, under current circumstances, too many judges may not be neutral observers in the relevant sense.

What Judge Jones did is standard practice. It's funny how you are not complaining about how it happens day in, day out because it is. It's just this one specific example you have a problem with of the completely logical situation where a Judge who has been persuaded by one side uses that sides own data, word for word in some cases, in his verdict.

Tag and dismiss tactics — which you (sadly, predictably) used — do not answer to that.

Hardly. The way I see it is that Nick is taking time out from doing more productive work to explain his work to you to prevent, as much as possible, misunderstanding. If you have a problem with what Nick is saying then perhaps you should collect your evidence and publish! As I suggested to Upright. Publish or perish KF! Links to an angelfire website (are they really still going) might as well be to the timecube guy for all the difference it's going to make. The guy you are arguing with cannot lose here, he wins, he wins. He loses, well, it's only you that's seen it. And according to you and everybody else he loses every time anyway so who's to know it's different this time? So, save your energy and publish in the only venue that matters! The only venue where you have a chance of persuading others of the validity of your point of view! A Nobel awaits for the first worked example of the Explanatory filter for a biological object, I'm sure! WilliamRoache

Mung:

Elizabeth Liddle:

Mung – there’s always Darwin’s

Do you’ve changed your mind? Darwin’s book did contain a theory of common descent?

You asked for a book that laid out the case for common descent. Darwin wrote one - that's why the title is "On The Origin of Species". However, the mechanism he is famous for proposing - natural selection acting on variation - can be applied even to the animals coming off the Ark. The proposed mechanism does not, in itself, depend on Common Descent being true. However, Darwin argued that the mechanism he proposed could account for common descent of all living species from "few forms...or one", and thus for the nested hierarchies identified by Linnaeus, and laid out the case in his book. Elizabeth Liddle

p.s. I was really hoping for more than just fossils though. I meant the big case. All the evidence. Including molecular, etc. The best case for common descent is a book on fossils? Mung

Nick Matzke:

If you aren’t convinced by these works, please come up with a better explanation for the evidence when you write your rebuttal.

Thanks Nick, I just ordered Prothero's book. 1-3 weeks delivery. I don't need an alternate theory. What I need is an argument and evidence for why I should believe yours. The fact that I can't explain something doesn't mean your theory is correct, or that it's even coherent. Heck, my theory is God pops everything into existence every second tuesday including fossils. According to that theory fossils don't tell us squat about common descent. Can you come up with a better theory than that? Mung

CLASSIFICATION, groups subordinate to groups - Natural system - Rules and difficulties in classification, explained on the theory of descent with modification Oh my. In his own words even. http://www.talkorigins.org/faqs/origin/chapter13.html Mung

Elizabeth Liddle:

Mung – there’s always Darwin’s

Do you've changed your mind? Darwin's book did contain a theory of common descent? Mung

William. Stop. Breathe. Reread. Upright BiPed

Dr Matzke: Dismissive, jaundiced rhetoric that fails to seriously address on merits. As for thermodynamics issues, it seems you have not attended carefully to the question being highlighted then and now: energy conversion to do constructive counter-flow work, and the means by which this is done. Tag and dismiss tactics -- which you (sadly, predictably) used -- do not answer to that. FYI, as the just linked notes on Clausius point out, an open system that imports raw energy tends to INCREASE its entropy. It is coupling to an energy converter that does interesting things, and this brings up front centre the issue of the origin of complex functionally specific converters. And if Judge Jones' blind copying of NCSE/ACLU submissions, gross errors and all, is anything to go by, under current circumstances, too many judges may not be neutral observers in the relevant sense. (Something my ancestors would doubtless find quite familiar.) Good day GEM of TKI kairosfocus

Upright,

How much more satisfying would it be if you didn’t have to tip toe around the evidence against you.

Then summarise this evidence, provide support for your theory and publish! What exactly is stopping you Upright? If this evidence is so persuasive and so available and so against Nick then why don't you hit him where it hurts with it? I.E. his peer group! Were you to publish a paper that used this claimed evidence and provided a counterpoint to Nick's claims then how is that not a very desirable thing from your (or ID's) point of view? If you are concerned about academic suppression, then don't worry. There is no single documented example of a paper being refused solely on the basis that it supports intelligent design! Not a single rejection letter! So have no fear on that regard! I look forwards to reading about how the evidence is in fact against Nick and how very wrong Nick is, but all in a nice peer reviewed format where your claims have been put to the test before being allowed to represent "science", as best as we poor mortals have found to do it as yet. WilliamRoache

114 kairosfocus 07/12/2011 5:58 am Dr Matzke: Above, despite abundant opportunity to do so [and even a link to the book in question], you again have refused to read the context to see how the words you view as red flags, are working in context.

And you are just putting on rosy-colored glasses in your interpretation of MLO, and ignoring all of the inconvenient evidence in favor of the position that it is a creationist work. Even if you could convince a neutral observer like a judge that creationists talking about "special creation" and "intelligent Creators", who clearly favor the creator-beyond-the-cosmos idea (citing the proposal of cranks like Hoyle & Wickramasinghe that INSECTS were the intelligent designers? C'mon, this is just interference thrown up to muddy the waters a little bit, no one takes it seriously, and neither did Thaxton et al.), there is yet more evidence that has to be considered by a fair observer. Bradley was, at the very time that book was being written, contracted as a creationist expert witness to defend Louisiana's "creation science" law, which would eventually be overturned by the Supreme Court in 1987. Kenyon, who wrote the forward to MLO, was also. Thaxton was, in the early 1980s, defending the "two-model approach", which was the strategy & language adopted by the creationists in that very Louisiana bill. Why does MLO cite and agree with, at the very end, an article by ultra-YEC creation scientist Jerry Bergman, endorsing the creation-science two-model approach? And finally, Bradley's informational thermodynamic argument in MLO and other places in the 1980s was quite clearly just an attempt to revive the long-discredited (well, except on UD) Second Law of Thermodynamics argument used by the YECs in slightly different form. NickMatzke_UD

Convinced about what Nick? Convinced that lifeforms change over enourmous periods of time? It must take a delicate personal and professional balance to remain so immodest when the support for your worldview can be reduced to such trivial observations. How much more satisfying would it be if you didn't have to tip toe around the evidence against you. Pity. Upright BiPed

It seems as if much of your argument is based on the assumption (albeit a shaky one) that the flagellum evolved via a Darwinian mechanism. Is there any phylogenetic evidence that indicates that a T3SS-like common ancestor preceded the flagellum and the modern T3SS? Evidence that is, that does not rest on the assumption that the flagellum evolved? Thanks.

Phylogenetics doesn't assume evolution through lineal descent, it tests it. If you end up with no statistical support for a tree structure, then you have no evidence of lineal descent. If you do, then you do. It is so incredibly common to see tree structure that most people don't mention the testing nature of it most of the time.

Incidentally, given that the modern T3SS is definitely not ancestral to the flagellum, you are left without any evidence as to where FliF, FliP, FliM, etc., might have come from.

In actual fact, phylogenetically we have, as further and further out sister groups: the "classic" flagellum of e.g. E. coli the spirochete and gram-positive flagella, which work but are missing some parts that are "crucial" in other flagella (~20 shared proteins, ~10 of them are axial filament proteins homologous to each other) the T3SS, which is either sister to flagella or right near the base of the divergence of the bacterial phyla (sharing ~10 proteins that are not axial filament proteins) a system in the bacterial phylum Chlamydiales that shares ~5 proteins with the flagellum and T3SS; probably some kind of intracellular transporter; this consistently branches very deeply even more deeply is the F1Fo-ATPase and relatives which is homologous to at least 3 flagellum proteins (it used to be 1, it increases every few years, this is what impressed Mike Gene) the core shared ATPase protein has many more even more remote homologs ...and lots of other individual flagellum proteins have known nonflagellar homologs, e.g. the motor proteins MotA and MotB, the muramidase, etc. NickMatzke_UD

Hi Nick, I’m one of those agnostics. Direct me to a good book, the best one you know of, that lays out the case for common descent. I’ll read it. So far no one has been able to direct me to any such book, so I remain agnostic. And I don’t mean they’ve directed me to a book and I disagree with the book. I mean, no book. Yet.

Well, how could you have missed these? 1. Prothero's book: Evolution: What the Fossils Say ...and... 2. Doug Theobald's 29+ Evidences for Macroevolution FAQ... http://www.talkorigins.org/faqs/comdesc/ If you aren't convinced by these works, please come up with a better explanation for the evidence when you write your rebuttal. NickMatzke_UD

Nick Matzke: Again, you are not thinking phylogenetically. If the flagellum and T3SS are sister groups, then we have evidence that the common ancestor preceded both systems, and had all of the parts which the two systems share (which are all of the core parts of the secretion system, so probably we would call that ancestor a T3SS if we saw it). The relative ages of the flagellum crown group and the T3SS crown group are irrelevant, if the two groups are sister groups. It seems as if much of your argument is based on the assumption (albeit a shaky one) that the flagellum evolved via a Darwinian mechanism. Is there any phylogenetic evidence that indicates that a T3SS-like common ancestor preceded the flagellum and the modern T3SS? Evidence that is, that does not rest on the assumption that the flagellum evolved? Thanks. Incidentally, given that the modern T3SS is definitely not ancestral to the flagellum, you are left without any evidence as to where FliF, FliP, FliM, etc., might have come from. LivingstoneMorford

F/N: Bradley's presentation is now here on the wayback machine. kairosfocus

Dr Matzke: Above, despite abundant opportunity to do so [and even a link to the book in question], you again have refused to read the context to see how the words you view as red flags, are working in context. Words do not carry a free-floating meaning, they draw meaning from usage in context; and they evolve. You know, or should know that c. 1985, there was no generally accepted terminology for what is now known as design theory, and so when:

1: TBO spoke of intelligent creators within the cosmos -- in a context explicitly citing Hoyle and Wickramasinghe [with INSECTS in the star role], 2: juxtaposed this with another alternative of a Creator beyond the cosmos, and 3: Explicitly acknowledged that:

The above discussion is not meant a s a scientific proof of a Crea-tor, but is merely a line of reasoning to show that Special Creation by a Creator beyond the cosmos is a plausible view of origin [as opposed to operations] science [211 - 12]

4: Also reasoning thusly:

Special Creation (whether from within the cos-mos or beyond it) differs from abiogenesis in holding that the source which produced life was intelligent.

5: Further arguing:

But does creation employ cause-effect and the principle of uniform-ity? Yes. In fact, it appeals to them a s the only way we can plausibly reconstruct the past. [--> Morris et al probably had a collective head shaking at this point, cf the key creationist premise here, from Job 38: those who were not there but speculate on projecting from present to past "darken counsel with words without knowledge" . . . ] Consider, for example, the matter of accounting for the informational molecule, DNA. We have observational evi-dence in the present that intelligent investigators can (and do) build contrivances to channel energy down nonrandom chemical path-ways to bring about some complex chemical synthesis, even gene building. May not the principle of uniformity then be used in a broader frame of consideration to suggest that DNA had a n intelli-gent cause a t the beginning? Usually the answer given is no. But theoretically, at least, it would seem the answer should be yes in order to avoid the charge that the deck is stacked in favor of naturalism. [ --> a la Lewontin et al] We know that in numerous cases certain effects always [--> i.e. per massive observation, a well supported induction] have intelligent causes, such as dictionaries, sculptures, machines and paintings. We reason by analogy that similar effects also have intel-ligent causes. For example, after looking up to see “BUY FORD” spelled out in smoke across the sky we infer the presence of a skywrit-er even if we heard or saw no airplane. We would similarly conclude the presence of intelligent activity [--> so close to the later terms] were we to come upon a n elephant-shaped topiary in a cedar forest. I n like manner a n intelligible communication via radio signal from some distant galaxy would be widely hailed a s evidence of a n intelligent source. Why then doesn’t the message sequence on the DNA molecule also constitute prima facie evidence for a n intelligent source? After all, DNA information is not just analogous to a mes-| sage sequence such a s Morse code, it is such a message sequence.76 The so-called Shannon information laws apply equally to the genetic code and to the Morse code. True, our knowledge of intelli-gence has been estricted to biology-based advanced organisms, but it is currently argued by some that intelligence exists in complex non-biological computer circuitry. If our minds are capable of imagining intelligence freed from biology in this sense, then why not in the sense of an intelligent being before biological life existed?77

. . . we are plainly seeing a fresh departure, something that is clearly not parallel to either Paley's Natural Theology, nor to biblical creationism's then strong tendency to present the evidence of design of life as pointing necessarily to the God of the Bible -- who was there and so tells us accurately what happened (more or less literally), on the typical pattern of creationist thought -- as creator of life on earth. The core concepts are plainly in place, what would be refined would be the distinct terminology that best communicates those concepts. Remember, too, this discussion is not in a context of debates over earth dating and flood remnants, but on the atmospheric composition of the early earth on the conventional timeline, on the interactions that would have deposited how much of what in the primordial oceans, and on the resulting thermodynamics of monomers in solution. That might be a theistic evolutionary context, related to the co-founder of modern evolutionism's thought [cf. here Wallace's The World of Life and intelligent evolution], but it is not Biblical creationism. The operative terms in TMLO -- one would hardly expect this in a high school supplementary text -- are entropy, enthalpy, Gibbs free energy, Brillouin's negentropy formulation of information [which has now been given significant support by the emergence of t6he informational approach to thermodynamics as a viable school of thought] and reaction kinetics for severely endothermic polymer molecules, on an adaptation of diffusion in light of the state not path function nature of entropy. The sharp contrast to say Morris' The Genesis Flood or his later Scientific Creationism COULD NOT BE more obvious. We find nowhere a trace of Gish's debate points over fossils and the like. This is very different, as in its own way another key ID foundational work of that era was, Denton's Evo, a Theory in Crisis. I put it to you, sir, that your refusal to acknowledge such major and patent conceptual and analytical distinctives speaks a lot, and not in your favour. As at now, you come across as a very familiar type to one such as the undersigned, who cut his intellectual eye-teeth on communist radicals. Namely, pardon a few plain words, as a closed minded, indoctrinated radical ideologue pushing favourite talking points regardless of evidence to the contrary, and in particular using the snipping of words out of their proper context to score debate points with those who do not know enough of the context to spot that this is a wrenching of ideas out of context. Since you have been corrected by several people from several perspectives, but insist on deceptively twisted debate points, I have but little choice other than to highlight that willful suppression of evident facts. And, to point out that this accords exactly with the sort of ruthless amoral factionism that Plato warned about as a typical characteristic of self-important evolutionary materialism 2350 years ago. An attitude I am all too familiar with from the communists of my youth. So, please stop dancin' wrong but strong. Now, of course, Dr Cudworth is correct to highlight that the current shape of design theory is distinct again from the way things were formulated in 1985 or so (and popularised in 1989 or so). Across the 1990s, the key issue that the real proper focus for scientific investigation was not on the agent that may be implied in a design event but on the empirical evidence that points to design as causal process. That tweredun, not whodunit. But even in 1985, it is plain that TBO realised this, as we can see from their observations above, which you chose to ignore. Similarly, it was recognised that thermodynamics was not he best way to address the signs of intelligence in what are credible artifacts of design [cf Bradley later, here], but to go direct to information theory and build on Orgel's concept of complex, specified information, in the context of the known empirically warranted source of such and the linked infinite monkeys analysis that highlights that beyond a certain threshold of complexity, observed specified and complex events E that jointly constitute a target zone T that is UN-representative of a wider space of possible configs, W, will not plausibly be reached by blind chance and mechanical necessity on the gamut of our solar system [500 bits] or our observed cosmos [1,000 bits]. This for the same reason why it is hard to find a small needle in a very large haystack if we are only able to make one small sample. Also, we would see that when we deal with multi-part, co-ordinated functionality it is not plausible that the parts would spontaneously be just right and in the just right organisation per a wiring diagram, by chance, mechanical necessity and blind co-option. When your car engine breaks down, you want specific parts, installed the right way int eh right place, or the whole will not work. Just a tiny misfit is often enough to break the whole down. On massive observation and related analysis, the only empirically well warranted source for such is the act of intelligent design. Indeed, on simple induction, the CSI and IC as just described are well-warranted, inductively strong signs of design as causal process. Onward they point to intelligent, choosing agents as the most credible cause. You may reject this, and you may provide arguments to substantiate that rejection, but one thing that is not legitimate, is to pretend that this is not a serious argument and a historic live option for serious scientific thinkers. But, consistently, I find, sir, that you and your ilk try to do just that which is illegitimate, and that too often you resort to illegitimate steps in logic and much more than logic. Multiply that by the sort of internet thuggery I have just experienced -- to the applause of too many of your party, sir -- and you will understand why I take an exceedingly dim view of such tactics. Cho man, do betta dan dat! GEM of TKI kairosfocus

Mung - there's always Darwin's :) Elizabeth Liddle

Nick Matzke, You still do not have a testable hypothesis nor any supporting data for the claim the T3SS and the flagellum evolved via accumulations of genetic accidents. Strange that for all of your bloviating you still refuse to address those facts. Joseph

Nick Matzke (108): It's absolutely irrelevant whether Thaxton, Bradley, etc. were at one time creationists or are now creationists. That has nothing to do with the truth of falsehood of ID, which as a theoretical position has nothing at all to do with creationism. You're wasting your life trying to score debating points on the internet about historical trivia. If this is how you intend to spend your career as a scientist, I predict that your accomplishments in evolutionary biology will be few. Thomas Cudworth

Nick Matzke:

Second, (a) the vast majority of ID guys constantly dispute macroevolution, on this blog and elsewhere; (b) disputing common ancestry is so scientifically ridiculous and in the face of so much scientific evidence that even being agnostic on macroevolution indicates massive problems with the scientific capacity of anyone who holds those positions

Hi Nick, I'm one of those agnostics. Direct me to a good book, the best one you know of, that lays out the case for common descent. I'll read it. So far no one has been able to direct me to any such book, so I remain agnostic. And I don't mean they've directed me to a book and I disagree with the book. I mean, no book. Yet. Mung

Well, if we define the flagellum as something along the lines of “a motility organelle composed of ~21 proteins (at minimum) which are known as MotA, MotB, FliG, FliF, etc. etc.” then, per that definition, it would seem that the flagellum is older than the T3SS. In other words – and I think this is the main point I am trying to make with regards to the age of the flagellum and T3SS – the actual protein FliF is older than its homologous counterpart YscJ. FlhA is older than YscV, FliP is older than YscR, etc. The implication of this, of course, is that for many of the flagellar proteins you have no homologous counterparts that could have served as precursor proteins in the distant past.

Again, you are not thinking phylogenetically. If the flagellum and T3SS are sister groups, then we have evidence that the common ancestor preceded both systems, and had all of the parts which the two systems share (which are all of the core parts of the secretion system, so probably we would call that ancestor a T3SS if we saw it). The relative ages of the flagellum crown group and the T3SS crown group are irrelevant, if the two groups are sister groups. NickMatzke_UD

This — as the highlights show — clearly documents a process of thought that is building on the past and moving towards a new frame, what we now call Intelligent Design. On the strength of this and its wider context, I can see the terminology in Pandas and its evolution against the backdrop of the conceptual development. Once I do that, I see that the sort of jaundiced, well-poisoning approach taken by Matzke and ilk is unwarranted and unfair.

Your very quotes of Thaxton et al.'s "Mystery of Life's Origin" explicitly endorse "special creation" and "intelligent Creator" -- the very language used by Paley himself! How can this not be considered creationism? How can Pandas be creationism, a position even Thomas so clearly acknowledges, and an earlier book on the same topic by the same authors, who at the time in the mid-1980s were explicitly defending creationism in various publications, not be creationism? MLO began as a book project at *Probe Ministries*, for goodness' sake. Have a look at what Thaxton and Bradley were doing in the early 1980s, just as they were starting the MLO project: http://www.icr.org/article/creation-science-korea/ NickMatzke_UD

Dr Cudworth: It is sad that you too have had to turn aside to answer a willful misrepresentation based distraction from the main point of the thread. But, you needed to set a point on record. And, while I think Pandas is more in the lines of an emergent work at the time when modern design theory [so far as life origins issues are concerned -- cosmological ID is significantly older . . . ] was in gestation, and point to the ways that "creator" was used in TMLO as material context, I can understand your own view. I think something more needs to be said; for, this is all about a new, evolutionary materialist magisterium dressed in the holy lab coat imposing their ideological will due to disproportionate cultural power. (And, I should note that for me, once I saw the sort of mafioso implied threat made against my family, I have had to take a far more stringent view of the sort of behaviour you very properly censured above.) Let us never forget what Lewontin had to say, in that infamous NYRB article in January 1997:

To Sagan, as to all but a few other scientists, it is self-evident [[actually, science and its knowledge claims are plainly not immediately and necessarily true on pain of absurdity, to one who understands them; this is another logical error, begging the question , confused for real self-evidence; whereby a claim shows itself not just true but true on pain of patent absurdity if one tries to deny it . . ] that the practices of science provide the surest method of putting us in contact with physical reality, and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test [[i.e. an assertion that tellingly reveals a hostile mindset, not a warranted claim] . . . . It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes [[another major begging of the question . . . ] to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. Moreover, that materialism is absolute [[i.e. here we see the fallacious, indoctrinated, ideological, closed mind . . . ], for we cannot allow a Divine Foot in the door . . . [Fuller excerpt and discussion here. (If you want to complain that the onward remarks JUSTIFY such a priori censorship and turn this into an out of context quote, kindly read there, and then reflect on how your own side has so willfully and consistently distorted those who have thought differently, i.e reflect kindly on the double-standard tactics implicit in such.)]

We could add here citations from the US NAS and NSTA -- read onwards at the linked -- to show that this is indeed dominant among such elite circles. And yet, it is a patent betrayal of the sacred charge of science, that -- however provisional and limited its methods and degree of warrant possible on inductive reasoning -- it should always prize and seek the truth about our world. Materialist ideology in a lab coat is a betrayal of the lab coat. I therefore find it utterly hypocritical for those who live in a materialist glass house, to be casting stones at those who are indeed trying seriously -- however imperfectly -- to genuinely discover what science can teach us about origins based on tested, empirically reliable signs. Philip Johnson's rebuke to such imposers of a priori materialist ideology, in First Things, later on in 1997, is apt:

For scientific materialists the materialism comes first; the science comes thereafter. [[Emphasis original] We might more accurately term them "materialists employing science." And if materialism is true, then some materialistic theory of evolution has to be true simply as a matter of logical deduction, regardless of the evidence. That theory will necessarily be at least roughly like neo-Darwinism, in that it will have to involve some combination of random changes and law-like processes capable of producing complicated organisms that (in Dawkins’ words) "give the appearance of having been designed for a purpose." . . . . The debate about creation and evolution is not deadlocked . . . Biblical literalism is not the issue. The issue is whether materialism and rationality are the same thing. Darwinism is based on an a priori commitment to materialism, not on a philosophically neutral assessment of the evidence. Separate the philosophy from the science, and the proud tower collapses. [[Emphasis added.] [[The Unraveling of Scientific Materialism, First Things, 77 (Nov. 1997), pp. 22 – 25.]

Now, can we return to the focal topic for this thread? I would indeed like to find out the actual balance on the merits on the subject of being actually current -- per participating actively in current professional discussions -- on technical evolutionary biology issues. GEM of TKI kairosfocus

Nick Matzke: “(a) that by itself provides no evidence the T3SS *descends* from the flagellum, which was the original contention.” Actually, my original contention was that “I am convinced that the T3SS is almost certainly younger than the flagellum,” irrespective of the contentions of other individuals debating here. “Also, the ‘age to the last common ancestor of (currently living, sampled) flagella’ is not going to be the same as the ‘age to the first thing that we would describe as a flagellum.’ Ditto for the T3SS.” Well, if we define the flagellum as something along the lines of “a motility organelle composed of ~21 proteins (at minimum) which are known as MotA, MotB, FliG, FliF, etc. etc.” then, per that definition, it would seem that the flagellum is older than the T3SS. In other words – and I think this is the main point I am trying to make with regards to the age of the flagellum and T3SS – the actual protein FliF is older than its homologous counterpart YscJ. FlhA is older than YscV, FliP is older than YscR, etc. The implication of this, of course, is that for many of the flagellar proteins you have no homologous counterparts that could have served as precursor proteins in the distant past. LivingstoneMorford

And as Mike Gene correctly notes in "The Design Matrix" Intelligent Design can trace its roots back to Aristotle, Plato, Socrates & Diogenes- the teleologists vs. the non-teleologists- namely Democritus, Leucippus of Elea, and Epicurus of Samos- Geez Nick do a little research. Joseph

Nick Matzke:

That’s what ID was initially conceived as — basically a compromise where the young-earth creationists and old-earth creationists would stop arguing about the age of the earth and instead focus on bashing “Darwinism”. Young-earth creationism + old-earth creationism = still creationism.

I would say, and judging by Anthony Flew's change of mind, ID was conceived as an a-religious approach to the origins and evolution/ development questions. ID does not have anything to do with the Bible and all formal definitions of Creationism require the Bible as the sole authority. Nick Matzke:

Second, (a) the vast majority of ID guys constantly dispute macroevolution, on this blog and elsewhere; (b) disputing common ancestry is so scientifically ridiculous and in the face of so much scientific evidence that even being agnostic on macroevolution indicates massive problems with the scientific capacity of anyone who holds those positions

The premise still remains untestable Nick, therefor it is out of the realm of science. Heck you can't even produce positive evidence for genetic accidents accumulating in such a way as to give rise to new, useful and functional multi-part systems. Evo-devo hasn't shed any light on what makes an organism what it is. What I am saying Nick, is it is just good scientific sense to challenge the concept of universal common ancestry. But then again you don't seem to care about that... Joseph

Elizabeth: I agree that Darwinists should stop calling ID proponents creationists, and that ID proponents should stop calling chemical origin of life theories Darwinist. But Matzke and Co. will never stop calling ID "creationist," because their interest is not in representing ID proponents as they wish to be understood, but in slanting the public image of ID so that it appears anti-scientific, anti-intellectual, connected with backward religion, etc. So take it up with Nick. Thomas Cudworth

Elizabeth: 1. Since you and Nick don't seem to understand a point that is obvious to all ID people and to all impartial observers, let me state it in large letters: OF PANDAS AND PEOPLE WAS NOT AN ID BOOK. IT WAS A CREATIONIST BOOK. IT HAS NO STATUS, ABSOLUTELY NONE, AMONG SERIOUS ID THEORISTS. In case that is not clear enough, I will elaborate. Yes, Behe endorsed *parts of* that book -- mainly the parts that he wrote. He showed discomfort with other parts of it, as the Dover Trial testimony plainly shows. Nick Matzke knows this, but conceals it from the public, because he wants to paint Behe as a creationist. This is part of what I mean by an unconcern with the truth. Nick is quite willing to lead people to believe what he knows not to be true, i.e., that Behe is a creationist. Behe is in fact an unapologetic evolutionist. Yes, the same publisher later *radically* revised Of Pandas and People (to the point where it was a in reality a new book), and the new book is not creationist in any sense of the word. Not one argument, not one sub-argument, depends on a prior assumption of the truth of creationism. If you don't know that, you haven't read the book. (I have.) And if you (and/or Nick) haven't read the book, you have no business talking about it. In sum: it doesn't matter if Of Pandas and People was the most blatant piece of creationism ever written. Its flaws, whatever they may be, have no bearing on what ID proponents contest for today. Anyone who raises *Of Pandas and People* is not concerned with the truth of ID, but is just trying to score debating points. 2. You may have great expertise in science (though I don't know that), but clearly you have no training in logic. I said that Nick's comment was puerile. It was. You protested that ID people, too, have made puerile comments. That is irrelevant to my charge against Nick. It like arguing that it's OK for a student to cheat on an exam if other students have cheated. The point is that Nick, after five years or more in this business, still hasn't learned to argue like a grown-up. This constitutes a case of arrested intellectual development. Other cases of this arrested development include Abbie Smith, P. Z. Myers, Larry Moran, and Jeffrey Shallit, all of whom typically argue like know-it-all teen-agers rather than earnest, dignified researchers and teachers. 3. "We are all concerned with the truth". For you, that may be a correct statement. For certain others, it is definitely false. Not all pro-Darwinists and anti-ID people are concerned with the truth, either about ID or about evolution, at all times. Many of them are animated by a desire to believe that there is no God; this causes them to wish to block any inference of a designer, because if a designer exists, that designer might be God. That is, many pro-Darwinist ID critics are motivated by an a priori commitment to atheism and all that follows from it (materialism, etc.). And this is plain from the way they argue. They do not politely rebut; they rage. They sneer. They frequently openly attack not merely ID arguments, but religion itself, the notion of objective morality itself, and so on. They have tipped their hand. They are not neutral. Others are determined to defend classic neo-Darwinism out of professional ego. If you have committed yourself to a theory, and had ridiculed all challenges to that theory, and slowly the evidence for the theory erodes, and the evidence for the challenger (e.g., Margulis's view, or self-organizational views) starts to look better, the pure scientist would simply abandon his old theory and embrace the new. But scientists are human, with egos, and they often stick to their guns, and even resort to underhanded means to try to stangle the new truths in their crib. This can be done in all kinds of ways, e.g., through hiring new faculty who support the old view rather than the new one, by denying tenure and grants to those who support the new view, etc. If you think that scientists never engage in such activities, if you think they are all pure seekers of knowledge who have transcended egoistic motivations, you are completely naive about what goes on behind the scenes in a modern university. There is further evidence against your claim. Someone who is totally open to truth argues in this way: "I grant you point A, but I still disagree with B" "Good point! I never thought of that. I can't think of a good rebuttal today, but give me a couple of weeks to mull it over, maybe do some research..." "I admit you are right that the precision of evolutionary models is not even close to the precision of models in chemistry and physics, though I still think evolutionary modelling is reasonable because..." "I admit that many on my side loudly proclaimed for an overwhelming preponderance of junk DNA, and I admit that the Darwinian side greatly erred in championing that, and I admit that design people were less hasty and more prudent on that point" Etc. Elizabeth, have you ever heard Nick Matzke or Larry Moran or P. Z. Myers argue in the above way against an ID proponent? No, that's not the way the culture-war Darwinists argue, Elizabeth, and if you are awake, with your eyes open, you know this. They *never* retract a point. They *never* grant that an ID theorist has a good point. All ID theorists are "IDiots", bad scientists, lack peer-reviewed publications, etc. Read the book reviews of Behe. I've been in the academic game a long time, likely longer than most readers posting here, and I know what book reviews written by honest academics look like. They engage in intellectual conversation with the spirit of the book. They mention not only bad points but also good points of the book they are reviewing. They don't motive-monger. They don't utter ad hominem arguments. Yet all the reviews of Behe's books by Darwinsts read like this: "Behe is wrong on Page 1. He's wrong on Page 2. He's wrong on Page 3. He's a creationist. He's wrong on Page 4. He's wrong on Page 5. Even a first-year biology student wouldn't have made so stupid an error. The Discovey Institute plans a secret theocracy. He's wrong on Page 6..." Repeat as desired. These are not honest academic reviews by scientists open to learning anything from Behe. These are diatribes written by people who decided Behe was wrong before they opened the front cover. (And on Amazon, we've *literally* had book reviews trashing ID books where the reviewer hasn't opened the cover.) And when ID proponents ask not for ID in the schools, but only for criticism of Darwinian mechanisms in the schools -- and not criticism based on religion, but based on *peer-reviewed scientific literature*, the NCSE uses all its resources, financial and rhetorical, to stop this. Those aren't the actions of an organization devoted to truth. An organization devoted to truth would say: "If there are criticisms of Darwinism in the scientific literature, then by all means let these criticisms be taught to high school biology students." But Eugenie doesn't want any doubts about Darwin in the high schools. That could give comfort to creationists, and we can't have that, can we? Even if the criticisms of Darwin are legitimate. So, Elizabeth, many ID critics and Darwin-defenders are governed by prejudice, metaphysical prejudice, professional prejudice, and prejudices springing from tactical needs, and that prejudice does affect the direction and quality of their science. It blinds them to certain possibilities, and it causes them to argue with gross unfairness, dishonesty and violence against other possibilities. So Elizabeth, maybe you are animated by a pure concern for the truth. But don't try to tell us that this is true of all the people you are defending. We all have the scars here to show otherwise. I am not of course saying that there are no evolutionary biologists who are concerned with the truth. I expect that many are. But they are not the ones who savage ID people daily; they are not the ones trying to control the school system so that it teaches exclusively neo-Darwinism. We ID supporters have no problem with evolutionary biology as such. We have objections to neo-Darwinian dogmatism, especially when it is accompanied by lies, insults, and deliberate misrepresentations. And many of the people I have named above have willfully perpetrated or at least condoned such lies, insults, and misrepresentations. These are not people who are concerned with the truth. Even if you are. Thomas Cudworth

Flannery: very well said. kairosfocus

PS: I see some further loaded conspiracy theorist speculation just above. I think that Dr Matzke should be called upon to answer to the fact that the foundational technical book for ID -- Thaxton et al's TMLO -- was a work as just clipped from in its epilogue, one that focussed its main effort on an analysis of the prebiotic environment, abiogenesiss theories and the issues connected to the thermodynamics of abiogensis. Indeed as the book bridged from surveying the relevant thermodynamics [ch 7] to address the origin of life in light of the entropy challenges implied [ch 8], its authors argued:

While the maintenance of living systems is easily rationalized in terms of thermodynamics, the origin of such living systems is quite another matter. Though the earth is open to energy flow from the sun, the means of converting this energy into the necessary work to build up living systems from simple precursors remains at present unspecified (see equation 7-17). The “evolution” from biomonomers of to fully functioning cells is the issue. Can one make the incredible jump in energy and organization from raw material and raw energy, apart from some means of directing the energy flow through the system? In Chapters 8 and 9 we will consider this question, limiting our discussion to two small but crucial steps in the proposed evolutionary scheme namely, the formation of protein and DNA from their precursors. It is widely agreed that both protein and DNA are essential for living systems and indispensable components of every living cell today.11 Yet they are only produced by living cells. Both types of molecules are much more energy and information rich than the biomonomers from which they form. Can one reasonably predict their occurrence given the necessary biomonomers and an energy source? Has this been verified experimentally? These questions will be considered . . .

I would think a discussion that pivots on entropy, Gibbs free energy, enthalpy and the like, and uses these to set up Chemical kinetics equilibrium calculations is not at all to be recognised in the above references to:

ID was initially conceived as — basically a compromise where the young-earth creationists and old-earth creationists would stop arguing about the age of the earth and instead focus on bashing “Darwinism”. Young-earth creationism + old-earth creationism = still creationism.

Frankly, Dr Matzke either knows better than this distortion, or he should (in the DUTIES OF CARE sense) know better. So -- pardon, but directness is called for at this point -- he is plainly being willfully misleading and distorted, in service to a rhetorical agenda long since addressed in the UD Weak Argument correctives top right this and every UD page, which he should read and take to heart, then amend his ways. Which takes us right back to the force of Plato's caution about the amorality of evolutionary materialism and its tendency to lead to ruthless amoral abusive facitonalism. We have been warned 2,350 years ago now. kairosfocus

To get back to the main point, I think the real lesson here is that for all the bombast and posturing by these "culture-war defenders" (an apt phrase), neo-Darwinism is far less crucial to biology than one might think. Steve Fuller updated Nicolas Rasmussen's 1994 study and found that of the 1,273,417 articles published from 1960 to 2005 and indexed in the two leading biology databases, only 12% contained "evolution" and its variants in the keywords and abstracts; "natural selection" was even scarcer at a paltry 0.4%. Fuller's conclusion seems ineluctable, "neo-Darwinism could be abandoned tomorrow, and most research programs in genetics - and other biological disciplines - would continue apace." (See his Science vs Religion?, 2007, pp. 131-132.) All truth claims aside, in actual practice Darwinism and its modern synthesis is simply not the indispensable paradigm in biology its greatest defenders would have us believe. "Although Darwin's theory is very often compared favorably to the great theories of mathematical physics on the grounds that evolution is as well established as gravity," David Berlinski wryly notes, "very few physicists have been heard observing that gravity is as well established as evolution. They know better and they are not stupid." Flannery

Nick you state: (b) Also, the “age to the last common ancestor of (currently living, sampled) flagella” is not going to be the same as the “age to the first thing that we would describe as a flagellum.” Ditto for the T3SS.' But yet you have ZERO evidence of any precursor: 'Since the flagellum is so well designed and beautifully constructed by an ordered assembly pathway, even I, who am not a creationist, get an awe-inspiring feeling from its 'divine' beauty.,, if the flagellum evolved from a primitive form, ...where are the remnants of its ancestor? Why don't we see any intermediate or simpler forms of flagella than what they are today? How was it possible that the flagella have evolved without leaving traces in history? - Shin-Ichi Aizawa - What Is Essential for Flagella Assembly? - 2009 - Pili and Flagella - Chpt. 6 i.e. Nick you assume the conclusion into the very question being asked!!! i.e. how did the flagellum arise?? By design or by chance??? seeing that you have no solid evidence to back up your allusions to ancient mystery precursors should not, if you trying to be honest, send up a huge red flag as to the point you wish to make??? The whole thing is begging the question Nick!!! Moreover Nick since you cannot make this 'trivial' transition from T3SS to Flagellum with any kind of empirical certainty, what in the world makes you think you can extrapolate the much more complex changes witnessed in the 'hypothesized' lineage of Homo from your non-existent empirical evidence for T3SS to Flagellum?? It simply does not follow for you to make such unfounded leaps!! ================ Getting Over the Code Delusion (Epigenetics) - Talbot - November 2010 - Excellent Article for explaining exactly why epigentics falsifies the neo-Darwinian paradigm of genetic reductionism: http://www.thenewatlantis.com/publications/getting-over-the-code-delusion Response to John Wise - October 2010 Excerpt: But there are solid empirical grounds for arguing that changes in DNA alone cannot produce new organs or body plans. A technique called "saturation mutagenesis"1,2 has been used to produce every possible developmental mutation in fruit flies (Drosophila melanogaster),3,4,5 roundworms (Caenorhabditis elegans),6,7 and zebrafish (Danio rerio),8,9,10 and the same technique is now being applied to mice (Mus musculus).11,12 None of the evidence from these and numerous other studies of developmental mutations supports the neo-Darwinian dogma that DNA mutations can lead to new organs or body plans--because none of the observed developmental mutations benefit the organism. http://www.evolutionnews.org/2010/10/response_to_john_wise038811.html bornagain77

Dr Cudworth: Pardon an aside, I do think that the loaded claims being advanced above need a measure of correction for record where they are being made, and so following up from my earlier remarks at 46 above. Do forgive me. I do think your main point is being well made, and the issue of a self-serving double standard on the part of the evolutionary materialism advocates needs to be faced on this front also. If necessary, I am amenable to set up a branch thread to further discuss these issues. So, to the aside, with a clip from TMLO, 1985, and I address Dr Liddle precisely because she has been reasonable: ++++++++++++++++ Dr Liddle: I do ask you to read the actual text of the rough drafts here [as previously linked], and note that in the 1980's the terminology we are now using did not exist as a standard. But, the line of thought that led to how we now speak and think was clearly being pioneered by that Cancer Survivor Chemist and his colleagues. I think you are making the error of seeing the word "creation" as a well-poisoning red flag, when in fact the usage of the terms and the context shows something sharply distinct from Biblical creationism and from traditional natural theology was coming about. And, the just made reference in TMLO shows plainly that this predates the 1987 decisions that were made so much of. In fact, we are looking at people who pioneered in developing the concepts and terms, and who as I noted earlier right from TMLO -- have you read e.g. the Epilogue in TMLO? -- were moving in a fresh direction:

Intelligent contrivances harness a portion of the energy flow for work in the human world. How some energy converting/coupling means might arise without intelligence in the inorganic world before life is difficult to say [p. 191] . . . . We cannot disagree that there is need for a n alternative to chemi- cal evolution. In recognition of the fact that Panspermia offers no theory of origins, it must implicitly assume chemical evolution on some other locale in the cosmos, where conditions are more favor-able than on earth. Many of the objections raised concerning terres-trial chemical evolution must, however, apply to other planets by the principle of uniformity. In any setting it comes down to the fact that natural forces acting alone must be capable of supplying the neces-sary configurational entropy work of building the protein, DNA, etc., and then assembling the cell. We know by experience that intelligent investigators can synthesize proteins and build genes. | We still have no evidence it can be done by unassisted abiotic means [193 -4] . . . . An adequate theory of origins requires a n information source capable of generating chemical complexity. Hoyle and Wickrama- | singhe argue that the evidence is overwhelming that intelligence provided the information and produced life . . . . Hoyle and Wickramasinghe deny the creator is the traditional supernatural God. They envision a creator within the total cosmos [196 - 7] . . . . In agreement with views of abiogenesis, and the foregoing view of Hoyle and Wickramasinghe, Special Creation by a Creator beyond the cosmos holds there was once a time in the past when matter was in a simple arrangement, inert and lifeless. Then at a later time matter was in the state of biological specificity sufficient for bearing and sustaining life. Special Creation (whether from within the cos-mos or beyond it) differs from abiogenesis in holding that the source which produced life was intelligent. Throughout history, many writers have attempted to describe the work of the Creator. What they all seem to hold in common is the idea that a n intelligent Creator informed inert* matter by shaping it a s a potter fashions clay. Some representations are quite anthropomor-phic, others less so. But there is considerable agreement that some-how a n active intellect produced life [200] . . . . It is doubtful that any would deny that an intelligent Creator could conceivably prepare earth with oxidizing conditions and create life. And, of course, the data discussed above are consistent (and compati-ble) with this view of Special Creation. What we would like to know,of course, is whether a n intelligent Creator did create life. The ques- tion, unfortunately, is beyond the power of science to answer. Another question which can be answered, however, is whether such a view as Special Creation is plausible [210] . . . . But does creation employ cause-effect and the principle of uniform- ity? Yes. In fact, it appeals to them a s the only way we can plausibly reconstruct the past. Consider, for example, the matter of accounting for the informational molecule, DNA. We have observational evi-dence in the present that intelligent investigators can (and do) build contrivances to channel energy down nonrandom chemical path-ways to bring about some complex chemical synthesis, even gene building. May not the principle of uniformity then be used in a broader frame of consideration to suggest that DNA had a n intelli-gent cause a t the beginning? Usually the answer given is no. But theoretically, at least, it would seem the answer should be yes in order to avoid the charge that the deck is stacked in favor of naturalism. We know that in numerous cases certain effects always have intelligent causes, such as dictionaries, sculptures, machines and paintings. We reason by analogy that similar effects also have intel-ligent causes. For example, after looking up to see "BUY FORD" spelled out in smoke across the sky we infer the presence of a skywrit-er even if we heard or saw no airplane. We would similarly conclude the presence of intelligent activity were we to come upon a n elephant-shaped topiary in a cedar forest. I n like manner a n intelligible communication via radio signal from some distant galaxy would be widely hailed a s evidence of a n intelligent source. Why then doesn't the message sequence on the DNA molecule also constitute prima facie evidence for a n intelligent source? After all, DNA information is not just analogous to a mes-| sage sequence such a s Morse code, it is such a message sequence.76 The so-called Shannon information laws apply equally to the genetic code and to the Morse code. True, our knowledge of intelli-gence has been restricted to biology-based advanced organisms, but it is currently argued by some that intelligence exists in complex non-biological computer circuitry. If our minds are capable of imagining intelligence freed from biology in this sense, then why not in the sense of an intelligent being before biological life existed?77 We believe that if this question is considered, it will be seen that most often it is answered in the negative simply because it is thought to be inappropriate to bring a Creator into science. The above discussion is not meant a s a scientific proof of a Crea-tor, but is merely a line of reasoning to show that Special Creation by a Creator beyond the cosmos is a plausible view of origin [as opposed to operations] science [211 - 12] . . . . When we are asked to consider "far out" or "strange" ideas such as Special Creation, a s were the authors just a few years ago, typically the response is exactly that mentioned by Bohm a s cited earlier. "His first reaction is often of violent disturbance." This was our reaction, too. However, as Bohm goes on to say, if one is willing to "stick with the inquiry rather than escape into anger or unjustified rejection of contrary ideas ... he becomes aware of the assumptive character of a great many previously unquestioned features of his own thinking." The process as Bohm described it can sometimes be painful (it was to one of the authors) but the quest for truth has never been easy, and has on more than a few occasions been known to make one unpopular. [213]

This -- as the highlights show -- clearly documents a process of thought that is building on the past and moving towards a new frame, what we now call Intelligent Design. On the strength of this and its wider context, I can see the terminology in Pandas and its evolution against the backdrop of the conceptual development. Once I do that, I see that the sort of jaundiced, well-poisoning approach taken by Matzke and ilk is unwarranted and unfair. Multiply that by Judge Jones' decision to exclude the publishers of Pandas from the trial, so the people who knew the most about the book used as the wedge to drive in the imposition of a priori materialism were no6t allowed to speak for themselves. This is an extreme form of the strawman tactic and it is a shameful moment in American jurisprudence. Surely, we can do better. GEM of TKI kairosfocus

Now let's stop discussing victory and start discussing truth. The truth is that you are misrepresenting the normal usage of "creationism" in American discourse. "Creationism" in common usage refers to a view, based on a literal or near-literal reading of Genesis, that the world and all living species in it were created directly by God, without any evolutionary process. To be sure, there are variants on creationism such as "old earth" creationism, which allow for limited microevolution within basic created kinds (cat kind, dog kind, horse kind, etc.) , but overall creationism denies the existence of macroevolution.

That's what ID was initially conceived as -- basically a compromise where the young-earth creationists and old-earth creationists would stop arguing about the age of the earth and instead focus on bashing "Darwinism". Young-earth creationism + old-earth creationism = still creationism.

This is not true of ID. ID *as such* takes *no position whatever* on macroevolution.

Even if this were completely true, it wouldn't reflect well on ID. It's a ridiculous position for a "scientific movement" to take, just as ridiculous as the previous idea of being agnostic about the age of the earth. What if the people who originated plate tectonics had proclaimed they were agnostic about the roundness of the Earth? Second, (a) the vast majority of ID guys constantly dispute macroevolution, on this blog and elsewhere; (b) disputing common ancestry is so scientifically ridiculous and in the face of so much scientific evidence that even being agnostic on macroevolution indicates massive problems with the scientific capacity of anyone who holds those positions, and (c) many, many ID publications, from Pandas on, put the question as design vs. common ancestry. Those that say ID is OK common ancestry only became somewhat common relatively recently, after the sting of the Kitzmiller trial and the revelations of the massive historical connections between ID and creationism, and nevertheless they are still a minority. At the very least, ID is dominated by creationists, majority old-earth creationists but with a young-earth creationist contingent, and a very small subset of random contrarians of various sorts, some of who are sometimes claimed as ID proponents even though at other times they have explicitly denied it (e.g. David Berlinski). NickMatzke_UD

And what do Creationists say- John Morris, the president of the Institute for Creation Research: === "The differences between Biblical creationism and the IDM should become clear. As an unashamedly Christian/creationist organization, ICR is concerned with the reputation of our God and desires to point all men back to Him. We are not in this work merely to do good science, although this is of great importance to us. We care that students and society are brainwashed away from a relationship with their Creator/Savior. While all creationists necessarily believe in intelligent design, not all ID proponents believe in God. ID is strictly a non-Christian movement, and while ICR values and supports their work, we cannot join them." === Hmmm... Strange how the people who understand Creation and ID the best know there is a difference and only the people with a warped agenda try to conflate the two.

I'll see your John Morris and raise you a Henry Morris. Yes, that Henry Morris, the grand old man himself, father of John, and of the ICR, and of the "scientific creationism" movement in general:

Our other hesitation to get on this bandwagon is their use of the same arguments and evidences we Biblical creationists have used for years, while simultaneously trying to distance themselves from us. Our adherence to Biblical literalism is ridiculed by evolutionists, and the ID advocates would be embarrassed to be tarred with the same brush. In fact, Dembski goes so far as to say belief in evolution itself is okay, as long as it's not naturalistic. He opens his chapter 23 with the following: Intelligent design does not require organisms to emerge suddenly or to be specially created from scratch by the intervention of a designing intelligence. . . . What separates intelligent design from naturalistic evolution is not whether organisms evolved or the extent to which they evolved but what was responsible for their evolution.2 It is not even necessary that the designing intelligence be God. Intelligent design is a strictly scientific theory devoid of religious commitments. Whereas the creator underlying scientific creationism conforms to a strict, literalist interpretation of the Bible, the designer underlying intelligent design need not even be a deity.3 Dembski himself may not believe such nonsense, but he is trying to build a very large tent, allowing anyone except pure materialists to take refuge there. These well-meaning folks did not really invent the idea of intelligent design, of course. Dembski often refers, for example, to the bacterial flagellum as a strong evidence for design (and indeed it is); but one of our ICR scientists (the late Dr. Dick Bliss) was using this example in his talks on creation a generation ago. And what about our monographs on the monarch butterfly, the bombardier beetle, and many other testimonies to divine design? Creationists have been documenting design for many years, going back to Paley's watchmaker and beyond. Dembski uses the term "specified complexity" as the main criterion for recognizing design. This has essentially the same meaning as "organized complexity," which is more meaningful and which I have often used myself. He refers to the Borel number (1 in 1050) as what he calls a "universal probability bound," below which chance is precluded. He himself calculates the total conceivable number of specified events throughout cosmic history to be 10150 with one chance out of that number as being the limit of chance. In a book4 written a quarter of a century ago, I had estimated this number to be 10110, and had also referred to the Borel number for comparison. His treatment did add the term "universal probability bound" to the rhetoric.

http://www.icr.org/article/design-revelation/ NickMatzke_UD

I don't have all the quotes handy, but here are some others from Pandas:

"This view proposes that only the long-held expectations of Darwinian theory cause us to refer to the inbetween areas as gaps. If this is so, the major different groups of living organisms do not have a common ancestry. Such a conclusion is more consistent with currently known fossil data than any of the evolutionary models." "Intelligent design means that various forms of life began abruptly through an intelligent agency with their distinctive features already intact: Fish with fins and scales, birds with feathers, beaks and wings." "Intelligent design means that various forms of life began abruptly." "Of Pandas and People is not intended to be a balanced treatment by itself. We have given a favorable case for intelligent design and raised reasonable doubt about natural descent." "The theories of intelligent design and natural descent both have an explanation for why living things share common structures." "Design proponents have a realistic and more cautious approach to the use of homologies. They regard organisms which show great structural differences, such as starfish and chimpanzees, as having no common ancestry." "This is precisely why a book that questions the Darwinian notion of common descent is so necessary."

...as quoted in the Kitzmiller case, when Behe tried to make the ID-ain't-about-common-ancestry point: http://www.talkorigins.org/faqs/dover/day11pm2.html#day11pm558 NickMatzke_UD

PS Well, I disagree with some of it, but it's still a good post :D Elizabeth Liddle

Yes, good post, junkdnaforlife :) Elizabeth Liddle

Liz:

Darwinists stop calling ID proponents Creationists. ID proponents stop calling abiogenesis theories Darwinist.

Absolutely, but you will have a hard time trying to sell that to your colleagues. But you bring up another important point. And that is that ID, from what I understand about it, encompasses origins and evolution. Darwinism draws a line between the two. ID is strongest when both are incorporated, and Darwinism's strength comes when they are separated. So you have two narratives that start at different points in time but overlap. junkdnaforlife

"Okay, thanks for your elaboration. Given that the common ancestor of extant flagella would be older than the common ancestor of extant T3SS, that would seem to prove the contention that the T3SS is younger than the flagellum, would it not?" Yeah, but: (a) that by itself provides no evidence the T3SS *descends* from the flagellum, which was the original contention. (b) Also, the "age to the last common ancestor of (currently living, sampled) flagella" is not going to be the same as the "age to the first thing that we would describe as a flagellum." Ditto for the T3SS. It's much like this situation: the age of the common ancestor of the *living* members of the genus Homo (Homo sapiens) is ~200,000 years. The age of the oldest fossil Homo, though, is something like 2.5 million years. The technical way of saying it is that molecular phylogenies provide the ages only of "crown groups", thus giving you only the minimum age of a feature of interest, not the actual age of the feature, which evolved somewhere on the stem group (although the actual age can be bracketed with certain phylogenetic techniques). NickMatzke_UD

But I wasn't being sarcastic! I just meant that I was no longer teasing (as I had been, mea culpa). My point was a serious one (hence the word): I'm not sure why IDists so hate it, or rather, given that they do (and I accept that they do) I'm not sure why the Pandas book was written with ID support (and authorship). It's not just that the word "creationism" and "intelligent design" seemed interchangeable to the authors, according to the released drafts, it's that the ideas ultimately described as ID ideas are much closer to creationist ideas (like that one about fish with scales and birds with feathers being created as is by an intelligent creator) than ID ideas. But I do understand that what you describe in your second paragraph must be intensely irritating, so I guess I should rephrase. It's not so much that I'm surprised that ID proponents mind being called creationist, is that I'm surprised that IDists endorsed the creationist ideas expressed in Pandas. And I'm glad you note that Darwin appealed to a Creator! Yes, indeed he did, and his theory did not account for abiogenesis. He did speculate about a "warm little pond" but made it very clear that it was speculation. So here's a treaty: Darwinists stop calling ID proponents Creationists. ID proponents stop calling abiogenesis theories Darwinist. Deal? Well, deal or no deal, it doesn't matter! It's much more interesting to discuss ID :) Cheers Lizzie Elizabeth Liddle

Liz: "Seriously: I don’t see why ID proponents get so hot under the collar about being allied with creationists." When someone writes "seriously" before they say something it generally means they are being sarcastic. A little condescending as well. The beloved strawmen of Neo-Darwinists is the creationist tag. I understand Liz you have to lawyer up like a good soldier but c'mon. You know it's a cheap tactic used to avoid being pressed on legitimate biological issues. Which you yourself are not afraid to engage in, so why use it? (Especially, when apparently, Darwin himself appealed to a Creator at one point.) Dialogue similar to this is common throughout the debate: How did the first self-replicating cell originate? Creationist! What biological mechanism can be attributed to the vast diversity of life in the Cambrian? Creationist! Has field observation of mut/selection show sufficient horsepower to explain the diversity of life on earth? Creationist! junkdnaforlife

Hi Thomas, A few random points (what do you expect?): You said:

I do not know how to assess a claim that a paper on polyadenylation has “a decided evolutionary flavor”.

I left a link on my blog so you could read the paper (or at least the title and abstract) for yourself. I should think that the evolutionary implications of a difference between animals and plants in so fundamental a process as polyadenylation would be obvious.

Is Dr. Hunt saying that his paper’s primary purpose was to discuss evolutionary mechanisms? And that it was presented for critical approval to scientists whose main work is to assess evolutionary mechanisms? If so, then obviously it counts as the sort of research that I was asking for.

Um, frankly, the scientists you are mentioning here can probably grouped into two classes - those who wouldn't know a poly(A) tail from a prehensile one, and those who would appreciate the fundamental evolutionary implications of a finding that a fundamental step in gene expression can vary over evolutionary time as we have come to learn. The first group has no business reviewing research papers on the subject, and the second would be most welcome to offer opinions.

As for Dr. Hunt’s claims that he knows more about this or that subject than Behe, Sternberg, Wells, etc., they are not relevant to our discussion here. I never claimed that ID proponents were better scientists than their critics.

But you are questioning whether ID critics are knowledgable enough, and if they are active researchers in the field, so that they can provide accurate and informed criticisms of ID advocates. I am saying that, in no uncertain terms, when it comes to Wells, Sternberg, alternative splicing, and junk DNA, I most certainly am in a position to point out their many errors.

For example, if I mentioned Dr. Hunt’s name to any of the Altenberg 16 – some of the world’s cutting-edge evolutionary theorists — would they have heard of him? Would Lynn Margulis recognize him as an evolutionary biologist?

Would Margulis even know what the term "polyadenylation" means? I am skeptical that she would. Which would make any further commentary from her about my statements and research on the evolution of the polyadenylation complex quite pointless. As for the Altenberg 16, any of the group who can Google or Pubmed would, I expect, be glad to correct your misconceptions about my research. I invite you to poke around my blog - I like to think that a lay person can pick up some of the basics there, and start to grasp the multifaceted nature of my research and interests. And please, ask questions. Arthur Hunt

Thomas Cudworth:

Elizabeth: I thank you for your comments, and for their dialogical tone (a pleasant change from the belligerent tone of most ID critics).

oops, I may have blotted my copybook since :) Please take it as a tease. I actually snickered at that animation when it first appeared. We all need to feed our inner child from time to time :)

In fact I can agree with much of what you have said. I will clarify my position on some points: You wrote: “you don’t have to be an original researcher in a domain to have the competence to spot flawed science. Sometimes you do, sometimes you don’t. I am not an evolutionary biologist at all, yet I consider myself competent to evaluate scientific arguments, on logic, if not on factual minutiae.” I agree. It is often possible for a non-specialist to spot difficulties in the theory favored by the specialists. This happened at the 1966 Wistar Conference, where some of the most high-powered, mathematically-trained nuclear physicists and engineers in the USA pointed out serious flaws in the mathematical models of the neo-Darwinian account of evolution. But the anti-ID people of whom I am speaking rarely grant the possibility of intelligent non-specialist criticism of Darwinian theory. When a non-biologist who is very well read in evolutionary theory points out problems in the sheer logic of a neo-Darwinian argument, he is routinely told that logic is not enough, and that he is “not competent” to criticize the views of a biologist unless he too is a biologist. I have even hear people say that Behe is “not competent” to talk about evolution because he is a biochemist and not a biologist! (But the same people never argue the same thing in relation to Larry Moran, also a biochemist – again the double standard.)

Yes, I'm with you there.

What I am arguing for is consistency. If we are going to play the “qualifications” game, then let’s play it consistently. I believe (am not sure, but believe) that most of the biologists at Biologos have never published a peer-reviewed paper in evolutionary biology in any secular journal. So if they are going to trot out the “peer-review” mantra, they had better be ready to apply it to themselves. Alternately, if they are going to say, no, such things don’t matter, all that matters is the quality of the argument, then fine; but then they have to withdraw a number of statements made about ID people not being formally competent, and start to address ID arguments.

Again, I agree, except that I'd say that having peer-review publications isn't much of a qualification, although it's a start. A very low bar though. Formal peer-review is just the first stage (well maybe the second, for multi-authored work) of the peer-review process, and many a paper that passes peer-review gets torn to ribbons at journal clubs around the world! What matters is good work - sound arguments well supported by good, rigorously collected, data.

Now, you make a distinction between having produced research papers in a field and being competent to criticize work in that field. I agree with you that the two are not identical. But they often overlap. Think of the specific context here. I read, e.g, on Biologos, columnists promoting a gene-centered vision of neo-Darwinian evolution which is essentially the view of Mayr and Dobhzhansky, a view that is now decades old. Then I read people whose specialty is evolutionary biology – the Altenberg group, for example – and many of them severely criticize the gene-centered model of evolution as inadequate to account for novel biological form. And where on Biologos I find column after column in praise of “randomness”, I read in Lynn Margulis, one of the most celebrated evolutionary biologists in the world, that random mutation is not at all the origin of novel biological form, and that she agrees with ID people — *on that point*. Now if the Biologos people were *active* in writing papers in evolutionary biology, going to evolutionary biology conferences, reading evolutionary biology journals, etc., they would be aware of the major shifts in evolutionary thinking which have in some quarters put traditional neo-Darwinian, population-genetics approaches on the firing line. They would at least provide footnotes or parenthetical references to indicate that they had read this material, even if they disagreed with it. The fact that they seem completely unaware of these developments – never mention them – raises the question whether they spend enough time in the field to have any competence of judgment. Would we trust someone who seemed completely unaware of the career of Stephen Hawking, and whose thought was doctrinaire Einsteinian, to make judgments in the field of cosmology?

Well, no, but I'm not sure I accept your premise. I'm not sure who "they" are - these dinosaurs who forget that natural selection operates at the level of the phenotype! Of course genes are vital, and of course "random" is a rather meaningless lay word. We know much more about the origins of genetic variance now, and once you know the mechanisms of variance "random" seems a much less good word to describe it. And yes, Dawkins, for one, seems very out of date. I wouldn't say the same for Myers. As for most people in the field - well, they have to keep up, or they end up writing poor papers that don't get published! Poor scholarship is a sound reason for rejecting a paper.So I'm not quite sure which windmill exactly you are tilting at, but it does seem to me that they are windmills! Margulis is a hero to many young scientists, and the discovery of hox genes and the whole science of "evo-devo" has revolutionised the field. So has computational biology, and, I'd say, non-linear modeling. I certainly find it a very exciting time to be in the life-sciences. I don't find support for ID in what I discover there :)

The same can be said of the exposition of evolution given in the writings of Ken Miller and Richard Dawkins. It is dated, formulaic neo-Darwinism of the crudest kind. There is no evidence that these authors have kept up on the specialist literature. Are they, then, competent to articulate evolutionary theory for 2011? Or would it be better if they remained silent, and let younger people, who keep up with the field, take on that job?

I agree with you to some extent about Dawkins. I enjoyed "Finding Darwin's God" though. But getting active researchers to write good books for lay people isn't that straightforward. Only a few people can do it. One I do recommend (and keep recommending!) is very short - an extended essay really: Denis Noble's "The Music of Life". If you don't know it, have a taster in this lecture: http://videolectures.net/eccs07_noble_psb/ It's a response to Dawkins' notion of The Selfish Gene. It's not actually about evolution at all, but it's highly relevant. I keep linking to it, because I think the ID proponents would love it! Not that Noble is an ID proponent, but if we are looking for truth - he's got a big chunk of it there, IMO.

Thus, my point is not so much that people have not published papers or attended conferences on evolutionary biology, as that they don’t keep up with evolutionary biology, yet pretend to expertise in it. The lack of publications and conference attendance is merely one measure of the degree to which these people have failed to keep up. It is not, I concede, an infallible measure. But it is not an irrelevant measure, either. Anyone really keen on understanding evolution, as opposed to merely defending it with culture-war fury, *will* keep up, out of natural scientific curiosity. And anyone who has voluntarily chosen *not* to keep up would perhaps do more good for the world by remaining silent than by blogging and expressing off-the-cuff opinions.

Well, maybe. But the great thing about the internet is that you can respond :) May the truth win. Elizabeth Liddle

Thomas Cudworth:

Nick Matzke (57): This comment: “OK then, it looks like I win … because … ” is puerile, and betrays a locker-room mentality that has no place in science or scholarship. Science and scholarship are not about “winning” but at getting at the truth. The problem with the lobby you belong to, Nick – the angry, vitriolic Darwin-defenders who hate the very idea of design and have dedicated their lives to making sure it never gets a foothold in science – is that it is not concerned with truth, but only with institutional and social victory.

I have to protest! Both "sides" are perfectly capable of puerility in this debate. The parody I alluded to in my post at 36 was, IIRC, an animation of several leading ID opponents, plus Judge Jones himself, um, farting. I believe the farts were provided by Dr Dembski. Dr Dr Dembski, in fact, so I guess at one PhD certificate per puerile incident, he still may have one to spare :) More seriously: you are wrong. We are all concerned with the truth. Nobody goes into science (or very few, and the only ones I know of are creationists) with a view to supporting an a priori view rather than finding out the truth. It would be so boring apart from anything else. Oddly enough, I'd say the prime motivator of scientists is curiosity. It's a most under-rated drive IMO.

Now let’s stop discussing victory and start discussing truth. The truth is that you are misrepresenting the normal usage of “creationism” in American discourse. “Creationism” in common usage refers to a view, based on a literal or near-literal reading of Genesis, that the world and all living species in it were created directly by God, without any evolutionary process. To be sure, there are variants on creationism such as “old earth” creationism, which allow for limited microevolution within basic created kinds (cat kind, dog kind, horse kind, etc.) , but overall creationism denies the existence of macroevolution. This is not true of ID. ID *as such* takes *no position whatever* on macroevolution. Many leading ID theorists or ID allies support macroevolution – Behe, Denton, Sternberg. Many others are open to it, and think it can be reconciled to ID insights. Dembski, for example, is not a macroevolutionist, nor is Meyer, but both have indicated that it is theoretically possible to view macroevolution through ID lenses. So ID is not creationism, and the deliberate manipulation of the truth by such phrases as “intelligent design creationism” (promoted by that culture-war organization you once worked for, the NCSE), is a conscious attempt to associate some very thoughtful scientific work with stereotyped images of dumb fundamentalists living in shacks in the Ozarks.

All this would be more persuasive if two Pandas drafts had not contained the following:

Creation means that the various forms of life began abruptly through the agency of an intelligent creator with their distinctive features already intact. Fish with fins and scales, birds with feathers, beaks, and wings, etc

Intelligent design means that various forms of life began abruptly through an intelligent agency, with their distinctive features already intact. Fish with fins and scales, birds with feathers, beaks, wings, etc

This description (and note the straight substitution of "Intelligent design" for "Creationism") is not a description of the ID you give here:

ID *as such* takes *no position whatever* on macroevolution. Many leading ID theorists or ID allies support macroevolution – Behe, Denton, Sternberg. Many others are open to it, and think it can be reconciled to ID insights. Dembski, for example, is not a macroevolutionist, nor is Meyer, but both have indicated that it is theoretically possible to view macroevolution through ID lenses.

On the contrary, it is a clear statement that ID, is, like creationism (as the earlier draft had it) is a theory that holds that various forms of life, including fish with scales and fish with feathers, were created by an intelligent agent, in other words that fish and birds do not have a common ancestor and scales were features of the original ancestral birds and fish. And yet Behe was an author, apparently.

The “creationism” charge should be eschewed by all participants in the ID/Darwinist debates.

Well, I'm glad to hear it. While I think ID arguments are fundamentally unsound, I do accept that they are less obviously unsound than most creationist arguments.

You should know all this, Nick, since you claim to be an expert on the ID movement, and claim to have studied its writings. But apparently either you do not read those writings carefully, or you suppress what you have read, for partisan purposes.

It sounds as though he read Of Pandas and People. If that gives a false impression of ID, then perhaps ID proponents ought to point that out.

In the first case, you are not competent to speak about ID; in the second case, your behavior is academically dishonorable, and you should turn in your Ph.D. (if you have completed it yet) as one unworthy to hold it.

Perhaps he'd better get a spare :) Seriously: I don't see why ID proponents get so hot under the collar about being allied with creationists. It's not even as though all creationists think alike. Indeed not even a single creationist seems to think much like he did in the argument he was previously making! (they do seem to be all "he"s in my experience). Todd Wood is a notable and honorable exception. And I have met many honorable IDists here - nonetheless they frequently disagree, on things like the nature of information, common descent, and what exactly CSI is. *ducks for cover* But I do agree: let's aim for the truth :) The truth will set [us all] free :) In peace, Lizzie Elizabeth Liddle

Elizabeth: I thank you for your comments, and for their dialogical tone (a pleasant change from the belligerent tone of most ID critics). In fact I can agree with much of what you have said. I will clarify my position on some points: You wrote: “you don’t have to be an original researcher in a domain to have the competence to spot flawed science. Sometimes you do, sometimes you don’t. I am not an evolutionary biologist at all, yet I consider myself competent to evaluate scientific arguments, on logic, if not on factual minutiae.” I agree. It is often possible for a non-specialist to spot difficulties in the theory favored by the specialists. This happened at the 1966 Wistar Conference, where some of the most high-powered, mathematically-trained nuclear physicists and engineers in the USA pointed out serious flaws in the mathematical models of the neo-Darwinian account of evolution. But the anti-ID people of whom I am speaking rarely grant the possibility of intelligent non-specialist criticism of Darwinian theory. When a non-biologist who is very well read in evolutionary theory points out problems in the sheer logic of a neo-Darwinian argument, he is routinely told that logic is not enough, and that he is “not competent” to criticize the views of a biologist unless he too is a biologist. I have even hear people say that Behe is “not competent” to talk about evolution because he is a biochemist and not a biologist! (But the same people never argue the same thing in relation to Larry Moran, also a biochemist – again the double standard.) What I am arguing for is consistency. If we are going to play the “qualifications” game, then let’s play it consistently. I believe (am not sure, but believe) that most of the biologists at Biologos have never published a peer-reviewed paper in evolutionary biology in any secular journal. So if they are going to trot out the “peer-review” mantra, they had better be ready to apply it to themselves. Alternately, if they are going to say, no, such things don’t matter, all that matters is the quality of the argument, then fine; but then they have to withdraw a number of statements made about ID people not being formally competent, and start to address ID arguments. Now, you make a distinction between having produced research papers in a field and being competent to criticize work in that field. I agree with you that the two are not identical. But they often overlap. Think of the specific context here. I read, e.g, on Biologos, columnists promoting a gene-centered vision of neo-Darwinian evolution which is essentially the view of Mayr and Dobhzhansky, a view that is now decades old. Then I read people whose specialty is evolutionary biology – the Altenberg group, for example – and many of them severely criticize the gene-centered model of evolution as inadequate to account for novel biological form. And where on Biologos I find column after column in praise of “randomness”, I read in Lynn Margulis, one of the most celebrated evolutionary biologists in the world, that random mutation is not at all the origin of novel biological form, and that she agrees with ID people -- *on that point*. Now if the Biologos people were *active* in writing papers in evolutionary biology, going to evolutionary biology conferences, reading evolutionary biology journals, etc., they would be aware of the major shifts in evolutionary thinking which have in some quarters put traditional neo-Darwinian, population-genetics approaches on the firing line. They would at least provide footnotes or parenthetical references to indicate that they had read this material, even if they disagreed with it. The fact that they seem completely unaware of these developments – never mention them – raises the question whether they spend enough time in the field to have any competence of judgment. Would we trust someone who seemed completely unaware of the career of Stephen Hawking, and whose thought was doctrinaire Einsteinian, to make judgments in the field of cosmology? The same can be said of the exposition of evolution given in the writings of Ken Miller and Richard Dawkins. It is dated, formulaic neo-Darwinism of the crudest kind. There is no evidence that these authors have kept up on the specialist literature. Are they, then, competent to articulate evolutionary theory for 2011? Or would it be better if they remained silent, and let younger people, who keep up with the field, take on that job? Thus, my point is not so much that people have not published papers or attended conferences on evolutionary biology, as that they don’t keep up with evolutionary biology, yet pretend to expertise in it. The lack of publications and conference attendance is merely one measure of the degree to which these people have failed to keep up. It is not, I concede, an infallible measure. But it is not an irrelevant measure, either. Anyone really keen on understanding evolution, as opposed to merely defending it with culture-war fury, *will* keep up, out of natural scientific curiosity. And anyone who has voluntarily chosen *not* to keep up would perhaps do more good for the world by remaining silent than by blogging and expressing off-the-cuff opinions. Thomas Cudworth

…under this phylogenetic hypothesis, the common ancestor of the extant flagella is older than the common ancestor of the extant T3SSs, and thus is more diverse in sequence, but they are sister groups nonetheless. Okay, thanks for your elaboration. Given that the common ancestor of extant flagella would be older than the common ancestor of extant T3SS, that would seem to prove the contention that the T3SS is younger than the flagellum, would it not? LivingstoneMorford

hmm, it took the spaces out of my text graphic so it looks silly, oops NickMatzke_UD

Incidentally Nick Matzke, in molecular evolution class we are taught that populations with less genetic diversity are generally younger than those populations with more genetic diversity. I don’t think you ever elaborated on the point you were trying to make with regards to monotreme mammals, placental mammals, and all that good stuff.

That logic is correct, but it only applies within interbreeding populations. Both mammalian species and the gene lineages of flagella/T3SS are separate populations. Really I need to draw this to make it clear, but I'll try with text. |------------ |--------|T3SS has lower diversity | |------------ -| | |------------------ |--|flag has higher diversity |------------------ ...under this phylogenetic hypothesis, the common ancestor of the extant flagella is older than the common ancestor of the extant T3SSs, and thus is more diverse in sequence, but they are sister groups nonetheless. (All of the above assumes something like a molecular clock to be valid; modern phylogenetic techniques don't require molecular clocks anymore, however.) You could replace "T3SS" with "monotremes" and "flag" with "marsupials+placentals" to get the mammal version of the analogy. (Although, this depends on the timing of the common ancestor of platypus + echidna, vs. placentals+marsupials, which I can't remember at the moment.) NickMatzke_UD

LivingstoneMorford and Nick, thank you both for your contributions: It seems Nick that LivingstoneMorford has made his point quite well in that both machines (T3SS and Flagellum) are exceedingly complex and that if any machine came from another machine, then the Flagellum first view is, by far, the most parsimonious explanation. Nick you seem to, grudgingly, accept LivingstoneMorford's analysis, as for you had two objections, both of which are curious. First you stated: 'Where was this amazing hidden information for a dozen or so additional novel proteins, and 10+ highly modified flagellar proteins, stored for all of those billions of years, I wonder?' Now this is very curious, for you seem to recognize that finding specific novel proteins is certainly no easy task for highly competent scientists, much less for neo-Darwinian processes, But the curious thing in all this, in you making this objection, is that it is you, yourself, that is trying to say it is impossible for the flagellum to 'devolve' into the T3SS, thus highlighting the much more absurd unlikelihood of the reverse position, of T3SS to flagellum, which you would prefer to hold. Thus Nick, not to sound mean, but thanks for making our argument for us! ,,,the second 'curious' thing you state is,,,; So Someone intelligently designed the flagellum so that it could later evolve into the T3SS and cause things like bubonic plague? What an mean guy! ,,, Now Nick this, as I'm sure you are well aware, is a theological objection, which has no bearing on the primary question at hand of whether design is present or not,,,, but just to call your attention to a recent, peer-reviewed, paper, It turns out that Darwin's book 'Origin of Species' was primarily a theological book; Charles Darwin, Theologian: Major New Article on Darwin's Use of Theology in the Origin of Species - May 2011 Excerpt: "In the Origin," Dilley writes, "Darwin used a specific theological view of God's relationship to natural laws in order to argue for evolution and against special creation." The Origin supplies abundant evidence of theology in action; http://www.evolutionnews.org/2011/05/charles_darwin_theologian_majo046391.html Now Nick if you want to argue the Theology instead of the science to make your case, as Darwin did, exactly what does this tell me of the actual empirical strength of your position??? It tells me that you have no real scientific evidence to support your position and thus resort to, excuse my frankness, 'extremely bad theology' to make your case!!! But again, if it is theology you want to argue,,, Is Your Bod Flawed by God? - Feb. 2010 Excerpt: Theodicy (the discipline in Theism of reconciling natural evil with a good God) might be a problem for 19th-century deism and simplistic natural theology, but not for Biblical theology. It was not a problem for Jesus Christ, who was certainly not oblivious to the blind, the deaf, the lepers and the lame around him. It was not a problem for Paul, who spoke of the whole creation groaning and travailing in pain till the coming redemption of all things (Romans 8). http://www.creationsafaris.com/crev201002.htm#20100214a etc.. etc.. ======================= Brooke Fraser- "C S Lewis Song" http://www.youtube.com/watch?v=GHpuTGGRCbY bornagain77

Typo. I meant: "The evolution of a novel outer membrane ring protein that is homologous..." Incidentally Nick Matzke, in molecular evolution class we are taught that populations with less genetic diversity are generally younger than those populations with more genetic diversity. I don't think you ever elaborated on the point you were trying to make with regards to monotreme mammals, placental mammals, and all that good stuff. LivingstoneMorford

"Well then, there goes Stephen Meyer’s book and 95%+ of the ID movement’s arguments and indignant protest against evolution." I believe that Stephen Meyer argues in his book that the first biological information could not have arisen from mindless processes, not that information cannot arise from the already-existing genomic information. LivingstoneMorford

Minimally, the T3SS (if it evolved from the flagellum) would need a novel outer membrane ring protein (homologous to outer membrane secretins), new pilus proteins, and new secreted effector proteins, sometimes including a complex that binds to the targeted eukaryotic cell IIRC. And all the interactions between those (and whatever proteins in the target cell are targetted). I guess I was referring just to the origin of the 10 proteins in T3SS that are homologous to flagellar proteins. The evolution of a novel outer ring membrane that is homologous to 'outer membrane secretins' could, again, evolve from those homologues -- in theory, unless the outer membrane ring protein happens to require more functional specificity than its homologues. As per the rest of the proteins that need to evolve, I would answer with the above argument. LivingstoneMorford

Nick Matzke: “According to the evidence posted in the thread, they are a *little bit* more tolerant than the flagellar proteins. They are still comparable to lots and lots of standard proteins, which as a general rule can (a) accept many random mutations and function, and (b) can exhibit 70+ sequence divergence and maintain the same basic structure and function, but (c) nevertheless have highly conserved functional regions and binding sites and which (d) ID advocates say are just the kind of high-information gene/protein sequence thing that could never, ever, no way, evolve.” Firstly, I think I’ve already sufficiently demonstrated exactly why it’s plausible for the T3SS proteins to evolve from their flagellar homologues, but it is less plausible for flagellar proteins to evolve from their T3SS counterparts. While a single truncating mutation would be sufficient for YscJ to evolve from FliF, a fairly large number of very specific mutations would have to occur for FliF to evolve from YscJ. Indeed, it certainly seems like there is no real obstacle to a flagellum à T3SS evolution, and just some truncating mutations would be needed for the T3SS proteins to evolve from their flagellar homologues (and, of course, some mutations would follow that would improve the overall T3SS structure, stabilizing it, etc.). That said, I will now point out where I think your argument is lacking in rigor: Do T3SS have highly conserved functional regions and binding sites? Yes, but here’s why it’s perfectly plausible for those features of T3SS to evolve, while it is not quite so plausible for those features to evolve in the flagellum. If the T3SS evolved from the flagellum, it would evolve with the binding sites that were in the flagellar proteins (unless a function evolved from the flagellum that did not require binding sites). In other words, the T3SS didn’t evolve any new binding sites – it just ‘inherited’ the binding sites that were present in the flagellum. The same argument is true, of course, for highly conserved functional regions et al. The conclusion? To my knowledge, no new binding sites or highly conserved functional regions would have to evolve in order for the T3SS to evolve from the flagellum. LivingstoneMorford

Nick Matzke (57): This comment: “OK then, it looks like I win … because … ” is puerile, and betrays a locker-room mentality that has no place in science or scholarship. Science and scholarship are not about “winning” but at getting at the truth. The problem with the lobby you belong to, Nick – the angry, vitriolic Darwin-defenders who hate the very idea of design and have dedicated their lives to making sure it never gets a foothold in science – is that it is not concerned with truth, but only with institutional and social victory. Now let’s stop discussing victory and start discussing truth. The truth is that you are misrepresenting the normal usage of “creationism” in American discourse. “Creationism” in common usage refers to a view, based on a literal or near-literal reading of Genesis, that the world and all living species in it were created directly by God, without any evolutionary process. To be sure, there are variants on creationism such as “old earth” creationism, which allow for limited microevolution within basic created kinds (cat kind, dog kind, horse kind, etc.) , but overall creationism denies the existence of macroevolution. This is not true of ID. ID *as such* takes *no position whatever* on macroevolution. Many leading ID theorists or ID allies support macroevolution – Behe, Denton, Sternberg. Many others are open to it, and think it can be reconciled to ID insights. Dembski, for example, is not a macroevolutionist, nor is Meyer, but both have indicated that it is theoretically possible to view macroevolution through ID lenses. So ID is not creationism, and the deliberate manipulation of the truth by such phrases as “intelligent design creationism” (promoted by that culture-war organization you once worked for, the NCSE), is a conscious attempt to associate some very thoughtful scientific work with stereotyped images of dumb fundamentalists living in shacks in the Ozarks. The “creationism” charge should be eschewed by all participants in the ID/Darwinist debates. You should know all this, Nick, since you claim to be an expert on the ID movement, and claim to have studied its writings. But apparently either you do not read those writings carefully, or you suppress what you have read, for partisan purposes. In the first case, you are not competent to speak about ID; in the second case, your behavior is academically dishonorable, and you should turn in your Ph.D. (if you have completed it yet) as one unworthy to hold it. Thomas Cudworth

Nick matzke:

if they were their arguments about information, no-new-genes, no-cooption etc. would seem even less credible than they do at present.

Why do you erect so many strawmen? ID does not say "no new genes". ID does not say "no-cooption"- as a matter of fact those only make sense in a design scenario. And that is why your arguments are not credible- you are tilting at windmills. Joseph

Nick Matzke:

Behe was an (unlisted) coauthor on Pandas, and a (officially listed on the front page) reviewer of the book. Why didn’t he fix the allegedly bad definition of ID back when he was “reviewing” the book?

The definition of ID in the GLOSSARY is OK. The quote-mine you are referring to pertains to the fossil record. Nick matzke:

Also, there are like 10 places where Pandas explicitly says that ID challenges common ancestry. Why didn’t Behe object to these?

How do you know he didn't? Also seeing that common ancestry is untestable everyone should challenge it. Besides that old book has been superseded by "The Design of Life". And taht says that ID does not argue against common ancestry. Joseph

Not if they were designed to evolve Nick matzke:

Where was this amazing hidden information for a dozen or so additional novel proteins, and 10+ highly modified flagellar proteins, stored for all of those billions of years, I wonder?

I take it you don't understand evolutionary algorithms very well. Nick matzke:

So Someone intelligently designed the flagellum so that it could later evolve into the T3SS and cause things like bubonic plague? What an mean guy!

Not necessarily. But do keep the strawmen coming... Joseph

"But anyway Dr Behe weighed in on that quote also:" Behe was an (unlisted) coauthor on Pandas, and a (officially listed on the front page) reviewer of the book. Why didn't he fix the allegedly bad definition of ID back when he was "reviewing" the book? Also, there are like 10 places where Pandas explicitly says that ID challenges common ancestry. Why didn't Behe object to these? All of this was brought up in the cross-examination of Behe, and Behe had no good answers. No wonder ID lost so big in Kitzmiller... NickMatzke_UD

Incidentally, I should like to know what new binding sites would have to evolve in order to get from flagellum to T3SS — I do not deny that new binding sites can evolve, I am just curious about this.

Minimally, the T3SS (if it evolved from the flagellum) would need a novel outer membrane ring protein (homologous to outer membrane secretins), new pilus proteins, and new secreted effector proteins, sometimes including a complex that binds to the targeted eukaryotic cell IIRC. And all the interactions between those (and whatever proteins in the target cell are targetted). It gets simpler if you assume that some of these proteins are homologous to flagellum proteins, but have changed so much that the evolutionary relationship is no longer statistically detectable, but (a) ID advocates are never, ever so generous, because (b) if they were their arguments about information, no-new-genes, no-cooption etc. would seem even less credible than they do at present. NickMatzke_UD

I thank Arthur Hunt for his reply, even though it came here only indirectly. I must first say that, while Arthur Hunt has been a critic of ID, he has not (to my knowledge) uttered the kind of below-the-belt criticisms that many others have. He has stuck to scientific discussion. For that, I salute him. I do not know how to assess a claim that a paper on polyadenylation has “a decided evolutionary flavor”. Probably half of the papers in biological journals make some direct or indirect reference to evolution – a phrase here, a sentence there, a footnote here, an allusion there. That does not make them papers in the field of evolutionary biology, any more than a passing reference to quantum theory in a paper on general relativity makes the general relativity paper a quantum theory paper, or the general relativity theorist an expert on quantum theory. Is Dr. Hunt saying that his paper’s primary purpose was to discuss evolutionary mechanisms? And that it was presented for critical approval to scientists whose main work is to assess evolutionary mechanisms? If so, then obviously it counts as the sort of research that I was asking for. Dr. Hunt mentions some of his work that is critical of ID. But papers that are critical of ID are not necessarily papers that are primarily concerned with evolutionary mechanisms. For example, one could criticize the notion of “information” in DNA without discussing evolution at all. As for Dr. Hunt’s claims that he knows more about this or that subject than Behe, Sternberg, Wells, etc., they are not relevant to our discussion here. I never claimed that ID proponents were better scientists than their critics. I said nothing about ID science at all. The discussion here is about whether Dr. Hunt would be recognized as a peer in the field of evolutionary biology by the professional evolutionary biologists, or whether he is a plant scientist who has unilaterally declared himself to be competent in evolutionary biology. For example, if I mentioned Dr. Hunt’s name to any of the Altenberg 16 – some of the world’s cutting-edge evolutionary theorists -- would they have heard of him? Would Lynn Margulis recognize him as an evolutionary biologist? “I’m a plant biologist, and from time to time I say something pertaining to evolution” doesn’t make one an evolutionary biologist, any more than “I’m an ancient Greek historian, and I’ve spotted a few interesting parallels between ancient Greek revolutions and the French Revolution”, makes one a historian of the French Revolution. What I am looking for are publications (oral or written) aimed at the professional body of evolutionary biologists – people like Coyne and Carroll and Orr and Margulis and Lima de Faria and Newman etc. -- and therefore submitting themselves to the professional judgment of such biologists. This means the papers must be primarily, not glancingly, about evolution. Their purpose must be to discuss evolutionary mechanisms, either to suggest such mechanisms, or to criticize already-proposed mechanisms on theoretical or empirical grounds. Has Dr. Hunt published any papers of this nature? If so, I will gladly retract his name from my list, with apologies for including him in a group to which he does not belong. Thomas Cudworth

This is not true of T3SS proteins: T3SS proteins seem to be capable of tolerating more amino acid substitutions than flagellar proteins.

According to the evidence posted in the thread, they are a *little bit* more tolerant than the flagellar proteins. They are still comparable to lots and lots of standard proteins, which as a general rule can (a) accept many random mutations and function, and (b) can exhibit 70+ sequence divergence and maintain the same basic structure and function, but (c) nevertheless have highly conserved functional regions and binding sites and which (d) ID advocates say are just the kind of high-information gene/protein sequence thing that could never, ever, no way, evolve.

Incidentally, I should like to know what new binding sites would have to evolve in order to get from flagellum to T3SS — I do not deny that new binding sites can evolve, I am just curious about this. And, of course, I accept the idea that new information can arise through mindless processes.

Well then, there goes Stephen Meyer's book and 95%+ of the ID movement's arguments and indignant protest against evolution. NickMatzke_UD

Not if they were designed to evolve

Where was this amazing hidden information for a dozen or so additional novel proteins, and 10+ highly modified flagellar proteins, stored for all of those billions of years, I wonder?

Not if they were designed to evolve, Nick- you know like Dawkins “weasel” program. Heck even Mike Gene’s front-loaded evolution covers that.

So Someone intelligently designed the flagellum so that it could later evolve into the T3SS and cause things like bubonic plague? What an mean guy! NickMatzke_UD

Nick Matzke:

But even the evolution of flagellum–>T3SS would require the evolution of a bunch of new proteins/new genes, and drastic modification of others, change of binding sites, change of function by cooption, etc. All of these are things that ID folks most vociferously deny — especially, the evolution of new information, which all of this would be. So again, ID loses if even this scenario is adopted.

Not if they were designed to evolve, Nick- you know like Dawkins "weasel" program. Heck even Mike Gene's front-loaded evolution covers that. Also what us ID folk say is that information is not reducible to matter and energy and neither matter nor energy can create information. Joseph

Typo. I meant: "A gene duplication followed by very specific amino acid substitutions would be needed to get from YscJ –> FliF, yet a simple deletion event would be needed to get from FliF –> YscJ." LivingstoneMorford

But even the evolution of flagellum–>T3SS would require the evolution of a bunch of new proteins/new genes, and drastic modification of others, change of binding sites, change of function by cooption, etc. All of these are things that ID folks most vociferously deny — especially, the evolution of new information, which all of this would be. Indeed? Consider the facts: The flagellar proteins are all longer than the T3SS proteins, with the exception of FliN (YscQ is the only T3SS protein that is longer than its flagellar homologue). Further consider that the flagellar proteins have a higher degree a "functional specificity" than their T3SS counterparts. By this I mean that, in order for the flagellar proteins to carry out their function, very specified amino acid residues need to be in the proteins. This is not true of T3SS proteins: T3SS proteins seem to be capable of tolerating more amino acid substitutions than flagellar proteins. The implication of this? Namely, very specific mutations would not be needed for the T3SS proteins to carry out their function. T3SS proteins are generally less stable than their flagellar counterparts, yet they can still carry out their function. Let's just take a look at one example of how it is very plausible for a T3SS protein to evolve from its flagellar homologue: FliF is ~550 amino acid residues in length, while its homologous counterpart (YscJ) is ~270 amino acid residues in length. Obviously, FliF has an extra ~200 residues because those residues are required for flagellar function, but those extra residues are NOT required for YscJ to function. A simple deletion event of those ~200 residues would result in the YscJ function. Yet, to get from YscJ to FliF would require very specific mutations, because those ~200 residues are rather specific and need to be specific in order to carry out the flagellar function. A gene duplication followed by very specific amino acid substitutions would be needed to get from YscJ --> FliF, yet a simple deletion event would be needed to get from YscJ --> FliF. So, not-very-specific mutations are needed to get from a flagellum to a T3SS. Incidentally, I should like to know what new binding sites would have to evolve in order to get from flagellum to T3SS -- I do not deny that new binding sites can evolve, I am just curious about this. And, of course, I accept the idea that new information can arise through mindless processes. In conclusion: while the evolution of a T3SS --> flagellum would require very specific mutations, the evolution of flagellum --> T3SS could be accomplished by just a few, not very specific mutations. LivingstoneMorford

For some reason, I don’t find that ironic at all. Firstly, in my view, the T3SS evolved from the flagellum via the stochastic processes of random mutation and natural selection. I.e., no intelligence was required for the origin of the T3SS if it evolved from the flagellum. Phylogenetic results then can be used to support the contention that the T3SS is younger than the flagellum without having to admit that the flagellum evolved via purely mindless processes.

But even the evolution of flagellum-->T3SS would require the evolution of a bunch of new proteins/new genes, and drastic modification of others, change of binding sites, change of function by cooption, etc. All of these are things that ID folks most vociferously deny -- especially, the evolution of new information, which all of this would be. So again, ID loses if even this scenario is adopted. NickMatzke_UD

Thomas Cudworth:

Elizabeth Liddle: You are being vague, and are evading the point.

I was making a general point!

Eugenie Scott, Ken Miller, etc. have all loudly shouted that ID is not good science, because if it were, ID people would have peer-reviewed publication in evolutionary biology. The Christian Darwinists at Biologos also loudly proclaim that ID is not good science regarding evolution. So the natural response is to ask these critics to supply some example of their own work in evolutionary theory. I am inviting them to do this.

Fair enough. But what I am saying is that you don't have to be an original researcher in a domain to have the competence to spot flawed science. Sometimes you do, sometimes you don't. I am not an evolutionary biologist at all, yet I consider myself competent to evaluate scientific arguments, on logic, if not on factual minutiae.

Some of our critics have actually done work in evolutionary biology: Coyne, for example. I already conceded that such people exist. But the bulk of our loudest and personally nastiest critics do not appear to have done a stitch of work in the field.

Well PZ Myers is a developmental neurobiologist, not an evolutionary biologist. But it's a good background for understanding evolutionary biology. Dawkins, I readily agree, is frequently simply out of date.

If I am wrong, if I have just missed the work, you may correct me by providing the names of conferences and journals in which the work appeared. Or they can.

Well, you can do a google scholar search, but PZ Myers doesn't seem to have published much recently. I'm not sure his job is primarily a research one. My point is that doesn't disqualify him from evaluating research - indeed, it may give him more time to do so, as he should if he is primarily involved in teaching.

Zs for “reading voraciously” and having a vast knowledge base, that certainly applies to Paul Nelson and William Dembski and Richard Sternberg and Michael Denton, but our critics simply dismiss the competence of those Ph.D.s to comment on evolutionary theory.

Well, I think we have apples and oranges here. On the one hand, ID critics point to the dearth of peer-reviewed work in ID as evidence of its lack persuasive ness. On the other hand, you point to the dearth of peer-reviewed work by specific critics of ID as evidence of their lack of competence to criticise. These two things are not the same :) There is no shortage of peer-reviewed work supporting evolutionary theory, and there is no shortage of people without peer-reviewed work criticising it. In other words we have two separable issues: One is: are people qualified to critique the science? And the other is: is the science any good? Peer-reviewed publications are offered as evidence in both cases, but the questions are different. The reason I think Dembski et al are wrong is not because they do not have peer-reviewed papers (which could, conceivably, be because their work is being deliberately suppressed) but because I think the work has serious errors. And the reason I think PZ Myers is probably qualified to critique it is because he generally makes what seems to me to be a persuasive case.

So again, there is a double standard. And that’s how dying theories hold onto power: by applying a double standard.

No, I don't think so. I do think that it's harder to get radical theories published than non-radical, but the quid pro quo is that if your radical theory is well-argued and supported, you get published in the highest impact journals. Novelty has to run a more taxing gauntlet than something run-of-the-mill, but the potential prize is, well, Nobel. So I don't accept the charge of double standard. PZ Myers and Dembski are equally entitled to critique the other's preferred theory, regardless of how much they have published. Whether they are competent can only be judged by how much competence they show. But whether they are right or not can be at least partly judged by whether, not they, but the theory they espoused, gets published. Yes, I'll give Dembski a temporary pass on that front because he has a harder row to hoe - maybe the first ID Nature paper is still to come. But only on that front - the reason that I think he is wrong, is not because I have a "double standard" but because, well, I think he is wrong. I don't think the science works. Elizabeth Liddle

Nick matzke:

Just that the founders and leaders of the ID movement are. Behe was a coauthor of Pandas, as Stephen Meyer. A host of other DI fellows were contributors or reviewers. Chunks of the book were hosted on the DI website for a decade or more. Dembski and Wells coauthored the 3rd edition.

What Dr Behe says: Intelligent Design is NOT Creationism (MAY 2000)

Scott refers to me as an intelligent design "creationist," even though I clearly write in my book Darwin's Black Box (which Scott cites) that I am not a creationist and have no reason to doubt common descent. In fact, my own views fit quite comfortably with the 40% of scientists that Scott acknowledges think "evolution occurred, but was guided by God."- Dr Michael Behe

Dr Behe has repeatedly confirmed he is OK with common ancestry. And he has repeatedly made it clear that ID is an argument against materialistic evolution (see below), ie necessity and chance. Then we have: What is Intelligent Design and What is it Challenging?- a short video featuring Stephen C. Meyer on Intelligent Design. He also makes it clear that ID is not anti-evolution. Next Dembski and Wells weigh in:

The theory of intelligent design (ID) neither requires nor excludes speciation- even speciation by Darwinian mechanisms. ID is sometimes confused with a static view of species, as though species were designed to be immutable. This is a conceptual possibility within ID, but it is not the only possibility. ID precludes neither significant variation within species nor the evolution of new species from earlier forms. Rather, it maintains that there are strict limits to the amount and quality of variations that material mechanisms such as natural selection and random genetic change can alone produce. At the same time, it holds that intelligence is fully capable of supplementing such mechanisms, interacting and influencing the material world, and thereby guiding it into certain physical states to the exclusion of others. To effect such guidance, intelligence must bring novel information to expression inside living forms. Exactly how this happens remains for now an open question, to be answered on the basis of scientific evidence. The point to note, however, is that intelligence can itself be a source of biological novelties that lead to macroevolutionary changes. In this way intelligent design is compatible with speciation. page 109 of "The Design of Life"

And that brings us to a true either-or. If the choice between common design and common ancestry is a false either-or, the choice between intelligent design and materialistic evolution is a true either-or. Materialistic evolution does not only embrace common ancestry; it also rejects any real design in the evolutionary process. Intelligent design, by contrast, contends that biological design is real and empirically detectable regardless of whether it occurs within an evolutionary process or in discrete independent stages. The verdict is not yet in, and proponents of intelligent design themselves hold differing views on the extent of the evolutionary interconnectedness of organisms, with some even accepting universal common ancestry (ie Darwin’s great tree of life). Common ancestry in combination with common design can explain the similar features that arise in biology. The real question is whether common ancestry apart from common design- in other words, materialistic evolution- can do so. The evidence of biology increasingly demonstrates that it cannot.- Ibid page 142

And from one more pro-ID book:

Many assume that if common ancestry is true, then the only viable scientific position is Darwinian evolution- in which all organisms are descended from a common ancestor via random mutation and blind selection. Such an assumption is incorrect- Intelligent Design is not necessarily incompatible with common ancestry.- page 217 of “Intelligent Design 101”

And what do Creationists say- John Morris, the president of the Institute for Creation Research:

"The differences between Biblical creationism and the IDM should become clear. As an unashamedly Christian/creationist organization, ICR is concerned with the reputation of our God and desires to point all men back to Him. We are not in this work merely to do good science, although this is of great importance to us. We care that students and society are brainwashed away from a relationship with their Creator/Savior. While all creationists necessarily believe in intelligent design, not all ID proponents believe in God. ID is strictly a non-Christian movement, and while ICR values and supports their work, we cannot join them."

Hmmm... Strange how the people who understand Creation and ID the best know there is a difference and only the people with a warped agenda try to conflate the two. Joseph

(a) this is new evidence, which doesn’t support the cut-n-paste contention made in this and many other UD threads that the matter was settled long ago by phylogenetic evidence... My point really isn't concerning when the issue was settled, my point is that, in my humble opinion, the evidence points in the direction of the idea that the T3SS is younger than the flagellum. The key issue isn’t the amount of divergence within the “flagellum group” and the “T3SS group”, the key issue is whether one or both of these isn’t a real “group”, because one includes the other group. There is more diversity in placental + marsupial mammals than there is in monotreme mammals, but that doesn’t prove monotremes nest within placentals+marsupials; phylogenetic evidence shows that they are sister groups. You're being just a touch vague here. Would you care to elaborate, particularly on this comment: "There is more diversity in placental + marsupial mammals than there is in monotreme mammals, but that doesn’t prove monotremes nest within placentals+marsupials." Are you saying that if one aligns, say, a protein of a placental animal and aligns that protein with a protein of a marsupial animal, that there will be greater genetic diversity (in general) than if one aligns a given protein belonging to monotreme mammals? The most ironic thing about this debate is that all the published work which ID guys cite in favor of “flagellum-first” rely explicitly on phylogenetics results, which only make sense if evolution is accepted. So to make these arguments at all they have to accept common ancestry over billions of years of evolution. Which, again, means they’ve lost the main debate. For some reason, I don't find that ironic at all. Firstly, in my view, the T3SS evolved from the flagellum via the stochastic processes of random mutation and natural selection. I.e., no intelligence was required for the origin of the T3SS if it evolved from the flagellum. Phylogenetic results then can be used to support the contention that the T3SS is younger than the flagellum without having to admit that the flagellum evolved via purely mindless processes. LivingstoneMorford

oops, link: http://aghunt.wordpress.com/2011/07/11/dust-up/ NickMatzke_UD

Art posted a response to the OP on his blog: ======== Dust-up It’s been awhile since I’ve done an ID post. Thomas Cudworth on UD goads me thusly:

From June 17 to June 21, 2011, at the University of Oklahoma (Norman) campus, the conference “Evolution 2011” was in session. It was co-sponsored by three scientific societies – The Society for the Study of Evolution, The Society of Systematic Biologists, and the American Society of Naturalists. It was billed by its promoters as “the premier annual international conference of evolutionary biologists on the planet.” … It is interesting to make a mental list of the Darwin-defenders who have been most active in the culture wars, whether by publishing popular books defending Darwin, by appearing as witnesses against school boards in court cases, by working for the NCSE, by running pro-Darwinian blog sites, or by attacking Darwin critics throughout cyberspace, and to see which of them either read papers or at least contributed to the research and writing of papers for this premier conference. … Among those who have not attacked religious belief, but have violently bashed ID and/or passionately upheld neo-Darwinian theory, Paul Gross (co-author of Creationism’s Trojan Horse) and plant scientist Arthur Hunt (who has debated ID people live and on the internet) were not listed as contributors to any of the papers. … The theme of my column is qualifications. The question is: are most of the Darwinian preachers in the culture-wars competent to discuss the latest developments in evolutionary biology? If they are not competent, shouldn’t the public know this? What I’m trying to do here is to give everyone a chance to say whether these people are or are not qualified. And I invite any of the named people — Falk, Venema, Moran, Miller, etc. — to write in here, listing their publications and conference papers in the field of evolutionary biology, and explaining why we should prefer their account of evolution to those of Darwin-critical specialists in evolutionary theory such as Lynn Margulis, Stuart Newman, Richard Sternberg, etc.

Well, Thomas, I’ll speak only for myself. It turns out that my first paper in the area of polyadenylation had a decided evolutionary flavor, and the implications of this finding weigh on my own research even today. Heck, I’ve done more actual wet-bench research on irreducibly complex systems than Mike Behe, who is, by all estimations, at the head of the ID biochemistry class. I’ve even gone so far as to directly measure the CSI for a specific protein-protein interaction, something no ID proponent anywhere has ever done. All in all, I think I can make a good case that I’m qualified to tell people like Richard Sternberg and Jonathan Wells that their ideas about RNA processing, alternative splicing, and junk DNA are bogus. So I’ve got a couple of questions. First, you may recall that the 2010 meeting of the RNA Society was held in Seattle, Washington. I was there, and I figured that the Discovery Institute would send a cohort to dazzle all those RNA scientists with the latest and greatest ID research that demolishes all manner of RNA science – from the studies on RNA aptamers and ribozymes that show how little CSI there actually is in living things, to all that work on splicing and introns that Wells and Sternberg have shown to be wrong, to that misleading research on ribosomes that looks to spell out a clear evolutionary history that marks the very beginning of life, to, um, well, you get the idea. That’s what I figured. But guess what – the DI couldn’t even scare up the intellectual curiosity to drive a few blocks and present a single, solitary poster on any ID research. What’s up with that, Thomas? I am hoping for more this August, when Wells and Sternberg are surely going to shock the Cold Spring Harbor Eukaryotic RNA Processing meeting with their definitive experimental proof that each and every nucleotide in each and every intron in the human genome has a clear and undeniable biochemical or evolutionary function. I was wondering if you could give the readers at UD a sort of sneak preview of their amazing presentation. What say ye, Thomas? Any possibility of this happening? One more thing – I would post this on UD, but your “moderation” is such that it wouldn’t actually be posted for anywhere from 48 to 480 hours. I apologize that you have to wander on over here to read my reply. ======== NickMatzke_UD

I am convinced that the T3SS is almost certainly younger than the flagellum. If one aligns the amino acid sequences of the flagellar proteins (that have homologous counterparts in the T3SS), and if one also aligns the amino acid sequences of the T3SS proteins, one finds that the T3SS protein amino acid sequences are much more conserved than the amino acid sequences of the flagellar proteins. There are two possible explanations for this: (1) The T3SS is younger than the flagellum, or (2) The T3SS proteins are under more functional constraints than flagellar proteins, and so the sequences in T3SS proteins cannot diverge as much. We may rule out option #2 in the light of both in vitro and in silico mutagenesis. For example, I performed an in silico alanine scan on flagellar proteins and their T3SS homologues using SNAPs and found that flagellar proteins are under more functional constraints than T3SS proteins. (E.g., ~39% of the positions in FliF result in a non-neutral mutation when an in silico alanine scan is performed, ~34% of the positions in YscJ result in a non-neutral mutation — YscJ is FliF’s T3SS homologue, for those of you who do not know).

Interesting. But (a) this is new evidence, which doesn't support the cut-n-paste contention made in this and many other UD threads that the matter was settled long ago by phylogenetic evidence (b) as is common amongst non-phylogeneticists, you are misinterpreting the conservation information. The key issue isn't the amount of divergence within the "flagellum group" and the "T3SS group", the key issue is whether one or both of these isn't a real "group", because one includes the other group. There is more diversity in placental + marsupial mammals than there is in monotreme mammals, but that doesn't prove monotremes nest within placentals+marsupials; phylogenetic evidence shows that they are sister groups. As far as the actual published phylogenetic results go on the flagellum question, they seem to indicate that the hypothesis that the T3SS and flagellum are sister groups is as supported (or more supported) than the hypothesis that the T3SS nests within the flagellum. As it's a very ancient event, it's hard to tell for sure, so the debate continues. Surely ID apologists should accurately convey the state of the scientific literature, and not pretend to their supporters that the literature says only one thing, the side the ID guys support? (c) The most ironic thing about this debate is that all the published work which ID guys cite in favor of "flagellum-first" rely explicitly on phylogenetics results, which only make sense if evolution is accepted. So to make these arguments at all they have to accept common ancestry over billions of years of evolution. Which, again, means they've lost the main debate. NickMatzke_UD

The Pandas book doesn’t prove what you claim it does. What it proves is that people who *are* creationists will sometimes adopt ID language in order to conceal the real basis of their argument.

OK then, it looks like I win...because...

It does not prove that ID itself is creationism.

Just that the founders and leaders of the ID movement are. Behe was a coauthor of Pandas, as Stephen Meyer. A host of other DI fellows were contributors or reviewers. Chunks of the book were hosted on the DI website for a decade or more. Dembski and Wells coauthored the 3rd edition. NickMatzke_UD

Elizabeth Liddle: You are being vague, and are evading the point. Eugenie Scott, Ken Miller, etc. have all loudly shouted that ID is not good science, because if it were, ID people would have peer-reviewed publication in evolutionary biology. The Christian Darwinists at Biologos also loudly proclaim that ID is not good science regarding evolution. So the natural response is to ask these critics to supply some example of their own work in evolutionary theory. I am inviting them to do this. Some of our critics have actually done work in evolutionary biology: Coyne, for example. I already conceded that such people exist. But the bulk of our loudest and personally nastiest critics do not appear to have done a stitch of work in the field. If I am wrong, if I have just missed the work, you may correct me by providing the names of conferences and journals in which the work appeared. Or they can. As for "reading voraciously" and having a vast knowledge base, that certainly applies to Paul Nelson and William Dembski and Richard Sternberg and Michael Denton, but our critics simply dismiss the competence of those Ph.D.s to comment on evolutionary theory. So again, there is a double standard. And that's how dying theories hold onto power: by applying a double standard. Thomas Cudworth

Thomas Cudworth: I'd say that being an active researcher in your field qualifies you to discuss recent developments in that field including your own (obviously you need to be aware of what is going on in your area), but not being an active researcher doesn't disqualify you. What qualifies you is having the knowledge base (theoretical and practical) to evaluate new papers, and the time to read them. And you can't necessarily tell that from someone's recent qualifications. Some of the people whose evaluations I most admire no longer do active research but have vast experience and read voraciously. In fact, being involved actively in research in some ways is a bar to reading lots of other stuff! It takes a heck of a lot of time. Elizabeth Liddle

just a note to thanks to LivingstoneMorford for his input. It has been informative. bornagain77

What I’m trying to do here is to give everyone a chance to say whether these people are or are not qualified.

I'm not qualified to say whether they are qualified. I don't think their failure to present papers at conferences is a fair way to judge their qualifications. Their failure to publish peer reviewed papers just shows what they are doing is not science, it does not speak to their qualifications. Mung

Pardon me for going after a red herring. kairosfocus

To all Commenters: I would greatly appreciate it if people would respond to the issues raised in my column, and not get off into side arguments about the literary history of the Pandas book or into arguments about the mechanics of evolution. The theme of my column is qualifications. The question is: are most of the Darwinian preachers in the culture-wars competent to discuss the latest developments in evolutionary biology? If they are not competent, shouldn't the public know this? What I'm trying to do here is to give everyone a chance to say whether these people are or are not qualified. And I invite any of the named people -- Falk, Venema, Moran, Miller, etc. -- to write in here, listing their publications and conference papers in the field of evolutionary biology, and explaining why we should prefer their account of evolution to those of Darwin-critical specialists in evolutionary theory such as Lynn Margulis, Stuart Newman, Richard Sternberg, etc. Thomas Cudworth

F/N: And BTW on their fossil forms comment, I think that while their expression is reflective of a first effort not fully thought through, we should also note from Gould:

. . . long term stasis following geologically abrupt origin of most fossil morphospecies, has always been recognized by professional paleontologists. [[The Structure of Evolutionary Theory (2002), p. 752.] . . . . The great majority of species do not show any appreciable evolutionary change at all. These species appear in the section [[first occurrence] without obvious ancestors in the underlying beds, are stable once established and disappear higher up without leaving any descendants." [[p. 753.] . . . . proclamations for the supposed ‘truth’ of gradualism - asserted against every working paleontologist’s knowledge of its rarity - emerged largely from such a restriction of attention to exceedingly rare cases under the false belief that they alone provided a record of evolution at all! The falsification of most ‘textbook classics’ upon restudy only accentuates the fallacy of the ‘case study’ method and its root in prior expectation rather than objective reading of the fossil record. [[p. 773.]

And in case you think this is a matter of artful snipping -- the usual snide dismissal of inconvenient admissions by Darwinists and fellow travellers -- I suggest you read the further discussion of that here in light of the relevant NYRB review by Flannery. kairosfocus

Response to Nick Matzke's comment: "...even Mike Gene has admitted evidence has come in that has supported the evolutionary model, particularly further evidence of homology between the flagellum, T3SS, and the F1Fo-ATPase." A Darwinian mechanism for the origin of the flagellum is not the only explanation for homology. Just take a look at the sequences designed by Fisher et al. If one aligns those designed, un-evolved sequences, one finds that they are homologous to each other. In short, designed sequences can also result in homology. In light of this, sequence homology can hardly be explained only by Darwinian mechanisms. References: Fisher et al. "De Novo Designed Proteins from a Library of Artificial Sequences Function in Escherichia Coli and Enable Cell Growth." LivingstoneMorford

Hello Dr Liddle, Do you have any idea when we can expect a reply from you in our ongoing conversation. The one regarding a simulation to falsify ID - the very thing that Matske and Company avoid doing. Upright BiPed

Nick, Years of culture-war politics, and your well-organized indifference to evidence, has wilted your ability to comprehend the central key fact of the debate. Let me help you out. It doesn't matter what was, or was not, included in an attempted school book. It doesn't matter who the proponents of ID are, or what things they may have said at this time or that. It doesn't even matter that there is a politically powerful lobby against ID. Those things may be interesting and important for their own reasons, but they do not change the only thing that really matters - and that is the evidence itself. The core evidence of design boils down to a central claim regarding the explanatory power of two distinct paradigms: Chance contingency + natural law -versus- choice contingency + natural law. At that critical level of the evidence, you have never published a single paper of experimental results which confirms your ideological assumptions. Nor has anone else. Upright BiPed

Onlookers: Above, Mr Matzke showed just why he and ilk are utterly unreliable and jaundiced on this matter. Had he bothered to actually read honestly to get a true and fair view, he would have seen that -- just as I noted -- even when the term "creationist" was present in the rough draft text, Thaxton et al were definitely divergent from the way that creationists argue. Notice -- and BTW I note how, consistently, this same point is brushed aside when I make it myself -- that in Pandas, the authors are clearly distinguishing their view from the Natural Theology of Paley and from the inference from signs of design of life forms to a specifically supernatural creator in light of religious tradition that is typical of creationist thought. In short, they clearly are not playing at stealth religious apologetics. In fact, just as in the prior -- 1985 -- technical work TMLO, they explicitly draw the point out that an inference to design does not as a scientific inference warrant a conclusion to a designer within or beyond the cosmos. That appears in TMLO, 1985. It appears in the rough draft for Pandas, and it appears and is sustained in the published editions. How much more specific, consistent and explicit can you get than that? As I often have put it, a molecular nanotech lab several generations beyond Venter would be a SUFFICIENT cause for what we see in life forms on earth. 20 years before Venter, Thaxton et al were making essentially the same point. Namely, the science warrants an inference to design, on say the FSCI in DNA [cf discussions here on for a quick look at why], but that is not in itself a warrant for inferring to a particular designer; whether within or beyond the cosmos. Now, I do believe there is a side of ID that does warrant an inference to a designer beyond our observed cosmos, the cosmological inference on fine tuning that suits our cosmos to support C-chemistry cell based life. But that is not what Pandas was about and it was not what TMLO was about. So, clearly, Matzke et al were more concerned to set up a handy creationist strawman than to present a true and fair view of Thaxton et al and their work across the 1980s. We should therefore weigh that credible fact soberly in evaluating any further thing that Matzke et al have to say. Indeed, this piece of strawman laced with ad hominem slander maintained by the NCSE et al for the better part of a decade in the teeth of repeated correction points straight back to the concerns about the sort of ruthless amoral factionalism triggered by the inherent amorality of evolutionary materialism that we have been warned against ever since Plato in The Laws Bk X, 2350 years ago. As a man whose family has just been held hostage by outing tactics and mafioso style threats of we know you, we know where you are and we know those you care for, from the same sort of ruthless amoral evolutionary materialist factionism, I must highlight this prolonged pattern of misbehaviour and call on us to make it very plain to such that enough is enough. Bydand GEM of TKI kairosfocus

So, given that option #2 is ruled out, it seems obvious to me that the T3SS is younger than the flagellum -- the T3SS proteins have not been around as long as the flagellar proteins and so they have not diverged as much. LivingstoneMorford

Response to Nick Matzke's comment: The research papers are split on the question, and the most recent phylogenetic research papers indicate the flagellum and the T3SS are sister groups about equally old, not that the flagellum is older. I am convinced that the T3SS is almost certainly younger than the flagellum. If one aligns the amino acid sequences of the flagellar proteins (that have homologous counterparts in the T3SS), and if one also aligns the amino acid sequences of the T3SS proteins, one finds that the T3SS protein amino acid sequences are much more conserved than the amino acid sequences of the flagellar proteins. There are two possible explanations for this: (1) The T3SS is younger than the flagellum, or (2) The T3SS proteins are under more functional constraints than flagellar proteins, and so the sequences in T3SS proteins cannot diverge as much. We may rule out option #2 in the light of both in vitro and in silico mutagenesis. For example, I performed an in silico alanine scan on flagellar proteins and their T3SS homologues using SNAPs and found that flagellar proteins are under more functional constraints than T3SS proteins. (E.g., ~39% of the positions in FliF result in a non-neutral mutation when an in silico alanine scan is performed, ~34% of the positions in YscJ result in a non-neutral mutation -- YscJ is FliF's T3SS homologue, for those of you who do not know). LivingstoneMorford

Elizabeth Liddle:

Now, I fully accept that ID doesn’t mean what is written above (at least it bears very little resemblance to anything I’ve read here about ID), so yes, what it may do is “prove… that people who *are* creationists will sometimes adopt ID language in order to conceal the real basis of their argument.”

Why were people supporting the Pandas in the trial? Look at what you wrote. Perhaps that's why. Other reasons might be that they were unaware of it's provenance. Or that they were only testifying as to specific questions which were asked of them. That's how our legal system works. Would you care to make a specific allegation? Why do you continue to advance the ID = Creationism argument when you know it's not true? Mung

Nick at 32, so you have, in essence, defaulted that you have no concrete examples demonstrating the 'real time' evolution of any molecular machine whatsoever?!? And Nick, just why would you be so sold on neo-Darwinism when even this 'trivial' level of molecular verification cannot be met for neo-Darwinism? Could it be because you get a paycheck for supporting such a evidentially weak position??? As well, I noticed you avoided providing a sufficient material cause to explain the non-local quantum information we now find in molecular biology. Nick, this is not about you winning a argument against ID proponents, this is about a genuine concern for finding the truth. If the material causes of neo-Darwinism are grossly inadequate to explain the staggering levels of integrated information we find in life, which is exactly what the evidence is telling us, why in the world would you fight so hard against this truth??? bornagain77

Elizabeth- Using a released version of the book the quote referred to the fossil record and is supported by (the theory of) punctuated equilibrium. But anyway Dr Behe weighed in on that quote also:

Dr Behe = A Q= pro-ID lawyer Q I would like to direct your attention to page 99, please. I would like to read to you and oft-quoted passage in this case thus far. If you’ll look at the bottom on page 99, it’s going to continue onto 100 as well. It says, quote, Intelligent design means that various forms of life began abruptly through an intelligent agency with their distinctive features already intact: Fish with fins and scales, birds with feathers, beaks and wings, et cetera. Some scientists have arrived at this view since fossil forms first appeared in the record with their distinctive features intact and apparently fully functional rather than gradual development. And I would like to get your reaction to that section? A- Well, it says — it says that some scientists have arrived at this view. I think that’s a way of saying that this is a matter of disagreement and dispute. I certainly do not think that intelligent design means that a feature has to appear abruptly. And I — I certainly would have written this differently if I had done so. Q Now, you say you would have written it differently. Is there another reference or another section in Pandas that you could direct us to to emphasize that point? A Yes. I wrote the section at the end of Pandas which is discussing blood clotting. And on page 144 of the text there’s a section entitled “A Characteristic of Intelligent Design.” And it begins, “Why is the blood clotting system an example of intelligent design? The ordering of independent pieces into a coherent whole to accomplish a purpose which is beyond any single component of the system is characteristic of intelligence.” Q And why did you direct us to that particular section? A Because I think it more clearly conveys the central idea of intelligent design, which is the purposeful arrangement of parts. Q Do you see that then as a, perhaps a better characterization, or more accurate characterization of intelligent design? A Yes, I like this a lot better.

Joseph

Nick are you sure your conference wasn't more like this? http://www.youtube.com/watch?v=X3Wp9dICOoA&feature=related lamarck

Nick Matzke:

flagellum — even Mike Gene has admitted evidence has come in that has supported the evolutionary model, particularly further evidence of homology between the flagellum, T3SS, and the F1Fo-ATPase:

1- You don't have a testable hypothesis for accumulations of genetic accidents p[roducing either a flagellum nor a T3SS 2- You don't have any evidence that accumulations of genetic accidents can construct new, useful and functional multi-part systems. 3- One man's homolog is another's homoplasy or evn part of a common design Joseph

Elizabeth, The sentence you cite is NOT from the glossary- rather it refers to the fossil record. The definition provided in the glosary does not match that sentence. Also the publisher was not allowed at the trial- but that 9is the only way to "win"- stop the people who know the best from testifying. Joseph

Joseph:

Charles Darwin said the following in a RELEASED edition of “On the Origin of Species…”: There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone circling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.”– last sentence, last paragraph, last chapter 6th edition (bold added)

Darwin said this? So the theories originator was a creationist? Then why wouldn't Behe and Dembski etc use Darwin's appeal to creationism at the Dover trial to support their appeal to an intelligent agency to argue against the Darwinists non-appeal to Darwin's Creator? This thing is confusing. junkdnaforlife

Well, what puzzles me, typo or non-typo, is that clearly the original Pandas book was written to promote creationism, not ID, and, at least according to the wiki, wrote that: "Creationism [later drafts: Intelligent design] means that various forms of life began abruptly through an intelligent agency, with their distinctive features already intact. Fish with fins and scales, birds with feathers, beaks, wings, etc" Now, I fully accept that ID doesn't mean what is written above (at least it bears very little resemblance to anything I've read here about ID), so yes, what it my do is "prove... that people who *are* creationists will sometimes adopt ID language in order to conceal the real basis of their argument." But in that case, why were the ID people supporting the Pandas in the trial? Shouldn't they have been the most outraged at the misrepresentation of their position? But in fact Behe (whose ID ideas bear no resemblance to the definition of ID in the Panda's passage above) took the stand in its defense, and Dembski, I understand, was originally going to, then declined, but nonetheless responded to the final judgement with an um amusing animated parody of Judge Jones. If Pandas was a misrepresentation of ID, why did IDists support it? And if it wasn't, why the outrage? Elizabeth Liddle

SCheesman:

Here’s a short list of papers/headlines I’d be looking forward to hearing: “Oldest trilobite discovered: Light sensitive spots found in place of eyes” “New pre-cambrian fossil graveyard discovered in Qinghai, China. Origins of 30+ phyla now clear.” “Self-organization in proteins: New analysis reveals hidden mechanism for production of novel functions in response to selection pressure.” “UNA: Universal nucleic acids form stable, reproducing life forms, bridging RNA and DNA worlds” “Beneficial mutations found to be 1000 times more common that previously realized; observer bias found to be culprit in earlier low estimates”

This exactly what I was looking for when I responded, "anything good", to homeboy's point: “Lots and lots of data and analysis and science.” Instead, the same fecal matter fight as usual. -- velikovskys: "Depends on the opponents ,you don’t need the Yankees to best a last place singleA team." You can make that analogy. But from there, you cannot argue that the single A team is not playing baseball. junkdnaforlife

Re: flagellum -- even Mike Gene has admitted evidence has come in that has supported the evolutionary model, particularly further evidence of homology between the flagellum, T3SS, and the F1Fo-ATPase: Mike Gene Admits Matzke was Right http://scienceblogs.com/dispatches/2008/09/mike_gene_admits_matzke_was_ri.php NickMatzke_UD

"FYI, here is what Thaxton has to say for himself, which is indeed reflected in both TMLO and Pandas and People:" Late-in-the-day rationalizations are a lot less convincing than contemporary evidence. In the early 1980s Thaxton et al. were advertising the book project as a creationist book. They hired two young-earth creation scientists, Dean Kenyon and Percival Davis, to write the draft of the "non-creationist" book. Not-very-subtle endorsements of Biblical and young-earth creationism remain in the published 1989 book, let alone the drafts. C'mon, we aren't required to have infinite gullibility here. NickMatzke_UD

Nick Matzke (15): The Pandas book doesn't prove what you claim it does. What it proves is that people who *are* creationists will sometimes adopt ID language in order to conceal the real basis of their argument. It does not prove that ID itself is creationism. Behe, Sternberg, Denton and many others are design proponents, but not creationists (as the term is normally used in American cultural discourse, to indicate a particular interpretation of Genesis). Dave Scot who used to be here was an ID proponent but not a creationist. Antony Flew, who concluded for ID on philsophical grounds, was not a creationist. Jewish, Muslim and Hindu ID proponents are not creationists. So, now that this standard move of yours has been refuted (yet again), how about answering my earlier questions? Thomas Cudworth

In most scientific areas, non-experts don’t pretend to stand in for experts.  You don’t see solid-state physicists rushing onto the blogosphere to defend the latest  view on black holes from Stephen Hawking.  They leave the defense of cosmology to the cosmologists. Depends on the opponents ,you don't need the Yankees to best a last place singleA team. velikovskys

Elizabeth, What you are suggesting means they didn't delete the whole word "creationists"- they left the "c" behind and then typed in "design proponentsists". My version has them deleting the whole word and then starting with a typo. That is the more simple solution. And we are STILL talking about a ROUGH draft and trying to play "mind-reader" of the author's intentions. Joseph

I didn't say that it ID = Creationism. I was merely responding to Joseph's suggesting that it was a typo, arising from the proximity of c and d on the keyboard. That seems unlikely seeing as a previous draft actually had "creationist" in the same spot. I guess I was being a bit of a lawyer :) Elizabeth Liddle

I have no problem accepting that c[design proponents]ists replaced c[reation]ists if that makes sense given the original context. And that deserves a big so what. It in no way follows that ID is creationism. And Elizabeth, why are you back on the ID = Creationism shtick? You know better. Mung

Joseph:

Elizabeth Liddle, Charles Darwin said the following in a RELEASED edition of “On the Origin of Species…”: There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone circling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.”– last sentence, last paragraph, last chapter 6th edition (bold added) That would mean, by Nick’s logic, the theory of evolution = Creationism. Anything else I can help you with?

No, that is fine, Joseph. It seems to make my point very well :) Elizabeth Liddle

Dr Liddle: Please look carefully at the actual draft text as linked here, noting that at the time no vocabulary was generally known for what Thaxton et al were plainly trying very hard to say. At some point they found/re-invented the right vocabulary for what they were trying to say and they systematically used it. IIRC, they heard someone with the term, talked it over and concluded this said what they were fishing for. I would take it that (at least to an unprejudiced mind) when the authors and editors of a book go through and change towards a key term systematically, and in line with the tenor of the argumentation long since being made --

1: note they are specifically distancing themselves from inference from signs of design in the world of life to the supernatural as the cause, and 2: they are specifically and for given reasons differing with Paley's natural theology argument --

. . . they are thereby showing that they have found something that better says what they want to say, and are going to use it. I long ago observed that as published -- what is most relevant to identifying intent, Pandas explicitly states:

This book has a single goal: to present data from six areas of science that bear on the central question of biological origins. We don't propose to give final answers, nor to unveil The Truth. Our purpose, rather, is to help readers understand origins better, and to see why the data may be viewed in more than one way. (Of Pandas and People, 2nd ed. 1993, pg. viii) . . . . Today we recognize that appeals to intelligent design may be considered in science, as illustrated by current NASA search for extraterrestrial intelligence (SETI). Archaeology has pioneered the development of methods for distinguishing the effects of natural and intelligent causes. We should recognize, however, that if we go further, and conclude that the intelligence responsible for biological origins is outside the universe (supernatural) or within it, we do so without the help of science. (pg. 126-127, emphasis added)

You would have to go far to be more direct than this. And that has a lot to do with say a certain late Mr Morris' objections, as a leading creationist, to the design movement. When I recently had occasion to contrast Wiki's coverage of CSI with what I know CSI to be about, I found the same pattern of a jaundiced, agenda-serving misreading. Something is deeply wrong here -- something that needs to be fixed forthwith, and that is why I spoke to Mr Matzke as I did above. There is something that has gone rotten down at the NCSE, and at the ACLU, as well as at the Louisiana Humanists. GEM of TKI kairosfocus

Nick, To dovetail into Dembski and Marks's work on Conservation of Information;,,, LIFE'S CONSERVATION LAW: Why Darwinian Evolution Cannot Create Biological Information William A. Dembski and Robert J. Marks II http://evoinfo.org/publications/lifes-conservation-law/ ,,,Encoded classical information, such as what we find in computer programs, and yes as we find encoded in DNA, is found to be a subset of 'transcendent' quantum information by the following method:,,, This following research provides solid falsification for Rolf Landauer’s contention that information encoded in a computer is merely physical (merely ‘emergent’ from a material basis) since he believed it always required energy to erase it; Quantum knowledge cools computers: New understanding of entropy – June 2011 Excerpt: No heat, even a cooling effect; In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy. Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.” http://www.sciencedaily.com/releases/2011/06/110601134300.htm ,,,And here is the empirical confirmation that quantum information is 'conserved';,,, Quantum no-hiding theorem experimentally confirmed for first time Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment. http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html bornagain77

Nick, as well, after you have supplied the proper literature for the demonstrated evolutionary origin of any molecular machine whatsoever,,, I would also appreciate if you be so kind as to provide a sufficient material cause for non-local quantum entanglement/information we are now finding, on a massive scale, in molecular biology??/ notes; Neo-Darwinian evolution purports to explain all the wondrously amazing complexity of life on earth by reference solely to chance and necessity processes acting on energy and matter (i.e. purely material processes). In fact neo-Darwinian evolution makes the grand materialistic claim that the staggering levels of unmatched complex functional information we find in life, and even the ‘essence of life’ itself, simply ‘emerged’ from purely material processes. And even though this basic scientific point, of the ability of purely material processes to generate even trivial levels of complex functional information, has spectacularly failed to be established, we now have a much greater proof, than this stunning failure for validation, that ‘put the lie’ to the grand claims of neo-Darwinian evolution. This proof comes from the fact that it is now shown from quantum mechanics that ‘information’ is its own unique ‘physical’ entity. A physical entity that is shown to be completely independent of any energy-matter space-time constraints, i.e. it does not ‘emerge’ from a material basis. Moreover this ‘transcendent information’ is shown to be dominant of energy-matter in that this ‘information’ is shown to be the entity that is in fact constraining the energy-matter processes of the cell to be so far out of thermodynamic equilibrium. notes: Falsification of neo-Darwinism; First, Here is the falsification of local realism (reductive materialism). Here is a clip of a talk in which Alain Aspect talks about the failure of ‘local realism’, or the failure of reductive materialism, to explain reality: The Failure Of Local Realism – Reductive Materialism – Alain Aspect – video http://www.metacafe.com/w/4744145 The falsification for local realism (reductive materialism) was recently greatly strengthened: Physicists close two loopholes while violating local realism – November 2010 Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview. http://www.physorg.com/news/2010-11-physicists-loopholes-violating-local-realism.html Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009 Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables. http://www.sciencedaily.com/releases/2009/07/090722142824.htm (of note: hidden variables were postulated to remove the need for ‘spooky’ forces, as Einstein termed them — forces that act instantaneously at great distances, thereby breaking the most cherished rule of relativity theory, that nothing can travel faster than the speed of light.) And yet, quantum entanglement, which rigorously falsified local realism (reductive materialism) as the complete description of reality, is now found in molecular biology on a massive scale! Quantum Information/Entanglement In DNA & Protein Folding – short video http://www.metacafe.com/watch/5936605/ Quantum entanglement holds together life’s blueprint – 2010 Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours (arxiv.org/abs/1006.4053v1). “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford. http://neshealthblog.wordpress.com/2010/09/15/quantum-entanglement-holds-together-lifes-blueprint/ The relevance of continuous variable entanglement in DNA – July 2010 Excerpt: We consider a chain of harmonic oscillators with dipole-dipole interaction between nearest neighbours resulting in a van der Waals type bonding. The binding energies between entangled and classically correlated states are compared. We apply our model to DNA. By comparing our model with numerical simulations we conclude that entanglement may play a crucial role in explaining the stability of the DNA double helix. http://arxiv.org/abs/1006.4053v1 Quantum Information confirmed in DNA by direct empirical research; DNA Can Discern Between Two Quantum States, Research Shows – June 2011 Excerpt: — DNA — can discern between quantum states known as spin. – The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team’s results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property. http://www.sciencedaily.com/releases/2011/03/110331104014.htm Information and entropy – top-down or bottom-up development in living systems? A.C. McINTOSH Excerpt: This paper highlights the distinctive and non-material nature of information and its relationship with matter, energy and natural forces. It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate. http://journals.witpress.com/paperinfo.asp?pid=420 i.e. It is very interesting to note that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale, for how can the quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy space/time) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own ‘causation’ in the first place? (A. Aspect) Appealing to the probability of various configurations of material particles, as neo-Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the energy/matter particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘specified’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place! ,,,To refute this falsification of neo-Darwinism, one must falsify Alain Aspect, and company’s, falsification of local realism (reductive materialism)! ,,, As well, appealing to ‘non-reductive’ materialism (multiverse or many-worlds) to try to explain quantum non-locality in molecular biology ends up destroying the very possibility of doing science rationally; BRUCE GORDON: Hawking’s irrational arguments – October 2010 Excerpt: For instance, we find multiverse cosmologists debating the “Boltzmann Brain” problem: In the most “reasonable” models for a multiverse, it is immeasurably more likely that our consciousness is associated with a brain that has spontaneously fluctuated into existence in the quantum vacuum than it is that we have parents and exist in an orderly universe with a 13.7 billion-year history. This is absurd. The multiverse hypothesis is therefore falsified because it renders false what we know to be true about ourselves. Clearly, embracing the multiverse idea entails a nihilistic irrationality that destroys the very possibility of science. http://www.washingtontimes.com/news/2010/oct/1/hawking-irrational-arguments/ ,,,Michael Behe has a profound answer to the infinite multiverse (non-reductive materialism) argument in “Edge of Evolution”. If there are infinite universes, then we couldn’t trust our senses, because it would be just as likely that our universe might only consist of a human brain that pops into existence which has the neurons configured just right to only give the appearance of past memories. It would also be just as likely that we are floating brains in a lab, with some scientist feeding us fake experiences. Those scenarios would be just as likely as the one we appear to be in now (one universe with all of our experiences being “real”). Bottom line is, if there really are an infinite number of universes out there, then we can’t trust anything we perceive to be true, which means there is no point in seeking any truth whatsoever. “The multiverse idea rests on assumptions that would be laughed out of town if they came from a religious text.” Gregg Easterbrook ================= Alain Aspect and Anton Zeilinger by Richard Conn Henry – Physics Professor – John Hopkins University Excerpt: Why do people cling with such ferocity to belief in a mind-independent reality? It is surely because if there is no such reality, then ultimately (as far as we can know) mind alone exists. And if mind is not a product of real matter, but rather is the creator of the “illusion” of material reality (which has, in fact, despite the materialists, been known to be the case, since the discovery of quantum mechanics in 1925), then a theistic view of our existence becomes the only rational alternative to solipsism (solipsism is the philosophical idea that only one’s own mind is sure to exist). (Dr. Henry’s referenced experiment and paper – “An experimental test of non-local realism” by S. Gröblacher et. al., Nature 446, 871, April 2007 – “To be or not to be local” by Alain Aspect, Nature 446, 866, April 2007 bornagain77

Nick, you state: 'Endless repetition of ID talking points while ignoring the literature doesn’t make the talking points more true.' ,,,In regards to the T3SS being devolved from the Flagellum,,, Perhaps they were designed individually Nick,,, I honestly don't know for sure,,, One thing I do know for sure is that no neo-Darwinists has ever come on this site and demonstrated the evolutionary origin of any molecular machine whatsoever!!! Nick I would be more than willing to 'read the literature' on the demonstrated evolutionary origin of molecular machines if you would be so kind as to present it! notes: Astonishingly, actual motors, which far surpass man-made motors in 'engineering parameters', are now being found inside 'simple cells'. Articles and Videos on Molecular Motors http://docs.google.com/Doc?docid=0AYmaSrBPNEmGZGM4ejY3d3pfMzlkNjYydmRkZw&hl=en Michael Behe - Life Reeks Of Design - 2010 - video http://www.metacafe.com/watch/5066181 And in spite of the fact of finding molecular motors permeating the simplest of bacterial life, there are no detailed Darwinian accounts for the evolution of even one such motor or system. "There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject." James Shapiro - Molecular Biologist The following expert doesn't even hide his very unscientific preconceived philosophical bias against intelligent design,,, ‘We should reject, as a matter of principle, the substitution of intelligent design for the dialogue of chance and necessity,,, Yet at the same time the same expert readily admits that neo-Darwinism has ZERO evidence for the chance and necessity of material processes producing any cellular system whatsoever,,, ,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’ Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205. *Professor Emeritus of Biochemistry, Colorado State University, USA Michael Behe - No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines http://www.metacafe.com/watch/5302950/ “The response I have received from repeating Behe's claim about the evolutionary literature, which simply brings out the point being made implicitly by many others, such as Chris Dutton and so on, is that I obviously have not read the right books. There are, I am sure, evolutionists who have described how the transitions in question could have occurred.” And he continues, “When I ask in which books I can find these discussions, however, I either get no answer or else some titles that, upon examination, do not, in fact, contain the promised accounts. That such accounts exist seems to be something that is widely known, but I have yet to encounter anyone who knows where they exist.” David Ray Griffin - retired professor of philosophy of religion and theology What I find very persuasive, to the suggestion that the universe was designed with life in mind, is that physicists find many processes in a cell operate at the 'near optimal' capacities allowed in any physical system: William Bialek - Professor Of Physics - Princeton University: Excerpt: "A central theme in my research is an appreciation for how well things “work” in biological systems. It is, after all, some notion of functional behavior that distinguishes life from inanimate matter, and it is a challenge to quantify this functionality in a language that parallels our characterization of other physical systems. Strikingly, when we do this (and there are not so many cases where it has been done!), the performance of biological systems often approaches some limits set by basic physical principles. While it is popular to view biological mechanisms as an historical record of evolutionary and developmental compromises, these observations on functional performance point toward a very different view of life as having selected a set of near optimal mechanisms for its most crucial tasks.,,,The idea of performance near the physical limits crosses many levels of biological organization, from single molecules to cells to perception and learning in the brain,,,," http://www.princeton.edu/~wbialek/wbialek.html bornagain77

Elizabeth Liddle, Charles Darwin said the following in a RELEASED edition of "On the Origin of Species...":

There is grandeur in this view of life, with its several powers, having been originally breathed by the Creator into a few forms or into one; and that, whilst this planet has gone circling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved."-- last sentence, last paragraph, last chapter 6th edition (bold added)

That would mean, by Nick's logic, the theory of evolution = Creationism. Anything else I can help you with? Joseph

Mr Matzke: That you and ilk find yourself maintaining stoutly as a drumbeat talking point what you know or should know is false and misleading, the "creationism in a cheap tuxedo" smear, instead of addressing issues on their merits; even while smuggling in materialism into an attempted ideological redefinition of science, is telling. GEM of TKI PS: FYI, here is what Thaxton has to say for himself, which is indeed reflected in both TMLO and Pandas and People:

I wasn't comfortable with the typical vocabulary that for the most part creationists were using because it didn't express what I was trying to do. They were wanting to bring God into the discussion, and I was wanting to stay within the empirical domain and do what you can do legitimately there. (Deposition of Charles Thaxton 52-53, Kitzmiller, No. 4:04-CV-2688 (M.D. Pa., July 19, 2005))

--> Much more is here, including a key "from the horse's mouth" where drafts that predate the 1987 USSC decisions make some very crucial distincitons from they typical views of Biblical Creationism, and BTW, specifically distinguishing on given grounds, the pattern of thought from Paley's Natural Theology too. kairosfocus

Joseph:

Yes Nick, I looked up “cdesign proponentsists”- it appears in a ROUGH draft of the book “Of Pandas and People”- a ROUGH draft. Now if one looks at a standard keyboard one would obseve that the “d” key and the “c” key are close enough together that one could hit them both when just trying to hit one of them. Endless reprition of evotard talking points while ignoring reality doesn’t make those talking points more true.

Except that "cdesign proponentsists" actually occurred in a sentence in which "creationists" had appeared in an even earlier draft. Or do you dispute this? Elizabeth Liddle

As for the T3SS, well it is irreducibly complex also- meaning your position can't explain its existence without relying on magical mystery mutations and poofing selection... Joseph

Yes Nick, I looked up "cdesign proponentsists"- it appears in a ROUGH draft of the book "Of Pandas and People"- a ROUGH draft. Now if one looks at a standard keyboard one would obseve that the "d" key and the "c" key are close enough together that one could hit them both when just trying to hit one of them. Endless reprition of evotard talking points while ignoring reality doesn't make those talking points more true. Joseph

About ID and creationism. Two words: cdesign proponentsists Look them up ;-) NickMatzke_UD

"Nick,,, Do you still believe that the T3SS is precursor to the Bacterial Flagellum, or have you modified your view, in the face of the new evidence that indicates the Flagellum was precursor to the T3SS??? i.e. that the T#SS ‘devolved’ from the flagellum??? " If you actually read the Pallen/Matzke paper, you wouldn't say such silly things. The research papers are split on the question, and the most recent phylogenetic research papers indicate the flagellum and the T3SS are sister groups about equally old, not that the flagellum is older. Endless repetition of ID talking points while ignoring the literature doesn't make the talking points more true. NickMatzke_UD

Evolutionary history of over 600 proteins involved in mitosis clearly established. Darwin vindicated. Mung

SCheesman at 10 :) bornagain77

Chance discovery leads to new insights into how evolution really works. Mung

Here's a short list of papers/headlines I'd be looking forward to hearing: "Oldest trilobite discovered: Light sensitive spots found in place of eyes" "New pre-cambrian fossil graveyard discovered in Qinghai, China. Origins of 30+ phyla now clear." "Self-organization in proteins: New analysis reveals hidden mechanism for production of novel functions in response to selection pressure." "UNA: Universal nucleic acids form stable, reproducing life forms, bridging RNA and DNA worlds" "Beneficial mutations found to be 1000 times more common that previously realized; observer bias found to be culprit in earlier low estimates" SCheesman

This post does raise an interesting dichotomy. Put simply, the people who describe and evolution to the public are often not the ones who are at the cutting edge of the research. This is partly because the skills that are needed are different - verbal communication is less important for doing research (as anyone who has seen Nick Barton talk can attest). And also because people's time is limited, so the top researchers will want to continue doing what they do best - research. The people who concentrate on communication are also time-limited, so meetings like the SSE and ESEB in Europe are a lower priority. There's also a related issue that I think a lot of people at UD miss (and, in fairness, a lot of other people who are interested in science, but who are not working scientists). Most of the cutting-edge work and thinking on evolution isn't being done by people who have a high public profile, so if you want to see the current thinking you have to read the journals (e.g. Evolution, American Naturalist, Journal of Evolutionary Biology, TREE). The popular press is OK for reports on specific pieces of work (as long as you ignore the Darwin was RIGHT/WRONG rhetoric), but not s good at giving a deeper context. It also ignores the more technical (but as important) literature that needs to be read if you're to understand current thought - Mike Lynch's recent work springs to mind. Heinrich

Yes Nick, evolution is everywhere in biology. However ID is NOT anti-evolution and you still cannot produce a testable hypothesis nor positive evidence for the claim that the bacterial flagellum (for example- seeing you co-authored a paper pertaining to them) "evolved" via accumulations of genetic accidents. Heck you can't even demonstrate that such a processes can construct new, useful multi-part systems. And seeing living organisms are full of them one would think that would count against your position. And that is why you and your ilk are running jokes around the world... Joseph

Hi Thomas, I don't know what to say. I don't like to travel that much, and my meeting appetite will be whetted nicely in Cold Spring Harbor in August. Besides, we're talking Oklahoma, in June. No offense to Sooners who are reading this, but .... In any case, seeing as we're on the subject of absentees, I'll remind you that the DI crowd was very conspicuous by its absence from the RNA meeting in Seattle awhile back. Heck, the world's largest RNA meeting, with lots of stuff relevant to evolution, OOL, information, and the like, and they couldn't even find the time to, like, drive a few blocks or so and make their case. What's with that? Your post gives me hope, though, that maybe I will meet up with a few ID advocates in Cold Spring Harbor. We'll see. Arthur Hunt

Oh, and by the way, Nick, I am quite sure you are right that I would learn something at a meeting of bona fide evolutionary biologists. The question I am raising is whether or not certain rather loud Darwin defenders are in fact bona fide evolutionary biologists, or just pretenders to the name. So if you can give us a list of peer-reviewed articles on evolutionary mechanisms published by Miller, Myers, Falk, etc. you can dispel all my concerns immediately. Oh, and one more thing: I'm not a creationist, and ID isn't creationism. Thomas Cudworth

Apparently, Nick, careful reading is not a skill covered in Ph.D. programs in biology. I clearly mentioned the scheduled talks of both Coyne and Miller. As for Eugenie Scott, I didn't ask if she ever received any awards for her political lobbying; I asked if she has written any scientific papers in the past ten years. Happily for me, you are well positioned to know the answer to that question. And while you are here, Nick, since you know about all the other meetings, tell me at which meetings in the past ten years I would have heard scientific papers (not popular addresses) on evolutionary mechanisms by P.Z. Myers, Larry Moran, Allan MacNeill, Darrel Falk, Kathryn Applegate, Dennis Venema, Steve Matheson, or the others I've mentioned? Do let us know what makes these people competent to pronounce on evolutionary biology, as they so frequently have. The public needs to know whether these people have been certified by the community of experts in evolutionary biology, or whether they are just self-appointed champions of Darwin who have biology degrees but no special expertise in evolutionary theory at all. Thomas Cudworth

Nick,,, Do you still believe that the T3SS is precursor to the Bacterial Flagellum, or have you modified your view, in the face of the new evidence that indicates the Flagellum was precursor to the T3SS??? i.e. that the T#SS 'devolved' from the flagellum??? notes: Bacterial Flagellum - A Sheer Wonder Of Intelligent Design - video http://www.metacafe.com/watch/3994630 Bacterial Flagellum: Visualizing the Complete Machine In Situ Excerpt: Electron tomography of frozen-hydrated bacteria, combined with single particle averaging, has produced stunning images of the intact bacterial flagellum, revealing features of the rotor, stator and export apparatus. http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRT-4M8WTCF-K&_user=10&_coverDate=11%2F07%2F2006&_rdoc=1&_fmt=full&_orig=search&_cdi=6243&_sort=d&_docanchor=&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=8d7e0ad266148c9d917cf0c2a9d12e82&artImgPref=F Electron Microscope Photograph of Flagellum Hook-Basal Body http://www.skeptic.com/eskeptic/08-08-20images/figure03.jpg Biologist Howard Berg at Harvard calls the Bacterial Flagellum “the most efficient machine in the universe." The flagellum has steadfastly resisted all attempts to elucidate its plausible origination by Darwinian processes, much less has anyone ever actually evolved a flagellum from scratch in the laboratory; Genetic Entropy Refutation of Nick Matzke's TTSS (type III secretion system) to Flagellum Evolutionary Narrative: Excerpt: Comparative genomic analysis show that flagellar genes have been differentially lost in endosymbiotic bacteria of insects. Only proteins involved in protein export within the flagella assembly pathway (type III secretion system and the basal-body) have been kept... http://mbe.oxfordjournals.org/cgi/content/abstract/msn153v1 Stephen Meyer - T3SS Derived From Bacterial Flagellum (Successful ID Prediction) - video http://www.youtube.com/watch?v=3c-EAzJ8_4U Phylogenetic Analyses of the Constituents of Type III Protein Secretion Systems Excerpt: We suggest that the flagellar apparatus was the evolutionary precursor of Type III protein secretion systems. http://www.horizonpress.com/jmmb/v2/v2n2/02.pdf "One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. ‘The most parsimonious explanation is that the T3SS arose later," Howard Ochman - Biochemist - New Scientist (Feb 16, 2008) Michael Behe on Falsifying Intelligent Design - video http://www.youtube.com/watch?v=N8jXXJN4o_A Michael Behe Hasn't Been Refuted on the Flagellum - March 2011 http://www.evolutionnews.org/2011/03/michael_behe_hasnt_been_refute044801.html The Bacterial Flagellum – Truly An Engineering Marvel! - December 2010 https://uncommondesc.wpengine.com/intelligent-design/the-bacterial-flagellum-truly-an-engineering-marvel/ bornagain77

Good Morning Nick, Nice to meet you. Would you be so kind as to stick around for a while to teach other evolutionists the art of "arguing effectively against creationist/ID silliness"? First of all, have you read Stephen Meyer's "Signature in the Cell" yet? Chris Doyle

Anything good? Toss us Neanderthals a bone. junkdnaforlife

"Lots and lots of data and analysis and science." junkdnaforlife

You mean except for Kenneth Miller and Jerry Coyne, who both gave keynote addresses? You also missed the attendance of: Joel Cracraft David Hillis Joe Felsenstein Carl Zimmer Louise Mead (until recently an NCSE employee) little ol' me, and many of these people: http://www.oklascience.org/ People who spoke at last year's Evolution meeting included: Doug Theobald Robert Pennock (past president of SSE) John Harshman 2 years ago Eugenie Scott got the award that Kenneth Miller got this time (the Stephen Jay Gould Award -- hey, there's another guy who was a DarwinDefender at the top of his field). All that said, evolution is everywhere in biology. Paleontologists like Kevin Padian do evo at paleontology meetings. Molecular evolution people go to the SMBE (Society of Molecular Biology and Evolution) meeting. Organismal biologists go to the Society for Integrative and Comparative Biology (SICB) meeting. Nematode people do evolution at the nematode meeting. The Evolution meeting for various historical reasons tends to get population geneticists and fields descended from that -- phylogenetics, computational biology, phylogeography, mathematical theory, genomics, etc. And, anyway, arguing effectively against creationist/ID silliness doesn't necessarily take an advanced degree, just an ability to double-check creationist statements against the facts. I did this for years as a hobby before I started doing evolution as a job. Nice try, though. You might try attending one of these meetings sometime, you might learn something. It's pretty much like any other science meeting, actually. Lots and lots of data and analysis and science. It is surprisingly unlike a dark cabal plotting to overthrow God, morality, mom and apple pie. Creationism/ID are a running joke at the meeting, not something many people even bother to rebut most of the time. NickMatzke_UD

Hey now, if you're goona use my term, spell it right ;) DarwinDefender Ilion