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

Rats, I left some out. http://bedejournal.blogspot.com/2011/12/how-bad-were-mongols.html http://bedejournal.blogspot.com/2011/12/this-is-bogus-statistic.htmlHouseStreetRoom

January 21, 2012

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"In return may I recommend “The Better Angels of our Nature” by Stephen Pinker – which has nothing to do with ID but is one of the most interesting and well argued non-fiction books I have read for a very long time." Allow me to recommend against taking Pinker's analysis seriously based on the following criticisms: http://bedejournal.blogspot.com/2011/11/steven-pinker-and-an-lushan-revolt.html http://bedejournal.blogspot.com/2011/11/pinker-tackles-albigensian-crusade.html http://bedejournal.blogspot.com/2011/11/steven-pinkers-medieval-murder-rates.htmlHouseStreetRoom

January 21, 2012

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Just a brief comment, Timaeus: Thanks for this clarification. It seems that the "immanent" intelligence to which you refer chiefly differs from my use by refering to intelligence intrinsic to the organism - I am talking about "intelligence" intrinsic to the population - the capacity of a population to optimise the phenotypes of its members to survive in any given environment. The interesting thing that Shapiro shows is that through between-population selection, this "intelligence" can be raised to a meta-level: populations whose members tend to produce variant offspring within a range likely to render the population more robust to environment change. This is not the same as "foresight" of course; more like making sure you have a large Swiss Army Knife with which to confront the unforeseen! A similar role has been proposed for epigenetic effects.Elizabeth Liddle

January 21, 2012

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T - thanks for your lengthy reply. I think we will have to agree to disagree on the meaning of the word "Darwinian". I have always found it to be a very ambiguous phrase which is bandied about without much thought - especially on Uncommon Descent - so I probably should not have used it myself. Of course I do not have an "inbuilt hatred for any writer who would even consider the possibility than there might intelligent design anywhere in the universe,"- else why would I have spent time reading Dembski and Meyer and Behe? I just need to decide where best to spend my time. I will make Denton my next ID book - which doesn't mean I will read it soon. In return may I recommend "The Better Angels of our Nature" by Stephen Pinker - which has nothing to do with ID but is one of the most interesting and well argued non-fiction books I have read for a very long time. It is a must read if you are interested in the moral state of society today.markf

January 21, 2012

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markf: Thanks for your restatement. First, "immanent design" was a phrase I made up on the spur of the moment, not one that is used generally by ID people, so don't agonize over the precise phrase. I've explained what I meant by it -- the organism has its own "intelligence," so to speak, by which it can respond creatively to its environment by actually changing its own genetic makeup. It doesn't have to wait until some cosmic ray or chemical strikes its DNA and makes an alteration that will just *happen* to be of some use. To some extent it makes its own opportunities. Now, as I've defined both Darwinism and neo-Darwinism at great length to Elizabeth, the idea that the organism could do such self-engineering is non-Darwinian. To the neo-Darwinists the notion is anathema, and as for Darwin, whose Origin I read with great care and great enjoyment a few years ago, the closest he came was in his flirtation with bits of Lamarckianism; but his overall scheme lay in a different direction from this. (I'm just giving the generally accepted reading of Darwin, here, nothing tricky or peculiar.) So, no matter how the discussion twists and turns, I am never going to accept the term "Darwinian" as a reasonable description of what Shapiro is arguing for. I don't believe in uses of words which equate two things which are substantially different. Regarding your Point A, we are using the word "unguided" in two different senses, and this is what is causing the problem. I consider Shapiro's model of evolution "guided," not in the sense that God or some supernatural agent is steering the process, but in the sense that the organism has its destiny, to some extent, in its own hands. Think of those bumper car rides that little kids go on in the parks and carnivals. The kids have a range of freedom, allowing them to avoid certain collisions and to initiate others. I see the organism, in Shapiro's model, as like that. It is self-guiding, to an extent, because it can control not only how it responds to its environment (as in Darwin), but can even remake itself. The self-guidance is not supernatural, nor is it "intelligent" in the sense that the organism is "thinking" how to handle its problems, but there is a feedback between environment and genetic material that does not exist in neo-Darwinism and was a most a minor ancillary to Darwin's own view. Now Margulis's view of evolution I *would* call unguided. She proposes that massive recombinations of genomes are relatively common and the major source of evolutionary novelty. But she gives no suggestion that these recombinations are any less accidental than the random mutations of neo-Darwinism. Her view of evolution, then, is equally "chancy". Its only advantage over neo-Darwinism is that it can achieve large leaps in biological form very quickly, and therefore doesn't face the problem of incrementalism with which the ID people (in agreement with her) have assaulted neo-Darwinism. Most of 20th-century evolutionary biology, whether it was neo-Darwinian or whether it laid more emphasis on "drift" or whether it threw in more radical notions such as those of Margulis, ultimately laid the creation of radically new biological form at the doorstep of "chance" -- contingent events not dictated by any natural law. Natural selection could play its role only after "chance" produced the new forms. ID contests that any such modes of generating novel biological form, or all of them put together, could suffice to generate selectable traits sufficiently often to generate what we observe. I'm not going to argue that case here; I'm just making a general point to classify models of evolution. Shapiro's view is quite different. Since, in his view, the interaction is two-way, with the initiation of organic change sometimes coming from the genome, but sometimes from the environment, and since there is an "intelligent" interface where the two sources of change can communicate, allowing the organism to make "decisions" (I need all the scare quotes because I don't think that Shapiro believes that genomes or cells have intelligence or planning in the normal sense of those words), the whole question of probability becomes less important. If organisms have to wait for the right mutation, or the right combination of two, three, or more mutations, before they gain any selection advantage, then the sort of arguments that Behe and Dembski make become very important (even if Elizabeth believes that their numbers are wrong, their concern is in principle right); but if organisms can, to a significant extent, reorganize their own genetic material, evolution could happen much more quickly than the ND or other merely stochastic models would allow for. Using scare quotes again, to show that I realize the inaccuracy of these terms if we are trying to be historically strict, Shapiro's view seems to be more "Lamarckian" than "Darwinian." And ID arguments don't apply against "Lamarckian" notions of evolution. Or at least, they would need to be radically reformulated in order to do so; the whole ID machine is tooled for the attack on neo-Darwinism. So ID can take two approaches to someone like Shapiro. It can take a skeptical approach, and deny that the evidence for self-engineering capacities is very great; in that case, Shapiro's evolution would boil down to something like NDE with just a few extra bells and whistles, occasionally a bit faster but otherwise largely dependent upon external contingencies. Or, if the evidence for Shapiro's view builds, and it looks as if organisms can reorganize their genomes in a serious way, in response to need, then ID can ask: "Where did organisms get this capacity?" After all, when human beings build computer systems that can respond to situations and make choices based on those situations, those computer systems are *designed*; they aren't the product of chance. If the DNA-protein-cellular system, from the get-go, already has capacities for choice, including the choice of self-reorganization, and if, as it seems, these capacities go far beyond any system human engineers have so far devised, we have to ask how this *system* arose. Could it have arisen without the planning or design of an intelligence external to itself? Analogy from human experience would suggest, "No." So ID proponents would then be able to congratulate Shapiro on his successful breaking of the Darwinian mold, but then argue that he should join the ID camp. Back to Denton. Because Denton takes the design beyond the design of the first living things back to the design of the fundamental particles and laws of nature, his view is more radical than Shapiro's, and more ambitious. Denton is aware that his view is speculative and he doesn't claim to have proved anything. However, the advantage of Denton's view for those who cannot accept the notion of "intervention," is that, unlike Shapiro, he doesn't just stop at the question how life got its quasi-intelligent properties, leaving a door open for a miracle; he tries to show that no intervention would ever be necessary if you get the laws of nature right at the time of the Big Bang. This throws the intelligent design of the universe back to the beginning, and leaves the intelligent designer out of the picture after that. So if you believe in some sort of God as the brains behind nature and life, but don't want him interfering in any way, Denton is the man for you. You get God, while getting rid of miracles -- for some people, the best of both worlds, because it retains an intelligent source of nature, while freeing up natural science completely from religious restrictions of any kind, allowing it investigate literally any past event without invoking miracles. The only scientifically inexplicable event is then the absolute beginning in which nature itself was created -- it is only there that intelligent design is tied to a particular creative action. So Denton's view compels the existence of God, but not the interfering God of revealed religion; Shapiro's view is silent about God, but leaves open the possibility that God directly created these marvellous self-engineering cells (though Shapiro himself doesn't appear to personally believe that). Both of them agree that once the cells are created, no miracles are needed to explain anything that happens later. I've given you this long explanation so that you can see exactly how, in my view, Shapiro and Denton differ from Darwinian thinking. In my view, you can only call either one a special case of "Darwinism" by overlooking very important differences, and the label "Darwinism" for either one would massively confuse anyone who was trying to understand how these writers think evolution works. If you choose to call either or both of them special cases of "Darwinism," despite my analysis, I cannot stop you. But now you know why I wouldn't use that term for either one of them, and so my obligation to explain myself is fully discharged. (I would add that Denton contrasts his own view with the Darwinian, and Shapiro contrasts his own view with at least the neo-Darwinian, so even if you don't find my discussion helpful, it might be wise not to classify these people with a terminology they would not accept.) As for your Denton/Meyer comparison, all I can say to you is that I have read both books, very carefully, and there is no comparison. Meyer's book has merit, but is much too long for its limited purpose, whereas Denton's book (his second book, *Nature's Destiny*, is the one I'm speaking of) is necessarily long because of the richness of detail of his discussion. And Denton's book is such that its content (a vast but integrated tour through cosmology, geology, biochemistry, etc.) is intrinsically interesting, outside of any reference to evolution, design, etc. His broad grasp of nature is impressive and he infects the reader with a love for the dazzling intricacy and sophistication of the natural world. Reading Denton is like reading Dawkins's *The Blind Watchmaker* or Sagan's *Intelligent Life in the Universe*. I don't see how anyone with any broad interest in natural science could fail to enjoy reading Denton's book, even if they disagreed with his conclusions. There is no book by any Discovery fellow anything like it. That is not to denigrate the books of Dembski, Meyer, Behe, etc. It's merely to indicate that Denton's book, while "id" in the generic sense, is not "ID" in the sense of belonging to the institutional program of Discovery. Anyone taking any position in the culture wars could enjoy it and benefit from it. So if you want one of the most thoughtful book-length treatments of evolution to appear in the past 20 years, Denton will satisfy. But of course, if you have some sort of inbuilt hatred for any writer who would even consider the possibility than there might intelligent design anywhere in the universe, you will not want to read Denton, since you will reject his conclusions a priori. But such a position would reflect an atheist dogmatism, not a genuine scientific curiosity about nature. T.Timaeus

January 21, 2012

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Timeaus I agree my comment was poorly expressed.  I have a little more time this morning. I will try to put it more carefully and clearly. Take your option (2):

(2) design that organic matter imposes upon itself by some set of intrinsic creative capabilities

My contention is that this is either compatible with Darwinism or indistinguishable from external design. First I assume you agree that evolution happens by a process of one organism being descended from one or two parents and the child being different from the parents.  I am not saying anything about the degree or mechanism of this variation at this point. There are two options for this variation.  A) There is a satisfactory unguided explanation of the variation.  By an unguided explanation I mean we can see a plausible route for how given the features of the parent the child could arise which is based on natural and understood processes.  For example, if the parent contained units of DNA that would be extremely useful to the child and all that was required was a simple shifting around of those units that would be plausible given the parent.  (Shapiro and Margulis both fall into this category). B) There is no satisfactory unguided explanation.  For example, in some inexplicable way the base pairs reorganise themselves in one go into a complicated structure that provides a whole new useful function for the child – such as a new appendage. In case (B), if  you are prepared to accept design as an explanation, then I cannot see that there is anything immanent about it.  There was nothing in the parent to make it happen.  If there had been it would have fallen under case (A).  Some external force must have caused the implausible leap. So immanent design must be case (A) – every child is descended by unguided processes from its parent(s) and anything that makes you think design arises from features of the parent.  So how far do you take this back?  We have said that every child is descended from the parent by unguided processes (or else we have an instance of external designer intervention). So we must go back at least to the origin of life and you seem to imply that Denton goes back to the Big Bang. So we can summarise immanent design as life evolved from the OOL (or before) through unguided processes and the design of life is a result of features of the first living things. But Darwin’s theory had nothing to say about the origin of life much the less the Big Bang (he speculated about OOL in informal letters but it was not part of his theory).  His was only a theory about how life evolved from the OOL onwards.  It can be summarised as life evolved from the OOL through unguided processes. It said nothing about the features of the first living things. Therefore immanent design is compatible with Darwinism. In fact it is a special case of Darwinism. I take your point about reading Michael Denton.  You have not yet convinced me it is worth it.  I wasted a fair amount of time spent reading Signature in the Cell because of similar taunts.  If someone can provide a convincing example of what is meant by immanent design I might change my mind. markf

January 21, 2012

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markf: I've run out of time on this thread, so briefly: I'm confused by your exposition. The alternatives Elizabeth and I were discussing were (1) design imposed upon organic matter by an outside mind, i.e., a direct creation model, and (2) design that organic matter imposes upon itself by some set of intrinsic creative capabilities. You now seem to be throwing in a third possibility -- continuous intervention -- which we weren't discussing. Why have you added this in? Regarding the two models were were discussing, my view is that position (2) above amounts to an indirect creation model. For how did these genius "self-engineering" cellular-protein-genome systems become such geniuses? They may have produced all species, but what is *their* origin? I'd argue that they must have been intelligently designed. So we would need an "external" designer to create these systems, after which they would operate as the "internal" designer of future evolutionary outcomes. The difference would be that the external designer would (in my view) have to be a conscious agent, whereas the internal self-engineering systme would not be a conscious agent, but would merely be a highly adaptive organic computer program (of a type far beyond what human engineering could produce today). This is why ID people are more sympathetic with Shapiro than with ND or Margulis; Shapiro's view lends itself to an ID interpretation, even if Shapiro himself refuses to speculate about the origin of the self-engineering, self-evolving systems. If you want the empirical evidence which Shapiro uses to shoot down classical ND mechanisms and support his own, don't guess and speculate; read what Shapiro has written. If you want to know how Denton's system would operate differently from Darwin's, and hence would yield different predictions, read Denton. Don't rely on me to summarize for you. I might do it inaccurately, and in any case, I have no more time. If you are really interested, you won't shirk the job. T.Timaeus

January 20, 2012

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Perhaps I should just start a list. :lUpright BiPed

January 20, 2012

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I have no problem with God creating the universe, except that it doesn't answer any questions about how things work. You still need science to figure out how stuff works. Science doesn't answer big questions such as why there is something rather than nothing, but it can describe the solar system and enable us to explore it. It can probably never answer the historical question of how live originated, but it can study and describe how living things behave.Petrushka

January 20, 2012

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Peter,

"...well, publish or perish!"

I can't fully appreciate all the intricacies of English even though I have lived more than 10 years in the UK. But at the face of it, it sounds quite rude to me. On the material point, it is up to you, guys, to explain how symbolic information transfer, control and function are possible via chance and necessity. Up to the time of Darwin, to be a scientist one needed just to be a strong independent thinker without necessarily having to publish stuff anywhere. And even now it takes genius, independence of thought and courage to be a genuine one. I think that the main design proponents have those qualities in much bigger quantities than ordinary blokes who publish scores of papers a year and peer review the same stuff by their colleagues in like numbers. I am sure in 100 years' time no one will even know who these mainstream personalities were (without calling names) but people will know who, say, Dembski or Abel were, for sure.Eugene S

January 20, 2012

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Champ, thank you for providing a link. I am perfectly happy to allow the previous exchange to speak for itself. Peter, I provided a link. I'll check back later, cheers.Upright BiPed

January 20, 2012

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Upright, Could I have a fer'instance?Peter Griffin

January 20, 2012

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It's a bit like asking which came first, males or females. Or which came first, the genetic code or the machinery that interprets it.Petrushka

January 20, 2012

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Upright, Apparently, once again, you are avoiding Nick's question. At least Eugene had the guts to admit that evolution can produce an increase in information.champignon

January 20, 2012

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Apparently, once again, there is no interest in discussing material evidence.Upright BiPed

January 20, 2012

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Eugene, That's not what I meant and you know it!

I just don’t see why science should be afraid of “design” as causation.

It's not afraid. When you have evidence for it, then science will examine that evidence! It's as simple as that! So, today for the next hour only, I'm not going to be afraid of design as causation. Eugene S, please tell me how ID explains the origin of ATP via design! You can't, of course. And that's the point. When you can it will be listened to. Until then, well, publish or perish!Peter Griffin

January 20, 2012

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Joe, When did the design get implemented Joe? A million years ago? 10 million 6000 years ago? Yesterday? Right now?

That said what you asked is what science is for. Also your position doesn’t have any answers.

A transitional fossil was predicted at a particular location. A transitional fossil was found at the predicted location. Case closed! Here's an answer for you Joe. You claim that ATP was designed. Here's evidence that it evolved! http://www.nature.com/nature/journal/v481/n7381/full/nature10724.html

Many cellular processes are carried out by molecular ‘machines’—assemblies of multiple differentiated proteins that physically interact to execute biological functions. Despite much speculation, strong evidence of the mechanisms by which these assemblies evolved is lacking. Here we use ancestral gene resurrection and manipulative genetic experiments to determine how the complexity of an essential molecular machine—the hexameric transmembrane ring of the eukaryotic V-ATPase proton pump—increased hundreds of millions of years ago. We show that the ring of Fungi, which is composed of three paralogous proteins, evolved from a more ancient two-paralogue complex because of a gene duplication that was followed by loss in each daughter copy of specific interfaces by which it interacts with other ring proteins. These losses were complementary, so both copies became obligate components with restricted spatial roles in the complex. Reintroducing a single historical mutation from each paralogue lineage into the resurrected ancestral proteins is sufficient to recapitulate their asymmetric degeneration and trigger the requirement for the more elaborate three-component ring. Our experiments show that increased complexity in an essential molecular machine evolved because of simple, high-probability evolutionary processes, without the apparent evolution of novel functions. They point to a plausible mechanism for the evolution of complexity in other multi-paralogue protein complexes.

Whereas the ID "explanation" for how ATP came to be is "it was designed" Sure, you can write page after page (and you have) as to why it's not possible it evolved but in fact you don't have a word to say about how it did come to be. Yet "Darwinism" does. I know you'll jump on this phrase "Despite much speculation, strong evidence of the mechanisms by which these assemblies evolved is lacking" I'd only note that "weak evidence" (i.e. not strong) is better then no evidence at all (i.e. what ID can offer with regard to the origin of ATP). And the point of that article is to provide such strong evidence in any case. Can ID offer anything with a comparable level of detail as to the purported intelligent design of ATP?Peter Griffin

January 20, 2012

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"...does design happen all the time everywhere?" Oh yes, it is happenning as we speak. You and I are using our keybords to write specific sentences and record them using appropriate media. I just don't see why science should be afraid of "design" as causation.Eugene S

January 20, 2012

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http://pandasthumb.org/archives/2007/01/92-second-st-fa.html

To summarize, the claims that have been and will be made by ID proponents regarding protein evolution are not supported by Axe’s work. As I show, it is not appropriate to use the numbers Axe obtains to make inferences about the evolution of proteins and enzymes. Thus, this study does not support the conclusion that functional sequences are extremely isolated in sequence space, or that the evolution of new protein function is an impossibility that is beyond the capacity of random mutation and natural selection.

http://sfmatheson.blogspot.com/2011/05/exploring-protein-universe-response-to.html

This does not mean that Axe and Gauger are incorrect in their hypothesis, namely that different proteins are separated by vast evolutionary wastelands that can only be traversed with the help of "design." That may be the case. But the newly-published work in BIO-Complexity gets them no closer to establishing that hypothesis as reasonable or even likely.

http://aghunt.wordpress.com/2008/12/26/axe-2004-and-the-evolution-of-enzyme-function/

To summarize, the claims that have been and will be made by ID proponents regarding protein evolution are not supported by Axe’s work. As I show, it is not appropriate to use the numbers Axe obtains to make inferences about the evolution of proteins and enzymes. Thus, this study does not support the conclusion that functional sequences are extremely isolated in sequence space, or that the evolution of new protein function is an impossibility that is beyond the capacity of random mutation and natural selection.

Obviously the quotes are just tasters, follow the links for the full detail. If, however, you choose to read the ID supporting point of view Darwinism has already been disconfirmed and they are just waiting for somebody to take away the remains!Peter Griffin

January 20, 2012

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Such as? I'd love to hear.Eugene S

January 20, 2012

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ID diiferentiates itself from Creationism by the mere fact that ID does not rely on the Bible. That said what you asked is what science is for. Also your position doesn't have any answers.Joe

January 20, 2012

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Peter, Evos never support anything.

And yet in another breath you say that ID is not about studying the designer and you can’t in fact study the designer.

You are seriouly demented as I have never said that. ID is not about the designer. that does not mean no one can try to determine who/ what it was. And context is important and obvioulsy you are too stupid to understand the context of what I posted even though I was responding to you.Joe

January 20, 2012

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Joe,

One design.

Typically you support your answer with reasoning.

can’t say until we can study them, duh.

And yet in another breath you say that ID is not about studying the designer and you can't in fact study the designer. Make your mind up!Peter Griffin

January 20, 2012

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Joe, One of the ways that ID can differentiate itself from creationism is to distinctly say when the design event(s) happened. Was there just one, a long time ago, or does design happen all the time everywhere?Peter Griffin

January 20, 2012

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Elizabeth, For one, modern medicine, including vaccines, have allowed some people to live when nature would have eliminated them.Joe

January 20, 2012

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Artificial selection is what is allowing people who shpuldn’t breed to breed.

What?Elizabeth Liddle

January 20, 2012

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Elizabeth, Artificial selection is what is allowing people who shpuldn't breed to breed. And yes maybe Provine is wrong but the arguments he makes are better than anything you have ever posted.Joe

January 20, 2012

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Joe, if eugenics is the deliberate policy of allowing some human beings to breed and not others (as it usually is) then Darwinism is not eugenics. Darwinism is about natural selection, not artificial selection. Darwinism is a scientific theory, not a policy Darwinism about how we, and all other species, came to be the way we are, not what we should do in order to becomes somethign else.Elizabeth Liddle

January 20, 2012

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Elizabeth (5.1.2.2.2): As you yourself point out, Elizabeth, words have different meanings for different groups of people. "Theistic evolutionist" has a sort of generic meaning, which probably covers what you used to be; but you made a little dig about the criticisms we here on UD make of theistic evolution, and *that particular form of theistic evolution* is an American development of the past 20 years, and we know it extremely well; some of our members here have been on the mats with TEs in numerous public venues. Many of us know all the nuances in the positions of Ken Miller, Karl Giberson, Darrel Falk, Dennis Venema, George Murphy, Francis Collins, Denis Lamoureux, etc. We have read scores of their essays, hundreds of their blog posts, and many of their books. If you aren't deeply familiar with these authors, your comments on the subject will be of no use to us. The theistic evolutionists of whom I have been speaking are indeed Christian Darwinists, which for most ID people is a contradiction in terms, meaning, in effect, "teleological anti-teleologists." ID people are not Christian Darwinists, because they are not Darwinists at all -- as they understand the term. My comment about your ID reading was not for the sake of one-upmanship. I think that some of your confusions spring directly from not reading enough ID material, and not collating it all in your mind, noting similiarities and differences, resolving apparent internal contradictions by noting careful qualifications, etc. You seem to prefer attacking single statements or articles on a piecemeal basis. I have noticed that this is a common approach among science-trained people who debate evolution on the internet. Arts-trained people operate differently. They read broadly and deeply when learning a new position, before trying to refute it. My comment about your vocabulary was meant as a compliment, not as a dig. I was saying that you were bright, and given that you said you used to spend much time reflecting on religious questions and reading the likes of Aquinas, I was surprised you didn't immediately translate "immanent" into some appropriate biological equivalent. In any case, I've now explained what I meant by it. We aren't going to agree on the supposed intrinsic intelligence or design in Darwinism. I just refuse to use the word intelligent or design unless we are talking about conscious minds. There is no design in Darwinism; what arises, arises without any intelligent planning. You can use words any way you want to; but there is no point in your continuing to disagree with people here about intelligence and design in Darwinian biology when no one in this camp is going to use the words with your definitions. Banging your head against that wall will produce only a sore head. T.Timaeus

January 20, 2012

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06:36 AM

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Joe: maybe Provine is wrong?Elizabeth Liddle

January 20, 2012

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06:33 AM

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