Thursday, January 19, 2012

James Shapiro Publishes on Evolution News & Views

James A. Shapiro, author of Evolution: a View from the 21st Century has been criticized for being an Intelligent Design Creationist, or at least a sympathizer. He denies it but his denials sound very much like someone who protests too much.

Shapiro has now been allowed to post an article on the main IDiot blog, Evolution News & Views [A Response to Ann Gauger's and Douglas Axe's Comments. I don't agree with his response but that's not the point. Do you know any respectable evolution supporter who would post on a creationist blog?

Can you imagine his University of Chicago Colleague, Jerry Coyne, posting an article on the flagship blog of the Discovery Institute?


26 comments :

  1. Jim seems to be much more of a drama queen, than an ID supporter. What better to compel attention, even if the wrong kind, than "publishing" in a discoveroid blog?

    His description of individual aminoacid changes as "Darwinian modifications," reminded me of those advertisements where, for example, a new knife is advertised for cutting bread, showing that the bread "crumbles" using the old knife (which is misused while the hand is actually doing the pushing for dramatically exaggerated effect).

    I would love to know how Darwin learned about genetics and molecular biology so early in time that he could build his theories at such a specific level of detail.

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  2. Larry, why do you insist on refusing to acknowledge that intelligent design is not creationism? It's the same old tactic, a discussion stopper. It's like saying "I know what I know, and that's all I need to know." Whatever happened to open, honest, humble debate about important ideas? What would prevent you from meeting ID at the table, unless you are deathly afraid that they're onto something?

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    1. You are a creationist if you believe in a creator. Everyone who promotes intelligent design is a creationist and the movement is accurately described as Intelligent Design Creationism. Read Creationism Continuum.

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    2. GT

      My answer would be:

      Why do you insist on refusing to acknowledge that ID is creationism? Just take a look and you will see that all that ID "offers" is regurgitated same-old creationist arguments and tactics: calculating probabilities for a straw-man of evolution, for example by equating evolution with pure randomness, or refusing to notice that entropy is not exactly "tendency to disorder," or that our planet gets more than enough energy to keep evolutionary processes going, and that thus evolution is not a process that would running against entropy. Long et cetera. They will ignore such little details no matter what, which becomes obvious when you make an observation they did not expect. Then their answer is too often something about materialism, which sounds oddly enough like creationism, doesn't it? I am also wondering how comes then that a main source of ID-shit posts so many entries about evil materialism/naturalism, or links from Darwin to Hitler. After all, those are creationist propaganda. How could I even start to think that ID might not be creationism if they insist on showing me that it indeed is creationism? Even their "new" arguments are about misinformed "improbability," such as "irreducible complexity," or classic creationist propaganda techniques such as cherry-picking and misquoting from selected articles while forgetting data to the contrary, such as in "the signature of the cell."

      Can you see the problem yet?

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    3. "why do you insist on refusing to acknowledge that intelligent design is not creationism?"

      Ummm, could that be because they aren't soooo much different after all?!
      ID is nothing but creationist agenda from which one takes away creator's label and one inserts illegitimate claims to be legitimate good science. Of course, that won't change its essence.

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    4. Professor Moran,

      Just a quick question. Would you call Thomas Jefferson and Tom Paine creationists? (Yes, I'm aware that they weren't Christians but Deists, that Jefferson was a materialist who believed in a cosmos that had no beginning, and that Paine was fervently anti-Christian. The fact of the matter is, though, that they both believed that the laws of Nature pointed to the existence of a Creator.)

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    5. sez globe trotter: "Larry, why do you insist on refusing to acknowledge that intelligent design is not creationism?"
      I can't speak for Professor Moran, but I can certainly tell you why I refuse to acknowledge that Intelligent Design is not Creationism: I don't like to propagate lies. And the statement "ID is not Creationism" most assuredly is a lie. More specifically, ID is the latest obfuscatory tactic adopted by Creationists in their continuing campaign to have their religious dogma taught in public school science classrooms.
      Consider that every last one of the arguments in the Discovery Institute's text EXPLORING EVOLUTION is an old, bogus, pre-refuted 'argument' that originated from Creationist 'argumentation'; how could that be, if ID actually were distinct from Creationism? It's also relevant that one of the authors of EXPLORING EVOLUTION is, himself, a Creationist…
      Consider that the so-called 'Wedge Document', which outlines the ID movement's tactics and overall goals, explicitly declares the ID movement's two "governing goals" to be, first, "To defeat scientific materialism and its destructive moral, cultural and political legacies", and second, "To replace materialistic explanations with the theistic understanding that nature and human beings are created by God". These 'governing goals' make perfect sense for a Creationist campaign to inject religious dogma into public school science classrooms, but not for an actual field of science.
      Consider that the earlier ID textbook, OF PANDAS AND PEOPLE, was an out-and-out Creationist text in its earliest drafts -- and all that seemed to be necessary in order to convert PANDAS from a Creationist text to an ID text, was a search-and-replace operation which changed strings like "Creator" to strikes like "Intelligent Designer" -- try googling for "cdesign proponentsists" for more details on a particularly glaring, and amusing, example of this. If ID is not Creationism, how come a simple change in phraseology is all that was needed in order to convert the original Creationist PANDAS into the final Intelligent Design PANDAS?
      Apart from all the other evidence that ID is a wholly-owned subsidiary of Creationism, it's worth noting that ID proponents themselves say that ID is Creationism. They generally don't use those exact words, true, but is that because of any essential difference between ID and Creationism, or is it because ID-pushers are aware that the US court system has consistently & repeatedly struck down attempts to inject Creationism into public school science classrooms?
      Consider that Philip Johnson, author of the seminal ID book DARWIN ON TRIAL, is on record as explicitly saying, in so many words, that ID "really means the reality of God".
      Consider that William Dembski, creator of the ID design-detection methodology called the 'Explanatory Filter', is on record as explicitly saying that "intelligent design is just the Logos theology of John's Gospel restated in the idiom of information theory".
      Consider that damn near every last ID-pusher there is, is a Christian -- and that ID-pusher Michael Behe is on record as acknowledging that ID seems much more plausible if you're a Christian. Curious, that.

      I could go on, but if the above bits of evidence don't suffice to support the proposition that ID is Creationism, more won't help. Does that answer your question, globe trotter?

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    6. Re Vincent Torley

      What do the views of Thomas Jefferson and Tom Payne on a scientific issue have to do with anything? Just for the information of Mr. Torley, Issac Newton, the most important scientist who ever lived, was also a creationist (in addition to believing that chemical processes could turn lead into gold). Charles Darwin was a creationist then he stepped on board the Beagle. Back in those days, the extent of scientific knowledge was insufficient to come to any conclusion as to the nature of life.

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  3. I'd say if Shapiro has the chance to address some of Gauger and Axe's misunderstandings on their home turf, that's not a bad forum to do it. Many of us post comments on ID blogs when sufficiently motivated by a particular error - so why not guest posts? There have, of course, been the odd guest post on Uncommon Descent from ID opponents, so this type of thing is not unheard of.

    Given this, the issue really should be whether he has adequately characterised contemporary understanding of the evolution of novel protein function, rather than the forum he has chosen to do it. As NE points out above, the use of "Darwinian" is unfortunate as this should implicate stepwise 'gradual' positive selection, rather than a more generalised model of nucleotide substitutions. But forgiving this, his wider point seems to have some merit - Gauger and Axe artificially restrict the models of evolution to ones that don't adequately characterise evolution - strawmen, in other words.

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  4. Still waiting for the open, honest debate from ID creationists where they admit openly and honestly what most of them believe, namely that the intelligent designer is the Christian god. Also waiting for evidence for ID, instead of just attempts to disprove evolutionary theory, followed by the implied syllogistic conclusion: therefore, goddidit.

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  5. Larry,
    I read Shapiro's post you linked to and would say it is a clever PR trick. He's basically telling IDudes and critics who regularly scan that ID-page to buy his book, because that's where all the answers are supposed to be found.

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  6. Laurence, Why don't you post my entire blog entry so your readers can judge for themselves? Here it is. As Joachim remarks, I naturally want to sell my book. That is why I wrote it. But no one needs to buy anything to use the free reference materials posted on my web page. Jim Shapiro

    A Response to Ann Gauger’s and Douglas Axe’s Comments

    Continuing a conversation initiated by Bill Dembski (“Is James Shapiro a Design Theorist?”), Ann Gauger wrote:
    So far, our research (http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2011.1 ) indicates that genuine innovation, a change to a function not already pre-existent in a protein, is beyond the reach of natural processes, even when the starting proteins are very similar in structure. No supernatural presuppositions here, just standard genetic engineering, with a result similar to what protein engineers have found any time they try to engineer a new function onto an existing protein template.

    Douglas Axe wrote:
    As an ID proponent, I've put forward the scientific case for thinking that the thousands of distinct structures that enable protein molecules to perform their specific tasks inside cells cannot have arisen in a Darwinian way (http://bio-complexity.org/ojs/index.php/main/article/view/25 ). Moreover, the facts of this problem seem to preclude any naturalistic solution, Darwinian or not.

    Ann and Doug, the problem of protein evolution is covered in detail in my book (http://www.amazon.com/Evolution-View-Century-Press-Science/dp/0132780933/ref=cm_cr_pr_product_top ), and a relevant periodically updated bibliography is posted online (http://shapiro.bsd.uchicago.edu/ExtraRefs.ModularDuplicativeNatureProteinEvolution.shtml ). The 2001 draft human genome paper in Nature contains two figures that summarize the revolution that has occurred in our understanding of protein evolution (Lander, Linton et al. 2001).

    Proteins evolve largely by shuffling and accreting functional subregions called “domains,” not through the Darwinian modifications of individual amino acids (Doolittle and Bork 1993). Domain accretion and shuffling are inherently natural genetic engineering processes (i.e. non-Darwnian) because they involve the rearrangement of extended DNA segments that encode the different domains. As my book details, we have many examples of this process mediated by mobile genetic elements in nature as well as its replication in living cells in the laboratory. Moreover, we know a great deal about the roles of mobile genetic elements as sources for completely novel domain coding sequences through the process currently known as “exonization” (http://shapiro.bsd.uchicago.edu/ExtraRefs.NaturalGeneticEngineeringAndEvolutionaryGenomicInnovation.shtml ).
    I suggest you review this literature to see that well-documented natural processes are more than adequate to explain how protein evolution for new functionalities can occur in a purely natural and combinatorial fashion. One of the motives behind my book was to acquaint readers with these and other poorly known examples of revolutionary discoveries in molecular genetics and genomics that allow us to view evolutionary processes in a new light.

    REFERENCES

    Doolittle, R. F. and P. Bork (1993). "Evolutionarily mobile modules in proteins." Sci Am 269(4): 50-56. http://www.ncbi.nlm.nih.gov/pubmed/8235550.
    Lander, E. S., L. M. Linton, et al. (2001). "Initial sequencing and analysis of the human genome." Nature 409(6822): 860-921. http://www.ncbi.nlm.nih.gov/pubmed/11237011.

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    1. James Shapiro asks,
      Laurence, Why don't you post my entire blog entry so your readers can judge for themselves?

      Because that's not the point. You are being accused of skating around the issue of intelligent design and publishing on the Discovery Institute blog seems like a very strange way to convince us that you oppose Intelligent Design Creationism.

      So let me ask you straight out ... do you or do you not believe that God played a role in the evolution of life on Earth, especially humans?

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    2. Jim,

      I have no issue with a concept of natural genetic engineering (unless it is seriously given an unnecessary teleological bent), but I do have issues with the presentation of "anything else" wrongly. Example: "Darwinian" cannot be "point mutations." Actually, your naturally genetically engineered organisms can and would be positively selected if they recombined the right stuff, which would make the process "Darwinian."

      If a presumably evolutionary biologist presents the "other concepts" the wrong way, those who perceive you as the expert will buy into it, and thus create lots of confusion across disciplines. As if common misunderstandings weren't enough.

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    3. Evolution occurs naturally, without supernatural intervention. How else could a scientist treat it? That's why I took pains to explain to the ID people that newer results and more up-to-date views of evolution solve problems that older ideas cannot. They were unaware of where science had gone in the last 60 years. Isn't that the way science makes progress? Many in both the public and even the evolutionist community are also in ignorance of recent molecular developments. That's what I am trying to convey in my book. As a scientist, I would have expected you to welcome making this information more widely available.

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    4. Larry, In addition, perhaps you should also post Dembski's original article and my reply to him. It would be helpful for your readers to see the whole exchange. I'll leave it to you to copy everything over. I hope you can keep all the links live. Jim

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    5. James,

      I suspect the reason why some are suspicious of your views may be due to the way you use the term "Darwinian", as in this passage:

      "Domain accretion and shuffling are inherently natural genetic engineering processes (i.e. non-Darwnian) because they involve the rearrangement of extended DNA segments that encode the different domains."

      I admit I'm not well-informed about your work, but having just read several of your online articles I find it hard to see why such rearrangement should be considered "non-Darwinian". I suspect that you are using the word "Darwinian" in quite a narrow sense and that your detractors (and ID advocates) are taking it in a much broader sense, and so see your "non-Darwinian" claim as much more radical than it really is. It seems to me it's not the substance of your views which is so controversial but your use of the word "non-Darwinian".

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    6. Evolution occurs naturally, without supernatural intervention.

      Thanks for responding. Do you believe that God created the universe?

      Many in both the public and even the evolutionist community are also in ignorance of recent molecular developments. That's what I am trying to convey in my book. As a scientist, I would have expected you to welcome making this information more widely available.

      I'm more than pleased to help explain recent developments in molecular biology and evolution. That's why I wrote a post showing where you went wrong in explaining the Central Dogma of Molecular Biology [http://sandwalk.blogspot.com/2011/08/revisting-central-dogma-in-21st-century.html].

      And that's why I've written dozens of posts over the years showing why you are wrong about most things in your book.

      There's no such thing as "natural genetic engineering." Evolution just happens.

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    7. There seems to be a fine difference in usage between those who see science as gradually developing and those who see it as stasis punctuated by revolutionary change. The gradualists call whatever their received view may be "Darwinian" and the new view arising from new discoveries "neo-Darwinian"; the revolutionists also call their received view "Darwinian" but the new view "non-Darwinian".

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  7. Professor Moran,

    As a regular contributor to the ID Website Uncommon Descent, I can tell you that we do sometimes invite people whose views are diametrically opposed to our own to write their own posts for our Website. One example would be the physicist Sean Carroll, who very courteously did just that last June. He's an outspoken atheist, but as far as I know, he's never said anything rude about people who disagree with his views. He also has a very clear and accessible style of writing.

    James Shapiro's post on Evolution News and Views was a model of courtesy, even as he made clear his strong disagreement with the views of Ann Gauger and Douglas Axe, who maintain that "a change to a function not already pre-existent in a protein, is beyond the reach of natural processes."

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    1. I believe you when you say that you sometimes invite outsiders to post on ENV. That's not the point.

      The point is what kind of person would accept such an invitation? If I were a scientist I would be very leery of accepting such an offer, especially if my colleagues were expressing doubts about my understanding of evolution and my opposition to creationism.

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  8. But Ann Gauger also says "No supernatural presuppositions here" which is at odds with the claim of being "beyond the reach of natural processes".

    Come on, 'fess up, you really think that god did it, don't you ?

    Or was it space aliens ?

    I note that IDiots took Richards Dawkins to task, when forced to come up with a possible hypothetical non Darwinain explanation for life on earth said - IF there were aliens that created us, then they'd have had to EVOLVED.

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  9. "a change to a function not already pre-existent in a protein, is beyond the reach of natural processes."

    So presumably ID offers a method for discovering which things are 'preexistent' in a protein and which are not, correct?

    I wonder if IDers will ever understand the idea of incremental change. Or maybe it's 'deep time' they don't understand. They are certainly incapable of combining the two.

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    1. Not only that, they have no idea that there are more than one way to do things. They think a protein has to have a very specific sequence or it won't work. Any changes leading to a different function had to be those exact changes, no other changes would have worked, et cetera.

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  10. Professor Moran,

    Just a quick question. Would you call Thomas torley said:

    "Jefferson and Tom Paine creationists? (Yes, I'm aware that they weren't Christians but Deists, that Jefferson was a materialist who believed in a cosmos that had no beginning, and that Paine was fervently anti-Christian. The fact of the matter is, though, that they both believed that the laws of Nature pointed to the existence of a Creator.)"

    Could that be any more irrelevant? And what's your point? An appeal to alleged authority?

    Your desperation is showing.

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  11. I now see that some of the words in my comment above are mixed up. This is a corrected version:

    torley said:

    "Professor Moran,

    Just a quick question. Would you call Thomas Jefferson and Tom Paine creationists? (Yes, I'm aware that they weren't Christians but Deists, that Jefferson was a materialist who believed in a cosmos that had no beginning, and that Paine was fervently anti-Christian. The fact of the matter is, though, that they both believed that the laws of Nature pointed to the existence of a Creator.)"

    Could that be any more irrelevant? And what's your point? An appeal to alleged authority?

    Your desperation is showing.

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