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    <title>The Panda&apos;s Thumb</title>
    <link rel="alternate" type="text/html" href="http://pandasthumb.org/" />
    <link rel="self" type="application/atom+xml" href="http://pandasthumb.org/atom.xml" />
    <id>tag:pandasthumb.org,2008-04-25://2</id>
    <updated>2008-09-05T06:40:34Z</updated>
    <subtitle>The Panda&apos;s Thumb is the virtual pub of the University of Ediacara.  The patrons gather to discuss evolutionary theory, critique the claims of the antievolution movement, defend the integrity of both science and science education, and share good conversation.</subtitle>
    <generator uri="http://www.sixapart.com/movabletype/">Movable Type Pro 4.21-en</generator>

<entry>
    <title>Looking for Dr. 900</title>
    <link rel="alternate" type="text/html" href="http://pandasthumb.org/archives/2008/09/dr-900.html" />
    <id>tag:pandasthumb.org,2008://2.3937</id>

    <published>2008-09-05T06:30:53Z</published>
    <updated>2008-09-05T06:40:34Z</updated>

    <summary>The National Center for Science Education is looking for a few good Steves to join them in standing up to the culture warriors that threaten the very foundations of science and science education. They need just a handful of new Steves to sign up, and then they can make “900” t-shirts.—At last count they had 895.—I only have three names, so I’m putting a call out to all my Steves, Stephens, Stephanies, et al., who’ve...</summary>
    <author>
        <name>Prof. Steve Steve</name>
        <uri>http://www.pandasthumb.org/</uri>
    </author>
    
        <category term="Steve Steve" scheme="http://www.sixapart.com/ns/types#category" />
    
    <category term="projectsteve" label="project steve" scheme="http://www.sixapart.com/ns/types#tag" />
    
    <content type="html" xml:lang="en" xml:base="http://pandasthumb.org/">
        <![CDATA[<div class="kw-format"><p class="kw-img-center"><img src="http://pandasthumb.org/archives/2008/09/05/weneed.jpg" alt="weneed.jpg" width="300" height="471" style="float:right;" /></p><p>The <a href="http://www.natcenscied.org" rel="external ">National Center for Science Education</a>  is looking for <a href="http://www.natcenscied.org/resources/articles/3541_project_steve_2_16_2003.asp" rel="external ">a few good Steves</a> to join them in standing up to the culture warriors that threaten the very foundations of science and science education.  They need just a handful of new Steves to sign up, and then they can make “900” t-shirts.—At last count they had <a href="http://www.natcenscied.org/resources/articles/meter.html" rel="external ">895</a>.—I only have three names, so I’m putting a call out to all my Steves, Stephens, Stephanies, et al., who’ve earned doctoral degrees, to join us in denouncing the campaign to box science into the ’30s—the 1530s.</p><p>Creationists love to name drop.  They compile lists of random people that hate evolution like they do—“my pa waz no munkie”—and then present those lists as expert testimony against the modern world.  In response, NCSE developed <a href="http://www.natcenscied.org/resources/articles/3541_project_steve_2_16_2003.asp" rel="external ">Project Steve</a>, a list of academics, scholars, and scientists that support evolution and oppose the anti-evolution movement.</p><p>There is just one catch: the signers have to be named after me.</p><p>I know, I know.  Some of you are asking, “who isn’t named after the illustrious Prof. Steve Steve?”  And I’ll tell you what, too many people are not named after me.  However, that top 1% that are named after me are the smartest people in the world, Stephen Baldwin excluded.  We Steves are so smart that even the US Congress has started focusing on <a href="http://pandasthumb.org/archives/2007/10/do-you-all-know.html" rel="">our opinions on important issues like global warming and polar bear biology</a>.</p><p>So what can we Steves do for the other 99%?</p><p>We can use our vast intellects and experience to agree with the following statement:</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>
Evolution is a vital, well-supported, unifying principle of the biological sciences, and the scientific evidence is overwhelmingly in favor of the idea that all living things share a common ancestry. Although there are legitimate debates about the patterns and processes of evolution, there is no serious scientific doubt that evolution occurred or that natural selection is a major mechanism in its occurrence. It is scientifically inappropriate and pedagogically irresponsible for creationist pseudoscience, including but not limited to “intelligent design,” to be introduced into the science curricula of our nation’s public schools.
</p>

</div></blockquote><p>Come on, all the other Steves are signing it, <a href="http://www.ncseweb.org/resources/articles/3948_want_to_become_an_ncse_steve_2_16_2003.asp" rel="external ">why don’t you</a>?
</p>

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    </content>
</entry>

<entry>
    <title>Tangled Bank #113</title>
    <link rel="alternate" type="text/html" href="http://pandasthumb.org/archives/2008/09/tangled-bank-11-2.html" />
    <id>tag:pandasthumb.org,2008://2.3936</id>

    <published>2008-09-03T14:31:41Z</published>
    <updated>2008-09-03T14:32:09Z</updated>

    <summary> You can view it in all of its time traveling glory at En Tequila Es Verdad....</summary>
    <author>
        <name>PZ Myers</name>
        <uri>http://scienceblogs.com/pharyngula/</uri>
    </author>
    
    
    <content type="html" xml:lang="en" xml:base="http://pandasthumb.org/">
        <![CDATA[
<a href="http://scienceblogs.com/pharyngula/tangledbank.php" title="The Tangled Bank"><img src="http://scienceblogs.com/pharyngula/tbbadge.gif" alt="The Tangled Bank" width="88" height="31" align="right" style="padding: 4px;" /></a>

<p class="lead">You can view it in all of its <a href="http://entequilaesverdad.blogspot.com/2008/09/tangled-bank-113-labor-day-carol.html">time traveling glory at En Tequila Es Verdad</a>.</p>]]>
        
    </content>
</entry>

<entry>
    <title>Carnival of Evolution!</title>
    <link rel="alternate" type="text/html" href="http://pandasthumb.org/archives/2008/09/carnival-of-evo.html" />
    <id>tag:pandasthumb.org,2008://2.3935</id>

    <published>2008-09-03T00:05:37Z</published>
    <updated>2008-09-02T23:11:19Z</updated>

    <summary>Good news! Thanks to the pioneering efforts of Daniel Brown, there is now a Carnival of Evolution. Better news! I will be hosting the next installment over at EvolutionBlog. So send your best evolution related writing to me at rosenhjd@jmu.edu. I&apos;m looking for good, original writing on anything related to evolution, so make sure you proofread your stuff before sending it to me. It&apos;s always nice to give a little link love to undeservedly obscure...</summary>
    <author>
        <name>Jason Rosenhouse</name>
        <uri>http://www.math.jmu.edu/~rosenhjd</uri>
    </author>
    
    
    <content type="html" xml:lang="en" xml:base="http://pandasthumb.org/">
        <![CDATA[<p>Good news! Thanks to the pioneering efforts of Daniel Brown, there is now a <a href="http://carnivalofevolution.blogspot.com/">Carnival of Evolution.</a> Better news! I will be hosting the next installment over at <a href="http://www.scienceblogs.com/evolutionblog">EvolutionBlog</a>. So send your best evolution related writing to me at rosenhjd@jmu.edu. I'm looking for good, original writing on anything related to evolution, so make sure you proofread your stuff before sending it to me. It's always nice to give a little link love to undeservedly obscure bloggers, so here's your chance to get some publicity. The deadline will be September 14.</p>]]>
        
    </content>
</entry>

<entry>
    <title>Steve Steve in London</title>
    <link rel="alternate" type="text/html" href="http://pandasthumb.org/archives/2008/08/steve-steve-in-2.html" />
    <id>tag:pandasthumb.org,2008://2.3934</id>

    <published>2008-08-30T11:26:43Z</published>
    <updated>2008-08-30T11:32:05Z</updated>

    <summary>Steve Steve is having the time of his life at the Nature Network conference. Right now, he’s slumped over on the podium, recovering from yesterday’s festivities. A picture is found below. The question for you is this: Who is Steve Steve explaining evolution to? View image...</summary>
    <author>
        <name>Mike Dunford</name>
        <uri>http://scienceblogs.com/authority/</uri>
    </author>
    
        <category term="Conferences" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="Steve Steve" scheme="http://www.sixapart.com/ns/types#category" />
    
    
    <content type="html" xml:lang="en" xml:base="http://pandasthumb.org/">
        <![CDATA[<div class="kw-format"><p>Steve Steve is having the time of his life at the <a href="http://www.nature.com/natureconferences/sciblog2008/programme.html" rel="external ">Nature Network conference</a>. Right now, he’s slumped over on the podium, recovering from yesterday’s festivities. A picture is found below. </p><p>The question for you is this: Who is Steve Steve explaining evolution to? </p><p><a href="http://pandasthumb.org/archives/2008/08/30/stevesteve1.html" rel="">View image</a></p>

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    </content>
</entry>

<entry>
    <title>Giardia lamblia, polyadenylation, and irreducible complexity</title>
    <link rel="alternate" type="text/html" href="http://pandasthumb.org/archives/2008/08/giardia-lamblia.html" />
    <id>tag:pandasthumb.org,2008://2.3932</id>

    <published>2008-08-30T00:07:05Z</published>
    <updated>2008-09-03T12:30:05Z</updated>

    <summary>(The following is a slight adaptation of this essay. Readers may post questions and/or comments there as well as here.) As this series of essays has explained, the polyadenylation of messenger RNAs is a vital aspect of gene expression in eukaryotic cells (and a not-so-unimportant facet of RNA metabolism in other contexts). Polyadenylation is mediated by a sizeable complex that includes various RNA-binding proteins, nucleases, and other interesting activities. Genetic studies in yeast indicate that...</summary>
    <author>
        <name>Arthur Hunt</name>
        <uri>http://aghunt.wordpress.com/</uri>
    </author>
    
        <category term="Evolution" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="Irreducible Complexity" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="Research News" scheme="http://www.sixapart.com/ns/types#category" />
    
    
    <content type="html" xml:lang="en" xml:base="http://pandasthumb.org/">
        <![CDATA[<div class="kw-format"><p>(The following is a slight adaptation of <a href="http://aghunt.wordpress.com/2008/08/08/giardia-lamblia-polyadenylation-and-irreducible-complexity/" rel="external ">this essay</a>.  Readers may post questions and/or comments there as well as here.)  As <a href="http://aghunt.wordpress.com/category/polyadenylation/" rel="external ">this series of essays</a> has explained, the polyadenylation of messenger RNAs is a vital aspect of gene expression in eukaryotic cells (and a not-so-unimportant facet of RNA metabolism in other contexts).  Polyadenylation is mediated by a sizeable complex that includes <a href="http://aghunt.wordpress.com/2008/07/18/the-polyadenylation-complex-rna-binding-proteins/" rel="external ">various RNA-binding proteins</a>, <a href="http://aghunt.wordpress.com/2008/07/31/the-polyadenylation-complex-endonucleases/" rel="external ">nucleases</a>, and other interesting activities.  Genetic studies in yeast indicate that virtually every subunit of the core complex is essential – for viability and for pre-mRNA processing and polyadenylation in vitro and in vivo.  (<a href="http://www.current-biology.com/content/article/fulltext?uid=PIIS0960982202013532" rel="external ">This review</a> is freely available and serves as a good starting point for readers who wish to explore the subject further.)  Biochemical and/or immunological depletion studies reveal a similar scenario in mammals, and a less-expansive set of studies suggests that a similar rule of thumb will apply in plants.  The bottom line of all of this is that almost all of the subunits of the polyadenylation complex seem to be essential – remove one, and the complex cannot function.  In the vernacular of a proponent of intelligent design, the polyadenylation complex would seem to be irreducibly complex.</p><p>It is in this context that the recently-completed genome of the parasitic organism <em>Giardia lamblia</em> enters the fray.  Last year, the complete sequence of <em>G. lamblia</em>, some 12 million base pairs, was determined and analyzed.  The authors of the <a href="http://www.sciencemag.org/cgi/content/abstract/317/5846/1921" rel="external ">study</a> published in <em>Science</em> noted a number of interesting things – a preponderance of genes encoding protein kinases, evidence for substantial horizontal gene flow from bacteria and archaebacteria, and a streamlined core gene expression machinery (transcription and RNA processing).  This streamlining is especially notable in the case of the polyadenylation machinery.  Remarkably, of all the subunits in the yeast complex, genes for only three* can be found in <em>G. lamblia</em> (see the figure that follows this paragraph - adapted from Fig. 1 of Morrison et al.).
</p>

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        <![CDATA[<div class="kw-format"><p><img src="http://pandasthumb.org/archives/2008/08/29/MorrisonFig1.jpg" alt="MorrisonFig1.jpg" width="463" height="606" style="float: left; margin: 0 20px 20px 0;" class="mt-image-left" />
Naturally enough, one of these is the poly(A) polymerase (PAP).   The other two polyadenylation-related proteins encoded by the <em>G. lamblia</em> genome correspond to Ysh1 and Yth1 (whose mammalian counterparts are CPSF73 and CPSF30, respective).  Interestingly, as summarized <a href="http://aghunt.wordpress.com/2008/07/31/the-polyadenylation-complex-endonucleases/" rel="external ">here</a>, these two subunits are the two to which nuclease activity has been ascribed.  Also interestingly, the only <a href="http://aghunt.wordpress.com/2008/07/18/the-polyadenylation-complex-rna-binding-proteins/" rel="external ">RNA binding subunit</a> amongst those seen is Yth1 (=CPSF30).  Other subunits are missing.  Thus, no other RNA binding subunits are apparent, none of the scaffolds (CPSF160/Yhh1, CstF77/Rna14, Fip1, symplekin/Pta1) are seen, and most of the subunits that have been shown to interact with the transcription complex (CPSF100/Ydh1, CstF50, and Pcf11, to name three) are absent.  Indeed, entire complexes (CstF, CFmI, CFmII) appear to be missing.</p><p>What might these startling omissions mean?  One possibility is that functional counterparts for most of these proteins exist, but that they have diverged so extensively as to be unrecognizable.  This might be the case for some of the missing proteins, but many of these are so highly-conserved between plants and animals that this seems an unlikely explanation.</p><p>Another possibility is that mRNAs are in fact not polyadenylated in <em>G. lamblia</em>.  This is apparently not the case, as cDNAs can be prepared using the usual methods (priming reverse transcription with oligo-dT).  Moreover, these cDNAs have untemplated poly(A) tracts, and some limited sequence-gazing can identify a putative polyadenylation signal.</p><p>Neither of these possibilities seems likely.  Which leaves us with the remarkable likelihood that mRNA polyadenylation in <em>Giardia</em> is mediated by a highly-reduced complex of but 3 proteins.  This in turn brings us to some fascinating discussion, about both function and evolution.</p><p>First, about function.  Absent some studies dedicated to polyadenylation mechanisms in <em>Giardia</em>, it’s hard to make sense of the absence of so many essential components of the polyadenylation apparatus.  But the fact that the <em>Giardia</em> complex consists of the two known endonucleases is interesting, as it suggests that the very core of the complex in eukaryotes is an endonucleolytic one.  It also suggests that, as we peer ever more closely into the complex in other organisms, these two subunits will attract more attention.  Other questions about RNA recognition and of links with transcription and splicing also come to mind.  For example, might the RNA-binding activity of Yth1/CPSF30 play a more prominent role in polyadenylation signal recognition than has been assumed?  Is there an obligatory link between transcription and polyadenylation? If so, what is the link in <em>Giardia</em>, and what might this suspected mechanism tell us about the analogous link in other eukaryotes?  Etc., etc., etc.</p><p>Which brings us to the evolution of the complex.  <em>Giardia</em> has gained some notoriety of sorts, having been identified at times as a very primitive, pre-mitochondrial eukaryote, or as a still-primitive eukaryote that lost its mitochondria.  These two scenarios regarding the mitochondria of <em>Giardia</em> give us a similar set of contrasting pathways regarding the evolution of the polyadenylation complex.  One scenario would be that the <em>Giardia</em> polyadenylation complex resembles the primordial eukaryotic complex, that the first polyadenylation apparatus consisted of little more than a nuclease and a polymerase.  The complex we seen in other eukaryotes would be derived from a series of co-options, recruitments, and duplication events, all building on this simple beginning.  Of course, the most exciting aspect of this scenario is that it gives us a remarkably clear link to <a href="http://aghunt.wordpress.com/2008/08/17/the-nuclease-aisle/" rel="external ">nucleolytic activities in bacteria</a>; this follows from the structural and functional similarities between CPSF73/Ysh1 and RNAse J (noted <a href="http://aghunt.wordpress.com/2008/07/31/the-polyadenylation-complex-endonucleases/" rel="external ">here</a>).</p><p>The alternative is that the <em>Giardia</em> complex has lost most of the subunits that we see in other organisms.  This seems unlikely, given the essential nature of most of the subunits in yeast.  However, some differences in this regard exist between yeast and other eukaryotes; thus, Yth1 is essential in yeast, but its <em>Arabidopsis</em> counterpart is <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0002410" rel="external ">dispensible for viability</a>.  In any case, this alternative would provide us with a clear example of how extensively an irreducibly complex mechanism can evolve.</p><p>Hopefully, this essay has taught readers a thing or two.  More importantly, in the best of cases, it has raised a number of questions.  There may be some answers, but for many of these there await much experimentation and exploration.</p><p>Morrison, H.G., McArthur, A.G., Gillin, F.D., Aley, S.B., Adam, R.D., Olsen, G.J., Best, A.A., Cande, W.Z., Chen, F., Cipriano, M.J., Davids, B.J., Dawson, S.C., Elmendorf, H.G., Hehl, A.B., Holder, M.E., Huse, S.M., Kim, U.U., Lasek-Nesselquist, E., Manning, G., Nigam, A., Nixon, J.E., Palm, D., Passamaneck, N.E., Prabhu, A., Reich, C.I., Reiner, D.S., Samuelson, J., Svard, S.G., Sogin, M.L. (2007). Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia. Science, 317(5846), 1921-1926. DOI: <a href="http://dx.doi.org/10.1126/science.1143837" rel="external ">10.1126/science.1143837</a></p><p>* - in the figure from Morrison et al., Pab1, RNA polymerase II and Glc7 are also noted as polyadenylation factor subunits.  Pab1 is one of two poly(A)-binding proteins that plays roles in polyadenylation in yeast; this protein, as well as the G. lamblia protein identified in this study, is distinct in sequence and domain composition from the nuclear poly(A) binding proteins seen in mammals and plant.  RNAP II is so considered because it is a scaffold of sots, upon which numerous other polyadenylation factors assemble; this function is needed for efficient polyadenylation.  Glc7 is a protein that consistently purifies with the yeast polyadenylation complex.  As it is not considered historically to be a core polaydenylation complex subunit, I have not elaborated on it in this essay.</p><p>[updated on Aug 30 - Carl Zimmer noted, if more briefly, the curious reduction of the Giardia polyadenylation complex in <a href="http://blogs.discovermagazine.com/loom/2007/09/27/carrying-ancient-history-in-the-gut/" rel="external ">this essay</a>.  I didn’t know of this until today, but thought it appropriate to mention.]</p>

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<entry>
    <title>Genome Biology: &quot;It is alive&quot; by Gregory A Petsko</title>
    <link rel="alternate" type="text/html" href="http://pandasthumb.org/archives/2008/08/genome-biology.html" />
    <id>tag:pandasthumb.org,2008://2.3931</id>

    <published>2008-08-29T16:16:37Z</published>
    <updated>2008-08-29T16:41:49Z</updated>

    <summary>In a Comment in the journal Genome Biology Gregory Petsko, Professor of Biochemistry and Chemistry Protein Crystallography at Brandeis University discusses the latest shenanigans of the Intelligent Design movement. ( Gregory A Petsko It is alive Genome Biology 2008, 99::106) They’re at it again. Armed with another new idea from the Discovery Institute, that bastion of ignorance, right-wing political ideology, and pseudo-scientific claptrap, the creationist movement has mounted yet another assault on science. This time...</summary>
    <author>
        <name>PvM</name>
        
    </author>
    
        <category term="Assault on Education" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="Assault on Science" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="Education and Legal" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="Expelled" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="Expelled Exposed" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="Expelled Flunked" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="ID/Creationism" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="Improving science education" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="Manufactroversy" scheme="http://www.sixapart.com/ns/types#category" />
    
    
    <content type="html" xml:lang="en" xml:base="http://pandasthumb.org/">
        <![CDATA[<div class="kw-format"><p>In a Comment in the journal Genome Biology  Gregory Petsko, Professor of Biochemistry and Chemistry Protein Crystallography at Brandeis University discusses the latest shenanigans of the Intelligent Design movement. ( Gregory A Petsko <strong>It  is  alive </strong>
<em>Genome Biology</em> 2008, 99::106)</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>
They’re at it again. Armed with another new idea from the Discovery Institute, that bastion of ignorance, right-wing political ideology, and pseudo-scientific claptrap, the creationist movement has mounted yet another assault on science. This time it comes in two flavors: propaganda and legislative. 
</p>

</div></blockquote><p>What is Petsko talking about?</p>

</div>]]>
        <![CDATA[<div class="kw-format"><p>The propaganda refers to the movie “Expelled” which Petsko appropriately describes as a “poorly written and badly acted movie” and observes how the movie failed quickly in the theatres.</p><p>The legislative assault refers to the Louisiana bill which promotes ‘critical thinking’ on such topics as evolution, origins of life and global warming.</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>
The bill is cleverly worded: it states in section 1C that it “shall not be construed to promote any religious doctrine, promote discrimination for or against a particular set of religious beliefs, or promote discrimination for or against religion or nonreligion.” In an interview with the conservative newspaper The Washington Times (12 June 2008), Jason Stern, vice-president of the Louisiana Family Forum, a Christian right-wing lobby group, insisted “It’s not about a certain viewpoint. It’s allowing [teachers] to teach the controversy.” 
</p>

</div></blockquote><p>Petsko wastes no words</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>
Let me say this as clearly as possible, so there can be no mistake about what I mean: there is no controversy. Just because a few misguided so-called scientists question the 
validity of the concept of evolution doesn’t mean there is a controversy. There are still some people who believe the  Earth is flat (there’s even a ‘Flat Earth Society’), but that 
doesn’t mean that a grade-school science teacher should teach his or her students that the Earth might be flat. </p>

</div></blockquote><p>So what about the ‘academic freedom’ argument? Again Petski quickly dismisses this argument </p><blockquote class="kw-quote"><div class="kw-quote-body"><p>
What about the academic freedom argument? If someone wants to teach creationism in a science class, shouldn’t they have the right to do so? Certainly - if they want to get fired. 
Because if they do that they deserve to get fired. It has nothing to do with academic freedom; it’s about basic competence. </p>

</div></blockquote><p>Similarly, creationists are trying to undermine science teachings in other states, for instance in Texas</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>
On 7 June 2008, the Houston Chronicle wrote that “strengths and weaknesses” language is “a ‘teach the controversy’ approach, whereby religion is propounded under the guise of scientific inquiry”. The editorial went on to say: “What students really need is to be able to study science from materials that have not been hijacked by creationists whose personal agenda includes muddying the science curriculum. Creationism is not a ‘system of science’.” 
</p>

</div></blockquote><p>Hear hear.</p><p>ID’s scientific vacuity has doomed it to a misleading approach called “teach the controversy” where teachers are indirectly encouraged to present ID materials to their students where it has failed to meet even the minimum standards of science. Such indoctrination efforts should be of concern to anyone interested in the quality of science. To Christians these efforts should be of concern as they practice the flawed  “God of the Gaps” approach to science where our ignorance leads us not to stimulate further scientific inquiry but rather to invoke a supernatural cause.</p><p>Our children deserve better than to be exposed to such nonsense.</p><p>As Darwin observed</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>
Savages like York minister who consider thunder and lightning the direct will of God were scarcely less primitive than the miracle mongering philosopher who says the innate knowledge of a Creator has been implanted in us … by a separate act of God, rather than evolving according to His most magnificent laws.
</p>

</div></blockquote><p>Full quote:</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>So ready is change, from our idea of causation, to give a cause (&amp; no one being apparent, one fixes on imaginary beings, many vicarious, like ourselves) that savages (Mem York Minster) 102 consider the thunder &amp; lightning the direct will of the God ((thus) &amp; hence Those savages who thus | argue, make the same mistake, more apparent however to us, as does that philosopher who says the innate knowledge of creator (is) /has been/ implanted in us (?individually or in race?) by a separate act of God, &amp; not as a necessary integrant part of his most magnificent laws. which we profane in thinking not capable to produce every effect of every kind which surrounds us. Moreover /it would be difficult to prove this/ this innate idea of God in civilized nations has not been improved by culture ((who feels the most implicit faith that through the goodness of God knowledge has been communicated to us)). &amp; that it does exist in different degrees in races.—whether in Ancient Greeks, | with their mystical but sublime views, or the wretched fears &amp; strange superstitions of an Australian savage or one of Tierra de Fuego.—</p><p>102. York Minster was one of three Fuegians brought back to Tierra del Fuego by Capt. FitzRoy and the Beagle.</p></div></blockquote><p><strong>Source</strong>: Barrett, P. H. 1974. Early writings of Charles Darwin. In Gruber, H. E., Darwin on man. A psychological study of scientific creativity; together with Darwin’s early and unpublished notebooks. Transcribed and annotated by Paul H. Barrett, commentary by Howard E. Gruber. Foreword by Jean Piaget. London: Wildwood House. </p>

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<entry>
    <title>Tangled Bank #112</title>
    <link rel="alternate" type="text/html" href="http://pandasthumb.org/archives/2008/08/tangled-bank-11-1.html" />
    <id>tag:pandasthumb.org,2008://2.3930</id>

    <published>2008-08-28T11:55:52Z</published>
    <updated>2008-08-28T11:56:43Z</updated>

    <summary><![CDATA[ The latest edition, Tangled Bank #112, is now available at Science Notes. This issue was delayed because I neglected to ride herd on it while I was off in the Gal&aacute;pagos, but the next edition, at En Tequila Es Verdad, will be on schedule next week, on 3 September. So get inspired by the latest and send in links to your science writing pronto!...]]></summary>
    <author>
        <name>PZ Myers</name>
        <uri>http://scienceblogs.com/pharyngula/</uri>
    </author>
    
    
    <content type="html" xml:lang="en" xml:base="http://pandasthumb.org/">
        <![CDATA[

<a href="http://scienceblogs.com/pharyngula/tangledbank.php" title="The Tangled Bank"><img src="http://scienceblogs.com/pharyngula/tbbadge.gif" alt="The Tangled Bank" width="88" height="31" align="right" /></a>

<p class="lead">The latest edition, <a href="http://sciencenotes.wordpress.com/2008/08/27/tangled-bank-112/">Tangled Bank #112</a>, is now available at <a href="http://sciencenotes.wordpress.com/">Science Notes</a>.</p>

<p>This issue was delayed because I neglected to ride herd on it while I was off in the Gal&aacute;pagos, but the next edition, at <a href="http://entequilaesverdad.blogspot.com/">En Tequila Es Verdad</a>, will be on schedule next week, on 3 September. So get inspired by the latest and <a href="mailto:pzmyers@gmail.com?subject=Tangled Bank submission">send in links to your science writing</a> pronto!</p>]]>
        
    </content>
</entry>

<entry>
    <title>The gift that keeps on giving: Steve Fuller</title>
    <link rel="alternate" type="text/html" href="http://pandasthumb.org/archives/2008/08/the-gift-that-k.html" />
    <id>tag:pandasthumb.org,2008://2.3925</id>

    <published>2008-08-25T15:39:01Z</published>
    <updated>2008-08-29T21:10:15Z</updated>

    <summary>Regular readers on this group may remember Steve Fuller whose contributions as an “expert witness” for the defense in the Kitzmiller law suit were quoted by the plaintiffs as well as the judge to show that ID was not science?Last year, Steve Fuller released a book titled “Science v. Religion? Intelligent Design and the Problem of Evolution” which was recently reviewed by Sahotra Sarkar in “Notre Dame Philosophical Reviews”. Sarkar’s scathing review exposes the vacuity...</summary>
    <author>
        <name>PvM</name>
        
    </author>
    
        <category term="Scientific Vacuity" scheme="http://www.sixapart.com/ns/types#category" />
    
    
    <content type="html" xml:lang="en" xml:base="http://pandasthumb.org/">
        <![CDATA[<div class="kw-format"><p>Regular readers on this group may remember Steve Fuller whose contributions as an “expert witness” for the defense in the Kitzmiller law suit were quoted by the plaintiffs as well as the judge to show that ID was not science?</p><p>Last year, Steve Fuller released a book titled “<em>Science v. Religion? Intelligent Design and the Problem of Evolution</em>” which was recently reviewed by Sahotra Sarkar in “<em>Notre Dame Philosophical Reviews</em>”. Sarkar’s <a href="http://ndpr.nd.edu/review.cfm?id=13887" rel="external ">scathing review</a> exposes the vacuity of Fuller’s arguments, a vacuity we have come to expect from ‘Intelligent Design’.</p><p>Not wanting to be left out, Denyse O’leary, validates the quality of the work by Sarkar by referring to him as a “third-rate Darwin hack”. Furthermore, Denyse, in her continued display of ignorance, responds to Sarkar’s observation that <em>Fuller predicts that Darwinism (by which he means the entire framework of evolutionary theory) will be dead by the end of the twenty-first century and will be replaced by something more akin to ID creationism </em> with “What about the Altenberg 16? “.
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        <![CDATA[<div class="kw-format"><p>Indeed, Denyse, what about the Altenberg 16? Contrary to common ID myth, these people are neither displacing Darwinism and certainly are not intent on replacing it with something more akin to ID creationism. But somehow, Denyse, contrary to common journalistic practices, refuses to do the customary research which would led her to the statements released by the “<a href="http://rationallyspeaking.blogspot.com/2008/07/altenberg-2008-what-happened.html" rel="external ">Altenberg 16</a>”. In addition, Massimo Pigliucci <a href="http://rationallyspeaking.blogspot.com/2008/07/is-there-fundamental-scientific.html" rel="external ">explains</a> the reasons behind this workshop.</p><p>Now ask yourself, what has ID contributed to our understanding of evolution and evolutionary theory? Nothing, exactly nothing.</p><p>Various bloggers, well known to PT readers, have commented on Sarkar’s review, such as <a href="http://scienceblogs.com/evolvingthoughts/2008/08/a_casual_disregard_for_facts.php#more" rel="external ">John Wilkins</a> at “Evolving Thoughts” and <a href="http://scienceblogs.com/strangerfruit/2008/08/sarkar_v_fuller_part_ii_now_wi.php" rel="external ">John Lynch</a> at “Stranger Fruit.</p><p>Sarkar’s review is full of funny quotes, I personally like the following</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>The third chapter turns to complexity, the emphasis on which is supposed to distinguish ID from “other versions of creationism” (p. 69). (I will happily follow Fuller in explicitly construing ID as a form of creationism but I doubt that most ID proponents will be quite as accommodating on this point.)</p>

</div></blockquote><p>Always willing to read such statements in full context, I decided to check out the quote for myself. </p><p>On p. 69 we read:</p><blockquote class="kw-quote"><div class="kw-quote-header">Fuller Wrote:</div><div class="kw-quote-body"><p>
Intelligent Design theory (sic) differs most markedly from other versions of creationism by the emphasis it places on complexity.
</p>

</div></blockquote><p>Of course, the well informed reader should know by now that complexity as defined by Intelligent Design is merely the negative base-2 logarithm of the probability that a particular feature can be explained by a particular scientific hypothesis. Once a hypothesis explains a particular “complex” feature, the feature ceases to be “complex”.</p><p>And somewhat surprisingly,  Fuller testified, under oath, during the Kitzmiller trial as follows</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>
Q. Thank you. Do you have an opinion concerning whether intelligent design is creationism?</p><p>A <strong>(Fuller)</strong>. I do, and it is not.
</p>

</div></blockquote><p>You can read Fuller’s full testimony at Talkorigins:  <a href="http://www.talkorigins.org/faqs/dover/day15am.html" rel="external ">Steve Fuller: Morning session</a> and <a href="http://www.talkorigins.org/faqs/dover/day15pm.html" rel="external ">Steve Fuller: Afternoon session</a></p><h4 class="kw-heading" id="kw-Fuller-responds">Fuller responds</h4><p>Despite, or perhaps because, the several hard hitting reviews of his book, Fuller has decided to ‘<a href="http://www.uncommondescent.com/education/in-the-face-of-an-aspiring-baboon/" rel="external ">respond</a>’. And what a better place than the bastion of ID ‘research’, Uncommon Descent. Somewhat disappointingly, Fuller does little to address the critiques. He responds that Sarkar missed the point and all his other errors, and mistakes are at best nothing more than editorial flaws, and distract from the real issues.</p><p>The real issue is that: </p><blockquote class="kw-quote"><div class="kw-quote-header">Steve Fuller Wrote:</div><div class="kw-quote-body"><p>Non-teleological accounts of the world do not inspire the sustained pursuit of scientific inquiry – and so not surprisingly there are no good Darwinian accounts of science’s own significance for Homo sapiens.</p>

</div></blockquote><p>In other words, Fuller’s argument is nothing more than that the role of ID is mostly limited to inspiring a sustained pursuit of scientific inquiry because in the early days, scientists were often motivated by their religious beliefs in pursuing a scientific exploration of the world around them. While historically true, I find the argument that religious faith is a requirement for a sustained pursuit of scientific inquiry somewhat lacking in logic and reason. In fact, it is not clear to me that the correlation between faith and science is not spurious since most scientists of those days all were men of faith. In fact, I could easily list some examples which seem to undermine the claimed correlation, such as the appeal to the supernatural to explain the unknown (something even Fuller’s best example, Newton, did not shy away from). Furthermore, I fail to see why Darwinian accounts should exist for the significant of science for Homo Sapiens. The suggestion that Darwinism is somehow the single explanatory factor seems rather simple minded. And yet, Fuller suggest, in what has become a common confusion amongst ID proponents, that there could not exist non religious motivations to pursue science or that Darwinian explanations could never exist. Not only do religious foundations not necessarily lead to good science, especially when religious foundations cause one to reject scientific evidence, it also seems a dubious claim that religion is somehow necessary as a stimulus for scientific inquiry.  For instance, we have recent examples from the Young Earth Creationists who insist, based on their religious faith, that science needs to be ignored when it disagrees with their Biblical faith.</p><h4 class="kw-heading" id="kw-Other-reviewers">Other reviewers</h4><p>On TalkReason we have an article by <a href="http://www.talkreason.org/articles/Fuller.cfm" rel="external ">Norman Levitt</a> helping us understand why Steve Fuller and ID are a “match made in heaven”.  Norm Levitt also <a href="http://www.skeptic.com/eskeptic/07-12-19.html#feature" rel="external ">reviewed</a> Fuller’s book</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>Merely out of mathematical whimsy, I want to consider Fuller’s very extensive discussion of “complexity” and “randomness.” This, as mathematicians and computer scientists are well aware, is a subject that has been thoroughly studied and analyzed for decades, generating a slew of deep results and fertile conjectures. Fuller, however, shows no awareness of the actual mathematical literature (even though much of it is accessible, at the basic level, to anyone with minimal mathematical skill). Instead, he seems content to take ID-theorist William Dembski as his guide.</p>

</div></blockquote><p>In a wonderful paragraph, Levitt exposes, like Sarkar, many of Fuller’s flawed arguments such as:</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>None of this is backed up by serious analysis of the working methods and logical structure of biology itself. Fuller complacently views the ascendancy of evolutionary thought as a “rhetorical” rather than a “scientific” development. His principal evidence? The paucity of Nobel Prizes awarded for work on evolution! Of course, he never pauses to consider that under the idiosyncratic organization of the Nobel awards, there is no prize for biology as such. Biologists are smuggled in under the “Medicine and Physiology” category, which is just expansive enough to accommodate ethologists like Lorenz or Tinbergen, but not hard-core evolutionary theorists. In all of these pronouncements, Fuller is hard-pressed to hide his scorn for actual scientists who, it is obvious to him, know much less about what they think and how and why than a social theorist like himself who is enormously content to cite his own work endlessly.</p>

</div></blockquote><p>In a debate between Fuller and Wolpert, Fuller <a href="http://bcseweb.org.uk/index.php/Main/RoyalHollowayCollegeDebate" rel="external ">argued</a> that</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>Steve Fuller: Well, I don’t know what that means. Sorry, that is mysterious. That is a science stopper. A designer without, design without a designer is a science stopper, as far as I am concerned. </p>

</div></blockquote><p>which is why Fuller is quick to identify the designer as God, so why can other ID proponents not be forthcoming about this, especially if “design without a designer” is a science stopper?</p><h4 class="kw-heading" id="kw-Fuller-and-Kitzmiller">Fuller and Kitzmiller</h4><p>Fuller’s contributions to the ruling include:</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>Third, Professor Steven William Fuller testified that it is ID’s project to change the ground rules of science to include the supernatural.  (Trial Tr. vol. 28, Fuller Test., 20-24, Oct. 24, 2005).</p>

</div></blockquote><blockquote class="kw-quote"><div class="kw-quote-body"><p>Moreover and as previously stated, there is hardly better evidence of ID’s relationship with creationism than an explicit statement by defense expert Fuller that ID is a form of creationism.  (Fuller Dep. at 67, June 21, 2005) (indicated that ID is a modern view of creationism).  
</p>

</div></blockquote><p>In fact, as Matt Brauer <a href="http://www.pandasthumb.org/archives/2005/12/and-a-shout-out.html" rel="external ">pointed out</a>, Fuller was cited 11 times in the final ruling.</p><p>See also Fuller’s <a href="http://www2.ncseweb.org/kvd/experts/fuller.pdf" rel="external ">expert witness report</a> which helps understand Fuller’s position, however whimsical.</p><h4 class="kw-heading" id="kw-Religious-motivation-and-science">Religious motivation and science</h4><p>Arguing that since historically people have done excellent science coming from a religious motivation that </p>

<blockquote class="kw-quote"><div class="kw-quote-body"><p>It’s on those grounds that I believe Intelligent Design should be supported</p>

</div></blockquote><p><a href="http://fora.tv/2007/10/28/Steve_Fuller_Intelligent_Design_and_Evolution" rel="external ">Source</a></p><p>In the same video clip, Fuller also admits that the textbook used in the Dover trial (Of Pandas and People) was a very poor textbook and that he said nothing good about it.</p><p>Fuller’s fascinations with ID seem to not be because he necessarily believes that ID has much relevance per se but rather because historically a belief in a Creator has been a foundation for doing science. In addition, Fuller seems rather impressed by (or should it be “under the impression that”)  ID’s claims that it provides a ‘worthy alternative’ to evolutionary theory. As such Intelligent Design together with evolutionary theory would benefit the science education.  Fuller’s position is that sociologists like him are in a better position to judge the nature of science than the scientists themselves, and that one need not understand the scientific arguments involved to judge the quality of said science. In fact, like so many ID proponents, Fuller seems to lack much of an understanding of either the science behind evolutionary theory but also Intelligent Design, taking Dembski and Behe’s word as the ‘Gospel’, while largely ignoring the many well qualified critics of their positions. It does not matter, Fuller envisions a science where anyone can ‘contribute’ and quality is less important than ‘participation’. </p><p>As one reviewer observes:</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>For Fuller, religion and science are compatible. He complains that evolutionary theory is being taught as dogma. It needs a “critical foil” and ID satisfies that function as well as anything else.</p>

</div></blockquote><p>Source: <a href="http://www.guardian.co.uk/education/2006/jan/31/academicexperts.highereducationprofile" rel="external ">Steve Fuller : Designer trouble</a> by #  Zoë Corbyn <em>The Guardian</em>, January 31 2006</p><p>In this context I also encourage the readers to listen to a discussion between <a href="http://www2.warwick.ac.uk/newsandevents/audio/id101105m.mp3" rel="external ">Cohen and Fuller</a> exploring the issues involved in the debate between intelligent design and evolutionary theory. It runs for slightly over an hour but it helps understand Fuller’s position and why Fuller’s interest is not so much in the details of scientific accuracy, something to be left best to scientists, but rather the argument that ID can contribute to science education through questioning science and providing a foundation on which scientific interest can be explained. Neither one seems particularly relevant nor convincing to me.</p><p>The point at the end of the day is that since scientists have done good science when they, based on their religious faith, decided to propose scientific mechanisms to explain how God created, Fuller believes that ID is worth to be considered in the science curriculum, <strong>even if it is wrong</strong>. From a perspective of a non-scientist, Fuller is quick to define the extent of science even though his own comments show that he is not very well versed in the scientific arguments. </p><p>Of course, other than as an audience for his claims and his books, I doubt that Fuller has much sympathy for the Intelligent Design position. He clearly defines ID’s designer to be “God”, is not concerned about the continued scientific vacuity of Intelligent Design and is even less worried about his sometimes heretical theological claims. Fuller and Intelligent Design are in many aspects, a “match made in Heaven”. In fact, ID’s ‘loving’ embrace of Fuller seems to have extended the Big Tent to include some interesting theological concepts.</p><h4 class="kw-heading" id="kw-Newton-God-and-science">Newton, God and science</h4><p>In a <a href="http://muse.jhu.edu/login?uri=/journals/canadian_journal_of_sociology/v031/31.3fuller.html" rel="external ">recent paper</a>, Fuller apparently argues that “[it] traces the roots of intelligent design theory to the aspiration of Newton and other scientific revolutionaries to regard the mechanical world-view as enabling humans to approximate the mind of God.” </p><p>Of course, I doubt that much of any attempt is made to validate the necessity of such an position, and in fact, Fuller may have forgotten how this world view caused Newton to argue that God was actively involved in correcting the orbits of planets, since according to his understanding of mathematics, such orbits could not be stable. Indeed, the roots of ID can clearly be traced back to Newton as he confused, just like the modern day ID proponent, the concept of ignorance with the concept of God.</p><p>As so many have so clearly and convincingly argued, such a position not only dooms ID to remain scientifically without content but also theologically risky. Perhaps by promulgating a theologically risky proposition, Fuller may very well be hastening ID’s demise amongst the faithful. As far as the scientific vacuity of ID is concerned, little hope exists that Fuller will challenge this either, as Levitt observes:</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>It is almost superfluous to add that Fuller has done little to come to terms with Dembski’s most trenchant critics, actual experts in complexity and information theory, such as Mark Perakh and Jeffrey Shallit, the latter of whom has justifiably damned Dembski’s work as “pseudo-mathematics.” Nor has Fuller been very accurate in describing Dembski’s intended program, which is to demonstrate “mathematically” that the evolution of complex life via natural selection is literally impossible. But to acquaint himself with this now-voluminous literature would violate one of his favorite axioms, viz., that a “social epistemologist” needn’t actually understand science in order to belittle it.</p>

</div></blockquote><p>Mike Dunford, states it <a href="http://www.michaelberube.com/index.php/weblog/comments/783/" rel="external ">clearly and succinctly</a>, catching Fuller in yet another scientific inaccuracy:</p><blockquote class="kw-quote"><div class="kw-quote-body">
<blockquote class="kw-quote"><div class="kw-quote-body"><p>    ‘Anything new in science comes when scientific work comes up with something new, and this is unpredictable. At the time that Linus Pauling gambled that the genetic material would be a protein, he knew that it was a gamble and that experimental work would decide it.’ But your own example shows that Pauling DID predict correctly…
</p>

</div></blockquote><p>
    (Steve Fuller, comment 60)</p><p>As has been pointed out already, Pauling bet wrong. DNA (deoxyribonucleic acid) is a nucleic acid. Proteins are polypeptides. The two are very different kinds of chemical. That is really very basic biology - high school level, in fact. (I suspect that Bob Weimann would be somewhat disappointed in you for forgetting that.)</p><p>The Pauling situation illustrates a number of the problems both with teaching intelligent design and with Steve’s participation in this issue.</p><p>To begin with, let’s look at what the Intelligent Design people are demanding. They are not demanding equal funding for empirical research. They are not demanding access to the scientific literature. They are not demanding to be allowed to participate in the scientific process. They are demanding to be allowed to bypass research and publication and to place their material in the high school classroom. In the Pauling example, it would be like immediately demanding, prior to the expected experimental confirmation, to teach that protein is the genetic material.</p><p>When it comes to moving new research into the classroom, science moves very slowly and very, very conservatively. This is done for good reason. The sciences are very complex fields. Conducting and critically evaluating new research requires an enormous knowledge base - if it is to be done competently. Putting brand new, controversial material into the classroom might sound like a good way to stimulate critical inquiry in the students, but critical inquiry in this case requires a knowledge base that students simply don’t have at that level.</p><p>It’s also a knowledge base that Steve apparently doesn’t have. He speculates in comment 38 that “some design-based paradigm will overtake evolution in about 100 years,” but he doesn’t appear to have the basic knowledge of biology to actually make that an educated guess. He might be basing his opinion on the way that other major scientific revolutions have progressed, but that’s hardly a safe (or particularly relevant) basis for speculating on the outcome of specific cases.</p><p>Carl Sagan summed that up well, I think:</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>
    But the fact that some geniuses were laughed at does not imply that all who are laughed at are geniuses. They laughed at Columbus, they laughed at Fulton, they laughed at the Wright Brothers. But they also laughed at Bozo the Clown.
</p>

</div></blockquote><p>By Steve’s own admission, ID has not progressed to the point of formulating or testing hypotheses. How, then, do we know that they aren’t Bozo. If it is possible that they are, why put them in the schools? </p>

</div></blockquote><p>Similarly, Ben Alpers argues in the same comments </p><blockquote class="kw-quote"><div class="kw-quote-body"><p>But, in fact, Fuller’s analysis of ID involves more than the boring old job of testing its knowledge claims.  It involves speculating on the possibility that in the future, in some inscrutible way, ID might generate knowledge claims that are testable.  And because we can speculate that it might generate future testible knowledge claims, we must ignore its current lack of such claims and teach it as science in high school classes. </p>

</div></blockquote><p>Which raises a relevant issue namely, is something worth teaching just because it speculates that science may be wrong, especially when it fails to contribute to science in any positive manner, and failing to be ‘testable’? Even if one were to accept the (slight) possibility that ID may stumble onto something of scientific interest, why should we accept its premises when ID refuses by its own nature to engage in scientific inquiry? Sure, people have the right to formulate hypotheses based on their religious faith, but the right to speak does not extend to a right to be heard, especially when history has shown them to be unable to listen. In several of his comments, Fuller suggests that the main reason science rejects Intelligent Design is because of its strong roots in Christian theology, ignoring cause and effect. Intelligent Design is ignored by scientists because scientists have looked at its claims and found it to be lacking in content, relevance and accuracy. That in addition, this scientific lack of content can be explained by its roots in theology is just ‘icing on the cake’.</p><p>In the end it all comes down to, what Mike Dunford describes as</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>“How can you possibly hope to formulate an informed, independent opinion if you don’t know the underlying science?” </p>

</div></blockquote><p>And yet, this is something which seems to be of little concern to both ID proponents as well as Steve Fuller. In fact, this appears to be a great tradition amongst ID defenders such as Phillip ‘Godfather of ID’ Johnson and Francis Beckwith. Although, I believe that Beckwith’s ‘love affair’ with Intelligent Design has come to a predictable ending.</p><p>And finally, in 2008, Fuller released yet another book on the topic of intelligent design, titled “Dissent Over Descent: Intelligent Design’s Challenge to Darwinism” which got a short <a href="http://www.guardian.co.uk/books/2008/jul/12/saturdayreviewsfeatres.guardianreview7" rel="external ">review</a> in the Guardian:</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>
Once upon a time, Fuller points out, most science was inspired by the possibility of understanding God’s creation. That is true, but it does not mean, as Fuller pretends, that contemporary “ID” is an alternative method of doing science: its remit is strictly anti-science, cynically positing a “God of the gaps” for political reasons. For his part, Fuller happily adopts ID’s rhetorical tactics: speaking of biologists’ “faith”; forgetting to mention (or merely being ignorant of) the wealth of evidence for evolution in modern biology that wasn’t available to Darwin himself; and even muttering about the “vicissitudes” of fossil-dating, thus generously holding the door open for young-Earth creationists, too. The book is an epoch-hopping parade of straw men, incompetent reasoning and outright gibberish, as when evolution is argued to share with astrology a commitment to “action at a distance”, except that the distance is in time rather than space. It’s intellectual quackery like this that gives philosophy of science a bad name.
</p>

</div></blockquote><p>Another, slightly <a href="http://www.timeshighereducation.co.uk/story.asp?storycode=402929" rel="external ">more positive review</a> in the “Times Higher Education” points out that</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>Upholders of theistic evolution usually espouse “methodological naturalism”, which Fuller characterises as a “pseudo-philosophy” fuelled by bigotry. I have always understood it to be the view that properly scientific explanations refer only to “natural” (spatio-temporal) data, without denying that other data (like God) may exist, and have some form of causal influence, not falling within the purview of observational and experimental science. Fuller claims it is a conflation of logical positivism (all factual statements must be verifiable) and metaphysical naturalism (only natural causes exist). This claim is puzzling, as methodological naturalism is a term invented precisely to contrast with metaphysical naturalism, and no naturalist is committed to a positivist doctrine of meaning and verification. I cannot see how it is “anti-religious bigotry” to say that God’s acts cannot be unambiguously verified by public observation, or repeated, or experimentally tested. Indeed, this seems to be a common religious view, and even to follow from the fact that God is not a material entity and that God’s acts obey no general causal laws.</p>

</div></blockquote><p>So what to make of all this? I believe that Fuller has a sincere though mistaken beliefs about the impact nay necessity of religion (preferably monotheistic) on scientific inquiry and curiosity and while I believe the evidence clearly shows him to be wrong, I can appreciate his position. However, to argue that Intelligent Design deserves a place at the table of science because it sounds plausible and sincere to Fuller and because it serves to ‘keep evolutionists’ honest seems to be rather a high price to pay. Especially when the request comes from a sociologist who seems to consider actual knowledge about the science involved to be a hindrance to evaluating if something deserves to be treated as science. This is particularly troublesome since so many have shown ID to be scientifically vacuous. It is thus not surprising that Fuller neither explains why ID is scientifically relevant nor explains why evolutionary theory is in need of an ‘ID’ opponent, and worse, why Fuller relies on the strawman that science and scientists reject ID because of its theological roots.
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<entry>
    <title>The AAAS responds to &quot;Expelled&quot;</title>
    <link rel="alternate" type="text/html" href="http://pandasthumb.org/archives/2008/08/the-aaas-respon.html" />
    <id>tag:pandasthumb.org,2008://2.3928</id>

    <published>2008-08-25T01:39:34Z</published>
    <updated>2008-08-25T01:50:48Z</updated>

    <summary>This video from the “American Association for the Advancement of Science, “ (AAAS), a non-profit science society, explains why religion and science need not be in opposition. It is a response to the intelligent design propaganda movie, “Expelled: No Intelligence Allowed,” with Ben Stein. AAAS also released a written statement. See AAAS Statement Decries “Profound Dishonesty” of Intelligent Design Movie For more on how AAAS works to promote constructive dialogue between religious and scientific leaders,...</summary>
    <author>
        <name>PvM</name>
        
    </author>
    
    
    <content type="html" xml:lang="en" xml:base="http://pandasthumb.org/">
        <![CDATA[<div class="kw-format"><p>This <a href="http://www.youtube.com/watch?v=58UDTq3kaZM" rel="external ">video</a> from the “American Association for the Advancement of Science, “ (AAAS), a non-profit science society, explains why religion and science need not be in opposition. It is a response to the intelligent design propaganda movie, “Expelled: No Intelligence Allowed,” with Ben Stein. AAAS also released a written statement. See <a href="http://www.aaas.org/news/releases/2008/0418expelled.shtml" rel="external ">AAAS Statement Decries “Profound Dishonesty” of Intelligent Design Movie</a> For more on how AAAS works to promote constructive dialogue between religious and scientific leaders, see <a href="http://www.aaas.org/evolution" rel="external ">this link</a></p><p>Enjoy the video below the fold</p><p>A powerful video addressing how science and faith can work together without damage to either.</p>

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<entry>
    <title>New Features</title>
    <link rel="alternate" type="text/html" href="http://pandasthumb.org/archives/2008/08/new-features.html" />
    <id>tag:pandasthumb.org,2008://2.3926</id>

    <published>2008-08-24T21:45:40Z</published>
    <updated>2008-08-24T21:53:12Z</updated>

    <summary>Well the school is starting up again, and this blog will be slower than usual for a while until the authors get into the swing of things.On my side of things, I have an upgrade planned for site now that Movable Type 4.21 has been released. I’m currently running it on my blog and will implement it when I’m satisfied with it and have enough time on a weekend.I’ve also revealed a secret project that...</summary>
    <author>
        <name>Reed A. Cartwright</name>
        <uri>http://dererumnatura.us/</uri>
    </author>
    
        <category term="Metatalk" scheme="http://www.sixapart.com/ns/types#category" />
    
    <category term="comment" label="comment" scheme="http://www.sixapart.com/ns/types#tag" />
    <category term="validation" label="validation" scheme="http://www.sixapart.com/ns/types#tag" />
    
    <content type="html" xml:lang="en" xml:base="http://pandasthumb.org/">
        <![CDATA[<div class="kw-format"><p>Well the school is starting up again, and this blog will be slower than usual for a while until the authors get into the swing of things.</p><p>On my side of things, I have an upgrade planned for site now that Movable Type 4.21 has been released.  I’m currently running it on <a href="http://dererumnatura.us/" rel="external ">my blog</a> and will implement it when I’m satisfied with it and have enough time on a weekend.</p><p>I’ve also revealed <a href="http://dererumnatura.us/archives/2008/08/test-away.html" rel="external ">a secret project</a> that I’ve been toying with off and on for a few months: pre-submission comment validation.  I hope to enable this technology on PT, to help out those of you who find writing valid markup difficult.  However, I need y’all to go give <a href="http://dererumnatura.us/archives/2008/08/test-away.html" rel="external ">it a hard time</a> to find the bugs.</p>

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    </content>
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<entry>
    <title>Padian&apos;s Takedown of &quot;Of Pandas and People.&quot;</title>
    <link rel="alternate" type="text/html" href="http://pandasthumb.org/archives/2008/08/padians-takedow.html" />
    <id>tag:pandasthumb.org,2008://2.3924</id>

    <published>2008-08-24T05:23:29Z</published>
    <updated>2008-08-24T05:26:38Z</updated>

    <summary>Commenting on the testimony of the plaintiffs’ expert witnesses in the Kitzmiller trial, someone said (paraphrased) “It was the biology course you never took but wish you had.” Reading the raw transcripts of the testimony one can easily believe that.But it gets better. I just discovered that Nick Matzke took Kevin Padian’s testimony and integrated Padian’s slides, so one can see what Padian was talking about as he described the paleontological evidence for evolution and...</summary>
    <author>
        <name>Richard B. Hoppe</name>
        
    </author>
    
        <category term="Assault on Science" scheme="http://www.sixapart.com/ns/types#category" />
    
        <category term="Kitzmiller Ruling" scheme="http://www.sixapart.com/ns/types#category" />
    
    
    <content type="html" xml:lang="en" xml:base="http://pandasthumb.org/">
        <![CDATA[<div class="kw-format"><p>Commenting on the testimony of the plaintiffs’ expert witnesses in the <a href="http://www.talkorigins.org/faqs/dover/kitzmiller_v_dover.html" rel="external ">Kitzmiller trial</a>, someone said (paraphrased) “It was the biology course you never took but wish you had.”  Reading the raw transcripts of the testimony one can easily believe that.</p><p>But it gets better.  I just discovered that Nick Matzke took <a href="http://www.sciohost.org/ncse/kvd/Padian/Padian_transcript.html" rel="external ">Kevin Padian’s testimony and integrated Padian’s slides</a>, so one can see what Padian was talking about as he described the paleontological evidence for evolution and the misrepresentations in <em>Of Pandas and People</em>.   I don’t recall it having been flagged here before.</p><p>That had to have been a heckuva job for Nick, but it was sure worth it.  Reading it with the slides right there, the flow of the testimony is beautiful.  The integrated presentation is a significant resource for teachers and others in this arena.  I commend it to folks’ attention.</p>

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    </content>
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<entry>
    <title>Von Neumann, Berlinski, and evolution: Who&apos;s the hooter?</title>
    <link rel="alternate" type="text/html" href="http://pandasthumb.org/archives/2008/08/von-neumann-on.html" />
    <id>tag:pandasthumb.org,2008://2.3923</id>

    <published>2008-08-20T21:01:38Z</published>
    <updated>2008-08-21T17:19:01Z</updated>

    <summary>by Douglas L. Theobald, Assistant Professor of Biochemistry, Brandeis UniversityJeffrey Shallit pointed me to a youtube video, in which David Berlinski makes the following remarkable claim: “… von Neumann, one of the great mathematicians of the 20th century, just laughed at Darwinian theory. He hooted at it.”For those even tangentially familiar with the Hungarian mathematician John von Neumann, this will come as a shock. One may ask, however, with some justification: who cares what a...</summary>
    <author>
        <name>Guest Contributor</name>
        <uri>http://www.pandasthumb.org/</uri>
    </author>
    
        <category term="Evolution" scheme="http://www.sixapart.com/ns/types#category" />
    
    <category term="berlinski" label="Berlinski" scheme="http://www.sixapart.com/ns/types#tag" />
    <category term="evolution" label="evolution" scheme="http://www.sixapart.com/ns/types#tag" />
    <category term="vonneumann" label="von Neumann" scheme="http://www.sixapart.com/ns/types#tag" />
    <category term="youtube" label="youtube" scheme="http://www.sixapart.com/ns/types#tag" />
    
    <content type="html" xml:lang="en" xml:base="http://pandasthumb.org/">
        <![CDATA[<div class="kw-format"><p><strong>by Douglas L. Theobald, Assistant Professor of Biochemistry, Brandeis University</strong></p><p>Jeffrey Shallit pointed me to <a href="http://www.youtube.com/watch?v=L-UCo7JQm-A" rel="external ">a youtube video</a>, in which David Berlinski makes the following remarkable claim:  “… von Neumann, one of the great mathematicians of the 20<sup>th</sup> century, just laughed at Darwinian theory.  He hooted at it.”</p><p>For those even tangentially familiar with the Hungarian mathematician <a href="http://en.wikipedia.org/wiki/John_von_Neumann" rel="external ">John von Neumann</a>, this will come as a shock.  One may ask, however, with some justification: who cares what a non-biological mathematician thinks about evolutionary theory?  After all, anyone speculating outside of their field of expertise is simply doing that, and their opinion should carry no more weight than anyone else who talks about something they know little about.  John von Neumann, however, is not just any mathematician, and his seminal work on <a href="http://en.wikipedia.org/wiki/Cellular_automata" rel="external ">self-replicating</a> <a href="http://en.wikipedia.org/wiki/Von_Neumann_universal_constructor" rel="external ">automata</a> and <a href="http://en.wikipedia.org/wiki/Game_theory#Biology" rel="external ">game theory</a> has had important, fundamental implications for evolutionary biology (as have, more indirectly, his contributions to ergodic theory, numerical analysis, and statistics).</p></div>]]>
        <![CDATA[<div class="kw-format"><p>Von Neumann is something of a legend, one of those people whose name keeps showing up again and again in the citations of technical papers in very disparate fields (somewhat reminiscent of Sir Ronald Fisher, but even more intellectually promiscuous). [<a href="#note-3923-1">1</a>]</p><p>So, Berlinski’s pompous bit spurred me to do a bit of digging and jogging of the memory.  I found that Berlinski’s unsubstantiated claim is—yawn—preposterous.  Von Neumann was demonstrably pro-evo, especially regarding the usual mut/sel/drift mechanisms, yet he may have been critical of abiogenesis hypotheses given his theoretical work with self-replicating automatons.  Regardless, the creationists have apparently wrung certain statements out-of-context and/or conflated evolution with abiogenesis (no surprise there).  Here are three bits of fact on the matter:</p><h4 class="kw-heading" id="kw-Statement-1">Statement 1</h4><p>There is one misleading, yet eye-raising, quote from von Neumann that I’ve seen repeated on creationist/ID sites:</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>I shudder at the thought that highly purposive organizational elements, like the protein, should originate in a random process.</p>

</div></blockquote><p>This may be the ultimate source of many of the claims that von Neumann was anti-evo.  However, this is clearly a partially mangled, out-of-context quote.  Here is the original source, from a personal letter written by von Neumann to <a href="http://en.wikipedia.org/wiki/George_Gamow" rel="external ">George Gamow</a> in 1955:</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>
I still somewhat shudder at the thought that highly efficient, purposive, organizational elements, like the proteins, should originate in a random process.  Yet many efficient (?) and purposive (??) media, e.g., language, or the national economy, also look statistically controlled, when viewed from a suitably limited aspect.  On balance, I would therefore say that your argument is quite strong.
<div class="kw-quote-ref">(von Neumann to Gamow, 25 July, 1955.  Gamow fld., von Neumann papers, LC.  Quoted in Lily E. Kay, <em>Who Wrote the Book of Life?: A History of the Genetic Code</em>, Stanford University Press, 2000, p 158.)</div>
</p>

</div></blockquote><p>The context was a discussion regarding the nature of the <a href="http://en.wikipedia.org/wiki/Genetic_code#Cracking_the_genetic_code" rel="external ">genetic code</a>, which at the time had not yet been solved.  Gamow came up with some random model for the distribution of amino acids in proteins (for which I don’t understand the rationale, and neither evidently did Francis Crick).  Von Neumann gave an analytical solution for the model, and Gamow found that the observed distribution didn’t match the theoretical one.  From other considerations, Gamow concluded that the deviation from randomness must be due to a nonrandom distribution of nucleotide triplets in DNA, and he used this as support for his non-overlapping, triplet, combinatorial code hypothesis.  Gamow made this argument to von Neumann, and von Neumann responded with the quote above.  Gamow’s specific hypothesis turned out to be wrong (particularly the combinatorial part)—but of course there <strong>is</strong> a non-random distribution of nucleotides in codons (which are indeed triplet and non-overlapping).</p><p>So von Neumann’s statement has nothing to do with protein evolution, but rather deals with how amino acids are coded for in the translation apparatus.  Obviously neither the genetic code nor translation in general are predominantly random processes.</p><h4 class="kw-heading" id="kw-Statement-2">Statement 2</h4><p>There  are two other similar quotes I have seen recounted by creationists, one from Harold F. Blum’s book <em>Times Arrow and Evolution</em> (Harper 1962) and another from A.G. Cairns-Smith’s book <em>Seven Clues to the Origin of Life</em>.  On page 178G Blum writes regarding abiogenesis theories:</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>As the late John von Neumann pointed out, a machine that replicates itself can, with some difficulty, be imagined; but such a machine that could originate itself offers a baffling problem which no one has yet solved.</p>

</div></blockquote><p>Similarly, Cairns-Smith says on page 15:</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>Is it any wonder that Von Neumann himself, and many others, have found the origin of life to be utterly perplexing?</p>

</div></blockquote><p>Both Blum and Cairns-Smith are respectable sources, and I don’t doubt their word, but in neither case are references given.  I have not seen anything specifically where von Neumann has criticized abiogenesis per se; however, the following source may be what Blum and Cairns-Smith refer to.</p><h4 class="kw-heading" id="kw-Statement-3">Statement 3</h4><p>Here von Neumann shows without question his acceptance of evolutionary theory, though there are hints that he may have had trouble seeing how a self-replicating and evolvable machine (i.e. an organism) could arise de novo.  I quote this at length as it may be of use in refuting creationist claims (and because it could easily be misunderstood or quote-mined when taken out-of-context).</p><p>In 1949 von Neumann gave a series of lectures at the University of Illinois on self-replicating machines.  They were published posthumously in 1966 under the title <em>Theory and Organization of Complicated Automata.</em>  Much of this will sound very fuzzy from the lecture transcription, but von Neumann actually published several papers (and a posthumous book) where self-replicating automata were formalized (see <a href="http://en.wikipedia.org/wiki/Von_Neumann_cellular_automata" rel="external ">von Neumann cellular automata</a> and <a href="http://en.wikipedia.org/wiki/Von_Neumann_universal_constructor" rel="external ">von Neumann universal constructor</a> for more info).</p><p>From the fifth lecture, entitled “Re-evaluation of the problems of complicated automata—Problems of hierarchy and evolution”:</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>
Anybody who looks at living organisms knows perfectly well that they can produce other organisms like themselves.  This is their normal function, they wouldn’t exist if they didn’t do this, and it’s plausible that this is the reason why they abound in the world.  In other words, living organisms are very complicated aggregations of elementary parts, and by any reasonable theory of probability or thermodynamics highly improbable.  That they should occur in the world at all is a miracle of the first magnitude; the only thing which removes, or mitigates, this miracle is that they reproduce themselves.  Therefore, if by any peculiar accident there should ever be one of them, from there on the rules of probability do not apply, and there will be many of them, at least if the milieu is reasonable.  But a reasonable milieu is already a thermodynamically much less improbable thing.  So, the operations of probability somehow leave a loophole at this point, and it is by the process of self-reproduction that they are pierced.</p><p>Furthermore, it’s equally evident that what goes on is actually one degree better than self-reproduction, for organisms appear to have gotten more elaborate in the course of time.  Today’s organisms are phylogenetically descended from others which were vastly simpler than they are, so much simpler, in fact, that it’s inconceivable how any kind of description of the later, complex organisms could have existed in the earlier one.  It’s not easy to imagine in what sense a gene, which is probably a low order affair, can contain a description of the human being which will come from it.  But in this case you can say that since the gene has its effect only within another human organism, it probably need not contain a complete description of what is to happen, but only a few cues for a few alternatives.  However, this is not so in phylogenetic evolution.  That starts from simple entities, surrounded by an unliving amorphous milieu, and produces something more complicated.  Evidently, these organisms have the ability to produce something more complicated than themselves.</p><p>The other line of argument, which leads to the opposite conclusion, arises from looking at artificial automata.  Everyone knows that a machine tool is more complicated than the elements which can be made with it, and that, generally speaking, an automaton A, which can make an automaton B, must contain a complete description of B and also rules on how to behave while effecting the synthesis.  So, one gets a very strong impression that complication, or productive potentiality in an organization, is degenerative, that an organization which synthesizes something is necessarily more complicated, of a higher order, than the organization it synthesizes.  This conclusion, arrived at by considering artificial automata, is clearly opposite to our earlier conclusion, arrived at by considering living organisms.</p><p>I think that some relatively simple combinatorial discussions of artificial automata can contribute to mitigating this dilemma.  Appealing to the organic, living world does not help us greatly, because we do not understand enough about how natural organisms function.  We will stick to automata which we know completely because we made them, either actual artificial automata or paper automata described completely by some finite set of logical axioms.  It is possible in this domain to describe automata which can reproduce themselves.  So at least one can show that on the site where one would expect complication to be degenerative it is not necessarily degenerative at all, and, in fact, the production of a more complicated object from a less complicated object is possible.</p><p>The conclusion one should draw from this is that complication is degenerative below a certain minimum level.  This conclusion is quite in harmony with other results in formal logics, to which I have referred a few times earlier during these lectures. …  There is a minimum number of parts below which complication is degenerative, in the sense that if one automaton makes another the second is less complex than the first, but above which it is possible for an automaton to construct other automata of equal or higher complexity. …</p><p>There is thus this completely decisive property of complexity, that there exists a critical size below which the process of synthesis is degenerative, but above which the phenomenon of synthesis, if properly arranged, can become explosive, in other words, where synthesis of automata can proceed in such a manner that each automaton will produce other automata which are more complex and of higher potentialities than itself.</p><p><div class="kw-quote-ref">(Reproduced in <em>Papers of John von Neumann on Computing and Computer Theory</em>, W. Aspray and A. Burks, eds., MIT Press, pp 481-482)</div>
</p>

</div></blockquote><p>Von Neumann goes on to explain how automata can mutate, replicate, and inherit mutations.  He obviously was convinced of both the power of natural selection and of the fact of phylogenetic evolution.</p>

<h4 class="kw-heading" id="kw-Notes">Notes</h4><ol class="kw-notes"><li id="note-3923-1">Von Neumann’s very existence is even used as evidence for extra-terrestrials.  Enrico Fermi once famously asked concerning the potential existence of aliens: “Where are they?”  Fermi reckoned that, given the size and age of the universe, many technologically advanced civilizations must exist and that the odds are that they should have visited us by now—an argument dubbed the “Fermi Paradox”.  Leo Szilard supposedly provided an answer: “Maybe they’re already here, and you just call them Hungarians.” (Of course there are other stellar Hungarian mathematicians and physicists, like Erdos, Wigner, Polya, and Szilard himself, but Fermi and Szilard were both good friends of von Neumann, and of the same age).</li></ol></div>]]>
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<entry>
    <title>The Sixth International Conference on Creationism</title>
    <link rel="alternate" type="text/html" href="http://pandasthumb.org/archives/2008/08/the-sixth-inter.html" />
    <id>tag:pandasthumb.org,2008://2.3922</id>

    <published>2008-08-19T23:29:05Z</published>
    <updated>2008-08-19T23:42:13Z</updated>

    <summary>The Sixth Intenrational Conference on Creationism was held from August 3-7, in Pittsburgh, PA. That being a mere five hour drive from my digs in Harrisonburg, I naturally attended. Unlike the revival tent atmosphere that prevails at Ken Ham&apos;s ubiquitous gatherings, the ICC&apos;s represent an attempt at a serious scientific conference on creationism. If you flip through the conference proceedings and just give it a quick skim, you could easily be impressed by the professionalism...</summary>
    <author>
        <name>Jason Rosenhouse</name>
        <uri>http://www.math.jmu.edu/~rosenhjd</uri>
    </author>
    
    
    <content type="html" xml:lang="en" xml:base="http://pandasthumb.org/">
        <![CDATA[<p>The Sixth Intenrational Conference on Creationism was held from August 3-7, in Pittsburgh, PA.  That being a mere five hour drive from my digs in Harrisonburg, I naturally attended.</p>

<p>Unlike the revival tent atmosphere that prevails at Ken Ham's ubiquitous gatherings, the ICC's represent an attempt at a serious scientific conference on creationism.  If you flip through the conference proceedings and just give it a quick skim, you could easily be impressed by the professionalism of the volume and the level of technical detail in the papers.  It's a side of creationism we rarely see, and serves as a reminder that these folks honestly believe what they are saying, and at least attempt to do science with their idiosyncratic interpretaion of the Bible as their starting point.</p>

<p>Alas, combining the scientific legitemacy of creationism with the turgid style of academic prose is not the formula for a pleasant conference.  I will be reporting on my experiences at the conference over at EvolutionBlog.  The first two installments are already up:  <a href="http://scienceblogs.com/evolutionblog/2008/08/report_on_the_sixth_internatio.php">Part One</a> and <a href="http://scienceblogs.com/evolutionblog/2008/08/report_on_the_sixth_internatio_1.php">Part Two</a>.  Comments can be left there.  Go have a look, and stay tuned for further installments.</p>]]>
        
    </content>
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<entry>
    <title>The evolution of Jeffrey P Schloss</title>
    <link rel="alternate" type="text/html" href="http://pandasthumb.org/archives/2008/08/the-evolution-o-7.html" />
    <id>tag:pandasthumb.org,2008://2.3917</id>

    <published>2008-08-12T20:16:40Z</published>
    <updated>2008-08-22T04:07:21Z</updated>

    <summary>Former Discovery Institute’s Senior Fellow Jeffrey P. Schloss has become the target of several ID Creationists’ ire, such as Dembski, Denyse O’Leary and Richard Weikart. While I can appreciate that the history and evolution of former Senior Fellow Schloss is of concern to some ID Creationists, they, perhaps inadvertently, present us with evidence that serious scholars find it necessary to abandon Intelligent Design as preached by the Discovery Institute. In addition, the replacements seem to...</summary>
    <author>
        <name>PvM</name>
        
    </author>
    
    
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        <![CDATA[<div class="kw-format"><p>Former Discovery Institute’s Senior Fellow Jeffrey P. Schloss has become the target of several ID Creationists’ ire, such as Dembski, Denyse O’Leary and Richard Weikart. </p><p>While I can appreciate that the history and evolution of former Senior Fellow Schloss is of concern to some ID Creationists, they, perhaps inadvertently, present us with evidence that serious scholars find it necessary to abandon Intelligent Design as preached by the Discovery Institute. In addition, the replacements seem to lack much of a scientific background (Medved comes to mind)</p><p> And in case of Schloss, the reasons are quite compelling as laid out in a recent <a href="http://www.asa3.org/ASA/resources/Schloss200805.pdf" rel="external ">ASA article</a>. The article itself causes Dembski to make some strong comments about ASA, and cause Denyse to lose her temper as I will discuss. However, before addressing some of the creationists’ responses, I will first attempt to discuss the evolution of Jeff Schloss and his excellent review of “Expelled” which seems to have caused so much concern amongst ID Creationists, and for good reasons as Schloss presents an extremely well argued and still balanced critical rebuttal of “Expelled”.</p></div>]]>
        <![CDATA[<div class="kw-format"><h4 class="kw-heading" id="kw-A-short-historical-overview">A short historical overview</h4><p>We can trace some of the fossils of this evolution via his presentations, and writings</p><p><strong>Joining the Discovery Institute</strong></p><p><a href="http://www.jeffschloss.com/" rel="external ">Jeffrey Schloss</a> joined the Discovery Institute as a Senior Fellow and ID supporter and seems to have abandoned said relationship in August 2003. From that moment forward, Schloss’s position on Intelligent Design has evolved significantly</p><p>Jeffrey Schloss was one of the signers of the “<a href="http://www.ideacenter.org/contentmgr/showdetails.php/id/1207" rel="external ">List of Intellectual Doubters of Darwinism”</a></p><p>10/24/2000 Jeffrey P. Schloss, Ph.D. Ecology &amp; Evolutionary Biology (Washington University in St. Louis, Missouri).</p><p><strong>Leaving the Discovery Institute</strong></p><p>In August 2003, Jeffrey Schloss left the Discovery Institute.</p><p>What happened?</p><p>In 2005, Schloss spoke out in a public interview published in the Sacramento Bee</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>Then Schloss realized that unless people like him spoke up, the public would never get to hear more moderate ideas on the subject - such as the notion that evolution and God are not mutually exclusive; that scientists are not by definition godless nor religion advocates brainless; and that extremists on both sides have been responsible for fueling a feud that need not exist. 
</p>

</div></blockquote><p>Source: Sacramento Bee “Some find middle ground in science-theology clash” By Edie Lau – Published 2:15 am PDT Monday, October 3, 2005 </p><p>Why did Schloss join the Discovery Institute?</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>Like Townes, Schloss believes science can contribute something to the question of whether the nature of the universe is accidental or purposeful. That’s why the Westmont College biology professor was an early supporter of the  Discovery Institute, which was founded in 1990. 
</p>

</div></blockquote><p>Why did he decide to ‘part ways’?</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>“Is there a way we can formalize (that understanding) and make it scientifically rigorous rather than intuitive?” Schloss said. “I think that’s a fully legitimate question.”  Schloss said that while he supports science applying its tools to the question, he disagrees strongly with the institute’s stance against evolution.  “I think evolutionary theory is compatible with faith,” Schloss said. </p>

</div></blockquote><h4 class="kw-heading" id="kw-A-First-Sign-of-Trouble">A First Sign of Trouble</h4><p>On Feb. 7 2007, Schloss presented at the Grove City College Society for Science, Faith and Technology and The Center for Vision &amp; Values at Grove City College, one-day conference on “Creatively Seeking a Creation Story: Evolution and Intelligent Design in America.” </p><p>11 a.m.       “Evolution and Design: Beyond the ‘or’ Wars” by Dr. Jeff Schloss, Professor of Biology, Westmont College</p><p>Dembski’s comments suggest that he was surprised and felt perhaps a bit betrayed by the evolution of Jeffrey Schloss who (according to Dembski)</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>has since been distancing himself from ID and even going on the offensive against it. I witnessed the beginnings of this offensive at a symposium featuring Ron Numbers, Howard Van Till, Schloss, and me in 2007 at Grove City College</p>

</div></blockquote><p>The “Collegian”, Grove City College’s newspaper,  reports in their February 23, 2007 issue</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>
Seybold said the purpose of the conference was for those who attended “to know what 
these two positions [Evolutionary Theory and Intelligent Design] are and also why many people do not think intelligent design is a good option.”
</p>

</div></blockquote><p>and</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>The first three speakers argued that science could not be used to prove God’s involvement, while Dembski attempted to show that it could.</p>

</div></blockquote><p>Source:  Emily Dalpiaz: Seeking a Creation Story</p><p>Dembski’s presentation, which focused on the so-called ‘complexity’ argument, seems to have been well-oiled but likely did not improve on his earlier, somewhat shaky ‘God of the Gaps’ arguments.</p><p>Jeffrey Schloss is now a member of  ISSR (the International Society for Science &amp; Religion, which was established in 2002 for the purpose of the promotion of education through the support of inter-disciplinary learning and research in the fields of science and religion conducted where possible in an international and multi-faith context). The ISSR website explains the ISSR’s stance <a href="http://www.issr.org.uk/id-statement.asp" rel="external ">on the Concept of ‘Intelligent Design’</a> reads</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>
We believe that intelligent design is neither sound science nor good theology. Although the boundaries of science are open to change, allowing supernatural explanations to count as science undercuts the very purpose of science, which is to explain the workings of nature without recourse to religious language.  Attributing complexity to the interruption of natural law by a divine designer is, as some critics have claimed, a science stopper. Besides, ID has not yet opened up a new research program. In the opinion of the overwhelming majority of research biologists, it has not provided examples of “irreducible complexity” in biological evolution that could not be explained as well by normal scientifically understood processes. Students of nature once considered the vertebrate eye to be too complex to explain naturally, but subsequent research has led to the conclusion that this remarkable structure can be readily understood as a product of natural selection. This shows that what may appear to be “irreducibly complex” today may be explained naturalistically tomorrow.</p>

</div></blockquote><p>No wonder Dembski and O’Leary are not amused.</p><h4 class="kw-heading" id="kw-The-Review-of-Expelled">The Review of “Expelled”</h4><p>Jeffrey Schloss recently did a review of the movie “Expelled” and his review was prominently presented on the ASA website as well as the <a href="http://www.counterbalance.net/expelled/index-frame.html" rel="external ">Counterbalance</a> website. It is also one of the best reviews of “Expelled” I have read so far.</p><p><a href="www.asa3.org/ASA/resources/Schloss200805.pdf" rel="external ">The Expelled Controversy: Overcoming or Raising Walls of Division?</a></p><p>Schloss addresses such issues as 
<a href="http://www.counterbalance.net/expelled/isevo-frame.html" rel="external ">“Is Evolution Wedded to Atheism?”</a>, and 
<a href="http://www.counterbalance.net/expelled/doant-frame.html" rel="external ">“Do “anti-science bigots…censor scientists and stifle science”?</a> and 
<a href="http://www.counterbalance.net/expelled/areid-frame.html" rel="external ">Are ID advocates being expelled?</a> which looks in detail at 
<a href="http://www.counterbalance.net/expelled/carol-frame.html" rel="external ">Caroline Crocker</a>, and 
<a href="http://www.counterbalance.net/expelled/richa-frame.html" rel="external ">Richard von Sternberg</a> and 
<a href="http://www.counterbalance.net/expelled/guill-frame.html" rel="external ">Guillermo Gonzalez</a> and even addresses the issue 
<a href="http://www.counterbalance.net/expelled/shoul-frame.html" rel="external ">Should ID advocates be expelled?</a>. Schloss also addresses the charges  
<a href="http://www.counterbalance.net/expelled/didda-frame.html" rel="external ">Did Darwin lead to Hitler?</a>. In his 
<a href="http://www.counterbalance.net/expelled/concl-frame.html" rel="external ">Concluding Comments: Walls Torn Down?</a> Schloss  ends up quoting Hugh Ross</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>Our main concern about Expelled is that it paints a distorted picture. It certainly doesn’t match our experience. Sadly, it may do more to alienate than to engage the scientific community, and that can only harm our mission.RTB Scholars Expound on Expelled, the Movie. <a href="http://www.reasons.org/resources/apologetics/expelled.shtml" rel="external ">http://www.reasons.org/resources/ap[&hellip;]pelled.shtml</a></p>

</div></blockquote><p>Even our friend Davescot <a href="http://www.uncommondescent.com/intelligent-design/jeffrey-schloss-and-now-richard-weikarts-reply-to-him/#comment-293703" rel="external ">observes</a></p><blockquote class="kw-quote"><div class="kw-quote-body"><p>This Darwin/Nazi stuff is pure politics and exceedingly bad politics at that. It’s turning off those who might otherwise have given us a serious hearing like nothing else I’ve seen. Words fail me in describing how ill-conceived it is to associate this with intelligent design.</p>

</div></blockquote><p>Not to be ‘left behind’ self described ‘journalist’ Denyse O’Leary adds</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>Jeffrey Schloss is an embarrassment to scientists who claim to be Christians and part of the ongoing disgrace of the American Scientific Affiliation.</p><p>His scholarship is unbelievably poor.</p><p>But, of course, anyone who attempts to deny that Hitler was influenced by the Darwinism of his day would have to sign on to poor scholarship just for starters.</p><p>It is one thing for a group of Christians in science to disavow young earth creationism on insufficient evidence, but quite another to deny design in nature and suck up* to atheistic materialists.</p><p>= Hey! Guess what! The atheistic materialists as worried about design as we are! They have the courage of their convictions but we don’t. Still, they and we are friends, and whoop, whoop, they have invited us to coffee! So we are no longer scum, like the ID theorists.</p><p>Any serious scientist who belongs to such an organization had better have a plan for rescuing it.</p>

</div></blockquote><p>I wonder what O’Leary means by “disavow[ing] young earth creationism on insufficient evidence” but I am even more amazed about the intense hatred of some of the leading (and following) ID Creationists towards theistic evolutionists.</p><p>Denyse’s contributions to ASA’s reflector were, quite predictably, met with ‘skepticism’ and given the nature of some of her writings, I would say with good reason.</p><p>I have to commend Davescot for standing up for reason and point out that Jeffrey Schloss somehow became ‘incompetent’ after he was employed as a Senior Fellow at the Discovery Institute. Furthermore, when people assert the “Expelled” was not about a link between Darwinism and Nazism, he observes</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>It sure seemed that way to many viewers including me. If the Holocaust connection wasn’t made to smear modern Darwinists what then what the hell was it included for? The movie was supposed to be about suppression of ID in academia. The Holocaust seems pretty far removed from that theme. What am I missing?</p>

</div></blockquote><p>Nothing really. You are just far more perceptive than the average ID groupie.</p><p>Of course, other perceptive people such as <a href="http://www.calvin.edu/archive/asa/200808/0093.html" rel="external ">David Opderdeck</a> quickly showed how Denyse was lacking in scholarship herself</p><blockquote class="kw-quote"><div class="kw-quote-header">David Opderdeck Wrote:</div><div class="kw-quote-body"><p>I’m baffled by Denyse’s claim that Schloss denies “that Hitler was influenced by the Darwinism of his day” (which, she says, is  “to sign on to poor scholarship just for starters”).  .Here is what Schloss actually says in his Exposed essay on the ASA website:</p><p>“That Darwin was used (or abused) in Holocaust thinking seems uncontestable.”</p><p>Schloss later concludes:</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>Both Darwin and the Bible were seized upon by anti-Jewish zealots in search of a legitimating ideology. Hatred is notoriously indiscriminate in what it cobbles together to justify itself. Hitler, in particular, evidenced little regard for learning and – as the historical sources cited by recent defenders and critics of Expelled acknowledge – he extracted whatever was useful to support his preconceptions, from widely ranging popular, crude sources. <strong>In the case of Darwinian and Christian tradition though, there really exist disturbing themes that were (and are) amenable to misuse</strong>. However the fundamental ideas of the Holocaust were not just absent from, but contrary to the founders of each tradition.   (Emphasis added).</p>

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</div></blockquote><p>I will discuss the various parts of Schloss’s outstanding contribution in separate postings and Weikart’s ‘response’</p><h4 class="kw-heading" id="kw-Dembskis-Questions-for-Schloss">Dembskis Questions for Schloss</h4><p>See also <a href="http://www.asa3.org/groups/expelled/blog/" rel="external ">ASA Responds</a></p><p>Dembski raised some ‘interesting’ questions for Schloss</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>
(1) ID raises important issues for science.<br />
(2) Politics aside, ID proponents ought to get a fair hearing for their views, and they’re not.<br />
(3) A climate of hostility toward ID pervades the academy, which often undermines freedom of thought and expression on this topic.<br />
(4) That climate has led to ID proponents being shamefully treated, losing their reputations and jobs, and suffering real harm.</p>

</div></blockquote><p>Schloss seems to have rejected most of claim (4) and seems to believe that ID contributes little to science thus rejecting (1).  As to question number (2) Schloss observes that “Would that be a denial of academic freedom? Academic freedom does not involve the liberty to say absolutely anything in the name of one’s discipline. Moreover, for non-tenured faculty on a probationary appointment, it doesn’t even involve the freedom to research any topic. “ and “While both are important, earning the “right to be heard,” as Ross emphasizes, is surely not the same as demanding the “right to speak,” as Expelled focuses on. Expelled never ends up convincingly demonstrating that the latter is in any real jeopardy, but sadly, it does much to jeopardize the former.”</p><p>In the end however it is the lack of content which causes ID to fail and in addition why “Expelled” failed.</p><blockquote class="kw-quote"><div class="kw-quote-body"><p>So in response to his own question - “does it deserve to be suppressed?” - Stein never really provides us with a justified answer. We do get a stirring tribute to those who have given their lives to protect freedom, along with a reading from the Declaration of Independence. “We hold these truths to be self-evident…” the document famously proclaims. But of course not all truths, much less all purporting to be truths, are self-evident. Some require argument. What Expelled lacks is exactly that.</p>

</div></blockquote><p>Speaking of failures: “Expelled” was released in Canada and received some <a href="http://sensuouscurmudgeon.wordpress.com/2008/06/21/ben-stein%E2%80%99s-expelled-coming-to-canada/" rel="external ">scathing reviews</a> and <a href="http://www.benedictionblogson.com/2008/06/27/expelled-no-intelligence-allowed-not-a-hit-with-canadian-reviewers/" rel="external ">poor attendance</a></p><blockquote class="kw-quote"><div class="kw-quote-body"><p>36 theatres $24,374.00.
36/3 showings/3 days= 324 showings.</p><p>That’s about 72 people per theatre, which works out to 7-8 people, give or take a person per showing.</p>

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<entry>
    <title>Shocking new Darwin letter discovered...I&apos;m not sure what to think</title>
    <link rel="alternate" type="text/html" href="http://pandasthumb.org/archives/2008/08/shocking-new-da.html" />
    <id>tag:pandasthumb.org,2008://2.3920</id>

    <published>2008-08-11T19:31:54Z</published>
    <updated>2008-08-11T19:36:59Z</updated>

    <summary>This news comes via PTer and historian of science John Lynch. I don’t know what to think about this, it contradicts everything I used to think about Darwin, but honesty demands that the public and the scholarly world be informed of the uncomfortable facts.A precious historical findCategory: History and Philosophy (often of Science) Posted on: August 11, 2008 2:35 PM, by John LynchAmazing letter from Charles Darwin to Klara Pölzl, one that likely to change...</summary>
    <author>
        <name>Nick Matzke</name>
        <uri>http://www.talkdesign.org</uri>
    </author>
    
    
    <content type="html" xml:lang="en" xml:base="http://pandasthumb.org/">
        <![CDATA[<div class="kw-format"><p><a href="http://scienceblogs.com/strangerfruit/2008/08/a_precious_historical_find.php" rel="external ">This news comes via PTer and historian of science John Lynch</a>.  I don’t know what to think about this, it contradicts everything I used to think about Darwin, but honesty demands that the public and the scholarly world be informed of the uncomfortable facts.</p><blockquote class="kw-quote"><div class="kw-quote-body"><p><strong>A precious historical find</strong></p><p>Category: History and Philosophy (often of Science)
Posted on: August 11, 2008 2:35 PM, by John Lynch</p><p><a href="http://sneerreview.blogspot.com/2008/05/darwin-exposed.html" rel="external ">Amazing letter</a> from Charles Darwin to Klara Pölzl, one that likely to change Darwin scholarship for the future. Written in 1881, a year before his death, Darwin could clearly see the vast implications of his life’s work for Twentieth century thought. I’m going to have to take some time to digest this before I comment.</p>

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