Updated photo from Friday night:

Castle Rock, Colorado—Despite the first major snowstorm of the season, and unrelenting efforts by malicious Darwinists to prevent people from registering, a huge crowd of around 1,000 people showed up Friday night to hear Dr. Stephen Meyer present the DNA evidence for intelligent design based on his new book Signature in the Cell. Meyer, Michael Behe, David Berlinski, and myself are in Colorado to speak at the Legacy of Darwin ID Conference sponsored by Shepherd Project Ministries. On Saturday, Michael Behe will present the evidence against modern Darwinism from his books Darwin’s Black Box and The Edge of Evolution; David Berlinski will talk about The Devil’s Delusion and The Deniable Darwin; and I will talk about my book Darwin Day in America. Any fair-minded person in the Denver-Castle Rock-Colorado Springs area who still wants to come is welcome to purchase tickets at the door on Saturday morning starting at 8:15 am. The conference is taking place at the Douglas County Events Center. As of tonight, the malicious jamming of the Shepherd’s Project website seems to be continuing. Not content to suppress free speech about Darwin’s theory in schools and colleges and the media, some Darwinist vigilantes are now apparently even trying to stop intelligent design proponents from speaking at private conferences. Fortunately, their suppression tactics don’t seem to be working!

Posted by John West at 9:03 AM | Permalink | TrackBacks (0)

“Go to hell!” said Ron Numbers cheerfully to me, as we greeted each other at the front of Rockefeller Chapel last night. “Hey, did I say that loud enough?” he asked, looking around at the various evolutionary biology and history and philosophy of science worthies – Lewontin, Kitcher, Sober, Ruse, Dennett, Richards, and so on – milling about. Ron’s smiling insult was a mocking attempt to redress the widespread criticism that he had let me off easy in our notorious Bloggingheads conversation. A spirit of raillery was in the air, given a vigorous kick at the beginning of the evening by Harvard geneticist Richard Lewontin. Little of the secular sanctimony of the 1959 Darwin centennial (see below) was in evidence.

To the talks:

Richard Lewontin
Rockefeller Chapel, the venue for the plenary sessions, is a Gothic cathedral, although an oddly Baptist one, almost entirely void of religious symbols. (I’m sure there’s a small cross somewhere in the building, but you’d have to look hard to find it.) Lewontin, who has turned down every invitation this year to speak at Darwin celebratory events, accepted the University of Chicago invitation, he said, “because Jerry Coyne [Lewontin’s former doctoral student at Harvard] is the best arm-twister around. But I didn’t know I’d be speaking in a church,” Lewontin continued, “and we should recognize the religiosity of this occasion. There is a certain worship of a great saint, Darwin, and his apostles, who provide the texts for the day.” He then cited contrasting chapter and verse from Sir Ronald Fisher and Sewall Wright, and explained that battles between their respective positions – the primacy of natural selection, versus the primacy of random events – had occupied evolutionary theory for decades. “I really wish I could have spoken from there,” Lewontin ended his introduction, wistfully pointing to the spectacular high pulpit on the opposite side of the chancel.

“I want to challenge the New and Old Testaments of evolution,” Lewontin noted. “The New Testament holds that genes make organisms. The Old Testament says that organisms adapt to their environments. Neither of these testaments is true. It is not true that genes make organisms. Genes don’t make anything.” Nor do organisms adapt to their environments, he argued, as if they were adjusting – ad-apting, in its original eytmology – to pre-established niches. The outcome of genetic (internal) responses to environmental (external) challenges “cannot be predicted – there is no predictability to how organisms will respond,” because that depends in a complex fashion on a range of factors, many unique. Lewontin then illustrated his theme with several examples, from the unpredictability of Drosophila bristle patterns to variations in human fingerprints. One cannot move smoothly from genes to phenotypes: “I made the point,” he concluded, “and I’m dogmatic about it.”

Lewontin then criticized the Old Testament of adaptation. Organisms don’t “fit” into their niches, he said, as if the world could be divided into cubbyholes awaiting organisms to occupy them. There is an infinitude of ways of putting together the world; what actually happens is that organisms construct their niches, taking what is available from their environments to make their living. Lewontin ended with a cautionary critique about the shortcomings of the theory of natural selection, which he said was “in trouble.”

All in all, vintage Lewontin. Plainspoken, funny, independent. (And youthful! – Lewontin looks almost exactly as he did when he was a U of C professor in the early 1970s.)

Ron Numbers
On Thanksgiving Day, 1959, at the University of Chicago Darwin centennial celebration, Julian Huxley delivered a speech entitled “The Evolutionary Vision.” Predicting the demise of “supernaturally centered religions,” Huxley projected the coming of “new religions” that would replace the Abrahamic faiths: “they are destined to disappear in competition with other, truer, and more embracing thought organizations – in this case, with the new religions which are surely destined to emerge on this world’s scene” (1960, p. 253). Huxley’s lecture is notable for its overt religious tone. Religion, he argued, is the inevitable product of human consciousness, and thus like all biological objects, is destined to evolve to higher forms. (It is fascinating to note that Huxley, unlike Lewontin, did speak from the magnificent Rockefeller pulpit. Talk about religiosity.)

Well – Huxley certainly got the imminent demise of religion wrong. His prediction, at least on a 50-year scale, has failed spectacularly. Ron Numbers began his summary of “Anti-Evolutionism from Scientific Creationism to Intelligent Design” by saying, “I feel like I’m crashing the party.” Around the world, he observed, a majority of people do not accept Darwinian evolution.

Numbers then sketched the history of American dissent from Darwinism, making two major points: (1) young-earth creationism (YEC) was not the mainstream anti-evolution position until the last third of the 20th century, and (2) intelligent design cannot be equated with creationism. “Although many critics of ID want to say that it is nothing more than the same old creationist bullsh-t dressed up in new clothes,” he argued, “there is really only one historical link between ‘scientific creationism’ and ID, namely, the textbook Of Pandas and People.”

ID in Numbers’s eyes was actually a far more radical, indeed dangerous, viewpoint. ID proponents, he said, have made methodological naturalism (MN) their target. But MN, so named by a Christian philosopher of science at Wheaton College, has proved its value to the practice of science for 150 years, Numbers urged, by making it possible “for believers and unbelievers to participate alike” in the scientific enterprise. “This [MN] is a compromise that even scientific creationists typically bought,” Number said. However, for ID proponents, he went on, MN sacrifices what ought to be the goal of science, the discovery of truth, for what amounts to practical atheism. Numbers then sounded the alarm (as he often does) about the goals and funding sources of the Discovery Institute. (It’s a bit mysterious to me how observers can think Ron cuts ID people too much slack. Ron puts the boot into ID with force.) He concluded by discussing the growth, worldwide, of skepticism about Darwinian evolution. “There is yet a lot of work to do.”

If Ron and I had talked before his lecture, I would have reminded him of Huxley’s failed 1959 prophecy. Maybe a more realistic view of the future of the ID / materialism debate is not to see “work yet to be done” – as in trying for quasi-religious conversions of those unsaved theists who have yet to take Darwin into their hearts – but in recognizing the permanence of dissent from naturalism. If philosophical naturalism were congruent with reality, as Dawkins, Coyne, Dennett, and others argue, it should have won long ago. The fact that it hasn’t ought to give its promoters pause.

The last speaker of the evening was Marc Hauser from Harvard, on the origins of morality. His talk – absolutely fascinating, and (I think) counterintuitive to many in the audience – presented so much new data, in a short time, that it deserves its own post.

So that’s up next.

Reference
Julian Huxley, “The Evolutionary Vision,” in Sol Tax and Charles Callender, eds., Evolution After Darwin, volume 3: Issues in Evolution (Univ. of Chicago Press, 1960).

Posted by Paul Nelson at 10:13 AM | Permalink | TrackBacks (0)

Tuesday night at the Beverly Hills Library, with David Berlinski debating an atheist before a mixed crowd of friends and foes of religion, I experienced a lifetime first.

As a journalist writing about people and events, I’ve often had occasion to change or withhold someone’s name or otherwise disguise his identity. Almost always this is because the person in question never asked to be part of my story, is not a public personality and never sought to be, did nothing seriously blameworthy, but would be embarrassed by having his words or actions reported in public. So I don’t identify him. On Tuesday, listening to the debate, for the very first time in my experience I encountered a situation where someone was indeed seeking to make a name for himself but I felt nevertheless it would be cruel to give his name or institutional affiliation in my account of the event.

David Berlinski’s atheist opponent is that person. The poor guy! He was so hopelessly outgunned and outmanned as a thinker, debater, and speaker that I just can’t bring myself to give you his identity. He probably has his name on a Google Alert. Who doesn’t? Even it was entirely his free choice to put himself up again Berlinski in defense of his non-belief, I don’t have the heart to worsen his embarrassment.

The debate was sponsored by the tireless and infectiously enthusiastic Avi Davis of American Freedom Alliance. Dr. Berlinski spoke first and was, as ever, amazingly eloquent. He began by reframing what’s called the “Darwin debate” as something different. Rather than opposing sides in a conflict, for or against “Western civilization,” he generously portrayed the difference of views as an argument between passengers in a lifeboat on the open seas. Our civilization is a sinking boat on the ocean. We’re all, atheists, agnostics, and believers, trying to bail out the sorry craft. The argument is over how best to save all of us. There are no enemies here.

Berlinski went on to summarize Thomas Aquinas’ strong case for atheism and Aquinas’ own reply to that case. He spoke of the mysteries of existence, the origin of the universe, or matter and life, hardly stressing the case against Darwin at all. Afterward, in the Q&A, a questioner addressed him with hesitation: “Mr. Berlinski, you’re so eloquent it makes me pause before expressing myself publicly to you.”

Then the opponent got up. “I didn’t know we’d be talking about the origin of the universe,” he explained. “I would have studied more!”

“It’s not too late!” someone called out from the audience.

“It’s kind of hard to know how the universe came out,” he went on. It went downhill for him from there.

“I have some other little ideas,” he said later. He complained of how hard it is to be an atheist seeing, for example, triumphant pro sports players pointing up to the sky after a score or other victory.

“Atheists have been taking a lot of crap for a lot of centuries, a lot of centuries,” he lamented. “If you’re not an atheist, you don’t know how grating that can be over time.”

I was sweating for him the whole time -- maybe the first time, too, that I felt so much sympathy and fellow feeling for an evangelizing atheist.

It reminded me of the story of David and Goliath but with a twist. In the Biblical narrative, the terrified Israelites refuse to offer one of their own warriors to fight the giant. But they are happy to let young David have a try, expecting he’ll be crushed. In this case, too, the famed atheist warriors -- Dawkins, for example -- would never dare debate a Berlinski, or Stephen Meyer, or Michael Behe. But they are happy to let this poor guy face the giant.

Of course, the Biblical story worked out, in the end, quite differently than the story Tuesday night at the Beverly Hills Public Library.

Posted by David Klinghoffer at 8:30 AM | Permalink | TrackBacks (0)

This just gets better. Remember the International poll we highlighted earlier this week? British Darwinists, confused by the results (You mean our constant barrage of DARWIN RULZ msgs aren’t convincing anyone?), has taken to that old defense mechanism every psychologist knows too well: projection.

That’s it! They must be confused about Darwin’s theory. After all, “scientific wording” like "intelligent design" tricks people into thinking what they couldn’t possibly think after all the money we’ve spent on advertising Darwin’s awesomeness.

I almost wish they didn’t make it this easy:

Surprisingly, this percentage [of support for teaching alternative theories] was higher than in the US – a comparative bastion of religious fundamentalism – and Egypt, where only a third as many people dissented from the scientific consensus.

As for Egypt’s lack of “dissent from the scientific consensus” (what a lovely phrase!), maybe that’s because 62% of respondents had never heard of Darwin and had no idea what they were being asked. Most people in Egypt didn’t know what to say in response to the question, “How should evolutionary theory be taught in science lessons at schools?” though the few who had heard of Darwin preferred alternatives there, too, 45% to 22%.

Perhaps if certain British Darwinists (we’re looking at you, Ekklesia) channeled the time and energy they spend on condescending to America, religion, dissent from Darwin, and oh yes, their own audience, into something more productive, like reading poll numbers accurately, they might be more effective.

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The science writer Carl Zimmer posted an invited reply on his blog from Joseph Thornton of the University of Oregon to my recent comments about Thornton’s work. This is the last of four posts addressing it. References appear at the bottom of this post.

At the end of his post Thornton waxes wroth.

Behe’s argument has no scientific merit. It is based on a misunderstanding of the fundamental processes of molecular evolution and a failure to appreciate the nature of probability itself. There is no scientific controversy about whether natural processes can drive the evolution of complex proteins. The work of my research group should not be misintepreted by those who would like to pretend that there is.

To illustrate his own grasp of probability Professor Thornton talks baseball.

[Behe] supposes that if each of a set of specific evolutionary outcomes has a low probability, then none will evolve. This is like saying that, because the probability was vanishingly small that the 1996 Yankees would finish 92-70 with 871 runs scored and 787 allowed and then win the World Series in six games over Atlanta, the fact that all this occurred means it must have been willed by God.

Which of those strange behaviors would the imaginary Yankees have to change to win a Series title? — All of them. And how long would it likely take if each season they randomly changed one behavior a bit (say, fielders ran in a direction 173 degrees from a hit ball instead of 180 degrees straight away from it)? — Very, very long. The bottom line is this: it is Thornton who, frankly, doesn’t understand probability applied to evolutionary possibilities. His set of conceivable examples is severely restricted to ones that simply have to work, or that lead inexorably in the direction he wants them to go, without comprehending that there is no evolutionary law that says anything has to work, or that the best current innovation has to lead along a path to something even better. The remarkable thing is that his own admirable laboratory research illustrates this, but he is too enthralled by Darwinian theory to see it.

As for “no scientific controversy,” even a brief excursion into the history of science shows many uncontroversial, widely-accepted theories that were in fact wrong. There was no scientific controversy in the 19th century about the existence of the ether, or the adequacy of Newton’s laws. And, if one relies on science journals for her entire perspective, there is no controversy today about whether undirected natural processes can account for the origin of life. Yet neither can any scientist today detail a plausible theory of the origin of life. So the bare question of whether some idea is or is not controversial within the scientific community is itself simply a sociological question, not a scientific one. And when the idea is defended so weakly by someone as intelligent as Professor Thornton, it would seem that sociology is pretty much all the idea has going for it.

References

1. Bridgham, J.T., Ortlund, E.A., and Thornton, J.W. 2009. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461:515-519.

2. Bridgham, J.T., Carroll, S.M., and Thornton, J.W. 2006. Evolution of hormone-receptor complexity by molecular exploitation. Science 312:97-101.

3. Ohno, S. 1970. Evolution by gene duplication. Springer-Verlag, Berlin, Germany.

4. Behe, M.J. and Snoke, D.W. 2004. Simulating evolution by gene duplication of protein features that require multiple amino acid residues. Protein Sci. 13:2651-2664.

Posted by Michael Behe at 10:25 AM | Permalink | TrackBacks (1)

Supporters of Darwin’s theory continue to distinguish themselves on America’s college campuses—not for their reason and logic, but for their incredible ill manners and an almost pathological inability to engage in civil discussion. Last week, a factually-challenged attack on intelligent design was published in The Nevada Sagebrush, the student newspaper at the University of Nevada, Reno. Nothing new in that; I see ill-informed articles on intelligent design all the time. But after my colleague Rob Crowther posted a short comment suggesting that readers might actually want to hear from intelligent design proponents themselves (imagine that!), the Darwinist thought-police came out in force. One writer who is so courageous that he hides behind the pseudonym “bobxxxx” fulminated:

Robert Crowther… and the rest of the theocratic morons of the Dishonesty Institute are traitors who want to destroy America’s science education. If it was up to me they would be put in prison for treason. They are enemies of America, no better than terrorists, and they should be treated like terrorists.

Traitors? Terrorists? Enemies of America? ID proponents should be “put in prison” for freely expressing their views?!! Perhaps the University of Nevada should consider requiring its students to take a course on the First Amendment. It's pretty obvious that some of them don't understand the value of free speech.

When another person had the temerity to observe on the newspaper's website that “anti-Intelligent Design advocates often post nasty, name calling, ignorant, and often just plain slanderous comments on websites but the ID support[er]s rarely respond in kind,” he provoked a denunciation from someone calling himself “Jumbalaya,” who opined:

In the early 1940s, many of the German militants occupying France were known to be real polite as well. But you know what…?

THEY WERE STILL NAZIS!

Good manners don’t excuse ID supporters for the filth they’re pushing to the public.

This is not free speech; it’s an attempt to suppress free speech by demonizing and intimidating others so they will be afraid to speak up. I have a suggestion for the Darwinist purveyors of such hate speech: If you really want to identify the opponents of a free society, try looking in the mirror.

Posted by John West at 12:30 AM | Permalink | TrackBacks (0)

A Colorado group is the target of malicious computer hackers in what appears to be a coordinated attempt to suppress information about an upcoming conference on Darwin and intelligent design in Colorado.

Earlier this month the Shepherd Project Ministries website was breached using a “brute force attack” to break the password. The hackers then deleted webpages containing information about an upcoming conference featuring Discovery Institute speakers Stephen Meyer, Michael Behe, David Berlinski, and John West.

“No question whatsoever about they were targeting,” said Shepherd Project Executive Director Craig Smith. “That was brazen. We were a little stunned, to be perfectly honest. We had seen some hostile language about the conference, but honestly we just assumed it was cyber-flaming. We didn’t really expect or anticipate any kind of actual attack.”

The pages were quickly re-posted and security protocols fixed to prevent further mischief being done, but since then a distributed denial-of-service (DDoS) attack crippled and even crashed the Shepherd Project website, preventing many from registering for the intelligent design conference. These attacks involve multiple people coordinated in an attempt to make a website unavailable, shutting down access to information in a form of modern-day book-burning.

These attacks reveal how even having a discussion about intelligent design is threatening to those who can't countenance free speech on evolution.

In today's ID the Future podcast interview, Craig Smith said, "It’s stunning to me how threatened they seem to be about the conversation that is taking place. It’s not a matter of, 'I disagree with the content' or 'I disagree with the conclusion,' it’s 'I disagree that the conversation should be allowed.'"

That same sentiment was behind the recent canceling of the Darwin's Dilemma by the California Science Center, and you can read it for yourself in the New York Times as Daniel Dennett's recent letter blasted them for daring to be respectful to those who doubt evolution!

The Legacy of Darwin Intelligent Design Conference targeted by these hackers takes place this weekend at Douglas County Event Center in Castle Rock, Colorado.

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After having the premier of Darwin’s Dilemma canceled by the California Science Center, Avi Davis’s American Freedom Alliance really pulled things together in heroic fashion in Los Angeles. The AFA found a new venue, hardly inferior, where academic freedom may be less endangered: the University of Southern California. The sizable crowd on Sunday night of about 230 people was appreciative and intelligent. There were university students representing both sides of the Darwin debate, high school students from a church school in Santa Monica on a field trip, and a mix of other folks from the community.

The film is a powerful document. The word that came to my mind watching it was “spooky.” Besides very lucidly and compellingly laying out its scientific case that the Cambrian explosion can’t be remotely explained in Darwinian terms, and that the event 530 million years ago virtually compels a conclusion that purposive design was involved, I was struck by the atmosphere of mystery that director Lad Allen evokes. What does explain the sudden appearance of most animal body plans in a space of maybe 5 to 10 million years? The film quotes Richard Dawkins unarguable statement that, “Without gradualness in these cases, we are back to a miracle, which is simply a synonym for the total absence of explanation.”

Allen, David Berlinski, and Jonathan Wells all spoke afterwards on a discussion panel. The inimitable Berlinski, the William F. Buckley of Darwin doubters, was in fine form, at one point amusingly decapitating a rambling student challenge from the audience with the concise answer, “No.” I also loved his insight that the ugliness of the results of the Darwinian idea, its effects on our culture, are far from irrelevant in judging the idea’s truth. This is another one of Darwin’s dilemmas. Berlinski cited Keats, “’Truth is truth, beauty truth,’ -- that is all/ Ye know on earth, and all ye need to know.” No, he pointed out, you can’t separate the consequences of Darwinian theory from its truth. Beauty may well be an aspect of truth.

Heady stuff, but Berlinski brought it down to earth the next morning in the studio of Dennis Miller in Culver City here, discussing the new paperback edition of The Devil’s Delusion: Atheism and Its Scientific Pretentions. The last segment included David’s very funny riff on how a cow-like creature could take to the seas as a proto-whale, per the Darwinian just-so story, including the challenge of developing nipples that work underwater. Miller took up the nipple image and developed it in a manner that I’m not sure belongs on a blog intended for all the family, but was very entertaining nevertheless.

Monday and Tuesday were taken up by meetings with Jews and Christians — including rabbis, headmasters of Jewish high schools, and a very different group at the Lighthouse Church in Santa Monica. Held at a synagogue and at L.A. Museum of Tolerance, our meetings with the rabbis left me with a strong sense of breaking through in a way I hadn’t before with the Jewish audience. The speakers were again Berlinski and Wells, along with myself, representing three quite different approaches to the Darwin debate. I’d like to share with you my remarks later. We again took our three-way presentation on the road at the Lighthouse Church. Dr. Wells does a particularly effective and concise Powerpoint presentation on the basics of intelligent design.

One lesson I took away with me is that out there in the real world, the evolution debate matters to people for reasons that may not be quite the same as the reasons it matters to many of us who are involved with it professionally. For them, it’s not about the scientific issue per se or about academic freedom. It’s about their children.

If you’re meeting with rabbis and speaking at a church, obviously faith is going to be front and center in the mind of your listeners. But it was not the theologically knotty problem of reconciling God and Darwin that was at issue so much as the effect of the cultural pollution pouring out of various smokestacks in public life, the media, and academia. One very tall and ominous smokestack is represented by Darwinism.

Our listeners were not fixated on science or theology, nor on the consequences of Darwin’s idea in the past (Nazis, eugenics, racist imperialism) but on how the culture right now is corrupted by animalism and nihilism -- the drumbeat of despair that tells young people they are animals just like our ape cousins, that life in the present, just like its origin and development in the past, is without meaning and purpose. Worry for their children is, I think, the chief reason that parents, unlike the California Science Center, won’t allow this debate to be canceled.

Posted by David Klinghoffer at 10:50 AM | Permalink | TrackBacks (0)

The science writer Carl Zimmer posted an invited reply on his blog from Joseph Thornton of the University of Oregon to my recent comments about Thornton’s work. This is the third of several posts addressing it. References will appear in the last post.

Now back to Thornton’s first point, the role of neutral mutations (which he sometimes labels “permissive” mutations). At several places in his post Thornton implies I’m unaware of the possibilities opened up by genetic drift:

Behe’s discussion of our 2009 paper in Nature is a gross misreading because it ignores the importance of neutral pathways in protein evolution.... Behe’s first error is to ignore the fact that adaptive combinations of mutations can and do evolve by pathways involving neutral intermediates.... As Fig. 4 in our paper shows, there are several pathways back to the ancestral sequence that pass only through steps that are neutral or beneficial with respect to the protein’s functions.

To restore the ancestral conformation by reversing group X, the restrictive effect of the substitutions in group W must first be reversed, as must group Y. Reversal to w and y in the absence of x, however, does nothing to enhance the ancestral function; in most contexts, reversing these mutations substantially impairs both the ancestral and derived functions. Furthermore, the permissive effect of reversing four of the mutations in group W requires pairs of substitutions at interacting sites. Selection for the ancestral function would therefore not be sufficient to drive AncGR2 back to the ancestral states of w and x, because passage through deleterious and/or neutral intermediates would be required; the probability of each required substitution would be low, and the probability of all in combination would be virtually zero. (my emphasis)

Let’s quote that last sentence again, with emphasis: “Selection for the ancestral function would therefore not be sufficient ... because passage through deleterious and/or neutral intermediates would be required; the probability of each required substitution would be low, and the probability of all in combination would be virtually zero.” If Thornton himself discounts the power of genetic drift when it suits him, why shouldn’t I?

In his blog response to me Professor Thornton wants to emphasize that selection-plus-drift can sometimes lead from one nearby function to another, as it did in his work on the ancestral MR-like to the GR-like receptor transition. (2) But I and virtually everyone else already thought that was true. That’s why at the time I called those results (perhaps impolitely, but accurately) “piddling”. A surprise it was not. In his 2009 paper investigating the reverse transition, however, Thornton wants to emphasize (because it is unexpected) that in some cases selection-plus-drift can not lead (with anything like reasonable probability) even to a very similar function. Now that was surprising to me and apparently to many other folks.

The immediate, obvious implication (which he clearly wants to keep far away from) is that the 2009 results render problematic even pretty small changes in structure/function for all proteins — not just the ones he worked on. (Thornton himself is betting on this: “We predict that future investigations, like ours, will support a molecular version of Dollo’s law: as evolution proceeds, shifts in protein structure–function relations become increasingly difficult to reverse whenever those shifts have complex architectures....”) (1) So how, other than begging the question, are we now to know that even the small differences we see in related protein systems came about by random mutation/selection (and, yes, drift)? Quite simply, we can’t. Yet if even small changes are problematic, then larger changes will be prohibitive, and very big changes essentially unattainable. Thanks to Thornton’s impressive work, we can now see that the limits to Darwinian evolution are more severe than even I had supposed.

Posted by Michael Behe at 10:00 AM | Permalink | TrackBacks (0)

The science writer Carl Zimmer posted an invited reply on his blog from Joseph Thornton of the University of Oregon to my recent comments about Thornton’s work. This is the second of several posts addressing it. References will appear in the last post.

Now to Professor Thornton’s reply. He writes at length but makes just two substantive points: 1) that neutral mutations occur and can serendipitously help a protein evolve some function (“[Behe] ignores the key role of genetic drift in evolution”); and 2) that just because a protein may not be able to evolve a particular function one way does not mean that it, or some other kind of protein, can’t evolve the function another way (“nothing in our results implies that, if selection were to favor the ancestral function again, the protein could not adapt by evolving a different, convergent, underlying basis for the function”).

I’ll start with the second point since I can just quote myself to answer it. I wrote in one of my previous posts on Thornton’s work:

Another point worth driving home in this post concerns the frequently encountered argument that, well, just because one kind of protein can’t develop a useful binding site or selectable property easily doesn’t mean that some other kind of cellular protein can’t. (In keeping with their Darwinian framework, Bridgham et al (2009) seem to allude to this.) After all, there are thousands to tens of thousands of kinds of proteins in a typical cell. If one of them is ruled out, the reasoning goes, many more possibilities remain.

This argument, however, is specious. For any given evolutionary task, the number of proteins in the cell which are candidates for helpful mutations is almost always very limited. For example, as I discussed in EOE, out of thousands of malaria proteins, mutations in only a handful are helpful to the parasite in its fight against chloroquine, and only one is really effective — the mutations in the PfCRT protein. Ditto for the human proteins that can mutate to help resist malaria — there’s just a handful. In the case of the hormone receptors discussed by Bridgham et al (2006), one can note that, out of ten thousand vertebrate proteins, the one that gave rise to a new steroid hormone receptor was an already-existing steroid hormone receptor. This should be quite surprising to folks who believe the many-proteins argument, because the steroid receptor was outnumbered 10,000 to 1 by other protein genes, yet it won the race to duplicate and form a new functional receptor. If all things were equal, we should be very surprised by that. But of course not all things are equal. The reason the receptor duplicated to give rise to a closely-related receptor is because no other protein in the cell is likely to be able to do so in a reasonable amount of evolutionary time.

Now let’s contrast Thornton’s blog reply to me with what he wrote in his paper. In the blog he writes: “nothing in our results implies that, if selection were to favor the ancestral function again, the protein could not adapt by evolving a different, convergent, underlying basis for the function.” Yet in his paper he wrote:

There may be other potentially permissive mutations, of unknown number, that could compensate for the restrictive effect of group W and allow the ancestral conformation to be restored. Reversal by such indirect pathways could be driven by selection, however, only if these other mutations, unlike those we studied, could somehow relieve the steric clashes and restore the lost stabilizing interactions ... and also independently restore the ancestral function when helix 7 is in its radically different derived conformation. Whether or not mutations that could achieve these dual ends exist, reversal to the ancestral conformation would require a considerably more complex pathway than was necessary before the ratchet effect of W evolved.

Posted by Michael Behe at 4:10 PM | Permalink | TrackBacks (0)

According to an international poll released by the British Council, the majority of Americans — 60% — support teaching alternatives to evolution in the science classroom. The percentage is the same for Britons, despite the fact that both countries have been inundated with pro-Darwin media coverage in this super-mega Darwin Year.

Of course, the British media reporting this are chagrined. Britain is the birthplace of Charles Darwin and his theory of evolution, and the official-sounding British Council, the UK group behind the “Darwin Now” campaign that commissioned the Ipsos MORI poll, have spent precious resources educating the world about Darwin. Now some believe the poll shows that efforts by Darwinist organizations aren't working.

Head of the British Council’s Darwin Now program Fern Elsdon-Baker said, “Overall these results may reflect the need for a more sophisticated approach to teaching and communicating how science works as a process.”

While Darwin’s apologists might try to explain the poll numbers as an example of ignorance influencing people’s beliefs, the numbers themselves suggest a different picture.

Across the board, most respondents from the ten countries polled thought that “other perspectives on the origins of species” “such as intelligent design and creationism” should be taught in science class*. When the poll is weighted to include only those respondents who have heard of Charles Darwin and know something about his theory of evolution, the percentage supporting alternate theories increases, from 60% to 66% in Britain and 60% to 64% in the U.S.

The correlation appears again when we consider which countries have more knowledge of Darwin’s theory. The highest numbers of those in support of alternative theories in the classroom correspond to the highest numbers of those familiar with Charles Darwin — 60% in Britain, 65% in Mexico, 61% in China, 66% in Russia, and 60% in the U.S. It appears that the more people know about Darwin’s theory, the more they want to see alternatives in science class.

The basic truth is that most people want evolution to have to compete for its place of dominance in their schools. Interestingly, the U.S. was the only nation with significant knowledge of Darwin where respondents chose the option “theories about the origins of species and development of life on earth should not be taught in science lessons at all.” 14% chose that, compared with 3% in Britain.

*This takes both those who select "other perspectives" only and those who select "other perspectives" together with "evolutionary theories." It should be noted that Discovery Institute opposes efforts to mandate teaching alternative theories in the science classroom — we'd rather have the whole picture of evolution, the scientific arguments both for and against the theory, presented instead.

Posted by Anika Smith at 10:30 AM | Permalink | TrackBacks (0)

The science writer Carl Zimmer posted an invited reply on his blog from Joseph Thornton of the University of Oregon to my recent comments about Thornton’s work. This is the first of several posts addressing it. References will appear in the last post.

I must say, it never ceases to amaze me how otherwise-very-smart folks like Zimmer and Thornton fail to grasp pretty simple points when it comes to problems for Darwinian mechanisms. Let me start slowly with a petty complaint in Carl Zimmer’s intro to the post. Zimmer is annoyed that I think Thornton’s latest work is “great,” yet I thought his previous work published a few years ago was “piddling.” “Why the change of heart?” wonders Zimmer.

It’s really not that hard to understand. Here’s a little analogy to illustrate. Suppose some company claimed they could build a super-crane (tip of the hat to Daniel Dennett) which could hoist a whole mountain using a novel technology. Though untested, the great majority of the relevant engineering community was serenely confident it would work as advertised. In a carefully-devised, initial, “proof-of-principle” experiment, a laboratory at the University of Oregon demonstrated that the crane-technology could lift a smooth pebble. The work was published in Science, accompanied by a breathless editorial and a story in the New York Times. In a subsequent careful study published several years later in Nature, however, the same lab unexpectedly showed that if a pebble were even somewhat rough, the crane-technology would not lift it. Since mountains tend to be rough, too, if a super-crane wouldn’t move a rough pebble, then it certainly wouldn’t lift a mountain.

Of course, the initial work, although technically well-done, can fairly be called “piddling” compared to the promised capacity of the crane. The subsequent work, again technically well-done, was “great” because it demonstrated formidable difficulties for the technology at a very basic level that no one — not even (ahem...) the few skeptics — had expected. (I hate to be so pedantic, but unfortunately it seems necessary on this topic.)

Posted by Michael Behe at 11:17 AM | Permalink | TrackBacks (0)

A few days ago we saw Ida fall from her overhyped status as an ancestor of humans. Now some scientists are claiming that Archaeopteryx should lose its status as an ancestor of modern birds. Calling Archaeopteryx an “icon of evolution,” the Wall Street Journal (WSJ) borrows a term from Jonathan Wells while reporting that “[t]he feathered creature called archaeopteryx, easily the world's most famous fossil remains, had been considered the first bird since Charles Darwin's day. When researchers put its celebrity bones under the microscope recently, though, they discovered that this icon of evolution might not have been a bird at all.”

According to the new research, inferences about growth rates made from studies of Archaeopteryx’s ancient fossilized bones show it developed much more slowly than modern birds. While the WSJ is reporting these doubts about Archaeopteryx’s ancestral status as if they were something new, those who follow the intelligent design movement know that such skepticism has been around for quite some time. In his 2000 book Icons of Evolution, Jonathan Wells discussed differences between Archaeopteryx and modern birds and the implications for Archaeopteryx's place as an alleged link between dinosaurs and birds:

But there are too many structural differences between Archaeopteryx and modern birds for the latter to be descendants of the former. In 1985, University of Kansas paleontologist Larry Martin wrote: “Archaopteryx is not ancestral of any group of modern birds.” Instead it is “the earliest known member of a totally extinct group of birds." And in 1996 paleontologist Mark Norell, of the American Museum of Natural History in New York, called Archaeopteryx “a very important fossil,” but added that most paleontologists now believe it is not a direct ancestor of modern birds.

(Jonathan Wells, Icons of Evolution, p. 116 (Regnery, 2000).)

There are lingering doubts that birds today are descendants of dinosaurs. Researchers at Oregon State University recently argued that the distinctive anatomy that gives birds the lung capacity needed for flight means it is unlikely that birds descended from dinosaurs like archaeopteryx and its kin. Their findings were published in June in the Journal of Morphology.

But old theories die hard, Ruben said, especially when it comes to some of the most distinctive and romanticized animal species in world history.

"Frankly, there's a lot of museum politics involved in this, a lot of careers committed to a particular point of view even if new scientific evidence raises questions," Ruben said. In some museum displays, he said, the birds-descended-from-dinosaurs evolutionary theory has been portrayed as a largely accepted fact, with an asterisk pointing out in small type that "some scientists disagree."

"Our work at OSU used to be pretty much the only asterisk they were talking about," Ruben said. "But now there are more asterisks all the time. That's part of the process of science."

("Discovery Raises New Doubts About Dinosaur-bird Links," ScienceDaily, June 9, 2009.)

Posted by Casey Luskin at 8:00 AM | Permalink | TrackBacks (0)

A few months ago, “Ida” was sitting on top of the world. She’d been lauded as the “eighth wonder of the world” whose “impact on the world of palaeontology” would be like “an asteroid falling down to Earth.” Falling, indeed. On October 21, Nature published an article announcing that “[a] 37-million-year-old fossil primate from Egypt, described today in Nature, moves a controversial German fossil known as Ida out of the human lineage.” Wired also published a story, noting that, “[f]ar from spawning the ancestors of humans, the 47 million-year-old Darwinius seems merely to have gone extinct, leaving no descendants,” further quoting a paleontologist calling Ida “a third cousin twice removed … only very distantly related to living and fossil anthropoids.”

But Ida was given quite a ride by the mainstream media, while it lasted. Originally:

Famed BBC broadcaster Sir David Attenborough got involved, making a documentary titled Uncovering Our Earliest Ancestor: The Link, to explain why Ida is “the link that connects us directly with the rest of the animal kingdom.” Co-sponsored by both the BBC and the History Channel, the program attracted a massive audience. …

Good Morning America and Nightline covered the fossil.

National Geographic called her the “critical ‘missing link’ species.”

ScienceDaily and a Discover magazine commentator praised Ida as our “47-million-year-old human ancestor.”

Skynews told the public that “proof of this transitional species finally confirms Charles Darwin’s theory of evolution.”

With Google’s eager assistance, Ida went viral: One of the leading search terms that day was “missing link found.” Even the Drudge Report was reeled in by the media frenzy, briefly featuring Ida as the headline story.

(Casey Luskin, “The Big Ida: The Rise & Fall of Another Missing Link & Other Media Hype,” Salvo 10 (Autumn, 2009).)

Teeth and ankle bones of the new Egyptian specimen show that the 47-million-year-old Ida, formally called Darwinius masillae, is not in the lineage of early apes and monkeys (haplorhines), but instead belongs to ancestors (adapiforms) of today's lemurs and lorises.

"Ida is as far away from the human lineage as you can get and still be considered a primate," says Christopher Beard, a palaeoanthropologist at the Carnegie Museum of Natural History in Pittsburgh, Pennsylvania, who was not involved in either research team.

(Rex Dalton, “Fossil primate challenges Ida's place,” Nature, Vol. 461:1040 (October 21, 2009).)

Where else have we seen an “overhyped debut” of a fossil, without “dialogue”? Exhibit A: “Ardi” (Ardipithecus ramidus).

In fact, with its article titled “Humanity Has New 4.4 Million-Year-Old Baby Mama,” Wired was one of the numerous major media outlets assisting in the overhyped debut of Ardi. But most of those abettors didn’t say anything about the ambiguity and dissent over Ardi’s reconstructed skeleton. It seems that other missing links also debut with a lot of hype and without much dialogue.

Calm, collected, and careful scientific analysis is going on somewhere in the background here, but little scientific dissent from the media’s storyline is being disclosed to the public. Instead, we see that the media, working with certain evangelistic tribes within the academy (see illustration at left), are unashamedly using these fossils as opportunities to push Darwin.

How long “Ardi” will retain favored link status is anyone’s guess.

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Originally, proponents of neo-Darwinian evolution lauded “junk” DNA as functionless genetic garbage that showed life is the result of blind and random mutational events. Then “junk” DNA was disproved by the discovery that the vast majority of DNA is being transcribed into RNA. Did the failure of this Darwinian assumption cause evolutionists to terminate their love affair with biological “junk”? Of course not. They just shifted their argument back, claiming that the cell is full of “junk RNA”—DNA that is being transcribed into RNA but still does nothing in the cell. Earlier this year we reported on a Nature paper suggesting function for “junk” RNA. Now a Science Daily NewsArticle is confirming that finding. Aptly titled “No Such Thing As 'Junk RNA,' Say Researchers,” the article reports that very small strands of RNA termed “usRNAs” (unusually small RNAs) perform important functions related to gene regulation.

Once again, the Darwinian “junk” mindset seems to have held back such discoveries, as the authors report, “until we did our experiments, we didn't realize that RNAs as small as 15 nucleotides, which we thought were simply cell waste, are surprisingly stable, and are repeatedly, reproducibly, and accurately produced across different tissue types. … We have dubbed these as usRNAs, and we have identified thousands of them, present in a diversity that far exceeds all other longer RNAs found in our study." One of the study’s authors, Dr. Bino John, concluded, "These findings suggest that usRNAs are involved in biological processes, and we should investigate them further."

While it’s heartening to learn they’re now on a better path towards fruitful research, it seems that progress is only made once experimental data—and not evolutionary presumptions—are permitted to guide scientific research. It’s no secret that the Darwinian-based “junk” mindset has hindered research into the actual function for biological features thought to be functionless evolutionary garbage. A 2003 article in Science explained how “junk” thinking has “repelled mainstream researchers” from studying the function of such important genetic structures:

Although catchy, the term ‘junk DNA’ for many years repelled mainstream researchers from studying noncoding DNA. Who, except a small number of genomic clochards, would like to dig through genomic garbage? However, in science as in normal life, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. Because of them, the view of junk DNA, especially repetitive elements, began to change in the early 1990s. Now, more and more biologists regard repetitive elements as a genomic treasure."

(Wojciech Makalowski, "Not Junk After All," Science, Vol. 300(5623):1246-1247 (May 23, 2003).)

Of course, an intelligent design paradigm would have predicted function for “junk” DNA or “junk” RNA all along, perhaps leading scientists to “investigate them further” much sooner.

Posted by Casey Luskin at 8:33 AM | Permalink | TrackBacks (0)

What do Discover magazine, The London Gazette, The Wichita Eagle, Commentary, Forbes, The Weekly Standard and UC Berkeley’s student paper, The Daily Californian, all have in common? They are just some of the publications that have published an essay or opinion piece by David Berlinski in the past 15 years. And those pieces are among 32 of Berlinski's finest finally collected together in one volume: The Deniable Darwin.

Berlinski, there is little argument, is a skeptic’s skeptic — the last of a dying breed. Lately it seems that everywhere one looks there is someone with the answer to everything. There are precious few true skeptics left, and Berlinski is certainly in the top rank in regards to the sciences.

When it comes to some of life’s most profound questions — the origins of life, of matter, of the universe itself — does modern science already have everything all figured out? Many scientists would like us to think they are mere steps away from solving all the deep enigmas of physical existence.

Consummate skeptic David Berlinski shows without that all such confidence is at best a bluff.
In essays about evolution using humor and wit, Berlinski shows how lost today’s scientists really are.

His new book, The Deniable Darwin, frees us from the superstition of preening scientism and illuminates the path to a renewal of real science.

In The Deniable Darwin & Other Essays (DI Press 2009) Berlinski wields his famous skepticism, excluding neither Darwinism nor intelligent design from his critical eye. Included among the 32 essays spanning 15 years are his award winning essays, "What Brings a World into Being?" and "On the Origins of Mind" (Best American Science Writing 2002, 2005, respectively).

The prolific author of numerous books on mathematics and logic, Berlinski has written a series of famously controversial essays on biology, physics, psychology, and mathematics in Commentary magazine, provoking each time an outpouring of dumbfounded letters to the editor. Berlinski’s replies are witty and sharp. For the first time, The Deniable Darwin collects all of these essays and exchanges, and others in a similar vein, into a single volume.

Here's some of the praise for his new book:

“Berlinski is to science writing what Tiger Woods is to golf. He can score from anywhere, against any opponent, on any course. The Deniable Darwin is a compulsive revel of his incandescent prose and jugular polemics. As irresistible as Gödel’s Proof.”
—George Gilder, author of The Israel Test, Wealth and Poverty, and Telecosm

“Berlinski’s ability to weave the lessons of history with the wonders of modern science is unmatched, as is his use of subtle humor that enlivens his text. These essays will delight many and annoy others, regardless of on which side of the ideological aisle of science you may stand—for science has an ideology as Berlinski so well documents.”
—Gerald Schroeder, author of God According to God: A Physicist Proves We’ve Been Wrong About God All Along and The Science of God

“Berlinski is a genuine intellectual hero, one whose challenge to the certainties of evolutionary biology and Big Bang cosmology--the comfortable certainties of conventional wisdom about the origin of man and the origin of the universe--does not come from allegiance to rival certainties such as biblical creationism. Instead, Berlinski turns the methods and assumptions of science on itself to demonstrate the implausibilities underlying the arrogant claims of the grand theorists.”
—Ron Rosenbaum, author of Explaining Hitler and The Shakespeare Wars

“Berlinksi’s rapier wit is the antidote to the insufferable smugness of modern scientism. When, without any seeming effort, he notes that ‘like the Communist Party under Lenin, science is infallible because its judgments are collective,’ the reader is forever immunized against grandiose claims for scientific ‘consensus.’ Much more awaits the readers of this wonderful collection.”
—Michael Behe, professor of biochemistry, Lehigh University, and author of The Edge of Evolution and Darwin’s Black Box

Posted by Robert Crowther at 9:19 AM | Permalink | TrackBacks (0)

A new paper from Richard Lenski’s group has appeared in Nature and has garnered a fair amount of press attention. Some people asked me for my thoughts about it.

The new paper continues the grand experiment that Lenski has been publishing about lo these many years — allowing a culture of the bacterium E. coli to continuously grow and evolve under his close observation. The only really new thing reported is a technical improvement — these days one can have the entire genome of E. coli "re-sequenced" (that is, determine the sequence of the entire DNA of the particular E. coli you're working with) done for an affordable cost. (There are companies which will do it for a fee.) So Lenski and collaborators had the whole genomes — each and every nucleotide — sequenced of the E. coli that they have been growing for the past twenty years. Since they froze away portions of their bacterial culture at different times along the way, they now have the exact sequences of the evolving culture at many time points, from inception to 2000 generations to 10,000 to 40,000. Thus they can know exactly which mutations appeared when — an almost-complete paper trail. Very very cool!

From that information they identify a couple score of mutations which they say are likely beneficial ones. That is almost certainly true, but what they don't emphasize is that many of the beneficial mutations are degradative — that is, they eliminate a gene or its protein's function. About half of the mutations they initially identified in previous work, but some they report here for the first time. They don't discuss what the new ones do (they may not yet know), but odds are high that most of them also are degradative, causing proteins either to stop working or to work less well. In any event, there is no indication that any of these are on their way to building some complex new system.

Interestingly, in this paper they report that the E. coli strain became a "mutator." That means it lost at least some of its ability to repair its DNA, so mutations are accumulating now at a rate about seventy times faster than normal. Lenski had reported years earlier that a number of other lines of the evolving population (they started with 12 separate cultures) had become mutators, too. So it seems that loss of ability to repair DNA is a common occurrence under these conditions.

Lenski is a very good self-promoter (no criticism intended; that’s a good thing — scientists have to interest other people in their work), and he always accentuates the positive. So if a gene is blasted to bits by a mutation, he talks cheerfully about how it is a beneficial change that helps the bacterium grow faster. One has to dig hard into the data to see that the bacterium is losing genetic info. In press coverage for this paper, he avows a “new dynamic relationship was established” in the bacterium’s evolution, and one has to read the details of the paper to find out that this is due to a degradative mutation that compromises its normal ability to repair its DNA.

Despite his understandable desire to spin the results his way, Lenski’s decades-long work lines up wonderfully with what an ID person would expect — in a huge number of tries, one sees minor changes, mostly degradative, and no new complex systems. So much for the power of random mutation and natural selection. For his work in this area we should be very grateful. It gives us solid results to point to, rather than having to debate speculative scenarios.

References
Barrick, J.E., Yu, D.S., Yoon, S.H., Jeong, H., Oh, T.K., Schneider, D., Lenski, R.E., and Kim,J.F. 2009. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature, doi:10.1038/nature08480.

Sniegowski, P.D., Gerrish, P.J., and Lenski, R.E. 1997. Evolution of high mutation rates in experimental populations of E. coli. Nature 387:703-705.

Posted by Michael Behe at 1:44 PM | Permalink | TrackBacks (0)

David Berlinski is currently stateside for his speaking tour of the U.S., and The Devil's Delusion is selling briskly, already in its second printing in paperback. Now there's a new discussion guide to complement Dr. Berlinski's powerful book.

Because Dr. Berlinski's enjoyable style makes the book so eminently readable, not to mention its importance as a response to the new atheists, The Devil's Delusion and its new discussion guide are a natural choice for book clubs, small groups, adult Sunday school classes, and anyone who wants to delve a little deeper.

The guide reads as if a college professor highlighted the book's most trenchant points and asked the class to chew on them, a style that proves fertile for book discussions (I speak from experience). With chapter summaries and discussion questions, readers have a scaffolding on which to build their thoughts and engage the central questions with others.

The discussion guide is available for free download here, and hard copies are available for purchase.

Posted by Anika Smith at 10:00 AM | Permalink | TrackBacks (0)

David Berlinski is embarking on a speaking tour around the United States. For the most part he will be presenting his book The Devil's Delusion: Atheism and its Scientific Pretensions as a lecture at various universities, conferences and other appearances. Here are the basic details with links to get more information, and there will be continued updates at www.devilsdelusion.com.

October 23 -- lecture at King's College, New York
October 25 -- Darwin's Dilemma screening, USC, Los Angeles
October 27 -- lecture and discussion, Beverly Hills Library, Beverly Hills
October 31 -- lecture at ID conference, Colorado Springs
November 3 -- lecture at Oberlin College, Oberlin, Ohio
November 4 -- lecture at Ohio University, Athens, Ohio
November 5 -- lecture at University of Akron, Akron, Ohio

Posted by Robert Crowther at 10:00 AM | Permalink | TrackBacks (0)

Those who live in the Los Angeles area are invited to attend a gala premiere screening of Illustra Media's new documentary, Darwin's Dilemma: The Mystery of the Cambrian Fossil Record next Sunday, October 25th at 7:00 pm at the University of Southern California. The event is sponsored by the American Freedom Alliance.

This premiere was originally scheduled for the California Science Center, but the Center canceled the event just a few days ago, leaving the organizers virtually no time to find a new location. If you live in the Los Angeles area, you can show your support for free speech to debate the evidence for intelligent design by attending this important event!

There is a free public reception starting at 5:30 pm. The film screens at 7:00 pm at the Embassy Auditorium of the Davidson Executive Conference Center at USC.

Tickets are available at the door or by calling the AFA office at (310) 444-3085. ($20 general admission; $10 for students) You may also download the registration/ticket order form at
http://www.americanfreedomalliance.org/microsite/darwindebates/register.htm, fill out the form, and fax it to the AFA office at 310-444-3086.

Filmed on four continents, Darwin's Dilemma examines some of the most important fossil discoveries ever made and with them, a mystery deeper than Charles Darwin ever imagined. For the fossil record of the Cambrian Explosion does not reveal the gradual development of life forms as Darwin posited in his work, but a period in which compound eyes, articulated limbs, sophisticated sensory organs and skeletal frames burst into existence seemingly out of nowhere. Produced by Illustra Films Directed by Lad Allen. To read more about the movie go to www.darwinsdilemma.org. Following the premiere will be a panel discussion featuring Lad Allen (director), Jonathan Wells, author of Icons of Evolution and The Politically Incorrect Guide to Darwinism and Intelligent Design, and David Berlinski, author of The Devil's Delusion: Atheism and Its Scientific Pretensions.

Posted by Anika Smith at 2:24 PM | Permalink | TrackBacks (0)

In his book Only a Theory, one of Dr. Kenneth Miller’s main response to Michael Behe’s arguments for the irreducible complexity of the blood clotting cascade is that sequence similarities between various blood clotting factors demonstrates that they share a common ancestry. Indeed, in his response to me on the irreducible complexity of the blood clotting cascade, Miller again conflates evidence for common ancestry with evidence for Darwinian evolution. At best, Miller's only evidence shows evidence of common ancestry--not Darwinian evolution--but on closer inspection it seems that even Miller's arguments for common ancestry may be weak.

As a first example of such a fallacious argument, Miller confuses evidence for common ancestry with evidence for Darwinian evolution in his book Only a Theory:

if two of the proteins, such as factors 9 and 10, diverged millions of years ago, as the pathway suggests, then we should be able to take any organism we like and discover that the pattern of relationship between their various factor 9 proteins matches the one we see for their factor 10 proteins, which similarly matches the one we see for factor 7. (Ken Miller, Only a Theory, p. 64)

There are two main problems with Miller’s argument.

First, Evidence of Common Ancestry is NOT Evidence of a Darwinian Pathway
As Michael Behe aptly observes, "modern Darwinists point to evidence of common descent and erroneously assume it to be evidence of the power of random mutation” (Behe, The Edge of Evolution, p. 95). Behe puts it even more clearly in Darwin’s Black Box:

"Although useful for determining lines of descent ...comparing sequences cannot show how a complex biochemical system achieved its function -- the question that most concerns us in this book. By way of analogy, the instruction manuals for two different models of computer put out by the same company might have many identical words, sentences, and even paragraphs, suggesting a common ancestry (perhaps the same author wrote both manuals), but comparing the sequences of letters in the instruction manuals will never tell us if a computer can be produced step-by-step starting from a typewriter....Like the sequence analysts, I believe the evidence strongly supports common descent. But the root question remains unanswered: What has caused complex systems to form?" (Darwin's Black Box, pp. 175-176)

Incidentally, when I was a graduate student at UC San Diego, I took a graduate seminar where Miller's authority, Russell Doolittle, was brought in to tell us what was wrong with Michael Behe’s arguments for irreducible complexity in blood clotting. The main point of Doolittle's lecture was to draw trees tracing protein relationships, all based upon mere comparison of sequence similarity. His argument that trees based upon sequence similarity somehow demonstrate Darwinian evolution and refute irreducible complexity left me unimpressed--it committed the very fallacy Behe warned about in Darwin's Black Box. I came to a deeper realization at that point of just how strong Behe’s argument was.

Second, Conflicting Phylogenetic Trees Show Miller's Prediction Often Fails
I would go further than Behe and contend that Miller’s evidence not only does not provide evidence for Darwinian evolution, but it also doesn't even provide very good evidence for common descent.

On the surface, his example of coherence between the phylogenetic trees generated by the different organisms is not surprising. For example, if you compared blood clotting factor 9 in a fish, a horse, and a human, and found that the factors in the horse and human were more similar to one another than they were to the factor in the fish, no one would find that observation very startling. Molecule-based phylogenetic trees are simply nested hierarchies reflecting comparative genetic similarities. All this data shows is that organisms that are more similar on the outside tend to be more similar on the inside.

Let’s scrutinize Miller’s “prediction of evolution” more closely. Miller’s prediction seems to be that taking different orthologous genes found in various species and using them, one at a time, to construct phylogenetic trees, will produce very similar and congruent trees. While perhaps this is found to be true for these few blood clotting factors, anyone who follows this field knows that systematists regularly bang their heads against the wall because this “prediction of evolution” commonly does NOT turn out to be true. To give a few examples:

The Cytochrome C phylogenetic tree is often touted as allegedly matching and confirming the traditional phylogeny of many animal groups, and this is said to bolster the case for common descent. But evolutionists rarely talk about the Cytochrome B tree, which has striking differences from the classical animal phylogeny. As one article in Trends in Ecology and Evolution stated: “the mitochondrial cytochrome b gene implied...an absurd phylogeny of mammals, regardless of the method of tree construction. Cats and whales fell within primates, grouping with simians (monkeys and apes) and strepsirhines (lemurs, bush-babies and lorises) to the exclusion of tarsiers. Cytochrome b is probably the most commonly sequenced gene in vertebrates, making this surprising result even more disconcerting.”

A 2006 paper in the journal PLoS Biology entitled, “Bushes in the Tree of Life.” The authors acknowledge that “a large fraction of single genes produce phylogenies of poor quality,” observing that one study “omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom.”

An article in the journal New Scientist stated earlier this year that “problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species.” This type of problem was observed even among higher organisms, as the article lamented: “[t]he problem was that different genes told contradictory evolutionary stories,” leading one scientist to say regarding the relationships of these higher groups, “We’ve just annihilated the tree of life.”

In Only a Theory, Miller attacks ID claiming it “cannot predict such patterns, and cannot even be tested” (p. 65), but unless Miller wants evolution to be falsified by the above examples, then he must too concede the point that evolution does not make clear predictions about whether individual gene-based trees should agree. At the very least, it’s clear that trees based upon individual genes commonly do not agree. What does this do to Miller's alleged "prediction" of evolution?

Pseudo-Arguments
In his response to me on irreducible complexity and the blood clotting cascade, Professor Miller also argued that irreducible complexity is refuted on the grounds that whales allegedly have a non-functional psuedogene instead of a functional gene for blood clotting Factor XII. Miller wrote: “Whales possess a Factor XII pseudogene, an inactivated version of the very same gene carried by land-dwelling mammals. That pseudogene is a direct mark of their common ancestry with other mammals, and disproves any suggestion that constraints on cetacean ‘design’ required the absence of Factor XII. Rather, ordinary genetic processes knocked out the gene, and today the pseudogene remains merely as evidence of their evolutionary ancestry.”

At best a shared psuedogene might provide evidence of common ancestry, but as noted above, evidence for evolutionary ancestry does not confirm a Darwinian pathway. And again, even here it's not clear that Miller's evidence provides unambiguous evidence for common ancestry. If Miller thinks that by slipping in the mention of a pseudogene that he’s provided conclusive evidence of common ancestry, then he should consider that the more we study "pseudogenes," the more we're finding that they can have function! As Evgeniy S. Balakirev and Francisco J. Ayala wrote in Annual Review of Genetics:

“Rather, pseudogenes that have been suitably investigated often exhibit functional roles, such as gene expression, gene regulation, generation of genetic (antibody, antigenic, and other) diversity. … Pseudogenes exhibit evolutionary conservation of gene sequence, reduced nucleotide variability, excess synonymous over nonsynonymous nucleotide polymorphism, and other features that are expected in genes or DNA sequences that have functional roles.”

(Evgeniy S. Balakirev, and Francisco J. Ayala, Pseudogenes, "Are They “Junk” or Functional DNA?,” Annual Review of Genetics, Vol. 37:123–51 (2003), emphasis added.)

D. Zheng and M. B. Gerstein, “The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?,” Trends in Genetics, Vol. 23(5):219-224 (2007).

S. Hirotsune et al., “An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene,” Nature, Vol. 423:91-96 (May 1, 2003).

O. H. Tam et al., “Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes,” Nature, Vol. 453:534-538 (May 22, 2008).

D. Pain et al., “Multiple Retropseudogenes from Pluripotent Cell-specific Gene Expression Indicates a Potential Signature for Novel Gene Identification,” The Journal of Biological Chemistry, Vol. 280(8):6265–6268 (February 25, 2005).

J. Zhang et al., "NANOGP8 is a retrogene expressed in cancers," FEBS Journal, Vol. 273:1723–1730 (2006).

The very fact that the beta-globin pseudogene appears to be conserved in humans, chimpanzees and gorillas speaks eloquently of the fact that this DNA has some important biological function. Genetic sequences are conserved and maintained when any mutation would render them non-functional (or less functional) and when any loss of activity is damaging the organism’s prospects of survival. Such sequences are said to be under purifying (or stabilising) selection which means that deleterious mutations are removed from the gene pool restricting genetic diversity. It is probably the most common mechanism of action for natural selection and leads to the maintenance of genetic integrity. It is certainly not the driving force behind evolutionary change. According to the recent review by Sasidharan and Gerstein:

Although pseudogenes have generally been considered as evolutionary 'dead-ends', a large proportion of these sequences seem to be under some form of purifying selection - whereby natural selection eliminates deleterious mutations from the population - and genetic elements under selection have some use [5].

In the case of the beta-globin pseudogene, Wanapirak et al. have reported amazing conservation in the fine structure of the DNA with identical super-helical twists in the human, mouse, bovine, rabbit and chicken genomes [6] . It needs to be remembered that maintenance of the genetic integrity of these structures is biochemically costly. It takes energy to duplicate DNA. The replicating machinery in the cell has built-in proof reading and excising enzymes that constantly check for mutation and damage. Numerous repair mechanisms have been identified to correct genetic damage and to excise incorrect sequences [7].

(The Changing Face of Pseudogenes, Truth in Science Blog)

Neo-Darwinian evolutionists like Ken Miller should understand that evidence of common descent is not necessarily evidence of Darwinian pathway, and that in many cases, the evidence for common ancestry is not nearly as strong as many would like to think it is. At the very least, this much is clear: None of this evidence has any bearing upon irreducible complexity of the blood clotting cascade.

Posted by Casey Luskin at 8:00 AM | Permalink | TrackBacks (0)

A couple of weeks ago I got an email from an editor at a Jewish publication soliciting from me an article "related to creationism." He asked that it be pegged to the coming Sabbath when Jews across the spectrum of Judaism begin a new cycle of Torah readings. That cycle begins with the account of creation in Genesis.

The editor seemingly wasn't aware that I'm not a creationist (i.e., a naïve Biblical literalist), or he didn't know what the word means, or who knows what. Anyway, I wrote and sent off to him the piece he seemed to urgently want, suspecting even as I did so that it would never run in this particular publication. The Jewish religious world -- from Haredi to Reform and just about everything in between -- is in general so scandalously indifferent and ignorant on scientific issues relating to life's origins and evolution that I felt there was a strong possibility whatever I wrote would never get past editorial scrutiny. Sure enough, a week and a half went by without a response from my correspondent. Finally, asked for a status update, the editor told me it likely wouldn't be appearing in their pages.

So with the relevant Sabbath approaching tonight at sundown, I offer to you the piece I wrote:

Orthodox Jews have almost a sixth sense for feeling out of place. Many of us know this experience: On a visit to an unfamiliar city, you head into a restaurant that you have been assured is strictly kosher. On entering, you look around at the crowd of diners, expecting to see identifiably religious Jews -- men wearing kippot -- but there are none. Uneasy, you ask to see the establishment's kosher certification. Maybe the place is no longer under rabbinic supervision? Maybe you're in the wrong restaurant altogether. The manager produces a piece of paper with a rabbi's name on it, which looks legitimate. And yet...something doesn't sit right.

If there are no frum Jews there, could it really be kosher? That is a question I'm often asked by other Jews of all stripes, if not in exactly those words, about what I do in my professional life. And what is that? Do I work as a pork butcher? As the door attendant at a radical Muslim mosque? No, I'm a senior fellow at a think tank, the Discovery Institute, well known for supporting research in intelligent design -- the scientific critique of and alternative to Darwinian evolution.

At first glance, you might think nothing could be more Jewish. Very shortly Jews around the world will be celebrating a new yearly cycle of Torah readings, beginning with Genesis, the parsha of Bereishit, narrating God's creation of the world. Like Shabbat, which similarly recalls the primordial sequence of divine creativity, studying Bereishit again is a time to re-center ourselves as Jews on a truth that today is widely forgotten or denied.

That truth is that we live in a world bearing testimony to purposeful design. The very idea is under widespread, influential attack from Darwinists who insist overwhelming scientific evidence demonstrates that life originated and developed as the product of blind, churning, purposeless natural forces. Answering the challenge is a scientific pursuit, but it has spiritual implications as well, just as Darwinism has its own implications that rule out purpose, meaning or design in life's history.

Many Jews, however, including many on the more liberal end of the Orthodox spectrum, see intelligent design as a purely Christian undertaking, with no support from Jewish tradition. The Wall Street Journal has promoted as a representative Jewish view that of Yeshiva University biologist Carl Feit "who is an ordained rabbi and Talmudic scholar.... Prof. Feit says that in nearly a quarter-century of teaching introductory biology, he has always taught evolution -- supported by traditional Jewish source material -- and that 'there has never been a blip on the radar here.' His assessment echoes the official line of the Modern Orthodox rabbinical association, which states that evolution is entirely consistent with Judaism."

If you read the entry about me on Wikipedia, which I could never succeed in editing for accuracy because some anonymous Internet user would just change it right back, you will find it insinuated that I'm guilty of ethnic treason if not outright heresy. The entry quotes as authoritative a person whom I won't name here but who is a writer and self-identified Orthodox Jew. He is cited as "charging," as if it were a crime, "that Klinghoffer is paid to promote his ideas by his employer, the Discovery Institute, which [the writer] identifies as a Christian think tank that is funded by organizations that seek to promote a 'Christian-friendly world view.'"

Imagine that. Paid by his employer. What a scandal!

Anyway, there you have it. Advocating an open attitude to finding scientific evidence of design in nature is a Christian, not a Jewish, undertaking. In a front-page news article in the New York Times, reporter Jodi Wilgoren falsely characterized the Discovery Institute as a "fundamentalist Christian" organization. The newspaper later had to publish a retraction. Intelligent design is "the hot new rebranding of Christian creationism," as New York magazine puts it -- missing the fact that between pseudo-scientific creationism and intelligent design there yawns a wide gap in thought, perspective, and intellectual credibility. For myself, I am rebuked as a "Christophile," as one obsessive Jewish commenter on my Beliefnet blog puts it.

What is the reality? On one hand, other Discovery Institute fellows include author and radio host Michael Medved, an Orthodox Jew, and mathematician David Berlinski, a Jewish agnostic. When a popular theatrical documentary film on the suppression of intelligent design on university campuses came out last year -- Expelled: No Intelligence Allowed, narrated by lawyer and comedian Ben Stein -- there was a memorable scene where Berlinski, Stein, and Orthodox Israeli physicist Gerald Schroeder (with a kippah) were shown touring the ruins of the Berlin Wall, a symbol of Darwinism's authoritarian tyranny in the academic world. They were the three Darwin-doubting Jewish musketeers.

After seeing the movie, a colleague of mine half-joked, "I didn't realize intelligent design was such a Jewish enterprise." I savored the comment.

On the other hand, when you get out into the wider world, Jewish hostility or indifference to everything I do remains very much the rule. There's no denying that conservative Christians for the most part understand what's at stake in the Darwin debate. They appreciate the scientists and writers in the intelligent-design movement. Jews, whether secular or religious, do not. In many Jewish minds, there is an instinctive distrust of anything well regarded by Christians. If Christians like it, it's got to be treif. If Christians think there's scientific evidence of design in nature, then a Jew must believe the opposite, that there is no such evidence.

Even from the Haredi community, I regret to say, I've noticed little interest in or understanding of the issue. These fervently religious Jews seem to assume that since we already know God made the world, there is, in a scientific vein, hardly anything else worth saying. We have the Torah. Why do we need science?

We need it because the Torah itself instructs us that this is a subject of which we can't afford to be ignorant. The Mishnah in Pirke Avot urges us to "Know how to answer an Apikoros" -- a heretic or literally an Epicurean. Rabbi Yehudah Ha'Levi and Ibn Ezra, among other authorities, explicitly define the term as a follower of the ancient Greek philosopher Epicurus who denied the existence or detectability of design in nature.

Perhaps they were secretly closet Evangelical Christians, suborned by the Discovery Institute. Don't forget to add other rabbinic greats, Rambam, Rabbeinu Bachya, Moshe Chaim Luzzatto, and Samson Raphael Hirsch, who similarly saw nature as the unfolding scientific evidence of God's purpose in the world, to the list of crypto-Christians.

The deeper truth is that, in a sense, Christianity has defined certain Jewish attitudes for centuries. In his terrific new book Why Are Jews Liberals?, Norman Podhoretz traces the phenomenon of Jewish liberalism back to the Enlightenment. From ancient times to the Middle Ages, the Church had been the Jews' great tormentor. Then came the Enlightenment philosophers who tirelessly attacked Christian teaching, while indulging in an equally spiteful anti-Semitism. Somehow the idea got lodged in the Jewish brain that "The enemy of my enemy is my friend." Meanwhile Christians especially in America came to reject old beliefs about Jews and Judaism, even embracing what can only be called philo-Semitism. Yet from then on, and down to today, any idea that corrodes Christian faith, as Darwinism does, was greeted by many Jews as a friend, even if it corrodes faith in Torah to no less a degree.

The upcoming Shabbat of Bereishit is the perfect opportunity to rethink these ideas, along with the broader, practical priorities of our Jewish community. How many frum Jews today, following the advice of Pirke Avot, could intelligently answer the challenge of a Darwinist? How many are troubled that they could not? How many in the Modern Orthodox community would simply crumple, declaring preemptive surrender to Darwinian evolution? What a shame that on this point, so crucial to a Torah worldview, we have allowed Christians to take the lead.

When we stand up in our homes on Friday night to say Kiddush in testimony to God's intelligent design of the heavens and the earth, when we read the opening chapters of Genesis the next day, there could hardly be a more powerful time to meditate on our calling as God's witnesses not only to ourselves and our families but to the world. That world, I promise you, is waiting for us to add our voices to the most important public debate of our time.

Posted by David Klinghoffer at 12:58 PM | Permalink | TrackBacks (0)

Introduction:
Scopes v. State is probably the most famous court case in the history of the evolution controversy. It’s most well known because a play, Inherit the Wind, was turned into a movie based loosely upon the trial, and has been shown in countless college and high school classrooms promoting a stereotype that Darwin-skeptics are ignorant, close-minded, intolerant ignoramuses. Ironically, today it’s the evolutionists who behave like the fundamentalists in the Scopes trial, holding all the power and banning viewpoints they don’t like.

1. Summary
In 1925, teacher John T. Scopes was convicted under the recently adopted Tennessee “Monkey Law” that had criminalized the teaching of evolution.¹⁰ In Scopes’s defense, attorneys working with the American Civil Liberties Union (“ACLU”) argued that it was unconstitutional to force a teacher to present only one view of humanity’s origin, namely the Biblical account of creation.¹¹ The Tennessee high court upheld the law, stating that because the prohibition of evolution did not establish an official government religion, the law did not violate the Establishment Clause.¹² Mr. Scopes’s conviction was later overturned on a technicality.¹³ Over four decades later, Scopes v. State was overruled by Epperson v. Arkansas, which recognized that it is illegal to prohibit, much less criminalize, the teaching of any scientific theory due to religious motives.¹⁴

2. Importance and Commentary
The widely-publicized “Scopes Monkey Trial” became famous as a radio-broadcasted courtroom trial that debated the validity of evolution versus the Biblical account of creation.¹⁵ Although Scopes “lost,” the public perceived that the pro-evolution side won after prosecutor William Jennings Bryan took the witness stand to be cross-examined by lead defense counsel Clarence Darrow.¹⁶ Popular notions of history, based upon the dramatized account portrayed in the play and movie Inherit the Wind, typically teach that Darrow humiliated Bryan with well-reasoned questions about the creation account in Genesis that Bryan was unable to answer. Yet evolutionary paleontologist Stephen Jay Gould reminds that:

[T]he most celebrated moment—when Darrow supposedly forced Bryan to admit that the days of creation might have spanned more than twenty-four hours—represented Bryan's free-will statement about his own and well known personal beliefs (he had never been a strict biblical literalist), not a fatal inconsistency, exposed by Darrow's relentless questioning.¹⁷

Cultural memory has recorded a version of the Scopes Trial that differs sharply from reality; but nonetheless, as a result of the trial, “Antievolutionists and Fundamentalists in general were portrayed as foolish, unthinking, religious zealots.”¹⁸

Despite its infamy, the Scopes case has little direct relevance to current law. The trial was later dramatized by the play and movie Inherit the Wind, which “contributed to the negative public image of Fundamentalists”¹⁹ and is still regularly shown to high school and college students.²⁰ Many Americans do not realize that this movie falsely casts the trial, as well as the entire debate over evolution, as being between close-minded, backwards, and religiously motivated “Christian fundamentalists” versus enlightened, progressive, and freedom-loving evolutionary scientists and educators.²¹ U.S. Supreme Court Justice Antonin Scalia calls this portrayal the “beloved secular legend of the Monkey Trial,”²² while another legal scholar calls it the “Inherit the Wind stereotype.”²³ Unfortunately, many people believe this stereotype is valid, unaware that a significant number of well-credentialed scientists find legitimate scientific reasons to question Darwin.²⁴ Moreover, this stereotype continues to be perpetuated by the media covering modern curricular battles because the story of enlightened Darwinian scientists and educators versus bigoted and unsophisticated fundamentalists riles emotions and sells newspapers just as well today as it did in 1925.²⁵ As will be discussed, this caricature has even infiltrated the minds of some judges who believe that opposition to evolution necessarily endorses fundamentalist Christianity. While the criminalization of teaching evolution by the Tennessee Legislature was inimical to freedom of inquiry and the fair administration of justice, Scalia believes that today we have “Scopes-inreverse,”²⁶ where viewpoints that do not support evolution are excluded from classrooms through misguided law and a climate of fear and intimidation.

[Editor’s Note: This survey of Scopes v. State is an excerpt from Casey Luskin's article “Does Challenging Darwin Create Constitutional Jeopardy? A Comprehensive Survey of Case Law Regarding the Teaching of Biological Origins,” Hamline University Law Review, Vol. 32(1):1-64 (Winter, 2009), published by Hamline University School of Law. This is the first survey in a series of 21 cases discussed in the article that will be surveyed here on ENV in the coming months. This excerpt covers the case Scopes v. State; the full article can be read here.]

References Cited
[10.] Scopes v. State, 289 S.W. 363 (Tenn. 1927).
[11.] Id. at 364.
[12.] Id. at 367.
[13.] Id.
[14.] Epperson v. Arkansas, 393 U.S. 97, 109 (1968).
[15.] See Edward J. Larson, Summer for the Gods (Basic Books 1997).
[16.] Jay D. Wexler, Note, Of Pandas, People, and the First Amendment: The Constitutionality of Teaching Intelligent Design in the Public Schools, 49 Stanford Law Review 439, 446-47 (1997).
[17.] Stephen Jay Gould, Rock of Ages, 137 (Ballantine Books 1999).
[18.] Eugenie Scott, Evolution vs. Creationism: An Introduction, 96 (2004). For an account of the Scopes Trial that is more accurate and complete than the popular Inherit the Wind versions, see LARSON, supra note 15.
[19.] Scott, supra note 18, at 96.
[20.] Id. at 97 (stating that Inherit the Wind is “often read and performed in high schools”).
[21.] For an excellent account of the actual historical events versus the Inherit the Wind version, see Larson, supra note 15; see also Phillip Johnson, Defeating Darwinism by Opening Minds; Scott, supra note 18, at 94-97.
[22.] Tangipahoa Parish Bd. of Educ. v. Freiler, 530 U.S. 1251, 1255 (2000).
[23.] See Johnson, supra note 21, at 24-36.
[24.] See generally A Scientific Dissent from Darwin
[25.] A recent popular book which makes heavy use of the “Inherit the Wind stereotype” while telling the story behind the Kitzmiller v. Dover lawsuit is Edwards Humes, Monkey Girl: Evolution, Education, Religion, and the Battle for America’s Soul (2007).
[26.] Edwards v. Aguillard, 482 U.S. 578, 634 (1987) (Scalia, J., dissenting).

Posted by Casey Luskin at 11:24 AM | Permalink | TrackBacks (0)

Over at CNSNews.com, Casey Luskin has an opinion piece about the controversy surrounding the California Science Center's caving in to pressure from the Smithsonian and cancelling a scheduled screening of Darwin's Dilemma.

There are two ways that modern evolutionists approach the Cambrian explosion, or what has been called “Darwin’s dilemma”:

A. Some freely acknowledge that the Cambrian fossil evidence essentially shows the opposite of what was expected under neo-Darwinian evolution.

B. Others deal with the Cambrian explosion by sweeping its problems under the rug and trying to change the subject.

Succumbing to pressure from Darwinian elites, the California Science Center chose option B.

Posted by Robert Crowther at 5:47 AM | Permalink | TrackBacks (0)

When intelligent design (ID) proponents press neo-Darwinian evolutionists on the inability of Darwinian evolution to produce new functional genetic information, a common response from evolutionists is that they get angry and engage in name calling. That’s what happened when Michael Egnor asked How does evolution produce new functional genetic information?, and it again seems to be the case now after Jonathan Wells bravely observed that “duplicating a gene doesn’t increase information content any more than photocopying a paper increases its information content.” Mathematician and ID-critic Jeffrey Shallit responded by calling Wells a “buffoon.” Dr. Shallit then proceeded to offer an irrelevant definition of information which supposedly showed that Wells was wrong. William Dembski has responded to Shallit here, but Shallit’s tactics and arguments are worth exploring further.

Shallit defines information as “Kolmogorov complexity,” which can be thought of this way: What is the minimum length of a computer program to generate string X? The more commands necessary, the greater the Kolmogorov complexity.

Returning to Wells’s analogy, let’s call the information in the paper being photocopied X. We’ll use a little pseudocode to explore what, according to Shallit’s logic, would be the algorithm necessary to generate the needed information. It would probably look like this:

1. Write X

1. Write X
2. Repeat last step

Does Shallit’s explanation have any bearing upon the question Wells is asking, i.e. how do explain how new functional genetic information arises? Of course not. What would be far more interesting is an explanation of how you could get a paper full of new information -- call it Y -- instead of 2 copies of X. Thus, Wells would like to see how we can get XY out of X, instead of merely XX.

Since biology is based upon functional information, Jonathan Wells is interested in far more important questions like, Does neo-Darwinism explain how new functional biological information arises? Shallit seems interested primarly in addressing simplistic, trivial questions like how one might duplicate a string, without regard for the all important question of whether those additional characters convey some new functional message.

Under Kolmogorov complexity, a stretch of completely functionless junk DNA that has been utterly garbled by random, neutral mutations might have more Kolmogorov complexity than a functional gene of the same sequence length. For example, consider the two following strings:

String A:
KOMOLGOROVINFORMATIONISAPOORMEASUREOFBIOLOGICALCOMPLEXITY

String B:
JLNNUKFPDARKSWUVWEYTYKARRBVCLTLOPDOUUMUEVCRLQTSFFWKJDXSOB

Both String A and String B are composed of exactly 57 characters. String A spells a sentence in English, and String B was generated using a random string generator. Yet since many of its characters could be predicted using the grammatical rules of English, String A actually has less Kolmogorov complexity than String B (for example, we could use a data compression algorithm to shorten String A dramatically). Yet clearly String A conveys much more functional information than the String B.

For obvious reasons, Kolmogorov complexity is not always a helpful metric of functional biological information. After all, biological information is finely tuned to perform a specific function, whereas random strings are not. A useful measure of biological information must account for the function of the information, and Kolmogorov information does not necessarily take function into account.

In fact, Kolmogorov information is very similar to Shannon information, where “In both cases, the amount of information in an object may be interpreted as the length of a description of the object.” But the length of the description says nothing about whether there is function, or how much fine-tuning is necessary for function. Thus you could have a very long random string that requires long descriptions, but it has no function. As any ID novice knows, we infer design when we find both complexity and specification. In rough terms, Shannon information or Kolmogorov information measure complexity, but not specification. Thus, such measures of information are not useful for measuring functional biological information. As a paper in the journal Theoretical Biology and Medical Modelling observes:

[N]either RSC [Random Sequence Complexity] nor OSC [Ordered Sequence Complexity], or any combination of the two, is sufficient to describe the functional complexity observed in living organisms, for neither includes the additional dimension of functionality, which is essential for life. FSC [Functional Sequence Complexity] includes the dimension of functionality. Szostak argued that neither Shannon’s original measure of uncertainty nor the measure of algorithmic complexity are sufficient. Shannon's classical information theory does not consider the meaning, or function, of a message. Algorithmic complexity fails to account for the observation that “different molecular structures may be functionally equivalent.” For this reason, Szostak suggested that a new measure of information -- functional information -- is required.

(Kirk K. Durston, David K. Y. Chiu, David L. Abel, Jack T. Trevors, “Measuring the functional sequence complexity of proteins,” Theoretical Biology and Medical Modelling, Vol. 4:47 (2007) (internal citations removed).)

[L]iving organisms are distinguished by their specified complexity. Crystals are usually taken as the prototypes of simple, well-specified structures, because they consist of a very large number of identical molecules packed together in a uniform way. Lumps of granite or random mixtures of polymers are examples of structures which are complex but not specified. The crystals fail to qualify as living because they lack complexity; the mixtures of polymers fail to qualify because they lack specificity.

(Leslie E. Orgel, The Origins of Life: Molecules and Natural Selection, pg. 189 (Chapman & Hall: London, 1973).)

Shallit would most likely define information that is “new” as mere copies or duplicates of some pre-existing stretch of DNA, even if the new copy doesn’t actually do anything new, or perhaps even when the new DNA doesn’t do anything at all. In contrast, ID proponents define “new” genetic information as a new stretch of DNA that actually performs some different, useful, and new function. For example, consider the following 42-character string:

DUPLICATINGTHISSTRINGDOESNOTGENERATENEWCSI

Now consider the following duplicate string:

DUPLICATINGTHISSTRINGDOESNOTGENERATENEWCSIDUPLICATINGTHISSTRINGDOESNOTGENERATENEWCSI

Whether or not we have increased the Kolmogorov complexity, we have not created any new meaning in the duplicated string. We have not increased the CSI in any meaningful sense.

The above example is of course analogous to the commonly cited evolutionary mechanism of gene duplication. New functional information is not generated by a process of duplication until mutations change the gene enough to generate a new function -- which may or may not be possible. As Professor of Neurosurgery Michael Egnor insightfully commented in a response to P.Z. Myers:

[G]ene duplication is, presumably, not to be taken too seriously. If you count copies as new information, you must have a hard time with plagiarism in your classes. All that the miscreant students would have to say is “It's just like gene duplication. Plagiarism is new information -- you said so on your blog!”

Posted by Casey Luskin at 9:02 AM | Permalink | TrackBacks (0)

Wednesday, Stephen Meyer will be a guest on The Dennis MIller Show. Listen in with Dennis' other 1.75 million fans as they discuss the California Science Center's recent banning of pro-ID film Darwin's Dilemma and Meyer's landmark book Signature in the Cell. The segment is scheduled live at 7:30am Pacific coast time, which is mid-way through the show's first hour.

Posted by Robert Crowther at 6:24 PM | Permalink | TrackBacks (0)

For those interested in the history and philosophy of origins and in the present controversy over the “establishment” understanding, this is a helpful book. For those wishing to have a better understanding of DNA and a “simple cell,” this is an astonishing book. For those who wish to honestly consider what is the best explanation for the origin of specified complex information found in living things, this is an invaluable book. For those who have for whatever reason gravitated to the general proposition that design seems to make intuitive sense, this is an essential book so you can appreciate there is a scientific foundation for your belief. For those who disagree with intelligent design this is the crucial book you must have so as to understand your opponent’s best arguments.

Posted by Robert Crowther at 8:56 AM | Permalink | TrackBacks (0)

Nature has recently published an interesting paper which places severe limits on Darwinian evolution. The manuscript, from the laboratory of Joseph Thornton at the University of Oregon, is titled “An epistatic ratchet constrains the direction of glucocorticoid receptor evolution”. The work is interpreted by its authors within a standard Darwinian framework, but the results line up very well with arguments I made in The Edge of Evolution. This is the last of three posts discussing it. (see here and here)

Bridgham et al (2009) are interested in the reversibility of evolution, and discuss their results in terms of something called “Dollo’s law.” Louis Dollo, an early 20th century paleobiologist, was interested in discerning phylogenies. He maintained that one could always distinguish ancestral forms from descendant forms. Stephen Jay Gould (1970) commented that Dollo’s “law” was not an empirical observation, but rather a postulate which he felt was necessary to properly construct phylogenies. Over the years the meaning of “Dollo’s law” transmogrified. In modern usage, the phrase has come to mean that complex traits, once lost, do not re-evolve in the same lineage. For example, whales do not re-evolve gills, even though they are aquatic creatures who descended from fish, because gills are a lost, complex trait in that lineage.

Dollo’s law is taken with a grain of salt by many biologists, and apparent exceptions to the law have been noted (cited in Bridgham et al 2009). Nonetheless, although Dollo’s law isn’t very reliable at the organismal level, maybe it can do better at the molecular level. Bridgham et al (2009) wanted to test that idea:

Evolutionary reversibility represents a strong test of the importance of contingency and determinism in evolution. If selection is limited in its ability to drive the reacquisition of ancestral forms, then the future outcomes available to evolution at any point in time must depend strongly on the present state and, in turn, on the past. Ready reversibility, in contrast, would indicate that natural selection can produce the same optimal form in any given environment, irrespective of history. The evolutionary reversibility of a protein can be evaluated at three levels: molecular sequence, protein function, and the structural/mechanistic underpinnings for that function. The latter is most relevant to understanding the roles of contingency and determinism in evolution. ... True reversal, involving restoration of the ancestral phenotype by the ancestral structure-function relations, would indicate that the forms of functional proteins can evolve deterministically, irrespective of contingent historical events.

We predict that future investigations, like ours, will support a molecular version of Dollo's law: as evolution proceeds, shifts in protein structure-function relations become increasingly difficult to reverse whenever those shifts have complex architectures, such as requiring conformational changes or epistatically interacting substitutions.

The old, organismal, time-asymmetric Dollo’s law supposedly blocked off just the past to Darwinian processes, for arbitrary reasons. A Dollo’s law in the molecular sense of Bridgham et al (2009), however, is time-symmetric. A time-symmetric law will substantially block both the past and the future, for well-understood reasons: Natural selection fits a protein to a current, not any future (nor any previous), task; thus it tends strongly to restrict other potential structures/functions. The very same considerations (“shifts in protein structure-function relations”, “epistatically interacting substitutions”, and so on) that frustrate the reacquisition of complex molecular features will tend strongly to stymie their acquisition in the first place, because no potential protein component would ever be without a prior history of selection. A time-symmetric Dollo’s law turns the notion of “pre-adaptation” on its head. The law instead predicts something like “pre-sequestration”, where proteins that are currently being used for one complex purpose are very unlikely to be available for either reversion to past functions or future alternative uses.

Yet here we are, with complex life all around us and in us. If a time-symmetric Dollo’s law were really such a big roadblock, how did life come to be? Here is where their Darwinian framework most seriously blinkers their vision. Bridgham et al (2009) aimed to test “the importance of contingency and determinism in evolution”. But chance and necessity are not the only things that exist. There are also mind and plan. In fact, in their own work the authors themselves reconstructed the ancestral protein from the descendant protein, easily overcoming the hurdle that they realized would block a Darwinian process. Their own minds directed events that chance and necessity never could.

References

The knee-jerk response of Darwin's defenders is to suppress any message that challenges Darwinian evolution's orthodoxy. Case in point, this past week the Los Angeles Daily News reported that the California Science Center, a “department of the State of California,” banned the screening of the new intelligent design film, Darwin’s Dilemma, after the screening became public knowledge and there was intense pressure to cancel.

And get this, from what we've heard the intense pressure came from the Smithsonian Institution with which they are affiliated. That's right, the very same Smithsonian Institution that trampled evolutionary biologist Richard Sternberg's academic freedoms. The very same Smithsonian Institution that apologized for allowing another ID film, The Privileged Planet, to be shown at the Institution's Museum of Natural History.

In this instance the American Freedom Alliance entered into what was presumably a legally binding contract with the California Science Center when it rented its facilities. That they would be a screening a pro-ID film was never a secret. The Science Center apparently had no problem with the film being screened there and okayed the contract. So, who did have a problem? Why did the screening have to be canceled?

Earlier this week, Discovery Institute issued its own press release (independent of AFA) announcing that the AFA would be hosting a screening of the film, followed by a discussion with Discovery scientists at a Smithsonian affiliated museum. That is apparently when the screening became a problem. The LA Daily News reports that Smithsonian spokesman Randall Kremer said "he saw the press release a few days ago and was concerned by its reference to the Smithsonian." It certainly seems that the Science Center didn't have a problem until the Smithsonian had a problem.

"The only reason I spoke with anyone at the California Science Center is I was concerned by the inference (in the press release that) there was a showing of the film at a Smithsonian branch, which is how the California Science Center was portrayed in the news release," Kremer said. "Of course, that is not the case. They are independent and any decisions they make on this are on their own."

It seems pretty clear that here you have a department of the California state government --a science center clearly affiliated with the Smithsonian-- that is breaking a legal contract (for undisclosed reasons) because someone (the Smithsonian?) was upset that a pro-intelligent design film was about to be screened at a well-known science center that is a Smithsonian affiliate.

We've contacted the Science Center by phone and e-mail and they have so far refused to answer any questions about pressure they may have received from the Smithsonian or indeed provide any concrete reason that the screening should be canceled. Their only response was to reissue their singularly uninformative talking point:

"The American Freedom Alliance event at the California Science Center was canceled due to issues related to the contract. With regard to your other questions, we do not discuss contract issues."

I'd wager good money that the American Freedom Alliance doesn't have time to return all the calls from attorneys wanting to take this case.

This isn't the first time a major academic or scientific institution has trampled academic freedom of scientists who are proponents of intelligent design. Dr. Guillermo Gonzalez was the victim of very shameful treatment by the faculty and board of regents at Iowa State University. Dr. William Dembski was hounded out of Baylor University for his views on intelligent design. There's an entire film that millions of people have seen, Expelled starring Ben Stein about what happens to people who are advocates of design theory. Even Stein was later sacked from his position at The New York Times, in part, according to him, for his having made that film.

Rather than debate the science, Darwinists try to suppress it. They simply can't stand to let people know the truth about the shoddy case for Darwinian evolution.

Posted by Robert Crowther at 7:49 AM | Permalink | TrackBacks (0)

A new podcast out today at ID the Future features breaking news that could affect your freedom to present views that dissent from Darwin in a public place. CSC Associate Director John West explains in an interview here.

Posted by Anika Smith at 6:31 PM | Permalink | TrackBacks (0)

Richard Dawkins’ new book, The Greatest Show on Earth, is being touted as a scathing rebuttal to intelligent design (ID), yet an actual response to mainstream ID thinking can hardly be found in the book. Though the book makes passing mention of “irreducible complexity” in a couple places, there are zero mentions of leading ID proponents like Michael Behe, William Dembski, Jonathan Wells, Phillip Johnson, Stephen Meyer, or any other well-known ID proponent. Instead, Dawkins refers extensively to “creationists,” repeatedly attacking young earth creationism, while also making heavy use of fallacious (and dubious) “poor design” examples that rebut no argument made by a leading advocate of design since perhaps the 19th century. It seems that Dawkins didn’t have the stomach to tackle the actual modern theory of intelligent design in his new book.

Dawkins Refutes Straw Men and Ignores ID Thinking on Evolutionary Research
The closest place Dawkins comes to actually dealing with actual ID is in Chapter 5 where he mentions irreducible complexity a couple times and discusses Richard Lenski’s E. coli experiments. In typical Dawkins fashion, he taunts “creationists” with their alleged inability to respond to Lenski’s research, which he claims they “hate”:

There is a comic sequel to this triumphant tale of scientific endeavor. Creationists hate it. Not only does it show evolution in action; not only does it show new information entering enomes without the intervention of a designer, which is something they have all been told to deny is possible (‘told to’ because most of them don’t understand what ‘information’ means); not only does it demonstrate the power of natural selection to put together combinations of genes that, by the naïve calculations so beloved of creationists, should be tantamount to impossible; it also undermines their central dogma of ‘irreducible complexity.’ So it is no wonder they are disconcerted by the Lenski research, and eager to find fault with it.

(Richard Dawkins, The Greatest Show on Earth, pg. 131 (Free Press, 2009).)

But no. As we already saw, Behe’s name appears nowhere in Dawkins’ book. Instead, Dawkins slams Conservapedia editor Andrew Schalfly—whom Dawkins carefully notes is “a lawyer” (pgs. 131, emphasis in original)—who apparently made a misguided attempt to impugn Lenski by wrongly implying the scientist would not release his original data. It's a boring anecdote and a straw man, especially considering that a rebuttal to Behe is nowhere to be found in The Greatest Show on Earth.

Dawkins’ Centerpiece Example of Biochemical Evolution Is Comfortably Within Behe’s ‘Edge of Evolution’

So what is it about Lenski’s work that Dawkins claims is so devastating to irreducible complexity? Dawkins lauds 2 achievements of Lenski’s experiments: (1) the ability of the bacteria to increase their size (there are no new genes here, just, as Dawkins admits, that they “had changed their levels of expression” of certain genes), and (2) the fact that Lenski’s E. coli apparently evolved the ability to metabolize citrate. It’s the latter example which Dawkins claims “undermines” the “central dogma of irreducible complexity.”

Dawkins doesn't even offer a hint to his readers about this, but Behe dealt with this research from Lenski when it was first published back in 2008. Dawkins states that “if only a mutant could ‘discover’ how to deal with citrate, a bonanza would open up for it. This is exactly what happened…” (pg. 127) but according to Behe, that ‘isn’t exactly what happened’:

Now, wild E. coli already has a number of enzymes that normally use citrate and can digest it (it’s not some exotic chemical the bacterium has never seen before). However, the wild bacterium lacks an enzyme called a “citrate permease” which can transport citrate from outside the cell through the cell’s membrane into its interior. So all the bacterium needed to do to use citrate was to find a way to get it into the cell. The rest of the machinery for its metabolism was already there. As Lenski put it, “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.” (1)

(Michael Behe, Amazon Blog, "Multiple Mutations Needed for E. Coli," June 6, 2008)

The major point Lenski emphasizes in the paper is the historical contingency of the new ability. It took trillions of cells and 30,000 generations to develop it, and only one of a dozen lines of cells did so. What’s more, Lenski carefully went back to cells from the same line he had frozen away after evolving for fewer generations and showed that, for the most part, only cells that had evolved at least 20,000 generations could give rise to the citrate-using mutation. From this he deduced that a previous, lucky mutation had arisen in the one line, a mutation which was needed before a second mutation could give rise to the new ability. The other lines of cells hadn’t acquired the first, necessary, lucky, “potentiating” (1) mutation, so they couldn’t go on to develop the second mutation that allows citrate use. Lenski argues this supports the view of the late Steven Jay Gould that evolution is quirky and full of contingency. Chance mutations can push the path of evolution one way or another, and if the “tape of life” on earth were re-wound, it’s very likely evolution would take a completely different path than it has.

I think the results fit a lot more easily into the viewpoint of The Edge of Evolution. One of the major points of the book was that if only one mutation is needed to confer some ability, then Darwinian evolution has little problem finding it. But if more than one is needed, the probability of getting all the right ones grows exponentially worse. “If two mutations have to occur before there is a net beneficial effect — if an intermediate state is harmful, or less fit than the starting state — then there is already a big evolutionary problem.” (4) And what if more than two are needed? The task quickly gets out of reach of random mutation.

(Michael Behe, Amazon Blog, "Multiple Mutations Needed for E. Coli," June 6, 2008)

In fact, Behe has done a lot more than just write about this topic; he’s published rigorous calculations and simulations in a peer-reviewed scientific journal, Protein Science (also totally ignored by Dawkins), showing that when more than two mutations are required to gain function, it’s very difficult to evolve the trait under normal population sizes and generation times, etc. Their paper concludes:

The fact that very large population sizes—10⁹ or greater—are required to build even a minimal [multi-residue] feature requiring two nucleotide alterations within 10⁸ generations by the processes described in our model, and that enormous population sizes are required for more complex features or shorter times, seems to indicate that the mechanism of gene duplication and point mutation alone would be ineffective, at least for multicellular diploid species, because few multicellular species reach the required population sizes.

(Michael J. Behe & David W. Snoke, “Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues,” Protein Science, Vol 13:2651-2664 (2004).)

So where exactly is the ‘edge of evolution’? Dawkins’ readers won’t find out because the examples Dawkins gives are comfortably within the edge offered by Behe before Lenski’s E. coli and citrate research was even published. There’s a fascinating scientific debate here going on here about the information generative ability of Darwinian evolution, and it's quite unfortunate that Dawkins hides this debate from his readers.

Perhaps Dawkins is right that creationists do indeed “hate” Lenski’s research. I don't really know. But Behe, who is no creationist, clearly embraces Lenski's E. coli research because it validates his arguments about the limits of Darwinian evolution’s ability to generate complex new functional biological features.

Dawkins Unwittingly Validates Behe
Dawkins probably was wise to avoid talking about Behe in The Greatest Show on Earth, because it turns out that some of Dawkins’ arguments sound very much like Behe’s arguments in The Edge of Evolution. First, let’s review some comments from Behe in response to Lenski’s citrate research:

In The Edge of Evolution I had argued that the extreme rarity of the development of chloroquine resistance in malaria was likely the result of the need for several mutations to occur before the trait appeared. Even though the evolutionary literature contains discussions of multiple mutations (5), Darwinian reviewers drew back in horror, acted as if I had blasphemed, and argued desperately that a series of single beneficial mutations certainly could do the trick. Now here we have Richard Lenski affirming that the evolution of some pretty simple cellular features likely requires multiple mutations.

(Michael Behe, Amazon Blog, "Multiple Mutations Needed for E. Coli," June 6, 2008)

What if the necessary biochemical wizardry to feed on citrate requires not just one mutation but two (or three)? We are not now talking about mutations that build on each other in a simple additive way. If we were, it would be enough to get the two mutations in any order. Either one, on its own, would take you halfway (say) to the goal; and either on its own would confer an ability to get some nourishment from citrate, but not as much as both mutations together would. That would be on a par with the mutations we have already discussed for increasing body size. But such a circumstance would not be rare enough to account for the dramatic uniqueness of Tribe Ara-3. No, the rarity of citrate metabolism suggests that we are looking for something more like the ‘irreducible complexity’ of creationist propaganda. This might be a biochemical pathway in which the product of one chemical reaction feeds into a second chemical reaction, and neither can make any inroads at all without the other. This would require two mutations, call them A and B, to catalyze the two reactions. On this hypothesis, you really would need both mutations before there is any improvement whatsoever, and that would really be improbable enough to account for the observed result that only one out of the twelve tribes achieved the feat.”

(Richard Dawkins, The Greatest Show on Earth, pg. 129 (Free Press, 2009), emphasis in original.)

Yet Behe was skewered by reviewers for using this same allegedly mistaken logic; they accused him of ignoring the possibility of stepwise mutations. Thus, in their reviews of The Edge of Evolution, Ken Miller, Jerry Coyne, and Paul Gross each challenged Behe’s claim that the rarity of chloroquine resistance implies multiple mutations are necessary for it to occur. All three biologists alleged that Behe failed to recognize that such resistance can evolve in a stepwise fashion. All three biologists missed Behe’s point.

The rarity of chloroquine resistance is not in question. In fact, Behe’s statistic that it occurs only once in every 10²⁰ cases was derived from public health statistical data, published by an authority in the Journal of Clinical Investigation. The extreme rareness of chloroquine resistance is not a negotiable data point; it is an observed fact.

According to Behe's (and Dawkins') logic, extreme rarity of a trait can imply it requires multiple mutations to arise; if there were a simple evolutionary pathway, resistance would not be so rare. Dawkins uses precisely the same logic, arguing that its rarity implies that multiple mutations are required, writing, “No, the rarity of citrate metabolism suggests that we are looking for something more like the ‘irreducible complexity’ of creationist propaganda. This might be a biochemical pathway in which the product of one chemical reaction feeds into a second chemical reaction, and neither can make any inroads at all without the other. This would require two mutations, call them A and B, to catalyze the two reactions.” (pg. 129)

Yet consider how Gross, Miller, and Coyne skewered Behe for similarly arguing that the rarity of trait implies that perhaps more than one mutation is required for the trait:

Gross: “Second, Behe assumes simultaneous mutations at two sites in the relevant gene, but there is no such necessity and plenty of evidence that cumulativeness, rather than simultaneity, is the rule. As Nature’s reviewer (Kenneth R. Miller) notes, ‘It would be difficult to imagine a more breathtaking abuse of statistical genetics.’” (The New Criterion, 2007)

Miller: “It would be difficult to imagine a more breathtaking abuse of statistical genetics. Behe obtains his probabilities by considering each mutation as an independent event, ruling out any role for cumulative selection, and requiring evolution to achieve an exact, predetermined result.” (Nature, 2007)

Coyne: “Behe requires all of the three or four mutations needed to create such an interaction to arise simultaneously. ... If it looks impossible, this is only because of Behe’s bizarre and unrealistic assumption that for a protein-protein interaction to evolve, all mutations must occur simultaneously, because the step-by-step path is not adaptive.” (The New Republic, 2007)

First, steps. The more intermediate evolutionary steps that must be climbed to achieve some biological goal without reaping a net benefit, the more unlikely a Darwinian explanation. …

… The eminent evolutionary biologist John Maynard Smith, who died in 2004, addressed this point over thirty years ago and reached an important conclusion:

The model of protein evolution I want to discuss is best understood by analogy with a popular word game. The object of the game is to pass from one word to another of the same length by changing one letter at a time, with the requirement that all the intermediate words are meaningful in the same language. Thus WORD can be converted into GENE in the minimum number of steps as follows: WORD WORE GORE GONE GENE

Because mutations are relatively rare, the monkey’s typing is almost always judged after a single keystroke. Bad changes are quickly eliminated. So, reasoned Smith, evolution has to slog along one tiny beneficial step at a time. If it needs two changes to help, it gets stuck. University of Rochester evolutionary biologist H. Allen Orr recently seconded John Maynard Smith’s reasoning:

Given realistically low mutation rates, double mutants will be so rare that adaptation is essentially constrained to surveying—and substituting—one-mutational step neighbors. Thus if a double-mutant sequence is favorable but all single amino acid mutants are deleterious, adaptation will generally not proceed.

If two mutations have to occur before there is a net beneficial effect—if an intermediate state is harmful, or less fit than the starting state—then there is already a big evolutionary problem….

…Random mutation is the perfect tool for the evolutionary job when steps are continuous and close together. When there are some broken stairs, with small gaps between steps, it’s a potential tool. …

…The Darwinian magic works well only when intermediate steps are each better (‘more fit’) than preceding steps, so that the mutant gene increases in number in the population as natural selection favors the offspring of people who have it.

(Michael Behe The Edge of Evolution pp. 104-108, 112 (Free Press, 2007).)

So how does Behe infer that multiple mutations were necessary to gain any advantage? It's based upon the observed extreme rarity of the trait. Yet this is the precise reverse-engineering type of logic used by Dawkins to make the exact same inference with regards to Lenski’s citrate evolution.

Somehow, something tells me that no one is going to skewer Dawkins for using this same logic—valid logic—as Behe.

But there is one other point, even more profound to be made here...

Fin
In closing, step back consider what’s going on here. Dawkins’ centerpiece evidence for biochemical evolution to "undermine" irreducible complexity is Lenski’s research on citrate on E. coli. But as Behe argues, this is a modest accomplishment, well within the edge of evolution. If Lenski’s results are about the best we've seen evolution do, then there's no reason to believe evolution could produce many of the complex biological features we see in the cell. As Behe concludes his rebuttal to Lenski's citrate research: “If the development of many of the features of the cell required multiple mutations during the course of evolution, then the cell is beyond Darwinian explanation. I show in The Edge of Evolution that it is very reasonable to conclude they did.”

Posted by Casey Luskin at 12:44 PM | Permalink | TrackBacks (0)

The Los Angeles Daily News this morning is reporting the California Science Center’s outrageous cancellation of a screening of the new intelligent design documentary, Darwin’s Dilemma: The Mystery of the Cambrian Fossil Record. The California Science Center is a “department of the State of California,” and its IMAX Theater had been rented by a private group, the American Freedom Alliance, to hold the Los Angeles premiere of the film as part of a series of activities commemorating the 150th anniversary of Darwin’s On the Origin of Species. But after the screening became public knowledge, the pressure from Darwinist censors apparently became too intense. So this week the Science Center expelled the film, possibly after being intimidated by the Smithsonian Institution, which clearly was upset by publicity promoting the screening that mentioned the true fact that the Science Center is an official “Smithsonian Affiliate.” The Science Center is now claiming that it canceled the event “because of issues related to the contract,” issues its spokesperson conveniently refuses to identify. If you believe that, I have some swamp land you might like to buy in Florida.

Censorship is apparently alive and well in southern California. Given that the Science Center is a state entity, its heavy-handed cancellation of this event raises significant free speech issues. This is viewpoint discrimination plain and simple. A state agency has decided to ban speech it doesn't like in a public facility that is supposed to be open to all citizens. And that's an outrage.

Posted by John West at 12:09 AM | Permalink | TrackBacks (0)

Today on the Michael Medved show, arch-Darwinist Richard Dawkins, author of The Greatest Show on Earth, was asked point-blank by Discovery Institute President Bruce Chapman why he wouldn't debate Stephen Meyer, author of Signature in the Cell. His response? Weak sauce:

I have never come across any kind of creationism, whether you call it intelligent design or not, which has a serious scientific case to put.

The objection to having debates with people like that is that it gives them a kind of respectability. If a real scientist goes onto a debating platform with a creationist, it gives them a respectability, which I do not think your people have earned.

No matter — Professor Dawkins made his position clear enough: address young earth creationism, then tell your audience that you've destroyed intelligent design... which of course, even Richard Dawkins admits, is not the same thing as young earth creationism.

Read the transcript of the entire exchange below — and note Bruce Chapman's great line about Expelled:

Bruce Chapman: … Dr. Dawkins, this is Bruce Chapman from Discovery Institute calling. [Dawkins, muttering under his breath: “Right.”] I was frustrated with this conversation because most of the time I hear straw man arguments about intelligent design. Your new book apparently doesn’t really deal with intelligent design. But it seems to me, that in your previous book, you said that it’s a question of science, that it is a scientific argument – I congratulate you for that -- But if it is, how about having a debate with Stephen Meyer, who is the author of another new book, Signature in the Cell, which deals with this question, and have this in a respectful, civilized, scholarly fashion where you look at the scientific arguments, pro and con?

Richard Dawkins: Now, when you say that I don’t deal with intelligent design, I do, because I deal with creationism and, of course, intelligent design is simply another name for creationism invented for political reasons.

Chapman: Well, if it’s another name for creationism, why did you distinguish between intelligent design and creationism very early in this program?

Dawkins: I don’t.

Medved: You did, earlier on, when we were talking about the Holocaust denier analogy, you said you applied that analogy to old earth creationists. Intelligent design advocates are not old earth creationists.

Dawkins: Sorry, um, I applied the history-deniers to young earth creationists.
Medved: I’m sorry, young earth creationists, yes, but you know intelligent design advocates are not young earth creationists.

Dawkins: I do, and that was precisely the distinction I was making. That’s why I said that I was not accusing intelligent design people of being history deniers, in that sense.

Medved: But you just said intelligent design is another name for creationism.

Dawkins: It is another name for creationism, but not young earth creationism.

Medved: Bruce Chapman?

Chapman: In that case, you’ve got an argument with your previous caller also, because that would be a theistic evolutionist proposition, which is also, by your definition, if it’s not Darwinian evolution, it’s creationism in some fashion. There isn’t any other kind of evolution, as far as you’re concerned.

Dawkins: Where do you guys think – do you think that God did it?

Chapman: I don’t know, I don’t think that the intelligent design people—

Dawkins: That’s what you say, you always pretend, you always pretend that an alien in outer space or something, but you know very well that what you mean is God.

Chapman: No, I think that was your line in Expelled. But I think that the thing that you really ought to consider, in all seriousness, is that by your own definition there is a scientific argument. Put that scientific argument to the test, not with somebody who’s a straw man that you bring up, but have somebody like Meyer, who has written a very scholarly book, to actually debate this topic with you…

Medved: All right, the proposal’s on the table, response from Professor Dawkins, thank you, Bruce.

Dawkins: I will have a discussion with somebody who has a genuinely different scientific point of view. I have never come across any kind of creationism, whether you call it intelligent design or not, which has a serious scientific case to put.

The objection to having debates with people like that is that it gives them a kind of respectability. If a real scientist goes onto a debating platform with a creationist, it gives them a respectability, which I do not think your people have earned.

Posted by Anika Smith at 4:28 PM | Permalink | TrackBacks (0)

As someone who has studied the concept of “junk DNA” for over twenty years, I am dismayed by two statements that appear repeatedly on various blog sites discussing evolution. No, I am not referring to arguments of the form “the onion has six times more DNA than do mammals; therefore, there is no deity,” that are invariably followed by terms of disparagement hurled at anyone who even marginally departs from the Darwinian perspective. Rather, my consternation stems from a half-truth and a false fact that are recycled ad nauseum by those who apparently believe that, despite all the genomic and transcriptomic data that have been obtained only in this decade—data that have overturned a number of trenchant assumptions—a certain hypothesis published in 1980 is outside the purview of serious questioning.

The half-truth is the oft-read comment that goes something like this: “No one ever asserted that junk DNA is without function…it was long suspected that these sequences have important roles in the cells,” Now, to be fair, it is correct to say that models for, say, repetitive DNA-based operations in metazoan development, have been proposed since the 1960s.¹ It is also true that the evolutionary process of exaptation—the accidental acquisition of a function—has been used to explain how the odd transposon here or there along a chromosome can regulate a locus. Nonspecific effects of “extra” DNA on the cell have also been suggested for around three decades, if not longer. That said, the junk DNA hypothesis that one commonly reads as being an unassailable observation, as an incontrovertible empirical conclusion, presents as a clear prediction that the vast majority of non-gene sequences are devoid of any precise specificational role in ontogeny. Allow me to explain.

Two papers appeared back to back in the journal Nature in 1980: “Selfish Genes, the Phenotype Paradigm and Genome Evolution” by W. Ford Doolittle and Carmen Sapienza² and “Selfish DNA: The Ultimate Parasite” by Leslie Orgel and Francis Crick.³ These laid the framework for thinking about nonprotein-coding regions of chromosomes, judging from how they are cited. What these authors effectively did was advance Dawkins’s 1976 selfish gene idea⁴ in such a way that all the genomic DNA evidence available up to that time could be accounted for by a plausible scenario. The thesis presented in both articles is that the only specific function of the vast bulk of “nonspecific” sequences, especially repetitive elements such as transposons, is to replicate themselves — this is the consequence of natural selection operating within genomes, beneath the radar of the cell. These junk sequences, it was postulated, can duplicate and disperse throughout chromosomes because they have little or no effect on the phenotype, save for the occasional mutation that results from their mobility. On the positive side, the C-value paradox, the longstanding puzzle that genome sizes have no correlation with perceived organismal complexity — a lily, for instance, can have twenty times more nuclear DNA than a mouse — was satisfactorily explained by the hypothesis. Also, the problem of repetitive elements of which the “variety and patterns of their interspersion with unique sequence DNA make no particular phylogenetic or phenotypically functional sense” ³ was argued to have a simple solution. Likewise, the finding in the late 1970s that protein-coding regions in eukaryotes are interrupted by nonprotein-coding “introns” could be understood…as perhaps the degenerate remains of old transposable sequences.

A careful reading of these papers reveals, though, in what ways nonprotein-coding DNA function were thought by these authors to be likely. At the risk of being accused of quote-mining, let me first note the definitions of junk or selfish DNA:

A piece of selfish DNA, in its purest form, has two distinct properties:

(1) It arises when a DNA sequence spreads by forming additional copies of itself within the genome.

(2) It makes no specific contribution to the phenotype.

[W]e shall use the term selfish DNA in a wider sense, so that it can refer not only to obviously repetitive DNA but also to certain other DNA sequences which appear to have little or no function, such as much of the DNA in the introns of genes and parts of the DNA sequences between genes…The conviction has been growing that much of this extra DNA is ‘junk’, in other words, that it has little specificity and conveys little or no selective advantage to the organism…in the case of selfish DNA, the sequence which spreads makes no contribution to the phenotype of the organism, except insofar as it is a slight burden to the cell that contains it. Selfish DNA sequences may be transcribed in some cases and not in others. The spread of selfish DNA within the genome can be compared to the spread of a not-too-harmful parasite within its host.³

Natural selection operating within genomes will inevitably result in the appearance of DNAs with no phenotypic expression whose only ‘function’ is survival within genomes.²

We do not deny that prokaryotic transposable elements or repetitive and unique-sequence DNAs not coding for protein in eukaryotes may have roles of immediate phenotypic benefit to the organism.²

It would be surprising if the host organism did not occasionally find some use for particular selfish DNA sequences, especially if there were many different sequences widely distributed over the chromosomes. One obvious use, as repeatedly stressed by Britten and Davidson, would be for control purposes at one level or another. This seems more than plausible.
[…]
A mechanism which scattered, more or less at random, many kinds of repeated sequences in many places in the genome would appear to be rather good for this purpose [of gene regulation]. Most sets of such sequences would be unlikely to find themselves in the right combination of places to be useful but, by chance, the members of one particular set might be located so that they could be used to turn on (or turn off) together a set of genes which had never been controlled before in a coordinated way. A next way of doing this would be to use as control sequences not the many identical copies distributed over the genome, but a small subset of these which had mutated away from the master sequence in the same manner.

On this picture, each set of repeated sequences might be ‘tested’ from time to time in evolution by the production of a control macromolecule…to recognize those sequences. If this produced a favorable result, natural selection would confirm and extend the mechanism. If not, it would be selected against and discarded. Such a process implies that most sets of repeated sequences will never be of use since, on statistical grounds, their members will usually be in unsuitable places.

It thus seems unlikely that all selfish DNA has acquired a special function…
[…]
In some circumstances, the sheer bulk of selfish DNA may be used by the organism for its own purpose. That is, the selfish DNA may acquire a nonspecific function which gives the organism a selective advantage.³

In other words, the opinion expressed these two works is that “excess” DNA is junk in the sense that it is largely devoid of phenotype-specifying information. This perspective was being discussed in the 1970s and it quickly became the consensus after this pair of papers appeared. Don’t take my word for it—follow the literature trail. Simply type in terms such as “junk DNA,” “selfish DNA,” “repetitive DNA,” “noncoding,” etc. using the Pubmed search engine and read the articles. What should become obvious is that the view expounded by Orgel and Crick on the one hand, and Doolittle and Sapienza on the other, has been considered by many cellular and molecular biologists to be the correct explanation for much of genomic DNA until very recently.

So the oft-read claim on the web that the term “junk DNA” never implied developmentally “non-functional DNA” is one that is made either out of ignorance or disingenuousness.

That said, the success of the junk DNA proposal was based in part on the narrative it provided. But its acceptance was also due to definitions and presuppositions that remain with us today. Regarding the former, a gene was described in 1980 as a discrete section of the chromosome that encoded a protein or in some instances an RNA, with the “one gene, one enzyme” model exemplifying this concept. Sequences of DNA that do not specify a protein were labeled “noncoding” or, as we have seen, “nonspecific.” By connotation, then, almost all genomic regions of any given eukaryote lack coding potential, which was understood then and now to mean being a part of the “genetic program.” Linked to this definition of a gene was the assumption that cross-species conservation of a DNA string implies that it has been retained by natural selection, because it embodies some instructions that enhance the fitness of an organism. Since a large fraction of nonprotein-coding DNA is often restricted to members of a species or a genus or a family, it fails the conservation test and thus is said to be dispensable: the refuse of the duplication and transposition process. In short, the backdrop of the junk DNA hypothesis was the premise that sequences like repetitive elements are noncoding in the strictest way—encoding no proteins or RNAs other than those used in their own manipulative, lascivious, and licentious replication; and their evolutionary lability reflects this lack of coding potential.

This brings me to the false fact. It has been said that 90% of all genomic DNA (in eukaryotes) is junk. No taxon is mentioned; no reference is cited…the value is just repeated by those commenting on evo blogs. To be sure, tagging a percentage to such a claim is a lot better than simply saying that “most DNA is junk.” In lieu of an actual piece of research that demonstrated support for this proclamation, let’s critically examine the 90% junk figure by focusing on human genomic DNA. Only around 1.5% of our chromosomal sequences encode proteins, which entails that 98.5% of the genome is noncoding by the classical definition. If someone wanted to make the equation noncoding = junk, then lo and behold functional sequences in Homo sapiens drop far below the 10% value. But we know that this equation is not valid. A surprising finding of ENCODE and other transcriptome projects is that almost every nucleotide of human (and mouse) chromosomes is transcribed in a regulated way ^{5 6 7 8 9 10 11 12 13 14 15}. Most of the RNAs produced are various nonprotein-coding transcripts that are copied from both strands in a cell type-, tissue type-, or developmental stage-specific manner ^{16 17 18}. These RNAs belong to a number of different functional classes and new categories are being discovered all the time ^{19 20 21 22 23 24}. Further, these nonprotein-coding transcriptional units extend into and arise from protein-coding segments. Many also map to the regions between protein-coding loci.²⁵ The RNA map of the mammalian genome has moreover been demonstrated to be hierarchical and far from random. ^{13 15 26}

Clearly, the “gene” definition that provided the framework for the junk DNA hypothesis is defunct^{27 28}, and much discussion now centers on providing an operational description.^{29 30 31 32} That is to say, the coding/noncoding distinction is being rethought. And if one considers functional DNA to be equivalent to transcription units that are developmentally expressed together with their regulatory regions, the fraction that can be dismissed as junk becomes startlingly small—this is what the results of recent studies imply. ³³

Indeed, if we accept the equation transcription units + control elements = developmentally functional DNA, then the number of loci in the human genome jumps from a paltry 20,000 to hundreds of thousands, and the percentage of non-junk DNA increases to well over 90%.

It could be argued that most of these RNA-encoding loci are really cellular “noise” due to transcription running amok, on the basis that so few are phylogenetically conserved—after all, didn’t Orgel and Crick foresee such a possibility in their definition of selfish DNA? Well, this line of argumentation doesn’t hold. Another counterintuitive result of the ENCODE project and other comparative genomic analyses is that known functional sections of the mammalian genome such as protein-coding segments appear to be diverging without constraint ^{5 34}, whereas a host of “junk” sequences are under some type of selective pressure—including most human “noncoding” DNA stretches. ^{35 36} The same has been repeatedly detected for the fruit fly genome, where most nonprotein-coding sequences appear to be under functional constraint—with the species-specific differences having the statistical hallmarks of being “adaptive” ^{37 38 39 40}. Even the Y chromosome of the fruit fly, long presented as “exhibit A” in the gallery of garbage DNA, has been shown to have diverse effects on the phenotype of this insect.⁴¹ Such results are exactly the opposite of what Orgel and Crick and Doolittle and Sapienza predicted.

Instead of 90% of the human or fly genome being junk, it seems that 90% or more of chromosomal DNA has some kind of specific developmental function, given the available data. Indeed, the emerging picture is that the species-specific nonprotein-coding regions encode numerous RNAs that help to shape the phenotype in ways that we are only beginning to understand.^{42 43 44 45 46} This is especially true for the transposable element fraction of human chromosomes—about 50% of our DNA—much of which is arranged and expressed in a taxon-specific manner. ^{33 47 48 49} Part of the reason for why a human is not a chimp is not a cow is not a whale, then, is that each species has its own set of sui generis “genes”—genomic texts specifying unique RNAs or even proteins that are used in embryogenesis.

To put everything into perspective, I’ll mine another quote from a paper worth reading:

We now know that more of the DNA in eukaryotic cells is copied into RNA than previously had been thought. Many of these transcripts serve regulatory instead of template functions in gene readout. Some of these newly recognized RNAs come from regions of the genome that had heretofore been deemed "junk DNA," yet no one could answer the obvious question: if "junk," then why still around? Before memory fades, we should note that there were some reasonably well articulated ideas 30-40 years ago that anticipated these recent discoveries.¹

Indeed, those were the very same well-articulated ideas that the selfish DNA hypothesis was supposed to have dispensed with, once and for all.

How things have changed since 1980.

References

¹ Pederson T. 2009. The discovery of eukaryotic genome design and its forgotten corollary--the postulate of gene regulation by nuclear RNA. FASEB J. 23(7): 2019-2021.

² Doolittle WF, Sapienza C. Selfish genes, the phenotype paradigm and genome evolution. Nature 284(5757): 601-603.

³ Orgel LE, Crick FH. 1980. Selfish DNA: the ultimate parasite. Nature 284(5757): 604-607.

⁴ Dawkins, R. 1976. The Selfish Gene. Oxford University Press, New York, New York.

⁵ ENCODE Project Consortium, Birney E, et al. 2007. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447(7146): 799-816.

⁶ Frith MC, et al. 2006. Pseudo-messenger RNA: phantoms of the transcriptome. PLoS Genet. 2(4): e23.

⁷ Katayama S, et al. 2005. Antisense transcription in the mammalian transcriptome. Science 309(5740): 1564-1566.

⁸ Kapranov P, et al. 2007. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316(5830): 1484-1488.

⁹ Wu JQ, et al. 2008. Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol. 9(1): R3.

¹⁰ Furuno M, et al. 2006. Clusters of internally primed transcripts reveal novel long noncoding RNAs. PLoS Genet. 2(4): e37.

¹¹ Amaral PP, et al. 2008. The eukaryotic genome as an RNA machine. Science 319(5871): 1787-1789.

¹² Dinger ME, et al. In press. Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications. Brief Funct Genomic Proteomic.

¹³ Kapranov P, et al. 2007. Genome-wide transcription and the implications for genomic organization. Nat Rev Genet. 8(6):413-423.

¹⁴ Kapranov P, et al. 2005. Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays. Genome Res. 15(7):987-997.

¹⁵ Carninci P, et al. 2008. Multifaceted mammalian transcriptome. Curr Opin Cell Biol. 20(3): 274-280.

¹⁶ Rinn JL, et al. 2007. Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129(7): 1311-1323.

¹⁷ Amaral PP, Mattick JS. 2008. Noncoding RNA in development. Mamm. Genome 19(7-8): 454-492.

¹⁸ Mercer TR, et al. 2008. Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A 105(2): 716-721.

¹⁹ Taft RJ, et al. 2009. Small RNAs derived from snoRNAs. RNA 15(7): 1233-1240.

²⁰ Taft RJ, et al. 2009. Tiny RNAs associated with transcription start sites in animals. Nat Genet. 41(5): 572-578.

²¹ Kawaji H, et al. 2008. Hidden layers of human small RNAs. BMC Genomics 9: 157.

²² Wilusz JE, et al. 2009. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev. 23(13): 1494-1504.

²³ Affymetrix ENCODE Transcriptome Project; Cold Spring Harbor Laboratory ENCODE Transcriptome Project. 2009. Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature 457(7232): 1028-1032.

²⁴ Borel C, et al. 2008. Mapping of small RNAs in the human ENCODE regions. Am J Hum. Genet. 82(4): 971-981.

²⁵ Khalil AM, et al. 2009. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 106(28): 11667-11672.

²⁶ Thurman RE, et al. 2007. Identification of higher-order functional domains in the human ENCODE regions. Genome Res. 17(6): 917-927.

²⁷ Gerstein MB, et al. 2007. What is a gene, post-ENCODE? History and updated definition. Genome Res. 17(6): 669-681.

²⁸ Gingeras TR. 2007. Origin of phenotypes: genes and transcripts. Genome Res. 17(6): 682-690.

²⁹ Scherrer K, Jost J. 2007. Gene and genon concept: coding versus regulation. A conceptual and information-theoretic analysis of genetic storage and expression in the light of modern molecular biology. Theory Biosci. 126(2-3): 65-113.

³⁰ Pesole G. 2008. What is a gene? An updated operational definition. Gene 417(1-2): 1-4.

³¹ Prohaska SJ, Stadler PF. 2008. "Genes". Theory Biosci. 127(3): 215-221.

³² Stadler PF, et al. In press. Defining genes: a computational framework. Theory Biosci.

³³ Faulkner GJ, Carninci P. 2009. Altruistic functions for selfish DNA. Cell Cycle 8(18): 2895-2900.

³⁴ Margulies EH, et al. 2007. Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res. 17(6): 760-774.

³⁵ Asthana S, et al. 2007. Widely distributed noncoding purifying selection in the human genome. Proc Natl Acad Sci USA. 104(30): 12410-12415.

³⁶ Eory L, et al. In press. Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes. Mol Biol Evol.

³⁷ Andolfatto P. 2005. Adaptive evolution of non-coding DNA in Drosophila. Nature 437(7062): 1149-1152.

³⁸ Kondrashov AS. 2005. Evolutionary biology: fruitfly genome is not junk. Nature 437(7062): 1106.

³⁹ Halligan DL, Keightley PD. 2006. Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison. Genome Res. 16(7): 875-884.

⁴⁰ Haddrill PR, et al. 2008. Positive and negative selection on noncoding DNA in Drosophila simulans. Mol Biol Evol. 25(9): 1825-1834.

⁴¹ Lemos B, et al. 2008. Polymorphic Y chromosomes harbor cryptic variation with manifold functional consequences. Science 319(5859): 91-93.

⁴² Glinsky GV. 2008. Phenotype-defining functions of multiple non-coding RNA pathways. Cell Cycle 7(11): 1630-1639.

⁴³ Bond CS, Fox AH. 2008. Paraspeckles: nuclear bodies built on long noncoding RNA. J. Cell Biol. 186(5): 637-644.

⁴⁴ Barak M, et al. In press. Evidence for large diversity in the human transcriptome created by Alu RNA editing. Nucleic Acids Res.

⁴⁵ Lee JT. 2009. Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes Dev. 23(16): 1831-1842.

⁴⁶ Guttman M, et al. 2009. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458(7235): 223-227.

⁴⁷ Faulkner GJ, et al. 2009. The regulated retrotransposon transcriptome of mammalian cells. Nat Genet. 41(5): 563-571.

⁴⁸ Tay SK, et al. 2009. Global discovery of primate-specific genes in the human genome. Proc Natl Acad Sci U S A. 106(29): 12019-12024.

⁴⁹ Walters RD, et al. 2009. InvAluable junk: the cellular impact and function of Alu and B2 RNAs. IUBMB Life. 61(8): 831-837.

Posted by Richard Sternberg at 12:39 PM | Permalink | TrackBacks (0)

I thought Richard Dawkins’ science was outdated, but I didn’t realize just how badly outdated until I watched this amazing You Tube clip from “The Genius of Charles Darwin,” a science documentary Dawkins hosted last year. If you watch until 7 minutes and 30 seconds into the clip, you will see Ernst Haeckel’s bogus embryo diagrams magically appear onscreen right before your very eyes:

That’s right, Richard Dawkins circa 2008 was still peddling fraudulent "evidence" for evolution that no self-respecting embryologist would defend, and that most biology textbooks dropped years ago due in large part to biologist Jonathan Wells’ masterful book Icons of Evolution, which shamed Darwinists into cleaning up their act. Randy Olson, call home. Armed with retro science like this, no wonder Dawkins is afraid to debate Stephen Meyer.

Posted by John West at 12:10 AM | Permalink | TrackBacks (0)

Scientists sometimes find themselves wishing things were different. In one sense that’s a thoroughly unremarkable observation. After all, scientists are human, and humans have always found themselves wishing things were different.

But what if some of the things scientists wish were different are the very things they have devoted themselves to studying? In other words, forget about salaries, teaching loads, and grant funding. What if some scientists want the brute facts of their own field of study to be other than what they really are?

As odd as it may seem, particularly to non-scientists, that tension between preference and reality has always been a part of doing science. Like everyone else, scientists don’t just have ideas—they favor them… even promote them. And for scientists, as for everyone else, sometimes those cherished ideas are just plain wrong.

For decades now, a growing minority of scientists have argued that the standard explanations of biological origins are prime examples of this—cherished ideas that are spectacularly wrong. That raises an interesting question. If these ideas are really so wrong, why do so many experts affirm them?

Some, of course, would call this a false paradox. By their way of thinking, the mere fact that so many experts accept these ideas shows that they can’t be badly wrong. But paradigm shifts do happen in science, and every time they do the world is treated to the memorable spectacle of lots of experts being badly wrong.

Even experts have ways of avoiding reality. When it comes to the improbabilities that plague naturalistic origins stories, the avoidance often takes the form of what I’ve called the ‘divide and conquer’ fallacy. [1] It works like this. Instead of asking what needs to be explained naturalistically, you concentrate on what can be so explained. Specifically, you look for some small piece of the real problem for which you can propose even a sketchy naturalistic solution. Then, once you have this mini-solution, you present it as a small but significant step toward the ultimate goal of a full credible story.

But the only way to tell whether small steps of this kind are taking us toward that ultimate goal or away from it is to examine them carefully in the context of the whole problem. If that analysis doesn’t give the intended result, it’s tempting to skip it and end on a happy note.

Consider the work that Lehmann, Cibils, and Libchaber recently published on the origin of the genetic code. [2] By one account they have “generated the first theoretical model that shows how a coded genetic system can emerge from an ancestral broth of simple molecules.” [3]

That would be huge alright. And huge claims always call for caution.

Let’s start with some background. The “broth” that Lehmann et al. are thinking of is sometimes called the “RNA world”—a hypothetical early stage in the evolution of life when RNA served both the genetic role that DNA now serves and the catalytic role that proteins now serve.

In modern life, most RNA performs a cellular function analogous to the function of the clipboard on your computer. It enables sections of ‘text’ to be lifted from a larger ‘document’ for temporary use. These sections are genes and the document is the genome. By providing in this way temporary working copies of genetic text, RNA contributes to the central purpose of genes, which is to provide the sequence specifications for manufacturing the functional proteins that do the molecular work of life.

This is where the genetic code comes in, and with it the daunting problem it poses for naturalistic accounts of origins. The key thing to grasp is that genes are as unlike proteins as successions of dots and dashes are unlike written text. Only when a convention is established, like Morse code, and a system put in place to implement that convention, can dots and dashes be translated into written text. And then, only meaningful arrangements of dots and dashes will do. Likewise, only a system implementing a code for translating gene sequences (made from the four nucleotides) into protein sequences (made from the twenty amino acids) can enable genes to represent functional proteins, as they do in life.

What makes it so hard to imagine how this system could have evolved is the need for it to be complete in order for it to work, coupled with the need for it to be complex in order to be complete. To agree that “•” stands for e is relatively simple, but not in itself very helpful. Only when a whole functional alphabet is encoded in this way do we have something useful. Similarly, it seems that an apparatus for decoding genes, and thereby implementing a genetic code, would have to physically match each of the twenty biological amino acids to a different nucleotide pattern. Whatever else that apparatus might be, it can’t be simple. Moreover, it can’t be useful without some meaningful genes (encoding useful proteins) to go with it.

This realization is enough to make even a committed materialist give up on the idea of an evolutionary explanation. Evolutionary biologist Eugene Koonin has. In his words, “How such a system could evolve is a puzzle that defeats conventional evolutionary thinking.” [4] Accordingly, he proposes the unconventional solution of an infinite universe (a multiverse) in which even the seemingly impossible becomes certain.

I think it’s fair to say that most biologists are uncomfortable with Koonin’s proposal. Part of what bothers them is the tacit abandonment of more conventional solutions, as though these have no hope of ever succeeding. In the wake of this, Lehmann, Cibils, and Libchaber are, in effect, refusing to throw in the towel, and that merits attention in itself.

Instead of making the universe bigger, they propose a way of making the genetic code smaller, hoping that this downsized version might feasibly arise in a conventional evolutionary way. But there’s a risk. Their efforts to simplify could easily lead to oversimplification.

They presuppose an RNA-world endowed with two kinds of tRNA molecules, each of which has dual functional capacities: at one end they attach an amino acid, and at the other they pair with a specific base triplet (codon) on an RNA gene. Their world also has steady supplies of two kinds of amino acid, at least one kind of RNA gene that restricts itself to the two codons recognized by the tRNAs, and “a ribosome-like cofactor” that cradles the complex formed between the tRNA that caries the new protein chain and the codon to which it is paired.

The immediate question is, how could a world that has never encoded proteins have done so much preparation to become a world that does encode proteins? We seem to be left with the familiar alternatives of extraordinary improbability or guided design. Here it has to be conceded that Koonin’s proposal is at least commendably frank, in that it acknowledges the improbabilities. Lehmann et al., like everyone else, prefer not to go there.

Maybe that’s because, like everyone else, they find themselves between a rock and a hard place. Since the modern system for implementing the genetic code is way too complicated to have appeared by accident, they know they need to look for not just a simplification, but a radical simplification. But if it’s hard to explain how even a modest simplification could leave the basic function intact, imagine how hard it becomes for a radical simplification.

Their efforts to find a workable compromise between sterile simplicity and complex functionality are both laudable and instructive, but unsuccessful nonetheless.

Their simplified proteins are built from two amino acids instead of twenty. People have tried to fish out life-like proteins from pools of random chains made from just a few amino acids, but nothing impressive has ever come of it. That’s not surprising when you consider how fussy real-life proteins are about their amino-acid sequences. The idea of forcing them to hand over eighteen of their constituent amino acids without so much as a complaint is just plain unrealistic.

Lehmann, Cibils, and Libchaber attempt to push their proteins even further. Their translation mechanism has an extraordinarily high error rate, resulting in about one wrong amino acid for every six added to a new chain. And that’s under ideal conditions. Things get much worse if the conditions deteriorate.

Let’s experiment with this. If you haven’t read the title of their paper, hold off and we’ll see if you can read a version of it that has been simplified along the lines of their proposal. Protein functions would have to be remarkably relaxed about protein sequences for their simplifications to have worked in early life. The test will be to see whether you are comparably relaxed about spelling when you read.

The most common vowel in the title of their paper is e, and the most common consonant is n. To mimic their proposed simplification of proteins, let’s replace all the vowels in their title with e and all the consonants with n, randomly mistaking vowels and consonants about one sixth of the time. The random errors make many versions of the title possible, but you don’t have to see many examples to convince yourself that this isn’t going to work:

This isn’t meant to be a proof, of course, just an illustration. It approximates the scale of simplification that Lehmann et al. have proposed for protein sequences, and in so doing it provides very reasonable grounds for suspecting they have oversimplified. Something closer to proof can be had by examining how fussy real protein functions are about protein sequences. That whole field of work, as I see it anyway, seems to confirm the suspicion.

So in the end, Lehmann, Cibils and Libchaber seem to have taken us a step further from a naturalistic explanation for life rather than a step closer. Some people will be more pleased with that conclusion than others, and that’s okay. From the standpoint of science, every step is progress.

This article is crossposted from Biologic Institute's Perspectives blog.

References:
[1] Perspectives, 1 April 2009

[2] Lehmann J, Cibils M, Libchaber A (2009)

[3] ScienceDaily

[4] Koonin EV (2007)

Posted by Douglas Axe at 6:54 AM | Permalink | TrackBacks (0)

Seattle – Richard Dawkins, the world’s leading public spokesman for Darwinian evolution and an advocate of the “new atheism,” has refused to debate Dr. Stephen C. Meyer, a prominent advocate of intelligent design and the author of the acclaimed Signature in the Cell: DNA and the Evidence for Intelligent Design.

“Richard Dawkins claims that the appearance of design in biology is an illusion and claims to have refuted the case for intelligent design,” says Dr. Meyer who received his Ph.D. in the philosophy of science from the University of Cambridge in England.

“But Dawkins assiduously avoids addressing the key evidence for intelligent design and won’t debate its leading proponents,” adds Dr. Meyer. “Dawkins says that there is no evidence for intelligent design in life, and yet he also acknowledges that neither he nor anyone else has an evolutionary explanation for the origin of the first living cell. We know now even the simplest forms of life are chock-full of digital code, complex information processing systems and other exquisite forms of nanotechnology.”

In Signature in the Cell, Dr. Meyer shows that the digital code embedded in DNA points powerfully to a designing intelligence and helps unravel a mystery that Darwin did not address: how did the very first life begin?

Signature in the Cell has just entered its third printing according to publisher HarperOne, an imprint of Harper Collins, and has been endorsed by scientists around the world, including leading British geneticist Dr. Norman Nevin, Alastair Noble, Ph.D. chemistry, formerly Her Majesty’s Inspector of Schools for Science, Scotland, and Dr. Philip Skell, a member of the U.S. National Academy of Sciences.

Dr. Meyer challenged Dawkins to a debate when he saw that their speaking tours would cross paths this fall in Seattle and New York. Dawkins declined through his publicists, saying he does not debate “creationists.”

“Dawkins’ response is disingenuous,” said Meyer. “Creationists believe the earth is 10,000 years old and use the Bible as the basis for their views on the origins of life. I don’t think the earth is 10,000 years old and my case for intelligent design is based on scientific evidence.”

According to Discovery Institute, where Dr. Meyer directs the Center for Science & Culture, the debate challenge is a standing invitation for any time and place that is mutually agreeable to both participants.

Posted by Anika Smith at 12:56 PM | Permalink | TrackBacks (0)

Nature has recently published an interesting paper which places severe limits on Darwinian evolution. The manuscript, from the laboratory of Joseph Thornton at the University of Oregon, is titled, “An epistatic ratchet constrains the direction of glucocorticoid receptor evolution.” The work is interpreted by its authors within a standard Darwinian framework, but the results line up very well with arguments I made in The Edge of Evolution. This is the second of several posts discussing it.

Using clever synthetic and analytical techniques, Bridgham et al (2009) show that the more recent hormone receptor protein that they synthesized, a GR-like protein, can’t easily revert to the ancestral structure and activity of an MR-like protein because its structure has been adjusted by selection to its present evolutionary task, and multiple amino acid changes would be needed to switch it back. That is a very general, extremely important point that deserves much more emphasis. In all cases — not just this one — natural selection is expected to hone a protein to suit its current activity, not to suit some future, alternate function. And that is a very strong reason why we should not expect a protein performing one function in a cell to easily be able to evolve another, different function by Darwinian means. In fact, the great work of Bridgham et al (2009) shows that it may not be do-able for Darwinian processes even to produce a protein performing a function very similar to that of a homologous protein.

Before reading their paper, even I would have happily conceded for the sake of argument that random mutation plus selection could convert an MR-like protein to a GR-like protein and back again, as many times as necessary. Now, thanks to the work of Bridgham et al (2009), even such apparently minor switches in structure and function are shown to be quite problematic. It seems Darwinian processes can’t manage to do even as much as I had thought.

(As an aside into the circus world of popular-level debates on Darwinism, the work of Bridgham et al (2009) nicely shows the fallacy of the anti-ID retort that, say, a mousetrap is not irreducibly complex because, if the catch and holding bar are removed, parts of it can still be used as a tie clip. The same principle that holds for cellular machinery would hold for all machinery. Something that was shaped by selection to work as a tie clip would not look like an ancestor of a mousetrap, or easily be converted to one by random changes plus selection. If you look at images of tie clips on the internet, none of them resemble mousetraps — except for those purposely designed by folks who were arguing against irreducible complexity.)

Another point worth driving home in this post concerns the frequently encountered argument that, well, just because one kind of protein can’t develop a useful binding site or selectable property easily doesn’t mean that some other kind of cellular protein can’t. (In keeping with their Darwinian framework, Bridgham et al (2009) seem to allude to this.) After all, there are thousands to tens of thousands of kinds of proteins in a typical cell. If one of them is ruled out, the reasoning goes, many more possibilities remain.

This argument, however, is specious. For any given evolutionary task, the number of proteins in the cell which are candidates for helpful mutations is almost always very limited. For example, as I discussed in EOE, out of thousands of malaria proteins, mutations in only a handful are helpful to the parasite in its fight against chloroquine, and only one is really effective — the mutations in the PfCRT protein. Ditto for the human proteins that can mutate to help resist malaria — there’s just a handful. In the case of the hormone receptors discussed by Bridgham et al (2006), one can note that, out of ten thousand vertebrate proteins, the one that gave rise to a new steroid hormone receptor was an already-existing steroid hormone receptor. This should be quite surprising to folks who believe the many-proteins argument, because the steroid receptor was outnumbered 10,000 to 1 by other protein genes, yet it won the race to duplicate and form a new functional receptor. If all things were equal, we should be very surprised by that. But of course not all things are equal. The reason the receptor duplicated to give rise to a closely-related receptor is because no other protein in the cell is likely to be able to do so in a reasonable amount of evolutionary time.

The bottom line is that, for a given evolutionary task, at best only a handful of proteins will likely be helpful to evolve, at worst none may help. To calculate the probability of, say, a helpful protein-protein interaction developing in response to any particular selective pressure, it’s mistaken to gratuitously multiply odds by the total number of proteins in a cell. Combined with the point made by Bridgham et al (2009), that even tiny structural/functional changes may not be achievable by random mutation/ selection, these considerations pretty much squelch the likelihood of Darwinian processes doing much of significance during evolution.

References
Bridgham,J.T., Ortlund,E.A., and Thornton,J.W. 2009. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461:515-519.

Bridgham,J.T., Carroll,S.M., and Thornton,J.W. 2006. Evolution of hormone-receptor complexity by molecular exploitation. Science 312:97-101.

Posted by Michael Behe at 12:26 PM | Permalink | TrackBacks (0)

Barbara Forrest has issued a press release protesting good rules adopted in September, 2009 by the Louisiana State Board of Elementary and Secondary Education (BESE) for implementing Louisiana’s Science Education Act (LSEA). The LSEA is an academic freedom bill passed into law in Louisiana last year. Dr. Forrest seems to think that by frequently inserting the word “creationist” into her press release and falsely labeling people like Darwin-doubting biologist Dr. Don Ewert as “creationists,” she can logically argue that the rules are “pro-creationist.” The reality is that BESE’s new rules are fair and pro-academic freedom, not "pro-creationist." But as will be seen, fairness and academic freedom are exactly what evolution lobbyists like Dr. Forrest fear the most.

Blatant Misrepresentations of Don Ewert
Last year’s Louisiana academic freedom bill was premised upon the idea that students should be able to hear an objective, non-dogmatic, and diverse presentation of credible scientific viewpoints when studying controversial scientific theories. It was passed with overwhelming bipartisan support from both houses of the Louisiana State Legislature, and now holds the force of law.

The LSEA includes a strong requirement of religious neutrality in public schools, stating 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.” All the law does is sanction the use of supplementary curricular materials to create an educational atmosphere that “promotes critical thinking skills, logical analysis, and open and objective discussion of scientific theories being studied including, but not limited to, evolution, the origins of life, global warming, and human cloning.” The LSEA does not protect or allow the advocacy of religion, so my guess is it’s the “logical analysis and open and objective discussion” about “evolution [and] the origins of life” that has Barbara Forrest worried.

In a press release attacking BESE’s newly adopted rules, Forrest rails against the half-dozen or so LSEA supporters who testified before BESE at the hearing in mid-September. She repeatedly calls them “creationists,” as an epithet, as if the label “creationist” undercuts their very humanity and any viewpoint they might have. Here’s a little taste of how Forrest’s 3500+ word press release attempts to impugn one of those scientists:

Oklahoma creationist Donald Ewert was brought in from out of state to testify. Ewert is a signatory to the Discovery Institute’s “Scientific Dissent from Darwinism”; his name appears on a list of “Intellectual Doubters of Darwinism” at the creationist IDEA Center website. In Oklahoma, Ewert promoted “academic freedom” legislation similar to the LSEA (SSPS audiotape, 9/16/09). He was involved in the creationist effort to influence state science standards in Texas in March 2009 (see below).” … At a hearing in March, Ewert presented pro-creationist testimony before the Texas Board of Education, just as he did at the SSPS Committee hearing on September 16 (SSPS Committee audiotape, 9/16/09).

Casey: Dr. Ewert, are you a creationist?

Dr. Donald Ewert: Not in the popularly understood meaning of that term. A creationist starts with a dogmatic view and tries to fit their findings with Genesis. I arrived at my conclusions by looking at the scientific data, and as a scientist my view is that the evidence for Darwinian evolution is not adequate. That's why I signed the Scientific Dissent from Darwinism list.

Casey: Are you a young earth creationist?”

Dr. Donald Ewert: No. Based on everything that I’ve studied, I accept the findings of modern dating methods that show the earth is very old.

Casey: Do you think creationism should be taught in public schools?

Dr. Donald Ewert: No, absolutely not, because it’s primarily a religious position.

Casey: How do you feel about Barbara Forrest calling you a “creationist”?

Dr. Donald Ewert: I don’t know how she claims to know so much about me even though she’s never spoken to me. By calling me a creationist, she is misrepresenting who I am and obviously has never spoken to me.

If you want to know some facts, and not misrepresentations, about Dr. Ewert, here’s a good place to start: Don Ewert earned his Ph.D. in microbiology from the University of Georgia in 1976, and did his post doc under the father of evolutionary immunology, Max Cooper, at the University of Alabama. This led to him publishing several papers in leading scientific journals comparing aspects of the chicken's immune system to that of humans. Later in his career, Ewert operated a basic research lab at the prestigious Wistar Institute in Philadelphia for almost 20 years. Supported by the NIH, NSF, and Dept. of Agriculture, his research has involved the evolution of bacterial populations, comparative and developmental studies of the immune system, molecular and structural analysis of viruses, and the genetic regulation of cancer and cell death. Ewert has also been a section editor of the journal Developmental and Comparative Immunology.

Don Ewert is a credible scientist if there ever was one, and he holds serious scientific doubts about neo-Darwinian evolution. Forrest’s tactic of response is to just smile big and friendly like they do in the South and call him a “creationist,” pretending that therefore his opinions on evolution hold no merit.

Who Is Creating a “Kangaroo Court”? Forrest Misrepresents the History of BESE’s LSEA Rules
Forrest ends her tedious 3500+ word press release by calling the rules adopted by BESE a “pro-creationist complaint procedure” that creates a “kangaroo court” for hearing complaints about supplemental materials that challenge Darwinism used under the LSEA. Once again, Forrest is badly misrepresenting the situation:

• The truth is that the rules adopted by BESE rejected provisions pushed by the Louisiana Department of Education (DOE) that would have allowed the DOE to grab power and obstruct due process when hearing challenges to instructional materials.

• The truth is that BESE’s rules create fairness. In fact, before Forrest used the “kangaroo court” line, this is the precise language that the pro-LSEA advocates were using to describe the effect of the DOE’s proposed rules.

• The truth is that the DOE is a bureaucracy filled with ardent evolutionists who have tried to avoid their legal duty to fairly implement the intent of the legislature in the LSEA. Want proof? Here it is:

Fact 1: The LSEA was intended to foster a climate of academic freedom in the science classroom by allowing students to hear about legitimate scientific viewpoints that might disagree about controversial scientific theories. The LSEA is premised upon the view that when students are taught one scientific viewpoint on controversial topics (like evolution) in a monolithic fashion, students miss opportunities for critical thinking and credible minority scientific viewpoints may be censored from their learning environment.

Fact 2: When the DOE previously selected a panel of experts to help it craft guidelines for teachers implementing the LSEA, the DOE selected a panel of “experts” comprised entirely of Louisiana evolution lobbyists, and the DOE intentionally excluded from the panel qualified Ph.D. scientists and professors from Louisiana who doubt Darwin and testified in favor of the LSEA. In a subtle attempt to scuttle the legislature’s intent in passing the LSEA, the DOE appointed individuals who opposed the LSEA to craft guidelines for implementing the LSEA!

Fact 3: The DOE’s proposed rules this September were basically an attempt to grab power for the Louisiana evolution lobby. The proposed rules would have granted the DOE effective authority to play both judge and jury for any challenges to supplemental materials used under the LSEA. Thus, the DOE’s proposed rules said “the DOE will select three reviewers” and “the DOE may elect to support, reject or modify the recommendations of the reviewers or may substitute its own recommendation.” When a government body gives itself authority to pick the jury and then throw out the jury’s decisions if it doesn’t like them, we call this unchecked and arbitrary authority and a potential abuse of power.

Because the DOE’s proposed rules would have given the DOE complete authority to appoint pro-Darwin-only reviewers who would reject anything that challenges Darwinism, Barbara Forrest lauded them. She claims in her press release that “DOE professionals, exercising their professional judgment, would do their jobs properly and preserve the integrity of Louisiana’s science curriculum.” The reality is that the DOE’s rules would have resulted in evolutionists being handpicked to scuttle the intent of the legislature by rejecting the use of any supplemental materials that scientifically challenge evolution. No wonder Forrest liked them so much.

Fact 4: Knowing the DOE’s history of picking “experts” who were evolutionists that opposed the LSEA, this past June I spoke with DOE staff member Nancy Beben, who helped draft the DOE’s proposed rules. I raised these concerns with Ms. Beben that the DOE’s proposed additions to the rules lacked express provisions giving due process to certain parties, like the publisher or the local school district, to defend the materials being challenged, and allowed the DOE to have arbitrary power to scuttle the decisions of the reviewers. Beben’s response to me told me everything I needed to know:

She snapped that “there are no parties in science,” just “facts.”

The implications of that comment are profound: Ms. Beben and the DOE apparently view science simplistically (and inaccurately) as a monolithic enterprise without credible dissenting minority viewpoints. This means their view is directly inimical to the premise underlying the LSEA, which is that there can be credible minority scientific viewpoints worth disclosing to students when instructing them about controversial scientific topics.

Apparently Ms. Beben and the DOE not only don't understand how science works, but their view is directly inimical to the intent of the LSEA. To put it bluntly, the DOE was trying to bureaucratically muzzle the intent of the Louisiana legislature and skirt state law by proposing rules that would effectively gut the LSEA.

Thankfully, BESE members saw potential for the DOE’s abuse of power, and adopted rules that prevented the DOE from selecting all of the reviewers, and that prevent the DOE from scuttling the decisions of the reviewers if the DOE doesn’t like them. There are now 5 reviewers, and DOE still gets to select more reviewers—2—than any other party, but there are guarantees that the challenger, the local school district, and the publisher can also appoint credible experts to review the supplemental materials. And the final decision rests with BESE, who can consider expert opinions from multiple viewpoints before making their final choice.

If there is any doubt that the DOE’s rules would have obfuscated the intent of the law, consider Forrest’s attack on the adopted rules:

There is no guarantee that the three non-DOE reviewers, especially the school district’s and the publisher’s appointees, will have the requisite expertise to evaluate contested materials.

Forrest's assertion here is not true because the adopted rules still retain all of the original requirements that reviewers have the necessary expertise, stating: “The reviewers should be experts who are capable of determining if the materials are grade-level appropriate, if the materials are scientifically sound and supported by empirical evidence, and if the materials do not promote any religious doctrine, promote discrimination for or against a particular set of religious beliefs, or promote discrimination for or against religion or non-religion.”

So what exactly does Forrest mean by “will have the requisite expertise”? You might be able to guess, but it becomes explicitly clear in her next sentences, where Forrest rails against the possibility that Darwin-skeptics might have some influence in decisions about permissible supplemental materials (and realize that when she says “creationist,” she includes people like Don Ewert, extremely well-credentialed scientists who doubt Darwin):

A school district that permits the use of creationist materials is likely to choose a creationist reviewer. The publisher of creationist materials is virtually certain to choose a creationist. … BESE’s amended complaint procedure guarantees that a creationist … will be allowed to review their own materials. … The same holds for reviewers appointed by publishers of materials such as the Discovery Institute’s stealth creationist textbook, Explore Evolution, and its creationist DVDs … Such reviewers would be manifestly unqualified to render judgments concerning materials for use in Louisiana’s public schools.

The reality is that the rules adopted by BESE create fairness by guaranteeing that all of the reviewers will be experts, but won’t be handpicked by the DOE to stifle the intent of the Louisiana legislature and the LSEA. The rules adopted by BESE guarantee that both the pro-Darwin DOE and Darwin-skeptics can have a voice at the table, as multiple parties can appoint reviewers. That means the adopted rules promote fairness.

The contrast with Forrest’s preferred rules is stark: Forrest wants all the reviewers to be anti-LSEA Darwin lobbyists, while proponents of the LSEA want credible viewpoints on both sides to have a place at the table. Do you see the difference? Simply put, we don’t want our viewpoint to be the only game in town, but we do want it to be heard; Barbara Forrest wants her viewpoint to be the only game in town, and she wants other viewpoints to be silenced because they are deemed "manifestly unqualified."

Forrest’s last complaint about the adopted rules says it all:

DOE staff will not be allowed to independently assess the reviewers’ reports but must instead transfer the reports directly to BESE for evaluation.

The final rules aren't perfect, but fairness, due process, and academic freedom permeate the final rules that were adopted by BESE, which is why exactly Barbara Forrest and the Louisiana evolution lobby are so upset. The fact that Forrest doesn’t like these rules speaks volumes about her non-commitment to fairness and her intolerance for other viewpoints.

Posted by Casey Luskin at 11:14 AM | Permalink | TrackBacks (0)

Norman, Oklahoma, that is.

Okay, so there aren’t any real beaches in Norman, Oklahoma. But when Steve Meyer and I went there recently, the Darwinists who have installed themselves as absolute dictators at the University of Oklahoma (OU) made our arrival feel like D-Day.

On September 28, Steve gave a talk on his best-selling book Signature in the Cell at the Oklahoma Memorial Union on the OU campus. The following evening, September 29, Steve and I answered questions after a showing of the new film Darwin’s Dilemma at the Sam Noble Museum of Natural History, again on the OU campus.

Darwinists at OU are still gloating over the abuse to which they subjected Dr. William A. Dembski in 2007. On September 14, 2009, one of the organizers of that abuse, OU graduate student Abbie Smith, announced on her foul-mouthed blog that Steve and I were coming to OU and urged her readers to give us the same treatment.

The day after her announcement, retired OU zoology professor Victor Hutchison, of the militantly Darwin-only Oklahomans for Excellence in Science Education (OESE), posted the following on Smith’s blog: “

Folks at OU are experienced in how to put down such events. An example is the thorough dismantling of Dembski about three years ago. I expect that there will be plenty of students and others well-prepared with good questions and comments at both scheduled events—especially on the crap the film will have about the so-called 'Cambrian Explosion.'… However, opponents should get to the events EARLY.”

“Shame on the Sam Noble Museum of Natural History,” Myers wrote. “This will put a little spot of schmutz on their glossy reputation, I fear. And they're planning to turn it into a real kookfest, with both Jonathan Wells (whose book, Icons of Evolution, revealed that he was an ignorant maroon on the subject of the Cambrian) and Stephen Meyer, the philosopher-creationist with his own book on molecular biology (hah!) to peddle, there to lecture at the opening. I guess any clown can rent the integrity of the U of Oklahoma for a day.”

“Although the museum does not support unscientific views masquerading as science, such as those espoused by the Discovery Institute, the museum does respect the religious beliefs of all people. Moreover, the museum is obligated to rent its public space to any organization that is engaged in lawful activities, free speech and open discourse. The museum does not discriminate against recognized campus organizations based on their religious beliefs, political philosophy, scientific literacy, or any other factors.”

On September 18, Smith applauded Mares’s letter, the extension of the museum’s hours, and Westrop’s planned lecture. She wrote:

“If you live in the OKC [Oklahoma City] area, you’ve got a problem. Sure, you want to go see the TARD [short for retard] parade at the Sam Noble Museum of Natural History, you can always count on Creationists for a good time. But the problem is, Wells and Meyer are incredibly stupid. While recreational exposure to Creationists can induce euphoria and irrepressible giggles… long-term exposure to pure TARD from DI [Discovery Institute] fellows can cause seemingly irreversible brain damage.” Smith also announced that she would “be around, completely uninvited,” at the showing of the film. “I’ll even talk to Johnny Wells about HIV-1 evolution, since he thinks neither of my research topics exists.”

A few days later, Oklahoma Daily columnist Jelani Sims criticized Mares’s letter on the grounds that it “assumes that those presenting the documentary and supporting it must be religious, have conservative political views and lack scientific literacy, while disguising the museum’s malicious shot at those people and groups as tolerance.” According to Jelani,

“the museum should not have opposed the event in this way. Rather than hijacking the night of the documentary presentation with an opposing seminar and free extra hours of operation, it should have let the event stand on its own. And, rather than releasing a statement of vehement opposition, thinly veiled in tolerance, it should have said nothing.
OU and the surrounding halls of learning and education should be places of academic freedom and the open exploration of ideas. Instead of fostering and working toward this ideal, the Sam Noble Oklahoma Museum of Natural History has chosen to align itself with the many mean-hearted voices that wish no one would hear any alternative outside of evolution.”

The ensuing Q&A was surprisingly friendly, with the exception of one man who insisted that most human DNA is junk and who persisted in this claim even after Steve pointed out that recently published scientific research shows that most so-called “junk DNA” is not junk at all. Abbie Smith was there, but she spent the entire time blogging on her laptop. Her entries included the following:

7.10 -- Meyer is clueless on origin of life and Darwin.

7.27 -- 'Origin of information in DNA'. HAHAHA I made all the mathematicians facepalm [place their hands over their eyes and shake their heads].

7.40 -- Bored. Now watching porn.

On September 29, The Norman Transcript announced the 5 PM lecture by Professor Westrop and the 7 PM showing of Darwin’s Dilemma. The article mentioned Steve’s position that the pairing of events was good because it allowed for students to get two views. “I think it’s great that students will be party to that,” Steve said. “That’s what an academic experience is all about.”

I attended the lecture by Professor Westrop, which was informative and entertaining. Westrop began by saying that the Cambrian explosion was no dilemma for Darwin. Indeed, if Darwin knew what we now know he would have celebrated the fossil record and written about it at length. Westrop disputed the idea that most of the animal body plans (“phyla”) emerged “almost overnight” in the Cambrian. Instead, he argued that they began to emerge much earlier, in the pre-Cambrian period known as the Ediacaran. He mentioned trace fossils (signs of worm burrows) and the “small shelly fauna” that are older than the two most famous sites for Cambrian explosion fossils, the Burgess Shale in Canada and the Chengjiang beds in China—both of which show exceptional preservation of even the soft parts of early animals.

Professor Westrop mentioned pre-Cambrian sponges and the fossil Kimberella, which most paleontologists think was an early mollusc. He went further, however, and claimed that the Ediacaran fossils Vernanimalcula, Parvancorina, and Arkarua were early bilaterians (bilaterally symmetrical animals), arthropods (the phylum that includes crabs and insects) and echinoderms (the phylum that includes sea urchins and starfish), respectively. This would push back the beginning of the Cambrian explosion and make its duration 40 million years instead of the 5-10 million years mentioned in Darwin’s Dilemma. (Steve later addressed this in the Q&A after the film; see below.)

Professor Westrop suggested that the explosion might have been due to an increase in atmospheric oxygen and/or the opening of ecological niches by a mass extinction event at the end of the pre-Cambrian. (I thought to myself that increased oxygen and new ecological niches may have been necessary for the Cambrian explosion, but they were far from sufficient. New body plans need new information, not just air and space.) Westrop concluded by taking exception to J.B.S. Haldane’s claim that finding a fossil rabbit in the pre-Cambrian would prove Darwin’s theory wrong. If such a fossil were found, Westrop said, paleontologists would simply revise their reconstruction of the history of life.

During the Q&A, one student asked him whether any fossil find could falsify Darwin’s theory, and Professor Westrop said “No,” since Darwin’s theory is really about natural selection, which operates on a much shorter time scale than the fossil record. Another student asked him whether he had seen the movie Darwin’s Dilemma; he said he hadn’t, but his lecture was not intended to be a response to the movie.

During the lecture I caught several people glaring at me; the tension was palpable. After Westrop’s lecture I toured the museum exhibit on evolution and the Cambrian explosion. It seemed factually accurate for the most part, emphasizing (among other things) that many of the Cambrian explosion fossils were soft-bodied—which puts the lie to the common explanation that their precursors are absent from the fossil record because they lacked hard parts. The exhibit also made it clear that the Ediacaran fossils went extinct at the end of the pre-Cambrian, so (with a few possible exceptions) they could not have been ancestral to the Cambrian phyla.

One particular panel in the exhibit caught my attention. It showed over a dozen of the Cambrian phyla at the top of a branching tree with a single trunk, but none of the branch points corresponded to a real living thing. Instead, the branch points were artificial technical categories such as “Ecdysozoa,” “Lophotrochozoa,” “Deuterostomia,” and “Bilateria.” The artificiality of the branch-points emphasized that the branching-tree pattern imposed on the fossil evidence was itself an artificial construct.

By 7 PM the auditorium was filled to standing-room-only capacity with about 200 people. During the film Steve and I waited outside; we came in for the Q&A as the film was ending and the audience was applauding enthusiastically.

Steve led off with a short statement explaining that we were not challenging the facts, but only the Darwinian interpretation of them. He acknowledged that there are disagreements over the duration of the Cambrian explosion—even among Darwinian paleontologists—but the real issue is the origin of information. Even if the Cambrian explosion had lasted 40 million years, as Westrop had claimed, there would not have been enough time for unguided processes to produce the enormous amount of specified complexity in the DNA of the animal phyla. Then Steve opened the floor to questions, as the moderator walked around the room with a hand-held microphone.

The first “question” came from Victor Hutchison of the OESE, who claimed that the filmmakers had deceived Simon Conway Morris and James Valentine into granting interviews that were now 9-10 years old. Steve responded that he had had tea with Simon just a few months earlier, and although Conway Morris was not a supporter of intelligent design (nor did the film make him out to be), his views on the Cambrian explosion were accurately portrayed in the film. Steve said he had not spoken with Valentine recently, and that the latter had every right to distance himself from the views promoted by the film; but both Conway Morris and Valentine had signed releases and accepted payment for their participation. (In fact, Illustra Media interviewed Conway Morris and Valentine for this project in October and November of 2006—less than three years ago. Both Morris and Valentine knew they were being interviewed by Illustra Media, which was well known for having previously produced two pro-intelligent design films, Unlocking the Mystery of Life and The Privileged Planet. They were not deceived in any way.)

The second question came from a man who was concerned that the film said nothing about the role of viruses in changing DNA. The retrovirus-derived gene PEG10, he argued, explains how mammals evolved placentas millions of years ago. I replied that biologists can establish that certain genes are necessary in the formation of specific organs, but they have never established that genes alone—much less any one gene—can account for any organ. Indeed, I pointed out, we can (and have) mutated the genes of fruit fly embryos in every possible way, and there are only three known outcomes: a normal fruit fly, a defective fruit fly, or a dead fruit fly. Not even a new species, much less a new organ. So the fact that PEG10 may be necessary for the development of a placenta does not justify the claim that a retrovirus caused the evolution of the first placenta. The questioner persisted, pointing out that PEG10 is widespread among mammals (which is irrelevant to whether it caused the origin of placentas), and when the moderator moved to another person the questioner got up and stalked out of the room with his hands in the air.

The next person—apparently a professor of developmental biology—objected that the film ignored facts showing the unity of life, especially the universality of the genetic code, the remarkable similarity of about 500 housekeeping genes in all living things, the role of HOX genes in building animal body plans, and the similarity of HOX genes in all animal phyla, including sponges. Steve began by pointing out that the genetic code is not universal, but the questioner loudly complained that he was not answering her questions. I stepped up and pointed out that housekeeping genes are similar in all living things because without them life is not possible. I acknowledged that HOX gene mutations can be quite dramatic (causing a fly to sprout legs from its head in place of antennae, for example), but HOX genes become active midway through development, long after the body plan is already established. They are also remarkably non-specific; for example, if a fly lacks a particular HOX gene and a comparable mouse HOX gene is inserted in its place, the fly develops normal fly parts, not mouse parts. Furthermore, the similarity of HOX genes in so many animal phyla is actually a problem for neo-Darwinism: If evolutionary changes in body plans are due to changes in genes, and flies have HOX genes similar to those in a horse, why is a fly not a horse? Finally, the presence of HOX genes in sponges (which, everyone agrees, appeared in the pre-Cambrian) still leaves unanswered the question of how such complex specified genes evolved in the first place.

The questioner became agitated and shouted out something to the effect that HOX gene duplication explained the increase in information needed for the diversification of animal body plans. I replied that duplicating a gene doesn’t increase information content any more than photocopying a paper increases its information content. She obviously wanted to continue the argument, but the moderator took the microphone to someone else.

The next questioner suggested the film might have been better if it had included some Darwinists skeptical of its conclusions. (I learned later that the producer/director had invited several such critics to be interviewed, but they had declined.) Steve agreed that the film might have been better if it had done that. I chimed in that there seemed little need for the producer to pay for such views when the University of Oklahoma was spending so much public money to provide them. (I wished later I had said that if OU were doing its job it would be providing students with both sides of the story in the first place, and there would have been no need to make the film.)

Someone asked why the film refers to “designers” in the plural. Steve answered that this merely followed from the application of Lyell’s explanatory method of inferring past causes from those known to produce comparable effects in the present. We can infer the need for intelligence, but single or multiple designers could be responsible. In response to another questioner who noted that the film apparently assumes the standard geological time scale, Steve said that both he and I hold to the antiquity of the Earth.

An emeritus professor of immunology pointed out that the immune system is essentially the same in all vertebrates, but the supposedly primitive lamprey has a completely different immune system. He regarded this as evidence of a molecular explosion comparable to the Cambrian explosion that also pointed to design.

Then someone suggested that there is a fundamental distinction between the time organisms first arise and when they appear in the fossil record. He said there is abundant fossil and molecular evidence that many animal body plans arose before the Cambrian. I pointed out that three of the pre-Cambrian fossils cited by Professor Westrop as precursors to Cambrian animals were disputed by other paleontologists. According to Stefan Bengtson and Graham Budd, the bilaterian interpretation of Vernanimalcula is “not well-founded” but an “artifact” of changes in the organism after death and changes in the sediment after deposition. [Bengtson, S. & G. Budd, “Comment on ‘Small Bilaterian Fossils from 40 to 55 Million Years Before the Cambrian’,” Science 306 (2004): 1291a.] According to James Valentine, Parvancorina is not “convincing” as an arthropod ancestor; it lacks a head, jointed limbs, compound eyes and antennae. Also according to Valentine, without more shared features with echinoderms the relationship of Arkarua “remains uncertain.” [Valentine, J.W., On the Origin of Phyla (Chicago: The University of Chicago Press, 2004), pp. 287, 397.]

I then pointed out that molecular evidence comes entirely from modern organisms; no biomolecules have been recovered from Cambrian fossils. The molecular data are fed into a computer that has been programmed to generate a branching-tree pattern; the computer is not given the option of concluding that the organisms may not share a common ancestor. Even then, different molecules—or the same molecule analyzed by different labs—can give different trees. So molecular phylogeny is riddled with inconsistencies, and when applied to the Cambrian phyla it is speculative at best.

Finally, someone mentioned Thomas Kuhn’s book The Structure of Scientific Revolutions, and asked whether the current controversy over Darwinism and intelligent design fits Kuhn’s description. Steve answered that in many respects it does—not only in the way the Darwinian scientific establishment is using all means at its disposal to suppress the new theory of intelligent design, but also in the way the very definition of science has become part of the controversy.

The formal Q&A ended, but many people came up afterwards to continue the conversation. Both we and the organizers—the courageous students of the OU Intelligent Design and Evolution Awareness (IDEA) Club—were pleased with the outcome. As IDEA Club secretary Trevor Clark wrote in the student newspaper on October 1, “One of the most spectacular features of these events was the broad spectrum of people who attended. I am thrilled that so many people with different viewpoints could converge to join a discussion about intelligent design.”

Darwinist blogger P.Z. Myers, who had scolded the museum for letting us show the film, did not come all the way from the University of Minnesota, Morris, to attend. Yet he wrote afterwards about Steve’s September 28 lecture:

“I knew ahead of time exactly what it was going to be: complexity, complexity, complexity, complexity, complexity, complexity, complexity, therefore, DESIGN. It doesn't follow. The logic is nonexistent. It's the kind of thing you'd expect a competent person with a Ph.D. in philosophy to recognize, but no, it's the same ol' thing, trotted out every time they get up to speak.”

That’s why Steve Meyer devoted an entire chapter to it in his book. In fact, it’s the chapter from which the book takes its name (Signature in the Cell HarperOne, 2009, Chapter 4.). If Myers had bothered to read Steve’s book, he would have known this. Indeed, you’d expect that a competent person with a Ph.D. who’s paid by the taxpayers of Minnesota to teach their children would read a book before ridiculing it. But no, it’s the same ol’ thing, trotted out every time Myers blogs on the subject.

Oh, and porn-watcher Abbie Smith was a no-show. In a blog post the day after Darwin’s Dilemma showed, she called Steve a stupid idiot, and gave as her reasons for not coming (1) “I’d be trapped in a theater!” and (2) “I got no response to my debate request re: Wells HIV/Evolution Denial... I just don’t understand why ID Creationists don’t want to debate me.”

A debate about HIV? I don’t know what relevance HIV has to the Cambrian explosion, and I didn’t receive any “request” to debate it, but I would have been willing to discuss the matter with Smith if she had had the guts to show her face.

So our landing at Norman was a success. Despite all their taxpayer-funded professors and museum exhibits, despite all their threats to dismantle us and expose us as retards, the Darwinists lost. We’re now moving inland, and the end of the war may be coming into view.

Posted by Jonathan Wells at 12:13 PM | Permalink | TrackBacks (0)

The missing link presently being touted in the media, Ardipithecus ramidus, has had more reconstructive surgery than Michael Jackson. Assuming that their "extensive digital reconstruction" of its "badly crushed and distorted bones" is accurate, what does A. ramidus (or “Ardi” as the fawning media is affectionately calling it) really show us that we didn’t already know? We already knew of upright walking / tree-climbing, small-brained hominids—that’s what Lucy, an australopithecine, was. We already knew that there were australopithecine fossils dating back to before 4 million years, and this fossil is only a little bit older. So what does this fossil teach us? Assuming all the reconstructions of Ardi's crushed bones are objective and accurate, this fossil teaches us at least one very important thing: prevailing evolutionary explanations about how upright walking supposedly evolved in humans, confidently taught in countless college-level anthropology classes, were basically wrong.

In particular, A. ramidus casts doubt on the long-repeated hypothesis that humans evolved upright walking on the African Savannah where taller creatures had an advantage to see over tall grass by walking upright. A. ramidus walked upright in a “grassy woodland with patches of denser forest.” Time magazine’s article on A. ramidus explains the implications:

This tableau demolishes one aspect of what had been conventional evolutionary wisdom. Paleoanthropologists once thought that what got our ancestors walking on two legs in the first place was a change in climate that transformed African forest into savanna. In such an environment, goes the reasoning, upright-standing primates would have had the advantage over knuckle walkers because they could see over tall grasses to find food and avoid predators. The fact that Lucy's species sometimes lived in a more wooded environment began to undermine that theory. The fact that Ardi walked upright in a similar environment many hundreds of thousands of years earlier makes it clear that there must have been another reason.

(Michael D. Lemonick and Andrea Dorfman, "Excavating Ardi: A New Piece for the Puzzle of Human Evolution," Time Magazine (October 1, 2009).)

There is one other option: A. ramidus wasn't bipedal. In fact, one Science article is reporting some serious scientific skepticism about A. ramidus being bipedal:

However, several researchers aren’t so sure about these inferences. Some are skeptical that the crushed pelvis really shows the anatomical details needed to demonstrate bipedality. The pelvis is “suggestive” of bipedality but not conclusive, says paleoanthropologist Carol Ward of the University of Missouri, Columbia. Also, Ar. ramidus “does not appear to have had its knee placed over the ankle, which means that when walking bipedally, it would have had to shift its weight to the side,” she says. Paleoanthropologist William Jungers of Stony Brook University in New York state is also not sure that the skeleton was bipedal. “Believe me, it’s a unique form of bipedalism,” he says. “The postcranium alone would not unequivocally signal hominin status, in my opinion.” Paleoanthropologist Bernard Wood of George Washington University in Washington, D.C., agrees. Looking at the skeleton as a whole, he says, “I think the head is consistent with it being a hominin, … but the rest of the body is much more questionable.”

(Ann Gibbons, "A New Kind of Ancestor: Ardipithecus Unveiled," Science, Vol. 326:36-40 (Oct. 2, 2009).)

Mr. Johanson, founding director of the university's Institute of Human Origins ... said, he expected the team's initial interpretations "will undoubtedly generate widespread debate," perhaps even including the question of whether Ardi is actually a human ancestor. Mr. Johanson said he was not among those who would raise that question. But, he said, "there must have been very rapid evolutionary change" for the human form to transform so quickly from Ardi to Lucy.

So what do we have with “Ardi”? We have an extremely crushed “Irish stew” fossil that has undergone extensive reconstruction in order to become part of a PR campaign to make bold claims of ancestral status to the human line, even though at base its qualities are very similar to previously known fossils, and there's a lot of skepticism about the claims being made. In other words, we have the typical media circus that we find every time a new "missing link" is found.

Posted by Casey Luskin at 8:35 AM | Permalink | TrackBacks (0)

Another new alleged missing link has been found, if you consider something discovered in the early 1990’s new. This fossil seems to have spent almost as much time under the microscope at Berkeley as it did in the ground in Ethiopia, when it was first buried about 4.4 million years ago.

Why did it take over 15 years for the reports on this fossil to finally be published, besides the fact that it allowed more time for planning the now-customary PR campaign? A 2002 article in Science explains exactly why: the bones were so brittle, “squished,” “chalky” and “erod[ed]” when cleaned such that many of the bone fragments had to be “reconstruct[ed]”—and that took a long time. Here’s the story from more than seven years ago:

[I]n 1992, the Middle Awash Research Team, co-led by [Tim] White, made a discovery that ended Lucy’s reign. About 75 kilometers south of Lucy’s resting place, at Aramis in the Afar depression of Ethiopia, the team found fossils of a chimp-sized ape dated to about 4.4 million years ago. … The team named this species Ardipithecus ramidus, drawing on two words from the Afar language suggesting that it was humanity’s root species. But skeptics argue that the published fossils are so chimplike that they may represent the long-lost ancestor of the chimp, not human, lineage.

The next field season, team member Yohannes Haile-Selassie found the first of more than 100 fragments that make up about half of a single skeleton of this species, including a pelvis, leg, ankle and foot bones, wrist and hand bones, a lower jaw with teeth—and a skull. But in the past 8 years no details have been published on this skeleton. Why the delay? In part because the bones are so soft and crushed that preparing them requires a Herculean effort, says White. The skull is “squished,” he says, “and the bone is so chalky that when I clean an edge it erodes, so I have to mold every one of the broken pieces to reconstruct it.” The team hopes to publish in a year or so, and White claims that the skeleton is worth the wait, calling it a “phenomenal individual” that will be the “Rosetta stone for understanding bipedalism.”

(Ann Gibbons, “In Search of the First Hominids,” Science, 295:1214-1219 (February 15, 2002).)

One problem is that some portions of Ardi's skeleton were found crushed nearly to smithereens and needed extensive digital reconstruction. "Tim [White] showed me pictures of the pelvis in the ground, and it looked like an Irish stew," says Walker. Indeed, looking at the evidence, different paleoanthropologists may have different interpretations of how Ardi moved or what she reveals about the last common ancestor of humans and chimps.

(Michael D. Lemonick and Andrea Dorfman, "Excavating Ardi: A New Piece for the Puzzle of Human Evolution," Time Magazine (October 1, 2009).)

But the team’s excitement was tempered by the skeleton’s terrible condition. The bones literally crumbled when touched. White called it road kill. And parts of the skeleton had been trampled and scattered into more than 100 fragments; the skull was crushed to 4 centimeters in height.

(Ann Gibbons, "A New Kind of Ancestor: Ardipithecus Unveiled," Science, Vol. 326:36-40 (Oct. 2, 2009).)

After Ardi died, her remains apparently were trampled down into mud by hippos and other passing herbivores. Millions of years later, erosion brought the badly crushed and distorted bones back to the surface. They were so fragile they would turn to dust at a touch.

Claims of bipedalism often depend upon precise measurements of the angles of key bones such as the pelvis, femur, and knee-bones. But if these bones were discovered in such a crushed, squished, etc. form, determining the precise contours of these bones might become a highly subjective exercise. I’m sure they spent a lot of time on their reconstructions (and it certainly sounds like they did) but at the end of the day, it’s difficult to make solid claims about extremely unsolid bones.

Anyone for some Irish stew?

Posted by Casey Luskin at 3:41 PM | Permalink | TrackBacks (1)

Seeking relief from the demands of geschaeft, The Washington Times reported recently, senior officials at the National Science Foundation routinely spend a great deal of their time (and our money) visiting pornographic sites on the Internet.

Just possibly, I suspect, they spend all of their time on stress relief and none on the public's business, stress relief so striking as to cancel its cause entirely.

"The problems at the National Science Foundation (NSF) were so pervasive," the Times reported, "they swamped the agency's inspector general and forced the internal watchdog to cut back on its primary mission of investigating grant fraud and recovering misspent tax dollars."

These are points that might be kept in mind the next time senior members of the scientific establishment appear in public, their begging bowl clasped firmly in hand, and a suppliant froth just crusting on their lips.

They are points to keep in mind, as well, the next time the NSF issues some solemn and idiotic diktat about Darwin's theory of evolution and its enthusiastic endorsement by the scientific community.

A scientific mandarin may spend his time wandering around the Internet corridors of Sophie's House of Pleasure, or he may spend his time trying to think of something intelligent to say.

It is remarkably difficult to do both.

Posted by David Berlinski at 11:17 AM | Permalink | TrackBacks (0)

The Los Angeles premiere of Illustra Media's new science documentary Darwin's Dilemma: The Mystery of the Cambrian Fossil Record will be held on Sunday, October 25th in the IMAX theater of the prestigious California Science Center, which describes itself as "the West Coast's largest hands-on science center." Sponsored by the American Freedom Alliance, the premiere starts at 7:00 pm and will also include a showing of the IMAX film Born of the Stars as well as a post-screening discussion of Darwin's Dilemma featuring the film's director Lad Allen; David Berlinski, author of The Devil's Delusion: Atheism and Its Scientific Pretensions; and biologist Jonathan Wells, author of The Politically Incorrect Guide to Darwinism and Intelligent Design.

For tickets or more information, call the American Freedom Alliance office at (310) 444-3085 or visit the group's website here.

Darwin’s Dilemma explores one of the great mysteries in the history of life: the geologically-sudden appearance of dozens of major complex animal types in the fossil record without any trace of the gradual transitional steps Charles Darwin had predicted. Frequently described as “the Cambrian Explosion,” the development of these new animal types required a massive increase in genetic information. “The big question that the Cambrian Explosion poses is where does all that new information come from?” says Dr. Stephen Meyer, a featured expert in the documentary and author of the book Signature in the Cell: DNA and the Evidence for Intelligent Design.

The film previously had regional premieres at the Seattle Art Museum in August and at the Sam Noble Oklahoma Museum of Natural History earlier this week.

Posted by John West at 10:05 AM | Permalink | TrackBacks (0)