This Sunday, May 30, Wilberforce Forum will feature a special online radio program featuring Dr. Stephen C. Meyer, Director and Senior Fellow of the Center for Science and Culture. He'll be discussing his new book, Signature in the Cell: DNA and the Evidence for Intelligent Design, demonstrating that the digital code embedded in DNA points to a designing intelligence and brings into focus an issue that Darwin did not address.

Go to http://www.blogtalkradio.com/wilberforceforum at 6 pm EST, 3 pm PST this Sunday to listen, and ask Dr. Meyer a question by calling in or by posting in the conference forum online.

Posted by Anika Smith at 7:00 AM | Permalink | TrackBacks (0)

(Cue music.) Or, rather, a lemur. Almost every TV channel it seems ran a commercial announcing a documentary about the fossil find of the century, The Link, which will be encored on the History Channel tonight. “Ida,” as the female holotype of Darwinius masillae has been playfully dubbed, is the prehistoric prosimian that is the focus of attention. The story of her discovery is the stuff of every good science-fiction B-movie from the 1950s : A “secret study” conducted by an “international team of scientists,” has led to earth-shattering results that can only now be revealed to the world. Think Creature from the Black Lagoon (because of the fossil find) meets When Worlds Collide (because of the impact that will be felt on your everyday life) and you’ll be close to the stated importance of the program. All that’s missing are some Tesla coils, a hidden lair in a dead volcano, the fallout from an atomic explosion, and a UFO landing on the National Mall. Presumably such extra features, along with more specifics about the significance of her all too brief life — “a child when she died, but she’ll change history forever” — can be gathered from the just-released book, The Link.

It’s just a jump to the left…

Of the cladogram, I mean. There is one clade of primates called the Strepsirrhini (“wet noses”) that includes the lemurs, the dwarf and mouse-lemurs, the Aye-aye, the lorisids, and the galagos. Ida falls within this suborder according to one hypothesis.

With your hands on your hips…

You will kindly note the other clade of primates termed the Haplorrhini, the sister group of the strepsirrhines. This taxon of the “dry noses” contains the apes, monkeys, and tarsiers. An alternative phylogenetic hypothesis would place Darwinius at the base of this assemblage.

All the brouhaha thus boils down to whether Ida had a wet nose or a dry nose that — given her status as a transitional form — was occasionally runny. The theme of The Link is that the latter is a sure bet. For myself, regarding these two alternative evolutionary scenarios, I say…Let’s do the Time Warp again…

Anyhow, there I sat yesterday evening, with voyeuristic intention no less, my gin and tonic prepared and my lit cigarette firmly affixed in its black holder, shivering with antici……pation. For, indeed, I wanted to go up to the lab in order to see what’s on that slab. But it wasn’t the rain that was to blame for my later symptoms of underwhelment. No. It was that after all the commercial hoopla, I expected to hear a speech close to that given by the indefatigable Dr. Furter (Tim Curry) just prior to the dramatic vivification of his creature. That is, my expectation was to see and listen to a pronouncement much like this:

Tonight my conventional unconventionalists, you are to witness a new breakthrough in phylogenetic research and career paradise…is to be mine!

It was strange the way it happened. Suddenly you get a break…All the pieces seem to fit into place. What a sucker you’ve been…what a fool. The answer was there all the time [on the fossil market, that is]. It took a small accident to find it…an accident! And that’s how I discovered the secret, that elusive ingredient, that spark…that is The Link. Yes. I have that knowledge. I hold the secret…to evolution itself!

My interest of course did not concern who actually said it. Or that he would be wearing a tee shirt and jeans as opposed to a green surgical smock over a corset and fishnets (and adorned with oversized pearls). Not at all. What I instead wanted to view was a program where the could-be’s and perhapses, the equivocations and qualifications, the oh so many “well, on the one hand…but, then again, on the other” semantic hedges, that are de rigueur in documentaries about evolution, had been dropped with an unabashed flair.

Is it not The Link? Does it not change everything? I asked.

Obviously, as no doubt anyone of you could have told me, my expectations were misplaced. Part of me also desired to see an animation of Ida throw a bone into the air and then have the scene immediately segue to that of a futuristic Pan Am spacejet on its way to an orbiting station called "Darwin 9000," set to the opening strains of Johann Strauss II’s "On the Beautiful Blue Danube." I was mentally blending genres in my hopes, true, but in my defense the commercial had promised so very much.

Alas, the disappointment that soon arose in me after the documentary stemmed from the vagueness of it all…that The Link is actually a kind of, sort of, n^th cousin m^th removed of the side lineage that some hypothesize possibly gave rise to the distant ancestors of what quite conceivably became the hominid branch of the Darwinian tree. And to think that I could have been watching reruns of Mystery Science Theatre 3000 or the cult classic, The Phantom of the Paradise.

To be certain, the authors of the PLoS One paper were appropriately circumspect in their paper, so one should not misconstrue my peeve as really being about the finer details of basal primate taxonomy. As far as I’m concerned, Ida may well be the transitional taxon linking the Strepsirrhini and Haplorrhini. Fine. Who is going to get strung out — to again borrow a phrase from the illustrious Dr. Furter — if the Notharctidae and Cercamoniinae are rendered by implication paraphyletic, wastebasket taxonomic groupings? Who? Nor is there a limit to such theoretical gratuity…should someone even want to posit that each and every genus in the Cercamoniinae, from Anchomomys to Darwinius to Pronycticebus, is in its own right a missing link — the same way, you know, that everyone’s special — no complaint will be uttered from this quarter. Not so much as a peep.

Irksome, though, was the way in which an old story was sold as something profoundly novel. While watching it, I could almost hear the creator of this work of science fiction (defined by that definitive fount of knowledge Wikipedia as “science-based depictions of phenomena that aren't necessarily accepted by mainstream science,” emphases mine) singing as the fossil was presented: In just seven days…I can make you a humaaaannnnnn. (My sincerest apologies to Richard O’Brien of the Rocky Horror Picture Show^R for the way I have twisted his lines and songs from the film.) But the issue is that a familiar feeling emerged while watching the piece, the one we have all had in the theater. It arises the moment you realize that you know the plot, the narrative. The only difference is that the characters and the actors playing them have changed, along with the music and the CGI effects. Eight years ago it was the Urwhale. Last year it was the Ursalamander. Last night it was the Urmonkey. Still, the same story…

That said, I would not have been so underwhelmed had someone just blurted out in the first few minutes — like the inimitable Charles Gray does at the end of Rocky Horror — the central theme of the documentary, that “crawling…on the planet’s face…some insects called the human race. Lost in time…lost in space…and meaning.”

^R(Rated R) — For mature audiences only.

Posted by Richard Sternberg at 3:40 PM | Permalink | TrackBacks (0)

Editor's Note: This is crossposted at Professor Scot McKnight's Beliefnet blog, Jesus Creed.

In his article “Five Streams of the Emerging Church,” Scot McKnight identifies with Eddie Gibbs and Ryan Bolger’s description of emerging Christians. One of the nine hallmarks of such Christians, according to the authors, is that they “create as created beings.” And it is this theme I would like to explore with reference to Darwinian evolution and intelligent design (ID) in a series of three posts. First, we will consider how to consider ID. Second, we’ll assess conceptions of God in this debate. And third, we will reflect upon aesthetics and Darwinian theory.

What to make of intelligent design?

Years ago, before I had heard of Neil Postman, before I had given much thought to the role pictures play in our mental life, I read Edward Larson’s Pulitzer Prize-winning Summer for the Gods. Upon putting it down, I was struck by one simple fact: Everything I thought I knew about The Scopes Monkey Trial of 1925 ‘just ain’t so.’

With reflection, the disturbing fact emerged that

I had absorbed the black-and-white images of “Inherit the Wind.” Sure, I knew it was a play. Yet apparently the part of my brain overseeing history is not divorced from the part processing art. Plato was right. Art can be dangerous, for it provides a window into the soul.

The same cautionary tale applies to the Christian in the case of ID. We had better be careful that we assess facts, evidence, and narrative carefully rather than absorbing the assessments of our secular peers by osmosis.

It is impossible for the thinking Christian to put down all the invisible cultural baggage he carries—both Christian and secular narratives—in order to consider ID’s claims on their own terms. But we can try to clear confusion. So let’s start with what ID is and is not. Contrary to popular assumptions, ID is not Biblical creationism. It does not get into the recesses of Old Testament exegesis, nor is it meant to reveal the full nature of God.

ID is more modest, asking a simple question: When all of the scientific (not religious) evidence is put on the table, are certain features of nature better explained by an intelligent cause or by unintelligent causes like natural selection?

Now where does the artist fit in? Well, let’s put down our culture war armor for a moment. Let’s drop the usual visuals. We are not dealing with men in white lab coats versus backwoods basement Bible-thumpers. My friends in the ID movement have doctorates from Cambridge, The University of Chicago, University of Pennsylvania, CalTech, etc. They’ve done post-docs at Columbia, Harvard, and other major institutions. So let us re-imagine the narrative for a minute, wipe away the horizion, you and me.

Let us see the ID theorist the way we see an art historian at the Smithsonian who has just received a heretofore lost and unsigned Renaissance masterpiece. She must do some detective work. Are there not systematic and scientific ways for the art historian to learn about the cause(s) of this painting?

I propose that this is the way we should view the ID theorist. Returning to nature, in this view we see the ID theorist looking for positive signs of intelligent design and running tests to see if mere material causes are adequate to explain the artifact. In the case of the painting, material causes will never be adequate. Perhaps nature is like this, too. We should not judge this a priori. This is not a question of proving God’s existence or of Biblical fundamentalism. This is about what sorts of causes are necessary to explain certain features of nature. The emerging Christian knows God is the ultimate author of nature, so perhaps this will be scientifically detectable, or perhaps it will not. We should encourage scientists to find out.

The sensitive-souled Christian will not let the Scopes narrative—and the charge that consideration of design in nature is somehow anti-intellectual—get in the way this legitimate pursuit for the causes of natural phenomena.

Posted by Logan Gage at 1:41 PM | Permalink | TrackBacks (0)

Editor's Note: This is crossposted at David Klinghoffer's Beliefnet blog, Kingdom of Priests.

A pair of dueling websites, one that just went live, are engaged in an important argument over whether religious believers should continue to be fed the "opium of the people." That's the famous phrase Marx Karl used to deride all of religion. One kind of faith actually deserves the description, however. It's called theistic evolution, a convoluted justification for thinking that belief in God and belief in Darwin's mechanism of blind, churning, unguided, and purposeless evolution can be meaningfully reconciled.

The new website is Faith and Evolution, from the Discovery Institute's Center for Science and Culture. It features all kinds of resources -- writing and video, debates, questions and answers, and much else, including a number of contributions from yours truly. Do check it out and let me know what you think.

Faith and Evolution presents a striking contrast with Dr. Francis Collins's theistic evolution site BioLogos, courtesy of the Templeton Foundation. Dr. Collins and his associate Karl Giberson also blog here at Beliefnet. At F&E, you'll find my analysis of Dr. Collins's ideas on religion and evolution. One very useful thing about F&E is that it highlights debates both on the science of evolution and on the social impact of Darwinism, whereas BioLogos is more like a single-perspective sermon.

Collins and Giberson are sincere Evangelical Christians -- as far as I, a Jew, can tell -- and undoubtedly innocent of all guile, but they represent an insidious trend in religious and intellectual life. This genuine opiate of the masses works as a stupor-inducing fog, enveloping the debate about intelligent design versus Darwinism. The fog lulls you with the thought that between the idea of design in nature, and that of no design in nature, there is actually no need to make a choice.

The human genome, for example, is written in the "language of God," as Dr. Collins wrote in the title of his bestselling book. Yet the genome is riddled with "Junk DNA" just as you'd expect from the product of a Darwinian process, driven by randomness and guided by no design or intelligence. Language of God? Language of Junk? Both are right! School's out! Everybody celebrate!

Not only is this theologically, intellectually and scientifically vacuous — actually, that wouldn't be so bad — it would not qualify as insidious. What does qualify is the way this fog-generating machine of theistic evolution, its influence spread by the media, has given to countless otherwise thoughtful people intellectual permission to turn off part of their brains, lowering their defenses. This is just what the Darwin Lobby needs, people of faith complacently casting their vote for a cultural force that undermines faith. Lenin is said to have called such people "useful idiots." He was not a very nice person.

You see the effect most poignantly in religiously and politically conservative circles. Conservatives should be the first to grasp that "ideas have consequences," as Richard Weaver put it. Darwinism's corrosive effects on faith, on belief in human dignity and the sacredness of human life; the sinister way Darwin's theory has had of inspiring social movements of organized evil -- these are solid reasons to go back and look again critically at the science. Does natural selection operating on random mutations really explain the history of life without the need for a guiding spiritual force outside nature? Did the software in the cell, DNA, really write itself?

For many of us who should know better, it's easier, whether intellectually, socially, or both, not to come too close to the edge of the sacred mountain of Darwinism.

My image is from Exodus 19, which Jews will be reading in synagogue tomorrow for the festival of Shavuot, or Pentecost. When God gave the 10 Commandments to Moses at Mt. Sinai, he warned that the people should "Beware of ascending the mountain or touching its edge; whoever touches the mountain shall surely die" (v. 12).

"Descend, warn the people, lest they break through to the Lord to see, and a multitude of them will fall. Even the priests who approach the Lord should be prepared, lest the Lord burst forth against them" (v. 21).

This was on the third day of the Israelites' preparation for receiving the Sinai revelation, when "there was thunder and lightning and a heavy cloud on the mountain" (v. 16).

Something of this same sacred awe surrounds Mt. Darwin, its holy peak lost in cloud and fog. People are afraid to violate its borders to see, lest the prestige of the Darwinian idea burst forth against them, and a multitude will feel socially humiliated at being associated with the phantom menace: "creationism."

I invite you to investigate for yourself. Faith and Evolution provides some very apt and accessible resources. Contrary to myth, this mountain may be ascended, the fog dispersed.

Posted by David Klinghoffer at 4:25 PM | Permalink | TrackBacks (0)

A Wall Street Journal (WSJ) article from last month, “Education Board in Texas Faces Curbs,” revealed how the Texas evolution-lobby has been seeking to use both censorship and power grabs to promote their agenda.  First, they sought to censor from Texas students any instruction on scientific weaknesses in evolution. Having lost that fight before the Texas State Board of Education (TSBOE), they have tried to use other tactics to punish the board for adopting science standards that teach evolution objectively, or to grab power away from the democratically elected board. 

In a move that can only be attributed to political retribution, today Texas evolutionists successfully blocked the reappointment of Dr. Don McLeroy as chair of the TSBOE.  Practically speaking, this move will change little, as it is almost guaranteed that a like-minded conservative will be appointed in McLeroy’s place to chair the TSBOE.  The travesty here is that, to my knowledge, no one has put forth any legitimate charges that McLeroy was not fair-minded in how he chaired TSBOE meetings.  If this move will have little practical impact and Dr. McLeroy is a competent chair, why did the Texas evolution lobby push so hard for this ephemeral and pyrrhic media victory? The answer is simple: it's political retribution from evolutionists who like to expel people whose politics don’t advance their pro-Darwin-only agenda. 

The attack on McLeroy hasn’t been the only power-grab sought by the Texas evolution-lobby in recent weeks.  A number of bills submitted this session have sought to strip the Texas State Board of Education of its power to do things like set the curriculum or approve textbooks, or alternatively, to make the Board non-elected.  As the WSJ reported:

Some lawmakers -- mostly Democrats -- say they have had enough. The most far-reaching proposals would strip the Texas board of its authority to set curricula and approve textbooks. Depending on the bill, that power would be transferred to the state education agency, a legislative board or the commissioner of education. Other bills would transform the board to an appointed rather than elected body, require Webcasting of meetings, and take away the board's control of a vast pot of school funding.

A Texas political commentary blog offered a keen observation about what is going on here:

A lot of politicians -- all too many of them Republicans -- love to campaign on socially-conservative themes like pro-life and family values but then behind the scenes in Austin treat the social right like a bunch of lepers. This session, these politicians see an opportunity because of the change in House leadership and board's recent highly publicized debate over the role of evolution in the science curriculum. So we've had a lot more hearings on bills to strip the board of its powers.

What makes evolutionists so scared that they must resort to these tactics? Contrary to the WSJ’s article, Texas students will not learn about “creationist objections” to evolution, but scientific challenges found in the mainstream peer-reviewed scientific literature. Teaching students about real science that challenges evolution is what the Texas evolution lobby fears the most. Thus, they are willing to resort to extreme tactics to enforce their agenda—even when it sharply contravenes the will of the people.

All this amounts to an attempt to take control of the public school curriculum out of the hands of qualified elected officials and taxpaying and voting parents and put it into the hands of bureaucrats. Once the Texas evolution lobby has total vertical control of the curriculum, they hope to then also control—through indoctrination—the minds of the next generation of voters. Perhaps then Texas evolutionists will feel safe returning power to the people.

Posted by Casey Luskin at 2:34 PM | Permalink | TrackBacks (0)

Since the beginning of 2008, we've seen the publication of some excellent popular books introducing the topic of intelligent design (ID), including Intelligent Design 101 (with contributions by Phillip Johnson, Michael Behe, J.P. Moreland, William Dembski, and Jay Wesley Richards) and William Dembski's Understanding Intelligent Design. Another book just out is a small self-published book that is a gem, titled Probability’s Nature and Nature's Probability, by Donald E. Johnson. Johnson holds two Ph.D.'s — one Ph.D. in Computer & Information Sciences from the University of Minnesota and another Ph.D. in Chemistry from Michigan State University. Given Johnson's background, it was unsurprising that he has a good grasp of the issues. What was pleasantly surprising was Johnson's ability to communicate some of the technical aspects of ID in an easy-to-understand form that is extremely well-referenced. Johnson's introduction to ID shows his grasp of the subject:

In recent years there has been much controversy concerning ID (Intelligent Design). Many in the scientific community have dismissed the concept as Creationism warmed-over. Many in the Biblical Creationism community have dismissed the concept as irrelevant since the God of the Bible is not portrayed as the Designer. This book will deal with the scientific aspects of ID, not addressing its implications. ... If it is argued that ID is compatible with (though not requiring) a deity, and therefore should be excluded from science, then by the same reasoning no atheist should be able to publish anything in support of undirected naturalism (which includes Darwinism) since that is a primary belief of those holding the atheistic view. This book will show that undirected naturalism lacks known scientific facts in several critical areas, and that some intelligent agent better accounts for many observations. (p. 4)

Johnson then moves to the evidence for design in higher-level biological systems, examining the ability of Darwinian evolution to produce new biological information. As Johnson writes regarding the origin of new genes:

While the mutation mechanism for gene formation makes an interesting story, there are a number of scientific difficulties with the scenario. Blind chance is the only known mechanism possible for such gene formation since a selective advantage was thought to require some manifestation that is genetically coded (such as making a particular protein). Since nothing prevents what would have become a mutated 'correct' codon from mutating again to become useless (mutation is by chance), the probability for a useful mutated gene is that all required mutations take place in one organism before or during reproduction. (p. 65)

Neo-Darwinians realize this problem, at least implicitly, and thus assert that new genes arise from pre-existing genes via gene duplication. But does that really change anything or solve this problem? Their whole point of generating a gene-duplicate is so that selection pressure can be relaxed so that one of the duplicated genes is free to mutate. But how does the duplicate acquire the requisite code for the new function in the first place? With selection pressure now essentially gone, the pressure driving this gene-duplicate to mutate and find some new function is really no better than blind chance, or a random walk. Stephen Meyer explains this point, albeit more technically:

[N]eo-Darwinists envision new genetic information arising from those sections of the genetic text that can presumably vary freely without consequence to the organism. According to this scenario, non-coding sections of the genome, or duplicated sections of coding regions, can experience a protracted period of “neutral evolution” (Kimura 1983) during which alterations in nucleotide sequences have no discernible effect on the function of the organism. Eventually, however, a new gene sequence will arise that can code for a novel protein. At that point, natural selection can favor the new gene and its functional protein product, thus securing the preservation and heritability of both.

This scenario has the advantage of allowing the genome to vary through many generations, as mutations “search” the space of possible base sequences. The scenario has an overriding problem, however: the size of the combinatorial space (i.e., the number of possible amino acid sequences) and the extreme rarity and isolation of the functional sequences within that space of possibilities. Since natural selection can do nothing to help generate new functional sequences, but rather can only preserve such sequences once they have arisen, chance alone--random variation--must do the work of information generation--that is, of finding the exceedingly rare functional sequences within the set of combinatorial possibilities. Yet the probability of randomly assembling (or “finding,” in the previous sense) a functional sequence is extremely small.

(Stephen C. Meyer, “The origin of biological information and the higher taxonomic categories,” Proceedings for the Biological Society of Washington, Vol. 117(2):213-239 (2004).)

Johnson grasps this basic obstacle for Darwinian evolution, and explains it in terms that any lay reader can understand: no matter how evolutionists try to push the question back, acquiring a new genetic function where previously there was none must face the fact that "[b]lind chance is the only known mechanism possible for such gene formation since a selective advantage was thought to require some manifestation that is genetically coded (such as making a particular protein)" and thus "the probability for a useful mutated gene is that all required mutations take place in one organism before or during reproduction." Can evolutionists provide a compelling — or even plausible — explanation for the origin of new genes?

Probability Nature and Nature's Probability also introduces the fossil evidence for design, irreducible complexity, and discusses junk-DNA in various sections. Johnson closes by explaining the importance of preserving academic freedom to follow the evidence wherever it leads. I don't necessarily agree with everything that Johnson writes, but his book is succinct enough and lucid enough on so many important ID topics that I would recommend it as an introduction to ID. As Johnson writes in his closing chapter:

The benefits of an ID model are potentially wide-ranging. If ID had been accepted, virtually all data recently found concerning the universe’s fine tuning, the complexity of life, and the information of life (including in “junk DNA”) would be seen as confirmation of the ID model. (p. 108)

Probability Nature and Nature's Probability is a unique introduction to the debate over ID, written by a highly qualified author who has a lucid grasp of the issues and is able to communicate core ID concepts for any reader. Check out Johnson's website at ScienceIntegrity.com.

Posted by Casey Luskin at 9:14 AM | Permalink | TrackBacks (0)

ID The Future podcast features a special interview worth highlighting to ENV readers:

Click here to listen.

This episode of ID the Future features CSC associate director John West interviewed by Anika Smith on the launch of the new website, FaithandEvolution.org, bringing clarity to the conversation between the new atheists such as Richard Dawkins and the new theistic evolutionists like Francis Collins. Is faith in God compatible with Darwinian evolution? Who is right, and why does it matter? Listen in, and learn more at FaithandEvolution.org.

Posted by Anika Smith at 4:02 PM | Permalink | TrackBacks (0)

It must be hard to be the Darwinist editor of a major science journal, to have to constantly maintain the party line that there is no scientific debate between intelligent design and evolution while publishing articles whose authors seem haunted by design arguments, often taking it upon themselves to stick up a straw man of ID to knock down with a puff of hot air.

It must be especially hard when a scientist like Michael Behe bothers you, thinking it his duty to advance the debate by correcting the Darwinists' mistaken views of irreducible complexity which you published, hoping that maybe he would go away.

Alas, for the editors of Science and Trends in Microbiology, Michael Behe has not gone away. In fact, he's publishing the letters himself at his Amazon blog, which you can read here and here. Because knowledge advances when arguments are best understood, not when they're ignored or (purposefully?) mistaken, those who follow the debate would do best to read what Behe has to say for himself:

Although some news reporters, lawyers, and parents are confused on the topic, “intelligent design” is not the opposite of “evolution.” As some biologists before Darwin theorized, organisms might have descended with modification and be related by common descent, but the process might have been guided by some form of intelligence or teleological driving force in nature. Darwin’s chief contribution was not the simple idea of common descent, but the hypothesis that evolution is driven completely by ateleological mechanisms, prominently including random variation and natural selection. Intelligent design has no proper argument with the bare idea of common descent; rather, it disputes the sufficiency of ateleological mechanisms to explain all facets of biology. Those who fail to grasp such distinctions are like people who can’t distinguish between the ideas of Darwin and, say, Lamarck.

Posted by Anika Smith at 12:11 PM | Permalink | TrackBacks (0)

In recent years, debates over faith and evolution have continued to intensify. On the one hand, “new atheists” like Richard Dawkins have insisted that Darwinian evolution makes it possible to be an intellectually fulfilled atheist. On the other hand, “new theistic evolutionists” like Francis Collins have assured people that Darwin’s theory is perfectly compatible with faith and need have no damaging cultural consequences.

Who is right? And why does it matter?

You can find out at FaithandEvolution.Org a new website being launched today by the Center for Science and Culture at Discovery Institute.

“FaithandEvolution.Org is for anyone who wants to dig deeper into the scientific, social, and spiritual issues raised by Darwin’s theory, but who is tired of the limited options they are currently being offered by the media,” says Dr. John West, Associate Director of the Center.

“Increasingly, the only voices being heard in the faith and evolution conversation come from two wings of the evolution lobby: atheist evolutionists like Richard Dawkins, and a handful of theistic evolutionists like Francis Collins. But there are a lot of thoughtful scientists and scholars who are skeptical of Darwin’s theory whose views aren’t being heard.”

“Thus, the first goal of FaithandEvolution.Org is to present the scientific information about evolution and intelligent design that is typically left out of the discussion,” says West. “A second goal is to tackle tough questions that are usually ignored about the consequences of Darwin’s theory for ethics, society, and religion.”

Visitors to FaithandEvolution.Org will find information addressing such questions as: Does evolution undermine belief in God? Are there scientific challenges to Darwinian evolution? What is the scientific evidence for intelligent design? And does Darwinism devalue human life?

FaithandEvolution.Org is packed with free tools and resources, including:

• Audio, video, and articles featuring leading scientists and scholars, including biologists Michael Behe and Jonathan Wells, mathematicians William Dembski and David Berlinski, and philosopher of science Stephen Meyer.
  
• A questions page answering people’s top questions about evolution, intelligent design, and related issues; and topics pages addressing key topics such as theistic evolution, evolution and science, evolution and ethics, and evolution and culture.
  
• Curriculum ideas and discussion questions for small groups, Sunday School classes, adult educational programs, and private school science classes.
  
• A searchable database of thousands of articles about evolution and intelligent design, and a glossary of key scientific terms.

“It’s ironic that many of the pro-Darwin groups that claim to be promoting ‘dialogue’ about science and religion are really offering only a monologue,” says West. “They do their best to exclude those who disagree with them. But we have nothing to fear from a free and open exchange of ideas. That’s why we decided to have a section of our site where people could explore divergent views on such issues as the evidence for intelligent design, the limits of Darwin’s theory, and the connection between Darwin’s theory and Social Darwinism.”

West explains that since its inception in 1996, the Center for Science and Culture has devoted most of its resources to supporting research, publication, and education about the scientific aspects of the debate over Darwinian evolution and intelligent design.

“Nothing is going to change that,” he says, adding that much of FaithandEvolution.Org is focused on presenting scientific information in a clear and understandable manner.

“But we’ve always been clear that science has larger worldview implications, and so we want to encourage open and informed discussion of the implications of Darwin’s theory as well. This has become especially important in recent years as both the ‘new atheists’ and the ‘new theistic evolutionists’ have tried to monopolize the faith and evolution conversation. FaithandEvolution.Org is an effort to inject some balance back into the discussion.”

Please help promote FaithandEvolution.Org by forwarding this email to your friends and encouraging them to visit FaithandEvolution.Org!

You also can download here a free flyer for the website suitable for use as an insert in church bulletins or for distribution to church schools or community groups.

Download file

Posted by Robert Crowther at 7:25 AM | Permalink | TrackBacks (0)

New Scientist, is calling The Universe: Order without design by Carlos Calle "excellent." Why?

There's nothing new here, just the same old multiverse stuff that has been critiqued. The author combines a bunch of highly speculative, mostly metaphysical, controversial theories to reach his conclusions: eternal inflation, string theory and colliding branes. There will ALWAYS be speculative, untestable "cosmological" theories, so someone can always point to the latest ones and say, "See no need for a beginning or fine-tuning by a designer—the latest science says so!" These speculative theories have half-lives measured in years, unlike the now well-established Big Bang theory.

In any case, multiverse speculations do not explain those aspects of our existence that are not necessary for our existence or survival, such as the discoverability of the universe.

Posted by Guillermo Gonzalez at 9:14 AM | Permalink | TrackBacks (0)

Just as it seemed the hullaballoo about Great Grandma Ida might go on forever, there is just the hint of some perspective on what the fossil find really means. That the hype around Ida is more selling then compelling is beginning to become clear. The New York Time's business page wrote about how it all seems nicely orchestrated to boost ratings of the History Channel's accompanying documentary. A tongue in cheek report from a London science writer also helped to highlight the fact that the welcome for Ida has been more than just a little over the top.

By the far the most insightful is this post from a science writer at the Smithsonian, offering some more tempered words than the Darwinian elders. In some ways this is a pretty stunning piece, even just appearing on his blog. As is known, the Smithsonian doesn't play nice with people who don't toe the line. Switek doesn't commit the sin of disavowing a strict Darwinian view, but he does chastise the establishment for overselling this latest "missing link."

He opens with this:

So the big day is finally here. "Ida", a 47-million-year-old primate skeleton from Messel, Germany has finally been unveiled on PLoS One and in a flurry of press releases, book announcements, and general media hubub. Under different circumstances I would be happy to see an exceptional fossil receiving such treatment, but I fear that Ida has become a victim of a sensationalistic media that values audience size over scientific substance.

This is a shame. I would have hoped that this fossil would receive the care and attention it deserves, but for now it looks like a cash cow for the History Channel. Indeed, this association may not have only presented overblown claims to the public, but hindered good science, as well. As Karen James has suggested, the overall poor quality of the paper and the disproportionate hyping of the find make me wonder if this research was rushed into publication so that the media splash would occur on time.

Posted by Robert Crowther at 6:14 AM | Permalink | TrackBacks (0)

Any critic making the inaccurate claim that Stephen C. Meyer is the "President of the Discovery Institute" is bound to be fairly uninformed about both intelligent design (ID) and the Discovery Institute.¹ Thus, when I recently viewed a YouTube video making this very mistake while allegedly “Challenging the Discovery Institute to Discover,” I first thought: Why should I accept a challenge from someone who can’t even correctly “discover” the identity of our organization’s president?

Regardless, this video was enlightening, but not in the way that its creators intended. Rather than posing any difficult challenge for ID, the video unwittingly exposes the unfortunate ignorance that apparently abounds regarding the nature of the theory of intelligent design and how we detect and test for design in nature. In this regard, I view this response to the video as an opportunity—hopefully a teachable moment for the 40,000+ people who have apparently viewed the video and the handful who have e-mailed us recently regarding it. That is, it’s a teachable moment for those who are interested in learning.

The basic problem is that the video’s “challenge” woefully misunderstands ID and the logic by which we infer design. It claims that ID only claims that a gene is “unambiguously designed” when we find that:

(1) No homology for other genes exist.

(2) No alternative or prior function exists.

Why Must Designed Structures Be Unique?
Regarding the first criterion, the homology criterion, the video claims that homology is found with at least 20% sequence identity over at least 100 amino acids, which would have an odds of less than 1/ 10²⁸ of happening by chance. There’s actually much debate about what constitutes homology and what a non-arbitrary measure of homology should look like. For example, Teichmann and Veitia (2004) suggest that homology should not be inferred when there is less than a 60% sequence identity.² If this is to be the measuring line, many claims of protein homology (including the claims in this video) would be in jeopardy. But for the sake of argument, we’ll take the video’s definition of homology.

The video’s argument effectively says that a gene must lack any known homologies and thereby be completely unique—basically an ORFan gene—in order for us to claim that it was designed. But why must this be so?

The video’s first criterion for detecting design seems eminently contrived and unreasonable as a test. As I explained in my recent Primer on the Tree of Life, designers commonly re-use similar components in different designs because they are effective at performing a common function:

why not consider the possibility that biological similarity is instead the result of common design? After all, designers regularly re-use parts, programs, or components that work in different designs (such as using wheels on both cars and airplanes, or keyboards on both computers and cell-phones)³

If there is no known homology for a given gene, then that would dictate that the gene is effectively an ORFan gene. The existence of ORFan genes poses a problem for evolution (from whence would such an ORFan come?), but their non-existence would not pose a problem or ID. After all, many ID critics are quick to remind that evidence against evolution does not necessarily therefore constitute evidence for ID. (ID requires a positive case for design.) Thus, these ID-critics are testing ID inappropriately by trying to affirm ID simply by challenging evolution. But when it comes to predictions about biological similarity, both common design and common descent predict that it might exist. Thus, the presence of shared functionally similar sequences between different organisms does not make a good test of discriminating between design and descent.

Even leading evolutionists like Francis Collins recognize this point. Collins writes in The Language of God that genetic similarity “alone does not, of course, prove a common ancestor” because a designer could have “used successful design principles over and over again.”⁴ Collins is right. To again show how the video’s argument fails by analogy, if one discovers two similar Buicks in a junkyard, one would not conclude one car descended from the other. Rather, one would conclude that intelligent engineers modified plans from the first Buick to make the second. In the same way, the genetic similarity of two different proteins—in itself—is compatible with either common descent or common design. So rather than failing to make a case “unambiguously” for intelligent design, homology fails to make a case “unambiguously” for common descent.

Ignoring the possibility of common design, the video assumes that shared functional similarity necessarily indicates common ancestry. This video is simply applying what I called in my recent Primer on the Tree of Life the “main assumption” of neo-Darwinian tree-building:

[T]he first assumption that goes into tree-building is the basic assumption that similarity between different organisms is the result of inheritance from a common ancestor. That is, except for when it isn’t. (And then the similarity is purportedly said to be the result of convergent evolution, etc.) But even if we take this claim at face value — that similarity between different organisms is the result of inheritance from a common ancestor — let’s recognize it for what it is: a mere assumption. But are there other possibilities?

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?"⁵

The Edge of Evolution: "[M]odern Darwinists point to evidence of common descent and erroneously assume it to be evidence of the power of random mutation."⁶

Criterion 2: Repeating Ken Miller’s Errors
When you only read the arguments of critics, sometimes you begin to think that they have the monopoly on a subject. This must be the case of the YouTube video’s creators, who mimic Ken Miller’s straw man tests for irreducible complexity by stating: "We don't want some protein that is used lots of ways or it can't be part of an irreducibly complex system."

Huh? These guys must be learning about ID from Ken Miller, and not from ID’s proponents. Miller has made similar arguments like this many times, and I wrote a lengthy response to Miller on this point in 2006 at Do Car Engines Run on Lugnuts? A Response to Ken Miller & Judge Jones's Straw Tests of Irreducible Complexity for the Bacterial Flagellum that explains Miller’s error.

To repeat Miller’s assertion, he testified during the Dover trial that irreducible complexity (IC) is refuted if one sub-system can perform some other function in the cell:

Dr. Behe's prediction is that the parts of any irreducibly complex system should have no useful function. Therefore, we ought to be able to take the bacterial flagellum, for example, break its parts down, and discover that none of the parts are good for anything except when we're all assembled in a flagellum.⁸

In The Origin of Species Darwin stated:

'If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.'

A system which meets Darwin's criterion is one which exhibits irreducible complexity. By irreducible complexity I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease functioning.⁹

Thus, Miller and the video mischaracterize Behe's argument as one which focuses on the non-functionality of subparts, when in fact Behe’s argument actually focuses on the ability of the entire system to assemble, even if sub-parts can have functions outside of the final system.

Two analogies will help explain the fallacy in the video.

To understand how Miller and the video’s test fails to accurately apply to Behe's formulation of irreducible complexity, consider the example of a car engine and a bolt. Car engines use various kinds of bolts, and a bolt could be seen as a small “sub-part” or “sub-system” of a car engine. Under Miller's logic, if a vital bolt in my car's engine might also to perform some other function—perhaps as a lugnut—then it follows that my car's whole engine system is not irreducibly complex. Such an argument is obviously fallacious.

In assessing whether an engine is irreducibly complex, one must focus on the function of the engine itself, not on the possible function of some sub-part that may operate elsewhere. Of course a bolt out of my engine could serve some other purpose in my car. However this observation does not explain how many complex parts such as pistons, cylinders, the camshaft, valves, the crankshaft, sparkplugs, the distributor cap, and wiring came together in the appropriate configuration to make a functional car engine. Even if all of these parts could perform some other function in the car (which is doubtful), how were these parts assembled properly to construct a functional engine? The answer requires intelligent design.

Behe asserts that a system is irreducibly complex if the system stops functioning upon the removal of one part. This is the appropriate test of Darwin’s theory because it asks the question, “Is there a minimal level of complexity which is required for functionality of this system?” Clearly my car’s engine has a core set of parts necessary in order for it to function. The ability of an engine bolt to also serve as a lugnut does not refute the irreducibly complex arrangement of parts necessary to make the final engine-system functional.

Behe never suggests that subsystems or sub-parts cannot play some other role in the cell—in fact he suggests the opposite. Rather, Behe simply argues that evolution requires that the total system must be built up in a slight, step-by-step fashion, where each step is functional. When a certain core number of parts must be arranged in a particular pattern for a system to function, we have irreducible complexity. Period.

Likewise, my laptop’s power cord might be able to also be used power my toaster. But does that mean that my laptop does not have a core number of parts that are required for it to function? You answer the question for yourself.

The video’s second criterion for detecting design is therefore also utterly fallacious.

Answering the Challenge, Challenging the Critics to Understand Intelligent Design
The video then claims that “you [Discovery Institute] have not pointed to a single gene that shows evidence of a non-evolutionary design,” saying that we haven’t “discovere[d].” To restate the obvious, apparently these critics simply aren’t familiar with Discovery Institute or ID literature.

In Darwin’s Black Box, Michael Behe has described systems with dozens of genes which, as they form irreducibly complex systems, show evidence of not having been produced by natural selection acting on random mutations, and instead show evidence of design.

Doug Axe's research likewise studies genes that it turns out show great evidence of design. Axe studied the sensitivities of protein function to mutations. In these "mutational sensitivity" tests, Dr. Axe mutated certain amino acids in various proteins, or studied the differences between similar proteins, to see how mutations or changes affected their ability to function properly.¹⁰ He found that protein function was highly sensitive to mutation, and that proteins are not very tolerant to changes in their amino acid sequences. In other words, when you mutate, tweak, or change these proteins slightly, they stopped working. In one of his papers, he thus concludes that "functional folds require highly extraordinary sequences," and that functional protein folds "may be as low as 1 in 10^77."¹¹ The extreme unlikelihood of finding functional proteins has important implications for intelligent design.

Since Darwinian evolution only preserves biological structures which confer a functional advantage, this indicates it would be very difficult for such a blind mechanism to produce functional protein folds. This research also shows that there are high levels of specified complexity in enzymes, a hallmark indicator of intelligent design: Only forward thinking intelligent agents could find the extremely unlikely amino acid sequences that yield functional proteins. Axe himself has confirmed that this study adds to the evidence for intelligent design, writing: “In the 2004 paper I reported experimental data used to put a number on the rarity of sequences expected to form working enzymes. The reported figure is less than one in a trillion trillion trillion trillion trillion trillion. Again, yes, this finding does seem to call into question the adequacy of chance, and that certainly adds to the case for intelligent design.”¹²

Biologist Doug Axe's research suggests that the "fitness landscape" for many enzymes might look something like this, where the y-axis can be seen as representing enzyme activity, and the x-axis represents possible amino acid sequences. If Axe's empirical studies are correct, then enzymes likely sit at the peak of their fitness landscapes (Point A), and there are extremely high levels of complex and specified information in proteins--informational sequences that would be unlikely to be found via blind trial-and-error Darwinian processes, and which point to intelligent design. The video taunts Discovery Institute to name a specific gene that shows evidence of design. At the risk of dignifying this highly misinformed video, some of the enzymes empirically studied in Dr. Axe's work were those containing β-lactamase domains in E. coli, such as TEM-1 penicillinase.

So Discovery Institute and ID proponents most certainly have described genes that show evidence of a non-Darwinian and intelligent design. We’ve simply done it through a viable mode of detecting design: finding biological systems that contain high levels of specified (including irreducible) complexity.

This is the proper way to detect design and to test for design, not inventing contrived criteria that claim that systems must be totally unique and perform only one function before they can be designed. Given that designers regularly re-use parts that work in different designs, and may even use a part to perform multiple functions, we can easily dispense with the video’s uninformed modes of detecting design.

The Signature in the Cell

The video opens by showing Stephen Meyer arguing that “when we find information in the DNA in this four-character digital code, it’s a logical inference and explanation to say that an intelligent agent of some kind played a role in the origin of those living systems.” The video then challenges Meyer and Discovery Institute to provide evidence backing this statement statement, which is amusing since there will be no better elaboration on the scientific case for intelligent design based upon the information in DNA than Dr. Meyer’s forthcoming book Signature in the Cell: DNA and the Evidence For Intelligent Design, which comes out next month.

The right question is, where does your information come from? Stephen C. Meyer has elegantly explained that we know only one source of high levels of complex and specified information:

[W]e have repeated experience of rational and conscious agents-in particular ourselves-generating or causing increases in complex specified information, both in the form of sequence-specific lines of code and in the form of hierarchically arranged systems of parts. … Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source from a mind or personal agent.¹³

References Cited:

[1.] Spending a short 2 minutes on Discovery Institute's website quickly uncovers that Stephen Meyer is a Senior Fellow, and Director of the Center for Science and Culture, whereas the President of Discovery Institute is Bruce Chapman.

[2.] Sarah Amalia Teichmann and Reiner Albert Veitia, "Genes Encoding Subunits of Stable Complexes Are Clustered on the Yeast Chromosomes: An Interpretation From a Dosage Balance Perspective," Genetics, Vol. 167:2121–2125 (August, 2004).

[3.] Casey Luskin, "A Primer on the Tree of Life"

[4.] Francis Collins, The Language of God, page 134.

[5.] Michael Behe, Darwin's Black Box, pgs. 175-176 (Free Press, 1996).

[6.] Michael Behe, The Edge of Evolution, pg. 95 (Free Press, 2007).

[7.] Francis Collins, The Language of God, page 134.

[8.] Kenneth Miller Kitzmiller Testimony, Day 1, PM Session, page 16.

[9.] Michael Behe, Darwin's Black Box, pg. 39 (Free Press, 1996).

[10.] Douglas D. Axe, "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds," Journal of Molecular Biology, 1-21 (2004); Douglas D. Axe, "Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors," Journal of Molecular Biology, Vol. 301:585-595 (2000).

[11.] Douglas D. Axe, "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds," Journal of Molecular Biology, 1-21 (2004).

[12.] "Scientist Says His Peer-Reviewed Research in the Journal of Molecular Biology "Adds to the Case for Intelligent Design"

[13.] Stephen C. Meyer, "The origin of biological information and the higher taxonomic categories," Proceedings of the Biological Society of Washington, Vol. 117(2):213-239 (2004).

Posted by Casey Luskin at 10:00 AM | Permalink | TrackBacks (0)

Editor's Note: This is crossposted at David Klinghoffer's Beliefnet blog, Kingdom of Priests.

Some readers thought I was unfair in a previous entry explaining the difference between my perspective on evolution and that of my fellow Beliefnet blogger Dr. Francis Collins over at Science and the Sacred. Am I really not being fair? Well, let's test that hypothesis by picking out one idea from Dr. Collins's book and from his website BioLogos. It's his treatment of the idea that somehow a moral law in every heart points us to the existence of God. 

Because BioLogos -- or theistic evolution, however we may designate the general approach -- surrenders so easily to naturalism, it must be willing to accommodate Darwinism's explanation of where that moral law comes from. Dr. Collins thinks radical acts of altruism may defy an evolutionary explanation, or maybe not. Thus quoth BioLogos:

Even if a purely natural account of moral development could be found, the simple fact that morality has evolved is something that would be expected in a world created by a just and loving God.

On the contrary, it would be another indication that religion is superfluous in our quest to grasp the answers to life's ultimate questions. Dr. Collins merely holds it out as a possibility that an evolutionary understanding of moral development could possibly be solidified. But other prominent Darwinists seem confident, as Darwin himself was, that the evolutionary explanation is already in hand.

A recent forum "Evolution and the Ethical Brain" explored the issue in honor of Darwin's 200th birthday. You can watch the video online or read the transcript. It was sponsored by the opulently endowed Templeton Foundation, which by the purest coincidence also funds Dr. Collins's BioLogos. With New York Times columnist David Brooks leading the amiable discussion, three evolutionary scientists explored their conclusion that morality is a human capacity whose development is no more mysterious than the evolution of adult lactose tolerance.

Literally, lactose. The example was given by University of Virginia psychologist Jonathan Haidt. Dr. Haidt also said at one point that "[A]s we know from domesticating animals, in a few dozen generations you can create a new species." Which is, not to put it too indirectly, an eyebrow-raising untruth. Nobody has ever generated a new species.

In any event, Professor Haidt's thesis, agreed to by his colleagues in the Templeton forum and by David Brooks, is that the moral sense is really just like the aesthetic sense. It may itself be a kind of aesthetic sense. You observe an action, find it morally pleasing or repugnant, then generate reasons justifying your gut-level response. Some moral instincts go back as far as mammals do. Others are more recent developments -- such as our "ideas about purity and divinity" which "are probably very, very new."

Nothing in Dr. Haidt's discussion points to anything transcendent behind those ideas of the pure and the divine. The same unguided, unplanned, unexpected process that gave many of us lactose tolerance also gave most of us a belief in God. The same process that gave each of us our individual tastes in art or food gave us our individual tastes in morality.

There may be hinted at here the broad outlines of a general body of moral guidelines. Some things -- well, most people just find them yucky. Like chicken-flavored ice cream, for instance. Or incest. But other things are just a matter of taste. In the same way that it would be absurd for me to judge your taste in music as somehow violating absolute norms, it would be absurd to judge anyone's moral ideas.

Most importantly, it would be absurd to judge yourself and your own actions by such a yardstick. How could a person ever justify telling himself no?

Far from my being unfair to anyone, these are inescapable extensions of the discussion at the Templeton event. From the perspective of theistic evolution, or BioLogos, I don't see how they can be avoided except by wishful thinking. This is the road down which the surrender to naturalism eventually leads. It is the road to relativism.

For a group of academics with tidy, functional lives, the message may be harmless enough. Their gut tells them to continue being productive, orderly members of society. Lucky for them. For much of the rest of humanity, the same idea, if it were disseminated and truly taken to heart, would be catastrophic.

Incidentally, see this smart comment by Carol Iannone at National Review Online on the hopelessness of reconciling Darwin and religious faith. Sincere, believing Christian that he is, Dr. Collins still fails to see this.

Posted by David Klinghoffer at 7:31 AM | Permalink | TrackBacks (0)

If they weren't atheists, you'd think the scientists raising the ballyhoo over Ida were hailing the second coming.

Here is yet another icon of evolution. Every time one of these discoveries is made, there’s a huge PR snow job from the Darwin lobby to make it seem like it answers all the questions and objections. I thought Tiktaalik did that. Or maybe Archaeopteryx. It goes at least as far back as Proconsul. Each time the Darwinists seem to forget they already found the missing link — the one fossil to rule them all — and re-find it all over again.

At least CBS News was a bit more

skeptical than Sky News when they reported it on Friday.

While the fossil doesn't relate to the more heated debate over whether chimpanzees and humans share a common identity - the fossil is not the so-called "missing link" — the two factions will likely pounce on this new find with evolutionists claiming the skeleton adds to the limited fossil record.

The discovery of the 95%-complete 'lemur monkey' - dubbed Ida - is described by experts as the "eighth wonder of the world".

I’ll go you one better with a 100% complete lemur monkey! Nine wonders of the world apparently aren’t too many.

They say its impact on the world of palaeontology will be "somewhat like an asteroid falling down to Earth".

Prof Hurum said when he first saw the blueprint for evolution - the "most beautiful fossil worldwide" - he could not sleep for two days. A home movie records the dramatic moment. "This is really something that the world has never seen before, this is a unique specimen, totally unique," he says, clearly emotional.

Posted by Robert Crowther at 10:40 AM | Permalink | TrackBacks (0)

Scientist and theologian Alister McGrath has a new essay over at Christianity Today, "Augustine's Origin of Species." Knowing how Augustine has often been co-opted by Darwinians as a proto-Darwinist, I came to this article rather skeptical. But I was delightfully surprised.

McGrath notes that Augustine's dominant image of the natural world's relation to God is that of a "dormant seed." As McGrath explains:

God creates seeds, which will grow and develop at the right time. Using more technical language, Augustine asks his readers to think of the created order as containing divinely embedded causalities that emerge or evolve at a later stage. Yet Augustine has no time for any notion of random or arbitrary changes within creation. The development of God's creation is always subject to God's sovereign providence. The God who planted the seeds at the moment of creation also governs and directs the time and place of their growth.

...any injection of teleology into evolutionary biology violates precisely the great advance of Darwin’s theory: to explain the appearance of design by a purely materialistic process — no deity required. In a letter to his mentor Charles Lyell, Darwin explicitly decried the idea of divine intervention in evolution:

I entirely reject, as in my judgment quite unnecessary, any subsequent addition ‘of new powers and attributes and forces,’ or of any ‘principle of improvement’, except in so far as every character which is naturally selected or preserved is in some way an advantage or improvement, otherwise it would not have been selected. If I were convinced that I required such additions to the theory of natural selection, I would reject it as rubbish. . . I would give absolutely nothing for the theory of Natural Selection, if it requires miraculous additions at any one stage of descent.

he does clarify nicely at the end. He summarizes:

Augustine would have rejected any idea of the development of the universe as a random or lawless process. For this reason, Augustine would have opposed the Darwinian notion of random variations, insisting that God's providence is deeply involved throughout. The process may be unpredictable. But it is not random.

As we like to say, evolution by intelligent design is intelligent design.

Posted by Logan Gage at 7:15 AM | Permalink | TrackBacks (0)

Editor's Note: This is crossposted at David Klinghoffer's Beliefnet blog, Kingdom of Priests.

Astute readers will have noticed that Beliefnet runs two blogs that deal with evolution on a more or less frequent basis but in very different ways: this blog and Science and the Sacred, where former Human Genome Project head Francis Collins and other contributors from the BioLogos Foundation share their thoughts. An Evangelical Christian, Dr. Collins would like to find a reconciliation between Darwinian evolution including its randomly driven, unplanned, unguided mechanism of natural selection, with Biblical religion, which is premised on God's creative guidance of life's history.

I wish Dr. Collins all the luck in the world. He'll need it. An Orthodox Jew, I find his to be an impossible quest, though attractive to believers who find it expedient to dodge the radical challenge to theistic religion posed by Darwinism.

Part of the appeal of "theistic evolution" lies in the prospect it holds out to Christians and Jews of being respected and accepted by the prestige academic world. In that world, Darwinism and atheism have a way of melding. Alas, the fondly wished for respect is often cruelly withheld. Prominent Darwinists like P.Z. Myers and Jerry Coyne have been amusingly contemptuous of the BioLogos concept -- "full of fluffy bunnies and pious weasels to reconcile science and faith" -- which Dr. Collins also elaborates on a website of that name and in his book, The Language of God.

Of course, they are unfair to Dr. Collins and his collaborator Karl Giberson. I enjoyed Language of God, and reviewed it favorably in The Weekly Standard, though I did note that Dr. Collins, who disdains intelligent-design theory, gives no evidence of having kept up with the latest that is being argued and written on the subject. His critique suffers from superficiality.

For example, Dr. Collins lays great stress on the purported evidence for Darwinian evolution from so-called "junk DNA." But see the latest knock-down of the argument by my colleague Richard Sternberg at Evolution News & Views.

Fundamentally, when it comes to Darwinian evolution, the conflict isn't between faith and science. It's between faith and unfounded science. Bad science. Who would think Judaism or Christianity can be reconciled with any and every science-flavored theory of how the world works that happens to come along?

Without going into a lot of details about what separates our perspectives, I think readers deserve a sort of thumb-nail explanation of where Dr. Collins and I part, and why we do. Interestingly, the contrast between our two ways of thinking about faith goes way back. It was noted more than a century ago by the great psychologist and philosopher William James.

In the Postscript to his book The Varieties of Religious Experience, James wrote about two species of "supernaturalism" -- meaning, in general, an openness to recognizing a reality beyond our natural, material world. The opposite would be naturalism, which denies the existence of such an unseen and unseeable realm. James distinguished between a "refined" or "universal" supernaturalism, which views the supernatural as being unable or unwilling to exert a meaningful guiding influence over material reality, and a "crass" supernaturalism, which perceives the invisible world as intersecting with the visible.

James himself identified as a crass supernaturalist. Religious but not a Christian, he found that refined supernaturalism "surrenders...too easily to naturalism." BioLogos is tempted by the refinement and the prestige of universal supernaturalism.

James wrote: "In this universalistic way of taking the ideal world, the essence of practical religion seems to me to evaporate. Both instinctively and for logical reasons, I find it hard to believe that principles can exist which make no difference in facts." Under refined supernaturalism, the "universe become a gnosticism pure and simple."

I particularly like the part about "surrendering" to naturalism too easily. That's exactly what BioLogos, a/k/a "theistic evolution," does. With it, practical religion is put in danger of evaporating.

James also gives an insight into why refined supernaturalism appeals to so many otherwise faithful believers. It seems refined, sophisticated, worldly, whereas the crass version seems crass. The latter "finds no intellectual difficulty in mixing the ideal and the real worlds together by interpolating influences from the ideal region among the forces that causally determine the real world's details." How backward and old-fashioned! Why it almost sounds like intelligent design. That would never go down in the faculty club.

Like William James, I'm happy to be crass. It's not bad company to be in.

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Note: This post is the last in a series reviewing Jerry Coyne's Why Evolution Is True. Read Part 1 here, Part 2 here, Part 3 here, Part 4 here, Part 5 here, Part 6 here, and Part 7 here.

Darwin called The Origin of Species “one long argument” for his theory, but Jerry Coyne has given us one long bluff. Why Evolution Is True tries to defend Darwinian evolution by rearranging the fossil record; by misrepresenting the development of vertebrate embryos; by ignoring evidence for the functionality of allegedly vestigial organs and non-coding DNA, then propping up Darwinism with theological arguments about “bad design;” by attributing some biogeographical patterns to convergence due to the supposedly “well-known” processes of natural selection and speciation; and then exaggerating the evidence for selection and speciation to make it seem as though they could accomplish what Darwinism requires of them.

The actual evidence shows that major features of the fossil record are an embarrassment to Darwinian evolution; that early development in vertebrate embryos is more consistent with separate origins than with common ancestry; that non-coding DNA is fully functional, contrary to neo-Darwinian predictions; and that natural selection can accomplish nothing more than artificial selection — which is to say, minor changes within existing species.

Faced with such evidence, any other scientific theory would probably have been abandoned long ago. Judged by the normal criteria of empirical science, Darwinism is false. It persists in spite of the evidence, and the eagerness of Darwin and his followers to defend it with theological arguments about creation and design suggests that its persistence has nothing to do with science at all.⁵⁰

Nevertheless, biology students might find Coyne’s book useful. Given accurate information and the freedom to exercise critical thinking, students could learn from Why Evolution Is True how Darwinists manipulate the evidence and mix it with theology to recycle a false theory that should have been discarded long ago.

Notes
⁵⁰ Paul A. Nelson, “The role of theology in current evolutionary reasoning,” Biology and Philosophy 11 (October 1996): 493 - 517. Abstract available online (2009) here.
Jonathan Wells, “Darwin’s Straw God Argument,” Discovery Institute (December 2008). Available online (2009) here.

Posted by Jonathan Wells at 8:00 AM | Permalink | TrackBacks (0)

Regis Nicoll at Break Point has an excellent article for those interested in understanding the relationship between faith and science (like so many seem to be these days *cough* Francis Collins *cough*):

In a recent essay in The New Republic, evolutionary scientist Jerry Coyne asked, “Does the empirical nature of science contradict the revelatory nature of faith? Are the gaps between them so great that the two institutions must be considered essentially antagonistic?” Coyne has no doubt that the answer is yes.

Religion is so hopelessly inimical to scientific progress that any attempt to reconcile them is futile. As Coyne explains, “Accepting both science and conventional faith leaves you with a double standard.” And to make sure you are clear on what religion is at issue, Coyne adds that “rational on the origin of blood clotting, irrational on the Resurrection; rational on dinosaurs, irrational on virgin births.”

While hallowed bodies, like the National Academy of Sciences, claim publicly that faith and science do not conflict, privately, their “dirty little secret” is that religion is a science-stopper. Their public face, Coyne lets on, is all in the interest of maintaining public trust—one that is overwhelming religious and, professedly, Christian—and with it, public funding.

To the illuminati, a believer lumbers to the edge of every frontier of knowledge, poised to retire his investigations with “God did it!” contentment. Meanwhile, dead ends caused by their own faith in scientific materialism remain unexamined—the premature designation of “vestigial” organs and “junk” DNA being two examples.

Contrary to modern criticism, the scientist who approaches the world as a product of intelligence, rather than of matter and motion, is less likely to stop short of discovery. Instead of dismissing a feature that, at first glance, appears inert, unnecessary or just plain mystifying, he is more inclined the push the envelope of investigation to unravel its function and purpose.

Posted by Anika Smith at 1:28 PM | Permalink | TrackBacks (0)

Note: This is Part 7 in a series reviewing Jerry Coyne's Why Evolution Is True. Read Part 1 here, Part 2 here, Part 3 here, Part 4 here, Part 5 here, and Part 6 here.

Coyne writes that Darwin “had little direct evidence for selection acting in natural populations.” Actually, Darwin had no direct evidence for natural selection; the best he could do in The Origin of Species was “give one or two imaginary illustrations.” It wasn’t until a century later that Bernard Kettlewell provided what he called “Darwin’s missing evidence” for natural selection — a shift in the proportion of light- and dark-colored peppered moths that Kettlewell attributed to camouflage and bird predation.⁴⁰

Since then, biologists have found lots of direct evidence for natural selection. Coyne describes some of it, including an increase in average beak depth of finches on the Galápagos Islands and a change in flowering time in wild mustard plants in Southern California — both due to drought. Like Darwin, Coyne also compares natural selection to the artificial selection used in plant and animal breeding.

But these examples of selection — natural as well as artificial — involve only minor changes within existing species. Breeders were familiar with such changes before 1859, which is why Darwin did not write a book titled How Existing Species Change Over Time; he wrote a book titled The Origin of Species by Means of Natural Selection. “Darwin called his great work On the Origin of Species,” wrote Harvard evolutionary biologist Ernst Mayr in 1982, “for he was fully conscious of the fact that the change from one species into another was the most fundamental problem of evolution.” Yet, Mayr had written earlier, “Darwin failed to solve the problem indicated by the title of his work.” In 1997, evolutionary biologist Keith Stewart Thomson wrote: “A matter of unfinished business for biologists is the identification of evolution's smoking gun,” and “the smoking gun of evolution is speciation, not local adaptation and differentiation of populations.” Before Darwin, the consensus was that species can vary only within certain limits; indeed, centuries of artificial selection had seemingly demonstrated such limits experimentally. “Darwin had to show that the limits could be broken,” wrote Thomson, “so do we.”⁴¹

In 2004, Coyne and H. Allen Orr published a detailed book titled Speciation, in which they noted that biologists have not been able to agree on a definition of “species” because no single definition fits every case. For example, a definition applicable to living, sexually reproducing organisms might make no sense when applied to fossils or bacteria. In fact, there are more than 25 definitions of “species.” What definition is best? Coyne and Orr argued that, “when deciding on a species concept, one should first identify the nature of one's ‘species problem,’ and then choose the concept best at solving that problem.” Like most other Darwinists, Coyne and Orr favor Ernst Mayr's “biological species concept” (BSC), according to which “species are groups of interbreeding natural populations that are reproductively isolated from other such groups.” In Why Evolution Is True, Coyne explains that the biological species concept is “the one that evolutionists prefer when studying speciation, because it gets you to the heart of the evolutionary question. Under the BSC, if you can explain how reproductive barriers evolve, you’ve explained the origin of species.”⁴²

Theoretically, reproductive barriers arise when geographically separated populations diverge genetically. But Coyne describes five “cases of real-time speciation” that involve a different mechanism: chromosome doubling, or “polyploidy.”⁴³ This usually follows hybridization between two existing plant species. Most hybrids are sterile because their mismatched chromosomes can’t separate properly to produce fertile pollen and ovaries; occasionally, however, the chromosomes in a hybrid spontaneously double, producing two perfectly matched sets and making reproduction possible. The result is a fertile plant that is reproductively isolated from the two parents — a new species, according to the BSC.

But speciation by polyploidy (“secondary speciation”) has been observed only in plants. It does not provide evidence for Darwin’s theory that species originate through natural selection, nor for the neo-Darwinian theory of speciation by geographic separation and genetic divergence. Indeed, according to evolutionary biologist Douglas J. Futuyma, polyploidy “does not confer major new morphological characteristics… [and] does not cause the evolution of new genera” or higher levels in the biological hierarchy.⁴⁴

So secondary speciation does not solve Darwin’s problem. Only primary speciation — the splitting of one species into two by natural selection — would be capable of producing the branching-tree pattern of Darwinian evolution. But no one has ever observed primary speciation. Evolution’s smoking gun has never been found.⁴⁵

Or has it?

In Why Evolution Is True, Coyne claims that primary speciation was observed in an experiment reported in 1998. Curiously, Coyne did not mention it in the 2004 book he co-authored with Orr, but his 2009 account of it is worth quoting in full:

We can even see the origin of a new, ecologically diverse bacterial species, all within a single laboratory flask. Paul Rainey and his colleagues at Oxford University placed a strain of the bacteria Pseudomonas fluorescens in a small vessel containing nutrient broth, and simply watched it. (It’s surprising but true that such a vessel actually contains diverse environments. Oxygen concentration, for example, is highest on the top and lowest on the bottom.) Within ten days—no more than a few hundred generations—the ancestral free-floating ‘smooth’ bacterium had evolved into two additional forms occupying different parts of the beaker. One, called ‘wrinkly spreader,’ formed a mat on top of the broth. The other, called ‘fuzzy spreader,’ formed a carpet on the bottom. The smooth ancestral type persisted in the liquid environment in the middle. Each of the two new forms was genetically different from the ancestor, having evolved through mutation and natural selection to reproduce best in their respective environments. Here, then, is not only evolution but speciation occurring in the lab: the ancestral form produced, and coexisted with, two ecologically different descendants, and in bacteria such forms are considered distinct species. Over a very short time, natural selection in Pseudomonas yielded a small-scale ‘adaptive radiation,’ the equivalent of how animals or plants form species when they encounter new environments on an oceanic island.⁴⁶

Exaggerating the evidence to prop up Darwinism is not new. In the Galápagos finches, average beak depth reverted to normal after the drought ended. There was no net evolution, much less speciation. Yet Coyne writes in Why Evolution Is True that “everything we require of evolution by natural selection was amply documented” by the finch studies. Since scientific theories stand or fall on the evidence, Coyne’s tendency to exaggerate the evidence does not speak well for the theory he is defending. When a 1999 booklet published by The U. S. National Academy of Sciences called the change in finch beaks “a particularly compelling example of speciation,” Berkeley law professor and Darwin critic Phillip E. Johnson wrote in The Wall Street Journal: “When our leading scientists have to resort to the sort of distortion that would land a stock promoter in jail, you know they are in trouble.”⁴⁸

So there are observed instances of secondary speciation — which is not what Darwinism needs — but no observed instances of primary speciation, not even in bacteria. British bacteriologist Alan H. Linton looked for confirmed reports of primary speciation and concluded in 2001: “None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of twenty to thirty minutes, and populations achieved after eighteen hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another.”⁴⁹

Notes
⁴⁰ Coyne, Why Evolution Is True, p. 116.
Darwin, The Origin of Species, Chapter IV (p. 70). Available online (2009) here.
H. B. D. Kettlewell, “Darwin’s Missing Evidence,” Scientific American 200 (March, 1959): 48-53.

⁴¹ Ernst Mayr, The Growth of Biological Thought (Cambridge, MA: Harvard University Press, 1982), p. 403.
Ernst Mayr, Populations, Species and Evolution (Cambridge, MA: Harvard University Press, 1963), p. 10.
Keith Stewart Thomson, “Natural Selection and Evolution's Smoking Gun,” American Scientist 85 (1997): 516-518.

⁴² Jerry A. Coyne & H. Allen Orr, Speciation (Sunderland, MA: Sinauer Associates, 2004), p. 25-39.
Coyne, Why Evolution Is True, p. 174.

⁴³ Coyne, Why Evolution Is True, p. 188.

⁴⁴ Douglas J. Futuyma, Evolution (Sunderland, MA: Sinauer Associates, 2005), p. 398.

⁴⁵ Wells, The Politically Incorrect Guide to Darwinism and Intelligent Design, Chapter Five (“The Ultimate Missing Link”), pp. 49-59.

⁴⁶ Coyne, Why Evolution Is True, pp. 129-130.

⁴⁷ Paul B. Rainey & Michael Travisano. “Adaptive radiation in a heterogeneous environment,” Nature 394 (1998): 69-72.
Frederick M. Cohan, “What Are Bacterial Species?” Annual Review of Microbiology 56 (2002): 457-482. Available online (2009) here.

⁴⁸ Coyne, Why Evolution Is True, p. 134.
National Academy of Sciences, Science and Creationism: A View from the National Academy of Sciences, Second edition (Washington, DC: National Academy of Sciences Press, 1999), Chapter on “Evidence Supporting Biological Evolution,” p. 10. Available online (2009) here.
Phillip E. Johnson, “The Church of Darwin,” The Wall Street Journal (August 16, 1999): A14. Available online (2009) here.

⁴⁹ Alan H. Linton, “Scant Search for the Maker,” The Times Higher Education Supplement (April 20, 2001), Book Section, p. 29.

Posted by Jonathan Wells at 10:00 AM | Permalink | TrackBacks (0)

I am often struck by how the topic of evolution in general, and chimp/human ancestry in particular, can be an immediate conversation opener that just as quickly becomes a conversation closer. Mind you, I don’t go around buttonholing people at, say, my favorite lounge (this music will conjure up the atmosphere) about some phylogenetic arcana — at least, I try not to do so. But for some strange reason, there exist individuals of good will who apparently feel called upon to “raise my consciousness” about some Darwinian facts that I’ve presumably gotten wrong. Not just a bit wrong, but astoundingly wrong. You see, to their way of thinking, I am in dire need of reeducation and they are there to charitably point the way to “help.”

Here is an example of how “chats” like the one I’m talking about begin. After I have been formally introduced (though sometimes not) to an emissary of enlightenment, my just-made acquaintance proceeds to ask whether I’ve read a certain book (title withheld) that purportedly shows four things: We are 99% chimp; our chromosomes contain “scars” that are shared with those of our simian cousins; the DNA scars, like 98.5% of our genome, are simply junk; and these facts change everything we “know” about God. In response I invariably say, “How interesting,” with a wan smile followed by, “Oh, sure, I’ve read parts of it.” For me this is a taxing turn in the conversation for I must all at once feign attention, ask the bartender for another drink, and work to suppress my desire to bolt out the door. Sensing my unease, my new friend usually seems to read my restlessness as one of intellectual discomfort — possibly fear. Anyhow, seeing me as the quarry, he leans in and expounds on each of the topics, his eyes glinting throughout with the impression that he is surrounding me via a four-pronged conceptual assault, a two-pincer strategy. (All the while, I am praising the heavenly host for the warm irreducible complexity of scotch.)

Then a lull in the barrage occurs. To his way of thinking, it is my guess, an opportunity is being provided for me to offer an unconditional surrender; or, at the very least, for me to acknowledge that pieces like the one just published in the Scientific American (Katherine S. Pollard, “What Makes Us Human? Comparisons of the genomes of humans and chimpanzees are revealing those rare stretches of DNA that are ours alone,” April 20, 2009) are right when they assert that “our DNA blueprints are nearly 99 percent identical” to the sequences of chimps. Awaiting the white flag, my conversation partner will now sometimes try to emphasize that I have been at the receiving end of a coup de grâce,

By the way, this is the apogee or climax of the conversation. It is strictly downward from here on. But at such a critical juncture I proffer no surrender and, indeed, I mount a counter-offensive. Yes, yes, I know: The audacity…the rudeness. Whether my attempts to make my case are ever successful is unknown for my responses sooner or later elicit an abrupt termination of discourse. Regardless, my turn at the conversation goes something like this…

One can seriously call into question the statement that human and chimp genomes are 99% identical. For one thing, it has been noted in the literature that the exact degree of identity between the two genomes is as yet unknown (Cohen, J., 2007. “Relative differences: The myth of 1%,” Science 316: 1836.). Part of the reason for this is if one decides to take into account the plethora of species-specific DNA insertions and deletions (“indels”) that are present along any segment compared between chimp and human, the percentage of identity drops. Another reason is that duplications, inversions, translocations, and transpositions at all scales uniquely characterize the two genome sequences — these have to be untangled before aligning the sequences in order to measure their similarity. Also, the 99% identity figure is often derived from protein-coding regions that only comprise about 1.5% of the two genomes. Many mammalian protein-coding regions are highly conserved, however. We also have to consider that a detailed comparison of certain “heterochromatic” chromosome regions between chimps and humans has yet to be made. In short, the figure of identity that one wants to use is dependent on various methodological factors.

As I continue in this vein, I notice that I am being given the universal gesture of “Wow, look at the time…it’s really getting late…I’d love to pursue this matter further but I have better things to do…” by my interlocutor: He keeps staring at his watch and asking the bartender for the time. Since I’m now getting warmed up, I lean in and suggest to him that he should try his own chimp-human alignments and not take so-and-so’s word for it — after all, the sequences are publicly available. Why trust authority? (I can tell from his sandals and ponytail that this late 1960s reference will appeal to him.) But he has to make a parting shot and so, after commenting that only creationists are as recalcitrant to logic as I seem to be, he presents to me the ultimate criterion of truth, the standard by which I have failed. That criterion, the one I missed in school, comes through in a single sentence he utters: “Everything you just said, well, I have never heard this before.” Taken aback and after I request that he repeat what I just heard, my now peeved acquaintance tells me (holding up his book) that since he has never read in his trusted sources that DNA sequence comparisons often require complicated alignments, that the data are filtered through software algorithms that in turn rest on a priori assumptions, etc., he must dismiss my first salvo.

He tallies the intellectual score as 4-0 in his favor.

At this break, three things happen. The bartender receives my nod that I want another drink and then, after he places it before me, I inquire as to whether he can play anything by Ethel Ennis — I now want to listen to something languorous, music that will soothe the feeling of ennui that has come over me. Next, or simultaneously, my sparring partner makes one of two moves. Either he places his book into his hand-woven Inca-nesque bag and leaves without so much as a farewell, or he decides to tarry a bit longer and says, “You have no answer for ITSs, do you?”

ITSs…interstitial telomeric sequences…the chromosome scars, the pieces of junk DNA he was lecturing me about earlier. As you know, telomeres are the ends of chromosomes. In many species, including chimps and humans, the DNA sequences that are found at these genomic tips are tandem repetitions of TTAGGG. That’s right…TTAGGGTTAGGGTTAGGG…over and over and over again. A notable exception to this rule is the fruit fly, an organism that in this regard has provided the junk DNA notion no succor, since its telomeres have complex combinations of three different retrotransposons instead of those six-basepair units. What is important to note, though, is that telomeric sequences are essential to the cell, and it seems that hardly a week does not pass without some new role being discovered for these elements.

How, precisely, are miles and miles of TTAGGG of significance? From the standpoint of chromosome architecture, the repetitive elements en masse have the propensity to form complicated topologies such as quadruplex DNA. These sequences or, rather, topographies are also bound by a host of chromatin proteins and particular RNAs to generate a unique “suborganelle” — for the lack of better term — at each end. As a matter of fact, the chromatin organization of telomeres can silence genes and has been linked to epigenetic modes of inheritance in yeast and fruit flies. Furthermore, different classes of transcripts emanate from telomeres and their flanking repetitive DNA regions, which are involved in various and sundry cellular and developmental operations.

I try to outline all the functions of telomeric repeats, but my friend tells me that I am getting off the subject.

He wants to me to focus on the ITSs, the tracks of the hexamer TTAGGG that reside within chromosome arms or around the centromere, not at the ends. I tell him that I was just coming to that topic. The story, you see, is that in the lineage leading up (or down, I forget which) to chimps and humans, a fusion of chromosome ends occurred — two telomeres became stuck together, the DNA was stitched together, and now we find the remnants of this event on the inside of chromosomes. And to be fair, I concede at this point that the 2q13 ITS site shared by chimps and humans can be considered a synapomorphy, a five-dollar cladistic term meaning a genetic marker that the two species share. As this is said, it is apparent that the countenance of my acquaintance lightens a bit only to darken a second later. For I follow up by saying that of all the known ITSs, and there are many in the genomes of chimps and humans, as well as mice and rats and cows…, the 2q13 ITS is the only one that can be associated with an evolutionary breakpoint or fusion. The other ITSs, I hasten to add, do not square up with chromosomal breakpoints in primates (Farré M, Ponsà M, Bosch M. 2009. "Interstitial telomeric sequences (ITSs) are not located at the exact evolutionary breakpoints in primates," Cytogenetic and Genome Research 124(2): 128-131.). In brief, to hone in on the 2q13 ITS as being typical of what we see in the human and chimp genomes seems almost like cherry-picking data. Most are not DNA scars in the way they have been portrayed.

Exasperated with my stubbornness, the caffeine from innumerable herbal teas having only enhanced his tension, he rises from the bar and asks: “How, then, do you account for such ITSs in the first place…everyone knows they are out-of-place junk.” I tell him that I do have an answer but that first I must be excused for a moment. While making my way back to the bar, I mentally rehearse so as to be as succinct as possible. My rejoinders are, simply, that ITSs reflect sites where TTAGGG repeats have been added to chromosomes by telomerases, that these repeats are moreover engineered — literally synthesized by the telomerase machinery, that ITSs have a telomere-like chromatin organization and are associated with distinct sets of proteins, and that many have been linked to roles such a recombination hotspots. And just as I begin to reflect on where the references are in my bag that supports those points I notice…he is gone.

Posted by Richard Sternberg at 11:06 AM | Permalink | TrackBacks (0)

Dr. Jeffery Shallit has a post on his blog Recursivity that really caught my eye. He comments derisively on an essay by McGill University ethicist Margaret Somerville titled, “Facing up to the dangers of the intolerant university: Bird on an ethics wire.” Somerville argues that universities are increasingly becoming intolerant of viewpoints that fall outside of a narrow leftist-atheist ideology. She notes that healthy democracies depend on respectful sharing of opinions, and university censorship and exclusion of competing opinions — especially opinions on ethical issues that derive from religious traditions — leaves our public discourse dangerously impoverished.

Dr. Shallit agrees with some of her criticism of suppression of speech on campus, but he finds her essay “very shoddily argued.” He mainly objects to her suggestion that religious views be given a place in the public forum and her view that ethical decisions based on religious faith be accorded respect. Dr. Shallit asks:

With respect to religion, why should religious dogma, which maintains ridiculous and unverifiable claims, be treated in the same way as science and rational thinking?

Subtle arguments about God being the ground for existence and about the role of Christianity in Western politics and culture aren't "ridiculous and unverifiable;" these arguments are central to philosophy and to any informed understanding of history. New Atheist boilerplate trivializes the profound issues that religious belief raises, and the New Atheist contribution to meaningful discussion of these fundamental issues is ...well... nil. For New Atheists, ‘rational thinking’ takes a backseat to ideological spittle.

But that’s not what caught my eye in Shallit's post. Here’s what did.

Dr. Somerville, in her essay on intolerance and academic freedom, writes:

[W]e need to balance intense individualism with a robust concern for the community, and we need to consider the collective impact of our individual decisions. In our interconnected world, an order unavoidably emerges from thousands of individual decisions. For example, Quebec is proposing to offer all pregnant women screening for Down’s Syndrome. Whether or not, as individuals, we think that is good and ethical, the cumulative effect at the societal level of each woman’s individual decision (including the decisions not to abort when the fetus is “normal”) is to implement a 21st Century form of eugenics. Only the decision not to abort when the fetus has Down’s Syndrome is not a eugenic decision.

Dr. Somerville is exactly right. In the 1950's, Fredrick Osborn, the president of the American Eugenics Society, advocated a shift away from the more explicit negative eugenics that had been discredited by the Nazi's uncommonly skillful implementation of eugenic theory. In a 1956 speech, "Galton and Mid-Century Eugenics," delivered to the Galton Society, Osborn stated:

"The very word eugenics is in disrepute in some quarters ... We must ask ourselves, what have we done wrong? I think we have failed to take into account a trait which is almost universal and is very deep in human nature. People simply are not willing to accept the idea that the genetic base on which their character was formed is inferior and should not be repeated in the next generation. We have asked whole groups of people to accept this idea and we have asked individuals to accept it. They have constantly refused and we have all but killed the eugenic movement ... they won't accept the idea that they are in general second rate. We must rely on other motivation. ... it is surely possible to build a system of voluntary unconscious selection. But the reasons advanced must be generally acceptable reasons. Let's stop telling anyone that they have a generally inferior genetic quality, for they will never agree. Let's base our proposals on the desirability of having children born in homes where they will get affectionate and responsible care, and perhaps our proposals will be accepted." (1)[emphasis mine]

"Every Child a Wanted Child"

Dr.Somerville is right to point out that voluntary unconscious selection — eugenics — permeates our culture.

Dr.Shallit comments:

...she says "Only the decision not to abort when the fetus has Down's syndrome is not a eugenic decision". But here she is begging the question: why are decisions that she labels as "eugenic" necessarily bad? Why, exactly, would the world be better off with more Down's syndrome children? By her reasoning, positive assortative mating would be considered "eugenic"; yet most of us practice some form of it. [my emphasis]

Shallit channels Osborn, questioning whether the selective abortion of Down's children is really "eugenic" and really "bad." He leaves us wondering, "Why, exactly, would the world be better off with more Down's syndrome children?"

Setting aside Shallit’s characterization of love and marriage as “positive assortative mating” (a poor rhetorical strategy for eligible Darwinists interested in reproductive success), it's worth noting that Shallit's second inference ("the world would be better off with fewer Down’s kids") refutes his first inference (that "selective abortion of Down’s children isn’t eugenics"). He clearly views selective abortion of Down’s syndrome children as eugenic, although he uses sneer quotes around "eugenics." Whatever the selective killing of unborn children with Down's syndrome is, he seems to endorse it.

Enough with Shallit’s muddled eugenic sophistry. The selective abortion of children with Down’s syndrome is obviously eugenic. The question that Dr. Somerville asks, and that she believes can only be answered in an open forum in which religious views are given equal voice, is this:

Is the eugenic abortion of children with Down’s syndrome moral?

Nature eliminates the unfit and preserves the fit… Her fool-killing devices were highly efficient in the olden days before civilisation came to thwart her. It is man, not Nature, who has caused all the trouble. He has put his whole soul to saving the unfit, and has timidly failed to do the other half of his duty by preventing them from perpetuating their traits.

“Why, exactly, would the world be better off with more disabled children?”

Here’s my view on eugenics. It is a view that Dr. Somerville strives to keep in the public square, and that Dr. Shallit strives to exclude from the public square. I don’t believe that man is the product of purposeless natural selection. I believe that man is created by God, for a purpose, and that each of us is in part the image of God. Our dignity is that we carry that image. We are not mere animals to be bred and culled. Our dignity is not that we are smart, or strong, or that we have prevailed in our struggle for survival. Our dignity is that we are human and carry our Creator’s image, and we retain that full dignity despite the accidents of illness or genetics.

We are each afflicted with disabilities of different sorts. Some are genetic disabilities, and some are moral disabilities. Advocacy of eugenics is a much deeper — and a much more pernicious — disability (of the moral sort) than Down’s syndrome. Yet I believe that the world is better off because of each of us, and that includes children with Down’s syndrome as well as atheist mathematicians who casually endorse killing handicapped children before they're born.

Why do I find eugenics not merely morally wrong but repellant? I have three reasons. First, as I noted above, I have fairly traditional Christian beliefs, and I find the assertion that people should be bred and culled like farm animals to be repugnant.

Second, eugenics has stained my profession. It’s fair to say that the medical profession’s participation in eugenics is the most shameful aspect of its history. Most prominent eugenicists have been Darwinist scientists, but it is also true that many physicians played (and continue to play) a central role in eugenics. Yet the fundamental tenet of medical ethics is that a physician must always act primarily for the benefit of his patient. The thought of a physician entering an examining room with the thought, "How can I most effectively end this patient’s germ line?" makes me sick. It is a deep violation of trust.

The third reason is personal. I am a pediatric neurosurgeon, and I take care of many children with profound genetic neurological handicaps. My kids are "unfit" in the extreme. Many are paralyzed and many have profound cognitive deficits. My kids are the referents in Dr. Edward East’s description of natural selection as a “fool killing device.” They are the people of whom Dr. Shallit and his eugenic soul mates ask rhetorically

“Why, exactly, would the world be better off with more of these children?”.

Chelsea (not her real name) is 8 years old, and she has Down’s syndrome. I’ve taken care of her since she was born. She has hydrocephalus (water on the brain), which is unusual for Down’s children, but it’s how I have come to know her. She’s had seven operations, in her eight years, to relieve pressure on her brain. She is very afraid of needles, and doesn’t like hospitals. But she really likes doctors and nurses, and she really likes, well…everyone. When she has to undergo a painful or frightening procedure (blood-drawing or the like), she cries, but does not struggle, and as soon as the procedure is over, she hugs each participant, assuring them that “It’s OK.” She loves people — all people — and she never seems to associate the sometimes unpleasant things that people must do to her with the people themselves.

When she visits the doctor’s office or the hospital, she is the center of attention. Merely the phrase “Chelsea’s here!” brings doctors, nurses, ward clerks, secretaries — anyone who knows her — to stop by for a chat. She’s pretty good with names, and everyone gets a hug. Like most Down’s kids, she is preternaturally happy. Is the world much better off with Chelsea in it? Without question it is. Even a room is much better with Chelsea in it.

David (also not his real name) passed away a few years ago, when he was ten. Like Chelsea, he had Down’s syndrome and hydrocephalus, but he had a much harder time. David never learned to talk or to feed himself or even to sit up. In addition to Down’s syndrome and hydrocephalus, he suffered from a heart disorder, scoliosis, and pulmonary and digestive problems. He too was a happy child, but his disabilities were profound. He suffered much in his life; he had more than a hundred operations, and he passed away several years ago from his heart problems.

He spent quite a bit of his life in the hospital. His parents and three older brother and sisters intensely devoted to him. Neighbors and people in her home town held fundraisers to help, and extended family and friends volunteered to stay with him in the hospital (he was never alone) when his mom and dad needed a break.

I attended his funeral. I found a standing-room only crowd, a couple of hundred people, spilling out into the hallway. I was surprised how many of the people I knew — other doctors and nurses, clerks and administrative people from the hospital who had come to know his family well, as well as neighbors and extended family who I had met many times over the years. The eulogy was given by the medical center’s Lutheran pastor, who had become very close to David and his family. He gave the most moving eulogy I have heard. He recounted the death of his own daughter from a congenital heart disorder several years ago, and what he had come to know, in a very personal way, about grief over the loss of a child. Then he said (I paraphrase):

It would be natural now to think of David’s life as wasted, as having fallen short of what he might have accomplished had he been born physically and intellectually whole. But that would be a misunderstanding. His accomplishments are many. He brought his family closer, and helped them learn about love and sacrifice in a deeply and at times painfully personal way. He catalyzed friendships [here he pointed to the hundreds of people filling and spilling out of the room], and he brought people together who might never have met. He taught us much about love and about life through his own life. Now of course he is whole, with God, who knows much about the expression of love through suffering. Any one of us would be counted fortunate to have lived a life that moved so many people to love and compassion as he has. It’s a much better world because David has been in it.

Emma (also not her real name) is 22 years old. I’ve taken care of her for 17 years. She was born with spina bifida, a genetic disorder; her spinal cord was exposed on her back. She’s paralyzed below the waist, and her legs are shrunken and deformed. She has never had any control of her bladder or bowels. She’s had surgery to graft a piece of her intestine to her bladder so she’s incontinent several times a day rather than several times an hour. She has hydrocephalus, which is the continuous accumulation of water in her brain, and she’s had more than 20 operations to repair the plastic tube that drains the water from her brain into her abdomen. She has had major surgery to remove pressure from the bones at the base of her brain, and she has metal rods in her spine so she can sit up.

She’s a fairly cheerful person, but she’s very afraid of surgery, and she cries each time I tell her that she needs another operation. Lately her greatest concern, aside from her visceral fear of the operating room, is that surgery will set her back. She has a lot to do.

She tries to schedule her surgery — even relatively urgent surgery — around her responsibilities. She takes her responsibilities to her fiancée and to her family very seriously. She works full time as an administrative assistant at a local hospital. In the evenings and on the weekends she attends college, and she’s close to getting her undergraduate degree. She plans to get her masters’ degree, and then a doctorate. During an office visit a few months ago, I told her that she would need another operation to relieve pressure that was gradually building on her brain. After we took a few minutes to deal with the emotions that such a recommendation evokes in her, I asked her what she was studying in college. Her spirits brightened.

“I’m studying medical administration. My dream is to be a hospital administrator and to run a hospital.” she said. Then she smiled. “I’m going to be your boss someday.”

The world is made better by every person.

1) From "Galton and Mid Century Eugenics" by Frederick Osborn, Galton Lecture 1956, in Eugenics Review, vol. 48, 1, 1956

Posted by Michael Egnor at 8:03 AM | Permalink | TrackBacks (1)

An announcement from Professor David Snoke:

"Grill the ID Scientist"

Tuesday, June 9
7 PM, University of Pittsburgh Campus (room TBA)

A network of scientists known as the Intelligent Design (ID) community continues to question basic tenets of Darwinism and origin-of-life scenarios. Not only are their views controversial in scientific circles — many in the evangelical world, who might be expected to embrace ID, are also not sold on the value of the ID program.

This event brings together a panel of scientists associated with the ID movement. After a short presentation, the bulk of the evening will be given to questions from the audience. This event is aimed primarily at researchers, graduate students and advanced undergrad students in the sciences. It is open to anyone, but participants must register in advance by sending email to snoke@pitt.edu. In the event of limited seating, preference will be given to grad students and researchers in the life sciences.

Panel:

-- Doug Axe, Biologic Institute (formerly of Cambridge University)
-- Michael Behe, Lehigh University
-- Ann Gauger, Biologic Institute
-- David Keller, University of New Mexico
-- John Sanford, Cornell University

+ others TBA

moderated by David Snoke, University of Pittsburgh

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Note: This is Part 5 in a 5-part series titled "A Primer on the Tree of Life." Read Part 1 here, Part 2 here, Part 3 here, and Part 4 here. The full article can be found, here.

Molecules Contradict Morphology
A final way that evolutionists overstate the evidence for common descent is by claiming that molecular phylogenies have confirmed or buttressed phylogenies based upon morphology. For example, in his book Galileo’s Finger, Oxford University scientist Peter Atkins discusses evolution and boldly states, “The effective prediction is that the details of molecular evolution must be consistent with those of macroscopic evolution,” further claiming, "That is found to be the case: there is not a single instance of the molecular traces of change being inconsistent with our observations of whole organisms."¹⁶ Likewise, when testifying before the Texas State Board of Education, David Hillis claimed that “there’s overwhelming correspondence between the basic structures we have about the tree of life from anatomical data, from biochemical data, molecular sequence data.” Yet a variety of studies — typically unmentioned when evolutionists promote common descent to the public — have recognized that evolutionary trees based upon morphology (physical characteristics of organisms) or fossils, commonly conflict with evolutionary trees based upon DNA or protein sequences (also called molecule-based trees).

One authoritative review paper by Darwinian leaders in this field stated, “As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened. Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology.”¹⁷ Another set of pro-evolution experts wrote, “That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists. Most of the latter know that the two lines of evidence may often be incongruent."¹⁸

For example, pro-evolution textbooks often tout the Cytochrome C phylogenetic tree as allegedly matching and confirming the traditional phylogeny of many animal groups. This is said to bolster the case for common descent. However, evolutionists cherry pick this example and 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.”¹⁹

The widespread prevalence of disagreement and non-correspondence between molecule-based evolutionary trees and anatomy-based evolutionary trees led to a major article in Nature that reported that “disparities between molecular and morphological trees” lead to “evolution wars” because “Evolutionary trees constructed by studying biological molecules often don’t resemble those drawn up from morphology.”²⁰ The article’s revelation of the disparities between molecular and morphological phylogenies was striking:

When biologists talk of the ‘evolution wars’, they usually mean the ongoing battle for supremacy in American schoolrooms between Darwinists and their creationist opponents. But the phrase could also be applied to a debate that is raging within systematics. On one side stand traditionalists who have built evolutionary trees from decades of work on species' morphological characteristics. On the other lie molecular systematists, who are convinced that comparisons of DNA and other biological molecules are the best way to unravel the secrets of evolutionary history. … So can the disparities between molecular and morphological trees ever be resolved? Some proponents of the molecular approach claim there is no need. The solution, they say, is to throw out morphology, and accept their version of the truth. “Our method provides the final conclusion about phylogeny,” claims Okada. Shared ancestry means a genetic relationship, the molecular camp argues, so it must be better to analyse DNA and the proteins it encodes, rather than morphological characters that can end up looking similar as a result of convergent evolution in unrelated groups, rather than through common descent. But morphologists respond that convergence can also happen at the molecular level, and note there is a long history of systematists making large claims based on one new form of evidence, only to be proved wrong at a later date.²¹

Despite the inaccurate claims of some evolutionists and their cherry picking of data, the truth is that there is great incongruence between these two different types of phylogenies, and that this incongruence is a huge issue, problem, and debate within systematics.

Conclusion
The methodology for inferring common descent has broken down. Proponents of neo-Darwinian evolution are forced into reasoning that similarity implies common ancestry, except for when it doesn’t. And when it doesn’t, they appeal to all sorts of ad hoc rationalizations to save common ancestry. Tellingly, the one assumption and view that they are not willing to jettison is the overall assumption of common ancestry itself. This shows that evolutionists treat common descent in an unfalsifiable, and therefore unscientific and ideological, fashion.

Meanwhile, as far as the data is concerned, the aforementioned New Scientist article admits, "Ever since Darwin the tree has been the unifying principle for understanding the history of life on Earth," but because "different genes told contradictory evolutionary stories" the notion of a tree of life is now quickly becoming a vision of the past -- as the article stated "today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded," and as scientists quoted in the article said, "We have no evidence at all that the tree of life is a reality" or the tree is being "annihilated." Perhaps the reason why different genes are telling “different evolutionary stories” is because the genes have wholly different stories to tell, namely stories that indicate that all organisms are not genetically related. For those open-minded enough to consider it, common design is a viable alternative to common descent.

References Cited:

[16.] Peter Atkins, Galileo's Finger: The Ten Great Ideas of Science, pg. 16 (Oxford University Press, 2003).

[17.] Patterson et al., "Congruence between Molecular and Morphological Phylogenies," Annual Review of Ecology and Systematics, Vol 24, pg. 179 (1993) (emphasis added).

[18.] Masami Hasegawa, Jun Adachi, Michel C. Milinkovitch, "Novel Phylogeny of Whales Supported by Total Molecular Evidence," Journal of Molecular Evolution, Vol. 44, pgs. S117-S120 (Supplement 1, 1997) (emphasis added).

[19.] See Michael S. Y. Lee, “Molecular phylogenies become functional,” Trends in Ecology and Evolution, Vol. 14:177-178 (1999) (emphasis added).

[20.] Trisha Gura, “Bones, Molecules or Both?,” Nature, Vol. 406:230-233 (July 20, 2000) (emphasis added).

[21.] Trisha Gura, “Bones, Molecules or Both?,” Nature, Vol. 406:230-233 (July 20, 2000).

[22.] Matthew A. Wills, "The tree of life and the rock of ages: are we getting better at estimating phylogeny," BioEssays, Vol. 24: 203-207 (2002), reporting on the findings of Michael J. Benton, "Finding the tree of life: matching phylogenetic trees to the fossil record through the 20th century," Proceedings of the Royal Society of London B, Vol. 268: 2123-2130 (2001).

[23.] W. W. De Jong, “Molecules remodel the mammalian tree,” Trends in Ecology and Evolution, Vol 13(7), pgs. 270-274 (July 7, 1998).

Posted by Casey Luskin at 7:10 AM | Permalink | TrackBacks (0)

Note: This is Part 4 in a 5-part series titled "A Primer on the Tree of Life." Read Part 1 here, Part 2 here, Part 3 here, and Part 5 here. The full article can be found, here.

Homology in Crisis
As Mayr suggests, there are other examples where genetic similarity appears in unexpected places. Biologically functional similarity that is thought to be the result of inheritance from a common ancestor is called “homology.”

The concept of “homology” has been thrown into a crisis via observations, like those of Mayr, that the same genes control the growth of non-homologous body parts. Pax-6 is just one example. Another is the fact that the same gene controls the development of limbs in widely diverse types organisms that have wholly different types of limbs, where their common ancestor is not thought to have a common type of limb.¹⁴ The methodology used to infer homology was also challenged when it was discovered that different developmental pathways control the growth of body parts otherwise thought to be homologous. As the textbook Explore Evolution observes:

In sharks, for example, the gut develops from cells in the roof of the embryonic cavity. In lampreys, the gut develops from cells on the floor of the cavity. And in frogs, the gut develops from cells from both the roof and the floor of the embryonic cavity. This discovery—that homologous structures can be produced by different developmental pathways—contradicts what we would expect to find if all vertebrates share a common ancestor. … To summarize, biologists have made two discoveries that challenge the argument from anatomical homology. The first is that the development of homologous structures can be governed by different genes and can follow different developmental pathways. The second discovery, conversely, is that sometimes the same gene plays a role in producing different adult structures. Both of these discoveries seem to contradict neo-Darwinian expectations.¹⁵

References Cited:
[14.] Paul Nelson and Jonathan Wells, “Homology in Biology,” in Darwinism, Design, and Public Education, John Angus Campbell and Stephen C. Meyer eds. (East Lansing: Michigan State University Press, 2003).

[15.] Stephen C. Meyer, Scott Minnich, Jonathan Moneymaker, Paul A. Nelson, and Ralph Seelke, Explore Evolution: The Arguments For and Against Neo-Darwinism, pgs. 44-45 (Hill House, 2007).”

Posted by Casey Luskin at 7:46 AM | Permalink | TrackBacks (1)

Note: This is Part 6 in a series reviewing Jerry Coyne's Why Evolution Is True. Read Part 1 here, Part 2 here, Part 3 here, Part 4 here, and Part 5 here.

Theological arguments are also prominent in The Origin of Species. For example, Darwin argued that the geographic distribution of living things made no sense if species had been separately created, but it did make sense in the context of his theory. Cases such as “the presence of peculiar species of bats on oceanic islands and the absence of all other terrestrial mammals,” Darwin wrote, “are facts utterly inexplicable on the theory of independent acts of creation.” In particular: “Why, it may be asked, has the supposed creative force produced bats and no other mammals on remote islands?” According to Darwin, “on my view this question can easily be answered; for no terrestrial mammal can be transported across a wide space of sea, but bats can fly across.”³⁴

But Darwin knew that migration cannot account for all patterns of geographic distribution. He wrote in The Origin of Species that “the identity of many plants and animals, on mountain-summits, separated from each other by hundreds of miles of lowlands, where Alpine species could not possibly exist, is one of the most striking cases known of the same species living at distant points without the apparent possibility of their having migrated from one point to the other.” Darwin argued that the recent ice age “affords a simple explanation of these facts.” Arctic plants and animals that were “nearly the same” could have flourished everywhere in Europe and North America, but “when the warmth had fully returned, the same species, which had lately lived together on the European and North American lowlands, would again be found in the arctic regions of the Old and New Worlds, and on many isolated mountain-summits far distant from each other.”³⁵

So some cases of geographic distribution may not be due to migration, but to the splitting of a formerly large, widespread population into small, isolated populations—what modern biologists call “vicariance.” Darwin argued that all modern distributions of species could be explained by these two possibilities. Yet there are many cases of geographic distribution that neither migration nor vicariance seem able to explain.

One example is the worldwide distribution of flightless birds, or “ratites.” These include ostriches in Africa, rheas in South America, emus and cassowaries in Australia, and kiwis in New Zealand. Since the birds are flightless, explanations based on migration over vast oceanic distances are implausible. After continental drift was discovered in the twentieth century, it was thought that the various populations might have separated with the landmasses. But ostriches and kiwis are much too recent; the continents had already drifted apart when these species originated. So neither migration nor vicariance explain ratite biogeography.³⁶

Another example is freshwater crabs. Studied intensively by Italian biologist Giuseppe Colosi in the 1920s, these animals complete their life cycles exclusively in freshwater habitats and are incapable of surviving prolonged exposure to salt water. Today, very similar species are found in widely separated lakes and rivers in Central and South America, Africa, Madagascar, southern Europe, India, Asia and Australia. Fossil and molecular evidence indicates that these animals originated long after the continents separated, so their distribution is inconsistent with the vicariance hypothesis. Some biologists speculate that the crabs may have migrated by “transoceanic rafting” in hollow logs, but this seems unlikely given their inability to tolerate salt water. So neither vicariance nor migration provides a convincing explanation for the biogeography of these animals.³⁷

An alternative explanation was suggested in the mid-twentieth century by Léon Croizat, a French biologist raised in Italy. Croizat found that Darwin’s theory did “not seem to agree at all with certain important facts of nature,” especially the facts of biogeography. Indeed, he concluded, “Darwinism is by now only a straitjacket… a thoroughly decrepit skin to hold new wine.” Croizat did not argue for independent acts of creation; instead, he proposed that in many cases a widespread primitive species was split into fragments, then its remnants evolved in parallel, in separate locations, into new species that were remarkably similar. Croizat called this process of parallel evolution “orthogenesis.” Neo-Darwinists such as Ernst Mayr, however, pointed out that there is no mechanism for orthogenesis, which implies—contrary to Darwinism—that evolution is guided in certain directions; so they rejected Croizat’s hypothesis.³⁸

In Why Evolution Is True, Coyne (like Darwin) attributes the biogeography of oceanic islands to migration, and certain other distributions to vicariance. But Coyne (unlike Darwin) acknowledges that these two processes cannot explain everything. For example, the internal anatomy of marsupial mammals is so different from the internal anatomy of placental mammals that the two groups are thought to have split a long time ago. Yet there are marsupial flying squirrels, anteaters and moles in Australia that strikingly resemble placental flying squirrels, anteaters and moles on other continents, and these forms originated long after the continents had separated.

Coyne attributes the similarities to “a well-known process called convergent evolution.” According to Coyne. “It’s really quite simple. Species that live in similar habitats will experience similar selection pressures from their environment, so they may evolve similar adaptations, or converge, coming to look and behave very much alike even though they are unrelated.” Put together common ancestry, natural selection, and the origin of species (“speciation”), “add in the fact that distant areas of the world can have similar habitats, and you get convergent evolution—and a simple explanation of a major geographic pattern.”³⁹

This is not the same as Croizat’s “orthogenesis,” according to which populations of a single species, after becoming separated from each other, evolve in parallel due to some internal directive force. According to Coyne’s “convergent evolution,” organisms that are fundamentally different from each other evolve through natural selection to become superficially similar because they inhabit similar environments. The mechanism for orthogenesis is internal, whereas the mechanism for convergence is external. In both cases, however, mechanism is crucial: Without it, orthogenesis and convergence are simply words describing biogeographical patterns, not explanations of how those patterns originated.

So the same question can be asked of convergence that was asked of orthogenesis: What is the evidence for the proposed mechanism? According to Coyne, the mechanism of convergence involves natural selection and speciation.

Notes
³⁴ Darwin, The Origin of Species, Chapters XIII (pp. 347-352) and XV (p. 419). Available online (2009) here.
³⁵ Darwin, The Origin of Species, Chapters XII (pp. 330-332). Available online (2009) here.
³⁶ Alan Cooper, et al., C. Mourer-Chauviré, C.K. Chambers, A. von Haeseler, A.C. Wilson & S. Paabo, “Independent origins of New Zealand moas and kiwis,” Proceedings of the National Academy of Sciences USA 89 (1992): 8741-8744. Available online (2008) here.
Oliver Haddrath & Allan J. Baker, “Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis,” Proceedings of the Royal Society of London B 268 (2001): 939-945.
John Harshman, E.L. Braun, M.J. Braun, C.J. Huddleston, R.C.K. Bowie,
J.L. Chojnowski, S.J. Hackett, K.-L. Han, R.T. Kimball, B.D. Marks, K.J. Miglia,
W.S. Moore, S. Reddy, F.H. Sheldon, D.W. Steadman, S.J. Steppan, C.C. Witt & T. Yuri, “Phylogenomic evidence for multiple losses of flight in ratite birds,” Proceedings of the National Academy of Sciences USA 105 (2008): 13462-13467. Abstract available online (2008) here.
Giuseppe Sermonti, “L'evoluzione in Italia - La via torinese / How Evolution Came to Italy - The Turin Connection,” Rivista di Biologia/Biology Forum 94 (2001): 5-12. Available online (2008) here.
³⁷ Giuseppe Colosi, “La distribuzione geografica dei Potamonidae,” Rivista di Biologia 3 (1921): 294-301. Available online (2009) here.
Savel R. Daniels, N. Cumberlidge, M. Pérez-Losada, S.A.E. Marijnissen &
K.A. Crandall, “Evolution of Afrotropical freshwater crab lineages obscured by morphological convergence,” Molecular Phylogenetics and Evolution 40 (2006): 227–235. Available online (2009) here.
R. von Sternberg, N. Cumberlidge & G. Rodriguez. “On the marine sister groups of the freshwater crabs (Crustacea: Decapoda: Brachyura),” Journal of Zoological Systematics and Evolutionary Research 37 (1999): 19–38.
Darren C.J. Yeo, et al., “Global diversity of crabs (Crustacea: Decapoda: Brachyura) in freshwater,” Hydrobiologia 595 (2008): 275-286.
³⁸ Léon Croizat, Space, Time, Form: The Biological Synthesis. Published by the author (Deventer, Netherlands: N. V. Drukkerij Salland, 1962), p. iii.
Robin C. Craw, “Léon Croizat's Biogeographic Work: A Personal Appreciation,” Tuatara 27:1 (August 1984): 8-13. Available online (2009) here.
John R. Grehan, “Evolution By Law: Croizat's ‘Orthogeny’ and Darwin's ‘Laws of Growth’,” Tuatara 27:1 (August 1984): 14-19. Available online (2009) here.
Carmen Colacino, “Léon Croizat’s Biogeography and Macroevolution, or… ‘Out of Nothing, Nothing Comes’,” The Philippine Scientist 34 (1997): 73-88.
Ernst Mayr, The Growth of Biological Thought (Cambridge, MA: Harvard University Press, 1982), pp. 529-530.
³⁹ Coyne, Why Evolution Is True, pp. 92-94.

Posted by Jonathan Wells at 9:00 AM | Permalink | TrackBacks (0)

Note: This is Part 3 in a 5-part series titled "A Primer on the Tree of Life." Read Part 1 here, Part 2 here, Part 4 here, and Part 5 here. The full article can be found, here.

Extreme Genetic Convergent Similarity: Common Design or Common Descent?
If common descent is leading to so many bad predictions, why not consider the possibility that biological similarity is instead the result of common design? After all, designers regularly re-use parts, programs, or components that work in different designs (such as using wheels on both cars and airplanes, or keyboards on both computers and cell-phones).

One data-point that might suggest common design rather than common descent is the gene “pax-6.” Pax-6 is one of those pesky instances where extreme genetic similarity popped up in a place totally unexpected and unpredicted by evolutionary biology. In short, scientists have discovered that organisms as diverse as jellyfish, arthropods, mollusks, and vertebrates all use pax-6 to control development of their very distinct types of eyes. Because their eye-types are so different, it previously hadn’t been thought that these organisms even shared a common ancestor with an eye. Evolutionary biologist Ernst Mayr explains the havoc wreaked within the standard evolutionary phylogeny when it was discovered that the same gene controlled eye-development in many organisms with very different types of eyes:

It had been shown that by morphological-phylogenetic research that photoreceptor organs (eyes) had developed at least 40 times independently during the evolution of animal diversity. A developmental geneticist, however, showed that all animals with eyes have the same regulator gene, Pax 6, which organizes the construction of the eye. It was therefore at first concluded that all eyes were derived from a single ancestral eye with the Pax 6 gene. But then the geneticist also found Pax 6 in species without eyes, and proposed that they must have descended from ancestors with eyes. However, this scenario turned out to be quite improbable and the wide distribution of Pax 6 required a different explanation. It is now believed that Pax 6, even before the origin of eyes, had an unknown function in eyeless organisms, and was subsequently recruited for its role as an eye organizer.¹²

That a structure like the eye could originate numerous times independently in very different kinds of organisms is not unique in the living world. After photoreceptors had evolved in animals, bioluminescence originated at least 30 times independently among various kinds of organisms. In most cases, essentially similar biochemical mechanisms were used. Virtually scores of similar cases have been discovered in recent years, and they often make use of hidden potentials of the genotype inherited from early ancestors.¹³

References Cited:
[12.] Ernst Mayr, What Evolution Is?, pg. 113 (Basic Books, 2001).

[13.] Id. at 205-207.

Posted by Casey Luskin at 1:20 AM | Permalink | TrackBacks (0)

In the wake of the Texas school board decision to require students to analyze and evaluate certains aspects of Darwinian evolution, CSC program officer for public policy Casey Luskin appeared on Fox & Friends this morning to discuss common problems regarding evolution still found in biology textbooks.

Posted by Robert Crowther at 2:15 PM | Permalink | TrackBacks (0)

Note: This is Part 2 in a 5-part series titled "A Primer on the Tree of Life." Read Part 1 here, Part 3 here, Part 4 here, and Part 5 here. The full article can be found, here.

The Molecular Evidence
When speaking to the public, evolutionists are infamous for overstating the evidence for universal common ancestry. For example, when speaking before the Texas State Board of Education in January, 2009, University of Texas evolutionist biologist David Hillis cited himself as one of the “world’s leading experts on the tree of life” and later told the Board that there is “overwhelming agreement correspondence as you go from protein to protein, DNA sequence to DNA sequence” when reconstructing evolutionary history using biological molecules. But this is not accurate. Indeed, in the technical scientific literature, one finds a vast swath of scientific papers that have found contradictions, inconsistencies, and flat out failures of the molecular data to provide a clear picture of phylogenetic history and common descent.

Indeed, the cover story of the journal New Scientist, published on the very day that Dr. Hillis testified, was titled, “Why Darwin was wrong about the tree of life.” Directly contradicting Hillis’ gross oversimplification of molecular systematics, the article reported that “The problem was that different genes told contradictory evolutionary stories.” The article observed that with the sequencing of the genes and proteins of various living organisms, the tree of life fell apart:

“For a long time the holy grail was to build a tree of life,” says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. “We have no evidence at all that the tree of life is a reality,” says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.²

The 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 B than species C, but a tree made from DNA would suggest the reverse.³

Syvanen recently compared 2000 genes that are common to humans, frogs, sea squirts, sea urchins, fruit flies and nematodes. In theory, he should have been able to use the gene sequences to construct an evolutionary tree showing the relationships between the six animals. He failed. The problem was that different genes told contradictory evolutionary stories. This was especially true of sea-squirt genes. Conventionally, sea squirts—also known as tunicates—are lumped together with frogs, humans and other vertebrates in the phylum Chordata, but the genes were sending mixed signals. Some genes did indeed cluster within the chordates, but others indicated that tunicates should be placed with sea urchins, which aren't chordates. “Roughly 50 per cent of its genes have one evolutionary history and 50 per cent another,” Syvanen says.⁵

Other scientists agree with the conclusions of the New Scientist article. Looking higher up the tree, a recent study published in Science tried to construct a phylogeny of animal relationships but concluded that “[d]espite the amount of data and breadth of taxa analyzed, relationships among most [animal] phyla remained unresolved.”⁶ Likewise, Carl Woese, a pioneer of evolutionary molecular systematics, observed that these problems extend well beyond the base of the tree of life: “Phylogenetic incongruities [conflicts] can be seen everywhere in the universal tree, from its root to the major branchings within and among the various taxa to the makeup of the primary groupings themselves.”⁷

Likewise, National Academy of Sciences biologist Lynn Margulis has had harsh words for the field of molecular systematics, which Hillis studies. In her article, “The Phylogenetic Tree Topples,” she explains that “many biologists claim they know for sure that random mutation (purposeless chance) is the source of inherited variation that generates new species of life and that life evolved in a single-common-trunk, dichotomously branching-phylogenetic-tree pattern!” But she dissents from that view and attacks the dogmatism of evolutionary systematists, noting, “Especially dogmatic are those molecular modelers of the ‘tree of life’ who, ignorant of alternative topologies (such as webs), don’t study ancestors.”⁸

Striking admissions of troubles in reconstructing the “tree of life” also came from a 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.”⁹ The paper suggests that “certain critical parts of the [tree of life] may be difficult to resolve, regardless of the quantity of conventional data available.”¹⁰ The paper even contends that “[t]he recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics.”¹¹

Unfortunately, one assumption that these evolutionary biologists aren’t willing to consider changing is the assumption that neo-Darwinism and universal common ancestry are correct.

References Cited
[2.] Graham Lawton, "Why Darwin was wrong about the tree of life," New Scientist (January 21, 2009) (emphasis added).

[3.] Graham Lawton, "Why Darwin was wrong about the tree of life," New Scientist (January 21, 2009).

[4.] W. Ford Doolittle, "Phylogenetic Classification and the Universal Tree," Science, Vol. 284:2124-2128 (June 25, 1999).

[5.] Graham Lawton, "Why Darwin was wrong about the tree of life," New Scientist (January 21, 2009).

[6.] Antonis Rokas, Dirk Krueger, Sean B. Carroll, "Animal Evolution and the Molecular Signature of Radiations Compressed in Time," Science, Vol. 310:1933-1938 (Dec. 23, 2005).

[7.] Carl Woese "The Universal Ancestor," Proceedings of the National Academy of Sciences USA, Vol. 95:6854-9859 (June, 1998) (emphasis added).

[8.] Lynn Margulis, “The Phylogenetic Tree Topples,” American Scientist, Vol 94 (3) (May-June, 2006).

[9.] Antonis Rokas & Sean B. Carroll, "Bushes in the Tree of Life," PLOS Biology, Vol 4(11): 1899-1904 (Nov., 2006) (internal citations and figures omitted).

[10.] Antonis Rokas & Sean B. Carroll, "Bushes in the Tree of Life," PLOS Biology, Vol 4(11): 1899-1904 (Nov., 2006) (internal citations and figures omitted).

[11.] Antonis Rokas & Sean B. Carroll, "Bushes in the Tree of Life," PLOS Biology, Vol 4(11): 1899-1904 (Nov., 2006) (internal citations and figures omitted).

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

Note: This is Part 1 in a 5-part series titled "A Primer on the Tree of Life." Read Part 2 here, Part 3 here, Part 4 here, and Part 5 here. The full article can be found, here.

Evolutionists often claim that universal common ancestry and the “tree of life” are established facts. One recent opinion article in argued, “The evidence that all life, plants and animals, humans and fruit flies, evolved from a common ancestor by mutation and natural selection is beyond theory. It is a fact. Anyone who takes the time to read the evidence with an open mind will join scientists and the well-educated.”¹ The take-home message is that if you doubt Darwin’s tree of life, you’re ignorant. No one wants to be ridiculed, so it’s a lot easier to buy the rhetoric and “join scientists and the well-educated.”

But what is the evidence for their claim, and how much of it is based upon assumptions? The truth is that common ancestry is merely an assumption that governs interpretation of the data, not an undeniable conclusion, and whenever data contradicts expectations of common descent, evolutionists resort to a variety of different ad hoc rationalizations to save common descent from being falsified.

Some of these ad hoc rationalizations may appear reasonable — horizontal gene transfer, convergent evolution, differing rates of evolution (rapid evolution is conveniently said to muddy any phylogenetic signal), fusion of genomes — but at the end of the day, we must call them what they are: ad hoc rationalizations designed to save a theory that has already been falsified. Because it is taken as an assumption, evolutionists effectively treat common ancestry in an unfalsifiable and unscientific fashion, where any data that contradicts the expectations of common descent is simply explained away via one of the above ad hoc rationalizations. But if we treat common descent as it ought to be treated — as a testable hypothesis — then it contradicts much data.

The Main Assumption
As noted, the first assumption that goes into tree-building is the basic assumption that similarity between different organisms is the result of inheritance from a common ancestor. That is, except for when it isn’t. (And then the similarity is purportedly said to be the result of convergent evolution, etc.) But even if we take this claim at face value — that similarity between different organisms is the result of inheritance from a common ancestor — let’s recognize it for what it is: a mere assumption. But are there other possibilities?

I'll explore more problems with the tree of life and other possibilities in a series of five total posts in this series.

Reference Cited:
[1.] Perry Mann, "The Dinky Insect That Helps Demonstrate Darwin's Theory," at http://www.huntingtonnews.net/columns/090427-mann-columnsmanntalk.html (April 27, 2009).

Posted by Casey Luskin at 7:12 AM | Permalink | TrackBacks (0)

Note: This is Part 5 in a series reviewing Jerry Coyne's Why Evolution Is True. Read Part 1 here, Part 2 here, Part 3 here, and Part 4 here.

Darwin argued in The Origin of Species that the widespread occurrence of vestigial organs — organs that may have once had a function but are now useless — is evidence against creation. “On the view of each organism with all its separate parts having been specially created, how utterly inexplicable is it that organs bearing the plain stamp of inutility… should so frequently occur.” But such organs, he argued, are readily explained by his theory: “On the view of descent with modification, we may conclude that the existence of organs in a rudimentary, imperfect, and useless condition, or quite aborted, far from presenting a strange difficulty, as they assuredly do on the old doctrine of creation, might even have been anticipated in accordance with the views here explained.”²⁵

In The Descent of Man, Darwin cited the human appendix as an example of a vestigial organ. But Darwin was mistaken: The appendix is now known to be an important source of antibody-producing blood cells and thus an integral part of the human immune system. It may also serve as a compartment for beneficial bacteria that are needed for normal digestion. So the appendix is not useless at all.²⁶

In 1981, Canadian biologist Steven Scadding argued that although he had no objection to Darwinism, “vestigial organs provide no evidence for evolutionary theory.” The primarily reason is that “it is difficult, if not impossible, to unambiguously identify organs totally lacking in function.” Scadding cited the human appendix as an organ previously thought to be vestigial but now known to have a function. Another Canadian biologist, Bruce Naylor, countered that an organ with some function can still be considered vestigial. Furthermore, Naylor argued, “perfectly designed organisms necessitated the existence of a creator,” but “organisms are often something less than perfectly designed” and thus better explained by evolution. Scadding replied: “The entire argument of Darwin and others regarding vestigial organs hinges on their uselessness and inutility.” Otherwise, the argument from vestigiality is nothing more than an argument from homology, and “Darwin treated these arguments separately recognizing that they were in fact independent.” Scadding also objected that Naylor’s “less than perfectly designed” argument was “based on a theological assumption about the nature of God, i.e. that he would not create useless structures. Whatever the validity of this theological claim, it certainly cannot be defended as a scientific statement, and thus should be given no place in a scientific discussion of evolution.”²⁷

In Why Evolution Is True, Coyne (like Darwin) cites the human appendix as an example of a vestigial organ. Unlike Darwin, however, Coyne concedes that “it may be of some small use. The appendix contains patches of tissue that may function as part of the immune system. It has also been suggested that it provides a refuge for useful gut bacteria. But these minor benefits are surely outweighed by the severe problems that come with the human appendix.” In any case, Coyne argues, “the appendix is still vestigial, for it no longer performs the function for which it evolved.”²⁸

As Scadding had pointed out nearly thirty years ago, however, Darwin’s argument rested on lack of function, not change of function. Furthermore, if vestigiality were redefined as Coyne proposes, it would include many features never before thought to be vestigial. For example, if the human arm evolved from the leg of a four-footed mammal (as Darwinists claim), then the human arm is vestigial. And if (as Coyne argues) the wings of flying birds evolved from feathered forelimbs of dinosaurs that used them for other purposes, then the wings of flying birds are vestigial. This is the opposite of what most people mean by “vestigial.”²⁹

Coyne also ignores Scadding’s other criticism, arguing that whether the human appendix is useless or not, it is an example of imperfect or bad design. “What I mean by ‘bad design’,” Coyne writes, “is the notion that if organisms were built from scratch by a designer—one who used the biological building blocks or nerves, muscles, bone, and so on—they would not have such imperfections. Perfect design would truly be the sign of a skilled and intelligent designer. Imperfect design is the mark of evolution; in fact, it’s precisely what we expect from evolution.”³⁰

An even better example of bad design, Coyne argues, is the prevalence of “dead genes.” According to the modern version of Darwinism that Coyne defends, DNA carries a genetic program that encodes proteins that direct embryo development; mutations occasionally alter the genetic program to produce new proteins (or change their locations); and natural selection then sorts those mutations to produce evolution. In the 1970s, however, molecular biologists discovered that most of our DNA does not encode proteins. In 1972 Susumu Ohno called this “junk,” and in 1976 Richard Dawkins wrote: “A large fraction of the DNA is never translated into protein. From the point of view of the individual organism this seems paradoxical. If the ‘purpose’ of DNA is to supervise the building of bodies, it is surprising to find a large quantity of DNA which does no such thing.” From the point of view of Darwinian evolution, however, there is no paradox. “The true ‘purpose’ of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.”³¹

Like Dawkins, Coyne regards much of our DNA as parasitic. He writes in Why Evolution Is True: “When a trait is no longer used, or becomes reduced, the genes that make it don't instantly disappear from the genome: evolution stops their action by inactivating them, not snipping them out of the DNA. From this we can make a prediction. We expect to find, in the genomes of many species, silenced, or ‘dead,’ genes: genes that once were useful but are no longer intact or expressed. In other words, there should be vestigial genes. In contrast, the idea that all species were created from scratch predicts that no such genes would exist.” Coyne continues:

Thirty years ago we couldn't test this prediction because we had no way to read the DNA code. Now, however, it’s quite easy to sequence the complete genome of species, and it’s been done for many of them, including humans. This gives us a unique tool to study evolution when we realize that the normal function of a gene is to make a protein—a protein whose sequence of amino acids is determined by the sequence of nucleotide bases that make up the DNA. And once we have the DNA sequence of a given gene, we can usually tell if it is expressed normally—that is, whether it makes a functional protein—or whether it is silenced and makes nothing. We can see, for example, whether mutations have changed the gene so that a usable protein can no longer be made, or whether the ‘control’ regions responsible for turning on a gene have been inactivated. A gene that doesn’t function is called a pseudogene. And the evolutionary prediction that we’ll find pseudogenes has been fulfilled—amply. Virtually every species harbors dead genes, many of them still active in its relatives. This implies that those genes were also active in a common ancestor, and were killed off in some descendants but not in others. Out of about thirty thousand genes, for example, we humans carry more than two thousand pseudogenes. Our genome—and that of other species—are truly well populated graveyards of dead genes.³²

But Coyne is dead wrong.

Evidence pouring in from genome-sequencing projects shows that virtually all of an organism’s DNA is transcribed into RNA, and that even though most of that RNA is not translated into proteins, it performs essential regulatory functions. Every month, science journals publish articles describing more such functions. And this is not late-breaking news: The evidence has been accumulating since 2003 (when scientists finished sequencing the human genome) that “pseudogenes” and other so-called “junk DNA” sequences are not useless after all.³³

Why Evolution Is True ignores this enormous body of evidence, which decisively refutes Coyne’s Darwinian prediction that our genome should contain lots of “dead” DNA. It’s no wonder that Coyne falls back again and again on the sort of theological arguments that Scadding wrote “should be given no place in a scientific discussion of evolution.”

Notes
²⁵ Darwin, The Origin of Species, Chapters XIV (p. 402) and XV (p. 420). Available online (2009) here.
²⁶ Darwin, Charles. The Descent of Man, First Edition (London: John Murray, 1871), Chapter I (p. 27). Available online (2009) here.
Kohtaro Fujihashi, J.R. McGhee, C. Lue, K.W. Beagley, T. Taga, T. Hirano, T. Kishimoto, J. Mestecky & H. Kiyono, “Human Appendix B Cells Naturally Express Receptors for and Respond to Interleukin 6 with Selective IgA1 and IgA2 Synthesis,” Journal of Clinical Investigations 88 (1991): 248-252. Available online (2009) here.
J.A. Laissue, B.B. Chappuis, C. Müller, J.C. Reubi & J.O. Gebbers, “The intestinal immune system and its relation to disease,” Digestive Diseases (Basel) 11 (1993): 298-312. Abstract available online (2009) here.
Loren G. Martin, “What is the function of the human appendix?” Scientific American (October 21, 1999), Available online (2009) here.
R. Randal Bollinger, Andrew S. Barbas, Errol L. Bush, Shu S. Lin & William Parker, “Biofilms in the large bowel suggest an apparent function of the human vermiform appendix,” Journal of Theoretical Biology 249 (2007): 826-831. Available online (2009) here.
Duke University Medical Center, “Appendix Isn't Useless At All: It's A Safe House For Good Bacteria,” ScienceDaily (October 8, 2007). Available online (2009) here.
²⁷ Steven R. Scadding, “Do ‘vestigial organs’ provide evidence for evolution?” Evolutionary Theory 5 (1981): 173-176.
Bruce G. Naylor, “Vestigial organs are evidence of evolution,” Evolutionary Theory 6 (1982): 91-96.
Steven R. Scadding, “Vestigial organs do not provide scientific evidence for evolution,” Evolutionary Theory 6 (1982): 171-173.
²⁸ Coyne, Why Evolution Is True, pp. 61-62.
²⁹ Coyne, Why Evolution Is True, p. 46.
³⁰ Coyne, Why Evolution Is True, pp. 81.
³¹ Susumu Ohno, “So much ‘junk’ DNA in our genome,” Brookhaven Symposia in Biology 23 (1972): 366-70.
Richard Dawkins, The Selfish Gene (New York: Oxford University Press, 1976), p. 47.
³² Coyne, Why Evolution Is True, pp. 66-67.
³³ A few of the many scientific articles published since 2003 that document the function of so-called “junk” DNA are:
E.S Balakirev & F.J. Ayala, “Pseudogenes: are they ‘junk’ or functional DNA?” Annual Review of Genetics 37 (2003): 123-151.
A. Hüttenhofer, P. Schattner & N. Polacek, “Non-coding RNAs: hope or hype?” Trends in Genetics 21 (2005): 289-297.
J.S. Mattick & I.V. Makunin, “Non-coding RNA,” Human Molecular Genetics 15 (2006): R17-R29.
R.K. Slotkin & R. Martienssen, “Transposable elements and the epigenetic regulation of the genome,” Nature Reviews Genetics 8 (2007): 272-285.
P. Carninci, J. Yasuda & Y Hayashizaki, “Multifaceted mammalian transcriptome,” Current Opinion in Cell Biology 20 (2008): 274-80.
C.D. Malone & G.J. Hannon, “Small RNAs as Guardians of the Genome,” Cell 136 (2009): 656–668.
C.P. Ponting, P.L. Oliver & W. Reik, “Evolution and Functions of Long Noncoding RNAs,” Cell 136 (2009): 629–641.

Posted by Jonathan Wells at 10:30 AM | Permalink | TrackBacks (0)

Update: On May 4, 2009, The New York Times, perhaps unsurprisingly, came out with a story casting the swine flu as an example of evolution, titled "10 Genes, Furiously Evolving." Similarly, the staunchly pro-evolution site LiveScience.com has an article on the swine flu that opens by mocking Darwin-skeptics, stating: "Anyone who thinks evolution is for the birds should not be afraid of swine flu. Because if there's no such thing as evolution, then there's no such thing as a new strain of swine flu infecting people." As is discussed in Luskin's piece below, such a claim is a cheap-shot that completely mis-states and misrepresents the position of Darwin-skeptics.

A few years ago, the media was abuzz over the scare of the avian flu virus, which led me to write a post titled Avian Flu: An Example of Evolution?. At the time, it wasn't clear whether the avian flu would evolve and "jump" into a highly virulent form that easily infected humans. Had the avian flu virus made the jump, then we would have witnessed a sort of evolution where viruses swap genetic material in a process known as "reassortment" and can then more easily infect new hosts, such as humans. As I explained at that time:

So our fight to combat the Avian flu is undoubtedly a fight against evolution. The question is, has there been a net increase in genetic information through this "evolution"? The Avian flu is essentially the swapping of genes--but its genes probably came from other pre-existing viruses.

Pigs are well-known crucibles for mixing viruses, able to harbour strains of flu that normally are specific to pigs, birds and humans. When present in the same animal, these viruses are able to swap genes as they replicate, which can result in a new strain and leap the species barrier to humans.

After All This "Evolution," It's Still a Virus
In his 2007 book The Edge of Evolution, Michael Behe observed that after our attempts to kill disease-causing bacteria and viruses, some can evolve via Darwinian selection to evade our disease-fighting strategies. Yet despite this evolution, they remain bacteria and viruses — with very little net change. As Behe writes:

Indeed, the work on malaria and AIDS demonstrates that after all possible unintelligent processes in the cell--both ones we've discovered so far and ones we haven't--at best extremely limited benefit, since no such process was able to do much of anything. It's critical to notice that no artificial limitations were placed on the kinds of mutations or processes the microorganisms could undergo in nature. Nothing--neither point mutation, deletion, insertion, gene duplication, transposition, genome duplication, self-organization nor any other process yet undiscovered--was of much use. (Behe, The Edge of Evolution, pg. 162)

To further show the alleged utility of evolution, Hillis discussed how mutations in one particular protein of the influenza virus allow it to escape detection by our immune system, stating “phylogenetic analysis … is a critical tool for developing flu vaccines every year,” and asserting that “knowledge of evolution helps millions of human lives be saved every year.” While there is no doubt that influenza “evolution” is a real phenomenon, we must ask the crucial questions: What degree of evolution is this? And can this sort of “evolution” be legitimately extrapolated to explain large-scale evolutionary changes? In other words, if we were teaching students about this type of “evolution,” should we teach them that it implies large scale macroevolutionary change that could explain the origin of complex biological features, such as new body plans?

The answer is clearly no. The truth is that the mutations in the hemagglutinin molecule testified about by Dr. Hills represent small-scale changes in a limited number of amino acids in one domain of the protein that do not change the virus’s function for this protein (it resides on the surface of viruses and its function is to bind the flu virus to the infected cell).³ Nothing in Dr. Hillis’s comments alters the fact that the flu virus remains a virtually identical virus after the microevolutionary changes he describes. Lives may be saved by studying functionally trivial amino acid changes in this protein, but it is not due to knowledge of any kind of evolution that can explain the origin of new species or body plans.

An Analysis of the Expert Testimony of Prof. David Hillis before the Texas State Board of Education on January 21, 2009

The Evolutionary Origin of Viruses? "Forever Obscure"
Evolution appears tightly constrained, yet we see a suite of complicated micro-killers like viruses. How did viruses arise in the first place? After reviewing some of the speculative, vague, and detail-free ideas about how viruses might have arisen, an article in Scientific American admitted last year, "At the end of the day, however, despite all of their common features and unique abilities to copy and spread their genomes, the origins of most viruses may remain forever obscure."

Let's just hope that a cure for the swine flu virus is less obscure than its ultimate origin.

Posted by Casey Luskin at 9:10 AM | Permalink | TrackBacks (0)