The Cambrian Conundrum: Stephen Meyer Says (Lack of) Fossils Trumps Genes

Darwin's Doubt is a book about the problems surrounding the Cambrian Explosion. It's written by a prominent Intelligent Design Creationist and, like most books by IDiots, the main theme is how scientists get everything wrong.

The "problem" is how to account for the very rapid appearance of complex animals about 530 million years ago. Intelligent Design Creationists think that they can ignore all of the evidence for evolution for the following 530 million years and focus on this one problem to discredit naturalistic explanations for the history of life.

You might expect that they would offer an alternative explanation. Like, perhaps, an intelligent being who visited Earth 530 million years ago, created a bunch of different animals with similar body plans, then allowed evolution to proceed for the next half a billion years?

Don't hold your breath waiting for a scientific explanation. They aren't that clever.

Stephen Meyer Explains the Origin of Information

 
Intelligent Design Creationism is struggling to maintain scientific credibility. The movement claims to be scientific, not religious, and it's strongest defense is that it offers credible scientific explanations of biological phenomena.

Most of us don't see it that way. All we see is a bunch of people who attack science in general and evolution in particular. They publish lots and lots of stuff that raises questions about standard scientific explanations—some of the criticisms are valid but most are nothing more than wishful thinking. What we never, ever, see is a true explanation of how intelligent design creationism actually works.

This video was published on the Evolution News & Views (sic) blog [Stephen Meyer on Intelligent Design: What is the origin of the digital information found in DNA?]. Watch it to see if Meyer¹ explains the origin of information according to the Intelligent Design Creationism Model. Wait right 'till the end to make sure you don't miss the explanation of how an intelligent creator put information into DNA. Learn who the creators(s) is/are and why they did it. Find out when she did it. Wait to see how this accounts for life as we know it today.

Folks, this is the best they have to offer. It's why we call them IDiots. There's nothing there but obtuse rhetoric about the origin of life and information. They have nothing to offer but criticism of evolution.

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1. Stephen Meyer is one of the founders of the Discovery Institute in Seattle. He has a Ph.D. in the History and Philosophy of Science from Cambridge University (UK).

What Do You Do When All the Reviews Are Bad?

Charles Marshall has reviewed Darwin's Doubt in last week's issue of Science. The title says it all: When Prior Belief Trumps Scholarship.

Here's a sample of what a bad review looks like.

... when it comes to explaining the Cambrian explosion, Darwin's Doubt is compromised by Meyer's lack of scientific knowledge, his "god of the gaps" approach, and selective scholarship that appears driven by his deep belief in an explicit role of an intelligent designer in the history of life.

Ouch!

So far the Intelligent Design Creationists have a perfect record. Every single review of Darwin's Doubt by a scientist has been negative. None of them like the book.

What do you do under those circumstances? Remember, that the minions of the Discovery Institute aggressively hyped this book in the Spring before it was published. It was supposed to be the book that destroyed Darwinism.¹

Not to worry. The IDiots have an excuse ... in fact they have several.

1. Ignore the main criticism and focus on details. This is what Stephen Meyer is doing in his response to Charles Marshall's review: When Theory Trumps Observation: Responding to Charles Marshall's Review of Darwin's Doubt.
2. Most reviewers ignore the main arguments. This is the defense offered by David Klinghoffer, that well-known defender of Intelligent Design Creationism, and a non-scientist: A Taxonomy of Evasion: Reviewing the Reviewers of Darwin's Doubt.
3. At least we got their attention. This is what makes David Klinghoffer proud, "Marshall's review stands out. It's important. Not only because Marshall is a distinguished paleontologist writing in one of the world's two most importance science journals ..." [Stephen Meyer Answers Charles Marshall on Darwin's Doubt]. Casey Luskin uses the same excuse in when he writes [Teamwork: New York Times and Science Magazine Seek to Rebut Darwin's Doubt,
   

   It's now evident that, their previous denials notwithstanding, Darwin defenders have been unnerved by Darwin's Doubt. On the same day last week, both the world's top newspaper (the New York Times) and one of the world's top scientific journals (Science) turned their attention to the problem posed by Stephen Meyer.

4. Publicize reviews by non-scientists That's what Denyse O'Leary does in Astonishing innovation: Bethell’s review of Darwin’s Doubt defies tradition, tells you what is in the book. David Klinghoffer does it too: The American Spectator Warmly Welcomes Darwin's Doubt.

That's what you do if all the reviews and bad and you are an IDiot.

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1. There were half-a-dozen earlier books that were also supposed to have destroyed Darwinism.

Darwin Doubters Want to Have their Cake and Eat it too

The phrase "to have your cake and eat it too" means that you can't have it both ways or "shouldn't try to have two incompatible things" [You can't have your cake and eat it].

The Intelligent Design Creationists are giving us a good example of just what this means. They have a new book coming out called "Darwin's Doubt." It's to be published by the religious arm of HarperCollins. The book will be available in a few months in the USA so the IDiots are ramping up the hype in preparation. We are told that this book, just like several previous books from the Discovery Institute, will definitively refute evolution and demonstrate the truth of Intelligent Design Creationism.

Here's how casey Luskin put it a few days ago [Three (or Four) Reasons Everyone Should Read Darwin's Doubt].

When published, Darwin's Doubt will be the single most up-to-date rebuttal to neo-Darwinian theory from the ID-paradigm. In this regard, one exciting element of Darwin's Doubt is that Meyer reviews much of the peer-reviewed research that's been published by the ID research community over the last few years, and highlights how ID proponents are doing relevant research answering key questions that show Darwinian evolution isn't up to the task of generating new functional information.

Here's how the strategy works. The IDiots are arguing the merits of Meyer's new book on the leading creationist blogs. They are generating lots of publicity and convincing their followers that the book is going to be a devastating rebuttal of "Darwinism." None of their followers have read the book but that doesn't matter. They won't have to.

How are scientist supposed to respond? None of us have read the book so we can't (yet) show that it is just more of the same old propaganda that we've seen before. What we can say is that we are very skeptical of the claims being made and we think it is disingenuous to promote those claims when we can't examine the "evidence." We can confidently speculate about what Stephen Meyer is going to say because he has a history and because he gives away some of his arguments in the publicity surrounding the book. The IDiots only sing one note and there's a very high probability that this isn't going to change.

That's exactly what Jerry Coyne said in his post: A (formerly) reputable publisher sells out to creationists. He puts it very nicely—and undoubtedly accurately— when he says, "But creationist Stephen Meyer, from the Discovery Institute, has apparently wrapped up the story. He’s hit upon the real reason for the Cambrian explosion: it’s intelligent design! Yes, baby Jesus made the phyla!"

Does anyone with an IQ over 50 think Coyne's prediction is wrong?

You know what's coming because we've seen it all before with the pre-publication hype for "The Myth of Junk DNA." "Science of Human Origins," and "Signature in the Cell." This time it's David Klinghoffer who is the designated whiner [Current Trends in Darwinian Book-Reviewing].

With a pub date of June 18, naturally no books are available. (Though you can preorder at a nice discount, for now, better than Amazon, over at DarwinsDoubt.com.) Nevertheless, at Why Evolution Is True, University of Chicago biologist Jerry Coyne assumes he knows what will be in the book. His absurd summary: "Yes, baby Jesus made the phyla!"

...

Darwinists have a curious way of responding to serious scientific and intellectual challenges to their beliefs. And it's getting more curious, isn't it? It's sort of evolving. If they had answers to ID's challenges, surely they would wait till they read the book, then accurately characterize what it says, and then tell us why Steve Meyer is wrong. But so far, and wasting no time, they have signaled in this strange prophylactic manner their unwillingness to do so.

The solution is obvious to everyone but the IDiots. Don't make outlandish claims about what's in a book until it's published and everyone can check for themselves. It you speculate about what the book is going to say then don't be surprised if others do as well.

You can't have your cake and eat it too.

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Two Books on the Cambrian Explosion

I finished reading The Cambrian Explosion: The Construction of Animal Biodiversity by Douglas Erwin and James Valentine. It's a wonderful book. It brings you up to date on the fossil record, dating issues, evolutionary developmental biology, climate change, and molecular phylogeny. The book offers a reasonable evolutionary explanation for the apparent rapid diversification of animal groups during the Cambrian (about 530 million years ago).

The important point is covered in a paper by Erwin et al. (2011). It shows that the main animal groups probably split gradually over a period of tens of millions of years before the "explosion" became visible in the fossil record [see The Cambrian Conundrum: Fossils vs Genes]. The authors show that the molecular data indicates an earlier divergence and trace fossils are consistent with that data.

The other book is about to be published. It's called Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design and the author is an expert paleontologist and evolutionary biologist named Stephen Meyer.

It certainly sounds exciting if you read the announcement on Evolution News & Views (sic) [Coming in June, a Game-Changing New Book: Darwin's Doubt, by Stephen Meyer].

We've been keeping something from you, dear readers, but now it can be told. The evolution debate is about to undergo a paradigm shift....

Here is a sweeping account, stunningly illustrated with gorgeous color photos, of the frontiers of the scientific critique of Darwinism and the case for ID. Exacting and thorough, yet remarkably accessible to the thoughtful lay reader, Darwin's Doubt introduces us to the challenges to Darwinism based on the study of combinatorial inflation, protein science, population genetics, developmental biology, epigenetic information, and more.

Meyer explains how post-Darwinian alternatives and adaptions of Darwin's theory -- including self-organizational models, evo-devo, neutral or nonadaptive evolution, natural genetic engineering, and others -- fall short as well. He demonstrates that the weaknesses of orthodox evolutionary theory, when flipped over head-to-foot, are precisely the positive indications that point most persuasively to intelligent design.

Evolutionary biologists studying gene regulatory networks and fossil discontinuity, among other fields, have come tantalizingly close to reaching this conclusion themselves.

The Cambrian event, fundamentally, represents an information explosion, the first but not the last in the history of life. As no book has done before, Darwin's Doubt spells out the implications of this fact. Dr. Meyer stands on the verge of turning the evolution debate in an entirely new direction, compelling critics of the theory of intelligent design, at last, to respond substantively and in detail. The book will be a game-changer, for science and culture alike.

It would not be fair to criticize Meyer's book before we get a chance to read it. It will be fun to see how the science compares with that in the book by Erwin and Valentine. I'm really looking forward to reading about the Intelligent Design Theory that explains all of the scientific data. I'm especially curious about why the designer did the deed 530 million years ago and why everything since then looks so much like evolution. I'm sure that's going to be covered. We can be practically certain that a paradigm-shifting book like this isn't just going to be several hundred pages of evolution bashing.

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Erwin, D.H., Laflamme, M., Tweedt, S.M., Sperling, E.A., Pisani, D., and Peterson, K.J. (2011) The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science 334:1091-1097. [PubMed] [doi: 10.1126/science.1206375]

Stephen Meyer Talks About Junk DNA

Stephen C. Meyer has a Ph.D. degree (1991) in the History and Philosophy of Science from Cambridge University in the UK. He is currently Program Director of the Center for Science and Culture at the Discovery Institute in Seattle, Washington, USA.

Meyer's book, Signature in the Cell: DNA and the Evidence for Intelligent Design, is an attempt to present Intelligent Design Creationism as genuine science. I'll have more to say about this later but for now I want to concentrate on one particular aspect of his case.

Mayer claims that one requirement of a genuine scientific theory is the ability to make falsifiable predictions. Does Intelligent Design Creationism make such predictions? Yes, one of the predictions is that genomes will not contain very much junk DNA. It will be instructive to see how Intelligent Design Creationists handle this issue, especialy since I've just finished a thorough review of The Myth of Junk DNA by Jonathan Wells.

Here's what Meyer says about junk DNA.

Darwin's Doubt: The Genes Tell the Story?

The main goal of Intelligent Design Creationism is to cast doubt on modern science, especially evolutionary biology. Most of the IDiot books are devoted to attacks on evolution. The underlying assumption is that if modern science is discredited then "god-did-it" becomes a viable alternative.

The latest book by Stephen Myer is no exception. The theme is that evolutionary biologists cannot explain the Cambrian Explosion; therefore, God must have created all the animals in the space of a few million years back in the Cambrian Era (about 530 million years ago).

Most of the book is about the lack of transitional fossils that document the slow transition from primitive worm-like creatures to modern phyla such as arthropods and chordates. Others have dealt with this and I'm not going to comment because it's outside of my area of expertise.¹

There is strong evidence from molecular evolution that the major animal phyla share common ancestors and that these common ancestors predate the Cambrian by millions of years. In other words, there's a "long fuse" of evolution leading up to the Cambrian Explosion. Meyer refers to this as the "deep-divergence" assumption.

There are many versions of these trees. The one shown here is from Erwin et al. (2011). It's the one shown in the book The Cambrain Explosion by Douglas Erwin and James Valentine. It isn't necessarily correct in all details but that's not the point.

The point is that molecular phylogenies demonstrate conclusively that the major groups of animals share common ancestors AND that the overall pattern does not conform to a massive radiation around 530 million years ago. Also, it's very clear that the pattern is consistent with evolution and not with God creating all the animals at once.

Stephen Meyer has to address this evidence because it casts doubt on his main theme (God did it). I suppose I don't need to tell you what he says ... it's typical creationist denial. He claims that the evidence doesn't exist. Here are his reasons ...

1. There are no fossils to support the earliest branches in the molecular phylogenies.
2. There are many different molecular trees and they don't all agree with each other in terms of branching order and timing.
3. Evolutionary biologists cherry-pick the data by only picking molecules that give reasonable trees.
4. The trees rely on questionable assumptions; namely, that the molecular clock ticks at a constant rate and that there is a universal tree.
5. The molecules being compared must be homologous but this is what is being tested so the argument is circular.

The conclusion is ....

Comparative genetic analyses do not establish a single deep-divergence point, and thus do not compensate for the lack of fossil evidence for key Cambrian ancestors—such as the ur-bilateran or the ur-metazoan ancestor. The results of different studies diverge too dramatically to be conclusive, or even meaningful; the methods of inferring divergence points are fraught with subjectivity; and the whole enterprise depends on a question-begging logic. Many leading Cambrian paleontologists, and even some leading evolutionary biologists, now express skepticism about both the results and the significance of deep-divergence studies.

I'm hoping to find time to go over each of Meyer's objections since they reveal a lot about IDiot misconceptions of evolution (and science) and a lot about how they employ strawmen, lies, quote-mining, and distortions in order to discredit an entire field (molecular evolution).²

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1. Most IDiots are experts in everything. I'm not as smart as they are.

2. It always amazes me to discover that IDiots like Stephen Meyer think they know more than thousands of expert biologists who do this sort of stuff for a living.

Erwin, D.H., Laflamme, M., Tweedt, S.M., Sperling, E.A., Pisani, D. and Peterson, K.J. (2011) The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science 334:1091-1097. [doi: 10.1126/science.1206375]

Facts Supporting Intelligent Design Creationism?

 
We all know that the Intelligent Design Creationist movement consists almost exclusively of attacks on science. The idea seems to be that if you can cast doubt on evolution then this is evidence in favor of God.

Some unnamed Professor has challenged students to come up with facts that support Intelligent Design Creationism. The only criterion is; "fact can be any observation in biology that is substantiated by publication in a scientific journal,"

Casey Luskin attempts to meet the challenge over on the Discovery Institute propaganda site, Evolution News & Views: Helping Students Answer a Professor's Challenge to "Find a Fact" That Supports Intelligent Design (Part 2).

Here's a list of "scientific" publications submitted by Luskin. I haven't read all of them but, of the ones I've read, there isn't a single one containing a fact that supports the existence of God, let alone evidence that he/she designed anything at all. Furthermore, many of them aren't from a scientific journal. It looks like Casey Luskin has goofed, once again.

Let me know if any of these publications contain evidence of Intelligent Design Creationism. Is this the best they can do? (I've put asterisks in front of the ones I've read.)

*Douglas D. Axe, "Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors," Journal of Molecular Biology, Vol. 301:585-595 (2000)

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

*Michael Behe, Darwin's Black Box: The Biochemical Challenge to Evolution (Free Press, 1996)

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

Geoff Brumfiel, “Outrageous Fortune,” Nature, Vol. 439: 10-12 (Jan. 5, 2006)

Bract, "Inventions, Algorithms, and Biological Design," in Progress in Complexity, Information, and Design (Vol. 1.1, 2002)

*William A. Dembski, The Design Inference: Eliminating Chance Through Small Probabilities (Cambridge University Press, 1998)

a. William A. Dembski and Robert J. Marks II, “Conservation of Information in Search: Measuring the Cost of Success” (In publication, 2009)

b. William A. Dembski and Robert J. Marks II, “The Search for a Search: Measuring the Information Cost of Higher Level Search” (In publication, 2009)

*William Dembski and Jonathan Wells, The Design of Life: Discovering Signs of Intelligence in Living Systems, (FTE, 2008) (see www.thedesignoflife.net)

*Wayt T. Gibbs, “The Unseen Genome: Gems among the Junk,” Scientific American (November, 2003)

Guillermo Gonzalez and Jay Wesley Richards, The Privileged Planet: How our Place in the Cosmos is Designed for Discovery, (Regnery, 2004)

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

Hiroaki Kitano, ”Systems Biology: A Brief Overview,” Science, Vol. 295: 1662-1664 (March 1, 2002)

Wolf-Ekkehard Lönnig, "Dynamic genomes, morphological stasis, and the origin of irreducible complexity," in Dynamical Genetics pp. 101-119 (Valerio Parisi, Valeria De Fonzo, and Filippo Aluffi-Pentini eds., 2004)

Casey Luskin, “Human Origins and Intelligent Design,” Progress in Complexity and Design, (Vol 4.1, November, 2005)

Casey Luskin, "Intelligent Design Has Scientific Merit in Paleontology," part of the "Does Intelligent Design Have Merit?" debate at OpposingViews.com (September, 2008)

*Wojciech Makalowski, “Not Junk After All,” Science, Vol. 300(5623) (May 23, 2003)

Stephen C. Meyer, Marcus Ross, Paul Nelson & Paul Chien, "The Cambrian Explosion: Biology's Big Bang," in Darwinism, Design, and Public Education (John A. Campbell and Stephen C. Meyer eds., Michigan State University Press, 2003)

*a. Stephen C. Meyer, “The Cambrian Information Explosion,” in Debating Design (edited by Michael Ruse and William Dembski; Cambridge University Press 2004)

b. 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)

Scott A. Minnich & Stephen C. Meyer, “Genetic analysis of coordinate flagellar and type III regulatory circuits in pathogenic bacteria,” in Proceedings of the Second International Conference on Design & Nature, Rhodes Greece (M.W. Collins & C.A. Brebbia eds., 2004)

Paul Nelson and Jonathan Wells, “Homology in Biology,” in Darwinism, Design, and Public Education, (Michigan State University Press, 2003)

*Richard v. Sternberg, "On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic– Epigenetic System," Annals of the New York Academy of Sciences, Vol. 981: 154–188 (2002)

J.T. Trevors and D.L. Abel, "Chance and necessity do not explain the origin of life," Cell Biology International, Vol. 28: 729-739 (2004)

D. L. Abel & J. T. Trevors, “Self-organization vs. self-ordering events in life-origin models," Physics of Life Reviews, Vol. 3: 211–228 (2006)

Øyvind Albert Voie, "Biological function and the genetic code are interdependent," Chaos, Solitons and Fractals, Vol. 28:1000–1004 (2006)

Jonathan Wells, "Using Intelligent Design Theory to Guide Scientific Research" Progress in Complexity, Information, and Design (Vol. 3.1.2, November 2004)

Jonathan Wells, "Do Centrioles Generate a Polar Ejection Force?," Rivista di Biologia / Biology Forum, Vol. 98:71-96 (2005)

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Donald Prothero Reviews Darwin's Doubt

Donald Prothero is a paleontologist. He has reviewed Darwin's Doubt [ Stephen Meyer's Fumbling Bumbling Cambrian Amateur Follies]. The reason why this is important is because the IDiots want a "real expert" to review the book [see IDiot Ironly.

Well, they got their wish. It's a long, detained review but here's the fun part.

The entire literature of creationism (and of its recent offspring, "intelligent design" creationism) works entirely on that principle: they don't like any science that disagrees with their view of religion, so they pick tiny bits out of context that seem to support what they want to believe, and cherry-pick individual cases which fits their bias. In their writings, they are legendary for "quote-mining": taking a quote out of context to mean the exact opposite of what the author clearly intended (sometimes unintentionally, but often deliberately and maliciously). They either cannot understand the scientific meaning of many fields from genetics to paleontology to geochronology, or their bias filters out all but tiny bits of a research subject that seems to comfort them, and they ignore all the rest.

Another common tactic of creationists is credential mongering. They love to flaunt their Ph.D.'s on their book covers, giving the uninitiated the impression that they are all-purpose experts in every topic. As anyone who has earned a Ph.D. knows, the opposite is true: the doctoral degree forces you to focus on one narrow research problem for a long time, so you tend to lose your breadth of training in other sciences. Nevertheless, they flaunt their doctorates in hydrology or biochemistry, then talk about paleontology or geochronology, subjects they have zero qualification to discuss. Their Ph.D. is only relevant in the field where they have specialized training. It's comparable to asking a Ph.D. to fix your car or write a symphony--they may be smart, but they don't have the appropriate specialized training to do a competent job based on their Ph.D. alone.

Stephen Meyer's first demonstration of these biases was his atrociously incompetent book Signature in the Cell (2009, HarperOne), which was universally lambasted by molecular biologists as an amateurish effort by someone with no firsthand training or research experience in molecular biology. (Meyer's Ph.D. is in history of science, and his undergrad degree is in geophysics, which give him absolutely no background to talk about molecular evolution). Undaunted by this debacle, Meyer now blunders into another field in which he has no research experience or advanced training: my own profession, paleontology. I can now report that he's just as incompetent in my field as he was in molecular biology. Almost every page of this book is riddled by errors of fact or interpretation that could only result from someone writing in a subject way over his head, abetted by the creationist tendency to pluck facts out of context and get their meaning completely backwards. But as one of the few people in the entire creationist movement who has actually taken a few geology classes (but apparently no paleontology classes), he is their "expert" in this area, and is happy to mislead the creationist audience that knows no science at all with his slick but completely false understanding of the subject.

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God, Science, and the Universe

Today's the day we find out "What's Behind It All?" The decision will be announced at the University of Toronto (Toronto, Ontario, Canada) by Lawrence Krauss when he educates the audience at Convocation Hall starting at 7 pm. Stephen Meyer (Intelligent Design Creationist) and Denis Lamoureux (Theistic Evolution Creationist) will also be there to learn the answer. (Spoiler Alert: the answer is "nothing.")

It's not too late to buy tickets. Email me if you want to join some of us for dinner before the event.

The event is being sponsored by Wycliffe College at the University of Toronto. This is an Anglican College that trains people to become Anglican Ministers (among other things). The college is the prime mover behind this series of events and it deserves a great deal of credit for the effort. Co-sponsors include the Centre for Inquiry, Canada and three Christian groups.

The event is being video-hosted at many locations around the world. See the list here. If you don't want to watch with others, you can see the live stream on YouTube at: Krauss, Meyer, Lamoureux: What’s Behind it all? God, Science and the Universe. It starts at 7 pm EST. (It's probably over already in Australia.)

The ID crowd is already anticipating defeat so they're preparing their audience by warning them that Lawrence Krauss will be nasty (i.e. refute their arguments) [see Watch Meyer Take on Krauss and Lamoureux, Streaming Live at Evolution News on March 19]. (Warning: check your irony meters before reading the first paragraph.)

Those on the Darwinist, materialist, atheist side of the debate that we follow here aren't normally very good at listening and responding to scientific perspectives at variance from their own. They are much more interested in condemning and ridiculing -- which has got to be a poor strategy for them if they want to persuade anyone.

With that as the background, as we noted already, it's refreshing that arch-atheist cosmologist Lawrence Krauss has agreed to participate in a public conversation with Discovery Institute's Stephen Meyer, joined by theistic evolutionist Denis Lamoureux. That will be March 19 at the University of Toronto's Convocation Hall. We're looking forward to it -- and here's the even better news. You won't have to be in Toronto to enjoy the discussion. The event will stream live here at Evolution News.

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IDiots Make a Falsifiable Prediction

The Intelligent Design Creationists, otherwise known as IDiots, are getting desperate. They have been relentlessly promoting Stephen Meyer's upcoming book Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design but so far they have pretty much failed to trick evolutionary biologists into trashing the book before it's published.¹ That must be a major disappointment to them.

The baiting continues with an article by David Klinghoffer on the Evolution News & Views (sic) site: What Darwin's Enforcers Will Say About Darwin's Doubt: A Prediction. Here's what he predicts ....

Among possible lines of attack against Stephen Meyer's forthcoming book, Darwin's Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design, I foresee some critics trying to argue that it's not fair game for Dr. Meyer to invite the general reading public to consider what's going on in peer-reviewed technical literature pertaining to evolution.

After all, biologists should have the opportunity to air their views in a semi-private professional setting without "creationists" barging in and telling the unwashed masses that many scientists have already given up on the Darwinian paradigm and are seeking post-Darwinian alternatives. Even though it's true, still it's wrong to publicize the fact, thereby leading the common folk astray and confirming their prejudice in favor of seeing life and the universe as reflecting some purpose.

This time I will rise to the bait if only for the purpose of preserving this prediction so we can revisit it in the future.

I'd also like to note, for the record, that the IDiots have published a number of books in the past and I don't recall anyone making the argument that Klinghoffer predicts. Can anyone out there point me to an article where scientists criticized the IDiots for pulicizing controversy within the evolutionary biology literature? It would be quite hypocritical for most bloggers to do so since criticizing the scientific literature is what we do.

Is it just my imagination or have evolutionary biologists also published books where they "expose" the controversies within evolution. If scientists do it routinely then why in the world would they criticize an IDiot for doing it? That doesn't make any sense, does it? (Oops, I inadvertently made the false assumption that IDiots are supposed to be rational.)

Finally, Udo Schüklenk alerted me to this creationist article because he is mentioned. Klinghoffer refers to a discussion about the ethics of infanticide and he thinks that his creationist² buddy Wesley Smith is being attacked for exposing a debate within the bioethics community. You should read the papers he links to along with Udo Schüklenk's paper [In defence of academic freedom: bioethics journals under siege] if you want to catch up on that discussion. As usual, the IDiots get it all wrong. Are you surprised?

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1. That's mostly because we don't care. We are not anticipating anything we haven't heard many times before although, I suppose, we could be surprised.

2. Smith is a lawyer and a Senior Fellow at the Discovery Institute. I don't know what kind of creationist he is.

Signature in the Cell

 
Denyse O'Leary can hardly contain herself 'cause Stephen Meyer's book is about to go on sale.

In case you can't wait, there's a Signature in the Cell website that explains the significance of this momentous event.

The foundations of scientific materialism are in the process of crumbling. In Signature in the Cell, philosopher of science Stephen C. Meyer shows how the digital code in DNA points powerfully to a designing intelligence behind the origin of life. The book will be published on June 23 by HarperOne.

Unlike previous arguments for intelligent design, Signature in the Cell presents a radical and comprehensive new case, revealing the evidence not merely of individual features of biological complexity but rather of a fundamental constituent of the universe: information. That evidence has been mounting exponentially in recent years, known to scientists in specialized fields but largely hidden from public view. A Cambridge University-trained theorist and researcher, director of the Discovery Institute’s Center for Science and Culture, Dr. Meyer is the first to bring the relevant data together into a powerful demonstration of the intelligence that stands outside nature and directs the path life has taken.

...

As a philosopher and a scientist himself, having worked in the field of geophysics for Atlantic Richfield, Meyer is able to step back from the fray of competing views about Darwinian theory and offer a searching, compelling investigation of life’s beginning.

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IDiots Don't Understand Punctuated Equilibria

Intelligent Design Creationism is a movement dedicated to discrediting evolution and attacking the rational explanation of nature.¹ The evidence is in the books and blogs and the propaganda distributed to local school boards and state legislators. The attack on science and scientists makes up about 99% of their activities.

Given their dedication to disproving evolution, you'd think that the IDiots must at least understand it. Maybe not all of them—because there are some really, really, stupid IDiots—but certainly some of the most prominent IDiots should know what they're talking about? Right? Doesn't that seem reasonable?

The facts say otherwise. Off hand, I can't think of a single IDiot who has an adequate understanding of the science they attack. Believe me, I've tried harder than most to find an intelligent believer.

WIRED on Junk DNA

Junk DNA is the DNA in your genome that has no function. Much of it accumulates mutations in a pattern that's consistent with random genetic drift implying strongly that the sequences in junk DNA are unimportant. In fact, the high frequency of sequence change (mutation plus fixation) is one of the most powerful bits of evidence for lack of function.

Catherine Shaffer is a science writer who describes herself like this on her website,

I am a writer specializing in biotechnology, genetics, genomics, and other molecular, biological sciences. I have experience with news and features. My strengths include a meticulous attention to detail, an absolutely fanatical devotion to scientific accuracy, and enthusiasm. Readers appreciate my clean, uncluttered prose; my crisp, novelistic style; and (sometimes) my zany sense of humor. I am a writer who always meets deadlines and is organized and dependable.

I studied biochemistry at the graduate level at the University of Michigan, and worked in the pharmaceutical industry for several years. I am especially knowledgeable about genomics, proteomics, biotechnology, drug discovery, and chromatographic separations.

She has written an article for WIRED on junk DNA [One Scientist's Junk Is a Creationist's Treasure]. Here's how the article begins,

Without your "junk DNA" you might be reading this article while hanging upside down by your tail.

That's one of the key findings of the opossum genome-sequencing project, and a surprising group is embracing the results: intelligent-design advocates. Since the early '70s, many scientists have believed that a large amount of many organisms' DNA is useless junk. But recently, genome researchers are finding that these "noncoding" genome regions are responsible for important biological functions.

The opossum data revealed that more than 95 percent of the evolutionary genetic changes in humans since the split with a common human-possum ancestor occurred in the "junk" regions of the genome. Creationists say it's also evidence that God created all life, because God does not create junk. Nothing in creation, they say, was left to chance.

"It is a confirmation of a natural empirical prediction or expectation of the theory of intelligent design, and it disconfirms the neo-Darwinian hypothesis," said Stephen Meyer, director of the Center for Science and Culture at the Discovery Institute in Seattle.

Advocates like Meyer are increasingly latching onto scientific evidence to support the theory of intelligent design, a modern arm of creationism that claims life is not the result of natural selection but of an intelligent creator. Most scientists believe that intelligent design is not science. But Meyer says the opossum data supports intelligent design's prediction that junk DNA sequences aren't random, but important genetic material. It's an argument Meyer makes in his yet-to-be-published manuscript, The DNA Enigma.

Hmmmm ... This is so confused that it's difficult to know where to begin. First, the connection between my junk DNA and whether I am an opossum completely escapes me. I don't know of any credible scientist who claims that it's changes in junk DNA that makes us so different from the common ancestor of opossums. (And none who claim that we are descended from opossums.)

Second, the implication that most junk DNA is turning out to have a function is completely false and the confusion about the difference between junk DNA and noncoding DNA is inexcusable from someone who claims to be an expert on genomics [see Noncoding DNA and Junk DNA, The Deflated Ego Problem].

Third, the idea that large amounts of evolution in junk DNA supports Intelligent Design Creationism is crazy. But, in fairness, I don't think Shaffer is making the connection between the sequence variation and Intelligent Design Creationism; instead, she's making the (factually incorrect) connection between the discovery of some functions in noncoding, nonjunk, DNA and Intelligent Design Creationism (IDC). I think Steve Meyer is suggesting that IDC predicts that junk DNA will have a function and that's why he's being quoted here in the article (see above).

Scientists have made several discoveries about what some call the "dark matter of the genome" in recent years, but they say the research holds up the theory of natural selection rather than creationism.

When sequences in noncoding DNA are conserved, this is taken as evidence of negative selection. In that sense, it supports the theory of natural selection. However, most of the sequence comparisons show that junk DNA is not conserved. This does not support the theory of natural selection. It supports Neutral Theory and the mechanism of evolution by random genetic drift.

The article then describes one recent study suggesting that some noncoding DNA is not junk (Lowe et al. 2007). It appears to be the justification for writing the article since it compares short stretches of sequences in the human and opossum genomes. This is not news so I won't bother commenting.

With scientists increasingly believing that so-called junk DNA regulates other genes, among other functions, creationists like Michael Behe, a biochemistry professor at Lehigh University in Pennsylvania and author of the controversial new book on intelligent design, The Edge of Evolution, are more than happy to point out their errors.

"From the very beginning Darwinism thought whatever it didn't understand must be simple, must be nonfunctional," Behe said. "It's only in retrospect that Darwinists try to fit that into their theory."

The concept of junk DNA is not based on ignorance in spite of what the IDiots say. It's based on good scientific evidence and deduction. Of course most IDiots wouldn't recognize scientific evidence even if it bit them on the ...

Is this just a way of getting in another quote from a prominent advocate of Intelligent Design Creationism? Why is Shaffer so interested in the IDiots? This seems to be more than just seeking out controversy since the proper way to do that would be to interview real scientists who can put the work into perspective and comment on it's significance (see below).

Part of the difficulty in studying junk DNA is that it's impossible to prove a negative, i.e., that any particular DNA does not have a function.

That's why T. Ryan Gregory, an assistant professor in biology at the University of Guelph, believes that nonfunctional should be the default assumption. "Function at the organism level is something that requires evidence," he said.

That's how a real scientist speaks [see A word about "junk DNA" and Comments on "Noncoding DNA and Junk DNA"].

This is getting to be a familiar pattern among science writers. Many of them seem to be incapable of sorting out the actual science from the rhetoric. In this case the problem is exacerbated by introducing IDiots as though their opinion had a bearing on the subject. Not only that, the poor science writing stands in sharp contrast to the claim that, "My strengths include a meticulous attention to detail, an absolutely fanatical devotion to scientific accuracy, and enthusiasm."

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Lowe, C.B., Bejerano, G. and Haussler, D. (2007) Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc. Natl. Acad. Sci. (USA) 104:8005-8010. [PubMed]

Darwin's Doubt: A Synopsis

David Klinghoffer wonders why I'm not criticizing Stephen Myer's new book Darwin's Doubt [see On Darwin's Doubt, Still Waiting to Hear from Big Shots in the Darwin Brigade].

Where is Jerry Coyne in this debate? Where is Dawkins? Even PZ Myers? Or Lawrence Moran, who promised "I'm planning to read [Darwin's Doubt] as soon as I can get a hold of a copy -- probably sometime in August in Canada." (I'm still puzzled by that one. The book was published in June in Canada as well.) It would seem noble for the generals to go into battle alongside the ordinary foot soldiers, putting themselves at risk as well, instead of hanging back at a safe distance.

I preordered the book three months ago and received my copy from Amazon.ca on August 1st. I've been busy with other things for most of the month so I've only turned my attention to the book in the past few days.

David Klinghoffer probably thinks that reviewing another creationist book is my highest priority. That's not the case. In fact, I never promised to review it and after reading it, I never will. There are plenty of others who know more about the subject and some of them are taking the book apart, chapter by chapter [Slaying Meyer’s Hopeless Monster]. If you want details, you can do no better than Darwin’s Doubt – A Review on Skeptic Ink.

For those of you who want a brief summary, I can do no better that point you to the tree of eukaryotes on the left (Keeling et al., 2005). It summarizes tons of molecular data showing the relationships of various eukaryotes. The tree is based on solid molecular evidence that Darwin never knew existed and that evidence is direct conformation of evolution, properly defined. It represents the fixation of nearly neutral alleles by random genetic drift. Of course, you have to read very carefully to find any mention of modern evolutionary theory in Meyer's book—he prefers to focus his attack on mutation + natural selection.

I've drawn a little red circle around the part of this tree that Stephen Meyer discusses in Darwin's Doubt. It's the evolution of animals and, in particular the early fossil evidence of multicellular animals. Most of these appear rather suddenly in the fossil record during the Cambrian (about 530 million years ago). Scientists have long been puzzled about this rapid evolution of complex animals and there are many hypotheses that attempt to account for it. In fact, there's a recent book by Douglas Erwin and James Valentine that summarizes the science behind The Cambrian Explosion. It all seems quite reasonable to me.¹ I don't know exactly why complex animals evolved so rapidly but I don't see any reason to doubt the facts of evolution and I don't see any reason to propose that God must have been responsible for this little bit of the tree of life.

Myer does and that's what his book is all about.

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1. I don't agree with everything in that book.

Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J. & Gray, M.W. (2005) The tree of eukaryotes. Trends in ecology & evolution 20:670-676. [doi: 10.1016/j.tree.2005.09.005]

The dynamic duo tell us about five problems with evolution

Here's a link to a remarkable radio interview with Stephen Meyer and Doug Axe. The subject is the Royal Society meeting last November on New trends in evolutionary biology: biological, philosophical and social science perspectives. The theme is not Intelligent Design Creationism, instead it's all about so-called problems with evolutionary theory. That's really what ID is all about in spite of what the IDiots may claim. [see A Royal Pain: Stephen Meyer and Douglas Axe on Five Problems for Evolution.]

Here are the five problems according to IDiots.

1. Fossil record (Cambrian explosion)
2. The origin of information (no known natural source of information)
3. The necessity of early mutations (you can't mutate regulatory genes that act early in development because all mutations in those genes are lethal)
4. Epigenetic information (you can't evolve new body plans by mutating DNA because development is controlled by non-DNA epigenetic information)
5. The universal design intuition that we all have (everybody thinks that people are created by a god-like designer, even atheists, so it must be true)

Stephen Meyer Explains Intelligent Design Creationism

 
Here's Stephen Meyer on The 700 Club explaining why Intelligent Design Creationism is likely to be true. This is about as good an explanation as you're ever going to get.

Keep in mind that Intelligent Design Creationism is a strictly scientific theory. It is not religious. It just so happens that an evangelical Christian television show has an audience that's very interested in science.

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Catherine Shaffer Responds to My Comments About Her WIRED Article

 
Over on the WIRED website there's a discussion about the article on junk DNA [One Scientist's Junk Is a Creationist's Treasure]. In the comments section, the author Catherine Shaffer responds to my recent posting about her qualifications [see WIRED on Junk DNA]. She says,

You might be interested to learn that I contacted Larry Moran while working on this article and after reading the archives of his blog. I wanted to ask him to expand upon his assertion that junk DNA disproves intelligent design. His response was fairly brief, did not provide any references, and did not invite further discussion. It's interesting that he's now willing to write a thousand words or so about how wrong I am publicly, but was not able to engage this subject privately with me.

Catherine Shaffer sent me a brief email message where she mentioned that she had read my article on Junk DNA Disproves Intelligent Design Creationism. She wanted to know more about this argument and she wanted references to those scientists who were making this argument. Ms. Shaffer mentioned that she was working on an article about intelligent design creationism and junk DNA.

I responded by saying that the presence of junk DNA was expected according to evolution and that it was not consistent with intelligent design. I also said that, "The presence of large amounts of junk DNA in our genome is a well established fact in spite of anything you might have heard in the popular press, which includes press releases." She did not follow up on my response.

His blog post is inaccurate in a couple of ways. First, I did not make the claim, and was very careful to avoid doing so, that “most” DNA is not junk. No one knows how much is functional and how much is not, and none of my sources would even venture to speculate upon this, not even to the extent of “some” or “most.”

Her article says, "Since the early '70s, many scientists have believed that a large amount of many organisms' DNA is useless junk. But recently, genome researchers are finding that these "noncoding" genome regions are responsible for important biological functions." Technically she did not say that most DNA is not junk. She just strongly implied it.

I find it difficult to believe that Ryan Gregory would not venture to speculate on the amount of junk DNA but I'll let him address the validity of Ms. Shaffer's statement.

Moran also mistakenly attributed a statement to Steven Meyer that Meyer did not make.

I can see why someone might have "misunderstood" my reference to what Myer said so I've edited my posting to make it clear.

Judmarc and RickRadditz—Here is a link to the full text of the genome biology article on the opossum genome: Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. We didn't have space to cover this in detail, but in essence what the researchers found was that upstream intergenic regions were more highly conserved in the possum compared to coding regions, but also represented a greater area of difference between possums and humans.

This appears to be a reference to the paper she was discussing in her article. It wasn't at all clear to me that this was the article she was thinking about in the first few paragraphs of her WIRED article.

Interested readers might want to read the comment by "Andrea" over on the WIRED site. She He doesn't pull any punches in demonstrating that Catherine Shaffer failed to understand what the scientific paper was saying. Why am I not surprised? (Recall that this is a science writer who prides herself on being accurate.)

So, yes, this does run counter to the received wisdom, which makes it fascinating. You are right that the discussion of junk vs. nonjunk and conserved vs. nonconserved is much more nuanced, and we really couldn't do it justice in this space. Here is another reference you might enjoy that begins to deconstruct even our idea of what conservation means: “Conservation of RET regulatory function from human to zebrafish without sequence similarity.” Science. 2006 Apr 14;312(5771):276-9. Epub 2006 Mar 23. Revjim—If you have found typographical errors in the copy, please do point them out to us. The advantage of online publication is that we do get a chance to correct these after publication.

Sounds to me like Catherine Shaffer is grasping at straws (or strawmen).

For Katharos and others—I interviewed five scientists for this article. Dr. Francis Collins, Dr. Michael Behe, Dr. Steve Meyers, Dr. T. Ryan Gregory, and Dr. Gill Bejerano. Each one is a gentleman and a credentialed expert either in biology or genetics. I am grateful to all of them for their time and kindness.

I think we all know just how "credentialed" Stephen Meyer is. He has a Ph.D. in the history and philosophy of science. Most of us are familiar with the main areas of expertise of Michael Behe and none of them appear to be science.

Was Louis Agassiz better in the concrete?

Back in the nineteenth century (i.e. more than one hundred years ago) there was a biologist named Louis Agassiz who didn't like Darwin's radical ideas about evolution. Agassiz, a very famous professor at Harvard, thought that there were major gaps n the fossil record and he lamented the apparent lack of transitional fossils. What he was looking for were fossils of direct ancestors of modern species and not their close cousins.

Stephen Meyer thinks this old debate is still relevant today so he writes it up in Darwin's Doubt as if nobody in the past one hundred years ever thought of an explanation. It fooled Denyse O'Leary (not hard) so she blogged about it today [Louis Agassiz: The selective incompleteness of the fossil record].

This reminds me of a famous photograph of the statue of Louis Agassiz embedded upside down in the courtyard in front of the zoology building at Stanford University. The statue tumbled from its place above the entrance during the San Francisco earthquake of 1906.

According to legend, a passing scientist remarked that,

Louis Agassiz was great in the abstract but not in the concrete.¹

Actually, it would be even better to say that Agassiz looks better in the concrete than in the abstract [see Agassiz in the Concrete and Persecution of Religious Scientists]. By the 1920s (earlier in Europe) Agassiz's reputation had been severely damaged by his willingness to let religious convictions dictate his science.²

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1. The story is apocryphal (a polite word for "false"). The quotation has been attributed to several men, including the President of Stanford, but all have denied it. Nevertheless, it's too good a story to abandon just because it happens to be untrue!

2. Stephen Jay Gould held the Alexander Agassiz Professor of Zoology Chair at Harvard from 1982 until his death in 2002. Alexander Agassiz was Louis Agassiz's son. Alexander served as President of the National Academy of Sciences.

Fishing for Creationists

Fishing for creationists is not a sport. All you need to do is dangle a bit of bait and dozens of creationists will fight for the right to impale themselves on the hook. The latest victim is Jonathan McLatchie who responded to criticism of Phillip Johnson [Maligning Phil Johnson, with Lots of Rhetoric but Little Substance]. I'm sure the other bloggers on Evolution News & Views don't see him as a fishy victim, they probably think of him as the designated hitter. (You could use "sacrificial lamb" if you want a Biblical metaphor.)

Jonathan M, as he prefers to be known, is studying in Scotland for a Master's degree in evolutionary biology. He's upset with Jeffrey Shallit for criticizing Phillip Johnson's 1993 video (see This Video Should Be Shown to all Biology Students). He's also upset with my critiques of the same video (see Phillip Johnson, One of the Very Best Intelligent Design Creationists).