April 8, 2007 - April 14, 2007 Archives

Dr. Michael Egnor, creationist neurosurgeon and Discovery Institute blogger, has a problem. Either he hasn’t figured out that we’re way past April Fools Day, or he has just managed to produce what might just be the single dumbest anti-evolution argument that I have ever seen. We’re talking about a demonstration of absolute, rock-bottom, Kent-Hovind-eat-your-heart-out, triple-distilled essence of pure stupid.

The argument today - and I warn anyone who knows anything at all about evolution to put down all food and drinks right now - is that if evolution was right, we should see some brain tumors acting to make better brains.

No, I’m not joking. That’s his latest argument, in response to a thorough fisking delivered last month by Yale neuroscientist Steve Novella. Brain tumors mutate and are subject to natural selection, so if evolution is correct they should produce better brains:

Read more (at The Questionable Authority):

Science has an article today on extracting and sequencing proteins from T. rex bones, and I'm already getting email from people wondering whether this is believable, whether it challenges the stated age of dinosaurs, whether this means we can soon reconstruct dinosaurs from preserved genetic information, and even a few creationists claiming this is proof of a young earth. Short answers: it looks like meticulous and entirely credible work to me, these fossil bones are really 68 million years old, and it represents a special case with limits to how far it can be expanded, so scratch "reassemble dinosaur from fragments" off your to-do list.

Continue reading "Stone soup; or, extracting protein fragments from T. rex bones" (on Pharyngula)

Here’s an update to “Is There A Systems Biologist In The House?”, in which I described how the head of the New Mexico chapter of the Intelligent Design Network (IDnet), Joe Renick, put a whole new spin on “Systems Biology” in an editorial commentary published in the Albuquerque Tribune (March 28th):

Joe Renick Wrote:

The greatest threat to the Darwinian dogma today is science itself.

There is a revolution underway in the biological sciences. A whole new field of biology called “Systems Biology” has emerged during the past 10 or 15 years. This revolution is just as profound for the biological sciences today as the transition in physics was from classical physics to quantum physics and relativity in the early part of the 20th century.

In this exciting new field, research is guided not by Darwinian principles but by design principles because design principles are needed to explain design-like features.

The teaching of evolution today in public schools is frozen in the past where it is based largely on a mid-20th century understanding of biology. Research in the biological sciences has moved far beyond that understanding because of the hopeless inability of Darwinian principles to explain the complexity observed in living things.

In my initial responses to Renick, found here and here (comments), I argued that

Sure, “Systems Biologists” use words like “design” occasionally, but that doesn’t automatically mean they think “designs” in nature must be “poofed” into existence by an un-named magical being.


Just bear in mind that Systems Biologists use evolution science, and do NOT utilize so-called “Intelligent Design” in any way, shape or form.

Recently, Joe Renick sent me a letter to clarify his position on Systems Biology and Intelligent Design, and allowed it to be published in the April NMSR Reports.

Renick said all this talk about him wanting to get ID into schools is baseless:

Joe Renick Wrote:

You and your colleagues are the ones making the conclusion to a designer, not me.

I kid you not. Read on below the fold.

Cool news, strengthening the Dinosaurs-Bird link

Tiny bits of protein extracted from a 68-million-year-old dinosaur bone have given scientists the first genetic proof that the mighty Tyrannosaurus rex is a distant cousin to the modern chicken.

Source: CNN

Thanks to Bob O’H (hat tip) I have discovered that my book review of E.O. Wilson’s The Creation: An Appeal to Save Life on Earth has been published in Trends in Ecology and Evolution (TREE). Wilson attempts to set aside the evolution/creation issue to encourage evangelicals to join him in saving biodiversity. The review is currently the online-before-print version, I assume it will be in the May issue. The journal requires a subscription but I will post a bit below.

I have to add that I take a little extra pleasure in getting to correct Wilson, in my opinion the world’s leading living biologist, for mistakenly talking about the “spinning bacterial cilium” when he meant “bacterial flagellum.” OK, I am still a tiny ant compared to Wilson (and Wilson literally is a god among ants, so that is saying something), but hey, I am on a crusade about the flagellum thing.

This news article reports on a topic that tugs at antievolutionist heartstrings: would the Pope, leader of the Catholic church, throw in with them, joining them in the “intelligent design” big tent? The answer, at least according to this news report, is “No”. Pope Benedict is reported to adopt theistic evolution, the idea that God’s method of creation is what science has discovered concerning evolutionary biology. And we know from William Dembski that “intelligent design theorists” are no friends of theistic evolution.

A lot of the coverage has concentrated on Benedict’s stance against atheism, which seems to me to be about as newsworthy as taking up the question, “Is the Pope Catholic?” Well, yes, it seems that he is.

Today, we have part 3 of John Mark Reynold’s four six-part exercise in rationalizing institutionalized ignorance of geology, aka young-earth creationism. See previous discussion of part 1 and part 2. The really fascinating thing about Reynolds is how he can contradict his own professed high principles within seconds of stating them. For example:

The question is: “What is true?”, not what fits my preconceived philosophy of science or theology.

Way to go, great sentiment. Clearly, then, we should look at the physical evidence and conclude that the earth is not young and the global flood of Noah did not happen – oh, wait:

Tangled Bank #77

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The Tangled Bank

It's time for Tangled Bank #77 at Aetiology, and it's another mega-collection of links to science articles.

You’ve gotta hand it to Bill Dembski. No one is as damaging to the ID cause as he is. I mean, we’ve tried to trip them up, and I think we’ve succeeded here and there, but ultimately, Dembski is our best warrior.

Case in point: he’s just gone on a tirade in which the very paper which he previously said was in favor of intelligent design has got it all wrong:

So let me spell it out: DIRECTED EVOLUTION IS NON-DARWINIAN. DARWINIAN EVOLUTION IS NON-DIRECTED…. Just because the word “evolution” is used doesn’t mean that homage is being paid to Darwin. “Directed evolution” properly falls under ID.

The sad thing is, this little outburst should really be directed at Matti Leisola and Ossi Turunen, the guys who wrote the paper under consideration, and not at me.

Here is what the authors wrote:

At one end is an approach commonly referred to as a rational design, which aims to understand the principles of protein structure and function well enough to apply them in designing new properties or even novel proteins using de novo design. The value of this approach in purely scientific terms is indisputable. However, because the difficulty is likewise indisputable, any approach that might succeed sooner is worth exploring. That realization has motivated work at the other end of the spectrum, where the emphasis is on finding what works rather than predicting what works. Darwinian evolution is the inspiration behind this. In the extreme form, this means avoiding protein design principles altogether and relying instead on huge sequence libraries and carefully designed selection methods.

Why didn’t Dembski, with all his brilliance, bother telling his ID author heroes that they were really talking about “intelligent design” the whole time? Instead they’re under the horrible misapprehension that directed evolution techniques were inspired by Darwinian evolution. And later they go on to say that there’s an “Overreliance on the Darwinian methodology”, meaning the directed evolutionary methods they spent the previous paragraphs describing.

Here’s more:

It is often said that random genetic methods to improve enzyme properties “rely on simple but powerful Darwinian principles of mutation and selection” (Johannes and Zhao 2006). We agree.

Whoa, what’s that? Leisola and Turunen agree that mutation and selection are “Darwinian principles”, and that these principles are responsible for the success of directed evolution? Say it ain’t so!

Tell me something Bill: Did you even read the paper?

An olden goldie from Sarkar, Director and Professor at the Biodiversity and Biocultural Conservation Laboratory, of the University of Texas-Austin, who had the good fortune (sic) to debate Paul Nelson.

“It wasn’t much of a debate, with Nelson conceding that intelligent design was far from being a scientific theory, that it had no legitimacy as part of a high school curriculum, and that it had to develop a laboratory research record before it can be taken seriously.”

Wow, was that all?

I've just learned that a very nifty old book has been posted at Project Gutenberg: At the Deathbed of Darwinism, by Eberhard Dennert. It was published in 1904, a very interesting period in the history of evolutionary biology, when Haeckel was repudiated, Darwin's pangenesis was seen as a failure, and Mendel's genetics had just been rediscovered, but it wasn't yet clear how to incorporate them into evolutionary theory. In some ways, I can understand how Dennert might have come to some of the conclusions he did, but still … it's a masterpiece of confident predictions that flopped. It ranks right up there with bumblebees can't fly, rockets won't work in a vacuum, and no one will ever need more than 640K of RAM…he specifically predicts that 'Darwinism' will be dead and abandoned within ten years, by 1910.

Today, at the dawn of the new century, nothing is more certain than that Darwinism has lost its prestige among men of science. It has seen its day and will soon be reckoned a thing of the past. A few decades hence when people will look back upon the history of the doctrine of Descent, they will confess that the years between 1860 and 1880 were in many respects a time of carnival; and the enthusiasm which at that time took possession of the devotees of natural science will appear to them as the excitement attending some mad revel.

Continue reading "Dennert and the deathbed of Darwinism" (on Pharyngula)

On UcD, Dembski posts a ‘response’ to Steve Reuland and others pointing out that the paper which Dembski called pro-ID wasn’t.

Dembski Wrote:

I posted a reference the other day to a peer-reviewed paper by two Finnish ID-supporters that I claimed supported ID. The paper highlighted that evolutionary methods work to the degree that they are directed. As is typical with our detractors, whenever a pro-ID paper by pro-ID scientists comes out in a peer-reviewed biology journal, they try their best to show that it doesn’t actually support ID. An example is the following post at PT by Steve Reuland:

The response seems to be that it was a paper by two ID supporters (interestingly enough Dembski may have out-ed the second author).

What is Dembski’s ‘devastating argument’? Now stop snickering and pay attention


The Egnor Files continued

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Egnor Wrote:

Dr. Cartwright is mistaken. Darwin asserted that all natural biological complexity arose by random undesigned variation and natural selection.

Anyone familiar with Darwin would understand that this is incorrect. In fact, Darwin is clear that he considers natural selection one of various mechanisms, although he considered it the most relevant one. Also, Egnor may want to familiarize himself with the concept of randomness as used by Darwin. In fact, Darwin used an analogy to artificial selection to formulate his thesis of natural selection, in other words, one may argue that in this sense, Darwin identified the designer.

Charles Darwin Wrote:

Furthermore, I am convinced that Natural Selection has been the main but not exclusive means of modification.

Source: Origin of Species, Introduction, page 6

On UcD announces the Temple lectures by Marcus Ross speaking about the Cambrian explosion and Dr Peter Dodson who is speaking for evolution (I wonder for what or whom Ross was speaking?).

Paul Nelson Wrote:

Also speaking (for evolution) will be dinosaur paleontologist Dr. Peter Dodson of the University of Pennsylvania. Dodson has been a skeptic of the dino-to-bird hypothesis, and has interacted with Ross at professional meetings. Their exchange today should be fascinating. The lectures begin at 6 and run to 8:30 PM. This event is free and open to the public.

While in early 2000 Peter Dodson may have been a skeptic of the dino to bird hypothesis, I have found two problems with Nelson’s claims, unless all he meant to say that Peter Dodson used to doubt the dino to bird hypothesis a decade or so ago but has changed his mind based on the evidence.

Those rascals at antievolution.org are like the Baker Street Irregulars of the evolutionary forces—they're always doing the legwork to come up with interesting bits of data. Like, for instance, this wonderful example of hypocrisy/inconsistency at Uncommon Descent.

This is what Dembski spat out today, complaining about us manipulative elites (he really deserves a Pastor Ray Mummert Award for it, too):

"Framing," as a colleague of mine pointed out, is the term that UC Berkeley Professor of Linguistics George Lakoff uses to urge Democrats that the public will agree with liberal policies if only the policies are described in different terms — "framed" in other words. Politics aside, framing is part and parcel with the condescension of our secular elite that the masses cannot be reasoned with and must therefore be manipulated.

And here's what Grima DaveScot said last year:

I will remind everyone again — please frame your arguments around science. If the ID movement doesn't get the issue framed around science it's going down and I do not like losing. The plain conclusion of scientific evidence supports descent with modification from a common ancestor...

I am amused, and I shall deign to give you peons leave to chortle quietly, if you promise to be decorous about it and not go on too long … … … that was long enough. Stop now, and go back to being mindlessly subservient.

John Mark Reynolds has put up the second part of an essay he is writing on the topic of how young-earth creationists like himself can rationalize sacrificing their scientific honesty on the altar of Biblical inerrancy. Here was my post on part 1.

Here’s a really stunning bit:

Christianity has a general view of the world that accounts for why science works … it allows the cosmos to be a cosmos (ordered) in a deep sense. Secularism lacks the same strength.


Two weeks ago, I demonstrated to Dr. Michael Egnor that his knowledge of early molecular genetics was severely flawed. He responded yesterday, calling me a “pseudo-Darwinist” because those experiments involved, according to him, “designed” variation and “artificial” selection, not random “undesigned” variation and “natural” selection.

He is of course wrong about the experiments, but his rantings about pseudo-Darwinism bring up an interesting point: Egnor himself is a “pseudo-Darwinist”, drawing an absolute dichotomy between natural and artificial selection when it suits him and blurring the two when it doesn’t. Eugenics, according to Egnor, is both the “single incontrovertible Darwinian contribution to the field of medical genetics” (3/28) and the “antithesis of Darwin’s theory” (4/9). But such rhetorical contradictions are what we have come to expect from creationists and ID activists.

For a more detailed trip to the woodshed you can read the following two posts.

My “Backed into a Corner, Egnor Cannot Keep His Arguments Straight

Orac’s “Irony meter about to explode. Must. Escape

On UcD, Dembski shows such a level of despair about the lack of fertility of the ID thesis that he is willing to claim anything which mentions the word Darwin(ism) and problem(atic) as ID friendly. While Dembski provides, as usual, little more than a snippet introduction and fails to formulate much of anything similar to what could be considered an argument, I argue that his claim that the paper is pro-ID is lacking in logic, supporting evidence and relevance.

It is helpful to remind ourselves of what Intelligent Design is, free from its rhetoric and equivocation: “The set theoretic complement of chance and regularity”. In other words, that which cannot be explained by chance and regularity is given the label ‘intelligent design’. In this case we notice that the authors are talking about science exploring a better understanding of proteins (in other words regularities) as well as Darwinian approaches to design proteins (regularity and chance).

Here’s a pro-ID article without the usual disclaimers (e.g., a ritualistic suck-up to Darwin, an obligatory sneer at ID). Perhaps this is a sign of things to come.

Protein engineering: opportunities and challenges Matti Leisola and Ossi Turunen

Journal Applied Microbiology and Biotechnology SOURCE: http://www.springerlink.com/content/d5147725155837…

|Abstract: The extraordinary properties of natural proteins demonstrate that life-like protein engineering is both achievable and valuable. Rapid progress and impressive results have been made towards this goal using rational design and random techniques or a combination of both. However, we still do not have a general theory on how to specify a structure that is suited to a target function nor can we specify a sequence that folds to a target structure. There is also overreliance on the Darwinian blind search to obtain practical results. In the long run, random methods cannot replace insight in constructing life-like proteins. For the near future, however, in enzyme development, we need to rely on a combination of both.

Steve Reuland already defused much of the ‘claims’ made in a posting on PT called The Pro-ID Paper That Wasn’t. I intent to focus instead on the scientific irrelevance that is better known as “Intelligent Design”

Few things are more ironic than young-earth creationist John Mark Reynolds (theologian at Biola, Discovery Institute fellow, leader in the ID movement) lecturing scientists about truth, stubborn facts, and having an “open philosophy of science.” If there’s an earthquake in LA today, it won’t be the tectonic plates shifting, it will be the simultaneous detonation of thousands of irony meters. How does the man get up in morning, when young-earth creationism is as hopelessly false on the empirical facts as anything ever has been in the whole history of science, and when the fundamentalist movement’s promotion of young-earth creationism is perhaps the biggest example of systematic fraud ever perpetrated on the American public? If you ever need an example of an ID advocate blathering lip service about “truth”, while shamelessly disregarding it in practice at the exact same time, here you go.

Bill Dembski and company are having a self-congratulatory session about a new “pro-ID” paper published by Finnish researchers Matti Leisola and Ossi Turunen in Applied Microbiology and Biotechnology. Looking at the paper, you wouldn’t know that it’s a “pro-ID” paper at all because it contains not one shred of evidence in favor of ID, nor does it even try directly arguing for ID (compare this to the Meyer paper, which while riddled with errors, at least put forth pro-ID arguments). On what basis could it possibly be a pro-ID paper? If it weren’t for the fact that Matti Leisola is a creationist, there would be no reason to believe it was intended as such at all.

Nevertheless, Dembski apparently thinks that it’s a pro-ID paper on the basis of its content, presumably because he conflates rational design methodology as used in protein engineering with ID. Of course this is nonsense, and in reality the paper is merely a redundant review of the current state of protein engineering techniques, with most of the space dedicated to the very long list of successes enjoyed by evolutionary methods. There are much better reviews out there, but nevertheless Leisola and Turunen give a decent (if too limited) overview of directed evolution experiments. Then they proceed to argue that rational design methods will start working better once we have more detailed knowledge of the mechanism by which the primary sequence of a protein determines its structure and function. This is an obvious and noncontroversial conclusion, so one is still left wondering how this could possibly be spun as “pro-ID”. I’ll say more about that in a minute, but first let me give a quick overview of the state of protein engineering as it exists today.

Over the past few days I have been reading the various blog commentaries on the recent Nature paper, Bininda-Emonds et al. (2007), “The delayed rise of present-day mammals.” The paper (1) constructed a “supertree” for virtually all extant mammal species (4,510 out of 4,554!!), (2) dated the tree using sequences from 66 genes and 30 fossil calibration points, and (3) concluded that placental mammalian orders arose before the K-T impact 65 million years ago, and that mammalian families arose a substantial time after the K-T impact.

Doing phylogeny on this scale is a substantial achievement, and the authors deserve the attention they are getting. But I am not sure that everyone commenting on the “Did the K-T event lead to modern mammals?” issue clearly understands the macroevolutionary concepts involved. [1] To illustrate, I will pick a particularly egregious, and therefore clear, example, from an ID blog. An IDist commentator named Bradford challenged the evolutionists as follows:

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