April 2007 Archives

Pandanapped!

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After having dinner with Dr. Irene Pepperberg, Prof. Steve Steve was pandanapped by a man in a top hat. Perhaps one of those intelligent-design activists at Telic Thoughts, who recently accused the professor of being a panda puppet. They seem to be more familiar with him than they should be.

I know it would mean a lot to Prof. Steve Steve if you friended him on Myspace or joined his fan club on Facebook.

It is spring and dandelion season. I am performing an interesting experiment in artificial selection. Every day, I go outside and pick dandelion flowers. Dandelion flowers are practically the only vegetable waste that I do not compost.

I usually take a bucket and pop the flowers off, as well as the buds. I am more likely to miss the shorter-stemmed flowers, because they are hidden below the grass, which normally needs mowing. I am therefore selecting for dandelions whose flowers mature and go to seed in less than 1 day or whose flowers grow shorter than the grass. It remains to be seen whether growing too short a stem is adaptive; possibly the grass will then prevent the dispersal of seeds by the wind. If so, we can expect to see a period of stasis.

Even after a few days I find that I am picking shorter-stemmed dandelions. Clearly, the later-maturing dandelions are acquiring the characteristics of those I have just picked – even though they are not descended from the previous generation. More surprisingly, the previous generation was not short-stemmed but only aspired to shortness before I nipped it in the bud. The effect depends on distance: there appears to be an inverse-square law, with more-distant dandelions less likely to inherit the shortness of their neighbors.

Dandelions undergo spontaneous generation. More surprisingly, they sometimes appear in their fully mature, adult form within less than 30 minutes: I can scour my backyard, find not a single dandelion, and then come back 30 minutes later and easily find more than one.

I have developed a quantitative theory that explains how the dandelions can appear spontaneously and bring with them characteristics that their neighbors only wished they had: Goddidit.

I anticipate green dandelion flowers any day now.

I don’t typically cross-post many of my infectious disease topics over here unless they have a clear evolution slant, but I thought I’d let readers know about a recent case in Australia, where a HIV+ man was convicted of endangering the lives of three women by exposing them to the virus via unprotected sex. He appealed, and the basis of his appeal was the assertion that HIV doesn’t exist, a claim backed by some so-called “HIV dissidents” who use tactics very similar to creationists: quote-mining, misrepresentation off the literature, etc. The judge came back with his decision on the whole circus today, and I discuss the results at Aetiology.

Just wanted to inform readers of The Thumb that I’m going to be appearing on a radio debate with Dr. Cornelius Hunter. The show will broadcast live from 10:05am to 11:30am EST Saturday morning April 28th. You can call in at 904.854.1320 or e-mail your questions/comments to [Enable javascript to see this email address.].

goys_radio_button.jpg

BCH

40 days and 40 nights

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I have been forgetting to mention that Darwin descendant Matthew Chapman‘s book 40 Days and 40 Nights: Darwin, Intelligent Design, God, OxyContin®, and Other Oddities on Trial in Pennsylvania has just appeared in the bookstores. Here is the publisher’s website with background material, an interview with Chapman in New Scientist, the Amazon page, a review, and Chapman’s February 2006 article on the Kitzmiller trial in Harper’s.

Yesterday, I wrote about Wiley Interscience and the Society of Chemical Industry making legal threats against fair use: Wiley Interscience: Where Science Meets Legal Threats.

Today, Shelley Batts received an apology from them:

We apologise for any misunderstanding. In this situation the publisher would typically grant permission on request in order to ensure that figures and extracts are properly credited. We do not think there is any need to pursue this matter further.

Congrats to everyone who helped get the word out about the threats. You helped Shelley and the rest of the science-bloggers out.

Theodore Roosevelt Wrote:

In the Grand Canyon, Arizona has a natural wonder which is in kind absolutely unparalleled throughout the rest of the world. I want to ask you to keep this great wonder of nature as it now is. I hope you will not have a building of any kind, not a summer cottage, a hotel or anything else, to mar the wonderful grandeur, the sublimity, the great loneliness and beauty of the canyon. Leave it as it is. You cannot improve on it. The ages have been at work on it, and man can only mar it.

Today marks the 60th anniversary of the signing of the bill setting aside Theodore Roosevelt National Memorial Park. Roosevelt was a large figure in the movement to establish the national park system, so it only seems appropriate to take up an issue about how the National Park Service is operating now.

The Public Employees for Environmental Responsibility (PEER) issued a press release on December 28th, 2006, that brought up the fact that the National Park Service (NPS) was then three years delinquent in delivering a promised review of its sale of a creationist book, Tom Vail’s “Grand Canyon: A Different View”. The release, unfortunately, included ambiguous phrasing whose most likely reading yielded a false claim that NPS had issued a “gag order” to its rangers and docents in the Grand Canyon national park to stay silent on the geological age of features in the park.

I’ve been doing some more digging concerning the situation with the national park interpretative exhibits, curricula, and bookstore merchandise. While there has not been an explicit, “Don’t talk about the age of the earth or park geology” directive given to rangers and docents, there is entirely too much credulous stuff that offers to take anti-science sources seriously. Rangers and docents are officially encouraged to tell park visitors about the “tenets and explanations of Creationism”. In evidence of a state of neglect when it comes to the accuracy of merchandise in the parks, it turns out that Tom Vail’s “Grand Canyon: A Different View” is not the only anti-science tome available for sale in park gift shops; Vine Deloria, Jr.’s “Red Earth, White Lies” may also be picked up at various stores.

Various people have accurately criticized the overblown claim of the original PEER press release concerning a gag order on interpretative staff telling visitors about deep time, essentially exonerating NPS of committing arson in its approach to science. But I feel that many have overlooked other data that does indicate a general administration strategy of encouraging dry rot instead, de-emphasizing the science content associated with park interpretative programs and credulously treating creationism and other anti-science stances.

Read on for the details.

Hexley.png

In another observation of pop culture’s war on ID, I bring you a remark by Wired:

Apparently feeling pressured by Tux, supporters of Darwin, an open-source version of the Mac OS, decided they needed their own mascot. The result is Hexley, a curious platypus who in some images is portrayed with horns and a pitchfork – enough evidence for several intelligent design theorists to offer him as proof of the satanic origins of evolutionary biology.

This is additionally funny to us because we run FreeBSD, whose mascot, Beastie, inspired Hexley.

Shelley Batts over at Retrospectacle was contacted yesterday by a representative of Wiley Interscience, who objected to her fair use of part of one figure from a paper. Shelley has posted the exchange on her blog.

Wiley’s legal threats are baseless because fair use allows people “to freely use portions of copyrighted materials for purposes of commentary and criticism.” In addition, this move by Wiley is very stupid given that Shelley was promoting a paper published in one of their journals. She was providing good press for them. But in one stupid move Wiley has turned that good press into bad press.

Because of this I will not be publishing in any Wiley journal for the foreseeable future, and I call on others to do the same.

If you want to email the journal about this, here is the contact information.

Update: Wiley has a record of acting dubiously. (via Afarensis.)

Update: An apology has been issued.

Tangled Bank #78

The Tangled Bank

The latest edition of the Tangled Bank is at About Archaeology. Read!

Are you getting bored with Earth? Maybe you should consider a move to 581 c:

For the first time astronomers have discovered a planet outside our solar system that is potentially habitable, with Earth-like temperatures, a find researchers described Tuesday as a big step in the search for “life in the universe.”

The planet is just the right size, might have water in liquid form, and in galactic terms is relatively nearby at 120 trillion miles away. But the star it closely orbits, known as a “red dwarf,” is much smaller, dimmer and cooler than our sun.

But don’t pack your bags just yet…

There’s still a lot that is unknown about the new planet, which could be deemed inhospitable to life once more is known about it. And it’s worth noting that scientists’ requirements for habitability count Mars in that category: a size relatively similar to Earth’s with temperatures that would permit liquid water.

Still, it’s a neat find. No word yet if the planet is “designed for discovery”, but presumably anyone living there would have discovered those things that are easy to discover, and will therefore conclude that the planet must be situated just right for discovery. At least if their species has creationists.

Below the fold I’ll add some more excerpts from the article. Or you can just read the whole thing.

As the discussion over the Liu-Ochman flagellum evolution paper continues, it is clear that I need to do a little more arguing to defend my position. Although some were convinced that skepticism was justified based the previous PT posts (basically: 1. this goes against much prior published knowledge and 2. just look at the obviously different structures), others have defended the paper or at least suggested that the alleged problems are not as overwhelmingly obvious as they seem to me. Two primary lines of argument have been raised. First, some have pointed out, correctly, that the reputation of the authors and journal in question far outweighs the reputation of a blogger like me, so why should readers trust me over PNAS? I will concede the case when it comes to reputation; all I can say is that over the years I have developed some familiarity with the literature pertinent to flagellum evolution, and as I read through the PNAS paper it became apparent that it was going against much of what was already known. This is not necessarily bad if a direct attempt is made to rebut conventional wisdom, but if assertions are made without much evidence of awareness that they go against previous work, that is problematic.

Over the weekend, another “Egnor” post appeared on the Discovery Institute blog. This one addresses a post I wrote two weeks ago discussing the “Framing Science” article. In his “response,” “Egnor” manages to completely distort pretty much everything about my article, in a way that is so ham-fistedly inept that it is simply impossible for me to continue to believe that the “Michael Egnor” articles are being written by a real person who really believes what he (or she) writes.

(For the record, I’m neither a “prominent Darwinist” nor a “prominent scientist.” Also, there are only two possible ways that someone could claim that “find a way to get people who aren’t interested in the science behind an issue to care about the issue itself” is the same thing as “recruit people who don’t care about science to the cause of Darwinism.” The author either has a level of respect for honesty that falls below the Roveian, or he has the reading comprehension skills of a repeatedly concussed chipmunk. In either case, I have real problems believing that it’s coming from a reportedly well-respected neurosurgeon.)

It’s been fun while it lasted, but the game’s over now. Would whoever is really writing this stuff please take this opportunity to own up to it? Please? Come on, I know it’s got to be someone who is a regular here.

Read more (at The Questionable Authority):

Uncommon Despair

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On UcD, Salvador Cordova, makes the common and fallacious argument that ID somehow predicted function in ‘junk DNA’. In fact, there is no logical foundation for this claim as ID lacks predictive power beyond ‘Darwinism does not explain X’. At most Sal can claim that people who are also proponents of ID have ‘predicted’ function for Junk DNA. But as such they are not much different from scientists who have predicted function for Junk DNA as well. Where they differ is in what motivated them to reach such a conclusion.

Cordova Wrote:

ID theory has provided positive inspiration toward scientific inquiry and participating in the reversal of “the greatest mistake in the history molecular biology”, a mistake inspired by Darwinist dogma.

ID has contributed little either in predicting or establishing function in ‘Junk DNA’ but it also seems to be basing its claims on further ignorance about the origin and evolution of the term Junk DNA (which originated from the ideas of proponents of neutral evolution and was originally limited to refer to pseudogenes). While it should not come as a surprise that ID attempts to ride on the coat tails of real science, such an attempt can be quickly countered.

Nevertheless, even in his enthusiasm, Sal seems to have downgraded ID’s contribution to ‘positive inspiration’. Even ID proponents seem to shy away from making claims that ID is scientifically fertile and are willing to settle for ‘inspirational’.

Already in 1998 Should Scientists Scrap the Notion of Junk DNA? Bob Kuska describes how science had come to realize the many treasures in ‘junk DNA”.

(Journal of the National Cancer Institute, Volume 90, Number 14 Pp. 1032-1033)

and Bring in Da Noise, Bring in Da Junk–the Semantics of Junk DNA

You have the brains of a worm…

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Well, not exactly… But the following press release allows us to explore a common confusion amongst ID proponents, in addition to providing more compelling evidence supporting common descent.

The origin of the brain lies in a worm: Researchers discover that the centralised nervous system of vertebrates is much older than expected

First of all, an “ancient” evolutionary prediction

The findings provide strong evidence for a theory that was first put forward by zoologist Anton Dohrn in 1875. It states that vertebrate and annelid CNS are of common descent and vertebrates have turned themselves upside down throughout the course of evolution.

So how come UcD ‘contributor’ DaveScot considers the findings an argument from incredulity? And what are ID’s explanations and or predictions?

Those who have been following the comments section of the first post on the PNAS flagellum paper, entitled “Stepwise formation of the bacterial flagellar system,” will see that there have been several developments: ScienceNOW at Science magazine has uncritically reported the PNAS paper’s all-flagellar-genes-came-from-one conclusion; Behe and other IDers are getting into the act, although they are so clueless they don’t really even understand why the PNAS paper is problematic; and PZ Myers and I have dropped hints that several of us PT bloggers are reaching the conclusion that this paper is looking worse, not better, after close examination. We will have more on the technical methodology issues in the next few days. For the moment I would just like to offer a simple response to some comments, and a simple but powerful reason that the “all core flagellum genes are descended from one ancestral gene” does not work.

First, the comments. Some commentators have reacted along the following lines: (1) maybe the paper isn’t so bad, just speculative; and/or (2) maybe I’ve misread the paper or its conclusion was poorly worded, and maybe the authors just meant to argue that some of the 24 core flagellar proteins were related, not all 24 proteins.

Unfortunately – and I mean unfortunately because I wish one of these options was true – neither idea is a supportable interpretation of the authors’ views. Have another look at Figure 3 from the Liu & Ochman paper:

Best Protest Signs. Ever.

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A detailed eyewitness report on the Discovery Institute’s conference revival at Southern Methodist University last weekend has been published. This bit (p. 3) is particularly good:

At this point, we were fed up with the sheer lack of science being discussed. (Remember, ID theorists claim to support a science, not a religion.) So we held up our signs. They bore questions such as, “Why do we have wisdom teeth if they do not fit our jaws?” and “Why did it take 20 species of elephant to go extinct to get two species that survived?” and “Why do the ribosomes (protein synthesizing machinery) in our mitochondria match those of bacteria?” to name a few.

The Onion scores again

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Some recent science journalism from The Onion: Unemployed Scientists Prove Dog Likes Beer

Over at After the Bar Closes, Steve Story has set up a poll asking for educational background from PT/AtBC participants. With 90 responses in, the results so far are:

  • PhD Science 32 [35.56%]
  • PhD Humanities 3 [3.33%]
  • BS/BA/Ma Science 39 [43.33%]
  • BS/BA/Ma Humanities 13 [14.44%]
  • High School 3 [3.33%]
  • Lots of Scientific American 0 [0.00%]
  • I Done Readed a Lot on the Internets 0 [0.00%]

Check it out.

by Douglas L. Theobald

As many of you undoubtedly know, neurosurgeon Michael Egnor is the Discovery Institute’s latest garrulous creationist mouthpiece. In a recent blog entry responding to Michael Lemonick of Time Magazine, Egnor claims that the 19th century scientists Michael Faraday and James Clerk Maxwell used “the inference to design” to study electricity:

“Let’s ask: what role did the inference to design play for scientists who gave us electricity? … The two scientific pioneers of classical electromagnetism, Faraday and Maxwell, were particularly devout Christians who inferred design everywhere in nature. They believed that God designed everything — including electricity. Their approach to science was pure design inference, undiluted by atheism or materialism. … They worked entirely from the design inference.”

Faraday and Maxwell were Christians who did indeed see design in nature. However, Egnor has it backwards.

Today the prestigious journal Proceedings of the National Academy of Sciences (PNAS) put out an Advanced Online Publication paper on flagellum evolution entitled, “Stepwise formation of the bacterial flagellar system.” The paper is freely available via Open Access. I was initially excited that PNAS had published a paper on this topic, and furthermore that it cited the Pallen/Matzke essay on flagellum evolution, and Ian Musgrave’s excellent book chapter in Why Intelligent Design Fails.

Unfortunately, as I read the paper, my delight turned to concern, and then dismay. The paper makes some potentially useful points and explores new territory in a few areas. But much of it ranges from dubious to just irremediably wrong.

Irony award goes to…

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Salvador Cordova (Young Earth Creationist)

Darwinian TE (Theistic Evolution) just doesn’t cut it scientifically.

What a riot, as opposed to the scientifically defensible Young Earth variant or the scientifically vacuous Intelligent Design variant?

conwaymorris1LR.jpgI missed this one a week or two ago. Simon Conway Morris and his colleague Jean-Bernard Caron published a paper in Science on a new Cambrian fossil called Orthrozanclus. The cool thing about the fossil is that it combines features from two other fossils that Conway Morris previously implicated as transitional stem groups between the modern crown groups (“phyla”) of mollusks, annelids, and brachiopods: Wiwaxia and Halkeria. Of course, according to Discovery Institute propaganda, transitional fossils like this don’t exist.

Here is a news summary. See also the Orthrozanclus post from PZ Myers, his post last year on another stem group mollusk-ish critter, Odontogriphus.

The SMU Campus newspaper carried an opinion piece written by Ben Wells who is a junior anthropology major.

The article starts out by describing the political and religious foundation behind the Discovery Institute’s actions

This weekend Dedman Law School’s Christian Legal Society will be hosting a controversial and well-known institute that preaches a religious message masked in a capsule of pseudoscience.

Indeed, the Wedge document outlines clearly how Intelligent Design is meant to be a religious and not necessarily a scientific issue.

A controversial document (reported as the Wedge Document, a 1998 internal memo) stated the Institute’s goal was to “drive a wedge” into “scientific materialism” in order to divorce it from its purely observational and naturalistic methodology and stop the deleterious effects of evolution on Western culture.

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):

This just in:

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)

ID? It’s all OUR Fault!

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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.

and

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.

Did T-Rex taste just like chicken?

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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

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?

Sarkar Lab: Debating a Creationist

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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?

Dennert and the deathbed of Darwinism

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

So let me spell it out: DIRECTED EVOLUTION IS NON-DARWINIAN. DARWINIAN EVOLUTION IS NON-DIRECTED.

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.

200px-Another_one_bites_the_dust.jpg

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

The despair of Intelligent Design

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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[…]72515583767/

|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:

In the March 28, 2007 edition of Scientific American, Douglas Fox reports on the results of renewed experiments based on the original work by Stanley Miller.

Miller became famous for his experiments with Urey where they used a sparking device to replicate early earth. Their experiment produced a brown mixture rich in amino acids. In later experiments, which more closely matched the actual composition of the early earth, Miller found that the amino acids were quickly destroyed.

Not surprisingly, creationists quickly jumped on these results to argue that evolution must be wrong, and by extension, creationism was correct.

Such arguments of course are extremely vulnerable to scientific knowledge and in this case, things are not much different.

Three years and counting

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I was just reminded that last year at this time I announced an anniversary. In March of 2004, I critiqued this mysterious abstraction called "ontogenetic depth" that Paul Nelson, the ID creationist, proposed as a measure of developmental and evolutionary complexity, and that he was using as a pseudoscientific rationale against evolution. Unfortunately, he never explained how "ontogenetic depth" was calculated or how it was measured (perhaps he was inspired by Dembski's "specified complexity", another magic number that can be farted out by creationists but cannot be calculated). Nelson responded to my criticisms with a promise.

On 29 March 2004, he promised to post an explanation "tomorrow".

On 7 April 2004, he told us "tomorrow".

On 26 April 2004, he told us he was too busy.

On 13 January 2005, he told us to read a paper by R Azevedo instead. I rather doubt that Ricardo supports Intelligent Design creationism, or thinks his work contributes to it.

Ever since, silence.

One day has stretched into three years. I would fear that Paul Nelson has fallen into a chronosynclastic infundibulum and come unstuck in time, except that he still pops up saying the same stuff at creationist conferences. Maybe he just forgot, and this thread will remind him so that he'll show up and post that promised explanation in a comment.

Tomorrow.

Jonathan Wells apparently felt the sting of my rebuttal of his assertions about Hox gene structure, because he has now repeated his erroneous interpretations at Dembski's creationist site. His strategy is to once again erect a straw man version of biologist's claims about genetic structure, show that biologists have refuted his dummy, and claim victory. The only real question here is whether he actually believes his historical revisions of what we've known about Hox genes, in which case he is merely ignorant, or whether he is knowingly painting a false picture, in which case he is a malicious fraud.

Continue reading "Wells on Hox structure: making the same mistakes over and over again" (on Pharyngula)

The latest issue of the journal Science includes a policy forum piece written by Sciencebloggers Chris Mooney (The Intersection) and Matt Nisbet (Framing Science). In the article, they argue that scientists do not, for the most part, use effective communications strategies when trying to defend science. Both Chris and Matt anticipate that this view is likely to be somewhat controversial, and that it is likely to spark a vigorous debate. I think that they are probably right about this, and not just because their article includes at least one paragraph that is likely to set PZ off faster than a lit match dropped into a five-gallon can of kerosene.

As Chris and Matt point out, we scientists tend to act under the assumption that the public will “get it” if we can just get them to understand the science. Larry Moran agrees with that perspective, and points out that people like Gould, Dawkins, and Sagan were pretty good at communicating science just that way. Larry does have a point there, but I think it misses the main point that Nisbet and Mooney were making: it’s also important to communicate concepts to people who don’t give a damn about the science. They also point out that the opponents of good science are very good at framing their views on stem cell research, the environment, teaching evolution, and other areas that fall at the intersection of science and politics.

I think Matt and Chris are right. We do need to spend more time (and thought) on communicating our views effectively, particularly to people who do not care about science.

Read More (at The Questionable Authority):

Hagfish embryos!

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hagfish_egg.jpg

I've been looking forward to seeing these little jewels in print since I saw Kuratani talk about them at the SICB meetings in January. Hagfish are wonderfully slimy jawless chordates that have been difficult to raise in the lab—although if you poke a whale corpse rotting in the cold deeps you'll find them swarming everywhere. The Kuratani lab has managed to keep animals of the species Eptatretus burgeri alive and healthy in a lab aquarium maintained at cold temperatures (16°C), and has even had success in breeding them. That object to the right is a single hagfish egg, brown and leathery-shelled and surprisingly big—it's an inch and a half long!

They collected 92 eggs, and then another limitation emerged: it took 5-7 months for embryos to develop in a small number of the eggs. Hagfish aren't going to be your typical fast-developing model system, I'm afraid, but they are extraordinarily cool animals, and it's good to see work beginning on them.



Continue reading "Hagfish embryos!" (on Pharyngula)

From YouTube:

Latest product of basic evolution program.

A creatures probability of survival is dependent its compatibility to the environment relative to its fellows.

Anyone who survives can breed.

This shows that evolution is an intrinsic property of any system where offspring are different from their parent, and suffer environmental attrition. Life is such a system.

Note that with the population sizes shown, it is more likely that random genetic drift will be stronger than selection. And chimps were not the ancestors of humans et al.

Creationist brain surgeon Michael Egnor has been busy over the last couple of days, posting first a “response” to Orac’s challenge then a “response” to Mark ChuCarroll’s repeated attempts to explain the concept of tautology to him. There have been several responses to these two posts over at various of the Scienceblogs already - PZ, Orac, Mark, and Kevin have all addressed one or both of Egnor’s latest claims, and all of their responses are worth reading. I’m actually feeling a little left out right now - after all, Egnor still hasn’t deigned to address the two specific examples I presented of cases where natural selection has and is playing a role in public health decisions.

I’m not going to address Egnor’s claims about the role of the design inference in medicine at the moment. The stupidity really does burn, and Orac did a superb job of working through the brain spasms to deal with that post. Kevin and Mark have also done a good job addressing some of Egnor’s claims in the more recent “tautology” post, but I think that there is something that I can add to their responses. An introduction - Dr. Egnor, I’d like to introduce you to Sir Ronald Aylmer Fisher, FRS.

Read more (at The Questionable Authority):

This evening, I am watching an episode of that marvelous and profane Western, Deadwood, as I type this; it is a most excellently compensatory distraction, allowing me to sublimate my urge to express myself in uncompromisingly vulgar terms on Pharyngula. This is an essential coping mechanism.

I have been reading Jonathan Wells again.

If you're familiar with Wells and with Deadwood, you know what I mean. You'll just have to imagine that I am Al Swearingen, the brutal bar-owner who uses obscenities as if they were lyric poetry, while Wells is E.B. Farnum, the unctuous rodent who earns the contempt of every man who meets him. That imagination will have to hold you, because I'm going to restrain myself a bit; I'm afraid Wells would earn every earthy sobriquet I could imagine, but I'll confine myself to the facts. They're enough. The man completely misrepresents the results of a paper and a whole discipline, and does it baldly on the web, as if he doesn't care that his dishonesty and ignorance leave a greasy, reeking trail behind him.

Let's start with Wells' own words.

Continue reading "Wells' flagrantly false commentary on Hox complex structure" (on Pharyngula)

Double-Take

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piratehead.jpg

Well, it was nice while it lasted, which was far longer than we projected; the SUCKERED post was indeed a prank on you, dear PT readers, pretending to reveal a Discovery Institute prank at our expenses.

We’re not sure whether this is a success or a failure on our part. On one hand, our prank was better executed than the ones at Uncommon Descent and Telic Thoughts and received lots of praise. On the other hand, many of our readers need to work on their critical observation skills. Maybe we can blame it on our good reputation; our readers trust the quality of our work.

Of course, it wouldn’t have been possible without the DI acolytes providing us with seemingly inexhaustible involuntary parodies themselves. Indeed, just as our prank went online, Michael Egnor himself out-pranked us with a real post containing this philosophy gem:

Materialism is nonsense, because if matter and energy are all that exist, then truth doesn’t exist (it’s neither matter nor energy). If truth doesn’t exist, then materialism can’t be true.

Dude, that’s like, so deep.—Seriously, how can you beat these guys?

Anyway, it all started with us honestly wondering, after Egnor appeared on the scene a few weeks ago, whether he was actually real.—The sweet onomatopoeia of his name and style was just too good to be true.—Alas, it quickly became clear he was a real person and surgeon. As April 1st approached, we considered writing a post claiming that he was, in fact, a prank, but that seemed too direct and obvious. So the LeCarréan double-twist was conceived of trying to fool you pretending that the DI fooled us.

Andrea wrote the SUCKERED post, Reed made up the faux “Evolution Views & News” page with some pompous-sounding rewrites by Douglas, and the rest of the PT crew provided the usual slew of commentary, suggestions, nagging, doubt, and advice. The sciencebloggers amplified the effect by feigning dismay on their sites.

We thought most of you guys would see right through it, but it worked so well that it even fooled PT contributor PvM, who needs to read his e-mail more often. I guess years of contending with the absurdities emanating from the DI can make anyone confused between what is real and what is farce . …

[BOW]

Stephen Meyer, Discovery Institute cofounder and major IDist, in support of the Designer on this somewhat trying day, offers this amazing discovery: Meyer proves that information of any sort, not just complex specified information, comes from out of this world! Meyer’s impeccable proof is so astonishing in its simplicity that it can be explained to a first grade class! Here it is.

Stephen Meyer, explaining why biological information cannot originate through a materialistic process, said:

One of the things I do in my classes to get this idea across to students is I hold up two computer disks. One is loaded with software the other one is blank. And I ask

“What’s the difference in mass between these two computer disks as a result of the difference in the information content that they posses?”

Meyer of Disco

And of course the answer is zero - none. There is no difference as a result of the information. And that’s because information is a massless quantity. Now if information is not a material entity, then how can any materialistic explanation explain its origin? How can any material cause explain its origin. And, this is the real fundamental problem that the presence of information in biology has posed. It creates a fundamental challenge to the materialistic evolutionary scenarios because information is a different kind of entity that matter and energy cannot produce. uhm  In the nineteenth century we thought that there were two fundamental entities of science: matter and energy. At the beginning of the 21st century we now recognize that there is a third fundamental entity, and it’s information. It doesn’t - it’s not reducible to matter, it’s not reducible to energy, but it is still a very important thing that is real, we buy it we sell it, we send it down wires. Now what do we make of the fact that information is present at the very root of all biological function? [picture of DNA] That in biology we have matter we have energy but we also have this third, very important entity, information? The biology of the information age I think poses a fundamental challenge to any materialistic approach to the origin of life.

SUCKERED

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OK, well, we have to admit it, this time our adversaries at the Discovery Institute completely fooled us. For several weeks many of us have been involved in a back-and-forth with Michael Egnor, a neurosurgeon at Stony Brook who, ironically, displayed an amazingly thick skull about anything concerning evolutionary biology. Not only did he deny the obvious facts of evolution and its importance for medicine and biology, but he kept contradicting himself, repeating empty statements, ignoring the evidence and demanding answers to questions which had been already answered many times over. It was maddening to think that a person with a high-level degree and an academic position in a major educational and research institution could be such a know-nothing fool.

Well, he isn’t, apparently. It was all a ruse by ID advocates to see how far they could pull our chain, and lead us to take his progressively more outlandish statements for real. The Discovery Institute Media Complaint Division site has now come clean, admitting to the prank and giving us a well-deserved raspberry. We should have known better: imagine having a guy who denies the obvious homology of our neural system to that of other vertebrates in charge of slicing off chunks of it in an operating room! Or someone who doesn’t believe bacteria evolve resistance to antibiotics dealing with the risk of post-operatory infections.

While we are ashamed to have fallen for such a crass caricature of a “dumb Creationist”, and apologize to our readers for the time wasted in countering his ludicrous arguments, we applaud the cleverness of the ID folks involved in this April Fool’s joke and their effortless impersonation of such a character.

How stupid of us not to have thought of that!

The PT Crew

April 2nd Update:

The above post is part of our April Fools’ prank on you, our readers. The Discovery Institute did not admit that Egnor was pranking us. That faux page was part of our ruse. Read all the comments in this thread to see who fell for it and who didn’t. Also check out this post, where we come clean.

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