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Musings from the mind of a mouse

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Casey Luskin is such a great gift to the scientific community. The public spokesman for the Discovery Institute has a law degree and a Masters degree (in Science! Earth Science, that is) and thinks he is qualified to analyze papers in genetics and molecular biology, fields in which he hasn't the slightest smattering of background, and he keeps falling flat on his face. It's hilarious! The Discovery Institute is so hard up for competent talent, though, that they keep letting him make a spectacle of his ignorance.

I really, really hope Luskin lives a long time and keeps his job as a frontman for Intelligent Design creationism. He just makes me so happy.

His latest tirade is inspired by the New York Times, which ran an article on highlights from the coelacanth genome. Luskin doesn't think very deeply, so he keeps making these arguments that he thinks are terribly damaging to evolution because he doesn't comprehend the significance of what he's saying. For instance, he sneers at the fact that we keep finding conserved elements in the genome, because as we all know, there are lots of conserved elements.

Happy 9th Paul Nelson Day!

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It's a dying holiday, I'm sorry to say -- I completely forgot it last year. But I was reminded this year, so I'll mention it again. I think the proper way to celebrate it is simply to laugh at a creationist today.

The source of the holiday is a remarkable exhibition from Paul Nelson, who like several other creationists, loves to register and present at legitimate science conferences. The barriers are low, and many conferences are intended to give students an opportunity to present, so you'll often find that all you have to do is send in a fee and an abstract and you'll be allowed to put up a poster in an allotted space for a few hours of time. So Nelson showed up at the Developmental Biology meetings in 2004 with a poster titled "Understanding the Cambrian Explosion by Estimating Ontogenetic Depth" in which he and Marcus Ross claimed to have been collecting data measuring some parameter called "ontogenetic depth" in various organisms.

I was at that meeting. I asked him about that in person, and also in blog posts afterwards. How do you measure ontogenetic depth? Share your procedure so I can assess and replicate it, which is what scientists are supposed to do. He hemmed and hawed and hmmphed and in typical Nelsonian fashion babbled and burbled on, and the upshot was that he couldn't tell me just then, but he had something he was writing and he'd polish it up and get it to me the next day, 7 April. He didn't. We've been watching the 7th of April pass by for nine years now.

I think he's felt the sting of mockery. In 2010 he announced that my criticisms were invalid, but he was inventing Ontogenetic Depth 2.0, which still isn't defined and still doesn't have a procedure.

In 2011 he posted some more essays on his fictitious method, in the first of which he announced that ontogenetic depth is A Biological Distance That's Currently Impossible to Measure. Yeah? So why was he presenting a poster at a serious scientific meeting in which he and his colleague claimed to have been measuring it? Sounds like scientific fraud to me.

But then, Intelligent Design creationism has been scientific fraud all along, so I guess he was just following hallowed tradition.

A favorite creationist mantra these days, and one you especially hear from young earthers, is that creationists and scientists both have the same facts, they just look at them differently. To laypeople that may sound reasonable. The handful of guys at Answers in Genesis look at the Grand Canyon and say it was formed by a flood about 4400 years ago when God got all pissed off at humans. The 24,000 members of the Geological Society of America (and virtually every member of the literally dozens of geological organizations listed at their web site*) look at the Grand Canyon and say it was formed over millions of years by natural processes that continue today.

Same facts; different conclusions. Some of us laypeople often hear these two positions and see them as equally valid positions on either side of a debate. But some of us scratch the surface, and it doesn’t take a very deep scratch to see a significant difference. Scientists do science and creationists don’t.

I consider myself pretty well-educated about creationism, and of course I know it’s all silly, but I pride myself on usually being able to understand what argument the creationists are trying to make, even when they are doing it poorly. But I need help with this one.

Via the Discovery Institute Blog/Misinformation Service, I came across this post from Hunter, which is his Monday post. I also read Hunter’s Sunday post and got confused.

Starting on Sunday, we have: Cornelius Hunter, Sunday, July 25, 2010, speaking about shared errors in pseudogenes:

This claim, that such shared errors indicate, or demonstrate, or reveal common ancestry, is the result of an implicit truth claim which does not, and cannot, come from science. It is the claim that evolution and only evolution can explain such evidences. It is the equivalent of what is known as an IF-AND-ONLY-IF claim.

Science makes IF-THEN statements (if evolution is true, then species with recent common ancestors should have similarities between them). IF-AND-ONLY-IF statements (if and only if evolution is true, then species with recent common ancestors should have similarities between them) cannot be known from science. [italics original]

OK, so here he’s saying, I guess, that science can only make if-then statements, and test hypotheses on that basis. Science cannot formally say that X is the ONLY possible explanation of Y, because, I suppose, there always might be some other explanation out there.

That is the title of an article to be published in The International Journal of Cardiology, a presumably reputable journal published by Elsevier. Avijit Roy, the editor of the pro-science website Mukto-Mona, published in both Bengali and English, takes Elsevier to task on Talk Reason here.

Once again, the Discovery Institute stumbles all over itself to crow victory over evolution, led by the inspiring figure of that squeaking incompetent, Casey Luskin. This time, what has them declaring the bankruptcy of evolution is the discovery of tetrapod trackways in Poland dating back 395 million years. I know, it's peculiar; every time a scientist finds something new and exciting about our evolutionary history, the bozos at the DI rush in to announce that it means the demise of Darwinism. Luskin has become the Baghdad Bob of creationism.

The grounds for this announcement is the bizarre idea that somehow, older footprints invalidate the status of Tiktaalik as a transitional form, making all the excitement about that fossil erroneous. As we've come to expect, though, all it really tells us is that Casey Luskin didn't comprehend the original announcement about Tiktaalik, and still doesn't understand what was discovered in Poland.

Of Weasels and weasling

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As everybody should be aware by now, Denyse O’Leary is offering a prize for the original code for Dawkins’ Weasel program which illustrates cumulative selection [1]. O’Leary’s offer arises from people challenging Dembski’s misrepresentation of the Weasel program, as he has misrepresented it yet again in a trivial non-id paper. To get some much needed perspective, read Joe Felsenstein’s excellent article (and its follow-up) and those of Chris Mark Chu Carroll (here and here)

Seriously, arguing over whether Dawkins “weasel” program implements locking is a bit like arguing over whether the measuring cylinder in the Measuring Cylinder/Tap model of drug clearance is emptied by a tube or a bloke with a cup. Both are simplified systems that make demonstrating a concept easy, and do much the same thing.

The point is that a leading light of the cdesignproponentsits has spent an enormous amount of time critiquing a toy demonstration of selection, and can’t even get the toy example right. Not only that, they can’t admit when they were wrong. Heck, no one in the cdesign proponetsists can admit Dembski is wrong about a toy program, even when presented with video evidence.

Let’s emphasise this again. It’s a non-issue except for the way it highlights the determined cluelessness of cdesign proponetsists. To use the metaphor of the Measuring Cylinder/Tap model of drug clearance again, Dembski is effectively arguing that Dawkins said the measuring cylinder is emptied by a man with a cup in his book, but anyone can go to Dawkins original book, read how he set it up, and understand that Dawkins specified a tube. Dawkins doesn’t specify how big the tube, or the flow rate of the tap, but it’s sort of obvious and you can easily make an analogous system which demonstrates the same things that Dawkins does. Everyone understands except Dembski who then makes a convoluted argument over the whole thing (see www.evoinfo.org and read their “explanation” of Dawkins program if you have a spare half-hour of your life you don’t mind wasting).

Now there is a video showing a measuring cylinder with a tube (metaphorically, see www.youtube.com/watch?v=5sUQIpFajsg (go to 6:15) for the real video showing the weasel program), Dembski goes “oh, Dawkins must have REALLY have used a cup in his book, then swapped to a tube for the video”. Aside from the convoluted mentality involved in this staggering piece of “reasoning”, it goes to the heart of the cdesign proponentists reliability.

When Dembski claims that Lenski et al., have “smuggled in information”, explaining why they are wrong can get quite technical, but when they claim Dawkins has “smuggled in information”, one can simply point to how deeply they have misunderstood Dawkins model, and if they can’t get Dawkins right (after being told repeatedly, having it explicitly demonstrated to them and being shown a video), what hope is there that they got Lenski right.

For more information on Dembski’s denial of the video evidence, see Dembski Weasels Out, for a wide compendium of Weasel programs old and new, including head to head comparisons of Dawkins version vs Demski’s locking version see Weasels on Parade (note it took over 23 days for the Uncommon Descent people to come up with any programs themselves). To see where I completely reconstruct the output shown in Dawkins book, see here.

[1] Why doesn’t O’Leary just ask Dawkins? The whole concept of running a competition to get Dawkins code instead of asking Dawkins is rather bizarre. While he may not have the original code, he can tell her how he did it.[2] [2] People have asked Dawkins before. It no longer exists. Just like the AppleBasic programs I wrote to calculate stimulation-induced radioactive outflow for our laboratory. Used for years but vanished into the mists of time. Seriously, even if there was a disk around with AppleBasic finding a machine to run it and make copies would be an adventure in itself.

William Dembski and Robert Marks have written a paper. No it won’t be going in the peer reviewed literature, but into another of Dembski’s anthologies. Mark C. Chu-Carroll of Good Math, Bad Math explains what is mind-bogglingly wrong with it here and here.

Beavers of the Gaps

There’s a very interesting article over at Uncommon Descent about beavers, and the things that they do. I’m not entirely sure why they posted the article - Barry seems to be trying to make the point that because Beavers clearly can commit criminal acts but just as clearly can’t form criminal intent, their brains are different from humans, and there’s therefore something “non-materialist” and special about the human brain. I’d like to take a look at the same story, but with a slightly different focus.

Here’s the story:

Green campaigners called in police after discovering an illegal logging site in a nature reserve - and rounded up a gang of beavers.

Environmentalists found 20 neatly stacked tree trunks and others marked for felling with notches at the beauty-spot at Subkowy in northern Poland.

But police followed a trail left where one tree had been dragged away - and found a beaver dam right in the middle of the river. A police spokesman said: “The campaigners are feeling pretty stupid. There’s nothing more natural than a beaver.”

Let’s look at this story from the perspective of detecting design. That’s a topic that’s particularly relevant right now, given that Dembski himself has recently abandoned, then abandoned his abandonment of, the explanatory filter.

The Luskin Follies, Part MCMLVIII

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Last month PvM posted on Casey Luskin’s misconceptions based on some remarks reportedly made by Catherine Boisvert in a news story on the resolution of the distal radials of Tiktaalik.

However, as PvM pointed out, Boisvert’s research using MicroCT scans, discussed in that news article, actually resolved those elements of a Tiktaalik:

The disposition of distal radials in Panderichthys are much more tetrapod-like than in Tiktaalik,” Boisvert wrote. “Combined with fossil evidence from Tiktaalik and genetic evidence from sharks, paddlefish and the Australian lungfish, it is now completely proven that fingers have evolved from distal radials already present in fish that gave rise to the tetrapod.

Now Chris of A Free Man, a geneticist in Australia, has interviewed Boisvert about Luskin’s misuse of her remarks and her work with the specimens. The money quote:

As you know, the “Discovery” Institute tactic is not to go to the primary literature in order to understand it but rather to use quotations from secondary, even tertiary sources, reorganise or use them out of context opportunistically to their own convenience. In this case, they used an article where the journalists unfortunately misunderstood me. Tiktaalik’s material is in fact exquisite, it is very well preserved, basically uncrushed and can be prepared out to be examined in three dimensions. I never said the quality was poor. I have simply explained that the morphology of the fin of Panderichthys is more tetrapod-like than that of Tiktaalik, which has nothing to do with the quality of the material.

That pretty much settles it, I’d say.

In a book review by Christopher Heard, Pepperdine University of Stewart, Robert B., ed. Intelligent Design: William A. Dembski and Michael Ruse in Dialogue Minneapolis: Fortress, 2007, we read how Dembski’s attempts to have design be a place holder for our ignorance, are doomed to fail.

The continued rise of ignorance

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On evolutionnews.org, lawyer Casey Luskin, ‘argues’ that Tiktaalik as an evolutionary icon is poor, in a retrospective confession of ignorance. Let’s see how he reached such a ‘conclusion’.

Casey Luskin Wrote:

The Rise and Fall of Tiktaalik? Darwinists Admit “Quality” of Evolutionary Icon is “Poor” in Retroactive Confession of Ignorance

How did Luskin reach this ‘conclusion’? Because he read an interview with the lead-researcher who made the following claim:

Boisvert Wrote:

Previous data from another ancient fish called Tiktaalik showed distal radials as well – although the quality of that specimen was poor. And the orientation of the radials did not seem to match the way modern fingers and toes radiate from a joint, parallel to each other.

A logical conclusion would be to accept the observation that the quality of the specimen was ‘poor’ regarding the details of ‘distal radials’, but instead Luskin decided to mine the statement to mean that the quality of Tiktaalik was poor.

Casey Luskin Wrote:

The “quality” of Tiktaalik as a fossil specimen was “poor”? When did we see Darwinists admit this previously? Never. They wouldn’t dare make such admissions until they thought they had something better.

But in fact, the ‘Darwinists’ had already admitted that the fossil specimen for Tiktaalik poorly resolved the distal radials.

The “best possible code”

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A paper written by Knight et al in 2000 has created some confusion as to the nature of the genetic code, leading some design proponents to jump to the conclusion that these findings show evidence of ‘design’ when in fact, the findings, in proper context show strong support for an evolutionary thesis of the origin and evolution of the genetic code. Let me explain.

Casey Luskin’s “Junk” Arguments

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In a classic ‘bait and switch’, Casey Luskin, ‘argues’ that the “classic “Junk DNA” icon of neo-Darwinism needs updating” because a Yale University news release shows how differences in the regulatory elements between humans and chimps explain the human thumb and foot development.

Regular readers on this group may remember Steve Fuller whose contributions as an “expert witness” for the defense in the Kitzmiller law suit were quoted by the plaintiffs as well as the judge to show that ID was not science?

Last year, Steve Fuller released a book titled “Science v. Religion? Intelligent Design and the Problem of Evolution” which was recently reviewed by Sahotra Sarkar in “Notre Dame Philosophical Reviews”. Sarkar’s scathing review exposes the vacuity of Fuller’s arguments, a vacuity we have come to expect from ‘Intelligent Design’.

Not wanting to be left out, Denyse O’leary, validates the quality of the work by Sarkar by referring to him as a “third-rate Darwin hack”. Furthermore, Denyse, in her continued display of ignorance, responds to Sarkar’s observation that Fuller predicts that Darwinism (by which he means the entire framework of evolutionary theory) will be dead by the end of the twenty-first century and will be replaced by something more akin to ID creationism with “What about the Altenberg 16? “.

The Louisiana Coalition for Science has released a press release calling for the Senate to reject the creationist bill approved by the Louisiana House

New group stands up for sound science education in Louisiana

LA Coalition for Science decries House support for SB 733, calls for Senate to reject bill

Baton Rouge, LA, June 11, 2008 — In response to numerous attacks on science education in the Bayou State, concerned parents, teachers and scientists are getting organized. The new group — Louisiana Coalition for Science — calls upon the Senate to oppose SB 733, a bill which will open the door to creationism in public schools.

Spread the news.

Thumbnail image for Allen_2007.jpgAllen MacNeill has yet another interesting contribution (as well as an announcement about a new course). Allen MacNeill:It’s very gratifying to see Lynn Margulis finally getting the recognition that she deserves. As the originator of the serial endosymbiosis theory (SET) for the origin of eukaryotes, Lynn’s work provides an excellent example of how ID should (but currently doesn’t) proceed. During the late 1960s, Lynn published a series of revolutionary papers on the evolution of eukaryotic cells, culminating in her landmark book Symbiosis and Cell Evolution, in which she carefully laid out the empirical evidence supporting the theory that mitochondria, choloroplasts, and undulapodia (eukaryotic cilia and flagella) were once free living bacteria (purple sulfur bacteria, cyanobacteria, and spirochaetes, respectively).

Read the rest at Serial Endosymbiosis and Intelligent Design

Allen makes an excellent case how science progresses and that while science may resist change, the only way to change science is to do hard work, research and show how your ideas form scientifically relevant contributions. This is particularly relevant when it comes to Intelligent Design, whose proponents have chosen it to remain scientifically vacuous, without content. And still they whine about being ‘expelled’ when in fact they are ‘exposed’.

Allen is also organizing Seminar in History of Biology: Evolution and Ethics: Is Morality Natural? at Cornell

COURSE LISTING: BioEE 467/B&Soc 447/Hist 415/S&TS 447 Seminar in History of Biology

SEMESTER: Cornell Six-Week Summer Session, 06/24/08 to 07/31/08

The Washington Post has an excellent editorial on the recent attempts by Intelligent Design Creationists to ‘teach the controversy’ and ‘academic freedom’, observing that

Red-herring arguments about ‘academic freedom’ can’t be allowed to undermine the teaching of evolution.

The editorial points out how these efforts to undermine science are at best misguided.

NO ONE would think it acceptable for a teacher to question the existence of gravity or to suggest that two plus two equals anything but four. It’s mystifying, then, that a movement to undermine the teaching of evolutionary biology is attracting some support. Equally perverse is that this misguided effort is being advanced under the false guise of academic freedom.

T Ryan Gregory at Genomicron who is an evolutionary biologist specializing in genome size evolution at the University of Guelph in Canada educates us (and perhaps some ID proponents) about some of the common pitfalls in phylogeny. In this case, the posting discusses the findings in a recent paper which argues that the comb jellies and not sponges are the earliest branch.

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