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It’s Paul Nelson Day, again

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wafflehouse

Solemn greetings, all. Today, as the more reverent among you know, is Paul Nelson Day. Today is the 12th annual feast day of St Nelson, patron saint of obtusity and procrastination, and we honor his contributions to science by...well, by not doing much of anything at all. You could make grandiose claims today and promise to make good on them tomorrow, a tomorrow that stretches out into a decade or more, I suppose, but that's too much work. Instead, maybe we should all just shrug and say we'll think about celebrating later.

Oh, jeez, shrugging? I don't have time for that. How about if we don't and just say we did.

I also thought about suggesting waffles as the perfect food for this day, but nah, I'd have to cook them, or go to a restaurant. I'm just going to say "waffles!" and put it off to some other day.

Anyway, if you don't know the story, Paul Nelson is a creationist who attended the Society for Developmental Biology meetings in 2004, with a poster in which he claimed to have developed this new evo-devoish parameter, Ontogenetic Depth, that supposedly measured the difficulty of developmental complexity to evolve. I quizzed him on it, and specifically asked him to explain how I could measure it in my zebrafish, for example, and he couldn't tell me, even though he seemed to be saying that he and a student had been doing these 'measurements'. But he promised to send me a paper he was working on that explained it all. Tomorrow! A tomorrow that never came.

So now we remind him of his failure every year. It's a good thing to point out to Intelligent Design creationists that they don't seem to be very good at fulfilling their grand promises.

He seems to sometimes notice that he's being mocked, at least. Last year, he tried to trot out Ontogenetic Depth 2.0, which was just as impractical and ill-conceived as the first non-existent version. Maybe he'll have a new beta for us this year, too?

Unlikely. Too much work. Not in the spirit of the day.

We have just received an e-mail from one of the Panda’s Thumb crew to the effect that a paper “demonstrating” the intelligent design of the human hand has been published in the refereed journal Plos One. The paragraphs that caught the crew member’s attention are these:

The explicit functional link indicates that the biomechanical characteristic of tendinous connective architecture between muscles and articulations is the proper design by the Creator to perform a multitude of daily tasks in a comfortable way.

In conclusion, our study can improve the understanding of the human hand and confirm that the mechanical architecture is the proper design by the Creator for dexterous performance of numerous functions following the evolutionary remodeling of the ancestral hand for millions of years.

Another crew member directs us to the website Retraction Watch, which quotes a Plos editor to the effect that

PLOS has just been made aware of this issue and we are looking into it in depth. Our internal editors are reviewing the manuscript and will decide what course of action to take. PLOS’ publishing team is also assessing its processes.

The Retraction Watch paper naturally engendered the response,

Where has tolerance and respect for the beliefs and opinions of others gone? One doesn’t need to agree, but bringing in a different idea in a civil manner seems more appropriate for an academic discussion.

buzzards.jpg

This was sent out by the Discovery Institute around a week ago. Note the bolded sentence.

Dear {Insert name of email recipient here}:

Max Karl Ernst Ludwig Planck, originator of modern quantum theories and 1918 winner of the Nobel Prize in Physics, was quoted as saying, “A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.”

Here in Discovery Institute’s Center for Science and Culture (CSC), we are living proof that no matter how powerful an idea is–and the idea of intelligent design (ID) is truly a powerful one–there is some truth to Planck’s statement. It is not just about convincing opponents about the merits of ID. While books such as Stephen C. Meyer’s Signature in the Cell and Darwin’s Doubt have been met with critical acclaim, there is still a long way to go.

Thanks to your generosity, we aren’t simply waiting for our opponents to die.

Since its inception almost 10 years ago, visionary CSC donors have enabled us to focus on educating young people through our Summer Seminar on Intelligent Design and C.S. Lewis Fellows Program– programs designed to raise up a new generation of scientists and scholars who are not afraid to follow the evidence wherever it leads. These programs are made possible by those who recognize that science needs an infusion of new minds and ideas.

We need your support to continue and expand these programs. Our summer programs attract students from the United States and around the world, including Europe, Africa, Asia, Australia, Central and South America, and the Middle East; more than we can admit. Most of these students cannot attend unless we pay their expenses.

You can help with your gift of any amount.

  • $75 will pay for the cost of ground transportation for one student.
  • $200 will provide books and other curricular materials to one student.
  • $800 will pay to house and feed one student for the entire program.
  • $2,500 will cover the full cost for admitting an additional student into the program.

Donate now to the Summer Seminar campaign and be a part of the transformation of science and culture, one student’s life at a time!

Creepy, or what? Discuss.

(Update: paper preprint and bonus material available free here)

It is 7 am in Australia, but this is finally out on Thursday afternoon in the U.S.…just in time for the tenth anniversary of Kitzmiller v. Dover! I will do a longer post a little later, but for now - be sure to check out the Supplemental Material!

Matzke, Nicholas J. (2015). “The evolution of antievolution policies after Kitzmiller v. Dover. Science, Published online Dec. 17, 2015. (http://www.sciencemag.org/content/e[…]057.abstract | http://dx.doi.org/10.1126/science.aad4057)

See also: PDF of character maps for characters 1-111 of the Matzke (2015) phylogeny of antievolution bills. These are the presence-absence characters; there are more characters but in a larger file, we’ll see how PT handles this one first

The War Before Kitzmas

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Over at Elizabeth Liddle’s “The Skeptical Zone” (TSZ) blog, Salvador Cordova had something to say about being banned from the “Uncommon Descent” (UD) blog, now being managed (loosely speaking) by Barry K. Arrington.

Arrington did something for Cordova that he doesn’t do for most people banned from UD, which was to send Sal an explanatory letter, which Sal included in his TSZ post. I’ll quote it below the fold.

Kitzmas is Coming!

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The tenth anniversary of the Kitzmiller v. Dover decision, which came out on December 20, 2005, is right around the corner. There have already been some good retrospectives, including a series of pieces by the York Daily Record, another series in Reports of the National Center for Science Education, and a “What If Intelligent Design Had Won?” discussion by Eugenie Scott and Kenneth Miller in York College, Pennsylvania, in November. There will undoubtedly be more to come; please post links in the comments when you see them come out.

This has been obvious from the start, but as far as I know it has taken 10 years for the ID guys to finally admit it. Winston Ewert writes at the Discovery Institute blog:

However, Felsenstein and English note that a more realistic model of evolution wouldn’t have a random fitness landscape. Felsenstein, in particular, argues that “the ordinary laws of physics, with their weakness of long-range interactions, lead to fitness surfaces much smoother than white-noise fitness surfaces.” I agree that weak long-range interactions should produce a fitness landscape somewhat smoother than random chance and this fitness landscape would thus be a source of some active information.

GAME OVER, MAN. GAME OVER! The whole point of Dembski et al. invoking “No Free Lunch” theorems was to argue that, if evolutionary searches worked, it meant the fitness function must be designed, because (logical jump herein) the No Free Lunch theorems showed that evolutionary searches worked no better than chance, when averaged over all possible fitness landscapes.

Emergency backup arguments to avoid admitting complete bankruptcy below the fold, just so I’m not accused of leaving out the context.

Last March Tom English and I posted an argument here here at Panda’s Thumb analyzing an argument by William Dembski, Winston Ewert, and Robert Marks. They had made an argument that evolutionary “search” would not do better than blind search; we proved that their argument showed no such thing.

In response to our analysis here of the Dembski-Ewert-Marks paper, Winston Ewert has replied at Evolution News and Views. As that site does not allow comments, I have finally gotten around to posting a response here (six months late). Tom has now put up a related thread at The Skeptical Zone; I will try to comment in both discussions.

Ewert rather dramatically reveals that Tom and I do not actually disagree with any of the theorems in their paper. And he’s right about that. How did they discover this remarkable fact? Perhaps it was by reading our post, where we said

We’re not going to argue with the details of their mathematics, but instead concentrate on what in evolutionary biology corresponds to such a choice of a search.

or by reading a comment in that thread where I also said:

As theorems they may be mathematically true, but the average poor performance of searches is true only because so many irrelevant and downright crazy searches are included among the set of possible searches.

Ewert is right that we did not question their theorems. Instead we concentrated on what would follow from their theorems. We showed in a simple model that once there are organisms that reproduce, with genotypes that have phenotypes and fitnesses, that evolution will find higher fitnesses much more effectively than random guessing. So is it true that having what they call Active Information, embodied in a fitness surface and in a reproducing organism whose genotypes have those fitnesses, requires that there be Design Intervention to set up that system?

The issue is not the correctness of their theorems but, given that they are correct, what flows from them. Dembski, Ewert, and Marks (DEM) may object that they did not say anything about that in their paper.

We don’t think that it is a stretch to say that DEM want their audience to conclude that Design is needed.

Let’s look at what conclusions Dembski, Ewert, and Marks draw from their theorems. There is little or no discussion of this in their paper. Are they trying to persuade us that a Designer has “frontloaded” the Universe with instructions to make our present forms of life? Let’s look at what Dembski and Marks have said about that (below the fold) …

December 20 will be the 10th anniversary of Kitzmiller vs. Dover Area School District – what Dave Thomas calls Kitzmas. Kitzmiller, I probably need not say, is the Federal court decision that established intelligent design creationism as, well, creationism and therefore ineligible to be taught as part of a biology course in the public schools. You can read a no longer so hot-off-the-press report by Wesley Elsberry here.

But to my task: Lauri “Devil in Dover” Lebo sent us the following press release from the ACLU of Pennsylvania, announcing a victory celebration at 7 p.m., Saturday, November 7, in the Abbey Bar at Appalachian Brewing Company, Harrisburg. The panel discussion features PT’s Nick Matzke, who was then a staffer at the National Center for Science Education and the discoverer of the infamous cdesign proponentsists.

But before I get to the press release, which I will display below the fold, let me ask that other people who want to announce Kitzmas celebrations give the specifics in a Comment. If we get a measurable number of celebrations, we will post the list and stick it to the top of the page through December 20.

OK, on to the details of the press release:

(edited to add a point on Aegirocassis and Parapeytoia)

This week, the Discovery Institute Press put out another book called Debating Darwin’s Doubt. I took one for the team and bought it, in part because a a decent chunk of the book is responding to me. I’m pretty sure I’ve never been mentioned so much in a book!

Sadly, though, looking through it, almost all of it is material re-hashed from the DI “Evolution News and Views” blog and is no better than it was the first time. There is, however, a new chapter (I think it is new) by Casey Luskin, chapter 9, “Cladistics to the Rescue?” responding to me. If you don’t want to buy the book, there is a free podcast at ID the Future (heh), “Debating Darwin’s Doubt: Casey Luskin on Classification of Organisms” that interviews Luskin (although I think he wrote the questions). It has mostly the same material.

Unfortunately, I do not have time at the moment to write the introductory-level-tutorial-from-square-one that would be required to really explain the basics of cladistics and phylogenetics to Luskin et al. I have literally just moved to Australia to start as a Discovery Early Career Researcher Award (DECRA) Fellow in the Division of Ecology, Evolution, and Genetics, Research School of Biology, at The Australian National University in Canberra. Once I have a bed and a computer in my office I may be in better shape to do things more thoroughly – I have a bit of a fantasy about writing an R vignette or R package called something like BasicPhylogeneticsForCreationistsEspeciallyLuskin (I’ll take suggestions on a better name/acronym).

However, below, I can briefly hit the high points on the small bit of Luskin’s chapter that was new.

adam-and-eve-cast-out-of-paradise-after-eating-from-the-tree-of-knowledge-in-the-garden-of-eden.pngI would like to introduce everyone to James Downard, and his website Troubles in Paradise (TIP). TIP is available at http://tortucan.wordpress.com/ or http://www.tortucan.com.

James Downard is an activist with decades of experience tracking the creationists, stretching back to encounters with Stephen Meyer in Washington state in the early 1990s. In 2010, he did a guest post for PT, “An Ill Wind in Tortuca”, available at: http://pandasthumb.org/archives/201[…]wind-in.html

Troubles in Paradise is a massive review of the creationism/ID movement, its people, and its arguments, along with a similarly massive review of relevant scientific evidence and literature. TIP primarily covers the movement up to about 2004, which of course was just about the peak of the ID movement, leading up to the 2005 Kitzmiller v. Dover case.

I think it is extremely valuable to the pro-science community to have such a historical review available: the ID movement actively tries to conceal what it was saying pre-Kitzmiller, and of course the “intelligent design” label itself was an attempt to disguise connections to creation science. (And, “creation science,” particularly the whitewashed version put forward for the Edwards v. Aguillard case, was its own attempt at obscuring connections to religious fundamentalism.) (On this, see especially: Matzke, N. (2009), “But Isn’t It Creationism? The beginnings of ‘intelligent design’ and Of Pandas and People in the midst of the Arkansas and Louisiana litigation.” In: But Is It Science?: The Philosophical Question in the Creation/Evolution Controversy, Updated Edition, eds. Pennock & Ruse, Prometheus Books, 377-413; google Scholar)

Today in 2015, it is not uncommon for commentators new to the creationism/ID debate to start producing writings almost totally ignorant of the history of the issue. Hopefully Downard’s effort will help correct this problem, and will serve as a resource that science fans can link to and cite.

Troubles in Paradise is really several books’ worth of work, so if you’ve ever gone to the bookstore and bought a science book, please think about making a similar donation so that Downard can continue his efforts.

Below, I post Downard’s short description of the project, which includes a Q & A email interview I conducted with him, and links to his GoFundMe page, www.GoFundMe.com/dseego. Please reblog, retweet, and spread the word! PS: James Downard’s Twitter is: @RJDownardNick Matzke

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Short description of Troubles in Paradise, by James Downard:

Welcome to TIP, a new open access resource for defenders of sound science who get really unsettled by the claims of antievolutionists (be they Young Earth Creationists or the newer brand of Intelligent Design) but may not have all the best science information ready to drop on their claims.

The TIP files (all in pdf format) cover all aspects of antievolutionism (from paleontology and biology to the social and political ramifications of antievolutionism as they play out in schoolrooms and school boards or in state legislatures, Congress, or even candidates for President.

The Old TIP files form the base of the project, drawing on over 5500 sources, and step by step I am updating that material with a much larger set of newer data (over 36,000 sources and counting, including over 14,000 technical science sources aimed at claims popping up in over 6000 antievolutionist works) to keep TIP constantly current. The new modules also have an index to help locating all specific topics and people covered.

There are more pdfs & offsite web links in Other Stuff, including the 3ME illustrated guide to the Cambrian Explosion, and the origin of birds and mammals, the perfect heavy brick to lob at antievolutionists who make the mistake of claiming “there’s no evidence for macroevolution.” 3ME not only shows how wrong that is, it also pulls back the curtain to see just how antievolutionists manage to evade all that evidence (not a pretty picture, but has to be done).

Check out all the material here on TIP, all open access to download and share freely with anyone you think needs evens stronger evidence to counter the claims of antievolutionists.

Q & A with James Downard:

Q: Why did you decide to call your project “Troubles in Paradise” (TIP)?

On August 14, William Dembski spoke at the Computations in Science Seminar at the University of Chicago. Was this a sign that Dembski’s arguments for intelligent design were being taken seriously by computational scientists? Did he present new evidence? There was no new evidence, and the invitation seems to have come from Dembski’s Ph.D. advisor Leo Kadanoff. I wasn’t present, and you probably weren’t either, but fortunately we can all view the seminar, as a video of it has been posted here on Youtube.

It turns out that Dembski’s current argument is based on two of his previous papers with Robert Marks (available here and here) so the arguments are not new. They involve considering a simple model of evolution in which we have all possible genotypes, each of which has a fitness. It’s a simple model of evolution moving uphill on a fitness surface. Dembski and Marks argue that substantial evolutionary progress can only be made if the fitness surface is smooth enough, and that setting up a smooth enough fitness surface requires a Designer.

Briefly, here’s why I find their argument unconvincing:

  1. They conside all possible ways that the set of fitnesses can be assigned to the set of genotypes. Almost all of these look like random assigments of fitnesses to genotypes.
  2. Given that there is a random association of genotypes and fitnesses, Dembski is right to assert that it is very hard to make much progress in evolution. The fitness surface is a “white noise” surface that has a vast number of very sharp peaks. Evolution will make progress only until it climbs the nearest peak, and then it will stall. But …
  3. That is a very bad model for real biology, because in that case one mutation is as bad for you as changing all sites in your genome at the same time!
  4. Also, in such a model all parts of the genome interact extremely strongly, much more than they do in real organisms.
  5. Dembski and Marks acknowledge that if the fitness surface is smoother than that, progress can be made.
  6. They then argue that choosing a smooth enough fitness surface out of all possible ways of associating the fitnesses with the genotypes requires a Designer.
  7. But I argue that the ordinary laws of physics actually imply a surface a lot smoother than a random map of sequences to fitnesses. In particular if gene expression is separated in time and space, the genes are much less likely to interact strongly, and the fitness surface will be much smoother than the “white noise” surface.
  8. Dembski and Marks implicitly acknowledge, though perhaps just for the sake of argument, that natural selection can create adaptation. Their argument does not require design to occur once the fitness surface is chosen. It is thus a Theistic Evolution argument rather than one that argues for Design Intervention.

That’s a lot of argument to bite off in one chew. Let’s go into more detail below the fold …

si-JulAug2014.jpg I’ve a brief new article in the new Skeptical Inquirer (July/August 2014) regarding Casey Luskin’s botched attack on the second episode of Cosmos. Here it follows - your comments are welcomed.

Fox TV’s Seth McFarlane has joined with astrophysicist Neil deGrasse Tyson and Ann Druyan, Carl Sagan’s widow and collaborator, to continue Sagan’s marvelous Cosmos series of decades ago. The new series is a splendid blend of homage to Sagan’s original one with dazzling new graphics–and new discoveries.

The second episode of the series, first broadcast March 16, 2014, covered evolution and natural selection. (Link) As expected, creationists were furious. The main promoter of “intelligent design,” Seattle’s Discovery Institute, has run several anti-Cosmos blogs on its Evolution News and Views (ENV) website.

In their zeal to attack Tyson and the Cosmos series, however, the Discovery Institute has created a stunning example of the straw man logical fallacy. This fallacy is so named because it involves attacking one’s opponent not by an honest dissection of his or her actual views but by attacking a caricature, a distorted misrepresentation of those views. The Discovery Institute’s attack on the evolution episode of Cosmos was a particularly egregious example of this fallacy–a straw man for the ages, as it were.

From the website of the Schilling School, “A Nationally Recognized K-12 [Charter] School for the Gifted in Cincinnati, Ohio”:

Dr. Michael Behe to present at Schilling. Mark your calendar for Sunday, April 6th from 7:00 pm - 9:00 pm to hear him present, “ Feeling left out by the Ham-Nye Debate? The Reasonable Middle Ground of Intelligent Design.” Call 489-8940 for ticket prices and group rates.

Congratulations to our 2014 U.C. Science Fair winners. All of our students won a cash prize. Two of our students Salma and Daniel have been invited to participate at the state science fair in Columbus next month. Good luck to the both of them!

And may they not be seduced by pseudoscience.

Acknowledgment. Thanks to an alert reader for sending us the link.

By Josh Rosenau.

Reposted from NCSE’s Science League of America blog.

Crystal Disco. ballA Crystal disco ball to celebrate the crystal anniversary of the Disco. ‘tute’s entry into the creationism business.

Fifteen years ago yesterday, a mail clerk in Seattle was handed a document to copy. As the Seattle Weekly reported, the packet was labeled “TOP SECRET” and “NOT FOR DISTRIBUTION,” and the cover sported an Illuminati-esque triangular design and a copy of Michelangelo’s “Creation of Adam.” The title: “The Wedge”; the author: a newly-created division of the conservative Discovery Institute, the Center for the Renewal of Science and Culture (CRSC). Later, the Center would drop “renewal” from its title to escape the religious reference, and also switched its logo from the Creation of Adam to a picture of God creating DNA, then to a more secular galactic nebula, and now a mashup of Leonardo’s Vitruvian man and a DNA strand.

The Wedge Document, as the packet came to be known, laid out a bold plan by which the Center would “re-open the case for a broadly theistic understanding of nature,” and “reverse the stifling dominance of the materialist worldview, and to replace it with a science consonant with Christian and theistic convictions.” From its first sentence, the document proclaimed its sectarian goals, stating: “The proposition that human beings are created in the image of God is one of the bedrock principles on which Western civilization was built. Its influence can be detected in most, if not all, of the West’s greatest achievements, including representative democracy, human rights, free enterprise, and progress in the arts and sciences.”

Robert Asher is a Cambridge mammal paleontologist, zoologist, phylogeneticist, author of Evolution and Belief, and generally really smart guy. He has just published a commentary at HuffPo on one aspect of Stephen Meyer’s arguments, namely, Meyer’s argument about “uniformitarianism.”

A Very Darwinian Halloween

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It’s Halloween, so it’s time for a roundup of the SCARIEST October stories in the evolution versus creationism wars!

Years ago, someone gave me a book on child-rearing, and I noticed afterward that it was on The New York Times bestseller list. I mentioned the fact to my father, an expert on child-rearing, and his only comment was, “That’s not why it is lousy.” My father would no doubt feel vindicated right about now: Stephen Meyer’s book, Darwin’s Doubt, will be on the Times‘s bestseller list this coming Sunday, July 7.

Acknowledgment. Thanks to Alert Reader for pointing out this depressing fact.

Update, July 5: As a commenter has pointed out, Darwin’s Doubt will not appear on the July 14 list. The book is evidently a flash in the pan—unless they moved it to the fiction section. Advance orders were evidently vigorously promoted, but no one is actually reading the book, which we may consider a blessing.

Note: I am extremely busy this summer, finishing grad school and moving to a postdoc. But when I got this book, I realized I wouldn’t be able to focus on my real work without having gotten my 2 cents in. This is a rough-and-ready piece, so typos and missing references, and missing explanations of technical terms are to be expected, although I’m sure they can all be figured out with a wee bit of googling. I am off to Evolution 2013 tomorrow and will be incognito, writing, after that. So I may not comment much. However I expect commenters to be reasonable discussants and polite and will ban people who break the spirit of this expectation. Cheers, Nick

Review of Stephen C. Meyer’s Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design

This week, a new book came out by Stephen Meyer, Darwin’s Doubt: The Explosive Origin of Animal Life and the Case for Intelligent Design. Having followed the ID movement and specifically its arguments on the Cambrian ‘Explosion’ for a long time, as well being somewhat up on the recent literature, and especially on phylogenetics, I feel that I have a pretty good sense of what to look for in any work purporting to be a capable commentary on the topic. As I read through Meyer’s book, though, in case after case I see misunderstandings, superficial treatment of key issues which are devastating to his thesis once understood, and complete or near-complete omission of information that any non-expert reader would need to have to make an accurate assessment of Meyer’s arguments.

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.

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