Photograph by Sarah Boosey.

Erinaceus europaeus, hedgehog, East Dereham, Norfolk, UK.

Due to scheduled electrical maintenance, this website and the rest of my scit.us server will be taken off line Monday night and will not come back on until some time Tuesday morning.

I just heard word that evolutionary microbiologist Carl Woese has died. Woese is probably most famous for defining the Archaea, the “third domain of life”.

Intelligent design proponents have touted Woese’s ideas about horizontal gene transfer as a challenge to evolutionary theory, even claiming that Woese argued there were multiple, independent origins of organisms. This was wrong, of course. Almost exactly a decade ago, I asked Woese to give his thoughts on his work and ID. I leave you with some of his comments:

It’s basically correct to say that I do not challenge common ancestry per se but rather the concept that there was a single common ancestor cell or organism that gave rise to the three cellular domains of life.

In a way my theory is more of a problem for creationists and their ilk than the old way of looking at things – though those folks do not seem to sense this yet. Special creation starts with a given type of form that may or may not change but in any case remains “true” to its original character. “Intelligent design” seems to see different mechanisms being designed individually, just as an inventor or engineer would do. Well, in my theory none of this is the case.

I have no trouble with a claim to the effect that God set the world up so that it progressed in an evolutionary fashion. That would affect my work no more than the belief that God’s world was a mathematical world affected Newton’s work; one can scientifically procede the same way with or without the assumption. And creationist or intelligent design views will be back where they belong, in the realm of (immature) religion.

Photograph by Roger Lambert

Photography contest, Honorable Mention.

A child discovers science at the American Museum of Natural History.

In association with the Santa Fe Institute, Melanie Mitchell will teach a free online course called Introduction to Complexity starting on January 28, 2013. Mitchell has been working in complex systems research for years. Her Ph.D. advisors were Doug Hofstadter of Gödel, Esher, Bach fame and John Holland, a towering figure in the study of complex adaptive systems, which is the title of his influential 1975 book. According to the intro video and the course FAQ, it’s is aimed at non-specialists:

This course is intended for anyone with an interest in complex systems. For this introductory course, there are no prerequisites, and no science or math background is necessary. The level will be similar to that of an interdisciplinary undergraduate class, though the topics are broad enough to be of interest to people ranging from high school students to professionals.

To register to earn a certificate of completion, go here. One can watch the course videos without registering, though one won’t take the final nor be able to participate in the student forum.

Hat tip to Sean Carroll.

Reporter James McNair recently reported in a Cincinnati newspaper that the attendance at the Creation Museum has dropped for four consecutive years and that Answers in Genesis lost over $500,000. These tidbits inspired my colleague Dan Phelps and me to look at AIG’s Forms 990. These are tax forms that must be submitted by nonprofit organizations to the US Internal Revenue Service and may be found if you have a (free) account on GuideStar.

According to various Forms 990 through the tax year ending June 30, 2011, in four consecutive years, AIG has run surpluses of approximately $2.1 million, $716,000, and $940,000, and a loss of $540,000. Not exactly a monotonic decline, but certainly a steep drop from a surplus of $2.1 million to a loss of $540,000 in three years. Can we expect similar losses due to the Ark Park? Maybe: Joe Sonka in the Louisville newspaper LeoWeekly reports that “… correspondence between Ark Encounter and the Tourism Cabinet reveal an application process that proceeded with remarkable speed, little scrutiny, and standards that appear different from that of [another applicant].”

The 2010 Form 990 (for fiscal year ending June 30, 2011) has some interesting information.

Photographs by Bob Gitzen.

Photography contest, Honorable Mention.

The left frame shows the 84% partial eclipse of the sun on May 20 in Concord, California, passing through deodar cedar branches and projected onto a patio shade as a collection of pinhole camera images. The right frame is the same time the next day, showing the dramatic difference in appearance.

This started as a comment on my earlier post responding to a comment by John Harshman, but it outgrew comment length so I’ll do it as a post. It may appear to be beating a long-dead horse that’s suffered enough, but there’s an aspect of Gauger’s commentary that is again part of the Disco ‘Tute’s efforts to undermine common descent and impugn the credibility and honesty of evolutionary scientists in general that deserves attention.

John Harshman wrote

I don’t deny that the green screen is a valid target for ridicule. And it is indeed a fine metaphor for the whole DI exercise (though I really like “cargo cult science”). I had two points:

1. There’s been too much attention to the green screen in proportion to its importance. This may be because it’s a subject for which those who don’t know much about the biology feel free to contribute. It might be that the green screen is equally understandable and meaningful for the ignorant public, and so should be emphasized, but I don’t think that argument is a strong one.

Nor do I think it’s particularly strong except as a manifestation of the ‘business as usual’ approach to rhetoric of the Disco ‘Tute. And having earned a degree in anthropology many decades ago, I too like the “cargo cult science” characterization.

Douglas Axe and Ann Gauger, both of the BioLogic Institute, have put out a series of videos summarizing some of the content of “Science and Human Origins.” They attempt to undermine the case for common descent, and in particular the descent of humans from non-human ancestors. John Harshman, in comments on my posts on the use of a commercial stock photo of a lab as a background for Ann Gauger’s blather about “… a hidden secret in population genetics and in evolution,” argued that the focus on the green-screening diverts attention from the real issue, which is her mangling of the science (see here for an example). While John is right that setting the record straight on the science is important, it’s also the case that the green-screening is but one aspect of a larger effort on the part of the Disco ‘Tute to erode public confidence in ‘mainstream’ science. And that effort is what underpins the newest strategy of the Disco ‘Tute and its fellow travelers, which is to promote legislation embodying so-called “academic freedom” for public school teachers who want to teach creationism and intelligent design (see here for an overview and here for a Barbara Forrest video on it).

This guest post is written by Paul Braterman and Mark Edon, and appears courtesy of the British Centre for Science Education.

BCSE has long maintained that the Seattle-based Discovery Institute (DI), of which Glasgow’s own Centre for Intelligent Design (C4ID) seems to be a satellite, is a religiously motivated Creationist organisation. Casey Luskin has now demonstrated this with great clarity in his response, in the misleadingly titled Evolution News and Views (“Serving the Intelligent Design Community”), to the recent opinion piece “Anti-Creationists need to think about tactics”, which we recently posted on our site. Thanks Casey.

As our title and opening words make clear, our piece is addressed by us, as individual nonbelievers, to other nonbelievers, giving our reasons for cooperating with believers in defending science against Creationism. It does not even mention DI, or C4ID, or Intelligent Design. Nonetheless, Casey seems to find our piece relevant to his mission. Perhaps his concern with religion is not surprising, since the foundation document of DI’s Centre for Science and Culture gives the restoration of a “theistic understanding” as a core objective. As for Intelligent Design, few people can still believe the pretence that it is anything more than a cover for Creationism (in the strict sense of the term as applied to biological diversity), but it is good to see our thoughts on these matters so authoritatively confirmed.

There are many more reasons why being attacked by Casey has been compared to being savaged by a dead sheep. Here are a few of them (remember here that Casey is a trained lawyer, and has published on law in an internationally recognised journal, so presumably he has read what he refers to and means what he says about it):

For reasons completely unknown to me, people who know nothing whatsoever about the ancient Mayans and, indeed, could not care less about the ancient Mayans think that the world ended yesterday. I had serious doubts, so I pinched myself and listened to the weather forecast before deciding that the world had not ended yesterday. My wife told me to shut up and go to sleep.

But when will the world end? That depends, of course, on what you mean by the world ending. If you mean when will Earth itself be destroyed, then that will happen roughly 5 billion years from now, when the sun becomes a red giant. Notice that I said 5 billion years, with a B, not, thank God*, a mere 5 million years, with an M.

If you mean, when will life on Earth be obliterated, that will happen in a more disquieting 1 billion years.

David Klinghoffer, Disco ‘Tute apologist, has responded to the recent kerfuffle involving Ann Gauger’s mangling of population genetics and phylogenetics (see Joe Felsenstein’s comment on Sandwalk) whilst green-screened over a stock laboratory photograph. Klinghoffer doesn’t bother to address the scientific nonsense Gauger promoted, of course–how could he?–but claims that the green-screened lab was convenient because

Typically, filming in a genuine location like this would be troublesome for us and bothersome for others who work there – a distraction for all involved, including viewers, when the intent is to focus on the argument. Many other times, in other contexts, we have similarly used backdrops where, to get to an actual locale, it would require travel not to mention complicated, time-consuming setup and many other headaches. Going with a green screen makes sense for an organization that operates under a constrained budget.

So in Klinghoffer’s head there are just two alternatives: use a stock photo and green-screen Gauger into it, or tape Gauger speaking in her own lab. Here’s a third alternative for Klinghoffer and the DI’s film producers: Take a still photo of Gauger’s lab, which might be 10 minutes or so of interruption of the horde of minions working in it, and then green-screen her into that photo. That would have saved $19.00 (the reported cost of the stock photo) for the constrained budget of the DI. But it would also mean escaping from a false dichotomy, and ID proponents seem to be cognitively unable to entertain more than two alternatives at once; witness their decades-long efforts to equate (mostly specious) critiques of evolution with evidence for ID.

Three major holidays occur in the next two days. First, there’s Kitzmas on Dec 20^th, the 7^th anniversary of Judge Jones’ 2005 ruling in Kitzmiller v. Dover.

Second, there’s the winter solstice on the 21^st, the beginning of winter. It’s the day the sun is at its lowest altitude above the horizon in the northern hemisphere and the day is the shortest of the year. The winter solstice is celebrated by many cultures, not including those who have to go to work in the dark of morning and return home in the dark of evening. But be of good cheer: The days will get longer again!

Finally, of course, both of those holidays are trumped by the ultimate on the 21^st, THE END OF THE WORLD! (Or maybe just a transition to a new world of sweetness, light, and endless beer for the FSMers.) At least some of the loonier wingnuts (see here for some descriptions) tell us the world will end, basing their story on a misinterpretation of the Mayan calender. Skeptics notwithstanding, you can watch the end of the world live here.

So, Merry Kitzmas, Happy Solstice, and I’ll see you on the other side of the end of the world (maybe…)!

In this note, Nick Matzke directs PT’s readers to this post, by Jerry Coyne. Jerry, you see, had received an e-mail from the prominent creationist Paul Nelson, in which Nelson cited recent work by several prominent scientists as challenging the efficacy of natural selection in crafting complex adaptations. Jerry went to the trouble of contacting the folks cited by Nelson, and he posted their replies at his website. You can probably imagine how it went for Nelson, but I recommend reading Jerry’s post nonetheless. Take a browse through the comments as well, since Nelson shows up to dig the hole a bit deeper.

In his e-mail, Nelson also called attention to this talk that he recently gave at Rick Warren’s Saddleback Church in California. He asks Jerry to comment on the argument he presents to the audience. Well, I can’t speak for Jerry, but I have listened to the presentation and present my own thoughts in this post over at EvolutionBlog. The short version: I think his argument has some flaws, to put it kindly. For the longer version follow the link, and feel free to leave comments over there.

This deserves its own post. Yesterday I pointed to a post at Larry Moran’s Sandwalk about a Discovery Institute video showing Ann Gauger, a “researcher” at the Disco ‘Tute’s BioLogic Institute, in which she mangles phylogenetics and population genetics. Commenters on Youtube and both Sandwalk and here have identified the laboratory in which Gauger was supposedly speaking. It is a stock photograph from a commercial photo site. It’s a green screen job, which is a peculiarly appropriate method by which to present the DI’s pseudoscience. Fake lab, fake science.

Can we say “pathetic”?

Course page here. Course description:

Introduction to Genetics and Evolution gives interested people a very basic overview of the principles behind these very fundamental areas of biology. We often hear about new “genome sequences,” commercial kits that can tell you about your ancestry (including pre-human) from your DNA or disease predispositions, debates about the truth of evolution, and why animals behave the way they do. This course provides the basic biology you need to understand all of these issues better and tries to clarify some misconceptions. No prior coursework is assumed.

Topic outline:

*Evidence for evolution
*Introduction to basic genetics
*Recombination and genetic mapping simple traits
*Complications to genetic mapping
*Genes vs. environment
*Basic population genetics and Hardy-Weinberg
*Gene flow, differentiation, inbreeding
*Natural selection and genetic drift
*Molecular evolution
*Evolutionary applications and misapplications
*Adaptive behaviors and species formation

Taught by Mohamed Noor, Earl D. McLean Professor of Biology at Duke and (IIRC) Jerry Coyne Ph.D. Ten weeks, 5-6 hours per week workload. Free!

Phylogenetics and population genetics, that is. Larry Moran calls attention to the confusion of Ann Gauger, ID-pushing BioLogic Institute “researcher.” My favorite comment in the thread is from (PT crew member) Joe Felsenstein:

I must be totally confused. I wrote a book on reconstructing evolutionary trees – and it’s the standard textbook in that area. But it does not mention many basic population genetics concepts. I have another book (a free downloadable e-book) that is a textbook of theoretical population genetics. And it does not mention homoplasy at all.

So I must misunderstand what “population genetics” is. And here I’ve been giving courses on it for the last 44 years. At the university where Ann Gauger got her Ph.D. degree, for that matter.

Silly me.

My second favorite is from Piotr Gasiorowski:

Cargo cult science

Precisely. The cult members gather in mock laboratories full of imitation equipment, where they mimic the way scientists speak and behave.

(crossposted from Recursivity)

One thing that separates pseudoscience from science is fecundity: real science takes place in a social context, with an active community of scholars meeting and exchanging ideas. The ideas in one paper lead to another and another; good papers get dozens or hundreds of citations and suggest new active areas of study.

By contrast, pseudoscience is sterile: the ideas, such as they are, lead to no new insights, suggest no experiments, and are espoused by single crackpots or a small community of like-minded ideologues. The work gets few or no citations in the scientific literature, and the citations they do get are predominantly self-citations.

Here is a perfect example of this sterility: Bio-Complexity, the flagship journal of the intelligent design movement. As 2012 draws to a close, the 2012 volume contains exactly two research articles, one “critical review” and one “critical focus”, for a grand total of four items. The editorial board has 30 members; they must be kept very busy handling all those papers.

(Another intelligent design journal, Progress in Complexity, Information, and Design, hasn’t had a new issue since 2005.)

By contrast, the journal Evolution has ten times more research articles in a single issue (one of 12 so far in 2012). And this is just a single journal where evolutionary biology research is published; there are many others.

But that’s not the most hopeless part. Of the four contributions to Bio-Complexity in 2012, three have authors that are either the Editor in Chief (sic), the Managing Editor, or members of the editorial board of the journal. Only one article, the one by Fernando Castro-Chavez, has no author in the subset of people running the journal. And that one is utter bilge, written by someone who believes that “the 64 codons [of DNA are] represented since at least 4,000 years ago and preserved by China in the I Ching or Book of Changes or Mutations”.

Intelligent design advocates have been telling us for years that intelligent design would transform science and generate new research paradigms. They lied.

I’ve had my disagreements with Jerry Coyne over a few things, but this is freakin’ genius. Bonus points for the Marshall McLuhan/Annie Hall reference.