Well, this is interesting! Pseudo-historian David Barton, whom we last heard from here on the Thumb declaring that America’s Founding Fathers had considered evolution, and rejected it for creationism, has had his newest book examined and rejected by a group of conservative authors headed by the Discovery Institute’s Jay W. Richards.

From the New York Times Artsbeat blog for August 14, 2012:

Last month the History News Network voted David Barton’s book “The Jefferson Lies” the “least credible history book in print.” Now the book’s publisher, Thomas Nelson, has decided to stop publishing and distributing it.

The book, which argues that Thomas Jefferson was an enthusiastic orthodox Christian who saw no need for a wall of separation between church and state, has attracted plenty of criticism since it appeared in April, with an introduction by Glenn Beck. But the death knell came after Jay W. Richards, a senior fellow at the Discovery Institute and the author, with James Robison, of “Indivisible: Restoring Faith, Family and Freedom Before It’s Too Late,” began to have doubts and started an investigation.

The Times blog refers to a detailed August 7^th, 2012 article by Thomas Kidd at World Magazine, which notes

Richards says in recent months he has grown increasingly troubled about Barton’s writings, so he asked 10 conservative Christian professors to assess Barton’s work.

Their response was negative. Some examples: Glenn Moots of Northwood University wrote that Barton in The Jefferson Lies is so eager to portray Jefferson as sympathetic to Christianity that he misses or omits obvious signs that Jefferson stood outside “orthodox, creedal, confessional Christianity.”

More on the story in an August 10^th report by Tim Murphy of Mother Jones, “The Right’s Favorite Historian Comes Apart at the Seams” :

Barton has turned the study of America’s Christian roots into a lucrative business, hawking books and video sermons, speaking at churches and political confabs, and scoring a fawning New York Times profile and interviews on the Daily Show. He’s got friends in high places: “I almost wish that there would be like a simultaneous telecast and all Americans would be forced–at gunpoint no less–to listen to every David Barton message,” Mike Huckabee told an Evangelical audience in March of 2011. “I never listen to David Barton without learning a whole lot of new things,” Newt Gingrich told conservatives in Iowa that same month.

That’s probably because much of what David Barton writes seems to have originated in David Barton’s head.

On Thursday, Barton’s publisher announced that it was recalling Barton’s newest book, The Jefferson Lies, from stores and suspending publication because it had “lost confidence” in the book’s accuracy. That came one day after NPR published a scathing fact-check of Barton’s work, specifically his claim that passages of the Constitution were lifted verbatim from the Bible.

Wow. We know how much the Discovery Institute needs to feed on disinformation and polemics. That one of their leaders had to reject Barton’s book is a strong indication that the book must be really, really, really bad!

Discuss.

As we all know, the new book from the Disco ‘Tute, Science and Human Origins, has taken a considerable amount of flak for various and sundry flaws. Paul McBride has a chapter-by-chapter review starting here. Amusing among the critiques was Carl Zimmer’s quest to get a reference from the authors for a specific claim, summarized here. Nick Matzke posted an equally amusing account of a Facebook exchange with (presumably) the authors in a thumb comment. The Disco Tute authors ended that exchange by closing comments on the thread, running for a venue that doesn’t allow comments.

Now Afarensis has dissected another claim made in an excerpt from the paleo chapter by Luskin (who is a lawyer writing on paleo) about what Luskin calls Later Hominins: The Australopithecine Gap, I strongly recommend Afarensis’ takedown to our readers. I particularly call attention to Afarensis’ analysis of Luskin’s quote-mining and misrepresentations about Lucy. Is anyone surprised?

By Dan Phelps, [Enable javascript to see this email address.]

Dan Phelps, right, armed for battle, with his new friend, Ken Ham.

On July 28, 2012, Answers in Genesis (AIG) held a “Behind the Scenes” event at the Creation “Museum’s” Legacy Hall. The event was free but with RSVP required via the Ark Encounter website. I made it a point to register well in advance and ask for a space for a guest. I invited reporter Joe Sonka from LEO Weekly to come along since he has done numerous critical news articles and blog postings on the Ark Park. Indeed it was Joe who asked Governor Beshear and Ark Encounter representatives some embarrassing questions revealing that the Ark would have dinosaurs on it when the project was announced in December, 2010. What follows is my account of the event and summary of the status of the proposed park.

… to enter the photography contest! I know you all have more good pictures in you, so let’s get cracking! The winners, do not forget, will receive autographed copies of Among the Creationists, by Jason Rosenhouse, which received a very favorable review from a very irascible critic.

Troy Britain has joined the Panda’s Thumb crew. Troy is a long-time veteran of the creationism wars. He blogs at Playing Chess with Pigeons. He is a TalkOrigins Archive volunteer, was a co-founder of the McLean v. Arkansas Documentation Project, and is a member of both NCSE and the Skeptics Society.

Welcome, Troy! We look forward to your posts.

I am a computational evolutionary geneticist, and in my research I develop software to analyze genetic data and study evolutionary questions. As part of my research, I work with a lot of simulation programs to generate evolutionary datasets. My most widely used program is Dawg, and I am currently putting the finishing touches on a new version.

In simulating molecular sequences, you start by simulating the ancestral sequence at the root of a phylogenetic tree and then evolve that sequence upwards, making point mutations and indels as you go. Depending on type of sequences being generated, the root would be a string of nucleotides, amino acids, or codons. To simulate the root sequence, we draw its characters from a discrete, stochastic distribution. For example, lets say that in your system the frequencies of A, C, G, and T are 26%, 23%, 24%, and 27%. In order to create a root sequences of length k, you simply sample k nucleotides from this distribution, e.g. AAGTGCA or GATTACA.

Therefore, the key step in the simulation of the root sequence is sampling repeatedly from an arbitrary discrete distribution. While I have been doing this for years, I recently went searching for doing it better and came across the following excellent article: Darts, Dice, and Coins, written by Keith Schwarz, a lecturer at Stanford. In this article, he describes many different methods for sampling from a discrete distribution and analyzes their performance. It turns out the best method is the Alias Method, first described in the 1970s and improved by M. Vose in 1991. I will describe it below, but before we get there, here are some alternatives.

Imagine that you want to sample from the following discrete distribution of nucleotides:

Let the heights of these bars be h₀, h₁, h₂, and h₃. Since these heights correspond to the probability that a random base is A, C, G, or T, the total area of the histogram is 1. Now to sample from this histogram, you can draw a uniform random number—call it u—between 0 and 1 and find which bar corresponds to that number. If u < h₀, you sample an A. If u < h₀+h₁, you sample a C, etc. This works, but is clearly inefficient since it requires you to search through the histogram from left to right every time you sample a nucleotide. Imagine if you were sampling from 64 codons.

I wish I had thought of that title, but it is actually an article by Joe Sonka in the Louisville newspaper, LEO Weekly. According to Sonka, the Ark Park (properly known as Ark Encounter) will have to raise $22 million before it can even start construction, and $44 million an additional $22 million to complete the project (it was unclear to me whether that is an additional $44 million, above the first $22 million). Sonka further estimates that the project will take at least 3 years to complete, and an estimated $53 million will have to be invested over the next decade. If the project takes that long to complete, however, they will presumably lose at least some tax incentives.

But cheer up! There is hope: If you invest $100,000, the minimum investment, they project a 20.6 % return on investment. At this point, I am torn between a quotation attributed to P. T. Barnum and a myth concerning the sale of the Brooklyn Bridge.

Ken Ham, the driving force behind the Ark Park, claims that PBS will air a documentary this fall, but I could find nothing on the PBS website besides this broadcast, a year ago. According to Sonka, Ham claims that the PBS documentary will net the Ark Park 2 million visitors per year, an attendance that Sonka says would rival that of a big amusement park in Cincinnati, a city of roughly 300,000. Grant County, by contrast, has a population of around 25,000 and is located at least an hour’s drive from any major metropolitan area.

It’s time for the annual birthday greeting to Jean Baptiste Pierre Antoine de Monet, Chevalier de Lamarck, born 1 August 1744. Born into the impoverished nobility, he distinguished himself in the army, then had to leave military life because of a peacetime injury. In Paris, he started writing books on plants and ended up as Professor in the Natural History Museum. He was the great pioneer of invertebrate biology (he coined the terms “invertebrate” and “biology”). But of course he is best known as the first major evolutionary biologist, who propounded a theory of evolution which had an explanation for adaptation. (A wrong explanation, but nevertheless an explanation).

This time let’s use an image of the tree of animals, from his Philosophie Zoologique (1809):

This is not entirely a tree of history: it is also paths up which evolution proceeds (actually, on this diagram, down which evolution proceeds). So it is not quite the same as the trees we use now. Note that not all animals are connected on this tree.

Of course, it goes without saying that Lamarck was not responsible for inventing or popularizing “Lamarckian inheritance”. He invoked it but everyone already believed it. And to add one last jibe: epigenetics is not in any way an example of the use-and-disuse mechanisms that Lamarck invoked.

The fourth Panda’s Thumb photography contest,

Lab rats,

begins – now!

We will accept entries from July 30 through August 13, inclusive.

The theme of the contest is lab rats, by which we mean any object of experimentation or observation, from single-celled organisms, through nematodes, fruit flies, rats, chimpanzees, and undergraduates to volcanoes, stars, and galaxies. In order not to omit theoreticians, we will consider computer-generated pictures and also photographs of equipment, such as computers. Photomicrographs and electron micrographs are likewise welcomed.

Similarly, in order not to omit laypersons, we encourage entries in a second, general category, which includes pictures of just about anything of scientific interest. If we get enough entries, consistently with Rules 12 and 13, we may divide either category and award additional prizes, presuming, of course, that we can find more prizes.

The winners will receive an autographed copy of Among the Creationists, by Jason Rosenhouse, which received a very favorable review here.

In 1999 I posted to the Talk Reason website a critical review of Professor Nathan Aviezer’s book In the Beginning [1] and of his article The Anthropic Principle published in the Jewish Action journal [2]. My review was titled The End of the Beginning (see here.) [3]. Soon afterward one of my friends (on his own initiative) sent a copy of that essay to Aviezer and asked him to respond. Professor Aviezer chose to ignore my friend’s request. Of course, Professor Aviezer was under no obligation to respond to critique. In the following years my essay evoked some discussion on the internet, but Professor Aviezer remained silent in regard to my critique. In 2003 my book Unintelligent Design [4] was published, wherein one chapter was a slightly modified and updated version of my essay in question. Professor Aviezer remained unresponsive to my critique. Suddenly, in February 2012, 13 years after my review of his work appeared, Professor Aviezer posted a reply (see torahmusings.com/2012/02/fossils-and-faith ) [5].

See the full text of this post here.

Erythropsidium – a protist with a simple eye, or ocellus. Figure 2.2 of Evolution’s Witness. Image © F.J.R. “Max” Taylor, Ph.D.

Who knew? A single-celled organism has a camera eye with a lens. A certain fish has two corneas and controls the intensity of light on its retina by injecting pigmented particles between them. Other animals can shield their rods (the receptors for low intensity) during the day. A conch can grow a wholly new eye. A flatfish has both eyes on the same side of its head, but starts life with bilateral symmetry. A sea snake has a light sensor in its tail to ensure that the tail is hidden under a rock. Some birds cram their corneas through their irises in order to focus on nearby objects under water. The woodcock can see behind its own head - in stereo. Some animals have two foveas in each eye, one for peripheral vision and one for binocular vision.

Late last night, I got word from Ed Brayton that Panda’s Thumb blogger Skip Evans was found dead at his Madison, Wisconsin home. Skip had been having problems with his cardiovascular system, and so far as we know now those problems appear to have been the cause of his death.

Skip should be well known to most of our readers, either by his posts here or by some of the contributions that he made to advancing science education and countering the socio-political machinations of the creationism movement. A couple of the high-profile things Skip did included much of the concept of NCSE’s “Project Steve” and its naming, plus taking on (now convicted felon) “Dr.” Kent Hovind concerning his “doctoral disssertation”. Skip personally requested a copy of Hovind’s dissertation from “Patriot University”, and they shipped Skip the original, including taped-in graphics Hovind had scissored out of science magazines.

I’ll plan to add some photos later, but I wanted this news to go out soonest to our community. Skip was a friend of mine, and I appreciated his good humor. I already miss him.

His colleague posted this comment on Facebook:

To ease the pain of Skip’s dear friends, please know that he has so many people who loved him here. He was only with our company a year, but brought more life and energy to us in that short time than most people do in a lifetime. I went to a presentation on the fallacies of creationism a few weeks ago, where Skip gave an irreverent and poignant and funny talk. Over 150 people were in stitches. We were lucky to know him.

Photograph by Nicholas Plummer.

Photography contest, Honorable Mention.

Hyla chrysoscelis – Cope’s gray tree frog.

In addition to being the bananaman, Ray Comfort is the co-popularizer of the crocoduck. Comfort believes that because modern biology shows that birds are descended from theropod ancestors, there must be a transitional form between extant birds and extant reptiles; hence a half-crocodile, half-duck. Here’s the video in which Comfort’s ex-child actor sidekick Kirk Cameron made that claim.

That general false claim–the claim that evolution predicts that there must be an evolutionary pathway directly linking two extant organisms or extant biological structures–is not unique to creationist loons, though. Doug Axe has posted a response to Paul McBride’s review of “Science and Human Origins” on ENV, and has disabled comments on his post. I won’t elaborate, but will note that an amusing part of Axe’s response is this:

Ann [Gauger] and I conducted experiments to find out how many changes would have to occur in a particular enzyme X in order for it to begin performing the function of another enzyme, Y. We found that they are too numerous for unguided evolution to have accomplished this transformation, even with the benefits of a massive bacterial population and billions of years. Having carefully made the case that our chosen X and Y are appropriate for the aims of our study, we think this result has catastrophic implications for Darwinism.

As has been shown, though, the research that Axe cites, The Evolutionary Accessibility of New Enzymes Functions: A Case Study from the Biotin Pathway, does not test an evolutionary hypothesis. By studying whether one extant enzyme in a family of enzymes could have evolved from another extant enzyme in the same family, when the evolutionary account is actually that both evolved from a common ancestor, Gauger and Axe are making precisely the same error that Comfort and Cameron made: the notion that “common descent” means that related extant populations evolved from each other, rather than from a common ancestral population. That about equivalent to claiming that common descent means that I am descended from my cousin Keith.

Even young-earth creationist biochemist Todd Wood rebutted that particular claim more than a year ago. Wood wrote

Instead of ancestral reconstruction, Gauger and Axe focused directly on converting an existing enzyme into another existing enzyme. That left me scratching my head, since no evolutionary biologist would propose that an extant enzyme evolved directly into another extant enzyme. So they’re testing a model that no one would take seriously? Hmmm…

Axe and Gauger quite simply didn’t test an evolutionary hypothesis in the paper Axe cited, but Axe continues to claim that it says something about the limits of evolution. But when even an honest young-earth creationist sees the error, persisting in it is no more than perverse. Axe is doing the equivalent of waving Ray Comfort’s crocoduck over his head, hollering “Evolution couldn’t do it!” Maybe Ray will have an opening in his ministry for Axe when the BioLogic Institute sinks beneath the waves.

The BioLogic Institute, the purported research arm of the Disco ‘Tute, now has a Facebook page where they post miscellaneous anti-evolution notes, many from the recent book by Ann Gauger, Douglas Axe, and Casey Luskin titled “Science and Human Origins”. One recent note was headed

From the scientific evidence, it is stubbornly uncertain how the first humans arose, whether from a lineage including ape-like creatures and far humbler ancestors or not.

Nick Matzke did a lovely job of rebutting that claim in the comment thread on the post. In the end, ‘BioLogic Institute’ abandoned the field, saying

I am closing this discussion because we are talking past each other. Our responses will be posted separately at www.biologicinstitute.org.

Where, as Jeff Shallit noted, comments are not allowed. As is their habit, when challenged the brave scientists of the Disco ‘Tute retreat to their insulated world, safe from those pesky critics’ comments.

Troy Britain at Playing Chess with Pigeons flays a post by Casey Luskin about a recent paper on proto-feathers on dinosaur fossils. Britain shows how Luskin doctors a quotation by replacing a comma with a period, uses strategic ellipses in quotations to conceal relevant context, and in the end questions the common descent of dinosaurs. Yup, that means that Luskin really did imply something like the separate creation of ornithischians, saurischians, and theropods, three major clades of dinosaurs.

In other news, dog bites man.

Photograph by Siromi Samarasinghe.

Photography contest, Honorable Mention.

Anthracoceros coronatus – Malabar pied hornbill, Bundala National Park, Sri Lanka.

Jason Rosenhouse moved from the east coast to Kansas for a postdoc. He had studied a bit about creationism while a graduate student at Dartmouth, so it would be an exaggeration to say that he was surprised to learn that not everyone in Kansas was a liberal Democrat (even by today’s standard of liberalism). Nevertheless, for reasons that are not made completely clear, he humored his inner anthropologist and attended a handful of creationist conferences over a period of several years. The result is the splendid book Among the Creationists: Dispatches from the Anti-Evolutionist Front Line, which both shows creationists as regular people, just like scientists, and also takes them seriously, without condescension or sarcasm.

Not that Rosenhouse cuts them any slack. He gets up to the microphone and asks pointed questions, and he is completely open about who he is and what he believes. He mingles with the conference attendees and is impressed by how very pleasant they are; he is pleasant in return, except for one apparently unfortunate interaction with Ken Ham. Nevertheless, however pleasant the creationists may be, Rosenhouse makes clear that he and his interlocutors are always talking past each other, and his critiques have virtually no effect - except occasionally, when he sees a young student listening intently and thinks he may have planted some seeds of doubt.