August 2012 Archives

That is the title of a YouTube video by Bill Nye, the Science Guy. The punchline is essentially this,

And I say to the grownups, if you want to deny evolution and live in your world, in your world that’s completely inconsistent with everything we observe in the universe, that’s fine, but don’t make your kids do it because we need them. We need scientifically literate voters and taxpayers for the future. We need people that can–we need engineers that can build stuff, solve problems.

An appalling fraction of the comments are negative.

See also here for an article to the effect that reports of Mr. Nye’s death are exaggerated.

Acknowledgment. Thanks to Yan Linhart for notifying me about the Slate article.

John Freshwater’s attorney, R. Kelly Hamilton, has filed a Merit Brief, the document that presents his arguments for the Ohio Supreme Court to overturn the decision of the Mt. Vernon, Ohio, Board of Education to terminate Freshwater’s employment as a middle school science teacher. In the brief, Hamilton–really, the Rutherford Institute–attempts to re-interpret two key decisions of the Supreme Court of the United States bearing on the teaching of creation science–Epperson v. Arkansas and Edwards v. Aguillard–while wholly ignoring Kitzmiller v. Dover, which firmly established the equivalence of intelligent design with creation science. However, the brief itself lumps them together, treating creationism and intelligent design as near-identical siblings, in one place even referring to “creation science/intelligent design” (p. 12). The brief also says

However genuine it may be, the Board’s apparent belief that creationism and/or intelligent design theories have no scientific value cannot be accepted. The theories suggest that the physical universe and life within it appeared suddenly and have not changed substantially since appearing. (p. 17)

Shades of “Of Pandas and People,” which used the same word-for-word definition for creationism and intelligent design in successive versions spanning the 1987 Edwards decision.

The Merit Brief assumes as a foundational premise (without visible support except for a citation from Justice Scalia’s dissent in Edwards v. Aguillard) that intelligent design and creation science are actually legitimate alternative scientific theories, the mysterious “competing academic theories” cited in Freshwater’s appeal to the 5^th District Court of Appeals and in his Memorandum in Support of Jurisdiction to the Supreme Court. Their religious implications are merely by-products, not central pillars. In fact, the Brief argues that teaching only evolution is tantamout to government endorsement of a religious view, secular humanism, and that therefore creation science and intelligent design should be taught alongside evolution! This has got to give the Disco ‘Tute boys a migraine.

The Rutherford Institute, using the Freshwater case as a vehicle and Freshwater’s attorney as a sock puppet, is attempting to induce the Ohio Supreme Court to endorse intelligent design and creation science as legitimate parts of public school science curricula. Accepting the arguments in Freshwater’s Merit Brief requires that we accept that teaching intelligent design and creationism is permitted–even desirable–in public schools. In the brief, filed by Hamilton on August 24, 2012, a main argument is that teaching intelligent design and creation science in public school science classes is not only Constitutionally permitted, it is damned near required by the desirability of “unbiased instruction” in science.

I’ll hit a few of the high spots below the fold, but the whole document, which runs 24 pages, is worth reading. There’s a 56-page Appendix that can be skipped, except, perhaps, for an extract from the District’s guidelines for handling controversial issues in the classroom:

A. When a controversial issue is not part of an approved course of study, its use must be approved by the Principal. (p. A52)

While it discussses the controversial issue policy, somehow the Merit Brief never quite gets around to mentioning that particular requirement, the first in the list of guidelines.

Photograph by Jon Woolf.

Photography contest, Honorable Mention.

Vishnu Temple at the Grand Canyon. This feature demonstrates the size and typical features of a Grand Canyon butte and also helps destroy the YEC explanation of the Grand Canyon.

I was figuring he would live to be 120 so that he could see a Mars landing. But he did leave this:

Neil Armstrong, first man on the moon, dies

Photograph by Dan Stodola.

Photography contest, Honorable Mention.

Rhacodactylus ciliatus – New Caledonian crested gecko.

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.