May 2009 Archives

Michael Shermer vs. Eric Hovind

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Anyone who thinks it’s worthwhile debating creationists should listen to this podcast of a recent radio ‘debate’ between Michael Schermer of Skeptic Magazine and Eric Hovind, offspring of Kent Hovind. Hovind’s arguments show up a lot out in the boonies and his videos are circulated among fundamentalist congregations. One was in a backpack in John Freshwater’s middle school science classroom in the spring of 2007. If you are involved in these kinds of discussions you must know the arguments that are used, bizarre though they may seem and as irony meter threatening as they are. (The management recommends the Line Noise Laboratories Mark V Excelsior with the new optional emergency override capability for extreme situations.)

The second edition of Larry Arnhart’s book Darwinian Conservatism is being published today. This edition adds a number of critical essays, including my own essay, “Evolution And The Limitations of Conservatism.” Despite some obvious and serious disagreements, I actually admire Arnhart’s work quite a bit. My thanks to him and to Ken Blanchard for inviting me to participate in this project.

But it’s not about religion …

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The Disco ‘Tute has announced the opening of a new site, Faith+Religion, which purports to discuss the relationship between evolution and religion. A brief survey of the site shows that it has two objectives. First, of course, is the traditional ID goal of denigrating evolutionary theory. Right up on the home page we see a review of Collins’ The Language of God by Moonie Jonathan Wells that says

Collins’s defense of Darwinian theory turns out to be largely an argument from ignorance that must retreat as we learn more about the genome–in effect, a Darwin of the gaps.

Sure thing, Jonnie. Wells knows more about the scientific implications of new genetic knowledge than the former head of the Human Genome project. Yup.

Don McLeroy was nominated to be the chair of the Texas State Board of Education.

Today, that nomination failed.

Eleven senators opposed the shenanigans the board got up to under his leadership, and his nomination failed.

Texas Freedom Network has a live blog of the proceedings.

This month marks the 50th anniversary of C.P. Snow’s famous Rede Lecture, “The Two Cultures And The Scientific Revolution.” A half-century later, the term “two cultures” is still well remembered, but many of the details, both of the history and of the philosophical foundations of the dispute–and the contributions of my hero, the scientist, philosopher, and future television celebrity Jacob Bronowski–have largely been forgotten.

The final chapter of my dissertation has finally been published in Molecular Ecology. I don’t have time to go into detail, so I’ll just cite the abstract that covers much of the motivation and large-scale results.

Abstract: Many self-incompatible plant species exist in continuous populations in which individuals disperse locally. Local dispersal of pollen and seeds facilitates inbreeding because pollen pools are likely to contain relatives. Self-incompatibility promotes outbreeding because relatives are likely to carry incompatible alleles. Therefore, populations can experience an antagonism between these forces. In this study, a novel computational model is used to explore the effects of this antagonism on gene flow, allelic diversity, neighborhood sizes, and identity-by-descent. I confirm that this antagonism is sensitive to dispersal levels and linkage. However, the results suggest that there is little to no difference between the effects of gametophytic and sporophytic SI on unlinked loci. More importantly both GSI and SSI affect unlinked loci in a manner similar to obligate outcrossing without mating types. This suggests that the primary evolutionary impact of self-incompatibility systems may be to prevent selfing, and prevention of biparental inbreeding might be a beneficial side effect.

The citation of the paper is

Cartwright RA (2009) Antagonism between local dispersal and self-incompatibility systems in a continuous plant population. Molecular Ecology 18:2327-2336. [doi:10.1111/j.1365-294X.2009.04180.x]

Unfortunately, there is not a free version available yet online. The research was partially funded by NIH, so a copy should show up in pubmed in several months. Until then, you can email me at [Enable javascript to see this email address.], and I’ll send you a reprint.

If you want to know how I fulfill the reprint requests, see this post on De Rerum Natura.

Fregata magnificens

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Fregata magnificens – Male frigate bird, displaying, Galápagos Islands.

Apparently, Michael Behe just doesn’t know when to pack it in. In reply to Travis’s essay in Science, “On the Origin of The Immune System” (see previous PT posts: 1, 2), Behe has posted a letter he sent to Science. Instead of just sucking it up and admitting that his statements in Darwin’s Black Box that

“As scientists we yearn to understand how this magnificent mechanism came to be, but the complexity of the system dooms all Darwinian explanations to frustration.” (Darwin’s Black Box, p. 139)

and

We can look high or we can look low, in books or in journals, but the result is the same. The scientific literature has no answers to the question of the origin of the immune system. (Darwin’s Black Box, p. 138)

…were wrong, or at the very least became wrong in the time between 1996 and 2005, Behe is still expressing proud, Kierkagaardian-esque defiance. In this (rejected) letter to the editor of Science, Behe reiterates his proud stand that the work of an entire field, the life’s achievements of hundreds of immunologists, complete with surprising experimental support for a surprising hypothesis (the transposon hypothesis), still has “no answers” to the question of how it evolved, and that Darwinian explanations are “doom[ed].”

AAAS Science Resource Prize

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The American Association for the Advancement of Science has called for nominations for a Science Prize for Online Resources in Education. The brief description is

The Science Prize for Online Resources in Education (SPORE) has been established to encourage innovation and excellence in education, as well as to encourage the use of high-quality on-line resources by students, teachers, and the public. In 2009, the prize will recognize outstanding projects from all regions of the world that bring freely available online resources to bear on science education.

More info, including eligibility rules and nomination procedures, are at the link above. The deadline is June 30, 2009.

Brief Freshwater Update Note

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Sorry for the delay in posting on the most recent days of the hearing in early May. I’ve been up to my eyebrows in alligators for the last few weeks. I’ve got 50 pages of notes on the most recent two days of the hearing but haven’t had the 10 or 12 hours to spare to write them up. Soon, I think. Meanwhile, the Mt. Vernon News ran stories on those days here, here, and here.

Following up on the Science story on the origin of adaptive immunity and the role it played in the Kitzmiller case, the Science Origins blog has a short interview they did with me while writing the article. It didn’t make the final cut for the print version, but it is nifty for it to be online. I hope I sufficiently acknowledged my PT collaborators and all the other friends/enemies on the net that made that particular bit of the Behe cross-examination seem like a good idea.

Also, while I am on this topic, I should mention that I have been invited to speak about the role of evolutionary science in the Kitzmiller case, with special focus on the immune system science and how it was used in the Behe cross-examination. This will occur on September 3, 2009 at the University of Nebraska at Kearney. Here is the link for the meeting, September 2-4, 2009: http://www.evolution2009.org/. It looks like a fantastic lineup of speakers. The early (cheaper) registration deadline is July 31. And yes, I am mentioned in the same sentence as another speaker, Jack friggin’ Horner, which is just weird. (PS: Email me if you’ll be in the area and want to meet up!)

Here’s the flier the organizer, Brad Ericson, sent me, and asked to have put up: Evolution2009_poster_Univ_Nebraska_Kearney.pdf

Darwinius masillae

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This is an important new fossil, a 47 million year old primate nicknamed Ida. She’s a female juvenile who was probably caught in a toxic gas cloud from a volcanic lake, and her body settled into the soft sediments of the lake, where she was buried undisturbed.

darwinius.jpeg

What’s so cool about it?

Stick science deadline approaching!

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The deadline for entries to the Florida Citizens for Science Stick Science Contest is fast approaching – it’s May 31, 2009. See the FCS site for da roolz. The general goal:

Your job is to create a cartoon that can be used to educate the general public and especially decision makers (state legislators, school board members) about the truth behind one false science argument. Choose an argument, either one I’ve mentioned above or another one you are familiar with, and create a cartoon that corrects the record.

Note that it is a science education goal, not creationist bashing:

Your cartoon can be funny or educational or a combination of both; however, the cartoon should not be mean-spirited or single out a real person for ridicule.

The judges are Genie Scott, Carl Zimmer, Phil Plait, and Kate Miller. Give them something to do, and win prizes to boot!

Genie Scott honored

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Scientific American has identified

Ten researchers, politicians, business executives and philanthropists who have recently demonstrated outstanding commitment to assuring that the benefits of new technologies and knowledge will accrue to humanity

Among them is Eugenie Scott, Executive Director of the National Center for Science Education. SciAm says of Scott

Thomas Henry Huxley was the 19th-century biologist known as “Darwin’s bulldog” for his defense of the great scientist’s ideas. The 21st century has a counterpart in the woman who describes herself as “Darwin’s golden retriever.” Eugenie Scott has emerged as one of the most prominent advocates for keeping evolution an integral part of the curriculum in public schools in her role as head of the nonprofit National Center for Science Education (NCSE). Eugenie Scott has emerged as one of the most prominent advocates for keeping evolution an integral part of the curriculum in public schools in her role as head of the nonprofit National Center for Science Education (NCSE).

Canine metaphors aside, Genie is a tireless and highly effective advocate for science education as well as a charming person, and we congratulate her.

This essay is the third of a series authored by Dave Wisker, Graduate Student in Molecular Ecology at the University of Central Missouri.

In previous essays in this series, I have discussed two issues with the fusion that resulted in human chromosome 2: its dicentric nature, and the fusion’s possible effect on fertility. I showed how one extra centromere may not result in inevitable damage to the chromosome during meiosis and mitosis, and demonstrated that the fusion did not necessarily have to result in greatly decreased fertility. Either of those situations would have effectively prevented the fusion from rising in frequency and eventually becoming fixed in the human population. We are now in the position to consider the probability of such a fusion becoming fixed. This essay will examine the fixation probability of the fusion in a small subpopulation, or deme.

Pelecanus erythrorhynchos

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Pelecanus erythrorhynchos — American white pelican. Note orange beak and horn on beak, both indicating breeding season. Walden Ponds, Boulder, Colorado.

(Updated) Denyse O’Leary and the bottom of the barrel

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Update at the bottom

In the context of some flailing against theistic evolution, Denyse O’Leary has finally scraped the bottom of the barrel. On Uncommon Descent she writes

I just got done reading a book published in Turkey called Evolution Deceit, which helps me understand why Turkey alarms many materialists - but more on that later.

“Evolution Deceit” is by Adnan Oktar, who publishes under the name Harun Yahya and is a Turkish creationist. It’s a standard issue creationist diatribe; nothing new to see there. That O’Leary cites it as a reason to be alarmed about Turkey is entirely appropriate, but not for the reason O’Leary wants us to believe. In fact it’s an indication that the creationist pathology infests more countries than just the U.S.

Recall that Harun Yahya is also the purported author of The Atlas of Creation that was mailed to thousands of scientists a while back. It’s also the book in which a fly fishing lure was presented as a photograph of an insect along with other obvious mistakes. I knew the ID creationists were getting desperate for allies, but this is a new low. Soon I expect to see Denyse wearing a burqa.

Update: Larry Arnhart at Darwinian Conservative notes that Denyse has now interviewed Oktar. See Arnhart’s post linked above for commentary on the interview, particularly Oktar’s claim that intelligent design is the product of a Masonic conspiracy to promote atheism and Deism. This just gets weirder and weirder.

New evolution resource site online

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There is a wide array of resources on the web about evolution, ranging from public access to technical papers available via PubMed to the excellent Understanding Evolution site operated by the University of California Museum of Paleontology and the National Center for Science Education. The grand daddy of them all, of course, is the TalkOrigins Archive.

Now a new resource has been established by T. Ryan Gregory, evolutionary biologist and blogger at Genemicron. It’s called Evolver Zone, and is “a resource for students, teachers, and researchers with an interest in evolution.”

Evolver Zone is a collection of a wide range of resources on evolution, from online databases to software to teaching resources to multimedia (including games!). I haven’t browsed the whole site yet, but what I’ve seen looks to be very useful, particularly for advanced high school and undergraduate classes. Gregory tells us the site is a work in progress, so check back often for new additions.

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.

2009 Skepticamp in Denver

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Now that my grades have been submitted on time, I can admit to you that I spent all day Saturday, May 9, attending the annual Skepticamp in Denver. Skepticamp is the brainchild of Reed Esau, and the 2009 Skepticamp is the third so far. Since their inception, there have been a half-dozen other Skepticamps in the US and at least one abroad. The 2009 Skepticamp lasted from 9 in the morning till 7 at night and was the shortest 10-hour conference I have ever attended.

Chrysaora achlyos

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Chrysaora achlyos – Black sea nettle, with H. sapiens in forefground, Monterey Bay Aquarium.

by Barbara Forrest, http://www.creationismstrojanhorse.com/

Francis Beckwith has communicated to me via e-mail (May 3, 2009) his disagreement with my referring to him as an “ID supporter” in the abstract of my recently published paper entitled “The Non-epistemology of Intelligent Design: Its Implications for Public Policy,” Synthese, April 15, 2009. (See also Tim Sandefur’s post in response to Beckwith’s complaints about Sandefur’s classifying him as a creationist.) Here is the abstract:

Intelligent design creationism (ID) is a religious belief requiring a supernatural creator’s interventions in the natural order. ID thus brings with it, as does supernatural theism by its nature, intractable epistemological difficulties. Despite these difficulties and despite ID’s defeat in Kitzmiller v. Dover Area School District (2005), ID creationists’ continuing efforts to promote the teaching of ID in public school science classrooms threaten both science education and the separation of church and state guaranteed by the U.S. Constitution. I examine the ID movement’s failure to provide either a methodology or a functional epistemology to support their supernaturalism, a deficiency that consequently leaves them without epistemic support for their creationist claims. My examination focuses primarily on ID supporter Francis Beckwith, whose published defenses of teaching ID, as well as his other relevant publications concerning education, law, and public policy, have been largely exempt from critical scrutiny. Beckwith’s work exhibits the epistemological deficiencies of the supernaturally grounded views of his ID associates and of supernaturalists in general. I preface my examination of Beckwith’s arguments with (1) philosopher of science Susan Haack’s clarification of the established naturalistic methodology and epistemology of science and (2) discussions of the views of Beckwith’s ID associates Phillip Johnson and William Dembski. Finally, I critique the religious exclusionism that Beckwith shares with his ID associates and the implications of his exclusionism for public policy.

By Greg Fish, http://worldofweirdthings.com/

If you’re a creationist, astrobiology is probably your nightmare. While there are only a small handful of astrobiologists out there today, the search for life in space is being funded with multi-billion dollar mission plans and the field is bound to grow. Combining the basic principles of evolution with theories about how stars and planets are formed, biologists, chemists, planetary scientists, and astronomers are dedicating a great amount of time, effort, and cash to answer the question of whether we’re alone in the universe. The core of their project is the idea that Earth isn’t unique, and if life arose here following certain rules, other life arose on other worlds in a relatively similar way from basic building blocks found throughout the universe.

But they’re worried and upset that creationists are making big strides towards developing a potential brain drain in their nascent field by constantly trying to undermine the teaching of evolution and basic astronomy in the classroom. If you want to be an alien hunter, you have to be well versed in the theory of evolution and understand that planets are billions of years old, not thousands.

I’ve been thinking about comets a lot lately, trying to image C/2009 G1, reading “The Hunt for Planet X”, wondering why Galileo was so wrong about them and recently reading a Young Earth creationist blog post on them. The latter referred to a very interesting pre-publication article. And I’d like to discuss this article, as this illuminates not only the origins of comets but also how science is done.

Freshwater hearing: A witness contradicted by a photo

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This will be a short – I have a slew of commitments and won’t get a full account done until sometime over the weekend. But one thing established today deserves immediate comment.

R. Kelly Hamilton, John Freshwater’s attorney, called Zachary Dennis to testify today. Zach had already testified during the Board of Education’s presentation and Hamilton passed on cross examination then, knowing he would call Zachary in his case and would have greater freedom of questioning than in cross examination. Zachary testified for all but half an hour of today’s hearing. One section of that testimony stands out and I’ll describe it below the fold.

Mt. Vernon, OH, school levy results

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One of the threats made by the fundamentalists both recently and during the 2003 attempt by John Freshwater to inject ID creationist material into the science curriculum is that they will punish the district and the board of education in elections if the board opposes their efforts to corrupt science education. So far that doesn’t seem to be working out real well for them. Yesterday voters in the Mt. Vernon City School District passed a renewal of an operating levy by a 61%-39% margin. Like the Dover, PA, school board elections in 2005, it appears that the ballot box clout of the fundamentalists is a whole lot less powerful than they’d like us to believe. I’m cautious about interpreting that vote simply as a referendum on the board of education or Freshwater, but I know I heard rumblings around the district about it prior to the election. It certainly doesn’t support any claims of general dissatisfaction with the district.

The hearing on Freshwater’s termination resumes tomorrow, with members of the Dennis family being called by Freshwater’s attorney, R. Kelly Hamilton. Recall that Hamilton passed on cross examining Zachary and his mother last fall during the presentation of the Board’s case by David Millstone, the Board’s attorney, knowing he’d call them as hostile witnesses during Freshwater’s presentation.

A court in California has ruled that the Establishment Clause was violated by comments a schoolteacher made against certain religious propositions. Ed Brayton has details here. Personally, I’m troubled by the ruling for reasons that First Amendment expert Eugene Volokh explains here.

Every year the folks at the Alliance for Science have themselves an essay contest. The topic is evolution-themed, and since 2009 is so relevant to Charles Darwin– being his 200th birthday and 150th anniversary of the publication of The Origin of Species– we asked students to identify a modern scientist that exemplifies the characteristics which led Darwin to make his monumental discoveries.

This year we had a very tight race… a 3 way tie for 3rd place. Do check out the winning essays, they are worth a read!

Tachyglossus aculeatus

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Photo courtesy of Kelly Lyon, kellylyonphotography.com

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Tachyglossus aculeatus–Short-beaked Echidna

All is not (yet) lost in Texas

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Occasionally one happens onto a person who raises one’s hopes for rationality and good science, even in Texas. One such person is Joel W. Walker, a candidate for the College Station, Texas, Schools Board of Trustees, the local school board. Walker is a theoretical physicist, a Republican self-described as being “both fiscally and socially conservative,” and a supporter of honest science education. On his campaign site Walker has posted a strong and informed essay as an open response to Texas State BOE chairman and creationist dentist Don McLeroy. I’ll quote just some bits of it – go read the whole thing.

Another anniversary missed

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Well, shoot. We missed the 5th anniversary of the founding of Panda’s Thumb. Belated happy blogiversary to us! :)

The Cover of The Auk

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Kristin Lamm, a graduate student in bioinformatics at NCSU and a member of our lab, has made the cover of the latest issue of The Auk, the official publication of the American Ornithologists’ Union, with her reconstruction of Palaeospiza bella, a mousebird from the late Eocene found in North America.

Cover of The Auk April 2009, Vol. 126, No. 2. Art by Kristin Lamm.

The reconstruction goes along with the following article:

Ksepka DT‌ and Clarke JA (2009)‌ Affinities of Palaeospiza bella and the Phylogeny and Biogeography of Mousebirds (Coliiformes). The Auk 126(2): 245–259. [link]

Abstract:
Palaeospiza bella was described as an oscine songbird in the late 19th century. The late Eocene age of the holotype specimen would make it the oldest Northern Hemisphere record of the Passeriformes. However, few recent workers have accepted the placement of P. bella within Passeriformes, and the higher relationships of this fossil have remained controversial. We show that P. bella is a member of the Coliiformes (mousebirds) and represents the latest North American occurrence of a clade with an exclusively African extant distribution. Coliiformes are now known from the latest Paleocene to the approach of the Eocene–Oligocene boundary in North America. We present a redescription of P. bella and a new phylogenetic analysis of fossil and living Coliiformes based on a matrix including 49 characters and 18 ingroup taxa. The results of this analysis place P. bella in Colii, the clade comprising taxa more closely related to Coliidae (crown mousebirds) than to the extinct Sandcoleidae. The oldest stem-group Coliiformes are late Paleocene (about 56.2–56.6 Ma) in age. However, no fossil taxon can be confidently placed within the crown clade Coliidae at present. Phylogenetic results imply that a minimum of three mousebird dispersals from Europe to North America occurred during the Early Cenozoic. Review of the early Eocene fossil Eocolius walkeri from the London Clay shows that this taxon lacks convincing coliiform synapomorphies and should be removed from the clade.

Our Bioinformatics Research Center is one of the sponsors of the Symposium on Life Science Education, being held May 26, 2009 at the North Carolina Biotechnology Center in Raleigh.

The Symposium provides a forum for researchers, educators, and students to meet, discuss and exchange ideas about the latest methods and tools in Life Science Education. A series of invited talks will focus on modern technologies and resources in Life Science education. Topics include:

  • Teaching the analysis of genome-scale data using R and Bioconductor: Software, documents, and experiments
  • Bioinformatics in Motion: Animations for teaching Bioinformatics
  • Cold Spring Harbor Laboratory: Tools to Teach Biology in the Genome Age
  • The Joint Genome Institute’s Microbial Genome Annotation Program for Undergraduates (Department of Energy)
  • The Full Spectrum of Online Tools: From Synthetic Biology Research to Introductory Biology
  • NCSU DELTA: Educational Technology in Distance Education

Registration for the Symposium is free, and participants are invited to submit posters presenting their work. Abstracts of accepted posters will be published in the Symposium proceedings, and presenters will receive $100 to cover expenses. Poster abstracts must be submitted electronically at: http://statgen.ncsu.edu/slse/submission.html. Poster submission is now closed.

Further information, including the speaker list and registration forms, is available at the Symposium web page: http://statgen.ncsu.edu/slse/.

Download a Flyer

One of the better ideas I’ve ever been associated with was the immune system cross that Eric Rothschild put Behe through in the Kitzmiller trial in 2005. It was one of those show-your-cards moments where, finally, at long last, the ID movement’s endless wild claims about the emptiness of evolutionary biology were put into direct conflict with the weight of the evidence. Everything was crystallized into a short episode – an amazing field of research (the 100+ years of discovery about the function and origins of the immune system), an amazing practical application of evolutionary biology (both common ancestry and variation/selection played absolutely critical roles in developing science’s understanding of the immune system), and a really obvious put-up-or-shut-up moment for the ID movement’s “irreducible complexity” argument, where it completely failed to put up (here’s a review of the ping-pong game the ID movement played with “IC systems”, and how the immune system cross called their bluff).

Anyway, the cross has gotten plenty of attention and all of the details are online, but it is gratifying that Science magazine has devoted one of its “Origins” essays to the history of immunology, the role played by Darwinian ideas (both common ancestry and variation/selection), and highlights the Perry Mason immunology moment from the Kitzmiller case. It also provides an update on the science, and comprehensive links.

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