Several years ago, I saw a fantastic talk at the Evolution meeting about Intraspecific macroevolution: variation of cranial shape in dog breeds. The talk was by Abby Drake, then a grad student, and reported on a huge digital morphometric comparison of the skulls of dogs and many representatives from the order Carnivora (dogs, cats, bears, sea lions, etc.).

Morphometrics basically consists of taking digital photos of e.g. bones from different angles, and then marking the same landmarks on homologous bones across a big group. Then you can quantitatively compare the differences in shape, independent of things like body size. This is a much more sophisticated analysis than is possible with just calipers, where you can only get length, width, etc.

Phylogenetic trees are essential tools for representing evolutionary relationships. Unfortunately, they are also a major conceptual stumbling block for budding biologists. Anyone who has taught basic evolutionary concepts to college undergrads (and probably high school students as well) has most likely dealt with students struggling to properly read and draw phylogenies.

Lucky for us, there is also a growing body of literature on the most effective ways to teach what has been dubbed “tree-thinking”. I have summarized this literature in a review due to be published in the journal Evolution: Education and Outreach (doi:10.1007/s12052-010-0254-9). The full text of the article is available at that link, and I have reproduced the abstract below.

Evolution is the unifying principle of all biology, and understanding how evolutionary relationships are represented is critical for a complete understanding of evolution. Phylogenetic trees are the most conventional tool for displaying evolutionary relationships, and “tree-thinking” has been coined as a term to describe the ability to conceptualize evolutionary relationships. Students often lack tree-thinking skills, and developing those skills should be a priority of biology curricula. Many common student misconceptions have been described, and a successful instructor needs a suite of tools for correcting those misconceptions. I review the literature on teaching tree-thinking to undergraduate students and suggest how this material can be presented within an inquiry-based framework.

I just realized/figured out that Lauri Lebo, the reporter of Dover fame, and co-resident at the International Beer Can Museum, has an RSS feed for her posts at Religion Dispatches. Lots of fun stuff there, including the upcoming end of the world. By the way, we’ve got a guy on the Berkeley campus, David Temple, who is regularly out on the quad handing out these weird scrawled predictions of the end of the world starting May 21, 2011. He also hits the Integrative Biology building a couple times a year. I’ve saved a few since I figured this would make for a really good party next year.

I always assumed that the scrawling and Bible-verse quoting meant that David Temple was doing his own Bible-based numerology, but maybe he’s getting it from Harold Camping? Does anyone have any insight? I know a lot more about the literalists who focus on the beginning times than I do about the end-times guys. (Although, as you can see, the two are intimately connected.)

(HT: John Pieret)

Every Saturday on the square in downtown Madison you can find a big box covered with tired, ridiculous claims of Young Earth Creationism. Standing nearby Larry and Kevin preach the Gospel of Jesus-On-A-Triceratops to the curious and appalled alike. Together they make sort of a “good cop, bad cop” of creationism: Kevin, sort of a naive and basically likeable innocent guy, and Larry, a blustering, know-it-all whose abysmal knowledge of science is only inversely matched by his inflated sense of how much he thinks he knows. With creationists like these, who needs evolutionists.

Read a description of my encounters with them over a few weekends this summer on another server, and post your comments here at Panda’s Thumb.

I consider myself pretty well-educated about creationism, and of course I know it’s all silly, but I pride myself on usually being able to understand what argument the creationists are trying to make, even when they are doing it poorly. But I need help with this one.

Via the Discovery Institute Blog/Misinformation Service, I came across this post from Hunter, which is his Monday post. I also read Hunter’s Sunday post and got confused.

Starting on Sunday, we have: Cornelius Hunter, Sunday, July 25, 2010, speaking about shared errors in pseudogenes:

This claim, that such shared errors indicate, or demonstrate, or reveal common ancestry, is the result of an implicit truth claim which does not, and cannot, come from science. It is the claim that evolution and only evolution can explain such evidences. It is the equivalent of what is known as an IF-AND-ONLY-IF claim.

Science makes IF-THEN statements (if evolution is true, then species with recent common ancestors should have similarities between them). IF-AND-ONLY-IF statements (if and only if evolution is true, then species with recent common ancestors should have similarities between them) cannot be known from science. [italics original]

OK, so here he’s saying, I guess, that science can only make if-then statements, and test hypotheses on that basis. Science cannot formally say that X is the ONLY possible explanation of Y, because, I suppose, there always might be some other explanation out there.

Update 2: There is no settlement yet. The start of the trial was postponed for ongoing settlement talks. My best guess is that it all depends now on the outcome of the hearing on sanctions scheduled for July 29. As I noted here, the sanctions requested by the Doe family would eviscerate Freshwater’s defense in the civil suit, so if the judge grants either of the sanctions (adverse evidentiary inference or defaul judgment) on July 29, Freshwater is in deep trouble in that case and the probability of a settlement will go way up.

Update 1: See this comment below. It’s not clear now that this is a “settlement.”

The Mount Vernon News is reporting that Doe v. Mount Vernon, the federal civil suit in which John Freshwater is the sole remaining defendant, has been settled. The trial was due to start today. No details on the settlement are yet available. I’ll update this post as and when I learn more.

The other federal civil suit, Freshwater v. Mount Vernon BOE, is still proceeding as far as I know now.

Photograph by James Wood.

Photography contest, Honorable Mention.

Tachyglossus aculeatus – short-beaked echidna, or spiny anteater, wandering along the edge of the Jordan River, Midlands, Tasmania. One of Australia’s two native monotremes. Echidnas in Tasmania are somewhat hairier than individuals on the mainland and are recognized as subspecies setosus, one of five recognized subspecies.

(earlier draft @ ERV)

Im sure everyone here is well aware of the fact we have ‘science education issues’ here in Oklahoma. Not only do we have a failing grade of 50% on the State Science Standards report card, we have a plethora of politicians and powerful religious leaders declaring scientists and science itself untrustworthy.

How do you get kids excited by science in this kind of landscape?

A childrens musician in Stillwater has a great idea going. Monty Harper pairs up with local scientists to give sweet presentations for kids at the Stillwater Public Library– Monty writes a catchy song about the scientist/their research, and the scientists talk about their research!

Monty has built up enough of a song-base now, he wants to make an album so he can help kids everywhere get excited about science. It will include songs on topics like phototaxic bacteria, stress hormones, wheat genomics, bacterial biofilms, bat taxonomy, x-ray crystallography, and luminescence dating! For real.

The lyrics on his song about how scientists study bat evolution are hysterical and awesome.

Here is where you can help– If you think this is a neato idea and would like to help it become reality, check out Montys page over at kickstarter.

Look at the donation tiers, and see where you want to help– you can donate and free CDs will be sent to a school of your choice, you can get a CD for yourself for your kids (Im giving mine to my nieces), you can get all kinds of insider exclusives, get your name in the CD booklet as an official donor, or at the highest tier– you can get a custom song of your very own, written about YOUR research or your FAVORITE branch of science if you arent a scientist, and be included on the CD!

Im contacting local freethought groups to see if they want to pitch in to get CDs sent to local rural schools– My parents teach at rural schools, and these kids (and their teachers) would appreciate a way to bring professional scientists and researchers into their classroom, even if its only vicariously. A pro-science, pro-family way to do some good.

If Monty doesnt reach his funding goal by August 21 (HIS BIRTHDAY), you wont be charged anything, Monty loses the window his producer has open, and he has to start all over.

Monty may not be a scientist, but he is using his passion and talent to actually DO something to promote science literacy and getting kids excited about science in a pretty harsh environment. I think thats just awesome.

Over on the Thinking Christian blog I have been challenged on my assertion in several publications (e.g. in this PNAS article) that “intelligent design” leader Dean Kenyon – a coauthor of Of Pandas and People and a Discovery Institute fellow – is actually a young-earth creationist and “creation scientist.” Usually I get these things right, but I was recently wrong about Cornelius Hunter, and only some of the evidence is on the Dean Kenyon entry on Wikipedia, so it is worth it to review the evidence.

There are many lines of evidence for the proposition that Kenyon is/was a young-earther. It is true that he wasn’t always like this – in the late 1960s he was a young origin-of-life researcher, and he coauthored the book Biochemical Predestination which accepted the standard view on evolution and the age of the Earth. But in the late 1970s he changed his mind:

“Then in 1976, a student gave me a book by A.E. Wilder-Smith, The Creation of Life: A Cybernetic Approach to Evolution. Many pages of that book deal with arguments against Biochemical Predestination, and I found myself hard-pressed to come up with a counter-rebuttal. Eventually, several other books and articles by neo-creationists came to my attention. I read some of Henry Morris’ books, in particular, The Genesis Flood. I’m not a geologist, and I don’t agree with everything in that book, but what stood out was that here was a scientific statement giving a very different view of earth history. Though the book doesn’t deal with the subject of the origin of life per se, it had the effect of suggesting that it is possible to have a rational alternative explanation of the past.”

Kenyon, Dean, and Pearcey, Nancy (1989). “Up From Materialism: An Interview with Dean Kenyon.” Bible-Science Newsletter, 27(9), 6-9. September 1989.

(Note: both A.E. Wilder-Smith and Henry Morris are famous young-earther creation scientists. Nancy Pearcey is a young-earther too – she once wrote that humans were contemporaneous with dinosaurs. And the Bible-Science Newsletter was a famously rabid young-earth publication that sometimes even flirted with geocentrism.)

Photograph by Kari Tikannen.

Photography contest, Honorable Mention.

Fraunhofer lines appear in sunlight reflected off a CD. The Fraunhofer lines are the dark absorption lines superimposed upon the colored spectrum.

R. Kelly Hamilton and John Freshwater have filed responses to the Dennis family’s memorandum of opposition to reconsideration of the sanctions against Hamilton and Freshwater ordered by the judge in Doe v. Mount Vernon BOE, et al.. I recently described the memorandum in Tightening the vise. The responses are masterpieces of misdirection. See Hamilton’s (pdf) and Freshwater’s (large pdf).

Recall that the memorandum of opposition made two principal allegations:

1. Hamilton and Freshwater claimed that they spent many hours in May 2008 preparing 15 affidavits to give the independent investigators. However, Hamilton’s billing records for the period from mid-April through the end of May 2008, obtained pursuant to a federal court order to the Board of Education’s attorney, show no evidence of affidavit-related activity.

2. Freshwater has been unresponsive to discovery requests and unresponsive to a court order to compel compliance with those requests.

More commentary below the fold

Photograph by Deanna Young.

Sciurus niger – fox squirrel. According to an article in the Times, his relative, the eastern gray squirrel, S. carolinensis, is considered an invasive species in Europe.

For some strange reason, CNN’s iReport website wants people to post photos of church signs. Given the existence of websites to create fake church signs, this seems ripe for abuse. While looking at an article today, one of the signs popped up in the side bar, and it was a “deep” insight into evolution. From Venice, Florida:

Five years of grad school destroyed by the “wisdom” of this church’s sign!

(Note: I got off on some tangents in this post – big tangents, not having written a Luskin-rebuttal in awhile. In some cases – most of them, probably – I may be the only person in the world who would bother to rebut these points. But, hey, everyone needs a summer vacation, and Luskin usually takes lack of response as evidence that he must be right. This is hilarious, but it’s funniest when he relies on an argument for many years, getting more and more confident in it. But, eventually someone has to pop the bubble. I really have to stop now so please point out errors, which must exist, and I will fix when I get a chance.)

Casey Luskin has responded to my recent article “The Evolution of Creationist Movements” in Evolution: Education and Outreach. My article is freely online, so you should read it and all of the other great pieces in that issue, which was a festschrift for Eugenie C. Scott (only a few of the articles are currently open access, however).

Luskin raises 3 issues. I will answer in 3 parts:

Possibly stimulated by Jerry Coyne’s post, there’s a spate of web attention to a survey concerning evolution, science, and religion performed by the Center for Public Policy of Virginia Commonwealth University (pdf here). The survey was purportedly performed in collaboration with VCU Life Sciences. I seriously wonder who they consulted in the Life Sciences. It surely could not have been an evolutionary biologist, because like so many such surveys, this one asks a stupid question, and commenter Kevin on Coyne’s blog nails it:

I have a HUGE problem with question 1.

“Which of these statements comes closest to your views on the origin of biological life:”

What? Are you talking about abiogenesis? How am I to know whether it happened all at once or gradually over time?

The alternatives offered were

– Biological life developed over time from simple substances, but God guided this process,
– Biological life developed over time from simple substances but God did not guide this process,
– God directly created biological life in its present form at one point in time?

[Note: the order of answers was randomized among people]

Kevin went on:

Now, if you’re talking EVOLUTION, that’s a different kettle of fish. That can be defined as “diversity of life forms on this planet.” That we know a LOT more about.

But “origins of life”? Not so much.

Bad poll question. Horridly bad. Almost designed to allow theists to wedge a god into a gap.

Exactly right. This poll in fact tells us precisely nothing about acceptance of evolution because of the sloppy wording of that question. Worse, asking the question that way merely propagates the creationist conflation of the question of abiogenesis and the reality of evolution. So again, I wonder who in the VCU Life Sciences they actually consulted on that question.

“Never slaughter a chicken in front of a monkey:”

A Chinese man who saved a one-armed, one-legged monkey says the primate has paid him back - by killing all of his chickens.

<bevis>
Good thing the monkey didn’t see the farmer choke his chicken.
</butthead>