Weekly sampler 24

1. Get your genome sequenced for $48,000. I would so do this. In the meantime, we bought the Matheson family DNA test for my dad for Father's Day.

2. I'm following this series at Siris: Philosophical Sentences explained. You know the old chestnuts: Cogito ergo sum, God is dead, virtue is its own reward, cleanliness is next to godliness... heh. Brandon tells us where they came from and a little about them. Latest installment is Santayana's famous quote etched at Dachau.

3. A very cool illusion that, like all good ones, tells us something interesting about how the brain processes visual information. Don't click till you're ready to follow these instructions: display the image on your computer screen so that you can slowly back away from the screen and still see the image. The idea is to view it up close then back up at least a few meters.

4. Two of my favorite bloggers, John Lynch (of Satan's University) and John Wilkins (from Down Under) have left ScienceBlogs and set up shop independently. Lynch formerly blogged at Stranger Fruit and his new place is called a simple prop. Wilkins is an important antidote to brainless anti-religious bellowings from Coyne and like-minded simps. Both are skeptics who know a lot about evolution. Recent important posts: Lynch on The Roots of ID and Wilkins on The Demon Spencer.

5. Strangest species discovered in the last year. The ghost slug wins for weirdness, but the big news is that someday we might be able to drink decaf that's still coffee.

6. Becoming Creation is an important blog by a homeschooler, evolutionary creationist, accomplished biologist and good guy: Doug Hayworth. Up right now is an interview with Denis Lamoureux, author of Evolutionary Creation.

7. A recent piece in the Chronicle of Higher Education presents a very interesting take on teaching science in the context of religion (and other social influences). The concluding paragraph:

Science professors should explicitly engage the rich social and ethical context of the subjects that they teach, engaging new generations of students in the science that so many now fear and reject. A careful, thoughtful approach to teaching the sensitive issue of evolution represents merely the beginning of a challenging, less-traveled-by path, but one that could, nevertheless, make all the difference.

8. My research concerns some very interesting proteins called formins. Michael Behe's scholarship includes a focus on the malaria parasite, P. falciparum. A recent paper reports that a formin protein in P. falciparum is critically involved in the process by which the parasite invades red blood cells. I always knew that Professor Behe and I were destined to be collaborators.

Weekly sampler 23

Okay, so not really weekly.

1. John Farrell has an interesting discussion of protein folding as a problem or challenge for evolutionary theory. His post includes quotes from experts with whom he has corresponded, and he cites the primary literature. (You know, peer-reviewed research articles written by people who are actually trying to understand the biochemistry of an early earth.) Here he's quoting Nick Matzke:

Even the very first polypeptides were pretty certainly not assembled all-at-once-from-scratch from a pool of 20+ kinds of amino acids in even proportions, in D- and L-form, as creationists and various beknighted physicists blithely assume. Probably the first time a proto-tRNA grabbed an amino acid and made a short chain, the chain was composed of glycine and few common hydrophobic amino acids and was quite short. Cavalier-Smith (2001) suggests that the original function may have just been a hydrophobic tail for association with a membrane. All of the improbability statistics are irrelevant in this sort of scenario, chirality isn't an issue, etc.

Let's go with 'benighted' lest anyone confuse an ignoramus in Glendora, California with, say, Sir John Polkinghorne.

2. I never really finished my junk DNA series, but there's still work to be done: falsehoods about non-coding DNA are beyond rampant. Recently at Adaptive Complexity, Michael White scored a direct hit on one of the major issues in this bogus controversy, and as usual it's a basic scientific principle (in this case, the concept of a null hypothesis). His post is required reading for those interested in any aspect of evolutionary genetics and especially those who have seen the standard genomic arguments of intelligent design creationists. Hat tip: Sandwalk.

3. Christians (and others) will find ThinkChristian.net interesting and provocative. I'll be writing there regularly starting this month. About science. And stuff.

4. Alister McGrath on Augustine on Darwin. His (very) basic point is a good one and he equivocates at the right times. But he seems to be allergic to randomness. After mentioning Augustine's emphasis on "divinely embedded causalities," he claims that "Augustine has no time for any notion of random or arbitrary changes within creation." More specifically, McGrath explores notions in Augustine's The Literal Meaning of Genesis that sound like ideas from a thoughtful design advocate. (Ideas, I'll add, that were articulated just as well by Howard Van Till in a slightly different context.) But, like most design proponents, he inveighs against randomness and then identifies it with Darwin:

Augustine would have rejected any idea of the development of the universe as a random or lawless process. For this reason, Augustine would have opposed the Darwinian notion of random variations, insisting that God's providence is deeply involved throughout. The process may be unpredictable. But it is not random.

I wonder if McGrath has thought hard about this. He may be right about Augustine, but I think it's a mistake to take such a hard line against "random variations." Why do so many people think that "embedded causality" is inconsistent with "random variation"? I don't get it.

5. And speaking of randomness, our reading group ("Random Readers") recently tackled some articles on determinism and evolutionary theory. We focused on a paper by Roberta Millstein titled "How Not to Argue for the Indeterminism of Evolution: A Look at Two Recent Attempts to Settle the Issue.” The "attempts to settle the issue" were responses to a paper that Millstein describes as a "full fledged defense of evolutionary indeterminism" that put the debate over evolutionary determinism "into high gear." That paper is "The Indeterministic Character of Evolutionary Theory: No 'No Hidden Variables' Proof But No Room for Determinism Either" by Robert N. Brandon and Scott Carson. Wait, Scott Carson? Yes, the same Scott Carson who writes one of the blogs I regularly follow: An Examined Life.

6. An answer to the famous question, "What is it like to be a bat?" Hat tip: Very Short List.

Weekly sampler 22

It was a week of celebration and remembrance. There was a major birthday. And celebrations of that day of the first fruits of bigger things, in unlikely places like Florida and Arizona. It's all very exciting.

1. So... you're tired of reading about why Darwin is [God/Satan/Abe Lincoln/Howard Stern] or whether Darwinism is [Nazism/Atheism/True religion/ID codeword]. You'd rather read about what evolutionary biologists are doing today, and what real scientists think of Darwin and his ideas, but you don't have access to most academic journals. Take heart! There are some very good free resources that have been posted in celebration of Jason Varitek's signing, and here are some that I think are worth a visit:

• An entire issue of Heredity devoted to the topic of speciation
• A section of Current Biology devoted to reflections of various scientists upon reading (or perhaps re-reading) the Origin
• A series of very nice posts on evolutionary biology at Not Exactly Rocket Science, one of the best science blogs out there
• A new issue of Evolution: Education and Outreach, with excellent articles by Ryan Gregory (on artificial selection and domestication) and Michael Majerus (on the peppered moth story), among others. (Professor Majerus died last month; you can read a lot more about him at a tribute page at the University of Cambridge.)
• A special issue of Science devoted to Darwin and speciation, with some features freely available
• A special section at Nature devoted to all things Darwin
• A superb article at National Geographic by David Quammen on Darwin's first fossil clues to common descent

2. Randy Isaac (executive director of the ASA) has been providing reports from the AAAS annual meeting in Chicago, focused on topics of interest to ASA folks. He attended a symposium on human origins and posted comments on the ASA email list.

3. The Vatican will be holding a conference on evolution next month, and reports indicate that ID will get a very critical eye. Via John Farrell.

4. At the end of the month I'll be in Dayton, Tennessee to participate in an interesting Darwin-themed event at Bryan College and to hang with my friend Todd Wood. (Ted Davis is another speaker.) I hope to have a Scopes trial-centered tour as well. And in June I'll be giving a talk in a symposium at the North American Paleontological Convention in Cincinnati. I'll post the abstract here once it's accepted.

5. Siris on why Jerry Coyne should either stick to genetics or take a high school-level philosophy course.

6. More amazing illusions, again at Scientific American and again via Very Short List, but this time we have sculpted illusions of "impossible figures."

7. Gordon Glover has posted some lectures by Dennis Venema at Beyond the Firmament. Dennis is a professor at Trinity Western University in British Columbia and a fellow evolutionary creationist and ID skeptic.

Weekly sampler 21

Well, it's the first sampler since June, but I won't try to make up for lost time.

1. Todd Wood has started a blog, and it's excellent. His slant is unique -- he's a young-earth creationist -- but his writing is superb and his expertise in genetics and genomics is world-class. My favorite entry so far: a commentary on a recent report describing genetic variation among humans. The most recent post deals with the principle of accommodation and one of its Enlightenment defenders, one John Wilkins. Todd hasn't activated comments, so expect a journal and not a conversation. But have a look, and consider the gigantic difference between Todd's work and Mike Behe's. There's just no comparison, and Todd is an example of why one should not grant respect based solely on someone's willingness to accept an ancient universe or universal common descent.

2. Okay, best segue ever. Speaking of John Wilkins, Evolving Thoughts (a blog at ScienceBlogs run by a philosopher of biology) has some very interesting recent posts defending "theistic evolutionists" like me. Back in September, he discussed "Darwin, God and chance" and concluded:

Why does this matter beyond a bit of mental gymnastics, especially since I am not a theist? Well it has one rather significant implication: it means that those who criticise theistic evolutionists (like Asa Gray) for being inconsistent or incoherent are wrong: it is entirely possible to hold that God is not interventionist, and yet hold that God desired the outcomes, or some outcomes, of the world as created. In simpler terms, there's nothing formally wrong with believing the two following things: 1, that God made the world according to a design or desired goal or set of goals; and 2, that everything that occurs, occurs according to the laws of nature (secondary causes). In other words, it suggests that natural selection is quite consistent with theism, solving a problem I discussed earlier.

Read the whole post to see how he arrived at this conclusion, and don't miss the work of his collaborator, one Phil Dowe. More recently, Wilkins has summarized the "theistic evolution" position as he sees it, and reiterated his contention that the position is not incoherent. (Well, duh, but there are plenty of axe-grinding nitwits who assert just that.) I'll discuss these ideas in a separate post soon; in the meantime, pay Wilkins a visit.

3. Steve Martin's blog An Evangelical Dialogue on Evolution has become the blogospheric world headquarters for multilateral discussion of evangelical approaches to the theological understanding of evolution. The most recent series tackled questions of evolution and original sin, centered on an article by George Murphy and featuring responses by Terry Gray, Denis Lamoureux and David Congdon. Congdon's blog, The Fire and the Rose, is one of my favorites.

Left, the human eye as sketched by Descartes. Right, the eye of a fruit fly as revealed by scanning electron microscopy. Courtesy of Wellcome Images, Creative Commons license.

4. The most recent issue of Evolution: Education and Outreach is devoted to the evolution of eyes. And it's all free. Includes an introduction by Ryan Gregory, who also points us to an issue of The Lancet that focuses on evolution. Sheesh, is there some kind of anniversary coming up? :-)

5. Illusions of various kinds are something of a hobby of mine. Hence my interest in an online collection of kinetic optical illusions at Scientific American (meaning that the images produce an illusion of movement). Something else that's cool about the collection: some of the illusions were created (or discovered) by Donald MacKay, a Christian neuroscientist who has influenced me and many of my colleagues through his vigorous and uncompromising approach to the relationship between science and Christian faith. (We read part of his Science, Chance and Providence in our randomness reading group.) Make sure you look at the third image -- it's the infamous Enigma illusion.

6. Here's another kind of illusion that is interesting and informative: synesthesia, in which a perception (such as smell or color) becomes associated with a seemingly unrelated experience (a number or a different sensation). V.S. Ramachandran devoted one of his Reith Lectures to this phenomenon, which he described as "mingling of the senses." A new report describes a new version: touch-emotion synesthesia, in which certain textures evoke particular emotions. The proposed explanation for how these peculiarities is worth a look, too.

7. Using bumps in the road to make music. It'll be a clue in National Treasure 3, you just wait. Note that this link comes courtesy of Very Short List, which is a delight.

8. Deb and Loran Haarsma's excellent book Origins got a nice review at the Reports of the NCSE. I'll write one of my own sometime this spring. When the next issue of RNCSE goes online, I hope it will include my review of Gordon Glover's Beyond the Firmament.

9. The most recent (January 2009) issue of Scientific American is all about evolution. Larry Moran has some typically excellent comments over at Sandwalk, addressing pop evolutionary psychology [gag], testing natural selection, and why everyone should learn evolution.

10. Now off to enjoy one of our family's holiday traditions, this time with a mix of Scotch and rum.

Weekly sampler 20

Wow, lots going on lately.

1. So, what is a species? The concept is much abused by creationists, so that an already-challenging topic is turned into an abyss of confusion and obfuscation. John Wilkins is a philosopher of science who runs a superb blog over at ScienceBlogs, Evolving Thoughts. He's an expert on this whole species thing, and he recently provided a fascinating commentary on the issue and on a Scientific American essay on the topic by the dashing Carl Zimmer. Warning: spoiler ahead!

So my answer to the question Carl proposes: what is a species? is that a species is something one sees when one realises that two organisms are in the same one. They are natural objects, not mere conveniences, but they are not derived from explanations, but rather they call for them...

2. Oh, speaking of Carl Zimmer, check out this deliciously disturbing story of manipulation in nature, starring some of the creatures that drove Charles Darwin to agnostic distraction: parasitic wasps. Don't read this one at night.

3. Okay, so I've been a little hard on Jim Watson around here. He was "forced out" of his position at Cold Spring Harbor after he was reported to have made some plainly racist statements. Richard Dawkins was indignant, probably because Watson is a fellow atheist who Dawkins fawns over in The God Delusion. I had mixed feelings. On one hand, I was outraged by Watson's nakedly disgusting racist remarks; on the other, I was concerned about the likelihood that his comments on evolution and cognition would be ignored (or worse, rejected) in the uproar.

Well, Watson was recently interviewed by Henry Louis Gates, Jr., at an interesting site called The Root. Watson says that he is "mortified" by "those three sentences in the Sunday Times article." I'm pretty sure all three sentences appear in this paragraph:

He says that he is “inherently gloomy about the prospect of Africa” because “all our social policies are based on the fact that their intelligence is the same as ours – whereas all the testing says not really”, and I know that this “hot potato” is going to be difficult to address. His hope is that everyone is equal, but he counters that “people who have to deal with black employees find this not true”. He says that you should not discriminate on the basis of colour, because “there are many people of colour who are very talented, but don’t promote them when they haven’t succeeded at the lower level”. He writes that “there is no firm reason to anticipate that the intellectual capacities of peoples geographically separated in their evolution should prove to have evolved identically. Our wanting to reserve equal powers of reason as some universal heritage of humanity will not be enough to make it so”.

It seems to me that a discussion of the last two sentences could be quite fruitful; Watson is right about evolution, but wrong about what that must mean about the "equality" of "them."

4. Here's an interesting place to hang out: The Galilean Library. When I first followed a link there, I assumed it was a repository along the lines of Darwin Online. But no: here's how the community is described:

The aim of TGL is to provide a venue for people interested in the sciences and humanities and the possibility of learning more about them in community with others. Its rules are strict, relative to other discussion forums, and standards of expected behaviour are high, but all users need to do is demonstrate a genuine commitment to friendly and respectful dialogue with others in good faith. It consists in a Library of essays, at both introductory and more advanced levels, alongside a Discussion Forum where members of our community meet to converse and debate.

Cool. And yes, they do have stuff by Galileo, including that masterpiece of science-faith dialogue, Letter to the Grand Duchess Christina.

5. Kevin Corcoran unearths ancient secrets of scientific explanation. Now I get it.

6. A slick new Tangled Bank is up at Syaffolee.

7. A recent post in Steve Martin's ongoing series on "Evangelicals, Evolution, and Academics," by Karl Giberson, led to a lengthy and robust discussion there and on the ASA listserv. And a new post in the series, by Gordon Glover, just went up. It has this in-your-face title: "Why Evolution should be taught in Christian schools." Required reading.

8. Hey! My wife and I are looking for scholars (or just friends) in Scotland and/or London who would be willing to help us with our January trip to London and Edinburgh to study Christianity and the Scottish Enlightenment. Doesn't that sound like a great time? Please get in touch if you agree.

9. Reasons To Believe is a morass of misinformation about biology and evolution, but this is a new low: some "guest scholars" have contributed a series on "Evolution as Mythology" which is a rancid concoction of dishonest quote mining and fallacious reasoning that should make any informed Christian seethe. So much for RTB's claim to respect science and scientists; that series is a tour de force of the kind of arrogance-fed ignorance that forms the backbone of the young-earth creationism that RTB claims to eschew. Here's a typically nauseating morsel:

Even though macroevolution seems improbable via the traditional pathway (and regulatory genes are a strong argument for creationism) the myth-like character of neo-Darwinism continues to keep it as the dominant theory. As Behe says, “Most biologists work within a Darwinian framework and simply assume what cannot be demonstrated.”²³ Evolutionists even claim regulatory genes make neo-Darwinism more plausible because punctuated equilibrium is more easily explained by regulatory genes, but this only emphasizes how the myth of macroevolution must be protected with religious zeal.

Note to RTB: your intellectual integrity is mediocre at best, and your failures are magnified, not hidden, by your attempts to claim moral high ground in "debates" involving science and faith. Your organization desperately needs reform.

Weekly sampler 19

A few interesting and/or important tidbits for Monday.

1. Brian at Laelaps provides a list of some very useful books available electronically for free. Authors include slouches like Cuvier, Lyell and Huxley.

2. PZ Myers has an excellent new column up at SEED Magazine, discussing the pufferfish genome and referring to Ryan Gregory's excellent work. (Larry Moran adds commentary, and is talking about a poll.) If you need a refresher on "junk DNA" and the worthless creationist arguments it has spawned, note that I've added a Junk DNA tag to my topics list.

3. Steve Martin at An Evangelical Dialogue on Evolution is in the midst of an important and informative series of guest posts on "Evangelicals, Evolution, and Academics." Last week, Richard Colling provided some thoughtful reflections on the delicate art of communicating evolution to believers. (Some of my readers will be glad to know that I read Colling's words carefully.) One early line that caught my eye: "Indeed, an ungodly and consuming fear of evolution has engulfed the Christian community." Up this week: yours truly, on the topic of evolution at Calvin College. I wonder if I should update my CV...

4. James Kidder describes himself thus: "I am a Christian, librarian, palaeoanthropologist, evolutionary biologist and web page designer with an all-consuming interest in apologetics and controversies in science and religion." His blog is called "Science and Religion: A View from an Evolutionary Creationist" and I recommend it very highly.

5. If you can't make it to the Field Museum in Chicago to see the Evolving Planet exhibition...well, first try harder. But if you really can't get there, check out this incredible animation of the Cambrian ocean. Wonderful Life, indeed.

6. Baseball meets intelligent design! On the ASA listserv last week, Randy Isaac posted a link to a video, and asked:

How would we apply the explanatory filter to this video? Can we determine by probabilities whether it was edited? Or designed?

You can read about the explanatory filter elsewhere if you must, but what I really want you to do is to simply watch the video with Randy's questions in mind, and see what you think. Then maybe leave a comment here.

7. Read Ken Miller on Expelled, and why he wasn't interviewed, in the Boston Globe.

8. Monkeys can control robotic arms with "just their thoughts." Whereas my non-robotic limbs are wired directly to my motor cortex, and I seem to have far less control of them than these monkeys do...

The brain of S.S. Korsakov (alt. Korsakoff), a dead Russian genius. From Vein and Maat-Schieman, Brain 131: 583-590, 2008.

Oh, and while we're on the subject of brains, you have to check out this post on brains of dead Russian geniuses. (Where are the brains of dead Russian morons?)

9. Ten optical illusions in two minutes. AWESOME video; don't miss it!

Weekly sampler 18

1. A nice new Tangled Bank went up yesterday at The Beagle Project Blog, which is a cool site worth visiting at other times, too.

2. Last week saw the unveiling of the Evangelical Manifesto, "an open declaration of who Evangelicals are and what they stand for," which seeks "to rally and to call for reform." The document has sparked some pretty intense discussion among Christians I know. Some of my colleagues at Calvin have denounced it fairly strongly, at least in part due to frustration with evangelical politics. Jamie Smith (another Calvin colleague) has some interesting remarks in three parts (II and III) at Generous Orthodoxy Think Tank, and profitable discussion ensued. Here's one excerpt of clear relevance here:

All too often we have disobeyed the great command to love the Lord our God with our hearts, souls, strength, and minds, and have fallen into an unbecoming anti-intellectualism that is a dire cultural handicap as well as a sin. In particular, some among us have betrayed the strong Christian tradition of a high view of science, epitomized in the very matrix of ideas that gave birth to modern science, and made themselves vulnerable to caricatures of the false hostility between science and faith. By doing so, we have unwittingly given comfort to the unbridled scientism and naturalism that are so rampant in our culture today.

All well and good, but it's the last sentence I don't like. It's certainly true that evangelical credulity and ignorance are potent fuels for New Atheist engines, but in my opinion that's not the primary danger of the malignancy of obscurantism. Evangelical buffoonery on scientific matters betrays a deep and latent gnostic infection – North American evangelicals, in my experience, too frequently veer right to the brink of outright Gnostic heresy. "False hostility between science and faith," it seems to me, is actually real hostility toward the natural world, as evidenced by a pervasive preference for supernatural action as "God's work." I would have written something very different at the end of that paragraph – something sort of like this:

By doing so, we have unwittingly given comfort to the unbridled gnosticism that is so rampant in Christendom today, a great and ancient heresy that cleaves the creation in two, inviting the open degradation of God's good work by those who mistakenly assume that what is natural or material is worthless.

But I do like the document overall, and I agree with one commenter at the Generous Orthodoxy Think Tank who pointed out that it's the discussion of the document that makes it come alive.

3. I'm currently engaged with a discussion on the ASA listserv with one pseudonymous Mike Gene. He's recently published a book, and blogs at a site promoting that book. But wait...he's one design proponent who seems to be swimming clear of the Discovery Institute wreckage, by virtue of uncharacteristic intelligence and intellectual integrity. It's still ID, and I'm not enthused about the pseudonymity, but if you're looking for a pro-ID thinker who actually acts like an adult, Mike Gene is someone to check out. James McGrath gives the book a strongly positive review over at Exploring Our Matrix.

4. ORFans are genes that seem to exist in isolation, say in one or only a few closely-related species. They seem to have just popped into existence in those species, amid a huge common collection of genes shared by, say, all animals. If this sounds weird or interesting to you, go to Panda's Thumb to learn more. (Yes, of course, ID fellows have seized on this as another piece of ignorance on which to build.)

5. Check out someone's illustrated list of the world's 25 weirdest animals. I'm pretty sure I saw Dobby in there.

6. Gordon Glover is continuing his excellent series on science & Christian education. What do the Antipodes have to do with evolution? Are they anywhere near the Antilles or the Galapagos? Well, I'm not going to tell you; Gordon does it better.

7. Publishers Weekly online has a little interview with Ken Miller. He mentions his part in the intriguing new Templeton effort in which they've gotten a collection of big-brained white men (and one woman) to address the question "Does science make belief in God obsolete?" Included is a debate between Miller and Christopher Hitchens.

8. On the ASA web site, Jeffrey Schloss of Westmont College has an extensive review essay on Expelled, "The Expelled Controversy: Overcoming or Raising Walls of Division?" A blog was set up to allow discussion among ASA members (I'm not a member, dang it); not much there yet, but maybe that will change soon.

Weekly sampler 17

It'll be a breakout week after a slow month on the blog. To the Edge of Evolution – and beyond!

1. Ian Musgrave over at Panda's Thumb provides a nice summary of the evolution of clotting systems and some new genomic data that could be used, by ID proponents like Michael Behe, to bolster their claims regarding the "irreducible complexity" of the clotting system. I've been saying it since the beginning here at QoD: genomic data has already made it nearly impossible to respectably doubt common descent, and it gets much worse every day.

2. Massimo Pigliucci gibbers on the Problem of Evil and Francisco Ayala. Not that I'm buying Ayala's theodicy either...

3. Dale Purves is an eminent neuroscientist whose work I've followed for two decades. In the last several years, he's expanded from developmental neurobiology into cognitive neuroscience. His lab's web page is loaded with good stuff, which is probably why it was recently honored by The Scientist. The resources page includes a bunch of interesting illusions and the full text of two of his out-of-print books.

Ebola virus, electron micrograph. Image from PHIL, ID# 1835.

4. The CDC (Centers for Disease Control & Prevention) has a free online image library called PHIL (Public Health Image Library). Now you know where to go to get your pictures of Ebola Virus for when you make your own Get Well Soon cards. Don't miss this little disclaimer:

WARNING: This library includes subject matter that might be unsuitable for children. Viewing discretion is advised.

Yikes!

5. Get to Gordon Glover's Beyond the Firmament blog for a superb series on "Science and Education" focused on questions surrounding natural science (mostly origins) and Christian education. He's covering folk science right now, in his excellent style. And you don't even have to pay.

6. Last week saw the unveiling of the platypus genome, and it included lots of interesting surprises. The media coverage has been typically spotty (with regard to accuracy); to get well-grounded, start with the brief piece at the New York Times then check out Ryan Gregory's thoughts (at his new blogging home) and perhaps the usual clarity dispensed by the cuddly PZ Myers.

Weekly sampler 16

Well, no sampler last week, so here are the answers to the last DNA content quiz.

• Top row: the beluga whale has a slightly larger genome than the brine shrimp (3.29 vs. 2.91).
• Second row: the damselfly, in all its beauty and intricacy, sports a genome half the size of that of the woodlouse hunter (1.50 vs. 3.00).
• Third row: the aardvark needs more than twice as much DNA as the American cockroach (5.87 vs. 2.72). Ah, now that must be due to "degree of advancement." Just what a well-conceived biblical creation model would have predicted. NOT.
• Bottom row: the chameleon's genome is almost 10 times the size of the leech's (2.24 vs. 0.23). Another victory for junk science!

Just don't speak of the mountain grasshopper (16.93) and the bald eagle (1.43).

So, what's been keeping me so busy that I can't attend to my blog?

1. I've made a lot of dumb decisions in my time, but one magnificent success covers for all of them: a quarter of a century ago, I somehow convinced Susan Massee to enter into a long-term collaboration which has been enormously fruitful. We have four great kids (two teenagers, one of whom has a blog of her own) and lots of stories, but only recently have we started collaborating professionally. We'll be teaching two classes together in the next several months, with the most exciting one taking us (we hope) to London and Edinburgh next January. The idea is to explore the Christian roots of the Scottish Enlightenment, with Harry Potter as a theme (you know, to get us in the mood), and superstars like Hume, Reid, Burns and Smith as favored ghosts. It'll be a blast; now we just need to get about 20 students to sign up. We've been working on promotion and planning, trying not to emphasize Scotland's January climate. (Which, of course, is a heck of a lot better than Michigan's.)

2. Susan did change her name (it was a long time ago), so you'll need to add my Scottish surname to hers when looking for her work online. Start at the fascinating online magazine Catapult, then check out Calvin's television program, Inner Compass.

3. John Farrell passes along an interesting take on Michael Behe and his weird new book that I've been discussing here; see Laelaps for discussion of Behe's curious absence from a recent propaganda film. Key point: the Discovery Institute seems unenthused by the book, probably because Behe gave away the store. Here's Richard Dawkins in his review in the New York Times:

Behe correctly dissects the Darwinian theory into three parts: descent with modification, natural selection and mutation. Descent with modification gives him no problems, nor does natural selection. They are “trivial” and “modest” notions, respectively. Do his creationist fans know that Behe accepts as “trivial” the fact that we are African apes, cousins of monkeys, descended from fish?

Well, heh, maybe now they do.

4. Sorry I'm late on this, but a week and half ago D.W. Congdon at The Fire and the Rose presented Four theses against Intelligent Design. Please check it out. I'm particularly interested in his comments on natural theology and his blunt equation of ID with a "god of the gaps." My friend and colleague Del Ratzsch has convinced me that design arguments need not evoke god-of-the-gaps fallacies, but I find the ID movement to be rife with that malignancy, and Congdon's harsh judgment of such errors is spot-on. When I comment further on Behe's The Edge of Evolution, I'll claim that the book is nothing more than a single, flawed, ignorance-based argument, with the desperate aim of creating a gap.

5. I recently heard Stephen H. Webb, American Theologian, give a talk and thereafter concluded that his web site is not the parody I initially took it to be. I won't say much about the talk, for various reasons. But after hearing him speak, and looking at some of his other writing, I was unsurprised to see that he wrote a comically uninformed positive review of The Edge of Evolution. The comments reveal that not all of the readers of Christianity Today are as gullible as Stephen H. Webb, American Theologian. That's encouraging, eh?

6. John Derbyshire is a columnist at National Review, which makes him a conservative. (I used to refer to myself in that way, but I really don't know what it means anymore.) You thought I can't stand ID? Check out his remarkable condemnation of the movement, Henry V-like in its merciless passion. The high point:

And now here is Ben Stein, sneering and scoffing at Darwin, a man who spent decades observing and pondering the natural world — that world Stein glimpses through the window of his automobile now and then, when he’s not chattering into his cell phone. Stein claims to be doing it in the name of an alternative theory of the origin of species: Yet no such alternative theory has ever been presented, nor is one presented in the movie, nor even hinted at. There is only a gaggle of fools and fraudsters, gaping and pointing like Apaches on seeing their first locomotive: “Look! It moves! There must be a ghost inside making it move!”

The “intelligent design” hoax is not merely non-science, nor even merely anti-science; it is anti-civilization. It is an appeal to barbarism, to the sensibilities of those Apaches, made by people who lack the imaginative power to know the horrors of true barbarism. (A thing that cannot be said of Darwin. See Chapter X of Voyage of the Beagle.)

I don't know what Derbyshire has against Apaches, but that's beside the point.

7. I've mentioned Francisco Ayala before: he's a real evolutionary biologist, the kind who performs research and co-authors scientific papers as opposed to the kind who keeps a blog or leads a religious crusade. Read about him and his new book at the New York Times, and let me know your thoughts on the book, which I'll read and review sometime in the next...year. :-)

Weekly sampler 15

Last quiz on genome size, with animals chosen at random. The first quiz post explains what this is all about, the second one has additional commentary, and the answers to both previous quizzes are in previous Weekly samplers.

Which organism has the larger genome?
	This one?	Or this one?
1
2
3
4

Here's some help for you. These are the C-values (amount of DNA per cell) for those animals, in ascending order:

0.23 -- 1.50 -- 2.24 -- 2.72 -- 2.91 -- 3.00 -- 3.29 -- 5.87

And here's a hint: the biggest number does not go with the biggest animal. Good luck!

1. We're living in the postgenomic era, and comparative genomics has already made it impossible to be an intellectually fulfilled anti-evolutionist. I've written before about genome sequencing and the imminence of large-scale and inexpensive sequencing. Well, the first super-fast (4 months vs. more than a decade for the Human Genome Project), super-cheap ($1.5 million vs. billions for the HGP) human genome sequence is now official. It's Jim Watson's genome. Blecch. Someone should use BLAST to search his coding sequences for this amino acid sequence:
Alanine - Serine - Serine - Histidine - Glutamine - Leucine - Glutamic acid
Don't get it? Think about this guy's conduct, then check out the amino acid code.

2. If you think I'm never nice to Reasons To Believe, check out the discussion this week at the ASA listserv. The topic: RTB's statement in which they distance themselves from Expelled.

3. Speaking of Expelled, which I will do infrequently, here's a good reason to avoid the movie and its cynical attempt to enlist and co-opt evangelical Christendom: its indefensible linkage of "Darwinism" with Nazism. If that's not bad enough, check out John Lynch's examination of the diabolical credentials of one "expert" interviewed in the film.

If you're a Christian who thinks that the Nazis are a useful polemical tool against evolution, then maybe you should read about some of Hitler's best-known influences. In my view, if you can read Luther's words and still think there's any moral high ground surrounding the Holocaust that can be claimed by Christendom, then you're crazy. The Holocaust is an unspeakably abhorrent stain on the Church, if you ask me, and it's not Darwinists (whoever they are) who have hard questions to answer. I, for one, believe that Christians should be overwhelmingly humbled by the occurrence of the Holocaust, and not because of the Problem of Evil.

Christopher Heard has several recent posts on Expelled that are worth checking out. Just promise me you won't give any money to these chowderheads.

I say: skip Expelled. Send the money to Compassion International. Or give it to a library or school. Say no to the minions of the Discovery Institute who have given up the pretense of "scientific" explorations of "design" and have lustily embraced full frontal culture war. [spits]

3. [Deep breath] So, were you alive in the 1980's? Remember Bloom County? It's my favorite comic strip of all time (apologies to Calvin & Hobbes). The strip often tracked current events; during the 1981 Arkansas creationism trial, Bloom County presented the famous "penguin evolution" trial in which "scientific penguinism" was being advocated by certain characters. Some classic excerpts from that brilliant series are illicitly available in the blogosphere; don't miss the one (second from the bottom) in which the scientific expert states, "Penguin evolution is a fib." You can find some similarly scintillating examples on Berkeley Breathed's site. My favorites: the first and the next to last.

4. Kevin Corcoran writes this about a recent piece by Stanley Fish on deconstruction:

John Searle said it first, but it applies here: it’s stuff like this that gives bullshit a bad name.

Now that's funny.

5. The online repository of Darwin's works at the University of Cambridge announced this week that they were making available a gigantic collection of Darwin's private papers, including "the first draft of his theory of evolution" and notes from the Beagle voyage. One little tidbit: apparently they sold tickets to lectures at the University of Edinburgh. Hmmmm. [rubs chin]
Via my brilliant brother, who works at HP and helps his wife run her cool small business.

6. There was a lot of cyberspace snickering when Answers Research Journal started up, and some of the articles there are pretty lame (the metaphysical piece would, I think, do poorly in a 200-level philosophy course at Calvin). But have a look at the new article on peer review; the authors are worth listening to, and their discussion of peer review from a Christian perspective is worth considering. I'm not crazy about the occasional proof-texting, and the authors frequently address the YEC community specifically. But here's the type of clear-headed wisdom you'll find in their paper:

By striving for excellence, we also love our neighbors. In our modern, western culture, many people view scientific pronouncements as authoritative. Christians who are also scientists therefore have an even higher duty to speak with excellence than the average Christian, simply because of the perceived authority that they possess. Errors made by Christians speaking in the name of science, no matter how well intentioned, can become “common wisdom” and thereby very difficult to correct. Even greater responsibility lies upon the scholar who professes ideas to the general public rather than just scholarly colleagues. In doing so, the scholar becomes a teacher, with all the attendant responsibilities (e.g., Matthew 5:19, 18:6; James 3:1). We therefore love our neighbors by striving to present the excellence of God in our written work and avoid the dangerous alternative of leading them into error.

I probably don't need to explain why that passage rang true. You might notice, by the way, the links take you to the New King James Version. What is it with the conservative/fundamentalist fondness for 400-year-old prose bearing the name of an English monarch?

Weekly sampler 14

Answers to Quiz 2. (Poor John Farrell.) Row 1: the deer tick on the right has a genome almost 8 times the size of the ladybird beetle's (C value of 2.48 vs. 0.33). I take it that the scholars of RTB would postulate that a deer tick is many times more "advanced" than is a ladybird beetle. Similarly, Hugh Ross would have to surmise that a grasshopper is 4 times as "advanced" as a bengal tiger (row 2; C value 2.71 vs. 12.66). Indeed, it would seem that this wonderful insect is far more "advanced" than every mammal ever examined. Row 3: let's see...which is more "advanced", a snail or a giraffe? Well, the snail, of course, though perhaps just by a hair (heh): 2.69 vs. 3.58.

We'll have one more of these quizzes, but next time the species will be chosen randomly. At least then the success rate of Hugh Ross' proposals has a chance of reaching 50%.

1. Back in the day, I learned about the cool Monty Hall puzzle on a Usenet newsgroup. I found the puzzle to be very interesting, in that those who understand probability fairly well are most prone to being tricked by the puzzle. Here's the problem.

You're playing Let's Make a Deal with Monty Hall, and you are offered a choice among three doors. Behind one of the doors is a new Toyota Prius, yours to keep if you reveal it, and behind each of the other two doors is a goat (which, presumably, you don't want to take home). The game always proceeds as follows. You announce your choice of a door. Then Monty says, "Hmmm. Are you sure about that? Here, let me show you something that might change your mind." He then opens one of the two doors you did not choose, revealing a goat. Then he asks you: do you want to stay with your first choice, or would you like to change your mind? And the question is: do your odds of winning change (i.e., improve) if you change your mind, and choose the remaining door?

Now, if you've never encountered this famous puzzle, stop and think about it. I've put the rest of this section at the end of the post. Note, though, that there is no trickery here; Monty will always show you a goat (that's important) and the solution has nothing to do with semantics or other uninteresting chicanery. It's all about probability.

2. The evolution (and prevalence) of sex has long been considered one of the most perplexing phenomena in biology. Some of the most creatively-named hypotheses in all of science are hypotheses addressing the adaptive nature of sexual reproduction.

Image from PLOS Biology, photo by William F. Duffy.

Enter the bdelloid rotifers, animals whose "scandalous" claim to fame is that they don't have sex. For centuries, it seems that the evidence that these microscopic animals are asexual amounted to the fact that no one had ever seen a male. A very nice recent review in Nature News explains how biologists have established that the bdelloids are actually asexual, and how these animals – alone among all others – pull it off. If you want more, PLOS Biology has an interesting review of how one famous theory of sexual evolution recently held up under duress.

3. Brain doping?! So, how many scientists are taking cognitive enhancers in order to outperform their competitors? And should federal granting agencies ban this practice, perhaps to motivate Major League Baseball to follow suit? (Beware of leftover April Fools jokes.) Some of my colleagues apparently do indulge in this practice. Some, I daresay, really should start.

4. I don't have much to say about Expelled, and I don't intend to spend any of my childrens' inheritance on it. (In fact, if you are contemplating such a foolish move, consider redirecting your expenditure in some more constructive direction.) But Chris Heard at Higgaion has posted a very important piece on Why Ken Miller isn't in Expelled. Check it out, and if you decide to waste synaptic activity on this issue, tune in to the NCSE's Expelled Exposed site.

5. According to Siris, philosophy is enduring a zombie invasion. David Chalmers must be pleased. I know I am.

6. Okay, back to Let's Make a Deal. The answer is: yes, you should change your guess to the other door. Your probability of winning is 2/3 if you do that.

When I first encountered the puzzle, I had a response that is typical among people who know a little about probability. I figured that Monty's little stunt with the goat is irrelevant; it couldn't change my chance of winning any more than any other silly behavior on his part. My chance of winning is 1/3, period. And of course I was partially correct. My chance of winning is indeed still 1/3 if I make my choice and just stick with it. But I was wrong in assuming that Monty's action is irrelevant. On the contrary, his goat-revealing gesture is determined by my choice. And it changes the situation entirely.

There are many ways to explain this, but here's my favorite. On average, 1/3 of the time I choose the car at the outset. In those situations, Monty gets to choose between the 2 goats, and I lose if I change my choice to the remaining goat. But 2/3 of the time I choose one of the goats at the outset. Monty is forced to reveal the sole remaining goat to me, and that means the car is behind the remaining door. So, I have a 2/3 chance of winning by randomly picking a door and then watching Monty show me the location of the car.

Why mention this on the blog? Well, for one, it's interesting. But also, this week the Monty Hall puzzle surfaced in a scientific context. Psychologists are debating the extent to which the Monty Hall phenomenon has affected the outcomes of numerous experiments examining so-called cognitive dissonance. Read about it at John Tierney's blog at the New York Times, and don't miss your chance to play the Monty Hall game yourself, especially if (like many others) you are unconvinced by my explanation.

Weekly sampler 13

First, answers to the quiz in last week's sampler. Row 1: the genome of the funnel-web spider on the left is more than 3 times as big as that of the bald eagle (C value of 5.36 vs. 1.43). Row 2: The monarch butterfly's genome is less than 1/8 the size of the alligator's (0.29 vs. 2.49). Row 3: The duck-billed platypus has a significantly smaller genome than that of the octopus (3.06 vs. 5.15). So how'd the "degree of advancement" criterion work out? You do the math. More quizzes to come.

1. As a Reformed Christian (and former Catholic), I typically feel that Catholics are kindred spirits when it comes to science and the arts, and those of us who embrace the Creeds and common descent are prone to pointing to various papal endorsements of evolutionary science. This makes it all the more alarming to see Catholics falling for the ID line. Enter John Farrell with a sharp piece this week, following up on a nice analysis by DarwinCatholic.

2. David Sloan Wilson is the big name (that I know) behind an interesting site at Binghamton University on the topic of "Evolutionary Religious Studies." The program is Templeton-funded, and as near as I can tell is focused on outreach and dissemination but is not a degree program. I'll poke around some more, and will be interested to hear from anyone who knows more about it.

3. Thursday on Pharyngula, PZ Myers posted an article with a sadly typical description of some evangelical idiocy, then voiced a challenge I've heard from him before:

But I would think the concerted and largely successful effort in our culture to equate Christianity with the idiocy of belief in a 6000 year old world or a god who meddles in trivialities or denying the facts of a natural world would piss you off. Unless it's true, that is, that you don't mind having your religious beliefs associated with flaming anti-scientific lunacy.

Maybe you should try squawking a little louder.

I responded in the comments and would be interested in feedback here.

4. Olivia Judson has a superb piece on mutations and randomness at The Wild Side.


5. This week sees a nice edition (#102) of Tangled Bank at Further Thoughts.

6. Like I need another reason to cook up an insane road trip to NYC? As reported in the NY Times.

7. And speaking of the newspaper of record, check out this interesting piece by a couple of neuroscientists, attempting to explain why I can eat salad and ride my bike, but can't resist playing Text Twist when I have three (or is it four) papers to write. The comments are enlightening too; it's like sitting in on a contentious platform session at the Society for Neuroscience annual meeting.

Weekly sampler 12

Shall we play a game? Recall Hugh Ross' fictional tale about the "team of physicists" that remade molecular genetics. Ross claimed, falsely, that:

They noticed that the quantity of "junk" in a species' genome was proportional to that species' degree of advancement.

The biological truth is the opposite: amount of DNA, "junk" or otherwise, is so uncorrelated with other aspects of biology that the situation was termed a paradox when it was first uncovered. Well...let's see the paradox in living color. In the next few Weekly samplers, I'll present you with some organisms (all animals) and we'll see how well you can guess their relative amounts of DNA (per genome) based on their "degree of advancement." Good luck! (Hint: use a quarter; it's easier to catch, and easier to find on the floor if you drop it.)

Which organism has the larger genome?
	This one?	Or this one?
1
2
3

Answers are here. Explanation can be found on the superb blog of one of the world's leading experts on genome size.

1. This story is 6 years old, but I never heard it till this week. A 52-year-old woman gets DNA testing to determine whether she can serve as an organ donor for her son. The tests reveal that she is apparently not the mother of two of her children. But...she is the mother of all of her children. How can this be?

She's a tetragametic chimera, meaning simply that her body is composed of cells descended from two genetically distinct embryos which evidently fused very early in development. Her ovaries are descended from one of those embryos, but her blood descends from the other. The result: she conceived children with gametes derived from one embryo, but her blood (which was used for the genetic tests) comes from the genetically-distinct other. Each of her cells has just one "parent", but as a whole she is derived from two distinct embryos, each of which arose from two distinct sperm/egg pairs; thus she, as a whole, is derived from four gametes instead of the typical two. Wild! And lots of fun for certain friends of mine who (like me) enjoy reflecting on human personhood and personal identity.

2. The newest issue of The Economist has an interesting piece on a large new European scientific collaboration.

“Explaining Religion”, as the project is known, is the largest-ever scientific study of the subject. It began last September, will run for three years, and involves scholars from 14 universities and a range of disciplines from psychology to economics. And it is merely the latest manifestation of a growing tendency for science to poke its nose into the God business.

Bring it on!

3. This View of Life is a nice-looking site that aims to be "a beginner's guide to a science-based understanding of evolution." I'd love to hear some feedback from anyone who's checked it out. (Via the ASA listserv.)

4. Read Ryan Gregory on the much-abused concept of Just-So Stories.

5. Earlier this week, I heard an interesting story on MarketPlace about "video games that are good for you." I think I'll ditch Text Twist and try this instead. The games "reduce stress and boost self-confidence." Do they have any that add time to the day?

6. At the Howard Hughes Medical Institute (HHMI), a site called BioInteractive is crawling with "free resources for science teachers & students." Lectures, animations, "virtual labs." It's a mixed bag, but very much worth a stroll. (Via Panda's Thumb.)

Weekly sampler 11

First day of spring, 2008.

Right.

1. PZ Myers blogged about this interesting new report: examination of the genes for yolk proteins and milk proteins reveals a clear story of the evolution of proteins that nourish embryos and young in vertebrate animals. Pseudogenes figure prominently, and the explanation makes no sense without them. The article (in PLoS Biology) was accompanied by a nice lay summary, but PZ's post is very good too.

Speaking of PZ, if you haven't heard about his hilarious expulsion from a screening of a propaganda film that I won't name, check out his description of the event, or Greg Laden's Blog for bunches of links.

If your kids ever ask you to explain the concept of irony, tell them that Alanis is very confused, then tell them about how PZ was expelled from a movie with a curious title.

2. Are you a former physicist who is feeling ignorant of basic principles of biology? Feeling silly about some of the things you've written about biology, that you now know are complete nonsense? Want to learn a little about biology? Just ask a biologist. They might misspell 'color' and 'honor', but they'll surely know plenty about genetics and evolution, and a quick consult might save you from the humiliation of being thought an arrogant ignoramus. Try it!

3. I've mentioned before that our little state of Michigan, with the worst economy in the U.S. and without any hope of affecting the Democratic presidential nomination, is a hotbed of world-class evolutionary biology. The walking whale Rodhocetus kasrani? In a free museum on the University of Michigan campus. The famous ongoing experiment on selection and evolution in bacteria? In a lab in East Lansing. I could go on. Here's this week's sample: the Digital Evolution Lab at Michigan State. Their simulation program is Avida, and they used it in a prominent study published in Nature in 2003. Lately, with NSF funding, they've been adapting Avida for educational use. I haven't tried it yet, but I'm very interested in the possibility of using it in the classroom.

4. Is it a waste of time – or even counterproductive – to engage folk science and/or pseudoscience? Brian at Laelaps and Abbie Smith at ERV are two of my favorite science bloggers, and they both took the bait when a blogger at ScienceBlogs suggested that responding to anti-science propaganda "enables" it. I assume you already know where I stand: with Brian and Abbie. Via Pharyngula.

5. Dr. Hunter O'Reilly, BioArtist. Very cool.

6. I just looked over an article called "Spending money on others promotes happiness." Reader's Digest? Joel Osteen? The Living Bible? Mr. Rogers? Give up? Here's a hint: the same issue of the same magazine includes an article on a proposal to let scientists edit GenBank, the massive genomic database, in essence turning it into a wiki. (Sounds smart to me.) The magazine is Science, and here's the abstract of that article on "promoting happiness":

Although much research has examined the effect of income on happiness, we suggest that how people spend their money may be at least as important as how much money they earn. Specifically, we hypothesized that spending money on other people may have a more positive impact on happiness than spending money on oneself. Providing converging evidence for this hypothesis, we found that spending more of one's income on others predicted greater happiness both cross-sectionally (in a nationally representative survey study) and longitudinally (in a field study of windfall spending). Finally, participants who were randomly assigned to spend money on others experienced greater happiness than those assigned to spend money on themselves.

I wonder if there's a pseudogene involved somewhere...