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Showing posts from November, 2009

The Truth about Creationism

Over the past month or so, with my posts about the truth about evolution, it might appear that I've built up a certain good will with a lot of anticreationists out there. OK, maybe "good will" is a bit strong. Whatever it is, I'm about to squander it. I am a creationist after all.

The truth about creationism is that it's not stupid, illogical, or irrational. Creationism is not based on "blind" faith (whatever that is). Creationism is not a modern theological abnormality, nor is it an outmoded pseudoscience. Creationism is not a threat to science or to science education or to human rights.

Don't get me wrong. I can see how all of these things could be true, given the present state of things. (Except maybe the "threat to human rights." That's just stupid.) Tracking the reaction to my posts on evolution has led me to some seedy corners of the internet. I've seen up close that most of what passes for creation/evolution debate b…

Darwin Week: The Darwinian Revolution

Shortly after becoming a genuine college professor, I started getting catalogues from The Teaching Company, which manufactures and sells video and audio recordings of special courses taught by genuine college professors (like me, only smarter). Their catalogue includes titles on just about every subject, and a year or so ago, I finally decided to give them a try. Since I travel a lot, I'm always looking for ways to pass the time in airports, and lugging around big, scholarly books isn't always ideal. Reading while I drive is also ... challenging. I can now say from personal experience with about six of their courses that they really deliver quality material. So when I saw "The Darwinian Revolution" on sale earlier this year, I couldn't resist.

The course is taught by Frederick Gregory, a professor of the history of science at the University of Florida and a graduate of the history of science programs at UW Madison (M.A.) and Harvard (Ph.D.). As usual, I opted for …

Darwin Week: The Darwin Myth

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This book has an unintentionally accurate title, since the version of Darwin's life presented in this book is mostly mythological. The Darwin Myth was written by Benjamin Wiker, who holds senior fellowships with the St. Paul Center for Biblical Theology and the Discovery Institute, according to the book jacket. Of course, the book jacket's accuracy is open to question. It also raves that the book "casts aside Darwinism's politically correct veneer and offers a critical, scientific analysis of Darwin's life and his history-changing theory." Scientific? Not even close.

The book suffers from a basic lack of evidence. It's a lot like Davies's The Darwin Conspiracy in that regard, inflating a story in the missing pieces of Darwin's life (to be fair to Wiker, this book does not repeat the "Darwin is a plagiarist" myth). Wiker's Darwin differs from the real Darwin in two significant ways:

(1) Wiker's Darwin is an evolutionist from the sta…

Darwin Week: The Voyage that Shook the World

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I finally watched The Voyage That Shook the World, the new Darwin documentary from Creation Ministries International. From the accounts I've read, it cost CMI more than $500,000 to make, and it definitely shows. It's quite a lovely film, and the re-enactments are fairly decent. CMI's strategy of setting up a production company called Fathom Media to covertly arrange the filming of historical sites and interviews generated some controversy, which of course they dispute. You can find a positive review by Ted Baehr at Movieguide (no surprise there) and a critical review from Jim Lippard here (also no surprise). To be fair, Lippard's review is pretty balanced and not overly fanatic, unlike Baehr's.

Initially, I thought I'd write a detailed review of the film, but after seeing it, I changed my mind. To be honest, it wasn't really all that bad. It wasn't great either. It's pretty much what I expected. If you're familiar with CMI's talking …

Darwin Week: The Works

With all the hubbub about the 150th anniversary of Origin, it's easy to forget that Darwin was more than just the father of modern evolutionary theory. He originally established his reputation with his geological research on the Beagle voyage. That was followed by the first extensive study of barnacles, published in four volumes (1851-1854). After that came Origin, which was followed by a book on orchid pollination. Darwin revised Origin five times and wrote related works on variation in domesticated animals and plants, the descent of man, and the expression of emotions in humans and animals. He produced other books, too, on such diverse topics as carnivorous plants and the action of worms.

I'm delighted to report that the works of Darwin have been reprinted once again by New York University Press. Previous hardback editions of this set of 29 volumes are priced at thousands, but this new paperback set goes for just $525. (Yes, CORE has a set on order.) Along with Darwin…

Darwin Week: The Annotated Origin

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I suppose it would be presumptuous of me to review Darwin's Origin of Species, but it seems fitting to kick off Darwin week by looking at a new edition of Origin. This year, Harvard University Press released The Annotated Origin, a facsimile of the first edition with new notes by James Costa. Costa is a professor at Western Carolina University and director of the Highlands Biological Station in North Carolina. According to Frederick Gregory's review in BioScience, the book is the result of Costa's course on Origin, which he has taught now for a decade (Gregory also highly praises Costa's work).

When Darwin was surprised by Alfred Russel Wallace's independent formulation of natural selection in 1858, he dropped the extensive manuscript he had been working on (about half finished at the time) and wrote instead a 450-page "abstract" of his theory of evolution by natural selection. OK, 450 pages is a little more than just an abstract, but Darwin intended t…

Darwin week: introduction

Exactly 150 years ago this week, Charles Darwin's Origin of Species began to change the world. In honor of that anniversary, I'm going to review five Darwin-related "products" (books, movies, etc.) this week, one each day. I'll kick off the series tomorrow with my review of The Annotated Origin, published by Belknap with annotations by James Costa. That will be followed on subsequent days by my comments on the complete works of Darwin (published by NYU Press), CMI's new movie The Voyage that Shook the World, Wiker's book The Darwin Myth, and Frederick Gregory's The Darwinian Revolution, an audio course from The Teaching Company.

In the meantime, I've made a list of all my other Darwin-related reviews from the past year:

1. Answers Magazine's Darwin issue
2. Janet Browne's Darwin biographies
3. The Darwin Conspiracy
4. "Darwin's Big Idea" exhibit at the Natural History Museum
5. "Darwin's Confession"
6. Darwin:…

Random bits 5

I see the maize genome is out today. That's pretty big news (in my little world, anyway), so I want to take my time before I comment. You'll find the articles at Science and at PLoS Genetics. I've got a lot of reading to do.

In other news, PNAS has a really nifty article by Bunce et al. on ancient DNA of New Zealand moas. Moas are those giant flightless birds that went extinct about 600 years ago. The (nonauthoritative) NCBI taxonomy database lists 14 different species in two families. Bunce et al. sampled 263(!) different moa specimens to reconstruct both the species phylogeny as well as a new view of the paleogeography of these species. They argue that the main morphological radiation of moas took place on the South Island. Definitely worth reading.

At least two creationists have now weighed in with their opinions of the Darwin biopic Creation, directed by John Amiel. John Mackay's website has a quasi-review signed by British creationist John Peet. Peet didn&…

In praise of peer review

There's an interesting piece in the latest Genome Technology (of all things) on the flaws of the peer review system. Peer review is the process whereby the proposals or papers of one scientists are privately examined by other scientists for technical quality and importance. One common theme in the GT article is the problem of volume: there are too many papers to review and edit, too many grant proposals for too little money, and not enough scientists who can take time to do a quality review. Fortunately, this is not the case with creationism.

Those who know me know that I'm pretty fanatical about peer review. I'm a tough editor and reviewer, and I make no apologies for that. I've even co-authored a paper on peer review. I don't want to rehash that entire article, but for those who don't want to read through the whole thing, here are a few thoughts.

I think the benefit of peer review is obvious: we get better papers. Peer review should give me the confidenc…

Questions on science and faith

Amidst all the silly emails and comments pitying me or telling me I'm wrong, I've actually started getting some thoughtful feedback from my series on faith and science. I like thoughtful feedback, so I'm going to answer a few questions here. The first comes from a "secular/atheist" and former Christian fundamentalist:
with your acknowledgement of the evidence for evolution, what keeps you from just taking a Stephen Gould, "two realms" position?That's easy. Gould's non-overlapping magesteria model (that science deals in fact and religion in morality) is wrong. Religion is not merely about morality and living a good life. Pretty much all religions make claims about reality. Some are metaphysical claims ("all have sinned"), while others are grounded in a kind of empirical claim, like Joshua making the sun stand still. Such claims might not be subject to empirical validation today, but presumably if you'd been there, you would ha…

Ciliate transposases redux

I got the latest issue of Genes & Development in the mail last week, which would be unremarkable except that I don't actually subscribe to Genes & Development. Weird but useful, since this issue of G&D has an article on a "domesticated" transposase in Paramecium tetraurelia that's used to excise internal eliminated sequences (IESs) when converting the micronuclear genome into a macronuclear genome. What in the world am I talking about? Some might recall my comments on the transposases of Oxytricha, where I explained that the ciliate genome is present in two strikingly different forms. One form is a visibly large nucleus called the macronucleus, where all the transcription and gene expression is going on. The other genome is found in a compact little storage nucleus called the micronucleus, which is used in sexual reproduction. After sexual reproduction, a new macronucleus is generated from the micronucleus by excising a huge amount of DNA to generat…

Reading: Already Gone

This is not a book review, because I haven't even finished the book yet, but I think this book is important enough that I wanted to share some preliminary impressions.

For a hundred and fifty years, antievolutionists and creationists have complained that evolution is not merely a scientific theory but that it brings consequences that are dangerous to individuals and to society as a whole. You know the kind of thing I'm talking about. "Evolution is an atheistic ideology." "Evolution teaches us we're no better than animals." And on and on. As a creationist, I've said similar things myself. But in every generation, we've said these things based on our own impressions or on anecdotes. In recent years, I've become a little skeptical of this line of thought, mostly because I've never seen any specific evidence for it (other than anecdotes).

Well, Already Gone might begin to change that. Answers in Genesis commissioned a survey of 1000 tw…

Chromosome fusion viability

Regarding my comment that "creationists claim that such chromosomal fusion or fission events are bad and don't happen" in this morning's post, A reader writes,
Who are these "creationists"? Is it a strawman, really big brush, I
don't know, I have it on good authority, or what? ... It would be far preferable to ... give names. Else it looks like everyone else except you, or it becomes a sentence evolutionists can use to attach any creationist.Fair enough. For the record, when I address creationist ideas in that way, I avoid mentioning names for two reasons:
1. It's a common enough argument, and I'm too lazy to look up specific references.
2. I don't want to name specific names because I'm not looking to pick a fight. People are way too sensitive about this sort of thing.

But my reader has a legitimate point. If this was a formal publication (and not just my own personal soapbox), I would be expected to give citations and never, ever refer…

Last week in Science

My weekend blog fast prevented me from noting two interesting pieces in last week's issue of Science. First was an extra-snarky review of David Prindle's book Stephen Jay Gould and the Politics of Evolution written by Vassiliki Betty Smocovitis. Read the whole review, and you get the idea that the book is less than ideal in its treatment of its subject, but that doesn't stop Smocovitis from using the review as a platform to vent a bit of frustration:
Stephen Jay Gould and the Politics of Evolution arrives just in time. Just when it looked like the "ultra-Darwinists" were winning the "year of Darwin" with their interminable love-fests, triumphalist narratives, and self-serving revisionist histories; when we were starting to think that Darwin was the only evolutionist to have lived in the past 150 years; and when we might conclude that nearly the entire evolutionary community had drunk the Kool-Aid of antiquarian Darwinism, David Prindle's book appea…

To publish or not?

We had an interesting problem in the BSG recently concerning editing of a paper that had been submitted to the Occasional Papers of the BSG. The question that arose concerned the grounds for rejection of a paper. We had a manuscript submitted that received four reviews that recommended against publication, And that after the paper had already been rejected by a different creationists journal. Sounds simple, right? If the reviewers say reject, then we should reject. What's the problem?

The problem was the point of the paper. The paper lays out an argument that the serpent of Genesis 3, the one that tempted Eve to eat of the forbidden fruit, was just a snake. Now as anyone with a conservative, evangelical background "knows," Eve was tempted by a manifestation of Satan, not just a snake. Except that's not what the Bible actually says. The closest you get to that idea is a single reference in the New Testament to Satan as "the serpent of old" in Revelat…

Increased mutation rates don't reduce fitness?

I'm back! I was recently challenged that I couldn't go a week without checking my blog stats. I scoffed at this notion of blogaholism, so I negotiated the time down to two days, and voila! Two days of blog-free existence. Even weirder? I didn't think about it that much.

So I'm back on this Monday morning (hey, it's still morning for another 23 minutes where I am) with a truly fascinating article from Genetics. There's so much that could be said about this research, but I'm going to just copy the abstract below. Check it out for yourself.

Springman et al. 2009. Evolution at a High Imposed Mutation Rate: Adaptation Obscures the Load in Phage T7. Genetics doi:10.1534/genetics.109.108803.
Evolution at high mutation rates is expected to reduce population fi tness deterministically by the accumulation of deleterious mutations. A high enough rate should even cause extinction (lethal mutagenesis), a principle motivating the clinical use of mutagenic drugs to…

Random bits 4

A while back I report on the creation sabbath that the SDA church was celebrating. Here's a report on the one at Loma Linda:
Adventist churches worldwide hold creation emphasis day
Sounds like an interesting meeting (although I don't think the reporter really understood the whale and turtle research).

The latest Acts & Facts arrived in my mailbox today, sans the advertisement inviting me to order Andrew Snelling's monumental, two-volume Earth's Catastrophic Past. It does indicate that the book will be available around Thanksgiving, but the order page on B&N is now gone. And you still can't pre-order it at ICR. Seriously, how hard is it to take pre-orders on what will likely be the most significant work on creationist geology in decades?

There's an interesting article on Science Daily on the Faulkland Islands wolf. I didn't even know there was a Faulkland Islands wolf.

Tim Heaton's got a new article in the October Science and Education that offer…

The Nature of Idolatry

(This will get me in trouble.)

Ever since I affirmed that the evidence for evolution is reasonable and that evolutionary theory has not failed, I've been explaining ideas about science and evidence leading up to this post. After many years in this debate, I've come to the uncomfortable conclusion that we creationists have made an idol of our own arguments. I don't say this lightly or flippantly either. This is a deadly serious problem, and the conservative wing of Christianity desperately needs to address it.

Now I realize that the apostle Paul commonly uses logic to develop his readers' understanding of Christian theology, but Paul is also the one who wrote this:
For to those who are perishing the message of the cross is foolishness, but to us who are being saved it is God's power. For it is written,
I will destroy the wisdom of the wise,
and I will set aside the understanding of the experts.
Where is the philosopher? Where is the scholar? Where is the debater of th…

The Vibrio pangenome

Shortly after I started grad school, the first bacterial genome sequences were published. In those days, genome sequencing resources were devoted to getting a broad sample of different bacteria and archaea. It was some time before different strains of the same bacterial species would be completely sequenced. When that finally happened, we were surprised to find that bacterial strains could have very different genomes, sometimes with thousands of different genes. In genomes that have only 2000-5000 genes to begin with, strains could differ by 20%. Along with other studies, this genome sequencing revealed just how much gene transfer goes on among bacteria and archaea.

From these came the concept of the "pangenome," the full complement of genes found in any genomes from a closely-related set of bacteria or archaea. The pangenome represents the full genetic potential of those organisms. An individual strain might have only a small fraction of this pangenome, but since gene…

New word for Monday: Girus

In a new paper in Virology Journal, Ogata et al. describe the PolB gene of a marine giant virus (AKA "girus") that infects a dinoflagellate. Dinoflagellates can poison fish and other marine critters when they bloom, but the dinoflagellate Heterocapsa circularisquama can be killed by Heterocapsa circularisquama DNA virus (HcDNAV). HcDNAV is a "giant virus" because it's giant, around 200 nm with a 356,000 nucleotide genome. Compared to the usual viruses that we're familiar with, that's quite big, actually approaching the size of the smallest bacteria.

Ogata et al.'s results indicate that the PolB gene of HcDNAV is surprisingly similar to the PolB gene from African Swine Fever Virus (ASFV). ASFV is a completely terrestrial virus that lives in wild pigs and ticks, where it causes no disease. In domestic pigs, it can cause a hemorrhagic infection with very high mortality rates. Ogata et al. present further phylogenetic evidence from environmental sa…