Monday, July 31, 2006

Checking In

I'm in Denver now and I've got a place to live (but haven't moved in yet) and I'm getting my paperwork for my job and stuff taken care of. The trip was interesting, and I'll have more to say about it when I find the time.

Tuesday, July 25, 2006

Heading Out.

Well, I'm taking the plunge and driving to Colorado. It will be at least a few days and possibly longer until I have internet access of any kind, so don't expect to see any updates here any time soon. And wish me luck.

Friday, July 21, 2006

Friday Animal Blogging -- Upstate Edition

I'm visiting my parents in Easley, SC this week, and while I thought this would give me some time for blogging, I was wrong. First of all, there are router problems with our cable modem, and secondly, I've been going out with old friends of mine who still live in the area and getting... utterly sauced. That just doesn't help anything.

But my parents' house has this nice little waterfall that they built in, and it's a magnet for frogs. Not those boring tree frogs that sing all night, but some bullfrogs who make rather amusing noises. Here's the waterfall:


And here's the frog. He's shy, and likes to dive into the water, but I got his ass on film.

Monday, July 17, 2006

The Brick Testament

I ran across this site awhile ago and bookmarked it. Someone decided to illustrate Bible stories using Lego characters, and the results are, well, interesting.

Here we have Deuteronomy 21:18-21 in which the Bible instructs us on the proper occassion and method to kill our uppity children.

"If a man has a stubborn and rebellious son who will not listen to the voice of his father..."
Then it goes on for a few more frames, and we get to the good part.

'All the men of the town must then stone him to death. You must banish this evil from among you.'
It's a good thing no one really believes you should do this... well, almost no one. There is the Christian Reconstructionist movement, which has the avowed goal of committing mass murder against gays, unchaste women, and pretty much everyone else whom the Bible condems. Funny coincidence, the prime financial backer of Christian Reconstructionism also happens to be the prime financial backer of the Discovery Institute. The jerks at the Discovery Institute like to blame the theory of evolution for being responsible for Nazism. But as it turns out, the closest thing to Nazism you can find in contemporary American politics is holding their purse strings.

Anywho, the whole Brick Testament page is one of those things that makes you wonder how we ever got along before the invention of the internets. I used to play with these Lego characters as a kid, but the ones we had were generic and crappy. They've come a long way. And someone with way too much time on his hands put a lot of effort into setting up each and every one of these scenes. Aside from the bad focal length, it's quite brilliant.

Saturday, July 15, 2006

My New T-shirt

About a week ago, I ran into a friend of mine in a bar who has taken to making his own T-shirts, and he does a pretty good job too. I liked the one he was wearing and managed to talk him into trading shirts with me right then and there. Here it is:


Anyone living in the Charleston area will get the gag. On the other hand, the Sasquatch Army is a secret known only to a select few. If you have detailed information on the Sasquatch Army, please email me so I can arrange to have you killed.

Speaking of defending James Island, in one of those odd cosmic coincidences, just yesterday I was driving around and decided to check out an area off to the side of the salt marsh on Folly Road, just because I always wondered what was back there. I found a place called Fort Lamar, at which the Battle of Secessionville was fought. It was the last time James Island was truly defended. You can still see the earthworks. There's an interpretive hiking trial there that I'm going to check out sometime before I leave.

Friday, July 14, 2006

Gervais Bridges, We Hardly Knew Ye...

Sad news: Gervais, the proprietor of Barbecue and Politics, one of the best blogs in South Carolina (or anywhere for that matter), is hanging up his hat. Gervais' posts were insightful, clever, and above all funny, and they were nearly always complemented by humorous photoshopped graphics. I've been half tempted to try to imitate his style, so that way I too could be original. I was pleased to see among the list of blogs he reads and plans to keep up with my blog, which tells me that I really have to do more to keep this baby updated on a regular basis.

Anyway, as a parting shot, he's got more info on how State Superintendent of Education Karen Floyd, who is a proponent of creationism-lite a la the Discovery Institute, is having her campaign bankrolled by Libertarian millionaire Howard Rich. As I discussed previously, Religious Right crazies and Libertarians make strange bedfellows indeed.

But this is starting to blow my mind. Gervais figures that 23% of her campaign funds are coming either directly through Rich or indirectly through one of his bogus front-groups. (Which means it's all Rich's money -- making it indirect is just a way to misdirect.) It's probably more than that if Gervais managed to miss any groups that didn't make it obvious by having the same address.

And it gets worse:

Another $17,500, or 16%, came from several companies -- Aspect Energy, Azimuth Energy, Walnut Software, etc. -- which share an address: 511 16th Street, Suite 300, Denver, CO, 80202. The address is also shared by a voucher organization called "Alliance for Choice in Education," whose name is not found in the ethics filing.
Either each of these several companies just so happen to have their offices all located not just in the same building, but in the same suite (not likely), and by strange coincidence all happened to contribute to an obscure campaign in a different state on the other side of the country (even less likely), or they're bogus companies. You don't impersonate software and energy companies as a means of skirting campaign finance law unless you know you're doing something wrong. Someone really needs to investigate this.

By the way, everytime I see the word "Suite" as some company's or non-profit group's main address, alarm bells go off. Here's why: I've been following the "Intelligent Design" movement for far longer than I like to admit, and one reason I never seem to get tired of it is that these guys are the perfect case study in unethical behavior. There is almost nothing that they won't try to pull, and their shenanigans, while tragic and occasionally infuriating, are also a source of endless amusement.

About four and half years ago, the Discovery Institute people announced, amid much fanfare, the creation of something called the International Society for Complexity, Information, and Design, or ISCID. If you think that this "society" does any research or actual work in those things which comprise its name, then you don't really understand how these things work.
As such, ISCID has the following address, still visible on its contact page:

ISCID
66 Witherspoon Street, Suite 1800
Princeton, NJ 08542

609-924-4424 (general)
609-924-0582 (fax)
Wow, Princeton! That's quite prestigious. On the contact page, you can also see information about their Office Manager and other things one would expect to exist in a real, genuine office. But someone decided to check out the actual address of the place and observe first hand just what it is that goes on there. Here's what he found:


Yep, the "Suite" is actually a box at Mailboxes Etc. There is no actual office. The "Office Manager" is apparently someone's girlfriend, and here is a list of her duties:

1. Live in Princeton.

It's a difficult job, but someone has to do it.

Anyway, back to the front companies mentioned by Gervais. My suspicion is that by being located in "Suite 300", their address actually consists of no more than a small box at a Mailboxes Etc. or something similar. Clearly, the Alliance for Choice in Education is hiding something from us, and at the risk of stating the obvious, I'll tell you what it is: They've discovered a way to shrink several whole offices down to the size of a cubic foot. When this gets out, it's going to be huge.

Friday Animal Blogging: Pest Edition

I don't know how much a millipede counts as a pest, but I found this little guy crawling around on my electric bill late one night:




He isn't nearly as large as the millipede I found back in the Spring. My guess is that it's the garden millipede, Oxidus gracilis. It is apparently common for them to wander into homes in South Carolina, but they're not a domestic species. They can become a pest in greenhouses, munching on plants, but that's about it.

He didn't want to hold still, so getting a clear picture of him was hard. Not to mention the low light and his small size. This was the best I could do.




I heard some whining noise just outside the other night, so I get a flashlight and there I find an injured rat. It appears to be a juvenile brown rat, Rattus norvegicus. This is the same species that we use for lab rats; I used to own one as a pet. This guy must have been attacked and dragged near the front door by Fluffy. She's normally a totally inept hunter, but she's gotten more proficient of late. I took the rat inside.




I briefly thought about trying to nurse it back to health, but then my roommate, who helped take these pictures, wasn't wild about the idea. And I was less inclined myself after the little fucker bit me. So I put him back outside in the brush by the woods, where he'd at least have a fighting chance.



*

Moving to Colorado

I've been busy doing stuff to get ready to move this last week, in addition to spending some time with friends (who think they're being helpful by taking me out and plying me with beer). As a consequence, I haven't been updating this blog.

I've accepted a position as a post-doc at the University of Colorado at the Health Sciences Center located just outside of Denver. I'll be working in the lab of David Pollock, doing experiments on protein structure and function, as I did during my grad school days, but this time I'll be testing hypotheses derived from evolutionary biocomputational methods. It's pretty much right up my ally.

Right now I'm going through closets that have accumulated years of junk, some of it actually mine, and choosing what to keep and what to cart off to Goodwill. I've dumped three car loads of stuff off at their collection center recently, and I'm doing another one today. If you purchase anything from a Charleston area Goodwill store in the next few months, there's a good chance that it once belonged to me.

Next week I will be visiting my parents who have a high speed connection, so hopefully I'll get to do some more blogging.

Friday, July 07, 2006

Friday Animal Blogging: Dogs

These are my parents' dogs, Sugar and Spice (take a guess which is which based on the color) with my nephew Aidan, sometime around Thanksgiving in 2003.



And here is Sugar disobeying local sanitation laws.


Monday, July 03, 2006

The Techno-Geek Speaks Greek

Discovery Institute co-founder and investment strategist George Gilder has written an article that will be appearing in the prominent conservative magazine National Review. The DI has the article available here, which is convenient for those of you who don’t have 5 subscriptions to the National Review like I do.

Would you believe that the article is terrible? In looking at reactions to Gilder’s previous articles, the most consistent criticism is that his writing is abstruse, incoherent, and filled with terminology that he either doesn’t understand or intentionally misuses (or worse, invents on his own). This piece continues that time-honored tradition.

First of all, very little of it has anything to do with evolution, whether by Darwinian means or any other. (He even spends several paragraphs plugging his own books, which have no clear relevance, but I guess the guy needs all the royalties he can get.) Staying true to the Discovery Institute’s tactics, he associates things with evolutionary biology that have little or no association at all, and in every case these just happen to be things that are disliked by right-wing ideologues such as George Gilder. People like him apparently need an all-purpose boogyman to make sense of the world, but it’s a poor substitute for genuine understanding. And in this case it has resulted in an article that consists mostly of disjointed ramblings with no coherent thesis. Secondly, Gilder has an bad habit of throwing in random quotes from noteworthy scientists, most of whom would probably have a very low opinion of George Gilder. In virtually no case do these quotes have any real relevance to whatever point, if there is one, that Gilder is trying to make. They appear to serve as the literary equivalent of name-dropping, lending a fa├žade of authority to an otherwise nonsensical piece. And then there is Gilder’s favorite tactic, which is to wax profound about one scientific advance or another (with no indication that he knows what he’s talking about), and pretend as if this alone somehow constitutes an argument. There is just painfully little that rises up to the level of coherence.

Below the fold I will try to address the few claims that are on-topic and comprehensible enough to address. That’s not many, but it’s worth clearing a few things up.

Early on, Gilder repeats the old canard about natural selection being a tautology: “…at its root, Darwinian theory is tautological. What survives is fit; what is fit survives,” he writes. This is really bottom-of-the-barrel stuff, requiring a willful misunderstanding of evolutionary theory. Let’s clear this up: Natural selection is about the probability of an organism surviving and reproducing relative to the rest of the population. The theory requires that some features of living things are more conducive to survival and reproduction than are others; hence if these features are heritable, they will increase in frequency over successive generations. Since there is no a priori requirement that this be true of the world, it’s hardly a tautology, now is it? We could live in a world where all organisms, regardless of their traits, were equally likely to survive and reproduce. But a century of experiment and observation shows that this isn’t the case. In their famous work on Darwin’s Finches, Peter and Rosemary Grant found that a difference as small as 0.5 mm in beak size was enough to cause a measurable change in the likelihood of survival. Obviously, given that those features which improve survival can be detected empirically, Gilder’s blather about everything being equally good is nonsense.

Gilder also goes on and on about how we biologists are apparently unaware that genetic information can be understood as information rather than as chemistry. This seems to be a favorite hobby-horse of his, as he has repeated it several times elsewhere, claiming, quite amusingly, that biologists are going to be left behind in the new Information Age. This must come as a big surprise to those of us who use information technology on a regular basis, whether it be with sequence alignments, BLAST searches, or even phylogenetic trees. There is in fact a large and thriving field of biology known as bioinformatics that specifically focuses on using information theory to analyze the massive amount of sequence information that’s being produced. And like everything else in biology, evolutionary theory is a critical part of this field. But in spite of the fact that most research institutions have bioinformatics programs — and in some cases, whole departments — Gilder is apparently oblivious that this discipline even exists. Instead he lectures biologists about the need to incorporate this revolutionary new idea called information he’s just discovered. I hate to break it to you George, but you’re a half-century behind on this.

Gilder also makes a big deal about the idea that the information inherent in DNA is completely independent of the medium, seeming to base a large amount of his thesis (whatever it is) on this claim. Here are a couple of examples:

I came to see that the computer offers an insuperable obstacle to Darwinian materialism. In a computer, as information theory shows, the content is manifestly independent of its material substrate.
[…]
“Like a sheet of paper or a computer memory chip, DNA bears messages but its chemistry is irrelevant to its content.”

But anyone paying attention to molecular biology over the last 20 years knows that this is completely false. Many of the vital functions performed by nucleic acids are a direct result of their chemical properties. Consider, for example, the structure below:

This is a stem-loop, one of the most basic secondary structures that nucleic acids (in this case RNA) can adopt. These structures are necessary for the binding of proteins and the regulation of transcription, translation, and just about everything else that is important in how nucleic acids transmit their information. And while secondary and tertiary structures are determined by the primary sequence of DNA, and thus can be reduced to sequential information, they would not work if expressed in a different medium. In many cases, the information contained within DNA and RNA manifests itself functionally by means of the chemical properties inherent in the sequence itself — hence you cannot separate the medium from the message.

But even if Gilder weren’t totally wrong about this, it’s not even clear why it matters. Assuming the medium were completely independent of the information contained therein, what of it? What does that say about evolution and how does that make “intelligent design” any more plausible? As with everything else, Gilder doesn’t explain. He just hand-waves and pretends as if exuding profundities is a proper substitute for having a clue.

Gilder is at his most absurd when he attempts to discuss the Central Dogma of molecular biology, which postulates that information flows from DNA to RNA to proteins. Gilder is under the bizarre misapprehension that this means that DNA must have preceded protein during the origin of life. Of course this is not the case; the Central Dogma applies only to modern organisms and says nothing about alternative systems that may have existed prior to the last common ancestor. But assuming DNA did come before proteins, how is this relevant? Gilder doesn’t explain. And he seems completely unaware of the RNA World hypothesis, which holds that RNA containing both catalytic and information storage properties preceded both DNA and protein. But given that Gilder seems amazed by his recent discovery that DNA contains information, we’ll just have to take things one step at a time.

Having a hard time understanding what the Central Dogma actually means, Gilder goes on to say some pretty silly things about it. This is one of my favorites:

Over at NASA, U.S. government scientists make an analogous mistake in constantly searching for traces of protein as evidence of life on distant planets. Without a hierarchy of informative programming, proteins are mere matter, impotent to produce life. The Central Dogma dooms the NASA pursuit of proteins on the planets to be what we might call a “wild goo chase.”

Is he serious? Obviously, NASA wants its probes to detect chemicals that correlate with living things. It doesn’t much matter which chemicals they look for just so long as they’re easy to detect and can be reasonably assured to indicate the presence of life. The fact that they look for protein doesn’t mean that they don’t think space bugs would have nucleic acids as well. The Central Dogma isn’t the least bit relevant here. (By the way: Looking on the web, I can find no NASA program that looks for the presence of proteins on “distant planets”, or even on not-so-distant planets. What Gilder is referring to is anyone’s guess.)

But it gets worse. Combining his poor understanding of the Central Dogma with a equally poor knowledge of the history of science, Gilder says things that are, to be as polite as possible, weird:

Throughout the 20th century and on into the 21st, many scientists and politicians have followed Darwin in missing the significance of the “Central Dogma.” They have assumed that life is dominated by local chemistry rather than by abstract informative codes. Upholding the inheritability of acquired characteristics, Jean-Baptiste Lamarck, Trofim Lysenko, Aleksandr Oparin, Friedrich Engels, and Josef Stalin all espoused the primacy of proteins and thus of the environment over the genetic endowment.

It is truly a challenge to pack so much ignorance into such a small space, but Gilder is a techno-guru and capable of marvelous feats. Where to begin here? First of all, Darwin couldn’t have known anything about the Central Dogma of molecular biology because he lived a full century before it was worked out. The same is true of Lamarck, who lived in the 18th and early 19th centuries (Gilder is off by 200 years here). And neither one could have known much if anything about proteins, and certainly nothing about DNA.

The inheritance of acquired characteristics has a long history, but suffice it to say that Larmarck is usually credited with having come up with the idea in pre-Darwin times. In present-day textbooks, Lamarckian evolution is often contrasted with Darwinian evolution as a means of explaining how natural selection is very much different from Lamarck’s view. (Lamarck really gets a bad rep for this; the inheritance of acquired characteristics was a widely held view in his time, not unique to Lamarck at all, but it has sadly overshadowed his truly valuable contributions to evolutionary thought.) When Darwin came along, his biggest problem was that he couldn’t explain heredity. His theory required that heredity existed, which everyone accepted as true, but he couldn’t explain how it worked, and this remained a major thorn in his side. He incorporated so-called Lamarckian ideas into his work, but he never quite cracked the nut of heredity. Then in the early 20th century, Mendel’s laws of heredity were rediscovered and the modern science of genetics was born. It was precisely the melding of genetics with evolutionary theory that comprised the neo-Darwinian synthesis. The Central Dogma of molecular biology, by showing that heredity creates phenotype, and not the other way around, makes this even more explicit. How badly confused must Gilder be to think that this constitutes a valid argument against Darwinian evolution? He is apparently ignorant of the fact biologists do not and have not taken the theory of acquired characteristics seriously for nearly a century. The only major exception was T.D. Lysenko and his followers in the Soviet Union, who accepted a Lamarckian version of genetics — a thoroughly anti-Darwinian view — out of a devotion to ideology. It just goes to show that attacking science for ideological reasons, as Gilder does, is doomed to failure. But of course the irony is lost on him.

And finally, somewhere in the last half of the article, by which point the piece has descended into complete gobblety-gook, we finally get introduced to intelligent design. You know, the so-called theory which Gilder previously admitted has no content. For Gilder to know nothing about biology is understandable, but one would at least think that he kept abreast of the pseudo-theory that is championed by the institute that he co-founded. That’s not quite the case:

But intelligent design is merely a way of asserting a hierarchical cosmos. The writings of the leading exponents of the concept, such as the formidably learned Stephen Meyer and William Dembski (both of the Discovery Institute), steer clear of any assumption that the intelligence manifestly present in the universe is necessarily supernatural.

Um, no. Dembski at least has argued on many occasions that the “intelligence” responsible for whatever the heck it’s supposed to be responsible for must be supernatural. The Discovery Institute’s creationist wing mentions prominently that they are at war with naturalism, and says quite directly that science should incorporate that which is beyond the natural — in other words, the supernatural. That is their entire purpose for existing and wasting everyone’s time. And Gilder, with his own railings against “materialism”, is effectively saying the same thing. It’s pretty dishonest of him to pretend otherwise.

Beyond that there is little left in the article that isn’t muddled and impertinent. Gilder’s habit of listing break-through scientific theories seems to have little purpose other than to awe his readers by showing them that he’s heard of things like quantum mechanics. The National Review is perhaps the best known conservative magazine in America, and its readers deserve better than this. The Discovery Institute, on the other hand, deserves what it gets.

(Cross-posted to the Panda's Thumb.)