Sunday, June 29, 2008

A Wedgie for Creationists

The creationists have got their panties in bunches over Richard Lenski's recent paper on bacterial evolution and evolutionary contingency. In brief, over the course of 44,000 generations, Lenski's lab of e. coli acquired the ability to metabolize citric acid. It appears that at least 3 mutations were involved.

Now, on one hand, you have Andrew Schlafly (of Phyllis and "Conservapedia" fame) demanding a right to Lenski's data and bacterial cultures. Lenski was partially funded by the government, and Schlafly is a taxpayer. It appears that Schlafly sees the paper as a severe affront to his beliefs, and strongly suspects some kind of fraud. Never mind that he is not qualified to read such technical papers, much less analyze the bacteria for himself. The whole brouhaha is detailed here and here.

On the other hand, you have Michael Behe, an intelligent design creationist, poo-pooing the paper. After all, he says, the machinery to metabolize citric acid was dormant in e. coli's DNA. The only mutations required were those to allow it through the bacterial membrane. A handful of point mutations (most likely) over 20 years is nothing to get excited about, according to Behe.

Obviously, there's quite a disparity between Schlafly's and Behe's views. Is the paper such a blow to creationism that it surely must be fraudulent? Or are the results entirely ho-hum?

Now (July 9), we've got "Answers in Genesis" chiming in with an interpretation that Lenski's results are neither ho-hum or fraudulently evolution-affirming, but pro-creationism. Such disparities are fairly commonplace in the world of creationism, where the only guiding principle is to attack evolution on every possible front. In the spirit of fraternity, it seems that debate between the various schools of creationism is supposed to be minimized. But the logical chasms are huge.

I'm not only referring to creationist arguments against evolution, but also to their own religious dogmas. It seems, for example, that these folks are rather divided over the existence of satan, and/or his role in evolution. There was a time, though creationists have conveniently forgotten it, when satan was accused of planting un-biblical dinosaur bones in the soil. Remnants of this view can still be found on the net. Unfortunately, it seems that flimsy creationists tracts that may have existed in laundromats 40 years ago have gone the way of soft-bodied pre-Cambrian worms. Now, of course, you've got a "creation museum" with displays of folks saddled on the behemoths, and satan is normally left out of creationist arguments against evolution (Lewis Black on creationists: "these folks think the Flintstones is a documentary").

My point: scientists should make a point of questioning the creationists, a tactic that is normally ignored. Of course, there's a good argument to be made that scientists should never debate these buffoons in the first place. But if we must debate, then the scientist needn't merely play the role of creationist error correcter. My own experience is that, given a quasi-earnest nudge, these folks are foaming at the mouth to spew the most ludicrous supernaturalisms. Such a process may reveal inconsistencies in their views toward both evolution and religion, leaving them to fend off not only the scientists, but other believers.

Some other questions for the creos:

*How often has the Designer interceded? While most young-earthers would say "once", and others might say "always", creationist darling Behe implies that he does so intermittently. (Question for Behe: do you think your "science" could pin down when these intercessions occured?)

*If you claim that ID is a science, could you offer up a handful of experiments that might falsify it?

Wednesday, June 25, 2008

The Thailand Bowling Resort

About three years ago, I had this notion of putting together the "Thailand Bowling Resort". Enthusiasm for my latest brilliant idea normally wanes within a week or two, but I was hyped for several months. I put together the graphics (see the bowling balls in the coconut trees?) and a five page business proposal, and even made some meager attempts to contact folks with big bucks.

I envisioned myself as the Willy Wonka of global bowling. Given the relatively cheap costs of bowling in Thailand, you could send members of your league over here, toss a few games, and then drink cocktails on the beach. There'd be 200 foot lanes, and lanes with Evel Knievel style "loop the loops". Banked, race-track style lanes. Lanes with 15 or 21 pins. For the serious bowlers, you'd be able to choose from any number of lane conditions, and actually toss all sorts of balls...not just cheap plastic house balls. Video would be available so you could check out your form. Etc.

It never happened, of course. All you venture capitalists can feel free to grab the idea. But you gotta give me rein to mysteriously wander the premises in the wee hours, with tuxedo, top hat, and cane.


Actually, I haven't tossed a bowling ball for nearly half a year now. My new focus is on Himalayan climbing...I'd really like to get up over 8,000 meters someday. More on that later. But it's not like all my bowling balls are going to waste...I build leg strength and endurance by stuffing the balls into my backpack and "trekking" up and down the stairs in the condo.

Not quite ready to compete with the guys below, though...

Saturday, June 21, 2008

Fun with Gene Expression (for Bio-Nerds Only)

Hop on over here and you'll be greeted with an awesome gene expression resource. It's a database of about 33,000 cDNA sequences that correspond to virtually every gene in the body. You could type something like "204285_s_at" (that's how these cDNA sequences are identified) in the search field. Alternatively, you could type something like "top2a" (which happens to be the symbol for topoisomerase 2A). Then you hit enter, and you see all sorts of expression data for that gene. You might see that it's heavily expressed in the pancreas, but not in the brain. You'll see links for papers that reference that gene. Etc.

Folks gawk at the achievement of sequencing entire genomes. Impressive, but personally I'm astonished with these DNA microarrays that tell you which genes, out of 20,000 or more, are being expressed in the tissue sample. Biochemists have been sequencing DNA for something like 50 years now, with various increments in efficiency along the way. But these microarrays required a whole new approach. Specifically, biochemists had to collaborate with experts in semiconductor lithography to create these "gene chips".

"How much would you pay for your own genome sequence?" is a question sometimes offered to various scientists. Currently, it would cost a few million dollars, I would think. But a fairly affluent individual can have a tissue sample analyzed via microarray right now, and the results would probably be quite a bit more useful (at this junction in history, at least).

It also amazes me that so many of these genes and their protein products have been analyzed in depth. Choose any of 20,000 genes. Which diseases are connected with its mutations? What sort of protein family/structure are we talking about? What is its function? How heavily is it expressed in any of 100 different tissues and cancers? Who has written papers on the subject? Nobody will win a Nobel prize here, because tens of thousands of researchers have contributed to this huge knowledge-base. And much of the data is freely available to anyone nerdy enough to probe it.

I'm one of those nerds. Having downloaded the aforementioned database, transformed the data, and squished it through my own statistical sausage machine, I now offer up the winners of the "Gene Expression Awards". Before continuing, I should make it clear that I'm taking the expression data at "face value", ignoring error bars, and the simple fact that heavy/light mRNA concentrations don't necessarily translate into heavy/light protein concentrations.

First, the award for Most Consistently Expressed Gene. Here, we're talking about a gene that is expressed across all sorts of tissues, not just a few. The winner is...Insulin-Like Growth Factor Binding Protein 6! You find it everywhere in the body. Runner-Up candidates include "proline arginine-rich end leucine-rich repeat protein", "phosphoinositide-3-kinase, class 3", and "glypican 4". Special mention should go to proteins like "gelsolin" and "growth arrest-specific 6", which are not only consistently expressed, but also heavily expressed.

How about the Least Consistently Expressed Gene? Here, we'll go with "myosin, heavy polypeptide 7, cardiac muscle, beta", found almost entirely in muscle tissue. Another good candidate would be "protamine 2", which is only expressed in testis tissue.

How about "Most Overexpressed in Cancer Cells"? Let's go with "phorbol-12-myristate-13-acetate-induced protein 1" as the champion. Runner ups include "neuromedin U", "topoisomerase (DNA) II alpha 170kDa", "phorbol-12-myristate-13-acetate-induced protein 1", "DNA replication complex GINS protein PSF2", "ribonucleotide reductase M2 polypeptide", "activator of S phase kinase", and more.

There are plenty of proteins that are essentially unexpressed in cancer cells. There's always a slim chance that these proteins must be actively suppressed in order for cancer cells to proliferate. Some examples: clusterin, fibronectin 1, v-fos FBJ murine osteosarcoma viral oncogene homolog, and insulin-like growth factor binding protein 7.

"Most Overexpressed in Adult Tissue" (i.e. least expressed in fetal tissue): "major histocompatibility complex, class II, DP alpha 1", followed by any number of other immunoglobulin-related proteins. "Prostaglandin D2 synthase 21kDa (brain)" should also figure in the list.

Conversely, there's "Most Underexpressed in Adult Tissue": "alpha-2-HS-glycoprotein", "glycophorin A ", "hemoglobin, gamma G", and more.

Some Trivia...

*genes that are generally heavily expressed tend not to be expressed in testis germ cells. Rather odd.

*want to know which genes are heavily expressed in the appendix? Look for genes that are also heavily expressed in the superior cervical ganglia. Why in hell should there be a relation between these two tissues? Heavy expression in the ovaries also correlates strongly with expression in the appendix...low expression in the ovaries correlates with low expression in the appendix.

*Heavy expression in the Spinal Cord correlates overwhelmingly with expression in the Olfactory Bulb. More reasonably, heavy expression in the Prefrontal Cortex and Hypothalamus also correlate strongly with with Olfactory Bulb expression.

*Various brain tissues cross-correlate very strongly. Strong expression in the whole brain is very well correlated with heavy expression in the amygdala, followed by the prefrontal cortex, occipital lobe, etc. The differences between these tissues are fairly subtle, apparently.

*Gene expression in the prostrate is strongly correlated to expression in the lung! Huh?

*Despite the proximity of the organs, expression in the prostrate is negatively correlated with expression in the testis.

*Heavy expression in the atrioventricular node (of the heart) corresponds to heavy expression in the skin!

*Heavy/low expression in the blood is negatively correlated with heavy/low expression in the brain. There are also inverse correlations between testis expression and whole blood expression.

*Low expression in the adrenal cortex is correlated with heavy expression in the Medulla Oblongata.

*If it's heavily expressed in smooth muscle, it's probably expressed in low quantities in skeletal muscle. This correlation isn't strong, but it's a bit surprising nevertheless.

*Proteins heavily expressed in adipocytes (fat cells) tend to be expressed in smooth muscle. Collagen and collagen binding proteins, for example, but also "melanoma associated gene" (ds2448), laminin, and more.

Sunday, June 8, 2008

One-Step Woo Identification

Who are the woo-meisters? They're easy to identify. Given two sides, they're the ones that cite conspiracies.

Creationism: Here, it's the "Expelled" play. Legions of brilliant ID/creationist scientists are supposedly being fired or denied tenure. The possibility that these folks are simply inept, inane, or insane is not explored. The fact that this entire issue seems restricted to the U.S.A. is also other country in the world would waste as much time and effort debating whether all viewpoints under the sun should be offered up for scientific debate. It's a democracy, we've got Oprah, and even the illiterates are "entitled to their opinions".

Below, the trailer for "Expelled". Check it out...eminent game-show-host/Nixon-speech-writer Ben Stein doesn't waste any time (16 seconds, to be precise) blaming "BIG SCIENCE" for the world's ills.

Global Warming: As above, thousands of institutions have conspired to shut the gates on the aspiring Einsteins of global warming denial. This argument is momentarily suspended, of course, when the denialists cite academic polls that supposedly show that large numbers of scientists agree with their point of view.

Anti-Vaccine Nuttery: Here it's Big Pharma. The multinationals want to poison our children and turn them autistic because...because...actually, I'm not sure why. It's not like the drug companies have expensive, existing treatments for autism. Maybe they're working on some. Perhaps Big Pharma is attempting to create a new generation of savants who can be employed by Big Pharma, churning out ever more insidious malady/treatment combos.

Given my tongue-tiedness, let's hear eminent scientists Jim Carrey and Jenny McCarthy elaborate...

The Moon Landing Hoax: Here it's NASA. Thousands of scientists, government officials, and Hollywood types were hired to fake six moon landings. Toss in one failure (Apollo 13) for realism, and the chance for future sequels. Kill off anyone who shows signs of whispering the truth to the public. Kill off all the NASA scientists who weren't aware of the absence of wind on the moon, too. And punch out the intrepid sleuths who are honing in on the truth....

9/11: Again, huge volumes of government officials conspired to 1) cause four large airplanes laden with Laden zombies (and a lot of fuel) to crash into various structures which 2) wouldn't have toppled without the assistance of planted explosives in order to 3) cause world-wide hatred of Muslims and sympathy for America, ushering in a new Golden Age for democracy. Forgetting about the tendency of metal reinforcement to weaken, if not melt, in high heat, George Bush's response...that of taking any and all actions that might inhibit expressions of sympathy...makes it clear that he had no foreknowledge of these sinister schemes.

HIV Denial: Again, Big Pharma with a malady/treatment combo that.....targets babies!!! Ingeniously, they cause AIDS with a cheapo drug called AZT, brainwash both the scientists and the public into believing the killer drug is actually the cure, and sell more of the drug. Fortunately, one progressive and enlightened society has seen through the lies...Thabo Mbeki's South Africa.

Suppression of Alien Technology: Who is behind this conspiracy? Is it the Russians? The Chinese? It's certainly not a traditional society where ghosts have long been engrained as the spooks of choice (Q: Why aren't there any aliens in Thailand? A: Because the aliens are afraid of the ghosts). It's the Americans, of course, who have appropriated and reverse-engineered all sorts of black technology from the myriad alien vehicles that never seem to crash-land outside the homeland. With the extraordinary efficiency of our efforts in Iraq and Afghanistan, how could anyone really doubt the presence of an alien assist?

Friday, June 6, 2008

A "Penalty Decision" from China, 1987

My father dug up this little treasure and sent it to me. Seeing it, I chuckle. It's a "penalty decision" for trespassing into off-limit areas in China.

The town was Yecheng. It's about 200 kilometers south of Kashgar, and maybe 1,000 kilometers north of Tibet. My goal was to get into Tibet from Kashgar, and passing through Yecheng was the only efficient way to do it. The alternatives might have added 5,000 kilometers to the trip.

My traveling partner, Mani, and I found a hotel in Yecheng. It wasn't long before a policeman arrived and roused us (I feigned sleep when he entered the hotel room...somehow that wasn't an effective strategy). We were donkey-carted off to the police station where we were hit with the above penalty, which didn't amount to much by Western standards. Nobody could speak English, but the police were able to communicate by opening a little notebook in which handwritten explanations of various offenses were available in English. The manual was quite detailed...they even had foreseen the various objections that offenders might offer, with rebuttals following.

I was also asked to write an "auto-confession" apology to the People's Republic of China. I could have written just about anything, given the total lack of English skills. I wrote that my ancestors would be ashamed of me.

Back out on the street, we purchased bus tickets back to Kashgar for the following day. If the police accosted us, we could simply show the tickets as proof that we certainly planned to head north. Of course, we didn't. Around 4:00 in the morning, we exited the hotel. Unfortunately, there was a chain link fence surrounding the hotel, and we had to quietly bust open the gate to get out.

We wandered south for a couple hours before catching a truck heading into Tibet. That's another longggg story....