Wednesday, June 30, 2010

Sunrise Over Titan

This is a picture of sunlight glinting off the liquid surface of Titan. Titan is one of Saturn's moons and the only other place in the universe that we are SURE has oceans on its surface. They're hydrocarbon oceans, and they're very very cold, but they're liquid alright.

Anybody want to go there? I'd love for a biochemist to travel to Titan, it would only take a few years. Ok, maybe a decade. And there would be no feasible way to return. If life could happen that looks very different from water-based life on earth, it still almost certainly would have to take place in a liquid environment, and Titan provides that. My hunch is that even simple life could not exist on Titan, but I'm not sure. Who wants to go take a look?

Monday, June 28, 2010

Every Scientist's Faith

I have an essay somewhere that I wrote when I came to SPU seven years ago for "New Faculty Seminar." At the time I had submitted several grant applications but had not heard back. I had an echoing, empty lab room next year and no idea what was going to happen. At the time I wrote about the faith I had to have that my project would work.

Then the grant came in, and we started to work on the project, and ... it didn't work. What was supposed to be working was just giving us more of the same. The second summer of research, I spent about half of it puzzling over strange results of things that would work for other, novel reasons, until we figured out we were stupidly using spoiled antibiotics. Entirely my fault, too.

At points like this you have to have faith that something will work out eventually. The zeitgeist would say "you have to have faith in yourself." But that's not really a scientist's faith. Sure, you can make some brilliant connection, maybe, and you can work hard and get successful results, usually, but a scientist does not have faith in the self. Having faith in myself would have meant that I kept using spoiled antibiotics over and over again. Rather, the scientist has faith that at some level, the world is an ordered place. The faith I'm talking about is faith that what's wrong with the situation is not nature but the experiment.

On the surface, experiments mess up all the time. Undergraduate research is an exercise in frustration, because by definition you are doing something new and so when something goes wrong, is it because of your technique or the controls or the fact that you're doing something new? The scientist sticks with it at that point and trusts that there is an order to find and that the right experiment done well will reveal that order.

This is why monotheism led to science. The polytheistic world was unpredictable and chaotic, rolls of the dice and competing gods determining whether your family would have food or whether you'd win in battle. But one God who made everything in six orderly days meant that nature obeyed God when he spoke. If God gave humans some of that authority, then we humans could also interrogate nature and eventually get an ordered, sensible answer back. And that's worked out pretty well for us as far as iPods and polio vaccines go. On the other hand, thermonuclear war. But I digress.

Scientists sometimes pretend it's easy, as if it's our unparalleled brilliance that squeezes the answers out of nature. But if nature didn't have an underlying order in the first place, organized experiments could never get consistent answers, and we'd be better off figuring out which powerful being was ticked off today and bribing that god with a sacrifice. In fact, that exact polytheistic system developed many times over.

The scientist's livelihood depends on an ordered, responsive, knowable universe. Every scientist knows that most experiments don't work, but that's not that universe's fault. It's ours. And then, once in a while, you figure out the order of the universe, and then you can do whatever you figured out seven hundred times and you'll get the same result. I don't know about you, but I'd look at that fact and call it good.

Wednesday, June 16, 2010

The LOST Island Map

Check out this map of the LOST island, made by a professional cartographer, at this link.

Go ahead and skip the comments, however. Something about comments brings out the people who get pleasure out of typing "LOST was bad"; at the same time, few comments are made about why so many people watched it for so long. Remember how a few posts back I mentioned that the comments were an example of the Internet working like it should? Well, this is the opposite.

Was Harry Potter this way? Because I feel like Harry Potter explained things about as well as LOST, and I don't remember this general vitriol toward the series after it ended.

Saturday, June 12, 2010

Book Review: Faster

There's nothing quite so depressing as reading a book written in 1999 about how much faster the world is getting and realizing how much faster it's gotten since 1999. This is a surprisingly boring book in which James Gleick, usually reliable, resorts to the old "list 50 variants of the same thing" trick at least 10 times throughout the book and chooses to describe the 1999 cutting edge in detail while skipping over a lot of potentially interesting historical background (which, paradoxically, would have made his writing that much more relevant to 2010). Count me disappointed.

And, yes, ironically, it takes a long time to read this book. There's little context and no overarching narrative. Why should I take time to read about how busy I am?

Friday, June 11, 2010

Pictures from Old Abandoned Theme Parks

Call it the Scoobie-Doo Hall of Fame, the Ozymandius-Meets-Mickey-Mouse Hybrid, call it what you like, but I'm fascinated by what happens to old theme parks when they're shut down.

Here is an article about 8 abandoned parks. The New Orleans one wins my vote for most haunting.

Also, here's photos from the Disney World water park River Country, closed in 2001.

And here's photos from Splendid China, closed about the same time near Disney World.

I still have a hand-drawn calligraphy poster of 1 Cor. 13 from Splendid China. It's actually one of my most valued possessions!

Of course, the scientist in me thinks these are first-hand examples of what the book The World Without Us predicts (reviewed earlier here). I'd like to see how much of that book is right and how much is not given these specific "experiments."

Wednesday, June 9, 2010

The Genes of the Jews

The journal Nature just published "The genome-wide structure of the Jewish people," a large-scale analysis of the genes of Jewish people from around the world, from India to Ethiopia to Europe to Iraq ... and it reminds me why I'm so excited about genetic analysis.

Two of the most interesting findings (in my view!):

1.) Despite large geographical and historical differences, the two major groups of Jews (Ashkenazim and Sephardim) are genetically extremely similar to each other. This is similar to the recent finding that Irish and Scottish genes are very similar. It is biologically accurate to refer to the Jews as, well, Jewish, whatever their history, and the biological evidence is that they have been a separate people for a long, long time. (This also shows that they rarely intermixed the people around them -- except in India and Ethiopia. Ethiopia is such a unique nation ... )

2.) The New York Times reports that the Iraqi and Irani Jewish communities branched out from the other Jewish communities 2500 years ago, correlating with the Babylonian exile and destruction of the first temple. So we can read that part of the Bible in the genes.

Now I want to know, can genetic analysis find the Lost Tribes mixed in with others? Probably not but ... I have tons of questions. Bring on the genes!

Monday, June 7, 2010

New Production of The Ring Cycle

This article is mostly about the new production of the Ring Cycle at The Met, but I instantly am drawn to the moving planks that provide the sets. The video "trailer" in the middle of the article is really amazing (and only about a minute long).

Have I gone off the deep end enough as a Wagner fan that I would fly to New York for this? (Well, this and also to see the play "Red" about Mark Rothko ... ) I know Laurie would enjoy it but what to do with the children? If we brought them along for all 18 hours of operas, they might become SO weird that they end up normal again. It ... just ... might ... work!

OK, so I'll probably have to settle for watching the trailer on the 2-by-3-inch square on my screen repeatedly. It's probably better to have my imagination fill in the rest anyway!

Sunday, June 6, 2010

What to Do with "Against Darwin"?

Jerry Fodor, Philosophy prof at Rutgers, has jumped into the evolution debates with a book that I don't have time to read, but I just got my hands on an essay that is 1.) Free and 2.) Shorter than a book, and therefore I can look over his argument. It looks like this distills the argument pretty cogently, in any case. The essay itself is here.

Fodor argues against natural selection and "adaptationism." He doesn't have any real bone to pick with evolution per se as far as I can tell, but he is fed up with evolutionary psychologists. And I'm with him on that. In psychology and literature in particular, egregious sins against reason are being committed by hand-waving "just-so" stories that boil motivations and choices down to evolutionary pressures to survive or reproduce. Fodor insists rightly that intentions and aims need to be preserved for psychology to make sense (although, as an atheistic naturalist, I wonder where he proposes we get this free will from that is so important to his field; from what I can tell he doesn't go for free will and argues that we are in a mire of unknowingness that we must summarize as "intention").

It's easy to pick on the evolutionary psychologists, and kind of fun, but Fodor doesn't stop there; he expands his critique to evolutionary biology, arguing that not only can't natural selection explain brain states and intentions but it can't even explain biology. This is what he's getting all the attention for, and this is where the argument either stands or falls. This is also where I part company with him.

Fundamentally, what you have in this essay is a Philosopher critiquing Biology for not being Physics (without any consideration of Chemistry at all). Fodor claims that the "law" of natural selection is not really a law of science in any useful way. I agree that it's not a law like the law of physics or the law of gravity, but his chipping away at natural selection doesn't include any positive value for actually doing biology. (What am I, a biochemist, supposed to do with it beyond being careful when I make historical arguments?) Fodor points out quite rightly that evolutionary biology is closer to historical narrative than it is to physical law. But then he claims that because historical narratives can't be reduced to repeatable laws, then there's no place for the law of natural selection in biology.

Well, what is biology then? You've basically defined biology out of science and into history with a narrow Procrustean philosophical definition of what a scientific law is. This has everything to do with a philosophical argument and nothing to do with actually doing science or describing the world at a biological level. The definition of "science" is so tight that it can hardly be applied to the past at all. I think it's a well-written piece of sophistry on the level of Xeno's paradox. Yes, you always have to cross half the distance to a certain point before you actually get there. Yet -- it moves!

The missing link here is chemistry. It troubles Fodor that biological laws are context-dependent, as if the fact that the environment (chemistry!!) matters to biology is somehow embarrassing. (I know chemists are embarrassing sometimes but let us in on the conversation occasionally!) The chemical link between the environment and evolution is a major feature of the RJP Williams books I keep harping on about, so I guess I've got some more to talk about to get those ideas in the exchange. In fact, the role of the second law of thermodynamics and evolution in RJP Williams's books may provide exactly the physical level of rigor that Fodor demands.

Fodor also will often focus on a single organism for his argument as if the interaction between organisms is not important. There's one graph in particular of pigments like chlorophyll that shows how all the pigments overlap to capture all available visible light from the sun. This kind of connection, in which any single pigment doesn't make a pattern but all pigments together make a pattern, doesn't find a place in Fodor's argument. He just argues that it's hard to imagine how frogs snapping at flies or spiders weaving webs could evolve. But if it's all a drive for food and sticky things in general catch more food, I have no problem with the examples he provides. The complex sticky structures easily could result from simpler easy structures. It makes biological sense. I'm not sure it's the only thing but it's better than saying it just is.

(Another specific side point: There indeed ARE historical counterfactuals; maybe not philosophically coherent counterfactuals, but I think that means the philosophy is too rigid, not that the counterfactuals don't exist.)

What's strange is to see a leading atheistic philosopher taking some of the same myopic arguments against evolution as people with theological objections to evolution. Of course the intelligent designists and others are all over this, but they should look closer. Fodor is arguing against biological explanation, not against evolution itself. He's arguing against arguing, in a sense. And one thing I've learned from science is that the universe had a beginning, time had an origin, and time carries us all in a direction. Because of that I think it's all historical narrative at a level, and some stories of evolution are nice historical narratives just like stories from the ancient Hebrews are nice historical narratives. If you adopt Fodor's view you begin to argue against science itself (or at least against biology itself). We do actually live in an understandable world, in which narratives have explanatory power, and it is heading in a direction, and repeating experiments will tell us something about how it works, even in biology! Just because some people have ridden that horse too far doesn't mean we should stay off that horse -- just that they should take it slower ("Hey, man, stop hogging the horse!").

Fodor has a point. So, evolutionary psychologists, stay off Fodor's lawn. But Fodor, stay off the biologists's lawn (and the undergirding chemistry) until you have a critique that matches how that particular science actually works.

Thursday, June 3, 2010

LEGO Printer

How did my student know that I (and my boys) would totally dig this invention? My LEGO fascination is well known apparently.

Video here:

Wednesday, June 2, 2010

The Word: "Sphingolipid"

[This is a draft of something that may be published soon. I'm just giving it a trial run here.]

If good fences make good neighbors, then good membranes make good cells. Sphingolipids are some of the "bricks" in the membranes of blood and brain cells. The first researcher to define them revealed his frustration in the name he coined a century ago: the prefix “sphingo-” refers to the Sphinx, the original mythological riddler and bane of ancient travelers.


There are at least 60 different sphingolipids, many still as enigmatic as, well, the Sphinx. Some general riddles have been solved. Sphingolipids are chemically well-built and sturdier than most other lipids in the membrane. Also, they are extroverted molecules that sit on the outside of the cell, pointing at and talking to the rest of the body. Your immune system constantly surveys your blood cells’ sphingolipids and has grown accustomed to them (cue Sinatra and Bono’s duet, “I’ve Got You Under My Skin”).


In fact, the shape of the sugars on your sphingolipids determines your blood type, whether A, B, or O. The difference between A-type and B-type blood is just six tiny atoms (one “N-acetyl” group), but your immune system detects the difference, like the princess and the pea. If blood is transfused into your bloodstream with an unfamiliar sphingolipid, your immune system concludes that it’s under attack and defensively musters up a life-threatening overreaction. Sometimes the immune system’s reaction to innocuous substances can be too much of a good thing.

Tuesday, June 1, 2010

It Looks Like a Matte Painting but It's Real.

From Guatemala, one of the sinkholes that has opened up. It boggles the mind. Pray for Guatemala. (One of my colleagues is still stuck there but is OK from what I hear ... )