Thursday, March 31, 2005

Daylight Savings Time

Donald Prerau recommends bringing the start of Daylight Savings Time forward from the first Sunday of April to the middle of March, and moving the end from the last Sunday of October to the first Sunday in November.

I largely agree in the springtime, if only that the beginning of Daylight Savings time, when the sun suddenly stays up until 7:30pm, always seems to me to herald the arrival of spring and always lightens my spirits after the dark winter. Every year, I'm surprised how much an hour of extra light in the evening cheers me up.

However, he provides an odd reason for the extension in the fall:
Daylight time now always ends just before Halloween - sometimes, as last year, on Halloween morning. Alarmingly, children's pedestrian deaths are four times higher on Halloween than on any other night of the year, and daylight time would provide another hour of light for young trick-or-treaters.
But trick-or-treating is no fun unless it's dark out. I remember one year when I was a kid, my parents made plans for our family to go out for dinner on Halloween, and I was really disappointed that I would have to go trick-or-treating around 5:30pm, thinking that it would still be light. Luckily for me, the end of daylight savings time meant that it was already pitch black by then. So, really, daylight savings time on Halloween would just make kids want to go trick-or-treating an hour later. (In any case, in northern cities the sun sets on Oct. 31 by 5:30pm even with daylight savings time, and trick-or-treating usually happens after dinner, so it's not clear how the extra hour of daylight would help.)

Wednesday, March 30, 2005

Boy Scout hypocrisy

The program director of the Boy Scouts has pled guilty to possession and distribution of child pornography:
The longtime program director of the Boy Scouts of America and chairman of its Youth Protection Task Force pleaded guilty in court today to a charge of possession and distribution of child pornography. ... The filing charges Mr. Smith with knowingly receiving and sending "computer images which contained photographs of minors engaging in sexually explicit conduct."
I can't help but point out the bitter irony that this man engaged in acts that harm children while heading up an organization that banned gays from being scoutmaster at least partly on the (false) insinuation that gay men are pedophiliacs who would prey on Boy Scouts if they were scoutmaster.

Airport propaganda

I was in Shanghai this weekend. When I arrived at Pudong International Airport, by the baggage claim I saw a big poster that said "AIDS" in big letters, apparently intended to raise awareness of AIDS. I was pretty impressed that China was making an effort to end its harmful coverups of AIDS in China and start to educate the population about HIV and how it is transmitted. When I left, I saw a similar poster in the check-in hall - which is when I realized that the only places I had seen this poster at all during my whole visit were in the international airport. I can't help but suspect that this reflects an effort by China to convince foreigners that it's doing a good job, when in reality it's not doing much of anything...

This story in China Daily (a state-run English-language newspaper) contains a picture of a similar poster (scroll down), in a Beijing subway station. Notably, not a poster from a rural village in Henan province, where even the government admits that 40% of people who gave blood between 1992 and 1996 became infected with HIV.

Friday, March 25, 2005

New vaccine

Hooray for vaccines!

Paradigms, anomalies, and ground-breaking discoveries

When I first read Kuhn's "The Structure of Scientific Revolutions," I was deeply disturbed. I'd grown up believing that scientists are dispassionate collectors and analyzers of data who don't allow anything to stand in the way of The Truth. Kuhn argued instead that scientists work within models ("paradigms") that structure the way they interpret data - including what data they toss out as "experimental error." Scientists are largely trapped within their paradigm until the number of anomalies increases to the point that the cognitive dissonance is too much, and someone eventually comes up with a new (often incommensurable) paradigm that solves the problem. Kuhn was careful to say that this was not a limitation of science - rather, it is the key to science's fantastic success, in that it focuses our attention on questions that can actually be answered. Still, I was not too happy with this idea - it seemed to cast doubt on the objectivity, and therefore the validity, of science.

Then I started doing actual research.

In fact, the uncertainties involved in actual experiments are so huge that there is no way you can make sense of anything without a paradigm. For anything beyond the most simple of experiments, you have to take a lot of things for granted. And the truth is that experiments fail so often that it is quite sensible to dismiss experiments that don't work as expected as unexplainable failure rather than a blow to the reigning paradigm, and to pursue more productive lines of research instead. But sometimes the paradigm really is wrong, and we just hope that Kuhn was right and eventually people get bothered enough by all the anomalies to toss out or revise the old paradigm.

I bring this up because of the finding reported in Nature that there may be inheritance of genetic sequence information outside of the DNA genome (or as the paper's title says, "genome-wide non-mendelian inheritance of extra-genomic information"). (The Nature article requires a subscription; NYTimes reports here.) Plant geneticists found that in the standard plant genetic model (Arabidopsis thaliana), parents that had both copies of a certain gene mutated sometimes produced offspring that inexplicably recovered the wildtype version of that gene.

This is the kind of bizarre finding that, if you are too stuck within a paradigm, you just toss out as some weird error. I used to work in a fruit fly lab, and we constantly worried about contamination of fly lines (i.e., if a stray fly sneaks its way in while you are transferring flies from one bottle to another). If you had a bottle full of fly mutants with white eyes (the wildtype is red), and suddenly one day some red eyes (or orange eyes, which is the heterozygous color) appeared, you'd think the stock got contaminated, and you'd just throw out the red-eyed flies (or, more likely, the entire stock).

Now, the genetic anomaly in the Arabidopsis case is not as severe - for example, contamination is less likely because plants don't move, and Arabidopsis can be self-fertilizing. But still, I imagine that if I had discovered this, my first thought would not have been "wow! this is something new and exciting!" but "oh God, what the hell went wrong this time?" When I read the paper, I got this sense a little - as if the researchers were frustratedly trying to find out what was going wrong with their experiment, only to find that every possible conventional explanation within a traditional Mendelian paradigm failed. (It wasn't an epigenetic modification, or a suppressor mutation, or contamination, or outcrossing, or high mutation rates in that part of the genome; nor is there any additional sequence for that gene in the DNA genome.) And that's when you get really excited.

You get excited because this finding reveals yet another hole in the so-called "Central Dogma" of molecular biology, that sequence information flows from DNA to RNA to protein. Now, the Central Dogma has been full of holes for a long time (retroviruses 'reverse transcribe' RNA into DNA; prions transmit information from protein to protein). But for eukaryotes, DNA has always been the permanent repository of genetic information - RNA is thought to be too unstable. Yet here you have the fixing of a mutated gene, clearly being fixed from a wildtype template, where the DNA genome does not contain another wildtype copy of the gene. The researchers have proposed double-stranded RNA "holdovers" from previous generations that can be used as templates for gene conversion if the plant is under stressful conditions. Multigenerational RNA stability is totally mad - but this is the least mad explanation there is. I'm excited to see what happens next.

Just imagine if the researchers had written it off as some unexplainable experimental mishap and moved on to a more productive (read: more conventional, understandable) line of research. Kuhn's paradigm theory relies on the willingness to escape the paradigm to explore the anomalies that become ground-breaking discoveries. And we should be thankful that people do take risks like this - it keeps science self-correcting, and interesting!

Thursday, March 24, 2005

Why should we respect the wishes of the dead?

Having become overloaded by commentary on Terri Schiavo in the past week, I'm reluctant to add to the whole mess. Still, I had one thought of a more philosophical nature spurred by PZ Myers and Abiola Lapite. Both of them expressed the view that, since Terri has no higher brain function and has no idea whether her pre-vegetative wishes for medical treatment are being adhered to or not, we need not consider her wishes. That is, she has no dignity left to preserve, since she is unaware of her surroundings, so there's no real reason to go either way.

This brings up a thought experiment I have heard a few times. Suppose I offered you $10, in exchange for which a room full of people far away from you would insult you behind your back, call you ugly, stupid, mean, and so on. That doesn't sound very appealing - generally we desire people not to insult us, even if these insults have no effect on us (e.g., it's not the case that these backstabbing insults cause anyone to treat you worse than they otherwise would have). But suppose I offered you $10, in exchange for which people would insult you but I would then erase your memory of our agreement, and you would believe I had just been very generous in giving you $10. That doesn't sound very appealing either. Most people's intuition is that they want their desires to be fulfilled even if they don't know about it.

This is similar to people's wishes about what happens after they die. People care about what kind of funeral they have, whether they get cremated or buried in a coffin, and so on. People usually don't want their corpses to be desecrated. People care about whether they are remembered well or poorly. And people care about abstract ideals like whether democracy will survive in the world, whether global warming will ruin the planet. This is the sentiment of "I can die happy now that I have accomplished long-lasting achievement X," or in the negative, "X must be turning in his grave now that his ideals have been betrayed."

Still, we're left with the question of why we should care about these wishes. There is no person who gets concretely harmed if someone's wishes are contravened after their death, or unbeknownst to them. "What you don't know can't hurt you," etc. Yet it still feels wrong. It feels like betrayal. Why?

One practical argument is that living people want to have confidence that their wishes will be obeyed. Every betrayal of a dead or unconscious person's wishes is a blow to that confidence, and thus harms (in a small way) almost all living people.

Yet that doesn't seem quite right either. Wish-betrayal also seems wrong even if you do it secretly such that no one else ever finds out. Moreover, my intuition is that wish-betrayal is bad relative to a specific person (i.e., the person whose wishes you're betraying), not just humanity in general. But how can this be, if that person never finds out that you have betrayed his or her wishes?

Let's try another tack: There is a badness to dying that is completely independent of whether you suffer - it is the ultimate harm, even though "you" are not really being harmed at all, if you don't suffer. Death seems to be bad because it causes us to lose all the life experience we might otherwise have lived. You lose your opportunity to fulfill your goals and desires, whatever they may be. So if those who survive you continue to fulfill your goals and desires, that makes it slightly less bad. This is so even though you are unaware of what actually happens - our intuition suggests that the goodness of fulfilling your desires and the badness of having them frustrated doesn't depend on you knowing about it.

Still, I'm stuck on the problem of the fact that after death, you no longer exist - there is no subject to relate to the fulfillment or frustrations of your pre-death desires. Could it be that intuition in this case is hopelessly confused? It wouldn't be the first time, after all. It may be that this intuition just arises from the desperate hope (even among atheists) that life continues in some form after death, and that preserving a dead person's wishes is just a way of assuring ourselves that the dead person still lives on in our hearts.

Thoughts, anyone?

Saturday, March 19, 2005

Biological and genetic causes

One of my pet peeves is the conflation of "biological" and "genetic"/"innate" when discussing the causes of behavior. As in the recent row over Summers' comments about women in science, people often refer to a "biological" explanation for X (e.g., scientific/mathematical ability) as opposed to a social-influences explanation, when what they really mean is a genetic or innate explanation.

In fact, all behavior has a "biological" explanation. This is true simply because the mind is the product of the brain. Any behavior you might be interested in has a cause somewhere in the brain, even if we can't yet figure out what it is. Similarly, any environmental influence that affects your behavior (learning, for example) necessarily has an effect on your brain because how else would the change in your behavior be implemented? Thus, if social pressures discourage women from entering science, this is because women encode these subtle societal biases as memory in their brains; and vice versa for men. It's simply nonsensical to describe "biological" explanations as being opposed to "social influences" explanations in any meaningful way.


Wow, so I'm really sorry about basically disappearing for an entire month. I'm finding that despite my hopes to the contrary there are only 24 hours in a day after all, and I just don't have time to update this site every day. But I will try to write posts more regularly in the future, just at a lower frequency than I had been before my prolonged absence...