Wednesday, August 31, 2005

The flooding of New Orleans

It seems that the aftermath of Hurricane Katrina will be of much greater concern than the storm itself. Eighty percent of New Orleans is currently under water. Two levees holding back Lake Pontchartrain and the Mississippi have burst and water is pouring in (Here is a map from the NY Times). Since most of New Orleans is below sea level, this water cannot drain out. It will have to be pumped out. As of now, workers are still trying to repair the levees. Science writer Mark Frischetti wrote about such a possible disaster in the October 2001 issue of Scientific American. The only good news is that most of the inhabitants evacuated before the storm and water did not overwhelm the levees initially.

The nightmare scenario is that a severe storm surge will flow over the levee walls and flood the city quickly. The levees that were then designed to keep water out will now keep water in. In such a scenario, all of New Orleans would be under water up to 10 or more metres. Right now, the parts of the city above sea level like the French Quarter may be spared. I know I'm a doom and gloom kind of guy but it could take months just to make New Orleans habitable again. Half a million people could be displaced for a long time. I know the sentiment will be to rebuild the city but this will not be the last time a major hurricane will pummel the city. Wetlands that used to protect New Orleans to the south and east are diminishing at a pace of an acre very 24 minutes. The city sits directly in the path of where the Mississippi really wants to go and to top it all off it is slowly sinking. Should we seriously consider if it is worth maintaining New Orleans?

Tuesday, August 30, 2005

The Flying Spaghetti Monster

I've always been partial to linguini but it turns out I've been worshipping a false prophet. We must now give praise to the Flying Spaghetti Monster, who came to Bobby Henderson in a divine vision. You can learn about the Church of FSM at Henderson has written an open letter to the Kansas State Board of Education arguing that if intelligent design is to be taught in schools then all forms of it including those involving the FSM must also be taught. He is threatening legal action if they don't comply. He has started a whole movement of followers including splinter groups. There was a humourous column about it in the New York Times yesterday. In that article the author wonders if anyone has every converted parody into a religion. Does the Church of Scientology qualify? Personally, I'm all for "teaching the controversy". After all, less than 50% of the population believes or even understands evolution anyway (see a previous post). It may even stir up some interest in science.

Wednesday, August 24, 2005

Mind enhancing drugs

An article appearing yesterday in PloS Biology reports that an Ampakine known as CX717 can alleviate cognitive impairment due to sleep deprivation. The study was done in monkeys although the company that produced the drug - Cortex Pharmaceuticals, has announced in a press release that there is evidence that it works in humans as well.

The monkeys were first tested on a simple cognitive task (delayed-match-to-sample). They performed significantly better when administered CX717. After sleep deprivation of 30 to 36 hours, the same monkeys showed a markedly decrease in ability to perform the task. However, when given CX717 afterwards their performance improved dramatically, even exceeding normal levels.

The brains of the monkeys were imaged with a PET scan for glucose use during these tests. The researchers found that the medial temporal lobe (MTL) and dorsal prefrontal cortex (DPFC) showed enhanced activity during the task. With CX717, there was a slight increase in activity in these two regions and a greater increase of activity in the precuneate cortex. Sleep deprivation caused an increase in activity in MTL and precuneus but a decrease in the DPFC. With CX717, the brain activity in the sleep deprived animals approached normal vehicle levels.

Ampakines are positive modulators of the glutamate AMPA receptor. Glutamate is the main excitatory neurotransmitter in the brain. The AMPA receptor when activated produces a short (few ms) excitatory post-synaptic voltage pulse. Ampakines can make this pulse stronger and last longer. The interesting thing is that the addition of CX717 to the sleep deprived animal increased activity in some areas but decreased it in others. This goes to show you that jazzing up excitation in the brain does not necessarily lead to increased activity. Unfortunately, PET scans can only tell us about changes in glucose usage and not the actual neural activity.

It will only be a matter of time when these drugs hit the streets and college campuses. Students already take speed to stay up and Ritalin to enhance concentration. NMDA and CREB enhancers to boost memory will also soon be on the market. The CB1 blocker rimonobant will soon be approved as an obesity drug. Personally, I wouldn't go near any of this stuff. We have no idea what long term effects these drugs will have. The brain is probably pretty optimized so any enhancement will have some trade-off. I think I would like to know what that cost will be before I decide to mess with my brain.

Sunday, August 21, 2005

Tenure and Welfare

One commonly held notion is that the university tenure system is instituted mainly to protect those in the social sciences who are critical of the current establishment or hold controversial views. This is of course highly valuable for a free society. Recently there has been some suggestion that tenure should be disbanded in the sciences and be replaced with 5 or 10 year renewable contracts. The main reason for this argument is that every department has unproductive faculty and there is no way to replace them.

However, it could be argued that academic freedom is just as important for the sciences. Faculty need the ability to pursue risky ideas that may have no return. If Andrew Wiles was on a five year contract, he may never have had the peace of mind to hole away in an attic for seven years to prove Fermat's Last Theorem. Progress is not possible without failure. The tenure process should be decided carefully but once conferred, not producing another piece of research for the rest of one's career must be considered to be an acceptable outcome.

The argument could be expanded for justifying unemployment as an acceptable career choice. A just and free society should provide a minimal standard of living for all citizens. There are both practical and moral reasons for this stance. Even in our current society, people do accept that some people either through misfortune or bad judgment fall through the cracks and need temporary help to get back on their feet. One could also argue, although I bet this gets less support, that welfare could serve as a stipend for segments of the society wishing to pursue interests in areas that have no current commercial value such as writing a novel or painting. This is akin to academic freedom on the society scale.

But the most compelling argument is a moral one. A person born into a structured society does not have the freedom to live in their natural state. They must follow the conventions imposed upon them. They have no choice to opt out. They cannot choose to become a hunter-gatherer. In fact, few of us have absolute choice over what we do to support ourselves. We have some choice in the area we are trained but the market ultimately decides where we are hired. Thus, one could argue that compensation for eliminating this freedom could be a welfare system. Now, obviously, if everyone chose to take welfare the system would collapse. So to make it viable, any form of work should have a higher compensation than welfare. Did I hear someone say minimum wage?

Tuesday, August 16, 2005


I've always found so-called innate behaviour to be much more puzzling than learned behaviour. I can somewhat fathom how a neural network might learn a complex task through training but how does a gene do it? My research program over the past ten years has basically been to show that just knowing the connections of a neural network is not enough to specify what it does. Details like time scales and synaptic strengths matter crucially. Although the neural circuit of the worm C. elegans has been mapped out for quite some time, we still don't know how the creature functions. Since most of the animal world functions just fine on genetically programmed traits, we must be missing something.

An advanced online paper in Nature (Manoli et al., June 15, 2005) has found that the fruitless (fru) gene in Drosophila is responsible for male courtship behaviour. This gene encodes a set of male-specific transcription factors that are expressed in about 2% of neurons in the central nervous system. Inactivating this gene completely wipes out all male courtship behaviour but seemingly preserves all other functions. Expressing the gene in females induces courtship behaviour. Yes, females with fru will attempt to mate with other females even though they lack the apparatus to do so.

Most interestingly is when the gene is selectively inhibited in specific systems like olfaction. Naive males will typically court all drosophila they encounter, male or female, but they quickly learn to not try to mate with other males. However, when fruitless is inhibited in the olfactory receptor neurons, the flies will persist in courting males. This fact has been played up in the press as evidence of a gay gene but it actually indicates an inability to distinguish between males and females. What is amazing to me is that a single gene (although it does encode for a number of proteins) has a nonmonotonic action. Knock it out everywhere and the fly won't mate; knock it out in a specific location and the fly won't stop mating.

We still have no idea what the gene does but this result seems to imply that male courtship behaviour is pre-programmed into the neural circuitry and is activated by priming a subset of neurons or neural connections. Now we need to do the electrophysiology on the neurons expressing fru and try to untangle this mystery.

Sunday, August 14, 2005


I've been occupying my time during my two hour train rides to work by listening to podcasts on my Apple iPod. My listening selections include The Science Show and All in the Mind, both produced by the Australian Broadcasting Corporation and Quirks and Quarks produced by the Canadian Broadcasting Corporation. I used to listen to Quarks on CBC radio when I was a kid in Toronto. It was hosted by David Suzuki in those days.

I'm amazed at how good the Australian shows are. They focus on a topic each week and interview several experts from all over the world. The hosts of the shows are highly knowledgeable. These shows are so much better than NPR's Talk of the Nation Science Fridays. It is rather sad that the United States does not have a decent science show on the radio. It is no coincidence that Canada and Australia are both Commonwealth countries that followed the tradition of a national network in the vein of the BBC.

Saturday, August 06, 2005

Stem cells, cloning and beginning of life

The stem cell debate and cloning was again in the news this past week. A South Korean team announced that they had successfully cloned a dog (a very cute Afghan named Snuppy). Dogs had been notoriously difficult to clone and the team only obtained one success in one thousand tries. This work shows that it is just a matter of time before primates including humans will be cloned.

In terms of therapeutic promise, this research implies that someday we will be able to extract genetic material from a person and create a blastocyst from which embryonic stem cells could be harvested. These cells would be pluripotent and potentially be able to replace or repair any tissue in the body. Additionally, they would be a complete genetic match to the donor eliminating the chance of rejection and the need for immunosuppressive drugs which have many side effects.

In order to make this work we first need to understand how to manipulate stem cells to create desired cell types. Right now we have very little understanding of what causes differentiation in cells. Implanted stem cells could possible replace damaged neurons but they could also become tumor cells. Currently, federal funding is restricted to research only on established embryonic stem cell lines. Unfortunately, many of these lines may be contaminated with other genetic material or damaged from repeated replication. While the rest of the world is pushing forward the US is beginning to lag behind.

However, the tide may be turning. In May, the US House voted overwhelmingly to repeal the ban on creating new stem cell lines. This past week, US Senate majority leader Bill Frist, shifted his position and is now supporting a bill to expand federal funding of stem cell research although the president is threatening to veto the measure.

The argument against the use of embryonic stem cells and cloning is the same as that against abortion and that is the destruction of an embryo is tantamount to taking a human life - the premise being that life begins at conception. The curious thing is that those that support this position don't seem to have a problem with in vitro fertilization where many eggs are extracted and fertilized to create an embryo but only a few ever make it to term. The rest are either frozen, donated or discarded.

That aside, the notion of a well defined moment where life begins is not so clear cut. Is it the moment that the sperm fuses with the egg or the moment that the formed zygote implants in the uterus? If it's the former, then why not make it the moment the sperm collides with the egg or even the moment the sperm will inevitably collide with the egg. Given that we now know any cell in the body can become a new life form, should we prohibit the destruction of any cell? Should we go further and prohibit the destruction of human genetic material of any form including the sequence itself?

Someday, the only thing we'll have left of monarch butterflies, giant pandas or blue whales will be the sequence. Currently, we can build a virus starting from just the genetic map but eventually we will be able to reconstruct any life form. What protection should the genetic code have when it's erasure implies the extinction of an entire species? Perhaps in the distant (or not so distant) future, we will reproduce entirely algorithmically. A computer could combine the sequences of two people and generate the genetic material for their child. Suppose there were only one copy of that sequence and it were destroyed. Would that be murder? When biology fully merges with computer science, how do we define life then?

Monday, August 01, 2005

Bursting of the low carb bubble

The backlash against the Atkins diet is definitely on. Atkins Nutritionals, the company founded by the namesake of the diet, filed for bankruptcy today. It is in debt for 300 million dollars. The company greatly expanded over the past few years when the hype over low carb diets was at it's frenzied highest. Earlier this year I predicted that this diet fad was in its waning moments. I also wrote about some of the theory behind the diet. Basically, all diets will fail within a couple of years. It is much more difficult to keep off weight than to lose it. Maybe Krispy Kreme donuts will now make a comeback.