Wednesday, September 28, 2005
Grass Power
A possible promising crop for biofuel may be a form of Elephant Grass (Miscanthus x giganteus). This tall grass hybrid could yield up to 60 tonnes of biomass per acre. It is currently being tested in Europe. It thrives in northern climates and requires very little fertilizer. It has a low water content so it can be easily harvested at the end of the growing season and simply burned for power. Stephen Long of University of Illinois calculates that if 8% of all the land in Illinois was dedicated to this crop, it could generate half of the electrical needs of the state. It also has little effect on the carbon balance because it simply releases the CO2 when burned that was sequestered when it was growing. The hybrid does not produce seeds so it can't spread. Further bioengineering could make it even more efficient. Who says I can't say something positive?
Thursday, September 22, 2005
Programmed for Failure
Every time I feel kind of optimistic about the future, I think back to the Roman Empire and realize that it could all end pretty quickly. It may be no accident that civilizations tend to have finite lives and our brains may be responsible. Jared Diamond(in his book Collapse) posits a framework for a society's demise but he basically believes it is some combination of bad decision making and management that leads to failure. I'm proposing that it may actually be embedded in how our brains work and how it reacts to success. What allows us to build great civilizations may ultimately be responsible for our undoing.
As has been written in countless columns and blogs, manufacturing, software development, clerical work and so forth is being or will soon be outsourced to an offshore location where labour costs are so much lower. Many have argued that the US can retain world dominance by remaining a source of innovation and ideas. However, Thomas Friedman and others have been screaming lately that the US is losing it's lead in technology and science and American students are falling behind the rest of the world in technical subjects.
The reason is not just that we've become lazy or stupid. The Flynn effect shows that average IQ's have actually been rising every generation and in the recent book Everything Bad is Good For You: How Today's Popular Culture Is Actually Making Us Smarter, Steven Johnson argues that video games and popular culture are actually making us smarter. So why is it that we are becoming less intellectual even though we are getting smarter?
I think it is related to the fact that it takes effort to concentrate on something. This effort is not because we're using more energy. Although it may seem that thinking hard burns more calories, there is in fact little evidence for this. So if there is no metabolic cost then why is it so difficult to think? The reason may be that the brain is a novelty machine that constantly seeks new stimuli. Advertising and marketing people know that they need to change a scene every 10 or 15 seconds in a commercial or people's attention will be lost. Our brains are designed to wander and seek new stimuli. This constant novelty seeking probably helps in the early stages of a civilization where things need to be built and everyone sees open opportunities for growth.
As a civilization matures, it takes longer and longer for the citizens to acquire and digest the accumulated knowledge required just to keep it running much less advance it. Years of training is necessary before anyone can make a contribution. Given our current comfortable circumstances, there is little incentive to undertake such an ordeal when there are so many other distractions to occupy us. In the past, scholastic learning might have been the most cognitively stimulating thing one could engage in. Now, our lives are filled with leisure activities that are much more interesting and entertaining than what we learn in school. For every high school kid with his nose stuck in an analysis textbook, there are hundreds or thousands of other kids who are playing video games, surfing the web, reading a Harry Potter novel or solving a Sudoku puzzle.
Is there a way out? I'm pessimistic. While it is true that those on the cutting edge are doing very interesting and stimulating things, the journey to get there is so long and arduous that fewer and fewer are likely to take it. No matter how appealing you may make calculus or organic chemistry, they just will never be able to compete with the endless variety of distractions in modern society. There will still be an educated elite but there won't be enough of them to keep the engine going.
The decline of the US could be very rapid. Even now, much of science and technology is being driven by foreigners. However, as the balance of power starts to shift overseas and the US remains xenophobic, that spigot could be shut off quickly. The incentive to come here will diminish and people may return to their native countries as things decline here accelerating the process.
It may be that the only hope for humanity is to maintain uneven economic development. If the entire world became comfortable simultaneously, it might completely collapse all at once. However, if the decline of the US is accompanied by the rise of China and India then at least some order in the world could be maintained. After a century or so, the US could rise again in a perpetual cycle of localized growth and decay.
As has been written in countless columns and blogs, manufacturing, software development, clerical work and so forth is being or will soon be outsourced to an offshore location where labour costs are so much lower. Many have argued that the US can retain world dominance by remaining a source of innovation and ideas. However, Thomas Friedman and others have been screaming lately that the US is losing it's lead in technology and science and American students are falling behind the rest of the world in technical subjects.
The reason is not just that we've become lazy or stupid. The Flynn effect shows that average IQ's have actually been rising every generation and in the recent book Everything Bad is Good For You: How Today's Popular Culture Is Actually Making Us Smarter, Steven Johnson argues that video games and popular culture are actually making us smarter. So why is it that we are becoming less intellectual even though we are getting smarter?
I think it is related to the fact that it takes effort to concentrate on something. This effort is not because we're using more energy. Although it may seem that thinking hard burns more calories, there is in fact little evidence for this. So if there is no metabolic cost then why is it so difficult to think? The reason may be that the brain is a novelty machine that constantly seeks new stimuli. Advertising and marketing people know that they need to change a scene every 10 or 15 seconds in a commercial or people's attention will be lost. Our brains are designed to wander and seek new stimuli. This constant novelty seeking probably helps in the early stages of a civilization where things need to be built and everyone sees open opportunities for growth.
As a civilization matures, it takes longer and longer for the citizens to acquire and digest the accumulated knowledge required just to keep it running much less advance it. Years of training is necessary before anyone can make a contribution. Given our current comfortable circumstances, there is little incentive to undertake such an ordeal when there are so many other distractions to occupy us. In the past, scholastic learning might have been the most cognitively stimulating thing one could engage in. Now, our lives are filled with leisure activities that are much more interesting and entertaining than what we learn in school. For every high school kid with his nose stuck in an analysis textbook, there are hundreds or thousands of other kids who are playing video games, surfing the web, reading a Harry Potter novel or solving a Sudoku puzzle.
Is there a way out? I'm pessimistic. While it is true that those on the cutting edge are doing very interesting and stimulating things, the journey to get there is so long and arduous that fewer and fewer are likely to take it. No matter how appealing you may make calculus or organic chemistry, they just will never be able to compete with the endless variety of distractions in modern society. There will still be an educated elite but there won't be enough of them to keep the engine going.
The decline of the US could be very rapid. Even now, much of science and technology is being driven by foreigners. However, as the balance of power starts to shift overseas and the US remains xenophobic, that spigot could be shut off quickly. The incentive to come here will diminish and people may return to their native countries as things decline here accelerating the process.
It may be that the only hope for humanity is to maintain uneven economic development. If the entire world became comfortable simultaneously, it might completely collapse all at once. However, if the decline of the US is accompanied by the rise of China and India then at least some order in the world could be maintained. After a century or so, the US could rise again in a perpetual cycle of localized growth and decay.
Sunday, September 18, 2005
Peak Oil Production
We all know that the supply of oil is finite so the big question is how much do we have left. Geophysicist M. King Hubbert created a model of known oil reserves in 1956 and proposed that American oil production would peak between 1967 and 1972. US oil production peaked in 1971 and it's been downhill ever since. Hubbert died in 1989 but other geologists have applied his theory to global production and predict a peak between 2000 and 2010.
This month both American Scientist and Technology Review have book reviews of James Howard Kunstler's book 'THE LONG EMERGENCY: Surviving the Converging Catastrophes of the Twenty-First Century. Kunstler's thesis is that the 20th century defied Malthus because we have been living on cheap oil but when it does run out we will be in big trouble. He argues that all alternative sources of energy like solar, wind, nuclear, biofuels, hydrogen are a pipe dream that won't even come close to replacing oil. He believes that the depletion of oil will lead to social unrest and upheaval of the likes we've never seen before. The 14th century with the black death and all was pretty bad so this is really saying something.
The events of the past few weeks has sent me into a "The World is Going to End" kind of mood so I'm rather susceptible to this message. However, I think that we still have a chance to save ourselves. Conservation measures could prolong the supply of oil for say another century. This would buy us time to bring all alternative energy sources online. We will probably have to depend on nuclear power for much of it. If we're really lucky, we might get fusion to work in 50 years but that will also bring it's own set of problems. We will have to use bio-derived fuels for plastic and to power airplanes. However, our current unstainable American standard of living will decline. How far it drops is up to us.
This month both American Scientist and Technology Review have book reviews of James Howard Kunstler's book 'THE LONG EMERGENCY: Surviving the Converging Catastrophes of the Twenty-First Century. Kunstler's thesis is that the 20th century defied Malthus because we have been living on cheap oil but when it does run out we will be in big trouble. He argues that all alternative sources of energy like solar, wind, nuclear, biofuels, hydrogen are a pipe dream that won't even come close to replacing oil. He believes that the depletion of oil will lead to social unrest and upheaval of the likes we've never seen before. The 14th century with the black death and all was pretty bad so this is really saying something.
The events of the past few weeks has sent me into a "The World is Going to End" kind of mood so I'm rather susceptible to this message. However, I think that we still have a chance to save ourselves. Conservation measures could prolong the supply of oil for say another century. This would buy us time to bring all alternative energy sources online. We will probably have to depend on nuclear power for much of it. If we're really lucky, we might get fusion to work in 50 years but that will also bring it's own set of problems. We will have to use bio-derived fuels for plastic and to power airplanes. However, our current unstainable American standard of living will decline. How far it drops is up to us.
Wednesday, September 14, 2005
Math and Biology
There's a nice article on the synergy between my two favourite subjects in the December 2004 issue of PLoS Biology.
Thursday, September 08, 2005
Pitch perception and beyond
American symphony orchestras tune their instruments to A 440 Hz (in Europe they tend to go a little sharper with A 444Hz). However, no instrument produces a single frequency. Instead, they tune their instruments so that it sounds like an A. Humans can do this quite easily but if you were to look at the spectrum you would see a mess of frequencies. If you removed the fundamental frequency and just listened to the harmonics of a sound you would still identify the pitch you hear as that of the fundamental. It has always been quite puzzling as to how the brain does it. In this week's issue of Nature, a group from Johns Hopkins reports that it has found neurons in the auditory cortex of the marmoset (Callithrix jacchus) that respond to pitch, the way a human responds. These neurons will fire when the animal is presented with the pure tone fundamental or a set of harmonics without the fundamental.
This is without a doubt a very nice and illuminating piece of work but I wouldn't say it was surprising. Ever since Hubel and Wiesel discovered orientation selective neurons in the visual cortex in the late fifties and early sixties, much of systems neuroscience has been driven to providing more and more exotic stimuli and looking for neurons that respond to them. Given the data from the past forty years, I would venture that for anything which we can sense, perceive or ideate, there exists some neuron who's activity is directly correlated to that thing. That is not to say there is just one neuron that responds to some given concept. The other lesson we learned from Hubel and Wiesel is that neurons are broadly tuned over some category. Thus, for any type of perception there will be a population of active neurons.
By any type of perception, I mean all aspects of a thought. So if you are viewing a Cezanne landscape for example, there will be neurons responding to primitive elements like shapes, lines, colours and so forth. Simultaneously, there will be other neurons that respond only to more specific things like a coloured square or to a pair of adjacent coloured squares. Then there will be neurons that respond just to trees or houses and if you know enough about art just to Cezanne paintings. What we don't know is what sorts of neural architectures and learning rules can give rise to such behaviour and how all this cacophony of activity gets sorted out. While there are some candidate ideas floating around, the jury is definitely still out.
This is without a doubt a very nice and illuminating piece of work but I wouldn't say it was surprising. Ever since Hubel and Wiesel discovered orientation selective neurons in the visual cortex in the late fifties and early sixties, much of systems neuroscience has been driven to providing more and more exotic stimuli and looking for neurons that respond to them. Given the data from the past forty years, I would venture that for anything which we can sense, perceive or ideate, there exists some neuron who's activity is directly correlated to that thing. That is not to say there is just one neuron that responds to some given concept. The other lesson we learned from Hubel and Wiesel is that neurons are broadly tuned over some category. Thus, for any type of perception there will be a population of active neurons.
By any type of perception, I mean all aspects of a thought. So if you are viewing a Cezanne landscape for example, there will be neurons responding to primitive elements like shapes, lines, colours and so forth. Simultaneously, there will be other neurons that respond only to more specific things like a coloured square or to a pair of adjacent coloured squares. Then there will be neurons that respond just to trees or houses and if you know enough about art just to Cezanne paintings. What we don't know is what sorts of neural architectures and learning rules can give rise to such behaviour and how all this cacophony of activity gets sorted out. While there are some candidate ideas floating around, the jury is definitely still out.
Wednesday, September 07, 2005
Aquarium of the Americas
My favourite aquarium was the one in New Orleans. It had the most spectacular jelly fish display I have ever seen. I use the past tense because CNN reports that most of the sea creatures have died because of the power loss which shut down the water oxygenation systems. A few of the animals like the 250 pound sea turtle, the white alligator, birds, sea dragons and sea otters have survived. Another loss in this major tragedy.
Friday, September 02, 2005
Agriculture's downside
Brad De Long has posted an opinion piece from Jared Diamond arguing that agriculture, which displaced hunting and gathering as the means for sustenance, was actually humanity's greatest mistake. The article contends that agriculture promotes a much larger population with a lower quality of life for most people except for a dominating elite. In a recent post, I argued that welfare could be considered compensation for eliminating the right to forage. According to Diamond, that would hardly be a fair deal.
Fragility of civilization
The disaster unfolding before our eyes is even more troubling because it could have been mitigated in so many ways. I don't need to add anything more to the disbelief and anger spreading across the nation but it is hard not to. Among the many lessons to be drawn is that we are just a few days away from a complete breakdown of civil society. If ever there was an argument that government serves an essential role then this is it. It is quite clear who was able to get out and who was not. To blame the victims for their predicament is beyond reproach. If a city gives a mandatory evacuation order it must also provide a means for evacuation and resources for the evacuees. I can only hope that this tragedy will make us reevaluate what a just and fair civilization really means. Given that "values" was an issue in the last election I will quote directly from the bible:
The righteous is concerned for the rights of the poor; the wicked does not understand such concern. Proverbs 29:7
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?
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 venganza.org. 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.
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?
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
Fruitless
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.
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
Podcasts
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.
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?
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.
Thursday, July 28, 2005
Echinacea
The herbal supplement industry is a multi-billion dollar juggernaut. It's nice to see some of their outlandish claims finally get put to the test. The New England Journal of Medicine today reports that echinacea ( E. angustifolia root) has no effect for curing the common cold. There is a nice story in the New York Times. I'm sure adherents that swear by it (like my parents) will continue to take it but perhaps this study will put a little dent into sales.
The study took 437 volunteers, challenged them with the cold virus and randomly assigned them with pretreatment, treatment or placebo. The result was that there was no evidence that any form of treatment with echinacea had any significant effect in combating the cold or alleviating its symptoms.
The study took 437 volunteers, challenged them with the cold virus and randomly assigned them with pretreatment, treatment or placebo. The result was that there was no evidence that any form of treatment with echinacea had any significant effect in combating the cold or alleviating its symptoms.
Sunday, July 24, 2005
Phosphorus and nitrogen
The six most important elements for life are carbon, oxygen, hydrogen, nitrogen, sulfur and phosphorus. The abundances of these elements in biomass approximately mirror what is found in the earth's crust except for phosphorus which is about 6 times more abundant in biomass. However, the abundance of phosphorus in the ocean is the same as that found in biomass. This is no accident. Oceanographer Alfred Redfield found 70 years ago that the nitrogen to phosphorus ratio was 16:1 in both sea plankton and the ocean. He noted that this was not a coincidence but that the plankton was setting the ratio of the ocean. There is no intrinsic need for this ratio as plankton grown in laboratory conditions can exhibit a wide range.
The phosphorus in the ocean comes from the weathering of rocks on land. It is sequestered by oceanic life forms like plankton and then precipitates to the ocean floor when these organisms die. The availability of phosphorus sets the limit to how much life can be sustained by the ocean. This then sets the balance between oxygen and carbon dioxide in the oceans which in turn affects the balance of carbon dioxide in the atmosphere.
Now, some have argued that the increase of carbon dioxide in the atmosphere will lead to more vegetation which will counter the growth in CO2. However, more vegetation can grow only if it can acquire enough phosphorus and nitrogen. Although the atmosphere is 78% nitrogen, plants, other than legumes, cannot utilize it. They must obtain their nitrogen from the soil which mostly comes from animal waste or decaying biomass. Land animals that eat fish will transfer some nitrogen from the ocean back to the earth. The bottom line is that life on earth is precariously balanced and we really have no idea what will happen when we begin to perturb the system.
The phosphorus in the ocean comes from the weathering of rocks on land. It is sequestered by oceanic life forms like plankton and then precipitates to the ocean floor when these organisms die. The availability of phosphorus sets the limit to how much life can be sustained by the ocean. This then sets the balance between oxygen and carbon dioxide in the oceans which in turn affects the balance of carbon dioxide in the atmosphere.
Now, some have argued that the increase of carbon dioxide in the atmosphere will lead to more vegetation which will counter the growth in CO2. However, more vegetation can grow only if it can acquire enough phosphorus and nitrogen. Although the atmosphere is 78% nitrogen, plants, other than legumes, cannot utilize it. They must obtain their nitrogen from the soil which mostly comes from animal waste or decaying biomass. Land animals that eat fish will transfer some nitrogen from the ocean back to the earth. The bottom line is that life on earth is precariously balanced and we really have no idea what will happen when we begin to perturb the system.
Tuesday, July 19, 2005
Modern Living
The June issue of Smithsonian Magazine has some interesting numbers:
Median Income $8,734/year
Median Rent $108/month
Median Home $17,000
Bacon $.97/pound
Eggs $.51/dozen
Bread $.24/loaf
Vitamin D Milk $1.14/gallon
First-Class Postage Stamp $.06
Harvard College Tuition $2,600/year
Compared to 2005, the cost of food has changed surprisingly little. The price for eggs and milk have only doubled over the last 35 years while Harvard's tuition and the cost of housing has gone up by more than a factor of ten. You only have to walk down the streets of any large American city to realize that getting enough food is no longer a major problem. The problem these days is finding affordable housing and putting your kids through college.
According to a February article in Amber Waves (a USDA publication):
The List: 1970 Price Index
Gasoline $.36/gallonMedian Income $8,734/year
Median Rent $108/month
Median Home $17,000
Bacon $.97/pound
Eggs $.51/dozen
Bread $.24/loaf
Vitamin D Milk $1.14/gallon
First-Class Postage Stamp $.06
Harvard College Tuition $2,600/year
Compared to 2005, the cost of food has changed surprisingly little. The price for eggs and milk have only doubled over the last 35 years while Harvard's tuition and the cost of housing has gone up by more than a factor of ten. You only have to walk down the streets of any large American city to realize that getting enough food is no longer a major problem. The problem these days is finding affordable housing and putting your kids through college.
According to a February article in Amber Waves (a USDA publication):
Between 1952 and 2003, the ratio of food prices to the price of all other goods has fallen by 12 percent. The drop is even more dramatic if you factor in `quality improvements'—the reduced time cost of acquiring and preparing food (convenience), greater variety, and omnipresent restaurants and vending machines.Foods that once were available only seasonally are now available year-round. Advances in food processing and packaging have introduced a multitude of ready-to-eat foods, available virtually anywhere and at any time.
Harvard University's David Cutler, Edward Glaser, and Jesse Shapiro have suggested that the increase in food consumption prompted by the falling time cost of food is the major cause behind the surge in obesity since 1980. They note: "Technological innovations—including vacuum packing, improved preservatives, deep freezing, artificial flavors, and microwaves—have enabled food manufacturers to cook food centrally and ship it to consumers for rapid consumption. In 1965, a married woman who didn't work spent over two hours per day cooking and cleaning up from meals. In 1995, the same tasks took less than half the time."
Sunday, July 17, 2005
Face Cells
The June 23, 2005 issue of Nature reports work by Christof Koch and colleagues on the existence of "face recognition" cells in the hippocampus of the brain. This paper got a lot of play in the popular press because some of the cells only responded to famous people such as Halle Berry. The group found that the cells were highly selective to various views of a given person but not to another person. I think this work confirms some current theories of memory (see for example McClelland et al. Psychological Review, 102:419 (1995)). It's also more proof that there isn't much difference between humans and other mammals.
It is known that cells in the hippocampus in the rat code for spatial location in the same way. A given cell will only fire when a rat runs through a given spatial location in a given environment. When the environment changes, that same cell will then code for a completely different location. Location is important to a rat, just as the recognition of people is important to humans.
When the hippocampus is removed, humans can no longer form long term memories. They can remember things as long as they pay attention to it but once they lose their train of thought, the memory is completely gone. It is thus thought that the hippocampus is a form of mid-term memory that stores lots of information that is then slowly uploaded to the cortex for longer term storage.
It's useful to have different memory systems for different time scales because every time you remember something new you run the risk of erasing something old. One way out of this conundrum is to separate long term memory from short term memory. Simplistically, your hippocampus would store whatever information comes in and indiscriminately overwrite old information. Then slowly over time, the hippocampus would upload information to the temporal cortex (perhaps during dreams) which would update its synapses in a controlled fashion making sure not to erase important old memories.
What this paper shows is completely consistent with this idea. From theoretical work on associative memory, we know that the capacity of any neural network is limited by how correlated the stored patterns are with each other. The more correlated the patterns, the more likely they are to interfere. Thus, one way to make sure you don't overwrite old memories is to make sure the input patterns are orthogonal. The hippocampus may serve this purpose. A very sparse code, where only a few neurons encode a given concept (like Halle Berry), automatically orthogonalizes the patterns representing given memories presented to the higher cortical areas.
A sparse code is not robust because if you knock out that particular neuron you lose the memory it coded. A more robust code would be a population code where a large group of neurons encodes a given concept. The problem with this type of memory is that it's hard to train a network. So the way to overcome the trade-off between robustness and speed is to have a fast but fragile system (hippocampus) feed inputs to a slow but robust system (temporal cortex).
It is known that inferotemporal (IT) cortex of monkeys also respond to faces among many other percepts and that a given cell in IT will respond to a wide variety of images. So, if they ever get a chance to implant electrodes in the temporal cortex of humans, I'm sure they'll find similarly behaving cells.
It is known that cells in the hippocampus in the rat code for spatial location in the same way. A given cell will only fire when a rat runs through a given spatial location in a given environment. When the environment changes, that same cell will then code for a completely different location. Location is important to a rat, just as the recognition of people is important to humans.
When the hippocampus is removed, humans can no longer form long term memories. They can remember things as long as they pay attention to it but once they lose their train of thought, the memory is completely gone. It is thus thought that the hippocampus is a form of mid-term memory that stores lots of information that is then slowly uploaded to the cortex for longer term storage.
It's useful to have different memory systems for different time scales because every time you remember something new you run the risk of erasing something old. One way out of this conundrum is to separate long term memory from short term memory. Simplistically, your hippocampus would store whatever information comes in and indiscriminately overwrite old information. Then slowly over time, the hippocampus would upload information to the temporal cortex (perhaps during dreams) which would update its synapses in a controlled fashion making sure not to erase important old memories.
What this paper shows is completely consistent with this idea. From theoretical work on associative memory, we know that the capacity of any neural network is limited by how correlated the stored patterns are with each other. The more correlated the patterns, the more likely they are to interfere. Thus, one way to make sure you don't overwrite old memories is to make sure the input patterns are orthogonal. The hippocampus may serve this purpose. A very sparse code, where only a few neurons encode a given concept (like Halle Berry), automatically orthogonalizes the patterns representing given memories presented to the higher cortical areas.
A sparse code is not robust because if you knock out that particular neuron you lose the memory it coded. A more robust code would be a population code where a large group of neurons encodes a given concept. The problem with this type of memory is that it's hard to train a network. So the way to overcome the trade-off between robustness and speed is to have a fast but fragile system (hippocampus) feed inputs to a slow but robust system (temporal cortex).
It is known that inferotemporal (IT) cortex of monkeys also respond to faces among many other percepts and that a given cell in IT will respond to a wide variety of images. So, if they ever get a chance to implant electrodes in the temporal cortex of humans, I'm sure they'll find similarly behaving cells.
Subscribe to:
Posts (Atom)