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.
Wednesday, May 25, 2005
Value
I am finally starting to recover enough from my recent wedding and honeymoon to start posting again. The June 2005 issue of Technology Review covers the topic of Intellectual Property. There is a debate between Lawrence Lessig who believes that new laws governing copyright known as "digital rights management" (DRM), will undermine creativity and culture and Richard Epstein who thinks we need strong copyright laws to protect creators who add value to society.
I think this issue revolves on how we should value things in our society. The music and film industry is very worried about digital piracy. CD sales have gone down since illegal downloading of music became prevalent. I think that it will be impossible to fully stop it. Will this be the end of music? No, but I think it will be the end of powerful record companies who restrict the supply of recording artists so the prices can remain high. The argument is that making a record is expensive and they prescreen for quality. However, with inexpensive recording software like Apple's GarageBand and the internet, anyone can make a record now. The old model will become obsolete.
I can see two models for how artists might support themselves in the future. One is that they distribute their music for free or for a low fee and make money on concerts. The Grateful Dead has used this model for years. Classical and jazz musicians basically make their money from performances. The second is that we could re-establish a system of patronage for the arts. Artists would be paid a salary and their music would be given away for free. This last model is essentially the model for science. Scientists have jobs in research labs or universities and their work is given away for free.
In either model, the millionaire recording artist will become extinct. However, this won't change the lives of that many people. In the current system, only a handful of lucky people "make it" and become incredibly rich while everyone else waits on tables. What separates the people often has little to do with talent. It always seemed rather unfair to me that the world's greatest harmonica player is probably just getting by while a well marketed, lip synching pop star with little talent makes millions.
The motion picture industry does have an argument that films cost a lot to make and thus they need to be compensated. However, I think people will always want to see movies on the big screen. VCR's and DVD's have not reduced ticket sales. What will likely happen here is that more and more pictures will become digital and movie stars may become obsolete. Actors may only be necessary for live theatre.
Even in this world, I'm sure there will still be those that rise to be top and become stars. They may not be as well compensated as they are today but they will be as popular and probably a lot happier.
I think this issue revolves on how we should value things in our society. The music and film industry is very worried about digital piracy. CD sales have gone down since illegal downloading of music became prevalent. I think that it will be impossible to fully stop it. Will this be the end of music? No, but I think it will be the end of powerful record companies who restrict the supply of recording artists so the prices can remain high. The argument is that making a record is expensive and they prescreen for quality. However, with inexpensive recording software like Apple's GarageBand and the internet, anyone can make a record now. The old model will become obsolete.
I can see two models for how artists might support themselves in the future. One is that they distribute their music for free or for a low fee and make money on concerts. The Grateful Dead has used this model for years. Classical and jazz musicians basically make their money from performances. The second is that we could re-establish a system of patronage for the arts. Artists would be paid a salary and their music would be given away for free. This last model is essentially the model for science. Scientists have jobs in research labs or universities and their work is given away for free.
In either model, the millionaire recording artist will become extinct. However, this won't change the lives of that many people. In the current system, only a handful of lucky people "make it" and become incredibly rich while everyone else waits on tables. What separates the people often has little to do with talent. It always seemed rather unfair to me that the world's greatest harmonica player is probably just getting by while a well marketed, lip synching pop star with little talent makes millions.
The motion picture industry does have an argument that films cost a lot to make and thus they need to be compensated. However, I think people will always want to see movies on the big screen. VCR's and DVD's have not reduced ticket sales. What will likely happen here is that more and more pictures will become digital and movie stars may become obsolete. Actors may only be necessary for live theatre.
Even in this world, I'm sure there will still be those that rise to be top and become stars. They may not be as well compensated as they are today but they will be as popular and probably a lot happier.
Wednesday, April 27, 2005
Suspended animation
In the April 22 issue of Science, a group from the Fred Hutchinson Cancer Center reports that a state of suspended animation can be achieved in (nonhibernating) mice when administered hydrogen sulfide (H2S). H2S is a reversible inhibitor of oxidative phosporylation. It is known that this induces hibernation in some animals.
When the mice were exposed to 80 ppm of H2S, their oxygen consumption dropped by 50% in the first 5 minutes. After 6 hours, their metabolic rate dropped by 90% and the core body temperature reached 15 degrees Celsius where the ambient temperature was 13 degrees. When the mice were returned to room air and temperature, their metabolic rate and body temperature returned to normal.
If this works in humans, we may now have a means of reducing metabolic demand after traumatic injury or surgery. H2S may become a standard part of the repertoire of paramedics. I won't bother to dwell on the space travel implications.
Hydrogen sulfide is the gas emitted by volcanos and geysers responsible for the rotten egg smell. It is usually considered toxic but now you know that if you see someone looking lifeless at the edge of a volcano, make sure to pull them out because they may note be dead but just be in a state of suspended animation.
When the mice were exposed to 80 ppm of H2S, their oxygen consumption dropped by 50% in the first 5 minutes. After 6 hours, their metabolic rate dropped by 90% and the core body temperature reached 15 degrees Celsius where the ambient temperature was 13 degrees. When the mice were returned to room air and temperature, their metabolic rate and body temperature returned to normal.
If this works in humans, we may now have a means of reducing metabolic demand after traumatic injury or surgery. H2S may become a standard part of the repertoire of paramedics. I won't bother to dwell on the space travel implications.
Hydrogen sulfide is the gas emitted by volcanos and geysers responsible for the rotten egg smell. It is usually considered toxic but now you know that if you see someone looking lifeless at the edge of a volcano, make sure to pull them out because they may note be dead but just be in a state of suspended animation.
Tuesday, April 12, 2005
Mathematical Biology
I am the first to admit that I'm not sure how much mathematics and theory has contributed to biology. Certainly the buzz is there. With the reams of data generated by the human genome project, biologists are begining to realize that they could use some help to understand all of this new data. The result has been a surge of available grant money and a flood of physicists, computer scientists and mathematicians into the field. (For the record, I made the jump over ten years ago when it was less fashionable.) I think it's safe to say that the jury is still out on whether or not the hype has been justified.
However, there has been one instance where mathematics has made a major difference and that is in the development of the triple cocktail treatment for HIV-AIDS. HIV is a particularly insidious virus because it attacks CD4 T cells of the immune system. However, it is rather slow acting. So often, when a person is infected with HIV, their virus load will remain low and CD4 counts will remain relatively high for a long period of time. Then, suddenly, the CD4 count will plummet and they will lapse into fully developed AIDS. It was first assumed that the virus replicated slowly and then accelerated at some point.
In the early 90's, David Ho and his group were testing treatments for HIV infection and decided that mathematically modeling the virus dynamics may give clues as to what was really happening. So they called in Los Alamos biological physicists Alan Perelson and Avidan Neumann (who is currently visiting our lab at NIH) to see if anything could be inferred about the virus. They used simple models of just a few ordinary differential equations to fit to the virus load during perturbation experiments where a potent protease inhibitor was administered.
Their simple model showed that the virus was far more active than previously believed. During the quiet phase where virus loads were low, the virus was actually replicating very rapidly but the immune system was running at high speed to compensate. Full blown AIDS developed when the immune system wore out and could no longer keep up with the virus. The implication was that any anti-viral treatment that targeted a single specific mechanism would fail because the virus would quickly evolve a defense. Thus the triple cocktail was invented. The virus would then need to evolve three separate defenses and this was difficult enough to keep it at bay. The results were published in two deservedly celebrated papers - the first in Nature in 1995 and the second in Science in 1996. I think their achievement represents the best example of how theoretical ideas can be useful in biology.
However, there has been one instance where mathematics has made a major difference and that is in the development of the triple cocktail treatment for HIV-AIDS. HIV is a particularly insidious virus because it attacks CD4 T cells of the immune system. However, it is rather slow acting. So often, when a person is infected with HIV, their virus load will remain low and CD4 counts will remain relatively high for a long period of time. Then, suddenly, the CD4 count will plummet and they will lapse into fully developed AIDS. It was first assumed that the virus replicated slowly and then accelerated at some point.
In the early 90's, David Ho and his group were testing treatments for HIV infection and decided that mathematically modeling the virus dynamics may give clues as to what was really happening. So they called in Los Alamos biological physicists Alan Perelson and Avidan Neumann (who is currently visiting our lab at NIH) to see if anything could be inferred about the virus. They used simple models of just a few ordinary differential equations to fit to the virus load during perturbation experiments where a potent protease inhibitor was administered.
Their simple model showed that the virus was far more active than previously believed. During the quiet phase where virus loads were low, the virus was actually replicating very rapidly but the immune system was running at high speed to compensate. Full blown AIDS developed when the immune system wore out and could no longer keep up with the virus. The implication was that any anti-viral treatment that targeted a single specific mechanism would fail because the virus would quickly evolve a defense. Thus the triple cocktail was invented. The virus would then need to evolve three separate defenses and this was difficult enough to keep it at bay. The results were published in two deservedly celebrated papers - the first in Nature in 1995 and the second in Science in 1996. I think their achievement represents the best example of how theoretical ideas can be useful in biology.
Wednesday, April 06, 2005
A new new world order
An excerpt from Thomas Friedman's book "The World Is Flat: A Brief History of the Twenty-First Century" appeared in last Sunday's New York Times magazine. The premise is that the information age has truly arrived and now people all over the world can compete on equal terms. Steve Hsu summarizes the idea in his blog. The tone of Friedman's excerpt and Hsu's posts is that the Chinese, the Indians, and the Russians are coming and we better get ready for the new competition. America's dominance over the world is beginning to decline and if we don't recognize it now our standard of living will fall with it as our wealth starts to diffuse across the globe.
I certainly believe this is happening and it is unavoidable. Improving our educational system or motivating our citizens won't solve the real problem and that is the US only constitutes five percent of the world's population and if life were fair, it should have only five percent of the wealth. Even given that life is not fair, having only five percent of the world's population means that we only have five percent of the brightest, most innovative, and most energetic people to create the wealth for the future. Eventually, things will equalize. It's a battle we just can't win.
So what should we do? One solution is to bring the rest of the world up to our economic level. Unfortunately, I don't think a world where everyone lives like an American is sustainable. See my estimate of energy use from a previous post. A possible scenario is that as the world catches up and begins to compete for scarcer and scarcer resources, the pecking order will be sorted out through military means. I truly hope we are sane enough to avoid that fate. My deluded, quasi-utopian vision, is that we all scale back and share. The pessimistic nihilist in me says that won't happen in my lifetime.
I certainly believe this is happening and it is unavoidable. Improving our educational system or motivating our citizens won't solve the real problem and that is the US only constitutes five percent of the world's population and if life were fair, it should have only five percent of the wealth. Even given that life is not fair, having only five percent of the world's population means that we only have five percent of the brightest, most innovative, and most energetic people to create the wealth for the future. Eventually, things will equalize. It's a battle we just can't win.
So what should we do? One solution is to bring the rest of the world up to our economic level. Unfortunately, I don't think a world where everyone lives like an American is sustainable. See my estimate of energy use from a previous post. A possible scenario is that as the world catches up and begins to compete for scarcer and scarcer resources, the pecking order will be sorted out through military means. I truly hope we are sane enough to avoid that fate. My deluded, quasi-utopian vision, is that we all scale back and share. The pessimistic nihilist in me says that won't happen in my lifetime.
Tuesday, April 05, 2005
The North Pole
The earth's magnetic field is generated by the motion of molten iron in the earth's core. The combination of convection and coriolis forces generates the right set of currents to establish a dipole field with the north and south poles approximately in line with the rotational north and south poles. We partially owe our existence to this magnetic field because it provides a shield against charged particles from the solar wind. Without it, we would be subject to ionizing radiation and may also lose our atmosphere.
Neither Mars nor Venus has a significant magnetic field and we're not fully sure why. Mars once had a thick atmosphere of CO2 that may have been blown away by the solar wind. It could be that the molten iron has solidified or that the pattern of flow no longer supports a magnetic field. In any case, I think the lack of a field on Mars should make us less secure that we'll always have ours.
The earth's dipole flips every 250,000 years on average. We're not exactly sure why but some recent magnetohydrodynamic simulations of the geodynamo have shown examples of field reversals due to instabilities in the turbulent flow. It's been 780,000 years since the last reversal so we may be due for another one soon. It will take approximately 4,000 to 10,000 years for a reversal to take place. During the transition, the magnetic field may lose its intensity as well as its dipole structure which may have implications for life on the earth.
Another consequence of the turbulent geodynamic flow is that the north pole is in constant motion. It usually moves about ten kilometres a year but recently it has been moving forty! If it keeps moving at this rate, in about fifty years it will leave Canada and reach Siberia. This increased speed of drift of the north pole may be nothing more than natural random variations but it definitely makes me worry just a little.
Neither Mars nor Venus has a significant magnetic field and we're not fully sure why. Mars once had a thick atmosphere of CO2 that may have been blown away by the solar wind. It could be that the molten iron has solidified or that the pattern of flow no longer supports a magnetic field. In any case, I think the lack of a field on Mars should make us less secure that we'll always have ours.
The earth's dipole flips every 250,000 years on average. We're not exactly sure why but some recent magnetohydrodynamic simulations of the geodynamo have shown examples of field reversals due to instabilities in the turbulent flow. It's been 780,000 years since the last reversal so we may be due for another one soon. It will take approximately 4,000 to 10,000 years for a reversal to take place. During the transition, the magnetic field may lose its intensity as well as its dipole structure which may have implications for life on the earth.
Another consequence of the turbulent geodynamic flow is that the north pole is in constant motion. It usually moves about ten kilometres a year but recently it has been moving forty! If it keeps moving at this rate, in about fifty years it will leave Canada and reach Siberia. This increased speed of drift of the north pole may be nothing more than natural random variations but it definitely makes me worry just a little.
Friday, April 01, 2005
Engineers in Government
Ever wonder why science and engineering policy doesn't make much sense. Here's an article from this month's Technology Review that may give a reason why.
Engineers and Political Power
by Ed Tenner, April 2005
In the united states, engineers don’t rule. According to a Congressional Quarterly survey of the 109th Congress, there are just four engineers in the House and one in the Senate. When the engineering specialties in the 2004–2005 Statistical Abstract of the United States are combined, there are 2.12 million engineers in the U.S. versus 952,000 lawyers and 819,000 doctors; yet 10 physicians now sit in the House and two in the Senate, and CQ lists 160 representatives and 58 senators with legal backgrounds.
One explanation for those discrepancies is that rapid technological change makes it hard for engineers to return from political office to professional life. In a 1992 interview with Technology Review, John H. Sununu, President George H. W. Bush’s chief of staff, acknowledged that as a consulting mechanical engineer, he was lagging ten years behind the field. Physicians, however, face equally great problems keeping up with the latest research, and by entering public service, they often forgo even greater potential income.
Another theory is that engineers are self-selected for social distance. Sylvia Kraemer is an intellectual historian who became a senior NASA official and interviewed 51 colleagues for her insightful study NASA Engineers and the Age of Apollo. She found that lab engineers and those promoted into management endorsed the reputation of awkwardness. A manager declared that most engineers "wouldn’t recognize an emotion if it hit them in the face." One rocket engineer flatly acknowledged, "I related to things."
This is an old American stereotype. In The Engineers and the Price System, the maverick economist Thorstein Veblen, championing what was later called technocracy, wrote that the public considered engineers a "somewhat fantastic brotherhood of overspecialized cranks, not to be trusted out of sight except under the restraining hand of safe and sane businessmen." He added, "Nor are the technicians themselves in the habit of taking a greatly different view of their own case."
But in many other cultures, especially in Eastern Europe, Asia, and the Middle East, engineers have been in the thick of power. The’ve been prominent in Marxist movements, such as the brief Hungarian Communist revolution of 1919. They became influential enough in the early Soviet Union that Stalin directed one of his first purges against them. Later, scientists and engineers were put to work in the gulags’ special research prisons, the sharashkas. After Stalin’s death, engineering degrees became desirable credentials for the politically ambitious. As the historian Kendall Bailes wrote in 1974, "What lawyers and businessmen are in the American political system—the major professional groups from which most politicians and policymakers are recruited—men with engineering backgrounds have become to a large extent in the Soviet Union."
In 2004, almost all two dozen members of China’s ruling Politburo had engineering degrees, including all nine members of the Politburo’s Standing Committee. In the Middle East, prominent engineers fill the political spectrum, from former president Süleyman Demirel of Turkey to the members of the Society of Muslim Engineers, pillars of the ayatollahs’ Iran, to the late secular nationalist Yasser Arafat. In many countries, engineering appeals -to the civic minded. On the other hand, disaffected young men recruited in European engineering schools were prominent among the September 11 hijackers. As R. Scott Appleby and Martin E. Marty observe in Foreign Affairs, "fundamentalists tend to read scriptures [as] engineers read blueprints—as a prosaic set of instructions and specifications." Civil engineer Osama bin Laden surely did.
Globally, then, the unpolitical Anglo-American nerd is the exception. The argument that gained credence in 19th-century France and was echoed in other regimes is that a state must be guided by a scientific and technological elite. Two forces kept that notion from taking hold in the United States. The first was American suspicion of central government. The second was industry’s appetite for engineers; at the turn of the 20th century, U.S. companies fearing manpower shortages resisted attempts to make elite postgraduate degrees the norm for engineers, as they were becoming for lawyers, doctors, and executives. So engineers in this country continue to design and implement everything but our laws.
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