Archive for the ‘Uncategorized’ Category
When I was in graduate school in the eighties, the dream job if you were in theoretical high energy physics or pure math was probably the Institute for Advanced Study in Princeton but for everyone else it was Bell Labs, on which Jon Gertner has a tribute in the New York Times today. Unfortunately for me, I never had the chance to go. Also just as I was finishing my PhD, the AT&T monopoly was being broken up and the slow decline of Bell labs had begun. Gertner points out that while we glorify silicon valley these days as the hot bed of innovation, it stilll doesn’t compare with how Bell Labs changed the world. The NIH may be the closest thing in the US right now (and it may not last) in terms of size and freedom to pursue risky projects but we’re scattered over a large campus and it can easily be months between talking to colleagues in other buildings even though it would be of great benefit to interact with them more often.
One of the big news stories last week was the publication in Science on the genomic sequence of a hundred year old Aboriginal Australian. The analysis finds that the Aboriginal Australians are descendants of an early migration to Asia between 62,000 and 75,000 years ago and this migration is different from the one that gave rise to modern Asians 25,000 to 38,000 years ago. I have often been amazed that humans were able to traverse over harsh terrain and open water into the complete unknown. However, I briefly watched a documentary on CNBC last night about Apocalypse 2012 that made me understand this much better. Evidently, there is a fairly large group of people who believe the world will end in 2012. (This is independent of the group that thought the world would end earlier this year.) The prediction is based on the fact that a large cycle in the Mayan calendar will supposedly end in 2012. According to some of the believers, the earth’s rotation will reverse and that will cause massive earthquakes and tsunamis. These believers have thus managed to recruit followers and start building colonies in the mountains to try to survive. People are taking this extremely seriously. I think this ability to change the course of one’s entire life on the flimsiest of evidence is what led our ancestors to leave Africa and head into the unknown. People will get ideas in their head and nothing will stop them from pursuing them. It’s what led us to populate every corner of the world and reshape much of the surface of the earth. It also suggests that the best optimization algorithms that seek a global maximum may be ones that have some ‘momentum’ so that they can leave local maxima and head downhill to find higher peaks elsewhere.
My old friend Ted Hsu (PhD in physics from Princeton) has been elected Member of Parliament of Kingston and the Islands in the Canadian federal election this past Monday. Ted represents a small but hopefully growing number of scientists and physicists entering public life. He’s had experience in academia and the private sector and is well positioned to make a big impact in government. Congratulations Ted!
Michael Lewis has a must-read article on the Irish economic crisis in Vanity Fair this month. The Irish situation is much, much worse then the United States. The country is in debt to the tune of a hundred billion Euros for a population that is one hundredth that of the US. This would be equivalent to the US being ten trillion dollars in debt, which is three times the US budget. Ireland had lagged behind the rest of Europe economically for most of its history and then astonishingly became one of the richest countries in the world right before the crash. It is now back to being a developing nation. The crisis was a result of an out of control real estate bubble fueled by completely irresponsible lending. Right after Lehman Brothers went under in September of 2008, the Irish banks came under extreme stress. Then in possibly one of the stupidest acts in modern history, the Irish government decided to guarantee all of the banks losses. This included both depositors and bond holders, the latter which included foreign countries and Goldman-Sachs. I think this is a sad example of how a decision based on either incomplete or fraudulent information can lead to such dire consequences. One bit changed the life of an entire nation. Here is an excerpt
Vanity Fair: Back in September 2008, however, there was evidence that he wasn’t. On September 17 the financial markets were in turmoil. Lehman Brothers had failed two days earlier, shares of Irish banks were plummeting, and big corporations were withdrawing their deposits from them. Late that evening Lenihan phoned David McWilliams, a former senior European economist with UBS in Zurich and London, who had moved back home to Dublin and turned himself into a writer and media personality. McWilliams had been loudly skeptical about the Irish real-estate boom. Two weeks earlier he had appeared on a radio show with Lenihan, and Lenihan appeared to him entirely untroubled by the turmoil in the financial markets. Now he wanted to drive out to McWilliams’s house and ask his advice on what to do about the Irish banks.
The big science news last week was the announcement and publication in Science that a strain of bacteria that lives on arsenic instead of phosphorous was discovered. Arsenic, which appears below phosphorous in the periodic table, is toxic to most life forms mostly because it is chemically similar to phosphorous. It had thus been postulated that there could be life forms that utilize arsenic instead of phosphorous. In fact, astrophysicist Paul Davies had long suggested that a proof of principle of the possibility of alien life could be obtained by finding an alternative form of life on earth. The new bacterium comes from Mono Lake in California, which is very rich in arsenic. The authors put some samples from the lake into a medium rich in arsenic but devoid of phosphorous to see what would grow and found a strain that grew robustly. They then found that arsenic was actually incorporated into the proteins and DNA within the cells. In a post from five years ago, I speculated that we might find some new organism living on toxic waste some day although this cell is probably of ancient origin. However, there has been strong criticisms of the paper since the announcement. For example see here. Hence, the jury may still be out on arsenic loving microbes.
I was in New York yesterday and gave a talk at NYU in a joint Center for Neural Science and Courant Institute seminar. My slides are here. The talk is an updated version of the talk I gave before and summarized here. The new parts include recent work on applying the model to Autism (see here) and some new work on resolving why mutual inhibition models of binocular rivalry do not reproduce Levelt’s fourth proposition, which states that as the contrast is decreased to both eyes, the dominance time of the percepts increases. I will summarize the results of that work in detail when we finish the paper.
The world’s population is nearing 7 billion and will perhaps hit 9 billion by 2050. In a previous post, I estimated that the earth could feed up to 15 billion based on the amount of arable land and current farm yields. Ever since Thomas Malthus, people have predicted that we would eventually reach saturation resulting in massive famine and global unrest. However, technology keeps coming along to make farming more and more efficient, pushing off the Malthusian crisis into the future. The green revolution led by Norman Borlaug, saved over a billion people from starvation in the mid-twentieth century. In fact, food production is so efficient now that it has led to an obesity epidemic in the developed world (e.g. see here).
The question then is what is a sustainable population. Currently, food production requires a lot of fossil fuels, which comes with its own set of issues. Scientific American recently published an article arguing that phosphorous, one of the three components of fertilizer, with nitrogen and potassium, may run out by the end of this century. Obviously, our current means of food production is not sustainable indefinitely. I think our situation is like the person walking across a railroad bridge with a train bearing down on her. She can either run towards the train or away from it to get off the bridge. Depending on the speed of the train and how fast she can run, there is a critical point on the bridge where running in one of the directions is optimal. For us, going backwards away from the train is to try to reduce population growth and try to find a sustainable level. Running towards the train is to rely on technological progress to increase food production. Given that good ideas seem to grow linearly with the population and possibly slower (e.g. see here), going towards the train actually means we should keep growing as fast as we can and hope that another Norman Borlaug comes along. Where we are on that bridge is anybody’s guess.
Now that we’re almost through the 2010 Winter Olympics in Vancouver, we have witnessed several examples of athletes excelling and underperforming. How an athlete responds to a high pressure situation could give interesting clues into the underlying neurobiology and evolutionary history of the brain. The brain has to operate under trade-offs. There is what Stephen Grossberg calls the plasticity-stability trade-off, where a system that learns must decide when to learn and when not to learn since learning involves overwriting previously learned patterns. There is also the question of how much cognitive control should be exercised. People talk about just letting their “muscle memory” takeover and go on “instinct” but what does that really mean neurobiologically? Recent research has shown that a movement resulting from a reaction is faster than one from an intention. These experiments found that people could hit buttons faster when they reacted to someone rather than when they initiated which shows that more cognitive control can make you slower.
I think it is quite clear that some athletes rise to the occasion under high pressure situations while others wilt. The question is why is there such variability. Naively, it would seem that always performing under pressure should be a good thing. The answer must be that rising to the occasion is not always optimal in an evolutionary sense. Let’s imagine in paleolithic times that you’re in a stressful situation where you’re trying to catch your dinner or are running away from something that wants you for dinner. That would be an analogous situation to a high pressure athletic event. I think that there is not always an optimal strategy. In some instances, you would want to simply run as fast as you can and being able to reach top performance would be helpful. In other instances, it may be better to hesitate and come up with a plan before acting.
The American health care system relies on a “fee for service” model, in which physicians are reimbursed for the procedures they perform. I think this is a perfect example of how organizational structure and in particular incentives can affect outcomes. Free market proponents argue that the only system that can optimally distribute goods and services is a free market. I tangentially posted on efficient markets a short time ago. However, even with a free market, the rules of the game determine what it means to win. For example, when physicians are reimbursed for procedures then it makes sense for them to perform as many procedures as possible. If it is the choice between an inexpensive therapy and an expensive one and there is no clear cut evidence for the benefit of either then why choose the inexpensive option. A provocative article in the New Yorker by Atul Gawande shows what can happen when this line of thought is taken to the extreme. Another unintended consequence of the fee for service model may be that there is no incentive to recruit individuals for clinical studies as detailed in this article by Gina Kolata in the New York Times. The interesting thing about both of these examples is that they are independent of whether health insurance is private, public or single payer. Gawande’s article was mostly about Medicare, which is government run. An alternative to fee for service is “fee for outcome”, where physicians are rewarded for having healthier patients. Gawande favours the Mayo Clinic model where the physicians have a fixed salary and focus on maximizing patient care. There must be a host of different possible compensation models that are possible, which I’m sure economists have explored. However, perhaps this is also a (critically important) problem where ideas from physics and applied math might be useful.
Olivia Judson’s blog on the New York Times today covers a topic that I have been very interested in the last five years. I really liked her post because she is one of the few people in the popular press that has questioned the thrifty gene hypothesis for the recent obesity epidemic. This theory proposed nearly 50 years ago is that we evolved during a time when food was scarce and famines were prevalent so that we are genetically optimized to pack on as much weight as we can when food is available. Hence, we are ill adapted to the modern age of plenty and as a result we are getting fat (as we should be).
Barack Obama has nominated Francis Collins to be the new Director of NIH. Here is the official announcement from the Secretary of HHS:
I am delighted to announce that, today, President Obama announced his intent to nominate Dr. Francis S. Collins to be Director of the National Institutes of Health. Dr. Collins is one of our generation’s great scientific leaders. A physician and geneticist, Dr. Collins served as Director of the National Human Genome Research Institute, where he led the Human Genome Project to completion. I hope the Senate acts quickly to confirm his nomination.
Today is Canada Day. It was July 1, 1867 when the four existing provinces of Canada were united into a single entity although still an effective colony of Great Britain. Unlike the United States, Canada gained independence slowly and gradually. The Queen is still our official head of state. Her local stand in is the Governor General of Canada. We have a beautiful national anthem that was originally written in French so the words in English are not entirely fixed. The version I hear now at hockey games is not quite the same as the one I learned as a kid. The new one is better I think. I usually don’t pay much attention to Canada Day but today for some reason I feel a bit of nostalgia for “my home and native land”.
There are three technological developments that I’ve been waiting for that could actually improve my life. The first is a letter-sized electronic reader that can hold every book and paper that I’ll ever need. Amazon Kindle is not it but a company named Plastic Logic is promising something like this soon. The second thing that I’m waiting for is a program that will read and sort my emails. It will know how to prioritize them, delete the ones I don’t need anymore, update my calendar for events and meetings, and save keepers in the correct folders (including creating folders for new topics when expedient) when I’m done reading them. (Actually, there is something like this already, known as an administrative assistant but I’m waiting for an electronic one.) It may be a (long) while before something like this is available. The third thing I’m waiting for is a remote collaboration tool. This would be something to interact with collaborators remotely that mimics the experience of standing together in front of a blackboard. Thus far, none of the things I’ve seen that are supposed to do this have gained traction with me. However, Google is coming out with something called Google Wave that may be closer to what I’m looking for. It is an online communication tool that will support latex. Terry Tao has a nice summary of how it could be useful for scientific communication on his blog.
Steve Strogatz is the guest blogger on the Wild Side on the New York Times today.
We’ve just uploaded a revised version of our paper: Systematic fluctuation expansion for neural network activity equations, by Buice, Cowan and Chow to the arXiv. Hopefully, this is more readable (especially the path integral section) than the previous version.
February 12 was the 200th anniversay of Charles Darwin and Abraham Lincoln. I’m not going to comment on either of the two directly in this post (given the large amount of press devoted to them recently) even though their impact on our lives cannot be overstated. What I do want to talk about is whether or not biology and economics can be more like physics. I will do this in two parts, with this post focusing on biology. By “not like physics”, I mean that there is not a more quantitative and unifying approach to biology. I think many physicists feel that biologists miss the big picture and that much more could be gleaned if they only started to think like physicists. This attitude is perfectly represented in biophysicist Bob Austin’s letter to Physics Today a decade ago, which can be found here. I think this view has evolved recently as more physicists work on biology but I still see it.
Although I am a former physicist, I’m going to take the side of the biologists. I’m not saying that biology couldn’t be more quantitative and better understood. I’m also not saying that ideas from physics couldn’t be useful. These are all probably true. What I am saying is that the reason biology is not more like physics isn’t because biologists are misguided (or as Bob Austin puts it “can’t reason their way out of a paper bag”) but because biology is different from physics.
Noted Harvard economist Greg Mankiw wrote an op-ed last week for the New York Times and posted to his blog, a letter to the president-elect. One of his recommendations was to listen to economists. Following up on Steve Hsu’s post on intellectual honesty, I think this exhibits an element of hubris since the majority of economists did not foresee this current financial meltdown. There were certainly those that were warning about the collapse of the housing bubble, like Robert Shiller, but other than Nouriel Roubini, I didn’t hear too much about it causing the worst crisis since the Great Depression. Even Paul Krugman admits that this took him by surprise. I could see that there was a housing bubble back in 2004, which is why I haven’t bought a house yet, but I had no idea that the bursting of a bubble could cause so much damage. The bursting of the internet bubble caused a lot of pain to some people but did not destroy the financial system.
The current crisis first became public knowledge when Bear Stearns went under in March of this year. Federal Reserve Chairman Ben Bernanke quickly engineered a buy out of Bear by JPMorgan and the market calmed for a while. Then in quick succession starting in September came the bailout of Fannie Mae and Freddie Mac, the sale of Merrill Lynch to Bank of America, the bankruptcy of Lehman Brothers, and the bailout of A.I.G. Shortly afterwards, Treasury Secretary Hank Paulson went to Congress to announce that the entire financial system is in jeopardy and requested 700 billion dollars for a bail out. The thinking was that banks and financial institutions had stopped lending to each other because they weren’t sure which banks were sound and which were on the verge of collapse. The money was originally intended to purchase suspect financial instruments in an attempt to restore confidence. The plan has changed since then and you can read Steve Hsu’s blog for the details.
Marine dead zones are regions of the ocean, usually near the mouths of rivers or waterways, which receive a large amount of nutrient (phosphorous and nitrogen) run off mostly from fertilizer. This causes a great phytoplankton and algae bloom that takes up carbon dioxide. However, when they die they sink to the ocean floor where other aerobic bacteria break them down with such vigor that they deplete the oxygen supply leaving an anoxic zone that cannot support marine life. The environmental movement is striving to curb fertilizer use in an attempt to mitigate these dead zones. There are also theories that the increase in the number of these dead zones are related to global warming.
I have a heretical thought on this regard and I haven’t been able to find any information on it so if anyone knows please enlighten me. The earth’s oxygen was originally created by cyanobacteria, which make up the algae that are causing the dead zones. So, could these dead zones actually be removing and sequestering carbon dioxide? Once the ocean bottom becomes anoxic, would the phytoplankton and algae fecal matter and remains pile upon the ocean floor and turn into fossil fuels in a few hundred million years? I don’t think we should necessarily encourage dead zones but is there any data out there that they could be mitigating global warming? I don’t want to be another one of those staunchly leftist youths going conservative in their old age so please set me straight if I’m wrong.
I’ve been trying to reconcile the current political environment in terms of a consistent framework. In particular, I’ve been interested in dissecting how issues have been divided between the so-called left and right in the United States. My premise is based on ideas set down in my previous post on the genetic basis of political orientation. In that post I proposed that the political thesis of the right is that the wealth should be distributed according to a person’s direct contribution while the left’s premise is that wealth should be distributed equitably regardless of standing in the community. I think these are fair definitions based on historical notions of the right and left. What I want to do now is to see how current issues should be divided between these positions in a perfectly rational world.
Let me first summarize some positions currently held by the US right: 1) low taxes, 2) small government, 3) deregulation of industries, 3) free trade, 4) gun rights, 5) strong military, 6) anti-abortion, 7) anti-gay rights, and 8 ) anti-immigration. I would say positions 1) through 4) seem consistent with the historical notion of the right (although regulation can be consistent with the right if it makes markets more transparent), position 5) is debatable, while positions 6) through 8 ) seem dissonant. The left generally but not always take the opposite positions except possibly on point 5), which is mixed. The strong military position was understood as a right wing position during the Cold War because of the opposition to communism. The rationale for a strong military waned after the fall of the Soviet Union but 9/11 changed the game again and now the military is justified as a bulwark against terrorism (more…)