Wednesday, March 30, 2005

Krakatoa and the Tsunami of 2004

The southern coast of Indonesia is one of the most active tectonic zones in the world because the Indian plate is subducting beneath the Burma microplate. This was borne out tragically in the Aceh-Andaman earthquake and Tsunami of 2004. In this week's Nature, Stein and Okal argue that the magnitude of that earthquake was 2.5 times greater than previously thought and should have been a 9.3 instead of a 9.0. Just this past Monday, another earthquake of 8.7 magnitude struck southern Sumatra. Fortunately, this one was in shallower water so much less water was displaced and thus no Tsunami was generated.

It was over a century ago, on August 27, 1883, that the volcano Krakatoa exploded nearby. The volcano was part of an island consisting of three main cones in the straight between Sumatra and Java. It stood nearly 800 metres high and had a diameter of 15 kilometres. Two of the cones were completely blown apart in the eruption. The Tsunami generated was estimated to be 40 metres high although it was of short wavelength so it didn't travel very far. It did kill 36,000 people in southern Sumatra and western Java. It carried a steamship 2 miles inland. The explosion was so loud it was heard as far away as Perth Australia and the atmospheric shock wave travelled around the world seven times. There were brilliant red sunsets for five years afterwards due to the 21 cubic kilometres of material thrown up.

The eruption was extremely well documented by the scientists of the day. The field of volcanology was invented to understand why the eruption was so violent. The current theory is that Krakatoa had been dormant for 200 years before the 1883 eruption and this allowed the magma to cool inside the volcano. About four months before the August eruption, Krakatoa became active and this cool magma escaped in a series of minor eruptions. It was then replaced by hot magma from below. The entering hot new magma heated up the remaining cool old magma releasing gases and built up tremendous pressure which was released in a massive explosion equivalent to 21,000 megatons of TNT. The amazing thing is that a new volcano has almost entirely replaced the old one. In just a hundred years, Anak Krakatau (child of Krakatoa) has risen to a height of 300 metres and is still growing. It is not expected to explode like it's parent in the near future but given recent events one never knows.

Monday, March 28, 2005


Scott Sandage, an associate professor in history at Carnegie Mellon University, has recently penned a book entitled - Born Losers - A History of Failure in America. An interesting fact that Sandage points out is that the concept of being a failure as a human being did not exist until the late nineteenth century. Prior to that, failure was only used to imply bankruptcy, a circumstance that did not necessarily imply any personal deficiency. Unlike today where a lack of ambition and vision is synonymous with being a loser, it was perfectly fine to be satisfied with one's lot. Social climbers, like Becky Sharp in Vanity Fair, were considered crass.

Sandage finds that the Civil War may have been a turning point. Prior to the war, America divided itself into citizens and slaves. However, after the war, the division changed to winners and losers. It was also a time where the robber baron class arose. These were usually self-made men such as Carnegie, Mellon and Rockefeller who rose to prominence in a burgeoning industries such as steel, banking and oil. They also defined success in American as earned (plundered?) wealth. This attitude is probably even more apparent today. It is only in America (until recently perhaps) that being called aggressive was a compliment. I'm not suggesting that we all return to a society without ambition but perhaps defining ourselves exclusively in terms of our achievements and finances may not be the most satisfying way to live.

Friday, March 25, 2005

Jurassic Park

The possibility of resurrecting extinct animals some day in the future may not be as far fetched as previously thought. A paper in this week's Science reports that soft tissue from a 70 million year old Tyrannosaurus Rex was found in Montana. The specimen contained blood vessels and possibly cells. Finding pieces of DNA is a long shot but remains a remote possibility.

In fact, extracting DNA from extinct animals is becomng more common A recent article in PLOS Biology reviews the many ways that ancient DNA has been used to ask questions about population genetics in the past. It is probably not surprising that there are signs that our current descriptions of the evolutionary process based on the fossil record and modern DNA is far too simple. Since DNA is a fragile molecule, most studies are limited to DNA less than 60,000 years old. However, that's still old enough to get some interesting information. The hardest thing to prove is that the sample is not contaminated with modern DNA.

Thursday, March 17, 2005

The X chromosome

This week's Nature has a picture of the X chromosome on the cover. The issue has two articles on the topic. The first contains an analysis of the recently completed sequence. As I wrote before on the Y chromosome, women have two copies of the X. Previously, it had been thought that one was suppressed and the other is expressed. In the second paper, it is shown that about 15% of genes are still expressed on the inactive chromosome. The same genes on the active chromosome are also expressed so this could mean that more of the protein is produced. This could provide a basis for the differences between individual women and for this month's hot button topic - the differences between women and men.

Ironically, the X chromosome may actually be more important for men than for women. Since men only have one X, any advantageous mutation for men will we be selected for strongly even if it is somewhat deleterious for women. Conversely, a deleterious mutation will be strongly selected against. It has been proposed by Horst Hameisterat of the University of Ulm in Germany that females may be responsible for intelligence in humans. His group proposes that early females had a preference for intelligence and if the genes for superior intelligence and the preference for intelligence are found near each other then they would be selected together and this could lead to an instability because both lead to enhanced survival. It had been known for some time that many of the genes related to mental retardation are found on the X and now it is confirmed that there are many crucial genes on the X for neural development. Hence, the X could be what makes humans human.

Tuesday, March 15, 2005


Congress has subpoenaed seven baseball players to testify about steroid use in major league baseball. This is a result of the recent BALCO scandal that implicated sprinter Marion Jones, Barry Bonds, Jason Giambi among others and the recent publication of Jose Canseco's book alleging steroid use by several stars including Mark McGwire. Given the current debates on our fiscal crisis, the Iraqi war, social security, the Arctic National Wildlife Refuge, North Korea, outsourcing and so on, aren't there more important things for Congress to do? I love sports and baseball as much as the other guy but come on it's just a game.

I believe that international sporting bodies must accept that medical enhancement will only increase in the future and there is virtually no chance to completely stop it. If they ever get gene therapy to work we'll be in real trouble. I think testing for cheating is the wrong strategy. What we will eventually need to do is to set physiological standards that athletes cannot exceed. So everyone is allowed up to some level of testosterone, human growth hormone, myostatin, red blood cells and so forth. You can do whatever you want to get to these standards but you can't go beyond. I suppose those that exceed the standards "naturally" would be able to petition the governing body to obtain an exemption. I agree that this would take away something from sport but in some sense it also levels the playing field. After all, isn't being born with better genes an advantage?

Sunday, March 13, 2005

Dyson's take on evolution

Freeman Dyson always has something interesting to say on most topics. In the March issue of Technology Review he summarizes Carl Woese's idea about the end of Darwinian evolution due to bioengineering. I don't think we've stopped evolving since we're still battling microbes but the thought is intriguing and terrifying.
Carl Woese published a provocative and illuminating article, A New Biology for a New Century, in the June 2004 issue of Microbiology and Molecular Biology Reviews. His main theme is the obsolescence of reductionist biology as it has been practiced for the last hundred years, and the need for a new biology based on communities and ecosystems rather than on genes and molecules. He also raises another profoundly important question: when did Darwinian evolution begin? By Darwinian evolution he means evolution as Darwin himself understood it, based on the intense competition for survival among noninterbreeding species. He presents evidence that Darwinian evolution did not go back to the beginning of life. In early times, the process that he calls horizontal gene transfer, the sharing of genes between unrelated species, was prevalent. It becomes more prevalent the further back you go in time. Carl Woese is the worlds greatest expert in the field of microbial taxonomy. Whatever he writes, even in a speculative vein, is to be taken seriously.

Woese is postulating a golden age of pre-Darwinian life, during which horizontal gene transfer was universal and separate species did not exist. Life was then a community of cells of various kinds, sharing their genetic information so that clever chemical tricks and catalytic processes invented by one creature could be inherited by all of them. Evolution was a communal affair, the whole community advancing in metabolic and reproductive efficiency as the genes of the most efficient cells were shared. But then, one evil day, a cell resembling a primitive bacterium happened to find itself one jump ahead of its neighbors in efficiency. That cell separated itself from the community and refused to share. Its offspring became the first species. With its superior efficiency, it continued to prosper and to evolve separately. Some millions of years later, another cell separated itself from the community and became another species. And so it went on, until all life was divided into species.

The basic biochemical machinery of life evolved rapidly during the few hundred million years that preceded the Darwinian era and changed very little in the following two billion years of microbial evolution. Darwinian evolution is slow because individual species, once established, evolve very little. Darwinian evolution requires species to become extinct so that new species can replace them. Three innovations helped to speed up the pace of evolution in the later stages of the Darwinian era. The first was sex, which is a form of horizontal gene transfer within species. The second innovation was multicellular organization, which opened up a whole new world of form and function. The third was brains, which opened a new world of cordinated sensation and action, culminating in the evolution of eyes and hands. All through the Darwinian era, occasional mass extinctions helped to open opportunities for new evolutionary ventures.

Now, after some three billion years, the Darwinian era is over. The epoch of species competition came to an end about 10 thousand years ago when a single species, Homo sapiens, began to dominate and reorganize the biosphere. Since that time, cultural evolution has replaced biological evolution as the driving force of change. Cultural evolution is not Darwinian. Cultures spread by horizontal transfer of ideas more than by genetic inheritance. Cultural evolution is running a thousand times faster than Darwinian evolution, taking us into a new era of cultural interdependence that we call globalization. And now, in the last 30 years, Homo sapiens has revived the ancient pre-Darwinian practice of horizontal gene transfer, moving genes easily from microbes to plants and animals, blurring the boundaries between species. We are moving rapidly into the post-Darwinian era, when species will no longer exist, and the evolution of life will again be communal.

In the post-Darwinian era, biotechnology will be domesticated. There will be do-it-yourself kits for gardeners, who will use gene transfer to breed new varieties of roses and orchids. Also, biotech games for children, played with real eggs and seeds rather than with images on a screen. Genetic engineering, once it gets into the hands of the general public, will give us an explosion of biodiversity. Designing genomes will be a new art form, as creative as painting or sculpture. Few of the new creations will be masterpieces, but all will bring joy to their creators and diversity to our fauna and flora

Thursday, March 10, 2005

Cold Spring

The weather has not been kind for us on the east coast these past few weeks. After a reasonably mild winter, late winter/early spring has been filled with snow, cold, and more snow. There may be a silver lining to this though. Here is my completely unsubstantiated account of North American weather patterns.

Anyone who watches the weather channel knows that when it is cold on the east it's because a cold front has moved in from Canada. I heard it being called an Alberta Clipper this morning. The atmosphere gets warmed or cooled primarily through contact with the ground since solar radiation mostly passes through the air and is absorbed by the ground. In the winter and spring, the air over north western Canada is cold while the air over the Gulf of Mexico and the southern US is mostly warm. Thus a pressure gradient can arise with high pressure in Canada and low pressure in the southern US. This causes air to flow from north to south.

Now all that air coming down must go somewhere so it makes it's way up the Atlantic coast and returns to the arctic. Along the way, it picks up warmth and moisture which often ends up as snow in New England. Hence, the more cold air there is coming from the north, the more warm air there will be returning to the arctic. This should then lessen the temperature and pressure gradient between the north and the south. So, perhaps a cold late winter may actually lead to a milder late spring.

Monday, March 07, 2005

Hans Bethe

Yesterday marked the passing of Hans Bethe, the last of the great physicists from the Manhattan Project. I had the privilege of seeing Bethe speak twice when I was a graduate student at MIT in the late 1980's. Bethe was in his early eighties at the time and was still sharp as a tack. One talk was on neutrino oscillations and the other was on disarmament policy. Both talks were well thought out and exhibited the clear thinking that marked Bethe's career.

The amazing thing about Bethe was that he remained relevant for much of the twentieth century. Bethe was held in the highest regard by both his peers and the political establishment throughout his life. He was Sommerfeld's graduate student. His Nobel Prize work on energy production in stars was done in 1938. He played an important role in the development of QED and was Richard Feynman's mentor. He was instrumental in pushing for arms limitation treaties and derailing the Star Wars space-based anti-missile defense during the Reagan administration. He and John Bahcall wrote a landmark paper outlining how the solar neutrino problem was finally solved in 1990. He was a true giant among giants.

Friday, March 04, 2005

The Y chromosome

DNA is packaged into discrete units called chromosomes. The chromosomes come in pairs with one from the mother and one from the father. There does not seem to be any rhyme or reason to the number of chromosomes a species may have. For example, humans have 23 pairs, the other three great apes have 24 pairs, mice have 21 and horses have 32. It appears that during the course of evolution chromosomes can undergo fission and fusion or be lost altogether.

It is not necessary for two species to have the same number of chromosomes to produce fertile offspring. For example, Przewalski's wild horse has 33 pairs yet when crossed with a domesticated horse with 32, the offspring are fertile and can mate with other domesticated horses (Chandley AC, Short RV, Allen WR, J Reprod Fertil Suppl 23:356-70, 1975). What happens is that two of the chromosomal pairs from the wild horse fuse in a process called Robertsonian translocation. This can happen in humans as well and some people are walking around with 45 chromosomes.

The X and Y chromosomes determine sex. Females have two X chromosomes and males have an X and a Y. While female offspring will obtain an X chromosome from each of their parents, male offspring will always inherit their father's Y chromosome. So mutations in the Y chromosome will always get passed on and thus can accumulate. Jennifer Graves of the Australian National University, believes that the Y chromosome is rapidly shrinking and may disappear altogether. The basis of her claim is from comparing the genomes of various mammals. For example, she has found that kangaroos diverged from humans 180 million years ago and the platypus 210 million years ago. These mammals also have analogues to human sex chromosomes. In the last 300 million years the Y has lost most of its original genes. She estimates that the remaining genes have about 10 million more years to go. Hence to avoid extinction, humans may need to evolve into a new hominid species.

There is some dissent though. David Page of the Whitehead Institute has discovered 78 genes on the Y (about twice as much as previously believed) and there could be more. He also found palindromic sequences so there could be some redundency. The Y might be able to repair errors by taking hairpin configurations. So are we men on our last legs? I guess we'll have to wait to see.

Wednesday, March 02, 2005

Out on the tail

As the world's population gets larger, should we expect more Newtons, Mozarts and Tiger Woods or should we expect fewer? By this, I mean should the gap between the best in a field and the second best, be larger than the gap between the second best and the rest? If you presume that the aptitude level of people for some enterprise is normally distributed then the answer is no. The probability to be between n standard deviations and n+1 standard deviations above the mean decreases exponentially. As you go out onto the tail, the probability of someone being a standard deviation better than you is decreasing very quickly. Thus we should see a lot of people bunched near the top.

So why is it that we have Tiger Woods? Tiger is dominating golf like no one since perhaps Bobby Jones in the twenties and Ben Hogan in the early fifties. He was more dominant over a stretch of five years than Jack Nicklaus ever was although his dominance declined slightly last year. There are many more golfers now then there were fifty years ago so if anything we should see a much more competitive environment. Except for Woods and perhaps Vijay Singh, this is true as there is very little separating the rest. Dominance is not just limited to golf. Ten years ago we had Michael Jordan in basketball and Wayne Gretzky in hockey. Right now we have Barry Bonds in baseball and Lance Armstrong in cycling. These people are dominating or have dominated their sports as much or more than anyone else before.

Part of the reason is surely that a normal distribution is a bad approximation for the tail. Anyone in finance certainly knows this. The central limit theorem does not converge uniformly over the entire range, so even though the bulk is well described by a normal distribution, the tail can still experience low number statistics. Thus as the population increases, more of the tail gets sampled and that could actually increase the probability of rare events not decrease it as would be expected. So my prediction is that we will see more dominant athletes in the future.

Now what about physics and music? By this argument we should see more anomalies in these areas as well. However, it is not clear who is the Newton of our day. Ed Witten maybe? I think the reason is that there are fewer objective measures of mastery in these areas as compared to sports. A lot of what leads to great impact in physics is the choice of problem. In this case, there is a greater element of luck. One could be way out on the tail in terms of sheer brilliance (if that can even be measured) but not have a great impact if they worked in a dead end field. In this case, physics may suffer from low number statistics in the bulk and the tail so there will be no correlation of dominance with population size.

Music has a similar problem. Who in the 20th century compared to Mozart? Diatonic Western classical music reached its acme with Mahler. After that, composers either became atonal or "popular". The 20th century was the century of performers. Perhaps if Rubenstein, Heifetz, or Yo Yo Ma was born in the 18th century they would have been great composers. The playing field changed in the 20th century so the question of dominance became more difficult to answer. In 200 years, we may look back at the 20th century and consider a Jazz or Rock musician to be the Mozart of the day.