It's been a hectic 72 hours. On Wednesday I gave a colloquium at the Perimeter Institute (in Waterloo, Ontario). Later I had dinner with Fotini Markopoulou and Lee Smolin at a great restaurant called Jane Bond; we talked about quantum mechanics. Thursday morning I got up early and rented a car. Waiting for the car rental company to pick me up, I ran into Jeffrey Bub, who turned out to have given a talk on Tuesday about the the importance of our inability to duplicate quantum information - also a theme of my talk. He'd asked a good question at my talk, but I hadn't recognized him!
Anyway, I drove an hour and a half to the University of Western Ontario (in London, Ontario) where I spoke to Dan Christensen about homotopy theory and gave a lecture on where we stand in fundamental physics. I had dinner at a Thai restaurant with Dan, his student Igor Khavkine and his postdoc Josh Willis. We talked about spin foam models, especially Josh's new paper. I spent the night in a hotel in London, and today (Friday) I had breakfast with Dan and we talked more about our joint math projects. Then I drove back to Waterloo, took a cab to Toronto, and flew to Boston.
Insane, really - I'm not really practiced enough to stay completely calm while trying to make so many connections. I easily imagine all the things that could go wrong. But it all somehow worked, despite getting lost about 4 times while driving to London, and a flight delay due to thunderstorms in Boston.
Now I'm in Cambridge Massachusetts, in Kendall Square - right next to my old grad school, MIT. I'm here for some top-secret business that I've love to talk about, but can't. I'm staying at the Kendall Hotel. I don't think it was here back when I was a grad student (1982-1986). It may have still been a firehouse. Kendall Square was pretty dumpy back then, but part of why I wanted to come here was to see how Cambridge has changed.
I can already tell it's gotten gentrified, just like everyone says. As I was checking in here, someone walking out asked their friend "Did you know this is the most trendy boutique hotel in Cambridge?"
Woooh! I feel like a bigshot now. They probably pay some guy to keep walking in and out, saying that. Back when I was a longhaired grad student, I don't think the phrase "boutique hotel" had even been invented. There were fewer rich people; fewer poor people too.
I need some sleep, even though internet access makes me want to
stay awake and have fun....
June 4, 2006
My father had a stroke. It sounded very scary in the email I
got from my sister yesterday. When I called my mom yesterday she
said he had already recovered to the point of being able to talk and
walk. She was making him do lots of exercise. Today I called her again
and my father answered. "Hi!" he said, "What a surprise!"
He was expecting my uncle.
I was the one who was surprised - shocked, in fact, that he sounded
so hearty, and so obviously not just faking it. Whew - amazing!
I was and
am planning to visit them in two days. I'm relieved that it won't be
a tragic occasion.
June 5, 2006
An interesting article on the rise of people who plan to remain single all their lives:
I'm back at the Perimeter Institute - back from visiting my parents in DC. I was immensely relieved to find my dad hadn't suffered visibly from that stroke, or whatever it was - it's not even clear what it was. He's not much changed from how I saw him last. Unfortunately, this means that he is forgetful, arthritic, and very weak; he needs a walker to get around, and moves very slowly. He only gets out of the house when my mother drives him to the library or to his physical therapist. He finds this depressing - he says it's like he's already entered the afterlife. Somehow he manages to soldier on. I naturally found myself thinking about his future, and mine... how we'll probably all wind up in nursing homes.
When we're young we do a great job of ignoring these issues. When we're middle-aged it's easy to lose ourselves in work and raising of children. It's surprising how long we can go on pretending old age and death are things that happen to other people. But the hand of time hangs heavy on us all.
I could say much more, but I'm not quite sure how personal I want this diary to be. Here's a picture of my parents' house:
You can also see a closeup - my mom helped design this house, and she's very proud of it. Also: my dad, my mom, and a necklace my mom made - she spends a lot time creating jewelry these days.
Here are some notes from the clash of civilizations, written while reading the Washington Post when I was visiting my parents in DC:
The Afghan government has been trying to eradicate the opium crops in the southern portion of the country. As a side-effect, there is now an alliance between wealthy drug traders and Taliban forces. So, the Taliban - who once banned opium throughout Afghanistan - are now being funded by it. Last year the Afghan trade in opium and heroin amounted to $2.8 billion dollars, about 90% of the world's supply. So, the Taliban now have access to lots of cash.
Somalia has lacked a coherent government since 1991, and in 1994 the US-dominated UN military force was trounced, leaving Somalia to a number of fighting clans. The political disarray allowed al-Qaeda operatives to take root there. They're believed to be led by a Kenyan named Fazul Abdullah Mohammed, also known as Harun Fazul. Fauzl has been indicted for the 1998 bombing of the US embassy in Nairobi. The US has long been interested in tracking him down, so while the Bush administration has been officially backing a transition government, the CIA has been secretly giving money to an "anti-terror" coalition of secular warlords who are fighting the Islamic Courts Union, a coalition of 11 clan-based courts who are trying to impose Islamic law.
On Tuesday, the Islamic Courts Union issued a letter saying they "categorically deny and reject any accusation that we are harboring any terrorists", and expressing their desire to establish peaceful relations with the rest of the world. On Friday, the Bush administration decided to convene an international meeting and form a Somalia Contact Group to deal with this.
Opinions vary as to the possible effects of Zarqawi's death. On the one hand, he was a vicious thug and a thumb in the eye of US attempts to quell insurgents and sectarian violence in the region. He served as a kind of proxy for al Qaeda after formally swearing loyalty to bin Laden in October 2004 and changing the name of his organization from Monotheism and Holy War Movement to Al Qaeda in Iraq. On the other hand, al Qaeda found his independence annoying and his brutality counterproductive - and told him as much. So, they may try to take advantage of his death to bring in their own men to control Al Qaeda in Iraq now that he's gone.
Today I went on a little tour of Institute for Quantum Computing with Scott Aaronson. Raymond LaFlamme showed me his nuclear magnetic resonance lab, and also the lab where they create entangled photons for quantum cryptography. With any luck, at the end of June they'll beam pairs of entangled photons to the IQC and Perimeter Institute from a taller building somewhere between the two. This will allow them to communicate in a way that nobody can intercept without it being noticeable. Not that the IQC and Perimeter Institute have anything secret to talk about! Just a demonstration.
After Indian food and lunchtime discussion at the IQC, I felt a bit listless from lack of sleep the previous night, which I'd spent writing "week234". Luckily, John Moffat came by my office to talk about a fiendishly clever attempt to solve the cosmological constant problems using parastatistics. Alas, my technical understanding of parastatistics is almost zilch, but we still had an interesting conversation.
Then I whiled away the rest of the day correcting the dissertation of my student Toby Bartels and attaching emails about music theory to the Addenda of "week234".
Right now I'm listening to Miles Davis' E.S.P., wondering yet again why more people don't say this is his greatest album.
The fact that I'm sitting here listing the things I did
today, instead of actually doing something, is yet another
sign that I'm feeling low-energy.
June 14, 2006
At 11 am I had an appointment to talk with Howard Burton, executive director of the Perimeter Institute. Among other things, we discussed the future of fundamental physics. We agreed that dark matter, dark energy and other cosmological issues are where it's at. He wondered: will we understand them better in 20 years or so? None of our current theories seem to be making much of a dent in these questions.
I tried out my latest idea on him: finding a real solution to these questions might require years of fumbling around with crude theories that seem "insufficiently elegant" to people raised on the Standard Model, string theory or loop quantum gravity. Something more like Balmer's formula or the Bohr atom than Schrödinger equation. Balmer was a teacher at a girl's school in Switzerland who dreamt up a formula for some of of the frequencies of light emitted by hydrogen. Later Rydberg generalized it to get the other frequencies.
If some high school teacher proposed this formula today, would we dismiss it as mere coincidence, noting that it doesn't work for other atoms? We seem to think physics has progressed beyond this point now... but has it, really? MOND (modified Newtonian dynamics) has a similar jury-rigged quality: it does surprisingly well as a competitor to dark matter for explaining the anomalous rotation of many galaxies, but it does badly on other things. Maybe it has a kernel of truth. Maybe it will take a Bohr to spot that kernel of truth, and then a Schrödinger or Heisneberg to formalize it.
Later, John Donghue gave a talk about quantum gravity corrections to the 1/r2 force law, derived from effective field theory. Nice stuff! Any solid piece of information about quantum gravity is a precious gem.
Another low-energy day - apart from the above, I mainly kept
myself occupied by adding comments to the Addenda section of
week234, which was about the math
of music. It's fascinating how many of my math friends
had deep things to say about this. It seems
to support the stereotype that a lot of mathematicians are
into music. Like math, music can take us outside ourselves, into
a beautiful world of abstract patterns, where everything is
right. For a while, at least, it lifts that hand of time
that lays so heavy on us.
June 15, 2006
Dan Christensen came by and we continued our work on smooth homotopy theory. The ups and downs of research: we almost decided to give up on this project, when I mentioned an idea we had at the end of our last session... we got excited, talked a bunch more, and when we had to quit, things seemed to be working just fine!
We took break for listening to talks about loop quantum gravity and black entropy by Danny Terno, Saurya Das and Arundhati Dasgupta. I think I've put in too much time working on this subject to find it interesting or even bearable anymore. It doesn't help that I have a headache.
Martin Rees writes:
Once the threshold is crossed when there is a self-sustaining level of life in space, then life's long-range future will be secure irrespective of any of the risks on Earth (with the single exception of the catastrophic destruction of space itself). Will this happen before our technical civilisation disintegrates, leaving this as a might-have-been? Will the self-sustaining space communities be established before a catastrophe sets back the prospect of any such enterprise, perhaps foreclosing it for ever? We live at what could be a defining moment for the cosmos, not just for our Earth.This is from:
At the moment, scientific effort is deployed sub-optimally. This seems so whether we judge in purely intellectual terms, or take account of likely benefit to human welfare. Some subjects have had the 'inside track' and gained disproportionate resources. Others, such as environmental researches, renewable energy sources, biodiversity studies and so forth, deserve more effort. Within medical research the focus is disproportionately on cancer and cardiovascular studies, the ailments that loom largest in prosperous countries, rather than on the infections endemic in the tropics. Choices on how science is applied shouldn't be made just by scientists. That's why everyone needs a 'feel' for science and a realistic attitude to risk - otherwise public debate won't get beyond sloganising. Jo Rotblat favoured a 'Hippocratic' Oath' whereby scientists would pledge themselves to use their talents to human benefit. Whether or not such an oath would have substance, scientists surely have a special responsibility. It's their ideas that form the basis of new technology.Simple stuff, but worth remembering. This is from:We feel there is something lacking in parents who don't care what happens to their children in adulthood, even though it's generally beyond their control. Likewise, scientists shouldn't be indifferent to the fruits of their ideas their intellectual creations. They should plainly forgo experiments that are themselves risky or unethical. More than that, they should try to foster benign spin-offs, but resist, so far as they can, dangerous or threatening applications. They should raise public consciousness of hazards to environment or to health.
The decisions that we make, individually and collectively, will determine whether the outcomes of 21st century sciences are benign or devastating. Some will throw up their hands and say that anything that is scientifically and technically possible will be done - somewhere, sometime - despite ethical and prudential objections, and whatever the laws say - that science is advancing so fast, and is so much influenced by commercial and political pressures, that nothing we can do makes any difference. Whether this idea is true or false, it's an exceedingly dangerous one, because it's engenders despairing pessimism, and demotivates efforts to secure a safer and fairer world. The future will best be safeguarded - and science has the best chance of being applied optimally - through the efforts of people who are less fatalistic. And here I am optimistic. The burgeoning technologies of IT, miniaturisation and biotech are environmentally and socially benign. The challenge of global warming should stimulate a whole raft of manifestly benign innovations - for conserving energy, and generating it by novel 'clean' means (biofuels, innovative renewables, carbon sequestration, and nuclear fusion). Other global challenges include controlling infectious diseases; and preserving biodiversity.
These challenging scientific goals should appeal to the idealistic young. They deserve a priority and commitment from governments, akin to that accorded to the Manhattan project or the Apollo moon landing.
I've spoken as a scientist. But my special subject is cosmology - the study of our environment in the widest conceivable sense. I can assure you, from having observed my colleagues, that a preoccupation with near-infinite spaces doesn't make cosmologists specially 'philosophical' in coping with everyday life. They're not detached from the problems confronting us on the ground, today and tomorrow. For me, a 'cosmic perspective' actually strengthens my concerns about what happens here and now: I'll conclude by explaining why. The stupendous timespans of the evolutionary past are now part of common culture. We and the biosphere are the outcome of more than four billion years of evolution,but most people still somehow think we humans are necessarily the culmination of the evolutionary tree. That's not so. Our Sun is less than half way through its life. We're maybe only the half way stage. Any creatures witnessing the Sun's demise 6 billion years hence won't be human - they'll be as different from us as we are from bacteria.
But, even in this 'hyper-extended' timeline - extending billions of years into the future, as well as into the past - this century may be a defining moment. The 21st century is the first in our planet's history where one species has Earth's future in its hands, and could jeopardise life's immense potential. I'll leave you with a cosmic vignette. We're all familiar with pictures of the Earth seen from space - its fragile biosphere contrasting with the sterile moonscape where the astronauts left their footprints. Suppose some aliens had been watching our planet for its entire history, what would they have seen? Over nearly all that immense time, 4.5 billion years, Earth's appearance would have altered very gradually. The continents drifted; the ice cover waxed and waned; successive species emerged, evolved and became extinct.
But in just a tiny sliver of the Earth's history - the last one millionth part, a few thousand years - the patterns of vegetation altered much faster than before. This signaled the start of agriculture. The pace of change accelerated as human populations rose.
But then there were other changes, even more abrupt. Within fifty years - little more than one hundredth of a millionth of the Earth's age, the carbon dioxide in the atmosphere began to rise anomalously fast. The planet became an intense emitter of radio waves (the total output from all TV, cellphone, and radar transmissions.)
And something else unprecedented happened: small projectiles lifted from the planet's surface and escaped the biosphere completely. Some were propelled into orbits around the Earth; some journeyed to the Moon and planets.
If they understood astrophysics, the aliens could confidently predict that the biosphere would face doom in a few billion years when the Sun flares up and dies. But could they have predicted this unprecedented spike less than half way through the Earth's life -these human-induced alterations occupying, overall, less than a millionth of the elapsed lifetime and se emingly occurring with runaway speed?
If they continued to keep watch, what might these hypothetical aliens witness in the next hundred years? Will a final spasm be followed by silence? Or will the planet itself stabilise? And will some of the objects launched from the Earth spawn new oases of life elsewhere?
The answer depends on us.
Reading a copy of The New York Review of Books in a cafe on a hot day here in Waterloo, sipping a raspberry-cranberry smoothie, I was struck by a couple of poems from this book:
Tonight, for the first time in many years
there appeared to me again
a vision of the earth's splendor:
in the evening sky
the first star seemed
to increase its brilliance
as the earth darkened
until at last it could grow no darker
And the light, which was the light of death
seemed to restore to earth
its power to console. There were
no other stars. Only the one
Whose name I knew
as in my other life I did her
injury: Venus,
star of the early evening,
to you I dedicate
my vision, since on this blank surface
you have cast enough light
to make my thought
visible again.
This was my last weekend in Waterloo. My student Jeff Morton showed up today - he couldn't make it sooner, since final exams just ended at UCR - and we talked a bit with Aristide Baratin about Freidel and Baratin's new paper describing a spin foam model that gives ordinary quantum field theory on Minkowski spacetime. I'm pretty excited, because we conjecture that this spin foam model is the same as Crane and Sheppeard's spin foam model based on a gadget I invented called the Poincaré 2-group. Higher category theory may finally be sneaking into ordinary physics!
But alas, in my conversations with Baratin and Freidel, we only made a little preliminary progress on proving this conjecture - and now I have to go. I return to Riverside on Tuesday, where Lisa awaits me. On Friday she leaves for Wuhan, for a conference on Chinese archaeology. A bit more than a week later, on Monday July 3rd, I'll meet in her in Shanghai, where we'll spend the summer.
So, Jeffrey and my other student Derek Wise will have to do their best to make sense of this stuff with Laurent and Aristide. But, I have some tricks up my sleeve which may allow me to make some progress while I'm in Shanghai.
Lisa and I hope to have wireless internet access in our apartment
in Shanghai, by the way. So, with any luck, this online diary
will continue. It should be an adventure - a summer in the biggest
city in China!
June 20, 2006
I got back home yesterday. Ah, it's nice just to see my back yard again...
It's so peaceful here.
In the news today, the Editorial Projects in Education research center reports that the 2006 graduation rate for US high schoolers is only 70%! In Los Angeles, the figure is only 44%! I'm curious how this compares to European countries. Does anyone know? Apparently the US dropout rate has been underestimated by the states - you can see details here. So, European figures could also be misleading....
On the bright side, a
study by Julio
Licinio et al reports that
suicide
rates in the US have dropped by about 15% since 1988 - the year
that Prozac went on the market. Suicide rates had been fairly
stable, around 12.9 per 100,000 per year, all the way from 1870 to 1988.
Since then the rate has dropped to 10.9. Nobody knows if this drop is
due to the introduction of Prozac and other selective
serotonin reuptake inhibitors, but it's a plausible hypothesis.
It would be really, really cool if suicidal despair could be
reduced by rejiggering serotonin levels in the brain.
June 21, 2006
Ever wonder why the US is bickering so much with Hugo Chávez, the President of Venezuela?
One reason is that Chávez is a leftist who likes to throw his weight around. But another is that Venuzuela is sitting on top of lots of heavy oil. This is a gooey substance - a form of "unconventional oil" - that our economy will naturally turn to as conventional oil supplies start running out. Let me quote a little of this paper:
Unconventional oil is an umbrella term for oil resources that are typically more challenging to extract than conventional oil. While many unconventional oil resources cannot be economically produced at the present time, two exceptions are extra-heavy oil from Venezuela's Orinoco oil belt region and bitumen - a tar-like hydrocarbon that is abundant in Canada's tar sands. These resources are already being economically produced and are likely, in coming years, to become increasingly important to global oil supplies generally, and to U.S. oil security in particular, given their close proximity to U.S. markets.Just to give you some sense of what this means: as of 2006, the Oil and Gas Journal said the total proven worldwide oil reserves were 1,293 billion barrels. (This counts the Canadian oil sands listed above, but not the Venezuelan heavy oil.) The Energy Information Administration, run by the US government, guesses that these reserves will grow by 730 billion barrels over time, and throws in a guess of 939 billion extra completely undiscovered barrels, for a guess of 2962 billion barrels of oil left worldwide.[...]
In 2002, the Oil and Gas Journal accepted Canada's classification of 174 billion barrels of oil sands as established reserves and Canada became the second largest oil reserve-holding nation in the world after Saudi Arabia. If the 235 billion barrels of extra-heavy oil that Venezuela considers recoverable, but that are not currently acknowledged as established or proven, are re-classified in the same way as Canada's oil sands, Venezuela would be credited with the largest oil reserves in the world.
In 2003 the world used 29 billion barrels of oil per year. By 2030, the EIA predicts this demand will grow to 43 billion per year.
They predict that oil use will peak sometime between 2055 and 2065, and crash quite rapidly after that. If something like this comes to pass, Venezuela will be very important in the years to come... and Canada too, but I'm sure the US feels more threatened by Venezuela!
For more information, try this:
I can't see the EIA prediction that oil use will peak around 2055-2065 on their website. I found it here:
Let's ponder that chart up there. Most people are arguing about when peak oil will happen, not whether. And, if we take the long view, the disagreements are minor: everyone who contributed a line on the chart says sometime between now and 2070. An updated version of the chart shows even better agreement.
So, the question is: what next?
This is actually a huge interlocking network of questions. How much does the whole "growth is good" philosophy of economics rely on the assumption of ever greater energy usage? When we hit the wall, what will happen? Can economic growth occur in ways that don't require greater energy usage?
Will we decide that perpetual economic growth is an unreasonable goal for occupants of a finite planet? Or could we revamp our concept of "economic growth" to make it a bit subtler and less destructive? There are, of course, vast untapped reaches of ethical, spiritual and intellectual growth waiting to be explored. Why are they almost neglected in our current definition of "economics"? Can we change this? Will we?
Or: are we so locked into our current course that the carbon burning economy gets pushed to its logical limit, despite the cost of global warming? On December 18, 2005 I mentioned an article in Wired listing various forms of carbon we have left to burn, measured in oil barrel equivalents. Here are the biggies:
We see here the last 4 glacials (or "ice ages") in the last 400,000 years BP - "before present". Notice the incredible red spike at the far far right of the graph: that's what we're doing now! If we burn through all the methane hydrates, this will shoot way off the graph, and so will global temperatures.
To get a feel for some numbers: in 2003, people around the globe consumed about 440 quintillion joules (420 quadrillion BTU) of energy, mostly fossil fuels. This is the energy equivalent of 72 billion barrels of oil, and it caused the emission of roughly 8 billion tons of carbon into the atmosphere.
Doing this sort of thing for about a century caused the red and blue spikes on the edge of that graph. Of course, energy usage started out much lower a century ago... so multiply all the numbers in the previous paragraph by about 20 or 50, and you'll get the figures for the last century.
But: to get the figures for what'll happen if we burn all the methane hydrates, you have to multiply those numbers by about a thousand!
Of course, we wouldn't burn this stuff all of a sudden, so there will be time for some CO2 to get eaten up by various processes.
Nonetheless, we're talking about a major disruption of the climate if we don't end our carbon addiction. Something orders of magnitude greater than what we've seen so far.
The moral: the oil peak may be upon us, but the end of cheap oil won't save our climate, because the carbon peak will be much bigger - unless we move towards other energy sources, or less energy consumption.
(Here are my calculations and sources, so you can catch my mistakes if
you want: there are lots of weird units involved.
About 420 quadrillion BTU of energy were used in 2003,
according to
the EIA, which doesn't use metric. A barrel of crude oil equals
roughly 5.8 million BTU. So, the energy usage
was equivalent to 72 billion oil barrels. The actual oil usage
was about 150 quadrillion BTU, or 25 billion barrels,
or 36% of all energy usage. Burning a quadrillion BTU of fossil fuel causes
the emission of roughly - roughly - 20 million tons of
carbon. Of course it actually depends on how much hydrogen
the fuel contains - so, 26 million tons for coal,
about 20 million for petroleum,
versus only 15 million for natural gas. But, I'm just trying for rough
estimates here, so I'm cutting all sorts of corners:
I should subtract the amount of energy not coming
from fossil fuels, for example - about 10% or so.
More carefully prepared statistics
on carbon dioxide emissions are available from the IEA.
Finally, a BTU is 1055 joules, so 420 quadrillion BTU is
about 440 quintillion joules, or 4.4 × 1020 joules.)
June 23, 2006
Lisa left for Wuhan at 2 a.m. today - she's going to a conference on Chinese archaeology. I spent the day catching up with James Dolan, who has been thinking a lot about an intricate web of ideas related to Dynkin diagrams, including Vaughan Jones' work on subfactors and its relation to the McKay correspondence.
I was happy to see that International Astronomical Union has officially approved names for the two newly discovered moons of Pluto - Nix and Hydra. Here's a picture of them taken by the Hubble space telescope:
While visiting my sister in DC a while ago, we saw a bunch of sparrows living in the huge mall at Tysons Corner. This made me wonder - yet again - about why some animals seem so much better than others at living around humans. Sparrows, rats, pigeons, cockroaches and coyotes do well. Turtles, frogs, manatees, passenger pigeons and lions don't. I believe all animals that don't do well around us will either go extinct or wind up living at our sufferance in zoos or game reserves.
So, we are selecting the animal kingdom for certain traits. Animals either need the traits that let them eke out an existence in a human dominated world, or they need to be cute enough that we'll take care of them. Otherwise they will die.
This is a strange new kind of selection pressure. It's part of what Bill McKibben calls The End of Nature.
So, what traits do animals need to survive well around us? My sister just sent me an interesting article about this:
Greenberg hypothesized that since humans create a rapidly changing environment, animals will less neophobia will fare better around us.
But, it turned out that some species closely associated with us are among the most neophobic of all! Mallards, which get along well with people, are more neophobic than wood ducks. Norway and black rats, ravens, crows, and house sparrows are all highly neophobic! This is why it's hard to trap or poison these critters. And that's part of why they do well around us.
In short, "persecuted commensals" - animals that require human presence to do well, but which we keep trying to kill - must balance adaptability with neophobia. They need to keep adapting to new environments and trying new foods, but avoid our sneaky traps. They need to be curious... but still cautious.
That's what Greenberg says. And it makes me wonder: does this balance require a kind of intelligence? Are we selecting for intelligence?
I drove to the coast with James Dolan to visit my friends Chris Lee and Meenakshi Roy. Among other things, we went on a long walk on the beach from Playa Del Rey almost down to Hermosa Beach. Chris and Meenakshi study cool stuff like alternative splicing in human genes and evolution of drug resistance in HIV. But, Chris wants to do more theoretical work on bioinformatics, and he's writing a book about it that starts with the fundamentals: Bayesian reasoning, entropy, and so on. So, we mainly talked about that sort of stuff. Chris described a conjecture about entropy maximization, and Jim came up with an interesting idea for deriving the maximum entropy principle from Bayes' law! I need to find out if someone has already worked on these ideas....
According to Chris, people in bioinformatics are expected to
run "labs", following the pattern in other branches of
biology. They spend lots of time managing grad students,
applying for grants, and so on - leaving little time to
talk with colleagues and dream up new ideas. Each lab is like a
little business competing with the rest in cranking out data.
It's very different in math and theoretical physics. There are
reasons for this, to be sure, but it seems that now there's enough
data in biology to create a niche for "theorists" who
spend some time thinking about what it all means.
June 25, 2006
More about animals living with people:
A sad thing about visiting my parents' beautiful house in Great Falls, Virginia was seeing how deer have overrun the woods. With no natural predators to keep their population down, they eat every last little bit of plant life they can get find; their population must be limited by starvation. So, the forest has no brush in it... and no new saplings! It's a dying forest.
I mentioned how coyotes have moved into this area. Unfortunately, coyotes don't eat deer. At least, not often - maybe occasionally they grab an unlucky doe, but they prefer much smaller food, like mice.
Luckily, my sister said that mountain lions have entered the area! I hope they eat lots of deer and not too many people. Here's an article on a similar phenomenon in New England:
I keep hearing that there are mountain lions in the park behind our house, but I've never seen one - which is just fine with me. Do you know what to do if you meet one?Tracking the Cats
Wendy Williams
Mountain Lions Roam Region's Forests - Origins a Mystery
Northern Sky News
June 2002
In September 2000, less than 150 miles north of Boston, hunter Roddy Glover was following a wildlife trail through the woods when a tawny-colored animal caught his eye. At first he thought it was a deer, but he soon realized it was some kind of cat. As the cat came closer, Glover saw that it was much too big for a bobcat, the only wild feline known to roam that area.
He lay low in the ferns to watch. “Then—it kinda shocked the hell out of me—I realized it was a mountain lion. And she had a kitten with her.”Mountain lions were extirpated from New England by early in the last century, often hunted for the bounty placed on their tails. For decades, sightings of mountain lions roaming in New England’s north woods have been steeped in controversy. Those who believe in the presence of mountain lions have often been considered apt to believe in Bigfoot. Today, most wildlife biologists agree that there is increasing evidence of mountain lions in the area. But whether or not the animals —also known as catamounts, pumas, cougars or panthers—are breeding here remains unclear.
As for Roddy Glover, he wanted proof that he wasn’t crazy. Seeing tracks left by the female mountain lion in the mud, he called state biologist Keel Kemper, who arrived at the Monmouth, Maine site within the hour, looked at the tracks, took photos and made a plaster cast.
“This is a big cat print,” says Kemper of his plaster cast. “But if I had only this cat print, I would be foolish to say there was no doubt it was a mountain lion. I have Roddy Glover, experienced outdoorsman, who watched the cats for at least five minutes, from only 50 yards away. I’m about as convinced as I could be.”
A week later at the same location, Glover found another set of what he believed were mountain lion prints left on railroad ties. This time a biologist who had done mountain lion research out west came. “Yep,” Glover quotes the biologist as saying, “those are mountain lion prints.”
In over 60 years, this is the first sighting of a mountain lion roaming free through New England’s forests that is officially confirmed by accompanying physical proof (the last was a lion killed in northwest Maine in 1938). But there have been a number of credible sightings and several other tantalizing occurrences in recent years. In 1997, near Massachusetts’ Quabbin Reservoir, wildlife tracker John McCarter found a deposit of large scat covered with debris in the fashion of a mountain lion. McCarter, and tracker and teacher Paul Rezendes, sent the scat to a DNA sequencing lab at New York’s Wildlife Conservation Society. Those tests showed it to be mountain lion scat, a finding later confirmed by a second qualified DNA testing lab at Virginia Polytechnic Institute.
Rezendes, author of Tracking and the Art of Seeing, has been following up on McCarter’s finding: “We’re going to make more of a concerted effort to find something. Now we’re going to set a track line out this winter... We will be following up any credible sightings. Anybody who has tracks, scat, anything like that that sounds credible—if we find something, I’ll be ready to go.”
Massachusetts state biologists accept that the scat was probably mountain lion, but question the animal’s origins. “One could speculate that a captive cougar escaped or was released in the area and survived long enough to feed on a beaver and leave this tangible evidence,” wrote Massachusetts wildlife biologist Susan Langlois.
Throughout northern Maine, Vermont and New Hampshire, an increasing number of sightings by very credible and experienced outdoorsmen have been reported. None of these have been confirmed by physical evidence, however. Some observers have followed tracks in the snow. In the Brattleboro-Putney area of southern Vermont, in the winter of 2000, a number of independent sightings were reported over a series of several days. But to date, nothing has been confirmed.
“We have a semiformal policy of taking all sightings and all calls,” says Vermont state wildlife biologist Doug Blodgett. “We’re documenting everything we get, including misidentifications. We’re putting it on a data base and we’re keeping track.” Blodgett says that when biologists follow up on many of the calls, the animal turns out to have been a bobcat, a feral house cat, a coyote—or even a deer.
Because of the similarity in coat color, it’s quite common for the most experienced people to mistake a deer in a low-crawl for a mountain lion. “I had that experience myself once,” says Blodgett. “One night I was certain I was seeing a mountain lion, but when I checked the tracks it was a deer.” Biologists across the continent tell similar stories of mistaken identities.
Nevertheless, many regional experts agree that, on at least a few occasions, observers are reporting valid sightings. But, says Blodgett, it is not clear where the lions are coming from. “We have a lot of people who are quite cranked up about this, who really want to believe that the lions are here,” he says. “Some have speculated that there have been some intentional releases. They’re commercially available—you can buy them on the Internet.”
Some good news: Santa Monica has banned styrofoam and other non-recyclable plastics for businesses like fast-food restaurants. This stuff is virtually indestructible and accumulates on beaches and elsewhere. It's made of petroleum, so it's getting more expensive, and people are naturally turning to cups and plates made from corn starch, sugar cane, and other biodegradable materials.
Some bad news: this summer we'll probably see lots of wildfires in the western USA. It's just as dry as it was in 2002, which was the worst wildfire season ever, and the sky here was full of smoke and ash for days - it looked like Hell.
Of course, wildfires may not be all bad in the grand scheme of things. It's hard to tell... hard to tell what the "grand scheme of things" really is! That's part of what I'm trying to figure out in this diary.
From Thin Ice, where
the author was interviewing climate scientist Lonnie Thompson:
"I think humans are like every other organism: they try
to maximize the system to their advantage, take every resource
they can use to make whatever it is they're trying to produce, and
they will keep doing it until that resource is no longer available
to them. Our economic system is based on that: maximum production.
And every country in the world wants to be like the Western countries -
same lifestyle, same air-conditioning, same TVs. We have fine
universities, we train people to think; but actions speak louder than
words, and as long as we stay on this path I don't think we're any
smarter than bacteria. We're behaving the same way they did. You can
do that until you exceed the boundaries of the system, and then it
will collapse."
"You mean the whole system will fall apart?" I asked.
"Oh no, the system will keep working. I'm very optimistic
about the system. The system will take care of itself. This is like
a cancer growing on the surface. The planet will react in a way
as to stop that cancer."
"The earth will stay healthy?"
"Yes. It might be big storms; it might be wiping out
Bangladesh or Africa; the world will go on, and there will be
creatures that will multiply in that new world. Plants like
CO2; maybe the world will be dominated by plants. Whenever
a creature exceeds its resource base, its population collapses -
think of lemmings - and I think that's ultimately what will happen
to humans."
Yesterday I talked to Danny Stevenson and Alissa Crans about
representations of Lie 2-algebras and Lie 2-groups. We were
mainly battling with the puzzle of giving our 2-category of
2-vector spaces a nice tensor product and hom. The last few
days I've also been talking with James Dolan about the McKay
correspondence and ambidextrous adjunctions between 2-vector
spaces.
In the first reported case of
fatal hilarity,
the Greek fortune-teller
Calchas
is supposed to have died of laughter on the day
he was predicted to die, when the prediction didn't
seem to be coming true.
Google has a new
mirror
site. Make sure to type in your entry backwards.
You can find many other
strange things on Wikipedia:
It'll be an adventure!
My 2003 summer in Hong Kong was great, so I'm not scared, but it will
be quite something living in such a huge city. We'll be near
Fudan
University, not the heart of town. You can see it near
the top of this
map.
Somehow I got a subscription to Cell magazine. One
issue had a neat article on the genetic origins of left-right
asymmetry in vertebrates, which I've summarized in the Addendum
to week73. But even more cool are
these two articles:
But the phenomenon of quorum sensing has recently turned out to be
far more common in less exotic circumstances. It causes
"competence" in Streptococcus, a state in which bacteria
can pick up DNA molecules and change their genetic properties.
It also controls virulence factor secretion,
biofilm formation
and sporulation.
These are various spooky tricks bacteria like to play....
The article describes many other forms of inter-bacterial
communication. For example, bacteria in water send water-insoluble
molecules to each other in little packages called
vesicles.
And, some of these packages are fatal to bacteria of other species!
As if this weren't enough, it turns out that advanced life forms
like us - eukaryotes,
to be precise - are able to pass on traits not just using their DNA
and RNA, but also using a trick called
histone
methylation. In eukaryotic cells, DNA is wound around
around proteins called
histones.
Adding one, two or
three methyl groups to these proteins controls whether and how
gene will be expressed in a given cell. This is one way
cells in our body get to be very different even though they
have the same DNA! It's quite complicated and interesting - and
in a surprising
twist reminiscent of Lamarckian evolution, a mother can apparently do
histone methylation to genes in her child's embryo! So, traits
picked up during her life, encoded not in DNA or RNA but in histone
methylation, can be passed on to her offspring.
In short, besides genetics we must also study epigenetics - the science of reversible but
heritable changes in gene expression that can occur without any changes
in our DNA!
Evolution is like a game that life has been playing for billions of years.
The strategies in play are surely far deeper than we've been able to
fathom so far. We're like kids watching grand masters play chess.
We should continue to expect surprises....
© 2006 John Baez
June 30, 2006
I'm gradually gearing up for my trip to Shanghai on Monday July 3rd.
This may be my last diary entry for a while, but Lisa has found an
apartment with broadband internet access - apparently quite common there -
so I should be back in business once we get set up.
The first article describes how bacteria communicate using chemicals.
For example, in a process called
quorum sensing,
bacteria emit traces of a chemical, which rises to a level they can detect
only when their population density reaches a certain threshold.
The chemical then affects their behavior!
For example, a bioluminescent bacterium in the ocean called
Vibrio harveyi glows only when it reaches a certain
density - and in an extreme case of this phenomenon, a glowing
patch of the Indian Ocean 15,000 square kilometers in size was
visible from space for three nights!
For my July 2006 diary, go here.
The [...] spirit will soar
eagerly into the heavenly spheres, but rarely stays
there: it returns to the workaday world: it insists
that ideals shall be translated into action, precept
into practice, the spiritual applied to the physical,
the abstract to the concrete. - Hugh Schonfield
baez@math.removethis.ucr.andthis.edu
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