August 30, 2006
Biological complexity: not what you think
I've long been skeptical of the idea that life forms can be linearly ordered in terms of complexity, with mammals (esp. humans) at the top and single-celled organisms at the bottom. Genomic research in the past decade has shown humans to be significantly less complex than we'd initially imagined, having only about 30,000 genes. Now, along comes the recently sequenced genome of the heat-loving bug T. thermophila, which inhabits places too hot for most other forms of life, showing that a mere single-celled organism has roughly 27,000 genes! What are all these genes for? For rapidly adapting to different environments - if a new carbon source appears in its environment, T. thermophila can rapidly shift its metabolic network to consume and process it. That is, T. thermophila seems to have optimized its adaptability via accumulating, and carrying around, a lot of extra genes. This suggests that it tends to inhabit highly variable environments [waves hands], where having those extra genes is ultimately quite useful for its survival. Another fascinating trick it's learned is that it's reproductive behavior shows evidence of a kind of genetic immune system, in which foreign (viral) DNA is excised before sexual reproduction.
From the abstract:
... the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. [...] The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance.
J. A. Eisen et al. Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote. PLOS Biology, 4(9), e286 (2006). [pdf]
Update Sept. 7: Jonathan Eisen, lead author on the paper, stops by to comment about the misleading name of T. thermophilia. He has his own blog over at Tree of Life, where he talks a little more about the significance of the work. Welcome Jonathan, and congrats on the great work!
The truth, but funny
Some of us have it worse than others, but when I laughed at this, it hurt a little, too.
August 23, 2006
A skeptic's skeptic
Dr. Michael Shermer, a long-time columnist for Scientific American, and founder of Skeptics Society, is one of the people at the front-lines in the interface between science and pseudo-science. His careful critiques of popular misconceptions were one of my early introductions to the conflict between science and myth. For instance, it was in one of his columns that I learned of an excellent explanation of why smart people often believe really bizarre things: their intelligence makes them particularly good at rationalizing those crazy ideas. In one of his earlier articles, I even learned that Einstein once conducted a little experiment to see if time would seem to pass more quickly around a beautiful woman (his conclusion: it did). Salon is currently running a short, but good interview with him. Apparently, Dr. Shermer used to be a creationist.
What caused you to see the light about evolution?
Like most creationists, you just know what you read in creationist books. When you read them, it makes the theory of evolution sound completely idiotic. What moron could believe in this theory? When you actually take a class in the science of it, it's a completely different picture. That's also when I realized I enjoyed the company of scientists and science people much more than religious people and theologians. It was this exciting, open-ended, participatory process that I could be involved in. We're all in this search together, and there's an actual method to do it, and a community of people who practice it, and a way of determining whether something is true or not. I fell in love with that.
August 22, 2006
Jon Kleinberg wins the Nevanlinna Prize
Jon Kleinberg, a computer science professor at Cornell, has done it again, this time winning the Nevanlinna Prize for major contributions to the mathematical aspects of computer science (given out every four years; created in 1982; Robert Tarjan was the first recipient). What's most gratifying about his work is that he manages to ask (and answer!) questions that directly effect the way our complex world works. For instance, his work on the small world phenonema (and its more practical side: decentralized search) was the inspiration of my first graduate school research project.
August 12, 2006
Your academic-journal dollars at work
Having now returned from a relaxing and rejuvenating trip to a remote (read: no Internet) beach with my family, I am trying to catch up on where the world has moved since I last checked. Comfortably, it's still in one piece, although I'm not thrilled about the latest draconian attempts to scare people into feeling safe about flying in airplanes. Amazingly, only half of the 300 emails I received were spam, and what remained were relatively quickly dispatched. In catching up on science news, I find a new movement afoot to stop Elsevier - the ruthless, and notoriously over-priced, academic publishing house - from organizing arms fairs via one of its subsidiaries. Having recently watched the excellent documentary Why We Fight, on the modern military-industrial complex, this makes me a little concerned.
I've only refereed once for any Elsevier journal, and I now plan to never referee for any of them again. This idea is, apparently, not uncommon among other scientists, e.g., here, here and here. Charging exorbitant prices to under-funded academics who produce and vet the very same content being sold is one thing - exploitative, yes; deadly, no - but arms fairs are a whole different kind of serious. Idiolect is running a petition against this behavior.
Update, Aug. 24: Digging around on YouTube, I found this interview with Eugene Jarecki, the director of Why We Fight.
August 03, 2006
Things to read while the simulator runs; part 1
To commemorate the creation of a new recurrent topic here, two things caught my attention today:
Cosmic Variance, always an indelible source of cosmological weirdness, has a wonderfully detailed discussion about Boltzmann’s Anthropic Brain. That is, the argument that Boltzmann used, while thinking deeply about the nature of this entropy business and its incessant drumbeat of chaos, to explain the origin of the universe. The discussion begins with a simple questions "Why is the past different from the future, or equivalently, why was the entropy in the early universe so much smaller than it could have been?" and proceeds apace.
The unexpected consequence of Boltzmann’s microscopic definition of entropy is that the Second Law is not iron-clad — it only holds statistically... Faced with the deep puzzle of why the early universe had a low entropy, Boltzmann hit on the bright idea of taking advantage of the statistical nature of the Second Law. Instead of a box of gas, think of the whole universe. Imagine that it is in thermal equilibrium, the state in which the entropy is as large as possible. By construction the entropy can’t possibly increase, but it will tend to fluctuate, every so often diminishing just a bit and then returning to its maximum.
You can see where this is going: maybe our universe is in the midst of a fluctuation away from its typical state of equilibrium. The low entropy of the early universe, in other words, might just be a statistical accident, the kind of thing that happens every now and then. On the diagram, we are imagining that we live either at point A or point B, in the midst of the entropy evolving between a small value and its maximum. It’s worth emphasizing that A and B are utterly indistinguishable. People living in A would call the direction to the left on the diagram “the past,” since that’s the region of lower entropy; people living at B, meanwhile, would call the direction to the right “the past.”
Sean, our tour guide for this picturesque stroll through Boltzmann's mind, proceeds to explain why there is more going on here. Although the argument is flawed for more classical reasons, it also fails more directly because it doesn't account for things we can't hold Boltzmann responsible for not knowing: things like General Relativity, Inflation theory and Quantum Mechanics. It seems that the mystery of the arrow of time (or of time at all!) remains.
And finally, in case you have not been hiding under a rock for the past two years, you may have heard of a game called Sudoku. Many of my non-academic friends have succumbed to the faddishness of them, and I spy my neighbors on the plane scribbling away in books of these things. Even my younger sister is playing them now, on her Nintendo DS - oh, how the tools of procrastination have advanced since my youth, when we were forced to entertain ourselves with poorly wrapped bundles of dead trees. But, I do find Sudoku to be an interesting computational puzzle. That is, how difficult is it to solve these things, in general? The problem is clearly in NP, but not clearly NP-complete.
Lance Fortnow uses its NP membership as a nice little vehicle to explain how you can do a zero-knowledge interactive proof using Sudoku.
Victor has tried and failed to solve the latest Sudoku game and exclaims no solutions exists. His wife Paula has already solved the game. How does Paula convince Victor that a solution exists without giving the solution away?
It turns out that this can be easily done without the usual mapping to graph coloring. The result is intuitively pleasant and, because of Sudoku's popularity, probably highly accessible outside computer science. Not a bad use of something that reminds me of a glorified constraint optimization problem, or of that unpleasant "analytic" section of the GRE. In fact, any "puzzle" that can be solved by manually running a simple backtracking algorithm, or via first-order logic on the initial configuration, seems like a waste of brain power to me. Why not just write a computer program to solve it, and instead spend your time reading something interesting?
Update, Aug. 24: in truth, even problems that admit a more elegant solution can be solved by brute force via backtracking or reduction to satisfiability, but Sudoku doesn't yet admit such elegance, and I've never met anyone who solves them by doing something other than the two (boring) methods I mention. So, in my mind, by extension, that makes Sudoku a boring activity.