Monday, February 28, 2005

Time isn't kind

(I didn't have enough time to fish out my intended title, which was to be from the riddle match between Gollum and Bilbo in The Hobbit. Time, time!)

Becoming a fossil requires hard work and a lot of luck. It's not enough to die in a nice mushy riverbank, although that's a start. Your remains could get obliterated, washed away, or dispersed, before they even get properly mineralized. And, eons later, you could get ground up by a Chinese apothecary, sold on Ebay, or waylaid in any number of other ways instead of being dug up, polished, argued over, and shelved.

It's very inefficient, but how inefficient? In fact all the oddball events in a fossilizable entity's natural history tend to average out. So paleontologists have had some luck in modeling the "population" of fossil relics from a given population over time. The equations make certain idealizations including a constant environment and a closed, homogeneous population, reproducing exponentially, and subject to no more than normal post-fossilization vagaries.

In last week's Science (subscription link; free link at the BBC is here ) these equations have been ported over to describe what seems to be a completely different phenomenon: the survival of medieval parchment manuscripts through the looting and pillaging of the ages. The gauging of how many are left behind has been the province of anecdote and wild guesses, but these fossil equations seem to describe what to expect rather well. The reason it works for manuscripts, as summarized by Sharon Gilman and Florence Glaze, is that, prior to the printing press, the numbers of technical manuscripts behaved like a biological population: they were reproduced exponentially (as copies were made of copies of copies), up to a saturation point, and destroyed with some probability. Death and destruction, although seemingly arbitratry, actually average out over time. Using the equations derived for predicting fossil survival, the author predicts that a very big fraction of technical works (he suggests 2 in 7) have survived since the parchment era.


In their fairly snarky synopsis of the work ("If he had teamed up with a historian in the first place, he could have written a much better essay"), Gilman and Gaze point out some limitations to the modeling regarding the idealizations necessary for the math. Manuscripts do not provide a homogeneous population (every text is different, and therefore copied and disseminated differently from the others); the population is not closed; and it hasn't been long enough for the "noise" in the processes of destruction to have averaged out from text to text. Still, I think it's a fascinating first stab, and the match between model and reality for Bede's manuscripts looks pretty impressive. Now, back to my parchments...

tangled bank 22 1/2

A few misplaced emails have broken this week's Tangled Bank carnival of science writing into two parts. I'm listed at Pharyngula , and the main set is at The Scian . Looks good!

Sunday, February 27, 2005

Am I a card-carrying nethead yet?

I was looking over Brad DeLong's blog (great blog!) and came across an older post about growing pains of Technorati. Within the post is this excerpt:

Unfortunately, a good deal of this is attributable to the increase of spam that's coming at us. The growing number of link farms creates a much greater load on our spiders.

And I understood every word. I think I need to pick up a novel, before I start comprehending slashdot.

But read the post. More information ecology thinking, from people whose paychecks depend on it.

Don't throw that away!

I know very little about this subject, but I was very interested in this Internet News article about the Sarbanes-Oxley act for corporate financial accountability has driven a boom in storage technologies. Companies are trying to comply with guidelines that require not only databases, but unstructured business-related communications such as emails, to be archived.
Emails turn out to be especially problematic, because they're so heterogeneous. To be compliant with Sarbanes-Oxley, you have to store, and quickly retrieve, "all relevant financial records," but at the same time you wouldn't want respond to a request by handing over company communications outside of the focus of the request. Moreover, you'd like to go in to the archives to identify and delete irrelevant emails.

In the end, the article concludes that this up-front pain of developing a compliant archive policy will be beneficial to information-heavy companies. Read the whole thing.

Saturday, February 26, 2005

Biotechnology and lifespan

I was curious about a google hit which arrived at my site via "Condolezza Rice boots" (I had indeed misspelled her name). I went to look at the hit list and ended up at the Claremont Institute's Writings page, and Ken Blanchard's post reviewing a book, Bioevolution: How biotechnology is changing our world about the coming wonders of biotechnology. Biotechnology researchers are working hard on solutions to pollution, cancer,and infectious disease, and people today who turn 80 in 2025 may be able to live on to 120.

Ken Blanchard rightly points out a pair of objections to this very optimistic view. First, it is a very long and rocky road "from the bench to the bedside," meaning from research to when a doctor can actually help a patient, or a waste dump can be remediated. The two anti-cancer strategies mentioned, anti-angiogenesis and anti-telemorase approaches, are at least 5 and 15 years from a publicly available drug, respectively, and I'm not so sure anti-telemorase strategies will be free of side effects.

Secondly, if a disease can be cured or managed, does it cause people to behave less responsibly? Blanchard chooses the example of liver cancer and alcoholism: If it becomes possible to buy a new liver, why not piss away the one you have? (Short answer: Anyone heard of rabies in transplants? ) I think the more germane example would be HIV+ people having unprotected sex. However, I don't think the existence of life-saving technologies will increase mortality by inspiring mass bad behavior.

But my strongest reaction relates to the ongoing and really tragic differences in life expectancy worldwide, due to infectious diseases that could be treated with existing technologies. This is only touched upon by Blanchard, but I cringed when reading this quote from the book, looking forward to 2025:

Disease still exists, but the great infectious scourges such as malaria, tuberculosis, diarrhea, hepatitis and AIDS have been virtually eliminated.

I don't know where the book's author lives, but people are dying, worldwide, preventably, from this stuff. And it's getting WORSE with time. It is ironic that the book's title invokes evolution, because antibiotic resistance and other recombination events are being selected for precisely via the "directed evolution" (the author's phrase; Darwin called it "unconscious selection" ) that the author trumpets as a method for discovery of new treatments. Unconscious selection is making the "known" microbial diseases more deadly with time, even in places where treatments are readily available. A further irony, given the book's praise of the powers of biotech, resides in the many solvable diseases which receive almost no attention from the biotech world. These will still be killing people in 2025. Please, please read this discussion in PLOS medicine on how to change the rules. I do not claim to have an answer to the economics of setting research priorities, nor do I think that researchers should tackle everything just because it's doable. I just think that infectious diseases are going to be a nasty fact of life and death for a long time yet.

UPDATE: Blogger's spellchecker suggests replacing "Condolezza" with "gondola."

The psychology of purchasing

The L.A. Times describes scientists measuring how the sight of a beautiful Ipod, or a trustworthy senator, affects the electrical activity of the brain. Marketers in a very crowded marketplace are hoping to use these measurements to predict how potential buyers will view their product:

For all their differences, objects and celebrity faces were reduced to a common denominator: a spasm of synapses in a part of the cortex called Brodmann's area 10, a region associated with a sense of identity and social image.

It would probably be unfair to point out that this study was done in Hollywood ( The reaction in both sets of brains was intense. The brains reflexively sought to fulfill desires or avoid humiliation ) so let's assume that people really do engage their brains before buying, or deciding how to vote. This is interesting information-- very interesting to me-- gotten using some very fancy electronics. But the marketing utility of what is being gained, especially given the smallish samples sizes, may not match the expense of the machinery. One of their success stories, Pepsi, clawed out a market for itself long before there was an MRI machine. There are plenty of low-tech approaches . My favorite story, no link, was that a videotape set up in a boutique showed that customers entering a store were more likely to glance left than to glance right. Low tech, large numbers, linked to purchases. Seems more effective to me.

More interesting to me is the thrill-o-meter being developed by British scientists. When you're really getting goosebumps, your skin conductance changes, via the same nervous system effect that lie detectors also try to catch. The scientists are interested measuring viewer responses to video games or movies, in order to stoke them up for thrill hounds. But I think they're missing the real potential. Ever since Harry met Sally , there has been public awareness of an information gap between men and women regarding how fun the sex is. Men supply a pretty reliable barometer, but I think these thrill-o-meters might find a ready market for people curious about women. Just slap it on, someplace discreet, maybe during the risotto , and for the rest of the night you'll get real-time efficacy measures.

On second thought, maybe I don't want to know.

Thursday, February 24, 2005

Walt Disney, call your office

Humans who have signed up to be frozen cryogenically may be thrilled to hear about a bacterial revival in the Alaskan permafrost. Tunnelers travelling through soil that has been frozen solid for 30,000 years streaked out a sample on a microscope slide, and were shocked to see newly thawed bacteria swimming around!

Someone go thump on Disney's tank!

More seriously, they have to check that they haven't contaminated their samples. And of course, life on mars, blah blah.

Wednesday, February 23, 2005

You can see an awful lot, just by looking

(With apologies to Yogi Berra)

The genome sequencing efforts are flooding public databases with raw data. It is becoming a real information science issue to manage what has already been logged, let alone cope with the incoming. On Eurekalert.org yesterday, I noticed a link on this topic regarding researchers at the institute for Genomic Research, or TIGR. These scientists have been doing what TIGRs love best (couldn't resist the pun), which is to hunt for new microbial sequences. But their hunt took them to an unexpected place: archival data generated by the fruit fly genome projects.

The bacteria that they identified are endosymbionts with flies, with the bacterial DNA probably a contaminant in the fly DNA samples using for sequencing. This is easy to understand, as the enzymatic procedures involved in sequencing do not distinguish the source of the DNA. What is suprising is the extent to which these microbes were sequenced, essentially by accident. One strain was represented with 95% coverage, equivalent to a first-pass shotgun run! Ten years ago, this would have been notable in itself. In fact the coverage was good enough to allow detect a few horizontal gene transfer events, and to compare the 3 new species with previously described endosymbiont bacteria.

So, to get back to the title of this post, a computer is getting to be as much an experimental tool as a pipetter. Have a look!

Gender Bias

My two older sons are at a psychological stage which involves extreme alliegance to their boyness and avoidance of anything remotely girly. Our house is infested with weaponry, dinosaurs, superheroes, and books on snakes. These days I'm starting to read them from the DK series of biology-related books. I got them hooked with the danger end-- insects, poisonous animals, etcetera-- but we have also started into microscopic life. One wrinkle has been that the textbooks are written in German. I didn't know I was reading about "Reproduction," for example, until we reached a blithe discussion of a molluscan chain fuck, and I had to start furtively paging ahead to see where exactly this text was headed. (Anatomically exact, cutaway depictions of fly-on-fly action. But mammalian fun 'n' games was limited to a pretty modestly photographed pair of cats)

Their boy ID is so strong that we actually got into a disagreement about the heroine of a chapterbook. Both sons were certain she was a boy-- I think they literally cannot concieve of a girl liking kickball-- and I kept saying, no, Junie B is a girl, just look at her name. But this series has been written with relatively infrequent use of gender pronouns, so I couldn't seal my argument.

The issue was finally settled when we arrived at an illustration. Oh, she must be a girl, Matthew said, upon inspecting the picture. She's got flowers on her shirt.

Tuesday, February 22, 2005

Aha!

We scientists spend a suprising amount of our time in thinly disguised drudgery, but moments of genuine insight,and the ability to act creatively on them, make up a huge perk which brings us back to the bench. Psychologists have historically used several criteria to distinguish insight-based problem solving from regular schlepping along. Solvers must get stuck, coming to an impasse in solving the problem. Then, some sort of processing occurs-- the solvers have trouble saying exactly what. Then--pow!-- the light bulb flashes. A solution arises, and the solvers immediately recognize the rightness of this solution, and often are psyched as hell. But what's going on in the brain?

Advances in imaging technology are enabling scientists to look at how the human brain does its amazing job. fMRI, or functional magnetic resonance imaging, is fast enough to allow scientists to see rapid (about 5 seconds) changes in brain activity. Early last year, scientists used this technique to investigate brain activity during the experience of insight.

To find out what goes on behind the curtain during insight, the researchers designed a set of verbal puzzles that would be solved insightfully about half the time, and more conventionally about half the time. Volunteers who were given the puzzles were asked to report whether they solved it by insight or by grinding by pressing an indicator button. Analysis of fMRI images showed that self-reported insightful episodes were associated with more brain activity in the right anterior superior temporal gyrus. The authors cite earlier studies of this brain area to speculate that the elevated activity represents a churn of semantic processing needed to solve the verbal problems. The scientists then used a second imaging technology, EEG, on a new set of volunteers, to confirm the activity in this region. In the EEG work, they even found a second electrical signature which seemed to correspond to a shift from unconscious to conscious knowledge of the solution.

It is important to realize that fMRI is being used to report differences in brain activity, which is why the authors had to take such care to match the volunteers' activities in every respect except the feature they were looking for. In fact, the major result of this work is that insightful problem solving really can be distinguished from other modes of arriving at an answer. You'd expect that a really thorny problem would tax many parts of the brain, regardless of the mode by which the answer was produced. In my own experience, insightful or "aha" progress, in which the nub of a problem finally becomes apparent, is usually followed very closely by a more conventional brainstorm or fleshing-out of the idea.

Meanwhile, the Mozarts all around me never even seemed to break a sweat. I wonder how they do it.

Sunday, February 20, 2005

remake yourself

Kristen Philipkoski at Wired has a great report on progress using stem cells to regrow injured or surgically removed tissues. Stem cells, which exist in many places (possibly all tissues) in adults, contribute naturally to injury repair in places like the skin and liver (I'm sipping a beer as I write this), and enhancements of this natural ability may be the first clinical applications which come from understanding of these cells. The improvements that Philipkoski covers include stem cell-produced fat cells for breast reconstruction, and possibly skin stem cells to reverse the signs of aging.

But all of this is too shortsighted. Any reader of Douglas Adams is going to want stem cells for what they can really do. In short, I want antlers. Get me some neural crest stem cells, ply them with fgf and whatever else is coking up the springtime brains of male ruminants, and implant those suckers under the skin of my forehead. Now we'll see who gets the last croissant.

Actually, the triceratops frill was also probably crest cell derived. Yeah, baby.

Makes it a problem to get in the car though. Hmm, the price of leadership.

Jose Canseco- say no more

Bryan Curtis has a hilarious review of Canseco's steroid-addled memoir, Juice, at Slate. My personal highlight has gotta be using a machine gun to shoot sharks. For a more contemplative perspective, check out Scamboogah!! (How do you pronounce that, anyway?)

Life on Mars? or recycled news?

UPDATE: NASA is backing away from this story. See the bottom of the post.


Space.com is reporting that scientists operating earth-based observatories have seeen additional spectral signatures of microbial life on Mars. For some time, several groups have seen methane in the Martian atmosphere, even with fluctuating levels. On Earth methane can be produced by microbes (i.e. cow farts) or by geothermal processes. Since Mars is tectonically dead, the presence of geothermal processes in itself would have been very interesting for life hunters. But, since methane is not unambiguous, the hunt has been on for spectral signatures of a second organic. For a while ethane was the hot ticket.

The recent work-- apparently only submitted so VERY preliminary-- is the result of studying microbial communities in Rio Tinto, Spain, (earth). This region is very acidic and has similarities to the geography observed near the Spirit Mars rover landing site. It you made it very cold and very dry as well, you might have Mars. Space.com is saying that scientists have found microbial life underground at Rio Tinto, which perhaps is releasing some diagnostic compound, which is not made by known geological processes. . I'm guessing it would be sulfur-based.

Wow, I have been popping around technorati. There is a ton of cut-and-paste blogging going on. I got the Space.com report verbatim at least 3 times. A couple of people, including Suicide Girls (I only read it for the articles, honest.) are talking about observations of the mineral jarosite , which is seen on earth near hot springs. Hmm, Suicide Girls and hot tubs? Anyway, According to wiki, this is also old news ("old" meaning 3 months old)

So what exactly is new here? Not sure, except maybe the explicit link to underground living.

UPDATE: Space.com has been contacted by NASA administrators who say that the work in question is not construed as proof of life. I have to say, from what i could gather, it appeared to be an incremental improvement over last year.

Still, this is very important. Proven life on 2 out of 2 known domains of liquid water means you can pretty confidently predict it's also somewhere else. Seeing and characterizing that life can tell you much more about what it takes. At the end of the day, these researchers can piss in a pot and send it to Nature, and it'll get in-- And I'll read it, too.

Friday, February 18, 2005

Titan emerges from the Haze

The Cassini spacecraft flew by Saturn's moon Titan on Tuesday, and in this case both optical and smog-penetrating radar instruments were trained on the same region of the planet. The combined effort revealed the only crater, a very large one , yet seen on Titan. The crater walls are heavily "weathered" with whatever is going on in Titan's atmosphere.
You can see pictures of the crater at the ESA site here , and a nice write-up at Wired is here.

The Eyrie also has a very interesting rumor about some new Mars observations. Go have a look. Now, where are my hiking boots?

Thursday, February 17, 2005

Anatomically modern Omo fossils are very old

The NYTimes reports on an article to appear in Nature today that fossil remains originally found in 1967 have been re-dated with a much older result than previously reported. The Omo remains (Omo I and Omo II) differ slightly, but Omo I is essentially modern human in its features. The new dates, 190,000 years old, make them the oldest modern remains yet found. Those dates also come into line with estimates of the age of the human lineage from genetic evidence. (A blog which covers mitochondrial DNA dating is Dinekes . ) Together, the case looks pretty strong that anatomically modern humans arose in Africa. The Times, and The New Scientist , emphasize that the older date for these fossils suggest that humans stayed in Africa quite a while before dispersing.

The distinct look of the Omo II remains, combined with the very close dating results, again emphasize that humans evolved for quite a while alongside many closely related hominids, including Hobbits and Neandertals. (The Omo fossil beds have also yielded Homo Sapiens Idatu (elder) .) Very likely H. Sapiens Sapiens (we) killed them all, either directly or by outcompeting for their ecological niches. Orangutans and gorillas are next.

UPDATE: The US National Science Foundation, which funded part of the work, has a good description here. The work of dating the fossils required some effort- they trouble locating the site of the 1967 dig. They finally were able to use National Geographic footage to find some landmarks, collect the stratigraphic samples, and date the remains. You gotta love the sidebar, with its pictures of spear-carrying natives. Come on!

Wednesday, February 16, 2005

Xtreme sports Mars

The ESA's Mars Express spacecraft takes amazing stereo photographs of the surface, which can then be rendered in "airplane's eye" perspective like this spectacular panorama of the Valles Marineris canyonlands. Makes me want to get my hiking boots. Oh, and my UV shield, oxygen supply, water, food, and full-body thermal protection.

Tuesday, February 15, 2005

Hobbits in limbo

Some very important paleontological remains are being kept away from their discoverers by another scientist. The bones of the "hobbits," small meter-high people who may well be an entirely new species of hominid, are being kept by an well-connected Indonesian anthropologist, Prof. Jacob, despite repeated requests for their return to the Indonesian Center for Archaeology. The situation is somwhat delicate, as Australians led the discovery team, and if they push too hard they may be denied permission to dig further.

Carl Zimmer at The Loom has also been following the dispute over these remains. He links to a translation of the Professor's defense, dated Decemberish. The professor says that it has been a longstanding agreement between the ICA and his lab that hominid remains go to him at his Yogykarta lab. He raises the possibilty that the physical anthropology in the original report was sloppy, then spends the rest of the long essay crying foreign interference and generally digging in his heels. It's pretty clear, as of that writing, he'll give them up when he's good and ready.

Casts of these remains have already been made (one set is at Oxford )
but the DNA in the original samples is priceless. High stakes stuff.

By the way, check out Zinken , a cool archeology site, which gave me the Oxford link.

Elections technology- getting better

Wired Magazine reports that on the Caltech-MIT Voting project(you can follow the Wired link to a pdf file) that the 2004 electoral returns showed an improvement on 2000 with respect to ballots scored as "residual," that is, without identified a presidential preference. Estimates run that about 1% of voters intentionally do not vote for president, but returns above that percentage suggest counting problems. The measure for residual votes were 1.1% in 2004, compared to 1.9% in 2000.

Wired reports that credit is due to, believe it or not, throwing money at the problem. States which improved ballot design and implemented tech upgrades (including Florida) showed the best drop in residuals.

There's still a lot to do, especially right at the polling place. Check out this older Tech Review piece by Ted Selker of the Voting Project for examples of poll place sloppiness.

Food chain

Joseph at Corpus-Callosum talks about a young girl he admitted as a medical student. He was suspicious about a sinus infection, and ordered sinus X-Rays, and it turned out that she was suffering from histiocytosis X, meaning her skull was full of holes. It was very lucky she'd gotten the test.

The point of his post is how the glory hogs took over a medical student's good guess and turned it into an advertisement for the university. This reminds me of my doctoral defense, in which my first slide was "ten signs it's time to graduate," modeled after David Letterman. Just before my talk, my advisor stole the joke! When I ribbed him about it, he didn't miss a beat. I should wait until I'm a group leader-- then I can steal material too.

And so it is. I'm getting ready to move up in the food chain. I hope I get students who guess lucky, so I get to hog some as my job description. Who says heterotrophs are more primitive than autotrophs?

Monday, February 14, 2005

Self-love

There's another take on the psychology of romance in the New Zealand Herald. In this view, called implicit egotism, people's good feelings about themselves cause them to be more greatly attracted to "nearly anything associated with the self." This can affect choice of dogs, places to live, or, of course, romantic partners, as shown by statistically measurable "assortive" choices.

I like this article because it does not try to relate this to an evolutionary drive but instead sticks to phenomenology. But at the same time, it's pretty weak phenomenology! The measures in the dog story are not far above statistical noise.

I think psychologists should consider that, for example, that the marriage market is not optimized (for example no one can meet all eligible partners worldwide),and for this reason alone a reasonable fraction of people are going to marry "within the village." Beyond that, I think compatibility is a big part of the work of marriage (or business partnerships), and shared cultural values can help. For both these reasons, I think physical resemblance and other traits which segregate with geography/culture might appear in marriages and partnerships for very trivial reasons. Once these geographical factors are subtracted out, I think you'll find very little self-love there. I can't explain the dog stuff though.

What I do believe very firmly is that the judgement of "like me" versus "not like me" informs pretty much our entire lives.

Friday, February 11, 2005

Blowing in the wind

The Huygens probe which touched down on Titan last month was a huge success, but amid all of the excitement it emerged that an experiment designed to measure atmospheric windspeeds might have been doomed, because the relevant relay on the orbiter Cassini was never turned on. Now, via Slashdot, the ESA is reporting that earth-based telescopes in fact were able to pick up much of the transmission.

Sounds like a good thing. I had read that the principal investigator had put more than a decade into designing the instrument, only to have the data lost in space...

Destined for each other

There's an interesting short in this week's Economist about people and their dogs. Volunteer observers were correctly able to match dogs to their owners, in individual photographs stripped of other information. They were able to do this at a significantly higher-than-chance rate. This only seems to work with pedigreed dogs- a second study (this is a hot topic!) found that volunteers were not able to reliably match mongrels with their owners.

The explanation offered is that humans tend to form emotional bonds on an "assortive" basis, most prominently in the choice of mate, but also apparently in choice of pets. Mongrels are less reliably matched, either because no one can predict what they'll look like, or because they get adopted under a wider range of circumstances compared to purebreeds.

They offer an explanation for the evolutionary basis for assortive bonding, which I found a little thin (avoid incest but optimise outbreeding). But it has indeed been documented that married couples can be identified in just this sort of test.
The scientific authors think this phenomenon might affect a number of "gut decisions," for instance choice of business partner. Of course, no one can yet explain Macintosh usage.


Subscription link (Journal of Ethology) is here. I was sorely tempted to break copyright and reproduce the figure 1, showing the lineup. There's some great hair going on there.

UPDATE: Oh hell, if you want to laugh, look here.

Thursday, February 10, 2005

Pay attention!

The NY Times describes how much desk time is actually spent on distractions . Software designers, combatting this trend, are trying to keep people focused. Yeah, right!

This story gets interesting when compared with the fantastic success of children's television shows at attracting and keeping the kids' attention. Psychologists, God bless 'em, have designed these shows to be "sticky, " getting kids to deeply commune with the idiot box. And this means daddy can do his blog in peace. Even the Gray Lady of kidcrap, Sesame Street, has been affected. The key seems to have been event pacing and a melding of fantasy and reality elements.

Of course, their valiant effort has had strange effects for some.

Now, would adult workplace productivity increase if Big Bird started flitting around every fifth minute? Maybe not. Our lab resembles the Teletubbies set in any case.

Next up: ant paratroopers

Today's Nature reports tree-dwelling ants who return to their home trunk by controlled free-fall. Scientists videotaped the bugs twisting their torsos to direct their flight path toward the home trunk, with an 80% success rate. (No word on the other 20%). Quoth the abstract, "a field experiment shows that falling ants use visual cues to locate tree trunks before they hit the forest floor." Who needs Tarzan?

Star Warts and all

Drew at Scamboogah catches a slip-up in a bully's rant, and tears him a new hole. Then he goes back to Dr. Who.

Wednesday, February 09, 2005

Genome to proteome

This is a great article in Technology Review about an effort to take the human genome, the DNA sequence, and figure out a whole lot more about the "proteome," the set of all the proteins it makes (usually with reference to a specific cell-type or stimulation condition).


UPDATE: I got over to GRID.org , the organization which is attempting this. Remember that the DNA sequence of the genome can, with first pass analysis, be broken down into regions which look highly similar to known genes, and other regions which look properly configured to be a gene but remain hypothetical. These are sometimes referred to as "open reading frames," or ORFs. (Bloggers are not the only ones saddled with a tin-ear jargon). What GRID would like to do is use computer power alone, lots of it, to predict the 3 dimensional structure of the proteins which would get made, in the case that the ORF is really a gene. It has been a strange empirical observation that structural data sometimes reveal similarities which are not apparent from sequence data alone.

So most of the novelty involves getting the computer power together to achieve this leapfrog calculation. So they're taking a page from the SETI search and asking people to donate their leftover desktop power to compute these structures. Based on their stats page, it looks like they have more that 1.2 million CPUs at work on any given day.
I think it's interesting to compare this way of doing things with the brute force approach of actually observing everything a microbe makes, at the RNA and protein level. I can't quite tell who's pulling more oxygen.

But I'd love to see those data...

Tangled Bank is up

The Tangled Bank carnival of science-related blogging is up over at about town. . I don't have any dog in that hunt, but there are some interesting posts.

I especially liked Revere at Effect Measure with a series of posts about the Avian Flu. I have noticed headlines saying that this year will be bad. There's quite a lot of info about the economics and public health situation in Southeast Asia that keep amplifying this process.

Darwin on steroids, or rather growth hormone, indeed.

Tuesday, February 08, 2005

World without Darwin

A pretty unwieldy essay by Freeman Dyson appears in technology review . Dyson, who's not afraid to think big , manages to summarize 3 billion years of earth life, and pummel biologists besides, all in about 500 words.

So to take a tiny piece of this essay, he talks about prebiotic chemistry on earth, in which chemical reactions resembling the essentials of earth life (see here for an introduction to the idea of a "minimal cell") took place probably in the absence of one another. In this case, Darwinian selection, in the sense of survival and propagation of organisms, would not take place, and instead the cocktail would be a community sharing resources (and possibly genetic information). This, Dyson says, is life before Darwinism.

Yes, I would say, "life" without beaks of finches, but not necessarily "life" without natural selection. In fact, quite a lot of speculation on the origin of life centers on the idea that the right kind of chemical soup might self-organize, with more efficient reaction centers somehow shouldering aside their less efficient neighbors-- i.e. natural selection at the level of individual lipid micelles, or grains of clay, depending who you read. Not that this is thought out-- not by a long shot-- but I would consider Dyson's restrictive definition of Darwinism as tossing out your tool kit right when you need it most.

Dyson goes on to say that humans are making a evolutionary hash of the biosphere. I agree, but again, natural selection predicts how exactly this is happening. Anthropogenic processes are making ever-more-powerful parasites and ever-more-vulnerable crops. But this isn't post-Darwinism. If anything, it's Darwin on steroids.

Automated rudeness

The Register describes an experiment in which a computer picks on volunteers. Experimental subjects play "catch" in an online ballgame, and are told the other participants are also humans. Actually, though, one is just a computer, and at a set point the computer starts ostracize the volunteer, preferring to throw to other players. Apparently this is a pretty traumatic experience. The volunteers' brains light up in the anterior cingulate, an area associated with distress, when the computer starts playing its little mind games. No word yet if you can actually hear a snicker from silicon-based life.

Following an unfortunate round of post-experiment downsizing, the computer found work at this food court .

Subscription link is here , and a possibly free link (Science 2003) is here. You'll have to wait for those fries, though.

Monday, February 07, 2005

Genomics is hard, part II

There's a nice synposis in PLOS Biology about measuring the power of comparative sequence analysis in decoding new genomes. Basically, the mammalian genomes already sequenced confers a great deal of power to this type of analysis, but the choice of the next genomes would affect how quickly the power of the analysis would increase. Using the measure described in this article can help set priorities, especially in an era when resources are limited.

The first line of attack in understanding any newly sequenced genome is to identify sequences which are conserved between your new genome and in some related organism (i.e. mouse-human). However, there is a law of limiting returns at work, especially as you try to determine the importance of very small features of the new genome. The availability of the a single reasonably close (but not too close) relative allows you to unambiguously score conservation of features down to around 50 base pairs (already incredibly small!). But to go smaller, down to 5 base pairs, you need 5 genomes, ideally from species which all diverged at the same evolutionary moment.
So the take home message (public access article) is that successful identification of "big" features (the author gives a measure for bigness) can be achieved by a relatively small number of genomes, but the effort for the "smallest" features requires asymptotically more effort, with the exact position of the curve depending heavily on the evolutionary distance among the input genomes. At one point the analysis talks about 130 genomes. I wonder if that would ever happen...

Dan Gillmore: open the gates

Dan Gillmore talks about how newspapers could benefit from the blog phenomenon. I think the phenomenon he is after is something like Wiki, where knowledge (and the effort spent communicating it) is collected from a large number of volunteers. Gillmore argues that newspapers could benefit from becoming clearinghouses in a similar fashion; where the newspaper's brand name and distribution advantages (bazillions of hits on their web pages, for one) mean they would bring something to the table as well. Give it a read. It's interesting stuff.

I spent part of the weekend clicking around Green political sites, and I see the Democratic party is also getting a lot of criticism, on many of the same points (wishy washy being prominent), from its left wing as comes from the right. There are some similarities here to Dan's scenario-- you have a beleaguered but respected institution, good DNA, just a little shopworn. Could bloggers help? I don't think politicians are as susceptible to the blog swarm as information vendors are, and let's face it, Dan's speaking from a position of strength when he's preaching to Knight-Ridder. I'll have to think about this.

UPDATE: While I'm thinking TAPPED has been at work, with write-in suggestions of "what does liberalism stand for?"



But also one should keep in mind that Google, which I consider the frontline of information evolution, is suffering from growing pains which look an awful lot like the tragedy of the commons. When you generate value, you have to defend it. This is trickier to do when you are working in an open environment, and Google has had a few missteps.

UPDATE: A little bit off topic, but Crooked Timber also talks about the interface between blogging and expertise, in this case scholar-bloggers (yech.) Anyone who quotes Nietzsche has a greater acid tolerance than I. (I did quote Graham Greene once.) But-- a legitimate point-- you can't be a scholar on every blog post. It's no fun, and-- hell, you can't.

What fraction of time do bloggers spend wondering about the significance of blogging? Short answers only.

Sunday, February 06, 2005

What's on your doctor's Ipod?

I feel kind of guilty about propagating this, but I can't resist. It looks like a radiologist intern has reprogrammed his Ipod to carry around CT scans. It's open-source software, so you can download it yourself if you follow the link.

The reason I feel guilty-- and you can sort of sense the exasperation of the radiologist-- is that the only reason anyone cares is because it involves an Ipod. They have a 40 gig capacity, which means you can put a lot of hernias in one place. But the intern only did it because the average file is too big for a DVD. Quote:"it's a matter of time before people figure out that the iPod is just [an extra] storage device."

But I could not remain silent when I learned that he only has filled 1% of his drive with music. Someone, please help this man!

Friday, February 04, 2005

Genomics the hard way

(UPDATED 8 Feb). In today's Proceedings of the National Academy of Sciences, the Shewanella Federation, a consortium of genomics-oriented labs and companies, will describe how they have "fleshed out" the genome of S. oneidensis, a bug which is capable of sequestering heavy metals and might be useful for bioremediation.

Sequencing of long stretches of DNA has become so fast, these days, that publishing a newly sequenced microbial genome hardly raises an eyebrow anymore. The problem researchers now face is that the work has only begun with the raw sequence. Much work goes into annotating the sequence, that is, figuring out which regions code for proteins, and how those proteins contribute to the life cycle of the microbe. One can take a shortcut if sequence analysis turns up a sequence for which the function in a close relative is known. But genomic data also yield large numbers of so-called "hypothetical genes," consisting of sequences which appear to be correctly configured to specify a protein, but which cannot as yet be confirmed as actually making something, let alone for what function.

The consortium's work here was huge: nearly 40% of the potential genes in S. oneidensis, nearly 1500 sequences, were considered hypothetical. They decided to tackle the whole set of hypotheticals by analysing large numbers of bacterial mRNAs and proteins using high-throughput methods. They managed to positively identify about a third of the hypothetical genes, about 540, as actually being made. But a larger number, 592, were identified using the protein efforts alone, and in fact some of the "dropout" candidates (identified by protein, but not protein+ mRNA) could be reconsidered for technical reasons. So they think that the protein test was probably the more critical for deciding if a given stretch of DNA was actually a gene.

I think the interesting trends here are the massive collaboration going on, and the careful selection of target organisms. Functional genomics is expensive to do, and these projects end up looking like big science as more commonly seen in physics. The worry is that these mammoth projects will suck the funds away from smaller scale stuff. I'm a small-scale guy myself, but I am really fascinated by the possibilities here.

But you don't want to do it on joe microbe. To throw that much money at a problem you'd better want to know answers pretty badly.

Doing the math

Phil Carter at Intel Dump predicts some spectacular infighting during this session of Congress, as budget cuts come to Defense. Slated to get retired: the aircraft carrier JFK, with home port in politically vital Florida.
It seems that these extended brawls are the price we pay for constitutional checks and balances.

In a later post, Phil describes the story of Paul R. Smith, who will receive the Medal of Honor for sacrificing his life for the safety of about 100 other soldiers and a medical clinic. It is just phenomenal what the people out there on the lines are capable of. (Links are copied from Phil.)

Thursday, February 03, 2005

Dial-a-ref

This is just awesome. The case of the corrupt ref has an even greater wrinkle : In a game which had been pre-arranged for 35,000 Euro, the ref Hoyzer gets a TEXT MESSAGE! on his CELLPHONE! at halftime, saying that, if he delivers the game, he gets 50,000 instead. What I'm looking for in the future is remote play-by-pay, possibly to be performed by Ebay: the ref blows his whistle, runs the auction, and decides whether the foul was a "play on" or should be punished by death. By the way, these mobsters had some cash if they're paying 50K for a B-league game.

Two other refs are implicated in the corruption scandal: a guy named Marks and another named Schiri Jansen. Now, Jansen is really a big fish, and referees A-league games. Klaus Topmoeller, the coach who lost his job (after a match that was called by Hoyzer) is now saying that Jansen threw a late-season match Leverkusen versus St. Pauli (same as the beer) in 2001. Jansen called a suspicious hand-ball in the closing minutes of that match which tied the score, and Leverkusen lost the season championship based on that result. Jansen is insisting on his innocence "otherwise may I be struck dead." Does he wear a cell phone to work? Topmoeller is a bit hard to believe, as he seems to be claiming now that every downturn in his whole career has been caused by bent officiating.

Mac Mini skepticism

I can't tell what I enjoy more- reading about new Mac toys, or reading the skewering reviews that always come a few weeks later. People seem to get their creative juices flowing either way....

Beer munchies

Laboratory rats have confirmed their place at the pinnacle of evolution: not only do mothers turn down cocaine in order to care for their young, but they even manage to reduce their calorie intake when they're drinking alcohol.

In the current study, UF researchers made alcohol more palatable by adding it to decarbonated, non-alcoholic beer, which also allows scientists to precisely measure the alcohol content. In a separate test they presented the alcohol mixed into a sweet gelatin. (emphasis mine) Both male and female rats cut back on their calories from food and maintained a consistent intake of overall calories during the experiments, even with access to plenty of food, fresh water and palatable alcohol.

Humans were apparently discouraged from participating.

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It could be your neighbor

This publicity blurb begins on a funny note:

One in five mammals living on Earth is a bat...


So don't expose your neck to just anybody!

Tuesday, February 01, 2005

Link spamming explained

The Register explains the economics and ethics of link-spamming, i.e. filling up a blog's comments with links to porn, pills, or casino (PPC) sites. This boosts the PPC site's Google rating Meanwhile, the poor blogger is swamped with unwanted and off- topic comments.
Here at Keats' Telescope, we (ahem) don't seem to suffer that problem. Still, it's interesting watching Darwinism at play with different toys.....

UPDATE: The Register had an earlier post about Google's nofollow tag. Basically blogs are doing weird things to the web economy. As Homer Simpson would say, "crisistunity!"