Saturday, April 30, 2005

Hot vent worms keeping cool

Science Now has a short article about Pompeii worms, which grow right near hot vents at temperatures up to 80 Celsius. The worms live inside little tubes and appear to keep cool by sucking sea water in via a kind of piston action. Colonies of tube worms then serve in effect as a heat-exchange device , cooling the magma heated waters, which in turn may make things a bit nicer for neighboring bacteria. So, inch by inch as you get away from the vent, the inhabitants change.

What continually amazes me about extremophile communities are the very narrow growth zones, defined by steep gradients of pH, humidity, and/or temperature. You get just a millimeter out of your zone and you're history. Of course, humans can only really live up to few miles above sea level themselves, because of limitations on lung function. Compared to the earth's radius, that could be considered a narrow niche as well.

Friday, April 29, 2005

Mixed review for Hitchhiker

Space.com is loving the Hitchhiker's Guide to the Galaxy.

Wired sees more of a mixed bag . I think Peter Jackson's Lord of the Rings trilogy did too good a job, so now anything less just doesn't feel right.

I love the books so much, I'm sure I'll go see it anyway.

Pyramid? why not dodecahedron?

Via metafilter, a nice parody of the new USDA food pyramid is at mypyramid.org.

(The actual release is at mypyramid.gov. )

Thursday, April 28, 2005

Apert's Syndrome and Selfish Sperm


(The sperm scene in Woody Allen's Everything you always wanted to know about sex )

If economics is the dismal science, then the study of the natural world can't be far behind. The continual message is that selfishness is everywhere. In he April 19 issue of PNAS Goriely et al. report that a mutation causing Apert's syndrome, a craniofacial condition with severe health consequences, occurs at far above background levels compared to other sorts of mutations. Even though its effects are very detrimental to the humans who have it, the mutation is "favored" because it confers an advantage to the sperm precursors which carry it.

The mutation in question affects the DNA sequence for FGF receptor 2, resulting in a mutant receptor protein, called Ser255Trp, which is known to have innapropriate activity. (This mutation is genetically dominant, meaning that one mutant copy is enough to cause disease.) Goriely et al. had earlier observed that de novo mutations resulting in Ser255Trp are exclusively inherited from the unaffected father. Moreover, these mutations occur at more than 200x background level, and in particular are seen more often than other possible mutations at the same site. These two observations together suggested that the frequency of the occurence of this particular mutation was being enhanced in the father's sperm.

The current work follows up on these observations with three additional experiments to strengthen the case that this mutation is under selection during spermatogenesis. First, they analysed semen DNA for mutations in the sequence FGF receptor 2, and found mutations creating Ser255Trp were detected at nearly 19 times the rate of mutations at nearby spots (just outside codon 255; overall rates are approximately 1 in a million sperm). Thus this DNA region is not just error-prone; sperm bearing mutations which lead to Ser255Trp are specifically enriched. Secondly, during this work the scientists identified a fourth instance of a person with TWO sequence substitutions on this same (codon) spot, a conjunction expected to occur less than once in the entire human population. Finally, and most importantly, they show that the FGF receptor 2 is present in normal testes during sperm production. Thus there is "motive" and "opportunity" for the excessive activity of the Ser255Trp protein to directly affect sperm production.

So sperm bearing mutant DNA encoding Ser255Trp are present in a highly skewed proportion. Earlier work has shown that diffferent FGFs (the proteins which which stimulate FGF receptor) are present in distinct spots in the adult testis, and affect proliferation of cells giving rise to sperm. What would really nail the story would be to show that FGF10 or FGF2, the FGFs which overstimulate the Ser255Trp receptor in the human Apert's syndrome, are present in these spots. (Remember that the Dad's bodies are negative for the mutation.) But for now, the story is quite convincing that more mutant precursor cells give rise to disproportionately many mutant sperm, which in turn gives those sperm a numerical advantage in the contest to fertilize the egg.

In the end, the constant proliferation giving rise to sperm sets conditions for genetic selfishness analagous to what is seen in tumors. In cancer biology, cells with excessive proliferative capacity are not penalized, but rather come to dominate the tumor, even to the detriment of the host's health.

Wednesday, April 27, 2005

Science by the people, for the people

There have been a number of posts on Metafilter and especially Buzzmachine about how the reduced costs of communication associated with the internet have changed the job description of the media. Reporters as specialists are being overwhelmed by numerous nonspecialists who, in aggregate, make up a kind of market wisdom-- the pajamahadeen (spelling?). Control of access, content, and even reportage are going to pass over to the consumers of news; and current organizations which ignore this trend will likely get bypassed. (I just spent part of the morning looking in vain for an RSS feed for the LA Times. Since the WaPo and NYTimes have them, this means my daily news aggregator includes them, and e.g. Slate, but not the LAT. )

What's important in this trend (see especially the Metafilter comments, which resemble the spats between the Palestinian People's Liberation Army and the People's Liberation Army of Palestine in Life Of Brian ) is that decreased costs define the sea change. Items which still cost are less affected. For example, it costs very little to be a blogger (caffeine expenses nothwithstanding) *BUT* is still costs quite a lot to maintain the internet backbone. (And Google runs blogspot with some anticipation of profit as well). So the costs of some kinds of dissemination have fallen through the floor, but, to stretch the metaphor, the house still has the same four walls.

I remain very interested in how these changes might influence the way science is done and disseminated. I operate in two distinct worlds as scientist blogger. On the blogger side, reduced information costs make it very cheap for me to learn quickly (at the dilettante level) about a big variety of things. I'm loving it, but don't take the product so very seriously. On the scientist side, what has not changed is thinking, messy results, and general banging of my forehead against rather pricey walls. This is Coturnix's repeated admonishment that good science is muddled out in pencil on paper, before beginning the technical side.

(Nevertheless, connectivity has made deep inroads. I have not been to the paper library at our institute in my entire 3 year stay, because I download everything.)

Back40 at Muck and Mystery gives a few hints about what a distributed science might look like. Diverse groups of problem solvers can outperform groups of high-ability problem solvers, within parameters. The distinguishing feature of this "skunkworks" model, in my opinion, is its (dare I say it?) collectivization of both effort and credit. And, within parameters, this is going to be the better way to do things. I think for some very hairy scientific problems, the pajamahadeen, distributed model is going to be the way to go. I'd better sit down with Ayn Rand and have a talk about this.

UPDATE: Some more thoughts: At Tech Central Station, Glenn Reynolds is a known blog triumphalist, but in any case he's saying similar things about changes in the media. I thought a bit more about the science side. It seems that institutional science is actually quite dynamic, with certain data-generating procedures very rapidly outsourced as soon as they become routine. In my own time, oligo synthesis and sequencing have become entirely outsourced; and cdna cloning is not far behind. That is, scientists' job descriptions migrate pretty steadily toward the expensive, the once-off, the technically demanding. This occurs for many reasons, but it may mean science is a different sort of beast entirely than the newspaper industry. (See Back40 on Celera's human genome coup however. There are disruptive technologies in science as well.)

YET ANOTHER UPDATE: Teambuilding at New Scientist . In their case a pecking order is built in.

Celera is getting out of the database business

From the New York Times today, Celera Genomics is going to stop selling subscription access to its genomics databases, instead transferring the information to the public. According to the Times, their subscriptions have been steadily declining, and this is a good way to generate goodwill. In our laboratory, we've been splitting the difference between Celera and the public databases for some time already.

Data brevia, ars longa. It is very hard for a scientist to sit still, even having amassed a few more data points than the other fellow (although it never hurts). Data are like new cars, losing a chunk of their value as they drive off the lot. Celera is an extreme example of this value decay.

Organic soup in Titan's atmosphere

The Cassini probe continues its looping through Saturn's moons. It flew by Titan in its closest approach yet on April 16, coming about 650 miles from the surface of the planet. (A great summary of Cassini's discoveries is here.

A major new result from the recent flyby has been that very complex organics (for example benzene and nitriles) were detected at this height above the surface. In fact, even larger compounds are suspected, but could not be detected, as they fall outside the calibration range of the mass spectrometer. It 's been known that photochemical reactions form these compounds, but at Titan's cold temperatures they should have rained out of the upper atmosphere. (Benzene is also a liquid on Earth.) So something is churning the atmosphere to keep stirring the soup.

The photochemistry of Titan is regarded as an example of potential sources for complex organics necessary for the emergence of life in early Earth. Photochemically generated organics, like those detected in Titan's atmosphere, might also have been generated on the early Earth (and they're still being made in urban smogs), and may have provided the early building blocks for life. Comets contain a similar suite of molecules. However, it's hard to see how cometary organics could make it safely to earth's surface, because the impact energies of big comets (micrometeorites-- space dust-- being an important exception) should incinerate any of these compounds.

Tuesday, April 26, 2005

Monday, April 25, 2005

You'll put your eye out

From the immortal Straight Dope series, you really can knock your eyeball out from its orbit, if you do it just right. I thought that's how they used to do lobotomies as well.

Laid up

I tweaked my back lifting groceries on Saturday and I've been hobbling around ever since. Most of the trauma comes from getting in and out of bed. I need that bed from Wallace and Grommit which dumps Wallace straight downstairs, through his pants, to the kitchen.

Friday, April 22, 2005

Suspended animation

Science magazine has a very brief letter reporting that mice which inhale 80 ppm of H2S (hydrogen sulfide, the stuff from rotten eggs) fall into a hibernation-like state with very low heart rate and oxygen consumption. The effect is reversible, so that the mice, when returned to normal air, recover. From what I could gather from the Science letter, H2S shuts off the mitochondrial energy supply, so this should have some similarity to cyanosis? Confusing.

A good BBC link about potential uses for this discovery with humans is here.

UPDATE: I couldn't believe that the mice could survive after being knocked unconscious by H2S. A longer story with a partial explanation is at Red Nova. . The story there is that the balance between oxygen and the H2S is critical. When they give the H2S they have to lower the oxygen a great deal. I have to say, I'm getting a bad feeling about this. Either there is sloppy reporting, or sloppy science, but I still don't have a reference trail to what's going on.

Thursday, April 21, 2005

Tougher than nails

There's a nice blurb at Eurekalerts about microbes growing in pH of 1, which is acidic enough to corrode nails. It seems that there's a whole ecosytem, including algae and mycobacteria, living just inside porous sandstone and possibly eating mineral or thermal energy.
The Editor's summary in Nature is here.

colorado042005_3sm
(Image is from the Eurekalert )

The astrobiology angle is basically that these microbes' niche is an extremely narrow physical space. If the rock bed is perturbed, the microbes are literally toast, generating a lifeless "instant fossil." A robot explorer, coming to an extinct hotspring, could detect this fossil band just by scraping the rock surface.

I didn't quite manage to get this post to talk about bacteria and steel. While googling around for rust and bacteria, I came across this great description of rusticles forming on the wreck of the Titanic. These are iron stalactites, where the iron has been bio-extracted from the Titanic's rotting steel superstructure. Very odd. Ozymandias in steel.

Tangled Bank- the anniversary edition

The 26th Tangled Bank carnival of science-related blogging is up at Circadiana.

Dinosaur vessels are *not* fresh meat

Over at The Panda's Thumb there has been some interesting fallout from the finding of blood-vessel like structures and even preserved red blood cells in a tyrannosaurus fossil. Creationists are seizing on the idea that the find contains its original components (from the living animal) to assert that the find is fresh-- i.e. Created. Dr. GH attacks the idea that the fossil contains original biocomponents, and then forcefully debunks the creationist take, in a long but very worthwhile post.

Dr. GH doubts that the microvessels contain any of the original material. Time is not kind to protein, and fossilization in particular involves rotting and maybe some higher temperatures than you'd like for preservation. Remember: fossils usually consist of just bones, with all the muscle etc long since gone. Moreover, Dr. GH points out that the scientists' methods, following recovery of the fossil, may have chemically trashed anything which may have remained. Removal of the rocky surrounds included harsh chemical treatments which may have extracted native materials. The specifics of the scientists' method were buried in the supplementary information for the paper (approximately four times the length of the maintext. Science magazine is infamous for its uselessly brief maintext methods sections) He quotes their one maintext concession to this point:

“Whether preservation is strictly morphological -- that is, just the shape is preserved; a different sort of fossil, but "just" a fossil-- and the result of some kind of unknown geochemical replacement process or whether it extends to the subcellular and molecular levels -- i.e. whether the original tissue is there-- is uncertain.” 

I have to be honest-- I'm not so sure Dr. GH is being fair here. I never went to the supplementary info, but I knew that the fossils had been extensively processed in order to expose the deeply-embedded bone vessels. I don't see any agenda in the presentation of the paper, even when told that important caveats are hidden in the Supplementary Info. When I read the caveat which I quote above, I thought they got it about right.

And their enthusiastic presentation is fully justified. Blood vessel fossils!!! It's awesome!

However, I may have benefitted from my training to be able to sense the limits of the work. For example, in the maintext they allude to having used anti-collagen antisera, which-- to a person who's never pulled a dirty blot-- might suggest preserved proteins. I just laughed. If I had a dollar for every protein blot which came up "positive..." Collagen-like molecules such as keratins from human skin are an enormous contamination headache, even in specialist labs. If they did a dot blot without a negative control, this would be a non-result that only a PI could love. Based on this sort of evidence-with-limitations, I had read the whole paper in the spirit of a "glass half full" presentation, emphasizing a positive take on the data. This is perfectly legitimate presentation strategy, although I can see that it does make it harder for an interested outsider.


The second half of Dr. GH's post is on the distortion of the data, which began with the lead scientists, got further muddied in the media, and then got willfully misrepresented on the listserves. Repeated references-- beginning with the lead authors and amplified e.g. on MSNBC-- to DNA recovery and Jurassic Park, may have led to a misunderstanding about the preservation status of the find. Dr. GH is unsparing in criticizing the whole media food chain. This is a matter for much more concern.

Tuesday, April 19, 2005

"Off the map" showing eccentrics and their houses

The CS Monitor Scitech page to a web-only special from PBS/Independent TV service. Off the map features images and histories of houses transformed by their owners. The presentation is very, very cool, but be warned-- it sucks up bandwith.

Antarctic smash-up

An iceberg the size of Luxemborg has crashed into a toungue of ice extending out from Antarctica proper. The ESAs polar Envisat page has some spectacular pictures.

22,514 digits of Pi

Science Now has a story about the memory methods of Daniel Tammet, who last year coughed up a whole lot of Pi in just over 5 hours. Tammet, an unusually articulate autistic savant, is able to explain what he does when he's thinking numbers. He sees numbers as landscapes:

"When I multiply numbers together, I see two shapes. The image starts to change and evolve, and a third shape emerges. That's the answer. It's mental imagery. It's like maths without having to think."

He could recollect the digits of Pi as if he were viewing a film. (I wonder what digit number 22515 was.)

These descriptions of what he's doing are very interesting to psychologists wanting to improve everyone's memories. The Science now blurb talks about an initial test of how important visualization is to Tammet's memorization prowess. Intriguingly, a seemingly mild perturbation-- presenting numbers printed in different size fonts-- greatly interfered with his recall. His performance was forced down to nearly normal levels.

Engaging more than one sense to assist recall is an effective mnemonic technique, so Tammet's speaking of a visual component to his recall (and his sensitivity to visual disruptions) is a very interesting hint. In particular Peg listing , assigns numbers to vivid sensory qualities- furry, red, slippery-- to boost recall of numbers.(link is to Wikipedia). This sounds a bit like Tammet's Pi-film. My other immediate though was of chess players whose memory, even when playing blindfolded, is highly visual.

A nice general site about memory, including the procedural memory of savants, is here . Also, check out Mixing Memory , a very well written cognitive science blog.

Sunday, April 17, 2005

New imaging helps decode Oxyrhynchus Papyri

Via Marginal Revolution , a set of badly defaced parchments (some images are here )containing Greek and Roman writings can now be read using infrared illumination. The Oxyrhynchus Papyri were found a century ago in a dump dating from the late Roman period.

The Independent article treats the news somewhat breathlessly, saying that every day something new is coming out. But the Oxyrhynchus Project seems to say that this multi-spectrum work has been going on since 1997. A bit of perspective at Carnivorous Conservative . The IR imaging seems to greatly extend the number of readable parchments.

UPDATE: via Dienekes , at least one papyrologist is fairly suspicions and is saying wait-and-see .

Take a look at this account of the Oxyrhyncus digs during the late Victorian era. Dust, guns, nervous breakdowns, and biscuit tins. Perfect for Mechant and Ivory, or Monty Python-maybe both together.

Saturday, April 16, 2005

"Water-ful" world

(Title with apologies to Louis Armstrong)

A pair of nice posts at Science and Sensibility about evolutionary insights from sea dwellers: sea squirts and sticklebacks . Calling Spongebob...

Friday, April 15, 2005

Nobody knows I'm a robot

At CNN, some MIT students used an automatic text generator to successfully submit an abstract to a CompSci conference. One gem, obviously indebted to my own soaring prose:

"the model for our heuristic consists of four independent components: simulated annealing, active networks, flexible modalities, and the study of reinforcement learning"

Got a problem with that?

Follwing revelations of the the author's true nature, the abstract's status has now come under review.

Domestication of animals may have taken time

I'm intentionally giving this an unexciting title because I'm disappointed. There's a great-sounding title in this month's Trends in Genetics: Genes of domestic mammals augmented by backcrossing , which unfortunately lacks a punch.

Sequencing of mitochondrial DNA (which is only inherited from mothers) from most domesticated mammals- cattle, sheep, goats, pigs, dogs - indicates that each species was probably adopted from the wild only a few times. This is in agreement (Wikipedia) with archeological data. The note of the current paper is that other DNA regions (in this case parts of the MHC locus) are far more diverse and require a bigger founding population. The proposed modification of the existing theory is that genetic diversity was augmented by crossing in wild animals (Males? They would not contribute to mtDNA) into the domesticated group.

I just don't think this should suprise anyone, not even the ones who published the mtDNA surveys. Of course there would be a transition period in domestications in which genetic flow was a bit more, well, fluid. Especially if the animals tend to end up as dinner, a backcross may have been the way to keep herd sizes reasonable.

What would get me excited would have been to map out regional MHC diversity- to take an extreme example, did Chinese pigs get backcrossed with Chinese boars, and British with British? Detection of "wild" MHC alleles in local domestic populations would have been a much more direct demonstration of the principle. DNA should not be that hard to come by..

Biophysics of fastballs

Noam Scheiber at Slate explains why fastball speeds probably won't ever go much more than about 100 mph. Basically the pitcher's arm really would come apart at the joints. Yeck.

Thursday, April 14, 2005

Bacteria from ancient brines: at least the brine is ok

Discovery magazine has an article revisiting a disputed claim from five years ago about recovery of living bacteria from 250 million year old salt crystals. Russel Vreeland and colleagues had removed salt crystals from a Permian rock layer from a mine about 500 meters underground; sterilized the outsides; and used drilled cores from these to inoculate growth medium. On three occasions the cores succesfully cultured bacteria related to modern salt-tolerant species- a literal sleeping beauty.

The initial work received a lot of attention but was not universally accepted. There were two concerns. The first one, which they tried heroically to address, is that the isolates were modern contaminants. I still don't think this is closed. The second is whether the salt crystals really belonged in the rock formation from which they were obtained. New salts can force their way into old rock layers.

The new work used two methods to judge if the salts belong in the aged formation. The first test was that the ion composition of the salts is consistent with a brine formed in a shallow sea (and not a modern mineshaft). The second is that gasses, trapped in fluid inclusions within the salt crystals, had been trapped between 60 and 80 degrees Farenheit- again consistent with formation in a seashore, not a mineshaft. (The method used, cooling nucleation--brand new to me-- is discussed here. ) So the salts are at least chemically consistent with belonging to the Permian rocks around them.

My inclination is to accept that bacteria could sporulate for a very long time, especially in high salt. I would be more comfortable with these particular isolates if the DNA were to be a bit more different than modern forms. (They sequenced the DNA for 16S RNA and got a 92% hit to a modern Bacillus).

Wednesday, April 13, 2005

Fuel Cells for your laptop

The Beeb is reporting that both IBM and Sanyo will build methanol-cell power modules to boost a laptop's working life.

If they're not going to let me take it on board the plane, I'm not interested.

I always thought laptops should come with an accelerator pedal. Dual exhaust can't be far behind.

UPDATE: What about Potato Batteries?

Tuesday, April 12, 2005

Micro-market

A quick juxtaposition: Jeff Jarvis of Buzzmachine with Scale doesn't scale, talking about how micro-marketers like EBay, who can connect buyers with sellers at a very small scale, are the future of everything; with Fiona Apple's saga , about a singer, a niche audience (certainly not including me, yeck)willing to pay for electronic download, and Sony. This kind of small potatoes is just not what Sony wants to do, so the album sits unreleased.

Two other remarks, just riffing: it is possible to have vast variety and still no choice-- see cable TV. Secondly, is science already distributed and aggregated into micromarkets? I'm doing my little thing, and corresponding with my colleagues all over, while the person at the next desk does hers....

Monday, April 11, 2005

Parasites in your genome-- it's a jungle in there!

Henry over at Webiocosm reminded me that parasitism appears over and over again in the living world. The cycle of defenses and counterdefenses drives an evolutionary spiral between host and parasite, sometimes even resulting in mutual dependence and benefit.

Recently this evolutionary perspective has been brought to bear on a superficially different phenomenon-- the masses of repetitive DNA, such as Alu repeats , which infest the human genome. Alu repeats, together with other repeat families, make up a staggering 40% of the genomic sequence, without coding for any genes. A recent article in Nature Genetics shows that Alu repeats and their compadres form interactions within the human genome resembling a jungle-like ecosystem. One family of repetitive elements, the LINEs, consists of a complete parasite package, with special DNA sequences flanking a minigene which encodes the enzyme necessary for making more copies of itself. The much smaller Alu repeats take the freeloading one step further, and appropriate the LINE recognition sequences, and therefore are parisitic on the parasites. The Alu repeats are present in the human genome to the tune of a million or so copies. Quite an ecosystem!

One feature to keep in mind with the parasite analogy is that, numerous as they are, these repeats do not increase in a single healthy human. Instead, a new Alu repeat is inserted on average in 1/200 live births. There are statistical indications that Alu repeats are also removed over time, possibly in the male germline, but on the whole, it is a very slow interaction relative to, say, fleas on a dog.

There are two costs to humans with carrying all these repeats. Stable repetitive DNA sequences must be copied along with the rest of the genome with each cell division, which costs a lot of energy. The host might prefer to put this energy other uses (think about a tapeworm with a third of your weight). Secondly, during the less frequent instances when a new copy is made, it may get inserted into an important genetic region, resulting in disease. Both these effects have been seen in fruit flies. More of these repetitive elements correlates with fewer hatched eggs . Thus, as with all parasites, their "success" ends up hitting a wall when the well-being of the host starts to suffer.

However, specific instances have been found of Alu actions on genomic function (I wrote about two examples here and here . In both cases, the location of an Alu repeat ends up influencing gene expression or gene repair). So this set of freeloaders has indeed influenced human evolution.

Petworking

Knee deep in correspondence today...
Wired discusses SNIF, a wearable tracking device for your dog. You can track where your dog goes, and the presence of other dogs wearing a SNIF collar. A central server will even cause your dog's collar to beep distinctive tunes if buddy dogs are headed out for walkies.


Does this have anything to do with toothing?

Caltech versus MIT pranks

Via Slashdot, a scorecard of the various hacks performed by Caltech undergrads during MIT's orientation weekend for pre-freshmen. This is quite a subculture. The CalTech pranks, in some cases, disrupted extra-programmatic activities already planned by the MIT counterhackers.

Sunday, April 10, 2005

Some new data about the earliest hominids

Carl Zimmer at the loom has a nice post about a few recent spectacular homid finds. The braincase of Sahelanthropus, a 7 million year-old fossil found in Chad, has been analysed, and is now definitively assigned to the hominid lineage. The locus of the find, well outside the rift valley regions in Ethiopia and Kenya, has caused some consternation for the camp which believes that Ethiopia is the cradle of hominid evolution. Possibly hominids dispersed far earlier than expected. Or, maybe the story is just too incomplete to judge.

Is it just me, or are these MRI scans of the braincases being given an awful lot of evidentiary heft? About two months ago, braincase scans of the hobbit skulls were also used to definitively assign homo floresiensis to a separate species. Don't get me wrong- the enlargement of the brain is the single most important feature definining the human lineage ( a nice review of recent findings is here ). But I get a bit nervous when everything's getting hung on a single hook. I'd be more comfortable when other fossils are found in Chad, for instance, or more hobbits.

See also John Hawks' weblog for a great writeup of the original Chad discoveries. Even if the braincase stuff doesn't hold for some reason, these are tremendously important fossils.

UPDATE: The New York Times also covers the Nature article. I had misunderstood the claims of the Nature paper: apparently they're asserting that the Chad fossils represent a common ancestors to chimps and humans exclusive of great apes.

Thursday, April 07, 2005

Blogger's performance woes are getting noticed

Wired Mag is running an article on the esteemed Blogger, the host of this blog and other virtual fishwrap. It has been very, very flaky over the last few weeks, and people are getting mad. Item of notein the article: a google search for Blogger sucks is now bringing up more than 750,000 hits.

Wednesday, April 06, 2005

Tangled bank XXV is up

The Tangled Bank Carnival of science blogging is up over at Orac Knows. It's written up as a highly realistic cover letter for a manuscript re-re-re-resubmission. (This literary form can rival Haiku for courtly construction and implied emotion, although, in traditional manuscript correspondence, the "negative space" is thematically limited to anatomical novelties and interpersonal violence. Orac reveals himself as a modern master.) Enjoy!

Non-homo sapiens hominids: think about it.

Both AE Brain and Orbis-Quintus have posted about Homo Sapiens's relatively recent (and maybe continuing) coexistence with other hominid species. Alan is pairing genomic evidence for a recent (relative to chimpanzee) constriction in the H. Sapiens lineage with news items about the global impact of a supervolcano. Not only H. Sapiens, but also Neanderthals and the hobbits came through the last supervolcano eruption. Would their DNA show a comparable bottleneck?

Badgerminor links to the pursuit of the Dwendi, a "little goblin" in the forests of Belize. I am taking the bigfoot/yeti class of stories a bit more seriously with the discovery of the hobbit fossils (which were, after all, only 20,000 years old.) The limit on speculation about contemporary hominid diversity is the global ability of H. Sapiens to eliminate even indirect niche competitors. Wolves are almost gone, because they sometimes eat our sheep. Would bigfoot stand a chance?

UPDATE: Via Syaffollee, the long-suspected cryptid monster-under-the-bed, P. Umbris. We have several in our house, who additionally seem to wet beds.

You only love me for my ipod

An article in LiveScience describes a study of the emerging sociology of public sharing of Ipod libraries. People see your library on the LAN, and they start forming opinions about you. One man was afraid that his Justin Timberlake back catalogue (his excuse: it's my wife's stuff, honest!) would doom his position in the company's pecking order. My favorite epiphenomena from this report, though, sound strangely like the blog world:

People sometimes claim to listen to others' libraries when in fact they aren't interested and don't listen. Some people think their own libraries are unique, while coworkers might view them as just like many others.

Lastly, nobody likes an anonymous deejay."Most people didn’t want to listen to anonymous collections, even though they didn’t always want to talk to the playlists’ creators," Grinter said. "They went to quite a bit of trouble to figure out which playlists belonged to whom. It’s a peculiar social phenomenon. They don’t want to live in a completely anonymous world, especially in the workplace."


I started off intending to make fun of this phenomenon (get a job, etc.) but I do think there's a truth about human nature involved here. I have just returned from a conference, and maybe I'm sensitive to the kind of posturing that this nervousness provokes in me. I have to fight a wish to be all things to all people. In any case, I'll finish this post with Alexis de Tocqueville:

"when one can no longer rely on tradition or authority, one inevitably looks to others for confirmation of one's judgements. Refusal to accept established opinion and anxious conformity to the opinions of one's peers turn out to be two sides of the same coin."


Anyway I like Justin Timberlake, especially his wardrobe malfunction song. My deepest Ipod secret? Kraftwerk. It's amazing listening to them on the trains.

Saturday, April 02, 2005

New staph isolate is the return of an old adversary

Staphylococcus aureus are relatively common bacteria which can inhabit humans without adverse effects. (Wikipedia is here.) However, if they penetrate the skin, these bugs are the cause of many ailments, from minor skin infections to blood infections and pneumonia. A staph strain called the 80/81 staph phage caused widespread infections in repeated outbreaks in the 1950s and 60s. This pandemic was brought under control using synthetic pennicilin analogues; and other staph strains became the predominant sources of infection.

But 80/81 did not disappear. In last week's issue The Lancet, scientists report that a recently characterized clone of staph infections (of the diagnostic category CA-MRSA, for community acquired methicillin resistant S. aureus), appears to be a direct descendant of the 80/81 strain. This variant is quite nasty, associated with skin boils and abcesses even in young and healthy people; and it retains several toxins from the ancestral strain. Right now the 80/81 related isolates can still be treated with a second class of antibiotic, the vancomycins; but other staph strains have become resistant to these as well. This new-old infectious agent could develop into a major public health challenge.

UPDATE: The Washington Post ran an article on April 6 which appears to refer to the same staph isolate (no name is offered). Scary stuff

Islet crossing: from transcription factor to stereo vision

Visual information detected by the retina is sent back to visual centers of the brain for further processing. Special retinal neurons called retinal ganglion cells send long wiry connections, called axons, to visual brain regions via the optic nerve. Most retinal ganglion cell axons cross over, so that neurons in the left retina mainly connect to visual areas on the right, and vice versa. However, a fraction of retinal ganglion cell axons do not cross, and instead connect "ipsilaterally." This arrangement allows the brain to integrate overlapping information coming from the left and the right eye, providing a major cue for mammalian depth perception.

The fraction of retinal ganglion cells which connect ipsilaterally varies from mammal to mammal. There is a fascinating, though imperfect, relationship among mammals between the degree to which the eyes' fields of vision overlap and the fraction of ipsilaterally projecting retinal ganglion cell axons within each retina. In general, species with forward set eyes, in which left and right eyes see more overlapping parts of the visual scene, have a greater percentage of ipsilaterally projecting retinal ganglion cells than animals with eyes set to the sides of the head. This may represent an evolutionary tradeoff between a greater retinal field (in grazing animals favoring panoramic vision) and greater steroscopic vision. Thus primates, with forward facing eyes and extensive reliance on depth perception (think about swinging between branches) have a very tidy separation of ipsilaterally and contralaterally (crossing) projecting retinal ganglion cell axons. Cats, ferrets, and other carnivores have many ipsilaterally projecting cells. Animals like horses, cows, and mice have far fewer. And it is known that sperm whales have essentially no overlap between their left and right eye fields of vision (harpooners used to try to sneak up on them from directly in front) but I don't think anyone has looked at their retinal ganglion cell axons.

During development, the axons of the retinal ganglion cells have to find their way to the correct side of the brain. The decision whether to cross, or to stay ipsilateral, occurs at the optic chiasm , the crossroads where the optic nerves lead to the optic tracts. In the last two years, scientists have figured out quite a lot about how retinal ganglion cells achieve this decision. It turns out that developing retinal ganglion cells whose axons are destined to cross at the optic chiasm express a different genetic program from the ones whose axons are destined to stay ipsilateral. A critical difference lies in two transcription factors (proteins which help control gene expression), Zic2 and Islet-2. Zic2 is expressed by retinal ganglion cells whose axons project ipsilaterally, and islet-2 is expressed by retinal ganglion cells whose axons project contralaterally. These two transcription factors not only control the receptors on the axon which are involved in the decision to cross or not to cross, but they antagonize each other's expression. Knockout mice for either transcription factor have increased numbers of retinal ganglion cells committing to the other decision.

But the coolest of all is that the expression of Zic2 in the retinas of different species reflects the number and location of retinal ganglion cells cells which are known to project ipsilaterally in that species. (Figure 5 in this link ). Mice showed a smaller percentage of these cells than ferrets. But even more intriguing, Zic2 retinal expression also varied in frogs between the panoramic tadpole stage and the partially binocular adults-- corresponding to the development of an ipsilateral retinal ganglion cell connection! Although the brain circuits for binocular vision differ between mammals and amphibians, it seems that these two transcription factors have been involved in the development of binocular vision for a very long time.

Friday, April 01, 2005

Famous Fools'

A few nice April Fools' posts:

Paris Hilton to increase Linux exposure

Steve Jobs to join Ikea with a few value-subtracted furniture items (the Torquemada chair is worth a look).

Bush cancels Space Shuttle: "We cannot find any justification to continue deficit funding of a program that has no application other that proving that with enough money America can do anything," said Bush.

"The whole world knows that already, so why keep spending money on it," he added.

Mutated clocks in early risers.

The National Geographic confirms what we've all suspected: that people who are ready to go in the early morning are definitely not like the rest of us. A group of people who have familial advanced sleep phase syndrome (FASPS),a dominant inheirited disorder, have their sleep/wake cycles (part of a "circadian rhythm) out of sync with normal people. They get sleepy in the early evening and wake back up in the wee hours. Scientists at UCSF report in Nature this week that people with this disorder express a mutant form of the enzyme casein kinase I-delta. The mutant enzyme has reduced activity, and affects the processing of a second protein called PER2, which is important for circadian rhythms. When this mutant enzyme was introduced into mice, the mice showed several disruptions of their daily activities. Their overall activity was lower compared to mice without the mutant enzyme. Also, when kept in continuous dark (so that the internal clock cannot be reset by the sight of daytime) their activity showed a shorter daily rhythm. Finally, when light and dark cues were restored, mice with the mutant enzyme had difficulty entraining their daily schedules back to the cues. Thus the presence of the altered enzyme, specified by the human genetic mutation, is sufficient to affect circadian rhythms.

I just know that Coturnix at Circadiana will have something to say about this paper, so I will link to him when it's up!

UPDATE, April 17: Lots more mutants over at Circadiana