Friday, October 28, 2005

Worst jobs in science

Via Slashdot, Popular Science has released their annual list of the 10 worst jobs in science. . It takes some patience to click past the ads and stuff, but they do a pretty good job of explaining why people are doing these jobs.

Money quote, from number 8, "do-gooders" (people who pay money to join environmentally-inspired digs as a vacation):

Volunteers dig soil pits, analyze dirt, measure the depth of frost melt, and play a game called Page Count: "You close your notebooks as fast as you can and see how many mosquitoes you kill," Kershaw explains. "I think the record is 56 mosquitoes in one whack."

Thursday, October 27, 2005

Tell it to the hand!

Carl Zimmer at the Loom talks about recent results in the search for the origin of language. The idea that language might have had its origins in hand gestures and specifically with a class of neurons called mirror cells, is gaining in popularity. In a special issue of Forbes Carl turns the tables back to voice communication as the evolutionary material for the emergence of language. Carl's contention in the main of the article is that primatologists may have excessively focussed on hand gestures of chimps, since recent evidence is that their vocalizations also contain a great deal of social communication.

Representing the defense, in the same issue of Forbes, is Desmond Morris (link is to Dienekes' discussion). Morris talks about the magisterial use of hand gestures as a supplement to vocalization in Southern Mediterranean cultures. (He neglects to mention honking the car horn.) From my own experience, there must be thirty hand motions which all indicate to a person that his presence is no longer required, with varying degrees of implication toward the ancestry, mental health status, and sexual proclivities of the addressee. As Dienekes says, a phylogeny is clearly needed.

Sounds like a great issue of Forbes.

Wednesday, October 26, 2005

Long nursing period for mammoths

There's a short article on the Discovery channel page about the longer weaning period of mammoths relative to modern elephants. Breast milk differs from the plant-rich diet of adults by being richer in heavy isotope nitrogen and poorer in 13-C. I couldn't understand from the article what the scientists did exactly, but I gather that as the tusk grows outward, the tips retain the isotopic signature of the early years, and the base of the tusk is added last (see this abstract from the Fisher group). Very likely then they analyzed segments from the tip and base of a relatively complete juvenile tusk for isotopic differences, and found evidence in the tips for six or more years of nursing.

Modern African elephants nurse their young for about five years. It could be that the harsher climate in which mammoths lived would have required prolonged access to high-fat milk for the kiddies.

Good doggy

The CS montior has a nice piece about the social intelligence of dogs as studied in the laboratory of Eotvos Lorand. Dogs are incredibly attuned to humans and in particular their owners. Lorand's group has been able to show that they consistently do better than wolves, and even chimpanzees, in tasks requiring rapport with the human minders.

The most interesting part to me is the implication that ability to interpret social cues is its own kind of skill, which may be very different from intelligence per se. The difference between dogs and wolves also suggest that this separate skill has been actively bred for in domesticated dogs.

I'd be very curious how horses come in in this sort of test.

Tuesday, October 25, 2005

NASA - Crop Circles in Kansas

Crop circles in Kansas

From NASA's image of the day page, these crop circles were photographed with the ASTER satellite. The different colors correspond to different crops, with corn being dark green; sorghum a paler color; and wheat the gold color.

Monday, October 24, 2005

The psychology of a cluttered desk

I think this piece of pop psychology caught my eye, because my desk is such a mess. The news article, in the News Observer, suggests that clutter which seems so common in American households somehow parallels to the obesity epidemic:

To many observers, clutter reflects the mind-set of the modern household -- overburdened, disorganized and compulsive. To others, clutter is a broader symbol of a culture dependent on easy credit, piling up debt and consuming a lion's share of the world's resources without considering the consequences.
"People's homes are a reflection of their lives," says Los Angeles psychologist and organizational consultant Peter Walsh. "It is no accident that people have a huge weight problem in this country, and clutter is the same thing. Homes are an orgy of consumption."

The article later postulates an evolutionary psychological requirement to hoard items against possible future famine. Also featured-- I'm not making this up-- is the National Study Group on Chronic Disorganization. I'm sure their meetings begin promptly.

Good paleolib that I am, I do believe that people could get by owning a lot less. But I'm not sure I believe the link that this article tries to make between clutter and overconsumption. "Overburdened, disorganized and compulsive" though I may be, my desk clutter seems to come mainly because I don't have the habit of putting things away promptly. In contrast,I seem to remember Imelda Marcos having all her shoes in tidy rows.

Junk DNA- somehow it's important

The classical picture of a functioning cell is that the proteins and RNAs are doing all of the work while the DNA containing all of the instructions sits in splendid isolation in the nucleus. In this point of view, any DNA which does participate in the making of proteins or RNAs would be considered junk, because it does not contribute in an obvious way to the cell's activities. In fact, quite a lot of mammalian non-coding DNA (about a third of the human genome) strongly resembles a parasitic overgrowth of retrovirus-derived seqeuences known as repetitive elements, like kudzu overgrowing the back of a barn.

Yet population genetics analysis of this hinterland frequently show it being defended over time against mutations, suggesting that it must contribute to fitness. Thus it has to be contributing somehow to the survival of the organism. A recent report in Nature (Nature, subscription) confirms this by comparing two closely related species of the fruit fly Drosophila.

The findings of this study to challenge the picture that junk is really junk. The way out suggested in the Nature minireview seems to be that mammalian genomes might be junky but smaller organisms like flies much less so. For example, flies seem to have fewer repetitive elements than humans, but the mouse genome seems human-like. The main point of both the work and the opinion is that given the large mass of non-coding DNA, even a statistically small role could really matter in the long run.

Saturday, October 22, 2005

1st Avenue Machine short animations

This is a very cool animation group. The five projects which are up on their page are all worth a click-and-look.

I was just fascinated with "Sixes Last," which shows biomorphic little beings-- blinking eyes, tendrils-- integrated with living flowers and tree trunks. The effect is half time-lapse fungal biology, and half science fiction. Wow.

Friday, October 21, 2005

Islands as the last resort

Nature has a news blurb about a find of mammoth bones that are only 5700 years old, in the Pribilof islands off Alaska. The pit on St. Paul Island contained the bones of animals which had fallen in and starved. Among these were a few bones of a smallish mammoth.

Mammoths became extinct in the Americas around 11500 years ago, which corresponds very approximately to both the arrival of humans and the last glacial minimum. But it seems that on the islands much more recent megafauna remains can be recovered-- see also sabre-toothed tigers on Hispaniola. The islands go through the same climate change but got colonized by humans later. Thus the trend suggests that people, not climate, were the change agent.

Mammoths were in Siberian islands even more recently, as recent as 3700 years ago.

John Hawks on who's-your-(great-great-grand-)daddy

John Hawks reviews a few recent papers about unique Y-chromosome haplotypes which are very widespread and thus likely reflecting recent historical events. Since the Y-chromosome is passed from father to son, a sufficiently detailed genetic map--a "fingerprint"-- which yields a match between two people means it's very likely that those men got their Y-chromosome from the same male lineage. When this all occurs in the same village that's no big deal; but when it's spread across continents, it suggests some male had a phenomenal number of surviving descendants.

The first case Hawks reviews is an unusual Y-chromosome fingerprint which occurs all the way from the Caspian Sea to the Pacific, inheirited by up about 8% of all males in this vast region, or 0.5% of ALL the males IN THE WORLD. Indirect genetic evidence and historical accounts suggest they are ALL direct male descendants from Ghengis Khan.

The second case is in its own way even more interesting. Many Chinese but hardly any Han (the main ethnic group) have a Y-chromosome fingerprint that may have arisen in the 1500s or so. This appears to be linked to the Manchu conquest of China, in which the Qing dynasty-- a partiarchy of up to 80,000 male descendants of Giocangga (died 1582)-- basically lived off the backs of the Han. Here the history and the genetics are in pretty good register, although the molecular clock method for calculating the age of this unique haplotype gives a very broad range of dates.

Hawks is very good at outlining the imperfect seams between the genetic and the historical data. Together they make a very interesting picture. Genetics in particular can illustrate the tremendous difference in descendants between Ghengis Khan and Farmer Brown.

Update: the Giocangga study got written up in Nature as well.

Thursday, October 20, 2005

Slate bashes the Human Genome Project

Arthur Allen at Slate goes with both barrels after the Human Genome Project, basically asking where are the instant cures which were promised during the effort. His tag line at the end reads, "for this you should pay $500?"

Allen has no idea. $500 per taxpayer is a TINY amount of money (and I should point out that the Celera efforts were even cheaper, and done on the stockholder's dime). But yes, if he'd rather have half a flat-screen TV so he can watch Lost, well, I guess that's his prerogative.

I would agree with Allen that the disease side of the human genome project was badly oversold, but the feeling on the basic science side is that the genome efforts (plural; Allen is ignoring the C. Elegans and Drosophila efforts which built up to the human sequence) remain an epochal event. The methodology of shotgun sequencing alone has had applications in microbial, environmental and ancient DNA sequencing, which in turn has greatly increased understanding of things like the extent of horizontal gene transfer among species and the contribution of phage to open-ocean ecosystems. The combination of exponentially growing databases and cheap, cheap sequencing is allowing whole new sets of questions to be looked at rigorously. And newer sequencing methods are coming in which will blow the current methods away.

The genome efforts also played midwife to a cultural change in the basic biology mindset. I remember a lecture Gerry Rubin gave, in 1998 or so, talking about knowing "all the genes in Drosophila" and thinking he was crazy. Now people talk all the time about the transcriptome, the proteome, etc, with the intent of knowing all the elements present in an organism at a single timepoint. It's doable now, and is seen as doable. I remain a one-gene-one-scientist person, but I would be crazy not to be following this work.

With respect to human biology, the availabilty of the genome has indeed allowed identification of nucleotide stretches associated with human variation-- disease, for Mr. Allen. The Tourette's syndrome paper from last week, and earlier studies of longevity associated genes were only found because the human genome scaffold is precise enough to detect small scale inversions.

I think that's $500 well spent indeed.

Tangled Bank #39

I've been so swamped I forgot to follow the Tangled Bank series of science writing. This week it's up over at The Questionable Authority . It looks very good, as usual!

I should be actively blogging next week sometime.

Monday, October 17, 2005

ADEPs: A possible new class of antibiotic

Many dangerous bacteria are showing up with resistance to current antibiotics, so new antibiotics are badly needed. Nature Medicine this month talks about an antibiotic substance that attacks bugs in a brand new way. The compounds, ADEPs, act by removing controls on an enzyme in the bacteria which is normally used to dispose of malfunctioning proteins. Without the control, this enzyme becomes hyperactive and attacks even normal proteins-- with the result that the bacteria essentially digest themselves. Since this class of compounds acts differently than current antibiotics, it is unlikely that cross-resistance will be a problem.

The original molecule of this series had been isolated as a naturally produced defense from a bacterial culture. It had been patented in 1985, and then essentially abandoned. The folks at Nature Medicine emphasize that the natural world is likely to continue to be a good source of compounds, and that many new compounds might already be sitting in the patent books.

As terrific as it is that new drugs might be on the way, antibiotics should not be the first line of public health defense. Bugs will inevitably develop resistance to any single compound, which implies a pharmaceutical treadmill in which new compounds are continually needed. Thus, hygiene still matters an awful lot. I have also been very interested in naturally occurring microbial ecosystems in which the various species keep each other in check via mutual inhibition. There is some still literature suggesting that pathogens might also respond to social controls. This approach is interesting to me because the pathogens are not killed, just socialized. What I don't know is how mutants which ignore these controls-- corresponding exactly to an antibiotic resistant clone or a cancer cell-- get dealt with in natural ecosystems.

Sunday, October 16, 2005

New science page at Ars Technica

Ars Technica, which is mostly a PC enthusiast web page, has started a daily science page called Nobel Intent. It looks very good!

Actually, Wired magazine is always worth a look, but I only see biology stuff once or twice a week.

I really love the whole silicon-meets-carbon trend.

Update: Wired links to The Nikon Small World 2005 prizes honoring photography made with a light microscope. Beautiful stuff. (Full disclosure: I like Leicas better)

Friday, October 14, 2005

Little Chucky Darwin

McSweeney's does a take on how Chucky Darwin really got on board the Beagle . It's true- his Dad didn't want him to go. That voyage almost didn't happen.

Myself I tend to be a bit Platonic (actually, Romantic) about scientific insight. The order in the world exists independently of perception by individual personalities. Thus I think it's a mistake to hang too much of the theory of descent by natural selection on Darwin. Still, that guy knew how to write an argument. I have a copy of Origin and I still page through it.

Hat tip: Pharyngula

Like a kid in a candy store

The CS monitor has a nice writeup of what's next for the two Mars rovers. They are both running well, long past their sell-by date, and both have more interesting formations in sight. Spirit, having climbed out of Gusev Crater, could possibly make it to Home Plate, a very oddly colored terrane out on the undisturbed Martian floor. Opportunity conversely is trying to get down into a crater.

My own opinion about the likelihood of life outside Earth has definitely changed over the last year-and-a-half because of all of the details of the water history of Mars. More fun to come!

Wednesday, October 12, 2005

Another hobbit fossil- a jaw

Head over to John Hawks for a peek at the latest fossil finds from Flores. A new jaw will be reported in this week's Nature-- and of course teeth can tell you an awful lot about their owner. It's still early days, but the fossils taken together suggest that hobbits are a very deep off-branch of the hominin lineage, with australopithecines (Lucy and co.) being the last shared ancestors with H. Sapiens.

And folks in Germany are trying to get DNA reads from the fossils! This could get really interesting.

Friday, October 07, 2005

6 degrees of Kevin Bacon

A post over at Crooked Timber talks about a new book raising doubts that the author of Shakespeare's plays was W.S. himself. This week's champion ghostwriter is Henry Neville.

What I liked about the discussion is the very learned comment thread. About midway down, an unexpected connection develops between the latest Shakespeare debunkers and--wait for it-- the Intelligent Design movement.

The detective work is all done by bloggers in pyjamas, wielding Google--which is, after all, mightier than the pen.

Thursday, October 06, 2005

First we take Manhattan

For people who still believe this kind of thing, Slashdot is talking up blog money. Yeah, right, the check's in the mail.

Some funny comments though.

Spongebob

135041main_PIA07740-516

This is Saturn's moon Hyperion, as imaged last week by the Cassini probe. Cool...

Tuesday, October 04, 2005

Why do folks order a smaller soda at the drive-in?

Via anthropologi.info , a cute story from this summer of a commercial anthropology detective story. Coca-cola had noticed that people consistently ordered a smaller sized drink at McDonald's when they used the drive-through compared to indoor customers. They couldn't figure out why, so (cue Indiana Jones) they hired an anthropologist.

Coke had already ruled out my first theory, which was fear of greater spillage (Ah, fatherhood: never pour more liquid than you're prepared to see on the rug.)

Of course, the best approach would be to interview the drive-in customers, but they're by definition going somewhere, which makes them impatient. Also, the author decided to dress in a suit and tie, which was off-putting:
So most of your interviews last about 22 seconds. It is hot, very hot. It is so hot that I am soaked right through and my camera person, Suz, has discovered that the sun block has run off her forehead into her eyes and she can barely see. At this point, we aren’t getting very much more on camera than we are in the interviews.

The answer (kept secret in the post) was arrived at intuitively, and has something to do with cooking in the sun. So the anthropology part of collecting data failed to contribute.

The point of the post was the frequent impracticality of jamming a camera in someone's face in order to get data. The anthropologist needs creativity, and a bit of humility in interviewing people: they are the expert and you are the supplicant.

Looks like this story was trackbacked by Kottke a while ago...

Potato origins

A paper to appear in PNAS this week uses genetic data to argue that Potatoes were domesticated only once in the region around Peru.

The pedigree of modern potatoes can be traced back to 1562 in Europe, but the ancestors of that crop could have been either one or several sources in South America. There are certainly two clades among modern cultivars which can be distinguished both genetically and based on things like daylight adaptation. The favored theory, until now, has been that these clades in fact are of ancient origin (representing independent domestication events), possibly introduced to Europe (and the world) by necessity. The 19th century potato blights, by this hypothesis, wiped out the older breeds, requiring hybridization to a different, blight-resistant, race of potato. This hybridization of two different gene pools contributed to modern spuds. David Spooner, the lead author in the current study, had earlier proposed just such a dual origin of potatoes, but with the second (Chilean) clade being prominent long before the 1840s.

The current study involves RFPL analysis surveys of wild potatoes in the South of Peru and north of Bolivia. The result of the new classification is that both the northern and southern clades of modern potatoes can be linked to a small set of species from this area. The data furthermore point to a need to look closely at this "set" of species, which may instead represent a single species.

In terms of bioprospecting, then, lots of useful potato genes could be tapped from just about anywhere else along the Andean chain.

This kind of analysis has been done on a number of major food crops including wheat, beans, and squash. After initial domestication, farming of these valuable plants has sometimes spread primarily along the east-west axis (wheat), and in other cases they spread north-south, or without an apparent latitude bias (corn, squash, beans). A while back, Jared Diamond stuck out his neck and speculated that agriculture of monoclonal crops would be spread with an east-west axis bias, because the similarity of climate is better preserved, whereas north-south spreading might require polyclonal domestication or extensive hybridization. Since Diamond's original thesis, both corn and now potato, both with prominent north-south historical spreads, have been shown to be genetically monoclonal. Send that one to the circular file.

DNA in the mud

Last week's Science had a really suprising short letter showing an enormous amount of extracellular ("dead") DNA in the top few centimeters of ocean sediments. The amount of "extracellular" DNA greatly exceeds the amount contained within the living prokaryotes and viruses in this ecosystem.There is so much DNA in the ocean floor-- 0.45 gigatons!!-- that the phosphorous content of this molecule (about 10% by weight)is a major reservoir of phosphate for all the ocean.

The most interesting possibility would be that this DNA is intact enough to have biological activity. For example, plasmid or virioid DNA can be complexed with protiens in a way that would resist (chemical) degradation for a very long time. If even a fraction of this DNA were still encoding genes, it could be taken up by bacteria and contribute to their genomes as a huge extension to the horizontal gene (DNA) transfer process which already occurs between living organisms.

A second, more practical, consequence of large amounts of relatively intact DNA in the ocean sediments is on metagenomic surveys of this ecosystem. Metagenomics-- a fairly new method which uses special cloning and computational methods to survey the genomic capacity of a particular environment-- cannot by itself "see" if the DNA molecule being sequenced was obtained inside or outside of an organism. The specific concern is that one set of genes (for example, belonging to one class of microbe) would be overrepresented in the extracellular, nonliving pool.
Thus the metagenomic clone counting, which is used to estimate the relative abundances of "genes" in the environmental sample, would lose its presumed linkage to the biological activity of the sample. That is, DNA does not make a gene unless it's inside something alive, and the identical sequence obtained from extracellular DNA should not be scored as contributing to the genomic capacity of the ecosystem.

The issue of extracellar DNA should also be considered for large microbial concretions such as stromatolites, which, in fact, have also been analyzed by the metagenomic approach.