Friday, September 23, 2005

Sedimentary rocks on Mars

Sedimentary rocks Terby Crater, Mars

This image shows sedimentary layers in Terby Crater, exposed by subsequent erosion. The rocks were likely to have been altered by water in some point in their history.

Breakfast science

There's a fun article at LiveScience about the Cheerios effect , in which cereal pieces floating in a relatively empty bowl tend to clump together. This effect is also seen with soda bubbles, or with hair shavings, on the surface of water.
Now I know everyone's been losing a lot of sleep over this, so luckily a physicist has put together an explanation. It's a combined action of buoyancy and surface tension, with the meniscus effect coming in to play at the edge of the bowl.

The cheerios floating on milk distort the surface, making a little dimple; and when two cheerios get near enough to one another they "fall" downward and consolidate into each other's troughs. Breaking this configuration would require the cheerios to go uphill.

The geometry of the milk surface near the rim of the bowl (the meniscus) also traps cheerios on the sides.

Wednesday, September 21, 2005

Tangled Bank 37 at Milk River Blog

Milk River blog is hosting this weeks' Tangled Bank of science-related blogging. The presentation is pretty neat- a vending machine with different candies for different blogs.

Tuesday, September 20, 2005


Kieran Healy at Crooked Timber gives the final word on the still-kicking plans to open a humanned base on the moon. Worth a read, and a laugh.

Monday, September 19, 2005

Biology as a termite mound

As with any communal project, the nomenclature of biology can get kind of quirky. The Curiosities of Nomenclature site is dedicated to fishing out some interesting ones.

My favorite Russian Doll nomenclature has always been the Drosophila series of mutations, sevenless, son of sevenless (sos), and bride of sevenless (boss), all of which are genes important for eye development. Sevenless mice are missing neuron number 7 in the small repeating arrays known as ommatidia. Sos was later identified in mouse and became m-sos; but then there are two variants, m-sos1 and m-sos2. More cool names from this family, including many allusions to German foods, are at FlyBase .

Southern exposure

Sir Edwin Southern has won this year's Lasker Award for his invention of a DNA blotting method. Southern's original idea is incredibly cool- you could analyze the fragmentation pattern of a complex mixture of DNA by using a "probe," which just consists of a short radioactively labelled fragment. The probe will only stick to its matching (complementary) sequence, and all other sequences stay blank. Using this simple idea and multiple probes, you can detect many different genetic changes, ranging in size from chromosomal rearrangements to loss of a single restriction site.

The method has proved so versatile that it has been adopted for RNA ("northern blot," a pun on Southern's last name), and then to protein ("western blot") and even to protein-protein interactions ( "far western" ). I am not aware of an eastern blot.

Southern later became an early advocate of microarray hybridization , which uses analagous techniques to a Southern blot. for biology

This month's Nature Cell Biology makes the science debut of connotea, a social bookmarking application like or flickr. The hope is that scientists will use the tagging system to link all sorts of web pages together.

Connotea seems to have been in beta since late last year but this is the first that I have heard of it. This description provides some startup help.

The NCB rollout article tries to address worries that sharing ideas in a community site(even as innocuous as linklists) might cause loss of a competitive edge. My bias is already against that concept, but I'm not sure they would convince a scientist who didn't want to share.

In the end the system will fly if it gets lots and lots of users. I personally would like to see the emergence of a system which is attractive to non-scientists as well. I have to emphasize: I'm a little confused even about delicious, so I'm just happy with the principle. Oktoberfest is going now, so I'm not sure when I'll do the mind-meld necessary to get started.

I think I would be remiss not to mention citulike , which is also a tag-based online library system. I've heard of this one, and done a few clicks, but I just haven't hit threshold yet.

John Hawks touches on related developments in anthropology toward the end of this post.

UPDATE on information theft in competitive situations: Via The Daily Transcript, I had forgotten the recent New York Times article about an ethical brawl between two groups of astronomers over discovery of an object orbiting outside Pluto. Apparently one group did some snooping deep in the web-based logbooks of the other just prior to announcing their discovery.
I assume that everything in this blog is on Google's servers for eternity; I guess I should assume the same about connotea information.

Saturday, September 17, 2005


The Open Science Project links over to videos of dangerous (read: boom!) chemical experiments. If you touch nitrogen triiodide with a feather, well...

The main list of videos is here.

Friday, September 16, 2005

Serotonin agonists and migraines

Migraines are a class of ferocious headaches, frequently with pain on only one side of the head, and often accompanied by nausea, visual illusions called aura, and a deep aversion to light or noise.

This month's Nature Reviews Drug Discovery has a review about progress in treating migraines. The most commonly chosen drugs, known as triptans, activate the Serotonin 1B and 1D receptors. This class of drugs has been the choice for persistent migraine cases since the late 80's. However, triptans (the best known is sumatriptan/Imitrex) act not only in the brain but also constrict blood vessels throughout the body, with potential cardiovascular side effects. The argument of this review is that pharma needs to design drugs that will disentangle the two effects.

The first section of the review explains the evidence that migraine is in the neurons of the brain and not the brain vasculature. (This is what brought me to the article. In fact the vascular actions of the drugs might have increased the confusion about which system mattered.) During attacks, brain activation is seen in specific areas which are associated with pain sensation in the head and the brain vasculature. (In fact the visual aura might be a blood flow effect.) But a specific electrical phenomenon known as a contingent negative variation (CNV) is altered before an oncoming attack and, if the attack is prevented with drugs, the CNV seems to become normalized. Thus migraine is associated with abnormal neuronal firing, and activation of specific brain regions associated with pain processing.

The author basically suggests that moving past the current therapy requires compounds targeting other, neuron specific, receptor systems. He runs down a pretty lengthy list of compounds which are in development. Of these the most interesting to me are the ones which are directly related to blocking nociception (the neuronal sense of "pain"). In any case, options for treating migraine will expand greatly in the near future.

A nice older review at NEJM is here .

PZ Myers on the evolution of senses

Via Panda's Thumb, P.Z. Meyers reviews the evolution of the senses. Our senses of sight, taste and smell (and also some pheremone responses) all first register items in the environment via a closely related set of proteins called G-protein coupled receptors. It turns out that this family is very ancient, and also occurs in bacteria. Other senses, namely hearing, touch, and balance,l register at the cell level when physical shearing of the cell surfacel activates a family of proteins known in mammals as TRP channels.

The new work discussed by Meyers, which appeared in Nature a while back, describes an ancient pedigree for the TRP-like channels as well. There are fungal and bacterial proteins which also register physical stress at the cell surface, and some are direct homologs to the mammalian proteins.

The hypothesis of the review is that bacteria evolved G-protein coupled channels to detect soluble items in their surround, and mechanosensory channels to detect physical stress. These inventions, once established, became highly portable widgets to solve a large number of sensory problems. Truly a great demonstration of the Panda's Thumb principle-- that natural selection tweaks working solutions rather than designing anew.

Here's looking at you

False color image of Minas

This false color image of Saturn's moon, Minas, shows the differences in surface texture. The impact which made the huge crater nearly destroyed the moon.

From the NASA's image of the day web page. .

Thursday, September 15, 2005

"Nutty professor"

(Edited quite a bit on Sept. 16th)

The Chronicles of higher Ed ran a story earlier this week about academics who are socially compromised:

Ask anybody what adjective goes best with the word "professor," and the answer will almost certainly be "absent-minded," or possibly "nutty." Popular culture is full of addlebrained academics....

The idea that scientists and artists are basically nuts is almost universally accepted, and popular studies linking odd behavior and creativity (in this case referring to schizotype personalities) seem to pop up every few months or so. There have been some efforts to actually measure rates of mental illness among creative professionals.. There are some interesting trends, including an apparent correlation between scientific eminence and rates of measurable pathology. But I think the equation of the two has become badly shopworn to the detriment of both groups. Not all scientists are crazy-- and certainly not everyone suffering from mental illness is going to be doing science or art. I think scientists can handle the moderate contempt implicit in this linkage, but people with mental illness must really despise the "beautiful mind" expectation that they start spouting equations.

The Chornicles of Higher Education article goes on to what I consider a more interesting topic-- the response of the faculty community to new hires suffering from moderate psychological disturbance. As with any other disruptive personality (some of which are considered normal) entering a small workplace, these people become "hot potatoes," passed on by glossing over their seriously marginal behaviors. But this part of the discussion is essentially about hiring and firing. I think it could have been pruned away from the nutty professor trope fairly well. I acually wish the essay had gone on longer in this vein-- the author seems only to recommend great care in hiring and probationary periods.

UPDATE: See another ambivalent reader, and comments, over at Crooked Timber

Mountain photographs at National Geographic

There are some very nice photographs of mountain scenes from the 2005 Banff Mountain Photography competition. Go and have a look!

Google blog search: still searching

Update from the comment: Google search hits Atom and RSS feeds

Google now has a search engine which is intended to hit blogs only. The engine searches only blogs with RSS feeds.
I had a look and it's not all the way there yet. .

On the more general topic, though, I've been steadily migrating over toward RSS feeds. I'm getting very interesting stuff by using Pubsub and Bloglines .

Tuesday, September 13, 2005

Peer pressure in the grocery store

Eurekalert is carrying a blurb about social cues affecting people's spending decisions. Consumers will choose a more expensive brand-name item if an unknown fellow-shopper is standing near them in the aisle. The cool thing about the effect is that the stranger is not directly involved in the transaction-- it is the "mere" social presence which has a measurable effect on the purchase choice. In fact, the researchers also chose an invisible product-batteries-- so that the social impact of the brand name should have been minimal after they were in use.

The effect of an onlooker gets stronger if there are more people, or if the onlooker gets physically closer. But the experimental subjects actually did not report any feelings of annoyance or defensiveness until there were three people up close. (The famous Wall-mart Oxygen Deprivation Effect.)

The items to be bought in this study were just batteries, but I can imagine the impact on deodorant sales. In fact, this consumer effect, which has been branded as "Social Impact Theory," probably contributes to the embarrassment effect on buying more socially visible things.

Monday, September 12, 2005

Is that your tongue in your mouth?

(First link is now correct)

The BBC is reporting parasitic louse found in a red snapper in Britain. Cymothoa Exigua drains blood from the fish's tongue and then takes up residence inside the mouth. It seems to even be a functional replacement for the tongue.
A nice picture is here.

The beeb quotes a scientist as being very excited by the find, but I spent 30 seconds on google and found references going back to the late 80s...An entry from early this year is at Stranger Fruit

Other lovely hitchhikers are described here.

Organics in comets

Last week Science Express published two papers ( here and here ) about the Deep Impact mission to comet Tempel. This spacecraft basically slammed into the comet to dig out the pristine material deep under the surface. When that stuff jetted out, both spacecraft and ground telescopes were able to identify the components by their spectra.
Based on the behavior of the comet flume, astronomers think that the comet is a very weak and dusty collection of dust-sized particles, with almost no solid surface. This may be bad news for the Rosetta mission, which is trying to send a lander down to the surface of a comet. It may just sink straight down once it lands.

The main chemical result from Deep Impact is that the inside of this comet is a whole soup of organics , including methyl cyanide, a reactive small organic which can easily polymerize into the precursors of DNA among other things. The earth was absolutely pummeled by comets and their kin during its early history; thus these objects may have delivered the precursors of life to the earth's surface.

A second finding of interest was the presence of clays and carbonates , which require liquid water. Thus the comet might be an agglomeration of material which formed in very different parts of the solar system. I think this mixing, maybe under the gravitational influence of the early Jupiter, may be an important part of making a terrrestrial planet. The rocky core has got to form close in, but the water and organics are best made further away. However this works out, the comets are a big part of the Earth's history.

See also the writeups at ..of Cabbages and Kings and plvs vltra .

Benjamin Fry at the Whitney

Via Metafilter, Benjamin Fry, who is interested in displaying large datasets in visual form, has an installation at the Whitney Museum. Of course I *should* be looking at the haplotype blocks comparing two humans' DNA, but I prefer the baseball salaries graphic. Ben Fry has put a lot of thought and documentation into this.

Take a look also at his Anemone which displays the click habits of visitors to the MIT media lab web page.

Very cool stuff.

Friday, September 09, 2005

Now THAT's a big bird

pterosaur gait interpreted from trackways

The BBC discusses pterosaurs, and recent evidence that they could have had wingspans of 18 meters. Actual fossils have been found of pterosaurs which should have had 14 meter wingspans; the larger figure is based on trackways. (The image, somewhat off topic, comes from this older article about pterosaur tracks, which match panel B-- quadriped gait-- much better than the hypothesized birdlike gait shown in panel A).

By contrast, the largest wingspan of a living bird is only 3.6 meters, for an abatross.

The pterosaurs seem to have been able to fly soon after birth ( as possibly were some ancestral birds ),which means that during this prodigious growth their aerodynamics had to be functional at all times. In contrast, modern birds are born flightless and only begin to fly at nearly adult size.

UPDATE: Orbis Quintus wants a real live thunderbird.

Web interface for Thebes archaeology

Jim Regan at the CS Monitor reviews the newly re-tooled Theban mapping project web page.He's interested in both web page design and the excavations themselves. The project page includes an aerial photograph (I wonder what Google Maps would give?) and lots of links. Regan is right in complaining that the site is a bandwidth hog.

I only wish there were an equivalent site with photographs of the artifacts. There is a small download section for tomb drawings.

Thursday, September 08, 2005

Toads at the disco

There's an item on the newswires that cane toads, an introduced species that's basically overrunning northern Australia, can be lured to traps using ultraviolet strobes. It's not yet clear if the toads are responding to the light itself or to the swarms of insects that are also attracted.

The reason for the big effort is that the toads are very poisonous and eat ravenously. In a public initiative to slow their spread, a story this spring introduced "whacking day" in which people were encouraged to go after the pests with golf clubs and cricket bats. A key comment from the text: "Two issues with golf clubs, one is they're fairly light, they don't have a lot of mass so whilst they hit cane toads and make a very healthy sounding smack when they do, they don't really have enough mass to crush the cane toad's skull," he told ABC radio.

Tangled Bank is up

The Tangled Bank of science-related blogging is up over at B and B.

Wednesday, September 07, 2005

Antioxidant treatment for medieval documents

rembrandt drawing- ink corrosionNature has a short blurb about chemical treatments to neutralize copper in medieval iron gall inks . This ink was the major ink used for centuries for treaties and drawings. The iron preparations used to make the ink also contain copper, along with the trace metals manganese and chromium. These metals generate free radicals which then attack the parchment. The new results suggest that the minor metals are even worse than the known effects of iron.

The antioxidant treatment, combined with alkali (to reduce acidification), is dissolved in heptane and ethanol. Since it is not water-based, it will not cause the books to swell and won't dissolve most inks.

A general history of Iron Gall inks is here. A link to the Metals-In-Paper conservation effort is here. A recent abstract from the Slovenia group is here.

If you want to live hot

Hyperthermophilic microbes often have close relatives which live at "normal temperatures." The evolutionary transition has been made in both directions by multiple families of archaea and bacteria. There is now enough structural information about closely related proteins to make generalizations about what is needed to keep functioning in kochwasser.

In this week's PNAS has an open access article about the physics and evolution of individual proteins retaining their ancestral functions in a new high temperature environment.What is perhaps not suprising is that different proteins manage in different ways. The two most commonly observed answers-- taking a page from my dad's repairs around the farm-- could be classified as "staple gun" or "ten penny nail." That is, either hot proteins are much more tightly compacted, with no single substitution apparently critical; or they are stabilized, without compaction, by a few major changes in the protein sequence that evidently nail everything together. What is interesting from the paper is that these strategies occur in isolation.

The scientists were able to see a trend in the strategies used and relate it to the evolutionary history of hyperthermophiles. Bacterial hyperthermophile proteins tend to use the sequence change (ten-penny nail) method, wherease archaea used the structural(staple gun) method. To quote from the summary:

We attribute such differences to the vastly different phylogenetic histories of these organisms: The primordial habitat for archaea is believed to be a hot environment. When archaea evolved in such a habitat, its proteins were "de novo" designed in a hot environment that necessarily biased both structural repertoire (as explained in more detail below) and sequences that had to be found to fold and be stable in such structures. On the other hand, T. maritima (the bacterium) is likely to have initially evolved as a mesophilic organism that later recolonized a hot environment. Its thermophilic adaptation required the enhancement of the thermostability of already existing proteins.

Based on their observations I'd predict that the tube worms and crabs living near hot vents are using the ten-penny nail method to hold their proteins together. What I did not grasp from this study is the physics of the reverse case- is it somehow less stressful to get cold, so that cold-dwelling archaea don't need whatever the opposite of a ten-penny nail would be to unblock their hot-adapted proteins? This is of some interest because of speculation that life originated at high temperatures (the present authors disagree with this idea), so that the epochal evolutionary event would be in managing in the cold.

The hunt for Peking Man

Duane Smith at Abnormal Interests says that the hunt for the original Peking Man fossils is heating up. These fossils, exemplars of homo erectus, were lost in the early days of World War II although casts and field notes survived. Duane's post has background information and links to subsequent finds at the site.

Wikipedia on Peking man, is here. The tourist center makes the La Brea Tar Pits look understated.

Monday, September 05, 2005

Dinosaur babies: chicks, but with teeth

Via Slashdot , the Times UK quotes paleontologist Gareth Dyke that dinosaur hatchlings could have been covered with mulitcolor fuzz like chicks. (He says "delicate feathery plumage.") This is based on finds at the Liaoning fossil bed in China, a site in which animals were buried in a volcalnic eruption with soft tissue details preserved.

I haven't been able to find a scientific paper specifically mentioning tyrannosaurus young. There was a Nature article last fall about feathery tyrannosauroids, and a 2003 story about a possible four-winged creature (i.e. both arms and legs) found at the site appears here and here .

I don't know why, I keep thinking about an easter basket with one of these little babies peeping out.

Data mining for text connections

SnowDeal is aggregating recent articles about text mining. A good statement of the problem is provided by BioNLP: The literature of the field of biology is the largest of all the sciences. The volume of biology literature each year, measured in bytes, is about fifty times the size of the entire human genome, junk and all. But locked in this literature is an enormous amount of information that can tell us much about the structure and function of genes, proteins, cells and organisms -- how they work as well as how they can fail.

Very interesting stuff.

Friday, September 02, 2005

You are what you eat- and what you eat ate you

There's a really icky story on CNN that Mad Cow disease may have arisen from cows eating human remains.

The cowfood in question was imported as bone meal from south asia. The CNN article goes on: "In India and Pakistan, gathering large bones and carcasses from the land and from rivers has long been an important local trade for peasants," the scientists wrote. "Collectors encounter considerable quantities of human as well as animal remains as a result of religious customs." That is, they'll haul stuff out of the Ganges no questions asked.

It should be said a second hypothesis is that the disease came from the bones of sheep infected with scrapie. The authors of the Lancet paper point out that the first case of mad cow was in 1986, even though sheep stuff had been recylced for decades. There is also some evidence that cows don't get scrapie "via the oral route."

I know, I know, it's all just protein. Yuck.

UPDATES: A bit of policy comment on this from Crumb Trail.

Coincidentally, "chronic wasting disease," or CWD, another prion disease seen in elk and deer, seems not transmissible to humans.

Chimp genome at Pharyngula

PZ Meyers has somehow found time to read the last issue of Nature. His summary of the chimpanzee work, is here .

Thursday, September 01, 2005

Left-handedness in amino acids

Amino acids exhibit chirality, which means they can come in a left-handed or right-handed version. Geological processes tend to make in exactly equal yields but life on Earth overwhelmingly uses only the left-hand versions. This strong bias is now necessary for proteins to fold together properly, but when did it begin? The New Scientist describes some speculation of how polarized light generates a bias in the chirality of amino acids prior to the emergence of life. Circularly polarized light, of the sort generated in vast amounts by white dwarfs can generate an excess of the left-handed racemer of the amino acid leucine. Possibly some such process at work in the early solar system meant that our common ancestor had an excess of left-handed amino acids to work with. The current polarized light experiments can generate excesses on the order of a few percent, but perhaps that's enough. It could be chemically amplified , or, once the bias was established, living things may have standardized and codified it. Some earlier work suggests that strong chiral bias in only one of the amino acids- serine- could force the other ones to come along.

Chimpanzee draft genome

The draft genome of the chimpanzee will be released today at Nature (some stuff is public access). Apparently there are some very interesting differences in the Y-chromosome relative to humans. Also some quantification of repetitive elements, essentially genetic parasites which make up about a third of the human genome. Some families of these little snippets have done very well indeed, specifically in humans. More later when I've done the reading-- wow, the Nature table of contents is full of goodies!

In the meantime check out Carl Zimmer as usual at the Loom, and Monsters and Critics .