Wednesday, August 31, 2005

Turn a turnip into cabbage

Not that my kids would eat either one..

Carl Zimmer at the New York Times (reg) and his blog, The Loom talks about large scale slicing and dicing of chromosomes and its impact on evolution. Big pieces of chromosome, with the details essentially intact, have been moved around in the interval separating rhesus monkeys from human. Intriguingly, the genes near the evolutionarily defined break points are often associated with congenital disease.

Carl is always worth a careful read.

Tuesday, August 30, 2005

Does the "Mozart effect" really exist?

Dave Munger at Cognitive Daily takes a look at the "Mozart effect," the belief, that listening to Mozart can enhance testing ability, which has become the basis for an entire cottage industry aimed at the parents of young children.

The original Mozart observation was that adults performed better on a specific spatial test after listening to Mozart compared to a group exposed to relaxation stimuli. The idea that a particular music would improve test scores erupted into a "Mozart makes you smarter" frenzy. Mozart also improves your smile, removes ugly blemishes and increases your goats' milk production. You get the idea.

Regardless of the pop culture phenomena, the original observations were pretty interesting. Dave discusses to two efforts to replicate them which came to opposite conclusions. It might be that the reported difference lies instead in the exact sort of relaxation of the control group. Experiments using verbal cues to relax result in the Mozart effect, whereas listening to relaxing music (Debussy) erased the effect.

So: avoid telling your kids to relax. Otherwise they'll go dumb, and your goats will dry up.

Hurricane Katrina- wavetops and clouds

esa082905 Hurricane Katrin water surface and cloudtops

Hurrican Katrin was imaged by the European Weather Satellite ENVISAT. The left image uses synthetic aperture radar to show surface roughness of the water. The eye is relatively calm and shows dark. The right image is a more conventional cloud-cover image made using the MERIS detector of reflected sunlight.

This was a beast of a storm. I'm glad that New Orleans escaped a direct hit.

UPDATE: There may still be trouble in New Orleans. A lakeside levee has been damaged, and water is coming in.

Image description is from Eurekanet

Alzheimer's and blood flow, revisited

I had blogged before about a minority view that Alzheimer's disease begins with circulatory problems, and the neuronal damage comes later. This hypothesis is emphatically a minority view, and has a lot of genetic data (my favorite) to explain away. However-- and this is important-- it is testable: there are very sensitive evaluations of blood flow in the brain (not least fMRI!), and prospective studies are presumably underway.

What is abundantly clear, though, is once the disease starts, that both neuronal and vascular function are compromised. Today's EurekaNet lists a story to appear in Radiology comparing both vascular flow and indicators of brain structural damage between patients with dementia (either Parkinson's or Alzheimer's) and age-matched controls with normal cognitive function. They found that total brain volume was comparable between patients and normal people, but vascular flow was strongly reduced. Thus the flow density is reduced in the persons with disease. Measures of brain structural damage as expected also showed the correlates of the diseases.

The conclusion is that vascular and neuronal measures both show damage in people with sporadic Alzheimer's even at an early stage of diagnosis. What remains critical-and with enough time, can be done-- is to ask which system is damaged first.

Sunday, August 28, 2005

Substance P inhibitor: the pain controller that wasn't

In the Pipeline has a nice history of efforts to develop a drug to block Substance P signaling in the treatment of pain. Substance P is a neurotransmitter peptide which is associated with intense and chronic pain, or so-called "bad pain" (as opposed to "good," necessary, pain which tells us to pull our hand away from the hot stove). Because the pain from several diseases seems to come from excessive substance P signaling, it would be a big help to control it. Merck has had a compound for some time, but unfortunately it does not seem to live up to its potential.

The story shows how difficult it really is to bring something from the laboratory to the hospital.

More background on Substance P is at Medscape.

Friday, August 26, 2005

Want to be creative? Do something else first

A review in press in Consciousness and Cognition discusses evidence for the "incubation effect", which refraining from conscious thought about a problem can result in a more creative response. Despite abundant anecodatal support for this idea (Einstein cutting himself while shaving, etc.) it has been very hard to demonstrate in a lab.

The authors are interested in the very first phase of creative thinking, the generation of new and original thoughts. They designed experiments which allow for open-ended answers.For example, 3 groups of people were asked to list "towns that begin with A." One group was allowed to begin immediately; one group was allowed to think about the problem for an interval; and a third group was given a highly distracting test for an equivalent time before returning to the question. The authors scored the "originality" of the lists based on the population size of the municipalities, with big, prominent towns considered a less original answer than small villages.

Every group managed to come up with a fair list of towns. Both delayed groups tended to give more total answers than the group asked to respond immediately.
The most dramatic effect, a nearly twofold higher number of small villages named, is seen between the group asked to answer immediately and the distracted group. The group which was allowed to consciously consider the problem got intermediate scores, although tending toward the immediate answer group. There is also a small tendency for the distracted group to come up with *fewer* "obvious" answers in their list.

My final reaction to this is that it's very interesting to see effects with such a simple experimental design. I myself feel refreshed and sharper especially after a vacation, so I'm inclined to believe there is a real cognitive effect which just needs careful experimental design to be teased out. I think I'd like to see the concept tested using a bigger variety of tasks (they always asks for written lists) and larger sets of people.

Update: there seems to be a fairly extensive literature all suggestive of a positive effect of being a way from a problem for a while.

More genetics of India

Dienekes blogs about the India diversity project, which will try to map human genetic diversity in India. A huge and fascinating effort.

Thursday, August 25, 2005

Liquid water as necessary for life

This week's Nature (subscription! possible workaround using Bugmenot ) has a brief note about why liquid water is considered so essential for life. I have been wondering about this for some time, and have only read a few reviews about alternative life chemistries.

The article starts with Steve Benner, who actually wrote the review I had read last December. Benner's position is that liquid water is literally a two-edged sword. It's an excellent solvent and is chemically both an electron donor and acceptor-- but these flexibilities also mean it will chemically attack just about any information storage molecule you care to think of. (My RNA preps can testify to that!)

The interesting part comes with a third property of water- it is highly polar (the hydrogens are weakly positive, and the oxygen weakly negative) which allows a much weaker class of bond called hydrogen bonding to exist. They get made and get broken, over time and energy scales we can live with. These hyrogen bonds, for example, zip DNA molecules together, and can be readily undone when it's time to copy them. When you get out of the temperature domain of liquid water, you'd have to rely on a new class of bonds-- or operate on a timescale wholly different than we think of as alive.

But we only have the single example of life on earth, and maybe our thinking is limited by only studying life which has clearly evolved with water in mind. Benner's favorite alternatives are cold domains, with liquid ammonia or nitrogen (which have subsets of water's properties). Cold means **slow**, but probably information storage is greatly simplified. Would we recognize something with a lifespan of millenia?

Some links:
The Benner Homepage
Astrobiology encyclopedia for liquid ammonia life
An earlier Nature pdf file on extreme life.
The physical chemistry of liquid water

Tangled Bank 35

The Tangled Bank Carnival of science-related blogging is up at Cognitive Daily . Perhaps not suprisingly, many scientists have been moved to discuss the inclusion of Intelligent Design in the classroom. Dave migrated those posts over to a personal blog. Both sets are worth a read.

Tuesday, August 23, 2005

The vascular hypothesis of Alzheimer's disease

Alzheimer's disease affects about 4 million Americans, and the numbers of cases are expected to rise as the population ages. The exact causes of Alzheimer's disease are unknown, and it is likely that non-heritable cases are triggered by more than one kind of environmental insult. The most prevalent theory has been that accumulation of a protein fragment called "A-beta," which is toxic to neurons, starts a vicious cycle of neuronal death and inflammation.

Although blood circulation problems can also cause dementia, the difference in the sequence of cognitive losses have led neurologists to consider vascular dementia to be distinct from Alzheimer's. However, even from the earliest reports of the disease, it has been known that people who die from Alzheimer's have not only neuronal damage but also pathologies in the blood supply to the brain. A subset of researchers in this very big field are suggesting that perhaps problems with the circulation are the first problem, and that neuronal toxicity comes later. (There is an intermediate position, which could be called the neurovascular hypothesis, which would hold that clearance of toxic A-beta by the vasculature is faulty.) To test whether changes in the blood supply or accumulation and toxicity by A-beta(or both!) are the beginnings of Alzheimer's, it is critical to identify people with the very earliest stages of the disease.

The notion that circulatory disorders can contribute to Alzheimer's-like pathologies got a big boost in a paper to appear in next month's Nature Medicine. Wu et al. report that brain endothelial (blood vessel) cells taken at autopsy from people with Alzheimer's disease are deficient in the vascular transcription factor GAX/MEOX2 and are less able to form tubules in vitro. When expression of this transcription factor was reduced in normal endothelial cells, those cells developed some of the same difficulties as the cells from Alzheimer's victims. Moreover, mice lacking one copy of this gene show reduced ability to grow blood vessels in the brain, and impaired clearance of A-beta.

So the molecule GAX/MEOX2 is reduced in humans with the disease, and reduction in human cells in vitro and in mice in vivo can cause blood vessel abnormalities like those seen in the progression of Alzheimer's disease. There are three limitations to the data at present. The first is that the authors have not yet ruled out that GAX/MEOX2 is also expressed by neurons, and could also function on the neuronal side of the neurovascular unit in mice (analysis of this possibility appears to be in progress by that lab). The second is that there is no mention if the mice show any kind of dementia, or amyloid plaques (accumulations of A-beta which are seen in Alzheimer's disease). This may be because the mice do not live long enough. Lastly, although heriditary Alzheimer's disease is very frequently associated with abnormal generation of A-beta, there has not been, to my knowledge, any human genetic abnormality which only affects the vasculature. (Several proteins related to the generation of A-beta are expressed in neurons and blood vessels.)

My own reaction is that the importance of neuro-vascular interplay cannot be overstated, and the sort of mild global cognitive impairment which seems to represent the earliest stages of Alzheimer's is suggestive of circulatory problems.

More comments on this work are at What's Next and at Science Daily .

Using water tension as a controlled adhesive

File this one under "invention of velcro." I just spent this morning peeling my rain-drenched bike pants off, so it seems especially appropriate!

A materials engineer is taking a page from a palm beetle-s book to make a reversible adhesive device composed of thousands of microscopic water droplets. The beetle has footpads loaded with oil droplet-laden hairs, and when attacked it simply grabs hold of a leaf, with a tensile strength corresponding to 60 times its body mass, and waits for the predator to go away. The adhesion is reversible, so the beetle can just walk off. During regular walking the miniature bristles are kept away from the leaf surface.

The engineered variant uses water and electricity. The water is doped with ions, so a tiny field can cause the droplet to migrate between the underside and the top of a small porous (glass) disk. The working model uses micron-size pores, and requires 5 volts or so; but the hope is that scaling down will improve the speed of performance and reduce energy requirements.

I want to walk like a gecko!

Monday, August 22, 2005

When in Rome: Chimps conform like humans.

There are discussions popping up all over about peer pressure in chimp social groups. The researchers designed a puzzle in which food could be obtained by two different solutions, and then trained high-ranking females from two groups in distinct ways to solve it. When the groups were reunited, everyone went along with the expert's distinct way, and a third group, without a ringer, was left nonplussed.

The hook is that the second solution was independently discovered in one group, and spread somewhat; but after the puzzle was removed for some months, everyone reverted to the leader's strategy. Quoted in the Scientific American:

"We have shown a non-human species conforming to a group norm, despite possession of an alternative technique that represents the norm of another group," the team writes in a report published online yesterday by the journal Nature. "Conformity fits the assumption of an intrinsic motivation to copy others, guided by social bonds rather than material rewards such as food."

Nice discussion of similar points is at science daily. . I will update when I find blog entries.

UPDATES: Thinking Meat, a very nice general-science blog, and PsyBlog , with focus on psychology, both have great, non cut-and-paste posts. (Both found via the increasingly balky Technorati search engine.) But first prize without doubt goes to "small-a" afarensis (spelling corrected in the blogroll), who goes into theories of culture and shows what those chimps are doing.
Coturnix at Science and Politics has more links.

Detecting organic molecules on Mars

There's a very nice interview in Astrobiology magazine with Pamela Conrad, an investigator at JPL, about searching for evidence of life via detection of indigenous complex organics. Dr. Conrad is much more of an Indiana Jane than I'll ever be-- she had to take rifle lessons against polar bear incursions during an Arctic expedition-- but the interview is very down-to-earth about her experiments.

porphyrinsThe plan of attack is to look for a class of ringed organic molecules called porphyrins. This naturally occuring reactive molecule (seen on the moon, for example) is very good at electron capture, and is central to both chlorophyll and cytochromes (in mitochondria), which appear throughout earth life. It is also very easy to detect by uv excitation, which means you can mount a little robot with essentially a black light, and (on Earth at least) everything that glows will grow.

The reasoning in this and other searches goes that electron capture is so central to both photosynthesis and oxygen respiration that some analogous chemistry (also involving big, fluorescent rings) have got to be part of microbial life outside of earth. Patches of flyorescent regions can be inspected more closely, for example by looking for a bias in chirality of the molecules.

CORRECTION: In this post I originally said porphyrins function in electron capture. Actually a metal atom fits right into the middle, and that metal carries the electrons.

Sunday, August 21, 2005

Dienekes: European Society of Human Genetics conference

Dienekes selects a few abstracts from the recent ESHG conference for discussion. It seems that Y-chromosome lineages are really going to refine the human family tree. Also mentioned are mitochondrial marker surveys of Hungarians--giving further evidence for the (maternal) Mongolian heritage of the Magyars-- and Czechs. Very interesting.

Illustrating the barely known

The CS Monitor reviews a compilation of old illustrations of animalsand seamonsters, with a general theme of paleontology. The site, Strange Science, also explains a bit what was guiding the artists' interpretations.

Apparently Renaissance scientists believed stingrays love "music, dance, and witty remarks." I'll have to go see if I can be witty.

Saturday, August 20, 2005

"Disappointment abounds, but that is no excuse to let our courage flag"

Via Metafilter, a fantastic multi-page development log for a portable apparatus for photographing flying insects. A camera with locked zoom is triggered by an electric eye monitoring the focal plane. The whole deal is worn in a harness and looks a bit like a dowser's water stick.

My favorite are the early failures, e.g. a bumblebee almost out of the frame (every other bug is too fast). Then, after machining his own shutter, triumph.

How sweet it is.

Friday, August 19, 2005

Origins of tuberculosis

The open-access journal group Public Library of Science will launch a new journal, PLoS Pathogens, in September. A preview article talks about the suprisingly homogeneous genomes of tuberculosis baccili.

The tuberculosis complex (approximately equivalent to genus) consists of 6 clone groups, of which M. Tuberculosis is the most commonly encountered in human disease. In contrast to other microbial complexes, this family shows extremely little inter-species variation, and almost no evidence of lateral gene exchange, leading to the suggestion that they all clonal progeny of a single, recent, highly successful ancestor.

In 1997, a novel tuberculosis isolate from Africa was described as having features of a possible ancestor baccilus. In the current work, the authors report 37 additional isolates of this smooth tubercule baccilus, enough to characterize them as a single species (with variance distances more common of microbes "in the wild") and a direct ancestor pool for all the modern, highly homogeneous pathogens.

The story gets pretty interesting in the discussion section. They point out a parallel between human genetic diversity (also at its apex in East Africa) and that of the tuberculosis progenitor. The two species were in prolonged contact, and may have exerted selection on each other prior to the emergence of modern pathogen (I mean the baccilus, of course), and even that they may have migrated out of Africa together. This last point would require more precise dating- the molecular clock data (difficult to make precise) for the tuberculosis bottleneck falls at 30,000 years ago, at which point the migrations of H. Sapiens which populated the rest of the world were already long gone. Still, it's interesting that the clone-like Mycobacterium which causes leprosy worldwide also appears to have originated in Eastern Africa Conceivably leprosy's forbears also made use of the greater palette of host genomes in East Africa during its emergence. See Carl Zimmer at the Loom (link below) for other examples of this.

For the purpose of fighting the disease it is always enormously helpful to find an outgroup, and an outgroup with variation amounts to a gold mine. The selection events which gave rise to such a homogeneous group can be read out by comparing with the ancestral gene pool. This may give insight into how tuberculosis persists for so long in human tissue, for example.

Wikipedia on tuberculosis is here. Additional open-access work on the ancestral TB strain is here .

UPDATE: Carl Zimmer at the Loom puts tuberculosis in context with other human pathogens, all of which likely shaped the modern H. Sapiens.

Thursday, August 18, 2005

Liquid lenses for cameras

Slashdot links to a new camera technology: very compact lenses which focus over a broad range using shape changes just as the human eye works.

Since I'm overdue for a new prescription (bifocals?) I couldn't help wondering how these lenses would hold up over time. Still, it looks fantastic.

The slashdot comments are interesting as always.

Tuesday, August 16, 2005

Will the future of science look like the future of journalism?

Jeff Jarvis spends a lot of time thinking about what journalism is going to look like now that the barriers to daily publishing have essentially vanished. Today he quotes Jay Rosen about how journalism schools ought to change their missions to embrace the larger group of people who report:

I used to teach it implicitly: journalism is a profession. Now I think it's a practice, in which pros and amateurs both participate. There were good things about the professional model, and we should retain them. But it'’s the strength of the social practice that counts, not the health of any so-called profession. That is what J-schools should teach and stand for, I believe. I don'’t care if they'’re called professional schools. They should equip the American people to practice journalism by teaching the students who show up, and others out there who may want help.

I keep looking for ways to introduce science methods and thinking to a more general public. The ongoing flap about intelligent design gives this sentiment some urgency. Not only would better explanation do some gohoweververI do think very well-informed people retain opposite views) , but I also think that genuine participation-- doing research-- would also diffuse ownership of the process, to everyone's discomfort, and ultimate benefit! What I cannot see is the equivalent to blogging, or online publishing, in terms of doing science. The basic sciences still involve quite a lot of infrastructure, which means money, which by itself guarantees an ivory tower.

UPDATE: See Coturnix for what other scientist bloggers are saying. Also, I guess I should say that the same reductions in cost of information exchange which are upending journalism already greatly enhance what I can do with this blog. Not science, but communication of science, even by non-specialists, is already happening at the plane I'd envision.

UPDATE#2: The Washington Post is reporting a clinical trial with extensive internet usage. They used the internet at every stage, from patient recruitment to data collection. In this case the patients reported anxiety levels via computer-- you would not want to try a administer a blood pressure drug trial like this.

Population genetics of India

NuSapiens gives a nice introduction about recent work documenting the population genetics of India. I am very interested, as usual in the nexus between migrations and human genetics (giving short shrift to culture), and have been unsuccessfully trying to get a perspective on the India literature.

The field appears to be moving very fast. Basically the mitochondrial DNA and Y-chromosome results from India suggest ancient and yet more ancient peoples and migrations. On the large scale, southwest asia still shows mtDNA variations that appear to date all the way back to the inital settlement of the subcontinent. But the north of the subcontinent has seen substantial mixing.

Dienekes has two recent posts as well. Indus valley mitochondrial DNA and Y-chromosome studies give tantalizing hints of successive waves of settlement that may reflect specific technological developments such as farming or the domestication of horses. An earlier post links to an article using STR DNA to explore genetic diversity among south India tribes.

Also worth a look (especially in tandem with NuSapiens) is an older comment on the catalysis of the caste system by the arrival of a west Asian group.

Monday, August 15, 2005

Metagenomics of stromatolites

Stromatolites pillow-shaped rock formations which are frequently formed by bacterial communities. They are of great interest for the origin of life on Earth because well-preserved examples are found as old as 3.5 billion years, which is only about 300 million years younger than the very oldest rocks. (There is some dispute about whether the oldest stromatolites are really biological in origin. See the very good-- possibly overly skeptical-- discussion in Wikipedia, the first link.)

Stromatolites take various shapes, and are classified based on the cyanobacteria inhabitants , but the community contains many members which cannot be directly cultured (grown in the laboratory for identification and sequencing). A paper to appear in Applied and Environmental Microbiology uses a DNA amplification strategy to identify the metagenomic composition and structure of the microbial community of modern stromatolites.

The biggest suprise from this effort was that cyanobacteria sequences were recovered less than 5% of the time, and instead proteobacteria (formerly, purple bacteria) sequences were about 1/3 of the whole take. Even on the surface, where you'd expect the photosynthetic cyanobacteria to be happiest, cyanobacteria were still a minor part of the community. Instead, the researchers found many representatives of anoxic photosynthetic microbes.

As fossil stromatolite formations are older than the cyanobacterial lineage this makes a kind of sense. The stone structure might even have enabled the community to survive by providing a shield against UV light in the early (oxygen- and cyanobacteria- poor) Earth. The cyanobacteria might thus be a much later addition to the stromatolite strategy.

The spread of a rumor in the internet

The really fascinating blog Data Mining is tracking a rumor spreading through the internet. The rumor, that Technorati (a blog search engine- use it!) will be bought out by a major search-engine player, began possibly on August 11, and he names the blog.

The parallels with the spread of an epidemic are really interesting to me. I hope Matthew posts an update in the next week or so!

Found, ironically enough, on Blogdex, which tracks "the most contagious information currently spreading in the weblog community."

Sunday, August 14, 2005

Use it or lose it

The Washington Post has an article today about lifestyle exercises to slow the brain's aging. The rate of slowing down with older people is a combination of genetics, environmental factors, and lifestyle. I don't have any doubt that keeping your mind active-- the woman described in the article is taking Italian classes and doing crossword puzzles-- will help with the third aspect.

The article does a good job keeping this work in perspective: no single person, for example, ever defeated Alzheimer's disease by doing crosswords, but in on average the disease hits later among people with active mental lives. (And people with early Alzheimer's can use mental exercises to improve their mental function. )

This idea with respect to Alzheimer's has been around for some time. I think what is new is that this appears to be a good idea for everyone.

Very interesting stuff.

Saturday, August 13, 2005

Friday, August 12, 2005

Nice kitty

A paper in this month's Current Biology uses ancient DNA to trace the taxonomy of North American cats, the sabre-toothed tiger and a cheetah-like cat. The DNA was amplified from specimens found in Patagonia (the methods are not online yet). The short recovered sequences show that the sabre-tooth tigers belong in a separate clade from surviving big cats; and the cheetah-like Miracinonyx is a relative of the New World puma.

A tangentially related piece at Discovery Magazine talks about what those pearly sabres were chomping. A big set of fossil teeth from sabre-tooth tigers and wolves, found at a fossil bed in South Carolina, were analyzed for carbon-13 content Carbon-13 is enriched relative to Carbon-12 as you go up the food chain, but this paper makes the additional assertion that C-13 is also enriched in open grassland compared to forest. The C-13 for sabre tooth tigers was much lower than for wolves, though both were top predators. The authors interpret conclude that sabre tooth cats preyed mainly on forest animals.
This reliance on forest may have been the downfall of the cats when the climate shifted.

Finally, (are we to Kevin Bacon yet?) a paper to come out in PNAS uses fossil evidence from Cuba and Hispaniola to suggest that North American megafauna extinctions at the end of the Quatenary period are more closely timed with the arrival of humans than with the climate changes of the ice age. Giant sloths persisted out in the islands until about 4500 BC, well after the last interglacial-glacial transition (between 15,000 and 9,000 years ago). Instead, the closely spaced extinctions in North and South America, and the much delayed island extinctions, are more consistent with humans being the change agent.

Wednesday, August 10, 2005

Tangled Bank #34 at Creek Running North

The Tangled Bank carnival of science-related blogging is up at Creek Running North. Enjoy!

Vikings: family guys

A nice article in the journal Heredity reviews genetic evidence of the last decade to re-assess the Viking image. In contrast to their reputation as "smash and grab" raiders, Vikings colonized islands in the North Atlantic islands (for example, the Shetlands) with both men and women, and it can be seen in the DNA of their descendants.

The evidence comes from the separate inheritance patterns of the Y-chromosome (passed from father to son) and mitochondrial DNA (inherited only from the mother). If Vikings were exclusively marauders, you would expect a male-dominated inheritance, so that the descendants would show Nordic origins on the Y-chromosome but not mtDNA. Admixture analysis shows a large Scandinavian input into the Shetland (about 44%), Orkney (about 30%) and the northwest coast of Scotland. But these contributions are both maternal and paternal, suggesting that whole families made the trip.

In contrast, Iceland seems to show an excess of Y-chromosome Scandinavian input. The review suggests that more distant areas might have been settled by unattached males. I guess the real "smash and grab" areas might be expected to have minimal lasting Scandinavian input.

I'd be curious to see what the deal was for Ireland, and also Russia. There is a tie-in to a human mutation, CCR5-delta32, which has gotten attention recently because it confers resistance to HIV. This mutation may have been spread by Vikings in their travels down the Volga. The map from that work suggests a very widespread Viking genetic impact.

In the end, the genetic data are already jiving pretty well with archaeological evidence. For example, the review mentions a Norse graveyard in the Isle of Man which had only male skeletons.

The search for the perfect espresso

A lengthy discussion on Boing boing about how to get a perfect espresso. Cory gets it right- a Bialetti stovetop, with Illy coffee (mmmmmmmmm....pesticide).

We just watched "Sideways" on rental a few weeks ago. Is there some sort of link between wine and coffee that makes people obsessive? In my experience, they're separate demographics, but the intensity of emotion is eerily similar.

Tuesday, August 09, 2005

Hatching 300 year old eggs: evolution of water fleas

The Philosophy of Biology links to an amazing story- you can recover water flea (Daphnia) eggs from the muck at the bottom of a lake, incubate them and get hatchlings. Even from 300 year old sediments! The scientist profiled, Charles Kerfoot, was able to document evolutionary changes in the Daphnia from different generations-- up to 3,000 generations' difference-- grown side-by-side. In epochs corresponding to a heavy predator burden, he hatched water fleas with tail spikes and helmets; and in epochs without many predators, the bulk of the eggs hatched lightly armored progeny.

Read the PoB link for a pep talk about the immense explanatory power of evolutionary biology, and the vigorous nature of scientific inquiry. Awesome!

UPDATE: This made me laugh: Don't forget to vote in the Intelligent Design poll over at BBspot. Vote twice!

Monday, August 08, 2005

Do dogs have human-like social skills?

A very interesting minireview to appear in Trends in Cognitive Sciences is asking if domesticated dogs' social skill in reading humans does not indicate a heritable trait selected for during domestication.

In specific tests of social cueing, dogs do far better than wolves-- and also even better than chimpanzees. The main example given is a test in which a new toy is hidden under one of identical buckets, and, as the dog enters the room, a human points to the correct bucket. Even litter-raised puppies, with little direct human contact, are able to understand that a human pointing a finger has an information content. Chimpanzees do not do well in this sort of test, but human infants as young as 14 months also perform it with ease.

Dogs will also prefer to "fetch" a ball back to an observer with open eyes over one with closed or masked eyes; and will carry the ball around to the front of an observer with back turned. Try to turn your back on a toddler!

What makes this interesting is that dogs are not exactly the top of the heap when it comes to problem-solving. It's rather social aspects, and the bond with humans, which seems to be where dogs shine-- even more than the quite social wolves. The authors believe that the genetic tendency to bond with humans, which was selected during domestication of dogs, led also to this ability to read social cues coming from people. They propose this when summarising a long-running (since 1959) experiment with domestication of foxes, which have been selected for (bred for) approaching humans without fear or aggression. The "domesticated" foxes were very good at the pointed-finger test, much better than the unselected control population, even though the breeding program had begun decades before that test was known.

Thus a specific social skill might be heritable, and selectable, and different from generic problem-solving intelligence. What makes this an interesting opportunity to a geneticist is the very big evolutionary distance between humans and dogs, and the availability of undomesticated wolves. It might be possible to tease out a genetic description of these tendencies.

It is obvious that many animal species are highly capable problem solvers, and that this reflects several flavors of intelligence. This is a tough field, rife with the danger of anthropomorphism. My own reaction on reading this story is needing to know more about the social skill intelligence of dogs and humans, its distinction from other cognitive skills, and how to develop a bigger range of tests around it. The second item would I think be to test feral dogs, who have not lived around the smell of humans. And lastly, I myself would want to re-read the chimpanzee data to see if this social intelligence is really completely absent from them.

UPDATE,August 9: Science Now (possibly subscription only) is also running a blurb on dog society. Dogs meeting at a free-run park use sterotyped signals to get one another's attention, like sniffing, galloping, play biting. The idea is they know if the other one is distracted or paying attention. (Note to self: could have applications in lab meeting.) From the blurb I'm again left wondering if this is unique to dogs, or part of the toolkit for a social animal. Cute pictures, though.
Proxima Centauri

From Red Nova , the closest star to our solar system is Proxima Centauri, the red star in the center of the image. It's extremely faint, so the exposure also reveals lots of brighter, more distant stars.

Not to spoil this peaceful image, but the Jesuit head of the Vatican Observatory (a fairly senior post in the hierarchy) has publicly and robustly contradicted Cardinal Schönborn's pro-Intelligent Design editorial. I think Catholic astronomers-- Galileo's heirs-- feel a special obligation to avoid getting theology injected into science matters. Read this for a more recent take on the chronology of Galileo's suppression, and Pope John Paul II's role, with then-Cardinal Ratzinger, in rehabilitating Galileo.

Fr. Coyne's editorial (registration required) is here .

Friday, August 05, 2005

Deep subsurface biosphere

Trends in microbiology has a minireview about bacterial cells growing as deep as 800 meters underneath the seafloor. The numbers of bacteria, and the size of marine sediments, means that these prokaryotic communities might be as much as 30% of the total earth biomass.

The main focus of the minireview is on efforts to count how many are actually alive. Early counts based on sulfur turnover gave values orders of magnitude smaller than surface counts, which suggested that a lot of the biomass down there was either dead or very metabolically slow. A new effort used an alternative technology (detecting ribosomal RNA) and came up instead with fairly constant numbers of alive cells from the surface all the way down. So the bacteria are dividing slowly, but they are alive and well.

800 meters underground!


Genome biology has an update on metagenomics, the genomic sequencing of multiple related organisms all in one go. Metagenomics was first invented for the purpose of getting sequence data from microbes which cannot be grown in the lab. (This is the vast bulk of all microbes). Places like acid pits in mines, the open ocean, or even the air in Manhattan are brimming with life, but scientists are not able to grow the individual organisms yet to the point where they could get enough DNA for sequencing.

Metagenomics gets around this problem by big improvements on the front and back ends of the sequencing effort. On the front end, DNA is just taken and sheared "shotgun" from an environmental source, and clever methods are used to clone the DNA (chemically join it to known sequences to make a recombined DNA package which bacteria will copy). This means that the DNA is recovered in a fairly unbiased way.
The sequencing is done all at once on the mixture of all DNAs which were available in the environmental sample.
On the back end, computer analysis is used to group (assemble) sequences, without knowing the source organism. In many cases, the sequences are similar enough that source organisms can be identified. The frequency with which a particular sequence is obtained hints at the relative numbers of its host organism in the environment.

What's interesting to me about the analysis is that the results produce a portrait of an ecosystem. Comparing the sequences found in one environment to another set can highlight the specializations characteristic of the whole assemblage of organisms, allowing meta-comparisons analagous to "Hollywood is all about movies and New York is about finance." (Probably at a similar level of resolution). For example, the open ocean (Sargasso Sea) sequences showed a huge variety and frequency of rhodopsin-like proteins, suggesting that photosynthesis is probably a property of very many pelagic species. Again, some have not even been identified yet except for their sequence! Soil samples show a diversity of cellubiose phosphorylase genes, again consistent with a community organized around decaying plant matter.

The point is that these descriptions, encompassing a kind of weighted average of the actual inhabitants of a particular spot, portray how microbes actually live in the wild. Microbes always occur in communities, and they rely on each other extensively. As a concrete example, the paper mentions an future effort at metagenomic analysis of the 10,000,000,000-strong community of microbes in and on the human body. There is as much DNA in those microbes as within the human genome, and its detailed makeup changes with every meal, even with every shower.

Thursday, August 04, 2005

Crunch time

Today's Nature has a study comparing the teeth of the hominins Australopithecus africanus and Paranthropus robustus. A new method for studying microwear in three dimensions allows the researchers to categorize the diets of ancient species:
the 'gracile' Australopithecus africanus ate more tough foods than Paranthropus robustus, and that Paranthropus ate more hard, brittle items as part of more varied diet.

But the bigger advance from the study was that the new method also allowed evaluation of overlap in diet. In the linked interview, the authors emphasize substantil overlap, and speculate that most of the time both hominins both preferred easy-to-get foods like fruits. The differences in wear may actually reflect seasonal specialization. So, to quote from the article:

This suggests that early hominin diet differences might relate more to microhabitat, seasonality or fall-back food choice than to oversimplified, dichotomous food preferences.

Updates on Mars and Methane has been running a series on methane on Mars and the possibility that it is being generated by microbial life. I think the bulk of the evidence is in favor of some geological process. The last article in the series goes over how to distinguish living from non-living sources of methane.

And the New Scientist talks about some of the most recent data. Methane is almost certainly being produced continuously, by spot sources.

Vive la difference- a bird's-eye view

The week's PNAS has a nice short article bringing up something I guess should have been obvious: birds can see differences among themselves that are invisible to the human eye. Birds have special cones which can see into the UV range, and several species of passerine birds, which are listed as not having sex differences, actually do have flares or tufts of ultraviolet bling-bling which distinguish males from females.

birds uv coloration This picture shows three males of different species. They appear very similar in visible light (left) but the uv shows differences.

The point is that when you have a difference, you can get a mating preference, and sexual evolutionary presssure is likely to be acting on these "drab-colored" birds just as much as on peacocks. Also, these patches were so common that maybe the focus should be on the converse case: explaining evolutionary pressure on the rare birds without any sexual dimorphism.

Tuesday, August 02, 2005

John Hawks and the Neanderthal Diet

No, John doesn't eat Neanderthals.

In a strange instance of dietary synchronicity, given that Atkins is going bankrupt, Hawks gets exasperated with attempts to figure out the heavily carnivorous Neanderthals diet. A number of studies have measured bone collagen nitrogen-15, a heavy isotope which gets enriched as you go up the food chain (but, as Hawks points out, maybe not in a simple way). A study to be published soon reports very high N-15 values in Neanderthal remains, and concludes that Neanderthals ate big beasties--rhinos and mammoth-- compared to horse-eating hyenas.

What's clear is Neanderthals have higher N-15 than contemporaneous hyenas, and it's thought on other grounds that Neanderthals ate up to 95% meat. The high isotope values are remarkable, and consistent with high N-15 found in mammoth of the same epoch. However, mammoth bones are not found in Neanderthal sites. Moreover, bones of Homo Sapiens peoples known to have relied on seafood (the South Beach diet?) give even higher N-15 values. Basically, Hawks thinks you can't conclude much about diet without more data than carbon and nitrogen isotopes.

The spread of Leprosy, and its demise

Leprosy , a disfiguring mycobacterial infection, was a feared illness in biblical and medieval times (the biblical term may have been a catchall for several skin diseases), and remains very persistent in the developing world. Like TB, leprosy is making a comeback in areas with high rates of HIV infection.

The genomic effort to sequence leprosy shows that leprosy worldwide is the result of an almost clonal population of mycobacteria (about 1/10th the number of SNPs compared to M. tuberculosis), so homogeneous that SNP analysis can reveal the human migrations which spread the disease. Specifically, the disease in the New World is West African in origin and almost certainly was brought by slave traders. The European variant is divergent from the India strain, so Alexander the Great brought the disease from a lot closer to home than previously thought.

In western Europe, the once common leprosy nearly vanished by the 16th century, even as tuberculosis, another mycobacterial disease, persisted. An old hypothesis suggested that cross-immunity to tuberculosis contributed to the disappearance of leprosy in Western Europe. However, a paper from February in PRSL-B suggests that the relationship between TB and leprosy is more complicated than previously thought, with co-infection historically being actually very common. PCR detection of the two microbes' DNAs revealed that co-infections with TB and leprosy occured in about 42% of human remains stretching from 100-1000 A.D. TB may thus historically have acted as the killing blow to people already suffering from leprosy.

So rather than cross-immunity within human hosts, it must be that social changes in the middle ages favored the persistence of TB and the demise of leprosy (and the rise of Foucault ).

Online neurologist

Mind Hacks links to an explanation of what neurologist are doing with all the poking and prodding during the exam. For example, ask someone to close their eyes, then push them in the chest. Malice? No, the Romberg test. (Just explain you're an overachiever.)

Then, take out your mallet and start clipping at their kneecaps.

Monday, August 01, 2005

Tornado Intercept Vehicle

Via Boing Boing , a modified pickup truck built by a cameraman for the purpose of driving into tornados. Looks like something from Star Wars.

Generalized cognitive losses in early Alzheimer's

Alzheimer's disease is thought to be cryptic for several years, with just mild cognitive losses, before a definitive diagnosis can be reached. There has been some evidence that episodic memory (e.g. face recognition) might be more specifically vulnerable in the early stages of the disease. However, a very large retrospective study of Alzheimer's case histories, to come out Neuropsychology tomorrow, shows that patients who later developed Alzheimer's had multiple cognitive losses at stretches up to 10 years before the definitive diagnosis was made:

The analysis showed that no matter what kind of study, people at the preclinical (undiagnosed) stage showed marked preclinical deficits in global cognitive ability, episodic memory, perceptual speed, and executive functioning; along with somewhat smaller deficits in verbal ability, visuospatial skill, and attention. There was no preclinical impairment in primary memory...

..The data also supported the emerging consensus that AD's preclinical period is characterized by an early onset followed by relative stability until a few years before diagnosis, when functioning plummets.

These changes, including a leveling-off of losses, are also seen in normal aging, which is what has made early-stage diagnosis so difficult. (A nice discussion is here )

The study also found that patients who were already under heightened scrutiny for general cognitive losses then showed a stronger episodic memory effect during the early stages; so episodic memory may be an effective metric for disease progression once an at-risk person has been identified. The authors suggest a multi-variable approach to catching the earliest stages of the disease. The huge advantage conferred by early detection is the possibility that treatments will have more effect.

The full article (pdf file) is here .
A nice summary at USA today is here.