Wednesday, March 30, 2005

Craters and tectonic activity on Mars

The New Scientist is reporting that a method used for dating ages for the surface of Mars is seriously flawed. Nadine Barlow, the person who has catalogued 42,000 craters on the Martian surface, says that recent images done by the Mars Odyessey project suggest that crater counts overestimate the number of impacts on Mars. This in turn would mean that most martian surfaces are somewhat younger-- and Mars has therefore been somewhat more active-- than has been calculated in the past.

The age of the surface of Mars is calculated by counting craters . Heavily cratered regions have been geologically still for a longer period, whereas lightly cratered regions have somehow "erased" their allotment. To assign a date to these counts, the crater numbers have been compared to regions on the moon , which in turn have been precisely dated by lunar rock samples.

Barlow's comment is that cratering occurs differently on Mars than on the Moon. Even smallish Martian craters have extensive rays of ejected material, suggesting ejection of much more material than calculated, and the creation of millions of small secondary craters as the "splash" from the first impact falls back down. Thus regions might acquire cratering faster than previously recognized, and a given region should be assigned a younger age than a strict Moon dating scheme would give.

I'm a little confused by this news, and I have not been able to pick it up anywhere except New Scientist. In fact, Dr. Barlow was apparently saying just the opposite in 2003: that Mars makes fewer secondary craters than the moon, arguing, at the time, because of subsurface ice. What is abundantly clear from Google is that she's the expert, so it may just be the reports which are confusing me.

In the meantime, check out the unfortunately named PIGWAD interactive map of Mars. I launched the Mars Craters survey and could zoom from the whole globe down to features of 5 km. Now if I could only use this to find my glasses....got 'em!

Fungus among us

Crumb Trail is blogging that Alaska, and Canada's Yukon territory, could get a bumper crop of morel mushrooms in late spring. Morels come on like gangbusters in seared soils the year after a wildfire. Last year 6.5 million acres of the interior of Alaska burnt, with four of the largest 10 fires of 2004.

Morels make for some good eating, but if you pick them yourself be sure you know what you're picking.

Tuesday, March 29, 2005

Plants,insects, and soils- the eternal golden braid

The March National Geographic describes research in two Amazon ecosystems in which differences in soil quality seem to drive the setpoint in the struggle between plants and insects. Plants mount all sorts of defenses against herbivorous insects, which are then under selective pressure to evade them; and once a plant's defenses are evaded, that species comes under pressure to develop something new. And this struggle is indeed very old: fossil beds from as long ago as the late Silurian (400 million years ago) already show land plants and the arthropods which eat them already in an ecological assemblage.
What's new about the National Geographic article is that plants seem to devote more resources to fending off insects-- poisons (like caffeine), spiky indigestible leaves, etc.-- when the soils are poor; and more on leaf production and growth when the soil is richer. This tendency is so strong that the Amazon soil districts have distinct sets of plants, even though much the same sets of insects are doing the eating. To me this sounds reminiscent of desert plants, who invest heavily in defense at the expense of slow growth. In a sense, then, the nutritional input determines the equilibrium point in the ecosystem.

Make the Connection

The vastly underrated neuroscientist and philosopher Horace Barlow has speculated that the human cortex is built to be a "coincidence detector," able to detect (or construct) patterns against noisy backgrounds. I was reminded of Barlow's thesis this morning when I read these items in rapid succession:

The Smiths to be studied in Manchester conference. The Smiths' music, already recognized for its medicinal properties, will now be put under the microscope for its cultural impact on mopey teenagers. (People forget the sarcasm-- Vicar in a Tutu, Sheila Take a Bow) I don't have nearly enough of their music on my Ipod. Morrissey's famous vow of celibacy has presumably been released by the patron saint of onanism .

And An Evolutionary Basis for Acne in which acne becomes celebrated for its contraceptive effects. A team of Birmingham scientists (can't find the link) believe that acne, with its pox-like symptoms, visibly flags immature humans who are not ready for reproduction.

And lastly, the Register suggesting that IPods carry a health warning:

(The Register/ Splinter Products )

Monday, March 28, 2005

Hard drives- smaller, roomier.

I don't usually gush about hardware, but this hard drive looks unbelievable. You could fit 4 Gig into your cell phone!

Given the trouble I'm having filling my ipod, maybe it's too much space? Of course you could put your MRI scans on it...

Sunday, March 27, 2005

Catch a comet by the tail

Micrometeorites are small particles of space dust, up to the size of grains of sand, which populate the inner solar system. Their speed relative to spacecraft makes them a bit of a hazard. But once captured in the Earth's atmosphere, they tend to drift to the earth's surface without getting completely melted, as larger metorites are. (Micrometeorites often form a melted "rind" around pristine material.)

Tons of micrometeorites enter the earth's atmosphere every day, making them the largest source of extraterrestrial material to arrive at the earth's surface. You can actually collect micrometeorites in your own backyard , by sorting through the grit at the base of a drainspout, because they stick to magnets whereas most other earth dusts will not. Visible under a moderately powered microscope, glossy spherules with pitted surfaces are likely to be from outer space.
(Micrometeorites collected in Antarctica; picture copyright US Army cold regions engineering lab)

Systematic efforts to collect micrometeorites are made in ice pack or from ocean sediments. Glacier melt-holes will have the same sort of grit (on a much larger scale) as found under a drainspout; and in pristine environments, this will be a fairly rich source. In Antarctica, US scientists have collected them by suctioning up the grit at the bottom of a covered meltwater drinking well; whereas a French group has been carefully melting ice cores under clean room conditions.

Micrometeorites are of interest mainly because their mineralology is much more varied than that of conventional meteorites. Many contain complex organics, and even amino acids , suggestive of an origin in comets. Therefore these particles are of interest in the origin of life because they might have delivered organics to an Earth which was effectively sterilized during the late heavy bombardment. The big question is whether organics supplied by this stardust could have helped the origin of life along.

Current research focuses on identifying compounds in micrometeorites, but it is made harder by the huge chemical heterogeneity. I'm guessing that microanalytical methods, working with batches of less than 100 or so, may produce something very interesting soon.

Friday, March 25, 2005

Clocky the persistent alarm clock

Via slashdot, an alarm clock which will roll off the nightstand and hide if you hit the snooze button. It hides in a different place every day.

Why not just have children? Better: take mine, between the hours of 5:30 and 7. My most memorable awakening (to date) was a drool droplet in my ear (no, it wasn't Heidi Klum), although the sick kids also always seem to find my side of the bed first.

Soft tissue from dinosaur bones

The New York Times (and yahoo, reuters, La times....) has the story coming out in today's science that scientists have recovered soft tissue, possibly blood vessels and blood cells, from within the incompletely fossilized bones of a tyrannosaurus rex. The vessels and cells look just like birds'.

From the science text it seems that they regard this fossil as unusual but not exceptional. They should be able to recover such structures in the future (they have already done it with a different tyrannosaur and a hadrosaur).

My interest in hearing about well preserved blood vessels in the bones was that it could add evidence as to whether dinosaurs were warm-blooded or not. Mammals and reptiles have different microcapillaries because the heat in lizards comes from outside whereas in mammals it's (in general) arising from within. But the bone vessels described here are not involved in heat exchange. There's a very nice discussion of these ideas here but basically the dinosaur's Haversian bone vessel system, although similar to mammals' and birds', might also have evolved for mechanical reasons.

UPDATE: The nearest citation I could find to my unreliable memory about skin differences is here . It looks like debate on dinosaur endothermy focuses on lungs and heart and nasal structures and not skin. Also these physiologies come in many flavors, with dinosaurs maybe having their own thing going.
UPDATE#2: For a really great discussion of how animals control body temperature, see here. An interesting point is that the heat budget of biggish animals like leatherback turtles is actually in the direction of too hot.

Thursday, March 24, 2005

Mind drugs and enhanced normalcy

I have interested for quite some time in performance-enhancing drugs for the mind, and the recent attention to steroid use by athletes has gotten me thinking about it some more. Several newer drugs, most famously Prozac and relatives, but also Provigil and others to come, target specific brain systems > and seem to have fewer side effects than anything which has come before. Thus there is a possibility that these drugs could be taken without risk by a wide range of people. It's very difficult to restrict one's writing about this topic, as it readily sends offshoots toward complex medical and public policy issues. I just want to pinch off the idea that the way the increased availability of these drugs is presented ends up somehow impugning the undrugged, "normal" mind.

At least since Listening to Prozac , and more explicitly last weekend with Kate Zernicke's article in the New York Times , it has been noted that people take neuroactive drugs not just in moments of distress, but also to enhance their everyday lives, either for specific reasons (pulling an all-nighter; in-law's visiting) or as a lifestyle choice. As Zernicke points out, newer drugs such as Ritalin and Provigil are part of a continuum of drugs including caffeine, beta-blockers, or alcohol, which, used moderately, help smooth life's bumps with minimal side effects. Zernicke furthermore quotes Arthur Caplan that this type of drug consumption is just another form of technological advance, like a PDA or a spreadsheet, which enhance capabilities and even competitiveness. What's the big deal?

Without going into detail, I think it's likely that excessive ingestion of anything, from super-sized fries to crack cocaine, will have measurable health effects. Thus I think the health-care industry might have a financial stake in knowing who's taking what.(For an idea of the potential complexity of this question, see here for actuarial considerations for smokers.) A second social concern with brain drugs is the idea that these drugs, if available to only some people, will give them an unfair advantage. The only concrete example I have is standardized entrance exams, where standardization is precisely the purpose of the exam. (It would be equally unfair to compare students subjected to random loud noises with those taking a test in silence; or to allow calculators for only half the class in an arithmetic exam.) This is essentially doping, which has been discussed to death with respect to competitive sports. After all the posturing is over, I do expect some kind of framework to emerge for running fair sports competitions. These standards could be ported over to mind drugs.

Professionals will always have enormous incentives to enhance their performance. What interests me more is the prospect of ordinary people taking these drugs. I think neither of the two concerns I mentioned above forms an absolute barrier to "lifestyle" use of mind enhancing drugs. Moreover, I have to note here that I drink 3 cups of coffee a day, in part because of the mental buzz. What I find more weird is the undertone of dissatisfaction with normal brain function, and in fact an effort to slight normalcy, which seems to be stoked by discussion of these little pills. One can see the trend, in another context, in the article in this week's New York Times about hypomania , a recently described mental state comprising increased, but controlled, brain activity. I think the accompanying figure says it all. People are running around in the middle of the night, writing, painting, succeeding. And all of them smiling:

At some point, almost everyone encounters them - restless, eager people, consumed with confident curiosity. Researchers suspect that their mental fever shares some genetic basis with that of bipolar disorder, known colloquially as manic depression, a psychiatric disorder characterized by effusive emotional highs and bouts of paralyzing despair.

....(snip)....

As one psychiatrist put it, Dr. Kessler said, "The goal in life is constant hypomania: you never sleep too much; you're on; you keep going."


Besides the idiocy of wishing everyone's setpoint to be 110% (shades of Spinal Tap), this attitude glosses heavily over the real struggles of people with bipolar disorder. The ones I know and love have no wish to hold on to their manic episodes. But look at the words surrounding hypomania: eager, curiosity, confidence. Did someone forget abrupt, irritable, can't hold a conversation? In the absence of a fuller portrait of abnormally elevated brain activity, the decision of normals to forego drugs which result in a simliar state somehow becomes technophobic. Moreover, there is a conceptual problem first noted by the great philosopher Syndrome of the Incredibles, if everyone is special, then no one will be. If use of the drugs becomes sufficiently widespread, than hypomania will be the new normal.

So my final problem with this trend becomes a cultural one, namely, who the hell cares if my teeth are sparkly white? Why should it be my goal to be hypomanic? I enjoyed this paragraph from Neela Thirugnanam very much:

Happiness void of repercussions is no more contained within a Prozac capsule as it is (sic) with any other drug. ... Prozac may call to us as the savior of those with minor depression, but its overuse can drown difference in sea of medicated sameness.

What people want is to be happy. Maybe we should start with that.

UPDATE: Via email from Andy Miah at Bioethics and Sport, a whole book about cosmetic pharmaceuticals Better than Well by Carl Elliot. Check out Dr. Andy's site!

Wednesday, March 23, 2005

Tangled Bank # 24

The Tangled Bank carnival of science-related blogging is up over at Syaffolee. It's looking very good!

Ice-9, coming to your solar system

Scientists modeling the H20 in the extreme conditions inside Neptune have now pushed the substance into a superionic state, as hard as iron and (thermally) glowing yellow. Based on what I could google, a superionic state is not yet hot and compressed enough to be metallic, so the hydrogen atoms have free run, but the oxygen remains in a crystal lattice. The superionic state for water is possible at a chilly 7000 K (about 12000 farenheit).
For an introduction to the technology involved, click here. I've had trouble locating a lattice definition of the state, but I did find this abstract list which suggests that the state may also be present in the earth's mantle, right after Ice-VI (no Vonnegut )

Tuesday, March 22, 2005

Germany: underdeveloped blogger nation

David's Medienkritik lists the top 10 reasons why Germans don't blog. My favorite: "7. On the internet no one cares about someone's Dipl-X or Dr."

Here in Germany, my neighbors, who know an alarming amount about my position, address me as "doctor" because of my Ph.D. It's very disorienting.

Also at Medienkritik, a run-down of the SPD's latest woes.

Genesis probe update:When life hands you lemons...

The Genesis space probe for solar wind particles, which landed with a thud in the Utah desert, may yet yield useable samples. If nothing else, click on this link to see the impact scene, which looks something out of Wile E. Coyote.


The shattered collection surfaces are being pieced together, and scientists are working at finding the solar wind particles amid all the terrestrial contamination. They have been successful enough that they are now accepting requests for distributions .

When the crash first happened, I felt real pain for the postdocs and grad students who just saw their projects obliterated.

Monday, March 21, 2005

A little bit more about Mars methane

I came across this journal article by Chris Webster, a JPL scientist, whose lab is building a small laser spectroscopy unit to detect methane on Mars . The device is fairly small, and is sensitive enough to detect methane at concentrations well below current estimates for the Martian atmosphere.

But to identify methane as coming from life, the device needs to compare isotopes in the gas. Living things prefer to use carbon-12 over carbon-13, whereas geological processes don't distinguish between them (this is the same method used to search for biogenic traces in very old earth rocks. I didn't realize this but the enrichment is on the order of 2-4%. The device will also be able to measure oxygen and hydrogen isotopes.) To measure the ratio of these two carbon isotopes, the device needs much higher concentrations of methane. Perhaps this limitation could be bypassed if a vent or other big source of methane could be located.

Some technical info about the laser spectrograph is available here. Subscription pdf file (Applied Optics) is here.

Sunday, March 20, 2005

"Alu" about translocations

It's important for the life of a cell that its chromosomes remain intact. DNA breakage can occur following radiation exposure, chemical damage, or viral infection. In some cases, breakage repair results in DNA pieces attached to the wrong chromosome. This phenomenon, known as a translocation, can cause certain cancers, such as acute myeloid leukemia.

In the latest issue of Molecular Cell, Elliott et al. investigated how mammalian cells rejoin DNA strands during translocation. Elliott et al. were especially interested in how translocations occur around the gene MLL, which is frequently the site of translocations in people with acute myeloid leukemia. In addition, they wanted to know in whether short, highly related DNA repeat regions known as Alu sequences , which appear to form hotspots of DNA breakage and rejoining events in tumors, could influence the mechanism of DNA repair.

Translocation breaks can be repaired either with loose ends, carrying possible insertions or deletions, simply joined together (this is called NHEJ, for non-homologous end joining), or via a mechanism called SSA (for single-strand annealing), which uses a match in sequences near the breakpoints as a template to "edit" the new junction and remove one copy of the match. (These mechanisms plus a third mechanism, homologous recombination, are also seen in chromosomal reattachments, when a fragment is re-joined to its original chromosome. In this more normal situation, junction editing makes sense, as extra DNA can be as damaging in the wrong context as a stray semicolon in computer code.)

chromosomal repair

To study the events surrounding translocation, the authors designed a test (see the picture) where genes encoding resistance to two different drugs (shown as a green region and a red region) were broken in two, and the halves were swapped, joined by a controlled breakage point called a restriction site and an Alu repeat (the blue box). Following DNA strand breakage, about 1 cell in 100,000 showed a chromosomal translocation in which the drug resistance genes were reconstituted. These rare cells were now drug resistant. The neomycin resistance gene (green) had additionally been designed with splicing donor and acceptor sites, a trick which allowed expression no matter how the translocation was joined. But for a cell to achieve puromycin resistance (red), a further constraint was that overlapping sequences (shown as complementary triangles) had to be edited via SSA. Thus, by evaluating the puromycin resistance of neomycin resistant cells, they could see whether the translocation occured by NHEJ or by SSA. (Of course the cells could elect to make one translocated juction by SSA and the other by NHEJ. )

Using this system, they found by far the most common translocation event (80% of all events) utilized SSA on both chromosomes. But they got a suprise when they tinkered with the system. The intervening Alu sequences (the blue box) had been identical to one another in the first run, but when they replaced one Alu sequence with a 25% divergent Alu sequence, neomycin resistance gene (green) translocations now occured almost entirely via NHEJ. The change to NHEJ was not the result of disabling the SSA machinery, as the translocations creating puromycin resistance continued to favor SSA. The total frequency of translocation was not affected, even though a different repair mechanism was used. But this was not completely random NHEJ. The weakly homologous Alu sequences somehow biased the joining event, because deletions associated with the NHEJ often occured within short stretches of identity between the Alu repeats!

The most important observation from this experiment is that translocations are strongly affected by the degree of sequence homology near the broken ends to be joined. If, as in the first experiments, the sequences match closely, an SSA mechanisn will edit the junction so that an overlap is removed. But translocations occuring near moderately related Alu repeats cannot evoke SSA, and instead favor NHEJ joining, with however a bias to the joining. The exact role of Alu repeats in biasing the joining remains a bit mysterious. The authors believe that the NHEJ is sensitive somehow to microhomologies within divergent Alu sequences in their system, and that this sensitivity may be significant in clinical leukemias as well.

Friday, March 18, 2005

I'm not THAT old! (Am I?)

Recent questions from my kids:

"Daddy, what's a typewriter?"
--a typewriter is a computer without the television part.

"Daddy, what's film?"
--film used to go in the back of cameras for you to make pictures.

They have also never seen a vinyl album or a portable CD player (I do have an ancient walkman).

Coming soon:
"Daddy, what's a library?"

Thursday, March 17, 2005

Martian methane

Red Nova talks about a possible interpretation of the methane signatures seen in the Martian atmosphere. People are excited because life is one big source of earth methane, but Mars is different enough that it may come from a process not familiar to earth.

Dorothy Oehler (pronounced "oiler" I'm sure) of NASA thinks that the methane might be coming from kerogens, or residues of past life, which on earth release methane as they slowly degrade during geothermal heating. In the case of Mars there is not likely to be geothermal heat. But Oehler thinks heat might come from a meteorite impact (and there are reasons to believe it's only forming in some regions). Alternatively, as there has been some evidence for seasonal differences in the rate of methane production, maybe the sun has something to do with it. In any case, in the kerogen scenario, the methane would be the hangovers of a long ago party.

For me this feels like a glass half full. Readers of this blog might have realized that I'm pretty excited about the idea of life outside earth. But having it long gone isn't any fun. ( Don't look in that egg! ) Alternatively, the picture on earth is that once life gets a toehold, evolution can allow survival in unbelievably harsh conditions. Maybe Martian life vigorous enough to deposit kerogen could have left descendants.

Kerogens of course are also of interest with respect to petroleum formation . See also this fairly technical discussion about whether earth petroleum arises from biological processes or deep-earth processes (the latter is not plausible for tectonically dead Mars).
I don't even want to think about oil deposits on Mars. How did all our oil get under their sand?

SeXed up

This week's Nature carries the genomic sequence of the human X chomosome. This chromosome was tricky to sequence because it is full of repetitive DNA sequences, which resemble each other quite closely, so the still 85% complete sequence arrives about 4 years after the publication of the draft sequence of the human genome.(Since sequencing of a whole chromosome involves breaking the chromosome into small pieces, sequenced, and reassembled, repetitive DNA acts like a jigsaw puzzle full of the color blue: every piece starts to look like every other.) Despite the special rules of inheritance for sex chromosomes, the sequence of the X chromosome reveals quite a bit of genetic exchange between the X and Y, which has been progressively shut off during evolution.

The X-chromosome is of very high interest to neuroscientists, because it is the site of a disproportionate number of human mutations resulting in mental retardation . Groups like the European Mental Retardation consortium are hunting through the X chromosome to find the estimated 20 different X-linked genetic defects which result in mental retardation.

Moreover, there are some hints from an identical twin study that the X Chromosome may harbor genes important for verbal skills and social behavior. Girl identical twins (who have two copies of their X chromosome) differ in which X chromosome is active in which cells, whereas boy twins don't "have a choice" and use the same X chromosome in all cells. This study found that boy identical twins had more highly correlated scores in tests of prosocial behavior and verbal ability. Interestingly, girls with Turner syndome (only one X chromosome) where the X came from the Dad have much better verbal skills than girls with Turner syndrome in which the copy came from the mother. Although the proposed mechanism, called imprinting, would have to be confirmed by identification of the causative gene, the Turner syndrome observation again suggests that there's a lot more to X than meets the Y. The X chromosome will be an interesting hunting ground for cognitive abilities we associate with being human.

The Beeb , reading the same Nature stuff, points out that the entire female X-chromosome is not inactivated but rather about 15% of the genes remain active. For these 15%, females are expressing two copies. This region may be a source of differences between the genders.

I can't leave a discussion of sex chromosomes without discussing my avatar, the platypus, which never seems to do anything the easy way. Platypusses have 5 X chromosomes, and males have 5 Ys; and they have to resort to a very strange subcellular chromosome chain during sperm formation to be sure all of the sex chromosomes, Xs and Ys, sort to the right place (which they do, a big percentage of the time). Al though platypusses lack SRY, the gene important for human male differentiation, their X chromosome number 5 actually has a relative of DMTR1, a gene implicated in bird sex determination.

Wednesday, March 16, 2005

Michelangelo had his anatomy down cold

Ok, it's a slow news day.. the Discovery Channel reports measurements of Michelangelo's David which dismisses the notion that the statue is of less than heroic proportions:

"David is not really highly gifted, but he is totally normal. His penis measures 15 cm which, considering the height of the statue, corresponds to 6-7 cm in an adult," Gulisano told Discovery News.

"Here we have a naked man who is about to fight. He has an orthosympathic activation consistent with the combined effects of fear, tension and aggression. A contraction of the genitals is totally normal in such conditions," he said.


Memorize those words, boys, orthosympathetic activation. They'll come in handy.

Too much information

An editorial in PLOS Medicine calls for reconsideration of how biologists publish work involving large datasets. Although this problem of data management is becoming widespread, the focus of the editorial (and they are really unsparing!) is the frequent poor presentation of microarray data from clinical trials, where, to quote the editorial, "studies involving large datasets..are so poorly reported..that many are not reproducible." In a later section they say "published studies are far from the level of evidence that would be accepted for virtually any other medical test."

Given this level of alarm, I wish they would give an example of a high profile association (i.e. one which received media attention) which fell through.

There appear to be two sets of issues in the editorial. The first set consists of tasks made harder by big data sets: analysis by authors, review by reviewers and editors,display by journals (which often resort to extensive web supplements that are never printed) and digestion by readers. The second set lands on the backs of the researchers themselves, and seems, in aggregate, to be that people are doing the experiments without adequate training. Both sets of issues are endemic in the array-using biology world, so there's no need to trot out sterotypes of M.D.s burning down the lab. (Is there?) Still, a false clinical association could put someone's health at risk.

PLOS, which is mainly a web journal, wants publications to include everything in an interactive E-document, from "primary data to statistical methods, figures and derived data together with textual documentation." That sounds a little extreme, but they do point to such a document already in existence. I can't help thinking, though-- haven't physicists already confronted the issue of data management? Aren't netheads designing data mining software?

I am a consumer of this kind of data, and I don't think an interactive document would help me much. In my own experience with "gene-gazing," I tend to go through the raw tables in the Supplementary Info, and, if the experimental design was especially relevant, I cook up the raw numbers myself. This is because I am an "old biologist"-- actually, literally pretty aged-- and my experiments are centered around 1:1 or 1:several interactions. Maybe I should call myself a hedgehog, compared favorably to the idiot foxes.

Sunday, March 13, 2005

Can past epidemics explain HIV resistance in Europeans?

There's a fascinating blurb in Nature news examining whether past epidemics which killed many Europeans can explain the prevalence of a mutation which confers resistance to HIV. At least 10% of Europeans, ranging from 4% of Sardinians to nearly 16% of Finns, have a mutation in a protein called CCR5, which HIV needs to infect macrophages and CD4 positive T-cells. (People homozygous for this mutation,called CCR5-delta32 , do not express any CCR5 protein on the surface of their macrophages. People heterozygous for CCR5-delta32 also have improved HIV resistance. The mutation is not cost-free, as it results, for example, in decreased responses to M. Tuberculosis.)

CCR5-delta32 appears to be relatively new in evolutionary terms (estimated origin in a single individual 1000-5000 years ago). This recentness may account for why the mutation is virtually absent outside of Europe. But conversely it becomes hard to understand how it got so prevalent within Europe. It must have come under huge positive selective pressure, meaning at some point people carrying the mutation must have out-survived their neighbors with normal CCR5.

One possible explanation is that this mutation helped Europeans survive during an earlier epidemic. For this to be the case, the epidemic would have to be devastating, cyclical, and have persisted in Europe for centuries. Nature cites a recent Hypothesis Essay in the Journal of Medical Genetics which proposes that the bubonic plague (Black Death), which dogged Europe from about 1350 into even the 1800s, could be the pest. This hypothesis, which has been around since the late 90's, is now revisited with a model of how the wheres and whens of the outbreaks, including the late persistence of bubonic plague in Scandinavia, might match a steady increase in the frequency of CCR5-delta32.

Two major problems with this idea are that bubonic plague is attributed to a bacterium, Y. Pestis, not a virus; and moreover CCR5-delta32 does not confer resistance against Y. Pestis infection. The bubonic plague proponents hypothesize that a virally borne hemmorhagic fever (not bacterial plague) may have contributed to the lethality of the Black Death, and thereby increased survival of people carrying CCR5-delta32. This idea is really threading a needle. The European mass graves from the time of the Black Death are absolutely crawling with Y. Pestis DNA. Resistance to a hypothetical virus would have trouble generating positive selection in the documented presence of a second massive killer, the bacterial plague, which is not affected by the mutation.

A second group believes that smallpox, a viral disease, may have been the guilty party. Poxviruses infect lymphocytes via a close relative to CCR5, so cross-resistance is easier to imagine. A difficulty with this hypothesis is that smallpox never appeared so cataclysmic as the Black Death, and may not have been sufficiently lethal, in population terms, to account for the prevalence of CCR5-delta32. Proponents of the smallpox theory counter by saying that the disease primarily killed children, who may not have made it into historical accounts; and that the cumulative effect of small scale smallpox epidemics over 700 years (lasting into the 20th century) killed far more than the Black Death did. I have to say, on balance, that their idea seems easiest.

One fascinating remaining observation is that sooty mangabeys, for whom SIV infection does not result in AIDS, also appear to control their CCR5 levels. . This receptor, then, could be a good target for efforts to prevent HIV infection.

Brief coda: The Telegraph claims that the CCR5-delta32 mutation arose somewhere in Mesopotamia. Impossible! Regardless of whether the mutation interferes with smallpox or Black Death, both diseases were widespread enough that CCR5-delta32 should have increased survival throughout southwest Asia. It has only been found in tiny percentage of people in Pakistan and the Middle East.

Friday, March 11, 2005

When did life begin on Earth?

There's a pretty important article in this month's Geology magazine (link is only to the abstract) which questions the geologic evidence used for the very beginnings of life. The article, reviewed by Stephen Moorbath , shows that rocks taken from Akilia, Greenland, which had been reported to show chemical traces of life, are not of the relevant type for this effort. Moorbath concludes, rather conservatively, that for the moment, the oldest certain traces of life are bacterial fossils "only" 2 billion years old. ( See Wikipedia for a timeline that needs to be reconsidered and general background.)

Everyone agrees that life has been around for a long time, but the very oldest rocks are hard to find, and frequently heavily distorted. Geologists can usually still identify heavily altered sedimentary rocks, and Australia and Greenland (in particular the Isua peninsula) have formations which are 3.8 million years old, corresponding to nearly the end of the Late Heavy Bombardment . Geologists can measure these rocks for "biogenic" (suggestive of life) traces, because living things preferentially use carbon-12 over carbon-13, whereas geological processes do not. It was therefore astonishing that graphite grains in the Akilia rocks were reported to have exactly this carbon signature, meaning that life emerged essentially right after the last big impact.

The current paper delivers a killing blow to the Akilia work. Not only is the dating of the rocks a bit problematic, but in fact the precise samples used don't have any graphite in them! These samples simply cannot have a carbon signature one way or the other. In his review, Moorbath, who has been heavily involved in work on nearby Isua, also says that those rocks have no distinctive carbon signature.

I should say that Moorbath is maybe a bit pessimistic. Although the carbon work is toast, I think the Banded Iron Formations , which must form in the presence of oxygen, at least show progressive transformation of the Earth's atmosphere. If this is taken as the product of life, then life would already be global at nearly 3 billion years ago.

These earliest dates are important because they affect surmises about the likelihood of life outside of Earth. Assuming life developed on Earth (and wasn't imported), faster occurence of life may imply less stringent requirements. That is, something which requires the conjunction of 5 sequential one-in-a-billion events would be expected,on average, to take longer than something which only requires 3 such events. We only have n=1 here, so I wouldn't hang my hat on it, and talk of averages is a bit improper. Nevertheless, if life is "only" 3 billion years old, my guess would be that it needed some time and a lot of luck to emerge here. If evidence of life is swimming around in the very oldest rocks we can find, that's really something, and maybe life really is elsewhere as well.

Earworm

The BBC science page discusses how songs get stuck in your head . Scientists used songs like the Rolling Stone's "Satisfaction" (yeah, you're already humming it, aren't you) They then manipulated the tune, removing snippets (presumably representing my air-guitar solo), and played the song back to volunteers hooked up to an fMRI machine. They report in Nature that many volunteers reported the subjective experience of familiar songs continuing through the artificial gaps despite the actual audio silence.

In people who heard the song continuing, their the auditory cortex also kept its activity. The exact form of the activity depended on whether the tune had lyrics. In tunes with lyrics, the region with biggest differences was the associative (higher-processing) auditory cortex, presumably reflecting a meaning-based reconstruction of the song. In worldless tunes like the Pink Panther theme, differences in brain activity extended into primary auditory cortex (the area of cortex to which the main sound pathway from the ears first connects), as if the volunteers "hearing" the tune were reconstructing the sounds themselves.

The scientists' conclusions, consistent with other work, is that memories with a strong sensory component are associated with elevated activity in the brain region which handled the original experience. There's a lot more going on with a memory, though, than a strict rewind. I'm thinking about Proust's famous madeleine, which induced several novels' worth of non-taste reveries. That was some cookie! But also of traumatic memories , which may vividly incorporate the sight of something which was never there.

Meanwhile, check out this slang dictionary, WordSpy . I don't really like their etymology of earworm (I always think StarTrek, Wrath of Khan) but "Meanderthal" sounds tailor-made for Germans out on their Sunday walk.

The Beeb refers to songs' persistence as "brain itch," which sounds unpleasant.

Thursday, March 10, 2005

The march of science

The Register picks up on the IgNoble prizes for improbable research with what, I have to say, is a prizewinner.

Tangled Bank 23

Tangled Bank 23, the carnival of science-related blogging, is up over at Living the Scientific Life. Grrlscientist has done an amazing job getting the posts organized by topics. Take a look!

Wednesday, March 09, 2005

Protein sequencing from Neanderthal Bones

Scientists in Leipzig, Germany, and St. Louis are reporting that they have been able to recover the bone protein osteocalcin from 75,000 year-old Neanderthal bones and even to obtain a protein sequence. They were then able to compare the protein sequence from Neanderthals to that of other primates including humans and gorillas. Interestingly, the ninth amino acid of the protein, identical in humans and Neanderthals, was different in gorillas, a difference the authors attribute to differences in diet among the species. We omnivores don't get as much vitamin C as gorillas do.

Some of these scientists have been involved in ongoing efforts to extract DNA from ancient material. The work on sequencing proteins, which has been made possible by big advances in mass spectrometry , a technique in which proteins are shattered and the masses and sequences of the fragments are measured. For the purposes of comparing species (especially very closely related species), DNA analysis would be preferred, because DNA sequences can have differences which are not apparent in the protein sequences. The specific modification reported here, hydroxylation of the proline, would of course have been missed in DNA work.

Orbis-quintus has a nice discussion, including links describing the site in Iraq where the bones were found (a Neanderthal burial ground?), and Zinken , who must have the world's fastest RSS reader, has a second post about the potential use of this method for retrieving REALLY old protein.

Tuesday, March 08, 2005

Chris McKay on searching for life

Red Nova has a blurb from Chris McKay of NASA/Ames (some would call it an advertisement) about the whys and wheres of searching for microbes on Mars. He's favoring looking for fossils in the oldest undisturbed portions of the planets, and drilling. It's not clear he would take no for an answer....

Life on the edge

This month's Trends in Microbiology has a review by David Thomas about the recent discovery of polar microbial communities which are capable of photosynthesis under extremely cold and dry conditions, and moreover with extremely low light levels. Work reported last September documented a "green band" of microbes colonizing the undersides of rocks near the edges of glaciers, where they are protected from UV irradiation, wind scouring, and drying out. There is only a narrow band along the bottom of the rock where they can live. Too far out, and they're exposed; too far under, and there's not enough light.

Many of the species of bacteria found here have also been seen in other very cold niches. For example, similar cyanobacteria also grow inside sandstone rocks in the Ross Desert in Antarctica. The microbes living in such extreme niches must develop extensive specializations such as antifreeze strategies. It would be interesting to know how these photosynthetic bacteria manage to survive during the long, dark winter. In Antarctic lakes, the protozoa just switch to eating bacteria or each other when light is short, allowing them to grow year-round.

Learning more about these cold-tolerant communities could lead to
new enzymes for molecular biology research, because their enzymes move are active at low temperatures (relative to humans' preference!) and can be easily inactivated at "room temperature." For example, my personal bugaboo, ligation, requires two DNA molecules to dock together long enough for an enzyme to join them permanently. The DNA moves less at low temperatures, but the current tradeoff is that the enzymes move less too. A ligase which prefers cold temperature might reduce my migrane levels.


A second interesting feature of these communities is their razor-thin niche. Any disturbance could result in the whole community getting dried out. However, this also means that they generate instant fossils , similar to the mummies discovered in present-day Peru, which are also preserved by the extreme dry and cold. Fossil bacterial mats of the sort described here would be sitting out in the open, unchanged, until perhaps the rock got jiggled back to an advantageous configuration. It might be that searching for life on Mars would not require drilling or astronauts, but rather just turning over the right kind of rock.

more KT science

Friday, March 04, 2005

Finding out the dirt on Mars

Via blogdex, an interesting newspaper article about the importance of dirt on Mars in scenarios for a manned mission to Mars. A ship carrying humans has to touch down a bit more elegantly than the rovers needed to, and so the landing device has to be designed with the surface conditions in mind. Moreover, given the long trip, astronauts would probably want to stay a while and have to dig out a shelter. Finally, dust control would be a big issue for any electronics (for example the rovers lost energy because of dust on their solar panels ).

The specific example in the newspaper article discusses camping out on soil overlaying an ice bed. Heat from the astronaut's activities might melt out a sinkhole. This is worth thinking about, because "rotten" subsurface ice is exactly where you'd expect microbial life, so you'd want astronauts right on top of it. Check out this Workshop for this spring's Mars fashions.

Maybe a robot or two first.

There's quite a lot more information in the Geology thread of Martian Soil. Also some links are available here.

Hobbit head

The NY Times and other papers are carrying news of the analysis of the small hominid "hobbit" fossils found in Indonesia last year. The analysis, appearing in this week's Science, carries the of the braincase casts from one of these fossils. The little people had very small total brain volume, about the size of a grapefruit. But the details of the shape of the brain indicate quite a bit of specialization, including very highly convoluted frontal lobes. The authors interpret these signs as being consistent with a highly intelligent species.
These observations, if they could be confirmed, would upend a longstanding idea of how Homo sapiens got to be top dog. In general, the enormouse expansion of brain volume was thought to have come "first." Instead it could be that complex wiring came first.

One must always keep in mind, though, that the hobbits were following their own evolutionary path, and their brain geometry will reflect their evolutionary niche with possible differences from the niche(s) occupied by Homo sapiens. Still, this is a really fascinating discovery.

UPDATE: A nice writeup by Joseph Verrengia at Salon.
UPDATE 2: Follow the trackback over to Sound and Fury for a more skeptical take on what, exactly, the H. Floresiensis fossils represent. And Nature News gives an update about the nearly-resolved squabble over the original fossils.

UPDATE #3: Carl Zimmer at The Loom has more on these data. He thinks it's a brand new species, and telling something about the sequence of hominid evolution. Check out the comments as well.

Thursday, March 03, 2005

Chromosomal changes in normal human brain cells

Yesterday's Journal of Neuroscience has a fascinating brief report describing a suprisingly high frequency of aneuploidy, or abnormal chomosomal number, in normal human brain cells. About 4% of all the human brain cells (this includes neurons and non-neuronal cells) obtained from normal subjects show increases or decreases in the number of copies of chromosome 21. ( Another group, with overall lower estimates, still arrives at about 5% of neurons with some chromosomal change.)

In any living creature, one of the most critical aspects of cell division is chromosomal segregation , which insures that each of the two daughter cells inheirits exactly the same number of chromosomes (for most animals, 2 of each non-sex chromosome) as the original mother cell. This process is very carefully checked, because a daughter with too many or too few chromosomes might express genes to incorrect levels or give rise to further generations of cells with even more changes. Abnormalities in chromosomal segregation, which result in aneuploidy , are associated with diseases including Down's Syndrome and cancers.

The authors of this study had shown several years ago that developing mouse brains have large numbers of aneuploid dividing cells. Most of the chromosomal mixup appears to occur during the last division of the neuroblasts (parent cells to the neurons), when the neurons themselves are being generated. Again in mice, they have been able to show that changes in chromosome number have measurable consequences in terms of changes in gene expression, although how these events affects the overall health of the animals is not certain. The same research grop has even more recently found a mouse mutant with increased numbers of these damaged cells, possibly because the damaged cells fail to be cleared during natural cleanup events which occur in the developing brain. The significance of the new human study is that they can show that these chromosomal changes in a new mammal, and that they survive into adulthood.

Getting back to Down's syndrome, it has been speculated that overexpression of certain genes on chromosome 21 (since there are 3 copies around) stresses and kills neurons, and that neuronal death may in turn cause some of the cognitive deficits in these people. In light of that theory, it seems really suprising, then, that up to 3 percent of "brain cells" in normal people have four copies of chromosome 21. How are these cells even alive??? The only explanations I can think of are that one needs a group effect to get toxicity, or that the "brain cells" getting scored don't include very many neurons.

Wednesday, March 02, 2005

World of Wikipedia

Wired.com has a story about Wikipedia, the massive open-source internet encyclopedia. Wikipedia differs from a more traditional encyclopedia because there are very many contributors, and the updating is continuous:

Most encyclopedias start to fossilize the moment they're printed on a page. But add Wiki software and some helping hands and you get something self-repairing and almost alive........Look up any topic you know something about - from the Battle of Fredericksburg to Madame Bovary to Planck's law of black body radiation - and you'll probably find that the Wikipedia entry is, if not perfect, not bad.

In my science posting, I link to Wikipedia very often, because it's open, well written, and contains link collections that save me time. The currentness of the Wikipedia effort is less of a concern to me, as I rely on the information in the main link for the immediate background. I think the Wired article has caught this good-enough assesment very well.

A lot of the issues raised by throwing by the open authorial gates-- open source vs. open sewer, Leonard Nimoy versus Toni Morrison, etc.-- are very reminiscent of the perils of blogging and blog-reading. (I was just blog-burned last week by a life on Mars post. It got me because I knew just enough, about the scientists and science involved, to bite. Right place, right time, wrong answer.) Wikipedia tries, with good success, to maintain a low bullshit content, via principles of neutrality and good faith writing.

But the high traffic, information aggregation aspects of Wikpedia generate epiphenomena which individual blogs never see, including entry trolls and "point of view warriors." Tackling these latter types of vandalism has forced Wiki from pure open source into a heirarchical system of reviewers and sysadmins, which does make me wonder how well Wikipedia will bear up. Still, there's some reason for optimism in the dedicated people who are addicted to the project. The people of Wikipedia functionas a collective bastion, defending the value of the project against vandals. Maybe there's a lesson here: some virtual cities will have less litter than others, just because of the people who live there.

UPDATE: The Wikipedia homepage is here.