Keats' telescope

Soaked at the outsource

2006-07-08T07:37:00.000+02:00

I just thought this was interesting- the monsoon season in India has knocked out a large number of call centers for tech firms like Hewlett-Packard. I know this shows my age, but I still can't get my head around the idea that I'm calling the other side of the world for tech support for something I bought down the street. Here's a quote that shows I'm not the only one:

"Is it just me, or is it madness that because of flooding thousands of miles away, I can't get a technician who probably lives a few miles away called out to fix our printer?"

And just for laughs, some of the funniest tech support stories.

Blonde and brunette mammoths

2006-07-07T12:59:00.000+02:00

Sequencing of ancient DNA from mammoth remains has revealed that these animals had genetic variations in hair color. The hair found with frozen or buried mammoths has been studied for a long time and can be quite variable in color, but it has always been uncertain if the hair color were natural or, well, if they were bottle blondes. Peat bogs as a hairdresser, who knew?
On a more serious note, this is the first complete gene sequence recovered from ancient nuclear DNA.

A companion paper in science shows that the same mutation observed in mammoth DNA has also
been under positive evolutionary selection in a population of beach dwelling mice.

I guess you'd have to call it a sandy blonde.

Ten most difficult feats in sports

2006-07-01T13:02:00.000+02:00

In honor of Jens Lehmann's heroics last night in the Germany-Argentina game, here's a list of the 10 hardest things to do in sports. . Blocking a penalty kick comes in 9th. Walking and chewing gum, my most recent feat, I assume requires a separate listing.

Does life shape the landscape?

2006-06-29T15:06:00.000+02:00

There are bazillions of stars out there, and untold numbers of planets, some of which are going to harbor life. How do you go about distinguishing those few from the many barren ones? You can narrow the list by thinking about the requirement for liquid water and a reasonably stable star (it turns out those aren't so common) but you've still got a lot of objects to look at.

One possibility is that a living planet will have an obviously different landscape compared to a barren one. On earth, plant roots hold the soil against erosion by rain and wind, which then affects the speed and sediment of rivers, which can then affect the profile of mountain ranges. It is also likely that life transformed earth's atmosphere, possibly several times.

But is there something about earth that would not have occured in the absence of life? A review in Nature last January compared Earth to Mars and came up with suprisingly few definitive differences on the scale of mountains or drainage valleys. What those authors did propose is that although the range of geologic features is similar, the distribution of these features on a biotic planet might be skew detectably relative to an abiotic one.

What struck me as I read the review, though, is that our cousin planets Mars and Venus, both definitely dead at the moment, have REALLY different geology from each other, not to mention Earth. If you saw a similar object around a completely different star, you might be hard pressed to say if it was behaving "normally" (without life) or not.

I was interested, then, to pick up this paper, from the lab of MT Rosing, which proposes that photosynthetic life on earth helped create the surface energy cycle required to form the continents. The basic argument is that plate tectonics requires a lot of energy-- more than the earth's internal heating should generate. However, chlorophyll and company harvest huge amounts of the sun's light, which tilted the whole-earth energy budget in favor of tectonic movement and stable continents (basically by increasing weathering of some rocks to contribute to the tectonic churn.) But this continental drift seems to be a consequence of things which are much easier to detect, like a transformed atmosphere and tons of liquid water.

UPDATE: Molecular biologists, this problem needs you! Check out this primer (subscription, unfortunately) at Current Biology. There's lots to think about.

"Who needs coffee when you have a family of sober organ donors?"

2006-06-29T14:19:00.000+02:00

Recent reports suggest that coffee can counteract the effects of alcohol on the liver. The Onion, of course, has the definitive reaction.

Viruses as engines of evolution

2006-06-26T14:04:00.000+02:00

There are two recent reviews about viral origins and contributions to life on earth at the open-source journal Genome Biology here and at Nature here . As parasites, modern viruses have evolved strategies for incredible levels of compaction, but this means their very compressed genomes do not leave a lot of evidence of their origin. There has been a huge amount of progress on this problem as more and more viruses get sequenced and especially with the discovery of "giant viruses" such as mimivirus. Genomic methods are being used to discover viruses literally everywhere, many of which contain previously unknown genomic sequences.

With the new evidence and new ideas, it looks possible that viruses evolved from a very ancient, independent branch on the tree of life. But here's where the story gets pretty wild- perhaps viruses, sporting the first DNA in order to evade RNA defenses, actually made the very first nucleus. In this case there's a little bit of virus in all of us.

The Nature article highlights that viruses in the present-day world grab sequences from their hosts and each other. This mixing of genetic information itself can shuffle genes between viruses and even animals, meaning that genes are in effect pooled across an entire population:

"When you look at a group of viruses, such as the algal viruses, there seems to be a very, very small core of conserved genes," says Curtis Suttle, a microbiologist at the University of British Columbia in Vancouver, Canada. "The rest is almost like a super-organism — a massive pool of genetic information that's being shared among all these different viruses." (from the Nature review).

Wow, the borg is here!
UPDATE: And we are the borg- a nice writeup from a few weeks back by Dan Vergano at USA Today about how humans and the bacteria in their gut together make a superorganism. Something just made me think of Taco Bell.

Science is the seed corn

2006-06-24T06:26:00.000+02:00

Check out emptywheel at the next hurrah for an impassioned appeal that the U.S. continue to invest in the sciences, and that specifically a political effort is made to improve the near-term funding of the NIH. I believe that science and technology are the keys to future American prosperity.

Supply and demand- laser eye surgery and the military

2006-06-20T19:22:00.000+02:00

There's a really interesting article in the NY Times about how the wide availability of corrective laser eye surgery in the Navy is affecting the application pools for the various postgraduate jobs. The big winners are aviation and special forces, both of which require perfect vision in applicants. They now select from a much larger pool. One loser is submarines, who used to get the glasses wearers but now have trouble filling their quota.

But don't worry- in 50 years, aerial combat will be perfomed drones, controlled by 10-year-olds on their PlayStation Xs-- and glasses will end up being cool.

The "HIV resistance mutation" might be very old

2006-06-19T16:15:00.000+02:00

This month's Trends in Genetics has an update on the story of CCR5-delta32, a human mutation present at high frequency in Europeans and Western Asians but rare outside this region. People who are homozygous for this mutation are resistant to infection by HIV. It has been thought that the allele has been under positive selection, that is, that it has improved the survival of people carrying it, long before HIV was around, and might have therefore have conferred resistance to some other epidemic such as plague or smallpox.

The update talks about data that CCR5-delta32 might not have been historically under such strong selection as previously thought. The main new argument is that the mutation has been found in Bronze age bones, which means it has been around for a long time and might not be ramping upward in frequency over time as would be expected for a resistance gene. Secondly, an analysis called linkage disequilibrium, used to show evidence for positive selection, has been repeated with larger data sets and gives more ambiguous results.

Even though the population measurements for this mutation are less certain in humans, the evidence that CCR5 is critical for the timecourse of HIV infection is still very strong, and the mutation might still be an interesting marker for Northern European migrations (i.e. the Vikings).

An open-access discussion of CCR5-delta32 is here . I have blogged about this mutation and some interesting historical hypotheses here .

Two-tongued but not tongue-tied

2006-06-18T12:47:00.000+02:00

"I speak French to my ambassadors, English to my accountant, Italian to my mistress, Latin to my God, and German to my horse."
Frederick the Great

True multilingual people have exquisite control of what language comes out of their mouth at any given time. (In contrast, I always mishmash my languages, putting German prepositions into my French.) At a cognitive level, this skill involves hearing and understanding the language and formulating a reply, while suppressing the other languages, as if a "language switch" is at work. But in MRI images of these people during writing or speech, the brain activity patterns are very similar no matter what language is being used. This is probably because most of the brain concerned with meanings embedded in the language is going to be independent of the language used.

A recent paper in Science used a trick to try to locate brain regions which were directly related to the choice of language at the level of words and meanings. The authors had multilingual subjects read word pairs, in which the paired words either showed a close relationship (i.e. trout-salmon) or were not closely related (trout-horse). By varying whether the words within the pair were obtained from the same language or different languages, they sought to specifically trigger the brain region that coupled language to meaning. (There's no telling what havoc recent American english adoptees such as 'angst' or 'samizdat' would wreak in this test!)The testees were wired up to PET scans or functional MRI to measure their brain activity during these tests.

Now this test is still not so simple, because differences in shapes and lengths of the words (German words were on average 7% longer than the English equivalents) in different languages will affect brain areas without being specifically concerned with the meaning of the words. Despite these difficulties, the scientists were able to see two new effects with this test: an area in the left temporal lobe was activated differently depending on the relationship between the word pairs, without being affected by the language; and activation in an area called the left caudate was reduced in same-language pairs compared to different-language pairs.

The left caudate is a very interesting candidate location for an internal "language switch" because of earlier data from patients with damage near this brain area. These people can understand languages, but spontaneously switch between languages in their own speech and writing.

I would be interested to see the social aspects of this language switch, as hinted at by the quote from Frederick the Great. There must be some sort of recognition for what language is best for a given audience. My wife and have I frequently noticed that peoples' speaking styles differ depending on the language. A person can be fairly formal and courtly in French, for example, and quite casual in English. I am not in full command of any language besides English, but it seems that a sort of style or swing-- a cultural expectation-- attaches itself to languages.

UPDATE: My wife pointed out that languages don't just have words but also grammar- which I again muddle, speaking French with German word-order. A little discussion of word-order differences in Basque-Spanish bilinguals is available here although I couldn't find a publication.

Re-thinking planets

2006-03-09T10:29:00.000+01:00

Michelle Thaller at the CS Monitor has a very nice article about rethinking the rules for formation of planets around stars. Our solar system is organized with rocky planets inside and gas giants outward (plus Pluto and planet X), and I remember being taught that the pressure of solar radiation tears the bulk of gasses off of planets whose orbits fall inside a certain radius. (Another idea I remember is that Jupiter formed at the orbital distance corresponding to the condensation point of water in the primordial dust cloud.) But the Spitzer telescope and other search methods are finding lots of examples of big gas giant-like planets very close to their star, along with planets orbiting brown dwarfs and a fair number of systems which likely resemble ours.

What I love about this is that the science is getting outside of an n=1 (our own system) and really sampling what is available in nature's palette. The next decade or so should be very interesting.

Yeast and ethanol production

2006-03-09T09:34:00.000+01:00

The February Trends in Genetics has a nice write-up of the evolution of alcohol production by yeast. Modern fermentation relies on the yeast metabolizing 6-carbon sugars but choosing to halt at the 2-carbon stage (like ethanol) rather than completing the process by going all the way to carbon dioxide. This is a loss of potential energy for the yeast-- even though it's a happy outcome for humans!-- so it's interesting to understand the natural selection events which favored this stopping short behavior.

Ethanol is metabolically a dead-end molecule, but it's a single enzymatic step away from the more central 2-carbon relative, acetaldehyde. The enzyme involved, alcohol dehydrogenase (ADH), can shuttle 2-carbon molecules back and forth between these two configurations, so it could have emerged during evolution either to gather in ethanol as a fuel source, or as a way to make ethanol from acetylaldehyde (think of a deserted railroad track where you're not quite sure which direction the trains run).

Evolutionary analysis suggests that ADH was initially used to make ethanol, suggesting that ethanol itself is useful to the cell. The current theory is that ethanol helps keep competitors away. Ethanol is toxic to other competing microbes, so-- as long as it's not needed for fuel-- the yeast can make enough ethanol to poison the waters for competitors. Later, when sugars run out, it can reel the ethanol back in and use it as a secondary fuel.

There's also a suggestion from molecular clock data that this ability to accumulate ethanol was favored soon after the emergence (50-100 million years ago) of fruiting trees. The six-carbon sugars which are the basis for modern fermentation became widely available then, so several yeasts jumped on the opportunity and evolved new ways of controlling their metabolism to generate this useful by-product.

Hobbitry

2006-03-09T09:23:00.000+01:00

Kate Wong at Scientific American has a nice writeup of the continuing back-and-forth about the "hobbit" skeletal remains found in Indonesia. The two theories are either that the bones belonged to a Homo Sapiens suffering from secondary microcephaly, or belonged to a previously unknown hominin (for example, possibly a remnant Homo Erectus?). If the second were true, the recent age of the bones suggested that we humans have had close relative species up to nearly the dawn of history. Kate seems to be weighing on the side of "abnormal human" rather than non-human.

Take a look at the comments, too- Kate has a great readership.

"Nessie" = "Dumbo?"

2006-03-08T17:46:00.000+01:00

The BBC is reporting a new theory of the Loch Ness Monster . With most of the sightings chalked up to too much time at the distillery, the remaining two-bumps-and- a-tube sightings are --wait for it-- circus elephants.
Here's your proof:

I'm going to have to place this somewhere between Monty Python and Calvin and Hobbes.

Wired magazine top 10 accidental discoveries

2006-03-07T13:16:00.000+01:00

The march issue of Wired lists 10 accidental discoveries. I really like that saccharin was initially isolated from coal tar. Seems to fit!

Polysorbate60sneezy-%$poultry9*capricorn

2006-03-03T17:51:00.000+01:00

Norm Bleichman has modest proposal for generating a *really* secure password.

Life outside of kids III: Things fall apart

2006-03-03T09:31:00.000+01:00

This is the third post, with maybe one more to come, to look at the "grandmother effect," in which human grandmas who are past their childbearing years can nevertheless contribute to the propagation of their genes indirectly by taking care of grandkids. The first post is here and the second post is here . This post is much more speculative.

What interested me when I first read about the grandmother effect was the possibility that human evolution had taken us (via the disposable soma ) out of the birth-reproduction-death treadmill and instead we as a species (or at least the females among us) were "programmed" for an extended, extragenetic-- probably social and cultural-- contribution to the species. This is probably true anyway, but more specifically, I was looking for some hint that humans would be capable of extreme longevity. I'm interested in long-lived cognitive function, and I have to emphasize that the rest is outside my expertise. With that said, I think the idea of greatly extended lifespans looks unlikely.

Among the killers of humans today are cancer, cardiovascular disease and dementia. These all start as failures of a specific system. One possible way to extend the average lifespan would be to plug holes-- to attack these diseases as they emerge, so that a major disease is delayed or the faulty part replaced, ab infinitum. An enthusiastic proponent of this approach (combined with other strategies) is Dr. Aubrey de Grey who pops up in the major media every now and then talking about lifespans on the order of centuries. De Grey's idea is that a mixture of delaying disease and replacing diseased tissue might allow great extensions. He was recently on the receiving end of a major smackdown for claiming that excessive pessimism on life extension by other gerontologists was costing lives .

So far, so comic. I guess what has me pessimistic about life extension by plugging holes is some very recent evidence that healthy tissue in elderly primates just gets worn out. A study in this week's Science shows that elderly captive baboons living develop sensescent cells in healthy tissues , suggesting that, well, they're getting old all over. Senescent cells were seen in vitro in skin and connective tissue cells, and were measured using three different measures. Moreover, the percentage of senescence went way up in cells from older animals. With a bit of extrapolation, you would guess that baboons of around 30 years of age are going to wear out in multiple places. Illnesses arising from this kind of senescent failure could not be fixed piecewise, and that makes me think that the lifespan of these animals is pretty near maxed out.

UPDATE: Aubrey De Grey is also written up in the Economist from last week.

Tangled Bank 48 at Aetiology

2006-03-02T10:59:00.000+01:00

The Tangled Bank carnival of science blogging is up over at Aetiology . It's pretty huge, and worth a look!

Operate on a beating heart

2006-03-01T16:11:00.000+01:00

The New Scientist describes a robotic system which can compensate for the motions of the heart, allowing surgery to continue while the heart beats (gently). The surgeon wears eyepieces which track his gaze. He first scans over the heart; then tracks the beating motion of a single region; and the machine calculates the topography of the heart and its motion from that point forward. This means that the surgical tools stay stationary with respect to the heart.

Wild.

Neandertals for dummies

2006-02-28T13:09:00.000+01:00

There's a (possibly subscription) brief description of recent research into Neandertals, in the form of a "quick guide," over at Current Biology.

An argument against Supplementary Data in publications

2006-02-28T12:37:00.000+01:00

Genome Biology is carrying an editorial by Gregory Petsko arguing that Supplementary Data is a losing game. Web versions of scientific papers often contain links to additional tables, methods, and results for which there is not enough space in the print version. In my experience this is often where the goodies are hiding, like the information that the experiment must be done only with certain reagents, or that a whole other line of experiments gave negative results and have to be interpreted cautiously.

Petsko has, uh, a different opinion:
I hate supplementary material. It's one of the worst ideas in the history of bad ideas. It's the scientific publishing equivalent of fighting a land war in Asia.

He and I actually on the same page (pun intended) about what these massive data supplements do: by eliminating the word limit, it means reviewers can demand quite a lot more out of submitting researchers; then this mass is organized such that the tidy results and diagrams go "up front" and the wet science drifts into the back pages. And I think the "land war in Asia" analogy is correct: looking through the February 10th Cell, I see papers with 1,8,4,1 and 3 supplemental figures. What that means is a huge amount of extra work has become "published" (which affects its money and communication status for the corresponding author). There is no longer an upper limit to the amount of data which could be sucked in. And finally, especially with Cell, those files are inconveniently organized in nests of links and slow to download-- so they are at a qualitatively lower accessibility than the main data, which comes in a single pdf.

However, it used to be that these details didn't go into the paper at all, especially in Nature and Science. I agree with his objection that critical methods are frequently absent from the main text. But wasn't that always the case?

Life outside of kids II: Great grandma

2006-02-27T13:10:00.000+01:00

This is the second one of about four posts dealing with the grandmother effect. Menopause, and the relatively extended life in human women after the cessation of reproduction, distinguishes humans from their primate relatives and possibly earlier hominins. The "grandmother effect" proposes that postreproductive women can nevertheless contribute to the propagation of their genes, specifically by helping their juvenile grandchildren reach adulthood. The first post talked about searching for the grandmother effect in other species. This post will talk about the evidence for the grandmother effect in humans and some speculation about the evolutionary mechanics.

It should be pointed out right away that the grandmother effect really does refer only to post-menopausal women. Men survive for similar lengths of time, but retain their fertility. This concept is only invoked to explain how the survival of the human species might have been enhanced by the presence of vigorous, non-reproductive women.

Strong evidence for grandmothers' contributions to survival of their grandkids came in a 2004 demographic study of 19th century Finnish and Canadian villages. In new families with a surviving mother-in-law, the newlyweds had their first child sooner, had more closely spaced kids, and those kids made it to adulthood with greater frequency. The Finnish records were detailed enough to show that the grandma's impact was greatest during the early post-weaning years, and might correspond to feeding and helping with young kids. So it's pretty clear that, in modern human societies, a grandma is a big help.

Comparative biology and the fossil record both suggest that "senior citizens" are a bigger proportion of human than non-human primate demographics. Among modern-day primates, the ratio of lifespan to age at maturity is relatively constant.Humans are at the far end of this relation, being very long-lived (thus with lots of surviving seniors) and very slow to grow up (both physically and cognitively). This special place on the curve is also true of hunter-gatherer societies.
A similar picture comes from the fossil record. By looking how worn-out the teeth are, especially the late-erupting 3rd molars (wisdom teeth), you can classify fossil jaws as belonging to a young adult or a "senior." Scientists who scored many fossils with this approach found the percentage of seniors keeps increasing in the hominin line, reaching a peak in upper paleolithic modern humans. It's important to keep in mind, though, that this analysis does not give the gender of the senior.

Putting it all together, the grandmother effect concept suggests that as human ancestors started taking longer to develop, it became advantageous for somone else with free hands to help. The increased number of humans surviving into old age would be a combination of better success of the human lifestyle and, perhaps, active selection for a vigorous grandma.

Another, gender neutral, factor which might have contributed to human longevity would be the complexity of the human lifestyle and the value of accumulated wisdom. This whole issue gets very interesting in the case of the Neanderthals, who probably grew up very fast but who had reasonable numbers of elders, And who might have cared for their elderly into their dotage. Neanderthal grandmas might have had a much less direct impact on the survival of the fast-growing grandkids, but the wisdom of the ages would still have been valuable.

UPDATEs: The Oscars and human evolution?

Also, I had this bookmarked but didn't get to it: the idea (from fossilized teeth)that Neanderthals grew up faster than H. Sapiens is disputed.

William Shakespeare's bust

2006-02-27T07:48:00.000+01:00

The Beeb says that a portrait bust sitting in a gentleman's club in England matches the death mask of wordsmith will. There's a bit more in the Scotsman (gotta love Google) which says that the forensic scientist making the match also sees evidence of tumors near his eye orbits in several of the authenticated Shakespeare portraits. Alas, poor Yorick.

From the Scotsman, a dose of skepticism:
Prof McLuskie said comparing images ran the risk of circular logic - one fake image might be confirmed by another that was based on it. "A lot of these portraits tend to be of a generic bald guy with a beard," she said.

Of course, I'm partial to his portrait with the earring.

In the zone

2006-02-24T13:23:00.000+01:00

National Geographic (and some other sites) are listing the five extrasolar planets estimated to be most habitable to life. Searching through our neighborhood they basically looked for stars of about our sun's age, with fair amounts of metals, which did not flare too often. Seems amazing that you could come up with a list of only five...

Life outside of kids Part I: The Fish Bowl

2006-02-23T13:12:00.000+01:00

Birth, copulation, and death. That's all the facts
when you come to brass tacks.
- T. S. Eliot, Sweeney Agonistes

As the fish from Monty Python's Meaning of Life could tell you, it's hard to understand the forces shaping lifespan-- not least because many get yanked from the tank prematurely. Natural selection, of course, puts a premium on living long enough to reproduce, and should even pay dividends for seeing the offspring make it to adulthood. But in many species, including humans, the natural lifespan extends far past the reproductive age. It's very interesting in this regard that extended lifespan seems to be relatively recent in human evolutionary history (more on this later).In humans, this added lifetime has been hypothesized to contribute to Darwinian fitness via the "grandmother effect," in which post-menopausal women help out with their grandchildren, and thereby promote the survival of their own genes over more than one generation. This effect should be greatest in cases where parents (or groups) take extended care of their offspring. But this idea has been difficult to test, and in fact baboons and lions, both of which do take care of their young socially, do not display "grandmotherly" lifespans.

An article in the December PLoS Biology takes an negative test of the grandmother effect by looking at lifespan in guppies. Guppies do not take care of their young, so the grandmother effect should not affect their lifespan. Reznick et al. took advantage of closely related guppies which have made major adaptations to high- or low- predation environments. Reznick et al. measured three features of reproduction in these fish- time at first brood; brooding interval; and life after brooding (which turns out to be non-zero). Guppies from high predation environments give birth early and often, and continued reproducing longer than those from low predation environments.
What is cool, though, is that this seems to operate independently of the lifespan after the last brood; so that in fact the guppies adapted to high predation lived longer. It's as if the extra reproductive rounds, necessary for life on the edge, were just plopped into the middle of the guppy lifespan (you can see this in Figure 4 of the paper). More to the point for the grandmother effect, lifespan of individuals after the the last brood was essentially stochastic, and the same in both groups(long-lived or shorter-lived). It follows a random decay, to risk a pun.
So guppies show no grandmother effect, which is predicted, since they don't care for their young. The authors of the paper point out, though, that this kind of actuarial analysis remains very hard to do for longer lived animals; and the positive presence of the grandmother effect in a place where it's expected might require some other approach.

This article was also referenced at the anti-ageing and science blog.