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.

Advancing science: Science education is crucial

2006-02-21T18:29:00.000+01:00

Via Pharyngula, Matthew Nesbit has a list of recommendations for engaging the public on scientific controversies . Advancing science in America requires both short term, politically informed tactics and longer term efforts at science education.

Very interesting reading.

The "coastal route" for populating the Americas

2006-02-20T11:30:00.000+01:00

Some talks at the AAAS meeting in St. Louis revive the discussion about the route taken by the first humans entering the Americas. These first peoples could have been big-game hunters following mammoth across the interior of the land bridge connecting Asia and North America, or they could have been fishers who followed the coasts. The coastal migration theory relies on the immense productivity of coastal kelp beds, and suggests that fishers could have made a very good living by just following the kelp highway.

The biggest difficulty with the coastal hypothesis has been the lack of archaeological evidence, presumably because the camps would be submerged as the ocean levels rose after thelast ice age. I have been able to see a few abstracts ( here and here ) suggesting that these data are slowly coming in.

It's not clear to me that these two routes are mutually exclusive. With that said, mtDNA from a tooth found in a coastal cave Alaska shows kinship with contemporary native americans throughout the New World, suggesting that at least the coastal people prospered.

Transitions- evolution blog aimed at high school students

2006-02-19T20:43:00.000+01:00

I only just became aware of Afarensis' effort called Transitions ,a blog aimed at high school to early college students who are fairly serious about evolutionary biology, with an emphasis on the fossil record. The posts I looked through are very well written. Take a look!

UPDATE: The BBC has a whole series called In our time dedicated to human evolution.
And, via Slashdot, science fair entries from hell . Pot muffins in Santa Cruz-- who woulda thought?

Electronic forms for U.S. government grants- Windows only?

2006-02-18T09:06:00.000+01:00

The Washington Post reported earlier this week that the new umbrella site for applying for U.S. government funding, grants.gov, uses electonic forms that won't work on Mac. A client program which reads and edits the forms only runs on windows. The government is scrambling to get this fixed, and the NIH will delay the requirement that the big R01 grants are submitted electronically (this affects me personally!). However the smaller NIH grants apparently must be sent via this program.

I was using the handy technorati feature that the Washington Post includes with its articles, and I found that Suresh has already written about this, including referring to an open-access workaround for Mac from the University of Wisconsin. If you're in grant-writing mode, this may be a solution.

This isn't a simple issue. Have a look at Behind the Curtain for electronic document issues, creating an acceptable umbrella standard, and some other history.

Mimiviruses-- a different kind of life

2006-02-18T07:10:00.000+01:00

[I got started on this post via Digg , a social version of Slashdot. Lots of science stuff pops up over there.]

Discover magazine's March issue has a great account of the discoverers of Mimiviruses, an extraordinarily large virus ( and maybe one of many ) which may have relevance to understanding the origins of life. Most viruses are very stripped-down infection machines, and their DNA or RNA contents are so spare that studying their deep evolutionary history via sequence comparisions is very difficult. The genome of Mimivirus, in contrast, is larger than that of some parasitic bacteria (in fact Mimivirus might be independently alive, and at a minimum blurs the boundaries. See Wikipedia ), and the full genome has been a gold-mine of evolutionary remnants.

Mimi's genome contains elements with similarity to many of the major DNA viruses known as NCLDV (including poxviruses), plus a whole lot more. This observation by itself strongly suggests that NCLDV viruses are descendants of an ancestor at least as complex as Mimi-- thus, possibly independently alive-- with their excess genetic material lost during reductive evolution in the transition to their current parasitic niche. In addition, several mimi genes and gene control elements seem to be equally related to eukaryotic and archaeal sequences, suggesting that the Mimi-like ancestor, and its NCLDV descendants, deserve their own branch in the tree of life next to eukaryotes, archaea, and bacteria. (This is controversial. See this technical comment and a well-written summary here. In my opinion the evidence for independent ancestry looks pretty good.)

I guess what's coolest to me as an outsider is how intimately locked in parasites are with evolutionary history. (Of course, we humans are parasites on plants.) Many evolutionary innovations have come as an attempt either by hosts to evade parasites, or for parasites to evade host defenses. Secondly, oddball organisms often have a lot to tell. Lastly, the nature of mimiviruses as probably barely alive means that the next few years could bring some pretty detailed ideas about what it means to be alive, here on Earth and elsewhere.

UPDATE: Some evidence based on conserved structure for an early origin of viruses

Paleoproteomics- getting protein out of fossils

2006-02-17T14:10:00.000+01:00

There's going to be a really cool symposium at the AAAS meeting in St. Louis about analysis of protein recovered from fossils. Some proteins and DNA can survive the fossilization process and be preserved for amazing periods. Meanwhile, methods for recovering and analyzing tiny amounts of these substances continue to get better and better.

One speaker at the symposium, Peggy Ostrom, is using mass spectrometry to sequence proteins (probably osteocalcin ) from bone powder half a million years old.

For an excellent article about the challenges still facing ancient DNA analysis, go here . The caveats and opportunities listed there are probably going to apply to paleoproteomics as well. For example, protein analysis of osteocalcin should be pretty hard to troubleshoot, because the human protein is going to be almost identical to what you'd expect from any mammalian fossil.

UPDATE: Some more details on the symposium at afarensis

Having trouble deciding? Don't think about it

2006-02-17T13:25:00.000+01:00

People have a lot of strategies for deciding among complex options. There are the list-makers, the snap-deciders, and the procrastinators. A study coming out in Science this week suggests that a good strategy for complex decisions is essentially to sleep on it. It seems that you can only hold so much information in your conscious mind at once-- good enough for fairly simple situations-- but that your unconscious mind might be better at dealing with all those variables. Here is a block quote from the Science blurb:

To test the idea, Dijksterhuis and colleagues asked volunteers to read brief descriptions of four hypothetical cars and pick the one they'd like to buy after mulling it over for 4 minutes. The researchers made the decision far simpler than it is in real life by limiting the descriptions to just four attributes such as good gas mileage or poor legroom. One of the cars had more plusses than the others, and most participants chose this car. But when the researchers made the decision more complex by listing 12 attributes for each car, people identified the best car only about 25% of the time--no better than chance. The real surprise came when the researchers distracted the participants with anagram puzzles for 4 minutes before asking for their choices. More than half picked the best car. The counterintuitive conclusion, Dijksterhuis says, is that complex decisions are best made without conscious attention to the problem at hand.

The BBC writeup is here .
An older story, that in emotionally charged situations we tend to go with our gut, is here . Finally, Zack Lynch at Brainwaves ran a story about how the pleasure centers of the brain can override the decision-making process, and speculates about drugs which could improve snap decisions by traders by affecting this balance.

Biology Direct- a completely different way to publish

2006-02-08T14:48:00.000+01:00

The open access journal collection BioMed Central is launching a very different biology journal called Biology Direct. Not only will the publication be open access, but the reviews of the paper will also appear, unedited (even if they're harsh), alongside the data.

The traditional way of publishing is that an editor referees the interaction between the submitting scientist and the reviewers, and makes the final call about whether something will be published. The costs (editor's salary and endless secretarial support) are generally recovered in part by subscriptions to the magazine in question, but there have been increasing complaints that this shuts out the public from work which is after all tax funded. Open access journals let you download all the publications for free, but still have the editor infrastructure, which is paid for in part by a fee charged to the researcher. I guess Biology Direct (which again charges the researcher) would fall one step closer to self-editing communities like Wikipedia, in that there is a in house stable of reviewers (the Editorial Board) who have to be approached by the scientists in order to get a review. If you get a review and you pay your dime, apparently, your work goes up on the web page.

This seems to put a lot on the Editorial Board, and also I wonder if reviewers won't pull punches since they know the full text of their critique is going up. I took a look at the most recent accepted paper, Glazko et al. (link is to abstract; the article, reviews, and responses to reviews are in one large pdf) and the reviewers did seem to have gone over the paper pretty thoroughly. It looks like revisions are put into the main body of the paper without special designation (this is the practice in more conventional publications).

A good statement of Biology Direct's working philosophy and rationale is here (keep scrolling down), and there's a very good and link-filled writeup of the rationale for the new proposal by Jamais Cascio over at worldchanging. Very interesting, and a bit of a risk.

Wallace and Grommit live!

2006-02-08T07:01:00.000+01:00

I laughed when I saw this on Digg : It's a sleeping back that also serves as your day clothes . Handy.

Bird-to-dinosaur transitional fossils

2006-02-07T08:38:00.000+01:00

Hedwig at Living the Scientific Life has a great summary of some recent fossil finds showing intermediate morphology between birds and dinosaurs. The expedition that identified these finds was documented by the Discovery channel and will appear on TV. It looks like the work is not yet published but should come out sometime this year.

Caffeinated soap

2006-02-06T20:17:00.000+01:00

Erik Bangemann at Ars Technica tries out Shower Shock, a soap laced with caffeine and peppermint oil. Erik's a coffee drinker and didn't get much except the peppermint pick-me-up, but his wife possibly got something. The article runs toward my first guess, which is that caffeine shouldn't penetrate skin very well. If you want to absorb the caffeine quickly you should wash your mouth out with the soap, or just make a bunch of small cuts. However, caffeine soap might help with psoriasis .

I googled around and see that Shower shock has been offered by thinkgeek for a while now. Dave Barry has weighed in with a serving suggestion.

...but you knew that already

2006-02-06T17:19:00.000+01:00

Gina Kolata at the NYTimes has an interesting article about discovering the already discovered. People working on new mathematical algorithms might publish and name an improvement, only to find out later that the math had been done under a different name years earlier. Worse, small scale drug trials, showing benefits of a drug after surgery, could be needlessly repeated (including placebo controls) because the work was not published.

Final word goes to Larry Shepp: "Yes, but when I discovered it, it stayed discovered."

Big....hoof

2006-02-04T08:00:00.000+01:00

Pharyngula describes an identification of Sasquatch, based on a tuft of fur found just after the beast was sighted. 9 Canadians saw this particular Sasquatch through the kitchen window. (They build big windows up there.)

I'll give you a hint-- it's not a biped.

Meanwhile, Scottish police are on the trail of the dread Beast of Balbirnie and even have pawprints. Or, possibly not.

UPDATE: Malaysians are seeking their local snaggle-toothed ghost . Look at the bones!

Was Oetzi the iceman infertile?

2006-02-04T07:08:00.000+01:00

The BBC is saying that initial DNA analysis of Oetzi, the Copper Age man found frozen in 1991 in the Italian Alps, has been completed. DNA samples were retrieved from inside his intestines and stretches of mitochondrial DNA were sequenced. They were able to get more sequence than a 1994 DNA analysis.

The main result is that his DNA falls into a known haplotype cluster called K1, which is still found in that region of the Alps, but his exact variant is difficult to place within subclusters of K1.

The Beeb also says that Oetzi had more than one mtDNA stretch associated with male infertility. The medical side of this is that the sperm rely on mitochondrial output to do their swimming, so faulty mitochondria can affect sperm motility . I can't find out just yet what mutations Oetzi might have had. Of course, he may not have been interested in having kids anyway.

Dienekes had this story about a week ago.

Hot dogs as a microbicide

2006-01-30T12:49:00.000+01:00

I just saw this on Science Blog : a common food preservative may be very powerful against the kind of bacterial infection which is so destructive to Cystic Fibrosis Sufferers. Mutations which cause CF in humans result in abnormally thick and acidic mucus. Bacteria such as Pseudomonas aeruginosa which can get in there are effectively shielded from the immune system by the mucus and their own deposits, which are referred to as alginate.

Now, in recent study of American CF patients, 84% of the Pseudomonas aeruginosa isolates themselves carried a mutation in the gene MucA. This mutation allows the bacteria to make more alginate, which in turn gives the mutant bacteria an improved shield against the immune system relative to the wild-type bugs. Here's where the story gets really cool- this same mutation makes the mutant bugs (which are frustratingly resistant to antibiotic or immune therapy) very sensitive to acidified sodium nitrite, a compound used as a preservative for hot dogs or bacon. So in principal this nitrite could be made into an aerosol and clear up the mutant bacteria; and other therapies could help get the rest.

The original reference is here.

For a description of recent work on saline washes as a way of getting the sticky mucus of CF sufferers out, see Aetiology.

It always rains on the fourth of July

2006-01-24T17:56:00.000+01:00

I came across this in the NASA/JPL web page and I thought it was pretty cool: there are places in Mars that have repeated, predictable weather patterns. These four photographs show a circular cloud appearing over the same terrain, near the Martian North pole, each Martian summer. Another example is here where a volcano gets a massive dust devil every year in the late Martian autumn. Here's the Mars Global Surveyor (MGS)report:

The wide angle cameras have shown us that Mars has fairly predictable weather, with some storms and cloud phenomena repeating every year, like clockwork. There are specific times of year and locations on Mars which have experienced the same dust storm patterns every Mars year since we began observing with the first MGS MOC approach image in July 1997.

Apparently Martian atmospherics are dominated by seasonal heating and local geological features, making for a much simpler picture than earth.

Cool..

Is it fake? Is it real? Mathematics and digital images.

2006-01-24T11:24:00.000+01:00

There's a very interesting article in todays New York Times about scientists and image editing software. Many of the most striking images, such as astronomy photographs, must be digitally enhanced even to be intelligible. But in the Photoshop world, it is very easy to beautify digital images beyond this in a way that leaves no visible trace-- in short, to fudge. However, since Photoshop is essentially a collection of math algorithms, the manipulations-- rotations, rubber stamps, contrast gradients-- can be detected by their mathematical signatures. The editors of the Journal of Cell Biology have been able to detect these little fudges, such as cutting out a background band or selective contrast enhancement. Even as outright deception by Photoshop appears to be very rare, fudging is suprisingly common. My brand of science is very visually driven so a great deal of attention, benign and otherwise, is lavished on the images.

A tangentially related problem was covered in a recent Slashdot thread, which describes researchers using digital analysis to authenticate a Rembrandt. Jumping the link to ZDNET blog , a quote from Dan Rockmore says it all:

"The fact that you can put everything on the computer means that everything is numbers," Rockmore says. "As soon as everything is numbers, it makes perfect sense to ask mathematical questions about what the numbers represent." If he's right — if computers can distinguish between artists more accurately than connoisseurs can — the art world is in for some high-stakes corrections."

The ZDnet article is really fascinating, and shows how this method was used to identify four different artists' hands in a large Renaissance painting. ZDnet also cites some pushback by art historians- for example, a Rembrandt might have eight layers of paint, so that a surface analysis might miss underlying information. I also know that in Renaissance workshops the master might put the finishing touches on a face blocked in by an apprentice. This mixed effort should look very confusing at the mathematical level.

UPDATE: But the final picture is so compelling! (Can't decide if this better suits scientists or Rembrandt.)

Meme: dusting off ancient history

2006-01-24T10:06:00.000+01:00

Coturnix tagged me with this meme:

1. Go into your archives.
2. Find your 23rd post.
3. Post the fifth sentence (or closest to it).
4. Post the text of the sentence in your blog along with these instructions.
5. Tag five other people to do the same thing.

Well, the relevant sentence is pretty strange when taken out of context:

In most of the Forstenrieder Wald, the oaks are continually replaced and rather young looking.

It comes from This post where I talk about the beautiful oak trees in my neighborhood in the south of Munich. I have to say, I love Bavaria in a way that only California can eclipse.

I had forgotten how bloggy I was in the old days!

I will try to update with people to tag later...

Ears that breathe

2006-01-22T10:44:00.000+01:00

The Scientific American Editor's blog has a very nice summary of some recent ideas about the transition from living in the sea to living in land . The bones of the inner ear of terrestrials, for example, may have been derived from a breathing hole that initially allowed clean water to be pumped over the gills independently of the mouth. (Nearer to my own work, the swim bladders of fishes were adapted to generate terrestrial lungs, and they have a whole slew of molecular similarities to our airbags.)

UPDATE: the lung/swimbladder story is not as simple as I thought. Apparently both structures emerged multiple times during fish evolution, and the current similarity is an example of convergent evolution. Hat tip to Lloyd .

In summary, a whole lot of body structures had to get refitted for this transition to happen. The post has very nice explanations, and lots of links!

Stardust returns

2006-01-19T14:16:00.000+01:00

Astrobiology magazine has a nice writeup about the initial assessment of the Stardust mission, which returned safely to earth last Sunday. The spacecraft had very large panels, coated with aerogel, which were hoped to capture particles from a comet's tail. Upon landing the scientists opened up the panels, and confirmed that about a million such particles were brought back. Very cool.

Lab humor doesn't translate

2006-01-19T10:40:00.000+01:00

There's a funny letter to Nature this morning about whimsical names for genes, as chosen by bench scientists, which don't play well in a clinical setting. Just off the top of my head, I could say that bazooka, gurken, pokemon (now under copyright challenge) or sonic hedgehog are cute when descibing a fly, but don't sound quite right when you're doing genetic counseling.

But the biggest such unpalatable genetic term wasn't even intentional: CATCH-22, for 'cardiac anomaly, T-cell deficit, clefting and hypocalcaemia' associated with Chromosome 22 deletions.

Diversify your reading!

2006-01-18T12:15:00.000+01:00

Professor Steve Jones in Connected complains that science writers need to broaden their horizons. Glancing this week through newspapers in English, French and German, he sees the same major science stories appearing again and again. He also makes the very interesting observation that the primary research in many cases originated in Nature , by most measures the world's premiere general science journal:

A glance at this week's newspapers and popular science magazines shows just how wide a range there is: global warming killing off frogs, new methods for generating stem cells, plants that make methane, and what space dust might tell us about the origin of the Universe.Those stories are interesting, varied and up-to-date; but they all share a hidden thread that links - or entangles - everyone who writes about science, for each of them first appeared in Nature.

Jones goes through a list of a huge trove of sources for interesting science available on the web: the Public Library of Science, the free side of highwire press (note: link was dead at the time of writing), and Google scholar. I would add to this list Wikipedia or Google itself.

While of course there are many sources (and "science" sections of newspapers are frequently just dumps of the AP wire) I think that Nature really does deserve special reading attention. For me, Nature is a brand name telling me that what's inside is very interesting to many people and has also been carefully reviewed. (the same goes for Science). As I often post well outside my expertise, I rely on the editors that the main premise of the paper I'm reading is at least self-consistent. It takes long enough to understand the stuff! And Google Scholar can turn up a lot of dodgy stuff especially with specialized searches.

With that said, right this second I'm reading in PLoS about goldfish longevity and its relevance to humans. Very, very cool.

The evolutionary value of laughter

2006-01-15T14:43:00.000+01:00

Maggie Witlin at the beta of SEED magazine (the one swallowing up science bloggers) has an excellent article on the practical side of humor . Laughing probably comes in two distinct flavors. "Emotional" laughter appears to be very ancient-- preceeding even language-- because apes will also make a distinct pant-grunt when they tickle each other. This ancient form might be a way of communicating safety or group cohesion. The other types of laughter, called "conscious laughter"-- anything from nervous laughing to Dr. Evil's cackle--involve different areas of the brain and might have a completely different evolutionary function.

Did viruses "invent" DNA?

2006-01-13T17:21:00.000+01:00

All modern cells are built with very similar components: A wall to keep everything in, DNA which stores the genome, and RNA and protein which take care of the mechanics and metabolism. These components are heavily interdependent, and it is actually something of a puzzle how the modern cell emerged from the prebiotic chemistry of early earth. (See Wikipedia here ).

RNA was likely to be among the very first of the modern cell components to emerge, because RNAs can do the jobs of genome storage (now done mainly by DNA) and enzymatic action (now done mainly by protein) whereas the other components cannot. Proteins might have come second, and DNA last. So how did DNA take over the job of genome storage?

This week's Nature has an amazing suggestion: DNA was "invented" by viruses as a way of evading the defenses of ancient cells. Ancient viruses, as with the ones today, could only make copies of themselves by succesfully infecting a host. So they become engines of innovation, thinking of every possible dodge to get inside the host cell. In an early, RNA-protein world, there would not be enzymes to degrade DNA, so a virus encoded by DNA would have a big survival advantage.

There are some clues from comparative genomics that the DNA world developed in pieces. The means of interpreting DNA genes (transcription, translation) are very similar among all the major domains of life, suggesting that these tools were present in the common ancestor of all present-day cells. In contrast, the means of handling and copying DNA vary quite a bit. DNA polymerases (the copying enzymes) in the various domains of life are in each case more closely related to viral proteins than to comparable proteins from the other domains of life. This suggests a scenario in which a clever parasite brings along DNA plus the means of copying it-- a different parasite for bacteria, archaea, eukaryotes-- and hijacks the cell's existing interpretation equipment. The merger of virus plus RNA/protein cell then created the modern cell.

With this topic it is important to realize that the ideas are very speculative. The attraction of this idea- that the parasite-prey relationship is a very old evolutionary engine- actually also makes trouble because modern day parasites and prey, especially in the microbial world, actually exchange whole chemical modules. Thus it remains very very hard to state what came first.

The original article (Biochimie) is here. An argument about DNA emerging in stages (TIGS) is here .

Human ancestors hunted by Eagles?

2006-01-12T19:05:00.000+01:00

A replica of the Tuang child find, image taken from Skulls unlimited

One of the very early Australopithecus africanus finds is the so-called Tuang child, which was discovered in a limestone cavern along with the bones of many other mammals including baboons and antelope. Because of the heap of bones, it was hypothesized that the Tuang child was the victim of a predator and ended up in the heap with all the other prey. The early money was on a leopard or hyena, but a theory which has been around for quite a while is that a predatory bird, such as the crowned hawk-eagle (which can prey on animals up to 30 kg; the Tuang child was probably about 20 kg) was the predator in question. The first argument in favor of a bird was based on the mix of prey present in the bone heap, with small animals predominating as might be expected for a bird that has to fly off.

A second line of argument (for example here ) favors predatory birds based on the pattern of bone damage to the Tuang skull. Leopards and their ilk do a lot of gnawing, but birds are limited to what they can slice open with their beaks (which is still an awful lot- they brain a lot of their prey via the palate, leaving the postcranial skull alone). The authors of this theory propose looking at the long bones of the various mammalsin the Tuang assemblage, because birds will slice the ends off to get at the marrow while hyenas can just crush them.

The news this week is now (also at afarensis ) is that the bones of the eye sockets of the Tuang child find have radial scratches of the sort that a bird's talons would leave. Birds will strike a treeborne monkey and puncture the skull, and then wait for the animal to die before hauling it off. Sounds like a shark's method.

I just finished reading the Hobbit to the boys. Wouldn't want to have been one of those goblins.

Saturn, its rings, and ring shadow

2006-01-12T19:01:00.000+01:00

From NASA's image of the day page:

Home experiments for kids

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

The Telegraph has a short article on some science-based experiments you can do at home with your kids. There's a trick to sticking a skewer all the way through a balloon..

Let c=cinnamon

2006-01-08T09:49:00.000+01:00

Brad deLong offers a modest proposal to triple the amount cinnamon in all recipes. This is followed by a lengthy and very geeky comments section. deLong theorizes that the level of cinnamon reccomended in older recipes was determined by the price, not taste.

Myself, I have not yet gotten gingerbread to taste gingery, even after tripling the dry ginger and shaving in fresh. A topic obviously crying out for investigation

A genetic taxonomy of cats

2006-01-07T10:22:00.000+01:00

Carl Zimmer at The Loom talks about new work in the evolution of the cat family. The mighty sequencers used in the genomics efforts have been used to compare large amounts of sequence from many different cats. They take this purely genetic tree and try to propose how the modern cats emerged, taking into account divergences and migrations.

Carl points out that some of the highest profile paelontololgy results are coming out of genetics labs. (At least one expert that Carl consults is not too happy that they didn't try to relate the genetics to the fossil evidence).

In the comments section the issue is raised that even distantly related cats can interbreed. This is a topic I've been meaning to learn about myself-- that the base definition that two animals are of different species when they cannot mate must be supplemented with lots of shades of grey.

For more information about how sequence data are transforming paleontology, take a look at this list of newspaper articles from the great news aggregator SnowDeal.

Revised, older dates for Croatian Neanderthal fossils

2006-01-06T18:14:00.000+01:00

It is known that Neanderthals co-existed with anatomically modern humans for some time in Europe, but the length of time during which the two populations might have interacted has been poorly defined. Neanderthal fossils found in Vindija Cave, Croatia had earlier been identified as the youngest of European Neanderthal finds at 28000 years ago.

A new paper appearing in this week's PNAS revists the dating of these fossils, still using C-14.The results suggest the fossils are about 4000 years older than was thought, that is, at least 33000 years old. This, combined with some revisions of modern Homo sapiens tools, tends to put an upper limit on how long or extensive the contact between the two species was. In their discussion the authors emphasize that there are just not many fossils of either kind available between 40000 and 30000 years ago.

UPDATE: A very good writeup at John Hawks. Apparently the younger dates obtained before from these fossils were due to contamination problems. Careful, careful, careful.....

Human genomics at The Economist

2006-01-05T17:45:00.000+01:00

Apparently the print edition of the Dec 24 Economist had a whole series of articles on human evolution and current human genomic research. The editor's note is here but the individual articles seem to be for pay.

I'll have to go get a print copy..

Stem cell scandal: Hwang risked his employees as well

2006-01-05T13:17:00.000+01:00

William Saletan at Slate has a very good discussion of the implosion of the stem cell claims from Hwang Woo-Suk's laboratory. :Hwang claimed that large numbers of stem cells were prepared, at good efficiency, from oocytes freely donated (at personal risk) by human women. Good efficiency was a huge deal, because it means reduced risk to future women.
It turns out that pretty much everything in that claim-- except the risk and the women-- is false. An especially heartbreaking twist is that he in fact he exposed women under his administrative control to much, much higher risks than he admitted.

Here's Saletan:
A scientific panel investigating his 2005 study announced that he'd lied about the number of eggs as well as their sources. Hwang said he'd used 185 eggs. A former colleague said he'd used as many as 1,100. Maybe Hwang's 2004 study, in which he claimed to have gotten one stem-cell line from 248 eggs, was a fraud like his 2005 study. Maybe the cost-benefit ratio wasn't 248 eggs to one stem-cell line. Maybe it was 1,100 to zero.

And there is a claim from at least one female junior scientist in her lab that he pressured her to donate. Wow.

Freedom for plumbers

2006-01-05T13:03:00.000+01:00

Via Wonkette, a court in Maryland ruled that it's not illegal to moon your neighbors.

Plumbers everywhere sigh in relief.

UPDATE: Check out Zoe Brain for gendered approaches to anatomy.

Tangled Bank #44 up at afarensis

2006-01-04T20:11:00.000+01:00

The Tangled Bank Carnival of science-writing is up at afarensis . Have a look!

Mozart's skull confirmed?

2006-01-04T11:33:00.000+01:00

Austrian scientists have been doing DNA tests on a skull sitting in a Salzburg museum to see if it really belongs to Mozart. Mozart was buried in a grave with 4 or 5 other bodies, but a gravedigger later went and got a skull which then ended up in the collection of a museum in Salzburg, Austria. This skull shows evidence of head injury , so if it really is Mozart's, then it could explain the headaches the musician suffered in his last year of life. Mozart's final illness went pretty fast, raising the question of foul play .

The new DNA tests compare DNA from the skull to DNA from the bones of known relatives, whose graves were identified in 2004. The results of the DNA testing will be televised at the end of this week.

UPDATE, Jan 11: It's a bust- the DNA tests were ambiguous

CS Monitor top 10 web pages

2006-01-04T11:18:00.000+01:00

Jim Regan at the CS Monitor lists his favorite web finds of 2005. I really enjoy his taste in sites-- for example The Theban Mapping Project is an interactive look at the vast archeological digs in the Valley of the Kings in Egypt. He has a few other really enjoyable ones. A great time sink!

Crashing to earth-- and surviving

2006-01-03T12:58:00.000+01:00

Astrobiology magazine points out a fascinating side-effect of the the Space Shuttle Columbia tragedy. As the space shuttle broke up, its entire cargo, including scientific experiments, fell to Earth. During the recovery search, it was discovered that a colony of C. elegans roundworms which had been on board the shuttle actually survived the fall to earth despite travelling at anywhere from 600-1000 km/hours and a calculated impact velocity of 45 m/s.
The C. elegans had been growing inside sealed cannisters designed to later be incorporated into a long-term automated spaceborne experiment. They were effectively embedded in a soft gel.(In earth-based laboratories they grow on top of bacterial plates, eating the bacteria.) But the cannisters were not at all designed for impact.

Apparently the worms did not get extremely hot. The inner linings, made of polystyrene (melting point about 80 degrees C), were not damaged, and in any case earthbound C.elegans die above about 40 degrees C.

The first potential significance of this is that even multicellular organisms could possibly survive planetary impact. Space probes sent from earth should be well sterilized to prevent forward contamination of outside bodies; but also, allowing spacecraft to break up in the atmosphere of other planets may not be sufficient to kill everything on board.

A more speculative possibility is that natural objects such as meteorites could transfer multi-cellular organims between worlds. For example, as the authors point out,
(free abstract with link to pdf) the Martian metorite ALH84001 (his friends call him AL) was also not heated past about 40 degrees. Of course, once you've survived impact you'd need to survive whatever you landed in. The main danger to the current C.elegans was that their culture plates were being overgrown by (terrestrial?) mold.

UPDATE: Of all people, the hilarious David Sedaris had already written about these worms. In his short story "Can of Worms" in the collection Dress your family... , he overhears about the space worms and wonders about their perspective. You can hear an audio version of the story here at This American Life.

Are humans the point of evolution?

2006-01-02T18:31:00.000+01:00

UPDATEs:
--The title of this post should be, "Are intelligent beings necessary?" or some such; see Ruse's title.
-- Via Three-toed sloth , a whole conference on complexity and evolution, and a book (reviewed by Cosma) about how the complexity of life on Earth might have been stabilized ("fixed") during natural selection. Clearly there's more going on here than I first appreciated, though I remain close to Gould.

Here's the original post:

Michael Ruse has a wonderfully written essay at Philosophy of Biology about the idea that humans are the pinnacle of evolution. A suprising (to me) number of thinkers, believe that a very common result of natural selection is an increase in complexity; and that, by extension, that Homo Sapiens or in any case a social, intelligent, environment-altering lifeform, is essentially inevitable. Here is E.O. Wilson as quoted by Ruse:

“the overall average across the history of life has moved from the simple and few to the more complex and numerous. During the past billion years, animals as a whole evolved upward in body size, feeding and defensive techniques, brain and behavioral complexity, social organization, and precision of environmental control – in each case farther from the nonliving state than their simpler antecedents did.”

A slightly less emphatic statement of the same idea comes from Conway Morris's notion of a sort of quantization of niches. For example, marsupials and placental mammals both gave rise to very similar-looking predators. Somehow intelligence and culture have beckoned in our era, the Cenozoic; thus Humans. (If not humans, then a cultural animal arising from a different lineage. Ninja turtles, anyone?)

Ruse himself does not come down with an opinion, so let me supply one: the law of natural selection by itself does not specify what will improve survival. (Ruse metntions this point, citing Stephen Gould, in his essay, then strangely abandons it at at the end). Thus, at the most basic level- given life on a World X would it *necessarily* become complex over time, I have to answer, emphatically, no, not necessarily. Whether the range of niches supplied by Cenozoic-era Earth led to an evolutionary gradient which our primate ancestors filled (with us) is speculative to the point of being a bit weird. Even the softer version of Wilson that simple "tends to" give rise to complex with time just does not feel written in stone to me.

Open access- the Royal Society says go slow

2005-11-28T15:04:00.000+01:00

UPDATE: I got this link from Snowdeal, which has a very nice set of links on this topic.

The Guardian ran an article last Friday in which the Royal Society of London argues against a rush to open access for scientific articles. At issue is a proposal by the Research Councils UK that scientists receiving funding from them be required to put a copy of their research online.

From the position paper of the Royal Society:

the Society believes that the approach of some organisations to the 'open access debate' is threatening to hinder rather than promote the exchange of knowledge between researchers. This is partly because some participants in the debate appear to be trying to pursue another aim, namely to stop commercial publishers from making profits from the publication of research that has been funded from the public purse.
...
The process of disseminating research results through peer-reviewed papers costs time and money. Authors must invest time in preparation of the paper, and in some cases must pay journal charges for typesetting and other services. Journals incur charges through the process of reviewing papers and then publishing those that are accepted. Journals recover these costs primarily by charging subscription fees, and occasionally through sponsorship and selling advertising space.

Thus the whole business model of society journals supporting themselves (and returning a bit of money to the society) would wilt unless they controlled access to the data. The Royal Society, which publishes the Proceedings, sees that no one will subscribe if the same data are available for free elsewhere.

The issues they raise are non-trivial: reviewing and editing are a lot of work, and in particular I cannot see who would step in for quality control in a completely open-sourced system. I would say this and further say that there will always be the need for a filter or explainer to put the significance of particular works into layperson's terms. And the society themselves agree that taxpayers have a right to see what they've paid for.

With that said, I think this statement is fighting against a pretty powerful tide. I see how well done the American PLoS journals are (follow the link in my sidebar), and I see the blogs and RSS feeds popping up in the Nature and Cell Press, and I have to believe that this is the future.

I would just hope that increased and improved access would translate into more widespread interest in science.

UPDATE: The Economist has a very interesting take on this issue: transparency is going to change the way that scientists work, and maybe sees a way around the problem of reviewing and quality control. Sorry for the block-quotes, but they do say it best:

All this could change the traditional form of the peer-review process, at least for the publication of papers. The process is organised by the publisher but conducted, for free, by scholars. The advantages afforded by the internet mean that primary data is becoming available freely online. Indeed, quite often the online paper has a direct link to it. This means that reported findings are more readily replicable and checkable by other teams of researchers. Moreover, online publication offers the opportunity for others to comment on the research. Research is also becoming more collaborative so that, before they have been finalised, papers have been reviewed by several authors.

I wouldn't be quite so rosy as this. In particular, people engaged in a collaboration are necessarily rather compartmentalized. Often the best critique of a particular experiment comes from the one other person-- usually a competitor-- who does exactly that. Still, every worker in the current system can tell a story of the vagaries of the current review process. It's not at all airtight.

Bad Vibes

2005-11-27T10:28:00.000+01:00

Bad Vibes is a survey of really horrible sounds- from someone retching to fingernails on a chalkboard. They're trying to figure out what components of a noise make the skin crawl. I'm going to have to bet that imagination plays a large role.

All in the name of science, of course.

Via Science Netwatch.

Ah, the good old days

2005-11-25T16:34:00.000+01:00

Brad deLong links to an interesting post by Charlie Stross about how well he would have fared in the distant past. Medical interventions which have been developed over just the last 60 years have decisively improved his quality of life. For example,antibiotics probably saved his life as a child: therefore, had he been born before 1942 he could not have lived to adulthood.

Stem cell star resigns

2005-11-24T15:17:00.000+01:00

Hwang Woo-suk, the South Korean pioneer of human stem cell work, has resigned from all of his public posts following news that he had obtained human eggs in violation of international medical standards. This is really huge. Before the last two weeks' events he had been one of the world's premiere researchers in this field.

You can find several posts on the story as it has developed this past week at Stem Cell Reseach Progress

A tutorial on short chromosomal duplications

2005-11-17T09:55:00.000+01:00

The awesome new-ish blog Flags and Lollipops has a tutorial about shortish duplications known as low copy repeats or copy-number polymorphisms which are being discovered very rapidly in the human genome. These doubled sections, each of which might carry a handful of genes, are very widespread in the human species and may actually contribute a great deal to human variation.

South Korean stem cell project under scrutiny

2005-11-17T09:41:00.000+01:00

I had seen news items here and there, but Glenn McGee at Bioethics.net says that the breakdown of a collaboration between stem cell star Wu Suk Hwang and an American scientist is much more than it appears. It might be that the human stem cells which contributed so much to Hwang's prestige were obtained from a junior scientist in his lab, raising the possibility that there was professional coercion for her to donate. Here's the Washington Post:

Embryo cloning requires human eggs, which are typically donated by women in a process that requires a month-long series of hormone injections followed by a minor but not risk-free surgical procedure. Because of the modest but real health risks involved, researchers who perform the procedure are required to get informed consent from donors and fulfill other ethics requirements.

Glenn argues that stem cell workers must to be squeaky clean, even beyond the statutory limits on their behaviors, because of the controversy around their work; and that Hwang may have damaged not only his own standing, but that of the field.

I am an interested outsider and can't really evaluate the potential impact of this. But the American, Gerald Schattner, was apparently a very big part of Hwang's international network. The Post again:

The impact of yesterday's (November 11) revelations could be far-reaching, Schatten and others acknowledged. Hundreds of scientists have visited Hwang's Seoul laboratories in the past two years, and many have initiated collaborations with him. The field has also been under scrutiny because of ethical concerns about the creation and destruction of cloned human embryos.

Both are worth a read.

UPDATE: Nature (subscription) is also very alarmed at the Schattner's accusation:

To maintain public support for any controversial field of science, researchers need to follow strict ethical guidelines — and be seen to be doing so. If for whatever reason that doesn't happen, responsibility jumps up a level. It then becomes the job of regulatory bodies and funding agencies to ensure that researchers are brought to account.

Dalai lama at the Society for Neuroscience

2005-11-16T15:57:00.000+01:00

Neville at Neurodudes has posted a liveblog of the Dalai Lama's speech at the opening of the Society for Neuroscience last Saturday-he came away underwhelmed.

My favorite is Neville's evocation of the cattle-car ambiance at SfN. They need to pipe some oxygen into those conference centers!

Blogs, the career killer

2005-11-16T15:19:00.000+01:00

Slate has another go at the idea that Blogs are the kiss of death for academics. I sure don't hope so! But I find the reasoning for (and against) this idea a bit unconvincing; there are just too many variables to assume that blogs would be definitive in either direction. I would guess the only certainty is publish or perish; so if you're writing on a blog, you're not doing your academic duty 24/7.

One very lame thing in the article is they mention John Hawks' anthropology blog as an example of a good academic effort-- and then they don't link to it. This is especially silly because John had a recent post lampooning the blogs=death meme.

Read to the end of the Slate essay for a happy ending.

UPDATE: Via Pharyngula , The Chronicle of Higher Education has an essay responding to their original cautionary tales . Again, though, it's one person's experience. I think it's going to be very tough to generalize. I like it, I do it, I hope to be employed.

Nancy Pelosi on increasing science funding

2005-11-16T12:29:00.000+01:00

Over at the next hurrah there's a discussion of a speech by house minority leader Nancy Pelosi about increasing the United States' commitment to (read:funding for) research. Quite a lot has been made of the U.S. gradually losing its edge especially in engineering. I have to say that I don't see such a sea change in competitiveness with respect to Europe, but in Asia it might be a different thing entirely. Regardless, I think increased money for science, if spent wisely (Gates foundation!) could really help the U.S. Good politics, and good policy, indeed.

A second point, not addressed in Pelosi's speech, is that changes in immigration policy in the wake of the September 11th attacks have the potential to hurt U.S. hi tech very badly. I don't have a constructive suggestion, but a large fraction of postdocs in the United States are foreign born, and losing them will cost.

Please see The Next Hurrah for a great comment thread- look for "emptywheel" on immigration, and multiple "emptypockets" comments on the glut of biology Ph.D.s. and on policy.

UPDATE: Pelosi's speech appears to have been a grab-bag of hi-tech initiatives. I feel less sure about this.

Forensic identification of human remains

2005-11-14T21:16:00.000+01:00

There's a nice story in the LA Times about the different methods used to identify military remains dating back to the war of 1812. The focus of the story is an airman who crashed in the California Sierras, probably in 1942, and whose remains were found by ice hikers last October .
When the remains were found, the name tag was corroded almost to nothing. The central identification lab is consulting with a manuscript expert to try to get words or numbers out of his 60-year old address book.

Moonwalk

2005-11-14T16:56:00.000+01:00

The Japanese mission to the asteroid Itokawa has met with partial success . The main spacecraft, Hayabusa managed to come within 70 meters of the asteroid's surface and release a foot-tall lander named Minerva. However, this approach was actually closer than had been intended, and the command to release Minerva came at a time that Hayabusa was rocketing away from the asteroid surface. So Minerva is basically lost in space.

Haybusa itself will try to land on the asteroid and return samples to earth. Several features, like a laser range-finder, worked well during this approach, so the mission might still yield samples.

A description of Minerva, which sounds a lot like a grasshopper, and of some results to date is over at Instrumentation News .

Cow tipping-- debunked

2005-11-14T16:32:00.000+01:00

A recent article in the Times UK claims that it's impossible for a human to tip over a cow. In this important matter, I will let the scientists speak:

Ms Boechler, now a trainee forensics analyst for the Royal Canadian Mounted Corps, concluded in her initial report that a cow standing with its legs straight would require five people to exert the required force to bowl it over.
A cow of 1.45 metres in height pushed at an angle of 23.4 degrees relative to the ground would require 2,910 Newtons of force, equivalent to 4.43 people, she wrote.
Dr Lillie, Ms Boechler’s supervisor, revised the calculations so that two people could exert the required amount of force to tip a static cow, but only if it did not react.

Persons well known to me have claimed to have tipped cows, so I am a bit at a loss to explain this. Possibly American cows have a narrower stance? Seriously, though, the impression given me--by persons who shall remain nameless-- was that the cows' legs buckled under.

A second observation from the article seems to seal the deal, though:

Another problem is that cows, unlike horses, do not sleep on their feet — they doze. Ms Boechler said that cows are easily disturbed. “I have personally heard of people trying but failing because they are either using too few people or being too loud.
“Most of these ‘athletes’ are intoxicated.”

Hat tip: Scientific American Editor's blog , now at a new url.

UPDATE: What about Kazakh cows?

Proposal-writing blues

2005-11-11T09:21:00.000+01:00

Some words of comfort, from a book review about an Einstein biography:

The ability to recognize something is broken is as important as the ability to fix it, and the ability to choose among the things that work and those that don’t is more important still.

The review is also worth a read for Einstein's religious impulses. He was a complicated man.

Search engines for medical information

2005-11-08T14:46:00.000+01:00

PLoS medicine has a nice, very basic introduction to the major search engines indexing medical information. Quite a lot of this is available to the general public. Take a look!

1918 was a bird flu- but who?

2005-11-08T09:44:00.000+01:00

The always good NY Times science page has a nice article by Gina Kolata about the genetic reconstruction of the 1918 flu . Pieces of that virus were amplified from its 1918 victims, and overall the virus quite clearly belongs in the avian influenza group.
The problem is, the details of the sequence look different from any of the known flu variants- different from strains found in american fowl; different from the H5N1, the current bird flu; and different even from avian flu obtained from preserved animals from 1918. Specifically, the hemagluttinin gene, which is necessary for the 1918 virus' huge virulence, has about 30 amino acid substitutions relative to known avian strains. These changes make a new structure for hemagluttinin which lets it infect mammalian cells.

The scientists involved are now examining migrating bird populations to isolate a closer relative of the 1918 monster flu.

Me Tarzan. You Jane.

2005-11-07T10:02:00.000+01:00

Via Metafilter, a scientific survey of the best pick-up lines. By scientific, they mean evolutionary psychology, which produces gems like this:

Chat-up lines, and other openings used to initiate a relationship with a woman, can be viewed as male displays. How well does their effectiveness accord with predictions from evolutionary psychology? 205 undergraduates (142 female, 63 male) rated 40 vignettes; in each vignette, a man approached a woman and the raters judged whether she would continue the conversation. Openings involving jokes, empty compliments and sexual references received poor ratings. Those revealing, e.g., helpfulness, generosity, athleticism, ‘culture’ and wealth, were highly rated. Although the length of the vignette—confounded here with item content—affected the rating, differences remained after the effects of length were eliminated. The success of openings which demonstrated culture was predicted from Miller’s (2000) ‘mating mind’ hypothesis; the success of others could be predicted from patterns of parental investment.

My favorite, and Metafilter's too:"Ten-ton polar bear."
"What," replied the young brunette at the bar. "Well, it breaks the ice, doesn't it," we said, optimistically.

UPDATE: the EvoPsych abstract was originally at Dienekes . Must have missed it.

Update: A pretty hilarious skewering of the evolutionary take.

Giant shoulders, held aloft by others

2005-11-06T10:29:00.000+01:00

Kieran Healey at Crooked Timber reviews a biography of Darwin which seems like a very worthwhile read. It rings true to me, in my own attempts to glimpse into the cloud of unknowing, that an alternation between very good scientific correspondence and moments without distractions (..uh, like blogging?) is a very healthy routine for thinking.

Read through the comments for some thoughts on the crisis Darwin provoked among Victorian believers. I think it may be a mistake to pin all of this on Darwin; a careful read of Voltaire can scald the retinas.

How Advanced Can a Civilization Become?

2005-11-05T19:13:00.000+01:00

Billyuns and billyuns..

No, seriously, my guess is that's it's pretty likely that microbial life exists in many many extraterrestrial locations. Of those worlds, some fraction have given rise to civilizations (although we will always have Madonna). If you enjoy skating way out onto thin ice, read this interview with Dr. Michio Kaku, about the next Copernican revolution.

Update: The perspective of an alien when visiting Earth.

Clay as a scaffold for the origins of life

2005-11-04T09:04:00.000+01:00

Nature news has a spot about some remarkable chemistry displayed by aluminum-silicate clays. Under conditions mimicking undersea hot vents, these clays are able to catalyze conversion of methanol to complex organic molecules. The work reported this week adds a new twist: at least one kind of clay, smectite, can also protect the organic molecules from degradation, and might even carry them safely away from the vent and release them elsewhere.

Life as we know it has a boundary- a cell wall, defining the living thing- and information molecules. Both of these features are so basic to what we consider life that it is a major puzzle which element could have come first. For example, it's hard to assemble DNA from its units without something to keep everything near at hand; thus a cell wall seems critical. However, a bag full of goodies doesn't have much chance in the game of life without the information to make copies of itself.

The clay line of thinking provides a way to make long molecules such as DNA without relying on a cell wall. Clays instead are very "sticky" for carbon-rich molecules, which can move along the surface of the clay and interact and react with each other in two dimensions rather than three. This feature of clays provides a potential substitute for the "corral" or scaffold that the cell membrane provides in life as we know it. Thus this line of thinking champions the idea that information molecules came first in the origins of life.

One hole in this theory-- literally!-- is that current cell walls don't just keep important things in, they also protect them. Cells with walls can control their internal pH and other aspects of their insides, because they're enclosed. A growing DNA molecule out on a clay surface is exposed to whatever the hot vent can throw at it.

So the significance of the current work is that smectite not only simplifies the organization problem, but also protects the organic molecules which result. Thus organic molecules can not only arise in the hot vent chemistry, but they also have a place to hide once they're made.

Technical note: A sidelight of the articles as written is that smectite will actually release the organics if the temperature comes down to that of the surrounding ocean. Since hot vents-- also known as chimneys or smokestacks-- expel all sorts of particles out into the ocean, you could imagine a it seeding the whole area around it with these newly forged molecules. In this scenario, you'd have a lot of things then- a gradient of temperatures and chemistry, and a mechanism for physical flux- that could be very helpful in initiating natural selection on the organic products.

A newspaper writeup is at the Guardian .
The abstract in Geology Magazine is here

A very nice general intro is at Biocrawler, which seems to be a biology version of Wikipedia-- read especially the entry on Wachtershauser. Anyone heard of Biocrawler before?

Best Science News Podcasts?

2005-11-04T08:03:00.000+01:00

Slashdot is running a comment thread on the best science podcasts. I don't listen to podcasts much, but I'm amazed at the variety that's out there.

Who's your daddy? Use Google to find out

2005-11-03T15:44:00.000+01:00

The New Scientist is running an interesting story of a boy who managed to identify his biological father, an anonymous sperm donor, by getting his own Y-chromosome sequenced and then hitting the internet.

He started by paying a service, FamilyTreeDNA.com, to sequence bits of his own Y-chromosome DNA. Since the Y-chromosome is handed down father-to-son, this DNA could have come only from the sperm donor. The service got him in touch with two other men with very similar Y-chromosome content to his. Those two men had very similar last names with a minor spelling difference (it took me a minute to remember that last names are also frequently patrilineal, thus serving as a real-world tracer of the Y-chromosome).

He used the sperm donor's birthdate-- which his mom knew-- to query a different database, Omnitrace.com, for every male born in a certain place on that date. Only one of these guys had the last name he was looking for.

As New Scientist remarks, "The news will be especially unsettling for men who donated anonymously before the power of genetics was fully appreciated. Donors were often college students who traded their sperm for beer money. Many have not told their wives or children and have never considered the implications of having a dozen offspring suddenly wanting to meet them."

I'm not at which step in this search the anonymity of the sperm donor could have been defended. Are you still cool with filling out information at the supermarket?

Worst jobs in science

2005-10-28T21:47:00.000+02:00

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

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

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

Tell it to the hand!

2005-10-27T10:42:00.000+02:00

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

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

Sounds like a great issue of Forbes.

Long nursing period for mammoths

2005-10-26T16:29:00.000+02:00

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

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

Good doggy

2005-10-26T12:23:00.000+02:00

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

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

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

NASA - Crop Circles in Kansas

2005-10-25T10:40:00.000+02:00

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

The psychology of a cluttered desk

2005-10-24T17:52:00.000+02:00

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

To many observers, clutter reflects the mind-set of the modern household -- overburdened, disorganized and compulsive. To others, clutter is a broader symbol of a culture dependent on easy credit, piling up debt and consuming a lion's share of the world's resources without considering the consequences.
"People's homes are a reflection of their lives," says Los Angeles psychologist and organizational consultant Peter Walsh. "It is no accident that people have a huge weight problem in this country, and clutter is the same thing. Homes are an orgy of consumption."
The article later postulates an evolutionary psychological requirement to hoard items against possible future famine. Also featured-- I'm not making this up-- is the National Study Group on Chronic Disorganization. I'm sure their meetings begin promptly.

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

Junk DNA- somehow it's important

2005-10-24T09:40:00.000+02:00

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

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

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

1st Avenue Machine short animations

2005-10-22T09:57:00.000+02:00

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

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

Islands as the last resort

2005-10-21T17:47:00.000+02:00

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

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

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

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

2005-10-21T10:45:00.000+02:00

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

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

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

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

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

Slate bashes the Human Genome Project

2005-10-20T09:33:00.000+02:00

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

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

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

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

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

I think that's $500 well spent indeed.

Tangled Bank #39

2005-10-20T09:31:00.000+02:00

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

I should be actively blogging next week sometime.

ADEPs: A possible new class of antibiotic

2005-10-17T09:30:00.000+02:00

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

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

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

New science page at Ars Technica

2005-10-16T16:12:00.000+02:00

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

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

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

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

Little Chucky Darwin

2005-10-14T09:47:00.000+02:00

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

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

Hat tip: Pharyngula

Like a kid in a candy store

2005-10-14T09:40:00.000+02:00

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

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