Sunday, July 31, 2005

A Calcium/Magnesium channel mutation in Guam Parkinson's

The Chamorros, the indigenous people of Guam, suffer from a neurodegenerative disorder known as lytico-bodig, which has a mixture of similarities to Parkinson's and Lou Gehrig's diseases, including muscle wasting, tremor, dementia and death. A 1958 survey estimated that 10% of Chamorro adults had this disease, which is about 100 times the incidence of Lou Gehrig's disease worldwide. The epidemic has greatly subsided since the 1970's.

Scientists interested in neurodegenerative disease have been going to Guam because of the high incidence of the disease and because the disease seems to be a mixture of pathologies seen in other degenerative conditions . However, despite 40 years of collecting blood samples, though, the causes of the disease have been difficult to sort out. The current consensus is that it is caused by a combination of genetic susceptibility and one or more environmental factors. The environmental insults have been variously proposed to be the cycad plant toxin BMAA , bacterial contamination in river water or magnesium deficiency.

Efforts to identify genetic factors which contribute to the disease have given mixed success. However, a advance publication to appear in PNAS is now reporting a point mutation in a calcium/magnesium channel in autopsy tissue from five patients out of 21 checked. The point mutation in TRPM7 removes a conserved phosphorylation site, and the mutant channel is thus more sensitive to magnesium inhibition. The authors propose that this channel mutation increases susceptibility to whatever environmental insult to result in the disease. The authors favor the magnesium dietary deficiency hypothesis, as it dovetails best with the defect seen in the mutant channel.

The strong point of this article is the identification of a somatic genetic alteration in a substantial fraction of lytico-bodig suffers. This point mutation is present in the public (SNP) databases, and seems to have occurred all over the world, i.e. it is not causative for the disease. However, the functional data in the paper on what this means for the channel and Ca/Mg homeostasis are really tantalizing.

In the end, the rapid disappearance of the epidemic argues against any strict genetic cause of this illness. The cycad hypothesis has received the most attention (possibly because Oliver Sacks was a co-author) and may account for the sufferers without this genetic predisposition.

I keep thinking about the human cost to these people of an epidemic of this horrifying disease, and what it must feel like for the affected families to be asked to give blood over and over again. The epidemiologist looking for mechanism might look right through the person. I have this problem generally with Sacks' writings. The NIH has been administering research into this disease since the late 50's, and hopefully there have been standards for sample sharing that are minimally onerous to the disease sufferers.

Friday, July 29, 2005

More maneuvering on Kennewick Man

Via The Panda's Thumb , the Progressive Reaction was at the hearings of the US Senate Indian Affairs Subcommittee on the McCain amendment to NAGRPA and is not happy with how it's going. The McCain amendment would allow Native American tribes to demand the return of remains, even in cases where they cannot prove a link to a modern tribe.

At the hearing, the speakers for the Native American perspective seemed to be on a roll, and the physical anthropologists were not holding up well. Progressive Reaction thinks this will go McCain's way.

Progressive Reaction also provides a list of Kennewick legal links.

For a thoughtful take on the science and religion aspects, i.e. scientists getting access to items of potential religious significance, see Bartholomew.

Dinosaurs and healthful chocolate

Seriously, though, there's a really interesting dinosaur embryology paper to come out in this week's Science. The remains, from a Massospondylus, an early Jurassic prosauropod species, shows that the babies were not ready for prime time:

An analysis of the embryos suggests they were born walking on four legs with short tails, long forelimbs and big heads. To morph into their adult shape -- walking on two legs with long tails, short forelimbs and small heads -- their various features must have grown at different rates.

"The proportions are just ridiculous," Reisz said.

Anyone seen a human baby recently? Ridiculousness is in the eye of the beholder.

In addition the dino babies lacked teeth, suggesting they needed lots of parental care. The remains furhtermore suggest that the four-legged gait of the later sauropod giants could have emerged directly by retaining the youthful form, rather than requiring a two-legged to four-legged lifestyle adaptation. But-- someone correct me-- aren't Diplodocus et al thought to have reared up on two legs on occasion?

Thursday, July 28, 2005

Blog Idol

Via Blogdex, Todd Mintz tells of an experiment comparing blog growth . He started pseudonymous blogs for each of the contestants of American Idol and posted with the same frequency for all.

The result was that the most popular Idol, Bo Bice, resulted in the most popular blog. Topic isn't everything, but it has a very big impact. I guess I'm not going to get anywhere blogging Alu repeats. New topic: dinosaurs. No, space dinosaurs deriving unexpected health benefits from chocolate.

The article does give some good blog advice, including focus and regular posting, which do seem to help me. And a few borderline sneaky things about gaming Google. For example, every time your chosen topic hits the news, you cut-and-paste blog from a prominent source, with the link. Soon you'll be indistinguishable from USA Today.

Ancient floods on Mars

I had complained earlier this week that geological evidence that Martian surface rocks have been cold for almost their entire history is hard to reconcile with Spirit and Opportunity findings of surface rocks with clear water alteration. The distinction seems to be between surface temperature, where the sun maybe can heat things, and deeper rocks. In any case, Science Now discusses the geology another very visible watery feature of Mars -- the huge arroyos, especially in the Valles Marineris system. These appear to be transient, catastrophic flood formations. A new hypothesis says the water was there, possibly trapped in sulfate salts, and released all at once maybe by vulcanism.

For fans, here's a whole poster session on whether, or how much, water mars has seen.

In the mean time, check out this perspective image of a (dry) canyon wall in Mars, from the USGS.
Perspective view of Candor Chasma, mars

Slashdot: Go East

(Updated 29.July)

Slashdot links to a National Bureau of Economic Research paper saying that China will lead the world in science and engineering . Obviously, the sheer size of China and India implies that if they built up like the United States, they wouldn't just have Caltech and MIT but, wow, tens of such universities.

However, that's a BIG if. Even a brief look at Simon World reveals all sorts of growing pains. It even seems a bit of a stretch to think that the Chinese technological edifice will have the same priorities as the current America-Europe-Japan juggernaut.

So I don't think the sky is falling, not nearly yet, although any alarmism designed to increase US science efforts is ok by me. The Slashdot crowd seems a bit more accepting of the paper's message.

Wednesday, July 27, 2005

Panda's Thumb follows up on Cardinal Schönborn's remarks

Reed Cartwright at the Panda's Thumb follows up on the recent New York Times Op-ed by Austrian Cardinal Schönborn. Schönborn's editorial contained phrases and concepts derived from the American Intelligent Design movement, and was received as an endorsement by the Catholic Church of that interpretation of the existing biological world. (Lots of background at the link.) I have a lot riding on this topic because of my Catholic heritage, and I have to say I read the Schönborn Op-ed with considerable dismay.

In subsequent clarifications, Schönborn seems to say that he wants only to criticize atheistic explanations of life, and he specifically remarks that the teaching of evolution is acceptable to the Church:
In follow-up remarks published July 11 by Kathpress, an Austrian Catholic news agency, Cardinal Schonborn cited Popes Pius XII and John Paul II as saying that the theory of evolution - as long as it remains within the realm of science and is not made into an ideological "dogma" which cannot be questioned - is in conformity with Catholic teaching.

I can live with the block quote. (However, the full text , despite its title, is not exactly what Richard Dawkins would say.) But I think the Cardinal is attacking a straw man. The whole point of working science is its etiological modesty and empiricism-- the exact opposite of normative "dogma" of the sort which the Cardinal dislikes. Specifically, the concept of the origin of species by natural selection as argued in Darwin's The Origin of Species is painstakingly developed, with repeated references to available data and to alternative interpretations. Here's Darwin in his last chapter:
That many and grave objections may be advanced against the theory of descent with modification through natural selection, I do not deny. I have endeavoured to give to them their full force. Nothing at first can appear more difficult to believe than that the more complex organs and instincts should have been perfected not by means superior to, though analogous with, human reason, but by the accumulation of innumerable slight variations, each good for the individual possessor...

Hardly a blowhard! He's trying to explain what he sees. It's very much worth a read even today. And it's important to note that Darwin had responses ready for a strict creationist. It is that person, and not the scientist, who is trying to put ideological constraints on the divine:
Authors of the highest eminence seem to be fully satisfied with the view that each species has been independently created. To my mind it accords better with what we know of the laws impressed on matter by the Creator, that the production and extinction of the past and present inhabitants of the world should have been due to secondary causes, like those determining the birth and death of the individual. When I view all beings not as special creations, but as the lineal descendants of some few beings which lived long before the first bed of the Silurian system was deposited, they seem to me to become ennobled.

So, to reiterate: the teaching of ecolution via descent with mpdification and natural selection does not in itself throw anyone's Uncaused Cause out of the window, and the Cardinal's revised argument does not affect institutional evolutionary science at all. The explicit refusal of science to treat with such matters should not be construed as a denial of anything, although individual scientists will of course have their private cosmologies. It is rather Intelligent Design which presumes to constrain the form of-- and therefore ideologically intrudes upon-- the divine within the biosphere.

I think it's appropriate to close with Darwin's famous "tangled bank" at the end of Origin:
There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

Limitless complexity arising from elegant simplicity, and an almost Platonic invocation of beauty. These features of science ought to have some appeal to the devout.

UPDATE, August5: Crooked Timber quotes Cosma Shalizi with a a far more elegant way of saying it.

A male contraceptive: the second sexual revolution?

There's a great article at Science and Spirit speculating about the release of a male contraceptive pill (maybe by the year 2010). It turns out to be something of a marketing challenge, even marketed to men in committed relationships, because of ideas about loss of virility. It's most successfully addressed by framing it as the caring, responsible thing to do.

What's even more interesting is the sort of game-theory sociology which emerges: if a man who's on the pill goes off the pill, there still won't be a pregnancy if the woman is on the pill. Yeah, but the converse is also true, right? And anyway if people know each other well enough to be having sex on a regular basis, doesn't it seem likely that they'd try to agree on their reproductive preferences?

Or is that just (wait for it) inconceivable?

Read the whole thing.

Dig Stonehenge:"Not an autopsy, but brain surgery"

The Guardian reports an research framework for the near future study of rhe area around Stonehenge. The immediate vicinity of Stonehenge (about 2000 hectares is designated a World Heritage Site) is full of ancient graves, many of which have never been excavated. A grave about 3 miles away revealed the cotemporaneous "Amesbury Archer," whose childhood may have been spent in the northern Alps, and whose rich burial ornaments came from as far away as Spain and France. (see links at archaeology UK) So the possibility of learning a great deal more about European Bronze Age culture is very great.

The framework would like to begin new small scale digs, and increase efforts to retrieve artifacts which have been taken from the site by any number of means. A timeline of historical digs is here.

For a very good summary of issues related to balancing science, public access, and preservation in a World Heritage site, see Save Stonehenge .

Tuesday, July 26, 2005

Cloning mammals

Making clones like Dolly the sheep is a very inefficient business. Just 1 to 5% of clones mammals survive to birth, and lots of those have health problems.
Science Now is saying that at least some of the problems can come from the specific stages in the development of the cloned embryo. Keth Latham's group has found that technical matters like changing the culture medium can enhance the number of survivors up to nearly 50%. The Science Now blurb also says that many very early cloned embryos show pretty massive disturbance of their gene expression patterns.

A much earlier report mentioning Latham's lab is here. In the older work, they found that the genetic fertilization and other initial steps went fine, leading to the current work where they considered later stages.

So there's some progress in identifying the scope of the problem. But it sounds like if you want to clone your pet kitty you're still going to have to wait.

Endangered raptor-- already flown?

Via discovery channel, the population of historical Cape Verde kites is not related to the group of kites, considered to be endangered, which live there now. Mitochondrial DNA sequences retrieved from museum specimens show that the original Cape Verde kites belonged to the red kite family, and the current inhabitants give mitochondrial DNA characteristic of black kites (common in Africa and Asia). This implies that the island's inhabitants were displaced at some point in the last 100 years by a maternal lineage related to African birds. This may knock the current birds a bit down the priority list for conservation efforts.

The link (Royal society of london) is here.

Miniature ice giants, supersize earth: planets outside our solar system

Astrobiology magazine has a short article about the hunt for planets outside the solar system. The most successful search method has found lots of Jupiter-plus planets, which are big enough to cause a noticeable wobble in the parent star's position. Refinements of this approach have led to detection last August of planets as small as Neptune, i.e. the theoretical smaller limit of an "ice giant".
However, all three of these "small" planets that have been successfully detected orbit very close to their parent star-- closer than Jupiter in our system. This may be an artifact of the search procedure (close in makes for more rapid stellar wobbles) but still, ice giants should be forming much farther out because it's too hot close in. Instead, they could be supersized rocky versions (similar to Earth's composition) or they could be icy despite their nearness, having migrated inward from a more distant birthplace. The astronomer Alan Boss is betting on a super-sized rock, especially because in 2 of the 3 systems where they've been seen the same system has a Jupiter-like planet further out. These big planets would be a big obstacle for an ice giant trying to migrate inward.

Monday, July 25, 2005

Mars on ice

Speculation about the possibility of earth-like microbial life on Mars took a little bit of a hit last week with publication of the thermal history of a piece of Mars. A rare class of meteorite, known as nahklites, are thought to actually be pieces of Mars which fell to Earth. The evidence in the article in Science suggests that these rocks have been very cold for almost their entire history on Mars. This would imply that the planet as a whole was never warm enough to support widespread near-surface liquid water, which in turn means that microbial life may never have had a chance.

In the Science study, the scientists re-analyzed old measurements of the ratio of radioactive potassium to its decay product argon. These analyses (and other radio-dating pairs) indicate that the meteorite ALH84001 (called AL by his friends) was formed underground on mars about 4 billion years ago. AL was kicked out of Mars (about 15 million years ago) by a not-very big impact, so he must not have been buried more than a few kilometers deep.

Argon formed by the decay of potassium will diffuse, and the warmer the rock gets, the faster argon will leak away. The scientists extensively modelled how much argon AL has still in him, and conclude that he could never have been very warm-- otherwise he'd have a whole lot less argon than is observed. The most likely temperature range they determine is around -60 degrees celsius, far below the freezing point of water. They conclude that the kilometer or so nearest the Martian surface has been in deep freeze for its entire history.

It's a little hard to see where this fits in with other Mars data. The Mars Rovers, especially Spirit, have observed lots and lots of rock formations which must come from exposure to liquid water. These are not just one-off volcanic rocks, but sedimentary layers requiring thousands of years to form. Of course, the Rovers' landing sites were preselected for the maximum chance of seeing just such formation; whereas AL and his nahklite relatives come to us from (presumably) a random event.

In the next few years the Mars Express MARSIS experiment will be using ground-penetrating radar to look for current subsurface water.

Wellcome trust medical images

Head of a dog tapeworm

The New Scientist links to this year's Wellcome medical images awards . I love images which also have some scientific content, so I have to say the Wellcome page is a bit of a disappointment. There are beautiful images, but they have very little explanation, and they want to sell them even for academic users. Still, this tapeworm head (by M.I. Walker)is weirdly beautiful.

A conservation hack for Google maps?

The Uneasy Chair wants someone to map data about the locations of endangered species with the Google maps interface. Google maps allows you to run your custom data sets through their collection of maps of the globe (see Wired for a history of this phenom). So a conservationist with a big set of GPS points could plug in, for example, the known range of the northern right whale, for example 20 years ago and then again today.

In a later post, Jon links to the World Wildlife Fund's wild finder which can be browsed by region or by species.

I would love to see GPS data from a single radio-tagged blue whale.

I am really drawn to the idea of making data widely available, especially if it comes prepackaged with an interface. For me this is not only for the purpose of popularizing science (in itself greatly needed), but also works toward the more elusive goal of genuinely participatory science. I just love the Wikipedia phenomenon-- an edifice built by thousands of hands. Conservation issues, in particular, rely on the goodwill (and brainpower) of so many people that increasing the involvement by many minds could only help the science and the policy.

UPDATE: COOL! Look at this page by U. Cal Berkeley with locations of major Miocene fossil beds.

Tuesday, July 19, 2005

Just don't call it junk

(All of these links appear to be behind subscription walls. It may be possible to get to the Science blurb using BugMeNot .)

Science Now talks about an idea emerging from comparing genomic sequences: basically there is an awful lot of conservation outside of coding DNA. This must be important stuff, but the function of this non-coding DNA is not yet clear.

The mouse (2.5 Gigabasepairs) and human (2.9 Gbp) genomes have a lot more DNA sequence than is used to directly specify protein (these are so-called coding DNA regions). In order to understand the function of the non-coding regions of the human genome, computational scientists look at which sequences are conserved between mouse and human (and other studies even compare human to fish, or fly). The result of these comparisions is that the total extent of non-coding sequences conserved between mouse and human is larger than that of coding sequences , and some "ultraconserved" sequences are actually better conserved than the protein-coding regions. .

The specific effort cited in Science actually shows that the abundance of these highly conserved non-coding DNA regions increases with the complexity of the organism pair being compared. When comparing yeast to roundworms, about 40% of the matches are non-coding; but when comparing fruit flies to vertebrates almost 2/3 of the conserved sequences are non-coding.

It's thought that these conserved non-coding regions are enhancer elements , meaning they contribute to the control of nearby protein coding regions. The idea would be that to make a more complex organism you'd need not just fancier building blocks (proteins) but also more precise control of where and when the proteins get put in. See also the references here in Pharyngula's reading list.

Life is everywhere

Live Science and others are reporting that a whole ecosystem has been revealed by the collapse of an antarctic ice sheet. A geological survey of the seabottom formerly covered by the Larsen Ice shelf showed clams and bacterial mats around mud volcanoes, or so-called "cold-seep" niches.
What's important about the region is that the Larsen shelf probably kept the area pristine for millenia until its 2002 collapse. It's sort of a footrace to get to these organisms before outsiders arrive.

John Hawks on the Kennewick frenzy

John Hawks blogs that the much-publicized examination of the Kennewick bones by scientists involes a lot less new science than appearances would suggest. The common perception (I've bought in, too) has been that no one has looked at these bones since the legal dispute blew up. In fact, Hawks links to a government-maintained data page summarizing extensive work already done on the remains. The current, publicized study appears to be mainly cross-checking.

Read his post to find out his take on what's going on.

Saturday, July 16, 2005

Popping a water balloon in microgravity

My kids really liked this one. Except for a surface spray, the water hangs together and eventually becomes spherical. Another cool one is the sausage shaped balloon which unsheathes itself before disintegrating.

New radiometrics for surface rocks

The US-European joint effort CRONUS is trying to standardize decay times for new radionuclides useful for dating surface rocks. (great acronym, by the way.) The series they're hoping to establish would be useful for an enormous time range- between 50 and 10 millon years, or nearly 6 orders of magnitude.

The nuclides of interest are generated by cosmic rays hitting the top 3 meters of the Earth's surface. (, my ultimate source for this, had a supernova tie-in. ) The high-energy rays generate a whole panoply of exotics- 3He, 10Be, 21Ne, 26Al and 36Cl-- that are not generated in deeper rocks. Ratios of these nuclides with respect to decay products, i.e. 10Be/9Be, could in effect say when the rocks left the surface.

I guess this approach would be limited to surface rocks that get shielded, by 3 m or more of overlying rock, in a short time relative to the age of the rocks. I was thinking about the 40,000 year old mexican footprints, which were left in volcanic ash and possibly promptly buried.

Friday, July 15, 2005

Deep Impact- not deep enough?

The science wire Eurekanet says that the comet Tempel-1 has gone quiet ten days after the collision with the Tempel-1 probe. The absence of a prolonged "active site," or jet, may limit observations from the pristine materials from the inside of the comet. Eurekanet links over to the European Southern Observatory which confirms that the comet does not have a visible jet.
Tempel-1 has been around the sun many times, so its exterior has been chemically modified. One goal of the impact experiment was to excavate through this outer part, to let out the inner stuff which would be representative of the chemistry of the forming solar system (in the vicinity of Jupiter). Without a prolonged jet, the astronomers have got "only" the 40 hours of observation from immediately after the collision. Coincidentally, an active site had opened up spontaneously before Deep Impact arrived, so the observatories will have that information as well.

I can't find much more on this topic yet.

Wikipedia is already up with a very nice summary of the mission. The technical demands of this mission are unbelievable.

Pharyngula on dinosaur lungs

Pharyngula writes about the recent evidence that dinosaurs had air sacs similar to the pumping system modern birds use to improve their lungs' function. He's got diagrams of the mammalian and the bird systems, and sketches of what therapod dinos must have had. Very cool stuff.

Thursday, July 14, 2005

Why is Harvey the Rabbit always male?

The BBC has a short segement on auditory verbal hallucinations . Auditory verbal hallucinations are a common symptom of schizophrenia, occuring in about half of all patients. Apparently more than 70% of these patients-- male or female-- report hearing a male voice during hallucinations. The false voices are furthermore likely to be middle-aged and carry derogatory messages. (The Beeb does not include these details, but the article says that the voice is also typically right-localized,external and speaks in a monotone, "like a BBC newsreader.")

A new article in NeuroImage proposes an explanation for the gender bias of these hallucinations. Normal healthy volunteers listening to computer-altered recordings showed different brain activity (by fMRI) in response to male, female, or indeterminate voices. Specifically, perception of a female voice correlated with increased activation of the superior temporal gyrus relative to perception of a male voice. The authors propose then that the brain state corresponding to hearing a (real) male voice is a kind of default, and the easiest for the brain to mimic during hallucinations. They want to go back and test these ideas on schizophrenia patients.

Perception of a female voice yields more complex responses both because of the shape of their larynx gives a more acoustically complex sound and because (English speaking?) women employ more melody while speaking. This makes me think that the authors should evaluate speakers of a tonal language and see whether the difference in brain activation based on speaker's voice would still hold.

Man fakes heart attack using electric underpants

In a product mod which would make the Slashdot crowd proud, the Register reports that a man trying to get product liability money from an iron maker faked the symptoms of a heart attack using electrical underpants . He first rigged an iron to short-circuit, then faked getting shocked. When his wife drove him to the hospital, he deployed the Austin Powers underwear to juice the EKG.

All this came out in court, however, and he was told to pay the iron manufacturer's legal fees. He didn't attend the final decision, having admitted himself to a hospital with depression and chest pains.

More underwear trauma is available from the Register, who show their ongoing commmitment to get to the bottom of everything.

Wednesday, July 13, 2005

RNA editing targets Alu repeats

One of my ongoing interests is the ecology the numerous repetitive, "parasitic" DNA sequences which make up almost a third of the human genome. These sequences are descendants of DNA stretches either containing information for moving themselves to a new location, or able to be moved by proteins encoded by other DNA. Movement by these elements causes changes which are almost always harmful to to the host (the human). For example, a novel parasitic DNA insertion can gum up the production of messenger RNAs (mRNAs) necessary for production of human proteins.

In this month's PLoS biology, computational biologists have pulled out evidence that human cells use RNA editing to target Alu repeats which occur in mRNA.

The main thrust of the article is an effort to understand "A-to-I" editing, a process with important consequences especially for certain neurotransmitter receptors in the brain. To learn more about A-to-I editing, the authors searched a database of mRNAs and found 26 examples of the specific mismatch which this editing generates. Interestingly, in all but one of these cases, the A-to-I editing happened within an Alu repeat. They believe this happenes because the machinery which does A-to-I editing seems to recognize special regions of mRNAs called hairpin duplexes. Hairpins can form when multiple Alu repeats integrate in opposite orientation in the same mRNA. A-to-I editing might weaken the base pairing which creates the hairpin.

Assuming that A-to-I editing is a sort of control mechanism (see more below), the evolutionary success of the Alu sequence repeats, which are self-similar by definition, in jumping into mRNAs seems to be the exact trait which is used to target them.

So what exactly is the impact of A-to-I editing? The story gets even stranger in the second half of the paper, in which they give examples in which an Alu repeat present in an mRNA changes that mRNA, and is changed again by this editing. Exons are made and lost, and mRNAs are spliced together into alternative forms under the influence of this process. In all, the authors think about 1500 mRNA transcripts, or about 1.4% of all transcripts, have changes in their exons because of editing of Alu repeats-- this means different protein products! They believe this is a conservative estimate because diversity among Alu sequences might have prevented detection of some editing events.

Finally, when the authors looked at which tissues are doing this the most, the answer came back that most transcripts are brain- or thymus- derived. (However, the trachea was also active. Go figure.) The reliability of this finding is a bit less robust because it relies on text annotations in the database.

So why? and why the nervous system? The activity of A-to-I editing follows the expression of (separate) adenosine deamidase enzymes within the nervous system and the immune system. These, in turn, may be active because of special features of those two organs. In particular, I still have not blogged about the recent Nature paper showing increased LINE element mobility during neurogenesis. Activity of the LINE family of jumping DNA sequences can also mobilize the far more numerous Alu repeats, so it may be that individual neurons in general have to cope with novel insertions in their transcriptome. The A-to-I editing might have originally arisen to break up cellular "indigestion" resulting from hairpins, and become successively adapted as an Alu-monitoring mechanism and finally a gene editing device. Thus relaxation of DNA "quality control" during neurogenesis and in the immune system (indicated e.g. by LINE mobility and tolerance of aneuploidy) seems to enable greater activity of parasitic repetitive elements. The host organism responds not by reinstating checkpoint controls, but by apparent ad-hoc countermeasures, and even by adapting to (more precisely, exapting) the changes introduced by the jumping genes.

If you can't beat 'em, enjoin 'em. But I guess the question is, why is DNA damage control relaxed in these specialized cells in the first place?

Update: there is a pretty considerable older literature about A-to-I editing, which I completely missed in this blog. See for example here .

Mars rovers writeup at Nature

This shows you what relying on the Web will do- I only just realized that last week's Nature had the Mars Rovers on the cover. The two rovers have continued to churn out geological information from their respective areas, and their observations have definitely changed my guess about the possibility of microbial life there.

Some conclusions of the Nature articles are excerpted at The take-home for me is the geological diversity of Mars and possible ongoing geological activity. Where there's a heat source, especially underground, I think the possibility of liquid water and then chemotrophic life goes up. An important caveat to this line of thinking is the abundant evidence of just how dry the rest of Mars seems to be. I blogged a while ago about large deposits of olivine, which appparently had not seen water in 3 billion years, sitting around on the Martian surface.

Tuesday, July 12, 2005

Afarensis on Kennewick man

Afarensis has a wide-ranging series of posts discussing the availability of the Kennewick skeleton for scientists to study. (The link is to the 3rd of a promised 4 posts.) The Kennewick remains, dated at 9000 years old, were found along the Columbia River in eastern Washington. The remains have been locked up in legal wranglings for some time but will be available this summer.

There are some indications that Kennewick's skull was of Caucasian rather than Mongolian form. Please see afarensis again for everything that can be learned from a single skeleton.

Tempel-1 collision was a real dust-up

The first data are already out about the collision between the Deep Impact probe and the comet Tempel-1 last week. The probe made a crater about 300 feet wide and of unknown depth.
Comets had been proposed to be "dirty snowballs," with water holding together a grab-bag of other materials. This has since been modified to icy dirtballs, with other materials predominating. Researchers were nevertheless suprised to see very little water in the fresh ejecta. Instead, the bulk of the material kicked out of the comet was very small-grained, on the order of talcum powder, suggesting that short-period comets might be more like interplanetary dust bunnies, stable only in the deep vacuum and low gravity of space. One interpretation that needs to be modelled out is that dessication from solar warming extended deeper into the comet than expected.

Lots and lots of observatories were watching the event, so it will still be some time before a final run-down of the insides of comets is available. Tempel-1 will return in 5 years and it may be possible to continue observatoins then.

Non-coding conserved DNA sequences- what do they do?

A recent review in last month's Genome Biology sets out the progress made in identifying non-coding conserved regions of the genome. These areas are conserved, or highly similar in the genome of different vertebrates, but non-coding, which means that they are not translated into protein. In some cases these sequences are shared between animals, like fish and humans, whose last commmon ancestor lived 300 million years in the past. Other sorts of sequences are shared between nearer neighbors such as rat and human. Both levels of conservation imply that these non-coding regions are important for survival of the organism.

Non-coding conserved stretches occur both in the near vicinity of "gene territories" and also remote from any known gene, although the latter tend to be less well conserved. It is proposed that non-coding conserved regions near gene territories help control that gene. However, early functional tests of this idea, by making mutations in the non-coding conserved stretches near the gene singleminded have not led to obvious abnormalities in that gene's activity.The review concludes by showing that at least the evolutionary distance between rat and human is near enough that at least some of the time sequences would not drift very far even without active measures (that is, under neutral selection).

A second paper on this topic from the folks at Hinxton tackles regions of DNA sequence similarity between the puffer fish Fugu and humans. Fugu has an incredibly compact genome (400 Mb versus 3000 Mb for humans), which is thought to enrich its sequences for critical genomic regions relative to organisms with big floppy genomes. Recent computer work had found about 1400 non-coding regions, conserved between humans and fugu, placed in clusters throughout the human genome. The current work took a closer look at the boundary regions around these stretches and found a sharp dropoff between the conserved sequences and their non-conserved neighbors. This pretty strongly suggests that these little regions are being actively husbanded while the genomic neighborhood is allowed to drift. Still, there's no known function.

Wednesday, July 06, 2005

More armpit research

A study suggests that dominant males' armpit sweat contains a pheremone that ovulating women find attractive. If I remember right, Austin Powers kept his mojo somewhere else...

Key conclusion: "Single women and those not ovulating were not overly aroused."

Tuesday, July 05, 2005

40,000 year old human footprints in Mexico

Via New Scientist (but also Dienekes and Orbis-Quintus ), there are sets of human and animal footprints in a fossilized lava bed in Mexico dating from 40,000 years ago. The earliest arrival of Humans in the Americas is generally thought to have been as recent as 11,000 years ago, and I have seen genetic distance modeling supporting dates (of genetic isolation from the Asian forbears) as recent as 7000 years ago. The New Scientist article makes clear that the dating was done by a number of different methods and always gave dates older than 38,000.

It sounds like people in the field are waiting for an independent confirmation of the dating results. If it's confirmed, it will upend a whole lot of thinking about the peopling of the Americas.

There doesn't seem to be any idea how the people could have gotten there so long ago.

I remember seeing that the dates for initial colonization of Australia may be getting pushed back as well.
UPDATE: Thanks to Badger minor for the Australia link.

"Tortise" and "hare" strategies in a family of infectious agents

There's an interesting short review in the June Trends in Microbiology about different epidemiology in three members of the Bortadella family . The ancestral Bortadella, B. bronchosepta, is endemic in nasal tissue of mammals, and has given rise to two highly virulent descendants, B. pertussis and B. parapertussis, both of which are unbelievably contagious and cause whooping cough in human children.

What is pretty cool about this family is the apparent tradeoffs under which all three are operating. The infectious versions can stay in a kid for about 10 days, and get spread to the next kid through little droplets expelled during coughing. In contrast, the ancestor version can stay put in wildlife for years. The review proposes that the infectious versions have become specialists in becoming maximally contagious and sacrificing their ability to live in any individual host. This strategy, like the hare in the story, increases the speed of propagation at the expense of persistence, and also increases risk of extinction- once everyone in sight (actually, coughing range) is infected, they either die or become immune, and you're left high and dry. This strategy might have become profitable when humans started living in big cities, which meant that there would be a year-round supply of fresh kiddies to infect.

The wildlife in which the ancestral form dwells never congegate enough to support an outbreak-directed strategy. The ancestral form instead follows a "tortise" strategy, with lower virulence and long persistence, giving it time to infect another target in dispersed host populations.

Human urbanization thus opened up a big niche opportunity, so much so that the jump to the "hare" strategy, high virulence/short persistence happened not one but twice. B. pertussis and B. parapertussis use different strategies to evade the human immune system, and even require different vaccinations, suggesting that the hare strategy was under strong selection no matter how it was implemented. These fast guys have succesfully competed away the ancestral form away in humans, so that B. bronchosepta is typically observed only in infants, people in contact with animals, and immunocompromised people.

Cat's Cradle

Via biology news net , this beautiful computer-generated dendogram (diagram of the lines of descent) of bacteria (grey) and archaea (green). Direct descent is shown by the vertical connectors, and lateral gene transfer (trading of DNA sequences between unrelated neighbors) is shown by the red "vines." The universal common ancestor is the yellow sphere at bottom center. This work was done by the computational folks at EMBL-Hinxton.

net of life1

Monday, July 04, 2005

Deep Impact hit the comet successfully

The Deep Impact probe successfully smashed into the comet Tempel-1. This should provoke a huge increase in the comet's brightness, just in time for the 4th of July. There will be periodic updates at

UPDATE: You can see a sort of jumpy view of the explosion here

Intra-ocular lenses

I am REALLY squeamish about stuff getting in my eye. I can (barely) handle contact lenses, but the scene in A Clockwork Orange where they were propping his eyes open had me crawling backwards out of my skin.

But I'm probably going to need bifocals pretty soon. Thus my interest in this article about implanting lenses directly. The technique was developed first for people with cataracts but can be used to correct far-sightedness.

I'm not sure how this should compare to LASIK.

Sunday, July 03, 2005

German Summertime Beer Myths

As Bavarians get ready to swarm the beergardens, the German site t-online is running a list of beer myths: (Take this with a grain of salt. I put in my own commentary with the rough translation)

1. Beer makes you horny: they say it's false.
2. Beer protects from hearing loss: They say it's true. If you drink 4.2 liters a week, you reduce the risk of old-age hearing loss by about 40%. The scientists (Americans- hah!) speculate that the health benefit comes because of improved circulation in the inner ear. If you really want to keep your hearing, stay away from Oktoberfest.
3. Beer is unhealthy: they say it's false, citing antibacterial activity and cardiovascular benefits. Yeah, that's right. It's a health food. (see below)
4. Beer is only for men: Although women might avoid inferior stuff, German beer brewed according to the Reinheitsgebot is naturally loved by everyone.
5. Beer leads to a beer-belly: False. You have to have the genetic tendency. Yeah right, it just happens that college-aged men all have the same genes. And even though it's only genetic, the same web page nevertheless links to a list of stomach exercises to get a washboard stomach. Presumably so that people who have both genetic tendencies can change their bellies back and forth.
6. Beer makes you hungry: true.
7. Beer is good for skin and hair: Ok, this is getting ridiculous. Beer has B-vitamins and minerals from the yeast. That's why drunks are famous for their glistening skin.
8. Beer improves (increases?) your circulation: True. Think flushed faces.
9. Beer makes your bones stronger. A single glass has 40% of your daily silicon. Look elsewhere for silicone.
10. Don't drink beer after wine: Doesn't matter anyway, you slob.
11. Wheat beer (Hefe) gives you headaches: This is personally true to me (maybe it's the company I keep). In any case they say it's false.
12. Beer makes you fat: they give a rundown of the relative calories. Wine has more per glass. But who drinks beer by the wine glass?

Friday, July 01, 2005

Just give me the cancer

Apparently the herb rosemary has antioxidant properties that could decrease the creation of carcinogens while grilling meat.

No way. I hate rosemary.

Copy number polymorphisms in the human genome

total sequences in human genome database
Total number of sequences deposited in the HTGS domain of GenBank as of 2000. Up-to-date numbers are here

I may need to start a separate blog just to keep track of genomic studies. The synergy between reduced sequencing costs and strategies and increased computational power has meant a surge of information about the human genome. More is known about the human genome than any other animal's, and possibly more than any other eukaryote. This has allowed people to ask very basic questions about the DNA content of such an organism, such as the level of diversity which exists among individuals of a species. I think lots more suprises are in store in just the next few years.

A review in the subscription journal Trends in Genetics talks about yet another category of variation: small changes (as small as 200 bases insertions and deletions) in the DNA sequences of normal humans known as copy-number polymorphisms (CNPs). Up to 200 such human CNPs have been identified in just two recent studies. The field is in its infancy, so there are no estimates how many would be expected in the genomes of humans. But analysis of this category of variation will complement the more famous single-nucleotide polymorphisms (SNPs) in population studies.

Complex origins of Homo Sapiens

John Hawks talks about some interesting complexities coming out of human genome studies. In a series of posts (for example here and here ) he discusses data suggesting that Homo Sapiens did not originate as a single interbreeding tribe (they were not panmictic ). Rather, there are portions of our genomes-- plural intended!-- which have been genetically separated for even a million years, i.e. last recombined before Homo Sapiens was a species.

The evidence is coming from the avalanche of high resolution data about human genomic variation. Over time, genome differences can occur in any organism via mutations, and if they do not interfere with survival, they can be kept in the descendants. In most cases, genetic mutations which occur far enough apart on a chromosome will tend to get exchanged between pieces of DNA, via a process called recombination . What is critical here is that recombination only occurs between chromosomes inside the same individual. If a group with a new variation never interbreeds with the main group, the variant and original chromosome will never "see" each other, and recombination will not occur.

Several groups studying small chromosomal regions (about 20 kilobases of sequence) find that tandem strings of differences have been preserved, thus that recombination has not occured. In the second case discussed by Hawks, two individuals in Africa were found to have a ten-step difference in a region of the X-chromosome relative to the more common allele. Recombination among the 10 differences had not occurred, even though the more common allele was obviously capable of recombination with other versions.

So, as Hawks says, the very low likelihood of observing this result under panmixia indicates that it is likely that parts of the ancestral population were out of genetic contact for some period of time. Additional data would be required to place these observations along the continuum from a highly dispersed population to admixture (breeding) between fully differentiated subspecies. The authors of the study are going for the latter end, and Hawks thinks support for this idea may reach a tipping point in 2005. The authors say "This inference supports human evolution models that incorporate admixture between divergent African branches of the genus Homo--" i.e., it is consistent with the idea that genetically divergent hominids interbred within the ancestry of Homo sapiens. In any case, the clean Out-of-Africa picture of a single interbreeding tribal origin of Homo Sapiens is in trouble.

Carl Zimmer on genetic clues to language

Carl Zimmer at the Loom has a nice summary of recent progress understanding the genetic basis for human language. FoxP2, a gene which is mutated in people with specific language difficulties, has a homologue in mice and chimpanzees (although the human variant seems to have been under intense selective pressure). Mice lacking FoxP2 show deficiencies in their communication via squeaking, suggesting that the evolutionary toolkit necessary for the emergence of human language has been around for a long time. (The exact brain deficiency in these mice does not appear to match the deficiency in humans with language aphasias).

The second half of his post concerns a better understanding of Broca's area, the area thought to be responsible for human speech. Monkeys have a similar area, and stimulation of this brain region elicits mouth and tongue movements. Again, the raw materials which natural selection has acted upon in humans seems to have been in place for a while.

What's that Twinkie going to see?

Via metafilter, a photomontage taken by a microcamera during its journey from mouth to anus. It seems to have come with its own flashbulb.

You have to scroll horizontally to see the images. The first one, just prior to ingestion, is looking up the guy's nostrils.