Wednesday, June 29, 2005

"The only depressing thing is that the representation is very small."

The Register reports that a German researcher has located the spot in the sensory region of the brain which corresponds to stimulation of the penis.

Also worth a look is Pharyngula's February treatise on the mechanics-- with diagrams: "it's all a glorified water balloon." Don't miss the comments section.

31st Tangled Bank is up

The 31st Tangled Bank carnival of science writing is up over at Science and Sensibility. Enjoy!

The New York Times on filesharing as a culture

John Markoff at the Times has an article today about Flickr and other services which use internet connectivity to share information in novel ways. As Jeff Jarvis at Buzzmachine continually emphasizes, the trend is that consumers will have more control over content (and businesses had better build that into their plans). Here's Markoff:

Indeed, the abundance of user-generated content - which includes online games, desktop video and citizen journalism sites - is reshaping the debate over file sharing. Many Internet industry executives think it poses a new kind of threat to Hollywood, the recording industry and other purveyors of proprietary content: not piracy of their work, but a compelling alternative.

What I love is "citizen journalism sites"--- by which he means blogs, and by implication the gaping holes blown in the Gray Lady's deck. The whole rest of the article continues with this sort of malapropism, as if Markoff is trying to describe the ivory-billed woodpecker from some third-hand account (or holding a piece of roadkill at arm's length). C'mon, it's not that hard! The Washington Post does really fine at this.

The article I really wanted to read from the Times was how is the Grokster decision going to affect the setpoint between open and institutional content. I guess I'll go to Slashdot to find out.

UPDATE: Jeff has already jumped on this.

UPDATE#2: Wired talks about inclusion of copywrighted sounds in a podcast. If Apple points you to the podcast, is that incitement?

More generically, I cut and past images, and others publish long quotes. I frequently write about science ideas which are behind subscription walls. Is Blogger.com guilty of incitement? Am I?

Mini-me: a brown dwarf solar system

Mini me solar system
(Credit:NASA/JPL/T.Pyle)

From the NASA homepage, the size of a brown dwarf solar system relative to our own. The star, OTS 44, is only 15 times the size of Jupiter.

Tuesday, June 28, 2005

Space.com user-submitted astronomy pictures

Space.com has an ongoing site with user-submitted astronomy images. You have to click on the photographs to get the captions, but it's worth it.

LINE retroposition yields instant regulatory pair

This is going to be a pretty technical post, but I do think the idea of what's going on is fairly cool. In layperson's terms, there are small pieces of DNA called LINEs in the human genome which carry the information necessary to move a copy of themselves to a new location in the genome. You could think of it as a short stretch of computer code which includes instructions to copy itself elsewhere inside a software program. This jumping, or "retro-transposition," by LINEs occurs very rarely in normal cells, and is basically like a parasite inside your DNA.

The really cool part about parasitic interactions is that they frequently are under evolutionary pressure to become symbiotic relationships. In situations of mutual benefit, the host then has less of a burden, and the parasite gets a happier host. A recent paper in Trends in Genetics shows that some LINEs have actually been subverted by their mammalian hosts into an instant regulatory mechanism. LINE derived micro-RNAs (miRNAs) can dock to existing LINE integration sites, which are frequently found in the 3'UTR of RNAs. This is like adding a new control button (if the host can harvest the opportunity).

miRNAs, which seem to be the topic du jour in the genomics world, are very short pieces of RNA which can control several aspects of regular messenger RNA biology including translation into protein and subcellular localization (for clarity, I will refer to messenger RNA as "messages"). miRNAs accomplish this by docking to very short sequences, which typically fall in the 3' untranslated end (the RNA sequence after the part which codes for protein) of the message. A given miRNA can recognize many target messages, thus bringing a whole set of genes under a single control.

As it happens, the 3'end of messages is also a region where LINEs can insert without damaging the protein, and this in fact is very frequently observed.

What is new about this paper is that mammals have evidently turned parasitic LINE integrations into an opportunity for transcriptional control, by converting sister LINE sequences to make a LINE-derived miRNA. Because the parasite copies are distributed in many places, the LINE-derived miRNA instantly matches a whole set of targets. And because the miRNA machinery is well established for other short pieces of RNA, the whole control module can be plugged in to an existing infrastructure. What was a bug, has become a feature.

"AMA to Seek Limits on Tanning, Video Games"

The American Medical Association is concerned as always about "our nation's most precious commodity." But aren't these two activities mutually exclusive?

Monday, June 27, 2005

Siebenschläfertag

June 27 is the German version of groundhog day. If it rains on seven-sleeper day, then it will rain for seven weeks more. The etymology supposedly derives from seven saints who slept in the cave of Ephesus for 195 years. But confusingly, a siebenschläfer is also a squirrel-like rodent which is active only in the summer months.

In any case it was sunny today.

Supreme court rules unanimously against Grokster

No comment yet, I just saw the Washington Post article.

"We hold that one who distributes a device with the object of promoting its use to infringe copyright, as shown by the clear expression or other affirmative steps taken to foster infringement, is liable for the resulting acts of infringement by third parties," Justice David H. Souter wrote for the court.

Word elsewhere is that pay-for-play services like iTunes will benefit greatly. A detailed who's who (written before the decision) is at ZDnet .

Helps you grow 9 ways

Doc John at World of Psychology enumerates the 9 different flavors of love. He's a little disappointed in the study being discussed, as they only interviewed about 50 people.
My personal favorite, not listed in the big 9, is Hassliebe (literally hate-love), the German expression for tough love toward children.

A quick look through Shakespeare or Pedro Amoldovar would probably yield a few more flavors.

The original story, in the Guardian, is here.

Keeping it simple at Pharyngula

PZ Meyers talks about the search for the earliest metazoan, the common ancestor of all animals. Maybe this common ancestor looked like one of the simplest animals surviving today, trichoplax .

Sunday, June 26, 2005

Ancient carbon... and modern artefacts

Science Now links to an article to come out in Geology magazine giving evidence that one class of diamonds is formed from biological residues. The Jagersfontein kimberlite formation, which is in a mine in south africa, originated near the earth's surface and was subsequently subducted by plate tectonics to about 250 km deep. Diamonds isolated from these rocks have a Carbon12/carbon 13 ratio consistent with living things, indicating that the carbon was already there at the time the rocks were laid down. The abstract says that shallower-forming diamonds do not show this skewed ratio.
Basically what goes down must come up, geologically speaking.

Also in last month's Geology was the finding of kerogen streaks in 3.2 billion-year-old slates. Kerogen (wikipedia) is a sort of precursor wax to oil deposits, and to see it in these shales suggests widespread microbial life at that early stage. I have written before about the difficulty in finding proof of the earliest life on earth.

And, as long as we're handing out wet blankets, a review in May's Trends in Microbiology takes Occam's buzzsaw to about 20 reports of very ancient DNA being recovered from amber, salt crystals (ouch!) or stone formations. They don't like any of them. What's the fun of that?

Friday, June 24, 2005

"Male sweat makes men opt for a manly read."

Via Marginal Revolution, the New Scientist is reporting that pheremones affect men's buying preferences. A compound present in armpit sweat leads men to rate mens' lifestyle magazines more attractive and even to buy them with greater frequency.

No word yet on sock odor.

Are you gonna eat that?

Via Boingboing, , the shelf life of assorted foods, including brown sugar and tabasco sauce.

Meanwhile, at the urban myth-debunker Snopes, it is revealed Twinkies are not immmortal. They're only fresh 'n' tasty for four weeks. However-- write this down, folks-- they will explode if you microwave them.

Thursday, June 23, 2005

Elusive Earths

There's a nice interview at Spaceref.com with planet hunter Geoff Marcy of U Cal Berkeley. Marcy thinks that rocky smallish planets should be formed with good frequency by any star that originated in a dusty disk-- that is, most stars.
In the hunt for planets, they are monitoring 1300 stars for velocity perturbations (i.e. gravitational tugs, from planets or other things) and they think that 5% are showing wobbles, with 85% of those not having a Jupiter-sized object-- thus possibly smaller objects closer in.

With all of this looking, maybe someone is looking back...
118733main_image_feature_353_ys_4
Dust cloud around Formelhaut. Dust has been swept clear near the star, possibly by a planet. (NASA/ESA)

Wednesday, June 22, 2005

"Better a teacher in Omaha than an Upper East Side internist."

William Bernstein at Efficient Frontier thinks there's no housing bubble. It's just that places like California and Boston are attracting disproportionate numbers of high earners.
Doesn't make it any more fun to look at prices though.

Here's a pretty grumpy renter's eye view of the housing boom. I think it unwittingly reinforces the idea that you've gotta buy no matter what the market is.

Tuesday, June 21, 2005

Photosynthesis on Europa?

CGD

I've seen a news item in several science pages about photosynthetic bacteria isolated from deep vents. The vents are so deep that surface sunlight must be negligible; instead the bacteria must be using the faint light emanating from the hot vents themselves. This electron microscope picture (from Beatty et al. )shows the light-collecting device as pale spots near the surface of the bugs.

Finding these bacteria growing in such low light suggests that the lower light limit photosynthesis organism might be very, very low. Even Jupiter's moon Europa might be bright enough. Wow.

UPDATE: Very nice writeup over at The Loom , who, in turn links to Alan Boyne at Cosmic log a MSNBC blog. (The cosmic log link is a bit dodgy; his entry is June 20. )

Seems that everyone took the scanning EM picture of the bacteria. I like the transmission EM better because it shows the antenna structures. Thinking a bit more about this, I think the amount of sunlight falling on Europa is almost besides the point. If hot vents are glowing, then photosynthetic life can be anywhere that has vulcanism and liquid water.

UPDATE#2: Oops, the way Carl and others write it, Europa is chosen as an example of buried hydrothermal vents. I'm not sure where I got the idea that sunlight levels were part of the argument... speak in haste, repent at leisure.

Tesselations

Via metafiler, this is a really lovely site with some animated tesselations. Tesselations are the style of drawing in which a plane is covered by interlocking images, as made famous by Escher. I really get sucked in watching the tesselated planes move in these demos. My favorite (unfortunately a bandwidth hog) is fish swallowing fish .

"Girl of Uchter Moor"

The German news site t-online.de has a news item about a 2500 year old girl's body found by peat harvesters in a moor near Hannover, Germany. Apparently the remains are in amazing condition (the harvesters called the police, thinking it was a murder victim) and there may be more in the vicinity of the find. There's not much else to the blurb, although there are some photos.

UPDATE: The news is appearing in the German press now. A slightly longer story, evidently relying on the same press release, is here.
UPDATE#2: An English version is available here .

It's what you eat

There's an interesting article and synopsis at the public access journal PLOS Biology about the effect of diet on fly longevity. Many organisms live longer if they are fed a restricted diet; in the case of mice the optimum seems to be cutting intake by about a third of their free intake. However, some recent data from the centers for disease control suggests that the link between human intake and longevity may be complex.

The current effort studied the mix in the diet on fly lifespan, by varying yeast (a source of protein and fat) and sugars. The authors found that reducing yeast honly as a more pronounced effect than reducing sugars only; although the best effect was seen when both were reduced.

Dietary studies always remind me of Woody Allen's Sleeper. I eagerly await news that steak is the secret for long life.

Monday, June 20, 2005

Human genome is a plural noun

There are a few recent genetics items which suggest that human brains have much more genetic diversity than the initial human genome release would have suggested. I have blogged before about aneuploidy (loss or gain of chromosome)which occurs in suprising numbers of normal mammalian brain cells, and the hints that these altered cells contribute to brain function.

More recently a human genetics meeting at Cold Spring Harbor was full of reports of fine-scale (up to several hundred bases) variation in DNA of normal humans, in some cases even affecting the copy numbers of whole genes. (The best known of these blips is a short inversion in chromosome 17 found in Icelanders by DeCODE genetics.) Some variations affect the interactions of humans with their environment-- including the immune and nervous systems-- and appear from population genetic data to be undergoing natural selection.

And lastly, in a topic which I hope to finish reading (and maybe blogging) this week, a really astonishing report in Nature last week that small pieces of DNA known as LINEs relocate themselves (Nature link) in the mouse nervous system. The sequences "jump" out from their place of origin and re-insert, frequently near genes which are active in the nervous system, changing that neuron's DNA relative to its neighbors. This means that even identical twins will not match between neurons and DNA content. (This was already known to be true for female identical twins because of differential inactivation of the X-Chromosome. What makes LINEs different is that the genetic variations are potentially a whole range of flavors rather than binary.)

Microarrays and the professional touch

There's an interesting commmentary in Nature Cell Biology this month about the sources of variability in microarray studies. Briefly, microarrays (Wikipedia entry) are arrays of spots of short stretches of DNA (it can be other substances as well). Each spot is designed to be complementary to (match; but more importantly, to bind) the product of only a single gene. Using some care, you can put on a complex mixture, and the fluorescence seen at each spot will correspond to the level of expression of that gene. The fluorescence is read by a digitizer directly onto a hard drive for analysis.

The promise of this method is that, in principle, it vastly multiplies the genetic description associated with a particular condition, and specifically brings in the chance that something completely unexpected will fall out of the description of a known cell state. The difficulties have been information management issues and, more importantly, lack of agreement between studies, especially when different hardware is used.

The recent comment in NCB reviews some progress towards standardizing this method toward increasing agreement between different conditions. I think the results won't shock anyone- some labs are able to do the same work on different platforms with good reproducibilty, and others cannot. The articles cited in the comment have a set of procedures affecting both sample preparation and initial data analysis which seem to improve reliability. Although it's really nice that the hardware is not always to blame, it still suggests that microarrays are not going to be nearly as portable as PCR. Perhaps they need to be ceded to big centers just as cDNA cloning is effectively done now.

In my end of the field, people are using microarrays as a screen to identify new genes, which are then followed up one at a time. Given all of the work that needs to be done even once you've gotten a good read, I have heard some thoughtful people suggest you'd be better off picking an interesting sequence at random.

UPDATE 22 June: Ouch. A paper in this weeks' PNAS takes down a prominent Nature Genetics finding from 2003. Ramaswamy et al. compared tumor tissue to healthy tissue and concluded that the metastatic potential of the tumor is contained within the bulk of the cells, a conclusion with pretty big therapeutic implications. The PNAS work goes over the raw data and suggests that this conclusion is highly dependent on the exact threshold chosen while reading in the fluorescent chip. (The link to Ramaswamy et al is the PubMed entry, which shows the paper had attracted some flack already.)

Friday, June 17, 2005

Fossil photo gallery

Bundenbach_Furcaster_palaeozoicus_4t from virtual fossil museumFrom Science Netwatch I got a link to this fantastic online fossil museum. .
This is a fossil starfish, Furcaster paleozoicus, from Bundenbach Germany, about 2 inches across. The specimen is owned by John Adamec.

Google Scholar gets the slashdot treatment

Over at slashdot there's a very lively discussion of how Google scholar shapes up against other academic search engines, free and subscription.

The starting point is this review by Thomson Gale corporation, which concludes that other free services and some subscription services (by coincidence including two Gale products) do a better job. Google is popular because of a combination of hype and "laymen's ecstasy," which must be either a fungal infection or a very attractive controlled substance. If you can't guess my opinion of the review yet, take a look at this quote:
The problem may be that Google developers have been working smart and hard to make heavy duty software excavators that dig up useful data from unstructured masses of data from zillions of Web pages. They were great for discovering the Web landfill, but not for digging scholarly archives — just as heavy duty excavators are inappropriate for archeological digging of Mayan tombs instead of tiny pick axes, chisels, shovels, trowels and brushes to extract, clean, bag and label the finds.
This begs the question of how the preciousss tombses are located in the first place. Has this guy never seen a field survey? We're talking about search, aren't we?? Moreover, this tone, which is used throughout the review, comes off like the anal-retentive chef in a new calling, and leaves me seriously wanting to ignore their products.

This is the kind of topic that slashdot does best, so it's worth reading the whole thread. I think the main meta-conclusion is that there is a LOT of interest in academic search-- so, if nothing else, Google is onto something. In terms of the specific debate, I use google scholar alongside the main free biology database ( PubMed ) and usually find what I'm looking for. The main limit on both of these is that electronic versions of anything published before about 1996 are nearly absent.

Thursday, June 16, 2005

Homo Floresiensis in limbo

Carl Zimmer at the Loom has another update about the hobbit fossils from Indonesia. The remains, potentially beloning to non-human hominids which lived up until very recently, have become the focus of a prolonged dispute between the mainly Australian discoverers and an eminence grise of Indonesian paleontology. Zimmer is taking the side of the Australians, although John Hawks (homepage appears to be down, sorry; the exact entry at the dead weblog was here ) has expressed doubts that the single hobbit skull can be assigned to a different species.

I think the worst part is that the digs have apparently been suspended, so that possible additional material is just going to have to sit there. I hope they've sealed the site!

UPDATE, 17 June: Carl at the Loom has another post on the topic adressing some specific reservations. The tiny fossils have been proposed to be dwarf homo sapiens, but there has been some concern that human brains should not become smaller with evolutionary pressure. Carl gives the counterexample of bat brains.

Meanwhile, John Hawks, who claims that he's not dead (see the comment), discusses some other fossils found in the same dig the Flores site. Remains of Stegadon, a now extinct relative of elephants, were proposed to also show dwarfism, giving the impression that the whole island ecosystem favored hobbitry. Hawks cites a recent paper suggesting that dwarf Stegadon had already died out prior to the dates of the hominid find. This counterclaim weakens the whole evidentiary heft of the fossil bed, and specifically the claim of multi-species, hence widespread, dwarfism on the island during the epoch in question. (For a flavor of the original logic here's the 60 minutes page. )

By the way, Stegadon also appears to be the name of a battle lizard from a role-playing game. That's Google for ya!

At the end of the day, the best way to settle the confusion is to continue digging and to quit with the role-playing games.

Wednesday, June 15, 2005

Rocket propelled bacteria

I came across this incredibly cool proteobacterium while reading up on genomic work. M. Xanthus changes its behavior from single bugs to "swarms" depending on food conditions, so people are looking at which genes are active during which behavior.
But I couldn't get over this organism. Starving M. Xanthus , like all Myxococci, will gather together into a fruiting body of about 100,000 individuals (a movie is available at the link). But M. Xanthus can also behave as a predatory swarm, which can glide across surfaces (more movies). During swarming, the colony starts to secrete all sorts of antimicobial substances which help with predation.
Sometimes individuals break off from the swarm in so-called adventurous motility. (social motility involves contractile ripples within the aggregate). Adventurous motility is accomplished-- I'm not making this up-- by a slime rocket. The working model is that slime accumulates inside the nozzle; gets wetted from outside, and the force of swelling expels the slime, providing propulsion.

slime rocket
Taken from Wolgemuth et al., Curr Biol 12:369 (2002).

Wow, see what I missed by taking neuroscience?

Computer based gene-hunting

Genomic DNA sequencing has been following its own version of Moore's law: the price is dropping while the quality (length) is increasing. (Meanwhile methods are also being used to assemble shorter reads.) The result is a jaw-dropping increase of incoming data, comparable to particle physics. Take a look at the physical plant needs for the Sanger Institute .

Also racing along, but not exponentially, are the methods for analysis of the raw sequence. In particular, although many genes are known, there are few absolute methods for predicting genes directly from the sequence. This is made a bit harder by phenomena like pseudogenes, which were likely once functional and thus have a lot of the sequence features expected of genes. Secondly, although there are reasonably shared features for the start of a gene, eukaryotic messenger RNAs are spliced together from pieces that can be far apart, and prediction of the exact splice sites has been very hard.

A recent set of papers from the Brent lab (an open-access article here describes analysis of chicken gemonic data) has evaluated TWINSCAN, a computer method with specific improvements in splice site prediction. The improvements from TWINSCAN derive by side-by-side comparision of two related organisms, since the splicing sites are likely to be preserved. The approach is sensitive to exactly how related the two organisms are: too close, and too much sequence will be identical, but too far, and genes will have diverged from each other. What is important here is that the main information are the genomic sequences themselves, and not accessory databases. It's all sitting on the hard drive. The level of computation required is daunting; but computation has in the best case the capability to scale up, wherease bench annotation still has to be done by us linear humans.

Once a hit comes up from TWINSCAN the Brent lab confirms that the predicted sequence is actually made into mRNA. They used RT-PCR. , a variant of PCR used for detection of RNA.

Their best case, which is what caught my eye, was comparing C. elegans to C. briggsae. These are two species of nematodes studied by geneticists. In this case, the TWINSCAN side-by-side computation of raw genomic data yielded predictions corresponding to 60% of the known genes, and predicted additional regions (later confirmed) which had not been predicted to be genes before.

Although TWINSCAN is efficient, the Brent lab themselves seem to use more than one program (ENSEMBL etc.) to predict genes, with the highest confidence being given to genes predicted by more than one analysis. A particular question which I didn't see addressed by TWINSCAN is the issue of splicing variants, in which different series of snips are stiched together from the DNA sequence. On the whole, though, I think these are interesting days for gene-hunters. There's quite a lot to be found by hunting the raw reads which are already sitting in the public databases.

Monday, June 13, 2005

Cave Bear DNA from a bloody mess

There has been an interesting story in Science Express earlier this month about being able to get sequence from a cave bear fossil (Nature subscription link; SciAm free link is here despite massive contamination with more recent DNAs. Cave bear fossils (and hobbit, and Neanderthal, by the way) are commonly found in cave floors, at more-or-less cave temperature, which is pretty rough on ancient DNA. Worse, the really interesting cavebeds have mixtures of different fossils overlaid by whatever microbes and more modern DNA contaminations happened by. To date, methods of recovering ancient DNA have relied on PCR amplification, which unfortunately prefers to amplify modern contaminating DNA. Thus recoveries have been limited to a few favorable instances, and usually targeted mitochondrial DNA.

In this work, they got around these twin problems by basically sequencing everything without PCR amplification, and then sorting out what came from bear by computational comparison with the recently completed dog genome (they still needed to be very stringent about excluding modern dog DNA from the analysis lab, still a much easier job than keeping microbes out. Some matching stretches were 90% identical to dog genomic entries.) They were able to use some computational tricks to identify additional, divergent stretches as very likely coming from bear. In all, they think that about 6% of their sequence is the genuine article.

Although Nature and SciAm are hyping the computer tools used, I think the real hero here is the improvement in cloning, the step in which foreign DNA fragments are molecularly joined to other stretches for preservation by bacteria. That they recovered 1000 little pieces to sequence from a single tooth just blows me away. They think they could get 10x coverage of the cave bear genome if the sequenced everything from this one tooth! It also doesn't hurt that sequencing is dirt-cheap these days either.

The point for these workers is the proof-in-principle that Neanderthal remains could be sequenced. There remains the problem of keeping modern human DNA out of the mix.

Friday, June 10, 2005

What were dinosaur spikes for?

Like Goth mall rats, plant eating dinosaurs sported lots of crests and spikes , but no one can be sure what good it did. Work in last month's Paleobiology takes a look at the stegosaur family. Their bony plates have been variously proposed to have been used as defensive weapons or heat exchangers, but they are actually poorly built for either purpose, being hollow (not good defense) and lined with apparently blind-ended blood vessels (not good for heat exchange). Support for these two ideas got even weaker in this work, when scientists considered the stegosaur ancestors. The ancestral plates lay very close to the skin and would not exchange heat at all, and were already hollow, arguing against an armor function.

The scientists propose that only use that makes sense is that these structures were for display, possibly for conspecifics to recognize each other. A reservation about this is that these things took a lot of energy to make. It's hard to believe that they were only an identifier. Couldn't they have worked out a secret handshake? For example, ants do it with odor.

There are lots of examples, including some very expensive ones, of males peacocking it up for sexual advantage; but stegosaur plates were similar between males and females.

Still, kooky exteriors are so widely seen in dinosaurs-- from the ceratopsians (spiky frills) to the hadrosaurs (head crests)-- so maybe species recognition was harder for them to accomplish than most.

UPDATE, June 14: Sort of an aside, but the turtle's shell seems to result from co-opting of the genes responsible for the arrangement of the ribs in other animals.

Consensus failures at Wikipedia

Via Blogdex, Wikipedia carries a list of its lamest edit wars ever. Since Wikipedia is a group effort encylopedia, with multiple levels of permission to edit, it can be very tough to arrive at a consensus on burning issues as to whether potato chips ought to be "flavored" or "flavoured." (Answer: seasoned.) I am drawn to ideas relying on community input, but there are hazards to this approach.

Thursday, June 09, 2005

Spamalot

Via Slashdot, a really interesting discussion of how Jef Poskanzer, owner of the "Acme.com" domain and spam magnet, deals with the millions of spam emails he receives per day . The filters and ideas he talks about foil spammers by mucking with their desire to transmit at random and in volume. Just forcing all incoming emails to wait for 5 seconds during SMTP (a greet_pause) seems incredibly effective.

"Galactic Gradients, Postbiological Evolution and the Apparent Failure of SETI "

I always get a kick out of theory-of-everything papers. This title seems to cover a fair amount of ground in a short space. The public-access article is 30 pages, with two figures.

The idea they're picking up on is that maybe SETI is looking for the wrong sorts of things. Specifically, the most advanced civilizations would be characterized by machine intelligences, possibly persisting long+wide after their biological forbears had snuffed themselves. (This includes a pretty loony discussion in which the fact that humans haven't immolated themselves, 60 years after inventing nukes, is used to strengthen the argument that civilizations don't always self-destruct. Glad to hear it.) Thus the information content of advanced civilizations makes an easier (spatially more dispersed, longer lasting) target for long-range detection than biosignatures. Information storage, per se, has different constraints than carbon soup, and might be seen in different places than terrestrial environments.

But I'm still confused. I thought the SETI project was searching for nonrandom radio signals (think Leave it to Beaver, starring Wookies). Won't the dispersed machine progeny need to communicate with one another, that is, via radio signals? I can't understand which assumption of SETI is undercut by this admittedly very interesting idea.

UPDATE, 17 June: I REALLY hate to bring this in, but this discussion of Star Wars touches on the same points about civilizations on a galaxy scale. Bottom line: machine intelligences will be doing the civlizing, thank you very much. Bio-intelligences have too long generation times.

Wednesday, June 08, 2005

MARSIS radar to look for deep water

The MARSIS radar experiment aboard the ESA's Mars Express satellite will come a bit closer in late June when the second dipole boom is deployed. These 20-meter-long structures will send very low frequency waves which will penetrate up to several kilometers deep. Reflections will indicate any sub-surface interface, including possible water or ice deposits (a nice diagram is here. ) Subsurface water is the best chance for life on Mars, as surface uv irradiation is very intense.

The antennae had been loaded in a telescoped configuration and there has been a fair amount of hassle getting the first one fully extended. What I especially appreciate about this saga is how it underscores that machines in space do not always behave as predicted in ground testing, so there's quite a lot of seat-of-the-pants adjustment going on.

Subsurface water may also be all there has been on Mars for some time. Some other work suggests that the atmospheric methane detected on Mars might be coming from breakdown of olivine by water. This "mineral source" (rather than microbial source) theory of ongoing methane production would require that the olivine had been kept dry since its creation in lava flows-- in this case, some 3 billion years. But in that case, where's the water coming from now?
UPDATE: More on the recent olivine-methane work is in last week's Nature .

UPDATE, 16 June: The second boom deployment seems to have gone smoothly but the gyroscope data are not yet in. Looking for water could start as soon as next week.

Monday, June 06, 2005

Pig genome to come out

A Chinese-Danish consortium will soon put the pig genome online. I can't help asking: was it a capitalist pig?

Jetlag

I'm more or less back at it today after a very addled few days. I was happy to see jetlag is making the news . It seems that shifts of 6 or more hours are especially tough because they can jar two parts of the superior chiasmatic nucleus "clocks" out of sync with each other. I have seen mention that you can reduce jetlag by changing the timing of your meals . I presume you wouldn't be allowed to have anything but beer and nuts, the Hitchhiker's Guide diet.

What is hardest for us is travelling with the kids, who seem to absolutely randomize their clocks (also relative to each other) for shifts of this size.

The best cure of all is taking lots of naps. You need a scientist to tell you that?