Monday, November 28, 2005

Open access- the Royal Society says go slow

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.

Sunday, November 27, 2005

Bad Vibes

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.

Friday, November 25, 2005

Ah, the good old days

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.

Thursday, November 24, 2005

Stem cell star resigns

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

Thursday, November 17, 2005

A tutorial on short chromosomal duplications

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

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.

Wednesday, November 16, 2005

Dalai lama at the Society for Neuroscience

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

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

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.

Monday, November 14, 2005

Forensic identification of human remains

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

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

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?

Friday, November 11, 2005

Proposal-writing blues

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.

Tuesday, November 08, 2005

Search engines for medical information

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?

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.

Monday, November 07, 2005

Me Tarzan. You Jane.

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.

Sunday, November 06, 2005

Giant shoulders, held aloft by others

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.

Saturday, November 05, 2005

How Advanced Can a Civilization Become?

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.

Friday, November 04, 2005

Clay as a scaffold for the origins of life

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?

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.

Thursday, November 03, 2005

Who's your daddy? Use Google to find out

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?

Friday, October 28, 2005

Worst jobs in science

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."

Thursday, October 27, 2005

Tell it to the hand!

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.

Wednesday, October 26, 2005

Long nursing period for mammoths

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

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.

Tuesday, October 25, 2005

NASA - Crop Circles in Kansas

Crop circles in Kansas

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.

Monday, October 24, 2005

The psychology of a cluttered desk

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

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.

Saturday, October 22, 2005

1st Avenue Machine short animations

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.

Friday, October 21, 2005

Islands as the last resort

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

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.

Thursday, October 20, 2005

Slate bashes the Human Genome Project

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

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.

Monday, October 17, 2005

ADEPs: A possible new class of antibiotic

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.

Sunday, October 16, 2005

New science page at Ars Technica

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)

Friday, October 14, 2005

Little Chucky Darwin

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

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!

Wednesday, October 12, 2005

Another hobbit fossil- a jaw

Head over to John Hawks for a peek at the latest fossil finds from Flores. A new jaw will be reported in this week's Nature-- and of course teeth can tell you an awful lot about their owner. It's still early days, but the fossils taken together suggest that hobbits are a very deep off-branch of the hominin lineage, with australopithecines (Lucy and co.) being the last shared ancestors with H. Sapiens.

And folks in Germany are trying to get DNA reads from the fossils! This could get really interesting.

Friday, October 07, 2005

6 degrees of Kevin Bacon

A post over at Crooked Timber talks about a new book raising doubts that the author of Shakespeare's plays was W.S. himself. This week's champion ghostwriter is Henry Neville.

What I liked about the discussion is the very learned comment thread. About midway down, an unexpected connection develops between the latest Shakespeare debunkers and--wait for it-- the Intelligent Design movement.

The detective work is all done by bloggers in pyjamas, wielding Google--which is, after all, mightier than the pen.

Thursday, October 06, 2005

First we take Manhattan

For people who still believe this kind of thing, Slashdot is talking up blog money. Yeah, right, the check's in the mail.

Some funny comments though.

Spongebob

135041main_PIA07740-516

This is Saturn's moon Hyperion, as imaged last week by the Cassini probe. Cool...

Tuesday, October 04, 2005

Why do folks order a smaller soda at the drive-in?

Via anthropologi.info , a cute story from this summer of a commercial anthropology detective story. Coca-cola had noticed that people consistently ordered a smaller sized drink at McDonald's when they used the drive-through compared to indoor customers. They couldn't figure out why, so (cue Indiana Jones) they hired an anthropologist.

Coke had already ruled out my first theory, which was fear of greater spillage (Ah, fatherhood: never pour more liquid than you're prepared to see on the rug.)

Of course, the best approach would be to interview the drive-in customers, but they're by definition going somewhere, which makes them impatient. Also, the author decided to dress in a suit and tie, which was off-putting:
So most of your interviews last about 22 seconds. It is hot, very hot. It is so hot that I am soaked right through and my camera person, Suz, has discovered that the sun block has run off her forehead into her eyes and she can barely see. At this point, we aren’t getting very much more on camera than we are in the interviews.

The answer (kept secret in the post) was arrived at intuitively, and has something to do with cooking in the sun. So the anthropology part of collecting data failed to contribute.

The point of the post was the frequent impracticality of jamming a camera in someone's face in order to get data. The anthropologist needs creativity, and a bit of humility in interviewing people: they are the expert and you are the supplicant.

Looks like this story was trackbacked by Kottke a while ago...

Potato origins

A paper to appear in PNAS this week uses genetic data to argue that Potatoes were domesticated only once in the region around Peru.

The pedigree of modern potatoes can be traced back to 1562 in Europe, but the ancestors of that crop could have been either one or several sources in South America. There are certainly two clades among modern cultivars which can be distinguished both genetically and based on things like daylight adaptation. The favored theory, until now, has been that these clades in fact are of ancient origin (representing independent domestication events), possibly introduced to Europe (and the world) by necessity. The 19th century potato blights, by this hypothesis, wiped out the older breeds, requiring hybridization to a different, blight-resistant, race of potato. This hybridization of two different gene pools contributed to modern spuds. David Spooner, the lead author in the current study, had earlier proposed just such a dual origin of potatoes, but with the second (Chilean) clade being prominent long before the 1840s.

The current study involves RFPL analysis surveys of wild potatoes in the South of Peru and north of Bolivia. The result of the new classification is that both the northern and southern clades of modern potatoes can be linked to a small set of species from this area. The data furthermore point to a need to look closely at this "set" of species, which may instead represent a single species.

In terms of bioprospecting, then, lots of useful potato genes could be tapped from just about anywhere else along the Andean chain.

This kind of analysis has been done on a number of major food crops including wheat, beans, and squash. After initial domestication, farming of these valuable plants has sometimes spread primarily along the east-west axis (wheat), and in other cases they spread north-south, or without an apparent latitude bias (corn, squash, beans). A while back, Jared Diamond stuck out his neck and speculated that agriculture of monoclonal crops would be spread with an east-west axis bias, because the similarity of climate is better preserved, whereas north-south spreading might require polyclonal domestication or extensive hybridization. Since Diamond's original thesis, both corn and now potato, both with prominent north-south historical spreads, have been shown to be genetically monoclonal. Send that one to the circular file.

DNA in the mud

Last week's Science had a really suprising short letter showing an enormous amount of extracellular ("dead") DNA in the top few centimeters of ocean sediments. The amount of "extracellular" DNA greatly exceeds the amount contained within the living prokaryotes and viruses in this ecosystem.There is so much DNA in the ocean floor-- 0.45 gigatons!!-- that the phosphorous content of this molecule (about 10% by weight)is a major reservoir of phosphate for all the ocean.

The most interesting possibility would be that this DNA is intact enough to have biological activity. For example, plasmid or virioid DNA can be complexed with protiens in a way that would resist (chemical) degradation for a very long time. If even a fraction of this DNA were still encoding genes, it could be taken up by bacteria and contribute to their genomes as a huge extension to the horizontal gene (DNA) transfer process which already occurs between living organisms.

A second, more practical, consequence of large amounts of relatively intact DNA in the ocean sediments is on metagenomic surveys of this ecosystem. Metagenomics-- a fairly new method which uses special cloning and computational methods to survey the genomic capacity of a particular environment-- cannot by itself "see" if the DNA molecule being sequenced was obtained inside or outside of an organism. The specific concern is that one set of genes (for example, belonging to one class of microbe) would be overrepresented in the extracellular, nonliving pool.
Thus the metagenomic clone counting, which is used to estimate the relative abundances of "genes" in the environmental sample, would lose its presumed linkage to the biological activity of the sample. That is, DNA does not make a gene unless it's inside something alive, and the identical sequence obtained from extracellular DNA should not be scored as contributing to the genomic capacity of the ecosystem.

The issue of extracellar DNA should also be considered for large microbial concretions such as stromatolites, which, in fact, have also been analyzed by the metagenomic approach.

Friday, September 23, 2005

Sedimentary rocks on Mars

Sedimentary rocks Terby Crater, Mars

This image shows sedimentary layers in Terby Crater, exposed by subsequent erosion. The rocks were likely to have been altered by water in some point in their history.

Breakfast science

There's a fun article at LiveScience about the Cheerios effect , in which cereal pieces floating in a relatively empty bowl tend to clump together. This effect is also seen with soda bubbles, or with hair shavings, on the surface of water.
Now I know everyone's been losing a lot of sleep over this, so luckily a physicist has put together an explanation. It's a combined action of buoyancy and surface tension, with the meniscus effect coming in to play at the edge of the bowl.

The cheerios floating on milk distort the surface, making a little dimple; and when two cheerios get near enough to one another they "fall" downward and consolidate into each other's troughs. Breaking this configuration would require the cheerios to go uphill.

The geometry of the milk surface near the rim of the bowl (the meniscus) also traps cheerios on the sides.

Wednesday, September 21, 2005

Tangled Bank 37 at Milk River Blog

Milk River blog is hosting this weeks' Tangled Bank of science-related blogging. The presentation is pretty neat- a vending machine with different candies for different blogs.

Tuesday, September 20, 2005

Moondoggle

Kieran Healy at Crooked Timber gives the final word on the still-kicking plans to open a humanned base on the moon. Worth a read, and a laugh.

Monday, September 19, 2005

Biology as a termite mound

As with any communal project, the nomenclature of biology can get kind of quirky. The Curiosities of Nomenclature site is dedicated to fishing out some interesting ones.

My favorite Russian Doll nomenclature has always been the Drosophila series of mutations, sevenless, son of sevenless (sos), and bride of sevenless (boss), all of which are genes important for eye development. Sevenless mice are missing neuron number 7 in the small repeating arrays known as ommatidia. Sos was later identified in mouse and became m-sos; but then there are two variants, m-sos1 and m-sos2. More cool names from this family, including many allusions to German foods, are at FlyBase .

Southern exposure

Sir Edwin Southern has won this year's Lasker Award for his invention of a DNA blotting method. Southern's original idea is incredibly cool- you could analyze the fragmentation pattern of a complex mixture of DNA by using a "probe," which just consists of a short radioactively labelled fragment. The probe will only stick to its matching (complementary) sequence, and all other sequences stay blank. Using this simple idea and multiple probes, you can detect many different genetic changes, ranging in size from chromosomal rearrangements to loss of a single restriction site.

The method has proved so versatile that it has been adopted for RNA ("northern blot," a pun on Southern's last name), and then to protein ("western blot") and even to protein-protein interactions ( "far western" ). I am not aware of an eastern blot.

Southern later became an early advocate of microarray hybridization , which uses analagous techniques to a Southern blot.

Del.icio.us for biology

This month's Nature Cell Biology makes the science debut of connotea, a social bookmarking application like del.icio.us or flickr. The hope is that scientists will use the tagging system to link all sorts of web pages together.

Connotea seems to have been in beta since late last year but this is the first that I have heard of it. This description provides some startup help.

The NCB rollout article tries to address worries that sharing ideas in a community site(even as innocuous as linklists) might cause loss of a competitive edge. My bias is already against that concept, but I'm not sure they would convince a scientist who didn't want to share.

In the end the system will fly if it gets lots and lots of users. I personally would like to see the emergence of a system which is attractive to non-scientists as well. I have to emphasize: I'm a little confused even about delicious, so I'm just happy with the principle. Oktoberfest is going now, so I'm not sure when I'll do the mind-meld necessary to get started.

I think I would be remiss not to mention citulike , which is also a tag-based online library system. I've heard of this one, and done a few clicks, but I just haven't hit threshold yet.


John Hawks touches on related developments in anthropology toward the end of this post.

UPDATE on information theft in competitive situations: Via The Daily Transcript, I had forgotten the recent New York Times article about an ethical brawl between two groups of astronomers over discovery of an object orbiting outside Pluto. Apparently one group did some snooping deep in the web-based logbooks of the other just prior to announcing their discovery.
I assume that everything in this blog is on Google's servers for eternity; I guess I should assume the same about connotea information.

Saturday, September 17, 2005

Boom!

The Open Science Project links over to videos of dangerous (read: boom!) chemical experiments. If you touch nitrogen triiodide with a feather, well...


The main list of videos is here.

Friday, September 16, 2005

Serotonin agonists and migraines

Migraines are a class of ferocious headaches, frequently with pain on only one side of the head, and often accompanied by nausea, visual illusions called aura, and a deep aversion to light or noise.

This month's Nature Reviews Drug Discovery has a review about progress in treating migraines. The most commonly chosen drugs, known as triptans, activate the Serotonin 1B and 1D receptors. This class of drugs has been the choice for persistent migraine cases since the late 80's. However, triptans (the best known is sumatriptan/Imitrex) act not only in the brain but also constrict blood vessels throughout the body, with potential cardiovascular side effects. The argument of this review is that pharma needs to design drugs that will disentangle the two effects.

The first section of the review explains the evidence that migraine is in the neurons of the brain and not the brain vasculature. (This is what brought me to the article. In fact the vascular actions of the drugs might have increased the confusion about which system mattered.) During attacks, brain activation is seen in specific areas which are associated with pain sensation in the head and the brain vasculature. (In fact the visual aura might be a blood flow effect.) But a specific electrical phenomenon known as a contingent negative variation (CNV) is altered before an oncoming attack and, if the attack is prevented with drugs, the CNV seems to become normalized. Thus migraine is associated with abnormal neuronal firing, and activation of specific brain regions associated with pain processing.

The author basically suggests that moving past the current therapy requires compounds targeting other, neuron specific, receptor systems. He runs down a pretty lengthy list of compounds which are in development. Of these the most interesting to me are the ones which are directly related to blocking nociception (the neuronal sense of "pain"). In any case, options for treating migraine will expand greatly in the near future.

A nice older review at NEJM is here .

PZ Myers on the evolution of senses

Via Panda's Thumb, P.Z. Meyers reviews the evolution of the senses. Our senses of sight, taste and smell (and also some pheremone responses) all first register items in the environment via a closely related set of proteins called G-protein coupled receptors. It turns out that this family is very ancient, and also occurs in bacteria. Other senses, namely hearing, touch, and balance,l register at the cell level when physical shearing of the cell surfacel activates a family of proteins known in mammals as TRP channels.

The new work discussed by Meyers, which appeared in Nature a while back, describes an ancient pedigree for the TRP-like channels as well. There are fungal and bacterial proteins which also register physical stress at the cell surface, and some are direct homologs to the mammalian proteins.

The hypothesis of the review is that bacteria evolved G-protein coupled channels to detect soluble items in their surround, and mechanosensory channels to detect physical stress. These inventions, once established, became highly portable widgets to solve a large number of sensory problems. Truly a great demonstration of the Panda's Thumb principle-- that natural selection tweaks working solutions rather than designing anew.

Here's looking at you

False color image of Minas

This false color image of Saturn's moon, Minas, shows the differences in surface texture. The impact which made the huge crater nearly destroyed the moon.

From the NASA's image of the day web page. .

Thursday, September 15, 2005

"Nutty professor"

(Edited quite a bit on Sept. 16th)

The Chronicles of higher Ed ran a story earlier this week about academics who are socially compromised:

Ask anybody what adjective goes best with the word "professor," and the answer will almost certainly be "absent-minded," or possibly "nutty." Popular culture is full of addlebrained academics....

The idea that scientists and artists are basically nuts is almost universally accepted, and popular studies linking odd behavior and creativity (in this case referring to schizotype personalities) seem to pop up every few months or so. There have been some efforts to actually measure rates of mental illness among creative professionals.. There are some interesting trends, including an apparent correlation between scientific eminence and rates of measurable pathology. But I think the equation of the two has become badly shopworn to the detriment of both groups. Not all scientists are crazy-- and certainly not everyone suffering from mental illness is going to be doing science or art. I think scientists can handle the moderate contempt implicit in this linkage, but people with mental illness must really despise the "beautiful mind" expectation that they start spouting equations.

The Chornicles of Higher Education article goes on to what I consider a more interesting topic-- the response of the faculty community to new hires suffering from moderate psychological disturbance. As with any other disruptive personality (some of which are considered normal) entering a small workplace, these people become "hot potatoes," passed on by glossing over their seriously marginal behaviors. But this part of the discussion is essentially about hiring and firing. I think it could have been pruned away from the nutty professor trope fairly well. I acually wish the essay had gone on longer in this vein-- the author seems only to recommend great care in hiring and probationary periods.

UPDATE: See another ambivalent reader, and comments, over at Crooked Timber

Mountain photographs at National Geographic

There are some very nice photographs of mountain scenes from the 2005 Banff Mountain Photography competition. Go and have a look!

Google blog search: still searching

Update from the comment: Google search hits Atom and RSS feeds

Google now has a search engine which is intended to hit blogs only. The engine searches only blogs with RSS feeds.
I had a look and it's not all the way there yet. .

On the more general topic, though, I've been steadily migrating over toward RSS feeds. I'm getting very interesting stuff by using Pubsub and Bloglines .

Tuesday, September 13, 2005

Peer pressure in the grocery store

Eurekalert is carrying a blurb about social cues affecting people's spending decisions. Consumers will choose a more expensive brand-name item if an unknown fellow-shopper is standing near them in the aisle. The cool thing about the effect is that the stranger is not directly involved in the transaction-- it is the "mere" social presence which has a measurable effect on the purchase choice. In fact, the researchers also chose an invisible product-batteries-- so that the social impact of the brand name should have been minimal after they were in use.

The effect of an onlooker gets stronger if there are more people, or if the onlooker gets physically closer. But the experimental subjects actually did not report any feelings of annoyance or defensiveness until there were three people up close. (The famous Wall-mart Oxygen Deprivation Effect.)

The items to be bought in this study were just batteries, but I can imagine the impact on deodorant sales. In fact, this consumer effect, which has been branded as "Social Impact Theory," probably contributes to the embarrassment effect on buying more socially visible things.

Monday, September 12, 2005

Is that your tongue in your mouth?

(First link is now correct)

The BBC is reporting parasitic louse found in a red snapper in Britain. Cymothoa Exigua drains blood from the fish's tongue and then takes up residence inside the mouth. It seems to even be a functional replacement for the tongue.
A nice picture is here.

The beeb quotes a scientist as being very excited by the find, but I spent 30 seconds on google and found references going back to the late 80s...An entry from early this year is at Stranger Fruit

Other lovely hitchhikers are described here.

Organics in comets

Last week Science Express published two papers ( here and here ) about the Deep Impact mission to comet Tempel. This spacecraft basically slammed into the comet to dig out the pristine material deep under the surface. When that stuff jetted out, both spacecraft and ground telescopes were able to identify the components by their spectra.
Based on the behavior of the comet flume, astronomers think that the comet is a very weak and dusty collection of dust-sized particles, with almost no solid surface. This may be bad news for the Rosetta mission, which is trying to send a lander down to the surface of a comet. It may just sink straight down once it lands.

The main chemical result from Deep Impact is that the inside of this comet is a whole soup of organics , including methyl cyanide, a reactive small organic which can easily polymerize into the precursors of DNA among other things. The earth was absolutely pummeled by comets and their kin during its early history; thus these objects may have delivered the precursors of life to the earth's surface.

A second finding of interest was the presence of clays and carbonates , which require liquid water. Thus the comet might be an agglomeration of material which formed in very different parts of the solar system. I think this mixing, maybe under the gravitational influence of the early Jupiter, may be an important part of making a terrrestrial planet. The rocky core has got to form close in, but the water and organics are best made further away. However this works out, the comets are a big part of the Earth's history.

See also the writeups at ..of Cabbages and Kings and plvs vltra .

Benjamin Fry at the Whitney

Via Metafilter, Benjamin Fry, who is interested in displaying large datasets in visual form, has an installation at the Whitney Museum. Of course I *should* be looking at the haplotype blocks comparing two humans' DNA, but I prefer the baseball salaries graphic. Ben Fry has put a lot of thought and documentation into this.

Take a look also at his Anemone which displays the click habits of visitors to the MIT media lab web page.

Very cool stuff.

Friday, September 09, 2005

Now THAT's a big bird

pterosaur gait interpreted from trackways

The BBC discusses pterosaurs, and recent evidence that they could have had wingspans of 18 meters. Actual fossils have been found of pterosaurs which should have had 14 meter wingspans; the larger figure is based on trackways. (The image, somewhat off topic, comes from this older article about pterosaur tracks, which match panel B-- quadriped gait-- much better than the hypothesized birdlike gait shown in panel A).

By contrast, the largest wingspan of a living bird is only 3.6 meters, for an abatross.

The pterosaurs seem to have been able to fly soon after birth ( as possibly were some ancestral birds ),which means that during this prodigious growth their aerodynamics had to be functional at all times. In contrast, modern birds are born flightless and only begin to fly at nearly adult size.

UPDATE: Orbis Quintus wants a real live thunderbird.

Web interface for Thebes archaeology

Jim Regan at the CS Monitor reviews the newly re-tooled Theban mapping project web page.He's interested in both web page design and the excavations themselves. The project page includes an aerial photograph (I wonder what Google Maps would give?) and lots of links. Regan is right in complaining that the site is a bandwidth hog.

I only wish there were an equivalent site with photographs of the artifacts. There is a small download section for tomb drawings.

Thursday, September 08, 2005

Toads at the disco

There's an item on the newswires that cane toads, an introduced species that's basically overrunning northern Australia, can be lured to traps using ultraviolet strobes. It's not yet clear if the toads are responding to the light itself or to the swarms of insects that are also attracted.

The reason for the big effort is that the toads are very poisonous and eat ravenously. In a public initiative to slow their spread, a story this spring introduced "whacking day" in which people were encouraged to go after the pests with golf clubs and cricket bats. A key comment from the text: "Two issues with golf clubs, one is they're fairly light, they don't have a lot of mass so whilst they hit cane toads and make a very healthy sounding smack when they do, they don't really have enough mass to crush the cane toad's skull," he told ABC radio.

Tangled Bank is up

The Tangled Bank of science-related blogging is up over at B and B.

Wednesday, September 07, 2005

Antioxidant treatment for medieval documents

rembrandt drawing- ink corrosionNature has a short blurb about chemical treatments to neutralize copper in medieval iron gall inks . This ink was the major ink used for centuries for treaties and drawings. The iron preparations used to make the ink also contain copper, along with the trace metals manganese and chromium. These metals generate free radicals which then attack the parchment. The new results suggest that the minor metals are even worse than the known effects of iron.

The antioxidant treatment, combined with alkali (to reduce acidification), is dissolved in heptane and ethanol. Since it is not water-based, it will not cause the books to swell and won't dissolve most inks.

A general history of Iron Gall inks is here. A link to the Metals-In-Paper conservation effort is here. A recent abstract from the Slovenia group is here.

If you want to live hot

Hyperthermophilic microbes often have close relatives which live at "normal temperatures." The evolutionary transition has been made in both directions by multiple families of archaea and bacteria. There is now enough structural information about closely related proteins to make generalizations about what is needed to keep functioning in kochwasser.

In this week's PNAS has an open access article about the physics and evolution of individual proteins retaining their ancestral functions in a new high temperature environment.What is perhaps not suprising is that different proteins manage in different ways. The two most commonly observed answers-- taking a page from my dad's repairs around the farm-- could be classified as "staple gun" or "ten penny nail." That is, either hot proteins are much more tightly compacted, with no single substitution apparently critical; or they are stabilized, without compaction, by a few major changes in the protein sequence that evidently nail everything together. What is interesting from the paper is that these strategies occur in isolation.

The scientists were able to see a trend in the strategies used and relate it to the evolutionary history of hyperthermophiles. Bacterial hyperthermophile proteins tend to use the sequence change (ten-penny nail) method, wherease archaea used the structural(staple gun) method. To quote from the summary:

We attribute such differences to the vastly different phylogenetic histories of these organisms: The primordial habitat for archaea is believed to be a hot environment. When archaea evolved in such a habitat, its proteins were "de novo" designed in a hot environment that necessarily biased both structural repertoire (as explained in more detail below) and sequences that had to be found to fold and be stable in such structures. On the other hand, T. maritima (the bacterium) is likely to have initially evolved as a mesophilic organism that later recolonized a hot environment. Its thermophilic adaptation required the enhancement of the thermostability of already existing proteins.

Based on their observations I'd predict that the tube worms and crabs living near hot vents are using the ten-penny nail method to hold their proteins together. What I did not grasp from this study is the physics of the reverse case- is it somehow less stressful to get cold, so that cold-dwelling archaea don't need whatever the opposite of a ten-penny nail would be to unblock their hot-adapted proteins? This is of some interest because of speculation that life originated at high temperatures (the present authors disagree with this idea), so that the epochal evolutionary event would be in managing in the cold.

The hunt for Peking Man

Duane Smith at Abnormal Interests says that the hunt for the original Peking Man fossils is heating up. These fossils, exemplars of homo erectus, were lost in the early days of World War II although casts and field notes survived. Duane's post has background information and links to subsequent finds at the site.

Wikipedia on Peking man, is here. The tourist center makes the La Brea Tar Pits look understated.

Monday, September 05, 2005

Dinosaur babies: chicks, but with teeth

Via Slashdot , the Times UK quotes paleontologist Gareth Dyke that dinosaur hatchlings could have been covered with mulitcolor fuzz like chicks. (He says "delicate feathery plumage.") This is based on finds at the Liaoning fossil bed in China, a site in which animals were buried in a volcalnic eruption with soft tissue details preserved.

I haven't been able to find a scientific paper specifically mentioning tyrannosaurus young. There was a Nature article last fall about feathery tyrannosauroids, and a 2003 story about a possible four-winged creature (i.e. both arms and legs) found at the site appears here and here .

I don't know why, I keep thinking about an easter basket with one of these little babies peeping out.

Data mining for text connections

SnowDeal is aggregating recent articles about text mining. A good statement of the problem is provided by BioNLP: The literature of the field of biology is the largest of all the sciences. The volume of biology literature each year, measured in bytes, is about fifty times the size of the entire human genome, junk and all. But locked in this literature is an enormous amount of information that can tell us much about the structure and function of genes, proteins, cells and organisms -- how they work as well as how they can fail.

Very interesting stuff.

Friday, September 02, 2005

You are what you eat- and what you eat ate you

There's a really icky story on CNN that Mad Cow disease may have arisen from cows eating human remains.

The cowfood in question was imported as bone meal from south asia. The CNN article goes on: "In India and Pakistan, gathering large bones and carcasses from the land and from rivers has long been an important local trade for peasants," the scientists wrote. "Collectors encounter considerable quantities of human as well as animal remains as a result of religious customs." That is, they'll haul stuff out of the Ganges no questions asked.

It should be said a second hypothesis is that the disease came from the bones of sheep infected with scrapie. The authors of the Lancet paper point out that the first case of mad cow was in 1986, even though sheep stuff had been recylced for decades. There is also some evidence that cows don't get scrapie "via the oral route."

I know, I know, it's all just protein. Yuck.

UPDATES: A bit of policy comment on this from Crumb Trail.

Coincidentally, "chronic wasting disease," or CWD, another prion disease seen in elk and deer, seems not transmissible to humans.

Chimp genome at Pharyngula

PZ Meyers has somehow found time to read the last issue of Nature. His summary of the chimpanzee work, is here .

Thursday, September 01, 2005

Left-handedness in amino acids

Amino acids exhibit chirality, which means they can come in a left-handed or right-handed version. Geological processes tend to make in exactly equal yields but life on Earth overwhelmingly uses only the left-hand versions. This strong bias is now necessary for proteins to fold together properly, but when did it begin? The New Scientist describes some speculation of how polarized light generates a bias in the chirality of amino acids prior to the emergence of life. Circularly polarized light, of the sort generated in vast amounts by white dwarfs can generate an excess of the left-handed racemer of the amino acid leucine. Possibly some such process at work in the early solar system meant that our common ancestor had an excess of left-handed amino acids to work with. The current polarized light experiments can generate excesses on the order of a few percent, but perhaps that's enough. It could be chemically amplified , or, once the bias was established, living things may have standardized and codified it. Some earlier work suggests that strong chiral bias in only one of the amino acids- serine- could force the other ones to come along.

Chimpanzee draft genome

The draft genome of the chimpanzee will be released today at Nature (some stuff is public access). Apparently there are some very interesting differences in the Y-chromosome relative to humans. Also some quantification of repetitive elements, essentially genetic parasites which make up about a third of the human genome. Some families of these little snippets have done very well indeed, specifically in humans. More later when I've done the reading-- wow, the Nature table of contents is full of goodies!

In the meantime check out Carl Zimmer as usual at the Loom, and Monsters and Critics .

Wednesday, August 31, 2005

Turn a turnip into cabbage

Not that my kids would eat either one..

Carl Zimmer at the New York Times (reg) and his blog, The Loom talks about large scale slicing and dicing of chromosomes and its impact on evolution. Big pieces of chromosome, with the details essentially intact, have been moved around in the interval separating rhesus monkeys from human. Intriguingly, the genes near the evolutionarily defined break points are often associated with congenital disease.

Carl is always worth a careful read.

Tuesday, August 30, 2005

Does the "Mozart effect" really exist?

Dave Munger at Cognitive Daily takes a look at the "Mozart effect," the belief, that listening to Mozart can enhance testing ability, which has become the basis for an entire cottage industry aimed at the parents of young children.

The original Mozart observation was that adults performed better on a specific spatial test after listening to Mozart compared to a group exposed to relaxation stimuli. The idea that a particular music would improve test scores erupted into a "Mozart makes you smarter" frenzy. Mozart also improves your smile, removes ugly blemishes and increases your goats' milk production. You get the idea.

Regardless of the pop culture phenomena, the original observations were pretty interesting. Dave discusses to two efforts to replicate them which came to opposite conclusions. It might be that the reported difference lies instead in the exact sort of relaxation of the control group. Experiments using verbal cues to relax result in the Mozart effect, whereas listening to relaxing music (Debussy) erased the effect.

So: avoid telling your kids to relax. Otherwise they'll go dumb, and your goats will dry up.

Hurricane Katrina- wavetops and clouds

esa082905 Hurricane Katrin water surface and cloudtops

Hurrican Katrin was imaged by the European Weather Satellite ENVISAT. The left image uses synthetic aperture radar to show surface roughness of the water. The eye is relatively calm and shows dark. The right image is a more conventional cloud-cover image made using the MERIS detector of reflected sunlight.

This was a beast of a storm. I'm glad that New Orleans escaped a direct hit.

UPDATE: There may still be trouble in New Orleans. A lakeside levee has been damaged, and water is coming in.

Image description is from Eurekanet

Alzheimer's and blood flow, revisited

I had blogged before about a minority view that Alzheimer's disease begins with circulatory problems, and the neuronal damage comes later. This hypothesis is emphatically a minority view, and has a lot of genetic data (my favorite) to explain away. However-- and this is important-- it is testable: there are very sensitive evaluations of blood flow in the brain (not least fMRI!), and prospective studies are presumably underway.

What is abundantly clear, though, is once the disease starts, that both neuronal and vascular function are compromised. Today's EurekaNet lists a story to appear in Radiology comparing both vascular flow and indicators of brain structural damage between patients with dementia (either Parkinson's or Alzheimer's) and age-matched controls with normal cognitive function. They found that total brain volume was comparable between patients and normal people, but vascular flow was strongly reduced. Thus the flow density is reduced in the persons with disease. Measures of brain structural damage as expected also showed the correlates of the diseases.

The conclusion is that vascular and neuronal measures both show damage in people with sporadic Alzheimer's even at an early stage of diagnosis. What remains critical-and with enough time, can be done-- is to ask which system is damaged first.

Sunday, August 28, 2005

Substance P inhibitor: the pain controller that wasn't

In the Pipeline has a nice history of efforts to develop a drug to block Substance P signaling in the treatment of pain. Substance P is a neurotransmitter peptide which is associated with intense and chronic pain, or so-called "bad pain" (as opposed to "good," necessary, pain which tells us to pull our hand away from the hot stove). Because the pain from several diseases seems to come from excessive substance P signaling, it would be a big help to control it. Merck has had a compound for some time, but unfortunately it does not seem to live up to its potential.

The story shows how difficult it really is to bring something from the laboratory to the hospital.

More background on Substance P is at Medscape.

Friday, August 26, 2005

Want to be creative? Do something else first

A review in press in Consciousness and Cognition discusses evidence for the "incubation effect", which refraining from conscious thought about a problem can result in a more creative response. Despite abundant anecodatal support for this idea (Einstein cutting himself while shaving, etc.) it has been very hard to demonstrate in a lab.

The authors are interested in the very first phase of creative thinking, the generation of new and original thoughts. They designed experiments which allow for open-ended answers.For example, 3 groups of people were asked to list "towns that begin with A." One group was allowed to begin immediately; one group was allowed to think about the problem for an interval; and a third group was given a highly distracting test for an equivalent time before returning to the question. The authors scored the "originality" of the lists based on the population size of the municipalities, with big, prominent towns considered a less original answer than small villages.


Every group managed to come up with a fair list of towns. Both delayed groups tended to give more total answers than the group asked to respond immediately.
The most dramatic effect, a nearly twofold higher number of small villages named, is seen between the group asked to answer immediately and the distracted group. The group which was allowed to consciously consider the problem got intermediate scores, although tending toward the immediate answer group. There is also a small tendency for the distracted group to come up with *fewer* "obvious" answers in their list.

My final reaction to this is that it's very interesting to see effects with such a simple experimental design. I myself feel refreshed and sharper especially after a vacation, so I'm inclined to believe there is a real cognitive effect which just needs careful experimental design to be teased out. I think I'd like to see the concept tested using a bigger variety of tasks (they always asks for written lists) and larger sets of people.

Update: there seems to be a fairly extensive literature all suggestive of a positive effect of being a way from a problem for a while.

More genetics of India

Dienekes blogs about the India diversity project, which will try to map human genetic diversity in India. A huge and fascinating effort.

Thursday, August 25, 2005

Liquid water as necessary for life

This week's Nature (subscription! possible workaround using Bugmenot ) has a brief note about why liquid water is considered so essential for life. I have been wondering about this for some time, and have only read a few reviews about alternative life chemistries.

The article starts with Steve Benner, who actually wrote the review I had read last December. Benner's position is that liquid water is literally a two-edged sword. It's an excellent solvent and is chemically both an electron donor and acceptor-- but these flexibilities also mean it will chemically attack just about any information storage molecule you care to think of. (My RNA preps can testify to that!)

The interesting part comes with a third property of water- it is highly polar (the hydrogens are weakly positive, and the oxygen weakly negative) which allows a much weaker class of bond called hydrogen bonding to exist. They get made and get broken, over time and energy scales we can live with. These hyrogen bonds, for example, zip DNA molecules together, and can be readily undone when it's time to copy them. When you get out of the temperature domain of liquid water, you'd have to rely on a new class of bonds-- or operate on a timescale wholly different than we think of as alive.

But we only have the single example of life on earth, and maybe our thinking is limited by only studying life which has clearly evolved with water in mind. Benner's favorite alternatives are cold domains, with liquid ammonia or nitrogen (which have subsets of water's properties). Cold means **slow**, but probably information storage is greatly simplified. Would we recognize something with a lifespan of millenia?

Some links:
The Benner Homepage
Astrobiology encyclopedia for liquid ammonia life
An earlier Nature pdf file on extreme life.
The physical chemistry of liquid water

Tangled Bank 35

The Tangled Bank Carnival of science-related blogging is up at Cognitive Daily . Perhaps not suprisingly, many scientists have been moved to discuss the inclusion of Intelligent Design in the classroom. Dave migrated those posts over to a personal blog. Both sets are worth a read.

Tuesday, August 23, 2005

The vascular hypothesis of Alzheimer's disease

Alzheimer's disease affects about 4 million Americans, and the numbers of cases are expected to rise as the population ages. The exact causes of Alzheimer's disease are unknown, and it is likely that non-heritable cases are triggered by more than one kind of environmental insult. The most prevalent theory has been that accumulation of a protein fragment called "A-beta," which is toxic to neurons, starts a vicious cycle of neuronal death and inflammation.

Although blood circulation problems can also cause dementia, the difference in the sequence of cognitive losses have led neurologists to consider vascular dementia to be distinct from Alzheimer's. However, even from the earliest reports of the disease, it has been known that people who die from Alzheimer's have not only neuronal damage but also pathologies in the blood supply to the brain. A subset of researchers in this very big field are suggesting that perhaps problems with the circulation are the first problem, and that neuronal toxicity comes later. (There is an intermediate position, which could be called the neurovascular hypothesis, which would hold that clearance of toxic A-beta by the vasculature is faulty.) To test whether changes in the blood supply or accumulation and toxicity by A-beta(or both!) are the beginnings of Alzheimer's, it is critical to identify people with the very earliest stages of the disease.

The notion that circulatory disorders can contribute to Alzheimer's-like pathologies got a big boost in a paper to appear in next month's Nature Medicine. Wu et al. report that brain endothelial (blood vessel) cells taken at autopsy from people with Alzheimer's disease are deficient in the vascular transcription factor GAX/MEOX2 and are less able to form tubules in vitro. When expression of this transcription factor was reduced in normal endothelial cells, those cells developed some of the same difficulties as the cells from Alzheimer's victims. Moreover, mice lacking one copy of this gene show reduced ability to grow blood vessels in the brain, and impaired clearance of A-beta.

So the molecule GAX/MEOX2 is reduced in humans with the disease, and reduction in human cells in vitro and in mice in vivo can cause blood vessel abnormalities like those seen in the progression of Alzheimer's disease. There are three limitations to the data at present. The first is that the authors have not yet ruled out that GAX/MEOX2 is also expressed by neurons, and could also function on the neuronal side of the neurovascular unit in mice (analysis of this possibility appears to be in progress by that lab). The second is that there is no mention if the mice show any kind of dementia, or amyloid plaques (accumulations of A-beta which are seen in Alzheimer's disease). This may be because the mice do not live long enough. Lastly, although heriditary Alzheimer's disease is very frequently associated with abnormal generation of A-beta, there has not been, to my knowledge, any human genetic abnormality which only affects the vasculature. (Several proteins related to the generation of A-beta are expressed in neurons and blood vessels.)

My own reaction is that the importance of neuro-vascular interplay cannot be overstated, and the sort of mild global cognitive impairment which seems to represent the earliest stages of Alzheimer's is suggestive of circulatory problems.

More comments on this work are at What's Next and at Science Daily .