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?