Uncommon Ground

This is hardly a surprise, but I thought I'd pass it along.¹

A recent National Science Foundation report shows that the agency once again received a record number of grant applications in fiscal year (FY) 2007.  The report, prepared for the National Science Board, indicates that in FY 2007, "NSF received a total of 44,577 proposals, the highest number of proposals to date. This is a 5 percent increase over the number of proposals received in FY 2006 and a 50 percent increase from the 29,508 received in FY 2000."  The average duration of grants awarded remains at about three years and the average annualized award size increased slightly to $146,200.

NSF made 11,463 awards in FY 2007 resulting in an agency-wide funding rate of 26 percent. However, the Biological Science Directorate (BIO) remains well below this average mark, and is the lowest in the NSF.   Many programs within BIO have single digit success rates.  In 2006, the BIO-wide success rate was a mere 14 percent.

For additional information about NSF funding for biology, please visit the AIBS Public Policy Office Federal Budget Resource at http://www.aibs.org/public-policy/budget_source.html and download a free fact sheet at

http://www.aibs.org/public-policy/resources/Bio_funding_March_2008.pdf . 

Scientists understand the world first by noticing regularities and second by explaining them. Linnaeus noticed that living things could be grouped into hierarchical categories more than a century before Darwin provided the explanation. Mendeleev noticed that elements could be grouped into a periodic table more than a century before the atomic theory explained why.

One of the challenges we always face is figuring out what patterns make sense. Take a bunch of nucleotide sequence data from a bunch of different nuclear genes within a large population of an outcrossing species, throw it into your favorite phylogeny program, and you'll get out a tree, one tree¹ -- even if each gene has a different evolutionary history.² Or take a bunch of data from a single gene and a bunch of different populations and throw it into the same programs, and you'll get out a tree -- even if the populations show a linear cline or isolation by distance.

Wouldn't it be great if you could throw your data into a program and have it figure out whether a tree is the best way to structure your data or if some linear order or a dominance hierarchy or something else made more sense? Well, hang on to your hats. There's a recent paper suggesting that it might just be possible.

Next April Ed Wilson will present the 2009 E.O. Wilson Biodiversity Technology Pioneer Awards at Montana State University in Bozeman. The awards honor those who "who have pioneered, invented, developed or used modern technology to help advance the biodiversity of life on planet Earth." In 2009 the awards will go to:

Jane Lubchenco
Mike Soulé
Steve Running
David Ward

The awards are sponsored by The American Computer Museum.

What can I say, except thanks to Gernot Wagner at Environmental Economics for pointing this out. He links to comments by Brad DeLong and Joseph Romm.

Western lowland gorillas are doing better than we thought they were. The news for other primates is not so good.

The first comprehensive review in five years of the world's 634 kinds of primates found that almost 50 percent are in danger of going extinct, according to the criteria of the IUCN Red List of Threatened Species™. (IUCN press release, 3 August 2008)

Chimps and gorillas get most of the attention, but it's the smaller species that are most at risk. 90% of primates in Vietnam and Cambodia are at risk of extinction, and more than fifty new species have been described since 2000.

Most primates are highly threatened. But Andy Revkin reported some good news yesterday. A survey by Congolese scientists and scientists affiliated with the Wildlife Conservation Society found more than 125,000 western lowland gorillas (Gorilla gorilla ssp. gorilla) in the northern Congo republic.

Just last year the IUCN Red List assessed the subspecies as Critically Endangered. As Steven Sanderson, president of WCS, puts it "While we don't want to relax our concern, it's just great to discover that these animals are doing well."

Click through for an abstract of the assessment from last year, or watch this video from the New York Times narrated by Andy Revkin.

I already have tenure after all, and I'm really enjoying the work we've started on Protea.

Last week in Vancouver I attended the Botanical Society of America's President's Symposium, Understanding the Crisis in Science Literacy: The BSA is Planting Science in the 21st Century. The first two talks, by Matt Nisbet and DIetram Scheufele, revisited ground that I've touched on before - the role of framing in mass communication. One example I hadn't seen before shows nicely how context influences interpretation. It's from Daniel Kahneman's Nobel Prize lecture on 8 December 2002.
The middle pair of marks look like a "B" in the top row and like the number "13" in the second row.¹ But the marks are identical. Only the context in which they appears differ. Here's what Kahneman has to say about the pair of figures:

An ambiguous stimulus that is perceived as a letter in a context of letters is seen as a number in a context of numbers. The figure also illustrates another point: the ambiguity is suppressed in perception. This aspect of the demonstration is spoiled for the reader who sees the two versions in close proximity, but when the two lines are shown separately, observers will not spontaneously become aware of the alternative interpretation.²

Why do I bring this up now? Because it's an excellent example of how context affects perception. If context has such a strong effect on what we see, surely the way in which we frame arguments will have a strong effect on how they're received.

Andy Revkin referred to this yesterday.  

ScienceDebate2008 didn't happen during the primaries, but the team behind the effort released 14 questions they wanted the candidates to answer a little over a month ago. So far as I know, neither candidate has yet made a formal response. They should. Science issues haven't received much press, but results of a poll released by Scientists and Engineers for America show that the public is very interested.

Until the candidates provide more detailed responses on their own, AAAS has compiled a table comparing the positions that McCain and Obama take on issues related to energy and climate change, health care, and competitiveness and innovation. The most detailed information is available for issues related to energy and climate change.

The information AAAS provides is informative. But I hope that the candidates will provide more. I urge them to tell us more about their views on the role of science in policy making, the role of the federal government in protecting water resources, and the role of the federal government in preparing students for careers in science and technology. I urge them to answer all of the 14 questions.

That's the headline in The Economist about this paper in the 18 July issue of Science. James Evans from the Department of Sociology at the University of Chicago studied a database including over 34 million citations to articles from 1945 to 2005. He studied the relationship between citation patterns and the availability of journals online. You'd expect citations to increase both in frequency and in breadth of coverage as journals came online.¹ But that's not what he found.

• The longer a journal has been available online, the younger the average age of its articles that are cited.
• As more articles became available online, fewer were cited.

Evans concludes that

These changes likely mean that the shift from browsing in print to searching online facilitates avoidance of older and less relevant literature. Moreover, hyperlinking through an online archive puts experts in touch with consensus about what is the most important prior work--what work is broadly discussed and referenced. With both strategies, experts online bypass many of the marginally related articles that print researchers skim.

The Economist puts it differently:

As a wag once put it, an expert is someone who knows more and more about less and less until, eventually, he knows everything about nothing. It would be ironic if that is the sort of expertise that the world wide web is creating.