OSTP Launches Public Forum on Public Access to Research

The Office of Science and Technology Policy wants you! On December 10 the office officially launched a Public Forum on Public Access to Federally Funded Research intended to solicit public comments on what the federal government's policy ought to be with regard to published, federally-funded research. They ask: "To what extent and under what circumstances should such research articles—funded by taxpayers but with value added by scholarly publishers—be made freely available on the Internet?"

In most cases, research publications are held behind journal subscription barriers. In research universities and other institutions of higher education, libraries are instrumental in providing access to this content. For those who do not have the benefit of an educational or institutional subscription, much of this research is inaccessible.

Advocates for Open Access encourage the public availability of all federally-funded research. Not only does Open Access make scientific literature available to anyone with an interest in it (for example: people with medical conditions, amateur or unaffiliated scientists), it also speeds scientific process and fosters competition.

Tell the OSTP what you think. The forum will run until January 7. Comments on policy implementation will be taken from December 10 to December 20; comments on features and technology will be taken between December 21 and December 31; comments on management and compliance will be taken between January 1 and January 7.

Neil Forbes interviewed on WFCR: The Power of Bacteria (2009-12-11)

On the radio this morning, we heard UMASS Amherst researcher Neil Forbes (Chemical Engineering) interviewed about his work using bacteria to target cancer cells. Have a listen.

WFCR: The Power of Bacteria (2009-12-11)

Science paper on glycosylation retracted

News from The Scientist by Jef Akst:

Researchers are retracting a highly-cited 2004 Science paper describing a new way of adding sugars to proteins -- a longstanding challenge in molecular biology -- citing their inability to repeat the results and the absence of the original lab notebooks with the experiment details, they announced in Science last Thursday (November 26).

It's a little curious - that absence of the original notebooks. Here's the retraction:

Science 27 November 2009: Vol. 326. no. 5957, p. 1187 DOI: 10.1126/science.326.5957.1187-a

Letters

Retraction

We wish to retract our Report (1) in which we report that β–N-acetylglucosamine-serine can be biosynthetically incorporated at a defined site in myoglobin in Escherichia coli. Regrettably, through no fault of the authors, the lab notebooks are no longer available to replicate the original experimental conditions, and we are unable to introduce this amino acid into myoglobin with the information and reagents currently in hand. We note that reagents and conditions for the incorporation of more than 50 amino acids described in other published work from the Schultz lab are available upon request.

Zhiwen Zhang,¹ Jeff Gildersleeve,² Yu-Ying Yang,³ Ran Xu,⁴ Joseph A. Loo,⁵ Sean Uryu,⁶ Chi-Huey Wong,⁷ Peter G. Schultz^7,*

"Regrettably, through no fault of the authors..." is a curious way to report this - absolving themselves, but not giving any other explanation. In an email to The Scientist, Schultz says again, "There are clearly complexities associated with suppression and cellular bioavailablity of these and other glycosylated amino acids that we did/do not understand, and, regrettably, we no longer have the notebooks to help resolve these issues (through no fault of any coauthors)." One wonders what happened.

Another animal 'cam' - on the backs of albatrosses - reveals possible explanation

Researchers had wondered how certain deep water prey had turned up in the diets of Black-browed albatrosses (Thalassarche melanophrys) - surmising that they had found these species in association with commercial fisheries.
[Photo caption: An iceberg photographed from the back of an albatross]

Now scientists report in the journal PLoS ONE that miniaturised cameras attached to the back of the birds have revealed the birds fly in groups and forage with killer whales.

"We went through thousands of images manually, we were so bored because most of images showed just 'featureless' ocean," says Professor Akinori Takahashi from the National Institute of Polar Research, Tokyo, Japan.

"Then we suddenly saw some albatrosses flying in front of the camera bird and then found the killer whale in the image."

"Finding the interaction of albatrosses with killer whales in the open ocean is unique, because it provides a clue to explain [how] some fish species unavailable within a diving range of albatrosses often appeared in their diet," he explains.

"World interest in Australian fishery impact test" - Press release from CSIRO

An Australian method for assessing the environmental impact of marine fisheries has caught the eye of fishery management agencies worldwide. [click on title to connect to source]
[CSIRO = Commonwealth Scientific and Industrial Research Organisation]

26 October 2009

Aspects of the 'ecological risk assessment' (ERA) method have been adopted in the US, Canada, Ecuador, and the Western and Central Pacific, and by the international eco-labelling organisation the Marine Stewardship Council.

The method was developed in research led by Dr Tony Smith and Dr Alistair Hobday from CSIRO’s Wealth from Oceans Flagship in association with the Australian Fisheries Management Authority (AFMA).

“AFMA needed a tool for assessing the ecological risk associated with a diverse range of fishing practices: from the hand-selection of rock lobsters in the Coral Sea, to the trawling of Patagonian Toothfish deep in the Southern Ocean,” Dr Smith says.

“We met the challenge with a three-step method that considers targeted and incidentally caught species, as well as threatened, endangered and protected species. Ongoing research is further developing the method for habitats and ecological communities.

“Each level of analysis potentially screens out issues of low concern and directs attention to higher risk issues. This helps fishery managers to guard against unacceptable changes to the ecosystem, while being strategic about where to focus dollars and time,” Dr Smith says.

Dr Hobday says the completion of ERA reports for more than 30 AFMA-managed fishing sectors has been a mammoth undertaking involving many years of work by a large research team.

“Our ERA reports document the most comprehensive assessment of the ecological impacts of fishing in Australia’s commercial fisheries and for any large set of fisheries in the world,” he says.

“More than 1200 species have been assessed, highlighting the diversity of Australian fisheries and pointing to risks requiring analysis and management, both for individual fisheries, and on a cumulative scale.”

The ERA process contributes to the strategic assessment of fisheries under the Environment Protection and Biodiversity Conservation Act 1999 and flags priorities for research, data collection, monitoring and management.

AFMA is responding with environmental risk management strategies for each fishery and other initiatives such as a guide for fishery managers to help manage shark bycatch. (Sharks and rays come out repeatedly as high-risk species across many fisheries.)

The research has also yielded a database of information on more than 1000 species of mammals, seabirds, reptiles, scalefish, and sharks and rays.

The Bureau of Rural Sciences, Fisheries Victoria, Fishwell Consulting, and the Queensland Department of Primary Industries and Fisheries assisted with the ERA research.

CSIRO initiated the National Research Flagships to provide science-based solutions to Australia’s major research challenges and opportunities. The 10 Flagships form multidisciplinary teams with industry and the research community.

Can USDA's NIFA be ag's NIH? - Bob Grant's NewsBlog from The Scientist

Commentary on prospects for agricultural and food research after the establishment of the National Institute of Food and Agriculture (new name and mission for the Cooperative State Research, Education, and Extension Service), looking in particular at the consequences of neglecting publicly available research, and issues for public/private collaborations.

...

Unlike university-based biomedical research, however, which in general has enjoyed robust funding in the recent past, academic agricultural research has withered under a USDA that has traditionally meted out small, non-competitive grants to land grant universities, often at the behest of US legislators trying to direct funds to their home districts or states. The result is an intellectual landscape where much of the knowledge surrounding plant science and agriculture resides not in universities but in industry, locked behind the walls of large agribusinesses.

"We're starting at a different point with NIFA than the one at which we find ourselves at NIH," said Keith Yamamoto, a University of California, San Francisco, molecular biologist who serves as an advisor to the NIH and led the agency's recent efforts to revamp its peer-review process. "The current tilt in the fundamental knowledge about plants, their growth, and development is on the industry side and I would say that it's precisely because of the lack of resources on the public side," he told The Scientist. "It's the basic, fundamental information that needs to be in the realm of the public sector."

The disparity between private and public agriculture research becomes apparent when one considers data from the US Patent and Trademark Office (USPTO). Lists of recent patent holders in technology classes related to biomedicine -- surgery, drugs, prosthesis, etc. -- are replete with universities, which typically hold patents generated by publicly-funded research. Agricultural patents from 2004-2008, however, are overwhelmingly held by large agribusinesses such as Monsanto, DuPont, and Syngenta. In the USPTO's "Multicellular Living Organisms and Unmodified Parts Thereof and Related Processes" technology class (which includes genetically modified organisms), six companies -- Pioneer Hi-Bred International, Monsanto Technology, Stine Seed Farm, DuPont, Syngenta, and Mertec -- were awarded a total of 255 patents in 2008, while the Regents of the University of California system, which held the most patents in that technology class out of any university or university system last year, was awarded only six. Other technology classes relating to agriculture, such as "Plant Protecting and Regulating Compositions" and "Planting," have been devoid of university-held patents over the past 4-5 years.
...

"What have we found out about the influenza A (H1N1) 2009 pandemic virus?" - article in Journal of Biology (BMC open access)

Question and answer format.
Published online September 18, 2009. Questions include:

The 1918 pandemic influenza virus is said to have started by causing relatively mild disease in the summer but to have become more severe in the winter. Do we know why, and might influenza A (H1N1) 2009 do the same?

What about the possibility that influenza A (H1N1) might recombine with other more virulent viruses?

Might immunity built up in the course of the Northern hemisphere summer lessen the impact of the pandemic in the winter?

...etc.