Bruce Byers on Scientific American Frontiers

We happened to catch this segment on Scientific American Frontiers, a PBS show hosted by Alan Alda. UMass Amherst biologist Bruce Byers and his colleagues show their fieldwork in a power line clearing in Savoy State Park in western Mass. The show was focused on the "Call of the Wild". In the segment, "Songs of Love and Betrayal":

Alan and Byers attempt to sort out the soap opera-like mating habits of the chestnut-sided warbler.
Only the male chestnut-sided warbler sings, and only during mating season, so the singing seems to be associated with successfully defending a territory and attracting a mate. To check his hypothesis, Byers captures and bands the individuals within one territory. The colored leg bands will help him keep track of which bird is doing what.

ArXiv.org - Cornell Proposes Model to Support Repository

From The Chronicle of Higher Education (January 21, 2010), a "Wired Campus" blog post from Jennifer Howard: "Cornell Library Proposes New Model to Keep arXiv Going."

Cornell University Library announced today that it wants the top institutional users of arXiv.org to help pay for the online scientific repository. "Keeping an open-access resource like arXiv sustainable means not only covering its costs, but also continuing to enhance its value, and that kind of financial commitment is beyond a single institution's resources," Oya Rieger, Cornell's associate university librarian for information technologies, said in a statement describing the new strategy.
...
It costs Cornell about $400,000 a year to maintain arXiv, according to Anne R. Kenney, university librarian at Cornell. The library's annual budget runs in the $40- to $50-million range. Some 200 institutions account for about 75 percent of the download traffic on arXiv, and it's that group that Cornell hopes will pony up first. The suggested contribution for the heaviest users is $4,000. Ms. Kenney says that most of the top 25 have said they will participate.

Broader questions are raised by this eminently reasonable proposal:

• Is this a sustainable arrangement?
• Should there be more governmental support for this kind of repository? And if so, what kind of precedents does this establish for other fields of study? (NSF already provides significant support. See http://arxiv.org/help/support/faq)
  
• How can academic institutions avoid paying for the same material in multiple formats?

UMass Amherst was 159th of the 200 most common users of arXiv in 2009, and so might be expected to bear some of the cost. Academic librarians and others are actively discussing these and related issues of access to and funding of scholarly and scientific information. Cornell asserts that arXiv will continue to be open access. More to come.

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.

"Scientists Decry Isotope, DNA Testing of ‘Nationality"

In the special issue of Science out today, a news item describes a dismaying misuse of science and technology. As one of its tests, the Borders Agency in Britain is piloting use of DNA analysis and isotope testing of soft tissues to verify (or not) whether a person applying for asylum in the U.K. comes from the country they claim to have come from.

"My first reaction is this is wildly premature, even ignoring the moral and ethical aspects," says Alec Jeffreys of the University of Leicester, who pioneered human DNA fingerprinting. ...

After reviewing the Border Agency's plans, Jeffreys [wrote] in an e-mail to Science: "The Borders Agency is clearly making huge and unwarranted assumptions about population structure in Africa; the extensive research needed to determine population structure and the ability or otherwise of DNA to pinpoint ethnic origin in this region simply has not been done. Even if it did work (which I doubt), assigning a person to a population does not establish nationality - people move! The whole proposal is naive and scientifically flawed."

Because the hue and cry over this is so widespread in the scientific community, I wondered if this might be a case of those in power trying to use science to intimidate rather than actually expecting to get at the truth. Questionable asylum-seekers might be threatened with the use of "scientific tests" in hopes that they will admit to falsifying their country of origin. This might be deemed reasonable if the tests would actually produce relevant information, but, instead, what is questionable is the attempt to assign country of origin by these means.

Ardipithecus ramidus - special issue of Science magazine

Science 2 October 2009:
Vol. 326. no. 5949, pp. 60 - 61
DOI: 10.1126/science.326_60a

from Introduction to the Special Issue, by Brooks Hanson, "Light on the Origin of Man"
...

This issue presents 11 papers authored by a diverse international team (see following pages) describing an early hominid species, Ardipithecus ramidus, and its environment. The hominid fossils are 4.4 million years old, within this critical early part of human evolution, and represent 36 or more individuals, including much of the skull, pelvis, lower arms, and feet from one female. The papers represent three broad themes. Five focus on different parts of the anatomy that are revealing for human evolution. These show that Ardipithecus was at home both moving along trees on its palms and walking upright on the ground. Three characterize Ardipithecus's habitat in detail, through analysis of the hosting rocks and thousands of fossils of small and large animals and plants. These show that Ardipithecus lived and ate in woodlands, not grasslands. The first paper presents an overview, and it and the last two papers trace early human evolution and synthesize a new view of our last common ancestor with chimps. One conclusion is that chimps have specialized greatly since then and thus are poor models for that ancestor and for understanding human innovations such as our ability to walk.

Data Sharing

The Nature Publishing Group has put out an interesting series of articles in their September 10 issue on data sharing: why, why not, and why the sciences are strongly disinclined to open up their harddrives.

Crowd-sourcing dinosaur science! The Open Dinosaur Project

Here's an innovative way to get science done, and get people involved at the same time. Three researchers asking for help from the public to enter data into a giant spreadsheet. There must be hundreds of projects that could progress this way.

From their organizing blog:


Introducing the Open Dinosaur Project
Posted September 8, 2009

Hello, and thanks for dropping by at the Open Dinosaur Project. This blog is part of a wider project, in which we hope — with your help — to make some science. We want to put together a paper on the multiple independent transitions from bipedality to quadrupedality in ornithischians, and we want to involve everyone who’s interested in helping out. We’ll get to the details later, but the basic idea is to amass a huge database of measurements of the limb bones of ornithischian dinosaurs, to which we can apply various statistical techniques. Hopefully we’ll figure out how these transitions happened — for example, whether ceratopsians, thyreophorans and ornithopods all made it in the same way or differently.
...
if you care about dinosaurs, and want to make some science, then you can be involved. It doesn’t matter whether you’re a seasoned professional palaeontologist, a high-school kid or a retired used-car salesman: so long as you can conduct yourself like a professional, you’re welcome here.

And now, for the gory details. . .

and so on - check it out here: http://opendino.wordpress.com/
Thanks to CoTurnix's A Blog Around the Clock for this.

Got moose? - with video

UMass Amherst grad student Dave Wattles' moose research described in an article in The Scientist - with video!
Click on title for full article.

Video of Dave tracking moose on YouTube:
http://www.youtube.com/watch?v=k_YN5UTshkU

The Scientist.com

Volume 23 | Issue 8 | Page 21

By Margaret Guthrie Got moose? Cadwell in fall Courtesy of Paul Lussier I’m sitting in the cab of a large pick-up whose roof bristles with radio antennae, on a narrow back road in the western, more wooded part of Massachusetts. On the seat between Dave Wattles and me is a radio the size of an automobile battery with knobs and dials on top. It’s emitting a low static hum punctuated by loud chirps. The chirps are from the GPS transponder on a radio-collared moose, in this case the Peru bull, one of Wattles’s 20 or so research subjects. The louder and closer together the chirps, the closer we are to the moose. It’s April, and Wattles is doing his monthly moose check-up. ...

Bee calamity clarified - Newsblog article from New Scientist

For full article click on title above

Posted by Bob Grant

[Entry posted at 24th August 2009 08:45 PM GMT]

An illness that has been decimating US honeybees for more than three years probably isn't caused by a single virus, but by multiple viruses that wear down the bees' ability to produce proteins that can guard them against infection, according to a new study.

Image: courtesy of Joseph Spencer

"We may not have the smoking gun," University of Illinois entomologist May Berenbaum, the study's main author, told The Scientist, but "we found the bullet hole."

Cells taken from bees that had succumbed to colony collapse disorder (CCD) were cluttered with ribosomal RNA fragments, suggesting that the bees had trouble translating genetic material into functional proteins, Berenbaum and her colleagues report today (August 24) in the Proceedings of the National Academy of Sciences.

"This is an elegant piece of work that weaves together data on host gene expression, microflora and observations of others into a coherent and compelling story," W. Ian Lipkin, a Columbia University researcher who was not involved with the study, wrote in an email to The Scientist.

"Furloughs for state school profs" - blog post from The Scientist

This hasn't happened at UMass Amherst yet... [To see the full article, click on the title of this posting]

Posted in The Scientist by Jef Akst

[Entry posted 22nd July 2009]

Universities across the US are forcing their employees to take unpaid leave, effectively reducing the salary budget without reflecting pay cuts on paper. But for most researchers, who cannot easily pause their studies, what furloughs really amount to is a simple reduction in income -- the same amount of work for less money. Image: Flickr/hoyasmeg "Especially in the sciences, [professors can't just stop] laboratory experiments or any ongoing monitoring they're doing," said John Curtis, Director of Research and Public Policy at the American Association of University Professors (AAUP). "In most cases, [the end result is] just that they get a pay cut." Last week (July 16), the University of California Board of Regents enacted a furlough plan to save $184.1 million by requiring their employees to take between 11 and 26 days of unpaid leave, amounting to a 4-10% reduction in pay. But the UC system isn't the first; several US schools have been quietly implementing similar plans in the past several months. The problem, of course, is that faculty aren't 9-to-5 employees, and walking away from academic work can be like trying to escape your own shadow. "The teaching load is not being reduced, [nor] the expectations for producing," Curtis said. "It's something we really hadn't heard of except in isolated cases, and then all of a sudden this spring, probably about 12 public colleges or universities announced furloughs of one kind or another." [...]

DNA may differ between tissues - blog post from The Scientist

Posted in The Scientist by Bob Grant on 20th July 2009 04:52 PM GMT. Click on the title above to see the full blog posting, which begins:

Recent findings may spell trouble for genome-wide association studies based on DNA obtained through blood samples: Genetic material may vary between blood cells and other tissues in a single individual, a study in the July issues of Human Mutation reports.

Image: Wikimedia

The study "raises a very interesting question," Howard Edenberg, director of the Indiana University School of Medicine's center for medical genomics, told The Scientist. Many genome-wide association studies -- especially studies on systemic diseases such as diabetes and atherosclerosis -- depend solely upon DNA harvested from blood samples to identify genes associated with medical conditions. But this study "suggests that looking only at blood, you may miss some things."

Searching for the genes behind a fatal condition called abdominal aortic aneurysm (AAA), researchers from McGill University in Montreal found that complementary DNA from diseased abdominal aortic tissue did not match genomic DNA from leukocytes in blood from the same patient. "We did not expect to find a difference in the tissue [genes] compared to the leukocyte [genes]," said endocrinologist Morris Schweitzer, who led the study.

ACS To Go Electronic Only

The Chronicle of Higher Education and Ars Technica report that the American Chemical Society, publisher of journals such as Chemical Reviews, Journal of Physical Chemistry B, Langmuir, and Nano Letters (to name a few), is preparing to publish their content electronically only and step away from print production.

What impact will this have? Both reports have some interesting comments.

Article from The Scientist on "Citation Amnesia"

Interesting comment on citation practice in journal articles. Below is quoted only the first few paragraphs. Full article and comments from readers are well worth reading. Click on the title of this blog post for a link to the article.

The Scientist: NewsBlog:

Citation amnesia: The results

Posted by Bob Grant

[Entry posted at 25th June 2009 03:57 PM GMT]

Citing past scientific work in present-day research papers can be a slippery business. Contributions from competing labs can be lossed over, pertinent studies accidentally left out, or similar research not mentioned in an attempt to give the study at hand a sheen of novelty. We at The Scientist often hear complaints from our readers concerning what they regard as either honest or purposeful omissions in the reference lists of high-profile scientific papers. So we conducted a study of our own to try and quantify the prevalence of these types of slights and ask our readers how the problem might be fixed. Image: Wikimedia Indeed, the vast majority of the survey's roughly 550 respondents -- 85% -- said that citation amnesia in the life sciences literature is an already-serious or potentially serious problem. A full 72% of respondents said their own work had been regularly or frequently ignored in the citations list of subsequent publications. Respondents' explanations of the causes range from maliciousness to laziness. ...

Journal of Biology editorial - Biologists Who Count

Editorial in a recent Journal of Biology discusses the debate about the importance of numeracy in the study of biology. First paragraph below. The title of this post is a link to the full text.

Biologists Who Count

Miranda Robertson

Journal of Biology 2009, 8:34doi:10.1186/jbiol146

Published:

27 May 2009

© 2009 BioMed Central Ltd

Editorial

The importance of mathematics in biology is a matter of perennial debate. The squabbles of early 20th century geneticists on the value of mathematics to the study of evolution have recently been revisited in Journal of Biology [1], and the 21st century has seen an explosion of information from various -omics and imaging techniques that has provided fresh impetus to the arguments urging the need for mathematical competence in the life sciences [2]. While there can be no question about the contribution of mathematics to many fields in biology, there is a curious tendency on the part of numerate biologists (often immigrants from the physical sciences) to insist that it is an essential part of the equipment of a biologist and none should be without it. This seems, on the evidence, extreme.