Friday, December 18, 2009

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.

Friday, December 11, 2009

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)

Monday, November 30, 2009

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



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. Schultz7,*

"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.

Monday, November 02, 2009

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.

Wednesday, October 28, 2009

"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.

Tuesday, October 27, 2009

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.

Friday, October 09, 2009

"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?

Friday, October 02, 2009

"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.

Friday, September 18, 2009

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.

Tuesday, September 08, 2009

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:
Thanks to CoTurnix's A Blog Around the Clock for this.

Tuesday, August 25, 2009

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:

Volume 23 | Issue 8 | Page 21

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.

Thursday, July 23, 2009

"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."


Monday, July 20, 2009

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.

Tuesday, July 14, 2009

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.

Monday, June 29, 2009

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.

Saturday, June 13, 2009

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


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.

Thursday, May 28, 2009

Peregrine falcon chicks atop Du Bois Library - photos of banding

Click on the blogpost title to see photos of the 'Class of 2009' falcon chicks from library staffer Lorraine LaPointe. There are 4 chicks in this year's brood, 3 females and one male. Lorraine says in her email:

The males are much smaller than the females. The male is in Richard Nathorst’s right hand in the group photo. If you don’t know who Richard is he is the one that looks like the “proud Papa”. Hopefully he will send some better photos.

Tuesday, May 26, 2009

Common Chemistry

“Common Chemistry” new CAS website

Chemical Abstracts Service (CAS; , a division of the American Chemical Society (ACS; has launched a new, free, web-based resource called Common Chemistry ( This resource is designed to help connect a chemical name to its CAS Registry Number. The CAS Registry Number is considered to be the most commonly used and unique identifier of a chemical substance.

Helpful to non-chemists this site contains approximately 7,800 chemicals of widespread and general interest as well as information about 118 elements from the periodic table. The results page provides the compound’s Registry Number, molecular formula, and chemical name (chemical name synonyms) and a Wikipedia link if available.

While not intended to be a comprehensive CAS Registry number look-up service, it does provide a good starting point for common chemicals. In testing the site my only concern is that it does not provide look-up service by entering a common drug name such as “Prozac.” If this site was truly designed for the non-chemist I would think that it would provide look-up service to those “common” household chemical names.

Thursday, May 14, 2009

Reaxys Database Trial through 6/30/09

The UMass Library is pleased to announce a database trial to Reaxys.

Reaxys is a web-based search and retrieval system for chemical compounds, bibliographic data and chemical reactions. Reaxys is based on data from Elsevier’s chemistry databases – CrossFire Beilstein, CrossFire Gmelin and Patent Chemistry Databases.

Offering a wealth of experimentally validated information, Reaxys brings a fresh look to synthetic chemistry with powerful functionality, combined content and relevant information.

Powerful Functionality
Reaxys search, analysis and workflow tools are designed around the needs and common tasks of users, including:
· Synthesis planner to design the optimum synthesis route
· Multi-step reactions to identify precursor reactions underlying synthesis of target compounds
· Additional search capabilities such as the ability to generate structure query from names or phrases
· Search result filters by key properties, synthesis yield, or other ranking criteria
· Results visualization
· Similarity search
· Transformation analysis

Combined Content

The merger of three prestigious databases puts all the relevant data at the user’s fingertips. A search across the Reaxys database delivers a single results set and each record provides details excerpted from multiple patent or journal sources.

Relevant Information
Reaxys contains an extensive repository of experimentally validated data that chemists need including structures, reactions (including multi-step reactions) and physical properties. Now chemists can get relevant data not found elsewhere, drawn from source publications carefully selected for their importance and relevance to synthetic chemists.

To access the database go to the Reaxys link on the database trials page:

Send comments to

Wednesday, May 13, 2009

NASA astronaut sends Twitter messages from Hubble

Article from the

Twitter has broken through the final frontier: it has gone into outer space, thanks to one of the NASA astronauts servicing the Hubble Telescope.

John Grunsfeld, Drew Good, Mike Massimino, Andrew Feustel: NASA astronaut sends Twitter message from space
(L to R) Mike Massimino, Drew Good, Andrew Feustel, and Jon Grunsfeld

Mike Massimino, a member of the crew sent to Hubble, has become the first person to use Twitter from space.

His first tweet proclaimed: "From orbit: Launch was awesome!! I am feeling great, working hard, & enjoying the magnificent views, the adventure of a lifetime has begun!"

His second, sent via the computers on board the space shuttle Atlantis, said: "From orbit: Getting more accustomed to living in space today and getting ready for our big rendezvous with hubble."

Twitter, the popular micro-blogging service, has been used by thousands of people in unusual and controversial locations – including the Mumbai terrorist attacks, a child's funeral, and even inside the womb, thanks a pregnant woman wearing a belt with a sensor, which automatically tweeted when it felt the baby kick.

NASA, however, confirmed that this Mr Massimino – who goes by the Twitter nickname Astro_Mike – was the first man to have sent a Twitter message from out of space.

"Tweeting happens every day down here on earth, so why not take it to beyond Earth?" a spokesman at the Kennedy Space Centre.

Mr Massimino started using the blogging service in April and until recently had just a few hundred followers.

He now has in excess of quarter of a million people following his updates on Twitter, thanks to his regular messages in the lead up to launch day on Monday, which gave small details about his preparations and fitness regime.

Twitter, which allows people to post small messages, of no more than 140 characters, has taken off this year, with celebrities, politicians as well as about 15 million of ordinary people using the service.

Two New International Telescopes Launching May 14 - watch the launch live!

Steve Lord, a graduate of UMass Amherst in Astronomy and Electrical and Computer Engineering, who now works at the Infrared Processing and Analysis Center, Jet Propulsion Lab at Cal Tech in Pasadena, CA, sent me this email:

Dear Friends,

Today [Tomorrow] - On the same day when the Space Shuttle astronauts reach NASA's Hubble Space Telescope to repair it and give it 5 more years of life, a new telescope will be launched from Kourou, French Guiana, South America:

The Herschel Space Observatory:

Herschel was built by 25 European countries with some help from the US - 1000 people x 10 years and 1 billion dollars. The US (NASA) gave 20% in instrumentation. I have worked on Herschel exclusively for 10 years.

Herschel (and another telescope, Planck) will be launched by the European Space Agency (ESA) and for a month steered to its Sun orbital position located five times further than the Moon.

The Herschel telescope is the largest telescope to be put into space by far, having more than twice the collecting surface area of the Hubble.

Herschel's instruments are cooled with liquid helium to near zero -273 C and the large mirror cools to -200C.

Herschel will observe the "cool" Universe for 3.5-5 years studing the origin of the Universe and the prebiotic chemistry taking place in space.

Herschel Launch time:
Thursday 14 May*/ /*by the French Aerospace Company

- Trois, deux, un

6:12 AM PST
9:12 AM EST

10:12 AM Rio Janeiro

2:12 PM GMT

3:12 PM CET

6:12 PM India

9:12 PM China

Watch the launch live here (it takes 25 min of burn)

Here are some Herschel info links:

Links from the European Space Agency (ESA) on

the Herschel and Planck Observatories

And the launch campaign:

Tuesday, May 12, 2009

Wikipedia misquotes the dead

Shane Fitzgerald wondered how accountable modern news media are. Do they check facts in a 24/7 news cycle? He got his chance to test the media's accuracy and research methods when French composer Maurice Jarre died on March 28. Within hours of his death, Fitzgerald added to the Wikipedia article on Jarre a quote he thought would be irresistible to obituary writers. Here it is:
  • "One could say my life itself has been one long soundtrack. Music was my life, music brought me to life, and music is how I will be remembered long after I leave this life. When I die there will be a final waltz playing in my head that only I can hear."
He supplied no source or attribution, and the administrators at Wikipedia quickly removed it. Before they did, though, the quote was lifted and appeared in newspapers around the world. So far only one of them, The Guardian, has publicly admitted that its writer copied the quote. Other newspapers have removed the quote but made no apology for the mistake.

This brings up two points: the frequently repeated, too-often-unheard warning about using Wikipedia as a source, and what happens to stories that incorporate inaccurate information. In this case, only one of the newspapers that made the mistake printed a retraction; the others quietly corrected it. What if someone used one of those stories as a source before the correction? The mistake would be carried on, even after it had been fixed. The shadow of Wikipedia is long and dark. And you can quote me.

Tuesday, May 05, 2009

Elephants on the brink

YouTube video - photographs of elephants by Karl Ammann with narration by Dale Peterson about a book they collaborated on Elephant Reflections, University of California Press, Berkeley, 2009.

Note from the book by Karl Ammann:

I believe that both the conservation community and most of the conservation media are far too content to go with the ivory story. It's a sexier tale, after all, and it allows us to focus our blame on a distant and rather vague "ivory mafia" in Asia rather than on particular poachers, lax law enforcement officers, and meat traders in Africa. The ivory story is also a simpler one to tell, and perhaps easier to bear. But the consumption of all kinds of wild animal meat in Central Africa has become profoundly commercialized during the past several years. This commercialization has, in turn, caused the consumption of game meat -- including elephant meat -- to explode in scope and impact. The uncontrolled nature of the commercial meat trade is now the most important threat to forest elephants, and it needs to be publicized, understood, and addressed by individuals, organizations and governments.

Post extracted from The Scientist, "A new book explores the many textures of African elephants", published 1st May 2009 04:59 PM GMT.

UMass Amherst Researcher Edward Calabrese Receives Marie Curie Prize for Work on Hormesis, Low-Dose Radiation and Health

May 1, 2009

Contact:Ed Blaguszewski

AMHERST, Mass. – Edward Calabrese, a professor in the School of Public Health and Health Sciences at the University of Massachusetts Amherst, has been awarded the Marie Curie Prize for “outstanding achievements in research on the effects of low and very low doses of ionizing radiation on human health and biotopes.”

At an international conference this week at UMass Amherst, Andre Maisseu, president of the Paris-based World Council of Nuclear Workers, announced that Calabrese is the council’s 2009 Curie Prize winner. Maisseu saluted Calabrese during the annual meeting of the International Dose-Response Society, of which Calabrese, an environmental toxicologist, is a founder and current director. Maisseu said the prize recognizes an entire body of research that has improved scientific knowledge of low-dose ionizing radiation effects on human beings and biological communities. A formal award ceremony will be held in Rio de Janeiro, Brazil, in September.

While Calabrese is the foremost expert in the world on a chemical dose-response phenomenon known as hormesis, he has done little dose-response work with ionizing radiation, he observes. However, he feels deeply honored by the council’s recognition. “I accept that I’m being given credit for bridging the gap between chemical hormesis and ionizing radiation,” he says, “and I do believe there is evidence to bridge it. What I have urged all along is for mainstream science to see hormesis as a basic biological principle.”

Hormesis describes the fact that low doses of some chemicals are stimulative or promote growth but higher doses are toxic or inhibit growth, for example. The Marie Curie Prize winner, who joined the UMass Amherst faculty in 1976, says, “We need to conduct the research―which has been long neglected―to understand hormesis more fully, with all its implications.”

The theory’s proponents suggest that low doses of minerals in multivitamin pills such as chromium and selenium, for example, boost health not because they provide required nutrients but because low doses of many toxins stimulate biological systems with beneficial mild stress, while higher doses are toxic. By contrast, the prevailing linear threshold model of toxin behavior says the absence of harmful effects below the threshold assumes there are no effects relevant to health.

Calabrese and colleagues’ work on chemical hormesis sparked vigorous scientific debate and a special section in the journal, Science, in 1989. Challenged to subject hormesis experiments to more rigorous statistical standards, Calabrese and his longtime UMass Amherst collaborator, Linda Baldwin, created a database of 21,000 papers. In 2003, they reported in a ground-breaking paper that the low-dose stimulatory effect of chemicals is typically about 40 percent enhanced growth, for example.

“It was a coming-out party for hormesis,” Calabrese recalls. “We made a credible case and we did it by following the scientific rules of the game,” he says of their work over the past 30 years. By contrast, he says, the two leading risk assessment models used by the Environmental Protection Agency and the Food and Drug Administration have been imposed on society and the scientific community without being vetted or validated.

Everyday implications of hormesis for risk assessment are significant. If chemical hormesis is a basic biological principle, Calabrese says, society is needlessly over-regulating the environment to protect against low exposures that are not dangerous, and we’re missing possible benefits. “The traditional threshold model is not very good at explaining or accounting for data that’s below the toxic threshold, and that’s where we live. But hormesis is quite good at that.”

Major Implications for Public Health Policy

Mark Mattson, chief of the Laboratory of Neurosciences at the National Institute on Aging, one of Calabrese’s past co-authors, agrees that the findings for which Calabrese is being recognized with the Marie Curie Prize “have major implications for public health policy regarding environmental ‘toxins,’ for the design of biomedical studies, and for the discovery of new therapeutic interventions for a range of diseases.”

Mattson adds that the UMass Amherst research clearly reveals that “hormesis as a widespread feature of biological systems (cells, tissues, organisms and populations) that was previously either unrecognized or ignored by scientists in the fields of biology, biomedical research and toxicology. Calabrese and colleagues have shown that biological systems very often respond adaptively to low amounts of toxins and other stresses (radiation, heat, etc.) so as to increase their resistance to more severe stress and disease.”

Maisseu says it’s unfortunate that most research on ionizing radiation conducted since nuclear weapons were developed has focused on its harmfulness. This has prevented valuable work on possible beneficial low-dose effects, including adaption and repair mechanisms, he feels. Further, anti-hormesis prejudice has deprived the scientific community of fundamental knowledge which might be uncovered, and which is needed to pursue the fight against the different forms of cancer, Maisseu adds.

He therefore salutes Calabrese’s “courageous opposition to this indefensible position with regard to scientific research.” Recalling the famous statement by the 15th century toxicologist, Paracelsus, that all substances are poison and only dose makes a poison, Maisseu adds, “Calabrese dared to undertake work making it possible to correctly appreciate the relationship between dose and effect in many areas of toxicology and biology, and to highlight numerous examples of the hormesis phenomenon.”

Edward Calabrese can be reached directly at 413/545-3164 or

Friday, May 01, 2009

"Merck published fake journal" - from The Scientist news article

Posted by Bob Grant
[Entry posted at 30th April 2009 04:27 PM GMT]

From the news article:
Merck paid an undisclosed sum to Elsevier to produce several volumes of a publication that had the look of a peer-reviewed medical journal, but contained only reprinted or summarized articles--most of which presented data favorable to Merck products--that appeared to act solely as marketing tools with no disclosure of company sponsorship.
The Australasian Journal of Bone and Joint Medicine, which was published by Exerpta Medica, a division of scientific publishing juggernaut Elsevier, is not indexed in the MEDLINE database, and has no website (not even a defunct one). The Scientist obtained two issues of the journal: Volume 2, Issues 1 and 2, both dated 2003. The issues contained little in the way of advertisements apart from ads for Fosamax, a Merck drug for osteoporosis, and Vioxx. (Click here and here to view PDFs of the two issues.)

Oldish news, to be sure, but still, a cautionary tale.

One of the "Honorary Editorial Board" of this "journal" was an Australian rheumatologist, who is quoted in this article.

"You get involved in a whole bunch of things at this level," Brooks said, adding that he had put his name on "a few advertorials" for pharmaceutical companies about 10 years ago.

As for the Australasian Journal of Bone and Joint Medicine, he said, "If it would have been put to me that [the journal] was just sort of a throwaway, then I would have said 'no'" to serving on its editorial board. He said he was never paid for his role, adding that he "didn't ever get [manuscripts] to review or anything like that," while on the board, because the journal did not accept original manuscripts for review.

Monday, March 30, 2009

A century's worth of bird data online

Geologists aren't just about rocks and dinosaurs. At the USGS Patuxent Wildlife Research Center, there is a project underway to make available online the notes of 3,000 birdwatchers who participated in the Bird Phenology Program. The notes, on forms called Migration Observer Cards, span almost a century, and document migration arrival dates in the spring and fall across the US and Canada. There are 6 million of the cards, and volunteers have undertaken the huge task of transcribing and entering the data.
The BPP has local roots-- it was started in the 1881 by Wells W. Cooke, who wanted to broaden knowledge and understanding of migration. Cooke was born in Haydenville, a village in Williamsburg, just west of Amherst on Route 9. In 1881 he was teaching in Minnesota and organizing volunteers to collect migration data when his efforts came to the attention of C. Hart Merriam, of the newly formed American Ornithologist’s Union. Merriam extended the network to the rest of the US and Canada, as well as parts of the West Indies. In the 1880's the program was taken over by the federal government, but as participation declined in the mid-20th century, the program closed in 1970. The records were curated, but largely ignored, and finally passed on to Jessica Zelt. Zelt is overseeing the the project and reviewing the program’s possible uses and potential for collecting new data. She hopes that the data will provide insights into the effects of climate change on migration patterns and habits.
You can be a part of this important project. No particular expertise is required. Sign up to enter records into the database, and be a member of the next generation of "citizen scientists."

Friday, March 20, 2009

First U.S. Public Access Policy Made Permanent

On March 11th 2009 President Obama signed into law the 2009 Consolidated Appropriations Act, which includes a provision making the National Institutes’ of Health (NIH) Public Access Policy permanent. This Act requires eligible NIH-funded researchers to deposit electronic copies of their peer-reviewed manuscripts into the National Library of Medicine’s online archive, PubMed Central. Full text articles will be made publicly available and searchable online in PubMed Central no more than 12 months after publication in a journal.

"Public access to publicly funded research contributes directly to the mission of higher education,” said David Shulenburger, Vice President for Academic Affairs at NASULGC (the National Association of State Universities and Land-Grant Colleges). “Improved access will enable universities to maximize their own investment in research, and widen the potential for discovery as the results are more readily available for others to build upon.”

For more information, visit the Alliance for Taxpayer Access Web site at

Tuesday, February 03, 2009

Google Earth: Dive! Dive!

Google Earth is finally paying attention to parts of the planet below sea level. According to a story in the New York Times Science Times this week, starting Monday (Feb. 9), Google Earth will enable users to cruise beneath the waves, add pictures and video to locales, or "... you can create narrated, illustrated tours, on land or above and below the sea surface, describing and showing things like a hike or scuba excursion, or even a research cruise on a deep-diving submarine." Sometimes when I can't get to sleep, I imagine myself as Sylvia Earle, piloting Alvin through the abyssal depths, so this will seem like a waking dream to me. (Sometimes I try to picture cruising beneath the Cretaceous seas, but that's for another post.) I'm excited about possibilities for teaching and learning using this technology.
Besides oceanography and marine ecology, another feature, Historical Imagery, compiles archives of satellite images to allow you to watch ways the land surface changes. (I don't know if there will be historical subsurface data.)
The new features require downloading the new version, free at

Thursday, January 29, 2009

Elevating Science, Elevating Democracy

Dennis Overbye had an essay in this week's Science Times, the Tuesday section of the New York Times, commenting on the value of science, indeed, on the values of science. It struck a chord with me.

To be honest, the restoration of science was the least of it, but when Barak Obama proclaimed during his Inaugural Address that he would “restore science to its rightful place,” you could feel a dark cloud lifing like a sigh from the shoulders of the scientific community in this country.

When the new president went on vowing to harness the sun, the wind and the soil, and to “wield technology’s wonders,” I felt the glow of a spring sunrise washing my cheeks, and I could almost imagine I heard the music of swords being hammered into plowshares.

Wow. My first reaction was to worry that scientists were now in the awkward position of being expected to save the world. As they say, be careful what you wish for.

My second reaction was to wonder what the “rightful place” of science in our society really is.

...Science is not a monument of received Truth but something that people do to look for truth.That endeavor, which has transformed the world in the last few centuries, does indeed teach values. Those values, among others, are honesty, doubt, respect for evidence, openness, accountability and tolerance and indeed hunger for opposing points of view. These are the unabashedly pragmatic working principles that guide the buzzing, testing, poking, probing, argumentative, gossiping, gadgety, joking, dreaming and tendentious cloud of activity — the writer and biologist Lewis Thomas once likened it to an anthill — that is slowly and thoroughly penetrating every nook and cranny of the world.

Click on the title above to read the rest.