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.