Tinkering with Proteins

Tucked into today's broadcast of NPR's Morning Edition was an exciting story not quite 4 minutes long, and easy to miss.  Listen to Joe Palca as he explains how "tinkering with proteins can have fundamental consequences on anything that's alive."  The research of Jason Chin and his group at Medical Research Council Laboratory of Molecular Biology, Cambridge, England, as described by Jim Collins at Boston University, has resulted in re-engineered ribosomes that can "read" quadruplets of thymine, adenine, guanine, and cytosine, the bases of DNA, rather than the standard triplets, leading to faster creation within certain bacterial cells of many more types of amino acids, capable of being strung together to construct novel proteins.  This technology, says Chin, could be used to develop "heartier" proteins with therapeutic properties, available in the body without being degraded.  The work of the research teams of both Chin and Collins is briefly reviewed in a news article on Nature's web site, along with other research challenges for synthetic biology.

A 2009 article on the technology developed by Chin appeared in PNAS: Proceedings of the National Academy of Science. PNAS May 26, 2009 vol. 106 no. 21 8477-8482

New Content in Web of Knowledge: BIOSIS and Science Citation Index Together

It is now possible to search BIOSIS Previews from the same search platform as Science Citation Index and the other citation indexes offered within Web of Knowledge.  In addition, we have access to a deeper back file of the databases, with indexing back to 1965 for Web of Science and 1969 for BIOSIS.

This is a wonderful development, since the great subject indexing of BIOSIS is made even more effective with the Refine Results options of the Web of Knowledge search interface.  In addition, citation indexing is linked from Web of Science to the BIOSIS search results so every BIOSIS article that has been cited by an article indexed in Web of Science is so tagged.

Start exploring the new options and content from the Science Citation Index link on the science library's web site.  Click on the Select A Database tab once you are at the Web of Knowledge site.

Need clarification on all of those names?

• BIOSIS Previews includes Biological Abstracts, a database of primary, peer-reviewed journal articles.  The expanded content and indexing of BIOSIS gives additional access to annual publications, conference proceedings, monographs, reviews, bibliographies, and other types of life sciences literature.
• ISI Web of Knowledge encompasses all of the databases and other products offered by Thomson Reuters
• ISI Web of Science includes the citation indexes, first created by the Institute for Scientific Information and acquired by Thomson Reuters.   
• Science Citation Index is the largest database of Web of Science.

Get more information from Web of Knowledge.

Commemorating African American Achievement in Science

What follows is a brief listing of web sites and guides to commemorate the contributions of African Americans in Science, Technology and Medicine.  It is appropriate to take a wide view of African American achievement during Black History/African American History Month, and there are many sources that do just that, beginning with the
Association for the Study of African American Life and History and the Library of Congress.

My intent is a narrower focus, superbly presented by Kenneth R. Manning in a number of essays on African American scientists.  Manning, Thomas Meloy Professor of Rhetoric (Program in Writing and Humanistic Studies and STS), MIT, Cambridge, is the author of Black Apollo: the life of Ernest Everett Just.

His keynote address, Reflections on E. E. Just, Black Apollo of Science, and the Experience of African American Scientists, given at the symposium honoring E. E. Just held on the campus of Howard University, November 21, 2008, was transcribed and published in Molecular Reproduction and Development 76 (2009): 897-902.

A more general essay by Manning is accessible from OBIS: African Americans in Science, offered in the Black Studies Center archived by ProQuest.

Other resources include:
African Americans in Science / Charles Carey (online encyclopedia from ABC/Clio)
Science Update - Spotlight: African American Scientists (from AAAS)
The Faces of Sciences: African Americans in Science

Finally, C&EN published a report in 2007 on Chemists of Color that stated many of the same sentiments expressed by Kenneth Manning.  Specifically, diversity in academia will not reflect the general population until all members of the academy work together to support scientists of color beyond the interview and hiring stage.  Critical decisions over tenure, promotion, funding, and hiring of graduate assistants all directly impact success and retention.

In Manning's words, at the conclusion of his keynote address:
"We have an opportunity now to get into another gear, to begin to aggressively try and nurture people who have not been part of the enterprise. 

"We have to recognize our roles as gatekeepers, as people who evaluate, and realize that evaluations do have meaning and message.  We should be as sensitive and wise as we can.  If we do that, I think the legacy of Just will carry on and our scientific enterprise will have the diversity that we want and deserve."

Temple Grandin on NPR's Fresh Air

Tune in to Fresh Air today on National Public Radio (3 pm, WKSU.org) and hear David Bianculli (of TV Worth Watching) review the HBO movie depicting the life of animal behaviorist Dr. Temple Grandin, Ph.D., to premier on February 6.  Or download the audio file, which just because available on the web site.  In brief, Bianculli declares the movie is wonderful.  Sitting in for Terry Gross, Bianculli then introduces a segment that draws upon three earlier interviews between Gross and Grandin, corresponding to publication of some of Grandin's books.  Grandin is the focus of one of "seven paradoxical tales" in An Anthropologist on Mars, by Oliver Sacks. 

See books by Grandin in OBIS.  Several of Oberlin's copies of Grandin's and Sacks' books are currently checked out, but you can find other copies to borrow in the OhioLINK catalog. 

Faculty Publication: Sean Decatur on Self-Aggregation of a Polyalanine Octamer in JACS

An Oberlin author alert from Science Citation Index brought this publication to our attention.  Co-authored by Sean Decatur, Dean of the College of Arts and Sciences:

Self-Aggregation of a Polyalanine Octamer Promoted by Its C-Terminal Tyrosine and Probed by a Strongly Enhanced Vibrational Circular Dichroism Signal.

J. Am. Chem. Soc., 2009, 131 (51), pp 18218–18219

The results of this research "offer considerations and insight regarding the de novo design of self-assembling oligopeptides for biomedical and biotechnological applications and highlight the usefulness of VCD as a tool for probing amyloid fibril formation." [from the authors' abstract]. 

Good Reading for Cold Nights

Now that the bright moon is waning and snow showers are headed our way, you might want to grab a few of the new books we just unpacked for the dark evenings ahead.

Science as a Contact Sport is my first choice, especially if you are concerned about the growing number of Americans who say they question the validity of scientific findings regarding anthropogenic climate change.  Author Stephen Schneider, Ph.D., National Geographic Society Fellow, recipient of a MacArthur "genius" grant, expert adviser to every president since Nixon, and recipient with his colleagues of the collective 2007 Nobel Peace Prize (awarded to the Intergovernmental Panel on Climate Change), writes clearly of complex issues and the danger of stereotyping individuals as either "pro" or "con" advocates relative to action on climate change.  This excerpt comes from his chapter The Media Wars: "If the public is bamboozled into thinking that each 'side' in a typical media debate is credible, a typical reaction is to say, 'Well, if the experts don't know, how can I know!  Let's just wait a while until they figure it out.'  That is precisely the strategy of the climate deniers, to create public confusion and apathy, which slows policies that help the planet and our children but hurt special interests who are vested in the status quo."

Schneider points out the difference between necessary scientific skepticism and climate deniers, who "simply ignore the preponderance of evidence presented.  Skeptics should question everything but not deny where the preponderance of evidence leads.  The latter is, at best, bad science or, at worst, dishonesty."

Denialism considers the impact of deniers on scientific progress in a broader context, and received a good bit of attention when it was released last fall.  Read it yourself and see how much you agree with the author's premise.  The New York Times and Grist Magazine reviewed the book within days of each other, and you'll find plenty of customer reviews on Amazon.com.

The new book shelf is burgeoning with many other great options, from Victorian-era science to modern day tragedies and triumphs of discovery.  Browse the shelves - online or in the library!

Salt Marsh Diary is Restorative

Salt Marsh Diary writer Mark Seth Lender was featured on Living on Earth last week, and I was led to his online diary. It is a welcome respite from the snow covered mud outside the library's windows, where no bird or even a lone squirrel is visible from this vantage point and the remains of a snow sculpture is but a hulk of frozen dirty slush.

Lender's words practically sing: "In the glass-calm morning the wading birds come walking, with their long feet talking, tickling at the bottom as they stop, then stride." [from Upon Reflection I]. Escape from northern Ohio briefly with the Mountain Bluebird in Wire to Wire. The photos and prose alike are beautiful. Thank you, Mr. Lender. Salt Marsh Diary is syndicated by the Connecticut River Gazette.

PLoS One to be indexed by Web of Science

As announced on the PLoS Blog, PLoS ONE will be indexed in Web of Science [access for OhioLINK users]. This is good news for our students and faculty, who have long relied on Science Citation Index, a core component of Web of Science, as an essential part of the research process. Read the PLoS Blog post for the whole story. While there, read the post for Jan. 6 as well - it's an excellent indication of the growing importance of PLoS ONE across many science disciplines ["PLoS ONE in the Science Superlatives"].

New publication: Simonson, Bruce, et al. Precambrian Research.

The newest faculty publication listed in Science Citation Index:

Simonson, Bruce M. (Oberlin College Geology Department); McDonald, Iain; Shukolyukov, Alex; Koeberl, Christian; Reimold, Wolf Uwe; Lugmair, Guenter W.

Geochemistry of 2.63-2.49 Ga impact spherule layers and implications for stratigraphic correlations and impact processes.

PRECAMBRIAN RESEARCH 175 (1-4): 51-76 DEC 2009 [access for OhioLINK users]

Partial abstract:
Thin layers rich in spherules formed during impacts by large extraterrestrial objects have the potential to shed new light on impact processes and aid in the long-distance stratigraphic correlation of Precambrian successions. Seven formations in Western Australia and South Africa clustered around the Archean-Proterozoic boundary each contain a single spherule layer...
Cr isotopic compositions are consistent with the formation of the oldest layers on both continents by a single impact event about 2.63Ga.

Why some ducks have such extravagant penises.

From Discover: "Kinkiness Byond Kinky"

"Female ducks can’t stop an unwanted male from delivering his sperm, but the obstacles in their oviducts may give them control over what happens to that sperm."

Need we say more? Get the whole story. Read Discover Magazine Blog.

Last regularly scheduled contribution from David Orr in Conservation Biology

David W. Orr, Paul Sears Professor of Environmental Studies and Politics, has published his last column for Conservation Biology. His essay in the December issue (published online November 24, 2009), Retrospect and Prospect: the Unbearable Lightness of Conservation, is an insightful review and nudge - or shove - onward. Read it. Then get cracking on what needs to be done.

The editors thanked Professor Orr with these words:

After some 20 years of providing columns for Conservation Biology, this is the last regularly scheduled contribution from David Orr, who has asked to retire from this position to devote time to other pursuits. The Board of Governors and Executive Committee of SCB wish to express their profound thanks and gratitude to Professor Orr for his extraordinary and unparalleled service for nearly the entire life of this journal to date. His columns were consistently stimulating, often edgy, and his many insights and observations always challenging to our readers. His writings have been unique in bringing science, politics, economics, and social and ethical issues under a robust and uncompromising vision of what it means to do conservation in our time. His understanding of conservation and devotion to this journal are without equal. The Society recognizes and thanks him for his numerous and diverse contributions; his presence is irreplaceable, and he will be sorely missed in these pages.

Luigi Boitani
SCB President, on behalf of the Board of Governors and Executive Committee

This final essay is important reading, chronicling breathtaking transitions and stupefyingly stuck legislators and policy makers. His contributions (63 columns since 1988) have marked many missed opportunities to slow the train of environmental disaster before we reach the last switch. It is enough to make you weep in frustration, or lie down in despair, but only in preparation for the next round.

The December issue of Conservation Biology will be archived at the OhioLINK Electronic Journal Center, where you can quickly search for all of David Orr's writings within that title since 1992. Older volumes are archived at JSTOR. A 1995 column caught my eye: None so blind, the problem of ecological denial. The column could have been written today, describing climate change deniers. Orr says "denial is manifest in ridicule and ad hominem attacks." That was certainly obvious at Lord Christopher Monckton's speech in Copenhagen on Dec. 9, when Lord Monckton referred to protesters as "Hitler Youth" and "nazis." [Story from It's Getting Hot in Here].

Thank you, Professor Orr, for your writing and advocacy.

Friends of Wetlands Newsletter, available to all

Friends of Wetlands (FOWL), a local all-volunteer organization, has just published its December Newsletter. Everyone is welcome (and invited!) to read and download the newsletter, to learn more about current challenges to wetland ecosystems in northern Ohio. FOWL actively works to educate the public about the essential and multiple roles wetlands have in the environment, and is completely funded by memberships and donations. Enjoy the newsletter, sign up for FOWL email alerts, and consider being active in the organization by participating in the Stakeholder's Meeting on January 9.

Exciting news in this newsletter: Robert F. Kennedy Jr. will be speaker at the 2nd Annual EcoWatch Green Gala. Kennedy, a visionary leader and advocate for the environment, spoke to thousands gathered at the 2007 American Library Association Conference in Washington, D.C. His address at the Green Gala is certain to be dynamic and inspiring.

Also included in the newsletter is William E. Stafford's poem, The Well Rising:

The well rising without sound,
the spring on a hillside,
the plowshare brimming through deep ground
everywhere in the field—

The sharp swallows in their swerve
flaring and hesitating
hunting for the final curve
coming closer and closer—

The swallow heart from wingbeat to wingbeat
counseling decisions, decision:
thunderous examples. I place my feet
with care in such a world.

This poem was chosen by a reviewer on NPR's April 14 "Morning Edition" news program (90.3, 89.7 FM) as the one which, if all people read it, would be most likely to save the planet.

Public Citizen's new blog: Citizen Energy

Public Citizen launched a new blog this week, Citizen Energy, with thoughts on the start of the Climate Conference in Copenhagen. The image of one ton of carbon dioxide, trapped in a threatening-looking balloon, is compelling (reproduced here without permission, but with attribution to america.gov, thank you very much).

Here is snippet from Citizen Energy's blog post: "Public Citizen understands that climate change is a transformative event that requires us to rethink our corporate model of centralized energy production. Rather than promote market-based solutions to protecting the planet that will hand billions of dollars in windfall profits to polluters and Wall Street, we need a decentralized energy system where families generate their power needs from rooftop solar, small scale wind and massive new investments in energy efficiency." Read more.

I like the message on the balloon: reduce every way YOU can. Now!

Alternative Gift Fair This Week! Science Center, Bent Corridor

The Alternative Gift Fair is a great place to buy gifts that support environmental sustainability, fair trade, and organizations that serve those who are unemployed (or underemployed), hungry and homeless. A number of tables are set up in the Bent Corridor of the Science Center from 11:30 am - 1:30 pm this week, representing different agencies or organizations. Each offers an opportunity for gifts that make a positive difference. You make an environmentally sustainable choice by buying gifts offered locally, without excess plastic packaging, thus reducing the fuel and petroleum-based materials associated with transport and packaging.

Come see! The Gift Fair catalog is online, too.

Opening Day for Copenhagen Climate Conference

From The Guardian, UK:

• by Adam Vaughan
• guardian.co.uk, Monday 7 December 2009 17.47 GMT

Newspapers, blogs and individuals around the world have welcomed a common editorial on the Copenhagen climate conference, which opened today. The editorial, which called on rich countries to commit to "deep cuts which will reduce their emissions within a decade", appeared on the Guardian front page and ran in 56 newspapers in 45 countries.

Alan Rusbridger, editor-in-chief of the Guardian, said: "No individual newspaper editorial could hope to influence the outcome of Copenhagen but I hope the combined voice of 56 major papers speaking in 20 languages will remind the politicians and negotiators gathering there what is at stake and persuade them to rise above the rivalries and inflexibility that have stood in the way of a deal." Read the common editorial.

It is a persuasive call for unity on this 68th anniversary of the bombing of Pearl Harbor.

Follow the Climate Talks blog at Environmental Defense Fund for conference updates and news coverage.

Enhanced Searching of PubMed with BioMedSearch

BioMedSearch was just reviewed in The Scout Report of the Internet Scout Project - excellent timing as we celebrate Science and Health during December in the Year of Science.

BioMedSearch is an "enhanced version of the NIH PubMed search that combines MedLine/PubMed data with data from other sources to make the most comprehensive biomedical literature search available. BioMedSearch also provides advanced account features that allow saved searches, alerts, saving documents to portfolios, commenting on documents and portfolios, and sharing documents with other registered users."

The cluster concept is interesting, bringing together papers related to one of 100 broad topics. Scanning through the top list of clusters is relatively efficient, but the subcluster lists (each with another 100 closely related topics) are harder to differentiate as many of the defining terms are repeated. Take a look at the population genetics subclusters, for example.

This maybe perfect for someone who needs an efficient way to follow all new publications in a specific area (polymorphism in schizophrenia, perhaps), and registering for BioMedSearch is free. Give it a try!

Science and Health: December's Theme in the Year of Science

The Year of Science comes to a close with a celebration of science and health - a very fitting focus for the month of December, which began with World AIDS Day, and given a year of concern over the H1N1 virus. Not to mention extraordinarily contentious debates over health insurance/health care reform, and the scrutiny given to health-care legislation in the U.S. Congress. [Track legislation with THOMAS from the Library of Congress]

The theme, though, is science and health, rather than politics, economics, behavior, or social aspects of health. The National Institutes of Health lists dozens of scientific interest groups that function as "assemblies of scientists with common research interests." Member lists for each group might help you identify a contact for an internship or Winter Term project, in addition to showing the broad reach of NIH research support.

The NIH is the "National Medical Research Agency," and is the provider of PubMed ("more than 19 million citations for biomedical articles from MEDLINE and life science journals"). Once only accessible by searching print volumes within a research library, MEDLINE via PubMed is freely available to anyone with an Internet connection. It is one of the great things that our government makes possible - thank you, NIH!

Obviously, you can find health and wellness advice everywhere on the Web, but for comprehensive searching of medical literature, and published studies of scientifically conducted clinical trials, MEDLINE is your best source. You can search it for free as PubMed, or in tandem with any number of EBSCOhost databases (for EBSCOhost subscribers). This is a very efficient way to search multidisciplinary research topics, with quick access to thousands of full-text articles. Link to Academic Search Complete from the Science Library's home page, and look for the "Choose Databases" link at the top of the search screen for a list of all EBSCOhost databases that can be searched simultaneously. Very cool.

AIDS Vaccine Research Shows Promise

World AIDS Day headlines heard on National Public Radio this morning included a report that research for an effective AIDS vaccine continues to look very positive. Follow progress on AIDS vaccine research at IAVI.org: the International AIDS Vaccine Initiative. See New Antibodies Found that Cripple HIV. Learn how you can be part of the effort at the National Institutes of Health site BeTheGeneration.

Abstracts of scientific papers given at the AIDS Vaccine 2009 conference, held October 19-22 in Paris, are freely accessible online in Retrovirology, vol. 6, supplement 3 (also in the OhioLINK Electronic Journal Center and at PubMedCentral). Related publications from those researchers may be found by searching PubMed, the public site for Medline.

A report by NPR's Richard Knox on All Things Considered, September 24, 2009 is a helpful overview of vaccine development and testing. Listen or read the transcript.

World AIDS Day, Tuesday Dec. 1

Looking ahead to World AIDS Day, skim a bit of this book in the OhioLINK ELectronic Book Center: Denying AIDS : Conspiracy Theories, Pseudoscience, and Human Tragedy / Seth C. Kalichman, Foreword by Nicoli Nattrass. Copernicus Books, an imprint of Springer, 2009. The introduction includes this observation:

"Denialism – like stigma, sexism, and homophobia – undermines the fight against AIDS. At the very least, denialism diverts attention and resources from the global AIDS disaster. At its worst, it disinforms affected populations about the importance of prevention, the necessity of HIV testing, and the availability of life-prolonging treatments. At its core, denialism is destructive because it undermines trust in science, medicine, and public health."

AIDS denialism should not be dismissed as the baseless opinion of a small, misinformed minority. Kalichman stresses that the rhetoric of denialism is quite harmful, especially to those who are HIV-positive:

"There are now countless HIV infected people who have avoided getting tested for HIV, rejected their HIV positive test results, ignored safer sex practices, failed to disclose their HIV status to sex partners, and refused HIV treatments for themselves and their children because they have believed denialists. Health decisions that are disinformed by denialist rhetoric are why we must care about denialism."

Be informed. Rely on factual sources, based on expert peer-reviewed medical research.
HIV Facts from:

• Centers for Disease Control and Prevention
• National Aids Trust (UK)

UN Climate Change Conference in Copenhangen: Prospects for Progress?

Living on Earth's Steve Curwood chatted with U.N. Foundation President, Tim Wirth, a former U.S. Senator and Under-Secretary of State for Global Affairs, as the Copenhangen Conference looms closer. Wirth stressed the urgency of the global warming, and the opportunity for China-US relations to make the biggest contribution worldwide in reducing carbon emissions saying, "we're the biggest developed world, they're the biggest developing country; between the two of us we have about 50 percent of the world's carbon emissions. So, if we can figure out together a joint program for moving toward a greener and ultimately low-carbon economy, then we have an opportunity together to really salvage the world."

Listen to the entire interview or read the transcript online.

COP15 Copenhagen. Denmark's host country web site on the convention.
CleanSkies.com news on the Copenhagen conference.