New Faculty Publications in Chemistry, Environmental Studies and Geology

Belitsky, Jason M., Chemistry
Sono K, Lye D, Moore CA, Boyd WC, Gorlin TA, Belitsky JM. 2012. Melanin-based coatings as lead-binding agents. Bioinorganic Chemistry and Applications :361803. [access at PMC]

Hubbard, Dennis, Geology
Lescinsky H, Titus B, Hubbard D. 2012. Live coral cover in the fossil record: An example from holocene reefs of the dominican republic. Coral Reefs 31(2):335-46. [access at EJC]

Page, F. Zeb, Geology
Blondes MS, Brandon MT, Reiners PW, Page FZ, Kita NT. 2012. Generation of forsteritic olivine (fo(99 center dot 8)) by subsolidus oxidation in basaltic flows. J Petrol 53(5):971-84. [access at EJC]

Shammin, Md Rumi, Environmental Studies
Bagstad KJ and Shammin MR. 2012. Can the genuine progress indicator better inform sustainable regional progress?-A case study for northeast ohio. Ecol Ind 18:330-41. [access at EJC]
 
Simonson, Bruce, Geology
Bottke WF, Vokrouhlicky D, Minton D, Nesvorny D, Morbidelli A, Brasser R, Simonson B, Levison HF. 2012. An archaean heavy bombardment from a destabilized extension of the asteroid belt. Nature 485(7396):78-81. [access at Nature]

Thompson, Robert Q., Chemistry
Thompson RQ, Chu C, Gent R, Gould AP, Rios L, Vertigan TM. 2012. Visualizing capsaicinoids: Colorimetric analysis of chili peppers. J Chem Educ 89(5):610-2. [access at ACS]

These six articles were found by searching "Oberlin Coll*" in the address field of Web of Science, limited to the last four weeks in Science Citation Index, then exporting the references to RefWorks and formatting the list according to the Ecology journal format.

Just in time... for you to have no time.

Recognizing that the first day of exams is not when most people will look at the new books shelf (more's the pity), I will highlight just two:

Pictured rocks of the Upper Peninsula is purely a personal choice, as a Michigander and someone who loves the northern parts of the state.  Spend just a few minutes with this book and you will feel refreshed and ready for the next exam:
Geology and landscape of Michigan's Pictured Rocks National Lakeshore and vicinity / William L. Blewett.
The world of trees  is my second choice.  The trees around Oberlin this spring are amazing! - in fact, anything that uses carbon dioxide for growth (anything plant-like, that is) is growing by leaps and bounds.  It's a bit alarming, to be honest.

Happy Buddha? Mycobacterial infection following tattoo

Annika Sullivan '12 is a co-author on a paper originating from the Oregon Health & Science University, Portland:

Happy Buddha? Kevin L. Winthrop; Cara D. Varley; Annika Sullivan; Robert S. Hopkins.  2012.  Clinical Infectious Diseases  54: 1670-1671.

Oberlin does not subscribe to this journal, but the publisher provided this link for limited number of free access views of the html version. The tattoo identified in the article as the origin of a mycobacterial infection depicts a joyful buddha in a standing pose, completed using a grey ink. The dye was created by mixing black tattoo ink with tap water, a common source of Mycobacterium chelonae.

The authors observed "Outbreaks associated with [Myccobacterium organisms] may occur when contaminated tap water is inappropriately used in surgical, cosmetic, or other procedures. Symptoms typically develop 2–3 weeks after exposure."

Today's lesson: when getting a tattoo, insist that purified water be used throughout the procedure.

University of Minnesota compiles database of peer-reviewed, open-source textbooks | Inside Higher Ed

This is an exciting development, and could dramatically change the learning process in undergraduate courses.  Reliable participation by faculty in many colleges and universities would be useful, to extend peer-review to a wider audience.
University of Minnesota compiles database of peer-reviewed, open-source textbooks | Inside Higher Ed

Something fishy online

We now have access to Elsevier's Encyclopedia of Fish Physiology online, at sciencedirect.com.  If you are asked to identify your institutional affiliation before gaining access, be sure to select the Oberlin College option (not Oberlin College/OhioLINK, which gives access to the journals archive only).

Here's a snippet to pique your interest:

"At a conservative estimate at least 40% of the world's vertebrates are fish. On the one hand they are united by their adaptations to an aquatic environment and on the other they show a variety of adaptations to differing environmental conditions - often to extremes of temperature, salinity, oxygen level and water chemistry."  One chapter begins with this truism:  "All fish are united by the requirement to obtain food, while (at least during some phase of their life) avoiding being food." It's a challenging life, beneath the water's surface.  Take the plunge and learn more.

New articles by faculty and students

Oberlin-authored articles published in April 2012 included the following:

From Emeritus professor of chemistry Norm Craig with Oberlin student Hengfeng Tian -
Craig N. C., H. Tian, and T. A. Blake. 2012. Analysis of the Rotational Structure in the High-Resolution Infrared Spectrum of trans-Hexatriene-1-C-13(1): A Semiexperimental Equilibrium Structure for the C-6 Backbone of trans-Hexatriene. Journal of Physical Chemistry A 116:3148-3155. [access at ACS]

From Neuroscience professor Jan Thornton with Oberlin students Sarah McConnell, Juliet Alla, and Elizabeth Wheat -
McConnell S. E. A., J. Alla, E. Wheat, R. D. Romeo, B. McEwen, and J. E. Thornton. 2012. The role of testicular hormones and luteinizing hormone in spatial memory in adult male rats. Hormones and behavior 61:479-486. [access at OhioLINK EJC or sciencedirect.com]
Curious about those hormones and spatial memory?  Here's the summary statement from the abstract:
"[The] data indicate that testicular androgens are important for maximal levels of spatial working memory in male rats, that testosterone may be converted to estradiol and/or dihydrotestosterone to exert its effects, and that some of the effects of these steroid hormones may occur via negative feedback effects on luteinizing hormone."  No indication is given on any possible linkage between testosterone and human male behavior vis-à-vis seeking directions while traveling through unfamiliar territory.  Sorry, couldn't resist.

Petersen article in Marine Ecological Processes

A recent publication from John Petersen, Associate Professor/Director of the Environmental Studies Program, was selected for inclusion in the treatise Marine Ecological Processes (2010), edited by J.H. Steele [borrow through OhioLINK]. Petersen's article first appeared in the Encyclopedia of Ocean Sciences, 2nd ed., which subscribers can access on sciencedirect.com.

Petersen, John E. & W.M. Kemp. 2008. Mesocosms: enclosed experimental ecosystems in ocean science. Encyclopedia of Ocean Sciences.  Elsevier, New York, pp 732–747.

New publications from faculty & students

Five recent publications by science faculty, some co-authored with current students or recent alumni, are higlighted here.  Oberlin affiliated authors are noted with bold text:

Craig, Norman C., Clay C. Easterday, Deacon J. Nemchick, Drew F.K. Williamson, Robert L. Sams  2012. Rotational analysis of bands in the high-resolution infrared spectra of cis,cis- and trans,trans-1,4-difluorobutadiene-2-d(1). Journal of Molecular Spectroscopy 272(1):2-10.

De Smet I., P. J. White, A. G. Bengough, L. Dupuy, B. Parizot, I. Casimiro, R. Heidstra, Marta Laskowski, M. Lepetit, F. Hochholdinger, X. Draye, H. Zhang, M. R. Broadley, B. Peret, J. P. Hammond, H. Fukaki, S. Mooney, J. P. Lynch, P. Nacry, U. Schurr, L. Laplaze, P. Benfey, T. Beeckman, and M. Bennett. 2012. Analyzing lateral root development: how to move forward. Plant Cell 24(1):15-20.

Glass B. P., Bruce M. Simonson. 2012. Distal impact ejecta layers: spherules and more. Elements 8(1):43-48.

Moran Sean D., A. M. Woys, L. E. Buchanan, Eli Bixby, Sean M. Decatur, and M. T. Zanni. 2012. Two-dimensional IR spectroscopy and segmental C-13 labeling reveals the domain structure of human gamma D-crystallin amyloid fibrils. Proceedings of the National Academy of Sciences of the United States of America 109(9):3329-3334.

Schmidt, Amanda H., A. S. T. Robbins, J. K. Combs, A. Freeburg, R. G. Jesperson, H. S. Rogers, K. S. Sheldon, and E. Wheat. 2012. A new model for training graduate students to conduct interdisciplinary, interorganizational, and international research. Bioscience 62(3):296-304.

Contentious Bird Flu Research Will Be Published

From the NPR health blog on March 30, 2012:
by Nell Greenfieldboyce

The National Science Advisory Board for Biosecurity "has reconsidered its advice to keep certain details of bird flu experiments secret. Revised versions of manuscripts that describe two recent studies can be openly published, the committee now says. The decision could help end a contentious debate that has raged within the scientific community for months."

Nature and Science are the two journals in the process of publishing the reports.  Nature's blog, in a post by Ed Yong, featured this headline last week: "Mutations behind flu spread revealed.  Details of one of two controversial mutant flu papers discussed in London."

Yoshihiro Kawaoka, of the School of Veterinary Medicine at the University of Wisconsin–Madison, revealed that an altered form of the H5N1 virus was able to reproduce in a ferret's airways, and that spontaneous mutations of that form of the virus resulted in three new mutations (not represented in any virus database) which allowed the virus to go airborne between infected and healthy ferrets.       

Read more about the research and the controversy surrounding it in Nature‘s mutant flu special and in news analysis dated April 6 from Science, by Jon Cohen and David Malakoff.

Open Access from Nature Climate Change

This comes from The Nature Publishing Group at Nature.com, in an email dated April 4, 2012:

"Nature Climate Change is one! To celebrate, the editors have pulled together a collection of highlights from the journal over the last year – free to view until the end of April 2012."

See the First anniversary highlights 

"Launched in April 2011, Nature Climate Change is a monthly journal dedicated to publishing the most significant and cutting-edge research on the impacts of global climate change and its implications for the economy, policy and the world at large. The journal is interdisciplnary and strives to forge and synthesize ideas across the physical and social sciences." 
While at Nature.com, read the news note "How carbon dioxide melted the world," summarizing research findings published yesterday: Shakun, J. D. et al. Nature 484, 49–54 (2012). NPR adds insight with a story from Christopher Joyce this morning: Shake it off: earth's wobble may have ended ice age.

Neurobiology books on exhibit, coincides with presentation by Jeffrey Burgdorf

From the book display
in the Science Library

First In Family Speaker Series features Jeffrey Burgdorf on Wednesday, April 4. Dr. Burgdorf will present "The Neurobiology of Positive Emotions: from laughing rats to a novel antidepressant in clinical trials for depression."  Stop in the science library to peruse a selection of books from our neurobiology section, on exhibit in conjunction with Burgdorf's talk.

Copies of recent papers by Burgdorf and collaborators are also on display, including "Frequency modulated 50 kHz ultrasonic vocalizations reflect a positive emotional state in the rat : neural substrates and therapeutic implications" by Jeffrey Burgdorf and Joseph R. Moskal in Handbook of behavioral neuroscience, v. 19.

From the OC Events calendar:
First In Family Speaker Series
WHEN: 4:30pm - 6:00pm
WHERE: Science Center, Norman C. Craig ’53 Lecture Hall @ 119 Woodland Street, Oberlin, OH 44074

Dr. Burgdorf earned a doctorate in 2005 at Bowling Green State University, where he validated that rat ultrasonic vocalizations reflect distinct positive and negative emotional states relevant to depression, and further explored the neuronal basis of these vocalizations. 

Poetry in Science

April is National Poetry Month; while the science library is full of instructive, enlightening and absorbing prose, poetry is harder to find in our stacks.  But poems with scientific imagery are not hard to find!  Try this book, as a starting place: Curve away from stillness : science poems / John Allman ; afterword by Peter S. Coleman. New York : New Directions, c1989.
Available in the OhioLINK ebook center or from the Main library.  There are enough poems in this little book to read one a day during the entire month (one per day for each workday, that is).

If you loved every minute of CHEM254 or BIO213 you are sure to appreciate the Biochemists' Songbook (complete with selected scores and detailed biochemical pathways).  It is in the Science library and also online.

Glorious Magnolias

This was a spectacular day last week - in the midst of midterms, the warming sun and sweet fragrance under the magnolias improved outdoor studying immeasurably.

The blossoms fell fast in the days following, and now litter the pavement in front of the Science Center.  The fragrance lingers, however, to lessen disappointment on this overcast, chilly day.  Such is spring break in Oberlin.

Sounds of the natural world = sounds of the divine

Living on Earth featured a marvelous conversation this week with Bernie Klaus, trained musician who is now an "acoustic adventurer."  Listen to the miraculous sounds he has recorded, including a haunting symphony by two packs of wolves, the scraping of insects' wings and sap moving inside trees.  Remarkable!

We will order Great Animal Orchestra: Finding the Origins of Music in the World's Wild Places, by Klaus, just published this year.   Listen to other sounds from nature in the Borror Laboratory of Bioacoustics archive in the OhioLINK DMC. The Birds of North America also offers audio files, as does Grzimek's Animal Life.

Klaus remarked, toward the end of the Living on Earth segment, that "the sounds of the natural world are the sounds of the divine."  You may share that conviction after listening to his recordings.

Sherwood Rowland, CFCs, ozone depletion and the public role of scientists

Sherwood Rowland, CFCs, ozone depletion and the public role of scientists
RealClimate has posted a fine tribute to Nobel Prize Winner F. Sherwood Rowland, who died on March 10 at the age of 84 (obituary in Nature).  This observation of Dr. Rowland, following a lecture that prompted questions from an audience member with slight understanding of atmospheric science, is particularly telling:

"While everyone else was enjoying a beverage, cookies, and conversation, Sherry had been off in the corner for about 30 minutes talking with the questioner, explaining basic principles of atmospheric science, how the greenhouse effect works, etc. It didn’t matter that one of the two of them had a Nobel Prize while the other may not have had any formal education. What mattered to Sherry is that he had an opportunity to educate someone about this important issue, and that mattered more than anything."

I greatly appreciate this quote from Dr. Rowland, spoken during this Nobel Prize acceptance speech:

“What’s the use of having developed a science well enough to make predictions if, in the end, all we’re willing to do is stand around and wait for them to come true?”

Chemistry books top the new books list

The preponderance of new books in our last shipment are chemistry related, from Philosophy of Chemistry and The Chemical Element to Chemical Crystallography.  The last title includes highly specialized chapters by different contributors (e.g., "Construction and structure of metal-organic frameworks with specific ion-exchange property," by Man-Sheng Chen), while the first two are aimed at a broader audience.  The Chemical Element was published in conjunction with the International Year of Chemistry (2011) and relates directly to the UN Millennium Development Goals.  It demonstrates how the science of chemistry is essential for solving the most critical goals related to energy, climate, food, water, poverty, education and health.  It is accessible, important reading for anyone concerned about achieving a sustainable future for 10 billion or more people.  More new books.

Caterpillars: beautiful, mundane, beneficial and destructive

Now on the new book shelf:
Owlet Caterpillars of Eastern North America, by  David L. Wagner, Dale F. Schweitzer, J. Bolling Sullivan & Richard C. Reardon.  Princeton Univ Press.

This arrived on approval from our book vendor, YBP (Yankee Book Peddler, a division of Baker & Taylor), and I was entranced.  The publisher's description speaks for itself, and the thousands of color photographs are indeed impressive.  This is more than a guide to identifying species; the accompanying text tells the important story of the essential roles caterpillars have in varying ecosystems.  Gain a new appreciation of such humble seeming invertebrates by spending a bit of time perusing this volume.

Complete Dictionary of Scientific Biography online

From Gale/Cengage

We have owned the print format of the Dictionary of Scientific Biography for many years, and can access it in the OhioLINK Electronic Books Center.  We now subscribe to the online version at the publisher's website (Gale/Cengage), part of the Gale Virtual Reference Library, where searching and browsing functions are very nicely supported.  Link to it from the OBIS catalog record.  Composed of 18 large print volumes, the title "Dictionary" does not do justice to this comprehensive encyclopedic work.  Take time to browse the index volume and jump from one entry to another, and you will gain a new understanding of the development of science and the people who advanced that knowledge throughout centuries.  Simply browsing the list of illustrations indicates the wide breadth of scientific information represented in the work.  Go discover!

In Memoriam: Sonali Seth, '02

We were so sorry to learn of the passing of Sonali Seth, '02 who was a bright, engaging and lively member of our student staff for two years.  Sonali's welcome to all who entered in the library was warm and genuine, and she was a wonderful reference assistant in the period of transition between the old and new library.  As a senior science major, Sonali was truly helpful to everyone getting their bearings in the new science center.  A 2005 graduated of the Johns Hopkins Bloomberg School of Public Health as a new MPH, Sonali had a passion for humanitarian assistance and health & human rights.  Her good works will be remembered by the hundreds of people whose lives she touched.  This photo was taken when Sonali first began work with us, in the fall of 2000, in the last year of operation of the library in Kettering Hall.

Energy Matters: Oberlin Project Blog is launched

Head over to Cindy Frantz's first post on the new Oberlin Project blog, where you can respond with your own thoughts on what is important about Oberlin and sign up for the project's e-newsletter.  Associate Professor of Psychology Frantz is also the Co-Chair of the Energy Planning Committee of the Oberlin Project.  Today's blog post appears in this week's Oberlin News Tribune, with the promise of future columns on "energy matters" in Oberlin and the immediate environs.  Frantz concludes her first column with these remarks:  "Energy matters in Oberlin because we care about each other, our community, and our planet.  We all want Oberlin to be healthy and prosperous.  By thinking carefully about our energy, we pave the way for a future we can all get excited about."  These are sentiments we can support throughout the community.  I encourage all residents - college and town - to learn more and be engaged in the Oberlin Project.

Spring Carrel Sign-Up Starts Today

Welcome to Spring Semester!  All carrels were cleared at the end of fall semester, and new carrel assignments for spring semester will be posted on Friday, February 10.
Carrel applications are on the circulation desk -- open to all students; preference is given to science majors, based on seniority.  Carrel regulations and an application form are also online, here.

Wild-eyed forerunners

Among the new books received today is this research monograph, with a strong emphasis on understanding evolution of the earliest non-mammalian therapsids through understanding their bone microstructure. Sixteen specialists contributed to the volume, edited by Anusuya Chinsamy-Turan (who also co-authored six of the book's eleven chapters).  

Detailed research findings on cranial microstructure, bone and dental histology, bone degradation, and vascularized bone tissue patterns fill most of the chapters, within the context of relating those minute observations to new understandings of how the earliest land vertebrates evolved into modern day mammals.  Fascinating stuff, evolution!  See the OBIS record for table of contents and contributors.

Other new books received today cover a wide range of subjects, from anthropology to geophysics, as well as polar bears facing extinction, a birdwatching guide controversy, bioconstitutionalism and genomics, mountains in Antarctica and beaches worldwide, plus an impressively chunky dictionary of entomology.  See the new book list.

Science Breakthrough of 2011: HIV Treatment as Prevention

Science's editors and news staff have selected "HIV Treatment as Prevention" as the Scientific Breakthrough of the Year 2011, based on findings by the HIV Prevention Trials Network (HPTN) that antiretroviral drugs reduced the risk of heterosexual transmission by 96%.  Read the full story.

Science is published by the American Association for the Advancement of Science (AAAS).

7 new publications by Karla Parsons-Hubbard and colleagues

All seven of the following articles by Associate Professor of Geology Karla Parsons-Hubbard are published in Palaeogeography, Palaeoclimatology, Palaeoecology, special issue:  The Shelf and Slope Experimental Taphonomy Initiative (SSETI): Thirteen years of taphonomic observations on carbonate and wood in the Bahamas and Gulf of Mexico.  [access for subscribers at OhioLINK EJC or ScienceDirect.com]

• Brett CE, Parsons-Hubbard KM, Walker SE, Ferguson C, Powell EN, Staff G, Ashton-Alcox KA, Raymond A. 2011. Gradients and patterns of sclerobionts on experimentally deployed bivalve shells: Synopsis of bathymetric and temporal trends on a decadal time scale. Palaeogeography Palaeoclimatology Palaeoecology 312(3-4):278-304.

• Heise EA, Raymond A, Parsons-Hubbard K, Walker SE, Staff G, Powell EA, Brett C, Ashton-Alcox KA. 2011. Wood taphonomy in a tropical marine carbonate environment: Experimental results from lee stocking island, bahamas. Palaeogeography Palaeoclimatology Palaeoecology 312(3-4):363-79.

• Krause RA, Jr., Parsons-Hubbard K, Walker SE. 2011. Experimental taphonomy of a decapod crustacean: Long-term data and their implications. Palaeogeography Palaeoclimatology Palaeoecology 312(3-4):350-62.

• Parsons-Hubbard KM, Brett CE, Walker SE. 2011. Taphonomic field experiments and the role of the shelf and slope experimental taphonomy initiative. Palaeogeography Palaeoclimatology Palaeoecology 312(3-4):195-208.

• Powell EN, Staff GM, Callender WR, Ashton-Alcox KA, Brett CE, Parsons-Hubbard KM, Walker SE, Raymond A. 2011. Taphonomic degradation of molluscan remains during thirteen years on the continental shelf and slope of the northwestern gulf of mexico. Palaeogeography Palaeoclimatology Palaeoecology 312(3-4):209-32.

• Powell EN, Staff GM, Callender WR, Ashton-Alcox KA, Brett CE, Parsons-Hubbard KM, Walker SE, Raymond A. 2011. The influence of molluscan taxon on taphofacies development over a broad range of environments of preservation: The SSETI experience. Palaeogeography Palaeoclimatology Palaeoecology 312(3-4):233-64.

• Walker SE, Parsons-Hubbard K, Richardson-White S, Brett C, Powell E. 2011. Alpha and beta diversity of encrusting foraminifera that recruit to long-term experiments along a carbonate platform-to-slope gradient: Paleoecological and paleoenvironmental implications. Palaeogeography Palaeoclimatology Palaeoecology 312(3-4):325-49.

Environmentalism at Oberlin

All things environmental at OC is the overarching goal of a brand new web site created by Annika Sullivan, Sustainability Literacy Intern (also one of the many dedicated student assistants in the science library).  Annika observed that this is a work in progress and will change as groups form, issues change and new initiatives emerge.  Feedback is welcome.  It looks great so far!

Go to Environmentalism at Oberlin.

Visualizing Photons @ MIT's Media Lab - the Camera Culture Group

Visualizing Photons in Motion at a Trillion Frames Per Second.  Remarkable!  The investigators offer these observations for the possible applications of their work: "Beyond the potential in artistic and educational visualization, applications include industrial imaging to analyze faults and material properties, scientific imaging for understanding ultrafast processes and medical imaging to reconstruct sub-surface elements, i.e., 'ultrasound with light'. In addition, the photon path analysis will allow new forms of computational photography, e.g., to render and re-light photos using computer graphics techniques."

Annual Reviews on your mobile device

annualreviews.org

This comes from Annual Reviews, Inc., publisher of some of our favorite titles in the library and now more convenient than ever!  Connect to the Annual Reviews mobile site before leaving campus for winter break, and you will be able to access anything on the site while you are away.

The mobile site includes articles formatted for personalized browsing, searching, and provide a reading experience optimized for a variety of mobile devices.  You can also download articles for offline reading and easily share article abstracts and links via email and social networks.

Visit annualreviews.org/page/about/mobile for more information.

While there, search "oberlin college" - an interesting list results, from personal narratives of scientists whose lives were influenced in some manner by Oberlin to in-depth review articles by past and present faculty members. Classic papers, such as Norm Henderson's Human Behavior Genetics, J. Milton Yinger's study on Ethnicity, and Birdsey Renshaw's early review on Nerve and Synaptic Transmission are followed by more recent reviews by Bruce Simonson on spherule layers and Daphne John on the division of household labor.

Whatever your research interests, there is an Annual Review title that undoubtedly includes an excellent article, written by a leading expert in the filed, that provides historical context, critical analysis of peer-reviewed literature and thoughtful conclusions to spur new investigations in that subject.  We no longer receive the volumes in print, so the web site is our best access point.  Take full advantage of all of the features now offered!

Predatory, open-access publishers

Beall's List of Predatory, Open-Access Publishers has been updated, including publishers who are essentially fraudulent in their claims of scholarly peer-review and others who are launching far too many journals to adequately ensure a quality editorial process.  Extraordinary author fees for manuscript submission do not guarantee an ethical, reliable scholarly communication cycle.  Some are hardly more than vanity presses, according to Jeffrey Beall, academic librarian at the University of Colorado Denver.  Researchers are forced into the position of "buyer beware" if sending a manuscript to one of these publishers, and, even more to the point for undergraduate students, readers must be very discerning to understand which papers have been given a rigorous peer-review by knowledgable scholars in the discipline of the article in question.

Journals from some of these publishers are listed in the Directory of Open Access Journals, which strives to list "quality controlled" scientific and scholarly journals.  Inclusion in the DOAJ may help assure the reader of peer-review, but does not preclude predatory practice by the publisher to garner as many authors' manuscripts as possible, at the highest price, in a process that may undermine the goals of scholarly communication.

First Snowfall in Oberlin, Gone by Midday

There was no hint of the early morning trace of wet snow by midday, as sun broke through gray clouds and blue skies chased away even the memory of slush on soggy ground.  

According to the new edition of The Weather Almanac, received today, the last time we scrapped through November with just a trace of snowfall was 2001.  The normal amount (mean) for the month is 5.1 inches (since 1980, as measured at Cleveland Hopkins Airport weather station).  The Weather Almanac is full of interesting data, as well as lengthy, factually accurate narratives on climate topics.   

The section on global warming and climate change is thoroughly updated.  If you want an well-organized, easy to read, detailed account of how climate is changing, minus the hype and political posturing, take a look at pp. 317-352.

Impact of Hydrofracturing for Natural Gas on Ohio's Forests

Buckeyeforestcouncil.org

Cheryl Johncox, Executive Director Buckeye Forest Council

will speak on

Impact of Hydrofracturing for Natural Gas on Ohio's Forests

Thursday Dec. 1, 2011 -  4:30 p.m. 

Heiser Auditorium, Kendal @ Oberlin

Ms. Johncox will describe the environmental hazards associated with fracking, and pressures being brought to bear on landowners to lease public and private lands for drilling.
Sponsored by the Kendal Environmental Concerns Committee and League of Women Voters of the Oberlin Area.  
Martha's Journal, official publication of the Buckeye Forest Council, is named for the last known Passenger Pigeon, who died in the Cincinnati Zoo in 1914.  The Passenger Pigeon, once numbered in the millions throughout eastern forests, in flocks so huge that they took hours to pass while migrating, was driven to extinction in part by human-caused destruction not unlike the continued fragmentation of forests still standing.  
Come learn what effect hydraulic fracturing could have on Ohio's forests.  The public is invited.

Connect with Buckeye Forest Council on Facebook.

Bill McKibben in Craig Auditorium, 7 pm, Nov. 28

Learn more about 350.org and Bill McKibben as a spokesperson for Tar Sands Action.

Read one of the dozen books by author Bill McKibben in the college library.

Read Nicholas Stern's review of Eaarth: Making a life on a tough new planet.  Review published in the New York Review of Books 57(11): 35-37, June 2010. Borrow a copy of Eaarth.

Most importantly - show up at the Craig Auditorium to hear one of the most influential environmentalists of our time, and learn more about the potentially disastrous consequences of hydraulic fracturing or fracking: a practice that consumes millions of gallons of water in order to force natural gas from shale beds thousands of feet beneath the earth's surface, leading to methane release in groundwater and surface contamination, in addition to many other negative effects.

Be informed.  More on fracking from the Buckeye Forest Council and New York Times Magazine (Nov. 17, 2011)

New publication from Norm Craig, in J Molecular Spectroscopy

From ScienceDirect

A new publication from Norman C. Craig, Emeritus Professor of Chemistry, published October 2011:

Boopalachandran P., N. C. Craig, and J. Laane. 2011. Gas-phase Raman spectra of hot bands of fundamentals and combinations associated with the torsional vibration of s-trans-1,3-butadiene and its deuterated isotopologues. Journal of Molecular Spectroscopy 269:236-241.

OhioLINK users can access this in the Electronic Journal Center.

Supplementary data for this article are available on ScienceDirect and as part of the Ohio State University Molecular Spectroscopy Archives. [download the suppl. figure]

On this date in 1772: Lavoisier changed chemistry for all time.

Source: Yale Univ Chem 125
history project

Here is a tidbit of chemistry history, from The Illustrated Almanac of Science, Technology, and Invention: "'A week ago I discovered that sulfur on being heated gained weight.  It is the same with phosphorus,' reported Antoine Lavoisier, 29, in a simple note to the Secretary of the French Academy of Sciences.  The discovery advanced and changed chemistry for all time." (November 1, 1772).  Lavoisier showed that the weight gained equaled weight lost in the air, and established his Law of Conservation of Mass: The mass of the products of a chemical reaction are equal to the mass of the individual reactants.

What seems so basic, now, to any high school chemistry student was of phenomenal importance in 1772, invalidating the old phlogiston theory and establishing Lavoisier as the "Father of Modern Chemistry due to his use of step-by-step experimental procedures, making careful measurements, and keeping accurate records." (Scientific Laws, Principles, and Theories: a reference guide / Robert E. Krebs, p. 205).

Royal Society opens its archives and launches Open Biology

Royal Society of London Open Access

Open access news from the Royal Society of London is very welcome.  Read more about the recently launched Open Biology, "a journal run for scientists by scientists." The Royal Society says that the editors and editorial board intend to "ensure a fair and speedy review process without recourse to unnecessary rounds of revision,"  It is very new, so check back often for more publications.

The Royal Society open archive announcement coincides with Open Access Week, and celebrates free access to any article  published more than 70 years ago. This is remarkable, considering the historically significant research findings published by the Royal Society.  Try the advanced search at the Royal Society site, and you'll find that the publication date range extends back to 1665. There are not many (any?) other sites on the Internet where you can find such an authentic and rich archive of scientific discovery. Explore!

PLoS Blogs: Making Science Understandable and Accessible

Today on one of the Public Library of Science (PLoS) Blogs is an interesting account of gathering sediment cores from tropical mud, to document changes in precipitation over thousands of years by measuring amounts of hydrogen ions in the sediment.  What's so great about mucking around in the tropics to measure hydrogen ions?  As author Conor Myhrvold of MIT SciWrite explains, it gathers "physical evidence of recent manifestations of tropical climate change several thousand years ago to make sure the parameters in the [climate change] models are grounded in reality."  Reading this will give insight into what it takes, physically, to amass reliable data for understanding climate change, and a deeper appreciation for climate scientists' assessment of those data.  At the very least, it's a good way to balance what you may have heard from certain politicians. 

While at the PLoS Blogs site, take a moment to see all of the other perspectives offered there and link to the many wonderful open access PLoS journals.  Open Access Week ends soon - take this open access challenge and find an article that interests you (try DOAJ for a start) to forward to a friend or colleague, confident that he or she will also be able to read it in its entirety.  No subscription required.

Going away for Fall Break? Need access to journal articles?

Information on remote access to the library's resources is here.  In a nutshell, do this:

1. Download the VPN Client (Cisco) from the CIT website.
2. Launch the client and login before trying to search library databases or download articles.
3. Be sure the barcode on the back of your OCID has been input into the library's circulation system, if you will be requesting any items on the OhioLINK library catalog.  We can do that over the phone, if needed.  440-775-8310.

Problems?  Questions?  Contact science.library@oberlin.edu or chat with us on Meebo IM.

Have a great break!  The library will be open all week, Mon-Fri, 9-noon and 1-4:30, if you're staying on campus.

PubMed Central 10th Anniversary Video

PubMedCentral (PMC) celebrated its 10th Anniversary in 2010, and this commemorative video was posted by NCBI NLM in July 2011.  Just 12 minutes long, and definitely worth viewing despite the time elapsed since the video was distributed.  Establishing the open access archive was one of the most important developments in scientific communication in the past decade, and the video chronicles its rapid rise to prominence and influence on other repositories of scientific articles.  In addition to its role as an archive, PMC leads directly to NCBI and PubMed databases, with links to protein or nucleotide data or citing articles beyond those in the PMC, among other options.  See this 2009 article co-authored by biology professor Michael Moore and explore some of those linking options:
Rosid radiation and the rapid rise of angiosperm-dominated forests.
Proc Natl Acad Sci U S A. 2009 March 10; 106(10): 3853–3858.

Committed to Biodiversity? Go Swim with Sharks!

Shark Tourism is a growing business with a helpful purpose that may not be entirely clear to thrill seekers in wet suits - preserving the diversity of predators essential for maintaining ecosystem balance.  Listen to this great segment on Living on Earth, October 14, 2011, featuring Samuel “Doc” Gruber, a marine scientist at the University of Miami, who has been studying lemon sharks for 20 years from the beachfront lab he started on Bahamas’ Bimini island.

If you're considering a dip with sharks (or would prefer to appreciate them from afar), check out this magnificent reference book on our new book shelf:  The Sharks of North America / José I. Castro ; color illustrations by Diane Rome Peebles.  New York : Oxford University Press, c2011

PubMed: access to free medical articles online is unmatched

www.ncbi.nlm.nih.gov/m/pubmed/

Open Access Gem of the Week:
For rapid, effective and entirely free (to the user) indexing to open access medical literature, PubMed can't be duplicated or surpassed.  If you need to limit your search to medical articles that are freely available, PubMed is simply the best.  Do any search and notice on the far right of the results screen a link to "Free Full Text" -- there are many other limits and very powerful search options, but this is one of the most obvious and helpful for the public.

Medline, the database underlying PubMed, can be simultaneously searched with Chemical Abstracts in SciFinder; with BIOSIS and the ISI citation indexes in Web of Knowledge; and with a whole host of databases in EbscoHost.  There are excellent reasons to search Medline in those different platforms, but none of them are freely accessible by the public, world-wide, and offer the same ease of quickly linking to free articles online.  PubMed:  our tax dollars at work, and worth every penny.  Try the advanced search interface with its "search builder" and be amazed at the options for creating a well-focused search.   PubMed Mobile provides access from just about anywhere, anytime.  Thank you, NCBI.

Cool Citation Tracking Tools @ the Geek Fest - Oct. 11

Come to the library's Geek Fest on Tuesday October 11 and have fun following citations.  Truly, it will be fun!

• Easily find Oberlin faculty members whose research has been referenced (cited) by hundreds of other authors in the past twenty years.  
• See who has cited any published paper that interests you, from any discipline or time period, using the Web of Science - and, in one more step, find all of the papers related to those citing papers with the shared reference feature.  
• Leaping (linking) from one citation to the next in mere milliseconds, all within the context of millions of scholarly articles indexed in the Web of Science - including Arts & Humanities Citation Index, Social Sciences Citation Index and the Science Citation Index.  Plus Conference Proceedings!

Once you've mastered the Web of Science, visit other stations around Azariah's Cafe, set up to delight you with new ways to find, store, organize and use information.  Food, beverages, friendly librarians, fellow students, writing tutors, prizes!  Mark your calendar...  be there!

Rain Barrel Workshop at the Oberlin Depot

Want to conserve water with your own rain barrel? Make your own? Head to the Oberlin Depot on Saturday, October 8, 2011.

OSWAMP-Oberlin Stormwater Management Project
Sign up for a RAIN BARREL WORKSHOP

Sat. Oct. 8, 2-5 pm
Oberlin Depot (beside the bike path, between S. Professor and S. Main St., just south of South Street)

Image from Chesapeake Bay Trust

Send $20 cash or check (made out to City of Avon Lake) before Oct. 1 to:
Annika Sullivan
OCMR 2515
Oberlin College
Oberlin OH 44074

Bring power tools!!!

Jennifer Crozier '09 published in Infectious Disease Reports

It is great to see a paper by former science library student assistant Jennifer Crozier '09 in Infectious Disease Reports, an Open Access, peer-reviewed journal published by PAGEPress, Pavia, Italy. Crozier is one of five authors of Nanoparticles containing siRNA to silence CD4 and CCR5 reduce expression of these receptors and inhibit HIV-1 infection in human female reproductive tract tissue explants. The article reports research under the direction of Susan K. Eszterhas and Alexandra L. Howell of the V.A. Medical Center, White River Junction, VT and Dartmouth Medical School Department of Microbiology and Immunology. PAGEPress is devoted to "open access knowledge" and credits Public Knowledge Project for Open Journal Systems (PKP | OJP)

Visit Open Access Week
Open Access Week will be celebrated world wide during Oberlin's Fall Break, so we will highlight Open Access resources in the sciences during the coming weeks. Some important Open Access journals are listed here. Have a favorite Open Access journal that isn't noted on the list? Let me know!

Summer slipped into September... need a study carrel?

After weeks of anticipation, the new academic year has begun!  It feels like late October already, but hot September weather is sure to hit us when we least need the distraction of summer breezes on top of September's academic expectations.  Regardless, the science library is a great place to study.  If you want a study carrel here, stop by and fill out an carrel application form.  Leave it at the circulation desk anytime before 4pm on Friday, September 9, and you will have complete consideration along with everyone else in your class and major (senior science majors are given priority).  More about Study Carrels in the science library.

Julia Bair, 5th year double-degree student, publishes in Eur. J. Neurosci.

Just indexed in ISI Web of Knowledge and co-authored by Julia Bair, double-degree Bassoon performance/Neuroscience major from Glencoe, Illinois:

What subcortical-cortical relationships tell us about processing speech in noise.
Parbery-Clark, Alexandra; Marmel, Frederic; Bair, Julia; Kraus, Nina

EUROPEAN JOURNAL OF NEUROSCIENCE 33 (3): 549-557  FEB 2011 [access @ OhioLINK EJC]

Bair's co-authors are based in various departments at Northwestern University, Evanston, Illinois, including the Auditory Neuroscience Laboratory.  The team investigated the "effects of background noise on both subcortical- and cortical-evoked responses, and the relationships between them, in normal hearing young adults."

See a sample issue of the journal at Wiley Online Library.

Amanda Schmidt's latest post from China: digging for snails

Assistant Professor of Geology Amanda Schmidt is studying the properties of loess in China, as part of an effort to understand the natural hazards of a region characterized with this sediment. She writes from China: "These [samples] will be used to determine how strong [loess] is, what makes it break in blocks, and what makes it flow. We suspect that the original loess is rather weak and flows easily, but that once it has flowed and set up again, it is quite a bit stronger." Schmidt's posts appear in the New York Times Scientist at Work blog. The bit about snails refers to finding snails buried in undisturbed loess sediments, to use for dating the deposition age. Schmidt includes a great photo of the 3-year old daughter of the park science translator, enjoying her first time "playing in dirt," and helping to sort snails from sediment.

Basic Protocols Freely Accessible in JoVE

JoVE: Journal of Visualized Experiments is a peer-reviewed online journal of videos and other forms of visualization that demonstrate complex procedures, most of which are rather more specialized than needed for our curriculum -- but the "Basic Protocols" section includes 56 videos that are freely accessible and of potential use in the undergraduate laboratory.  See, for example, Generation of Single-Cell Suspensions from Mouse Neural Tissue, by Sandra Pennartz, Sandy Reiss, Rebecca Biloune, Doris Hasselmann, and Andreas Bosio. Free access to the protocol, which is accompanied by a written abstract and pdf describing the technique, is sponsored by Miltenyi Biotec.

Biology major Dylan Holmes co-author in Animal Behavior

About the Journal

Congratulations to junior Dylan Holmes, who co-authored a paper appearing in the current issue of Animal Behavior:

Sing softly and carry a big stick: signals of aggressive intent in the song sparrow.
Akcay, Caglar; Tom, Mari E.; Holmes, Dylan; Campbell, S. Elizabeth; Beecher, Michael D.
Animal Behaviour 82 (2): 377-382 August 2011 [access at OhioLINK EJC]

Also recently published is an article by chemistry professor Matt Elrod:
Kinetics Study of the Aromatic Bicyclic Peroxy Radical plus NO Reaction: Overall Rate Constant and Nitrate Product Yield Measurements.  Elrod, Matthew J.
Journal of Physical Chemistry A 115 (28): 8125-8130 July 21, 2011 [access at ACS Publications]

Diving bell spider, sea urchin, Arctic ground squirrel: on journal covers this week

View this cover online (subscribers only)

We maintain print subscriptions to many journals still, even for those we also access online.  Serendipitous discovery motivated by intriguing journal covers is one benefit of maintaining a print collection.  Three issues received yesterday have gorgeous photographs that are best appreciated in hand - stop by and pick one up!

Seymour, R. S. and Hetz, S. K. (2011).  The diving bell and the spider: the physical gill of Argyroneta aquatica.  J. Exp. Biol. 214, 2175-2181.  Photo, Stefan K. Hetz.

The cover of Development (July 1)  shows the "mouth of an adult sea urchin (Lytechinus variegatus) as the animal attempts to consume a fragment of seaweed.  This still frame from a rapid time-lapse sequence taken by Sarah A. Elliott and Nobuo Ueda at the 2010 Woods Hold MBL Embryology Course was chosen by readers of the Node."  (Cover explanation taken from the table of contents)

Arctic ground squirrel (Urocitellus parryii)

A hibernating Arctic ground squirrel graces the cover of The Journal of Neuroscience, July 27, illustrating an article beginning on page 10752.

Jinka, T. R., O. Toien, and K. L. Drew. (2011).  Season primes the brain in an arctic hibernator to facilitate entrance into torpor mediated by Adenosine A1 receptors.  J. Neurosci. 31, 10752-10758.

Photo by Lesa Hollen and Leone Thieman.

Structure for cis,trans-1,4-Difluorobutadiene

View cover at acs.org

New publication by Professor Emeritus of Chemistry Norm Craig:

Semiexperimental Equilibrium Structure for cis,trans-1,4-Difluorobutadiene by the Mixed Estimation Method.  Demaison, Jean F.; Craig, Norman C.
Journal of Physical Chemistry A 115 (27): 8049-8054 published online June 8, 2011
[access at American Chemical Society Publications, for subscribers]

Belitsky Lab Research Presented at ACS Spring Meeting

The abstracts of two presentations by Associate Professor of Chemistry Jason Belitsky have been published as part of the proceedings from the 241st National Meeting and Exposition of the American Chemical Society, held in Anaheim, CA, March 27-31, 2011.

The first presentation was a collaboration with Oberlin students (Lye and Moore both graduated in 2011, Ellowitz expects to graduate in 2012).

Melanin-based coatings for environmental applications.
Lye, Diane; Moore, Christine; Ellowitz, Micah; Belitsky, Jason M.
Abstracts of Papers of the American Chemical Society 241:  CHED-547 March 27 2011

Structure image
from Wikipedia

This work involved immobilizing melanin from human hair and testing the binding of melanin and its synthetic analogs with heavy metals and dyes, and efforts toward heavy metal sequestration.

Melanin molecular recognition. Belitsky, Jason M.
Abstracts of Papers of the American Chemical Society 241: ORGN-676 March 27 2011
Belitsky's talk focused on analogs of eumelanin and their interactions with metal ions and boronic acids.  His research furthers understanding of colorimetric sensors for lead and inhibitors of synthetic melanin, including applications for molecular imprinting and inhibition.

The abstracts do not appear on the ACS website for viewing by the public, but may be found in SciFinder.

"It was a lark." -- Freeman Dyson, on the early Los Alamos community

On the new book shelf today is a very slim pamphlet, containing the transcript of the PBS production The Day After Trinity: J. Robert Oppenheimer and the Atomic Bomb (1981).  Transcribed and printed by PTV Publications, Kent, Ohio, this written record of the public broadcasting production by Jon Else gives a fascinating picture of gathering the best physicists and their students in the "boom town" of Los Alamos.  Under Oppenheimer's leadership, this group of brilliant thinkers, with "kind hearts and humanist feelings," went to work on a weapon of mass destruction.  The Day After Trinity explores how and why the atomic bomb was developed, in the context of relationships of the scientists working together under great stress.  "Their average age was 29, and their job was to construct a mechanism which would trigger, in a millionth of a second, a violet chain reaction.  They had two dance bands, a soda fountain, Boy Scouts, Girl Scouts, a radio station with no call letters, aa cyclotron, and 7,000 fire extinguishers," says the narrator.  Freeman Dyson, then a physicist with the Institute for Advanced Study, Princeton University, remarked "The most striking contraction is the fact that this man [Oppenheimer], who was so unworldly, so unpolitical in his youth, such a great scholar, so fond of metaphysical poetry, should suddenly emerge as the great administrator who put Los Alamos together and produced the atomic bomb."

It is still very thought-provoking reading, 30 years after the making of the documentary.  As we approach the 66th anniversary of the destruction of Hiroshima and Nakasaki, Oppenheimer's words remain relevant:  "I think the only hope for our future safety must lie in a collaboration, based on confidence and good faith, with the other peoples of the world."  [OBIS catalog record]

Faculty publication: Tracie Paine, in Neuropsychopharmacology

More into @ Nature.com

A new publication by Assistant Professor of Neuroscience Tracie Paine:

Schizophrenia- Like Attentional Deficits Following Blockade of Prefrontal Cortex GABA(A) Receptors.
Paine, Tracie A.; Slipp, Lauren E.; Carlezon, William A., Jr.
Neuropsychopharmacology 36 (8): 1703-1713 July 2011 [read the abstract]

Oberlin College Library does not have access to this journal (a print subscription costs $2,846 and an online site license would be considerably more).  We can obtain a copy through Interlibrary Loan.

Climate Scientists Face Hostility, Undermining Scientific Freedom

From the American Association for the Advancement of Science:
"Reports of personal attacks on climate scientists, including harassment, legal challenges, and even death threats, have created a hostile environment that inhibits the free exchange of scientific findings and makes it difficult for factual information to reach policymakers and the public, the AAAS Board of Directors said in a statement of concern."

Read “Statement of the Board of Directors of the American Association for the Advancement of Science Regarding Personal Attacks on Climate Scientists.” [pdf] Approved on June 28.

Faculty-Student co-authored publication in J PHYS CHEM

Recent publication by Adam Birdsall, '11 and Professor of Chemistry Matt Elrod, as found in ISI Web of Science:
Comprehensive NO-Dependent Study of the Products of the Oxidation of Atmospherically Relevant Aromatic Compounds.
Birdsall, AW.; Elrod, MJ.

Journal home page

JOURNAL OF PHYSICAL CHEMISTRY A 115 (21): 5397-5407 JUN 2 2011. [subscriber access, @ ACS publications]

Imams add their support for teaching evolution

The Clergy Letter Project expands and creates opportunity for Muslims to support evolution, explains Michael Zimmerman in a recent Huffington Post column (posted June 2, 2011).   

Extracted from Zimmerman's column:
"One of the overarching goals of The Clergy Letter Project is to demonstrate that the battle that so many want to portray as being between religion and science is actually something very different. In fact, there are religious individuals whose beliefs are at odds with science, and those people, typically fundamentalists regardless of their religion, are convinced that their perspective is the only "correct" one; that all other religious views are wrong. But, regardless of how much attention these people receive, they are in the minority and their views are every bit as much in conflict with the broader religious world as they are with the perspectives of the scientific community. These fundamentalists are attempting to claim all of religion for themselves by casting it in their own image while working feverishly to redefine science in a way that privileges their idiosyncratic readings of ancient texts."

Related reading:
Being human in Islam : the impact of the evolutionary worldview / Damian A. Howard
Abingdon, Oxon ; New York, NY : Routledge, 2011

Black lung disease is back with a vengence

Living on Earth on May 27, 2011 presented a sobering story on a highly aggressive form of black lung, or coal workers’ pneumoconiosis, saying "An investigation into last year’s [Massey Energy's Upper Big Branch] coal mine disaster in West Virginia reveals a tragedy within a tragedy: autopsies show most of the men who died in the explosion also had black lung."  The prevalence of black lung had been declining since the 1970s, due to stricter regulations governing the amount of coal dust permitted in active work areas. "Lax enforcement and monitoring of dust" are considered likely contributors to the increased incidence and severity of black lung, coupled with changes in mining practice that result in more silica dust as well as coal dust in smaller, confined areas.

The Government Accountability Office in 2008 found that 87% of miners' claims for disability benefits due to black lung were initially denied (Black Lung Benefits Program, report to U.S. Senate Subcommittee on Health Care, Committee on Finance).

Ironically, Senate Hearing 110-527 [Coal: a Clean Future] does not once mention black lung in its 252 pages (hearing before the U.S. Senate Subcommittee on Energy, Natural Resources, and Infrastructure, Committee on Finance).  The "clean future" does not, apparently, include miners' lungs -- or the environment around coal mining sites.

More about --
Black lung:  National Institute for Occupational Safety and Health (NIOSH)
Massey's denial of culpability for the disaster: Wall Street Journal, June 3.
Mountain top removal for coal extraction.