Happy Halloween From NSF (and me)

Happy Halloween, Eckerd!

It's a grey, windy day, perfect for this spooky night. The National Science Foundation has put together a "ghoulish" newsletter. Find out why we like scary movies, how to be eco-friendly for Halloween, and the truth behind monsters.

The best of algal blooms

If you're a marine science or environmental studies student interested in marine issues, and you are not familiar with SeaWeb, I would like to introduce you to this excellent resource via algal blooms. Red tide...It's something we know well here on the coast. A family I know lives on Boca Ciega Bay, and a bad red tide can mean dead fish on their little beach, horrendous smells, and more.

SeaWeb was mentioned in another recent blog post, as the sponsor of the the Marine Photobank. SeaWeb is a nonprofit working for healthy oceans. The Web site is full of information and resources, such as its program "Too precious to wear," which highlights the plight of corals being used for jewelry and furniture accessories.

One of my favorite resources offered by SeaWeb is Ocean Citations. Ocean Citations lists literature on topics dealing with marine and coastal environmental issues. The 2007 list on algal bloom contains 17 citations from high-profile journals such as Limnology and Oceanography and Ambio. At least 3 of the articles study Florida and the marine areas near Eckerd. Other topics for citations include marine mining, introduced species, fisheries, and more. What an easy way to find specific resources!

In addition, users can sign up to receive updates on citation lists and others valuable resources. If we don't own a journal, remember you can always order the article on interlibrary loan. Take a moment to check out the best of 2007 in algal bloom literature and surf around SeaWeb to see how it can help you in your studies.

Scitopia reaches final version

It has been a crazy week with meetings for me first in Ohio and then in Fort Myers. Therefore, instead of my take on the new Scitopia, I am going to direct you to an excellent article in Information Today. In brief, Scitopia has improved the XML to provide more exact results. The patent search includes Japanese and European patents, as well as those in the United States. In addition, the article claims that in comparison to one expensive database, the coverage is better. No names are used but at Eckerd, I know for our subject guides, I will be directing you to Scitopia over a few smaller search pages such as SIAM or AGU, since Scitopia covers their content.

Biological and ecological data comes recommended

NatureServe Explorer was brought to my attention through a reference librarian journal, Reference & User Services Quarterly. According to the review,

With its colorful Web site and troves of animal, plants, and ecological data, NatureServe, a nonprofit conservation organization, is a superb resource for academics and members of the public.

From my experimentation with the Web site, I feel Eckerd students studying animals and plants from an environmental perspective will find this free site extremely helpful. The Online Encyclopedia of Life provides information on 70,000+ species of plants and animals. Information is not comprehensive for all entries, however many entries include conservation status, distribution, ecology & life history, and population delineation. Maps and images are also prevalent. For example, I decided to search for Roseate Spoonbill because I saw one on campus the other day. The search allows common or scientific names. As shown in the distribution map below, populations in Illinois (dark blue) are "presumed extirpated," in Florida (orange) are "imperiled," in Mississippi (red) are "critically imperiled," in Louisiana (yellow) are "vulnerable," and in Texas (green) are "apparently secure."


Ridgely, R.S., T.F. Allnutt, T. Brooks, D.K. McNicol, D.W. Mehlman, B.E. Young, and J.R. Zook. 2003. Digital Distribution Maps of the Birds of the Western Hemisphere, version 1.0. NatureServe, Arlington, Virginia, USA.

You can also search by ecological systems as defined by ECOLOGICAL SYSTEMS OF THE UNITED STATES: A WORKING CLASSIFICATION OF U.S. TERRESTRIAL SYSTEMS . I found this search more difficult to use, but the option to search by state was effective. In this manner, I was able to access data about the ecosystem "Southwest Florida Dune and Coastal Grassland." I learned the vegetation distinctive to this area, as well its lack of distinctive animal species.

It is important to choose "New Search" even if you have moved from one search tab to another. Otherwise the parameters of your first search seem to remain.

A second component for this product is InfoNatura, which provides information on birds, mammals, and amphibians in Latin America. My first search was for Galapagos Sealion, since I had a student Meebo me a question on these mammals a few days ago. I was curious to see how much this might have helped the student. I was disappointed to find the information on this animal very limited. On subsequent searches within InfoNatura, I found some species with more data, but overall this aspect of the database seemed less extensive than what is available for North America and Canada.

Formula of belief

An exhibit put together by The World Question Center and the Serpentine Gallery in London displays the formulas, equations, or algorithms from more than 80 scientists and premier thinkers. At once, it reminded me of the "This I believe" media project, whereby people offer their deeply held beliefs in a oral essay. Yet, these formulas are much simpler, much more exact, and in some ways, more beautiful. The breadth of formulas is astounding: from ones describing the path to happiness to work philosophies to formulas I can't understand at all. Take a moment to check them out for yourself. Make sure to scroll to the bottom of the page to see the full set. And if, by chance, you are inspired to share your own formula, I would be happy to put it up on this blog.

Open Access publishing for Eckerd

As a participant in The Oberlin Group, a consortium of liberal arts college libraries, Eckerd College is a Supporter Level member of Biomed Central (BMC). What does this mean for our researchers? We receive a discount for publishing in any one of 182 peer-reviewed, open access journals published by BMC. As a supporting member, The Oberlin Group has its own Web page, where its researchers are featured. Functionality on the page filters articles that Oberlin Group researchers have published recently, as well as articles that have been accessed the most within a month and a year. This feature provides extra exposure to authors from Oberlin Group institutions.

According to BioMed Central, some of the reasons for publishing in a BMC open-access journal are the speed of publication, international exposure, a highly dedicated promotional process undertaken by BMC, inclusion in major bibliographic indices (e.g., PubMed), and now, and the addition of a Thomson ISI impact factors for some journals. Additional promotion is available through BioMed's "Highly accessed" designation, which can be mentioned as a measurement when authors refer to their work.

Authors for BMC retain copyright over their own work through a Creative Commons license. Work published in BMC journals are made available for free through BMC permanently. Works are archived in various locations so if BMC loses control of its works, open access articles will remain available through other venues.

Some of the recent titles from Oberlin Groups researchers include the following:

Toward the automated generation of genome-scale metabolic networks in the SEED
Matthew DeJongh1, Kevin Formsma1,2, Paul Boillot1, John Gould1, Matthew Rycenga3,4 and Aaron Best2

1. Department of Computer Science, Hope College
2. Department of Biology, Hope College
   
3. Department of Chemistry, Hope College
4. Department of Chemistry, University of Washington

BMC Bioinformatics 2007, 8:139 doi:10.1186/1471-2105-8-139

Analysis of the Saccharomyces cerevisiae proteome with PeptideAtlas
Nichole L King, EricWDeutsch, Jeffrey A Ranish, Alexey I Nesvizhskii, James S Eddes, Parag Mallick, Jimmy Eng, Frank Desiere, Mark Flory, Daniel B Martin, Bong Kim, Hookeun Lee, Brian Raught, and Ruedi Aebersold

Abstract: We present the Saccharomyces cerevisiae PeptideAtlas composed from 47 diverse experiments and 4.9 million tandem mass spectra. The observed peptides align to 61% of Saccharomyces Genome Database (SGD) open reading frames (ORFs), 49% of the uncharacterized SGD ORFs, 54% of S. cerevisiae ORFs with a Gene Ontology annotation of 'molecular function unknown', and 76% of ORFs with Gene names. We highlight the use of this resource for data mining, construction of high quality lists for targeted proteomics, validation of proteins, and software development.

Genome Biology 2006, 7:R106 (doi:10.1186/gb-2006-7-11-r106)

Blog Action Day!

photo/Rob Partington for openphoto.net CC:Attribution-ShareAlike

I have to admit, I forgot about Blog Action Day in which participants would blog about environmental issues on October 15, 2007. Fortunately, as karma would have it, this weekend, my significant other and I made some environmental pledges to ourselves. Baby steps, as we say. It seems appropriate to discuss some of them on Blog Action Day. There are more than 16,000 blogs participating, and that doesn't include people like me who never registered their blog. The resources for Blog Action Day are excellent. I particular like TreeHugger's How to Green Guides, including How to Green Your Pet; How to Green Your Meals; and How to Green Your Sex.

So what are we doing? We are riding bikes or public transportation at least 3 days a week to work. Furthermore, same rules apply for anything within 5 miles of our house. No more running out for milk in the car. If we have more shopping than can fit on a bike, we plan it around other car activities, such as a day when someone might be driving to work. We are no longer using disposable napkins or sponges. We have cloth napkins, and I am knitting washable cotton cloths for cleaning dishes. We will hang up a clothesline instead of drying our reusables in the dryer. Finally we joined the new Pinellas Sweetwater farm, community-supported organic farming.

Is this all that can be done to promote a sustainable lifestyle? Not by a long shot! But with smaller goals, we can work toward a greener way to live. Once we incorporate a few lifestyle changes, perhaps others will become easier. We have decided on a reward if we stick to our goals. If it works, I will report in about 4 months.

I would love to hear some of the things Eckerd students are doing to keep the campus green.

2007 Nobel Peace Prize

Because the Peace Prize this year has been awarded for efforts to disseminate and collate information on global change, I thought it appropriate for this blog. Both the Natural Sciences Collegium and Eckerd College have been proponents of environmental wellness. This year's award will be split between Al Gore Jr. and the Intergovernmental Panel on Climate Change (IPCC). The IPCC was established in 1988 by the World Meteorological Organization and the United Nations Environment Programme. The organization publishes assessments based on peer-reviewed literature. Al Gore has dedicated a portion of his career to the effects of climate change, most recently with a book and an Academy-award winning movie.

2007 Nobel Prize in Chemistry

German surface chemist Gerhard Ertl is the single recipient of this year's Nobel Prize in Chemistry. According to the Royal Swedish Academy of the Sciences,

This year’s chemistry laureate Gerhard Ertl has succeeded in providing a detailed description of how chemical reactions take place on surfaces and has in this way laid the foundation of modern surface chemistry. He is awarded the prize for showing how reliable results can be obtained in this area of research.

Surface reactions are vital in many processes today

• in catalytic cleaning carbon monoxide oxidates on platinum,
• freons used in air conditioning systems, for instance, reduce the ozone layer by reacting on the surfaces of small ice crystals,
• rusting takes place when an iron surface is exposed to oxygen,
• surface reactions are used in the electronics industry to manufacture semiconductor materials for components,
• artificial fertilizers contain ammonia which is produced when nitrogen and hydrogen react on an iron surface,
• renewable fuels can be produced using catalytic surfaces.

Image and quotes from The Royal Swedish Academy of Sciences. (2007). Information for the public: the Nobel Prize in Chemistry 2007. Retrieved from Nobelprize.org: http://nobelprize.org/nobel_prizes/chemistry/laureates/2007/info.html

Ertl laid the groundwork for a branch of chemistry that is difficult to quantify, yet has extremely practical applications. Ertl's modelling of hydrogen reaction on metal surfaces in the 1970s advanced conversations on catalytic mechanisms. A much more thorough discussion of Ertl's contributions for both scientists and the public is available here.

2007 Nobel Prize in Physics

PETER GRUNBERG (left); ALBERT FERT (right)
(pictures from Nobel Prize.org)
















The Nobel Prize in Physics will be split between a French and a German physicist, Albert Fert and Peter Grunberg, respectively, for

the discovery of Giant Magnetoresistance

With this discovery, the ability to read data on hard drives became more refined, and therefore, applicable to smaller storage devices such as your ipod. The Nobel Prize Web site has an excellent article on the science behind Giant Magnetoresistance (GMR) available here.

Marine photos available for educational use

The Delray Beach, Florida, ocean outfall discharges 13 million gallons per day of treated sewage up-current of a coral reef./ Jim Cagle, Palm Beach Reef Rescue/Marine Photobank

Marine Photobank provides easily accessible images of human effect on marine life. Photographers--some professional, some amateur,some researchers from universities and nonprofits--furnish photos of sea lions wrapped in filament, otters blanketed in oil, corals bleaching, hurricanes swirling over land, and many more. According to the organization's mission statement:

The Marine Photobank aims to literally shed light through photos on pressing marine issues and human-related impacts on the ocean ecosystem.

In frustration over the lack of compelling images, philanthropist and photographer Wolcott Henry joined Green Media Toolshed to collect images that document the widespread destruction throughout the world's oceans and coastlines. In 2004, the photobank became part of SeaWeb, a nonprofit advancing the cause of ocean conservation.

Users can register to both download and upload photographs. There are two types of download registrations, one in which you designate your photo use as nonprofit (e.g., in an educational context) and one in which you designate your use for the media or other for-profit use. Upon registering for nonprofit, your membership must be accepted by the organization. In my case, this took approximately 24 hours. I did not register to upload photos, but students and faculty who spend time photographing research may want to contribute to this database.

Photographs will be excellent for presentations made by either students or faculty on marine and coastal issues. The site offers an extensive collection of exceptional, vivid, and troubling images. The images are arranged in subject galleries, such as Reefs in Peril, Deep Sea Habitat, and Coast Development, which makes for easy browsing. In addition, the search function permits searching by keywords, concepts, or photo ID number.

Some images have been turned into "photo stories," which may be best described as downloadable informational posters on a marine issue. In addition, educational materials for classroom use are under development. Another cool feature is the photo wishlist. Members can request certain images. Currently, there is a lengthy wishlist, so prospective photographers also might be interested to see what members wish for.

Furthermore, I see Marine Photobank serving a social/networking function also. Photographers are listed, some with biographies and contact links. Many of the photographers are also researchers, providing a method of finding people studying issues that you might also find interesting, hope to study, or are studying yourself.

2007 Nobel Prize in Medicine or Physiology

This morning the Nobel Prize for Medicine or Physiology was awarded to Mario R. Capecchi, Martin J. Evans, and Oliver Smithies for

their discoveries of "principles for introducing specific gene modifications in mice by the use of embryonic stem cells"

An excellent summary and illustration of the research done by these scientists is available at the Nobel Prize Web site. The prize money will be split equally three ways between Capecchi, who is a U.S. citizen born in Italy, Evans, a British citizen, and Smithies, a U.S. citizen born in the United Kingdom.

The house that Flickr built

This Friday I bring you a super cool demo for an application under development called Photosynth. Microsoft Labs architect, Blaise Aguera y Arcas, demonstrates how Photosynth reconstructed a three-dimensional model of Notre Dame using photos from Flickr.

Computational Science for the classroom

Computational Science Education Reference Desk (CSERD) is dedicated to introducing students to computational science, especially through its use in the classroom. According to CSERD, computational science involves the use of a computational architecture in combination with an algorithm to solve a scientific problem. For a more thorough definition, as well as a model, see the article from CSERD at http://www.shodor.org/refdesk/Help/whatiscs. CSERD is a partnership of National Science Digital Library, the Virtual Reference Desk, and the Gateway to Educational Materials.

At the CSERD site (http://www.shodor.org/refdesk/), both students and faculty can browse resources by subject, educational level, resource type, audience, or any configuration of these. In addition to providing resources, CSERD offers the opportunity for students and/or faculty to review and add resources. Once a user registers at no cost, they are able to conduct the following tasks:

Ask and answer questions in the forum.
Review material in the catalog.
Add items to the catalog.
Submit modules to be included in CSERD's resources.
Submit in depth verification, validation, and accreditation reviews.

CSERD tracks user participation and will submit letters to appropriate administrators regarding contribution.

NCSE promotes evolution education

September 29 through October 6 marks the American Libraries Association's Banned Books week. In honor of this event, I did a brief database search on the censorship and science. One idea the emerged was the national discussion on evolution versus creationism/ intelligent design in science classrooms of public schools. Therefore, I decided to introduce a Web site that, in the organization's words, educates "the press and public about the scientific, educational, and legal aspects of the creation and evolution controversy, and supply needed information and advice to defend good science education at local, state, and national levels." This organization is the National Center for Science Education (NCSE). Often in my library instruction, I discuss the evaluation of Web sites and their possible bias. In this vein, I would like to note that this organization is firmly on the side of evolution as necessity in science classrooms. Therefore, arguments for the teaching of creationism are not present.

The Web site for NSCE includes news on the debate divided by state and national issues, an events pages, and a resources page. In addition, the journal of the organization Creation/Evolution Journal is available in full text from 1980-1990. Furthermore, full text to some important works on this topic are also available, such as Eugenie C. Scott's article "Antievolutionism and Creationism in the United States" (Annu. Rev. Anthropol. 1997. 26:263-89).