Bibliographies for the 21st century, why Zotero rules!

Byoliveridley

Many scientists now manage the bulk of their bibliographic information electronically, thereby organizing their publications and citation material from digital libraries. However, a library has been described as “thought in cold storage,” and unfortunately many digital libraries can be cold, impersonal, isolated, and inaccessible places. In this Review, we discuss the current chilly state of digital libraries for the computational biologist, including PubMed, IEEE Xplore, the ACM digital library, ISI Web of Knowledge, Scopus, Citeseer, arXiv, DBLP, and Google Scholar. We illustrate the current process of using these libraries with a typical workflow, and highlight problems with managing data and metadata using URIs. We then examine a range of new applications such as Zotero, Mendeley, Mekentosj Papers, MyNCBI, CiteULike, Connotea, and HubMed that exploit the Web to make these digital libraries more personal, sociable, integrated, and accessible places. We conclude with how these applications may begin to help achieve a digital defrost, and discuss some of the issues that will help or hinder this in terms of making libraries on the Web warmer places in the future, becoming resources that are considerably more useful to both humans and machines.

via PLoS Computational Biology: Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web

zoteroInteresting look at how to manage scientific information. I use zotero these days. Zotero is a firefox addon that works within the browser, hence is platform independent. It is incredibly powerful, automatically imports meta data from a lot of journal sites, links to microsoft word and openoffice for “cite as you write” and bibliographic generation behaviour, stores pdfs, word docs, excel files, etc as attachments to your citations so if you have a little calculation routine you got from a paper, you can put that in an excel spreadsheet and always have it linked to the paper.

You can synchronize the database to the cloud. And, if you have access to a server with webdav, you can synchronize your attachments as well (i have not tried this yet).

Best of all, it is free and open source.

Anyway, the days of ridiculously expensive and arcane tools like endnote are over.

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One Strike for Open Access Journals

Byoliveridley

Now, if only the US government, which funds the bulk of all research in this country, insists on open access for all research it funds! A man can dream!

Chemical & Engineering News: Latest News – HHMI Will Require Free Access To Journal Articles

Howard Hughes Medical Institute has announced a new policy regarding articles authored by biomedical researchers supported by the prestigious philanthropic organization. Beginning in January 2008, HHMI investigators will be required to publish only in those journals that make articles freely accessible in a public repository within six months of publication.

HHMI supports more than 300 investigators, some of whom publish in American Chemical Society journals. Investigators who publish in an ACS journal can satisfy HHMI’s requirement by utilizing the society’s AuthorChoice option. For a $1,000—$3,000 fee, ACS provides free reader access to an article via the ACS website immediately upon online publication and deposits a copy of the article in the National Institutes of Health’s free PubMed Central repository.

HHMI may be the first U.S. funding institution to impose a mandatory public-access policy on its investigators. In the U.K., the Wellcome Trust, which funds biomedical research, already has a mandatory public-access policy.

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Organic agriculture can feed the world

Byoliveridley

That’s the conclusion reached by the authors of this study based on 293 examples in the developing and developed world.The authors also conclude that yields in the developing world are higher for organic agriculture than for conventional agriculture. Why? Well, since the paper is not open access, I can’t read it, or critique it, I’ll have to wait to get to the library before I can download it. But, maybe it’s because organic agriculture tends to be more labor intensive than conventional agriculture as practised by the developed world, and in the developing world, labor is cheap!

Anyway, this is a good news study and should be examined a little more thoroughly.

CJO – Abstract – Organic agriculture and the global food supply

The principal objections to the proposition that organic agriculture can contribute significantly to the global food supply are low yields and insufficient quantities of organically acceptable fertilizers. We evaluated the universality of both claims. For the first claim, we compared yields of organic versus conventional or low-intensive food production for a global dataset of 293 examples and estimated the average yield ratio (organic:non-organic) of different food categories for the developed and the developing world. For most food categories, the average yield ratio was slightly 1.0 for studies in the developing world. With the average yield ratios, we modeled the global food supply that could be grown organically on the current agricultural land base. Model estimates indicate that organic methods could produce enough food on a global per capita basis to sustain the current human population, and potentially an even larger population, without increasing the agricultural land base. We also evaluated the amount of nitrogen potentially available from fixation by leguminous cover crops used as fertilizer. Data from temperate and tropical agroecosystems suggest that leguminous cover crops could fix enough nitrogen to replace the amount of synthetic fertilizer currently in use. These results indicate that organic agriculture has the potential to contribute quite substantially to the global food supply, while reducing the detrimental environmental impacts of conventional agriculture. Evaluation and review of this paper have raised important issues about crop rotations under organic versus conventional agriculture and the reliability of grey-literature sources. An ongoing dialogue on these subjects can be found in the Forum editorial of this issue.

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The LA Times and the American Chemistry Council

Byoliveridley

Giving the American Chemistry Council a forum to sing paeans to its chemical du jour is kinda like giving Donald Trump an Op-Ed column on the harmlessness of gambling. The ACC is a trade association that gets all its funding from the chemical industry and is the reliable source on producing just about enough fudge to create “reasonable doubt” about chemicals. The ACC is notorious for its various astroturf websites including the Phthalate information center, the Plastic Resource, dioxin facts (seeing a pattern here?), and many other websites that propagate biased industry funded research, outright misinformation, and unrestrained cheerleading. They also spend vast amounts of money lobbying congress. Bora, and other Open Access advocates, note the similarities in the arguments used in the above websites to some recent attacks on Open Access, the imprint of Nicholas-Dezenhall is all over the ACC’s strategies!

Harvard votes on Open Access

Byoliveridley

Faculty members are scheduled to vote on a measure that would permit Harvard to distribute their scholarship online, instead of signing exclusive agreements with scholarly journals that often have tiny readerships and high subscription costs.Although the outcome of Tuesday’s vote would apply only to Harvard’s arts and sciences faculty, the impact, given the university’s prestige, could be significant for the open-access movement, which seeks to make scientific and scholarly research available to as many people as possible at no cost.

Harvard Proposal to Publish Scholarly Research Free on the Internet – New York Times

This could be huge. Of course, expect ACS, Elsevier and others to complain, but their lobbyists can’t touch Harvard, with its giant endowment.

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Harvard Open Access Update

Byoliveridley

Yes they can, and they did! Harvard votes for Open Access!

Harvard University’s arts and sciences faculty approved a plan on Tuesday that will post finished academic papers online free, unless scholars specifically decide to opt out of the open-access program. While other institutions have similar repositories for their faculty’s work, Harvard’s is unique for making online publication the default option.

Harvard Opts In to ‘Opt Out’ Plan :: Inside Higher Ed :: Jobs, News and Views for All of Higher Education

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Feds punt on Bisphenol A

Byoliveridley

By studiously ignoring all the subtle hormone disruption effects of bisphenol A and concentrating on easily observable neurological effects, the CERHR essentially does the industry’s bidding.

Some risk linked to plastic chemical – Los Angeles Times

A federal panel of scientists concluded Wednesday that an estrogen-like compound in plastic could be posing some risk to the brain development of babies and children.

Bisphenol A, or BPA, is found in low levels in virtually every human body. A component of polycarbonate plastic, it can leach from baby bottles and other hard plastic beverage containers, food can linings and other consumer products.

Culminating months of scientific debate, the decision by the 12 advisors of the Center for the Evaluation of Risks to Human Reproduction — part of the National Institutes of Health — is the first official, government action related to the chemical. Their recommendation will be reviewed for a federal report that could lead to regulations restricting one of the most used chemicals.

The scientists ranked their concerns about BPA, concluding they had “some concern” about neurological and behavioral effects in fetuses, infants and children, but “minimal” or “negligible” concern about reproductive effects. The findings put the panel roughly in the middle — between the chemical industry, which has long said there is no evidence of danger to humans, and the environmental activists and scientists who say it is probably harming people.

For a detailed look at how bisphenol research has been corrupted by industry sponsored “focused counter research” – where the goal is to show no effects and the experiment is tiled to ensure this goal, read this excellent article in the The Public Library of Science Biology Open Source Journal. Note, because it is Open Access, you can actually read it without selling a kidney! Some highlights…

The moment we published something on bisphenol A, the chemical industry went out and hired a number of corporate laboratories to replicate our research. What was stunning about what they did,” vom Saal says with a mix of outrage and bemused disbelief, “was they hired people who had no idea how to do the work. Each of the members of these groups came to me and said, ‘We don’t know how to do this, will you teach us?’”

More…

The HCRA report, commissioned before Schwartz’s tenure, concluded that “the weight of the evidence for low-dose effects is very weak” [15]. Industry groups hailed the report as a comprehensive review by independent experts and quickly disseminated its findings. Yet the “comprehensive” report reviewed just 19 of 47 studies available in April 2002, and when it was published more than two years later, three panelists asked not to be listed as authors.

What the hell, just read the whole article, especially the bit about the Harvard Center for Risk Analysis and its well documented industry shillness.

The key to understanding bisphenol research is to realize that it is a hormone disruptor that works at low doses. At high doses, normal toxicological testing doses that is, it floods the hormone receptors and slows down the receptor pathways. So, the usual technique of testing in rats and mice at high doses and extrapolating will not work.