open_science - Taryn . on Diigo

11 Sep 09

PLoS Medicine: Ghostwriting: The Dirty Little Secret of Medical Publishing That Just Got Bigger

While readers expect and assume that the named academic authors on a paper carried out the piece of work and then wrote up their article or review informed by their professional qualifications and expertise, instead we see a prime example of “ghostwriting

www.plosmedicine.org/...10.1371%2Fjournal.pmed.1000156 - Preview

publishing_industry pharmaceutical open_science

01 Sep 09

Scientist at Work - Eric Schadt - Enlisting Computers to Unravel the True Complexity of Disease - Biography - NYTimes.com

The problem is no surprise to Dr. Schadt. “It turns out that common diseases involve thousands of genes and proteins interacting on complex pathways,” he said.

In 2003, Dr. Schadt was first noticed as a co-author of a paper in Nature that articulated t

www.nytimes.com/...25prof.html - Preview

genetics disease prediction statistics genome-environment_interaction open_science

06 Aug 09

Ghostwriters Paid by Wyeth Aided Its Drugs - NYTimes.com

But the seeming consensus fell apart in 2002 when a huge federal study on hormone therapy was stopped after researchers found that menopausal women who took certain hormones had an increased risk of invasive breast cancer, heart disease and stroke. A late

www.nytimes.com/...05ghost.html - Preview

pharmaceutical industry corruption open_science cancer women

30 Jul 09

Projects

(citizen science projects)

sciencecheerleader.com/...projects_activities - Preview

open_science

26 Jun 09

Viral Spiral | The New America Foundation

a discussion with David Bollier, author, Viral Spiral, on how commoners built a digital republic of their own
@36:00 digital citizenry

www.newamerica.net/...viral_spiral - Preview

creative_commons social_network intellectual_property open_education open_science democracy telecom journalism newspaper video

23 Mar 09

PLoS ONE: Clickstream Data Yields High-Resolution Maps of Science

www.plosone.org/...10.1371%2Fjournal.pone.0004803 - Preview

data_visualization research digital_media open_science academia

03 Mar 09

John Conyers and Open Access (Lessig Blog)

Pushed by scientists everywhere, the NIH and other government agencies were increasingly exploring this obviously better model for spreading knowledge. Proprietary publishers, however, didn't like it. And so rather than competing in the traditional way, t

www.lessig.org/...n_conyers_and_open_access.html - Preview

open_access open_science business model academia publishing_industry politics transparency

11 Feb 09

Stanford Neuro Research Lectures

www.youtube.com/view_play_list - Preview

video neuro reference open_education open_science

New Web Site Maps Endocrine Disruptors to Human Development: Scientific American

The Web site compiles information from hundreds of studies and inserts it on timelines that show the development of key bodily systems in both people and animals, including the male and female reproductive tracts, immune system and nervous system. By laye

www.sciam.com/article.cfm - Preview

pollution hormone endocrine health bisphenolA data data_visualization pregnancy collaboration open_science

07 Nov 08

Ready or Not, Here Comes Open Access

The plan to bring open access publishing to scientists' attention in this way — fighting traditional publishers on their own turf — misses the point of the open access vision. If your options are running a fleet of mediocre journals or publishing a high-q

www.genome-technology.com/...150414-1.html - Preview

open_science science publishing publishing_industry research academia library

Of course, open access advocates say the money's all coming from the same place. Whether it comes from a university to pay a subscription or from a research lab to pay an author fee, the money probably started out as government funding — and virtually every penny of it came from the taxpayers' pockets. While the costs of author-pays models are not well understood on a large scale, the costs of journal subscriptions are: they're rising at rates "radically outstripping the cost of living," Wilbanks says. High-profile journals can cost a research library $20,000 or more per title every year, adds Linke. In the open access movement, the solution is simple: take the funding away from subscriptions and channel it to author fees instead.
People who study the scientific publishing world at a systems level will notice three items of interest. First, that government funding agencies control almost all of the money. Second, that university libraries control subscription agreements. And third, that the main financial beneficiaries of both the scientific results produced by grant funding and the subscription fees are the publishing firms.
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- Journals that are less selective cost significantly less to produce. PLoS, for example, has shored up its revenue base by publishing a suite of journals with lower rejection rates, as well as its experimental online journal PLoS One (see PLoS description below), that bring in enough revenue to pick up much of the financial slack for the high-end titles. To many detractors, this is a fundamental failing of the open access model: that it can only survive when publishing mediocre-quality journals.

02 Oct 08

The Carnegie Commons - Opening up Education

John Seely-Brown gives a great intro. Read online or download pdf: http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid=11309. Lots of talk about science education as a model in the accompanying forums.

commons.carnegiefoundation.org/openingupeducation - Preview

teaching education open_science open_education video

31 Aug 08

Out in the open: Some scientists sharing results - The Boston Globe

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science open_science academia wisdom_of_crowds publishing publishing_industry crowd_sourcing

the open-science movement, with many of its leaders in the Boston area, encourages scientists to share techniques and even their work long before they are ready to present results
It is an attempt to bring the kind of revolutionary and disruptive change to the laboratory that the Internet has already wrought on the music and print media industries. The idea is that opening up science could speed discoveries, increase collaboration, and transform the field in unforeseen ways.
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- the entire system of credit in science is based on being the first to publish a finding in a reputable journal; there's no incentive to post on blogs or community websites. Scientists try to get their findings published in the top journals in their fields, and major scientific prizes are awarded to those who make breakthroughs.
  Despite these concerns, the counterculture scientific movement is gathering steam, and not just among junior researchers.
- OpenWetWare.org
- Science Commons

A Blog Around The Clock : The Web: how we use it

great aggregate

scienceblogs.com/...the_web_how_we_use_it.php - Preview

science open_science social_change social_network

They really don't care about 99% of the things I care about. FriendFeed? Yeah, right, they haven't even heard of it, and if I try telling them about it, they say "why would I do that?" See, most people just want to work their 9 to 5 jobs, go home, pop open a beer, sit on the couch, watch some movies, play with their kids, etc.
The activity is the thing to focus on, not the technology. Technology enables the activity, and people will get excited about the technology if they're excited about the activity first and the benefits of the technology has been explained to them. But you don't make passionate photographers by showing them lenses, you make passionate photographers by showing them pictures that rip your heart out.

Michael Nielsen » The Future of Science

michaelnielsen.org/blog - Preview

open_source open_science science academia publishing innovation creativity information wikipedia

The adoption and growth of the scientific journal system has created a body of shared knowledge for our civilization, a collective long-term memory which is the basis for much of human progress. This system has changed surprisingly little in the last 300 years. The internet offers us the first major opportunity to improve this collective long-term memory, and to create a collective short-term working memory, a conversational commons for the rapid collaborative development of ideas. The process of scientific discovery - how we do science - will change more over the next 20 years than in the past 300 years.
leading edge of the greatest change in the creative process since the invention of writing.

Science is an example par excellence of creative collaboration, yet scientific collaboration still takes place mainly via face-to-face meetings.
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- there are major cultural barriers which are preventing scientists from getting involved, and so slowing down the progress of science.
- The adoption of the journal system was achieved by subsidizing scientists who published their discoveries in journals. This same subsidy now inhibits the adoption of more effective technologies, because it continues to incentivize scientists to share their work in conventional journals, and not in more modern media.
- We should aim to create an open scientific culture where as much information as possible is moved out of people’s heads and labs, onto the network, and into tools which can help us structure and filter the information. This means everything - data, scientific opinions, questions, ideas, folk knowledge, workflows, and everything else - the works. Information not on the network can’t do any good.
- extreme openness. This means: making many more types of content available than just scientific papers; allowing creative reuse and modification of existing work through more open licensing and community norms; making all information not just human readable but also machine readable; providing open APIs to enable the building of additional services on top of the scientific literature, and possibly even multiple layers of increasingly powerful services.
- To create an open scientific culture that embraces new online tools, two challenging tasks must be achieved: (1) build superb online tools; and (2) cause the cultural changes necessary for those tools to be accepted. The necessity of accomplishing both these tasks is obvious, yet projects in online science often focus mostly on building tools, with cultural change an afterthought. This is a mistake, for the tools are only part of the overall picture. It took just a few years for the first scientific journals (a tool) to be developed, but many decades of cultural change before journal publication was accepted as the gold standard for judging scientific contributions.
- a top-down strategy that has been successfully used by the open access (OA) movement [3]
- second strategy is bottom-up. It is for the people building the new online tools to also develop and boldly evangelize ways of measuring the contributions made with the tools. To understand what this means, imagine you’re a scientist sitting on a hiring committee that’s deciding whether or not to hire some scientist. Their curriculum vitae reports that they’ve helped build an open science wiki, and also write a blog. Unfortunately, the committee has no easy way of understanding the significance of these contributions, since as yet there are no broadly accepted metrics for assessing such contributions. The natural consequence is that such contributions are typically undervalued.
- Is it possible to scale up this conversational model, and build an online collaboration market [4] to exchange questions and ideas, a sort of collective working memory for the scientific community?
- Rather than hoarding their questions and ideas, as scientists do for fear of being scooped, the programmers revel in swapping them. Some of the world’s best programmers hang out in these forums, swapping tips, answering questions, and participating in the conversation.
- Innocentive’s business model is aimed firmly at industrial rather than basic research, and so the incentives revolve around money and intellectual property, rather than reputation and citation.
- FriendFeed allows messages to be passed back and forth in a lightweight way, so communities can form around common interests and shared friendships.
- Lacking widely accepted metrics to measure contribution, scientists are unlikely to adopt FriendFeed en masse as a medium for scientific collaboration. And without widespread adoption, the utility of FriendFeed for scientific collaboration will remain relatively low.
- Expert attention, the ultimate scarce resource in science, is very inefficiently allocated under existing practices for collaboration.
  
  An efficient collaboration market would enable Alice and Bob to find this common interest, and exchange their know-how, in much the same way eBay and craigslist enable people to exchange goods and services. However, in order for this to be possible, a great deal of mutual trust is required.
- In economics, it’s been understood for hundreds of years that wealth is created when we lower barriers to trade, provided there is a trust infrastructure of laws and enforcement to prevent cheating and ensure trade is uncoerced. The basic idea, which goes back to David Ricardo in 1817, is to concentrate on areas where we have a comparative advantage, and to avoid areas where we have a comparative disadvantage.
- recommend Bill Hooker’s series of essays on open science, Mitchell Waldrop’s article in Scientific American, and the Science Commons as starting places. There are some great communities of people online engaged in building a more open scientific culture - many of those people can be found in the Life Scientists and Science2.0 rooms on FriendFeed.
- whenever the stakes are that high, secrecy pays off - and the science community is not alone in this. The shoe-salesman Bob may have high stakes in his business, but for Alice it is probably just one of many pairs of shoes. Analogies only go so far

15 Aug 08

For-Profit Scientific Publishers and the Culture of Entitlement.

scienceblogs.com/...rofit_scientific_publisher.php - Preview

science open_science publishing_industry academia file_sharing

scientists are not only the end customers for journals, they're also the people who provide the content. For free.
the major academic publishers seem to feel that they are entitled to continue to make enormous profits selling scientific research to scientists at outrageously inflated prices.
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- Harvard University's Faculty of Arts and Sciences adopted a policy this evening that requires faculty members to allow the university to make their scholarly articles available free online.
- we scientists are willing to torpedo ourselves by continuing to allow those expensive journals such respect. Nature, Science, and other journals' prices would drop like stones if we simply took out papers elsewhere. But no one wants to be the first to try it.
- P2P seems to actually function as free advertising with a beneficial net effect on sales

PLoS Biology - Going, Going, Gone: Is Animal Migration Disappearing

biology.plosjournals.org/perlserv - Preview

bird migration ecology conservation open_science biodiversity world government

Birdwatchers in North America and Europe, for example, complain that fewer songbirds are returning each spring from their winter quarters in Latin America and Africa
the threats to migrants fall into four nonexclusive categories: habitat destruction, the creation of obstacles and barriers such as dams and fences, overexploitation, and climate change
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- Protecting the abundance of migrants is the key to protecting the ecological importance of migration. As the number of migrants declines, so too do many of the most important ecological properties and services associated with them.
- But if migration is seen as a phenomenon of abundance, then its protection will require decision makers to adopt a much more proactive approach to conservation—in effect, to protect species while they are still abundant.
- species with large breeding or wintering ranges and diffuse migratory routes may be less vulnerable to individual threats, yet more difficult to conserve.
- The long-term conservation of the cerulean warbler (and, we suspect, many other migrants as well) will require a broad-based, mixed strategy: creation of numerous reserves in the breeding and wintering grounds (largely by government agencies); identification and protection of key stopover sites (by government agencies and private organizations); and the use of financial incentives to encourage landowners to protect smaller patches of habitat that may be important to the warblers during their migration.

24 Jul 08

Science schmience: How to make sense of a published study | BlogRivet.com

At some point, you may very well want to read and understand a published scientific study for the sole purpose of writing about it.

blogrivet.com/...ake-sense-of-a-published-study - Preview

open_science reference

If You Have a Problem, Use Innocentive to Ask Everyone - NYTimes.com

www.nytimes.com/...22inno.html - Preview

innovation open_science open_source

The process, according to John Seely Brown, a theorist of information technology and former director of the Xerox Palo Alto Research Center, reflects “a huge shift in popular culture, from consuming to participating” enabled by the interactivity so characteristic of the Internet.
“most laboratories, most R & D endeavors still work on the premise ‘we can accumulate and make sense of all the knowledge that is relevant.’ The open-source models and a model like InnoCentive show that other approaches can help.”

10 Oct 07

Journal Clubs - think of the future!

scienceblogs.com/...nal_clubs_think_of_the_fut.php - Preview

open_science science scienceblogs

It is not the matter so much of here-and-now as it is a contribution to a long-term assessment of the article, providing information to the future readers

06 Sep 07

J. Craig Venter - In the Genome Race, the Sequel Is Personal - New York Times

www.nytimes.com/...04vent.html - Preview

biotech genetics genome human open_science

Like James Watson, the co-discoverer of DNA, whose genome is also being decoded, Dr. Venter believes strongly in making individual DNA sequences public to advance knowledge and hasten the era of personalized genomic medicine.
Biologists had estimated that two individuals would be identical in 99.9 percent of their DNA, but the true figure now emerges as much less, around 99.5 percent, Dr. Scherer said.
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- Dr. Venter reports that he has variants that increase his risk of alcoholism, coronary artery disease, obesity, Alzheimer’s disease, antisocial behavior and conduct disorder.
  
  But these predictions are far from certain. As more individual genomes are decoded, the information from them will become more valuable, Dr. Venter said, provided that people can overcome “irrational fears of even seeing their genetic code.”
- That a scientist of his ability has been forced to work outside the N.I.H.’s peer-review system puts peer review in a strange light. If his diploid human genome should become a standard, the success is one that he will have earned by perseverance and defiance of long odds.

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