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Posts Tagged ‘data sharing

Science Policy Around the Web – August 1, 2017

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By: Sarah L. Hawes, PhD

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Climate Science

Conducting Science by Debate?

Earlier this year an editorial by past Department of Energy Under Secretary, Steven Koonin, suggested a “red team-blue team” debate between climate skeptics and climate scientists. Koonin argued that a sort of tribalism segregates climate scientists while a broken peer-review process favors the mainstream tribe. Science history and climate science experts published a response in the Washington Post reminding readers that “All scientists are inveterate tire kickers and testers of conventional wisdom;” and while “the highest kudos go to those who overturn accepted understanding, and replace it with something that better fits available data,” the overwhelming consensus among climate scientists is that human activities are a major contributor to planetary warming.

Currently, both Environmental Protection Agency Administrator, Scott Pruitt, and Department of Energy Secretary, Rick Perry, cite Koonin’s editorial while pushing for debates on climate change. Perry said “What the American people deserve, I think, is a true, legitimate, peer-reviewed, objective, transparent discussion about CO2.” That sounds good doesn’t it? However, we already have this: It’s called climate science.

Climate scientists have been forthright with politicians for years. Scientific consensus on the hazards of carbon emissions lead to the EPA’s endangerment findings in 2009, and was upheld by EPA review again in 2015. A letter to Congress in 2016 expressed the consensus of over 30 major scientific societies that climate change poses real threats, and human activities are the primary driver, “based on multiple independent lines of evidence and the vast body of peer-reviewed science.”

Kelly Levin of the World Resources Institute criticizes the red team-blue team approach for “giving too much weight to a skeptical minority” since 97% of actively publishing climate scientists agree human activities are contributing significantly to recent climactic warming. “Re-inventing the wheel” by continuing the debate needlessly delays crucial remediation. Scientific conclusions and their applications are often politicized, but that does not mean the political processes of holding debates, representing various constituencies, and voting are appropriate methods for arriving at scientific conclusions.

(Julia Marsh, Ecological Society of America Policy News)

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Data Sharing, Open Access

Open Access Science – getting FAIR, FASTR

Advances in science, technology and medicine are often published in scientific journals with costly subscription rates, despite originating from publicly funded research. Yet public funding justifies public access. Shared data catalyzes scientific progress. Director of the Harvard Office for Scholarly Communication and of the Harvard Open Access Project, Peter Suber, has been promoting open access since at least 2001. Currently, countries like The Netherlands and Finland are hotly pursuing open access science, and the U.S. is gearing up to do the same.

On July 26th, bipartisan congressional representatives introduced The Fair Access to Science and Technology Research Act (FASTR), intended to enhance utility and transparency of publicly funded research by making it open-access. Within the FASTR Act, Congress finds that “Federal Government funds basic and applied research with the expectation that new ideas and discoveries that result from the research, if shared and effectively disseminated, will advance science and improve the lives and welfare of people of the United States and around the world,” and that “the United States has a substantial interest in maximizing the impact and utility of the research it funds by enabling a wide range of reuses of the peer-reviewed literature…”; the FASTR Act mandates that findings are publicly released within 6 months. A similar memorandum was released under the Obama administration in 2013.

On July 20th, a new committee with the National Academies finished their first meeting in Washington D.C. by initiating an 18-month study on how best to move toward a default culture of “open science.” The committee is chaired by Alexa McCray of the Center for Biomedical Informatics at Harvard Medical School, and most members are research professors. They define open science as free public access to published research articles, raw data, computer code, algorithms, etc. generated through publicly-funded research, “so that the products of this research are findable, accessible, interoperable, and reusable (FAIR), with limited exceptions for privacy, proprietary business claims, and national security.” Committee goals include identifying existing barriers to open science such as discipline-specific cultural norms, professional incentive systems, and infrastructure for data management. The committee will then come up with recommended solutions to facilitate open science.

Getting diverse actors – for instance funders, publishers, scientific societies and research institutions – to adjust current practices to achieve a common goal will certainly require new federal science policy. Because the National Academies committee is composed of active scientists, their final report should serve as an insightful template for federal science agencies to use in drafting new policy in this area. (Alexis Wolfe & Lisa McDonald, American Institute of Physics Science Policy News)

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Written by sciencepolicyforall

August 1, 2017 at 7:38 pm

Science Policy Around the Web – January 12, 2016

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By: Tad Davenport, Ph.D.

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Biomedical Resources

Funding for key data resources in jeopardy

The goal of science is to push boundaries of knowledge. In a letter to John Locke, Isaac Newton famously wrote about his own discoveries, saying: “If I have seen further, it is only by standing on the shoulders of giants.” The pace of scientific discovery is accelerating, and the findings accumulate rapidly – this means that the giants whose shoulders we stand on today have never been quite so gigantic nor have they ever grown so quickly.

Increasingly, biomedical researchers rely on curated databases such as UniProt, OMIM, FlyBase and others to rapidly sort through enormous (and rapidly growing) volumes of information. These databases provide digestible, searchable access to descriptions of protein function and interactions, post-translational modifications, mutations associated with disease, and changes in protein and RNA levels during the development of model organisms including fruitflies and zebrafish. These databases are essential for generating hypotheses and designing experiments to understand basic biology and disease mechanisms.

A recent report by Jocelyn Kaiser for Science magazine describes the fiscal challenges faced by the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) in supporting the maintenance of these databases.  It is estimated that over $110 million or the NIH’s $30 billion annual budget is spent on maintaining these databases, and the cost is likely to continue growing in parallel with rapid expansion of genomic and other data.  To address the long-term “sustainability problem”, leaders of NHGRI have initiated discussions on alternative funding sources and mechanisms, including subscriptions and use-based fees. The enormous value of these databases for scientific progress is difficult to estimate, and every effort should be made to ensure easy accessibility for all researchers. (Jocelyn Kaiser, Science)

Vaccine Research

Unfilled Vials – Accelerating and Prioritizing Vaccine Development

Vaccines are a highly cost-effective means of preventing transmission of infectious agents. Unfortunately, vaccine development does not always make fiscal sense for pharmaceutical companies. In order to encourage pharmaceutical companies to take on the substantial financial burden of developing and testing vaccines in human clinical trials, it is likely that public-private partnerships, designed to mitigate the financial risk to companies, will play a critical role.

In a recent Science magazine article, Jon Cohen describes some recently proposed mechanisms for igniting private interest in developing and testing vaccines for pathogens that do not typically impact wealthy nations. One important step toward this goal is generating consensus regarding which pathogens should be prioritized for vaccine development.

Based on a poll of twelve vaccine experts, Science magazine generated its own list of the top ten pathogens that should be prioritized in designing new vaccines. Number one on the list was Ebola Sudan, a pathogen known and feared by many in the United States and other wealthy countries. However, a number of the pathogens on this list are less well-known in the United States (but no less important), including Chikungunya, Schistosoma, and Hookworm.  In ranking the pathogens, the contributors considered the pathogen’s impact on human populations, its transmissibility, its “potential to cause economic and social chaos”, and importantly, the feasibility of developing an effective vaccine (based on the immunity generated by natural infection, or preliminary results from tests in animal models). Cohen’s article enlightens the reader by presenting a balanced review of the challenges of vaccine development and a rational mechanism by which much-needed vaccines might be brought to market. (Jon Cohen, Science News)

The Future of Science

Interviews: Big ideas for better science

In a 2015 year-end interview with Kendall Powell of Nature magazine, four notable scientists made recommendations for how to improve the practice and culture of scientific research.

Jin-Soo Kim from Seoul National University suggests that eliminating the one-directional anonymity of the peer review process and openly crediting reviewers would reduce the potential conflict of interest in which a competing scientist is asked to review a colleague’s paper.

Jean-Baptiste Mouret at the French Institute for Research in Computer Science and Automation, recommends improving the openness and accessibility of computer programs used in research, with numerous potential benefits including better reproducibility and faster scientific progress.

Maria Cristina De Sanctis at the Institute for Space Astrophysics and Planetology in Rome emphasizes the importance of encouraging women in science from the very earliest ages.

And Danielle Edwards from the University of California, Merced recommends instilling more humanity in scientific research by providing a safer, more understanding work environment for people with varied experiences of life and its associated challenges.

These can be thought of as “New Year’s Resolutions” for science. How do you resolve to improve science, and more broadly, the world, this year? (Kendall Powell, Nature)

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Written by sciencepolicyforall

January 12, 2016 at 9:00 am

Science Policy Around the Web – September 4, 2015

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By: Amanda Whiting, Ph.D.

Scientific Publishing

Fake Peer Review Scandal Shines Spotlight on China

On August 18th, Springer, one of the world’s largest academic publishers, announced that it was retracting 64 articles from 10 of its journals after the discovery that those papers were associated with fake email addresses and that “subsequent internal investigations uncovered fabricated peer review reports”. The fake addresses led back to study authors writing their own peer reviews and to peer review “services” which sold names and contact information for fake experts with positive reviews. The latest aspect of this controversy is that nearly all of the retracted papers were authored by Chinese academics, based on a search for retracted papers on Springer’s site. While William Curtis, executive vice-president for publishing, medicine and biomedicine at Springer said that the retractions “do not offer a representative picture of the quality and ground-breaking research being published by researchers in China”, other researchers recognize the pressure many academics are under to publish at all costs. “We don’t think that Chinese researchers are any worse than anybody else. But what we know is that the pressure to publish — for example in Western journals — is enormous in China,” said Dr. Charlotte Haug, vice-chair of the U.K.-registered Committee on Publication Ethics (COPE). Publishers are starting to implement polices to help prevent this type of abuse of the peer review system, such as no longer allowing authors to suggest reviewers for their own papers and mandating that peer reviewers communicate through institution-based email addresses only. (Felicia Sonmez, Wall Street Journal)

Biomedical Research and PMI

Giant study poses DNA data-sharing dilemma

Next month, a working group run by the National Institutes of Health (NIH) for the Precision Medicine Initiative (PMI) is set to release a project plan and observers are keen to find out the answers to one really big question – how much information about disease risk (including genetic data) will the project share with the people who participate? PMI aims to collect health data including genomic information, health records and physiological measurements from up to 1 million people in order to have a large cohort to study how genetics, environment and lifestyle influence disease risk and the effectiveness of treatments. Within this large amount of data could be trends that influence disease treatments for public health as a whole, but it could also include more specific information about individual participants and diseases/conditions they never even knew they had. Proponents of data-sharing believe that participants should at least be given the option of seeing their own data, truly making them “active partners in the process” of research, as it would allow them to further investigate findings related to their own health. Opponents believe that it would be irresponsible to just dump data onto people since the raw information can be challenging to interpret and of uncertain significance. If data sharing does go ahead, it raises new challenges such as how to actually share the data, what level of quality the data must be at to be shared (for clinical decision making vs. research), and whether data on deceased patients could be released to their families. Given the size and profile of the PMI, the decisions of this working group could have a significant effect on how biomedical research on human cohorts is conducted in the future. (Sara Reardon, Nature News)

Drug Policy

F.D.A. Warns 5 Producers of Powdered Caffeine

The Food and Drug Administration (FDA) stated that it has sent warning letters to five producers of pure powdered caffeine over concerns of public safety and overdose risks. While caffeine is legal substance that can be found naturally in coffee and tea and is added in small amounts to gum and energy drinks, a teaspoon of pure caffeine is equivalent to approximately 28 cups of coffee and a tablespoon’s worth can be lethal. According to the FDA’s statement from September 1st, “the difference between a safe amount and a toxic dose of caffeine in these pure powdered products is very small.” The statement goes on to say that “safe quantities of these products can be nearly impossible to measure accurately with common kitchen measuring tools.” Bulk powdered caffeine has been linked to the deaths of two young men in otherwise good health in 2014. Laura MacCleery, regulatory affairs director of the Center for Science in the Public Interest consumer advocacy group, celebrated the move by the FDA and hoped that this was merely the first step towards a product ban. In explaining the dangers of bulk purified caffeine she said that “[p]eople assume something this dangerous would not be sold to consumers in this form. They are used to seeing warning labels and childproof caps on aspirin. And this is just a zip-lock bag.” (Sabrina Tavernise, New York Times)

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Written by sciencepolicyforall

September 4, 2015 at 9:00 am