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Posts Tagged ‘peer review

Science Policy Around the Web – February 17, 2017

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By: Thaddeus Davenport, PhD

Source: pixabay

CRISPR

Decision in the CRISPR-Cas9 Patent Dispute

This week, Heidi Wedford from Nature News reported that the United States Patent and Trademark Office (USPTO) made a decision on the disputed patents for the gene editing technology known as CRISPR-Cas9 in favor of the Broad Institute of MIT and Harvard. The CRISPR-Cas9 system has been widely publicized, and this publicity is arguably not out of proportion with the potential of this technology to simplify and accelerate the manipulation of DNA of both microbial (prokaryotic) and higher order (eukaryotic) cells for research and therapy. A simplified, programmable version of CRISPR-Cas9 for use in gene editing was initially described by Charpentier and Doudna, and it was rapidly translated for use in eukaryotic cells by Zhang and colleagues at the Broad Institute in parallel with Doudna, Charpentier, and others.

The USPTO decision follows a dramatic and ongoing dispute over whether the patent application submitted by the University of California on behalf of Doudna and Charpentier – which was submitted before that of the Broad Institute, and described the technology in broad terms as a method of cutting desired DNA sequences – was sufficient to protect the CRISPR-Cas9 intellectual property when the Broad Institute later filed a fast-tracked patent application describing the use of CRISPR-Cas9 for use in eukaryotic cells. Because the Broad Institute’s application was expedited, it was approved before the University of California’s application. In January of 2016, the University of California filed for an ‘interference’ proceeding, with the goal of demonstrating to the USPTO that Doudna and colleagues were the first to invent CRISPR-Cas9, and that the patent application from the Broad Institute was an ‘ordinary’ extension of the technology described in the University of California application.

On February 15th of this year, the USPTO ruled that the technology described in the Broad Institute’s application was distinct from that of the University of California’s. The importance of this decision is that the patents granted to the Broad Institute for the use of CRISPR-Cas9 in mammalian cells will be upheld for now. It also creates some complexity for companies seeking to license CRISPR-Cas9 technology. Because of the overlapping content of the CRISPR-Cas9 patents held by the University of California and the Broad Institute, it is possible that companies may need to license the technology from both institutions. The University of California may still appeal the USPTO’s decision, but this is a significant victory for the Broad Institute for the time being. For many scientists, this dispute is a dramatic introduction to the inner workings of the patent application process. We would do well to familiarize ourselves with this system and ensure that it works effectively to accurately reward the discoveries of our fellow scientists and to facilitate the transfer of technology to those who need it most, without imposing undue economic burden on companies and consumers. (Heidi Wedford, Nature News)

Scientific Publishing

Open Access to Gates Foundation Funded Research

Also this week, Dalmeet Singh Chawla reported for ScienceInsider that the Bill and Melinda Gates Foundation had reached an agreement with the American Association for the Advancement of Science (AAAS) that will allow researchers funded by the Gates Foundation to publish their research in the AAAS journals Science, Science Translational Medicine, Science Signaling, Science Immunology, and Science Robotics. This agreement follows an announcement in January in which the Gates Foundation decided that research funded by the foundation would no longer be allowed to be published in subscription journals including Nature, Science, and New England Journal of Medicine, among others, because these journals do not meet the open access requirements stipulated by the new Gates open-access policies. The new Gates Foundation policy requires its grant recipients to publish in free, open-access journals and to make data freely available immediately after publication for both commercial and non-commercial uses. A similar policy is being considered by the nascent Chan Zuckerberg Initiative.

In the agreement with AAAS, the Gates Foundation will pay the association $100,000 in order to make Gates-funded published content immediately freely available online. Convincing a journal as prominent as Science to make some of its content open-access is a step in the right direction, but it is perhaps more important as a symbol of a changing attitude toward publishing companies. Michael Eisen, co-founder of the Public Library of Science (PLoS) open-access journals, was interviewed for the ScienceInsider article and noted, “[t]he future is with immediate publication and post-publication peer review, and the sooner we get there the better.” This sentiment seems to be increasingly shared by researchers frustrated with the hegemony of the top-tier journals, their power over researchers’ careers, and the constraints that subscription-based journals impose on the spread of new information. Funding agencies including the Gates Foundation, Howard Hughes Medical Institute, and the National Institutes of Health are in a unique position to be able to dictate where the research they fund may be published. A collective decision by these agencies to push the publishing market towards an improved distribution of knowledge – through open-access publishing and post-publication peer review – and away from the historical and totally imagined importance of validation through high-tier journal publication would enrich the scientific ecosystem and accelerate innovation. In this regard, the efforts by the Gates Foundation are laudable and should be extended further. (Dalmeet Singh Chawla, ScienceInsider)

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February 17, 2017 at 12:44 pm

Science Policy Around the Web – December 13, 2016

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By: Allison Dennis, BS

Source: pixabay

Whistleblowers in Science

Keep your reviewers close and your online, anonymous, post-publication reviewers closer

A recent ruling by the Michigan Court of Appeals has ruled that anonymous online scientific reviews are a protected form of speech. Fazlul Sarkar, a former researcher at Wayne State University, had sued the site PubPeer in 2014 in an attempt to reveal the identity of several anonymous online reviewers to mixed success. Sarkar claimed that the defamatory and public nature of several online reviews posted anonymously to PubPeer had cost him a forthcoming tenure position at the University of Mississippi, one that came with a $350,000 a year salary. These reviews brought into question the validity of several images found in his published works.

While the initial ruling in March of 2015 largely sided with PubPeer to protect the anonymity of their online posters, a follow-up just two weeks later compelled PubPeer to reveal the IP address of a user who had gone as far as to repost quotes from an email response from the Senior Executive Assistant to the President of Wayne State University confirming their knowledge of the online allegations.

PubPeer filed an appeal of the decision by the end March, which garnished the collective support of science and internet moguls, Bruce Alberts, and Harold Varmus, Google, and Twittter in addition to the ACLU who filed amicus briefs in support of online anonymity. The summer brought more trouble for Sarkar as thirteen of his papers were retracted.

On December 9, 2016, the Michigan Court of Appeals found upon further review that Sarkar was “not entitled to unmask the identities of any speakers on pubpeer.com” citing “anonymity protections afforded by the First Ammendment.” Although this ruling does not dismiss Fazlul Sarkar’s case against John and Jane Doe, the protection of anonymity makes the suit moot. (Adam Marcus and Ivan Oranksy, STAT)

Federal Funding

Bipartisan cure found for stalled 21st Century Cures Initiative

In an end of the year push, the House and Senate passed the 21st Century Cures Initiative, a bill aimed at bringing legislation and regulation up to speed with biomedical research. At the end of November, a draft of the bill emerged from negotiations that were largely palatable to both Republican and Democrats across the House and Senate. A previous draft of the bill had successfully passed the House in July. However agreement over the source of funding could not be reached, arresting any further progress of the bill. The passing months brought Fred Upton, the Republican Representative who had originally spearheaded the bill close to the term limit afforded, as the chair of the Energy and Commerce Committee. The results of the recent elections seemed to be enough to incentivize compromise for Democrats in the final months of the Obama administration. Both parties returned to negotiations settling on a combination of funds derived from the selling of petroleum reserves and the Affordable Care Act.

In the end, the bill won 392-26 in the House and 94-5 in the Senate. Highlights of the bill under the title of Development include the accepted substitution of “data summaries” for full clinical trials when a new indication is to be added for a previously approved drug and expansion of off label-uses. The FDA has been tasked with evaluating evidence from the real world in an effort to speed-up and improve patient access. Highlights under the title of Discovery include a $4.8 billion boost to the NIH budget and $1.8 billion power pack for Joe Biden’s Cancer Moonshoot. A complete play-by-play of the winners and losers of the final version of the bill can be found in Sheila Kaplan’s article on STATnews. (Sheila Kaplan, STAT)

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December 13, 2016 at 10:38 am

Science Policy Around the Web – June 7, 2016

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By: Thaddeus Davenport, Ph.D.

Amazon Manaus forest” by Phil P Harris. – Own work. Licensed under CC BY-SA 2.5 via Wikimedia Commons.

Conservation Policy

A collaboration between science and religion for ecological conservation

Science has the potential to solve many of the world’s problems, but it may be overly optimistic to think that science alone can cure the world of all that ails it. Climate change and loss of biodiversity threaten humans in a way that we have yet to fully comprehend, and yet these problems emerged not as a result of some mysterious force, but rather because of simple human choices – the collective action (and inaction) of humans over the course of many years. This suggests that the solution to these most grand challenges does not only require scientific breakthroughs. Instead, the solution presents itself to us with a disappointing and somewhat undesirable simplicity: a problem created by humans might also be solved by human cooperation, responsibility, and ownership of our world and our problems. Indeed to tackle the world’s most complex challenges, science and society will need to work together.

Christine A. Scheller reported in March that the American Academy for the Advancement of Science (AAAS) annual meeting featured a dialogue on science, ethics, and religion (DoSER) discussion, which addressed the potential opportunities for collaboration between conservation scientists and religious communities in stemming the loss of biodiversity. The speakers included conservation biologist, Karen Lips, wildlife ecologist, Peyton West, and theologian, William Brown. Lips, the director of the Graduate Program in Sustainable Development and Conservation Biology at the University of Maryland, College Park discussed the decline of amphibious species and noted that while scientists may understand the causes of the problem and potential solutions, the efficacy of any conservation effort will require participation and engagement of those communities where species are going extinct. Similarly, West, the Executive Director of the Frankfurt Zoological Society-U.S. described the important and unique role of religious leaders in shaping the beliefs and behavior of their followers and highlighted the efforts of Catholic, Buddhist, and Islamic leaders to discourage ivory trafficking. Finally, Brown, a Columbia Theological Seminary Professor of the Old Testament observed that nature is represented in the Bible as the dominion of man – a perspective that has been historically “unhelpful” in encouraging conservation. He ended more positively, however, noting that “[m]uch of scripture affirms God’s love for all creation and acknowledges humanity’s vital connection with the nonhuman animal world.”

Science and religion are arguably the two most powerful thought systems in our global society. There is enormous potential to transform our world for the better if we can align the goals of each system toward creating a more just, balanced, healthy world and to identify opportunities for collaboration to achieve these goals. The DoSER program is an exciting forum in which these collaborations may take root. (Christine A. Scheller, AAAS)

Human Genetics

Why try to build a human genome from scratch?

Last week, a group of scientists released a report in the journal Science outlining their goals of building a complete human genome from scratch. This goal was initially discussed in a closed-door meeting, which drew criticism from those concerned about the ethics of such a proposition. The recent report is the product of that meeting and is intended to achieve transparency and to initiate an open discussion on the value, as well as the ethical and practical considerations of such a goal.

The proposed initiative is named “HGP-write” for human genome project – write, to differentiate it from the first, highly fruitful stage of reading the sequence of the human genome (HGP-read), which was completed in 2004. Perhaps in response to their initial criticism, the authors begin the report by acknowledging the ethical questions that will arise over the course of the project and emphasize that they hope to ensure responsible innovation by allocating a portion of research funding to facilitate “inclusive decision-making”. These will likely be valuable discussions with the potential to yield regulatory decisions that should be relevant for emerging gene-editing technologies, such as CRISPR, as well.

The authors go on to say that just as HGP-read produced a significant decrease in the cost of DNA sequencing, one of the goals of HGP-write is to develop technology that will make synthesizing large pieces of DNA faster and cheaper – they cite an optimistic goal of decreasing “the costs of engineering and testing large (0.1 to 100 billion base pairs) genomes in cell lines by over 1000-fold within ten years.”

But how would this technology be applied? The authors provide a number of examples, notably focused on the cell and organ level, including: to facilitate the growth of transplantable human organs in other animals and to engineer cell lines or organoids for cost-efficient vaccine and pharmaceutical development, among others. Additionally, the authors note that this ambitious project would begin by synthesizing small pilot genomes and DNA fragments, and that even these small-scale projects would be of substantial value, for example to synthesize an entire gene locus including associated noncoding DNA may provide insight into the regulatory role of noncoding DNA in gene expression and disease. The project is expected to begin this year with an initial investment of $100 million from a variety of public and private sources, and the authors estimate that in the end the project will cost less than the $3 billion spent during HGP-read.

Without a doubt, there is much good that could come from HGP-write – the ethical debate, the technological advances, a better understanding of the so-called “junk” DNA that makes up the majority of the human genome, and the applications of synthesized genomes. It is an exciting proposition that should be approached carefully and inclusively.

Peer Review Process

Confronting Bias in Peer Review

Humans are unavoidably flawed, and one of our greatest flaws is that each of us carries subtle biases – preconceptions about the world that shape our view and simplify our interaction with an unimaginably complex world. The essential role of peer-review in the scientific endeavor is founded on the assumption that our peers are able to think and make objective assessments of the value and quality of our work, without bias. In a system of thinking and observation that depends entirely on objective, measurable truths, there should be no value placed on who made the observation. Unfortunately, science and decisions about publishing and funding scientific research are exclusively human activities, and thus they are subject to the irrational biases that are so characteristically human.

No one – not even a scientist – is free of bias, and a recent AAAS-sponsored forum sought to highlight the presence of bias in scientific peer-review. Ginger Pinholster wrote about this forum on intrinsic bias in a Science magazine article from May 27th. Pinholster reports that multiple speakers observed that bias in scientific peer-review is not only a problem of fairness.  Geraldine Richmond, the AAAS Board Chair, noted that “unconscious assumptions about gender, ethnicity, disabilities, nationality, and institutions clearly limit the science and technology talent pool and undermine scientific innovation.”

Editors from the New England Journal of Medicine and the American Chemical Society pointed out a US-centric bias in peer-review. Gender bias was discussed as well by Suzanne C. Iacono, head of the Office of Integrative Activities at the National Science Foundation (NSF). Though success rates in grant funding from NSF were similar for men and women in 2014, women submitted only one quarter of the total grant applications. Iacono also noted that success rates for NSF applications submitted by African-American scientists were lower than the overall success rate of submitted applications (18% vs 24%), but more worrisome is the fact that only 2% of the submitted applications were submitted by African-American scientists. Similarly Richard Nakamura, director of the Center for Scientific Review at the National Institutes of Health (NIH) cited that African-American scientists have a success rate of funding from NIH that is approximately half that of white applicants.

While a number of potential interventions to minimize bias were discussed, including double-blind peer-review, it is clear from the relatively small number of funding applications from women and African-Americans that larger structural changes must occur to support and retain women and minority scientists early in their scientific development. The interest of AAAS in studying and addressing problems of bias in scientific peer-review is commendable. Understanding the problem is an important first step and finding a solution will require practice in self-awareness, as well as cooperation between high schools, universities, and finally funding and publishing agencies. (Ginger Pinholster, Science)

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June 7, 2016 at 10:00 am

Science Policy Around the Web – April 1, 2016

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By: Ian McWilliams, Ph.D.

photo credit: Matti Mattila via photopin cc

Federal Research Funding

House budget plan would rearrange and restrict federal research portfolio

Since the financial crisis of 2008, much attention has been given to the state of the economy. With recent optimism about the health of the economy, the president’s new budget plan for 2017, increases the NIH budget in FY 2016, and initiates new research spending for the Cancer moonshot. However, not all agencies are benefiting from the proposed budget. A report filed recently by the U.S. House of Representatives’ budget committee could curtail research spending for the National Science Foundation (NSF), the Department of Energy (DOE), and could lead to reshuffling sections of the Department of Commerce (DOC) into other agencies. Current DOE budget speculation is that there will be a decrease in funding for “several high-risk projects” that should be picked up in the private sector. While NSF biology, computing and information science, and math and physical sciences research directorates are to receive “stable funding”, the omission of specific plans for engineering, geoscience, and the social and behavioral sciences is ominous. It is unclear how the reorganization of the DOC will contribute to decreases in discretionary spending. The DOC is responsible for the research portfolios of the National Oceanic and Atmospheric Administration (NOAA), the National Institute of Standards and Technology (NIST), and the Census Bureau. (Jeffrey Mervis, ScienceInsider)

Science in the Public Eye

Controversial anti-vaccination documentary pulled from Tribeca Film Festival

In 2010, The Lancet retracted a highly controversial paper by Andrew Wakefield which proposed to link the Measles, Mumps, and Rubella (MMR) vaccine to autism. Since the original publication in 1998, this paper has been a cornerstone for the anti-vaccination movement, even after the paper has been discredited and retracted. Recently, Wakefield himself has directed and co-written a documentary titled “Vaxxed: from cover-up to catastrophe,” which claims that the CDC falsified and omitted crucial data linking vaccines to autism. This divisive film was to be screened at the Tribeca film festival , but was pulled, likely due to the backlash over screening the film. The original plan, put forth by Tribeca co-founder Robert De Niro, was to give an “opportunity for a conversation around the issue,” but he later decided after consultation that “we do not believe it contributes to or furthers the discussion I had hoped for.” In response, Wakefield and Del Bigtree, a producer for the film, released a statement that “We will be pressing forward and sharing our plans in the very near future.” With both sides pointing fingers, this argument will likely continue for some time to come. (Jason Ukman, StatNews)

Medical Devices and Testing

Study of Theranos Medical Tests Finds Irregular Results

The first peer-reviewed results of finger prick blood tests offered by Theranos have been published this week and bring more questions about the accuracy of its tests. Theranos, the medical start-up that provides direct-to-consumer blood tests, has come under increased scrutiny after an independent study found irregular results from tests offered by the company. The study, published in the Journal of Clinical Investigation, compared results from 22 different tests offered by Theranos to conventional blood test results from two national diagnostic laboratories, Quest Diagnostics and LabCorp.

Theranos has received much attention for their claims to offer blood tests that require small amounts of blood as a low-cost alternative to conventional laboratory testing. The company offers over two hundred different tests that require only a finger prick compared to vials of blood needed for conventional tests. Elizabeth Holmes, CEO of Theranos, touts the convenience and consumer experience of Theranos’s tests. However, the company has been reluctant to release data regarding their tests and has been mired in controversy after a Wall Street Journal article questioned the accuracy of the results of these tests. Furthermore, Theranos’ Newark, California laboratory has been cited by The Centers for Medicare and Medicaid Services for problems that “pose immediate jeopardy to patient health and safety.”

The current study used 60 healthy, adult volunteers who were tested at separate laboratories on the same day and found more measures outside of their normal range for Theranos’s finger prick blood tests when compared to measures from conventional blood tests. Results from Theranos were out of range for 12.2 percent of measurements compared to 7.5 and 8.3 percent for Quest Diagnostics and LabCorp, respectively. Although variability was seen in results from all three labs, Eric Schadt, one of the authors of the study, said that “Theranos was outside of range in ways that would impact clinical decision-making.”

Theranos’ laboratory directors responded to the study by sending a letter the journal calling the study “flawed and inaccurate.” They claim that a large blood draw from a vein could affect the results from a finger prick test and that the study authors did not attempt to determine which measurements were correct. (Andrew Pollack, New York Times)

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April 1, 2016 at 9:00 am

Science Policy Around the Web – March 29, 2016

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By: Thaddeus Davenport, Ph.D.

Source: Ashley Fisher / Flickr

Modernizing Scientific Publishing

Handful of Biologists Went Rogue and Published Directly to Internet

Peer-reviewed scientific journals are essential for science. They motivate and reward high-quality experimental design and facilitate the dissemination of knowledge that drives innovation. A recent article in the New York Times nicely captures some of the complexity of modern scientific publishing by examining a recent push by some researchers to publish their findings directly to ‘preprint’ servers – a practice already common in physics and mathematics.

Preprint publishing has the potential to significantly speed up publishing, allowing for faster and wider dissemination of ideas into a free, modern digital forum. Some researchers worry that bypassing the traditional peer-review process might eventually erode the quality of research. Though, it could be argued that so long as articles published to preprint servers are treated as preliminary findings (as, perhaps, we should treat all findings published in even the highest tier journals), the online forum has the potential to be a more transparent, robust peer review process than the current model in which a small number of anonymous reviewers decide the value of research.

The article notes other potential hurdles to the widespread adoption of preprint publishing that are deeply embedded in the culture of research. For example, papers are the currency of science. If authors bypassed this system, they would also bypass the possibility of attaining the classic badges of honor associated with publishing in high tier journals, potentially decreasing their competitiveness when applying for jobs and grants.

A change in publishing practices will also, likely, need to coincide with a change in the culture and value system of scientific research, but it is exciting to watch publishing move into the modern world. Scientific progress thrives on new ideas, and the resources of the digital age have the potential to broaden the reach of ideas and to increase the speed of their communication. (Amy Harmon, New York Times)

Economic Policies

A “Circular Economy” to Reduce Waste and Increase Efficiency

Our current economy can largely be described by a linear flow of material in which natural resources are harvested, combined, refined, and converted into products. These products are purchased, and after some amount of use, ultimately recycled or discarded at the discretion of the owner.  In a Nature special this week, Walter R. Stahel describes the potential economic and environmental benefits of a different sort of economy – a “circular economy” – that “replaces production with sufficiency” by encouraging reuse, repair, and recycling over remanufacturing.

Originally conceived by Stahel and his colleague Geneviève Reday-Mulvey in the 1970s, the concept of a circular economy “grew out of the idea of substituting manpower for energy.” For example, Stahel observed that it requires “more labour and fewer resources to refurbish buildings than to erect new ones.” Applying this model to all products has the potential to reduce greenhouse gas emissions substantially and expand the workforce because “remanufacturing and repair of old goods, buildings and infrastructure creates skilled jobs in local workshops.”

To support a transition to a more circular economy, Stahel recommends – among other things in his article –  a change in the way economic success is measured. Rather than trying to maximize our gross domestic product (GDP), a measure of the flow of resources, perhaps we should attempt to optimize the “value-per-weight” or “labor-input-per-weight” of the manufactured products. Policies and tax structures designed to maximize these economic indicators might be effective in encouraging stewardship of the earth’s limited resources and cultivating job growth. (Walter R. Stahel, Nature News)

A Second Chance for Grants

New funding matchmaker will cater to NIH rejects

The majority of NIH grant applications do not receive funding, not necessarily because the applications are of poor quality, but rather because there are simply more good ideas than the government has the capacity to support. A recent article in Science news by Kelly Servick describes a pilot program started earlier this month by NIH in collaboration with Leidos to address this gap in funding.

The program, known as OnPAR, aims to establish a more open market in which NIH grant applications that score well (within the thirtieth percentile) but do not receive funding would then be made available to private organizations and funding agencies for consideration. It seems that this system would be of substantial benefit to grantwriters – increasing the efficiency of grant-writing and review by allowing “recycling” of grants and their associated peer reviews, which are expensive to produce in terms of time and energy, and thus, money.

Funding agencies may see value in this program through expanded access, possibly finding themselves in the position to fund and motivate inquiry for researchers who may not have applied to their organization directly. However, private funding agencies are often in a position similar to that of the federal government – they receive more good applications than they have resources to support, and Servick notes that “the success of the project will hinge on whether private funders see value in using OnPAR in addition to their existing grant review process.”

If funders do find value in OnPAR, it is conceivable that they might allocate a percentage of their annual budget for OnPAR grants. Time will reveal the ultimate value of OnPAR, but it is a step in the right direction. How else might we increase the efficiency of the scientific production cycle? (Kelly Servick, Science News)

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March 29, 2016 at 10:00 am

Science Policy Around the Web – May 5, 2015

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By: Amy L. Kullas, Ph.D.

Global Health

Antibiotic Resistance: Combating Deadly ‘Superbugs’ Weak In Most Countries, World Health Organization Report Says

According the the World Health Organization (WHO)’s recent report, most countries are still failing to address the serious issue of antibiotic misuse, and are ill-prepared for the resulting increase in drug resistant microbes, allowing previously-treatable diseases to become killers. This statement was delivered approximately a year after the organization released its first global report on antibiotic resistance, which should have sounded an emergency alarm to the world, but essentially went unheard or ignored. At that time, Charles Penn, WHO coordinator on antimicrobial resistance, had this warning for reporters: “We will lose the ability to treat a range of serious conditions such as blood stream infections, pneumonia, tuberculosis, malaria, and HIV, and the benefits of advance medical treatment, such as cancer chemotherapy and major surgery will also become much riskier and may well be lost.”

For the current report, a only dismal 34 of the 133 countries that even responded to the WHO survey, currently have comprehensive national plans to combat resistance to antibiotics and other antimicrobial medicines. Counterfeit and low-quality drugs plague many regions of the globe, “resulting in sub-optimal dosing.” Additionally, many countries do not have standard treatment guidelines, which may allow the overuse and over-consumption of drugs. As a result, the WHO has drafted a Global Action Plan for addressing antimicrobial resistance and plans to ask all 193 member states to approve the plan at the next World Health Assembly, being held in Geneva, Switzerland later this month. By approving the plan, the countries will agree to develop their own national plans over the next two years and hopefully try to stem the tide of antimicrobial resistance. (Elizabeth Whitman, International Business Times)

Climate change policy

Analysis: In boosting climate goals, California daring others to follow

Californian governor, Jerry Brown, took action for climate change policy by issuing an executive order on April 29th requiring the state to reduce greenhouse gas emissions by 40% of the 1990 level by 2030. This level is consistent with scientifically established levels needed in the United States to limit global warming below 2oC, the threshold implicated for “major climate disruptions,” such as rising sea levels, changes in the ocean currents or extensive droughts. Governor Brown stated, “With this order, California sets a very high bar for itself and other states and nations, but it’s one that must be reached-for this generation and generations to come.” Californians usage of renewable resources, such as LED lighting and electric and hydrogen fuel cell cars, will have to leap from the current “25% to at least 50%” while halving their oil consumption. Further, Dan Kammen, an energy professor at the University of California-Berkeley, has estimated “$27 billion of venture capital and other financing has flowed into California clean technology companies since 2006” and almost 460,000 payroll positions have been generated in the past year. California’s effort will be successful on a global level only if other states and nations make set similar goals for themselves. (Marianne Lavelle, ScienceInsider; Adrienne Alvord, The Equation)

Gender equality in science

‘Sexist’ peer review causes storm online

Controversy has erupted after comments made by a reviewer for the journal PLOS ONE about a manuscript submitted by two female researchers were made public last week on Twitter. The reviewer felt that “one or two male biologists” co-authors would improve the manuscript written by the two female researchers to verify that data were interpreted appropriately and to “serve as a possible (fact)check.” The anonymous peer reviewer further stated that men have “better health and stamina” which may contribute to why men publish in higher impact journals and more successful in the highest jobs in science.

Dr. Fiona Ingleby, a postdoctoral fellow in evolution, behavior, and environment at the University of Sussex in the United Kingdom, tweeted sections of the letter that she and her co-author, Dr. Megan Head, received after rejection of their manuscript. The manuscript highlights the progression of Ph.D. graduates in the life sciences to postdoctoral positions and “found that men finished their PhDs with more other-author papers than women, but no difference in number of first-author publications.” According to Dr. Ingleby, “the reviewer acknowledged that they had looked up our websites prior to reading the manuscript” suggesting that the reviewer may not have been an unbiased referee.

As a result, PLOS ONE has requested the editor involved in the situation to step down from the editorial board and removed the anonymous reviewer from the database. Furthermore, the journal “sincerely apologize(s) for the distress the report caused the authors, and …completely oppose(s) the sentiments it expressed.” This incident highlights that while women in science have made significant strides towards gender-equality, more still needs to be accomplished. (Holly Else, Times Higher Education; Rachel Bernstein, ScienceInsider)

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May 5, 2015 at 9:00 am

Science Policy Around the Web – March 31, 2015

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By: Julia Shaw, Ph.D.

An Ebola treatment unit in Guinea. Photo by Samuel Hanryon/MSF

Ebola Drug and Vaccine Trials

Scientists Argue over Access to Remaining Ebola Hotspots

In contrast to previous outbreaks which were much smaller and relatively quickly contained, the current Ebola outbreak in West Africa is the worst the world has seen, causing close to 25,000 cases and 10,000 deaths. Although tragic, the scale of the outbreak should benefit the development of future vaccines and treatments for Ebola as studies advance through phase I safety studies to begin phase III efficacy testing. However, as the epidemic winds down, tensions are mounting as multiple organizations seek to complete their large-scale vaccine and drug studies.

Researchers at the National Institutes of Health (NIH) are hoping to move a vaccine study from Liberia, where new cases are few and far between, to Guinea, which reported 45 new cases last week. Yet Guinea is already host to a vaccine trial sponsored by Doctors Without Borders (MSF) and the World Health Organization (WHO) which began vaccinating last Monday. While Clifford Lane of NIH suggests “a country like Guinea is big enough to do at least two studies,” Peter Smith, an epidemiologist and chair of the board of the Norwegian Global health and Vaccination Research Program (which is co-funding the MSF/WHO vaccination trial) stated, “it would not be feasible to successfully run both trial in Guinea at the same time (unless there is a radical change in the epidemiology of the disease in Guinea and disease rates increase. . .).” The two sides have yet to meet in person to discuss the options. An assistant director-general at WHO, Marie-Paule Kieny, noted that “A compromise could be to run the two trials one after the other.” Lane contends that the ring-vaccination study approach adapted by WHO-MSF does not adequately assess longer term protection and that the NIH’s randomized controlled trial is a better approach “to get the most effective vaccine as quickly as possible to the largest number of people possible” and should not be delayed. Similarly, an NIH-led trial to test the therapeutic antibody cocktail, ZMapp, is expanding from Liberia to Sierra Leone where researchers from the University of Oxford have already begun a therapeutic trial of TKM-Ebola, another treatment which uses small interfering RNAs to limit viral replication. Lane is working with the government of Sierra Leone to provide patients with access to ZMapp which has shown better results in animal studies compared to TKM-Ebola. According to Lane, the government of Sierra Leone decides what treatment units will participate, and Port Loko, site of the TKM-Ebloa study, is currently not included in the list. However, if  ZMapp is introduced into treatment units that already have trials underway, Peter Horby, lead investigator of the TKM-Ebola study, says this would “jeopardize ongoing trials and lead to conflict.” (Kai Kupferschmidt, ScienceInsider)

Scientific Peer Review

Major Publisher Retracts 43 Scientific Papers Amid Wider Fake Peer-Review Scandal

United Kingdom-based BioMed Central, publisher of 277 peer-reviewed journals, recently retracted 43 papers due to “fabricated” peer reviews. Peer review is the process by which experts in a scientific field anonymously read and critique a submitted manuscript, judging whether it should be published based on scientific merit. Unfortunately, the process can be weakened or manipulated by poor reviewers, cronyism and outright fraud. In an investigation that began last year, BioMed Central’s associate editorial director for research integrity, Jigisha Patel, describes suspicions that surfaced due to a pattern of unusual e-mail addresses among reviewers and the discovery that the same author was reviewing different, highly specialized topics. Ultimately it was found that the scientists identified as reviewers had not actually written the reviews; someone else had simply used their names. A retraction associated with the articles states, “A systematic and detailed investigation suggests that a third party was involved in supplying fabricated details of potential peer reviewers for a large number of manuscripts submitted to different journals.” The pressure to publish may open the door for these third party agencies that offer language and publication assistance. According to Patel, “if authors are naïve and want to get their manuscripts published, they can be exploited.” The Committee on Publication Ethics, which includes over 9,000 journal editors, issued a statement calling attention to the “systemic, inappropriate attempts to manipulate the peer review processes of several journals across different publishers,” indicating this type of fraud is widespread and in no way limited to BioMed Central. (Fred Barbash, The Washington Post)

Pharmaceutical Regulation

Makers of Generic Drugs Challenge F.D.A. Plan for Updated Warnings

In 2013, the Food and Drug Administration (FDA) proposed requiring generic drug companies to update their labels if previously unknown health risks are discovered. Currently, generic drug producers cannot alter labels to reflect new health warnings unless it is ordered to do so by the FDA, while brand-name manufacturers do make changes as risks are discovered and the changes are later approved by the FDA. Public Citizen, a consumer advocacy group, supports the proposed rule, noting that the FDA lacks the resources to monitor changes for the numerous generics on the market. The drug industry counters that the proposed rule would make them vulnerable to expensive lawsuits resulting in increased costs. They further argue that they lack the full range of data available to the FDA from the brand-name producer and other sources with the end result being confusion as companies making the same drug might have different warning labels. The director of the health research group at Public Citizen, Dr. Michael Carome, admits generics are a great benefit to the public but maintains, “. . . because they dominate the market, it’s critical that they have full incentives to engage in robust monitoring of safety.” In response to the strong resistance from the generic industry including threats to sue, the FDA has reopened the period for public comment on the proposed rule until April 27th. (Sabrina Tavernise, The New York Times)

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Written by sciencepolicyforall

March 31, 2015 at 9:00 am