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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 – May 10, 2016

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By: David Pagliaccio, Ph.D.

Source: Ashley Fisher / Flickr

Scientific Publishing

Who’s downloading pirated papers? Everyone

Sci-Hub is an online repository for millions of scientific and academic articles, which has sparked major controversy among the scientific and publishing communities. The site, launched in 2011 by Alexandra Elbakyan, a graduate student in Kazakhstan, provides free access to ‘pirated’ articles. These articles would otherwise only be accessible through personal or institution journal subscriptions or by purchasing individual articles, which often can cost ~$30 each. Recent analysis of Sci-Hub’s 28+ million download requests from September-February 2015 found that requests were coming from over 3 million different IP addresses (potentially many more individual users as those sharing university internet network will often share an IP address). These download requests came from all over the world and across all types of scientific fields. Download rates reached more than 200,000 per day. An opinion survey regarding Sci-Hub found that at least half of users download articles from Sci-Hub because they do not otherwise have access to the articles at all. Interestingly, many others use Sci-Hub purely out of convenience when they would still have access through their institution. Many respondents also use Sci-Hub in objection to the profits made by publishers off of academics and feel that efforts like Sci-Hub have the power to disrupt the status-quo of science publication. That said, Elsevier, of the largest publishers affected by Sci-Hub, launched a lawsuit against Elbakyan last year for infringing on their legal rights as copyright holders. Despite having their domain seized during the lawsuit, Sci-Hub is largely beyond the reach of the U.S. legal system by being based in Russia. This is an still evolving situation and debate, which may have large effects on the state of scientific publishing today particularly given the major support from much of scientific community. (John Bohannon, Science News)

Mental Health

New Study Shows Mental Health Diagnoses and Treatment Vary Significantly by Race and Ethnicity

The Department of Research and Evaluation at Kaiser Permanente published result of a large study in the journal Psychiatric Services regarding the diagnosis and treatment of mental health conditions. The study included data from electronic health records of 7.5 million adult patients. The patients were part of 11 private, not-for-profit health care systems participating in the Mental Health Research Network. The results indicated that 15.6% (1.17 million) of these patients received a mental health diagnosis in 2011. This varied by race and ethnicity from 7.5% among Asians to 20.6% among Native American/Alaskan Native patients. Most groups had generally lower diagnosis rates than non-Hispanic white patients. Importantly, regardless of race and ethnicity, all patients with a diagnosed mental health condition were much more likely to receive psychiatric mediations (73%) than they were to receive formal psychotherapy treatment (34%). While the study does not point to any specific causative factors, they do indicate a need for evaluation of the causes and effects of racial and ethnic differences in diagnosis and treatment of mental health conditions as well as those relating to the vast discrepancy in treatment by medication vs. therapy. (PR Newswire)

Child Development Policies

Bringing Brain Science to Early Childhood

Researchers at Harvard’s Center on the Developing Child are pushing better use of developmental psychology and neuroscience research in the creation and implementation of policy regarding early-childhood programs. Particularly, they critique incentives in the current policy system and call for research and development on the most effective early-childhood programs for stemming intergenerational poverty. Programs for child development should all be based on the rapidly evolving knowledge base in the scientific field and should be allowed to develop as we learn and understand more. Work in this area has shown lifelong consequences of early childhood stress as well as lifelong benefits of early positive parenting both on mental and physical health. The Center has already been to pilot programs in Washington state aimed at improving executive function and self-control among parents and children and hopefully to improve parental engagement. This work allows for testing and refining of new interventions based on data collected from the pilot testing. On the other hand, many interventions have previously been enacted at large-scale without adequate follow-up testing or methods for improvement based on outcomes. For example, they cite that the Head Start program, which aims to help young disadvantaged infants and children, has but has not utilized the infrastructure to evaluate the effectiveness of their various programs and to identify which programs benefit which types of individuals most. As research suggests, intervening early in development can be incredibly impactful, and thus we should be capitalizing on our scientific understanding to implement the most evidence-based programs and utilizing outcomes data to constantly improve our programs. (Emily Deruy, The Atlantic)

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May 10, 2016 at 9:00 am

Science Policy Around the Web – April 24, 2015

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By: Danielle Friend, PhD

photo credit: DSC03602.JPG via photopin (license)

Genetic-based Drug Discovery

23andMe will invent drugs using customer data

As of March 2015, 23andMe will no longer simply be known for direct-to-consumer genetic tests. 23andMe has now made progress toward their long-term goal of influencing drug discovery. 23andMe claims to have collected DNA from approximately 850,000 consumers through marketing of their $99 kit, and the company plans to use this genetic information to identify new drug targets. Additionally, 23andMe reports that approximately 80% of the consumers that purchase the kits have agreed to allow 23andMe to use their genetic information for this research. To help lead these discovery efforts, 23andMe recently hired Richard Scheller, who formerly lead research and development at Genetech, as the chief scientific director and head of operations. In addition to these in-house efforts, 23andMe has also recently formed partnerships with pharmaceutical companies, including both Pfizer and Genetech who plan to use the genetic information to develop drugs for diseases like Parkinson’s disease. Although the partnerships with companies like Pfizer and Genetech are clearly defined to help identify drug targets for particular diseases, 23andMe plans to organize their in-house research as a broad sweep through their databases without a particular disease in mind. However, 23andMe has mentioned that they have a particular interest in metabolic and immune system disorders, eye disease, and cancer. (Mathew Harper, Forbes; Ron Winslow, Wall Street Journal)

Transparency in Clinical Trial Data

World Health Organization calls for increased transparency in clinical trials

In mid-April, the World Health Organization (WHO) released a statement recommending that findings from all clinical trials be made public regardless of the results of the study. Dr. Marie-Paule Kieny, the assistant director-general for health systems and innovation with the WHO, stated that the goals of this new mandate are to “…promote the sharing of scientific knowledge in order to advance public health.” Additionally, Dr. Kieny also stated that, “failure to publicly disclose trial results engenders misinformation, leading to skewed priorities for both [research and development] and public health interventions,” and that “it creates indirect costs for public and private entities, including patients themselves, who pay for sub-optimal or harmful treatments.” Several factors may come between completed research and the publication of results. However, unpublished results (even if negative) can lead to the perception that treatments are more or less effective than they are. The WHO mandate requires that results from clinical studies be submitted to peer-reviewed journals within 1 year after the completion of data collection, and that the work should be published within 24 months in an open access journal. The WHO also asks that “key outcomes” — limited details of the study including the number of participants, main findings, and adverse events — be made available online within a year of study completion. Although these new requirements are a step in the right direction for clinical trial transparency, it remains unclear just how the WHO plans to enforce these recommendations. (Chris Whoolston, Nature Research Highlights; Martin Enserink, Science Insider; The World Health Organization)

Ebola Clinical Trials

Lack of patients hampers Ebola drug and vaccine testing

As attention on the Ebola outbreak in Africa has increased, more resources and medical assistance have been provided. Although the number of Ebola cases has significantly decreased due to these interventions, an unexpected troubling scenario has developed: Ebola vaccine clinical trials are now having trouble testing the efficacy of their vaccines due to the lack patient populations. In fact, one company has altogether halted their trial. Chimerix, a company running a trial for their antiviral drug, brincidofovir, has decided to end the trial altogether due to a lack of patients. In fact, the World Health Organization’s weekly report from April 19 states that new cases of Ebola are now down to a total of 33. Because of the dramatic decrease in Ebola cases, the public health community faces ethical issues regarding whether more promising drugs should be prioritized and given preferential access to patients and geographical regions. (Andrew Pollack, The New York Times; Richard Harris, National Public Radio; The World Health Organization; Kai Kupferschmidt, Science)

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April 24, 2015 at 9:00 am

Science Policy Around the Web – March 24, 2015

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By: Courtney Pinard, Ph.D

Open Access

NSF unveils plan to make scientific papers free

The National Science Foundation (NSF) unveiled a plan last week that will require their grantees to make their peer-reviewed research papers freely available within 12 months of publication. This plan comes two years after the White House Office of Science and Technology Policy ordered U.S. federal science agencies to devise their own public-access policies. According to the plan, archives of full-text articles will be available on the publisher’s website. The push for public-access policies by some scientists and activists has been happening since the late 1990s with the National Institutes of Health (NIH) leading the effort with PubMed Central repository. Many publishers critical of repositories like PubMed Central say that public access policies infringe on their copyright and decrease their revenues. In response to these concerns, NSF has decided to work with the Department of Energy to create a system called PAGES (Public Access Gateway for Energy and Science). PAGES will contain abstracts, authors, and other metadata, but not the full-text paper. Instead, PAGES will provide a link to the full-text paper on the publisher’s website. In the future, NSF may allow open access to full-text papers through other repositories. (Jocelyn Kaiser, ScienceInsider)

Infectious Disease

Is Tuberculosis Still a Risk?

Tuberculosis is a widespread, and in many cases fatal, infectious disease caused by various strains of mycobacteria. Tuberculosis (TB) was once the top killer in the U.S. during the 19th century. With the advent of antibiotics, TB cases have steadily declined. In 2013, for example, 9,588 cases were reported in the U.S. Because of antibiotic resistant strains, there has been a surge in the number of people falling sick with TB in recent decades. Just last week, 27 people tested positive for TB at Olathe Northwest High School in Olathe, Kansas after a single case prompted testing. Due to the strength of their immune systems and access to proper antibiotics, none of these 27 people had symptoms, nor were they contagious. Without the correct treatment, however, more than 80% of people die from the infection. In fact, TB is the second leading cause of death in adults world-wide after HIV, and affects 1 million children each year. Two-thirds of the drug-resistant cases are found in the BRICS countries – Brazil, Russia, India, China and South Africa. Health policy officials in these countries started working on a TB treatment access plan more than two years ago, but little progress has been made. According to a report by the World Health Organization (WHO), three million people developing tuberculosis in BRICS countries are missed by national notification systems each year and only a fraction of cases are being treated. The WHO report emphasized the need to improve vulnerable populations’ access to quality tuberculosis care in low- to middle-income countries. Maybe, one day, TB-infected individuals in BRICS countries will have similar access to TB medical testing and treatment as those in Olathe, Kansas have. (Jacob Creswell, WHO; Dr. Salmaan Keshavjee, NPR)

Global Health and Agriculture

For the love of pork: Antibiotic use on farms skyrockets worldwide

As the developing world becomes richer, more and more people are consuming meat. Increased meat production will lead to the skyrocketing use of antibiotics, according to a study published last week in the Proceedings of the National Academy of Sciences. The study estimates that of the 228 countries who use antibiotics in livestock, total consumption will increase 67% from 63,151 tons in 2010 to 105,596 tons by 2030. The authors suggest that a huge rise in farm drug use will be especially prevalent in middle-income countries, where there is no regulation of antibiotic use on farms. That being said, although the United States Food and Drug Administration has made efforts to limit antibiotic use, critics say U.S. policies passed so far support “voluntary cooperation,” not binding regulation. (Michaeleen Doucleff, NPR)

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March 24, 2015 at 9:00 am

Science Policy Around the Web – December 2, 2014

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By: Amanda Whiting, Ph.D

photo credit: AJC1 via photopin cc

 

Federal Funding and Dual Use Research of Concern

U.S. urged to clarify extent of funding moratorium on risky virus research

The National Science Advisory Board for Biosecurity (NSABB) has called upon the US government to clarify its position and urged it to give guidelines to scientists affected by a recent funding moratorium on certain types of infectious disease research. The NSABB statement was intended to give voice to some of the concerns of scientists and uncertainty surrounding the October 17th announcement and ask for “clear definitions and pathways to exceptions where they are needed” said NSABB Chair Samuel Stanley, president of Stony Brook University, New York. The pause in new federal funding applies to gain-of-function (GOF) research on influenza, MERS and SARS viruses that could potentially make these pathogens more transmissible in mammals or more pathogenic. The moratorium on new research is intended to give experts, such as those at NSABB, a year to advise on and help formalize a U.S. government-wide policy for reviewing the risk and benefits of GOF studies. Researchers whose studies are already funded or have non-U.S. support are encouraged to join a voluntary moratorium while the policy is under development. Concerns over the possible misuse of viral research arose in 2012, after the publication of two NIH-funded studies of H5N1 transmissibility and pathogenesis in ferrets.  (David Malakoff, ScienceInsider)

Open Access Publishing

Gates Foundation announces world’s strongest policy on open access research

Beginning January 1st, 2015, researchers with funding from the Bill & Melinda Gates Foundation will be required to agree to some very, very open access publishing requirements! According to the open access policy announced on November 20th, authors funded in whole or in part by the foundation, must make their resulting papers and underlying data-sets open with unrestricted access immediately upon publication and allow reuse of their data for commercialization. During a two year transition period, authors may still apply for a 12-month embargo on the open publication of their data. This year-long delay in open access is similar to other life sciences funding sources, such as the NIH. However, after 2017, this option will no longer be available and could potentially prevent Gates Foundation researchers from publishing in top-tier journals such as Science and Nature, which currently make the delay mandatory. The ability to re-use data for commercial purposes also goes far beyond what is required by most open access policies. The Gates Foundation has taken a major stance on open access – and time will see just how far journals will go to continue to publish and distribute research or who else might follow suit. (Richard Van Noorden, Nature News Blog)

Public Health Policy

More public health interventions required to tackle grim reaper of ‘lifestyle’ diseases

A new paper published in the journal Critical Public Health, pushes the idea that public health policy should focus more breaking the (bad) habits of the public on the whole, rather than focus on an individual’s behavior as a way to better overall public health. Common behaviors, such as eating while watching TV or walking the dog after dinner, represent “social practices” that could be targeted for potential intervention with policy. The lead author, Dr. Stanley Blue says, “Smoking, exercise and eating are fundamentally social practices, therefore we need to re-shape what is deemed socially acceptable and normal in order to change them.” The authors cite changed attitudes towards smoking as one example of practice-oriented public health – as the social relationship with smoking changed, public health policies emerged that target the “practice” of smoking such as bans on smoking in restaurants or bars or in cars with children. “Current public health policy is dominated by the presumption that individuals are capable of making ‘better’ choices for themselves on the basis of information given to them by the government or other agencies. This does not account for the fact that practices like those of smoking and eating have histories of their own. Public health policy will have to find the courage to break away from its traditional mold if it is to stand a chance of confronting the grim reaper of lifestyle diseases.” (Science Daily)

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December 2, 2014 at 9:00 am

Science Policy Around the Web – November 8, 2013

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By: Tara Burke

Photo credit: Ryan Thompson via photopin cc

Photo credit: Ryan Thompson via photopin cc

Our weekly linkpost, bringing you interesting and informative links on science policy issues buzzing about the internet.

F.D.A. Ruling Would All But Eliminate Trans Fats – Yesterday, the Food and Drug Administration outlined measures to rid the nation’s food supply of trans fats, a major contributing factor to heart disease. The announcement ends a thirty-year fight by public health advocates against trans fats, which are created when liquid oil is treated with hydrogen gas to make a solid. The Institute of Medicine has found that there is no allowable amount of consumption of artificial trans fats and therefore, the FDA recommends that trans fats be removed from the legal category “generally recognized as safe”. The complete removable of trans fats from the American diet is expected to significantly cut down on health care costs and heart attacks. (Sabrina Tavernise)

U.K. Researchers Launch Open-Access Genomes Project – The United Kingdom announced this week the establishment of a British Personal Genome Project (PGP-UK). This program will recruit volunteers to provide DNA as well as health data; both DNA and health data will be available with no restrictions on their use. Britain’s PGP, headed by Stephan Beck from University College London, stems from a 2005 Harvard study. While the Harvard PGP currently has less than 200 genomes available, the study has many volunteers waiting. Other countries continue to see the value in personal genome databases as a way of furthering our understanding of DNA’s contribution to disease as Britain’s PGP joins other programs currently underway in Canada and Korea and one launching soon in Germany. (Elizabeth Pennisi)

More Asteroid Strikes Are Likely, Scientists Say – Traditionally, asteroid strikes have been thought of as an extremely rare event. However, in a paper published Wednesday in the journal Nature, scientists estimate that asteroid strikes may occur as often as every decade or two. These findings, along with the recent asteroid explosion over the Russian city of Chelyabinsk are elevating the topic of planetary defense. The United Nations is expected to recommend the establishment of an International Asteroid Warning Network, a way for countries to share information. They are also likely to recommend an advisory group to explore technologies that can deflect asteroids. (Kenneth Chang)

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November 8, 2013 at 5:40 pm

Science Policy Around the Web – August 29, 2013

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By: Jennifer Plank

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photo credit: Teseum via photopin cc

Measles outbreak tied to Texas megachurch sickens 21 – A visitor to the Eagle Mountain International Church that previously traveled to Indonesia and became infected with measles, has spread the infection to the largely unvaccinated congregation. To date, 16 people in Tarrant County, including a 4 month old infant, and 5 people in Denton County have contracted the illness and the number is expected to increase. All of the individuals infected have been linked to the church. As many as 1,000 people may have been exposed to the disease. Due to the outbreak, the church will be holding vaccination clinics for uninfected individuals. (JoNel Aleccia)

Government must step in to halt Fukushima leaks – A leak at the Fukushima Daiichi plant has resulted in the spillage of hundreds of tons of radioactive water, and experts believe the power company overseeing the plant is unable to cope with the leak. Therefore, many are calling on the Japanese government to intervene. Initially, the leak was labeled a Level 1 incident, but as of this week, it has been upgraded to Level 3. Several countries have offered to help Japan deal with the leak. (Quirin Schiermeier and Jay Alabaster)

Free papers have reached a tipping point, study claims – A study funded by the European Commission demonstrates that 50% of all scientific papers published are freely available after 1-2 years from publication, and the number is set to increase. US agencies funding scientific research and the European Commission are proposing plans for papers to be open access within 12 and 6 months, respectively. (Jocelyn Kaiser)

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August 29, 2013 at 10:43 am