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Posts Tagged ‘CRISPR

Science Policy Around the Web – February 24, 2017

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By: Alida Palmisano, PhD

Source: usda [Public domain], via Wikimedia Commons

Public Access to Data

Lawsuit Aims to Force USDA to Repost Scrubbed Animal Welfare Records

“Put the records back on the internet.”

An article published in Science discusses a lawsuit filed on February 13 against the U.S. Department of Agriculture (USDA) by an animal law expert at Harvard University. According to the plaintiffs, USDA violated the federal Freedom of Information Act (FOIA) when it removed thousands of animal welfare inspection reports and other records from a publicly accessible website. USDA generated records that document animal facility inspections, enforcement actions, animal censuses, and other information collected by the agency in the course of enforcing the federal Animal Welfare Act.  The law covers animals in more than 7800 facilities, including zoos, roadside circuses, and research laboratories at government agencies and academic medical centers.

The decision to remove the public access to these records may have been a response to a lawsuit involving another law, the Horse Protection Act. The plaintiffs in a 2016 Texas lawsuit accused USDA of violating their rights under the Privacy Act by posting inspection documents required by the Horse Protection Act. A resulting USDA review of all its public postings led the agency to scrub from its website documents generated under both the Horse Protection Act and the Animal Welfare Act.  In the future, the agency announced, people who want access to those records will need to file a FOIA request. The agency’s most recent FOIA report states that it takes an average of 94 days for the agency to respond to a simple FOIA request and 234 days on average for more complicated requests.

In February 13’s lawsuit, the plaintiffs invoke a section of FOIA that requires agencies to make publicly available electronically all records that it has released under FOIA which “because of the nature of the subject matter, the agency determines have become or are likely to become the subject of subsequent requests for substantially the same records.” (Meredith Wadman, ScienceInsider)

Science and Immigration

Grad Students, Postdocs with U.S. Visas Face Uncertainty

While U.S. courts are busy handling President Donald Trump’s travel ban on immigration from seven majority-Muslim countries, the temporary shut down of the executive order, the appeal to reinstate the travel ban, the rejection of the immediate restoration of the ban, and more appeals and rulings, graduates and postdoctoral students already in the United States are weighing their options and trying to plan rationally in an unpredictable and fluid situation.

Many scientists in the U.S. are on student or other working visas. All these visas may not be renewable, depending on future executive orders and regulations. The dilemma “simply ruins their future. It’s a catastrophe,” says a Yemeni biologist who is on a university faculty on an H-1B, a 3-year visa for professionals. For years, lawmakers in Washington have tried to reform abuses of visa regulations by companies using visas to bring workers to the U.S. to learn the ropes, and then send the trained workers to other countries where the job can be done cheaply. The H-1B system is contentious: on one side labor advocates want the exploitation of the H-1B system to stop supporting an outsourcing business model. On the other hand, tech companies like Google and Facebook say they can’t get enough visas for top foreign talent, as the cap on the number of H-1Bs issued every year means that sometimes foreign graduates from top U.S. universities, places like the Massachusetts Institute of Technology and the University of California, Berkeley, can’t get one. The travel ban already has harmed the top universities in the U.S., stranding students, faculty and scholars abroad, and making foreign schools more attractive to some of the world’s brightest students.

In papers filed in Brooklyn federal court, the schools (that include Columbia, Duke, Harvard, Johns Hopkins, Princeton, Stanford, Yale, Massachusetts Institute of Technology and several more) said that the order blocking travel from seven predominantly Muslim countries threatens their abilities to educate future leaders from every continent. They said the executive order has “serious and chilling implications” and that the ban “casts doubt on the prospect and value of studying and working here for everyone,” the papers said. (Meredith Wadman, Richard Stone, Science)

Genetic Engineering

US Science Advisers Outline Path to Genetically Modified Babies

“Scientists should be permitted to modify human embryos destined for implantation in the womb to eliminate devastating genetic diseases such as sickle-cell anaemia or cystic fibrosis — once gene-editing techniques advance sufficiently for use in people and proper restrictions are in place. That’s the conclusion of a 14 February report from the US National Academies of Science, Engineering, and Medicine.”

The report follows a 2015 National Academies summit between scientists, ethicists, legal experts and patient groups from around the world. At the time of the meeting, given the outstanding scientific, ethical and legal questions surrounding the issue, the organizers concluded that scientists shouldn’t yet perform germline editing on embryos intended for establishing a pregnancy. However, the organizers also stated that altering human embryos for basic research was acceptable.

The latest iteration of this ongoing CRISPR debate moves the bar a little further. The report recommends restricting the technique to severe medical conditions for which no other treatment exists. Eric Lander, president of the Broad Institute of MIT and Harvard, said, “It’s a very careful, conservative position that’s just a little bit beyond an absolute bar.” In the report, the committee also called for international cooperation, strict regulatory and oversight framework, public input into decisions and long-term follow-ups of children who have edited genomes. The report adds that for now, genome editing should not be used for human enhancement, such as improving a person’s intelligence or giving them super-strength.

The report drew immediate criticism from a California-based non-profit organization called the Center for Genetics and Society. “This report is a dramatic departure from the widespread global agreement that human germline modification should remain off limits,” said Marcy Darnovsky, executive director of the center. “It acknowledges many of the widely recognized risks, including stigmatizing people with disabilities, exacerbating existing inequalities, and introducing new eugenic abuses. Strangely, there’s no apparent connection between those dire risks and the recommendation to move ahead.” (Sara Reardon, Nature)

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February 24, 2017 at 11:23 am

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 – August 26, 2016

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By: Leopold Kong, PhD

Adipose Tissue  Source: Wikipedia Commons, by Blausen.com staff, “Blausen Gallery 2014“.

Health Policy

Is there such a thing as ‘fat but fit’?

Nearly 70% of American adults are overweight or obese, raising their risk for health problems such as heart disease, diabetes, and high blood pressure. However, about a third of obese individuals appear to have healthy levels of blood sugar and blood pressure. Whether these ‘fat but fit’ individuals are actually “fit” has been controversial. A recent study published in Cell Reports has sought to dissect differences in the fat cells of the ‘unfit’ obese versus the ‘fit’ obese using tools that probe the patterns of genes being turned on or off. Fat from non-overweight people were also examined in the study. Interestingly, fat of non-overweight individuals and obese individuals differed in over 200 genes, regardless of ‘fitness’. However, the fat of ‘fit’ versus ‘unfit’ obese individuals only differed in two genes. Dr. Mikael Rydén, the lead author of the study commented: “We think that adds fuel to the debate. It would imply that you are not protected from bad outcomes if you are a so-called fit and fat person.” The study also highlights the complexity of fat’s influence on health, and raises the possibility of ‘fat’ biopsies. For example, fat from normal weight individuals following an unhealthy lifestyle may have marked differences that are diagnostic of future obesity. With the rising cost of treating chronic diseases associated with being overweight, further studies are warranted. (Lindzi Wessel, Stat News)

Biomedical Research

Half of biomedical research studies don’t stand up to scrutiny

Reproducible results are at the heart of what makes science ‘science’. However, a large proportion of published biomedical research appears to be irreproducible. A shocking study by scientists at the biotechnology firm Amgen aiming to reproduce 53 “landmark” studies showed that only 6 them could be confirmed. The stakes are even higher when it comes to pre-clinical cancer research. In fact, they are $30 billion higher, according to a recent study, suggesting that only 50% of findings can be reproduced. Primary sources of irreproducibility can be traced to (1) poor study design, (2) instability and scarcity of biological reagents and reference materials, (3) unclear laboratory protocols, and (4) poor data analysis and reporting. A major stumbling block may be the present culture of science, which does not reward publishing replication studies, or negative results. Higher impact journals generally prioritize work that demonstrates something new and potentially groundbreaking or controversial. When winning grant money and academic posts hinges on impact factor, reproducibility suffers. However, with such high potential for wasting substantial funds on medically significant areas, radical changes in science policy towards publishing, peer review and science education is urgently needed. The recent reproducibility initiative aiming “to identify and reward high quality reproducible research via independent validation” may be a step in the right direction. However, a paradigm shift in scientists’ attitudes towards what constitutes important research might be necessary. (Ivan Orannsky, The Conversation)

Biotechnology

In CRISPR fight, co-inventor says Broad Institute misled patent office

The intellectual property dispute over the multibillion-dollar CRISPR gene editing technology has grown increasingly heated in the last months. With the FDA giving the go-ahead for the first U.S. clinical trial using CRISPR and with China beginning a clinical trial this month using this technology, the tension is high. On one side of the dispute is University of California’s Jennifer Doudna whose initial work established the gene-editing technology in a test tube. On the other side is Broad Institute’s Feng Zhang, who within one year made the technology work in cells and organisms, and therefore broadly applicable for biotechnology. Was Zhang’s contribution a substantial enough advance to warrant its own patents? Was Doudna’s work too theoretical and basic? This week, a potentially damning email that emerged from the legal filings of the dispute was made public. The email is from a former graduate student of Zhang’s, Shuailiang Lin, to Doudna. In addition to asking for a job, Lin wrote that Zhang was unable to make the technology work until the 2012 Doudna publication revealed the key conceptual advances. Lin adds: “I think a revolutionary technology like this […] should not be mis-patented. We did not work it out before seeing your paper, it’s really a pity. But I think we should be responsible for the truth. That’s science.” A spokesperson for the Broad Institute, Lee McGuire, suggested that Lin’s claims are false, and pointed out that Lin was in a rush to renew his visa, and had sent his explosive email to Doudna after being rejected for a new post at the Broad Institute. With CRISPR technology promising to change the face of biotechnology, the drama over its intellectual property continues to escalate. (Antonio Regalado, MIT Technology Review)

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August 26, 2016 at 9:00 am

Science Policy Around the Web – August 9, 2016

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By: Thaddeus Davenport, Ph.D.

Infectious Diseases

Local Transmission of Zika Virus in Miami

Most of the world became aware of Zika virus earlier this year when doctors in Brazil noticed a correlation between Zika virus infection in pregnant women and microcephaly in their newborn children. Recent articles in the New York Times on July 29th and August 1st report a notable shift in the course of the Zika virus epidemic – local transmission of the virus within the United States. In the last year, there have been over 1600 cases of Zika virus detected in the United States, but nearly all of these were imported infections, in which individuals became infected while traveling in Zika-endemic regions or through sexual transmission of the virus from people traveling outside of the United States. Because the Zika-carrying mosquito species, Aedes Aegypti is resident in parts of the continental United States, many people expected that it was only a matter of time before Zika virus would be transmitted locally within the United States. On July 29th, the Centers for Disease Control and Prevention and the Florida State Department of Health reported that Zika virus was transmitted to at least four individuals in the Wynwood neighborhood of Miami. By August 1st, the number of individuals infected in the neighborhood had risen to fourteen, and the CDC issued a travel advisory discouraging pregnant women from traveling to the affected area. Though Congress went to recess last month without passing a bill to provide funding for the fight against Zika virus, perhaps, and hopefully, the news of local Zika transmission will motivate bipartisan action in Congress to fund mosquito control efforts and basic research on this still poorly understood virus. (Pam Belluck, New York Times)

Clinical Research

First CRISPR-based clinical trial set to begin this month

The gene-editing technique commonly referred to as CRISPR-Cas9 has received significant attention over the last year because of its impressive potential to target, cut, and modify nearly any sequence of interest within a genome. David Cyranoski reported for Nature News that scientists in China are poised to be the first to use CRISPR-Cas9 technology in a human clinical trial. The trial will enroll individuals with metastatic, non-small cell lung cancer, for whom other treatment options have failed. T cells, immune cells capable of killing infected, cancerous, or otherwise afflicted cells, will be removed from these individuals and modified using CRISPR-Cas9 to delete the gene for a protein called PD-1, which plays a role in downregulating the immune response. It is hoped that removing PD-1 will make the participants’ T cells better able to mount an immune response against cancer cells. As an additional measure of safety, the genome of modified cells will be sequenced in order to confirm that there are no off-target modifications outside of the PD-1 gene that might impact the safety or validity of the study. Initially the trial will test the safety of introducing CRISPR-Cas9-modified cells into ten individuals at three different dosages, while also monitoring the effect of the treatment on cancer progression. A similar trial is set to begin in the United States later this year. These will be important proof-of-concept studies to show that CRISPR-Cas9 can be applied safely and effectively in the treatment of disease. (David Cyranoski, Nature News)

Drug Development – Antibiotic Resistance

New Funding for Antibiotics Development

Bacterial resistance to antibiotics is a significant and emerging threat to public health. Methicillin resistant Staphylococcus aureus (MRSA) – a commonly reported and widely feared strain of S. aureus – is one example of a bacterium that was once readily treatable with penicillin and related antibiotics, but which became difficult to treat after acquiring resistance genes. As current antibiotics become less effective against pathogenic bacteria, doctors are running out of tools to treat infections. An important hurdle to addressing the problem of antibiotic resistance is obtaining the funding necessary to support basic research. Unlike drugs to treat chronic health problems, effective antibiotics designed to cure infections of limited duration, are not necessarily a good investment for pharmaceutical companies. Asher Mullard reported for Nature News that CARB-X – Combating Antibiotic Resistant Bacteria Biopharmaceutical Accelerator- a public-private partnership supported primarily by the US government, Wellcome Trust, and the UK-based Centre for Antimicrobial Resistance hopes to provide US $350 million to motivate and accelerate the development of new antibiotics over the next five years. While many biotechnology companies support the initiative, some researchers, including Kim Lewis a researcher at Northeastern University, worry that CARB-X is too heavily focused on drug development instead of the discovery of novel antibacterial compounds. Despite their limitations CARB-X and other similar programs will likely provide valuable incentives for biotechnology and academic researchers to work towards better antibiotics for the common good. (Asher Mullard, Nature News)

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August 9, 2016 at 9:00 am

Science Policy Around the Web – June 28, 2016

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By: Sterling Payne, B.Sc.

Licensed via Creative Commons

Bioengineering and Human Trials

First CRISPR clinical trial gets green light from US panel

Since its discovery, CRISPR-Cas9 has become one of the hottest and most sought-after techniques and area of research in science. Whether owing to its ease of use, wide accessibility, or myriad modifications, the research and public health worlds are captivated by CRISPR. Almost one week ago, on June 21st, the National Institutes of Health (NIH) opened the door for the first use of CRISPR in humans as a potential therapeutic in a clinical trial. The trial in question focuses on the use of T-cells to fight cancer by introducing exogenous genetic material via CRISPR-Cas9, followed by the infusion of the cells into cancer patients.

This is not the first time that a gene-editing technique has been used to edit human cells. In 2014, Carl June, an immunologist at the University of Pennsylvania and scientific adviser on the current trial, led a trial that used zinc finger nucleases to edit T-cells in hopes of preventing viral infection. However, the recent approval of this single CRISPR proposal will most likely pave the way for many more, and in a short amount of time. The advancement of CRISPR-Cas9 in the past few years and its potential use in humans is staggering. However, an influx of clinical trials involving this technique will pose more policy discussions and questions to assure scientists and the public that the technique is being used humanely and ethically. It will be interesting to see how the definitions of what is humane and ethical in the eyes of policy-holders potentially changes in the coming years thanks to CRISPR. (Sara Reardon, Nature News)

Brexit and Research

Researchers deplore U.K. decision to leave the European Union 

On June 23rd, 2016, the electorate of Britain voted in a referendum to leave the European Union, creatively named the “Brexit”. Fast forward several days, and the consequences of the vote on multiple levels – such as global markets, immigration, employment, timelines and next steps – are still being determined. At it’s core, the U.K.’s decision to leave was not largely based on research science. However, multiple British science authorities are flabbergasted by the decision, a majority of whom believe was a mistake.

With Britain’s decision to leave the EU, it will be interesting to see how policymakers deal with the inevitable battles in terms of funding, personnel, and travel. One particular talking point is the fate of the U.K.’s standing in the Horizon 2020 program, a massively financed research initiative with 9 billion British pounds of funding over seven years (2014-2020). The initiative provides a means of support for collaboration across different European countries, and if the U.K. would like to continue as a player in the initiative, they will have to make a decision now and start preparing the necessary documents necessary to become an “associate”, for example. Policymakers have a long, winding road ahead of them in order to ensure the survival of the myriad collaborations and research projects headed by Britain. (Daniel Clery, Science News)

Patent Law

The Supreme Court decision that’s shaking up biotech 

The Supreme Court recently rejected the request to hear an appeal from Sequenom (San Diego, CA), a biotech. company specializing in prenatal testing. Sequenom’s test, MaterniT21, relies on the presence of fetal DNA in the plasma of the mother, allowing for a non-invasive method of analyzing the fetus for certain conditions such as Down’s syndrome (trisomy 21). The patent for the test remained intact until 2013, where in a case against Ariosa Diagnostics, a lower court ruled the patent as invalid. The Supreme Court’s failure to hear Sequenom’s appeal means that the previous ruling stands, and that poses a problem with implications far beyond a single biotech company.

Sequenom turned to the Supreme Court for thorough consideration and a final decision on whether or not their patent remains valid, although it does rely on the naturally occurring process of fetal DNA showing up in plasma. The highest justice’s silence in this situation creates an ambiguity around all patents in the biosciences. At what point does novelty evanesce into nature? Should patents, the protectors of intellectual property, really be granted in a case where natural processes are required to retain their validity? These are the types of questions that are being asked as a result of the Court’s silence, and that could plague future investments in biotechnology, a field that is highly represented by startups. (Douglas C. Pizac, AP/STATnews)

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June 28, 2016 at 2:30 pm

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 – March 11, 2016

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By: Sophia Jeon, Ph.D.

Photo source: pixabay.com

Patent law and Intellectual Property

Accusations of errors and deception fly in CRISPR patent fight

Clustered regularly-interspaced short palindromic repeats, better known as CRISPR, is getting a lot of attention as a promising molecular engineering technique that can easily edit genes in laboratories and potentially, for therapeutic uses. Last year, Chinese researchers successfully used the technique in human embryos, raising serious ethical concerns. Perhaps designing your own pets or human babies won’t happen in the immediate future but before CRISPR can even be considered for any commercial use, two research teams at UC Berkeley and at the Broad Institute will have to settle the issue of who gets to benefit financially from its use.

In May 2012, a team led by UC Berkeley’s Jennifer Doudna submitted a patent application for CRISPR-Cas9 technology. Several months later in December 2012, Feng Zhang’s research team at the Broad Institute also initiated the process to file for a patent but ended up getting the patent before Berkeley team since they used the expedited review program. The Berkeley team requested a patent interference, which will determine who actually invented the technology first. However, the issue becomes a bit more complicated by the fact that in March 2013, the U.S. patent law was switched to a system in which whoever files first gets the patent from a system that awarded patent to whoever invented first.

So how does one go about proving that someone invented or thought of something first, especially in this age of open access journals and public data sharing? The investigation process could be messy and could take months, or even years. However, both sides seem to have a number of strategies to weaken each other’s arguments, revealing mistakes in the application process and pointing fingers at insufficient data or misrepresented information in the application. Patent fights like this aren’t too rare with biotechnologies that could be used commercially (e.g. the recent lawsuit surrounding DNA sequencing technique between Oxford Nanopore Technologies and Illumina, Inc.) but it is interesting to see such a huge legal dispute between researchers from academia. (Kelly Servick, ScienceInsider)

Abortion law and Social Science

The Return of the D.I.Y. Abortion

In the recent years, abortion clinics have been vanishing from certain states (e.g. Texas, Mississippi, Missouri, North Dakota, South Dakota, Wyoming, Florida etc.) at a record pace. Planned Parenthood facilities are many of those clinics and these closures are partially due to passage of the bill to defund Planned Parenthood and other abortion restrictions in those States. However, the more important question is whether these restriction laws have actually result in lower abortion rates. Social scientists and health experts say there are multiple factors to consider. Some argue that abortion rates were going down even before clinic closings accelerated in the first place, due to increasing acceptance of single motherhood, the recession, and more effective birth control use.

How does law affect public health or more specifically, personal decisions regarding women’s bodies? Does limited access to abortion clinics make women turn to alternative methods such as self-induced abortion? It turns out that Google searches may provide some insight. Because there aren’t large enough surveys to track behavior in different states and also because surveys often don’t tell the real story (since people can lie), Seth Stephens-Davidowitz did an interesting study using Google searches to find correlation between the number of abortion clinics and interest in self-induced abortion. Sadly, the search terms he found related to self-induced abortion methods indicated that women might be driven to risky methods such as purchasing abortion pills online, punching one’s stomach, bleaching one’s uterus, or abortion using a coat hanger.

A previous study found that a vast majority of women would be willing to travel to other states with legal abortion if needed. However, underage girls or low-income women with unwanted pregnancy could be googling for and trying alternative abortion methods that could lead to adverse health outcomes. This June, the Supreme Court is expected to make a decision about a Texas law that restricts access to abortion clinics and whether or not it places an “undue burden” on women’s rights to abortion. The justices should make decisions based on hard evidence and well-balanced research. The study using Google search methods may be limited in certain ways as it is difficult to find out about their health outcomes or whether they actually succeeded in abortions, but it is one way to look at human behavior and how law could affect public health. (Seth Stephens-Davidowitz, New York Times)

Clinical Trials and Data Sharing

STAT investigation sparked improved reporting of study results, NIH says

The results of clinical trials are required by a federal law to be publicly reported on clinicaltrials.gov at the end of the trial. The goal is to promote transparency in any clinical research and to share data among the research community and physicians, as well as enhance patient empowerment by returning the results to the participants. However, according to a 2014 analysis published in JAMA, “a recent analysis of 400 clinical studies revealed that 30% had not shared results through publication or through results reporting in ClinicalTrials.gov within 4 years of completion.”

Last December, STAT also did a quite extensive investigation looking at clinical trials led by companies, universities, hospitals and even NIH-led trials to determine who actually reported their findings and how long after study completion. Many top research institutions failed to report on time and the federal government has not imposed fines on a single trial, which was “very troubling” according to the NIH director, Francis Collins said. Possible reasons for the delay in reporting are that the investigators continue to analyze data which can take a long time even after the trial has ended, that investigators wait until they publish their findings in a peer-reviewed journal and that in some cases drug companies intentionally want to hide negative results. Whatever the reason is, there should be consequences for withholding data that could be useful for doctors and patients.

The STAT investigation has named names and it seems to have worked. The data released by NIH showed that between December 2015 and January 2016, there was a 25 percent rise in new submissions and a 6 percent increase in reporting of corrected results for trial findings that had previously been submitted. Deborah Zarin, director of Clinicaltrials.gov, said the agency’s own outreach to researchers and training efforts are paying off as well. NIH is currently working on developing a new policy to clarify, expand, and enforce the requirements for clinical trial registration and results submission. (Charles Piller, STATnews)

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Written by sciencepolicyforall

March 11, 2016 at 9:00 am