Covid-19: What Are The Consequences Of The Unprecedented Rush For Knowledge?

By SalM on April 4, 2021 in COVID-19

Typically, the time between a research paper being submitted to an academic journal and it being published is 3-4 months. However, during the COVID-19 pandemic, many researchers have turned to preprint servers to make their work publicly available immediately, before peer review.

Despite the increase in early-career biomedical researchers supporting the use of preprint servers before the pandemic to gain timely recognition of their work, this field has been particularly slow in embracing these publications. Unlike physics, only a minority of all articles in life sciences and medicine are preprinted. This reluctance can be explained, at least in part, by the potential of flawed research leading to changes in clinical practice that could harm patients.

Since January 2020, around 30,000 preprints on COVID-19 have been published. Overall, only around 20%, of these preprints have been converted into peer-reviewed articles. This is mainly due to the time it takes to carry out peer review. The percentage goes up to about 50% when looking only at preprints that appeared in January-February.

Publishers have embarked in various initiatives to speed up the peer review process. These include the COVID-19 rapid review initiative, which allows the transfer of referee reports and articles between journals owned by different publishers, and developing online platforms that enable researchers to review each other’s work openly, such as Rapid Reviews: COVID-19 by MIT press.

Some publishers have also been able to invest in staff and/or artificial intelligence (AI) functionality to accelerate peer review and increase their output. This may not necessarily be beneficial.

Peer review isn’t perfect. It can fail to identify weaknesses or in some cases major flaws in a paper, resulting in a retraction. To date, Retraction Watch lists contains 37 retracted COVID-19 papers, including a couple in very prominent journals on the safety of malaria drugs and blood pressure medications for treatingCOVID-19 patients.

“There are lots of little changes we can make to raise the overall quality of the review system and of the outputs,” says Adam Marcus. He thinks that journals should be more diligent in checking reviewer suggestions made by authors (to make sure they’re real people and/or don’t have conflicts of interest with the authors themselves), and in detecting image manipulations or flawed statistical methods before papers are published rather than after.

According to Ludo Waltman, COVID-19 is changing the way we assess scientific literature: “The pandemic is forcing everyone, … researchers, journalists, policymakers to … gradually move away from the dichotomy between research in journals, that has been peer reviewed and is supposed to be reliable, and other types of work that don’t have this ‘stamp of approval’.”

Rather, readers face a continuum: from really low-quality research that hasn’t gone through any form of quality control at one extreme, to work that has been through a thorough peer review at the other, with research in journals that carry out a more superficial peer review and preprints that have benefitted from a certain level of quality control and expert feedback in between.

“We are still in the process of developing clear markers that inform researchers (and the public at large) about the level of trust you can have on a research output. We need to find a language that is easily understood, by doctors, journalists, policymakers…, and conveys different levels of soundness or trust you can have in the findings,” he explains.

“Further understanding of how research is organised and published will inform better ways of disseminating the information to different sectors of society,” says Waltman. And, as Marcus points out, electing politicians who value science and expertise is crucial for putting the emerging knowledge about COVID-19 into practice effectively.

Written by Monica Hoyos Flight.

This article has originally been published by the European Science and Media Hub and it is accessible here.

How Science Beat the Virus

By SalM on March 25, 2021 in COVID-19

In fall of 2019, exactly zero scientists were studying COVID‑19, because no one knew the disease existed. The coronavirus that causes it, SARS‑CoV‑2, had only recently jumped into humans and had been neither identified nor named. But by the end of March 2020, it had spread to more than 170 countries, sickened more than 750,000 people, and triggered the biggest pivot in the history of modern science. Thousands of researchers dropped whatever intellectual puzzles had previously consumed their curiosity and began working on the pandemic instead. In mere months, science became thoroughly COVID-ized.

Much like famous initiatives such as the Manhattan Project and the Apollo program, epidemics focus the energies of large groups of scientists. In the U.S., the influenza pandemic of 1918, the threat of malaria in the tropical battlegrounds of World War II, and the rise of polio in the postwar years all triggered large pivots. Recent epidemics of Ebola and Zika each prompted a temporary burst of funding and publications.

In a survey of 2,500 researchers in the U.S., Canada, and Europe, Kyle Myers from Harvard and his team found that 32 percent had shifted their focus toward the pandemic. Neuroscientists who study the sense of smell started investigating why COVID‑19 patients tend to lose theirs. Physicists who had previously experienced infectious diseases only by contracting them found themselves creating models to inform policy makers. Michael D. L. Johnson at the University of Arizona normally studies copper’s toxic effects on bacteria. But when he learned that SARS‑CoV‑2 persists for less time on copper surfaces than on other materials, he partially pivoted to see how the virus might be vulnerable to the metal. No other disease has been scrutinized so intensely, by so much combined intellect, in so brief a time.

But the COVID‑19 pivot has also revealed the all-too-human frailties of the scientific enterprise. Flawed research made the pandemic more confusing, influencing misguided policies. Clinicians wasted millions of dollars on trials that were so sloppy as to be pointless. Overconfident poseurs published misleading work on topics in which they had no expertise. Racial and gender inequalities in the scientific field widened.

Open data sets and sophisticated new tools to manipulate them have made today’s researchers more flexible. SARS‑CoV‑2’s genome was decoded and shared by Chinese scientists just 10 days after the first cases were reported. By November, more than 197,000 SARS‑CoV‑2 genomes had been sequenced. About 90 years ago, no one had even seen an individual virus; today, scientists have reconstructed the shape of SARS‑CoV‑2 down to the position of individual atoms. Researchers have begun to uncover how SARS‑CoV‑2 compares with other coronaviruses in wild bats, the likely reservoir; how it infiltrates and co-opts our cells; how the immune system overreacts to it, creating the symptoms of COVID‑19. “We’re learning about this virus faster than we’ve ever learned about any virus in history,” Sabeti said.

COVID-19 lessons for research

By SalM on March 12, 2021 in COVID-19

As we mark the 1-year anniversary of the declaration by the World Health Organization (WHO) of COVID-19 as a global pandemic, the world has suffered a staggering and tragic human toll. During this dark time, the scientific community has been called to rise to the occasion in unprecedented ways. The intensity of the work and the sense of urgency have been unremitting and exhausting. As we sort out the triumphs and frustrations, we can begin to reflect on what we have learned.

The rapid development of vaccines has been breathtaking. Moving at least five times faster than ever before, the design, development, rigorous testing, and manufacture of multiple vaccines using different platforms have been astoundingly successful. This was only possible because of decades of investment in the long arc of technology development—working out the details of a messenger RNA strategy, for instance, was a 25-year journey. To prepare for future pandemics, we must extrapolate this lesson to the most likely pathogens lurking in the future. We should also learn from the experience of vaccine trial recruitment, where special efforts like the U.S. National Institutes of Health (NIH) Community Engagement Alliance (CEAL) were needed to reach out to communities of color, where the disease has taken its highest toll in the United States. Diversity in clinical trial enrollment is not just a nice idea—it is essential if the results are going to be meaningful to all groups.

Therapeutics that have proven beneficial for COVID-19 include an antiviral (remdesivir), immunosuppressives (dexamethasone, baracitinib), several outpatient monoclonal antibodies, and anticoagulants. Important contributions were made by the Randomised Evaluation of COVID-19 Therapy (RECOVERY) trial in the United Kingdom and the Solidarity Trial sponsored by WHO. In the United States, a public-private partnership, Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV), brought together government agencies, academics, and 20 pharmaceutical companies, ably managed by the Foundation for the NIH. With a priority on therapeutic agents, ACTIV designed master protocols and coordinated rigorous, well-powered randomized controlled trials. Operation Warp Speed, a public-private partnership initiated by the U.S. government, provided billions of dollars for trial operation and at-risk manufacturing. One lesson learned, however, was that many clinical trials in the United States were not initially well suited to a public health emergency. Far too many small and poorly designed trials (many focused on hydroxychloroquine, which turned out to be a dead end) were initiated in the early days of the pandemic—all with good intentions but contributing relatively little in terms of new knowledge. Another lesson is that the necessary short-term dependence on repurposing existing drugs will not often produce true successful outcomes. For the future, we should begin to work on potent oral antivirals against all major classes of potential pathogens, with the goal of having drugs ready for phase 2/3 efficacy trials when the next threat emerges.

Another major challenge was the need for fast, widely accessible, and highly accurate virus testing. For all their merits, the first-arriving nucleic acid tests, which generally had to be conducted in central labs, took too long to produce the rapid results urgently needed to prevent spread. This inspired an innovative response—the NIH Rapid Acceleration of Diagnostics (RADx) program in which test developers drew on a “shark tank” of engineering, business, and manufacturing experts. From over 700 applications, 137 went through an intense evaluation, and those judged most promising were provided with additional resources. As a result, today there are 28 novel diagnostic platforms collectively contributing an additional 2.5 million tests daily. An analysis of the potential benefits of widespread home testing is about to get under way. This approach, whereby NIH took on the role of venture capitalist, should be considered in the future when rapid development of new technologies is the goal.

In the past, the world has rallied to confront new pandemics, only to lapse into complacency as the risk faded. Having now experienced the worst pandemic in 103 years, we must not make that mistake again.

Source: eurekalert.org

Public Engagement in the Time of COVID-19

By SalM on March 5, 2021 in COVID-19

This sense of dualism is also at play in public engagement spaces within and beyond the academy. In trying times, it is especially critical that we continue to create and maintain effective dialogues between scholars and communities in order to generate equitable and sustainable solutions to the problems that matter most.

Our objective in writing this post is to reflect on the continued importance of public engagement in the current moment and to highlight the unique challenges communities face during a time of crisis. By sharing these examples of effective public engagement – as well as new efforts to build capacity for even greater transformation – we hope to learn from this moment and reflect on ways that universities can support this critical work.

The academic community is rallying to meet the crisis with waves of new research and creativity in engaging with different publics; public scholars have recognized and acted upon myriad opportunities during the pandemic. There have been outstanding examples of researchers engaging with media professionals to share expertise and shape stories, and interest in writing op-eds or for outlets like The Conversation is incredibly high. Opportunities to participate in research on SARS-CoV-2 or work with researchers to co-design possible antivirals are expanding rapidly. Demand for online teaching and learning is spiking, and universities and other organizations are producing just-in-time learning opportunities addressing the novel coronavirus or sharing fun experiences for kids and families at home.

At the same time, community partners who work with academic scholars are experiencing huge impacts, and few have the same security that the shelter of a university offers. Zoos, museums, and other spaces for informal learning are shuttered and have been forced to furlough or lay off workforces. Schools are closed for the year. Non-profit organizations – especially those focused on alleviating poverty, housing, and food insecurity – are working to survive and hold the line. And engagement opportunities relying on virtual tools and environments underscore access disparities to technology and the internet, widening existing gaps which disproportionately affect people who are poor and people of color.

It is in this dual reality of intense struggle and remarkable human accomplishment where the importance and value of public engagement efforts become even more clear. Heartbreakingly, sometimes the communities with the greatest capacity to understand problems – especially through lived experience and other ways of knowing which aren’t rooted in academic expertise – are the most strained on the front-lines of crisis. Therefore the time of COVID-19 reinforces the responsibility and trust that institutions of higher education – especially public research universities – hold in serving the public good. Such institutions have much greater capacity to weather these trying times. We must leverage our relative stability and unique strengths and take active steps to be of service to our communities.

In addition, the pandemic – including all the associated challenges and opportunities – will become an anchor for the cohort’s reflective practice throughout the experience. We hope that continuing to offer this experience for Fellows during the time of COVID-19 will reinforce core tenets of ethical engagement work, including recognition, respect, and equitable partnership, and reinforce the need to be of service and to partner in mutually-beneficial ways with our communities in the times ahead.

We’ve highlighted just a few ways that the academic community continues to engage in important public engagement work. Certainly there are many more. There is also more work to be done – especially in the context of supporting scholars and community partners to be able to pursue this work sustainably and equitably.

  • How might institutions of higher education learn from the current moment – especially in how they value products of engagement work that aren’t rooted in grants and publications?
  • What infrastructure and policies are necessary to institutionalize a commitment to respectful and equitable engagement, including honoring the expertise and compensating the efforts of long-time public partners? How might such a commitment extend the shelter of the university to our communities during times of crisis?
  • How might universities help to address disparities to accessing much of the public engagement effort currently requiring a device and internet connection?
  • What other opportunities do you see to strengthen or support public engagement in a time of crisis?

The duality of this crisis truly poses an opportunity for all of us to reflect on the multiple roles we occupy and the communities of which we are members – both within and beyond institutions of higher learning. We hope to learn from this moment and use these lessons to build towards a more resilient future.

Pandemic Shows Significance of Open Data

By SalM on March 3, 2021 in COVID-19

Since March 2020, we have witnessed numerous parallels between COVID-19 and the climate crisis, including a lack of cohesive, coordinated global intervention and a laissez-faire response to a global emergency.

Inadequate government response to the pandemic has led to preventable deaths from a highly contagious virus, just as inadequate government responses to the climate crisis could result in exacerbated effects by drought, fires or flooding as well as rising food insecurity. These risks are fast approaching their tipping points.

COVID-19 has inundated our lives with numbers and social media updates to the point of statistical overload, a phenomenon WHO refers to as an ‘infodemic.’ The flood of information has occasionally caused the public to question the veracity of certain claims, which in turn has hampered effective public health responses. Nonetheless, the vast availability of data encourages scientists and citizen scientists across the world to disseminate models, ideas and scenarios for better progress against the virus.

Open Data for Forests

The pandemic reinforces the importance of data for interpretation and dissemination. It is a resource that needs to be carefully curated, because leaders, whether in health or in climate science, need to make informed decisions in order to respond to global agendas such as the Sustainable Development Goals (SDGs). Likewise, citizens will need assurance and transparency to act as individuals and communities, and to advocate for data-driven policy development.

Likewise, forest data transparency is key to supporting higher levels of ambition for the roles of forests in climate change action. Progress in National Forest Monitoring Systems (NFMS) in the past ten years has catalyzed solutions for forests and climate action, such as for REDD+. In many countries, greater transparency of countries’ forest-sector data and information has resulted in improved national decision-making, and for the first time, detailed and transparent forest data has been reported internationally, with 50 countries having submitted forest reference emissions levels to the UN Framework Convention on Climate Change (UNFCCC).

Still, countries’ efforts towards forest data transparency must be strengthened. Under the Enhanced Transparency Framework of the Paris Agreement, robust data collection is central for reporting on emissions and removals, as well as for tracking the progress of Nationally Determined Contributions. An NFMS that is transparent, reliable, relevant, accessible, and sustainable can support climate action on the ground.

What lessons can forest monitoring practitioners take from the ongoing pandemic?

  1. Sharing openly can flatten the curve: With COVID-19, countries that have embraced data acquisition through frequent testing and have been transparent about infection rates have mostly succeeded in flattening the curve of infections. In Germany, testing, tracing, and transparency are credited with building public trust. Likewise, improved data availability combined with transparency could catalyze more collaborative solutions to the climate crisis that could equally buy some precious time to achieve the terms of the Paris Agreement.
  2. Climate policies need up-to-date and integrated information: Data sets can be shared at unprecedented speed. While the availability of COVID-19 related data has often overwhelmed data consumers and resulted in conflicting guidance, frequent and integrated forest data is likely to enhance public engagement and collaboration on relevant solutions for forests.
  3. Public money means public information: Enormous financial resources have been poured into COVID-19 monitoring. Likewise, national forest data is primarily collected through taxpayer finances, either through national or international cooperation funds. Greater public financing of large-scale data collection and sharing ultimately means greater information available to the public, enhancing public trust and increasing opportunities for investors and researchers. Open, transparent, and reliable forest data can also enhance private investment, which is urgently needed to trigger transformation of forest and land management for climate action and other multiple benefits. Accurate and reliable forest data created from public funds needs to be open and accessible to the public.
  4. Overcoming obstacles to sharing: Under the pandemic, open data has accelerated science, but also introduced vulnerabilities. Both media and politicians have sometimes reported promising results before they have been scientifically validated. Among the obstacles to sharing forest data is the concern of inadequate use of the data and lack of intellectual property recognition. Barely 14% of researchers in 2018 shared their data in repositories. Yet, twisting the tragedy of the commons, while 74% researchers value others’ data sharing as beneficial to their own research, both scientists and governments show reluctance to share their own data.

To overcome this resistance, legal agreements that release individual contributors from conflicts with the institutions involved in data sharing are needed, with updated and harmonized measures to ensure anonymity of legal subjects and/or spatial coordinates. Further, data ownership recognition standards should encourage data sharing. Government officials and researchers need to follow the FAIR (findable, accessible, interoperable, reusable) guiding principles for data management and stewardship, thereby making the case that in the end the benefits of sharing outweigh the disadvantages.

Forest Open Data Platforms and FAO’s Support

Some existing microdata platforms, such as the Global Forest Biodiversity Initiative GFBI, largely compile and share global field data for academic research and require strict rules on confidentiality and control of users. Yet, forest-related information still remains largely scattered across multiple platforms. FAO is working with UN Member States to overcome obstacles to open forest data. Our current efforts include:

  • the Global Forest Resources Assessment 2020, which provides country validated forest data, accessible through an interactive platform and dashboards.
  • the Hand-in-Hand geospatial platform launched recently, representing a major step towards accessible and transparent cross-sectoral geospatial data across agriculture, fisheries, and forestry.
  • a set of free and open source tools (Open Foris) developed by FAO to facilitate flexible and efficient data collection, analysis, and reporting helping to enhance forest monitoring at national level.
  • A new FAO project ‘Building global capacity to increase transparency in the forest sector (CBIT-Forest)’ to establish a Global Field Forest Observation Repository with a view to harmonizing legal assurances in data confidentiality, redistribution policies, and quality assurance conditions meeting international data documentation protocols. Microdata inclusion on this platform would contribute to increased standardization, accessibility and data usage.

A New, Transparent Normal?

COVID-19 has increased awareness about the power of data sharing. We hope that this motivates governments and forest monitoring practitioners to share forest data. At the same time, it is important that open databases follow standards to minimize misuse and misinterpretation. We believe that open forest data can strengthen our collective effort to identify and apply solutions for forests as a key response to the climate emergency.

FAO’s support to forest monitoring aims to strengthen data openness standards, while solving conflicts with data protection and confidentiality. In order to achieve reusability, clear and accessible data use licenses must exist. Legal certainty through license to redistribute agreements, ensure data robustness alongside data sensitivity. A Global Field Forest Observation Repository to facilitate data sharing of forest microdata to technicians and academics while supporting international reporting requirements across countries, is a step towards fostering that necessary transparency.

Source: sdg.iisd.org

What are the ethics around research during a global pandemic?

By SalM on February 26, 2021 in COVID-19

By Elizabeth Kiely and Ciara HeavinUCC

Yet another survey has just arrived into our email inbox to explore how we were coping with our new normal. We coined the term “covidata” to describe the insatiable need and demand for data currently being driven by the pandemic and likely to continue for some time.

Social research ethics committees are reviewing Covid-19 related studies and considering a range of research questions exploring the effect of the global pandemic on different groups’ knowledge, attitudes and practices. These include university students, academics working in their new virtual environments and employees working in small and large business and not-for-profit organisations. Against the current backdrop, these studies are asking questions about how we work and live, what we are buying, our experiences of homeschooling and how we are coping with the stress/pressure/anxiety as we deal with all of our new, albeit temporary, reality.

There is no doubt that the coronavirus has created new opportunities for big research ideas that could potentially directly inform local, national, and international practice, policy and research during and after the pandemic. However, ethical, mindful and responsible researchers need to give careful consideration to the timing and the manner by which research is conducted. For example, a recent article published in the Lancet Psychiatry noted that some studies in the area of self-harm and suicide have been paused for a number of reasons. These include the unknown unnecessary burden they may be putting on participants who may not have the same access to the services and supports they used pre-pandemic.

Certainly, Covid-19 is presenting researchers and students with new challenges in the research field, which can cause stress and anxiety. We are now required to reorient our inquiries, adopt new methodologies or modes of engagement and develop revised ethical protocols as required. Our research may be moving online posing new ethical challenges that require careful consideration. Timelines and budgets for research projects commenced pre Covid-19 have to be reconsidered.

In times of stress such as this one, speedy solutions are sought and there is the risk that extraordinary measures introduced during extraordinary times continue to be used in ordinary times and can be re-purposed in ways that were not foreseen. For example, various technological solutions such as digital contact tracing apps have been adopted or proposed by governments in different countries to prevent virus transmission. Their use at the time of a pandemic does not remove or downplay human rights, privacy or cost concerns. They must be rigorous questioning as to the risks these solutions pose and the limits of what they promise.

It seems more important than ever that ethical standards required for the conduct of research are not slackened. Rather, the current situation provides opportunity for everyday ethical engagement. Writing in Nature, Gemma Derrick speculated that this new era may prompt us to examine our research motivations.

We could use the momentum of Covid-19 to firmly embed kindness into research practice

“A once narrow, competitive drive to collect data for our individual research ambitions has been replaced by dialogue about whether now, with everyone’s mind otherwise occupied, is really the best time to be collecting data?”, Derrick wrote. “This goes beyond concerns about data reliability and reproducibility, towards a type of empathy and foresight that is the bedrock of research kindness. We could use the momentum of Covid-19 to firmly embed kindness into research practice, extending greater goodwill beyond this, temporary, situation.”

As we pause our “normal” lives, is it also time to pause for thought to critically reflect on our motivation to conduct particular types of research? While pausing, we might consider what naturally occurring or already existing data is available that can be successfully mined to answer new questions. For instance, how can data gathered during previous pandemics / epidemics be of benefit to us during this one?

We can turn to secondary data collection or identify further potential in previously collected primary datasets.  We can conduct systematic reviews, rapid reviews, meta-analyses or advance new inquiries using already existing datasets held in digital repositories.  Undoubtedly, reflective diaries, lockdown journals, oral histories, and other creative outputs produced during Covid-19 will provide rich resources for research.

We can do our utmost to ensure that the data we are gathering is adding value

As the demand for “covidata” intensifies, we need to be mindful not to cause research fatigue. We need to consider how vulnerable individuals and constituencies can be real beneficiaries of our research while taking care not to over-research them or to compound their vulnerability. We can direct our research gaze upwards so that the activities of corporate elites, key decision makers, and powerful actors during Covid-19 do not evade the research spotlight.

We can take account of who is benefitting from our research findings and in what ways. We can guard against ourselves or others over-claiming the significance of our research findings, which may require considered analysis and interpretation as to their relevance for ‘normal’ times. We need to assess how and why our research findings may find their way into policy and practice or if not, why not.

If we produce careful data management plans at the outset of our research projects, we can better ensure the preservation of the data we gather for future use by ourselves and others facilitating opportunity for re-analysis and new interpretation. We can do our utmost to ensure that the data we are gathering is adding value and that our research outputs are FAIR (Findable, Accessible, Interoperable, and Reusable) and timely.

Dr Elizabeth Kiely is a Senior Lecturer in the School of Applied Social Studies at UCC. She is a former Irish Research Council awardee. Dr Ciara Heavin is a Senior Lecturer in Business Information Systems in the Cork University Business School at UCC. She is a former Irish Research Council awardee

Source: rte.ie

COVID-19 triggered unprecedented collaboration in research

By SalM on February 9, 2021 in COVID-19

The pandemic has both spurred on and demonstrated the value of open science, but has also exposed gaps in science policy. Now is a good time for reform, says OECD.

Unprecedented global collaboration between scientists has greatly accelerated understanding of the COVID-19 virus, the infection it causes, and the testing and development of therapies and vaccines to treat and prevent it.

This exemplar could form the basis for creating effective and long lasting models for open science, with enhanced international coordination and more targeted funding of research and development, which would  leave the world better prepared to respond to future pandemics, says the OECD’s Science and Technology Innovation 2021 report published today.

The report warns economic fallout from the pandemic is likely to severely reduce corporate spending on research and innovation, at the same time as it leaves debt-laden governments struggling to fund national R&D programmes. This could hamper innovation at a critical time.

Key findings of the report include:

  • In the first few months of the pandemic, national research funding bodies in countries for which data is available spent around $5 billion on emergency funding of COVID-19 R&D. That includes $850 million invested in Europe.
  • Across OECD countries, companies in the digital and pharmaceutical sectors increased R&D investments in 2020, while the automotive, aerospace and defence sectors saw their R&D spending decline, as sales and profitability decreased.
  • Around 75,000 scientific papers on COVID-19 were published in the 11 months to the end of November 2020. The US and China were major contributors, with a quarter of their COVID-19 papers co-authored with researchers in other countries. The highest level of collaboration was between scientists in the US and in China.
  • Over three quarters of scientific papers on COVID-19 were published with open access, making the content freely available to other researchers to access, as scientific publishers removed paywalls around COVID-19 research.

The research response to the COVID-19 pandemic provides a potent illustration of the value of collaboration, but the pandemic has also pointed to defects in the organisation and funding of research, highlighting the need for governments to reform science policy, the report says.

Science in the public eye

Beyond their research activities, scientists have been called upon to provide expert input on public health and other policy responses to the pandemic, with many becoming media personalities, communicating science to the general public. They have had to communicate evidence that is unavoidably incomplete and changing, and to do so in ways that promote public confidence and trust.

The way in which researchers have stepped forward to explain their findings has been an important contribution to managing the pandemic. But for various reasons, scientific advice to policy makers and the public is increasingly contested. The report says this requires governments to carefully communicate uncertainties, provide a balanced presentation of potential scenarios and be transparent about mistakes.

Despite the disruption, scientists have continued their work during the crisis, using digital tools and open data infrastructures to continue to function outside of their usual laboratory or field environments, underlining the importance of investment in digital infrastructure for scientific research.

The private sector has played a critical role, delivering a wide range of innovative products to help cope with the health emergency, The biopharmaceutical industry, often in partnership with academia, has launched hundreds of clinical trials targeting COVID-19 drugs and vaccines and academic start-up companies and SMEs have played a significant part in this.

In summary, the report says, the COVID-19 crisis has accelerated trends already underway. It has further opened access to data and publications, increased the use of digital tools, enhanced international collaboration, spurred a variety of public-private partnerships, and encouraged the active engagement of new players. “These developments could speed the transition to a more open science and innovation in the longer run,” OECD says.

Source: OECD

Citizen science has become a powerful tool assisting Covid pandemic response in India

By SalM on February 8, 2021 in COVID-19

Even before India reported its first case of Covid-19, WhatsApp messages began circulating, replete with advice on how to prevent and cure the SARS-CoV-2 infection. One message advised the reader to drink water every 15 minutes, another said the virus could be killed by breathing hot air from the sauna or a hair dryer.

In March 2020, the deputy commissioner of Mangaluru directed officials to take action against individuals spreading Covid-related fake messages on WhatsApp. However, such measures do not address the systemic lack of scientific understanding in society.

Apart from being potentially life-threatening, the rise of pseudo-scientific messaging during the pandemic has also exposed that India’s educational system hasn’t done enough to impart scientific temper and understanding among our citizens. While these fault lines were often visible during sporadic events in the past, Covid brought them to the fore.

Now, there is a new alternative that could help bridge this gap between the public and science — it’s called ‘citizen science’, and it has emerged as a powerful tool during the pandemic.

How citizen science aided pandemic response

Disseminating real-time and reliable information to the public during a pandemic plays a critical role in controlling the spread. This need led to the creation of Covid19Kerala.info, a crowdsourced citizen science project managed by the Collective for Open Data Distribution-Keralam (CODD-K) team.

“CODD-K collected Covid-19 data in real-time, curated it, and made it available to the public through a bilingual (English and Malayalam) user-friendly dashboard,” said Dr Neetha N. Vellichirammal, a CODD-K team member working at the University of Nebraska Medical Center in the US.

Many such citizen science projects have been initiated, which are assisting the pandemic response both in India and globally.

“Since the details are deposited in a public repository for longevity and reusability, it opens up opportunities for future studies and provides insights for future policymaking,” added Dr Neetha.

Other benefits of citizen science projects

Citizen science projects can be beneficial for all the stakeholders involved. Volunteers get first-hand experience by associating with a scientific exercise; acquire knowledge and learn to appreciate the process behind coming to the scientific conclusions.

Citizen science can also provide an innovative means of data collection for research, which otherwise may not have been possible, or would have been too expensive.

Apart from data collection during a pandemic, examples of citizen science research include monitoring and management of natural resources, including land, air, water, minerals and forests etc. In such large-scale and complicated projects, researchers can get the required data by distributing the workload among a larger group of volunteers, which drastically reduces the cost and time for implementation.

“Over the last few years, there has been a discernible interest and spurt of citizen science initiatives in India. The growth and permeation of ICT (information and communication technology), the availability and access to aggregation platforms, and the interest and awareness of citizens have all contributed to this growth,” commented Dr Prabhakar Rajagopal, coordinator of the India Biodiversity Portal and director of Strand Life Sciences.

“However, in a large and populous country like India, we are still at the tip of the iceberg in leveraging the potential power and possibilities of citizen science in India. Greater societal support with a favourable policy environment would help its growth and development,” he added.

How to harness it

One potential way to harness citizen science is by developing a framework for institutionalising it. However, several aspects for design and implementation would need to be considered during this process.

The National Achievement Survey conducted by the NCERT stated that students across 12 states scored significantly below the national average in mathematical ability, and also identified “learning” as a big challenge facing Indian education. The designing of specific citizen science projects and inculcating them at school and higher education levels could provide an effective learning tool for students.

In developed countries, most citizen science initiatives originate in the higher educational institutes. For example, many iconic projects such as ScienceAtHome and eBird started at Aarhus University, Denmark, and Cornell Lab of Ornithology, US, respectively.

Similarly, top higher educational institutes in India, such as the IITs and IISERs, could help in spearheading and initiating such projects at the undergraduate and post-graduate levels. Many universities abroad now also have dedicated centres to coordinate and guide citizen science activities, but the Centre for Citizen Science (CCS), Pune, is currently the only one in India.

Currently, the number of citizen science projects is highly skewed in the south Indian states, and mainly focussed in the areas of environment and ecology. Various primary and higher educational institutes in India can be key to inclusion of students at different educational levels and geographies.

Ensuring data quality

A policy framework for citizen science also needs to address another important issue: Ensuring data quality.

“While the first assumption for a citizen science project is that knowledge and expertise is not confined to the ‘citadels of science’, citizen data would have observer biases. As data grows, simple machine algorithms and heuristics could provide the first level of automated validation and outlier detection,” said Dr Prabhakar Rajagopal.

To ensure data standardisation, several countries have framed and provided access to guidelines and best practices for citizen science. For example, the US Environmental Protection Agency (EPA) has a site on Quality Assurance Project Plan for citizen science projects which serves as a blueprint for how your project should run.

A ‘national online portal’, combined with a dashboard, based on an example like SciStarter, could act as a repository of all citizen science initiatives in India, and facilitate inter-regional connections and expand the coverage of citizen science projects.

The Department of Science and Technology in 2019 released the draft policy on Scientific Social Responsibility (SSR), which aims to strengthen the link between science and society. While the policy recognises the need for science outreach to strengthen the knowledge ecosystem, it fails to recognise the potential impact citizen science could have in this endeavour. However, the recently released draft of Science and Technology Policy does provide provisions for promoting ‘public engagement in science’ in general, and citizen science in particular.

With our demographic and ever-increasing penetration of technology, the potential of citizen science in India is vast and largely untapped. An evidence-based framework for citizen science policy has immense potential in contributing to not just in increasing scientific literacy and temper of the country, but also to Indian science as a whole.

Source: theprint.in

Scientists call for fully open sharing of coronavirus genome data

By SalM on February 4, 2021 in COVID-19

Hundreds of scientists are urging that SARS-CoV-2 genome data should be shared more openly to help analyse how viral variants are spreading around the world.

Researchers have posted huge numbers of SARS-CoV-2 genome sequences online since January 2020. The most popular data-sharing platform, called GISAID, now hosts more than 450,000 viral genomes; Soumya Swaminathan, the chief scientist at the World Health Organization (WHO), has called it a ‘game changer’ in the pandemic. But it doesn’t allow sequences to be reshared publicly, which is hampering efforts to understand the coronavirus and the rapid rise of new variants, argues Rolf Apweiler, co-director of the European Bioinformatics Institute (EBI) near Cambridge, UK, which hosts its own large genome database that includes SARS-CoV-2 sequences.

“The openness of SARS-CoV-2 sequence data is crucial for the rapid response against the biggest health threat to humankind in a very, very long time,” says Apweiler.

In a letter released on 29 January, Apweiler and others call for researchers to post their genome data in one of a triad of databases that don’t place any restrictions on data redistribution: the US GenBank, the EBI’s European Nucleotide Archive (ENA) and the DNA Data Bank of Japan, which are collectively known as the International Nucleotide Sequence Database Collaboration (INSDC).

Anyone can anonymously access the INSDC’s data and use them as they want, but GISAID requires that users confirm their identity and agree not to republish the site’s genomes without permission from the data provider. This means that studies building on GISAID data — such as those that create evolutionary trees analysing how SARS-CoV-2 variants are related — can’t publish full data so that others can easily check their analyses or further build on their data set. They must direct readers back to the GISAID site.

The letter says the scientific community should “remove barriers that restrain effective data sharing”, but doesn’t mention GISAID specifically. It is signed by more than 500 scientists, including the 2020 chemistry Nobel laureate Emmanuelle Charpentier, and the head of the COVID-19 Genomics UK Consortium, Sharon Peacock. Where scientists have already established submissions to other databases, the letter states, “these submissions should continue in parallel”.

Feature not flaw

Many researchers who work with GISAID say that its terms of access are a benefit, because they encourage hesitant researchers to share data online speedily, without fear that others will use the results without credit. “The reason so many labs have provided SARS-CoV-2 genomes to GISAID is precisely because of the data-access agreement that restricts public resharing,” says Sebastian Maurer-Stroh, a bioinformatician at Singapore’s Agency for Science, Technology and Research. GISAID has worked with many labs to assist them to share data, he says.

GISAID stands for the Global Initiative on Sharing Avian Influenza Data; an international consortium of researchers helped to set it up as a nonprofit foundation in 2008, to address researchers’ reluctance to share data on influenza strains. Some nations, including Indonesia, a hotspot for avian flu, feared that pharmaceutical firms would create drugs and vaccines using the sequence data without crediting the original data providers or sharing the benefits of the work with them. But they were persuaded to share sequences rapidly in GISAID; in March 2013, for instance, China published sequences of H7N9 avian flu in the database on the same day it informed the WHO of three infections in people. “GISAID encourages and incentivizes real-time data sharing by parties who would otherwise be reluctant to share, by ensuring that they retain their rights in their data,” says a spokesperson for the initiative.

“This issue is not only about science, but also about sovereignty and equity,” says Marie-Paule Kieny, a vaccine researcher at INSERM, the French national health-research institute in Paris. “GISAID empowers the rapid flow of SARS-CoV-2 sequence data with maximal impact,” she says, because scientists depositing sequences can trust that their rights will be respected by data users.

Senjuti Saha, a microbiologist who works on SARS-CoV-2 genomes at the Child Health Research Foundation in Dhaka, says that she appreciates the call for open data beyond what GISAID offers, but worries that it may further dissuade researchers in low- and middle-income countries (LMICs) from uploading data until they have analysed them. During the pandemic, she says, some LMICS have started doing more viral sequencing, although labs often lack computational infrastructure. She says that she’s seen LMIC coronavirus data taken out of context by academics in wealthier countries who don’t consult or credit the data-providers. “We really want to share our data, but it is heart-breaking and demotivating when we know we worked so hard to generate data, but we don’t get the credit for it,” she says.

The letter, says Kieny, “seems to me like an initiative from European and high-income countries not fully informed on the critical need to ensure that low-resource countries accept to share sequences freely, so that the public-health impact of sequencing of pathogens such as SARS-CoV-2 is maximized”.

ENA head Guy Cochrane says the EBI is aware of the global issues around data and benefit sharing, and is actively involved in finding benefit-sharing mechanisms that empower countries in the global south and keep data open. But even well-resourced European countries could do more to share their data openly, he says.

Data challenges

Some researchers told Nature that besides arguments about equity and openness, there is an issue with GISAID’s differential control over how registered users can download its data. Some users must download files in small batches, for instance, but others can get an entire data set in bulk with GISAID approval. The GISAID spokesperson said that’s because the initiative needs to know who is using its data and for what reason, so that nothing is erroneously redistributed.

Cochrane adds that another challenge with GISAID’s platform is that researchers post ‘assemblies’ — or reconstructions — of viral genomes from the chunks of data read off sequencing machines, rather than the raw data. Assembly always involves some interpretation of inevitable errors in the sequencing process, Cochrane says, and this can lead to what look like mutations in a genome that are in fact artefacts of sequencing. Access to the raw data of many genomes helps scientists dig into these issues, and Cochrane says researchers should share their raw and assembled sequencing data, which they can do at the INSDC even if they also post on GISAID. Maurer-Stroh, however, says that GISAID is aware of such issues and already provides quality-control checks to flag potential mistakes in submitted genomes. Cochrane says such processes can only reduce, not eliminate, artefact errors.

An EBI-hosted data portal that brings together fully open COVID-19 data sets submitted to the INSDC currently hosts more than 270,000 raw SARS-CoV-2 sequences and 55,000 assembled genomes — fewer than GISAID. “We have a fog of incomplete knowledge,” says Apweiler. He says that some scientists might think, incorrectly, that submitting data to GISAID means that the results will automatically be shared openly at the INSDC — and he hopes that the call to share data without restriction will boost the INSDC’s data trove.

But telling scientists to resubmit their SARS-CoV-2 data to the INSDC is complex, says David Haussler, who directs a genomics institute working with INSDC and GISAID data at the University of California, Santa Cruz. Bioinformaticians are in crisis mode, rushing to get genome data and analyse it in detail, and want to share as much as they are permitted to publish about key new mutations in sequences, he says. He did not sign the open letter — although he supports restriction-free data sharing — because he hopes instead that GISAID can temporarily drop some of its access terms during the pandemic, perhaps to coordinate with the INSDC.

Kieny, however, says that could lead to some scientists losing trust in GISAID and not filing their sequences with the database so quickly. “There is no obstacle, for those who want to do it, to deposit their sequences into the INSDC,” she says.

Source: nature. com

The COVID-19 pandemic is pushing open access forwards

By SalM on October 30, 2020 in COVID-19

This year’s Open Access Week is a very special occasion. 2020 has shown – for all the good and bad reasons during a global pandemic that continues to affect us all – the power of open access. But, while the unprecedented growth of open access papers and preprints has been a crisis mode reaction, it is now time to make open access a permanent feature of the research system.

Twenty years after the Budapest Open Access Initiative, we are at a crucial moment: 2021 has all it needs for open access to become the norm for researchers in Europe.

First and foremost, Horizon Europe will require immediate and irrevocable open access to publications resulting from research projects funded by the programme, alongside a set of other elements mainstreaming ‘open science’. According to the European Commission, costs for hybrid publishing will no longer be eligible and researchers will retain the rights to share their results.

In parallel, the Open Research Europe publishing platform is a prime example of a research funder supporting a publishing ecosystem that is innovative, equitable and open. The European University Association (EUA), as a supporter of sustainable and open scholarly publishing, welcomes these changes in Horizon Europe.

Of course, this does not mean that the work is over. Horizon Europe will have to step up its backing for universities managing this transition and enable them to support all the scientific communities so that they can reach this objective.

Furthermore, the long-awaited and, at times, hotly debated ‘Plan S’ will finally come into action on 1st January 2021. While the plan itself and its conditions have evolved – also due to constructive input from universities and other stakeholders – its core is as relevant as it was at its launch in September 2018.

Open licences, sustainable business models and copyright retention must be ensured. A welcome development has been the more strident work on rights retention to ensure Green Open Access and the growing attention to non-commercial publishing venues – Diamond Open Access – in the quest to create a publishing system that is less dependent on a few commercial publishers and more diverse, community-driven and scholar-led.

Plan S is a crucial piece in a transition to open access driven by stakeholders in the academic community, and we at EUA look forward to continuing our engagement with Coalition S in the coming year.

Career assessment reforms

Likewise, at the core of the transition to open science is a re-thinking of the ways in which we assess researchers and academic careers.

EUA has been at the forefront of discussions on career assessment reforms and will continue this work. Based on this, we, in a partnership with the Declaration on Research Assessment and the Scholarly Publishing and Academic Resources Coalition Europe, will soon release materials and case studies that will support and inspire universities to reform their internal assessment mechanisms and requirements.

Going global

Finally, we need to look beyond Europe. Science, scholarly publishing and the means of assessment are issues with global implications. There are understandable and legitimate concerns about Europe moving ahead without due consideration of what it means for others – an often-heard concern is pay-to-publish business models being hurdles for countries with lower incomes or disciplines which are not supported by external funding agencies.

This is why we need a diverse and equitable publishing landscape. EUA supports such a vision of an open and inclusive system for the UNESCO Recommendation on Open Science, which is scheduled to be adopted in late 2021. This UNESCO recommendation, which already appears very promising in its draft version, has the potential to enshrine a global commitment to sustainable open access – and will, it is hoped, make 2021 the year that open access and open science go global.

Source: www.universityworldnews.com