Biosecurity in an age of open science

How will we prepare for an uncertain future? The value of open data and code for unborn generations facing climate change

As the impacts of climate change continue to intensify, humans face new challenges to long-term survival. Humans will likely be battling these problems long after 2100, when many climate projections currently end. A more forward-thinking view on our science and its direction may help better prepare for the future of our species. Researchers may consider datasets the basic units of knowledge, whose preservation is arguably more important than the articles that are written about them. Storing data and code in long-term repositories offers insurance against our uncertain future. To ensure open data are useful, data must be FAIR (Findable, Accessible, Interoperable and Reusable) and be complete with all appropriate metadata. By embracing open science practices, contemporary scientists give the future of humanity the information to make better decisions, save time and other valuable resources, and increase global equity as access to information is made free. This, in turn, could enable and inspire a diversity of solutions, to the benefit of many. Imagine the collective science conducted, the models built, and the questions answered if all of the data researchers have collectively gathered were organized and immediately accessible and usable by everyone. Investing in open science today may ensure a brighter future for unborn generations.

Establishing a national biosafety and biosecurity agency for the United States

The rapid advancement of biological research and biotechnology requires a novel and robust regulatory agency to ensure uniform biosafety and biosecurity governance in the United States. The current fragmented regulatory landscape needs to be refocused to address the complexities of modern biological research, including risks associated with accidental, inadvertent, and deliberate biological incidents. An independent government agency, which we call the National Biosafety and Biosecurity Agency (NBBA), that is devoted to biosafety and biosecurity could effectively address these challenges. The NBBA would consolidate various regulatory functions, streamline processes, and enhance oversight. This oversight would encompass life sciences research in the United States, regardless of the source of funding or level of classification. The agency could also contribute to the bioeconomy by streamlining requirements to safeguard public health and the environment while fostering scientific and commercial progress. The proposed agency would govern high-risk biological pathogens, manage the Federal Select Agent Program, enforce policies related to dual use research of concern, pathogens with enhanced pandemic potential, and nucleic acid synthesis screening, administer regulations on the use and care of laboratory animals, as well as regulate other relevant biosafety and biosecurity activities. The goal would be to provide one-stop shopping for the biomedical research and biotechnology sectors subject to oversight by the Federal government. To ensure leadership in global biosafety and biosecurity, the agency's mission would include international collaboration, applied research, education, workforce development, and coordination with national security initiatives. Creating an agency like the NBBA will be politically challenging but presenting a comprehensive vision and engaging stakeholders early and frequently, and being transparent in the process, will be essential for garnering support. Creating a unified biosafety and biosecurity governance system in the United States will ensure the safe and secure advancement of biological research while sustaining innovation and maintaining international competitiveness.

Limiting open science? Three approaches to bottom-up governance of dual-use research of concern

Governing dual-use research of concern (DURC) in the life sciences has become difficult owing to the diversification of scientific domains, digitalization of potential threats, and the proliferation of actors. This paper proposes three approaches to realize bottom-up governance of DURC from laboratory operation to institutional decision-making levels. First, a technological approach can predict and monitor the dual-use nature of the research target pathogens and their information. Second, an interactive approach is proposed in which diverse stakeholders proactively discuss and examine dual-use issues through research practice. Third, a personnel approach can identify the right persons involved in DURC. These approaches suggest that, going beyond self-governance by researchers, collaborative and networked governance involving diverse actors should become essential. This mode of governance can also be seen in light of the management of research use. Therefore, program design by funding agencies and publication screening by journal publishers continuously contribute to governance at the meso-level. Bottom-up governance may be realized by using an appropriately integrated design of these three approaches at the micro-level, such as dual-use prediction and monitoring, stakeholder dialogue, and background checks. Given that the term 'open science' has been promoted to the research community as part of top-down governance, paying due attention on site to research subjects, research practices, and persons involved in research will provide an opportunity to develop a more socially conscious open science.

Biomedical publishing: Past historic, present continuous, future conditional

Academic journals have been publishing the results of biomedical research for more than 350 years. Reviewing their history reveals that the ways in which journals vet submissions have changed over time, culminating in the relatively recent appearance of the current peer-review process. Journal brand and Impact Factor have meanwhile become quality proxies that are widely used to filter articles and evaluate scientists in a hypercompetitive prestige economy. The Web created the potential for a more decoupled publishing system in which articles are initially disseminated by preprint servers and then undergo evaluation elsewhere. To build this future, we must first understand the roles journals currently play and consider what types of content screening and review are necessary and for which papers. A new, open ecosystem involving preprint servers, journals, independent content-vetting initiatives, and curation services could provide more multidimensional signals for papers and avoid the current conflation of trust, quality, and impact. Academia should strive to avoid the alternative scenario, however, in which stratified publisher silos lock in submissions and simply perpetuate this conflation.

Anthrax revisited: how assessing the unpredictable can improve biosecurity

B. anthracis is one of the most often weaponized pathogens. States had it in their bioweapons programs and criminals and terrorists have used or attempted to use it. This study is motivated by the narrative that emerging and developing technologies today contribute to the amplification of danger through greater easiness, accessibility and affordability of steps in the making of an anthrax weapon. As states would have way better preconditions if they would decide for an offensive bioweapons program, we focus on bioterrorism. This paper analyzes and assesses the possible bioterrorism threat arising from advances in synthetic biology, genome editing, information availability, and other emerging, and converging sciences and enabling technologies. Methodologically we apply foresight methods to encourage the analysis of contemporary technological advances. We have developed a conceptual six-step foresight science framework approach. It represents a synthesis of various foresight methodologies including literature review, elements of horizon scanning, trend impact analysis, red team exercise, and free flow open-ended discussions. Our results show a significant shift in the threat landscape. Increasing affordability, widespread distribution, efficiency, as well as ease of use of DNA synthesis, and rapid advances in genome-editing and synthetic genomic technologies lead to an ever-growing number and types of actors who could potentially weaponize B. anthracis. Understanding the current and future capabilities of these technologies and their potential for misuse critically shapes the current and future threat landscape and underlines the necessary adaptation of biosecurity measures in the spheres of multi-level political decision making and in the science community.

The use and acceptability of preprints in health and social care settings: A scoping review

BACKGROUND

Preprints are open and accessible scientific manuscript or report that is shared publicly, through a preprint server, before being submitted to a journal. The value and importance of preprints has grown since its contribution during the public health emergency of the COVID-19 pandemic. Funders and publishers are establishing their position on the use of preprints, in grant applications and publishing models. However, the evidence supporting the use and acceptability of preprints varies across funders, publishers, and researchers. The scoping review explored the current evidence on the use and acceptability of preprints in health and social care settings by publishers, funders, and the research community throughout the research lifecycle.

METHODS

A scoping review was undertaken with no study or language limits. The search strategy was limited to the last five years (2017-2022) to capture changes influenced by COVID-19 (e.g., accelerated use and role of preprints in research). The review included international literature, including grey literature, and two databases were searched: Scopus and Web of Science (24 August 2022).

RESULTS

379 titles and abstracts and 193 full text articles were assessed for eligibility. Ninety-eight articles met eligibility criteria and were included for full extraction. For barriers and challenges, 26 statements were grouped under four main themes (e.g., volume/growth of publications, quality assurance/trustworthiness, risks associated to credibility, and validation). For benefits and value, 34 statements were grouped under six themes (e.g., openness/transparency, increased visibility/credibility, open review process, open research, democratic process/systems, increased productivity/opportunities).

CONCLUSIONS

Preprints provide opportunities for rapid dissemination but there is a need for clear policies and guidance from journals, publishers, and funders. Cautionary measures are needed to maintain the quality and value of preprints, paying particular attention to how findings are translated to the public. More research is needed to address some of the uncertainties addressed in this review.

The Need for Biosecurity Education in Biotechnology Curricula

The growth of biotechnology in recent decades and the dual-use nature of most bioscience research are making their misuse, or accidental misuse or release, more likely and present as threats to biosecurity. A proactive approach is through educating the next generation of scientists to be more security conscious. However, current educational and professional programs in biosecurity are lacking. In this perspective, we recommend that biosecurity educational opportunities should be implemented and expanded for undergraduate and graduate students who will likely use one or more methods in the field of biotechnology. We then propose that biosecurity education is a key factor in a path toward sustainable and safe research. Finally, a set of 17 biosecurity competencies organized into 6 distinct themes is outlined.

Must-have Qualities of Clinical Research on Artificial Intelligence and Machine Learning

In the field of computer science, known as artificial intelligence, algorithms imitate reasoning tasks that are typically performed by humans. The techniques that allow machines to learn and get better at tasks such as recognition and prediction, which form the basis of clinical practice, are referred to as machine learning, which is a subfield of artificial intelligence. The number of artificial intelligence-and machine learnings-related publications in clinical journals has grown exponentially, driven by recent developments in computation and the accessibility of simple tools. However, clinicians are often not included in data science teams, which may limit the clinical relevance, explanability, workflow compatibility, and quality improvement of artificial intelligence solutions. Thus, this results in the language barrier between clinicians and artificial intelligence developers. Healthcare practitioners sometimes lack a basic understanding of artificial intelligence research because the approach is difficult for non-specialists to understand. Furthermore, many editors and reviewers of medical publications might not be familiar with the fundamental ideas behind these technologies, which may prevent journals from publishing high-quality artificial intelligence studies or, worse still, could allow for the publication of low-quality works. In this review, we aim to improve readers’ artificial intelligence literacy and critical thinking. As a result, we concentrated on what we consider the 10 most important qualities of artificial intelligence research: valid scientific purpose, high-quality data set, robust reference standard, robust input, no information leakage, optimal bias-variance tradeoff, proper model evaluation, proven clinical utility, transparent reporting, and open science. Before designing a study, one should have defined a sound scientific purpose. Then, it should be backed by a high-quality data set, robust input, and a solid reference standard. The artificial intelligence development pipeline should prevent information leakage. For the models, optimal bias-variance tradeoff should be achieved, and generalizability assessment must be adequately performed. The clinical value of the final models must also be established. After the study, thought should be given to transparency in publishing the process and results as well as open science for sharing data, code, and models. We hope this work may improve the artificial intelligence literacy and mindset of the readers.

A guide to open science practices for animal research

Translational biomedical research relies on animal experiments and provides the underlying proof of practice for clinical trials, which places an increased duty of care on translational researchers to derive the maximum possible output from every experiment performed. The implementation of open science practices has the potential to initiate a change in research culture that could improve the transparency and quality of translational research in general, as well as increasing the audience and scientific reach of published research. However, open science has become a buzzword in the scientific community that can often miss mark when it comes to practical implementation. In this Essay, we provide a guide to open science practices that can be applied throughout the research process, from study design, through data collection and analysis, to publication and dissemination, to help scientists improve the transparency and quality of their work. As open science practices continue to evolve, we also provide an online toolbox of resources that we will update continually.

Open science has become a buzzword in the scientific community that too often misses the practical application for individual researchers. This Essay, provides a guide to choosing the most appropriate tools to make animal research more transparent.

The context matrix: Navigating biological complexity for advanced biodesign

Synthetic biology offers many solutions in healthcare, production, sensing and agriculture. However, the ability to rationally engineer synthetic biosystems with predictable and robust functionality remains a challenge. A major reason is the complex interplay between the synthetic genetic construct, its host, and the environment. Each of these contexts contains a number of input factors which together can create unpredictable behaviours in the engineered biosystem. It has become apparent that for the accurate assessment of these contextual effects a more holistic approach to design and characterisation is required. In this perspective article, we present the context matrix, a conceptual framework to categorise and explore these contexts and their net effect on the designed synthetic biosystem. We propose the use and community-development of the context matrix as an aid for experimental design that simplifies navigation through the complex design space in synthetic biology.