Metaphors in search of a target: the curious case of epigenetics

Carrying out research in genetics and genomics and communicating about them would not be possible without metaphors such as “information,” “code,” “letter” or “book.” Genetic and genomic metaphors have remained relatively stable for a long time but are now beginning to shift in the context of synthetic biology and epigenetics. This article charts the emergence of metaphors in the context of epigenetics, first through collecting some examples of metaphors in scientific and popular writing and second through a systematic analysis of metaphors used in two UK broadsheets. Findings show that while source domains for metaphors can be identified, such as our knowledge of electrical switches or of bookmarks, it is difficult to pinpoint target domains for such metaphors. This may be indicative both of struggles over what epigenetics means for scientists (natural and social) and of difficulties associated with talking about this, as yet, young field in the popular press.     

Maps, books and other metaphors for systems biology

We briefly review the use of metaphors in science and progressively focus on fields from biology and molecular biology to genomics and bioinformatics. We discuss how metaphors are both a tool for scientific exploration and a medium for public communication of complex subjects, by various short examples. Finally, we propose a metaphor for systems biology that provides an illuminating perspective for the ambitious goals of this field and delimits its current agenda.     

A priority paper for the societal and ethical aspects of synthetic biology

As synthetic biology develops into a promising science and engineering field, we need to have clear ideas and priorities regarding its safety, security, ethical and public dialogue implications. Based on an extensive literature search, interviews with scientists, social scientists, a 4 week long public e-forum, and consultation with several stakeholders from science, industry and civil society organisations, we compiled a list of priority topics regarding societal issues of synthetic biology for the years ahead. The points presented here are intended to encourage all stakeholders to engage in the prioritisation of these issues and to participate in a continuous dialogue, with the ultimate goal of providing a basis for a multi-stakeholder governance in synthetic biology. Here we show possible ways to solve the challenges to synthetic biology in the field of safety, security, ethics and the science–public interface.     

Policy on Synthetic Biology: Deliberation,Probability, and the Precautionary Paradox

Synthetic biology is a cutting‐edge area of research that holds the promise of unprecedented health benefits. However, in tandem with these large prospective benefits, synthetic biology projects entail a risk of catastrophic consequences whose severity may exceed that of most ordinary human undertakings. This is due to the peculiar nature of synthetic biology as a ‘threshold technology’ which opens doors to opportunities and applications that are essentially unpredictable. Fears about these potentially unstoppable consequences have led to declarations from civil society groups calling for the use of a precautionary principle to regulate the field. Moreover, the principle is prevalent in law and international agreements. Despite widespread political recognition of a need for caution, the precautionary principle has been extensively criticized as a guide for regulatory policy. We examine a central objection to the principle: that its application entails crippling inaction and incoherence, since whatever action one takes there is always a chance that some highly improbable cataclysm will occur. In response to this difficulty, which we call the ‘precautionary paradox,’ we outline a deliberative means for arriving at threshold of probability below which potential dangers can be disregarded. In addition, we describe a Bayesian mechanism with which to assign probabilities to harmful outcomes. We argue that these steps resolve the paradox. The rehabilitated PP can thus provide a viable policy option to confront the uncharted waters of synthetic biology research.     

The future of education in the molecular life sciences

The changing landscape of education in biochemistry and molecular biology presents many challenges for the future, for students and educators alike. The exponential increase in knowledge, the genomics, proteomics and computing revolutions, and the merging of once separate fields in biology, chemistry, physics and mathematics, mean that we need to rethink how we should be preparing today's science undergraduates for the future. What do we need to change, and how will we implement it?     

Animal Metaphors and Metaphorizing Animals: An Integrated Literary, Cognitive, and Evolutionary Analysis of Making and Partaking of Stories

Humans use metaphors to explore their relationship with nature. Our ability to make and understand metaphors appears to be an automatic cognitive process, one that likely evolved along with our ability to create and understand language. Because metaphors are processed automatically, without conscious appraisal, they can be used to rapidly communicate, or manipulate. Applying theories of evolutionary psychology and cognitive science to literary texts, we explored the role of animal metaphors in the making and partaking of stories in the context of a course in environmental studies. We investigated how humans are animals and yet use culture to shield themselves from this reality. We read and analyzed literature in which animal metaphors are central, such as Honoré de Balzac’s short story Passion in the Desert and Langdon Smith’s poem “Evolution.” Throughout the course, the overarching theme is that animal metaphors are powerful tools for framing our relationship with the environment and that they can be best understood in the context of humans as evolved animals.     

Bioethics,politics and the moral economy of human embryonic stem cell science: the case of the European Union's Sixth Framework Programme

Public communication of science is still largely conceptualized within a ‘transfer’ paradigm that describes it as a displacement of results and ideas from the specialists to the lay public, problematizing the public, the media, (sometimes) science, but very rarely the notion of communication itself. This paper is a preliminary attempt to see if the discourse about genes and the genome can help us to problematize the concept of communication in relation to science, rethink our models of public communication of science and, more generally, the metaphors we employ to describe communication. It is suggested that the relationship between science and the public could be understood better by viewing communication through metaphors drawn from contemporary biology, e.g. as ‘cross‐talk’ between the specialist and public discourse or as a ‘double helix’ coupling the two dimensions under certain conditions.     

Preaching to the choir or composing new verses? Toward a writerly climate literacy in introductory undergraduate biology

Climate change is one of the most pressing issues facing society today, yet a wide range of misconceptions exist in society about whether or why climate change is happening, what its consequences are, and what can be done to address it. Large introductory biology courses present an opportunity to teach a large number of students—some of whom may never take another course focused on climate, ecology, or the environment—about climate change. However, content knowledge alone may not be enough to prepare students to transform their knowledge into action. To begin understanding how content knowledge interacts with student constructions of climate change solutions, we administered and quantitatively analyzed a survey that examined student views of climate change and how they shifted with instruction during an undergraduate introductory biology course at a large Midwestern university. Almost all participants entered the course agreeing that climate change is occurring, and their certainty about the science of climate change increased after instruction. After taking the course, more participants described climate change as having more immediate impacts, reporting that climate change is already harming people and that climate change will harm them personally. However, both at the beginning and end of the course, participants tended to think that humans would either be unable or unwilling to reduce climate change. They were also more worried about climate change at the end of the course than they were before. Increased concern might result from students becoming more certain of the science and severity of climate change, while remaining pessimistic that humans will effectively act on climate change. This pattern suggests instructors have opportunities to modify curricula in ways that leave students with a greater sense of empowerment and efficacy; we suggest questions that instructors can ask themselves in order to modify their courses with this goal in mind.     

Integrating microscopy,art, and humanities to power STEAM learning in biology

Close observation is central to both art and science as practitioners in both disciplines describe, compare, and seek to understand or interpret the natural world. Indeed, as the artist and writer Guy Davenport noted, “The vision by which we discover the hidden in nature is sometimes called science, sometimes called art.” In the last decade, the movement to integrate science, technology, engineering, and mathematics with arts and humanities (i.e., STEAM learning) has gained traction in K–12 education. A recent National Academies report (2018) examines the case for integrating humanities and the arts in undergraduate STEM education. Microscopy provides an excellent vehicle for engaging all kinds of students in integrative (STEAM) learning about biology and for encouraging them to observe the world closely. In this essay adapted from my keynote address to the American Microscopical Society in 2020, I highlight activities and approaches that use microscopy to engage learners of all kinds, examine how using microscopes changes students’ attitudes about science and biology, and explore the intersection of microscopy and visual art.     

Shaping the science–industry–policy interface in synthetic biology

Current advances in the emerging field of synthetic biology and the improvements in key technologies promise great impacts, not only on future scientific development, but also on the economy. In this paper we will adopt the triple helix concept for analyzing the early stages of a new field of science and innovation, namely synthetic biology. Synthetic biology is based on the creation and assembly of parts in order to create new and more complex structures and functions. These features of synthetic biology raise questions related to standardization and intellectual property, but also to security and public perception issues that go beyond the classical biotechnology discussions. These issues concern all involved actors in the synthetic biology field and affect the interrelationship between science, industry and policy. Based on the results of the recently finished EU FP-6 funded project TESSY (http://www.tessy-europe.de), the article analyzes these issues. Additionally, it illustrates the setting of clear framework conditions for synthetic biology research and development and the identification and definition of common goals for the future development of the field which will be needed for efficient science–industry–policy interaction. It was shown that it will be crucial to develop approaches that consider the needs of science and industry, on the one hand, and comply with the expectations of society, on the other hand. As synthetic biology is a global activity, the involvement of national decision-makers in international initiatives will further stimulate the development of the field.     

合成生物学伦理、法律与社会问题探讨

合成生物学是以基因组学、系统生物学知识和分子生物学技术为基础,综合了科学与工程的一门新兴交叉学科。它使生命科学和生物技术研发进入了以人工设计、合成自然界中原本不曾出现的人造生命体系,以及对这些人工体系进行体内、体外优化,或利用这些人造生命体系研究自然生命规律为目标的新时代。然而,合成生物学研究在迅速发展、表现出巨大潜力和应用前景的同时,也引发了社会各界对相关社会、伦理、安全,以及知识产权等问题的重视与讨论。就世界各国针对合成生命对传统意义上生命概念的挑战、合成生物学产品存在的潜在风险危害、合成生物学研究的风险评估与监管等问题进行回顾综述和相关探讨。     

Professionalization as a governance strategy for synthetic biology

This article considers professionalization as a governance strategy for synthetic biology, reporting on social science interviews done with scientists, science journal editors, members of science advisory boards and authors of nongovernmental policy reports on synthetic biology. After summarizing their observations about the potential advantages and disadvantages of the professionalization of synthetic biology, we analyze professionalization as a strategy that overcomes dichotomies found in the current debates about synthetic biology governance, specifically “top down” versus “bottom up” governance and scientific fact versus public values. Professionalization combines community and state, fact and value. Like all governance options, professionalization has limitations, particularly regarding war and peace. It is best conceptualized as potentially part of a wider range of governance mechanisms working in concert: a “web of prevention”.     

Epigenetic metaphors: an interdisciplinary translation of encoding and decoding

Looking at the new and often disputed science of epigenetics, we examined the challenges faced by scientists when they communicate scientific research to the public. We focused on the use of metaphors to illustrate notions of epigenetics and genetics. We studied the “encoding” by epigeneticists and “decoding” in focus groups with diverse backgrounds. We observed considerable overlap in the dominant metaphors favored by both researchers and the lay public. However, the groups differed markedly in their interpretations of which metaphors aided understanding or not. We conclude by discussing the role of metaphors and their interpretations in the context of a shift from pre-deterministic genomic metaphors to more active, dynamic and nuanced epigenetic metaphors. These reflections on the choice of metaphors and differences in encoding/decoding are important for science communication and scientific boundary-maintenance.     

Synthetic biology: mapping the scientific landscape

This article uses data from Thomson Reuters Web of Science to map and analyse the scientific landscape for synthetic biology. The article draws on recent advances in data visualisation and analytics with the aim of informing upcoming international policy debates on the governance of synthetic biology by the Subsidiary Body on Scientific, Technical and Technological Advice (SBSTTA) of the United Nations Convention on Biological Diversity. We use mapping techniques to identify how synthetic biology can best be understood and the range of institutions, researchers and funding agencies involved. Debates under the Convention are likely to focus on a possible moratorium on the field release of synthetic organisms, cells or genomes. Based on the empirical evidence we propose that guidance could be provided to funding agencies to respect the letter and spirit of the Convention on Biological Diversity in making research investments. Building on the recommendations of the United States Presidential Commission for the Study of Bioethical Issues we demonstrate that it is possible to promote independent and transparent monitoring of developments in synthetic biology using modern information tools. In particular, public and policy understanding and engagement with synthetic biology can be enhanced through the use of online interactive tools. As a step forward in this process we make existing data on the scientific literature on synthetic biology available in an online interactive workbook so that researchers, policy makers and civil society can explore the data and draw conclusions for themselves.     

Epigenetic determinism in science and society

The epigenetic “revolution” in science cuts across many disciplines, and it is now one of the fastest-growing research areas in biology. Increasingly, claims are made that epigenetics research represents a move away from the genetic determinism that has been prominent both in biological research and in understandings of the impact of biology on society. We discuss to what extent an epigenetic framework actually supports these claims. We show that, in contrast to the received view, epigenetics research is often couched in language as deterministic as genetics research in both science and the popular press. We engage the rapidly emerging conversation about the impact of epigenetics on public discourse and scientific practice, and we contend that the notion of epigenetic determinism – or the belief that epigenetic mechanisms determine the expression of human traits and behaviors – matters for understandings of the influence of biology and society on population health.     

Social and ethical checkpoints for bottom-up synthetic biology, or protocells

An alternative to creating novel organisms through the traditional “top-down” approach to synthetic biology involves creating them from the “bottom up” by assembling them from non-living components; the products of this approach are called “protocells.” In this paper we describe how bottom-up and top-down synthetic biology differ, review the current state of protocell research and development, and examine the unique ethical, social, and regulatory issues raised by bottom-up synthetic biology. Protocells have not yet been developed, but many expect this to happen within the next five to ten years. Accordingly, we identify six key checkpoints in protocell development at which particular attention should be given to specific ethical, social and regulatory issues concerning bottom-up synthetic biology, and make ten recommendations for responsible protocell science that are tied to the achievement of these checkpoints.     

Programmable bacterial catalysis - designing cells for biosynthesis of value-added compounds

Bacteria have long been used for the synthesis of a wide range of useful proteins and compounds. The developments of new bioprocesses and improvements of existing strategies for syntheses of valuable products in various bacterial cell hosts have their own challenges and limitations. The field of synthetic biology has combined knowledge from different science and engineering disciplines and facilitated the advancement of novel biological components which has inspired the design of targeted biosynthesis. Here we discuss recent advances in synthetic biology with relevance to biosynthesis in bacteria and the applications of computational algorithms and tools for manipulation of cellular components. Continuous improvements are necessary to keep up with increasing demands in terms of complexity, scale, and predictability of biosynthesis products.     

Meeting report: Synthetic DNA - Writing with the Letters of Life: January 24, 2012, Frankfurt, Germany

The one-day meeting on Synthetic DNA (January 24, 2012) organized by and held at the DECHEMA in Frankfurt attracted about 100 participants from academia and industry interested in synthesizing DNA and its applications in synthetic biology. In recent years the cost for synthetic DNA reduced from 7€/bp to 0.35€/bp which has opened up many new possibilities for molecular biology. You can purchase the gene, cDNA, oligo library or full vector specifically for a particular expression host and apply synthetic biology principles to produce or create new drugs, vaccines or any other biotechnological products. There are, however, great concerns within society to produce organisms that do not exist in nature, and the potential misuse of them. Adressing these concerns and to use a clear terminology that do not cause misunderstandings are important issues within the field, which were also discussed at this meeting.