<Emphasis Type="Bold">Ethics and Epistemology of Big Data</Emphasis>

In this Symposium on the Ethics and Epistemology of Big Data, we present four perspectives on the ways in which the rapid growth in size of research databanks—i.e. their shift into the realm of “big data”—has changed their moral, socio-political, and epistemic status. While there is clearly something different about “big data” databanks, we encourage readers to place the arguments presented in this Symposium in the context of longstanding debates about the ethics, politics, and epistemology of biobank, database, genetic, and epidemiological research.     

Mobilizing and integrating big data in studies of spatial and phylogenetic patterns of biodiversity

The current global challenges that threaten biodiversity are immense and rapidly growing. These biodiversity challenges demand approaches that meld bioinformatics, large-scale phylogeny reconstruction, use of digitized specimen data, and complex post-tree analyses (e.g. niche modeling, niche diversification, and other ecological analyses). Recent developments in phylogenetics coupled with emerging cyberinfrastructure and new data sources provide unparalleled opportunities for mobilizing and integrating massive amounts of biological data, driving the discovery of complex patterns and new hypotheses for further study. These developments are not trivial in that biodiversity data on the global scale now being collected and analyzed are inherently complex. The ongoing integration and maturation of biodiversity tools discussed here is transforming biodiversity science, enabling what we broadly term “next-generation” investigations in systematics, ecology, and evolution (i.e., “biodiversity science”). New training that integrates domain knowledge in biodiversity and data science skills is also needed to accelerate research in these areas. Integrative biodiversity science is crucial to the future of global biodiversity. We cannot simply react to continued threats to biodiversity, but via the use of an integrative, multifaceted, big data approach, researchers can now make biodiversity projections to provide crucial data not only for scientists, but also for the public, land managers, policy makers, urban planners, and agriculture.     

Scientific perspectivism: A philosopher of science's response to the challenge of big data biology

Big data biology—bioinformatics, computational biology, systems biology (including ‘omics’), and synthetic biology—raises a number of issues for the philosophy of science. This article deals with several such: Is data-intensive biology a new kind of science, presumably post-reductionistic? To what extent is big data biology data-driven? Can data ‘speak for themselves?’ I discuss these issues by way of a reflection on Carl Woese’s worry that “a society that permits biology to become an engineering discipline, that allows that science to slip into the role of changing the living world without trying to understand it, is a danger to itself.” And I argue that scientific perspectivism, a philosophical stance represented prominently by Giere, Van Fraassen, and Wimsatt, according to which science cannot as a matter of principle transcend our human perspective, provides the best resources currently at our disposal to tackle many of the philosophical issues implied in the modeling of complex, multilevel/multiscale phenomena.     

Citizen Science

Citizen science Citizen science is performed on a honorary basis. Citizen scientists (”Citizen Science proper“) have no professional employment in the relevant field of research and differ very much in their educational background, specific knowledge and amount of time dedicated to the subject of research. Today, citizen science has become especially important in some fields neglected by professional science, e.g. regional research. Recently, another form of citizen science has gained much attention, in which usually many citizen scientist are active (”Citizen Science light“). Internet, smartphone and georeferencing by GPS are important tools for collecting, documenting and communicating the observation data. Besides the scientific results, social relevance through participation and information of citizens (e.g. for conservation issues) play a very important role in these projects. The recently strongly increasing interest in and contribution to citizen science plays an important role to strengthen the link and communication between science and society.     

Conceptual and ethical problems in the epistemology of genetic information

My thesis will be that the identification of genetic features and their medical interpretation follow at least partially from reductionist premises: “Genes are charging the gun, life(-style) will trigger it.” This simplistic metaphor illustrates a problem of genetic diagnosis: from the viewpoint of philosophy of science, concepts of the gene and the genome are vague and confused. Until now these concepts have not been defined satisfactorily. Partly on account of this there is an additional problem in applying genetic tests in medical diagnostics. The epistemic status of predictive genetic diagnosis in many cases can justifiably be called “opaque.” But a predictive genetic test is designed to reveal genetic knowledge of and for a client on the basis of scientific research. Methodologically the diagnosis of the scientific problem in genetics as a science is developed philosophically as an epistemological argument. The problem of genetics as applied science in medicine and society is the danger of irrationality due to reductionist premises of science. This problem is to be revealed by philosophical analysis. The major result of the argument is that the assessment of applications of basic research in genetics should include considerations from epistemology and philosophy of science. The epistemological status of scientific concepts and reasonableness of advice are interrelated. My thesis is that at the interface between theory of science in genetics and reasonableness of “genetic advice” is the responsibility of the researchers for concepts of their science.     

Botanical gardens and citizen science: An (as yet) under-exploited potential

Participation of citizens to research activities probably began with a “Christmas bird count” in 1900. Citizen science (CS) activities can aim at several purposes: long-term monitoring, environmental education, preservation of traditional ecological knowledge. Citizen scientists can collect data, support scientists in the field, involve decision-makers, plan new research activities, etc. While CS may have critical issues, especially as far as data quality is concerned, it has several relevant advantages as well (reduced costs, production of “big data”, awareness raising, etc.). However, especially in Europe, there is still an under-exploited potential for botanical gardens to act as drivers for CS initiatives.     

“Second generation” refugees and multilingualism: identity,race and language transmission

This paper explores the language practices, attitudes to languages and the inter-generational transmission of heritage languages amongst the UK-born adult children of refugee parents. The paper draws on empirical data from a research project based on 45 qualitative interviews with three groups of “second generation” refugees, whose parents came as Tamil refugees from Sri Lanka, Kurdish refugees from Turkey and as refugees from Vietnam. The paper explores the ways in which language is central to political discussions and to national policies on race, cohesion, diversity, “Britishness” and citizenship. These debates and policies ignore and often silence the positive role of heritage languages. This paper highlights the importance of heritage languages as a signifier for a number of wider issues of identity, which intersect with race and refugee backgrounds in complex ways.     

Using provenance to manage knowledge of in silico experiments

This article offers a briefing in one of the knowledge management issues of in silico experimentation in bioinformatics. Recording of the provenance of an experiment-what was done; where, how and why, etc. is an important aspect of scientific best practice that should be extended to in silico experimentation. We will do this in the context of eScience which has been part of the move of bioinformatics towards an industrial setting. Despite the computational nature of bioinformatics, these analyses are scientific and thus necessitate their own versions of typical scientific rigour. Just as recording who, what, why, when, where and how of an experiment is central to the scientific process in laboratory science, so it should be in silico science. The generation and recording of these aspects, or provenance, of an experiment are necessary knowledge management goals if we are to introduce scientific rigour into routine bioinformatics. In Silico experimental protocols should themselves be a form of managing the knowledge of how to perform bioinformatics analyses. Several systems now exist that offer support for the generation and collection of provenance information about how a particular in silico experiment was run, what results were generated, how they were generated, etc. In reviewing provenance support, we will review one of the important knowledge management issues in bioinformatics.     

The Living State

As biologists we can contribute to quantum chemistry only by clearing up the mechanism of some of the biological processes, thereby opening the way to their quantum chemical analysis. We have tried to do this by isolating and identifying the central catalysts of those processes. One of us (A.S.-G.) studied biological oxidations first in the plants that turn dark on exposure to air such as potatoes, apples and pears. He found the central catalyst of these oxidations to be a catechol derivative that oxidized to o-diquinol which forms dark complexes with protein. After this, he turned to the oxidation of plants that do not turn dark and identified two catalysts, one of which was ascorbic acid, the other succinic acid. His third problem was the generation of motion, the function of muscle. This study led to the discovery of a new protein, which he discovered with I. Banga at the University of Szeged, Hungary. They called it “actin” because it made the inactive myosin act to contract. This discovery has an unusual history. It was never published because just when they were about to publish, Hitler occupied Hungary and Szent-Gyorgyi had to disappear “underground” separated from Banga and science. Our present interest is in the “Living State”, one of the most important phenomena, the central substance of which seems to be methoxyhydroquinone (1–6).     

Clinicians’ views and expectations of human microbiome science on asthma and its translations

Human microbiome science examines the microbiota that live in and on the human body and their role in human health. This paper examines clinicians’ views and expectations of microbiome science in asthma care. Drawing on qualitative interviews with 10 clinicians in Canada, we explore their perspectives for insights into translation of human microbiome science. The emphasis on novelty in much microbiome scholarship, we suggest, does not account fully for the ways in which microbiome science translations may be taken up in multiple ways that are both disruptive to and continuous with contemporary biomedicine. We suggest that clinicians drew on scientific discourses of “evidence” and “facts” as a form of boundary work to re-establish a separation between western biomedicine and alternative health practitioners, and clinical expertise and lay knowledge. We conclude with a discussion of human microbiome science and the emergence of post-Pasteurian modes of health in western biomedicine.     

An integrated,modular approach to data science education in microbiology

We live in an increasingly data-driven world, where high-throughput sequencing and mass spectrometry platforms are transforming biology into an information science. This has shifted major challenges in biological research from data generation and processing to interpretation and knowledge translation. However, postsecondary training in bioinformatics, or more generally data science for life scientists, lags behind current demand. In particular, development of accessible, undergraduate data science curricula has the potential to improve research and learning outcomes as well as better prepare students in the life sciences to thrive in public and private sector careers. Here, we describe the Experiential Data science for Undergraduate Cross-Disciplinary Education (EDUCE) initiative, which aims to progressively build data science competency across several years of integrated practice. Through EDUCE, students complete data science modules integrated into required and elective courses augmented with coordinated cocurricular activities. The EDUCE initiative draws on a community of practice consisting of teaching assistants (TAs), postdocs, instructors, and research faculty from multiple disciplines to overcome several reported barriers to data science for life scientists, including instructor capacity, student prior knowledge, and relevance to discipline-specific problems. Preliminary survey results indicate that even a single module improves student self-reported interest and/or experience in bioinformatics and computer science. Thus, EDUCE provides a flexible and extensible active learning framework for integration of data science curriculum into undergraduate courses and programs across the life sciences.     

Science and Restoration Under a Big, Demon Haunted Tent: Reply to Giardina et al. (2007)

In a recent editorial, I discussed how the culture of science, heterogeneity of nature, and real‐world human complexities can limit the practical relevance of formal scientific research and argued that less formal approaches might often be more efficient and effective. Giardina et al. criticized this editorial and argued that formal science has and increasingly will play a central role in ecological restoration in particular and human progress in general. Here, I respond to these arguments and expand upon the ideas presented in my previous editorial. I further illustrate how despite superficial appearances the utilitarian value of formal science may often be largely indirect. I also argue that the complexities of ecological and human systems combined with the subjective values and political beliefs underlying restoration make transforming this discipline into a unified “hard science” virtually impossible. Because values and politics also underlie most environmental conflicts, and scientific inquiry is inherently unsuitable for resolving these kinds of disputes, the future success of restoration may depend more on political support than scientific progress. Dogmatic, nonfalsifiable faith in the universal superiority of “rigorous” scientific knowledge and methodologies can foster arrogance and intolerance and blind us to the ephemeral nature of scientific “truths” and the double‐edged sword of scientific “progress.” My hope is that Society for Ecological Restoration International (SERI) will remain a big inclusive tent that embraces a healthy diversity of foci and approaches that emulate the extraordinary diversity we find within the natural ecosystems and human cultures we strive to preserve, restore, and reconnect.     

Les Mollusques Céphalopodes dans les Annales de Paléontologie

About more than forty papers on cephalopods have been published in the ninety one issues of the “Annales” during one century. Most are monographs contributing to enlarge our knowledge on the biodiversity of these Molluscs which play an important part in the fossil record. Jurassic and Cretaceous ammonites are well illustrated; Palaeozoic and Triassic ones, Orthoceratoidea, Nautiloidea and Dibranchiata are seldom studied. As successive issues are published, hypothesis concerning palaeontological and geological applications are proposed by authors: systematics, phylogeny, biostratigraphy, palaeoecology, palaeobiogeography. However, these ones cannot be argued every time because of incomplete knowledge or adapted concepts. Several years or decades later, these hypothesis, reconsidered in a different context and other scientific publications, are the starting point of new ideas, at once developed and then accepted. From this point of view and by their contents, the “Annales” have answered to there vocation of publishing data, carried on year by year and enriched with the discoveries of each new palaeontologists generation.     

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.     

大学化学知识融入本科核心课程生物化学的教学刍议

本科的化学基础知识是生命科学专业的核心课程"生物化学"的重要基础.本文在对生物化学与大学化学知识的密切关系进行学理分析的基础上,对无机化学、有机化学、分析化学和物理化学四门课中与生物化学内容密切相关的知识点进行梳理和总结.以肽键、酶作用机制、蛋白质纯化为例,给出化学基础知识对生物化学知识点的关联性.借助第二课堂启迪学生...     

Policy Language in Restoration Ecology

Relating restoration ecology to policy is one of the aims of the Society for Ecological Restoration and its journal Restoration Ecology. As an interdisciplinary team of researchers in both ecological science and political science, we have struggled with how policy‐relevant language is and could be deployed in restoration ecology. Using language in scientific publications that resonates with overarching policy questions may facilitate linkages between researcher investigations and decision‐makers' concerns on all levels. Climate change is the most important environmental problem of our time and to provide policymakers with new relevant knowledge on this problem is of outmost importance. To determine whether or not policy‐specific language was being included in restoration ecology science, we surveyed the field of restoration ecology from 2008 to 2010, identifying 1,029 articles, which we further examined for the inclusion of climate change as a key element of the research. We found that of the 58 articles with “climate change” or “global warming” in the abstract, only 3 identified specific policies relevant to the research results. We believe that restoration ecologists are failing to include themselves in policy formation and implementation of issues such as climate change within journals focused on restoration ecology. We suggest that more explicit reference to policies and terminology recognizable to policymakers might enhance the impact of restoration ecology on decision‐making processes.     

The epistemic logic of asylum screening: (dis)embodiment and the production of asylum knowledge in Brazil

The current era demands our thoughtful attention to how states process asylum seeker claims for safe haven, yet we know little about the practices through which asylum officials carry out that work. Building from literature on the body and knowledge production, this paper illuminates the workings of (dis)embodiment in the asylum process. I use the term (dis)embodiment to refer to an arrangement of separate yet interdependent practices of disembodying and embodying knowledge. These practices of knowledge production together form an integral part of what I call the “epistemic logic” of asylum – the techniques and processes of reasoning used to produce and analyse information to determine if an asylum seeker qualifies for refugee status. Through an ethnography of the asylum process in Brazil, I document how officials produce and privilege disembodied knowledge, while they contrastingly constrain the knowledge of asylum seekers to their bodies and lived experiences.     

Combining field work and laboratory work in the study of financial risk-taking

A contribution to a special issue on Hormones and Human Competition.Financial markets are periodically destabilized by bubbles and crashes during which investors display respectively what has been called “irrational exuberance” and “irrational pessimism”. How can we best study these pathologies in competitive and risk-taking behaviours? In this article, we argue that a science of risk-taking and of the financial markets needs to draw heavily on physiology and especially endocrinology, due to their central roles in moderating human behaviour. Importantly, this science of competition and risk requires the same spectrum of research protocols as is found in mature biological and medical sciences, a spectrum running from field work conducted within financial institutions themselves to more controlled laboratory studies, which permit cause to be distinguished from effect. Such a spectrum of studies is especially important for translational behavioural science.     

Using Google trends data to assess public understanding on the environmental risks

This study proposes a method to assess the public understanding toward themes related to environment, biodiversity conservation and fishery. Since the Internet traffic is seen as the proxy of the public interest, this article analyzes the related Google Trends data to explore the cognitive map of the public. Patterning changes in the search volume (synchronous increase and decrease) were detected by using the association analysis. Weekly search volumes of the United States for the last 5 years have been gathered and were converted into values ranging between –1 and 1, indicating the gradual level of increase/decrease by the time. Apriori algorithm was used to determine the associations between search volumes of the keywords. As a consequence, several patterns were detected with a significant support indicating synchronous increases/decreases of the volumes. Upon the development of cognitive maps based on the detected patterns, it is found that the terms “Environment” and “Pollution” were the most significant and central terms. The search volume of the terms such as “Conservation,” “Ecology,” “Climate change,” “Invasive species” and “Endangered Species” increases as the search increases in the central terms. Therefore, these terms can be seen as the drivers/triggers of the Google search for some central words. It is apparent that the public has awareness of the central terms and further interest should be provoked and fostered on the environment-related concepts.