Against reduction

In Molecular Models: Philosophical Papers on Molecular Biology, Sahotra Sarkar presents a historical and philosophical analysis of four important themes in philosophy of science that have been influenced by discoveries in molecular biology. These are: reduction, function, information and directed mutation. I argue that there is an important difference between the cases of function and information and the more complex case of scientific reduction. In the former cases it makes sense to taxonomise important variations in scientific and philosophical usage of the terms “function” and “information”. However, the variety of usage of “reduction” across scientific disciplines (and across philosophy of science) makes such taxonomy inappropriate. Sarkar presents reduction as a set of facts about the world that science has discovered, but the facts in question are remarkably disparate; variously semantic, epistemic and ontological. I argue that the more natural conclusion of Sarkar’s analysis is eliminativism about reduction as a scientific concept.     

Understanding the Human Genome Project: a biographical approach

This article analyzes a number of recently published autobiographies by leading participants in the Human Genome Project (HGP), in order to determine to what extent they may further our understanding of the history, scientific significance and societal impact of this major research endeavor. Notably, I will focus on three publications that fall under this heading, namely The common thread by John Sulston (2002/2003), The language of God (2006) by Francis Collins and A life decoded by Craig Venter (2007).1 Sulston's autobiography was co-authored by science writer Georgina Ferry. What may we learn from these autobiographical sources about the dynamics of scientific change? What is their added value in understanding science in general and the HGP in particular? These questions will be elaborated in three directions: on the level of knowledge (epistemology), power (politics) and the Self (ethics). On the epistemological level, genomics is often presented as a paradigm shift in the life sciences, a tremendous up-scaling of research, an “informatization” of life. Autobiographies may reveal how this shift – usually discussed in more general terms from a philosophy of science or science studies perspective – manifests itself on an individual scale, on a micro-epistemological level. On the political level, autobiographies may inform us about the micro-politics of scientific change. Finally, on the level of Self, autobiographies may allow us to analyze how researchers, through practices of Self, are actively engaged in constituting themselves as responsible subjects in the face of unpredictable dynamics and unforeseen dilemmas.     

Strategies for severe drought survival and recovery in a Pyrenean relict species

In the context of future climate change new habitats will be threatened and unique species will be forced to develop different strategies to survive. Saxifraga longifolia Lapeyr. is an endemic species from the Pyrenees with a very particular habitat. We explored the capacity and strategies of S. longifolia plants to face different severities of drought stress under both natural conditions and controlled water stress followed by a re-watering period of 20 days. Our results showed a role for abscisic acid (ABA), salicylic acid (SA) and cytokinins (CKs) in plant survival from drought stress, and as the stress increased, ABA lost significance and SA appeared to be more associated with the response mechanisms. Moreover, photo-oxidative stress markers revealed that both xanthophyll cycles played a photoprotection role with a stronger participation of the lutein epoxide cycle as the stress was more intense. Severe drought decreased the maximum efficiency of photosystem II (F_v/F_m) below 0.45, being this the limit to survive upon rewatering. Overall, our results proved different strategies of S. longifolia plants to cope with drought stress and suggested a F_v/F_m threshold to predict plant survival in high-mountain environments.     

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.     

IS EVOLUTIONARY BIOLOGY STRATEGIC SCIENCE?

There is a profound need for the scientific community to be better aware of the policy context in which it operates. To address this need, Evolution has established a new Outlook feature section to include papers that explore the interface between society and evolutionary biology. This first paper in the series considers the strategic relevance of evolutionary biology. Support for scientific research in general is based on governmental or institutional expenditure that is an investment, and such investment is based on strategies designed to achieve particular outcomes, such as advance in particular areas of basic science or application. The scientific community can engage in the development of scientific strategies on a variety of levels, including workshops to explicitly develop research priorities and targeted funding initiatives to help define emerging scientific areas. Better understanding and communication of the scientific achievements of evolutionary biology, emphasizing immediate and potential societal relevance, are effective counters to challenges presented by the creationist agenda. Future papers in the Outlook feature section should assist the evolutionary biology community in achieving a better collective understanding of the societal relevance of their field.     

Fleck and the social constitution of scientific objectivity

Ludwik Fleck’s theory of thought-styles has been hailed as a pioneer of constructivist science studies and sociology of scientific knowledge. But this consensus ignores an important feature of Fleck’s epistemology. At the core of his account is the ideal of ‘objective truth, clarity, and accuracy’. I begin with Fleck’s account of modern natural science, locating the ideal of scientific objectivity within his general social epistemology. I then draw on Fleck’s view of scientific objectivity to improve upon reflexive accounts of the origin and development of the theory of thought-styles, and reply to objections that Fleck’s epistemological stance is self-undermining or inconsistent. Explicating the role of scientific objectivity in Fleck’s epistemology reveals his view to be an internally consistent alternative to recent social accounts of scientific objectivity by Harding, Daston and Galison. I use these contrasts to indicate the strengths and weaknesses of Fleck’s innovative social epistemology, and propose modifications to address the latter. The result is a renewed version of Fleck’s social epistemology, which reconciles commitment to scientific objectivity with integrated sociology, history and philosophy of science.     

Beyond Trust: Plagiarism and Truth

Academic misconduct distorts the relationship between scientific practice and the knowledge it produces. The relationship between science and the knowledge it produces is, however, not something universally agreed upon. In this paper I will critically discuss the moral status of an act of research misconduct, namely plagiarism, in the context of different epistemological positions. While from a positivist view of science, plagiarism only influences trust in science but not the content of the scientific corpus, from a constructivist point of view both are at stake. Consequently, I argue that discussions of research misconduct and responsible research ought to be explicitly informed by the authors’ views on the relationship between science and the knowledge it produces.     

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.     

Reports from the high table

David Sepkoski and Michael Ruse’s edited collection The Peolobiological Revolution covers the changes in paleontological science in the last half-century. The collection should be of interest to philosophers of science (particularly those interested in non-reductive unity) as well as historians. I give an overview of the content and major themes of the volume and draw some lessons for the philosophy of science along the way. In particular, I argue that the history of paleontology demands a new approach to philosophical delineation of sciences.     

Managing ethical challenges around misattributed parentage within the clinical context: Insights from an African moral theory

This study argues the thesis that a set of guidelines ‐ firmly rooted in a particular interpretation of African moral theory, specifically, Ubuntu – will do a better job than current medical ethics frameworks, in addressing ethical challenges around misattributed parentage within the clinical context. Incidental information such as information with significant personal/health implications raises unique challenges for medical professionals. For example, withholding information of misattributed paternity accidentally discovered in clinical interactions may be seen by a patient as a violation of his/her right‐to‐know. Contrarily, disclosure where a patient has not requested information – or where establishing paternity is not the purpose of clinical visit/interaction – may be taken by the patient as a violation of his/her right ‘not‐to‐know’. Resolving these challenges remain a herculean task. African moral theory contains an under‐emphasized value for addressing such ethical challenges around misattributed parentage in the field of transplant. I seek to contribute this knowledge; and enhance clinician‐patient relationship. This study builds off three completed systematic reviews, which aimed to answer the following questions: “what are the ethical challenges regarding information health professionals face within the clinical contest?” and “what core aspects (or common themes) of Ubuntu can be identified in existing literature describing the same?” In this present study, I applied the definition of Ubuntu which captures the core aspects of the theory in ethical literature on the same, to address ethical issues around unsought information of misattributed parentage in the field of transplant.     

Half a Century on the Concepts of Innateness and Instinct: Survey,Synthesis and Philosophical Implications

This paper first surveys and criticizes the various attempts by students of behavior to define the concept of innateness. A new definition, based on these (especially that of Lorenz), and reformulable in terms of now classic notions in genetics and evolutionary theory, is then offered: A trait is innate if, and only if, it is canalized and such that any phenotype in the reaction norm which does not possess the trait is a morphose — hence maladapted — and such that all modifications do possess the trait. A narrower definition of innateness, based on the first definition, is suggested to delimit what is called “the Lorenzian notions of innateness” and to provide a framework within which to discuss the notion of a fixed action pattern. Evidence, from the recent literature, is adduced to show the existence and importance of such patterns — even for human behavior. In the final section, it is argued that a paradigm shift has indeed occurred and that although this scientific revolution has been accompanied by many of the irrational elements noted by the Kuhnian school of philosophy of science, the shift has in fact been made upon perfectly rational grounds. That this should be true of so controversial a field is strong evidence against the irrationalist thesis in philosophy of science.     

In search of the Holy Grail: Media discourse and the new human genetics

It has widely been recognized that the media play a key role in framing debates about genetic issues. This paper provides an overview of the major areas of debate within the social scientific literature on media, public understanding of science and human genetics. It evaluates current approaches to assessing the role of the media in influencing public policy debates. It argues that an analysis of the strategies of news sources should occupy a central role in furthering understanding about the ways in which various social actors seek to influence public policy agendas. At present, within the field of human genetics, only a handful of researchers have systematically examined the strategies of news sources from the perspective of the sources themselves. While recent research has focused upon identifying the major sources and how they are used in science reporting, there remains much to be done in uncovering the processes of negotiation and contestation among social actors prior to issues gaining media coverage.     

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.     

Uexküllian <Emphasis Type="Italic">Umwelt</Emphasis> as science and as ideology: the light and the dark side of a concept

The concept of Umwelt, in particular the interpretation originally developed by Jakob von Uexküll, played an important role in the development of biological thought of the first half of the twentieth century. The theory of Umwelt (Umweltlehre) was one of the most original ideas that appeared in German biology at that time. It was the first attempt to introduce subjectivity into a science about organisms; it laid down the foundations of behavioural research and inspired the development of ethology. However, the theory of Umwelt has also been used to support more sinister activities and even some dangerous ideologies. The concept of Umwelt is of interest not only to historians: within some intellectual circles, it is still broadly used today. Our aim was to analyse the notion’s historic development within the context of biological thought of the first half of the 20th century. In particular, we focus (1) on how the concept was adopted and adapted for various, often widely diverging purposes; (2) on interactions between the Umweltlehre and other contemporary worldviews. We argue that in order to understand the developments that occurred in twentieth century biology, one needs to properly appreciate the role which Umweltlehre played in these. Even more importantly, the Umweltlehre is a worldview that influenced not only science but also politics and social affairs. In this respect it functioned rather like a number of other scientific and ideological frameworks of that time, such as Synthetic Darwinism.     

The Role of History in Science

The case often made by scientists (and philosophers) against history and the history of science in particular is clear. Insofar as a field of study is historical as opposed to law-based, it is trivial. Insofar as a field attends to the past of science as opposed to current scientific issues, its efforts are derivative and, by diverting attention from acquiring new knowledge, deplorable. This case would be devastating if true, but it has almost everything almost exactly wrong. The study of history and the study of laws are not mutually exclusive, but unavoidably linked. Neither can be pursued without the other. Much the same can be said of the history of science. The history of science is neither a distraction from “real” science nor even merely a help to science. Rather, the history of science is an essential part of each science. Seeing that this is so requires a broader understanding of both history and science.     

Reinterpreting Responsiveness for Health Systems Research in Low and Middle‐Income Countries

The ethical concept of responsiveness has largely been interpreted in the context of international clinical research. In light of the increasing conduct of externally funded health systems research (HSR) in low‐ and middle‐income countries (LMICs), this article examines how responsiveness might be understood for such research and how it can be applied. It contends that four features (amongst others) set HSR in LMICs apart from international clinical research: a focus on systems; being context‐driven; being policy‐driven; and being closely linked to development objectives. These features support reinterpreting responsiveness for HSR in LMICs as responsiveness to systems needs, where health system performance assessments can be relied upon to identify systems needs, and/or responsiveness to systems priorities, which entails aligning research with HSR priorities set through country‐owned processes involving national and sub‐national policymakers from host countries. Both concepts may be difficult to achieve in practice. Country ownership is not an established fact for many countries and alignment to their priorities may be meaningless without it. It is argued that more work is, therefore, needed to identify strategies for how the responsiveness requirement can be ethically fulfilled for HSR in LMICs under non‐ideal conditions such as where host countries have not set HSR priorities via country‐owned processes. Embeddedness is proposed as one approach that could be the focus of further development.     

The democratic side of science-fiction

Suspicion towards technological advances has progressively grown during the xx(th) century. However, in the XXI(st) century, reading the NBIC (nanotechnology, biotechnology, information technology and cognitive science) report of the National Science Foundation, we can note that science has caught up with science fiction. These changes in public mentality on one side and in scientific capacities on the other argue for an evolution of the debate on sciences. The recent example of the national debate on nanotechnology in France has clearly shown that the public is no longer waiting for additional sources of scientific knowledge but rather waiting for the recognition of its authority to participate in the definition of the national R&D priority and associated scientific strategies. This is all the more legitimate that these strategies will have profound impact on the future of our societies and therefore cannot be decided only by scientists. Hence, it is crucial to identify innovative tools promoting debate on sciences and their technological spin-off. Here, we contend that science fiction has major assets that could face this challenge and facilitate the dialogue between sciences and society.     

The unfalsifiability of cladograms and its consequences

Popper's falsificationism provides the normative reference system in recent discussions regarding theory and methodology of systematics. According to Popper, the falsifiability of a hypothesis represents a necessary precondition for its corroborability. It is shown that cladograms, independent of “strict”, “methodological” or “sophisticated” falsification, are not falsifiable in principle. No present observation is prohibited by any tree hypothesis and, thus, no Popperian test of cladograms exists. It is shown that the congruence test, which is commonly said to represent a Popperian test of cladograms, instead tests sets of apomorphy hypotheses. Three different strategies that have been proposed to circumvent this problem are discussed and refuted: (1) referring to Popper's convention to renounce ad hoc maneuvers; (2) referring to Popper's treatment of probability hypotheses; and (3) decoupling corroboration from falsification. As a consequence, within a Popperian framework the unfalsifiability of cladograms implies that cladograms cannot explain any present day observation and, thus, represent metaphysical hypotheses. However, Popper's falsificationism has been criticized and questioned by many philosophers before and it seems to be about time that phylogeneticists develop their own philosophy of phylogenetics that meets their specific requirements of a historical science that is not seeking for universal laws and regularities, but instead reconstructing particular historical events. © The Willi Hennig Society 2007.     

Advancing Ecosystem Science by Promoting Greater Use of Theory and Multiple Research Approaches in Graduate Education

Since the inaugural edition of Ecosystems was published in 1998, ecosystem science has undergone substantial changes including the development of new research methods and an increasing emphasis on collaborations across traditional academic boundaries. In response to this transformation, we reflect on the current state of theory in ecosystem science, and make recommendations for training the next generation of Ph.D.-level ecosystem scientists. Specifically, we call for increased integration of theory into ecosystem science and outline the utility of iterating between theory and data generated by observations, experiments, and quantitative models. We recommend exposing graduate students to these three major approaches for generating data and propose strategies that students, advisors, and departments can employ to ensure this exposure. Ultimately, a successful training program will provide students with an understanding of key theories related to ecosystem science and how they interact with data, an appreciation for the interconnectedness of approaches to scientific inference, and a well-developed skill set in at least one approach—thereby empowering them to confidently tackle our pressing environmental problems. Although this is a daunting list of goals, continuing to advance our understanding of how ecosystems function necessitates a rigorous and well-developed training program.