Causality, randomness, intelligibility, and the epistemology of the cell

Because the basic unit of biology is the cell, biological knowledge is rooted in the epistemology of the cell, and because life is the salient characteristic of the cell, its epistemology must be centered on its livingness, not its constituent components. The organization and regulation of these components in the pursuit of life constitute the fundamental nature of the cell. Thus, regulation sits at the heart of biological knowledge of the cell and the extraordinary complexity of this regulation conditions the kind of knowledge that can be obtained, in particular, the representation and intelligibility of that knowledge. This paper is essentially split into two parts. The first part discusses the inadequacy of everyday intelligibility and intuition in science and the consequent need for scientific theories to be expressed mathematically without appeal to commonsense categories of understanding, such as causality. Having set the backdrop, the second part addresses biological knowledge. It briefly reviews modern scientific epistemology from a general perspective and then turns to the epistemology of the cell. In analogy with a multi-faceted factory, the cell utilizes a highly parallel distributed control system to maintain its organization and regulate its dynamical operation in the face of both internal and external changes. Hence, scientific knowledge is constituted by the mathematics of stochastic dynamical systems, which model the overall relational structure of the cell and how these structures evolve over time, stochasticity being a consequence of the need to ignore a large number of factors while modeling relatively few in an extremely complex environment.     

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.     

Synthetic biology between technoscience and thing knowledge

Synthetic biology presents a challenge to traditional accounts of biology: Whereas traditional biology emphasizes the evolvability, variability, and heterogeneity of living organisms, synthetic biology envisions a future of homogeneous, humanly engineered biological systems that may be combined in modular fashion. The present paper approaches this challenge from the perspective of the epistemology of technoscience. In particular, it is argued that synthetic-biological artifacts lend themselves to an analysis in terms of what has been called ‘thing knowledge’. As such, they should neither be regarded as the simple outcome of applying theoretical knowledge and engineering principles to specific technological problems, nor should they be treated as mere sources of new evidence in the general pursuit of scientific understanding. Instead, synthetic-biological artifacts should be viewed as partly autonomous research objects which, qua their material-biological constitution, embody knowledge about the natural world—knowledge that, in turn, can be accessed via continuous experimental interrogation.     

On the Epistemological Crisis in Genomics

There is an epistemological crisis in genomics. At issue is what constitutes scientific knowledge in genomic science, or systems biology in general. Does this crisis require a new perspective on knowledge heretofore absent from science or is it merely a matter of interpreting new scientific developments in an existing epistemological framework? This paper discusses the manner in which the experimental method, as developed and understood over recent centuries, leads naturally to a scientific epistemology grounded in an experimental-mathematical duality. It places genomics into this epistemological framework and examines the current situation in genomics. Meaning and the constitution of scientific knowledge are key concerns for genomics, and the nature of the epistemological crisis in genomics depends on how these are understood.     

THE RELATIONSHIP BETWEEN EVOLUTIONARY BIOLOGY AND RELIGION

Belief in creationism and intelligent design is widespread and gaining significance in a number of countries. This article examines the characteristics of science and of religions and the possible relationship between science and religion. I argue that creationism is sometimes best seen not as a misconception but as a worldview. In such instances, the most to which a science educator (whether in school, college or university) can normally aspire is to ensure that students with creationist beliefs understand the scientific position. In the short term, the scientific worldview is unlikely to supplant a creationist one for students who are firm creationists. We can help students to find their evolutionary biology courses interesting and intellectually challenging without their being threatening. Effective teaching in this area can help students not only learn about the theory of evolution but better appreciate the way science is done, the procedures by which scientific knowledge accumulates, the limitations of science, and the ways in which scientific knowledge differs from other forms of knowledge.     

Scientific Authority in the Creation–Evolution Debates

At the heart of debates among creationists and evolutionists are questions about scientific integrity and rigor. Creationists often justify their rejection of biological evolution by claiming that the methodologies and interpretations of evolutionary scientists are flawed. A consideration of creationists’ critiques of the scientific data, however, reveals a deficient understanding and appreciation of the nature of the scientific process. It is essential that our schools educate students about the character of scientific inquiry. Clarifying the nature and limitation of scientific knowledge for our students will equip our students to evaluate evolutionary or creationist arguments critically. Recognizing and teaching both the strengths and limitations of the scientific process will do much to further the ongoing dialogue between science and religion.     

Estimating stomatal and biochemical limitations during photosynthetic induction

Understanding stomatal and biochemical components that limit photosynthesis under different conditions is important for both the targeted improvement of photosynthesis and the elucidation of how stomata and biochemistry affect plant performance in an ecological context. Limitation analyses have not yet been extensively applied to conditions of photosynthetic induction after an increase in irradiance. Moreover, few studies have systematically assessed how well various limitation analyses actually work. Here we build on two general ways of estimating limitations, one that sequentially removes the effect of a limitation (elimination) and one that uses a tangent plane approximation (differential), by including the ternary effect and boundary layer conductance so that they are consistent with gas exchange data. We apply them to the analysis of temporal and time‐integrated limitations during photosynthetic induction, calculating limitations either independent of the time course (one‐step) or make use of the entire time course (stepwise). We show that the stepwise differential method is the best method to use when time steps are small enough. We further show that the differential method predicts limitations near exact when the internal CO₂ concentration stays constant. This last insight has important implications for the general use of limitation analyses beyond photosynthetic induction.     

Scientific discovery as a combinatorial optimisation problem: How best to navigate the landscape of possible experiments?

A considerable number of areas of bioscience, including gene and drug discovery, metabolic engineering for the biotechnological improvement of organisms, and the processes of natural and directed evolution, are best viewed in terms of a 'landscape' representing a large search space of possible solutions or experiments populated by a considerably smaller number of actual solutions that then emerge. This is what makes these problems 'hard', but as such these are to be seen as combinatorial optimisation problems that are best attacked by heuristic methods known from that field. Such landscapes, which may also represent or include multiple objectives, are effectively modelled in silico, with modern active learning algorithms such as those based on Darwinian evolution providing guidance, using existing knowledge, as to what is the 'best' experiment to do next. An awareness, and the application, of these methods can thereby enhance the scientific discovery process considerably. This analysis fits comfortably with an emerging epistemology that sees scientific reasoning, the search for solutions, and scientific discovery as Bayesian processes.     

Translational Science: Epistemology and the Investigative Process

The term “translational science” has recently become very popular with its usage appearing to be almost exclusively related to medicine, in particular, the “translation” of biological knowledge into medical practice. Taking the perspective that translational science is somehow different than science and that sound science is grounded in an epistemology developed over millennia, it seems imperative that the meaning of translational science be carefully examined, especially how the scientific epistemology manifests itself in translational science. This paper examines epistemological issues relating mainly to modeling in translational science, with a focus on optimal operator synthesis. It goes on to discuss the implications of epistemology on the nature of collaborations conducive to the translational investigative process. The philosophical concepts are illustrated by considering intervention in gene regulatory networks.     

Eliminating the mystery from the concept of emergence

While some branches of complexity theory are advancing rapidly, the same cannot be said for our understanding of emergence. Despite a complete knowledge of the rules underlying the interactions between the parts of many systems, we are often baffled by their sudden transitions from simple to complex. Here I propose a solution to this conceptual problem. Given that emergence is often the result of many interactions occurring simultaneously in time and space, an ability to intuitively grasp it would require the ability to consciously think in parallel. A simple exercise is used to demonstrate that we do not possess this ability. Our surprise at the behaviour of cellular automata models, and the natural cases of pattern formation they mimic, is then explained from this perspective. This work suggests that the cognitive limitations of the mind can be as significant a barrier to scientific progress as the limitations of our senses.     

Species of thought: A comment on evolutionary epistemology

The primary outcome of natural selection is adaptation to an environment. The primary concern of epistemology is the acquistion of knowledge. Evolutionary epistemology must therefore draw a fundamental connection between adaptation and knowledge. Existing frameworks in evolutionary epistemology do this in two ways; (a) by treating adaptation as a form of knowledge, and (b) by treating the ability to acquire knowledge as a biologically evolved adaptation. I criticize both frameworks for failing to appreciate that mental representations can motivate behaviors that are adaptive in the real world without themselves directly corresponding to the real world. I suggest a third framework in which mental representations are to reality as species are to ecosystems. This is a many-to-one relationship that predicts a diversity of adaptive representations in the minds of interacting people. As “species of thought”, mental representations share a number of properties with biological species, including isolating mechanisms that prevent them from blending with other representations. Species of thought also are amenable to the empirical methods that evolutionists use to study adaptation in biological species. Empirical studies of mental representations in everyday life might even be necessary for science to succeed as a normative “truth-seeking” discipline.     

God is in the Data: Epistemologies of Knowledge at the Creation Museum

In contemporary American public culture, interest groups increasingly mobilise social constructionist arguments in order to discredit strains of scientific knowledge. According to Latour [2004. Why Has Critique Run out of Steam? From Matters of Fact to Matters of Concern. Critical Inquiry, 30:225–48], the field of science studies has contributed to this trend by exposing the ways that scientific facts are socially mediated. In this article, I examine how a narrative of social construction is articulated in the Creation Museum, a young earth creationist museum in Northern Kentucky, USA. I compare the epistemology of science in the Creation Museum with that of conspiracy theory and of social constructionist science studies. I examine how, in the Creation Museum, social constructionist critique is combined with a framing of the Bible as a source of factual data. It is argued that science studies, conspiracy theory and creationism overlap in their critiques of the transparency and objectivity of science. However, they diverge in terms of the degree of recursivity they allow.     

Evolutionary epistemology as a scientific method: a new look upon the units and levels of evolution debate

Evolutionary epistemology can provide a unified scientific methodology that enables scholars to study the evolution of life as well as the evolution of cognition, science, culture and any other phenomenon displayed by living organisms. In this article, three heuristics are provided that allow for a thorough search for the units, levels and mechanisms of evolution. Contrary to previous approaches, units, levels and mechanisms are not identified by pointing out essential features, but rather ostensive definitions are preferred. That is, units are considered as such if a level of evolution and a mechanism of evolution is identifiable. Levels are levels if one can point out units that evolve at that level according to evolutionary mechanisms, and mechanisms are considered as such if one can point out units and levels where the mechanism is active.     

Medicine and the call for a moral epistemology

For over a century, medicine has prided itself on its scientific orientation and technological accomplishments. But a conceptual crack lies at the foundation of contemporary medicine, one that may be characterized as a conflict between medicine's scientific epistemology and its moral philosophy. Moral refers to value, and more specifically in the clinical setting, to how facts must be ordered by the values attached to them. A "moral epistemology" seeks to bring these two domains into closer proximity. Clinical facts always reside in a complex array of systems that confer specific and often unique meanings to any finding. An integration of unsteady norms and the intuitive inference arising from the individuality of disease expression require that judgments order facts into their proper placement. And beyond this relaxed view of objectivity, clinical care must also incorporate judgments arising from the patient's (as well as the physician's) social and psychological realms that are removed from scientific concerns. Together, these various kinds of value judgments erect the scaffold of clinical care, in which a more complex moral epistemology emerges. A comprehensive biopsychosocial model of illness and its treatment articulates this integrated orientation, but until medicine embraces a philosophy that legitimates the full integration of facts and values, the appeal of such an approach will remain limited and its application ineffective.     

The hunt for sustainable biocontrol of oomycete plant pathogens,a case study of Phytophthora infestans

Late blight caused by the oomycete Phytophthora infestans is considered to be one of the most severe diseases of potato and tomato worldwide. Whilst current synthetic fungicides are efficient at controlling this disease, they are an environmental and economic burden. In line with EU directives to reduce the use of synthetic pesticides and increase the use of sustainable alternative disease control strategies that can form part of integrated pest management systems, practical biological control solutions are urgently needed. Despite the fact that there has been a large body of scientific research into microorganisms with potential for the biological control of late blight disease, relatively few commercial biocontrol agents, licensed to control late blight, exist. Furthermore, the practical uptake of those in Europe is lower than might be expected, suggesting that such solutions are not yet feasible, or effective. Here we review the scientific literature, focusing on the most recent developments in the hunt for efficient and sustainable biological control of late blight disease. We discuss the progress in our mechanistic understanding of mycoparasite–prey interactions, in the context of late blight and the challenges and limitations to the use of such knowledge in practical disease control within a European context.     

The Crisis of Reproducibility,the Denominator Problem and the Scientific Role of Multi-scale Modeling

The “Crisis of Reproducibility” has received considerable attention both within the scientific community and without. While factors associated with scientific culture and practical practice are most often invoked, I propose that the Crisis of Reproducibility is ultimately a failure of generalization with a fundamental scientific basis in the methods used for biomedical research. The Denominator Problem describes how limitations intrinsic to the two primary approaches of biomedical research, clinical studies and preclinical experimental biology, lead to an inability to effectively characterize the full extent of biological heterogeneity, which compromises the task of generalizing acquired knowledge. Drawing on the example of the unifying role of theory in the physical sciences, I propose that multi-scale mathematical and dynamic computational models, when mapped to the modular structure of biological systems, can serve a unifying role as formal representations of what is conserved and similar from one biological context to another. This ability to explicitly describe the generation of heterogeneity from similarity addresses the Denominator Problem and provides a scientific response to the Crisis of Reproducibility.