Checks and balances: the welcomed tension between philosophy and science

There is a tension between science and philosophy, but this tension need not engender enmity or derision. Scientists and philosophers can work together, and we argue that working together is beneficial to both, even if it is sometimes uncomfortable. We offer examples of how philosophy can autonomously and effectively inform scientific practice. Science and philosophy share certain methodological concerns and practices; therefore, scientists who disregard philosophy are vulnerable to critical conceptual mistakes. If our arguments are correct, and if it can also be shown that science informs philosophy, then, while it is possible for both disciplines to operate autonomously, each should welcome the checks and balances that each provides for one another in the investigation and explanation of reality.     

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.     

On the Neurobiology of Truth

The concept of truth arises from puzzling over distinctions between the real and the apparent, while the origin of these distinctions lies in the neurobiology of mammalian cerebral lateralization, that is, in the evolution of brains that can address the world both indicatively and subjunctively; brains that represent the world both categorically and hypothetically. After some 2,500 years of thinking about it, the Western philosophical tradition has come up with three major theories of truth: correspondence, coherence, and pragmatist. Traditional philosophy has nevertheless failed to arbitrate much among these views; certainly no clear winner has emerged. I argue, however, that contemporary neuroscience provides adequate theoretical grounds for a unified theory of truth. More specifically, I contend that the correspondence, the coherence, and the pragmatic utility of symbols are each biological features of our neurophysiological information processing systems—that is to say, our brains. On my view, the traditional trifurcation of philosophical accounts of the predicate, “is true”, stems from a trifurcation of focus on the information latent in sensory, motor, and somatosensory cortices of the human brain.     

What history tells us

The history of science was long considered to be something peripheral to science itself. By supplying interesting stories and gossip, it seemed, at best, to provide material for enlivening lectures. In general, it was deemed a suitable activity for retired scientists. This view has been revised considerably in the past years and indeed, today seems hopelessly out of date. History and philosophy of science are increasingly held to be an essential component of the education of scientists. By becoming acquainted with these areas, practicing scientists — and in particular biologists — can better appreciate the significance of the models and theories that underpin their research, especially with the accelerating succession of one idea by the next. The present series, of which the article that follows is the first, aims to give historical glimpses that bear on contemporary biology. The hope is that these glimpses will be both a source of inspiration and of help in resisting useless fashions.     

Do we need theory to study disease? Lessons from cancer research and their implications for mental illness

This article applies general ideas from contemporary philosophy of science--chief among them that much good science proceeds without theories and laws--to the science of medicine. I claim that traditional philosophical debates over the nature of disease make demands on medicine that are mistaken. I demonstrate this philosophical error by applying the perspective of the philosophy of science to understanding the nature of disease in two concrete cases, cancer and depression. I first argue that cancer research produces various kinds of piecemeal causal explanation and does so without any well-developed theory of normal and malignant functioning, despite the rhetoric of some leading cancer researchers. I then defuse doubts about the scientific status of psychiatry, by demonstrating that it is not necessary to have a theory of normal functioning in order to understand and treat depression.     

Towards disciplinary disintegration in biology

Interdisciplinary integration has fundamental limitations. This is not sufficiently realized in science and in philosophy. Concerning scientific theories there are many examples of pseudo-integration which should be unmasked by elementary philosophical analysis. For example, allegedly over-arching theories of stress which are meant to unite biology and psychology, upon analysis, turn out to represent terminological rather than substantive unity. They should be replaced by more specific, local theories. Theories of animal orientation, likewise, have been formulated in unduly general terms. A natural history approach is more suitable for the study of animal orientation. The tendency to formulate overgeneral theories is also present in evolutionary biology. Philosophy of biology can only deal with these matters if it takes a normative turn. Undue emphasis on interdisciplinary integration is a modern variant of the old unity of science ideal. The replacement of the ideal by a better one is an important challenge for the philosophy of science.     

Definition of the real domain of the history of sciences and exploring the relationship with the philosophy of science

The specific field of the history of science is the study and explanation of the origin and transformation of the structures of scientific knowledge. The historian of science should render understandable the reality of scientific research. The relationships between the history of science and the philosophy of science are examined stating that (1) the philosophical theories on the development of science have a scientific content only as much as they may be compared with the results of the history of science, and (2) the philosophy of science does not refer to an immediate historical reality but to an intellectual reconstruction of the past.     

What is stemness?

This paper, addressed to both philosophers of science and stem cell biologists, aims to reduce the obscurity of and disagreements over the nature of stemness. The two most prominent current theories of stemness—the entity theory and the state theory—are both biologically and philosophically unsatisfactory. Improved versions of these theories are likely to converge. Philosophers of science can perform a much needed service in clarifying and formulating ways of testing entity and state theories of stemness. To do so, however, philosophers should acquaint themselves with the latest techniques and approaches employed by bench scientists, such as the use of proteomics, genome-wide association studies, and ChIP-on-chip arrays. An overarching theme of this paper is the desirability of bringing closer together the philosophy of science and the practice of scientific research.     

Scientific Citizenship and good governance: implications for biotechnology

In the wake of public distrust regarding biotechnology, it has been suggested that the debate should be moved "upstream", whereby the public help to set research priorities. Although many scientists see this as an illogical reaction to a loss of faith in science, we argue that the boundaries between science and its technological applications have become blurred and this produces conflicts of interests that have led to this crisis of trust. Furthermore, this distrust is also a crisis in governance that calls for a new open and democratic approach to scientific research. We propose that the concept of Scientific Citizenship, based on good governance, will help to restore public trust and bridge the gap between science and the society that it serves. Integral to this is the suggestion that the governance of science forms part of the training for scientists.     

Reverend Paley's naturalist revival

This paper analyzes the remarkable popularity of William Paley's argument from design among contemporary naturalists in biology and the philosophy of science. In philosophy of science Elliott Sober has argued that creationism should be excluded from the schools not because it is not science but because it is 'less likely' than evolution according to fairly standard confirmation theory. Creationism is said to have been a plausible scientific option as presented by Paley but no longer to be acceptable according to the same standards that once approved it. In biology C. G. Williams and Richard Dawkins have seen in Paley a proto-adaptationist. This paper shows that the historical assumptions of Sober's arguments are wrong and that the philosophical arguments themselves take alternatives to science to be alternatives in science and conflate the null hypothesis, chance, with a competing explanatory hypothesis. It is also shown that the similarity of Paley's adaptationism to that of contemporary biology is not what it is made out to be.     

Save the planet: eliminate biodiversity

Recent work in the philosophy of biology has attempted to clarify and defend the use of the biodiversity concept in conservation science. I argue against these views, and give reasons to think that the biodiversity concept is a poor fit for the role we want it to play in conservation biology on both empirical and conceptual grounds. Against pluralists, who hold that biodiversity consists of distinct but correlated properties of natural systems, I argue that the supposed correlations between these properties are not tight enough to warrant treating and measuring them as a bundle. I additionally argue that deflationary theories of biodiversity don’t go far enough, since a large proportion of what we value in the environment falls outside bounds of what could reasonably be called “diversity”. I suggest that in current scientific practice biodiversity is generally an unnecessary placeholder for biological value of all sorts, and that we are better off eliminating it from conservation biology, or at least drastically reducing its role.     

Subjectivity and flexibility in invasion terminology: too much of a good thing?

Invasions biologists have frequently debated whether the definition of invasive should include ecological and economic impacts. More recent criticisms posit that objective definitions are impossible in any absolute sense, while subjectivity is desirable for its flexibility and motivational qualities. We argue that such criticisms underestimate the extent of subjectivity already present in invasion biology. Ecological questions may be methodological if they relate directly to other ecological theories and models, or motivational if they focus on issues important to society as a whole. Motivational questions are important for engaging scientists, improving public understanding of science, and often have applied benefits. In contrast, methodological questions are constrained by established scientific theories, and are therefore more efficient for the development of scientific knowledge. Contrary to recent critiques, we suggest that greater objectivity is both achievable and desirable for the discipline of invasion biology and ecology generally.     

What is truth – in science and beyond

Truth is threatened in our societies and one might wish that scientists should stand up for truth, but in order to do so, one needs to know what is truth and how it can be recognized. The oldest and most widely accepted concept of truth is the Correspondence Theory requesting a fit of propositions and reality. In the Coherence Theory truth is a consistent property of a whole system of propositions. In the Pragmatic Theory truth works in practical terms. Scientists have defined criteria to verify true statements by experiments and by the simplicity of theories. Aristotle proposed parsimony claiming the superiority of theories which derive from fewer hypotheses. David Hume suggested probability arguments to assess the force of evidence. Nicolai Hartmann elaborated a model based on the congruence of a priori logical arguments with a posteriori empirical observations. Karl Popper introduced the falsification of testable theories as a way to better theories. The analysis shows that scientific and medical research uses classical philosophical criteria of truth in their daily work. Humanities use different, hermeneutic criteria of truth. Finally, societies need for their coherence a dialectic approach to truth based on honest discussion of opposing views.     

A ribonucleopeptide world at the origin of life

The structural flexibility of RNA and its ability to store genetic information has led scientists to postulate that RNA could be the key molecule for the development of life on Earth, further leading to formulate the RNA world hypothesis that received a lot of success and acceptance after the discoveries of the last thirty‐five years. Despite its highly structural and functional significance, the difficulty in synthesizing the four nucleobases that form the RNA polymer from the same primordial soup, its low stability, and limited catalytic repertoire, make the RNA world hypothesis less convincing even though it remains the best explanation for the origin of life. An increasing number of scientists are becoming more supportive of a more realistic approach explaining the appearance of life. In this review, I propose an enhanced explanation for the appearance of life supported by recent discoveries and theories. Accordingly, amino acids and peptides associated with RNA (e.g., ribonucleopeptides) might have existed at the onset of RNA and might have played an important role in the continuous development of self‐sustaining biological systems. Therefore, in this review, I cover the most recent and relevant scientific investigations that propose a better understanding of the ribonucleopeptide world hypothesis and the appearance of life. Finally, I propose two hypotheses for a primitive translation machinery (PTM) that might have been formed of either a T box ribozyme or a ribopolymerase.     

Interdisciplinary integration in biology? An overview

Philosophical theories about reduction and integration in science are at variance with what is happenign in science. A realistic approach to science show that possibilities for reduction and integration are limited. The classical ideal of a unified science has since long been rejected in philosophy. But the current emphasis on interdisciplinary integration in philosophy and in science shows that it survives in a different guise. It is necessary to redress the balance, specifically in biology. Methodological analysis shows that many of the grand interdisciplinary theories involving biology actually represent pseudo-integration covered up by inappropriate, overgeneral concepts. Integrationism is not bad, but it must be kept within reasonable bounds. If the present analysis is appropriate, there will have to be fundamental changes in research strategy both in science and in the philosophy of science.     

The function of function

Contemporary analyses of biological function almost invariably advocate a naturalistic analysis, grounding biological functions in some feature of the mind-independent world. Many recent accounts suggest that no single analysis will be appropriate for all cases of use and that biological teleology should be split into several distinct categories. This paper argues that such accounts have paid too little attention to the way in which functional language is used, concentrating instead on the types of situation in which it is used. An example of the role of teleology in science is examined and, on the basis of conclusions drawn from this, an alternative unifying analysis is proposed. It is suggested that, contrary to naturalistic accounts, teleology in biology carries no ontological commitment whatsoever to any class of mind-independent entities or properties. Instead, it is best regarded as a methodological device which is used to focus interest, formulate research perspectives and facilitate the structuring of certain questions or types of question that are pertinent in a given context of interest.     

Interpreting evidence: why values can matter as much as science

Despite increasing awareness of the ways in which non-epistemic values play roles in science, many scientists remain reluctant to acknowledge values at stake in their own work. Even when research clearly relates to risk assessment and establishing public policy, contexts in which the presence of values is less likely to be contentious, scientists tend to present such research as merely involving empirical questions about what the evidence is. As a result, debates over policy-related science tend to be framed as purely epistemic debates over the state of the evidence. We argue that this neglects the important ways that ethical and social values play legitimate roles in judgments about what we take to be evidence for a particular policy. Using the case of recent disputes about the relative safety of home birth, we argue that although the debate has been framed as a purely scientific one about the empirical evidence for home birth, it actually involves disagreements about underlying value assumptions. If our claims are correct, then in order to move the debate forward, scientists will need to engage in a critical discussion about the values at stake.     

Innateness and the Sciences

The concept of innateness is a part of folk wisdom but is also used by biologists and cognitive scientists. This concept has a legitimate role to play in science only if the colloquial usage relates to a coherent body of evidence. We examine many different candidates for the post of scientific successor of the folk concept of innateness. We argue that none of these candidates is entirely satisfactory. Some of the candidates are more interesting and useful than others, but the interesting candidates are not equivalent to each other and the empirical and evidential relations between them are far from clear. Researchers have treated the various scientific notions that capture some aspect of the folk concept of innateness as equivalent to each other or at least as tracking properties that are strongly correlated with each other. But whether these correlations exist is an empirical issue. This empirical issue has not been thoroughly investigated because in the attempt to create a bridge between the folk view and their theories, researchers have often assumed that the properties must somehow cluster. Rather than making further attempts to import the folk concept of innateness into the sciences, efforts should now be made to focus on the empirical questions raised by the debates and pave the way to a better way of studying the development of living organisms. Such empirical questions must be answered before it can be decided whether a good scientific successor – in the form of a concept that refers to a collection of biologically significant properties that tend to co-occur – can be identified or whether the concept of innateness deserves no place in science.