One of the foundational problems of biochemistry concerns the conceptualisation of the relationship between the composition, structure and function of macromolecules like proteins. Part of the recent philosophical literature displays a reductionist bias, that is, the endorsement of a form of microstructuralism mirroring an out-dated biochemical conceptualisation. We shall argue that such microstructuralist approaches are ultimately committed to a potentialist form of micro-predeterminism whereby the macrostructure and function of proteins is accounted for solely in terms of the intrinsic properties and (...) potentialities of the components of the primary structure as if they were self-contained or essentially immutable entities. We shall instead suggest that a conceptualisation of the relationship between proteins’ composition, structure and function consistent with contemporary biochemical practice should account also for the causal role of the cellular, organismal and environmental relations in protein development. The analysis of the folding process we propose suggests that microstructure-laden reductionist approaches are ontologically indefensible. Rather than a potentialist form of micro-predeterminism, our analysis ultimately supports a relational-construction-based view of protein development and potentialities formation, which requires an indispensable analysis of the dynamical interplay between the micro-level of the parts and the macro-level of the relational structures of their systems. (shrink)

This open access book features essays written by philosophers, biologists, ecologists and conservation scientists facing the current biodiversity crisis. Despite increasing communication, accelerating policy and management responses, and notwithstanding improving ecosystem assessment and endangered species knowledge, conserving biodiversity continues to be more a concern than an accomplished task. Why is it so?The overexploitation of natural resources by our species is a frequently recognised factor, while the short-term economic interests of governments and stakeholders typically clash with the burdens that implementing conservation (...) actions imply. But this is not the whole story. This book develops a different perspective on the problem by exploring the conceptual challenges and practical defiance posed by conserving biodiversity, namely: on the one hand, the difficulties in defining what biodiversity is and characterizing that “thing” to which the word ‘biodiversity’ refers to; on the other hand, the reasons why assessing biodiversity and putting in place effective conservation actions is arduous. (shrink)

After having reconstructed a minimal biological characterisation of species, we endorse an “empirical approach” based on the idea that it is the peculiar evolutionary history of the species at issue—its peculiar origination process, its peculiar metapopulation structure and the peculiar mixture and strength of homeostatic processes vis à vis heterostatic ones—that determines species’ identity at a time and through time. We then explore the consequences of the acceptance of the empirical approach in settling the individuals versus kinds dispute. In particular, (...) while conceptual arguments have been proposed to show that species can be equally treated as individuals and kinds because mereology’s and set-theory’s languages are inter-translatable, we advance instead a causal argument to sustain the claim that each species is both a kind and an individual. (shrink)

Biologists and philosophers often use the language of determination in order to describe the nature of developmental phenomena. Accounts in terms of determination have often been reductionist. One common idea is that DNA is supposed to play a special explanatory role in developmental explanations, namely, that DNA is a developmental determinant. In this article we try to make sense of determination claims in developmental biology. Adopting a manipulationist approach, we shall first argue that the notion of developmental determinant is causal. (...) We suggest that two different theses concerning developmental determination can be articulated: determination of occurrence and structural determination. We shall argue that, while the first thesis is problematic, the second, opportunely qualified, is feasible. Finally, we shall argue that an analysis of biological causation in terms of determination cannot account for entangled dynamics. Characterising causal entanglement as a particular kind of interactive causation whereby difference-making causes ascribable to different levels of biological organisation influence a particular ontogenetic outcome, we shall, via two illustrative examples, diagnose some potential limits of a reductionist, molecular and intra-level understanding of biological causation. (shrink)

This paper will critically assess Popper’s evolutionary philosophy. There exists a rich literature on the topic with which we have many reservations. We believe that Popper’s evolutionary philosophy should be assessed in light of the intriguing theoretical insights offered, during the last 10 years or so, by the philosophy of biology, evolutionary biology and molecular biology. We will argue that, when analysed in this manner, Popper’s ideas concerning the nature of selection, Lamarckism and the theoretical limits of neo-Darwinism can be (...) appreciated in their full biological and philosophical value. (shrink)

The COVID-19 pandemic poses extraordinary public health challenges. In order to respond to such challenges, most democracies have relied on so-called ‘evidence-based’ policies, which supposedly devolve to science the burden of their justification. However, the biomedical sciences can only provide a theory-laden evidential basis, while reliable statistical data for policy support is often scarce. Therefore, scientific evidence alone cannot legitimise COVID-19 public health policies, which are ultimately based on political decisions. Given this inevitable input on policy-making, the risk of arbitrariness (...) is ubiquitous and democratic scrutiny becomes essential to counter it. During the COVID-19 pandemic, the standards of scientific and democratic scrutiny have been, as a matter of fact, substantially lowered. This erosion potentially damages democracy. (shrink)

Abstractabstract:Public health emergencies are fraught by epistemic uncertainty, which raises policy issues of how to handle that uncertainty and devise sustainable public health responses. Among such responses, a herd immunity policy might be an option. Particularly before the development of vaccines, the current COVID-19 pandemic has highlighted the polarized nature of the political debate concerning the ethical feasibility of herd immunity strategies. This article provides a conceptual framework tailored to uncover the ethical rationale behind such strategies. Clarity on this issue (...) is important in order to facilitate the terms of the political debate when tackling future health emergencies. (shrink)

This edited book is the outcome of a conference that was planned to take place in Lisbon at the Centro de Filosofia das Ciências (CFCUL) of the Faculdade de Ciências da Universidade de Lisboa. It was originally organized in the usual on-site form to which we were accustomed before the start of the Covid pandemic. The conference was postponed many times, with the hope to hold it on-site, to no avail. After many postponements, to our disappointment, the conference had unfortunately (...) to be organized in a purely online form between 14th and 15th of October in 2021. The only advantage of all this is that we saved public money. (shrink)

The protein folding problem is one of the foundational problems of biochemistry and it is still considered unsolved. It basically consists of two main questions: what are the factors determining the stability of the protein’s native structure and how does the protein acquire it starting from an unfolded state. Since its first formulation, two main explanatory approaches have dominated the field of protein folding research: a thermodynamic approach focused on energetic features and a kinetic approach focused on the temporal development (...) of protein chains and structural considerations. Although these two approaches are tightly intertwined in biochemical practice and largely agree on which are the parts and activities in which the phenomenon under study should be decomposed to, there nevertheless exist important contrasts that have had repercussions on the development of the field and still engender vigorous debate. We shall analyse the historical development of the field and crucial aspects of current scientific debates. On this basis, we argue that the main sources of disagreement centre on the causal interpretation of thermodynamic and kinetic explanations, on the explanatory relevance assigned to different features of the phenomena under study and on the status of the ontological assumptions concerning the entities under study. (shrink)

This Open Access book addresses the epistemological and ontological significance as well as the scope of new mechanism. In particular, this book addresses the issues of what is "new" about new mechanism, the epistemological and ontological reasons underlying the adoption of mechanistic instead of other modelling strategies as well as the possibility of mechanistic explanation to accommodate a non-trivial notion of emergence. Arguably, new mechanism has been particularly successful in making sense of scientific practice in the molecular life sciences. But (...) what about other sciences? This book enlarges the context of analysis, addressing the issue of the putative compatibility between the current ways of conceiving new mechanism and actual scientific practices in quantum physics, chemistry, biochemistry, developmental biology and the cognitive sciences. (shrink)

In this article we focus on the emergence of biological individuality by association, trying to formulate some theoretical conditions to think about the process of collective individualization. The starting point of our analysis is the notion of “major evolutionary transition.” A major evolutionary transition is the result of the integration of a multiplicity of initially independent biological entities that, by managing to organize their interactions, become a collective of components having an identity oriented towards a common goal. When biological organisms (...) are concerned, a major transition corresponds to a phenomenon of fusion between them. We shall argue that the emergence of a new biological level of individuality implies the establishment of constitutive relationships between individuals that change their status as autonomous entities. As a result, the emergence of a new type of entity in the living world implies that individuals enter into relationships that intrinsically transform them, a transformation sufficient for a “whole” to become a “part” that forms another “whole”, that is, a new level of organismality. (shrink)

In this article we analyse the issue of what accounts for developmental potential, i.e., the possible phenotypes a developing organism can manifest during ontogeny. We shall argue in favour of two theses. First, although the developing organism is the unit of development, the complete causal basis for its potential to develop does neither lie entirely in itself as a whole nor in any specific part of itself (such as its genome). Thus, the extra-organismal environment must be counted as one of (...) the three necessary, partial and complementary causal bases for development potential. Secondly, we shall defend a constructivist view of the developmental process. If the genome, the developing organism and the extra-organismal environment are to be counted as proper elements of the causal basis for an organism’s developmental potential, the latter is not a given. Rather, it is the result of an interaction-based construction, a process sometimes generating genuine developmental novelty. We will thus argue for an interactionist multi-causal basis view of developmental potential construction. We contend that our view provides a biologically tenable and metaphysically coherent account of developmental dynamics. (shrink)

La versión estadística del concepto de naturaleza humana sigue siendo un concepto central en muchas ramas de las ciencias humanas. La clave del concepto es que existe un núcleo de fenotipos específicos que caracteriza a las especies biológicas, incluyendo la nuestra. Llamo a esta perspectiva esencialismo estadístico. Voy a sugerir que la tipicidad y la uniformidad fenotípica se consideran supuestos legítimos en muchas ciencias humanas, ya que el desarrollo biológico se interpreta como un proceso inherentemente conservador que utiliza sólo recursos (...) endógenos, mientras que la evolución se interpreta como un proceso de normalización que destruye la variación fenotípica. Llamo a esta visión perspectiva homeostática. Voy a criticar la perspectiva homeostática presentando argumentos apoyados en consideraciones teóricas y empíricas. En particular, voy a destacar dos prejuicios anacrónicos que se encuentran en el corazón de la perspectiva homeostática: en primer lugar, su visión monomórfica de las especies, así como su visión monoorganísmica y monogenómica del organismo; en segundo lugar, su compromiso con una visión causal endógena del desarrollo. Finalmente voy a argumentar que el esencialismo estadístico es problemático porque respalda los mismos prejuicios monistas y endógenos que caracterizan la perspectiva homeostática. Parafraseando a Margulis y Sagan, los científicos pueden engañarse fácilmente al descuidar la investigación sobre la diversidad humana y la plasticidad del desarrollo. A statistical version of the concept of human nature remains a major foundational concept in many branches of the human sciences. The kernel of the concept is that there exists a core of species-specific phenotypes that characterises biological species, including ours. I call this view statistical essentialism. I will suggest that phenotypic typicality and uniformity are considered legitimate assumptions in many human sciences because biological development is interpreted as an inherently conservative process utilising only endogenous developmental resources, while evolution is interpreted as a normalizing process destroying phenotypic variation. I call this view homeostatic perspective. I will criticise the homeostatic perspective by presenting arguments supported by both theoretical considerations and empirical evidence. In particular, I will emphasise two anachronistic biases at the heart of the homeostatic perspective: first, its mono-morphic view of species as well as mono-organismic and mono-genomic view of the organism; secondly, its commitment to an endogenous view of developmental causation. I will finally argue that statistical essentialism is problematic because it endorses the same monistic and endogenous prejudices characterising the homeostatic perspective. Paraphrasing Margulis and Sagan, human scientists can easily fool themselves by neglecting research on human diversity and developmental plasticity. (shrink)

RESUMENEl desarrollo embriológico es un fenómeno que ha inspirado la especulación filosófica desde temprano en la historia del pensamiento. Desde los tiempos de Aristóteles dos modelos conceptuales antitéticos se han utilizado tradicionalmente para comprender la embriogénesis: o el embrión posee ya una forma o estructura, o ésta se forma de nuevo en cada generación. Nuestro objetivo en este artículo es mostrar que el contraste entre la posición preformacionista y epigenética persiste a pesar de los formidables avances teóricos y experimentales de (...) la biología del desarrollo contemporánea. El preformacionismo y la epigénesis han perfeccionado constantemente sus posiciones en el curso de la historia con el fin de responder a los retos conceptuales de la época. Este continuo proceso de transformación ha dado lugar a una convergencia parcial entre las dos posiciones. Sin embargo, vamos a argumentar que, a pesar de los esfuerzos por conciliar ambas posturas, esta antinomia, que se erige como una de las más fundamentales de la biología, no será fácil de superar. ABSTRACTThe process of development of the embryo has inspired philosophical speculation since the advent of Western thought. Since the time of Aristotle two antithetical conceptual models have traditionally been used to understand embryogenesis: either form or structure is preformed in the embryo or it is newly formed with each generation. Our aim in this article is to show that the contrast between the pre-formationist and epigenetic positions persists despite the formidable theoretical and experimental advances of contemporary developmental biology. Pre-formationism and epigenesis have constantly refined their positions in the course of history in order to answer the conceptual challenges of each epoch. This process of continuous transformation has resulted in a partial convergence of the two positions. However, we shall argue that, despite the partial successes of this process of continuous convergence, one of the most fundamental antinomies in biology persists. (shrink)

It is frequently claimed that our species is responsible for climate change, for a new impending mass extinction, for destabilising ecosystems dynamics etc. These claims might be interpreted literally as meaning that it is our species, not merely its constituent organisms, that is causing climate change, biodiversity loss and ecosystem upheaval. Such literal interpretation depends on what kind of answer is given to the general theoretical question concerning whether supra-organismal biological entities such as groups, populations and species can be morally (...) responsible for anything as collectives. I shall argue that organismality is the biological property grounding species collective moral responsibility. The question is thus whether our species is organismal enough to make it a morally responsible causal agent. (shrink)