Pattern Cladistics and the ‘Realism–Antirealism Debate’ in the Philosophy of Biology

Despite the amount of work that has been produced on the subject over the years, the ‘transformation of cladistics’ is still a misunderstood episode in the history of comparative biology. Here, I analyze two outstanding, highly contrasting historiographic accounts on the matter, under the perspective of an influential dichotomy in the philosophy of science: the opposition between Scientific Realism and Empiricism. Placing special emphasis on the notion of ‘causal grounding’ of morphological characters (sensu Olivier Rieppel) in modern developmental biology’s (mechanistic) theories, I arrive at the conclusion that a ‘new transformation of cladistics’ is philosophically plausible. This ‘reformed’ understanding of ‘pattern cladistics’ entails retaining the interpretation of cladograms as ‘schemes of synapomorphies’, but in association to construing cladogram nodes as ‘developmental-genetic taxic homologies’, instead of ‘standard Darwinian ancestors’. The reinterpretation of pattern cladistics presented here additionally proposes to take Bas Van Fraassen’s ‘constructive empiricism’ as a philosophical stance that could properly support such analysis of developmental-genetic data for systematic purposes. The latter suggestion is justified through a reappraisal of previous ideas developed by prominent pattern cladists (mainly, Colin Patterson), which concerned a scientifically efficient ‘observable/non-observable distinction’ linked to the conceptual pair ‘ontogeny and phylogeny’. Finally, I argue that a robust articulation of Antirealist alternatives in systematics may provide a rational basis for its disciplinary separation from evolutionary biology, as well as for a critical reconsideration of the proper role of certain Scientific Realist positions, currently popular in comparative biology.     

Synthesizing insight: artificial life as thought experimentation in biology

What is artificial life? Much has been said about this interesting collection of efforts to artificially simulate and synthesize lifelike behavior and processes, yet we are far from having a robust philosophical understanding of just what Alifers are doing and why it ought to interest philosophers of science, and philosophers of biology in particular. In this paper, I first provide three introductory examples from the particular subset of artificial life I focus on, known as ‘soft Alife’ (s-Alife), and follow up with a more in-depth review of the Avida program, which serves as my case study of s-Alife. Next, I review three well-known accounts of thought experiments, and then offer my own synthesized account, to make the argument that s-Alife functions as thought experimentation in biology. I draw a comparison between the methodology of the thought-experimental world that yields real-world results, and the s-Alife research that informs our understanding of natural life. I conclude that the insights provided by s-Alife research have the potential to fundamentally alter our understanding of the nature of organic life and thus deserve the attention of both philosophers and natural scientists.     

Meaning in Nature: Organic Manufacture?

The paper examines Marcello Barbieri’s (2007) Introduction to Biosemiotics. Highlighting debate within the biosemiotic community, it focuses on what the volume offers to those who explain human intellect in relation to what Turing called our ‘physical powers.’ In scrutinising the basis of world-modelling, parallels and contrasts are drawn with other work on embodied-embedded cognition. Models dominate biology. Is this a qualitative fact or does it point to biomechanisms? In evaluating the 18 contributions, it is suggested that the answers will shape the field. First, they will decide if biochemistry and explanatory reduction can be synergised by biosemantics. Second, they will show if our intellectual powers arise from biology. Does thinking use—not a language faculty—but what Marko? and colleagues call semiosis by the living? Resolution of such issues, it is suggested, can change how we view cognition. Above all, if the biomechanists win the day, cultural models can be regarded as extending natural meaning. On such a view, biomechanisms prompt us to act and perceive as we model our own natural models. This fits Craik’s vision: intellect gives us the alphanumerical ‘symbols’ that allow thoughts to have objective validity. For the biomechanist, this is explained—not by brains alone—but, rather, by acting under the constraints of historically extended sensoria.     

Ectogenesis and gender-based oppression: Resisting the ideal of assimilation

In a recent article in this journal, Kathryn MacKay advances a defence of ectogenesis that is grounded in this technology’s potential to end—or at least mitigate the effects of—gender-based oppression. MacKay raises important issues concerning the socialization of women as ‘mothers’, and the harms that this socialization causes. She also considers ectogenesis as an ethically preferable alternative to gestational surrogacy and uterine transplantation, one that is less harmful to women and less subject to being co-opted to further oppressive ends. In this article, I challenge some of the assumptions that underlie MacKay’s case in favour of ectogenesis by questioning whether the relationship between women’s capacity to gestate and birth children and gender-based oppression is as strong as MacKay makes it out to be. I subsequently argue that—even if MacKay’s reading of this relationship is accurate—ectogenesis is not a desirable means to end gender-based oppression. It embodies a strategy that could be used to pursue liberating projects that follow what Iris Marion Young defines as ‘the ideal of assimilation’, but that must be resisted. I then concur with MacKay’s contention that ectogenesis is better than gestational surrogacy and uterine transplantation. My argument is that many of the problematic issues that MacKay herself sees as features of these practices will not disappear with ectogenesis. Finally, I conclude that MacKay’s narrow focus on women’s biology and ectogenesis as a solution to gender-based oppression results in the overlooking of broader systemic issues that contribute to the upholding of oppressive norms.     

The tribunal of philosophy and its norms: history and philosophy in Georges Canguilhem’s historical epistemology

In this article I assess Georges Canguilhem’s historical epistemology with both theoretical and historical questions in mind. From a theoretical point of view, I am concerned with the relation between history and philosophy, and in particular with the philosophical assumptions and external norms that are involved in history writing. Moreover, I am concerned with the role that history can play in the understanding and evaluation of philosophical concepts. From a historical point of view, I regard historical epistemology, as developed by Gaston Bachelard and Georges Canguilhem, as a conception and practice which came out of the project, elaborated in France from the 1920s to the 1940s, of combining history of science and philosophy. I analyse in particular Canguilhem’s epistemology in his theory and practice of history of science. What he called ‘normative history’ is the focus of my analysis. I evaluate the question of the nature and provenience of the norm employed in normative history, and I compare it with the norm as discussed by Canguilhem in Le normal et le pathologique. While I am critical of Canguilhem’s treatment of history, I conclude that his philosophical suggestion to analyse the formation of scientific concepts ‘from below’ represents a useful model for history and philosophy of science, and that it can be very profitably extended to philosophical concepts.     

Lessons from EEO: Toward a Universal Evolutionary Curriculum

We propose a human-centered evolutionary curriculum based around the three questions: Who am I? Where do I come from? How do I fit in? We base our curriculum on our experiences as an evolutionary biologist/paleontologist (NE) and as a secondary level special education science teacher (GE)—and not least from our joint experience as co-editors-in-chief of this journal. Our proposed curriculum starts and ends with human biology and evolution, linking these themes with topics as diverse as the “tree of life” (systematics), anthropology, Charles Darwin, cultural evolution, ecology, developmental biology, molecular evolution/genetics, paleontology, and plate tectonics. The curriculum is “universal” as it is designed to be taught at all levels, K–16. The curriculum is flexible: “modules” may be expanded and contracted, reordered, or modified to fit specific grade level needs—and the requirements and interests of local curricula and teachers. We further propose that students utilize workbooks from online or printed sources to investigate the local answers to the general questions (e.g., “Who am I?”), while classroom instruction is focused on the larger scale issues outlined in the modules of our curriculum.     

Gould on Laws in Biological Science

Are there laws in evolutionary biology? Stephen J. Gould has argued that there are factors unique to biological theorizing which prevent the formulation of laws in biology, in contradistinction to the case in physics and chemistry. Gould offers the problem of ’’complexity‘‘ as just such a fundamental barrier to biological laws in general, and to Dollo‘s Law in particular. But I argue that Gould fails to demonstrate: (1) that Dollo‘s Law is not law-like, (2) that the alleged failure of Dollo‘s Law demonstrates why there cannot be laws in biological science, and (3) that ’’complexity‘‘ is a fundamental barrier to nomologicality.     

An Indigenous Philosophical Ecology: Situating the Human

Can Indigenous ecological knowledge contribute to major debates in Western science and philosophy? I argue that it offers a ‘philosophical ecology’ that works synergistically with Western eco‐philosophy and some streams of ecological science. This paper takes up the challenge offered by Val Plumwood: that anthropology can contribute to the work of re‐situating the human. It examines an ecological philosophy of mutual benefits, and shows patterns, and a broader meta‐pattern, in which life is both for itself and for others, and in which connectivity and stability are achieved through densely recursive benefits. I identify these and other contexts as areas for further dialogue.     

The emerging structure of the Extended Evolutionary Synthesis: where does Evo-Devo fit in?

The Extended Evolutionary Synthesis (EES) debate is gaining ground in contemporary evolutionary biology. In parallel, a number of philosophical standpoints have emerged in an attempt to clarify what exactly is represented by the EES. For Massimo Pigliucci, we are in the wake of the newest instantiation of a persisting Kuhnian paradigm; in contrast, Telmo Pievani has contended that the transition to an EES could be best represented as a progressive reformation of a prior Lakatosian scientific research program, with the extension of its Neo-Darwinian core and the addition of a brand-new protective belt of assumptions and auxiliary hypotheses. Here, we argue that those philosophical vantage points are not the only ways to interpret what current proposals to ‘extend’ the Modern Synthesis-derived ‘standard evolutionary theory’ (SET) entail in terms of theoretical change in evolutionary biology. We specifically propose the image of the emergent EES as a vast network of models and interweaved representations that, instantiated in diverse practices, are connected and related in multiple ways. Under that assumption, the EES could be articulated around a paraconsistent network of evolutionary theories (including some elements of the SET), as well as models, practices and representation systems of contemporary evolutionary biology, with edges and nodes that change their position and centrality as a consequence of the co-construction and stabilization of facts and historical discussions revolving around the epistemic goals of this area of the life sciences. We then critically examine the purported structure of the EES—published by Laland and collaborators in 2015—in light of our own network-based proposal. Finally, we consider which epistemic units of Evo-Devo are present or still missing from the EES, in preparation for further analyses of the topic of explanatory integration in this conceptual framework.     

EQUALITY AND THE DUTY TO RETARD HUMAN AGEING

Where does the aspiration to retard human ageing fit in the ‘big picture’ of medical necessities and the requirements of just healthcare? Is there a duty to retard human ageing? And if so, how much should we invest in the basic science that studies the biology of ageing and could lead to interventions that modify the biological processes of human ageing? I consider two prominent accounts of equality and just healthcare – Norman Daniels's application of the principle of fair equality of opportunity and Ronald Dworkin's account of equality of resources – and conclude that, once suitably amended and revised, both actually support the conclusion that anti‐ageing research is important and could lead to interventions that ought to be considered ‘medical necessities’.     

Molecular pathways and the contextual explanation of molecular functions

Much of the recent philosophical debate on causation and causal explanation in the biological and biomedical sciences has focused on the notion of mechanism. Mechanisms, their nature and epistemic roles have been tackled by a range of so-called neo-mechanistic theories, and widely discussed. Without denying the merits of this approach, our paper aims to show how lately it has failed to give proper credit to processes, which are central to the field, especially of contemporary molecular biology. Processes can be summed up in the notion of ‘pathway’, which is far from being just equivalent to that of ‘mechanism’ and has a profound epistemological and explanatory relevance. It is argued that an adequate consideration of pathways impels some rethinking of scientific explanation in molecular biology, namely its functional and contextual features. A number of examples are given to suggest that the focus of philosophical attention in this disciplinary field should shift from the notion of mechanism to the notion of pathway.     

Forty years of research on the assembly and infection process of bacteriophage

This short biographical note was written as part of the lead-in material for a festschrift kindly organized for me on the occasion of my 70th birthday. The collection of articles assembled in this issue range within the spectrum of the topics covered in the special issue ‘Multiscale structural biology—biophysical principles and practice ranging from biomolecules to bionanomachines.’ Here I describe some of the high points of my 40 years of research science conducted in the USA, Switzerland and Japan. I also use this opportunity to express my sincerest thanks to my former colleagues and the very many contributors who so kindly contributed to this special issue.     

The problem of teleology in biology as a problem of biology-teacher education

The paper sketches the ways ‘the problem of teleology’ appears in pupil-texts, teacher-guides, and college-level texts. Excerpts from the literature in the field of philosophy and history of science are then quoted, which illustrate that ‘the problem of teleology’ cannot be handled dogmatically, as if the issues were indisputable. It is pointed out, that teacher-education does not enable the prospective teacher to analyse the teacher and pupil texts objectively and critically as to their philosophical implications. Suggestions are made which might alter this situation.     

Interview with Sydney Brenner

The following text is an edited version of a recent interview with Sydney Brenner who has been at the forefront of many developments in molecular biology since the 1950s. It provides a participant’s view on current issues in the history and epistemology of molecular biology. The main issue raised by Brenner regards the relation of molecular biology to the new field of systems biology. Brenner defends the original programme of molecular biology—the molecular explanation of living processes—that in his view has yet to be completed. The programme of systems biology in contrast he views as either trivial or as not achievable since it purports to deal with inverse problems that are impossible to solve in complex living systems. Other issues covered in the conversation concern the impact of the human genome sequencing project, the commercial turn in molecular biology and the contested disciplinary status of the science.     

Bioethics,politics and the moral economy of human embryonic stem cell science: the case of the European Union's Sixth Framework Programme

Public communication of science is still largely conceptualized within a ‘transfer’ paradigm that describes it as a displacement of results and ideas from the specialists to the lay public, problematizing the public, the media, (sometimes) science, but very rarely the notion of communication itself. This paper is a preliminary attempt to see if the discourse about genes and the genome can help us to problematize the concept of communication in relation to science, rethink our models of public communication of science and, more generally, the metaphors we employ to describe communication. It is suggested that the relationship between science and the public could be understood better by viewing communication through metaphors drawn from contemporary biology, e.g. as ‘cross‐talk’ between the specialist and public discourse or as a ‘double helix’ coupling the two dimensions under certain conditions.     

Technologies of immortality: the brain on ice

One of the first envatted brains, the most cyborgian element of J. D. Bernal’s 1929 futuristic manifesto, The world, the flesh and the the devil, proposed a technological solution to the dreary certainty of mortality. In Bernal’s scenario the brain is maintained in an ‘out of body’ but ‘like-body’ environment—in a bath of cerebral–spinal fluid held at constant body temperature. In reality, acquiring prospective immortality requires access to very different technologies—those that allow human organs and tissues to be preserved in a quite ‘inhuman’ life-world—the cryogenic storage chamber. Like Bernal, today’s cryonicists consider that immortality can be secured through preservation of the brain alone. In this article I trace attempts to preserve or suspend life, and especially brain function, through the application of new ‘technologies of immortality’. Drawing together historical information on the development of refrigeration, cryopreservation, transplantation, and nanotechnologies, I explore the uneasy relationship between cryonics and the technology on which it depends for its success—cryogenics. In so doing, I argue that the ability to successfully realize the science fiction fantasy of human immortality will rest on a moral and scientific parasitism: the capacity to use the biotechnological artifacts or proxies—cryogenically preserved brains, archived brains, tissues, and immortalized cell lines—derived from the dead, in order to prolong life.     

Procedural understanding in biology: the ‘thinking behind the doing’

Several developments in science education aim to improve pupils' ability to ‘think scientifically’. This paper argues for the explicit teaching of the ideas that pupils need to ‘think about’ to do this; ideas related to the design of investigations and the collection, presentation, analysis, and evaluation of the resulting evidence — ideas which are important both for pupils who continue to study or work with biology and for all pupils to become biologically literate. This paper considers some of the concepts of evidence which are particularly important to biology, and discusses how and why the ideas could be taught.     

A user's guide to animal welfare science

Here, I provide a guide for those new to the burgeoning field of animal welfare science as to what this comprehensive, relatively young discipline is all about. Drawing on all branches of biology, including behavioural ecology and neuroscience, the science of animal welfare asks three big questions: Are animals conscious? How can we assess good and bad welfare in animals? How can we use science to improve animal welfare in practice? I also provide guidelines for an evidence-based approach to welfare issues for policy makers and other users of animal welfare research.     

The proximate/ultimate distinction in the multiple careers of Ernst Mayr

Ernst Mayr's distinction between “ultimate” and “proximate” causes is justly considered a major contribution to philosophy of biology. But how did Mayr come to this “philosophical” distinction, and what role did it play in his earlier “scientific” work? I address these issues by dividing Mayr's work into three careers or phases: 1) Mayr the naturalist/researcher, 2) Mayr the representative of and spokesman for evolutionary biology and systematics, and more recently 3) Mayr the historian and philosopher of biology. If we want to understand the role of the proximate/ultimate distinction in Mayr's more recent career as a philosopher and historian, then it helps to consider hisearlier use of the distinction, in the course of his research, and in his promotion of the professions of evolutionary biology and systematics. I believe that this approach would also shed light on some other important “philosophical” positions that Mayr has defended, including the distinction between “essentialism: and “population thinking.”