Philosophy of Biology

Explanation in biology

by Arno Wouters

To appear in Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota (Eds.) Encyclopedia of Systems Biology (Springer). (http://refworks.springer.com/mrw/index.php?id=3051)

Biological function

by Arno Wouters

To appear in Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota (Eds.) Encyclopedia of Systems Biology (Springer). (http://refworks.springer.com/mrw/index.php?id=3051)

Functional explanation

by Arno Wouters

To appear in Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota (Eds.) Encyclopedia of Systems Biology (Springer). (http://refworks.springer.com/mrw/index.php?id=3051)

Engineering love

by Brian Earp

Savulescu, J. and Sandberg, A. (2012). Love machine: Engineering lifelong romance. New Scientist, 2864, 28-29.

Essay partially adapted from Earp, B. D., Sandberg, A., and Savulescu, J. (2012). Natural selection, childrearing, and the ethics of marriage (and divorce): Building a case for the neuroenhancement of human relationships. Philosophy & Technology, forthcoming [see "profile" box in article].

Available at the New Scientist website: http://www.newscientist.com/article/mg21428646.200-love-machine-engineering-lifelong-romance.html

New Scientist BIG IDEA section, May 2012.

With break-up and divorce a major part of modern life, it looks... more New Scientist BIG IDEA section, May 2012.

With break-up and divorce a major part of modern life, it looks like we may be outliving our inborn capacity to love. But there could be a way to outwit evolution and make love last.

Also available at New Scientist: http://www.newscientist.com/article/mg21428646.200-love-machine-engineering-lifelong-romance.html.

Applied Evolutionary Epistemology: A new method to enhance interdisciplinary research between the life and human sciences.

by Nathalie Gontier

pdf download here: http://kairos.fc.ul.pt/nr%204/Applied%20Evolutionary%20Epistemology.pdf

Biological Interests, Normative Functions, and Synthetic Biology

by Sune Holm

L’organisme : concept hybride et polémique

by Charles Wolfe

Texte soumis en 2010 ; à paraître dans  J.-J. Kupiec, dir., Une histoire critique de la biologie, Paris, Belin, 2012

Une réflexion sur le concept d'organisme, à cheval entre biologie et philosophie, et en tant que concept polémique. Une réflexion sur le concept d'organisme, à cheval entre biologie et philosophie, et en tant que concept polémique.

De la biologie moléculaire à la biologie des systèmes. Le rôle des rythmes et du temps biologiques

by Nicola Bertoldi

The problem addressed in this paper concerns the epistemology of chronobiology, i.e. the study of biological rhythms,... more The problem addressed in this paper concerns the epistemology of chronobiology, i.e. the study of biological rhythms, especially circadian ones, and their influence on organisms and ecosystems. I take this particular field of biology to be an instance of a scientific paradigm with two largely complementary concepts at its roots : the concepts of “program” (especially “genetic program”) and of “mechanism”. My analysis argues the case for this paradigm having emerged in the field of molecular biology, as a result of the interplay between biologists, physicists and philosophers. Hence, this paper defines it “the molecular paradigm”.
The first part of my work tracks the evolution of the concept of “genetic program” along a period stretching from the seminal work of Erwin Schrödinger (What is life ?) to the later writings of Jacques Monod and François Jacob. I argue as well that this concept is deeply connected to the notion of “mechanism” and that this special relation has been brought out in the last thirty years by a host of philosophical analyses, focusing mainly on molecular biology and neurobiology. These works have thus set a new trend in contemporary philosophy of science, “new mechanistic philosophy”, whose main concern is to describe and asses the way practicing biologists try to detect mechanisms and explain their workings.
The second part argues that chronobiology has assimilated this paradigm, thereby conceiving the study of biological rhythms as the search for molecular clocks. This claim is supported by the analysis of some founding papers in this field, like the one of Colin Pittendrigh on the existence of “free running” circadian rhythms in insects and microorganisms. To substantiate further my point, I review a paper of William Bechtel and Adele Abrahamsen, who account for the discovery of drosophila's “clock gene” per, located in some neurons of the Suprachiasmatic Nucleus (SCN), and of the corresponding system of regulation through a negative feedback loop in fully mechanical terms. I contend that this account is no more tenable, since the complex function of this gene cannot be reduced to the interaction of a cluster of independent mechanisms. Then, alternative accounts must be taken into consideration, such as the one of Denis Noble and the one of Pierre Bailly, Giuseppe Longo, Mael Montevil, the latter proposing to represent biological time not as an oscillatory pattern, but by use of a two-dimensional geometrical model. The paper interprets this model on a philosophical background that extensively draws on the tradition of french “historical
epistemology”, as well as on the “biological thought” of Immanuel Kant. Concerning the latter one the paper aims to highlight the link between his reflexions on finality and organization in the living world and the emergence of new trends in the biology of his time, such as the embryological theory of Caspar Friedrich Wolff. In doing so, the argument turns to the studies of Philippe Huneman, in order to show how Kant connects three fundamental concepts – finality, self organisation and contingence – in a coherent conception of the organism. This short detour into kantian philosophy proves useful to the paper's last conclusions, via the concept of “organisational closure” introduced by Matteo Mossio and Alvaro Moreno. In these conclusions, I propose a radically new conceptual interpretation of biological rhythms, not as properties of biological clocks, but as properties of “temporally closed systems”.

Is Conservation Biology a Scientifically Legitimate Discipline

by Sandra C. Neill

Co-authored with Mart R. Gross (University of Toronto). Presented at League for Innovation in the Community College STEMtech conference, Orlando FL 2010

La filosofía de la biología como campo interdisciplinar

by Antonio Diéguez

Published in 'Ludus Vitalis', vol. XIX, nº 36, pp. 261-265.

Breve contribución solicitada para el foro organizado por la revista Ludus Vitalis bajo el siguiente epígrafe:... more Breve contribución solicitada para el foro organizado por la revista Ludus Vitalis bajo el siguiente epígrafe: "Desde su práctica profesional, ¿usar lenguajes y discursos de disciplinas distintas a la suya ha resultado signficativo en su trabajo? Dicho de otro modo, ¿la interdisciplina es una necesidad y una posibilidad productivo o forma parte del catálogo de las buenas intenciones inscritas en la corrección política en boga?"

Fitness

by Timo Maran

Published in: A More Developed Sign. Interpreting the Work of Jesper Hoffmeyer (Tartu Semiotics Library 10), Favareau, Donald; Cobley, Paul; Kull, Kalevi (eds.), Tartu: Tartu University Press 2012, 147-149.

Slaying the Chimera: a Complementarity Approach to the Extended Mind Thesis

by Mirko Farina

Supervisors : Andy Clark, Julian Kiverstein, Tillman Vierkant
Examiners: Michael Wheeler and Mark Sprevak

The Rise and Fall of Biotic Nativeness: A Historical Perspective

by Andrew Hamilton

Co-authored with Matt Chew. Appears in Fifty Years of Invasion Ecology: The Legacy of Charles Elton, Edited by David Richardson.

From types to individuals: Hennig’s ontology and the development of phylogenetic systematics

by Andrew Hamilton

Contemporary phylogenetic systematics was framed, in part, as a response to a resurgent idealistic morphology in the... more Contemporary phylogenetic systematics was framed, in part, as a response to a resurgent idealistic morphology in the German‐speaking world in the first half of the 20th century. There were also conceptual and methodological challenges from Anglo‐American researchers who were skeptical about whether a phylogenetic approach to systematics could be made to work. This paper describes these challenges as a way of providing context for some ontological innovations made first by Walter Zimmermann and then by Willi Hennig. The principal argument of this paper is that what has become known as the individuality thesis played a much more important role in the conceptual foundations of Hennig’s version of phylogenetic systematics than has been widely appreciated. Understanding Hennig’s ontology illuminates his responses to objections to phylogenetic systematics from both sides of the Atlantic and sheds substantial light on the extinction part of the dichotomy rule. Although many have taken Hennig’s claim that parent species go extinct at speciation to be an arbitrary and biologically unrealistic rule, extinction of the parent follows directly from the way Hennig understands species and how they are individuated.

Review of The Species Problem by Richard Richards

by Catherine (Katie) Kendig

Kendig, Catherine (2012). “Review of The Species Problem by Richard Richards.” The Philosophical Quarterly 62: 247, 405–408.

Cross-Species Databases

by Sabina Leonelli

Published in Social Studies of Science, April 2012.

Models in philosophy of biology: a pragmatic approach

by Emanuele Serrelli

Serrelli E (2012). Models in philosophy of biology: A pragmatic approach. Logic and Philosophy of Science, forthcoming. ISSN 1826-1043

ABSTRACT. A pragmatic approach to models in philosophy of biology can be adopted in order to understand a given case... more ABSTRACT. A pragmatic approach to models in philosophy of biology can be adopted in order to understand a given case of scientific modeling. The approach consists, I argue, in three epistemological moves: (1) acknowledgement of the existence of many presently valid notions of what a model is; (2) explicit selection of the notion which is most suitable for the case of philosophical interest; (3) fidelity to the initial choice, although with the possibility to start over the analysis with a different notion. I illustrate the idea and need for a pragmatic approach in an example: adaptive landscapes in evolutionary biology. Then I get to the conditions of appropriateness of the approach.

Index:
1. Introducing the example: adaptive landscapes in evolutionary biology
2. Narrowing the usage of model
3. Reaction: defending the plurality of model
4. The umbrella effect
5. Semantic variability and extension: the metaphor incident
6. Where does a pragmatic approach make sense?

In what way can considering evolution contribute to a philosophical epistemology?

by Christian Spahn

Models for Prediction, Explanation and Control: Recursive Bayesian Nets

by Phyllis Illari

With Lorenzo Casini, Federica Russo and Jon Williamson.

Theoria 26(1) (2011): 5-33.

The Recursive Bayesian Net (RBN) formalism was originally developed for modelling nested causal relationships. In this... more The Recursive Bayesian Net (RBN) formalism was originally developed for modelling nested causal relationships. In this paper we argue that the formalism can also be applied to modelling the hierarchical structure of mechanisms. The resulting network contains quantitative information about probabilities, as well as qualitative information about mechanistic structure and causal relations. Since information about probabilities, mechanisms and causal relations is vital for prediction, explanation and control respectively, an RBN can be applied to all these tasks. We show in particular how a simple two-level RBN can be used to model a mechanism in cancer science. The higher level of our model contains variables at the clinical level, while the lower level maps the structure of the cell's mechanism for apoptosis.

Mechanisms are real and local

by Phyllis Illari

With Jon Williamson

In Causality in the sciences, edited by P. McKay Illari, F. Russo, and J. Williamson. Oxford: Oxford University Press (forthcoming 2011).

Mechanisms have become much-discussed, yet there is still no consensus on how to characterise them.  In this... more Mechanisms have become much-discussed, yet there is still no consensus on how to characterise them.  In this paper, we start with something everyone is agreed on – that mechanisms explain – and investigate what constraints this imposes on our metaphysics of mechanisms.  We examine two widely shared premises about how to understand mechanistic explanation: (1) that mechanistic explanation offers a welcome alternative to traditional laws-based explanation and (2) that there are two senses of mechanistic explanation that we call ‘epistemic explanation’ and ‘physical explanation’.  We argue that mechanistic explanation requires that mechanisms are both real and local. We then go on to argue that real, local mechanisms require a broadly active metaphysics for mechanisms, such as a capacities metaphysics.