Daniel Liu

Phylogenetic models traditionally represent the history of life as having a strictly-branching tree structure. However, it is becoming increasingly clear that the history of life is often not strictly-branching; lateral gene transfer, endosymbiosis, and hybridization, for example, can all produce lateral branching events. There is thus motivation to allow phylogenetic models to have a reticulate structure. One proposal involves the reconciliation of genealogical discordance. Briefly, this method uses patterns of disagreement – discordance – between trees of different genes to add lateral branching events to phylogenetic trees of taxa, and to estimate the most likely cause of these events. I use this practice to argue for: (1) a need for expanded accounts of multiple-models idealization, (2) a distinction between automatic and manual de-idealization, and (3) recognition that idealization may serve the meso-level aims of science in a different way than hitherto acknowledged.

It has become customary to conceptualize the living cell as an intricate piece of machinery, different to a man-made machine only in terms of its superior complexity. This familiar understanding grounds the conviction that a cell's organization can be explained reductionistically, as well as the idea that its molecular pathways can be construed as deterministic circuits. The machine conception of the cell owes a great deal of its success to the methods traditionally used in molecular biology. However, the recent introduction of novel experimental techniques capable of tracking individual molecules within cells in real time is leading to the rapid accumulation of data that are inconsistent with an engineering view of the cell. This paper examines four major domains of current research in which the challenges to the machine conception of the cell are particularly pronounced: cellular architecture, protein complexes, intracellular transport, and cellular behaviour. It argues that a new theoretical understanding of the cell is emerging from the study of these phenomena which emphasizes the dynamic, self-organizing nature of its constitution, the fluidity and plasticity of its components, and the stochasticity and non-linearity of its underlying processes.

Philosophy of biology before biology Edited by Cécilia Bognon-Küss & Charles T. Wolfe   Table of contents Cécilia Bognon-Küss & Charles T. Wolfe. Introduction 1. Cécilia Bognon-Küss & Charles T. Wolfe. The idea of “philosophy of biology before biology”: a methodological provocation Part I. FORM AND DEVELOPMENT 2. Stéphane Schmitt. Buffon’s theories of generation and the changing dialectics of molds and molecules 3. Phillip Sloan. Metaphysics and “Vital” Materialism: The Gabrielle Du Châtelet Circle and French Vitalism 4. John Zammito. The Philosophical Reception of C. F. Wolff’s Epigenesis in Germany, 1770-1790: Herder, Tetens and Kant Part II. ORGANISM & ORGANIZATION 5. François Duchesneau. Senebier and the Advent of General Physiology 6. Tobias Cheung. Organization and Process. Living Systems Between Inner and Outer Worlds: Cuvier, Hufeland, Cabanis. Part III. SYSTEMS 7. Georg Toepfer. Philosophy of Ecology Long Before Ecology: Kant’s Idea of an Organized System of Organized Beings 8. Ina Goy. "All is leaf". Goethe's plant philosophy and poetry 9. Snait Gissis. ‘Biology’, Lamarck, Lamarckisms POSTSCRIPTS 1. Lynn Nyhart. A Historical Proposal Around Prepositions 2. Philippe Huneman. Philosophy after Philosophy of Biology before Biology Cécilia Bognon-Küss and Charles T. Wolfe. Conclusion  

The word ‘environment’ has a history. Before the mid-nineteenth century, the idea of a singular, abstract entity—the organism—interacting with another singular, abstract entity—the environment—was virtually unknown. In this paper I trace how the idea of a plurality of external conditions or circumstances was replaced by the idea of a singular environment. The central figure behind this shift, at least in Anglo-American intellectual life, was the philosopher Herbert Spencer. I examine Spencer’s work from 1840 to 1855, demonstrating that he was exposed to a variety of discussions of the ‘force of circumstances’ in this period, and was decisively influenced by the ideas of Auguste Comte in the years preceding the publication of Principles of psychology (1855). It is this latter work that popularized the word ‘environment’ and the corresponding idea of organism–environment interaction—an idea with important metaphysical and methodological implications. Spencer introduced into the English-speaking world one of our most enduring dichotomies: organism and environment.

This essay is an attempt to explain why Charles Sanders Peirce’s evolutionary metaphysics would not have seemed strange to its original 1890s audience. Building on the pioneering work of Andrew Reynolds, I will excavate the scientific context of Peirce’s Monist articles—in particular “The Law of Mind” and “Man’s Glassy Essence,” both published in 1892—focusing on the relationship between protoplasm, evolution, and consciousness. I argue that Peirce’s discussions should be understood in the context of contemporary evolutionary and physiological speculations, many of which were featured in late- 1880s issues of Open Court, sister journal to the Monist.