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The construction and use of phylogenetic trees is central to modern systematics. But it is unclear exactly what phylogenies and phylogenetic trees represent. They are sometimes said to represent genea...
Modeling causal structures:Volterra's struggle and Darwin's success
Modeling Causal inference Volterra Predator-prey-model Darwin Coral atolls
2016/6/15
The Lotka-Volterra predator-prey-model is a widely known example of model-based science. Here we reexamine Vito Volterra's and Umberto D'Ancona's original publications on the model, and in particular ...
Natural Kindness
natural kinds homeostatic property cluster kinds HPC stability biological kinds projectibility
2016/6/15
Philosophers have long been interested in a series of interrelated questions about natural kinds. What are they? What role do they play in science and metaphysics? How do they contribute to our episte...
Fitness:Philosophical Problems
environment evolution fitness drift measurement natural selection propensity interpretation tautology
2016/6/15
Fitness plays many roles throughout evolutionary theory, from a measure of populations in the wild to a central element in abstract theoretical presentations of natural selection. It has thus been the...
On the Application of the Honeycomb Conjecture to the Bee’s Honeycomb
Honeycomb Conjecture Application Honeybees Lyon Colyvan Baker
2016/6/15
In a recent paper, Aidan Lyon and Mark Colyvan have proposed an explanation of the structure of the bee’s honeycomb based on the mathematical Honeycomb Conjecture. This explanation has instantly becom...
Eco-phenotypic physiologies:a new kind of modeling for unifying evolution,ecology and cultural transmission
evolutionary theory economics cultural transmission mathematical modeling philosophy of biology niche construction phenotypic plasticity ecology
2016/6/15
Mathematical modeling can ground communication and reciprocal enrichment among fields of knowledge whose domains are very different. We propose a new mathematical model applicable in biology, specifie...
Putting Process and Product Conceptions of Natural Selection and Genetic Drift to the Test
natural selection genetic drift process product outcome causation
2016/6/15
This paper argues for two claims. First, despite a persistent appearance to the contrary in the philosophy of biology literature, the question of whether natural selection and genetic drift should be ...
Immunity and the emergence of individuality
Immune system individual individuality organism superorganism evolutionary transition major transition symbiosis immunology philosophy of immunology complexity adaptation innate and adaptive immunity
2016/6/15
Since (Buss 1987), it has become clear that individuality is not to be considered as a given, but rather as something which needs to be explained. How has individuality emerged through evolution, and ...
The speed of change:towards a discontinuity theory of immunity?
Immunology philosophy of immunology continuity-discontinuity theory self identity self-nonself theory model molecular biology
2016/6/15
Immunology, though deeply experimental in everyday practice, is also a theoretical discipline. Recent advances in the understanding of innate immunity, how it is triggered, and how it shares features ...
Microbial diversity and the “lower-limit” problem of biodiversity
microbial diversity definition of biodiversity biodiversity scope biodiversity measure units of biodiversity definition of life
2016/6/15
Science is now studying biodiversity on a massive scale. These studies are occurring not just at the scale of larger plants and animals, but also at the scale of minute entities such as bacteria and v...
A number of areas of biology raise questions about what is of value in the natural environment and how we ought to behave towards it: conservation biology, environmental science, and ecology, to name ...
Emergence,closure and inter-level causation in biological systems
Emergence biological organisation downward causation constraints
2016/6/14
In this paper, we advocate the idea that an adequate explanation of biological systems requires appealing to organisational closure as an emergent causal regime. We first develop a theoretical justifi...
Distinguishing ecological from evolutionary approaches to transposable elements
transposable elements ecology evolution multivariate analysis philosophy of science
2016/6/14
Considerable variation exists not only in the kinds of transposable elements (TEs) occurring within the genomes of different species, but also in their abundance and distribution. Noting a similarity ...
Varieties of Noise:Analogical Reasoning in Synthetic Biology
Synthetic biology interdisciplinarity analogical reasoning engineering sciences complex systems noise
2016/6/14
The picture of synthetic biology as a kind of engineering science has largely created the public understanding of this novel field, covering both its promises and risks. In this paper, we will argue t...
I introduce a theoretical framework, due originally to Lewis and Skyrms, used in several talks in the PSA symposium "Signaling Within the Organism." I contrast sender-receiver systems as they appear w...