Categorial modal realism.

The current conception of the plurality of worlds is founded on a set theoretic understanding of possibilia. This paper provides an alternative category theoretic conception and argues that it is at least as serviceable for our understanding of possibilia. In addition to or instead of the notion of possibilia conceived as possible objects or possible individuals, this alternative to set theoretic modal realism requires the notion of possible morphisms, conceived as possible changes, processes or transformations.

What is Interpretability?

We argue that artificial networks are explainable and offer a novel theory of interpretability. Two sets of conceptual questions are prominent in theoretical engagements with artificial neural networks, especially in the context of medical artificial intelligence: (1) Are networks , and if so, what does it mean to explain the output of a network? And (2) what does it mean for a network to be ? We argue that accounts of "explanation" tailored specifically to neural networks have ineffectively reinvented the wheel. In response to (1), we show how four familiar accounts of explanation apply to neural networks as they would to any scientific phenomenon.

The role of purifying selection in the origin and maintenance of complex function.

Fitness contribution alone should not be the criterion of 'function' in molecular biology and genomics. Disagreement over the use of 'function' in molecular biology and genomics is still with us, almost eight years after publicity surrounding the Encyclopedia of DNA Elements project claimed that 80.4% of the human genome comprises "functional elements".

On causal roles and selected effects: our genome is mostly junk.

The idea that much of our genome is irrelevant to fitness-is not the product of positive natural selection at the organismal level-remains viable. Claims to the contrary, and specifically that the notion of "junk DNA" should be abandoned, are based on conflating meanings of the word "function". Recent estimates suggest that perhaps 90% of our DNA, though biochemically active, does not contribute to fitness in any sequence-dependent way, and possibly in no way at all.

What Is the Tree of Life?

A universal Tree of Life (TOL) has long been a goal of molecular phylogeneticists, but reticulation at the level of genes and possibly at the levels of cells and species renders any simple interpretation of such a TOL, especially as applied to prokaryotes, problematic.

Aims and methods of biosteganography.

Applications of biotechnology to information security are now possible and have potentially far reaching political and technological implications. This change in information security practices, initiated by advancements in molecular biological and biotechnology, warrants reasonable and widespread consideration by biologists, biotechnologists and philosophers. I offer an explication of the landmark contributions, developments and current possibilities of biosteganography-the process of transmitting secure messages via biological mediums.

Multilevel Selection Theory and the Evolutionary Functions of Transposable Elements.

One of several issues at play in the renewed debate over "junk DNA" is the organizational level at which genomic features might be seen as selected, and thus to exhibit function, as etiologically defined. The intuition frequently expressed by molecular geneticists that junk DNA is functional because it serves to "speed evolution" or as an "evolutionary repository" could be recast as a claim about selection between species (or clades) rather than within them, but this is not often done. Here, we review general arguments for the importance of selection at levels above that of organisms in evolution, and develop them further for a common genomic feature: the carriage of transposable elements (TEs).

Distinguishing between "function" and "effect" in genome biology.

Much confusion in genome biology results from conflation of possible meanings of the word "function." We suggest that, in this connection, attention should be paid to evolutionary biologists and philosophers who have previously dealt with this problem. We need only decide that although all genomic structures have effects, only some of them should be said to have functions.