Homology

Thanks for blogging about this, John! As the special issue title The Importance of Homology for Biology and Philosophy indicates, the contributions address issues relevant for biologists (taxic and developmental accounts of homology, homologous functions in molecular and developmental biology, ...) as well as for philosophers (individuating behavioral and cognitive kinds, different notions of 'function', scientific concepts, ...). Let's see what responses we special issue contributors get from these two target audiences.

In line with Paul's "The phenomena of homology" paper (and with your thoughts about species), I plan to write a historical paper challenging the received wisdom that the advent of evolutionary theory introduced of a post-Darwinian 'evolutionary homology concept' distinct from the pre-Darwinian 'idealistic homology concept'. (This mirrors past philosophical and historical debates about the species concept.) Philosophically, my focus will be on the different components that make up a scientific concept--pointing to large continuity regarding several components of the homology concept, while also explaining the post-Darwinian innovations regarding other aspects of the concept. The aim is to illustrate this with a detailed historical study of the use of homology in different parts of the 19th century.

Yes, it is odd that those who think Darwin's idea of the world was evolutionary seem to want to make the assertion that he caused, not an evolution of ideas, but a revolution.

My slogan with respect to species is that people were not stupid bad observers before Darwin and they did not suddenly become sophisticated and smart after him. Yes, notions of species changed... gradually. Likewise notions like homology. These terms had a foundation in existing practice, that he and his followers found it necessary to explain, not redefine.

I believe you should call this something like "phenomenal biology" to get the idea across. Mind if I do?

I like Paul's talk about homology being a phenomenon or a set of phenomena, but find your above "homology is a phenomenal, rather than a theoretical concept" problematic (and your talk about species not being a "theoretical objects" potentially misleading). For it suggests using the logical positivist distinction between observational vs. theoretical terms (concepts, objects). This distinction was part of a foundationalist epistemology where observational facts were epistemically direct, certain, and unproblematic and which provided the foundational basis for the verification of theoretical statements. This conception erroneously assumed that there is a clear-cut distinction between observational and theoretical terms such that statements containing observational terms can be directly verified without any recourse to theory (they are not theory-laden). In his paper, Paul is fortunately clear about the fact that he does not maintain that homology assessments are not theory-laden (rather, his point is that homology can be assessed independently of the explanatory theories that attempt to explain the existence of homologies).

In this logical positivist context, one way to spell out observational (as opposed to theoretical) ideas was phenomenalism, which started out with subjective phenomena or sense data (features of the mind rather than the external world), and tried to construct knowledge of the external world (including theoretical objects) from this basis. So talk about 'phenomenal concepts' (or 'phenomenal biology') can be misread as either assuming that there is theory-free biological practice, or even as the endorsement of phenomenalism / idealism.

As it was a major intellectual achievement to establish the homology concept and the pre-Darwinian homology criteria were very sophisticated, and given this concept's central status for biological practice and theorizing, I am happy to call homology a 'theoretical concept'. Often, however, I simply call it a 'scientific concept' (so as to avoid the impression of endorsing a notion of theoretical concept as opposed to observational concept). What I will stress in the future paper is that homology criteria and how the homology concept was used in actual research practice are central features of this concept (even though there are more theoretical or explanatory aspects to it as well). This emphasis on practice aligns with your statement that "These terms had a foundation in existing practice".

These considerations also explain why Paul and I do not like loose philosophical talk about homology or species 'definitions'. What biologists call 'definitions' are simply (empirically defeasible) explanations of phenomena. For a philosopher, a definition is something that established the meaning of a term and the reference of a concept. Different definition entails different meaning and different concept entails different reference (raising incommensurability issues). Paul and I prefer to talk about different accounts (or conceptions) of homology, where different such accounts can express the same concept and refer to the same phenomenon.

I understand homology, in the doing phylogenetic analysis sense, to be an evolutionary novelty invented by the unique common ancestor of a lineage. The challenge to the phylogeneticist is sorting the homologies out from among the noise of parallel evolution, convergent evolution, loss of characters, etc, etc. Is this a reasonable understanding of the nature of homology in that context?