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Comment by bee_rider | Hacker News Reader

I guess it depends on on why you are doing the clustering, right?

If you want to cluster animals that sort of fuzzily behave similarly together — if it looks like a duck and walks like a duck, it probably acts like a duck, haha.

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The point of making trees is almost always to understand the fundamental sources of phenotypic diversity and making simple models that explain how the new (complex, organismal) phenotypes arise, how they are shared through various forms of reproduction and gene transfer, and how those relate to molecular phenotypes.

Nobody that I am aware of is clustering things based on similar functionality simply to say "look, these two things are similar", without having some sort of "explanation".

Except phylogeny generally was used to categorize how hereditarily related things were. Whether sequence alignment or physical taxonomy are better determinants is perhaps an open question in some cases, although I’m firmly on the side of sequence alignment, since DNA is an important component of inheritance

The side you are on has already won. Sequence data are universally accepted in systematics as the ultimate arbiters of evolutionary relationships, just delve into the modern classification of any extant group. One example of where molecular evidence overturned physical evidence long thought to be unambiguous, leading to a complete and essentially uncontested taxonomic overhaul: coprinoid mushrooms. Morphological characters are still used in paleontology for obvious reasons, but again within a higher-level framework provided by molecular phylogenetics.

Really? Cool! This was still pretty much unresolved in 2003 when I worked in the area and I had been told people were still arguing about this recently.

Are you proposing that we apply the notion of duck-typing to plants?

If it acts like a classification scheme, we should treat it as a classification scheme!

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