@scd @Rumraket @T_aquaticus @John_Harshman
This paper might be useful with regards to the discussion about the differences between nested hierarchies in biology vs designed objects. The 2 links are to the same paper, but the first is just a scan of a paper copy, so text can’t be highlighted, copied, or pasted. I put the second link in there for this purpose for those who feel they can overcome the terrible ethical quandary of avoiding a paywall.
https://sci-hub.tw/10.1662/0002-7685(2005)067[0283:bonbpe]2.0.co;2
The paper is published in “The American Biology Teacher”, a journal for (you guessed it) Biology teachers, presumably mostly those of the American persuasion. It discusses the pros and cons of the common classroom exercise used to teach students the basic principles of phylogenetics: constructing a phylogenetic tree by coding characters of (gasp) designed objects like nuts and bolts, screws and nails, etc. I myself experienced this exercise years ago, and I remember that the teacher made the point to emphasise both the utility of the exercise, but also the clear differences it had with actual biological phylogenetics. These differences are well-described in the paper, and it’s a fairly quick read.
The basic point has already been described in this thread already: producing phylogenies of designed objects will always be problematic because there are just so many different ways of producing the tree - different characters will give very different tree topologies. In contrast, actual biological organisms produce much more congruent trees because their sets of characters aren’t arbitrary, they’ve been shaped by a branching pattern of common descent.