But before genetics existed, people had to rely on some notion of “similarity” between species. It strikes me as strange that this concept is now being denied, contrary to common sense.

Well, I’m not a biologist.

But as for “common sense”, it is the first victim of science, it doesn’t apply in the face of facts. Specifically here, if you go too far you end up in too erroneous “folk taxonomy”, as Wikipedia terms it. (I.e. “bugs” for spiders et cetera.)

In fact, I found the series of Wikipedia article informative and helpful in this. Various kinds of taxonomy _are_ used in biology, for various reasons. Cladistics happens to be helpful when you want to map to evolution, which is after all the basic biological process.

Sure, we share a more recent common ancestor, but in terms of the number of mutations that separate us, aren’t we farther? And why doesn’t anybody seem to think that should matter in classification?

I’m not sure what you are asking for, since similarity can be as helpful as dissimilarity.

For one example, cephalopod eyes shows how similar to ours but in some ways more efficient eyes can develop. For another, our similarity to rats helps us to research biology and medicine, while the dissimilarities (breeding cycle, proliferation, size, age, not too close to “moral kin”, et cetera) is what makes it possible.

So again, perhaps there are good measures for similarity respectively dissimilarity in function, and perhaps they can be used for classification if you want, see above.

Except that placozoa was a sister to us, instead of branching off before sponges. Bummer; at a ~ 11 k genes they were simpler than ~18 k gene sponges. Who ordered that?

as long as cells have been cooperating within a single body, they have needed to guard against the threat of cancer.

I thought the article argued that the relation to cancer, which is general (programmed cell death before oncogenes), applied only in animals (and perhaps fungus)? Plant cells are totipotent (plants can grow from cuts, while most or all animals can’t), which change the game.

I googled that galls can be caused by Agrobacterium tumefaciens (and related species), which bacteria inserts uncontrolled growth genes (and opine secretion promoters) in the specific cells they want to feed off by way of plasmids. But that is highly provoked and local, I don’t think the gall tumor cells will spread by themselves, it is more like a virus attack.