Quote Originally Posted by squark View Post
A phylogenetic tree is basically a diagram of relationships, something that comes from observation and making categories. Iow, from taxonomy patterns developed and were noticed which then became an explanation and theory later. And this is how things typically progress or have progressed in Biology. It's how things have progressed in Astronomy, Physics etc and so on as well. Humans are good at noticing patterns, and organizing those patterns into a system gives you a basis from which to work. Why does the sun rise northeast in the summer and southeast in the winter? You start asking why, and that's where theories are developed.
That sounds more like phenetics, which is a classification of organisms based on observable similarities. Which is also pretty much what Socionics is.

A phylogenetic tree is not necessarily based on observations, since it requires an interpretation of what the DNA means. Which is a theory, not an observation.

Quote Originally Posted by squark View Post
So yeah, a category isn't an explanation, and if your categories are wrong, your explanations are likely wrong as well. Imagine if frogs were lumped in with fish because they both can swim, and otters and diving ducks . . . the categories themselves would be so wrong that you couldn't make heads or tails of anything. Darwin's theory developed from taxonomy, not outside of it. It isn't something separate, but rather a natural evolution itself: patterns --> theory behind the patterns. You can't start with a theory, or idea to explain patterns if you don't know what the patterns are.
I think you have the cart before the horse. We make categories because we have explanations of some kind (which may only exist in our heads) in order to categorize them in a certain way. We may rely on observable similarities, or we may rely on non-observables, such as interpretations of what the DNA means. And those require theories to do so.

The point is that you couldn't possibly have come up with Darwin's theory of evolution by just categorizing similarities. No amount of categorizing would have come up with that. It required a completely new way of thinking that things gradually evolved into something different, as in, there are similarities, even though there are no immediate similarities between them. You'd have to take a guess and imagine how things were in the way back before time. This required a bold guess to make that giant leap.

It couldn't have been done with an observation, but it could be done with a theory. This is why Darwin made a guess, and not just recognize some patterns or categorize a bunch of organisms.