> All taxonomies are broken, full stop. Your categories are gonna be completely wrong and everybody’s going to argue over every single thing. There is no such thing as a tree. Is this a serious statement? If so, wouldn't it be incompatible with the theory of evolution? Would an alien taxonomy of human binary numbers not be a legitimate tree?
It's very much not. The thing is that every model is a lie, but they can often be very useful lies. The reason we use taxonomic trees is because they're "good enough" but there are tons of places where this really breaks down.
For example, horizontal gene transfer is a huge problem in microorganisms. If you take a soil fungi from one environment and put it in a completely new one it'll become so stressed out that it somehow increases it's rate of HGT and can borrow genes from completely different clades of life like bacteria or algae. HGT actually happens at more macro scales as well. Many of our GMOs take genes from bacteria and put them into plants. Parasitic plants like dodders are known for taking (and spreading) genes from the wide variety of plants it can parasitize (though this might be the wrong word to use given that we now know it plays a host of beneficial ecological roles to its hosts like acting as an above-ground myccorhizal network allowing plants to "talk" to each other). We also know that HGT is quite common across completely unrelated fish and sometimes we even have certain animals, like the hoatzin (Opisthocomus hoazin), that push scientists to completely reevaluate their "tree of life" assumptions[0] (aside: this one's particularly bizarre because it even looks like a medieval depiction of a hybrid beast that took different parts of different animals and mashed them together).
Another more obvious problem is just simple hybridization. It can happen across species with regularity (especially in some plant families), but over the deep history of time much larger jumps seem less "rare". On the micro scale it happens so often that "species" is rarely a useful category. Both botany and microbiology often refer to "species complex" instead
Additionally, it's not really clear what an "organism" often is. For example, lichen are actually a partnership between algae and fungi but are given their own species name. Neither of the two can live without each other. And actually we're finding that it's basically a whole ecosystem of many different algae and a fungi. That might not seem as complex but consider that millions of years ago a germ ate another germ and that eaten germ continued to live and reproduce inside it and eventually came to be known as "mitochondria" and form the basis of basically all animals and plants. To this day they have their own DNA but their reproduction is completely tied to us. Also consider the fact that a human is actually mostly germs. Germs outnumber the number of cells in your body (well this can vary based on antibiotic treatments or how long since your last shit). These complex ecosystems that play critical roles in our skin, eyes, guts, and even brains are necessary to our survival. We wouldn't be able to EAT without them! Lastly, take the example of the man o' war. Similar to lichen, it seems at some point ~13 or so different animals came together and worked together so strongly that they essentially merged and became a single organism. Some of the parts of a man o war can even survive without the rest of the "colony" for a short while (imagine if your kidney could just do it's own thing). But, like lichen, it gets its own species name
As you can see there's a number of flaws in the "tree" view of evolution. It works well enough for most cases and that's why we still use it. But try looking up the debates around a taxonomy of human languages. In theory the same approaches should be able to be applied and the same problems (cultural equivalents of "HGT", "hybridization", and blurry lines between "symbiosis and dependency") can apply.
Edit: oh hole #4: ring species!
[0] https://www.newyorker.com/science/elements/the-bizarre-bird-...