Nah they aren't. The 'tree' of life is more of a full-fledged graph and the whole kingdom-order-genus-species thing is muddy and ill-defined. Most of the 'hierarchy' we find in natural systems is just our own projected deformation of much more complex relationships.

> the whole kingdom-order-genus-species thing is muddy and ill-defined

Well yes, it's somewhat an arbitrary construct for human convenience, but isn't much of the muddiness down to our limited understanding of the true relationships?

Regarding "cadherin/catenin or how epithelia are formed to see how a tissue is much more than a bundle of cells." could you give a link cos this is so far outside my area I really don't know what to look for (wiki article on Catenin wasn't very revealing of your point, sorry if I missed it)

Species S may no longer interbreed with species T, but that does not imply they’ve separated completely. There may exist intermediate species U...Z that link them together (https://en.wikipedia.org/wiki/Ring_species)

Viral infections modify host DNA, and can also incorporate host DNA -- this is a mechanism by which lateral gene transfer can occur between macroscopic organisms. The platypus has mammal, reptile and avian DNA, and they seem to have come about long after those branches diverged -- evidence that lateral gene transfers occur between macroscopic organisms.

Show me some paper on this. I mean an actual scientific paper, not a paper used to roll a yard-long spliff.

https://news.ycombinator.com/newsguidelines.html

(I took a quick look at your account's past comments and didn't see any previous history of this, which is great.)

https://news.ycombinator.com/newsguidelines.html

Regardless, horizontal gene transfer certainly does happen.

But then accidentally discovered this about gene transfer albeit in another area: https://www.sciencedaily.com/releases/2018/07/180709101216.h...

"This process is called horizontal transfer, differing from the normal parent-offspring transfer, and it's had an enormous impact on mammalian evolution." For example, Professor Adelson says, 25% of the genome of cows and sheep is derived from jumping genes.

OK, thanks!

Okay I suppose that it becomes a DAG if you zoom into the actual ancestral relations between individual organisms (which is where things become muddy). And I guess the concept of 'species' kind of forces a tree structure upon this DAG (although not exactly, but then the biologists didn't think to use a definition that provably produces a tree, in fact being of the same species isn't even an equivalence relation).

This hierarchical way of thinking is only designed for humans - because it helps us think more clearly. It's a crutch when you're attempting to learn, but at some point it becomes a hindrance when you want to run.

Now, mapping non hierarchical things to a hierarchy works well. But imposing that as a truth fails miserably.

But, if I understand it correctly, nominal hierarchies can also scale really well, like DNS addresses.

My point is imagine if the network had to only have the organization that is present in dns names.

Root, TLD, domain holder, sometimes further delegation depending on the domain holder.

For most of the cases, you will never be hitting root at all.

If the system was as hierarchical as it was proposed in the parent it would never be stable enough to work due to a single point of failure at root.

Ergo, hierarchies are not natural.

I use it all the time and find it perfectly abstracts things. Yes you can shoot yourself in the foot if you're not careful but wasn't that something we used to like about cpp? If a language is more expressive, I'd wager on average it's more likely to have bugs, but the benefit is an easier expression of skill and brilliance.

Again, they can be useful. No, they are useful. But they are fragile. And are but one way to look at things.

That’s why you throw up your hands and build property webs instead of heirarchies.1

It seems to me that a directed acyclic graph, rather than a tree, is a more accurate model in this case. (Directed because time always flows in one direction.)

A phylogenetic tree also fails to capture information about life that people might reasonable find interesting. Suppose for instance you want to study all organisms that fly. Bats, birds, insects and pterosaurs all fly[flew] but don't share common flying ancestors. The "flying organism" classification doesn't fit into that simple hierarchical tree.

How I model it, personally, is that as we learn more about the world, or learn about more things, we can increase the resolution of our categories, i.e. have more of them at a finer level of detail. From this process, my personal mental model goes, hierarchies tend to emerge as kind of "meta-categories." It's our attempt to overlay some predictability.

Mostly, it works okay, but when you hit a certain level of resolution, hierarchies get exposed as a very leaky abstraction. Busting out of that hierarchical mindset is, in my model, what happens when I "think outside the box:" Putting things which aren't "supposed" to be on the same level on the same level.

In my experience, thinking through things in this way leads to interesting places.

Even here, flows are often not entirely directed -- a river system experiences evaporation, precipitation, ground seepage, and aquifer flows, in addition to its dominant gravity-induced current. A tree has flows which originate at leaves (photosynthesis) and roots (water, mineral sourcing), as well as elsewhere (flowers, parasites and symbiotes, community flora and fauna). Similarly, evolutionary trees represent not only ancestral inheritance, but cross-species gene transfers -- bacteria, viruses, mitochondria, even other higher-order organisms (generally through an intermediary).

A true ontology to me is a largely nondirected graph. This may be a union of several directed graphs, a region of low-directedness within a larger directed space, or (fairly rarely) a near-universal truly nondirected system. Given that even cosmological megastructures are defined in terms of attractors and repellers, that is: gradients, truly nondirected spaces seem. likely rare. Though that's describing physical entities, conceptual spaces seem to me similar -- at least analogous, perhaps even more than that.

A tremendous risk in conceptual spaces is to equate some gradient with a moral, ethical, or social value gradient. This isn't -always_ a mistake, but it very frequently at least obscures more than it reveals, and can cause tremendous harm. The trait and tendency seems quite innate, dating. to earliest histories and likely earlier in the sociological and anthropological. It's all but certainly part of our neural wiring, "human nature", if not far deeper than that: a fundamental trait of representational modelling systems operating under constraints of perceptions, models, prior data, and processing and response capacity. Hierarchical value judgements are, by fundamental constraints of information systems theory, necessary (and very flawed) heuristics.

Or in fewer words: all models are wrong, some are useful.

Because both personal and sociocultural identities become wedded with values, they become rigid and defining. Good if certainty, speed, and consistency are required, not so much when flexibility and adaptation are.

In the context of TFA (and yes I'd submitted this): both hierarchical and ontological constructs are useful. I most often tend to think along the multi-hierarchical model -- that there are numerous centres, attractors, and repellers, with some phenomena behaving as both: a star or galaxy radiates light whilst attracting matter -- the same phenomenon is both a source and a sink.

I see networks of elements, trends, or traits, often with gradients not only of intensity but of complexity. This ... seems to serve fairly well.

Also worth noting: it's fascinating looking at classification schemes throughout history and which of those had central organising principles now seen as utterly unfounded. As well as some which have survived, or at least strongly suggested modern schemas.

For informational classifications associated with physical records such as the Dewey Decimal or Library of Congress Classification, a key contraint is that records must exist within physical space, at one and only one location. Looking at other classification systems (say, the LoC Subject Headings), this constraint does not exist, and works can be described, non-hierarchically, under multiple subjects simultaneeously. At the same time, many of the subject sections themselves have a strongly hierarchical structure, though also with notable idiosyncracies within specific areas. The law classifications, to my mind, most especially so.