[simiansays]

> 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?

[jmillikin]

The thing with taxonomies is that trying to make a category more precise tends to exclude things you want to include in it, and vice-versa. It is especially easy to find examples of this in nature, because nature has existed since long before humans had opinions about how things should be organized.

What is a cat? It's a small furry quadruped in family Felidae.

- Exception: cats may be quite large (lions, tigers).

- Exception: cats may have no fur (sphinx cats).

- Exception: cats may have fewer than four legs (e.g. due to injury).

Even questions that seem like they should be quite easy to settle, like "are these two gulls of the same or different species?", might be impossible to define formally due to things like <https://en.wikipedia.org/wiki/Ring_species>.

With the specific example of "no such thing as a tree", the category of plants that humans call "trees" isn't a genetically coherent group. Lots of different types of plants have woody stems and bark and leaves, and you can't group together all the things humans call trees without also including things that we definitely don't.

[simiansays]

I definitely understand that the majority of taxonomies are problematic for the reasons you cited. When OP said "no such thing as a tree", I thought OP meant a taxonomic tree, not a literal plant tree, hence my example of binary numbers! Thanks for clarifying.

That said, taxonomic groupings can have both wide consensus and be useful, can't they? (Hand on chin... monotremes? hominids??)

[jacobr1]

The CS specific analogy might be, "Abstractions are leaky," or more broadly the, "map is not the territory."

Any complex-phenomena that is modeled with with a simplification will have places where that simplification fails. But models can still be highly useful, you just need to choose an appropriate level of abstraction, accept and manage any tradeoffs with exceptions, and move to better paradigm if one emerges.

[jhbadger]

Although if you want to get get technical, even evolutionary relationships are only trees if you throw out some of the information that doesn't fit the tree. It's truer to speak of phylogenetic networks that can take into account things such as horizontal transfer of genes and recombination.

https://en.wikipedia.org/wiki/Phylogenetic_network

[KingMob]

As George Box supposedly said, "All models are wrong, but some are useful."

[all2]

I've pondered the "taxonomies as trees" as insufficient and broken. What I arrived at as "maybe this will work" is taxonomy as a high-dimensional sponge, where a thing may rest at a given point in high dimensional space (where the dimensions are characteristics of that thing) and may or may not be clustered with other things on certain axes.

Sort of like how word/semantic clustering works in LLMs.

This obviously isn't a fully formed idea, but it might make creating taxonomies easier? Taxonomic clusters? Something like that.

[bryanrasmussen]

should probably also reference metacrap here https://chnm.gmu.edu/digitalhistory/links/pdf/preserving/8_1... especially section 2.5 Schemas aren't neutral

[kirushik]

Well, this clearly references this wonderful article: https://eukaryotewritesblog.com/2021/05/02/theres-no-such-th...

The idea is that our taxonomy selects a group named "trees", but there's little internal coherence in that group, which probably results in more online hilly wars in the plant-loving communities than we the laypeople can think of.

See also: is Pluto a planet?

[dwohnitmok]

I don't think this article is referring to physical organisms known as trees (as your article does). It's talking about abstract tree structures, in particular:

1. There is a coherent parent-child relationship

2. Children have only one parent

3. Children have no lateral relationships with other children

4. Relationships are mediated through parents, not e.g. grandparent-child directly.

5. We can coherently differentiate between different children

etc.

All of these are assumptions that greatly simplify analysis and therefore useful in any situations, but almost always fail in some way on closer inspection.

More generally we go to the saying "all models are wrong, some are useful."

[throw10920]

I'm 95% sure that the author (who is on HN[1]) is at least referring to the article "There's No Such Thing As A Tree" in his line "There is no such thing as a tree." - regardless of the fact that the article as a whole isn't about trees made of wood.

It's possible that he's additionally making a double entendre about abstract tree structures.

[1] https://news.ycombinator.com/user?id=hwayne

[hwayne]

Yeah, I was thinking about biological trees. In retrospect, I should've gone with "there's no such thing as a fish."

[jerf]

My favorite example is "berry". Everything that you think is a berry isn't botanically a berry... but tomatos and bananas are.

OK... technically it's almost everything you think is a berry isn't. But it sure feels like it's everything.

[simiansays]

Haha yes please! I thought you were talking about literal taxonomic trees.

[culi]

> our taxonomy

What exactly do you mean by "our taxonomy". There's no plant order, family, or genus called trees. It's just a common plant form. Do you just mean some people's personal mental model?

[simiansays]

Yeah I definitely did not get the reference, I thought OP literally meant that taxonomic trees in general are useless and/or don't exist!

[ummonk]

Consider: https://en.wikipedia.org/wiki/Ring_species

[madhadron]

I spent some time working on replacing the formulation of descent as a tree of species with a chain-complete partial order of organisms. Then you start trying to define things like "species" or "strain" or "genus" on that and realize that they don't correspond to any typical clumping of graphs.

Someone else already linked to ring species. In microbiology, the definition of species is "stop asking, we agreed to stop fighting about that, no, really, la-la-la-la." Horizontal gene transfer between species is ubiquitous.

In the end I started talking about populations occupying a niche in a specific place at a specific time, and very cautiously tracing properties among linkages of those. But I'm also the one who kept insisting to my labmates that a gene is not a locus of DNA.

[jrochkind1]

The theory of evolution requires large and fundamental changes in organisms over time due to natural selection over diverse populations with characteristics being passed on by reproduction. Such that very different organisms can have common reproductive ancestors.

It does not in fact require a specific number of clearly delineated categories of organisms where all individual organisms are in one and only one category.

That part is a human invention to try to make sense of the world, rather than part of the mechanics of the world itself. The categorization is probably a necessary invention to try to make sense of the world in a scientific systematic way, and is also inevitably a broken inconsistent subjective biased over-simplified map of the territory.

[cratermoon]

I have a couple of sources that agree with the proposition that taxonomies are broken, linked below. The short summary is that they can be useful, but they are always just models of the real world. As such, they will always be broken in some way. Even the example of number is incomplete. Is infinity odd, even, or something else?

Voodoo categorisation and dynamic ontologies in the world of OER: https://web.archive.org/web/20190505064655/https://blog.mood...

Ontology is Overrated: Categories, Links, and Tags: https://web.archive.org/web/20070119210402/http://www.shirky...

[ajuc]

Taxonomy is just bureaucracy, evolution is real and breaks taxonomy, because evolution works on the level of individuals and genes, when taxonomy works on leaky abstractions called species and groups of species.

[btilly]

Where in a taxonomy of humans would you put the estimated 8% of our genome that is from viruses trapped in our DNA?

https://www.science.org/content/article/ancient-virus-may-be... https://www.discovermagazine.com/planet-earth/mammals-made-b...

[Errancer]

This would be incompatible only if we require realistic interpretation of our taxonomies and theory of evolution can be true regardless of our (anti)realistic commitments.

[dragonwriter]

> If so, wouldn’t it be incompatible with the theory of evolution?

It would be incompatible with viewing some past views of the mechanisms of evolution as complete; the “theory of evolution” beyond broad outline is something of a moving target that accommodates things like the ways in which taxonomies are approximate abstractions that aid in discussion rather than exact descriptions of reality.

[darksaints]

What is the difference between a biological mutation and a new species? There are thousands of years of grey area between the two. The Theory of Evolution is a tree-like model to summarize billions of years of biological mutations into neat little branches, but we essentially have to ignore the vast periods of grey area in order to turn that into a tree.

[spenczar5]

Are you sure evolution is tree like? https://en.m.wikipedia.org/wiki/Convergent_evolution

That said, some categories are real, precise, and useful, like integers vs reals vs complex numbers.

[masklinn]

Convergent evolution doesn't make evolution non-tree-like, that's just a tree with similar-looking branches or leaves at different locations. Pretty standard really. Convergent evolution makes taxonomy less tree-like.

Carcinization is a good example: it makes lots of things crab-like, so from a surface taxonomic point of view a flattop crab, a coconut crab, and marbled crab are all pretty crabby. But they're completely different evolutionary lineages, and only one of them is a "true crab".

Where evolution gets less tree-like is MGEs (https://en.wikipedia.org/wiki/Mobile_genetic_elements) as some of them can move between branches.

[spenczar5]

> Convergent evolution makes taxonomy less tree-like.

Yes, exactly. "All taxonomies are don't broken" is not at all "incompatible with the theory of evolution," is the point. The taxonomic layer is pasted on top.

[simiansays]

Sorry, as stated above I misunderstood "There is no such thing as a tree." to mean that OP though taxonomic trees were fundamentally broken in some way, I misunderstood OP!

That said, if we had perfect knowledge of the speciation process over the years, would our taxonomy not be extremely close to a perfect tree, where every node has 2+ branches, and branches don't converge to being species-compatible for breeding?

I get convergent evolution, but among large (let's say 10g+) organisms, I'm not aware of convergent evolution resulting in compatible species that would not otherwise have been compatible?

I'm super rusty on this topic, but if there is theory that large organism actual DNA-level speciation (resulting in individuals who cannot reproduce together) has eventuated to convergence back to a new species (who can reproduce together), I'd love a source. I definitely could have very rusty knowledge on this but it seems intuitive to me?

[oldgradstudent]

I've been saying it for years. Life is not a tree, it's a DAG.

[klyrs]

Are real numbers actually "real" or do they just have good PR?

[culi]

> If so, wouldn't it be incompatible with the theory of evolution?

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-...

[simiansays]

I get convergent evolution, but among large (let's say 10g+) organisms, I'm not aware of convergent evolution resulting in compatible species (with fertile offsping) that would not otherwise have been compatible?

I'm super rusty on this topic, but if there is theory that large organism actual DNA-level speciation (resulting in individuals who cannot reproduce together) has eventuated to convergence back to a new species (who can reproduce together with fertile offspring), I'd love a source. I definitely could have very rusty knowledge on this but it seems intuitive to me?

[culi]

I never once mentioned convergent evolution. Convergent evolution is irrelevant in modern phylogeny-based taxonomy. I'm talking about the actual genes themselves

[cratermoon]

One word: siphonophores

[culi]

(I mentioned them already :P)

[cratermoon]

Oh, I missed it. Is man o' war (Physalia physalis) a siphonophore?

[culi]

Yes exactly! Sorry, should've specified that

[mcguire]

Have you ever heard a discussion betweeen biologists about where to put a given species in the family tree?

Taxonomies are a human construction.