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There’s no such thing as a tree (phylogenetically)

eukaryotewritesblog.com

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Re: There’s no such thing as a tree (phylogenetically)

#81

Post by HPsquared »

Zababa wrote: post #56
yesenadam wrote: post #13

Well, I thought this was a fascinating and well-written article. p.s. I learnt not long ago that there's no such 'thing' as an antelope: "The term antelope is used to refer to many species of even-toed ruminant that are indigenous to various regions in Africa and Eurasia. Antelope comprise a wastebasket taxon (miscellaneous group) within the family Bovidae, encompassing all Old World ruminants that are not bovines, c…

A good reminder that the map is not the territory. Lately I've started to see more and more "categories" in general as a very human construct, probably made to save on processing power when thinking about things. Reality is hard and very complex and you can't be thinking about all the details all the time.

"The Treachery of Images"

"The famous pipe. How people reproached me for it! And yet, could you stuff my pipe? No, it's just a representation, is it not? So if I had written on my picture "This is a pipe", I'd have been lying!

— René Magritte"

https://en.m.wikipedia.org/wiki/The_Treachery_of_Images

Re: There’s no such thing as a tree (phylogenetically)

#82

Post by pfdietz »

ajuc wrote: post #53
yesenadam wrote: post #13

Well, I thought this was a fascinating and well-written article. p.s. I learnt not long ago that there's no such 'thing' as an antelope: "The term antelope is used to refer to many species of even-toed ruminant that are indigenous to various regions in Africa and Eurasia. Antelope comprise a wastebasket taxon (miscellaneous group) within the family Bovidae, encompassing all Old World ruminants that are not bovines, c…

Biology is what happens when you try to decompile code written in assembler into OO language.

Clade computing.

Re: There’s no such thing as a tree (phylogenetically)

#83

Post by williamdclt »

da39a3ee wrote: post #73
bejelentkezni wrote: post #10

Earlier quoted context omitted.

I was under the impression that what made a tree was its woodenness so I was probably more of the target audience, and was impressed by the article.

You’re right that is what makes a tree. But don’t you feel that it’s obvious that different lineages of plants could acquire, and lose, woodenness independently of each other? And therefore 100% unsurprising that “tree” is not a monophyletic group.

Definitely not obvious. I have no idea how complex "woodiness" is, evolutionarily. It's like if you asked me "don’t you feel that it’s obvious that different lineages of animals could acquire, and lose, feathers independently of each other": probability is certainly non-zero but is it negligible or is it actually likely? No idea, I'm not an evolutionary biologist, and would read an article about it with interest

Re: There’s no such thing as a tree (phylogenetically)

#84

Post by verisimi »

The world is whatever it is.

The classification we overlay on what we perceive might (or might not) relate to physical reality. One is objectively real, one is theoretical.

We can have all sorts of theories about how things have come to be, but again these might (or might not) relate to reality.

We do not and cannot achieve a theory of everything, even if we kid ourselves that we can be papering over the cracks. Physical reality just isn't that sort of thing that we can know as well as all that.

And this doesn't even mention how our data perception in only on a narrow range. Nor the fact that our theories drive the observations, rather than observations driving the theories.

We can certainly hack bits, and get them to do things, understand nature's tricks and re-implement them in a different context. But really understanding it? Not so much.

PS very interesting that the author mentions 'neoteny'. This is where a 'species' stays in a prolonged juvenile state.

I've long thought that this sounds like modern life, where people do not want to take personal responsibility for their lives, but instead look to various authorities (government, corporations, their mum) to do it for them.

Re: There’s no such thing as a tree (phylogenetically)

#85

Post by camtarn »

da39a3ee wrote: post #74
samus wrote: post #9

I don't get the premise of the article. A tree is just a growth shape of a plant (plants are quite flexible regarding growth shapes, and often adapt to the environment), and a category that our minds place a plant species into. And its clearly an ancient ability common to all vascular plants to develop woody tissues. So why would we expect the tendency of a plant to become a tree to depend on its position in the phyl…

Precisely. I think this has been on HN before, or if not then another “Wow you’re gonna be surprised by this — trees aren’t monophyletic!” article. Given all the surprising examples of convergent evolution, and given human tendencies to give vernacular names to paraphyletic groups, and given that it’s obviously easy for plant lineages to increase or decrease the woodiness of their stems, it is baffling that anyone wo…

'Anyone'? Really?

I think you massively overestimate how much general knowledge about biology people have. For a lot (I would reckon most, but obviously I have no evidence of that) of people, terms like 'paraphyletic' are literally not in their vocabulary.

Re: There’s no such thing as a tree (phylogenetically)

#86

Post by dsr_ »

Zababa wrote: post #72
jacquesm wrote: post #63

Earlier quoted context omitted.

Categories are an optimization. It is also a leaky abstraction and there are a large number of errors in our thinking due to this optimization, which is often premature.

I'm not sure that it's premature. We use categories all the time, the time when they fail us seem to be rare in proportion.

Rare but often important.

We all work with computers all the time, and so we have a tendency to try to represent the universe in the simplest abstractions that capture the necessary detail for the project we are currently contemplating. When those abstractions fail to capture a necessary detail, it can be due to:

- a bad abstraction in the first place

- a new use for the representation that we hadn't thought about

- insufficient understanding of what we are trying to represent

I have seen all three of these situations repeatedly. They are all quite common.

Re: There’s no such thing as a tree (phylogenetically)

#87

Post by abrowne »

medstrom wrote: post #76
lproven wrote: post #66

Earlier quoted context omitted.

I dispute that. Speaking as a vegetarian, I think the key problem is that a lot of people don't know WTF a fish is. Q: Do you know what's the best gift to give a vegetarian who eats fish? A: A dictionary.

I don't see how the culinary definition of fish is related to cladistics. Even if they were, I don't see what you dispute, because they agree on this point; if "vegetarian" means "avoid meat" and "meat" means "flesh of animal", then vegetarian also means to avoid fish. Come to think of it, eggs would also be included in that definition.

A lot of Indian religious vegetarians don't eat eggs. E.g. https://www.nytimes.com/2021/12/13/world/asia/india-eggs-hin...

Re: There’s no such thing as a tree (phylogenetically)

#88

Post by bradrn »

This is one of my favourite articles! But as someone who has recently become interested in botany, what I find really crazy about this is that there are so many different ways for plants to become trees. A listing (surely incomplete):

• Normal trees, like what you see every day, with bark and wood and so on

• Monocots like yucca and aloe and Draecena, which have no bark and become woody through ‘abnormal secondary growth’ (which I don’t properly understand but has something to do with wood development being scattered throughout the plant instead of in a ring around the edge), and tend to avoid branching except when the growing tip is disturbed

• Other monocots like palm trees and Strelitzias, where the ‘wood’ is actually the bases of dead leaves wrapped very very tightly together, firmly enough to keep the plant standing up

• Fern trees, which… I’m not at all sure about, but seem to work on the same principle where leaf bases sorta get fused together. But the Dicksonia in my front yard seems to extrude some sort of thin fiber — does that perhaps help to hold the trunk together in some way?

• And then there’s things like papaya and banana and giant horsetails, which become trees without any wood at all, and have presumably innovated other ways of holding themselves up

It’s interesting to walk around my neighbourhood and realise that many of the trees I see have evolved almost completely different methods to get to the same result!

Re: There’s no such thing as a tree (phylogenetically)

#89

Post by camtarn »

causi wrote: post #46
inglor_cz wrote: post #37

Earlier quoted context omitted.

How many people know what clade means, though? I had a pretty rigorous and extensive course of biology in high school, we spent a lot of time poring over various details, but the word clade never even fell. (Granted, that was 1992-1996, so things might have changed.) I only met the expression cladistics and clade much later in some popsci literature.

Most HN readers I'd wager. Regardless, "Trees are not a distinct evolutionary group" or "Trees are not all related to each other" or any number of other accurate or semi-accurate headlines are better than "There's no such thing as a tree".

I would happily wager against you.

I made a similar comment further up the page: I think some people massively overestimate the amount of general knowledge people have about biology. Like the article says, a lot of people are still at the 'did you know a tomato is a fruit??!' stage.

Re: There’s no such thing as a tree (phylogenetically)

#90

Post by lordgrenville »

jakear wrote: post #6

I’ve become increasingly interested in what I think would be called “computational botany” if it were to be fleshed out. In looking at this and articles like it, and speaking with both trained and amateur botanists, a common thread is that the appearance of a plant has become increasingly detached from its scientific classification. A frequent refrain in nature hikes I’ve been a part of goes along the lines of: “this…

Weird use of the term "computational". More like "visual", maybe.
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