Convergent evolutions are fascinating. It also gives me a hope that we'll find other non-earth life that will have some things axiomatically common with us (due to convergence).
One question I’ve always had with the Drake equation is if it needs another line for scale. That we are roughly the same size, and experience time at roughly the same rate.
Would we notice an alien civilization sending a signal with a small message over the course of hundreds of years, at a bit a century frequency? Would we recognize each other as life if one is the size of a galaxy or the size of an atom?
I second the suggestion at the bottom of the (very enjoyable) post, pointing readers to the Crime Pays But Botany Doesn't content on YouTube - their passion and their approach are fantastic.
Minor warning, to my recollection, their language can be a little robust (that's a euphemism for sweary), but the creator is very interesting to listen to, and clearly very knowledgeable. Definitely a recommendation.
If anyone knows of something similar for UK flora and fauna then please point me to it.
If all plant life evolved into grasses, that would create an opportunity to do something different - to grow taller than grasses are able, for example. Monocultures are not optimal.
Tangentially related, but grasses are, in fact, a very recent evolutionary turn. We live in a very grass heavy epoch to the extent that it is hard for me to imagine a world with out grasslands. In some sense grasses seem primitive and foundational to us compared to a flowering tree like the magnolia, but no - grasses are actually really complicated and impressive organisms that filled an unexpectedly large niche.
There is such thing as a tree. There is such thing as a fish. Maybe even conceding that dolphins and whales aren’t fish was already too much. After all, cladistics isn’t everything.
The same thing we've always done: pattern matching based on characteristics with fuzzy boundaries. Cladistics is useful as a way of classifying things for biologists, but not very useful in day-to-day life. e.g. if someone says "let's go sit under those trees", or "let's chop down some trees for firewood", replying that there is no such thing is a tree is not a very useful response.
We don't have these arguments about bipeds because we never assumed that all bipeds shared an exclusive bipedal common ancestor.
I think the best alternative is to use different names depending on what we're highlighting (cladistics versus functionalism, for instance).
The -id/-ine suffix (e.g. ursid / ursine) seems to do this.
It would be clarifying to distinguish hodgepodge groupings such as "fish", and groupings such as "ducks" that are basically monophyletic with some exceptions removed from the group. Ducks are just small Anatidae.
Child pyschological development is always a entertainingly fuzzy science, but I think there's at least some good reason to believe that the ability to apply multiple categorization systems to a set of objects at a time is something that will take until the teen years to really come in. Some people never really grok it.
With my younger kids, I settled on just introducing the ideas of multiple overlapping systems, but not pushing on it too hard until they're older. They're only now getting to that age and I've been folding it in to some conversations lately more strongly. I think having some fun with it early as you are is a very strong approach to the topic.
I sort of dislike the framing of this sort of article, as well as the "actually nothing's really a berry" and similar culinary silliness, because this is a really important cognitive skill for higher-level thinking and introducing it with an approach virtually guaranteed to produce resistance and associating it with trickery rather than clear thinking is a real disservice, in my opinion.
This article, once it gets going, is good; I'm only complaining about the framing, not the content.
I will complain about the culinary version of this, where the trickery I'm referring to is "You think that a strawberry is a berry (often heavily implied, 'dumbass'), but really it's an aggregate accessory fruit (often heavily implied, 'as I am smarter for knowing than you')." The whole frame is wrong; it isn't really one thing or the other, it is both, and several other things besides. The multiple classifications all exist at once and they aren't better or worse than each other, they are better or worse for certain uses, and there certainly isn't one classification that is the "real" one and all the rest are fake. For people pushing this, it's like, yeah, you almost get the idea that multiple classifications can exist at once, but you've still completely missed the point.
For practical purposes, tomatoes are vegetables, peanuts are nuts, and palm trees are trees.
Tomatoes and peanuts are primarily known to be useful as food, and in the context of food, they fill the niche of vegetables and peanuts, respectively. Palm trees are useful pretty much only decoratively and to provide shade (unless you harvest them, which most people don't) so they have exactly the same utility as trees, making them trees.
It's interesting to think about how these things are biologically different from the other things in their practical category, but we strip away the utility of placing things into categories if we try to apply them outside of the context in which the category is... useful. So unless you're in a biology lesson (or you are a botanist, or just having fun with facts), tomatoes are vegetables.
Tomatoes are vegetables and fruit. "Fruit" is a botanical category, including plenty of things that are inedible for various reasons. "Vegetable" is a culinary category, including many things that are fruit (aubergine/eggplant, cucumber, and many more).
All fruits are vegetables; not all vegetables are fruit. Tomato is a fruit because it's the fleshy reproductive body of a plant containing seeds.
What's interesting about peanuts is that it seems to have the same allergenicity profile as nuts that cause allergies. Kind of odd for a legume, if you ask me.
If I hand you a tomato and you've never seen one before, how will "that's a fruit" guide you in your experience? I feel like common sense pragmatism is being ignored here.
- "Be it known that, waiving all argument, I take the good old fashioned ground that the whale is a fish, and call upon holy Jonah to back me."
- "To be short, then, a whale is a spouting fish with a horizontal tail."
He even notes right there that he knows about Linnaeus' work (a century old at this point) that concludes that whales are not fish. He simply decides not to care. Looks like Walrus is where he draws his line.
Came here to say the same:
"wtf how are bananas and pineapples trees? Shall we get him to look up the pictures or ask some AI model to get the images of wikipedia and to classify them?"
There are fern trees (Tree Fern to be precise), but they only grow in tropical regions. Bananas and pineapples are clearly grass with huge leaves.
I think it's interesting how I discover in this comment section that many people use the word grass for any member of the order Poales, where I would only use it for members of the family Poaceae, and even then only when speaking in very general terms when it comes to things like bamboo.
But bananas? Who calls bananas grasses? They're not even in Poales!
Humans care about wood, so they made tree (thing which produces wood) a category, as it can be used to build bridges, ships and other structures. Wood being dense also made it a better feedstock for charcoal (one can use grass, however).
As far as why trees don't seem to evolve into grasses, (or grasses into trees), it might be all about C3 vs C4 carbon metabolism, the latter being a complex structural system that pre-concentrates atmospheric CO2 before feeding it into the photosynthetic biochemistry (which is the right way to do artificial photosynthesis as well). This is apparently difficult to do in trees?
> "Since C4 photosynthesis was first discovered >50 years ago, researchers have sought to understand how this complex trait evolved from the ancestral C3 photosynthetic machinery on >60 occasions. Despite its repeated emergence across the plant kingdom, C4 photosynthesis is notably rare in trees, with true C4 trees only existing in Euphorbia."
All grasses are monocots (single part seeds) - https://en.wikipedia.org/wiki/Monocotyledon and its got things like corn, oats, lawn grasses, wheat, horsetail grass ... and sugar cane, bamboo, Joshua trees, and palm trees.
The big split between flowering plants is between monocots (grass, palm trees) and dicots (say a Rose bush and a Apple Tree.)
You can find non-trees and trees that are monocots and dicots and also non-flowering trees and non-trees for that matter. The main issue is that when plants get big they get woody and take on the characteristics of trees.
I like the irony of that title that a "tree" (in the computer science sense) is the basic unit of phylogeny with the caveat that it is broken at the top because the three operating systems for a cell are described here
they do show a tree on that page based on a particular set of genes but if you picked a different set of genes you would get a different tree because complex cells have a mixture of Archaea and Bacteria because they merged in some horizontal gene transfer event long ago.
Idk if you've dealt with palm wood but most of it is very very soft. You would not want to try to do anything you would recognize as structural framing with it.
Depends. What are you referring to? "Dicots" is not a category with any significance.
Grass is mostly characterized by having blades instead of leaves. Other plants would be called... whatever they're called. If you want a generic term, it's "plants".
If you want a term that refers to the specific function of covering what would otherwise be bare earth, that term is "ground cover", but ground cover is not restricted to plants. It applies just as well to gravel.
I'm confused. If you know clover is different from the green stuff with narrow leaves that grows in lawns, but you call clover grass, then what do you call the green stuff with narrow leaves?
Conifers (pine, cedar, fir) are trees but neither dicot or monocot, so outside the scope of this question.
Magnolias are trees and dicots (so expected).
Cabbage is a dicot but not a tree - not all dicots are trees. Maybe you misinterpreted my parent comment as me suggesting all dicots were trees? I more wanted to illustrate the key difference between grasses (which are monocots) and most trees
> The Jersey cabbage (Brassica oleracea longata) is a variety of cabbage native to the Channel Islands that grows to a great height and was formerly commonly used there as livestock fodder and for making walking sticks. It is also known as Jersey kale or cow cabbage, and by a variety of local names including giant cabbage, long jacks, tree cabbage and the French chour and chou à vacque.
> The 'Jersey cabbage' develops a long stalk, commonly reaching 6 to 10 feet (1.8 to 3.0 m) in height, and can grow as tall as 18 to 20 feet (5.5 to 6.1 m). ...
>As far as why trees don't seem to evolve into grasses
There is obviously no non-teleological answer for this, but it can be much much more straight forward than metabolism.
Think of plants as basically solar panels. We can think of the 'grass' phenotype as competing through r-type selection. Lots and lots of individuals, lots of surface area, short life cycles. Short bursty growth, convenient loss resilience, easy mobility.
'Trees' are the also optimizing for surface area (among other things), but are relying on k-type selection. Longer life-cycles, lower probability of successful reproduction, specialized pollinators, and very significantly, vertically stratified growth habit. Being an individual in a k-type species is like a very significant advantage for that individual, since its unlikely that the vast majority of k-type seeds will successfully reproduce.
Being k-type may not be more competitive for the species overall, but it may result for a selection bias at the individual member resolution, and so may be unlikely to be selected against.
There are many many advantages to lignification when your whole thing is basically being solar panels on a pole. It would seem extremely unlikely this has anything to do with metabolism other than 'doing more of it'. We already know why monocots don't make trees more significant than palms (read: vascular bundles and eusteles). My money goes to species level versus individual level selection in k versus r.
When I see the ground under an oak tree covered in acorns, most of which will be food, my first thought is definitely not that the tree is engaging in k-selection.
The tree relies on squirrels to disperse the acorns (hiding them and then forgetting where they were buried, or being eaten by a grue before retrieving the acorns).
Fruit is another common way to disperse seeds. Animals & birds eat the fruit, and then disperse the seeds with a dollop of fertilizer (poop).
Have you considered evolutionary selection as reason for c4 not being adapted by trees?
Grasses profit much more from growing quick than trees, where new opportunities (e.g. trees dying, fires etc) are rather rare & being able to grow extremely quickly wouldn't provide much of a benefit?
> ... being able to grow extremely quickly wouldn't provide much of a benefit?
After any substantial ground clearing event (eg bushfire, etc), wouldn't the subsequent "winners" be those who grew the fastest to capture the available sunlight + suppress their competitors?
So true. I live in an area that was clearcut a century ago. The battle of the first movers vs the usurpers is well underway if you know what to look for. It's a fight to the death, in very very slow motion.
My wife and I disagree quite strongly on the crossover point fairly consistently. I also saw some research showing a supposed gender gap in that observation. Whether or not the gender part is true it seems very much that different people crossover some of these at different points.
Welcome to "A thousand plateaus" by Gilles Deleuze and Felix Guattari.
ATP is a political book, albeit not a book about politics. But in the process of building their radical political theory, they build a radical general systems theory that's u-n-m-a-t-c-h-e-d. We have no choice but to study it.
When I read Wikipedia (or any treatment) on philosophy, I can't help but feel like laymen are trying to science without getting their hands dirty and while trying to sound fancy. I know that's the wrong take, but I can't get over it.
The linked article for this thread is about how "tree" biology keeps springing up and disappearing - the molecular biology, genetics, convergent evolution -- and how the human concept of "tree" doesn't really map cleanly. All of that, to me, is intuitive.
But philosophy is lost on me. Neither your linked Wikipedia article or the article on the book you suggest [1] make much sense to my non-philosophical science brain. My eyes just glaze over.
For me it is the other way around. Scientist sound like laymen in philosophy when they want to bring their data into a larger context. They stumble to explain why certain connection can/cannot be made and how they come up with the implications.
^This applies mostly to epistemology.
I like my philosophy in the format of what the youth calls 'schizo-posts'. Weird, out-there, grasping to find right words and closer to art than anything else.
I think philosophy is somewhat like math in that there is an attempt to create a logically self consistent system. Except it's not rigorous like math because the logic often have gaps that gets filled with observations (anecdotes), and it tries to explain the observed world.
Philosophy is also not science, since there is no attempt to rigorously test the theories with experiments or data.
So I lump philosophy with art. It's strongly tied with a person's sense of aesthetics as well as the culture around them.
The philosophical sciences (I use this word in the classical sense, not the narrow modern/Anglo-American sense) can be said to couple the deductive rigor of math with general empirical observation. For example, consider metaphysics. Metaphysics often begins from very basic and general observations like "things change", observations that, btw, everyone generally presupposes, including the empirical scientist. From these observations, we can infer what must be true about reality in general and necessarily so. Metaphysics gives us the principles characteristic of being as being, or being in general. Such principles are therefore true of all things. If this seems very abstract, you would be right, as metaphysics concerns the most general things. Concrete-minded people will have a difficult time.
Sadly, because of ignorance, many take philosophy to be some kind of idle speculation or some kind of put on where anything goes. This may be a result of either bad experiences or simply a lack of preparation to understand what is being said. Also, certain philosophical "schools" seem to be notorious for their unintelligibility (Derrida has this reputation). But read someone like Aristotle or Thomas Aquinas, or better yet, recent commentators and didactic works, and you will breathe fresh air and feed your mind. Perhaps it won't be easy, but the clarity and value are there and there is plenty to chew on.
Philosophy also investigates the entailments of various held positions. For instance, your view of philosophy, science, mathematics, aesthetics, of what constitutes knowledge, etc, all very much present in your comment, all fall under the jurisdiction of philosophy. The assumptions you are making are philosophical in nature and they have profound logical consequences that make shock you and cause you to revise your views. For instance, a kind of quasi-/amateur positivist, scientistic materialism seems to be popular on HN. But a rather modest philosophical examination shows that logical positivism, scientism, and materialism are all self-refuting or incoherent. You can't escape philosophy. You can either do it well, or do it poorly.
You might enjoy reading at least a summary of existentialism. It is somewhat anti-scientific at its root - but like economics - philosophy exists in a somewhat untestable area. One cannot make a laboratory of the mind or use human beings as it’s lab rats.
Physics and maths tend to poopoo any line of thinking which considers human experience - and there is amazing utility in that! No opinions are important for calculation of a trajectory. However, human experience does exist, and operating rationally on it, despite the lack of ability to experiment, leads one into a world that mathematicians might scoff at, but is still a completely valid field of inquiry.
People will say “philosophy is a soft science! No experiments!” Without understanding that experiments cannot be done in this realm.
I recommend Michael Segrue on YouTube - his lectures are fantastic as an intro to philosophy. Particularly his into to Kierkegaard touches on the birth of existentialism out of the furnace of pure scientific rationality.
> One cannot make a laboratory of the mind or use human beings as it’s lab rats.
That isn't the only way to subject philosophical ideas to empirical scrutiny, but whenever people use the historical evidence to determine things like how well different economic systems behave, for example, all of a sudden a lot of people get very angry and defensive and refuse to acknowledge the validity of prior experience.
> People will say “philosophy is a soft science! No experiments!” Without understanding that experiments cannot be done in this realm.
Some kinds of philosophy can be experimented on in some respects. For example: Does unquestioning obedience produce an ethical system that minimizes arbitrary killings? Well, I think we can look to the historical record and find the answer to that one, and conclude that it doesn't.
More deeply, though, how do we conclude that we care about arbitrary killing? That's a kind of question that we can't answer through experimentation, because the world doesn't outright tell us what values we should adopt. The most we can do is reason through the problem and then use experimentation (even retrospective experiments, as in history) to try to figure out which ethical systems support those values best.
That said... We're not blank slates. We're humans, we're social animals, so we care about certain things instinctively and, thus, some ethical systems are more humane than others in their outcomes.
> but whenever people use the historical evidence to determine things like how well different economic systems behave, for example, all of a sudden a lot of people get very angry
I mean, I tend to agree here with the straw man! That's why, for example, when arguing against commonwealth planning, one can't point at the Soviet Union as an example. One instead has to start from epistemology[1]! Then, folks don't respond with anger, they respond with glazed eyes.
> like laymen are trying to science without getting their hands dirty and while trying to sound fancy. I know that's the wrong take, but I can't get over it.
It's actually the reverse—multiple sciences started out as subfields of philosophy, that got useful enough on their own that they were peeled out into their own thing. It would be more useful to think of as philosophy as a soup of proto-sciences that are developing, that some might prove useful, and some might die out.
That's not really all philosophy is, but at least it's a more historically accurate way to look at it.
> Whereas the other subfields of philosophy don't (yet) have ways to fully validate them, and/or make them reproducible?
I think it depends on the field. Reproducibility is more of a recent concern, whereas this process has been going on since the ancient Greeks, I'm sure.
Probably more recently the criterion is "commercial value".
What do you mean their general systems theory is unmatched? Unmatched for what? I have read a bunch of D&G (as well as D on his own) and generally enjoy their writing, but I find it basically useless in my every day life and work (software engineering), my attempts to understand science and the world, etc. For example the "body without organs" is a cool idea that unites a lot of seemingly disparate phenomena, but other than that it kind of useless. It does not lend itself to making predictions, drawing causal connections between things. I don't think it's even a good intuition pump, in Dennett's sense. Most of the "use" of D&G's philosophy that I'm familiar with boils down to "oh hey this thing is kind of rhizomatic and look at how it antagonizes capitalist structures". Would love to be proven wrong, since I spent hundreds of hours and thousands dollars getting an education with a strong emphasis on this kind of stuff.
I think this is basically the point. Understand the world around you, and especially the connections and influences between different components of a system (broadly defined), to form and verify more holistic, nth-order models rather than disconnected, first-order-only analyses.
I think it goes beyond "cool idea" and really strikes at the same kinds of intuitions that many on HN appreciate as regards simple models that explain complex phenomena. In this sense, then, D&G's work is a sort of "meta-model" for guiding intuitions when building specific models about specific systems.
It is not a predictive framework. I guess I would call it an "ontological/architectural" framework.
For me, the sense in which it "unites a lot of seemingly disparate phenomena" is not that different than the sense in which "purple" unites a lot of purple things. It is true that they are all purple, but ultimately not very interesting or useful. Of course as a concept it is more complex and richer than "purple" hence why academics are able to write so many books and articles using it. I just don't recall ever having read anything that used these concepts to describe phenomena X and then felt like I better understood phenomena X, other than that I know realized it was sort of rhizomey.
> I spent hundreds of hours and thousands dollars getting an education with a strong emphasis on this kind of stuff.
(I laughed)
> I find it basically useless in my every day life and work
D&G is of utility in architecture, for one. You need to have some philosophical decoration for your doodle. The art is in mapping bs to doodle. In general, useless philosophy is a faithful companion in bullshit fields. Where in software we could use D&G then? I suggest crypto space.
In software engineering, monkey patching and use-after-free are some examples of lines of flight. Broadly though, an ossified and financialized academy is never going to embody a rhizome. Check out the interview with the IDF commander who "use"s deterritorialization. If you want predictions, Nick Land was full of them
A rhizome, maybe. The article is about literal trees (e.g. dogwoods, oak) and not mathematical structures, but it has a decidedly philosophical bent, and I find the idea of rhizomes to be relevant to that, at least.
I’m not yet persuaded this is relevant, at all. This isn’t a case where hierarchy fails us: we have a perfectly good and natural hierarchical model of speciation based on descent from common ancestors. That model doesn’t give us the common-sense notion of a tree, but that’s fine: so much the worse for common sense.
If instead we used a D&G rhizome that “connects any point to any other point” — we’d be dropping the notion of time (ie, ancestors precede descendants). Which when we’re talking about evolution, seems bad.
If horizontal gene transfer were a big part of the story here, that’d be different. Or if your ecology has time travel, or interstellar exchange ala Butler’s Xenogenesis, then sure, rhizome away.
your concept of time is one which puts ancestry front and center as the obvious most important factor, but is in no certain terms the only method of interpretation. there are many other factors, and in fact, that reinterpretation is the point of rhizomatic thinking.
and that's exactly what we see in the article, right? if a species took a path A-B-C-D to exhibit features of D, and another took A-F-G-D and so also exhibits features of D, then isn't there more to the history there than simply genetic change via ancestry over time? there's a reason why convergent evolution is so weird and surprising.
epigenetics, for example, is an interesting manifestation of what sorts of new domains you can explore as you broaden the horizon for asking questions beyond "linear ancestry" or "natural heirarchy" - arborescent vs rhizomatic thinking. blasting out of these constraints is the process of deterritorialization/reterritorialization D&G put forward as necessary and essential.
To put this in a statistical paradigm; time is always an important predictor in your model of organism traits (outcome) but there also a whole lot of other predictors that sometimes, or often, are more important/correlated than time.
> and that's exactly what we see in the article, right?
I think we see the opposite! We start with a naive and non-hierarchical view of relatedness: trees are tall woody things, fish live in the water and have fins. And the piece argues that we should let go of our common-sense categories and use the descent-based ones, like the biologists do.
Anyway --- I didn't say that ancestry is the only factor. I said it was natural, and useful. Epigenetics is fascinating, really! But it's not 'blasting out' of anything, it adds a bit of detail and complexity around the edges. A sense of proportion is important; we shouldn't miss the forest for the...never mind.
The Axolotl tanks of Tleilaxu. I wonder if Frank Herbert got that from these creatures or is this some crazy coincidence that Axolotls are subjected to genetic 'shape shifting'.
Useful abstractions. Exploring their usefulness can be fun (the pedantic kind) and even sometimes illuminating.
Obviously right from the start "taxonomy" itself is arbitrary. A more universal tool than naming, establishing branches, starting and end points is the concept of "most recent common ancestor" [0]. From that nameless unclassified vantage point I find it interesting to see (as OP pointed out) how "woodiness" or "treeness" evolutionary speaking is clearly a "strategy" (convergent evolution) and nearly impossible to chase down "phylogenetically" through MRCAs. Intuitively before reading this article I would have guessed this to be more straightforward.
I worked in phylogenetics for a while and it was a pretty confusing area. Originally, phylogenetic trees (not the biological trees that are the subject of the OP) were created by finding physical features (yes, just like ML) and using those to build a semi-supervised tree-structure of classifications. However, eventually we began to use DNA sequences to compare organisms, which restructured the tree in many ways, even close to the root. It was a controversial time as the the historical physical-feature classifier group was certain their way was right, and same for the DNA folks. I sort of assumed that the DNA would be a much higher quality source for clustering but it hasn't really always worked out that way.
I guess it depends on on why you are doing the clustering, right?
If you want to cluster animals that sort of fuzzily behave similarly together — if it looks like a duck and walks like a duck, it probably acts like a duck, haha.
Except phylogeny generally was used to categorize how hereditarily related things were. Whether sequence alignment or physical taxonomy are better determinants is perhaps an open question in some cases, although I’m firmly on the side of sequence alignment, since DNA is an important component of inheritance
The side you are on has already won. Sequence data are universally accepted in systematics as the ultimate arbiters of evolutionary relationships, just delve into the modern classification of any extant group. One example of where molecular evidence overturned physical evidence long thought to be unambiguous, leading to a complete and essentially uncontested taxonomic overhaul: coprinoid mushrooms. Morphological characters are still used in paleontology for obvious reasons, but again within a higher-level framework provided by molecular phylogenetics.
Really? Cool! This was still pretty much unresolved in 2003 when I worked in the area and I had been told people were still arguing about this recently.
The point of making trees is almost always to understand the fundamental sources of phenotypic diversity and making simple models that explain how the new (complex, organismal) phenotypes arise, how they are shared through various forms of reproduction and gene transfer, and how those relate to molecular phenotypes.
Nobody that I am aware of is clustering things based on similar functionality simply to say "look, these two things are similar", without having some sort of "explanation".
I thought the article was going to be talking about phylogenetic trees aren't really trees (in the data structure sense) because the prevalence of horizontal gene transfer and hybridization helplessly muddies things.
Please do elaborate for a non-biologist - how and when is DNA sequencing worse at phylogenetic grouping than physiology? I had assumed the latter was embarrassingly outdated and easily duped (by convergent evolution, etc)
It's been about 20 years since I last looked into this but I think there were a few cases where people had "golden classifications" (IE, some sort of external proof of the grouping) that were more consistent with character features.
To be honest I'm not the best person to ask because every time I dip my toes in the area I realize (a) how little I know and (b) just how ugly these debates get. and (c) how much scientists like to treat some side observation as golden data that is absolutely right when trying to build support for their theory
Am I the only one drilling down in this thinking it might be about tree data structures? Not really having a clue what "phylogenetically" might mean, but kind of assuming it was about "those" other natural trees.
Interesting article, though I thought this was going to be about the fact the the "phylogenetic tree" is not in fact a tree but a hypergraph, owing to the existence of sexual reproduction.
I’ve been thinking it would be fun to build a simple game where you get three organisms and you’re supposed to identify which two are most closely related, for example, strawberry, apple, orange, or hippopotamus, horse, rhinoceros or for the big challenge, squid, earthworm, fish.
If you turn it into a mobile friendly site, and then reveal the common ancestor of the two closest, and the ancestor of all three, that would turn into basically my favorite educational addiction ever.
Bonus points if there are maps showing world geographical distributions.
Trying to track down common ancestors would be a challenge (not to mention that in most cases the common ancestor is unknown), I figure I’d be instead indicating how far up the kingdom-phylum-class-order-family-genus-species hierarchy you need to go.
Reminds me a little of the fact that "vegetable" is not a botanical term.
People who say "tomatoes are fruits, not vegetables" are guilty of performing an incorrect hypercorrection. Tomatoes are vegetables just as cucumbers, green beans, asparagus, lettuce, fennel and carrots are. "Vegetables" is a culinary and dietary term, not a biological one.
So some fruits are also vegetables? That doesn't seem right. I would think they're mutually exclusive because fruit is more precisely defined. If tomato is a fruit, then necessarily it is not a vegetable. It's a simple distinction between the product of a plant (what it produces) and parts of the plant.
The common way to distinguish between the definitions is to say a tomato is a culinary vegetable and a botanical fruit, but not a culinary fruit.
> The question of whether the tomato is a fruit or a vegetable found its way into the United States Supreme Court in 1893. The court ruled unanimously in Nix v. Hedden that a tomato is correctly identified as, and thus taxed as, a vegetable, for the purposes of the Tariff of 1883 on imported produce. The court did acknowledge, however, that, botanically speaking, a tomato is a fruit.
They are not mutually exclusive because they are defined in orthogonal ways.
"Vegetable" is defined by how a plant is cooked and eaten, and so has a lot of cultural and context specific influences. A vegetable can be a root (potato), a stalk (celery), a fruit (cucumber), seeds (beans), even non-plant fungi (mushroom).
A fruit has a very specific definition (especially in a biological or botanical usage). It's the "seed-bearing structure in flowering plants that is formed from the ovary after flowering" (Wikipedia).
The part of the cucumber we eat is the fruit (you can see its seeds). But the way we prepare and eat it means we classify it as a vegetable.
This reminds me of carcinisation. Where natural selection tends to heavily favor crab-shaped animals even though they come from different lineages. Natural selection seems a lot like physics. Given similar initial conditions and a population of organisms, you’re going to get similar results across groups after a period of time.
Surprised there's no mention of Lepidodendrons. OK, they're long extinct, but they were trees, even though they were closer genetically to club mosses and quillworts than any modern trees.
> First, what is a tree? It’s a big long-lived self-supporting plant with leaves and wood.
Also, do pineapple and banana plants have wood? I didn't think so.
My partner, who is a biologist, hates this take as a mostly grammar trick. Then again, she has no patience for philosophy in general, so that probably explains it.
I think the awesome takeaway of this post isn't about the naming and categorization of things (like "tomato is a fruit" or "humans are fish") but the shocking (to me, at least) fact that trees evolved and unevolved so many different times, and not just once.
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[ 2.7 ms ] story [ 279 ms ] threadWould we notice an alien civilization sending a signal with a small message over the course of hundreds of years, at a bit a century frequency? Would we recognize each other as life if one is the size of a galaxy or the size of an atom?
If anyone knows of something similar for UK flora and fauna then please point me to it.
Would like to hear if anyone knows. If you look at onion or garlic growing, it basically looks like a very long piece of grass.
Perhaps they're doing exactly that. But grasses evolved far more recently than trees.
There are billions of dollars of peanuts, fish, etc., being traded across the world every week.
I think the best alternative is to use different names depending on what we're highlighting (cladistics versus functionalism, for instance).
The -id/-ine suffix (e.g. ursid / ursine) seems to do this.
It would be clarifying to distinguish hodgepodge groupings such as "fish", and groupings such as "ducks" that are basically monophyletic with some exceptions removed from the group. Ducks are just small Anatidae.
She has a hard time believing me — tomatoes was ok, but for peanut she said “no daddy, there’s nut in the name”
And so now we call it pealegume and jelly sandwiches
There’s also pea in the same. It’s kinda like a pea and kinda like a nut.
With my younger kids, I settled on just introducing the ideas of multiple overlapping systems, but not pushing on it too hard until they're older. They're only now getting to that age and I've been folding it in to some conversations lately more strongly. I think having some fun with it early as you are is a very strong approach to the topic.
I sort of dislike the framing of this sort of article, as well as the "actually nothing's really a berry" and similar culinary silliness, because this is a really important cognitive skill for higher-level thinking and introducing it with an approach virtually guaranteed to produce resistance and associating it with trickery rather than clear thinking is a real disservice, in my opinion.
This article, once it gets going, is good; I'm only complaining about the framing, not the content.
I will complain about the culinary version of this, where the trickery I'm referring to is "You think that a strawberry is a berry (often heavily implied, 'dumbass'), but really it's an aggregate accessory fruit (often heavily implied, 'as I am smarter for knowing than you')." The whole frame is wrong; it isn't really one thing or the other, it is both, and several other things besides. The multiple classifications all exist at once and they aren't better or worse than each other, they are better or worse for certain uses, and there certainly isn't one classification that is the "real" one and all the rest are fake. For people pushing this, it's like, yeah, you almost get the idea that multiple classifications can exist at once, but you've still completely missed the point.
Tomatoes and peanuts are primarily known to be useful as food, and in the context of food, they fill the niche of vegetables and peanuts, respectively. Palm trees are useful pretty much only decoratively and to provide shade (unless you harvest them, which most people don't) so they have exactly the same utility as trees, making them trees.
It's interesting to think about how these things are biologically different from the other things in their practical category, but we strip away the utility of placing things into categories if we try to apply them outside of the context in which the category is... useful. So unless you're in a biology lesson (or you are a botanist, or just having fun with facts), tomatoes are vegetables.
Human languages are great, aint they?
What's interesting about peanuts is that it seems to have the same allergenicity profile as nuts that cause allergies. Kind of odd for a legume, if you ask me.
Huh? Peanut allergy is distinct from nut allergy; people with peanut allergies can generally eat nuts fine, and vice versa.
Strawberries aren't berries but bananas are.
Unless, that is, you intended for your comment to be a very bland summary of the piece, and not some kind of insightful counter-argument.
You may also find this referenced blog post interesting: https://slatestarcodex.com/2014/11/21/the-categories-were-ma...
In the sense that they share an ancestor with all fish.
It just also happens to be one of your ancestors too.
- "Be it known that, waiving all argument, I take the good old fashioned ground that the whale is a fish, and call upon holy Jonah to back me."
- "To be short, then, a whale is a spouting fish with a horizontal tail."
He even notes right there that he knows about Linnaeus' work (a century old at this point) that concludes that whales are not fish. He simply decides not to care. Looks like Walrus is where he draws his line.
[1]: Moby Dick, Chapter 32: Cetology
There are fern trees (Tree Fern to be precise), but they only grow in tropical regions. Bananas and pineapples are clearly grass with huge leaves.
But bananas? Who calls bananas grasses? They're not even in Poales!
As far as why trees don't seem to evolve into grasses, (or grasses into trees), it might be all about C3 vs C4 carbon metabolism, the latter being a complex structural system that pre-concentrates atmospheric CO2 before feeding it into the photosynthetic biochemistry (which is the right way to do artificial photosynthesis as well). This is apparently difficult to do in trees?
https://pubmed.ncbi.nlm.nih.gov/32409834/
> "Since C4 photosynthesis was first discovered >50 years ago, researchers have sought to understand how this complex trait evolved from the ancestral C3 photosynthetic machinery on >60 occasions. Despite its repeated emergence across the plant kingdom, C4 photosynthesis is notably rare in trees, with true C4 trees only existing in Euphorbia."
And here we have the world's largest Euphorbia:
https://www.wikidata.org/wiki/Q5851367
Arecales (palms)
Commelinales (spiderwort, water hyacinth)
Poales (grasses, rushes, bromeliads)
Zingiberales (gingers, banana)
So depending on how you measure, palms and "grasses" are distinct but closely related groups of plants.
You can find non-trees and trees that are monocots and dicots and also non-flowering trees and non-trees for that matter. The main issue is that when plants get big they get woody and take on the characteristics of trees.
I like the irony of that title that a "tree" (in the computer science sense) is the basic unit of phylogeny with the caveat that it is broken at the top because the three operating systems for a cell are described here
https://en.wikipedia.org/wiki/Domain_(biology)
they do show a tree on that page based on a particular set of genes but if you picked a different set of genes you would get a different tree because complex cells have a mixture of Archaea and Bacteria because they merged in some horizontal gene transfer event long ago.
They are different branches of the tree of life. Dicots (trees) vs monocots (grasses)
The least tree-like tree ever
>A lot of grasses are dicot
Such as?
Wiktionary doesn't even list a sense for "grass" that would include clover, and anyone can just add glosses there.
Grass is mostly characterized by having blades instead of leaves. Other plants would be called... whatever they're called. If you want a generic term, it's "plants".
If you want a term that refers to the specific function of covering what would otherwise be bare earth, that term is "ground cover", but ground cover is not restricted to plants. It applies just as well to gravel.
It's on the lawn, it's green, it's not a weed. Therefore, it's grass. ;)
Magnolias are trees and dicots (so expected).
Cabbage is a dicot but not a tree - not all dicots are trees. Maybe you misinterpreted my parent comment as me suggesting all dicots were trees? I more wanted to illustrate the key difference between grasses (which are monocots) and most trees
I give you the Jersey cabbage https://en.wikipedia.org/wiki/Jersey_cabbage
> The Jersey cabbage (Brassica oleracea longata) is a variety of cabbage native to the Channel Islands that grows to a great height and was formerly commonly used there as livestock fodder and for making walking sticks. It is also known as Jersey kale or cow cabbage, and by a variety of local names including giant cabbage, long jacks, tree cabbage and the French chour and chou à vacque.
> The 'Jersey cabbage' develops a long stalk, commonly reaching 6 to 10 feet (1.8 to 3.0 m) in height, and can grow as tall as 18 to 20 feet (5.5 to 6.1 m). ...
https://www.atlasobscura.com/articles/jersey-kale
There is obviously no non-teleological answer for this, but it can be much much more straight forward than metabolism.
Think of plants as basically solar panels. We can think of the 'grass' phenotype as competing through r-type selection. Lots and lots of individuals, lots of surface area, short life cycles. Short bursty growth, convenient loss resilience, easy mobility.
'Trees' are the also optimizing for surface area (among other things), but are relying on k-type selection. Longer life-cycles, lower probability of successful reproduction, specialized pollinators, and very significantly, vertically stratified growth habit. Being an individual in a k-type species is like a very significant advantage for that individual, since its unlikely that the vast majority of k-type seeds will successfully reproduce.
Being k-type may not be more competitive for the species overall, but it may result for a selection bias at the individual member resolution, and so may be unlikely to be selected against.
There are many many advantages to lignification when your whole thing is basically being solar panels on a pole. It would seem extremely unlikely this has anything to do with metabolism other than 'doing more of it'. We already know why monocots don't make trees more significant than palms (read: vascular bundles and eusteles). My money goes to species level versus individual level selection in k versus r.
Fruit is another common way to disperse seeds. Animals & birds eat the fruit, and then disperse the seeds with a dollop of fertilizer (poop).
Lots of co-evolution going on.
Grasses profit much more from growing quick than trees, where new opportunities (e.g. trees dying, fires etc) are rather rare & being able to grow extremely quickly wouldn't provide much of a benefit?
After any substantial ground clearing event (eg bushfire, etc), wouldn't the subsequent "winners" be those who grew the fastest to capture the available sunlight + suppress their competitors?
So no, being the first does not give you a clear advantage.
https://en.m.wikipedia.org/wiki/Ecological_succession
ATP is a political book, albeit not a book about politics. But in the process of building their radical political theory, they build a radical general systems theory that's u-n-m-a-t-c-h-e-d. We have no choice but to study it.
This doesn't do it justice, but it's a fair beginning. https://en.wikipedia.org/wiki/Rhizome_(philosophy)
This is an illustrated audio reading of the first chapter of ATP (the one dedicated to rhizomes): https://www.youtube.com/watch?v=0XYc2scuJrI&t=64s
The linked article for this thread is about how "tree" biology keeps springing up and disappearing - the molecular biology, genetics, convergent evolution -- and how the human concept of "tree" doesn't really map cleanly. All of that, to me, is intuitive.
But philosophy is lost on me. Neither your linked Wikipedia article or the article on the book you suggest [1] make much sense to my non-philosophical science brain. My eyes just glaze over.
[1] https://en.wikipedia.org/wiki/A_Thousand_Plateaus
^This applies mostly to epistemology.
I like my philosophy in the format of what the youth calls 'schizo-posts'. Weird, out-there, grasping to find right words and closer to art than anything else.
Philosophy is also not science, since there is no attempt to rigorously test the theories with experiments or data.
So I lump philosophy with art. It's strongly tied with a person's sense of aesthetics as well as the culture around them.
The philosophical sciences (I use this word in the classical sense, not the narrow modern/Anglo-American sense) can be said to couple the deductive rigor of math with general empirical observation. For example, consider metaphysics. Metaphysics often begins from very basic and general observations like "things change", observations that, btw, everyone generally presupposes, including the empirical scientist. From these observations, we can infer what must be true about reality in general and necessarily so. Metaphysics gives us the principles characteristic of being as being, or being in general. Such principles are therefore true of all things. If this seems very abstract, you would be right, as metaphysics concerns the most general things. Concrete-minded people will have a difficult time.
Sadly, because of ignorance, many take philosophy to be some kind of idle speculation or some kind of put on where anything goes. This may be a result of either bad experiences or simply a lack of preparation to understand what is being said. Also, certain philosophical "schools" seem to be notorious for their unintelligibility (Derrida has this reputation). But read someone like Aristotle or Thomas Aquinas, or better yet, recent commentators and didactic works, and you will breathe fresh air and feed your mind. Perhaps it won't be easy, but the clarity and value are there and there is plenty to chew on.
Philosophy also investigates the entailments of various held positions. For instance, your view of philosophy, science, mathematics, aesthetics, of what constitutes knowledge, etc, all very much present in your comment, all fall under the jurisdiction of philosophy. The assumptions you are making are philosophical in nature and they have profound logical consequences that make shock you and cause you to revise your views. For instance, a kind of quasi-/amateur positivist, scientistic materialism seems to be popular on HN. But a rather modest philosophical examination shows that logical positivism, scientism, and materialism are all self-refuting or incoherent. You can't escape philosophy. You can either do it well, or do it poorly.
Physics and maths tend to poopoo any line of thinking which considers human experience - and there is amazing utility in that! No opinions are important for calculation of a trajectory. However, human experience does exist, and operating rationally on it, despite the lack of ability to experiment, leads one into a world that mathematicians might scoff at, but is still a completely valid field of inquiry.
People will say “philosophy is a soft science! No experiments!” Without understanding that experiments cannot be done in this realm.
I recommend Michael Segrue on YouTube - his lectures are fantastic as an intro to philosophy. Particularly his into to Kierkegaard touches on the birth of existentialism out of the furnace of pure scientific rationality.
That isn't the only way to subject philosophical ideas to empirical scrutiny, but whenever people use the historical evidence to determine things like how well different economic systems behave, for example, all of a sudden a lot of people get very angry and defensive and refuse to acknowledge the validity of prior experience.
> People will say “philosophy is a soft science! No experiments!” Without understanding that experiments cannot be done in this realm.
Some kinds of philosophy can be experimented on in some respects. For example: Does unquestioning obedience produce an ethical system that minimizes arbitrary killings? Well, I think we can look to the historical record and find the answer to that one, and conclude that it doesn't.
More deeply, though, how do we conclude that we care about arbitrary killing? That's a kind of question that we can't answer through experimentation, because the world doesn't outright tell us what values we should adopt. The most we can do is reason through the problem and then use experimentation (even retrospective experiments, as in history) to try to figure out which ethical systems support those values best.
That said... We're not blank slates. We're humans, we're social animals, so we care about certain things instinctively and, thus, some ethical systems are more humane than others in their outcomes.
Kind of a necessary, but not sufficient, condition for a question to be a philosophical one.
I mean, I tend to agree here with the straw man! That's why, for example, when arguing against commonwealth planning, one can't point at the Soviet Union as an example. One instead has to start from epistemology[1]! Then, folks don't respond with anger, they respond with glazed eyes.
[1] https://cdn.mises.org/economic_calculation_in_the_socialist_...
It's actually the reverse—multiple sciences started out as subfields of philosophy, that got useful enough on their own that they were peeled out into their own thing. It would be more useful to think of as philosophy as a soup of proto-sciences that are developing, that some might prove useful, and some might die out.
That's not really all philosophy is, but at least it's a more historically accurate way to look at it.
Does that mean "they figured out ways to make it reproducible and/or validate it"?
Whereas the other subfields of philosophy don't (yet) have ways to fully validate them, and/or make them reproducible?
I think it depends on the field. Reproducibility is more of a recent concern, whereas this process has been going on since the ancient Greeks, I'm sure.
Probably more recently the criterion is "commercial value".
The problem here is postmodernism, which is absolutely a meaningless word salad designed solely to impress the gullible.
I think this is basically the point. Understand the world around you, and especially the connections and influences between different components of a system (broadly defined), to form and verify more holistic, nth-order models rather than disconnected, first-order-only analyses.
I think it goes beyond "cool idea" and really strikes at the same kinds of intuitions that many on HN appreciate as regards simple models that explain complex phenomena. In this sense, then, D&G's work is a sort of "meta-model" for guiding intuitions when building specific models about specific systems.
It is not a predictive framework. I guess I would call it an "ontological/architectural" framework.
(I laughed)
> I find it basically useless in my every day life and work
D&G is of utility in architecture, for one. You need to have some philosophical decoration for your doodle. The art is in mapping bs to doodle. In general, useless philosophy is a faithful companion in bullshit fields. Where in software we could use D&G then? I suggest crypto space.
A rhizome, maybe. The article is about literal trees (e.g. dogwoods, oak) and not mathematical structures, but it has a decidedly philosophical bent, and I find the idea of rhizomes to be relevant to that, at least.
IDK, I barely understand what's going on here.
If instead we used a D&G rhizome that “connects any point to any other point” — we’d be dropping the notion of time (ie, ancestors precede descendants). Which when we’re talking about evolution, seems bad.
If horizontal gene transfer were a big part of the story here, that’d be different. Or if your ecology has time travel, or interstellar exchange ala Butler’s Xenogenesis, then sure, rhizome away.
and that's exactly what we see in the article, right? if a species took a path A-B-C-D to exhibit features of D, and another took A-F-G-D and so also exhibits features of D, then isn't there more to the history there than simply genetic change via ancestry over time? there's a reason why convergent evolution is so weird and surprising.
epigenetics, for example, is an interesting manifestation of what sorts of new domains you can explore as you broaden the horizon for asking questions beyond "linear ancestry" or "natural heirarchy" - arborescent vs rhizomatic thinking. blasting out of these constraints is the process of deterritorialization/reterritorialization D&G put forward as necessary and essential.
I think we see the opposite! We start with a naive and non-hierarchical view of relatedness: trees are tall woody things, fish live in the water and have fins. And the piece argues that we should let go of our common-sense categories and use the descent-based ones, like the biologists do.
Anyway --- I didn't say that ancestry is the only factor. I said it was natural, and useful. Epigenetics is fascinating, really! But it's not 'blasting out' of anything, it adds a bit of detail and complexity around the edges. A sense of proportion is important; we shouldn't miss the forest for the...never mind.
Previous discussions
https://news.ycombinator.com/item?id=27094382
https://news.ycombinator.com/item?id=29621646
Cool article either way.
There’s no such thing as a tree (phylogenetically) - https://news.ycombinator.com/item?id=29621646 - Dec 2021 (132 comments)
There’s no such thing as a tree, phylogenetically - https://news.ycombinator.com/item?id=27094382 - May 2021 (207 comments)
There’s no such thing as a tree (phylogenetically) - https://news.ycombinator.com/item?id=27026812 - May 2021 (1 comment)
The Axolotl tanks of Tleilaxu. I wonder if Frank Herbert got that from these creatures or is this some crazy coincidence that Axolotls are subjected to genetic 'shape shifting'.
Wikipedia on Axolotls
> It is unusual among amphibians in that it reaches adulthood without undergoing metamorphosis.
Obviously right from the start "taxonomy" itself is arbitrary. A more universal tool than naming, establishing branches, starting and end points is the concept of "most recent common ancestor" [0]. From that nameless unclassified vantage point I find it interesting to see (as OP pointed out) how "woodiness" or "treeness" evolutionary speaking is clearly a "strategy" (convergent evolution) and nearly impossible to chase down "phylogenetically" through MRCAs. Intuitively before reading this article I would have guessed this to be more straightforward.
[0]https://en.m.wikipedia.org/wiki/Most_recent_common_ancestor
If you want to cluster animals that sort of fuzzily behave similarly together — if it looks like a duck and walks like a duck, it probably acts like a duck, haha.
Nobody that I am aware of is clustering things based on similar functionality simply to say "look, these two things are similar", without having some sort of "explanation".
To be honest I'm not the best person to ask because every time I dip my toes in the area I realize (a) how little I know and (b) just how ugly these debates get. and (c) how much scientists like to treat some side observation as golden data that is absolutely right when trying to build support for their theory
If you turn it into a mobile friendly site, and then reveal the common ancestor of the two closest, and the ancestor of all three, that would turn into basically my favorite educational addiction ever.
Bonus points if there are maps showing world geographical distributions.
People who say "tomatoes are fruits, not vegetables" are guilty of performing an incorrect hypercorrection. Tomatoes are vegetables just as cucumbers, green beans, asparagus, lettuce, fennel and carrots are. "Vegetables" is a culinary and dietary term, not a biological one.
If you put it with ice cream it is a fruit, if you put with a roast it is a vegetable.
Pineapple is an odd one.
> The question of whether the tomato is a fruit or a vegetable found its way into the United States Supreme Court in 1893. The court ruled unanimously in Nix v. Hedden that a tomato is correctly identified as, and thus taxed as, a vegetable, for the purposes of the Tariff of 1883 on imported produce. The court did acknowledge, however, that, botanically speaking, a tomato is a fruit.
https://en.wikipedia.org/wiki/Vegetable#Terminology
"Vegetable" is defined by how a plant is cooked and eaten, and so has a lot of cultural and context specific influences. A vegetable can be a root (potato), a stalk (celery), a fruit (cucumber), seeds (beans), even non-plant fungi (mushroom).
A fruit has a very specific definition (especially in a biological or botanical usage). It's the "seed-bearing structure in flowering plants that is formed from the ovary after flowering" (Wikipedia).
The part of the cucumber we eat is the fruit (you can see its seeds). But the way we prepare and eat it means we classify it as a vegetable.
https://chireviewofbooks.com/2020/04/15/why-fish-dont-exist-...
https://www.nosuchthingasafish.com
> First, what is a tree? It’s a big long-lived self-supporting plant with leaves and wood.
Also, do pineapple and banana plants have wood? I didn't think so.