There’s no such thing as a tree, phylogenetically
eukaryotewritesblog.com
eukaryotewritesblog.com
I don't even know where to start.
In re: TFA, most annuals that we use for crops have perennial versions. I just planted a "thicket bean" (Phaseolus polystachios) which should grow for years! There are perennial kales that grow into small tree-like "canes". There's a thing called a "strawberry tree" that is exactly what it sounds like: a tree that grows strawberry-like fruit. It goes on and on.
One take-away is that agriculture as it has been practiced is about the dumbest way to grow food. :( Check out Gabe Brown's videos on regenerative agriculture to see how we can grow food and increase fertility and volume of soil by incorporating more species and doing less work. See also the "food forest" concept: imagine a park or botanical garden where every species is edible. It takes a while to set up but then it is self-sustaining with low labor, you mostly just harvest.
Another take-away is that we mostly already have all the technology we need to make a really fun and enjoyable civilization. We have all these species that can develop food, medicine, clothing, fiber, wood, etc. such that the vast majority of our needs can be fulfilled in a garden.
> imagine a park or botanical garden where every species is edible.
Make it happen! If the way we’ve been doing things is dumb then there is a massive market opportunity. Save the world, become the first trillionaire.
It does seem like folks are catching on though. Business can be slow to adapt, especially in agriculture, but farmers are pragmatic. Brown's talks seem well-attended.
e.g. An idea to plant a garden with entirely toxic plants is just as valid, but not as valuable.
Useful models are still models after all.
Money does represent value of some kind, right? Whether that's time, labor, or [fill-in-the-blank]. It's a tool to represent generic value.
I'm interested to hear what you think a better unit of measurement might be for determining whether or not an idea is 'valid' or worth doing. Can you elaborate?
It turns out that when we understand what the plants and animals are doing in detail (through science) we can arrange them in time and space in ways that are vastly more efficient than what we've been doing these last ~12k years.
Think about it, if it wasn't so that would mean that our ancestors discovered optimal farming in antiquity, eh?
Just think: we used to burn chaff rather than composting it. It turns out that that is not a good idea. It's that sort of thing that I'm thinking of when I call ag "the dumbest way" to grow food.
Farming has undergone several fundamental changes throughout history after that though, notably in medieval times and then everything industrialization brought
Can you name some that can't be reduced to "but on a [insert new machine]"? The only one I can think of is artificial fertilizer, which isn't a sustainable practice in the long run either.
Compared to that every other revolution in farming was insignificant.
It may take years for new practices to be widespread and accepted, but I assure you, if you can make that chart continue to go up, ~every grain farmer in the US will happily be on board.
There is a certain world-view and a romanticizing to farming, but at the end of the day, farmers are businessmen who just want to grow as much food as possible, as cheaply as possible. They may grumble as much as a software developer when forced to learn new tools, and they won't drop everything for an unproven promise, but they'll happily abandon their old ways in favor of new ones once they're proven.
This assumes both systems are optimizing for the same thing.
We know that evolution is optimizing for continuation or duration (technically "evolution" isn't a thing, it's a non-volitional chemical tautology with no purpose or intrinsic meaning so "it" cannot optimize, however, in practice, life is optimizing for more and continued life, overcoming radiation, impacts, and it's own consequences (like the advent of oxygen and aerobic metabolism)) so what is the other system optimizing for?
(As an aside, is "life is optimizing for more and continued life" a definition for "life"?)
In large farms, seeds are mass produced, engineered, and go through a QA and testing process to prevent certain diseases. There are many good reasons, BTW, why farms don't grow perennials and engage in mono-cropping, or use herbicides and genetically engineered crops instead of no-till. The trade-off in abandoning these practices almost always involves sacrificing yields and the mechanization of labor.
Or how about vineyards?
> There are many good reasons, BTW, why farms don't grow perennials and engage in mono-cropping, or use herbicides and genetically engineered crops instead of no-till.
But sometimes the pests and disease are caused by these same practices, right? Like, I'm aware the Cavendish banana we all eat is very susceptible to a fungal disease that is slowly spreading around the world. Because we produce so much of a single variety, where all plants are clones, a single disease can be highly disruptive. If production was evenly distributed over many varieties, and if plantations had banana plants separated by other useful crops, the whole system might be more resilient.
> The trade-off in abandoning these practices almost always involves sacrificing yields and the mechanization of labor.
The problem (that cannot be escaped) is longevity. Any system of agriculture that does not increase over time soil fertility and volume/mass is doomed.
Systems of agriculture that deplete [various measures of biological health] over time are akin to mining. Once the underlying resources are exhausted the story ends (the resources in question could be water, or biodiversity, or climate stability, etc...)
Even if we compensate with technology, we are substituting our managed system for a automatic system that has been (meta-)stable for billions of years. We should proceed carefully. The billions of people who owe their lives to the Haber-Bosch process (and other innovations) may come to rue it if we crash due to environmental destruction. By some scientific estimates this is the decade when our biomass and the biomass of our agriculture outweighs naturally occurring biomass. For better or worse the world has become our farm.
That's why Gabe Brown (et. al.) seems so important to me: he is integrating modern practices with new (scientifically-validated) regenerative practices and his farm is both profitable and healthier year after year.
How old is it? How is the taste? Is the cane woody or is it more like bamboo or something else? Does it flower?
Cool reference that I hadn't heard of before, so I just looked this up. The fruits of this tree look absolutely nothing like strawberries (more like lychees, IMHO), so I don't think this is a good example for what you're describing.
https://en.wikipedia.org/wiki/Potentilla_indica
Incidentally: from a botanical perspective, strawberries are not berries. Nor do they even taste like straw!
Today I learned that papaya is closely related to cabbage.
cran-, elder-, lingon-, among others.
(Also, the fruit of the strawberry tree, unlike either strawberries or mock strawberries.)
[1] https://i0.wp.com/oaeblog.com/wp-content/uploads/2018/06/Ger...
No plant nursery will sell you a Raspberry Jam Tree, but you can buy seeds on Etsy: "Acacia acuminata".
They are interesting also because the leaves (which aren't leaves, but "phyllodes") and bark have a high concentration of interesting tryptamine alkaloids.
There are many other fascinating details about A. acuminata. Millions of fenceposts in Australia more than a century old (and more every year!) are made of its wood.
It still loses in profit per investment to modern industrialized farming, so (almost) nobody cares. If you want people to care - tax soil degradation.
Turns out with artificial fertilizers and modern technology neither work nor soil degradation is as important as quick adaptation to market forces and economies of scale.
I just want to point out that the way modern agriculture came to be is not dumb at all, the thing is that its focused on maximizing yield above other things. 7 billion people eat something (almost) everyday, I find it quite impressive that the infrastructure to support that, exists.
I hope the world could be stopped (as it happened, more or less, with COVID) in order to fix some of these problems, but in the case of food, it's going to be hard to ask people to stop eating for a while.
> One take-away is that agriculture as it has been practiced is about the dumbest way to grow food. [...]
One very useful technique in modern agriculture is crop rotation. https://en.wikipedia.org/wiki/Crop_rotation
You grow each year a different crops, because they have different fertilizer requirements (and some even fix Nitrogen) and also helps to reduce some plagues. It's also possible to plant different crops in succession, so you get multiple harvests in the same year.
For these, a perennial version is bad.
But if you like those, you should try the berries of haw and ash. They're similar in texture, lack of flavor, and seediness, but their mouthfeel is significantly improved by the lack of scales.
However the honey from them is absolutely special and delicious. The honey is bitter. I fell in love with the honey from the strawberry trees in Corsica.
It takes volunteers real work to keep it tame enough for a city, but they’ve done it for as long as I’ve lived here and it’s a really beautiful spot.
One perk of this style of gardening is that, for various reasons, pest moderation seems to happen automatically. No pesticides are required, the garden is watered by humans only a handful of times in summer, and no fertilizers besides city compost are used. Everything is lush and happy. Insects are everywhere, and perhaps birds are eating those instead of berries. It's hard to say exactly how each biome functions, but this one is very productive and animals aren't a problem for it.
Sometimes annuals are just handy to use the land in a more efficient way. You can obtain three crops in two years in the same land with annual species
But I haven’t encountered enough scientific spoken American to have developed an instinct for whether or not Americans actually pronounce the ‘h’ in ‘herb-‘ words like ‘herbivore’ or ‘herbaceous’; so in this text I was a bit thrown by encountering both “a herbaceous plant”, and “an herbaceous plant”. Wondering whether this is situational pronunciation? A variation on the hyper correct ‘an precedes words that start with H if the first syllable is unstressed’ rule that gives you “an hotel” and “an historic event”? Just error?
Can anyone enlighten me?
ˈ(h)ər-bə-ˌvȯr
As for "an" and "a", I was taught to follow the rule you stated in school. To my eye, using "a" is informal and mimicking speech, whereas "an" is "correct".
> Usage Note: In writing, the form a is used before a word beginning with a consonant sound, regardless of its spelling (a frog, a university, a euphemism). The form an is used before a word beginning with a vowel sound (an orange, an hour). · An was once a common variant before words beginning with h in which the first syllable was unstressed; thus 18th-century authors wrote either a historical or an historical but a history, not an history. This usage made sense in that people often did not pronounce the initial h in words such as historical and heroic, but by the late 19th century educated speakers usually gave their initial h's a huff, and the practice of writing an before such words began to die out. Nowadays it survives primarily before the word historical. One may also come across it in the phrases an hysterectomy or an hereditary trait. These usages are acceptable in formal writing.
According to the Usage Notes, both "an" and "a" are correct in written form (since both pronunciations are correct). If you're reading it out loud, "an herbacious" should be pronounced with a silent "h", and "a herbaceous" should be pronounced with an aspirated "h".
As someone who grew up in the US and has never left the country, "an herb" really bothers me because I've always pronounced the "h".
Words that are not commonly used in spoken English may often be mispronounced. Common words are subject to drift.
Then there are regional variations in the US. But then also people move from one region to another. And of course different dialects may coexist.
Fun story!!! Seagrasses are like whales, in that their ancestors lived on land, and now they live completely submerged.
Seagrasses are nowhere closely related to grasses. Quote: 'They just… both did that.' They're at least three, maybe four distinct 'back to the sea' events in the seagrasses, with distinct lineages that went back separately, but show convergent loss of genes.
Most seagrasses look a lot like grasses, bringing me back to OP's 'grass strategy' - under water it's a very successful strategy!
This document from the Minnesota DNR expresses just how hard it is to kill it: https://files.dnr.state.mn.us/natural_resources/invasives/te...
Specifically it suggests cutting it to the ground and then, if you don't want to use herbicide, to cover it with a black plastic for one to two years. And it says the seeds it drops remain viable for five.
Native here. Is the host of two nice butterflies and a terrific an totally unexpected substitute for conifers. Many people would mistoke it by a small Cypress.
Great for making forts in as a kid.
Tall, hard woods. Great smells of the dank forest floor and the tannins of the redwoods. Birds twittering, squirrels barking.
Dust, duff.
Your imagination running buckwild about ancient castles or being an ewok. Mom calls at dusk for dinner, red spaghetti and bugjuice.
Coolness creeps in and the scrubjays squawk at another.
Just dark enough for flashlight tag.
And running through church columns in twilight and you never get tired and you never get old.
And everything is perfect.
https://www.google.com/search?q=redwood+fairy+ring&source=ln...
https://robertogreco.tumblr.com/post/10973003737/idrawninten...
There's also quite a few trees that can be a pain if you want them gone. You can cut them down to stumps and they'll just send suckers up and try to grow again. My dad has been having it out with a lilac bush since I was a kid. He gets pissed off at it - I don't know why as it's a lovely bush - and lops it down to the ground. It's usually back within the year. I know sumac in particular is incredibly stubborn. When you're trying to remove them in prairie management, the general practice is to lop them off a couple inches above the ground and then apply herbicide to the cut. Otherwise and sometimes even in spite of this, they just grow right back.
Historically, the prairies would burn every couple years. Native prairie grasses and flowers are adapted for this and regrew, but shrubs and less-established trees didn't fare as well. When humans figured out how to prevent the wildfires, those shrubs and young trees started to move into the grassland. Sumac tends to be one of the first infiltrators. Once a sumac stand is established, they shade out the grass. Larger trees follow and what was once grassland becomes a forested area.
A testament to how important agroforestry was to the English people, I suppose.
Then we moved to composability + interface, realizing it's easier to compose attributes (often related to a given set of functions) to make any graph of structures instead of just a tree.
Just two days ago looking at how virus recombined themselves in the most random ways, i wondered if the species classification of the previous centuries based on trees were not destined to follow the same path.
> First, what is a tree? It’s a big long-lived self-supporting plant with leaves and wood.
That is such a broad thing that it's hardly remarkable. I find carcinization, or independent evolution of eyeballs from completely different tissues to be more remarkable.
This is no more remarkable than that animals independently evolved to be large, and in doing so evolved different hard support structures to support this, which for instance worms lack.
Maybe in some way most things can be viewed from the lense of a compiler/interpreter. "Structures" are really just existing meta-cache for how to efficiently traverse the language to enforce semantics that result in computations.
e.g. tail call optimizations are basically structures in the compilers that help to traverse a subset of the language (i.e. tail recursion) more efficiently time-and-space-wise
- The Tao of programming by Geoffrey James: https://www.mit.edu/~xela/tao.html
- An Analytical Approach to Programs as Data Objects by Olivier Danvy https://cs.au.dk/~danvy/DSc/00_dissertation-for-printing.pdf
- Maps of Meaning: Gautama Buddha, Adam and Eve by Jordan B Peterson - https://www.youtube.com/watch?v=F7T5cg1a77A
- Theories of Programming Languages by John C. Reynolds https://www.amazon.com/Theories-Programming-Languages-John-R...
Have you ever been into chemistry-oriented programming models ?
You're describing a (for the lack of a better term) "fad cycle". Our industry, like all, goes through cycles where a given practice is declares holy and sacrosanct, doctrine evolves around it, eventually flaws in the idealistic view appear and because the entire foundation before was "this is flawless and essential" and turns out it's not flawless and essential, the practice is wholly rejected. It's swinging to extremes. Neither of which is useful.
Experienced developers neither considered inheritance crucial property of OOP, nor they avoid it completely now.
Inheritance is static decoration. Decoration is a form of composition. It's all forms of the same thing, where you can make some choices AOT and some choices JIT and you pay for AOT vs JIT in terms of ending up with a different performance/flexibility balance.
I don't think we'll ever get back to modelling purely with strict trees of concepts, because this is simply not how things are in the real world.
[0] two organism can evolve light sensing because of appropriate context and some luck for instance, but you can't search for a common ancestor based on this
It’s only really a little bit about fish, the founding president of Stanford (who was an obsessive ichthyologist), and his eugenics agenda. It’s also part memoir. I found it very touching and quite good 4 the ole empathy.
[1] https://www.simonandschuster.com/books/Why-Fish-Dont-Exist/L...
The theory goes on about how mountains are actually the stumps of trees of the past, which, in turn, were thousands of miles high.
The theory came from the flat earth direction.
The title reminded me of this and I found the idea hilarious back when I read it.
Depending what the final goal of the worldbuilding is, the difficulty might be making it into something useful / relevant.
Thanks!
Because as we know... birds aren't real, either.
But I really wished they would have picked something else. There are tons of posters and "legitimate"-sounding text positing this theory, which very likely has led to people harming birds to "expose" the truth of mechanization
Please don't.
Their posters typically just say "Birds aren't real" with a link to the website - https://birdsarentreal.com/
A cash grab no doubt (the merch is front-and-centre after all), but their claims are presented with the closest thing to a "straight face" one can muster online.
Forget Gödel's wall (incompleteness theorems) and keep digging searching for imperfect answers to build our existencial puzzle. Thank you for the post.
> First, what is a tree? It’s a big long-lived self-supporting plant with leaves and wood.
I have some vines that are clearly capable of wood formation and sometimes seem to do so at places for reasons I can't understand.
“tree” is clearly a horizontal classification; it is as surprising as as that not all animals that can fly have common ancestors that can.
> You know birds? Imagine if actually there were amphibian birds and mammal birds and insect birds flying all around, and they all looked pretty much the same – feathers, beaks, little claw feet, the lot. You had to be a real bird expert to be able to tell an insect bird from a mammal bird. Also, most people don’t know that there isn’t just one kind of “bird”. That’s what’s going on with trees.
I do not find trees looking similar at all.
When folks say "forest", like "I'm going to go hiking in the forest", they usually don't specify what species or genus of tree. A street could be lined with "trees", or a "tree" could fall on someone's car. We categorize trees together because they tend to occupy the same enough overall role and profile.
Now if there was a "baobob tree" forest, or a "palm tree" fell on a car, those are distinct to merit specification.
That sounds like something that could very much be different in different languages.
well, no, because there aren’t usually multiple forests that could be meant that would be disambiguated to a single forest (warranting the definite article) by genus of trees, there is either one candidate (requiring no qualification) or multiple but needing some other qualification (like specific name of the forest or direction from the current location.)
I've certainly heard people mention the kinds of trees when talking about small stands of trees (ex: "this stand of pines over here.")
The birds bit is an analogy. It's not about looking identical, it's about looks (tall woody thing) and shared name (tree) not corresponding to phylogenetics.
What trees are you talking about ? or you mean in general ?
In particular, many trees grow from a central strem that is nearly perfectly vertical, and many have a more organic growth pattern. I see no reason to assume these have common ancestors that were trees any more than crabs and jellyfish.
Some examples where your description doesn’t hold up so well
- palm trees
- bamboo
- fringe tree (Chionanthus virginicus)
- Hydrangea paniculata
- sunflowers
- crape myrtles can have so many variations that it’s crazy
It's not very much like e.g. an oak tree. More like a scaled-up celery.
It is pretty obviously an enormous grass. Woody? Yes. Tree? No.
Woody hollow stems which don't grow rings, are canes. If less woody and more herbaceous, it's a reed.
The "tiebreaker" if you will, is palm wood. No rings, but it's dense, not hollow, it has a grain and it's lignin-rich. You can make planks with it. It's a weird wood, but it's wood. https://en.wikipedia.org/wiki/Coconut_timber
Ultimately "wood" is just a word, people will use it however they do.
Canes take the adjective "woody" but not the noun "wood". Bamboo can make some interesting laminate materials, but these are not normally referred to as wood either, although they are lumber.
I've done a fair amount of woodworking, but I don't think I've ever worked with bamboo. But if I were to, I'd be a lot more attuned to the distinction.
Palm trees do "grow from a central stem that is nearly perfectly vertical", and are woody, and conventionally are considered trees. Bamboo matches both of those criteria, in fact, but it has a "just look at it" grassness to it. Growing in clusters from rhizomes is pretty un-tree-like, but no one of these things is diagnostic.
What is and isn't a tree is more cultural than biological, which is, I believe, the original author's point.
Imagine that we had grouped together all of the animals that were purple. Or all of the animals that were edible. That wouldn't mean that there was an evolutionary link between them that could distinguish them from all the things that weren't purple or edible.
Energy tells you how difficult it is to put a bunch of particles (atoms, for example) in a given state. Entropy is how many of such states are possible. Ordered states (like crystals) have lower entropies than disordered states (like liquids), because there are fewer ways of arranging atoms and still get a crystal compared to the combination of possible positions for each atom in a liquid. In systems that are isolated (i.e. they cannot exchange energy with anything else), entropy cannot decrease on average. In non-isolated systems, anything goes and entropy can go up or down locally all the time.
We don’t measure it directly. What we can do usually is measure how much something heats when we give it energy, and work from there to deduce any entropy change using equations from thermodynamics or statistical Physics. It is impossible to measure an absolute entropy in general (in the same way as it is impossible to measure an absolute energy in general).
There are lots of caveats, asterisks, and cases that look like exceptions; that’s a quick and dirty description.
Mind if I ask follow-up question, what is a "state"?
Doesn't the entropy change when I change my definition of the state? If I go to the extreme and there is only one kind of state, an actual arrangement of particles, fields etc., the entropy would be the same of each and everything (one possible arrangement per state).
Does that make entropy an entirely subjective measure?
Sure. Actually there are two main things we call states. The first one (macroscopic state, or macrostate) is what we think as characteristic properties of a bit of matter, e.g. "1 kg of liquid water at 300 K under atmospheric pressure" compared to "1 kg of solid water at 250 K under atmospheric pressure".
The second one (microscopic states, or microstate) is the way the particles that constitute this bit of matter are arranged. The naming is a bit unfortunate and it can get technical quite quickly, but the distinction between macroscopic and microscopic states is crucial.
So, a more precise version of my previous post would be something like that. In the liquid example, there are many, many ways of distributing the H2O molecules that would result in the same macroscopic description. This means that there are many microscopic states that are consistent with the macroscopic state we observe. And, looking at a glass of water, we cannot say where the molecules are.
On the other hand, in a perfect ice crystal, the positions of all the atoms constituting al the H2O molecules are uniquely determined by the crystal structure. So, looking at a perfect ice cube we can say where every molecule is. It gets a bit more complicated in reality because no crystal is ever perfect. There are defects that introduce some disorder, so there are more than one microscopic state, but much fewer than in the liquid.
Entropy is larger for things that have more microscopic states consistent with their macroscopic state. You can also see here a hint of the link with information entropy in CS, if you think about the number of microscopic states as our knowledge of the molecules' positions.
> Doesn't the entropy change when I change my definition of the state? If I go to the extreme and there is only one kind of state, an actual arrangement of particles, fields etc., the entropy would be the same of each and everything (one possible arrangement per state).
It does sound very subjective. The conventional naming is a bit unfortunate and a consequence of the historical roots of statistical Physics in 19th-century thermodynamics. After all, there is no clear boundary between macroscopic and microscopic.
If this bothers you, you can say that "macroscopic" refers to the thing you are looking at as a whole, and "microscopic" to its constituents. This framework works as long as the stuff you are studying is made up of smaller things. We commonly use atoms and molecules in examples because it is somewhat intuitive, but you could consider an atom itself as a macroscopic system and its quarks as its constituents. Or the universe and its galaxies clusters.
The caveat is that the mathematical formalism is exact in the limit where the number of constituents is infinite, but might break down if their number is too small. That's why the distinction between macroscopic and microscopic is helpful.
> Does that make entropy an entirely subjective measure?
In a way, a bit. You can define the constituents seemingly arbitrarily (like considering molecules, or atoms as separate entities or not, adding electrons, etc). Adding more details gives a more accurate answer, but at some point it becomes irrelevant. So it is actually less subjective than relative.
To keep (ab)using the water example, a molecule is made up of 3 atoms, each one having a position (3 positions, each one being a 3-dimensional vector, so 9 parameters in total). But when grouped in a molecule these positions are not independent, and need to be consistent with the O-H bond length and the H-O-H angle. A molecule is characterised by a position (3-d vector), an orientation along the axes of the reference frame (3 other parameters), an angle and two bond lengths (again 9 parameters in total). So there is no more information if you describe the ice cube as a collection of atoms than as a collection of molecules, even though the choice seems arbitrary.
Take a deck of cards, say, a pre-ordered one (technically, you know what microstate it's in) - so let's say that its "disorder" is "zero", and your entropy about it is zero.
Now shuffle it face down really well, now both its "disorder" and your entropy about it is pretty high (it has a specific microstate that you don't know, and the ensemble of all potential microstates form a macrostate).
Now look at this shuffled deck face up again - it's "disorder" is still high, but now your entropy about it is zero again, because you know what microstate it's in.
In what details are they different ?
http://www.av8n.com/physics/thermo/entropy.html
EDIT : Perhaps more relevant:
http://www.av8n.com/physics/thermo/s-relevance.html#ch-s-rel...
EDIT2 : A specific example where both the Thermodynamic entropy and the Shannon entropy can be experimentally seen to be equivalent :
http://www.av8n.com/physics/thermo/expt-basis.html#sec-demag
EDIT3 : Ah, found the chapter discussing this specific point :
http://www.av8n.com/physics/thermo/entropy-more.html#sec-s-i...
The state of each card. If you define a macrostate in such a way as it can have only one microstate, then yes, entropy is 0. It is also completely artificial.
> EDIT : Perhaps more relevant: > http://www.av8n.com/physics/thermo/s-relevance.html#ch-s-rel...
I am not impressed with that website in general, but in this instance I don't see anything wrong with that section. Note in particular:
> Very roughly speaking, the items higher on the list can be assigned to the “information theory” camp, while the items lower on the list can be assigned to the “thermodynamics” camp. However, there is tremendous overlap between the two camps.
There is indeed some overlap (I have personally worked for a couple of years on applying information theory to calculate entropy in glass-forming materials), but not enough that you can just apply random concepts from one field to the other. Basically, your interpretation is that "we know a lot about the system, therefore entropy is low", whilst in a physical system it's the other way around: "entropy is low, therefore we know a lot about it". Knowing something does not change the state of the system you are observing.
> EDIT2 : A specific example where both the Thermodynamic entropy and the Shannon entropy can be experimentally seen to be equivalent : > http://www.av8n.com/physics/thermo/expt-basis.html#sec-demag
Entropy goes to zero when spins align, but it does not mean that entropy is non-zero until we check that the spins are aligned. Entropy itself is whatever it is even before we bother calculating it, and we can estimate it different ways. Sure, we can use Shannon's formula in some cases, which is really just Boltzmann's formula with different units.
Entropy is a thermodynamical property of a bit of stuff, regardless of what we know about it. The conservation of Gibbs free energy does not suddenly break down because we stop (or start) looking.
Obviously, a deck of cards can be in a lot of different microstates, I'm not sure what do you mean ? Consider that "macrostate" is another name for "distribution" ?
> There is indeed some overlap (I have personally worked for a couple of years on applying information theory to calculate entropy in glass-forming materials), but not enough that you can just apply random concepts from one field to the other. Basically, your interpretation is that "we know a lot about the system, therefore entropy is low", whilst in a physical system it's the other way around: "entropy is low, therefore we know a lot about it". Knowing something does not change the state of the system you are observing.
This is why having two different terms "entropy" and "lack of information" that correspond to the same underlying physical concept is problematic : it causes this kind of confusion.
Knowing a lot about a system is equivalent to having low entropy about it.
> Entropy itself is whatever it is even before we bother calculating it, and we can estimate it different ways. [...] Entropy is a thermodynamical property of a bit of stuff, regardless of what we know about it. The conservation of Gibbs free energy does not suddenly break down because we stop (or start) looking.
"Looking" (aka "measurement" or "observation") is not a "free" operation. To go back to the example of the deck of cards, the deck would have needed to be prepared beforehand to be "ordered", and the action of "looking" at it and to check in what order each card is in is not "free" either. In the same way, neither constructing an aligned spin system nor checking its alignment are "free".
As another example, consider the Szilard engine, which allows us to "extract" energy "from" information :
https://www.pnas.org/content/111/38/13786
(Semi-)Classical entropy is defined in terms of probability, it's a functional that depends on a specific probability distribution (aka macrostate) : it's the expected value (aka weighted average) over the surprisals (aka information contents) of all the possible outcomes (aka microstates).
(There's also a generalization of it for the situations where we have entangled microstates and quantum mechanics really come into play.)
As far as we know, this model works for all the situations where the two nuclear forces and/or relativistic effects can be neglected.
http://www.av8n.com/physics/thermo/entropy.html#sec-s-not-kn...
(Yes, it is indeed context-dependent.)
Life is just one big chemical reaction that's been going on for a billion years. It's structured only so-so - not perfectly. In sexually reproducing organisms, genes of two parents mix up randomly(ish) to create offspring, which would suggest a tree structure - except when it doesn't. Sometimes genes mix wrong. Gametes can and do accumulate random mutation. Viruses occasionally inject genes into places where they can get carried to future generations. Incest happens. Not all life forms reproduce sexually. Cells can pick up free-floating genetic information from the environment. At the level of single-cellular organisms, this is arguably the bulk of what's happening. Bacteria exchange genes like people exchange cooking recipes.
The way you take this messy reality and arrive at a "tree of life" (and it's always a tree of life, not the tree of life) is by looking at how some set of genes seem to have spread across life forms. It's always conditioned on what particular genetic marker you're looking at, and is equivalent to selecting an interesting spanning tree in a highly interconnected graph. Pick a different genetic marker, you'll get a different tree.
Sure, once you get to studying trees and dogs and humans, gene transfer becomes more tree-ish - but it's a difference of degree, not of a kind.
No? Tree structure is a simplified model of asexual reproduction, where each organism has one parent, not two.
Unidirectional acyclic graphs also allow for Neanderthals reproducing with humans, for random mutations, for bacteria exchanging genes asexually, and for genes inherited from virus infections. But "tree of life" is just so much more sexy than "unidirectional acyclic graph of life"
The biological classification matches intuition in overwhelming majority of situations.
All of these systems of categorization are necessarily arbitrary in a way, since all of life is a big messy tangle of related organisms, and there is nothing to clearly tell you where to draw lines to separate them. That's the source of your confusion right there. Turns out, groupings that seem obvious to someone who hasn't looked closely can be really difficult to delineate clearly.
So, biologists try to define rules by which to do that, which they can apply unambiguously. One of the possible rules to apply is that groups should be paraphyletic, i.e. only contain (some of the) organisms with a shared common ancestor, or monophyletic, i.e. contain all of the organisms with a shared common ancestor.
Other groupings do not fulfill those criteria, those are called polyphyletic. Grouping organisms that way has somewhat gone out of fashion, now that evolution is well understood. What this article is saying is that trees form a polyphyletic group. In addition to that, even just defining a group (for example, based on structural or functional properties of the plant) that neatly maps to what people usually consider to be a "tree" is harder than it sounds. Since all of that might be surprising, you see it here on HN.
This example seems reasonable in that way because there isn't some parallel definition of "tree".
A layman, on hearing that (according to evolutionary biologists) "birds are dinosaurs" might reasonably assume that evolutionary biologists will also say that dolphins are fish. Alas, no -- "dinosuar" has a parallel phylogenetic definition that differs from the lay one, but "fish" doesn't.
Botany is a source of this sort of confusion a lot. Raspberries and strawberries and blackberries are culinary berries, but not botanical berries. (A tomato is a botanical berry, though. -EDIT, said culinary originally.)
I'm of two minds about it. If you need a word, maybe it's best to use an existing one when there's a large overlap. But then again, the closeness of many legal terms ("murder", say) to their lay definitions arguably causes more confusion when those definitions differ. With biologists "just assume their meaning is totally different to yours" is a good heuristic, and with lawyers (or mathematicians talking about "knots" and "sets") the similarity causes perhaps more difficulty.
What’s surprising is that you can exclude sharks and rays from your definition of ‘fish’ and this statement will still be true - you are more closely related to a salmon than a salmon is to a shark.
We know that traits are heritable, so when you have a bunch of different organisms that exhibit the same characteristic, if you can trace back and determine they are all specialized descendants of some ancestor which first developed that characteristic, that’s the complete story right there.
But when we see the same behavior appear in different organisms without them sharing a common root for that characteristic that’s interesting precisely because we need another means to explain it.
I mean, if grizzlies and polar bears could interbreed even though their nearest common ancestor was, say, some kind of small Cretaceous rodent, then weld have some explaining to do, right?
[1] https://scienceblogs.com/gregladen/2010/09/09/one-could-say-...
I'm not confused about the categorical parts of biology. I don't understand it all, but that's OK, I don't need to. What's irritating is the pedantry that comes from articles like this.
If I wrote an article like, "There's no such thing as a strawberry, cryptographically," I imagine it would be entirely uninteresting.
If I write a tree categorization algorithm that categories what I call a "tree" as something else, my algorithm would be buggy.
But, in all seriousness, I didn't think the article was like that at all. The title is meant to grab your attention and then tell you lots of (to me, at least) interesting things about the evolution of trees.
If you were able to write insightfully about strawberries from a cryptography perspective, that title you suggested might be completely fine.
That said, I, too, remember people telling me things about how X wasn't actually Y because ...
IMO, these types of arguments come across as pedantic when they're framed as basically being just about using words the right way, without also telling you something deeper about why something looks like an X but in many non-obvious ways is closer to a Y.
My favorite example of that is the statement "Black is not a color". I heard that a lot as a child, and I would agree that that is unnecessarily pedantic. Learning about how color perception works, and how black is unlike other colors, is still super interesting.
It’s why we have scientific names in Latin, military beds are called a rack, and whose life matters.
Is this (joke) because it's a living fossil with a long lifespan, or something more?
To me "tree" simply has to do with being big and tall. Just like the term "whale" excludes porpoises and dolphins, purely based on size, with toothed whales and baleen whales being the actual biological subdivisions of cetacean. (and of course with the oddity that dolphins and porpoises are not whales per se, but they are members of toothed whales i.e. odontocetes)
On another level, should we obtain knowledge of a distant, life-filled world orbiting a distant star, we could expect it to be forested by woody plants, and filled with crabs.
> When we say a bird is a dinosaur
Lol no, you're not getting away with that. As long as you bastards are going to keep harassing the populace with the "fun fact" that birds are dinosaurs, then fish are monophyletic, dinosaurs are fish, birds are fish, and so are whales. Eat what you ordered.
I'm definitely no expert, but as kids in the nineties, banana plants were always cited as the example of how large plants are not always trees. Did they get recategorized?
I am expecting responses to the tune of "eyes are not that complicated" and "wood is actually incredibly complex."
Do all creatures with a brain share a common ancestor? Even more fundamentally, do all creatures share a common ancestor? The answer appears to be "maybe," which I find to be fascinating [1].
1.https://www.researchgate.net/publication/44593277_A_formal_t...
I'm very curious about why this comment got downvoted.
1.https://en.m.wikipedia.org/wiki/Cephalopod_eye
2.https://en.m.wikipedia.org/wiki/Parallel_evolution > Parallel evolution is the similar development of a trait in distinct species that are not closely related, but share a similar original trait in response to similar evolutionary pressure.
3. https://en.m.wikipedia.org/wiki/Convergent_evolution > Convergent evolution is the independent evolution of similar features in species of different periods or epochs in time.
OK, OK, I'll go check on that debate... But given the quotes of the definitions you posted here, it sure seems pseudo-.
Pineapples do not, by anybody's definition, grow on trees.
A "monophyletic" set of organisms is defined to be a set for which there exists a common ancestor, which ancestor has no descendents outside the set. (Try to ignore sexual reproduction when thinking about that; think about "lineages" of "species" first.)
This concept is the basis of modern biological taxonomy.
A "tree" is a plant with very pronounced woody structures.
There is nothing about the botanical concept of a "tree" that immediately suggests they should be monophyletic. At least to someone with general biological knowledge, it would seem entirely possible that this woody morphological form could have arisen multiple times independently, and indeed that is what one would suspect, given knowledge of the prevalence of convergent evolution elsewhere.