5 ms·

Evolution is not a tree of life but a fuzzy network

100 points by ALee 4y ago

Flankk 4y ago
Darwin believed that each successive generation of a species had increasing mutations leading to a gradual divergence. Another school of thought believes that a species remains at equilibrium until some environmental stressor activates a rapid divergence. If this "punctuated equilibrium" is true, climate change will give rise to many new species, as would all mass extinctions.
- seandhuine 4y ago
  What Darwin knew about biology is incommensurate with a modern understanding of the word "mutation". A generation later than him, biologists still believed cells were formless blobs of jelly, so to speak. Punctuated equilibrium is even less defensible given our present understanding of the molecular basis of genetics.
  - Flankk 4y ago
    Mutation means the same thing now as it did back then. What has changed is that we now understand how it works. The concept of punctuated equilibrium was introduced in 1972. It is the leading theory based on present understanding. I'm not sure what you mean by "less defensible."
    - seandhuine 4y ago
      That a hypothesis that has no feasible molecular basis can be called "leading" is a mark of the bankruptcy of Darwinian evolutionary theory.
      - whatshisface 4y ago
        Punctuated equilibrium still involves gradual Darwinian change, but over very short periods of time compared to the long periods where the species is adapted as well as it can be (without major, unlikely changes) to its present environment.
        seandhuine 4y ago
        I'm hoping that gradually over a very short period of time folks will realize the contradiction in terms that is called "punctuated equilibrium". It has no feasible molecular basis. Without such, it might as well be fairy dust for its explanatory power. But gradual fairy dust, that operates over very short periods of time. The pertinent question remains: at the molecular level, how?
        whatshisface 4y ago
        Large interbreeding populations are "locked in" and recessive traits are rare. Small isolated populations can make recessive traits permanent. This is well-known to everbody who has stopped to consider what conditions produce major genetic changes in human morphology (inbreeding). Large gene pools protect against morphological changes in humans and animals alike. Species are sent back and forth between those two extremes by changes in the environment brought on by our planet's constantly changing climate, topography and ecosystems. Sometimes, when the isolation ends, the combination of made-permanent recessive traits turns out to be harmful and the isolated population is replaced by the larger one (if the larger one survived), and other times it is helpful and they spread out into the larger environment. It isn't a contradiction any more than first and second gear on your bike are - you can't have them both at once, but they are switched between by systems external to the bike itself (the rider). The idea is that every species is descendant from a highly inbred population of another species. Curiously, this happens in the Bible (Noah's ark). The molecular basis is the same as that of Darwinian evolution (transcription errors plus whole-organism natural selection), combined with the usual laws of population genetics.
        seandhuine 4y ago
        Right at the end of all that, there's an IOU for a molecular explanation of puntuated equilibrium. How is the IOU cashed out? Oh, "transcription errors" plus some non-molecular magic. Transcription errors...think about that. Gradual errors (which are nearly always either neutral or deleterious -- in the real world, mind) that suddenly operate over a very short period to create a new species. Let me attempt to paraphrase the motivation for PE: "We can't see it happening because it's gradual, but it needs a catastrophe oh there it just happened!" Or it must have, because reasons. Errors, or something. Fairy dust.
oldgradstudent 4y ago
I've always said it's not the Tree of Life, but rather the DAG of Life.
- User23 4y ago
  It may not even be acyclic. For example it appears fetal DNA is permanently detectable in mothers and may even have health benefits that conceivably increase the mother’s evolutionary fitness.
  - jfarmer 4y ago
    The hypergraph of life?
    - taliesinb 4y ago
      Yup. Genetic recombination means some genotypes are the result of crossover of two parents. Horizontal gene transfer has a similar implication. This means the true structure is a directed hypergraph.
  - westurner 4y ago
    How can it be acyclic? A phylogenetic tree is a DAG. Organisms sharing DNA? That's definitely a cyclic graph. If there were Schema.org/Animal and/or schema:AnimalInstance classes, what do you list under a :breed property to indicate that e.g. one parent is breed X and another is breed Y?! That's definitely not a DAG; that looks like a feature clustering dendrogram. DNA barcoding > Mismatches between conventional (morphological) and barcode based identification https://en.wikipedia.org/wiki/DNA_barcoding#Mismatches_between_conventional_(morphological)_and_barcode_based_identification https://en.wikipedia.org/wiki/DNA_barcoding#Mismatches_betwe... Taxonomy (biology) https://en.wikipedia.org/wiki/Taxonomy_(biology) https://en.wikipedia.org/wiki/Taxonomy_(biology) FWIU, there's at least one DNA-based organism naming system; IDK how much that helps resolve :Animal and :AnimalInstance if at all?
    - sixstringtheory 4y ago
peter303 4y ago
5% - 8% of human genome appears to be from [retro]virus inserts. Thats outside the tree of descent.
MathMonkeyMan 4y ago
It's certainly a tree of individuals, though with single-celled division even that is not clear. Things get tricky when you talk about species, because species are (arbitrary?) equivalency classes of individuals.
- Tagbert 4y ago
  Species are approximations that can be useful to discuss populations but they are very fuzzy at the edges. There is not single definition of species that applies in all cases. In that sense they are somewhat arbitrary but terms can be arbitrary and useful at the same time.
  - lurquer 4y ago
    It seems the article is merely about the ‘wonder’ and ‘Eureka’ moment of realizing one’s definition of species is over or under inclusive. To summarize the article (using a more familiar animal): Polar Bears and Grizzly Bears are different species… Yet they can reproduce! Good god, that means they were once the same species, then different species, and now the same species again! My minds blown! Silly…
    - em-bee 4y ago
      that was my thought too. the general principle hasn't changed, just the understanding of how much divergence is necessary before the branches are truly separate. what's surprising is that it took so long to realize that. we only need to look at dogs to see an immense variety that is still interbreedable. and if dogs can, why not sharks or bears? i think the only reason we don't don't see that more often is because they each live in different habitats and opportunities for interbreeding are rare. i expect genetics will be able to give a better answer as to how much variety is needed before interbreeding no longer works.
      - AlotOfReading 4y ago
        There isn't a single answer to give re: the viability of interbreeding. It depends on the particular individuals and the particulars of their offspring and a whole lot of environmental luck besides. As individuals get farther apart, the chances of successful reproduction simply decrease. Beyond a certain point, fertilization simply ceases to take place and the issue is moot. In general, the babies that are born have already passed through a nightmarishly difficult biological gauntlet to survive. If they fail at any stage, the pregnancy is simply terminated. The majority of fertilizations never lead to births as a result.
LB232323 4y ago
Evolutionary biology is sincerely beautiful, the biological history of our species is a meta-history to human history. On a grander scale, the biological history of life itself weaves the career of the human race into a context of profound interconnectivity. It's natural to contemplate your origins, the place and culture you come from, your ancestors and the history of your family. It's even more profound to contemplate your biological origins, your ancestry into species unrecognizable from your own. It really is a humbling experience to trace a path thousands and even millions of years into the past. The end result is an increased appreciation for the beauty of nature and for the inseparable unity of the human race.
- deltaonefour 4y ago
  But also remember that billions died so you could exist. Natural selection is what it is... selection, and those that are not selected.. are silenced. Be awed by the beauty but also be wary of the horror that is existence. Awe, beauty and horror are human concepts. Do not let that bias cloud your logic. When something is beautiful to you, you become blind to the horror. When something is horrible to you, you become blind to the beauty. Best way to view something, is to ignore both, and judge it dispassionately. Nothing is beautiful, nothing is horrible. That is true understanding.
- ygmelnikova 4y ago
- packetlost 4y ago
  What's interesting is if you frame evolution as a system for producing and propagating increasingly efficient (given a context or state) behaviors through time (such that "living things" can amass more energy or manipulate their environment more), and take into account what makes humans unique, it's really eye opening as to the nature of intelligence, learning, emotions, and really just why we are the way we are. It seems the things that make humanity unique is how extremely efficient we are at propagating knowledge through time via means that are not merely genetic, yet our brains are still fundamentally limited by the chemical processes that make them up. What would happen if we were able to find a way to create a self-regulating, autofeedback system that made decisions at the speed of, say, electricity (nearly c)
newaccount1234 4y ago
Seeing that the article was about the "Tree of Life" metaphor and Coral, it is surprising that it didn't mention that Darwin actually suggested that a "Coral of Life" metaphor was superior to a "Tree of Life" metaphor in his notebooks (or maybe I missed it?). I'm not a biologist, but I found this paper (Podani, 2019) about the "Coral of Life" metaphor interesting: https://link.springer.com/content/pdf/10.1007/s11692-019-09474-w.pdf https://link.springer.com/content/pdf/10.1007/s11692-019-094...
- peterburkimsher 4y ago
  A couple of weeks ago, I went to Fiji and met my parents there. We stayed at Navini Island Resort, the kind of luxury I'd never choose for personal travels, but it was a nice holiday on an island in the South Pacific. The corals were particularly memorable. My dad's also from a comp sci background, and noticed how the coral colours are RGB. From other HN posts, I'd been thinking about the Tree of Life, and wondering about roots. Trees are basically mirrored around ground level. But coral grow without roots! So yes, I like the "Coral of Life" metaphor. It fits well with the Big Bang model, of having a single starting point and growing from there.
xyzrr 4y ago
I find that a lot of things are really DAGs or full on graphs but are easier to reason about as roughly trees. Website structures, for example. All knowledge, even. For some reason, trees are so much easier to hold in the head.
deleted 4y ago
[deleted]

100 points by ALee 4y ago

Darwin believed that each successive generation of a species had increasing mutations leading to a gradual divergence. Another school of thought believes that a species remains at equilibrium until some environmental stressor activates a rapid divergence. If this "punctuated equilibrium" is true, climate change will give rise to many new species, as would all mass extinctions.

seandhuine 4y ago
What Darwin knew about biology is incommensurate with a modern understanding of the word "mutation". A generation later than him, biologists still believed cells were formless blobs of jelly, so to speak. Punctuated equilibrium is even less defensible given our present understanding of the molecular basis of genetics.
- Flankk 4y ago
  Mutation means the same thing now as it did back then. What has changed is that we now understand how it works. The concept of punctuated equilibrium was introduced in 1972. It is the leading theory based on present understanding. I'm not sure what you mean by "less defensible."
  - seandhuine 4y ago
    That a hypothesis that has no feasible molecular basis can be called "leading" is a mark of the bankruptcy of Darwinian evolutionary theory.
    - whatshisface 4y ago
      Punctuated equilibrium still involves gradual Darwinian change, but over very short periods of time compared to the long periods where the species is adapted as well as it can be (without major, unlikely changes) to its present environment.
      - seandhuine 4y ago
        I'm hoping that gradually over a very short period of time folks will realize the contradiction in terms that is called "punctuated equilibrium". It has no feasible molecular basis. Without such, it might as well be fairy dust for its explanatory power. But gradual fairy dust, that operates over very short periods of time. The pertinent question remains: at the molecular level, how?
        whatshisface 4y ago
        Large interbreeding populations are "locked in" and recessive traits are rare. Small isolated populations can make recessive traits permanent. This is well-known to everbody who has stopped to consider what conditions produce major genetic changes in human morphology (inbreeding). Large gene pools protect against morphological changes in humans and animals alike. Species are sent back and forth between those two extremes by changes in the environment brought on by our planet's constantly changing climate, topography and ecosystems. Sometimes, when the isolation ends, the combination of made-permanent recessive traits turns out to be harmful and the isolated population is replaced by the larger one (if the larger one survived), and other times it is helpful and they spread out into the larger environment. It isn't a contradiction any more than first and second gear on your bike are - you can't have them both at once, but they are switched between by systems external to the bike itself (the rider). The idea is that every species is descendant from a highly inbred population of another species. Curiously, this happens in the Bible (Noah's ark). The molecular basis is the same as that of Darwinian evolution (transcription errors plus whole-organism natural selection), combined with the usual laws of population genetics.
        seandhuine 4y ago
        Right at the end of all that, there's an IOU for a molecular explanation of puntuated equilibrium. How is the IOU cashed out? Oh, "transcription errors" plus some non-molecular magic. Transcription errors...think about that. Gradual errors (which are nearly always either neutral or deleterious -- in the real world, mind) that suddenly operate over a very short period to create a new species. Let me attempt to paraphrase the motivation for PE: "We can't see it happening because it's gradual, but it needs a catastrophe oh there it just happened!" Or it must have, because reasons. Errors, or something. Fairy dust.

oldgradstudent 4y ago

I've always said it's not the Tree of Life, but rather the DAG of Life.

User23 4y ago
It may not even be acyclic. For example it appears fetal DNA is permanently detectable in mothers and may even have health benefits that conceivably increase the mother’s evolutionary fitness.
- jfarmer 4y ago
  The hypergraph of life?
  - taliesinb 4y ago
    Yup. Genetic recombination means some genotypes are the result of crossover of two parents. Horizontal gene transfer has a similar implication. This means the true structure is a directed hypergraph.
- westurner 4y ago
  How can it be acyclic? A phylogenetic tree is a DAG. Organisms sharing DNA? That's definitely a cyclic graph. If there were Schema.org/Animal and/or schema:AnimalInstance classes, what do you list under a :breed property to indicate that e.g. one parent is breed X and another is breed Y?! That's definitely not a DAG; that looks like a feature clustering dendrogram. DNA barcoding > Mismatches between conventional (morphological) and barcode based identification https://en.wikipedia.org/wiki/DNA_barcoding#Mismatches_between_conventional_(morphological)_and_barcode_based_identification https://en.wikipedia.org/wiki/DNA_barcoding#Mismatches_betwe... Taxonomy (biology) https://en.wikipedia.org/wiki/Taxonomy_(biology) https://en.wikipedia.org/wiki/Taxonomy_(biology) FWIU, there's at least one DNA-based organism naming system; IDK how much that helps resolve :Animal and :AnimalInstance if at all?
  - sixstringtheory 4y ago

peter303 4y ago

5% - 8% of human genome appears to be from [retro]virus inserts. Thats outside the tree of descent.

MathMonkeyMan 4y ago

It's certainly a tree of individuals, though with single-celled division even that is not clear. Things get tricky when you talk about species, because species are (arbitrary?) equivalency classes of individuals.

Tagbert 4y ago
Species are approximations that can be useful to discuss populations but they are very fuzzy at the edges. There is not single definition of species that applies in all cases. In that sense they are somewhat arbitrary but terms can be arbitrary and useful at the same time.
- lurquer 4y ago
  It seems the article is merely about the ‘wonder’ and ‘Eureka’ moment of realizing one’s definition of species is over or under inclusive. To summarize the article (using a more familiar animal): Polar Bears and Grizzly Bears are different species… Yet they can reproduce! Good god, that means they were once the same species, then different species, and now the same species again! My minds blown! Silly…
  - em-bee 4y ago
    that was my thought too. the general principle hasn't changed, just the understanding of how much divergence is necessary before the branches are truly separate. what's surprising is that it took so long to realize that. we only need to look at dogs to see an immense variety that is still interbreedable. and if dogs can, why not sharks or bears? i think the only reason we don't don't see that more often is because they each live in different habitats and opportunities for interbreeding are rare. i expect genetics will be able to give a better answer as to how much variety is needed before interbreeding no longer works.
    - AlotOfReading 4y ago
      There isn't a single answer to give re: the viability of interbreeding. It depends on the particular individuals and the particulars of their offspring and a whole lot of environmental luck besides. As individuals get farther apart, the chances of successful reproduction simply decrease. Beyond a certain point, fertilization simply ceases to take place and the issue is moot. In general, the babies that are born have already passed through a nightmarishly difficult biological gauntlet to survive. If they fail at any stage, the pregnancy is simply terminated. The majority of fertilizations never lead to births as a result.

LB232323 4y ago

Evolutionary biology is sincerely beautiful, the biological history of our species is a meta-history to human history. On a grander scale, the biological history of life itself weaves the career of the human race into a context of profound interconnectivity. It's natural to contemplate your origins, the place and culture you come from, your ancestors and the history of your family. It's even more profound to contemplate your biological origins, your ancestry into species unrecognizable from your own. It really is a humbling experience to trace a path thousands and even millions of years into the past. The end result is an increased appreciation for the beauty of nature and for the inseparable unity of the human race.

deltaonefour 4y ago
But also remember that billions died so you could exist. Natural selection is what it is... selection, and those that are not selected.. are silenced. Be awed by the beauty but also be wary of the horror that is existence. Awe, beauty and horror are human concepts. Do not let that bias cloud your logic. When something is beautiful to you, you become blind to the horror. When something is horrible to you, you become blind to the beauty. Best way to view something, is to ignore both, and judge it dispassionately. Nothing is beautiful, nothing is horrible. That is true understanding.
ygmelnikova 4y ago
packetlost 4y ago
What's interesting is if you frame evolution as a system for producing and propagating increasingly efficient (given a context or state) behaviors through time (such that "living things" can amass more energy or manipulate their environment more), and take into account what makes humans unique, it's really eye opening as to the nature of intelligence, learning, emotions, and really just why we are the way we are. It seems the things that make humanity unique is how extremely efficient we are at propagating knowledge through time via means that are not merely genetic, yet our brains are still fundamentally limited by the chemical processes that make them up. What would happen if we were able to find a way to create a self-regulating, autofeedback system that made decisions at the speed of, say, electricity (nearly c)

newaccount1234 4y ago

Seeing that the article was about the "Tree of Life" metaphor and Coral, it is surprising that it didn't mention that Darwin actually suggested that a "Coral of Life" metaphor was superior to a "Tree of Life" metaphor in his notebooks (or maybe I missed it?). I'm not a biologist, but I found this paper (Podani, 2019) about the "Coral of Life" metaphor interesting: https://link.springer.com/content/pdf/10.1007/s11692-019-09474-w.pdf https://link.springer.com/content/pdf/10.1007/s11692-019-094...

peterburkimsher 4y ago
A couple of weeks ago, I went to Fiji and met my parents there. We stayed at Navini Island Resort, the kind of luxury I'd never choose for personal travels, but it was a nice holiday on an island in the South Pacific. The corals were particularly memorable. My dad's also from a comp sci background, and noticed how the coral colours are RGB. From other HN posts, I'd been thinking about the Tree of Life, and wondering about roots. Trees are basically mirrored around ground level. But coral grow without roots! So yes, I like the "Coral of Life" metaphor. It fits well with the Big Bang model, of having a single starting point and growing from there.

xyzrr 4y ago

I find that a lot of things are really DAGs or full on graphs but are easier to reason about as roughly trees. Website structures, for example. All knowledge, even. For some reason, trees are so much easier to hold in the head.

deleted 4y ago

[deleted]