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Evolution is not a tree of life but a fuzzy network

aeon.co

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Re: Evolution is not a tree of life but a fuzzy network

#31
post #8
post #5

Earlier quoted context omitted.

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.

The hypergraph of life?

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.

Re: Evolution is not a tree of life but a fuzzy network

#32

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-…

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.

Re: Evolution is not a tree of life but a fuzzy network

#33
post #9

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 contempl…

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)

Re: Evolution is not a tree of life but a fuzzy network

#34

Earlier quoted context omitted.

That a hypothesis that has no feasible molecular basis can be called "leading" is a mark of the bankruptcy of Darwinian evolutionary theory.

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.

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?

Re: Evolution is not a tree of life but a fuzzy network

#35

Earlier quoted context omitted.

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.

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?

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.

Re: Evolution is not a tree of life but a fuzzy network

#36

Earlier quoted context omitted.

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?

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 extr…

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.
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