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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

#21

Post by seandhuine »

Flankk wrote: post #15
seandhuine wrote: post #6

Earlier quoted context omitted.

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.

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."

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

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

#22

Post by sixstringtheory »

westurner wrote: post #13
User23 wrote: 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.

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 (mor…

My assumption as someone not formally trained in advanced biology is that the phylogenetic tree has an implied arrow of time, and each node of the tree is a point where a mutation occurred that was sufficient to create a new and separate family/order/genus/etc afterwards, with leaf nodes representing species.

In this sense a cycle can’t occur because a branch would need to reach back in time and rejoin with an ancestral branch. It would be a different kind of grandfather paradox: who would be the ancestor and who the descendant in a cycle?

Maybe someone could help point out the flaws in this model.

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

#23

Post by pphysch »

Tagbert wrote: post #11
MathMonkeyMan wrote: post #7

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.

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.

Also applies to "individuals". It's all fuzzy

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

#24

Post by flobosg »

sixstringtheory wrote: post #22
westurner wrote: post #13

Earlier quoted context omitted.

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 (mor…

My assumption as someone not formally trained in advanced biology is that the phylogenetic tree has an implied arrow of time, and each node of the tree is a point where a mutation occurred that was sufficient to create a new and separate family/order/genus/etc afterwards, with leaf nodes representing species. In this sense a cycle can’t occur because a branch would need to reach back in time and rejoin with an ancest…

Your assumption is true, but only for rooted phylogenetic trees. In unrooted trees the node representing the most ancestral state is absent and thus no directionality can be determined.

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

#25

Post by lurquer »

AlotOfReading wrote: post #20
em-bee wrote: post #18

Earlier quoted context omitted.

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 th…

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…

It isn’t a continuum, though. There are distinct discontinuities. Chromosome count is one such example. Polar bears and grizzlies have 74 chromosomes. A panda has 42.

You can’t gradually go from one to the other.

Absent some mechanism we don’t know about, conception simply doesn’t work when the sperm and eggs have different numbers of chromosomes.

To be clear, the concept of chromosome isn’t as objective as one might think… nevertheless, it’s an example of the type of genetic difference that simply precludes reproduction.

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

#26

Post by whatshisface »

seandhuine wrote: post #21
Flankk wrote: post #15

Earlier quoted context omitted.

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."

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.

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

#27

Post by agumonkey »

Swizec wrote: post #12
agumonkey wrote: post #10

Earlier quoted context omitted.

I'd go full mad and say the space continuum of life. Context is what drives life. Similar context breed similar forces and genes.

> Similar context breed similar forces and genes Flight is so useful, it evolved 4 times independently. With very similar solutions. https://en.wikipedia.org/wiki/Flying_and_gliding_animals And crustaceans keep evolving into crabs. https://www.popsci.com/story/animals/why-everything-becomes-... And who even knows how many different times high level intelligence has evolved. I think octopi, birds, and mammals are all…

I believe Darwin envisioned that, and the Tree of Evolution was just an introductory notion (I never read his book) before going into subtler reasons for new traits.

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

#28

Post by AlotOfReading »

lurquer wrote: post #25
AlotOfReading wrote: post #20

Earlier quoted context omitted.

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…

It isn’t a continuum, though. There are distinct discontinuities. Chromosome count is one such example. Polar bears and grizzlies have 74 chromosomes. A panda has 42. You can’t gradually go from one to the other. Absent some mechanism we don’t know about, conception simply doesn’t work when the sperm and eggs have different numbers of chromosomes. To be clear, the concept of chromosome isn’t as objective as one might…

Horses and Donkeys have differing numbers of chromosomes and yet (extremely rarely) produce fertile mules. In a more common case, women with down's syndrome have an extra chromosome and yet are sometimes fertile. I understand that this is extremely common with plants, but that's pretty far outside my wheelhouse.

I don't think we're disagreeing here, just simplifying like all conversations about biology.

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