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Long term evolution experiments (LTEE) reveal too much complexity to be “disentangled”

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E. coli 1000x/USDA

So much for Darwinism. Joshua B. Plotkin writes at Nature:

Ecological interactions emerge spontaneously in an experimental study of bacterial populations cultured for 60,000 generations, and sustain rapid evolution by natural selection. (paywall)

Yes, that’s the abstract. It’s a model of economy.

This is from the article:

The authors’ most profound discovery is the spontaneous emergence of ecological interactions that fuel ongoing evolution (Fig. 1). Persistent subgroups have previously been identified in one of Lenski’s populations, but Good et al. reveal that at least 9 of the populations divide into two separate clades (genetic groups). These clades co-exist for tens of thousands of generations, and so must be maintained by some form of interdependence.

These emergent ecologies sustain ongoing adaptation at a roughly constant pace throughout the entire experiment, even though the benefits of ongoing adaptation to the entire population have been shown to decline over time4. Mutations sweep through a clade at generation 50,000 nearly as frequently and rapidly as they sweep through a population at generation 5,000. Indeed, the characteristic pattern of multiple competing beneficial mutations7 that occurs in the early phase of Lenski’s populations continues to occur in each clade throughout the experiment.

For all the statistical regularities that Good et al. reveal, the discovery of pervasive ecological interactions in the LTEE will complicate future work.

Not only can ecological and evolutionary processes co-occur, but it now seems impossible that they can be disentangled. More.

Ecology and evolution cannot be disentangled? Ramming textbook Darwinism down everyone’s throat without coercion just got a little harder.

See also: Study: Darwinian fitness does not overcome mutational decay during tens of thousands of bacteria generations

21 Replies to “Long term evolution experiments (LTEE) reveal too much complexity to be “disentangled”

  1. 1
    PaV says:

    This is the most intriguing part of the quote–without acces to the entire article:

    Persistent subgroups have previously been identified in one of Lenski’s populations, but Good et al. reveal that at least 9 of the populations divide into two separate clades (genetic groups). These clades co-exist for tens of thousands of generations, and so must be maintained by some form of interdependence.

    This contradicts Darwin’s central assertion of the OoS: the Law of Divergence. That is, one of these ‘clades’ should have displace the other ‘clade’ entirely. But, instead, they co-exist.

    This ‘co-existence’ only makes sense from a teleological perspective.

  2. 2
    Dionisio says:

    Embedded Variability Framework (EVF), fully designed and implemented within the biological systems. That’s all.
    The rest is speculative gossiping of the worst kind.
    Still don’t get it?
    Ok, let’s try another approach.
    Ever heard of MSFT .NET?
    No? OK, read about it: https://www.microsoft.com/net/
    Then you might understand what EVF is all about.

  3. 3
    Bob O'H says:

    PaV @ 1 – huh? I’m not aware of Darwin*s “Law of Divergence”, and TBH I can’t see how any laws about divergence would apply here. We’re well aware of different ways in which groups can co-exist, so I don’t see why there has to be a problem here. In the papers the authors point to a couple of similar examples they have found in the past.

  4. 4
    PaV says:

    Bob O’H:

    Are you aware of Darwin’s “principle of divergence”?

    The principle is that one species, having evolved, will displace the ‘parent’ species. This doesn’t happen here. Parent and progeny live side-by-side.

    Natural selection, as has just been remarked, leads to divergence of character and to much extinction of the less improved and intermediate forms of life. (Origin, 128)

    From this paper.

  5. 5
    Bob O'H says:

    PaV – The quote you give is about divergence of character. In ecology it’s called competitive exclusion. There’s really no conflict with what’s going on here – presumably the two lineages are specialising on different resources, so they are diverging in their traits. Whether this fits in with what Darwin suggested doesn’t bother me too much – we know that he was wrong about a lot of things. What’s more important is if we can explain these results using our current knowledge of ecology and evolution.

  6. 6
    News says:

    Bob O’H at 5: “What’s more important is if we can explain these results using our current knowledge of ecology and evolution.”

    Ah! Anyone can explain anything according to their current knowledge. That’s not where the bar is set.

    The question of whether current models offer better interpretations than others is where the bar is set.

  7. 7
    ET says:

    PaV:

    This contradicts Darwin’s central assertion of the OoS: the Law of Divergence. That is, one of these ‘clades’ should have displace the other ‘clade’ entirely. But, instead, they co-exist.

    Earlier this year I read a book titled “Life”, edited by John Brockman. It has chapters with Dawkins, Venter, Dyson, Ridley, Jones, et al. In Chapter 9 Dawkins says the following during an interview about a discussion with Dyson:

    Schoolboy howler. I did use that phrase, and that was about that one point- about suggesting that natural selection is about one species displacing another species, and that is a schoolboy howler. A lot of people think Darwinian selection means that one species goes extinct and another takes over. That is not Darwinian selection; that’s species extinction. It’s a totally different kind of process.

    Then Venter concurred

  8. 8
    Origenes says:

    So, the fact that countless transitional species have all been erased has nothing to do with darwinian selection? Thinking that it does is a “schoolboy howler”?

  9. 9
    ET says:

    I think Dawkins is playing with words. Darwinian selection is about the elimination of the less fit. And if a new species is more fit than its parent population then it should be Darwinian selection. However we do know that many different species can occupy the same ecosystem so it may not be as simple as that.

  10. 10
    Bob O'H says:

    News @ 6 – go on then. Tell me what explanation ID offers for these data.

    FWIW, my point was that we don’t use 150 year old theories to explain phenomena we observe now – we use current theories (which, yes, may have been developed from 150 years ago, but it’s rare that they will be exactly the same).

  11. 11
    ET says:

    Bob O’H:

    FWIW, my point was that we don’t use 150 year old theories to explain phenomena we observe now – we use current theories (which, yes, may have been developed from 150 years ago, but it’s rare that they will be exactly the same).

    Which current theories are you talking about?

  12. 12
    goodusername says:

    Origenes,

    So, the fact that countless transitional species have all been erased has nothing to do with darwinian selection? Thinking that it does is a “schoolboy howler”?

    Darwin was attempting to explain why we have such a diversity of life around us, and how populations adapt. So his theory is about how diversity increases, and what drives change in a population.
    Species A invading a territory and replacing, or wiping out, species B is neither. Extinction is a decrease in diversity and no change in a population has taken place.

    Sure species compete and even wipe each other out at times; people knew about that long before Darwin came along. They aren’t denying that that happens, but it’s hardly evolution, and that isn’t what Darwinism “is about”.

  13. 13
    Origenes says:

    Goodusername @12,

    I was talking about darwinian selection, which, as we all know, only acts on what already exists and therefore does not create anything — selection explains only why some things are not, not why some things are.
    You are, instead, talking about evolutionary change which is allegedly produced by random mutations.
    Now, darwinian selection is in fact a process of elimination, which is, rather obviously I would say, closely linked to extinction.

    Natural selection is a sieve. It creates nothing, as is so often assumed; it only sifts. It retains only what variability puts into the sieve. Whence the material comes that is put into it, should be kept separate from the theory of its selection. How the struggle for existence sifts is one question; how that which is sifted arose is another.
    [Hugo de Vries]

    . . . it is indeed the animal or plant breeder who selects certain superior individuals to serve as the breeding stock of the next generation. But, strictly speaking, there is no such agent involved in natural selection. What Darwin called natural selection is actually a process of elimination.
    [Ernst Mayr, ‘What Evolution is’, (117)]

  14. 14
    PaV says:

    Bob O’H:

    Whether this fits in with what Darwin suggested doesn’t bother me too much – we know that he was wrong about a lot of things. What’s more important is if we can explain these results using our current knowledge of ecology and evolution.

    So, you’re throwing Darwinism to the one-side. OK, then what theory explains evolution?

    Random genetic drift with an occasional assist from NS?

    Can this explain the Cambrian Explosion? Yes, or no.

    As Origines points out above, there are very few intermediates. Will random genetic drift + NS, or whatever prevailing scientific consensus is in effect, explain the absence of these intermediate forms? Or, are intermediate forms not needed?

    But, of course, if intermediate forms are needed, then extinction must be invoked, which is part-and-parcel of the Principle of Divergence.

    Hand-waving won’t do.

  15. 15
    Bob O'H says:

    PaV – modern biology does the trick quite nicely. See my explanation at 5. It may be that there’s another explanation, but I honestly don’t see any conflict with the results here and modern theory. The adaptive dynamics guys have lots of models where they produce bifurcations like this – they call it evolutionary branching. It’s also possible that one of the branches will die out, but it’s taking a long time.

    TBH, I’d like to see a stronger argument for why these results are so unlikely (and, to be fair, I’d also like to see more research on what these bacteria are doing, i.e. more about the mechanics).

    BTW, as Denyse has dropped out of this discussion, can you help her out by telling me what explanation ID offers for these data?

  16. 16
    PaV says:

    Bob O’H:

    There’s really no conflict with what’s going on here – presumably the two lineages are specialising on different resources, so they are diverging in their traits.

    “There’s really no conflict …”, but then, “presumably the two lineages are specializing on different resources.”

    I guess this is how evolutionary theory works: no conflicts exist because we can always come up with some explanation for it—even if we don’t know if the explanation holds water.

    Are you sure that there are two different resources involved?

    I don’t think that’s the point the authors are trying to make. Instead, they see two “genetic groups” living side-by-side.

    As to the ID reasoning: the species is “designed” to maintain a genetic diversity it wouldn’t otherwise have if only ONE “genetic group” formed the given culture. This gives it the best chance at long-term survival given variable environmental conditions over time.

  17. 17
    Origenes says:

    Bob O’H @15: as Denyse has dropped out of this discussion, can you help her out by telling me what explanation ID offers for these data?

    Which data? The untraceable intermediate forms postulated by Darwin?

  18. 18
    ET says:

    Bob O’H:

    BTW, as Denyse has dropped out of this discussion, can you help her out by telling me what explanation ID offers for these data?

    Creation explains the data as reproduction and variation within a Kind. And your imagined modern theory doesn’t have a mechanism capable of producing anything but more populations of prokaryotes given starting populations of prokaryotes. And that means your alleged modern theory cannot explain the diversity of life.

  19. 19
    Origenes says:

    ET @18: … your imagined modern theory doesn’t have a mechanism capable of producing anything but more populations of prokaryotes given starting populations of prokaryotes.

    The mechanism is not natural selection, at least not according to prof PZ Meyers:

    I think if selection were always the rule, then we’d never have evolved beyond prokaryotes — all that fancy stuff eukaryotes added just gets in the way of the one true business of evolution, reproduction…

  20. 20
    ET says:

    Gee Origenes, now I owe PZ an apology. Perhaps he isn’t as stupid and ignorant as I have been saying. 😉

  21. 21
    Bob O'H says:

    PaV @ 16 –

    I guess this is how evolutionary theory works: no conflicts exist because we can always come up with some explanation for it—even if we don’t know if the explanation holds water.

    Are you sure that there are two different resources involved?

    I’m not sure. But this can be tested, to see if the explanation holds water (by looking at the differences between the two groups, to see what they are doing differently. If they are specialising on different resources, that suggests that being able to use both means that one source can’t be used as efficiently, for example, so that can be tested). I hope this is being done – it’s an obvious next question to ask.

    As to the ID reasoning: the species is “designed” to maintain a genetic diversity it wouldn’t otherwise have if only ONE “genetic group” formed the given culture. This gives it the best chance at long-term survival given variable environmental conditions over time.

    How would you test this idea? Also, why two groups, rather than (say) one large gene pool?

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