Design by Natural Selection: The LTEE

Lenski’s Long Term Evolutionary Experiment

Richard Lenski began the LTEE with 12 populations (six Ara^+ and six Ara^-) of the bacterium Escherichia coli on 24th February, 1988. The experiment is currently housed at Michigan State University and has run continuously apart from a short break while relocating to the present site and another during the height of the Covid-19 outbreak.

The method is very straightforward. Each 24 hours, from flasks of the bacterium in a growth medium known as Davis minimal broth dosed with glucose at 25 mg per litre (DM25), are extracted by pipette a random sample of 0.1 ml which is added to a new volume of 9.9 ml DM25 in new flasks which are then incubated at 37°C for 24 hours and the procedure repeated indefinitely.

What the experiment does is to provide a consistent, stable and simplified niche for the twelve lines allowing them to proceed in parallel isolation (great care is taken to avoid cross-contamination). This allows the researchers to test whether evolutionary change is inevitable, repeatable or unpredictable.

One objection often made by critics is that, being designed, the experiment is not a true test of natural evolution. But Lenski chose the environment, he does not design the bacteria. A random (the flasks are continuously agitated on a mixing plate to ensure uniform distribution of cells) sample makes it through to the next generation (70,000 and counting in the thirty years the experiment has been running) but, over time, the twelve lines have undergone changes that can be observed. Cells have become larger, redundant (in the experimental niche) parts of the genome have become broken.

The most spectacular change so far has been the arrival of the ability of one line to metabolise citrate aerobically. The change has been well-studied because deep-frozen samples are retained every 75 days and DNA sequences (thanks to cheaper and quicker DNA sequencing) can be compared to match genomic changes against phenotypic changes. The ability to digest citrate involved changes at more than one locus, a beautiful illustration of neutral evolution and genetic drift.

The LTEE also is an excellent refutation for Creationist John Sandford and his “Genetic Entropy” idea. I’m sure others can point out errors but this OP is meant only to provoke discussion and not to be authoritative so please jump in with comments.

0

247 thoughts on “Design by Natural Selection: The LTEE

  1. Nonlin.org: You gather nonsense. The argument against “evolution” is not religious. It’s strictly scientific.

    What I cannot gather is what you think evolution IS. I strongly suspect that there are sound scientific arguments against whatever you think evolution is, so I’ll tentatively agree with you here. Conversely, there might be sound scientific arguments in favor of demons, depending on how they are defined.

    So would you be so thoughtful as to provide a brief description of evolution according to your understanding? Without any such description to work with, you could be anything from fully informed to full whackaloon, and nobody could tell.

    0
  2. Flint,

    I hesitate to suggest this but you could have a look at nonlin’s website (follow link in his name). There’s a wealth of misunderstanding, misconception, and misrepresentation there.

    0
  3. Can “natural selection” explain the humans? No. Both supposed evolutionary branches survived and developed in the same African environment. Why “struggle for survival” did not eliminate either one of the branches has yet to be plausibly explained*. In addition, the supposed “common ancestor” is a regular chimp, so no evolution of any kind on that branch of the “common tree”. Why then would the human branch explode with changes from bipedalism to superintelligence? Felines, canines, bovines, and primates ex humans are all more or less the same on all family branches. There is no feline/canine/bovine/etc. human equivalent. No “evolutionary arms race” can possibly account for human brains being able to make sense of the quantum and the cosmos – notions far removed from everyday survival. As far as we know, no other organism has such a removed capability inexplicable on the account of “natural selection”.

    *My emphasis

    0
  4. To increase the chances that this discussion will provide something useful for once, here is the closest that Nonlin ever came to defining evolution:

    A hypothesized process responsible for “the origin of species” (aka their hypothesized transmutation from one to the other).

    Go read back the rest of that thread to appreciate the effort that went into getting Nonlin to stop dancing around and write down something.

    0
  5. Nonlin.org: The argument against “evolution” is not religious. It’s strictly scientific.

    Heh, if the shoe fits … Flint didn’t say that the argument against evolution is religious. He said that you perceive evolution to be imaginary and evil. You yourself have made statements on multiple occassions to the effect that evolution is like a unicorn and that it is Godless.

    0
  6. Thanks, Corneel. Déjà-vu all over again. Nearly a year later and no-one has cracked nonlin’s carapace. That’s some determined resistance to change and evidence. Nonlin regresses to his norm.

    0
  7. Alan Fox quotes Nonlin’s version of “why there’s still chimps?”:
    Both supposed evolutionary branches survived and developed in the same African environment. Why “struggle for survival” did not eliminate either one of the branches has yet to be plausibly explained.

    That’s what the word “branches” means in evolutionary biology, they’re separated. Believe it or not, Africa is large enough to have more than one environment. So, one branch started off in the savannah, the other in tropical forests. Why would separate populations “eliminate” each other?

    It’s fucking simple.

    0
  8. Alan Fox quoting Nonlin’s babble:
    In addition, the supposed “common ancestor” is a regular chimp,

    Not really. Today there’s two species in the other lineage: chimps and bonobos.

    Alan Fox quoting Nonlin’s babble:
    so no evolution of any kind on that branch of the “common tree”.

    So, yes evolution on that other branch, it branched further into two species.

    Alan Fox quoting Nonlin’s babble:
    Why then would the human branch explode with changes from bipedalism to superintelligence?

    Superintelligence? Has anybody read Nonlin’s babble?

    0
  9. Entropy: That’s what the word “branches” means in evolutionary biology, they’re separated. Believe it or not, Africa is large enough to have more than one environment. So, one branch started off in the savannah, the other in tropical forests. Why would separate populations “eliminate” each other?

    Indeed; Here’s a link to peripatric speciation for nonlin to ignore.

    It’s fucking simple

    I spent much time arguing with an opponent of Darwinian evolution, John A. Davison, who proclaimed there could be no speciation as sexual reproduction would inevitably mix the variation into the whole population. (He advocated the “Hopeful Monster” scenario). It took me a while to see that speciation requires genetic isolation of populations whereas adaptation doesn’t.

    +1
  10. Entropy: Superintelligence? Has anybody read Nonlin’s babble?

    I did enjoy the bit about making “sense of the quantum and the cosmos”. I’m pretty sure that humans haven’t figured either out just yet. I am certain that nonlin…

    +2
  11. Alan Fox: It took me a while to see that speciation requires genetic isolation of populations whereas adaptation doesn’t.

    Took me a while to understand that genetic isolation does not require physical isolation. In fact, that it can happen gradually within a population, and speciation can be deemed to have occurred even though there may still be gene exchange between the branched populations for a long time. During a branching process, which might take millions of years, there can be legitimate dispute as to whether or when it qualifies as having produced separate species.

    0
  12. Alan Fox,

    Incomplete lineage sorting made me dizzy for a while. It really needs thinking of populations and sexual reproduction. Normally, even if we know better, the process is imagined as if it were individuals that evolve, rather than the population.

    0
  13. Alan Fox: Indeed; Here’s a link to peripatric speciation for nonlin to ignore.

    I spent much time arguing with an opponent of Darwinian evolution, John A. Davison, who proclaimed there could be no speciation as sexual reproduction would inevitably mix the variation into the whole population.

    That is kind of built into the mathematical framework too, to be honest (pace any watching population geneticists!). The useful fiction of a panmictic population with no representation of geometry or gene-flow ‘viscosity’ seems to lose traction around speciation (though this perception may result from ignorance on my part).

    And of course (as I will bore anyone foolish enough to hold my gaze for more than a split second!), exporting this useful fiction beyond the bounds of the sexual population itself into treatments of secondary asexuality leads to some dodgy thinking, viz: ‘the Twofold Cost of Sex’. 😁

    +1
  14. Allan Miller: The useful fiction of a panmictic population with no representation of geometry or gene-flow ‘viscosity’ seems to lose traction around speciation (though this perception may result from ignorance on my part).

    All models are wrong but some are useful.

    0
  15. Allan Miller: As I’ve remarked before, though, it’s heartwarming to see the joy and comfort Faith brings…

    Very funny and soo true: https://evolutionnews.org/2021/02/james-tour-episode-4-on-the-origin-of-life-the-devil-is-in-the-details/
    “Atheists: Follow the science!
    Dr. Tour: Here’s the science.
    Atheists: But you’re a Christian!
    Dr. Tour: But this is pure science.
    Atheists: La la la I’m not listening!”

    Being such an isolated case, I can’t fathom why my experience is so common. Haha.

    Flint: What I cannot gather is what you think evolution IS.

    Not “IS”. “ISN’T”.

    The “mechanism”. Yes, that one – the one with no relationship with anything real and the same one that can be easily dismantled with the scientific method fake stone by fake stone.

    Take this thread for instance:
    How would Lenski’s outcomes have been different, if “evolution” were not true.

    Alan Fox: I hesitate to suggest this but you could have a look at nonlin’s website (follow link in his name).

    Blasphemy! Darwinist style. Haha.

    Corneel: To increase the chances that this discussion will provide something useful for once, here is the closest that Nonlin ever came to defining evolution:

    Awesome! Let me commend you on not being entirely illogical all the time. Hope is NOT dead.

    Corneel: Flint didn’t say that the argument against evolution is religious.

    He said “like a demon”, to be accurate. Is that the new species of little monkeys we keep seeing on TSZ?

    DNA_Jock: I did enjoy the bit about making “sense of the quantum and the cosmos”. I’m pretty sure that humans haven’t figured either out just yet.

    Whaaat? Next you’ll tell me “evolution” is not true? Haha!

    DNA_Jock: I’m with you on this one, and (as I understand it) so is our senior resident population geneticist.

    Pure comedy! Love it.

    Btw, is anyone even trying to explain the disconnect between nature, where we just observe phenotypes, genetics, and outcomes; VERSUS the never ever observed “fitness”, “natural selection”, or “evolution”?!? http://theskepticalzone.com/wp/design-by-natural-selection-the-ltee/comment-page-3/#comment-284184

    0
  16. Nonlin.org:
    https://evolutionnews.org/2021/02/james-tour-episode-4-on-the-origin-of-life-the-devil-is-in-the-details/

    Two points:
    1. Abiogenesis, the problem of how life started on Earth nearly 4 billion yearts ago, is not yet solved, though there are many ideas and hypotheses. As I remarked before, we only have one data point, that life is first observed on Earth nearly 4 billion years ago. I await data point number two when we see what the Perserverance rover finds. It is a separate issue from the theory of evolution, so well evidenced it is accepted as uncontroverial fact.
    2.James Tour is a chemist well respected in his field, indeed a Nobel prize winner*. His field of expertise is not abiogenesis and he is not a biologist or biochemist.

    Have you watched the videos? (He asked innocently!) Can you summarize beyond “Ha ha”?

    ETA correction (H/T Entropy)

    +1
  17. Alan Fox,

    And his videos show a guy who gets more into rhetorics than science.

    (I did not see anything about him getting a Nobel prize.)

    0
  18. Nonlin (presenting some incoherent bullshit): Here’s the science you bunch of retards!!! Haha.

    Atheists: That’s not science Nonlin, that’s incoherent bullshit, you cannot even agree with yourself.

    Nonlin: La la la I’m not listening!

    +2
  19. Entropy: And his videos show a guy who gets more into rhetorics than science.

    I still wonder if nonlin actually watched them.

    0
  20. Entropy:
    Alan Fox,

    And his videos show a guy who gets more into rhetorics than science.

    (I did not see anything about him getting a Nobel prize.)

    Apologies. I seem to have screwed up a comment of yours in trying to reply to it then trying to edit it. I was confirming that Tour is not a Nobel recipient. I was so convinced I’d seen that somewhere that I didn’t bother to check before posting, sorry.

    0
  21. Alan Fox:
    Rumraket fell into a similar Nobel trap.

    https://discourse.peacefulscience.org/t/rumraket-response-to-dr-tour-on-abiogenesis/4242/5

    Ahh yes, thanks for reminding me of that thread. It was funny re-reading the exchange I had with that Ronald_Cram fellow, who appeared incapable of fathoming the subject of the discussion, which was me analyzing one of James Tour’s popular press articles arguing that the origin of life is chemically impossible, and showing that Tour failed to carry that case. It’s amazing how many theists are unable to wrap their heads around this.

    “Oh gee Tour does make it seem like it’s hard to make RNA from the ground up under plausible early Earth conditions, I guess the OOL is impossible”. I trust that a cognitively healthy person can see the non-sequitur there, because the average fundamentalist Christian sure as hell can’t.

    +2
  22. Nonlin.org:
    He said “like a demon”, to be accurate. Is that the new species of little monkeys we keep seeing on TSZ?

    I used “demon” as an example of something imaginary for which we have a name. But naming something doesn’t mean it exists. For example, we have the name “evolution” (and even widespread understanding of what it references), but just having a name doesn’t reify it.

    So I was asking you what you believe others using the name “evolution” might be trying to describe. In other words, what you regard as the nature of their misunderstanding. For most of us, this name really does refer to “observed phenotypes, genetics, and outcomes.” The word “evolution” ALSO refers to proposed mechanisms driving these observations.

    0
  23. Don’t forget Tour was the closet Creationist who claimed a few years back “there is no scientist alive who understands macroevolution”. Numerous scientists offered to educate him, most notably Dr. Nick Matzke of the NCSE with the one condition the session be recorded so no one could dispute what was said by each side. Tour of course refused. He had no desire to have a permanent record of his belligerent ignorance.

    Tour is a “Born Again” who has been in bed with the DI for a number of years now. In 2019 Tour made an anti-science anti-OOL video specifically for the DI’s YouTube site. Late last year a science educator, Dave Farina, made a rebuttal video pointing out the errors and disinformation in Tour’s flick. This infuriated Tour and the DI so much Tour is now posting a 13 part series on YouTube specifically attacking Farina and claiming once again OOL is impossible and OOL research is a fraud to scam public money. It’s just a repeat of his 2019 bullshit with a lot more fluff and filler. Tour himself rants and screams like a madman in the presentations, like an old style fire and brimstone preacher. The comments from Tour’s religious groupies are also priceless. There’s everything from YECs to IDiots to “jets leave chemtrails to control our brains” nutters. Of course every other post mentions God or Jesus as life’s Creator.

    0
  24. Adapa:
    It’s just a repeat of his 2019 bullshit with a lot more fluff and filler.

    It’s just that as far as I saw.

    0
  25. Adapa: Of course every other post mentions God or Jesus as life’s Creator.

    There are, as far as I can tell, some good honest scientists who are also devoutly religious — so it can’t be the case that religion requires dishonesty or ignorance. Yet these seem to go hand in hand with relentless consistency. Why?

    I’d be surprised if our resident religious anti-evolution voices (as far as I’ve read, ALL of our anti-evolution voices are devoutly religious) haven’t been asked WHY evolution is incompatible with their faith, and why evolution can NOT be their god’s chosen process. But I must have missed it.

    +1
  26. Flint,

    Well, yes, someone has suggested that to the creationists, the latest answer, from a creationist superstar (in his own eyes only), was “sure, as if God would start everything and then leave it to Darwin”. the tone I cannot paraphrase well enough, but it’s as if it would be offensive for this all powerful magical being to leave things to a process described by someone as offensive as Darwin.

    Somehow the creationist superstar decides what this magical being can and cannot do, despite, you know, the being being all powerful and such shit.

    0
  27. Entropy:

    Well, yes, someone has suggested that to the creationists, the latest answer, from a creationist superstar (in his own eyes only), was “sure, as if God would start everything and then leave it to Darwin”. the tone I cannot paraphrase well enough, but it’s as if it would be offensive for this all powerful magical being to leave things to a process described by someone as offensive as Darwin.

    What disqualifies the notion that the creationist god is manipulating reality in real time, and Darwin was simply one of the earliest to observe their god’s ministrations in any detail? Surely the creationists must believe their god is present and active today and in all time? Even if nobody had ever noticed what we now refer to as evolution, couldn’t their god still be doing it?

    Really, what is there about evolution that prohibits their god from using it? The closest I’ve been able to get is, there is an implication that humans weren’t always people as we know them. But hey, most of us have had weird ancestors. What’s the big deal?

    +2
  28. Nonlin.org: Awesome! Let me commend you on not being entirely illogical all the time.

    Wow! Thanks for not being completely obnoxious all the time.

    Nonlin.org: He said “like a demon”, to be accurate. Is that the new species of little monkeys we keep seeing on TSZ?

    He was using the phrase as an analogy. Yeah, he should’ve known that would be lost on you.

    +1
  29. Flint: There are, as far as I can tell, some good honest scientists who are also devoutly religious

    Even better, in my days as an evolutionary biologist I had several colleagues who were openly religious; All very skilled scientists. Lovely people too!

    Flint: Really, what is there about evolution that prohibits their god from using it? The closest I’ve been able to get is, there is an implication that humans weren’t always people as we know them. But hey, most of us have had weird ancestors. What’s the big deal?

    This interests me too. The very idea of evolution seems to be deeply offending to them and I cannot fathom why. The problem is that no creationist lets on about their underlying motives. They all seem to have convinced themselves that they were swayed by the scientific arguments, even though most of them clearly have an appallingly bad understanding of the subject as well as an evident religious motivation.

    Like you, I noticed that the majority of them have a strong commitment to human exceptionalism. Perhaps creationists are just unable to let go of the idea that humans were created with the personal attention of their God.

    0
  30. Flint: There are, as far as I can tell, some good honest scientists who are also devoutly religious…

    I’m sure Tour is good at his job which in a recent video discussion with Josh Swamidass he confirmed is certainly not abiogenesis but religion is the centre of his life and thoughts.

    Not too good at posting links by phone but it’s easy to find.

    Tour Swamidass abiogenesis

    ETA https://m.youtube.com/watch?v=yJgr38h_3H0

    ETA2 I’m not suggesting you or anyone watch the whole video (frankly, I haven’t). A few minutes at the beginning is enough to get the flavour of Tour.

    0
  31. Entropy: Nonlin: La la la I’m not listening!

    That complete lack of self awareness made me laugh out loud. I seriously wonder if he recognizes his own reflection in the mirror.

    0
  32. Nonlin.org: “Atheists: Follow the science!
    Dr. Tour: Here’s the science.
    Atheists: But you’re a Christian!
    Dr. Tour: But this is pure science.
    Atheists: La la la I’m not listening!”

    As noted, the objections raised were scientific objections, not religious ones. You have merely converted legitimate objections into ones you think you can ignore.

    Presumably you can quote someone refusing to listen to the science and making objections that Tour was a christian instead?

    If not, then you are the one who is not listening. You are not listening to the science yourself, because science is not just about one person’s opinion.

    If Tour is right and everybody else is wrong, and that is demonstrable on a scientific level then why are all these other scientists not convinced? Because Tour is religious? But as noted there are plenty of religious scientists. So it can’t be that.

    But you need it to be that, don’t you? And so it is that .

    Your cognitive dissonance will eventually catch up with you.

    Tour is a scientist. Therefore everything he says or does is based on science? Hardly. Have you actually watched any of the videos linked here?

    Why is it that a scientist saying what you want to hear is 100% right and any objections raised against him are unscientific whereas any scientist saying what you don’t want to hear is simply wrong?

    If you really want to play the science game you have to accept the opinions of more than just people who are already saying what you want to hear.

    +1
  33. Finding myself early for an appointment, I watched twenty minutes or so of Tour vs Swamidass. Tour, apart from strawmanning with Miller-Urey and misrepresenting the field of abiogenesis science as having answers, argues the improbability is too, well, improbable. It’s boilerplate arguing by personal incredulity.

    +1
  34. Corneel: That complete lack of self awareness made me laugh out loud. I seriously wonder if he recognizes his own reflection in the mirror.

    Yep. Makes me wonder is the title of some other OP is even right.

    +1

Leave a Reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.