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.

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348 thoughts on “Design by Natural Selection: The LTEE

  1. colewd: Are you claiming it is ok to insult some people and not others?

    My personal view is that an argument is weakened if it relies on insulting your opponent.

    Regarding whether the founder’s rules are still written in stone is a discussion for the moderation issues thread.

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  2. colewd: Are you claiming it is ok to insult some people and not others? This does not appear to support the philosophy of this blog.

    I pretty much concur with Alan. I do not think that is ok to insult anyone: it does not further the discussion.
    For instance, Bill, you quite often insult scientists on this blog. I think that it is unintentional, but you do it and we ignore it. By and large.
    An orthogonal issue is that there are some people who deserve to be insulted. Still doesn’t make it ok to insult them, but it is more understandable.

    +2
  3. Corneel: But let me get this straight: You actually consider blowing one’s nose as an act of Intelligent Design?

    Depends. Are you painting with that? Are any infamous Darwinsts involved?

    Alan Fox: Thankfully, even when nonlin insults one of the World’s leading geneticists, we can’t help not being offended.

    The only insults I see are from an angry little monkey. But who pays attention to little monkeys? And anyway, you’re OK with that, right?

    Also, whothat “World’s leading geneticists”? If true, maybe they can explain the hypothetical link, as tenuous as it might be, between “evolution” and genetics?

    Finally, where in the world is the phlogiston I ordered?

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  4. Nonlin.org to someone else (doesn’t matter):
    The only insults I see are from an angry little monkey. But who pays attention to little monkeys? And anyway, you’re OK with that, right?

    You reap what you sow little monkey. They’re not insults, but biblical lessons.

    Nonlin.org to someone else (doesn’t matter):
    Also, who that “World’s leading geneticists”? If true, maybe they can explain the hypothetical link, as tenuous as it might be, between “evolution” and genetics?

    Explain something that’s self-evident to you? Nobody can explain anything to you, not even something that basic. You’re an illiterate monkey, as you admit every time you ignore my devastating criticisms.

    Nonlin.org to someone else (doesn’t matter):
    Finally, where in the world is the phlogiston I ordered?

    Up your simpleton’s ass. Careful, it might blow up in flames if you continue talking out of there.

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  5. Nonlin.org: Also, whothat “World’s leading geneticists”? If true, maybe they can explain the hypothetical link, as tenuous as it might be, between “evolution” and genetics?

    Heh you’ve already been ‘peer’ reviewed and failed. And you don’t even know it. How un-self-aware.

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  6. Nonlin.org: Me: You actually consider blowing one’s nose as an act of Intelligent Design?

    Nonlin: Depends. Are you painting with that?

    Is that necessary? My hanky is designed, you know. Therefore everything I do with my hanky is 100% ID.

    Incidentally, did you know toilet paper is designed as well?

    Nonlin.org: whothat “World’s leading geneticists”

    It wouldn’t surprise me in the least if Nonlin really doesn’t know.

    +1
  7. Nonlin.org: Also, who that “World’s leading geneticists”? If true, maybe they can explain the hypothetical link, as tenuous as it might be, between “evolution” and genetics?

    To nonlin. Because perhaps spending time explaining to you is pointless for two main reasons.
    1) You have rejected explanations provided so far. 2) You appear to be exerting no influence whatever on others.

    You remain an isolated pseudonymous commenter at an obscure website. You don’t merit the attention.

    +1
  8. The ‘evolution has nothing to do with genetics’ stuff is so profoundly ignorant, it renders all attempts at communication redundant. I can’t visualise what version of ‘evolution’ goes on in nonlin’s head that does not have a hereditary component, and he’s such a poor communicator, I doubt I ever will. It’s #1 in nonlin’s Greatest Hits, just edging out ‘allele frequencies don’t add up to 100% unless you count them’ and ‘growth is decay backwards’.

    +4
  9. Allan Miller: The ‘evolution has nothing to do with genetics’ stuff is so profoundly ignorant, it renders all attempts at communication redundant.

    Exactly.

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  10. Corneel: Is that necessary? My hanky is designed, you know. Therefore everything I do with my hanky is 100% ID.

    Whatever.

    Alan Fox: To nonlin. Because perhaps spending time explaining to you is pointless for two main reasons.
    1) You have rejected explanations provided so far. 2) You appear to be exerting no influence whatever on others.

    You remain an isolated pseudonymous commenter at an obscure website.

    1. Should I accept bad and fake explanations instead? No, I am not asking for your opinion.
    2. Sleep easy then. Some people see the problems I raise, but not you. What do I care?
    3. I must be very isolated because ID is “dead” and “evolution” rules supreme. In other news, James Tour obliterates the evo-hype: https://www.youtube.com/watch?v=tqbpd3CmBgE . But he too is isolated, so no worries.

    And he’s not even aware of the “entropy forbids abiogenesis” angle. He’s just looking at the chemistry. Which he obviously masters!

    I love this one (min11:14): https://www.youtube.com/watch?v=tNbl-g8QoAg&t=3s

    Allan Miller: The ‘evolution has nothing to do with genetics’ stuff is so profoundly ignorant, it renders all attempts at communication redundant.

    Outrageous! I’m sure you could disprove this in no time: http://theskepticalzone.com/wp/design-by-natural-selection-the-ltee/comment-page-3/#comment-284184 . If you wanted… But you don’t… Don’t even ask…

    Allan Miller: Or rather (I hate to misrepresent!) ‘abiogenesis is decay backwards’.

    Now you got it. Except no “is”, but “would be”… if true.

    As far as Sum(alleles) = 100%, I’m still waiting for the reference. Which you could produce… If you wanted… But you don’t… Don’t even ask…

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  11. The part of Allan’s comment quoted by Nonlin, with a slight highlight, since Nonlin seemed to miss its meaning:

    Allan Miller:
    The ‘evolution has nothing to do with genetics’ stuff is so profoundly ignorant, it renders all attempts at communication redundant.

    Which means that it would be impossible to communicate with Nonlin. Naaaah! Really?

    The part that Nonlin “missed”:

    Allan Miller:
    I can’t visualise what version of ‘evolution’ goes on in nonlin’s head that does not have a hereditary component, and he’s such a poor communicator, I doubt I ever will.

    As an “answer” Nonlin wrote:

    Nonlin.org:
    Outrageous! I’m sure you could disprove this in no time: http://theskepticalzone.com/wp/design-by-natural-selection-the-ltee/comment-page-3/#comment-284184 . If you wanted… But you don’t… Don’t even ask…

    We’d imagine that link would lead to a clear-cut explanation as to how evolution and genetics have nothing to do with each other, proving that Nonlin is a rather excellent communicator. Let’s take a look:

    Nonlin.org:
    Of course mathematical models do what their creators want, so that’s 100% ID. As far as nature, we just observe phenotypes, genetics, and outcomes. Never any “fitness”, “natural selection”, or “evolution”.

    I’m surprised. I absolutely expected some clear-cut explanation as to how evolution and genetics could not possibly be related at all, and I find this thing about Nonlin’s inability to understand some concepts in evolution. But a clear lack of relationship between evolution and genetics? None. So what’s here to “disprove”? That Nonlin doesn’t understand some concepts is not a surprise, and not in dispute, except perhaps in Nonlin’s farts, which Nonlin pretends to pass for thoughts. Nothing else.

    There was another thing in there, but it doesn’t look like a clear-cut explanation about the lack of relatinship between genetics and evolution, but I’m putting it here so that Nonlin won’t imagine I didn’t see that:

    Nonlin.org:
    Food for thought:
    The same exact thing we see with “evolution” happened with the caloric, aether, vitalism, phlogiston, etc. https://en.wikipedia.org/wiki/Superseded_theories_in_science

    So. Nothing. Nothing pointing to genetics having nothing to do with evolution.

    I suspect Allan was right.

    🤣

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  12. Nonlin.org to whomever:
    As far as Sum(alleles) = 100%, I’m still waiting for the reference. Which you could produce… If you wanted… But you don’t… Don’t even ask…

    Now a reference is needed for a simple mathematical transformation from counts to percents? Of course, Nonlin’s problem starts with the formula, which might be on purpose, but I doubt Nonlin’s that smart.

    So, maybe this reference will work, since the web site has been used by Nonlin at some point:

    How to Calculate Percentages From the Total

    Maybe Encyclopaedia Brittanica:

    Percentage

    Maybe this one is closer to Nonlin’s level:

    Basics of percent – a free lesson*

    Perhaps Nonlin’s mother could help if she followed some instructions to teach Nonlin about percentages:

    How to Teach Children the Basics of Percentages

    Maybe Nonlin’s problem is some inability to deal with particulars, which, given Nonlin’s problems to deal with abstractions, wouldn’t be too surprising. So Nonlin might need an example with alleles:

    Allele Frequencies Example

    While genotypic frequencies look at the expression of the genes, allele frequencies look at the number of times a specific allele occurs in a population. To find the allele frequency of B in this example multiply 50 by two as there are two B’s in the BB genotype.

    Then add the people with the BG genotype as they also each have a B allele, giving a total of 123 B alleles. Finally, divide 123 by 200 as each person in the population carries two alleles, giving an allele frequency of 0.615 or 61.5 percent.

    Next, do the same for the G allele. By multiplying the 27 people with GG alleles by two and adding the 23 people who also have a G allele then dividing this number, 77, by 200, results in 0.385 or 38.5 percent.

    Check for mistakes by ensuring that all the allele frequencies add up to 1 or 100 percent. Here, 61.5 added to 38.5 equals 100.

    I doubt that’ll reach Nonlin’s brain, but, heck, it’s too basic to need a scientific article just about it. It’s used in scientific articles, but it’s not presented as some kind of amazing discovery, since it’s just a very basic mathematical tool.

    🤣

    ————

    * The site presents an example with birth defects, which is ironic given that Nonlin thinks that some magical being in the sky builds the baby in the mother’s womb, no damned bullshit genetics involved.

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  13. Nonlin.org: I must be very isolated because ID is “dead” and “evolution” rules supreme.

    The evidence supports you there, indeed! 🙂

    +2
  14. Corneel: Incidentally, did you know toilet paper is designed as well?

    Yup. And everything you do with your toilet paper is designed as well. 🙂

    +2
  15. Alan Fox,

    Joe’s kindness is astounding. He must be converting every atheist to Christianity by that show of absolutely unconditional love.

    The LTEE doesn’t show any design by natural selection.

    It doesn’t? Woa, I’m about to learn something new!

    That’s because there isn’t any evidence that natural selection produced prokaryotes.

    This doesn’t follow. The prokaryotes are already in the broth, so I doubt anybody is trying to prove that natural selection produced prokaryotes using the LTEE.

    There isn’t any evidence that the mutations were all just chance events, as natural selection mandates.

    This one will become a contradiction of terms pretty soon. Pay attention. Still, natural selection doesn’t “mandate” for mutations to be chance events. It just “mandates” that sufficient variation arises for there to be something to select. If the variation happened because there was some mutagen in the broth, for example, wouldn’t be a problem for natural selection to occur.

    Alan Fox is just a question-begging coward.

    Someone is a question begging coward for not thinking in the equivocating terms and mistaken notions of an ignorant, or perhaps desperate, creationist? How’s that cowardice? How’s that “question begging”?

    Alan spews:

    The most spectacular change so far has been the arrival of the ability of one line to metabolise citrate aerobically.

    OK. Seems reasonable to me, but I guess Joe is about to explain how that’s not the most spectacular result. Maybe there’s a better one. Or maybe Joe is about to obliterate the result. Let’s see.

    All that happened was the gene for citrate transport was duplicated. And the duplicate just happened to be placed under the control of an existing binding site that also just happened to be active in the presence of oxygen. You see E. coli have the ability to utilize citrate. It’s just that in the presence of oxygen the citrate transport gene isn’t expressed. So the only possible gene that could help in this situation was duplicated.

    Two “just happeneds”!! But there’s no evidence that the mutations arose by “chance events”?

    🤣

    Oh! And these “just happened” happenstances were a “response to an environmental cue”!!

    🤣

    Only a desperate evoTARD would think the LTEE is actually helpful to them. And only a desperate evoTARD would think the LTEE refutes genetic entropy. Enter Alan Fox, cowardly, lyimg evoTARD.

    This looks more like only a creotard would unconsciously contradict his own claims while trying desperately to “demolish” some interesting result in the LTEE.

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  16. This reminds me of colewd’s ‘event zero’, the thing that convinced him ID was true.

    I don’t quite recall but he was looking at some biological structure and said to himself if this is controlled in such and such a way then it must be Intelligent Design, and he checked and it was. Or some such. Much like he was absolutely sure there was no precursor to C no doubt.

    I do remember asking him what other ways that question could have been answered and how he justifies his leap to ID empirically, but he never even acknowledged the question. I’ll dig up the thread one day.

    But it’s the same for both, they come to the conclusions they do by literally shoving aside the actual evidence and once that’s been disposed of they are free to proclaim ID did it in good faith. So they think. Not sure why they bother myself.

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  17. Joe G, at least, appears to grasp the connection between evolution and genetics. That puts nonlin below Joe G in the grasping-the-subject-he-opposes stakes. Ouch.

    +3
  18. Also to note that Joe invokes genetic entropy, which is based upon a computer model which, so we are told, makes it ID, designed to give the desired result. That too is worth a good ‘snurk’.

    +3
  19. Allan Miller:
    Also to note that Joe invokes genetic entropy, which is based upon a computer model which, so we are told, makes it ID, designed to give the desired result. That too is worth a good ‘snurk’.

    Joe G has long been a fan of John Sanford and “genetic entropy”, the idea that the genes are degrading too fast for evolution to sustain and populations of organisms will inevitably go extinct. There’s no such effect observed with the LTEE even after thirty years and more than 70,000 generations.

    ETA Apologies to Joe G for mixing up John Sanford with Lee Spetner and it is Spetner that Joe admires.

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  20. Entropy: And these “just happened” happenstances were a “response to an environmental cue”!!

    And yet they “just happened” in only one of the twelve cell lines, all from two sets of six identical cells strains in identical niches.

    +1
  21. Alan Fox,

    Yes. He has this obsequious habit of always referring to ‘Dr’ Spetner, too. Not that there’s anything fundamentally wrong with addressing people that way, but it is a distinctive tic, and inconsistently applied.

    His nails are few but well-bashed.

    +1
  22. Alan Fox,

    There’s no such effect observed with the LTEE even after thirty years and more than 70,000 generations.

    Sniff. Still bacteria though … 😁

    +1
  23. Alan Fox: And yet they “just happened” in only one of the twelve cell lines, all from two sets of six identical cells strains in identical niches.

    Which, as you must already know, is also the logic of one of the classic founding experiments of microbial genetics, the Luria-Delbrück experiment. It showed that the variation in outcome after a change of environment was too great to have the result come from direct response to the environment, but was consistent with selection on inherited mutants.

    +2
  24. Joe Felsenstein: Which, as you must already know, is also the logic of one of the classic founding experiments of microbial genetics, the Luria-Delbrück experiment.It showed that the variation in outcome after a change of environment was too great to have the result come from direct response to the environment, but was consistent with selection on inherited mutants.

    I confess I knew little about it other than being a significant milestone. Looking at it now. Simple and elegant.

    https://en.m.wikipedia.org/wiki/Luria–Delbrück_experiment

    +1
  25. Entropy: This one will become a contradiction of terms pretty soon. Pay attention. Still, natural selection doesn’t “mandate” for mutations to be chance events. It just “mandates” that sufficient variation arises for there to be something to select.

    Bullshit of the highest order.

    You didn’t refute Joe’s main point at all:

    And yet that was a very meager thing. The change also fits in with Dr. Spetner’s “built-in responses to environmental cues”. All that happened was the gene for citrate transport was duplicated. And the duplicate just happened to be placed under the control of an existing binding site that also just happened to be active in the presence of oxygen. You see E. coli have the ability to utilize citrate. It’s just that in the presence of oxygen the citrate transport gene isn’t expressed. So the only possible gene that could help in this situation was duplicated.

    No new proteins were made. No new protein machinery has been formed. the LTEE has demonstrated the severe limitations of evolutionary processes.

    Your fake refutation is more like “So, big deal! ….” Pretty empty.

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  26. phoodoo: So, big deal!

    If it is not a “big deal” why didn’t the same thing happen in any of the other eleven cell-lines?

    0
  27. Joe G (or his ghostwriter)phoodoo: You see E. coli have the ability to utilize citrate. It’s just that in the presence of oxygen the citrate transport gene isn’t expressed.

    This is correct. But as Lesnski’s experiment demonstrates, unless the gene switch preventing the enzyme from being switched on is affected (either by anaerobic conditions or mutation in the switching mechanism) the bacteria can be rolling in citrate for years and remain unable to digest it.

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  28. Alan Fox,

    Alan Fox: If it is not a “big deal” why didn’t the same thing happen in the other eleven cell-lines?

    What makes you think the same thing happened in the eleven other cell lines?

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  29. phoodoo: What makes you think the same thing happened in the eleven other cell lines?

    I don’t think that. The mutations that resulted in aerobic citrate metabolism happened only in one of the twelve LTEE populations.

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  30. phoodoo: That’s what Lenski’s experiment demonstrates.

    What Lenski’s experiment demonstrates is given enough time, variation though random mutation followed by selection happens and thus evolutionary change happens even in an utterly stable niche.

    It also demonstrates purifying selection,

    – and that genetic entropy exists only in the head of John Sanford and supporters.

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  31. phoodoo:
    Bullshit of the highest order.

    You didn’t refute Joe’s main point at all:

    Joe refuted it himself. He contradicted his own stance.

    phoodoo:
    Your fake refutation is more like “So, big deal! ….”Pretty empty.

    Nope, it’s more like Joe said the mutations weren’t random, then he said they were random.

    Joe had no point either way, but the contradiction was fun.

    +2
  32. Allan Miller: Joe G, at least, appears to grasp the connection between evolution and genetics. That puts nonlin below Joe G in the grasping-the-subject-he-opposes stakes.

    No one in his/her right mind sees an “evolution” connection to anything real. Not even you, based on your inability to prove your point. And no, I am not vouching for your mental sanity.

    Joe Felsenstein: Which, as you must already know, is also the logic of one of the classic founding experiments of microbial genetics, the Luria-Delbrück experiment.

    And the “evolution” connection is… nowhere in sight. Of course.

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  33. Nonlin.org: No one in his/her right mind sees an “evolution” connection to anything real.

    This is just stupid, nonlin. There are thousands of working bioligists who accept and work with evolutionary theory. And there’s you and whatever you are doing.

    Not even you, based on your inability to prove your point. And no, I am not vouching for your mental sanity.

    Surely you must realise by now that your opinions (idiosyncratic, unsupported, incoherent) hold zero sway in the real world.

    +2
  34. Alan Fox to an incoherent, self-unaware, creationist:
    This is just stupid, nonlin. There are thousands of working bioligists who accept and work with evolutionary theory. And there’s you and whatever you are doing.

    That’s why Nonlin jumps at Joe Felsenstein, hoping to be seen by the adult Nonlin perceives as the one who can make a difference, the one who could make Nonlin’s “spectacular” ideas famous. It’s rather pathetic.

    Alan Fox to an incoherent, self-unaware, creationist:
    Surely you must realise by now that your opinions (idiosyncratic, unsupported, incoherent) hold zero sway in the real world.

    Nonlin will remain unaware of it until (s)he grows up. Unless (s)he ends-up like Joe G.

    Sadly, I’m serious.

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  35. Entropy,

    You’re probably right that he (I just don’t see him as female) isn’t going to change. I wouldn’t mind if I could see any chance of dialogue, in attempting to see a contrary view. Maybe I’m guilty of the same thing but it’s very hard to see what his position is other than being rabidly antithetical to evolutionary theory.

    +2
  36. I think it’s great that people like nonlin and phoodoo can have the time and space to publish their ideas on the internet, such as they are, without having to fend for themselves in an uncaring social system. Obviously there is some net that has caught them, allowing them to spend their time away from productive society, indulging their conceits.

    https://www.thevintagenews.com/2018/11/15/three-christs/

    It’d be great to have nonlin, phoodoo and colewd duke it out on a thread, winner takes all, losers have to concede. Winner then takes on actual science.

    As in the above link and the three christs, I’m sure it’d end badly, but damm it’d be amusing.

    nonlin, this is just a chatroom. It’s ephemeral. The posts may persist but no fucker’s reading them. You could have written a hundred papers and tried to get them published and learnt from the feedback in the time you’ve spent here convincing nobody of nothing.

    And even if you do convince someone here of something, so what? At that rate you’ll get another 2-3 people then game over for nonlin and his ‘ideas’.

    +1
  37. Nonlin.org: No one in his/her right mind sees an “evolution” connection to anything real.

    There are plenty of religious evolutionary biologists who do good science. Are they not in their right mind?

    +1
  38. OMagain: There are plenty of religious evolutionary biologists who do good science. Are they not in their right mind?

    Nope. Some are so brainwashed, they go as far as voting for the Satanists. And remember, science and “evolution” are incompatible.

    But there’s hope. People are waking up. Only not much in the tsz lala land.

    0
  39. Nonlin.org:
    Nope. Some are so brainwashed, they go as far as voting for the Satanists. And remember, science and “evolution” are incompatible.

    I’d talk about the irony of trying to teach scientists what’s incompatible with science, especially after that religiously-nut comment, but it would be lost on poor Nonlin.

    Nonlin.org:
    But there’s hope. People are waking up. Only not much in the tsz lala land.

    Or the irony of making such a religiously-nut comment and then calling the blog a “lala land.” But, again, it would be lost in poor Nonlin.

    +1
  40. I kind of gather that for nonlin, “evolution” is kind of like a demon; something both imaginary and evil. But who are the “satanists”?

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  41. Nonlin.org: Nope. Some are so brainwashed, they go as far as voting for the Satanists. And remember, science and “evolution” are incompatible.

    But there’s hope. People are waking up. Only not much in the tsz lala land.

    Blimey.
    What can men do against such reckless idiocy?

    +1
  42. As I’ve remarked before, though, it’s heartwarming to see the joy and comfort Faith brings…

    +2
  43. Flint: I kind of gather that for nonlin, “evolution” is kind of like a demon; something both imaginary and evil.

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

    0

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