Lenski’s Long Term Evolutionary Experiment | The Skeptical Zone

Evolutionary/phylogenetic relationships between proteins is a better predictor of protein function than % residue similarity.


A recent example …

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And he’s wrong. Because he makes several assumptions that are nonsense to anyone with a basic grasp of evolutionary theory. Mistaken assumptions hilariously continued after he has already been corrected on them, as though he hadn’t actually read Lynch’s response to his earlier writings on the topic.


Evolution is absolutely a falsifiable theory. To claim otherwise is just silly. Doing so in practice would be a bit tricky, considering it has passed each test so far, like when we figured out how DNA works, for example.


But that’s besides the point, because we’re not playing “I know you are, but what am I?”. This, on the other hand, gets right to the heart of the problem:

That is the thing being tested. The hypothesis is “systems that are irreducibly complex cannot evolve”. If we’re defining IC as “cannot evolve”, then the hypothesis is just “systems that cannot evolve cannot evolve”. It’s begging the question.

So I’m asking for some objective criteria that allow us to say “this system is irreducibly complex”. Behe provides some criteria that get at that, but his criteria, at least the formulations I’ve read, fail on the “cannot evolve” measure, because we’ve observed the evolution of systems that meet his criteria. But you’ve said you disagree with Behe’s criteria. So what are yours?


The specific error he makes there (or one of them) is his continuing to insist that the 1 in 10^20 number casually tossed in as an aside in a paper on malaria is a rigorous and universal measure of the number of generations required for any trait arising that requires the number mutations necessary for chloroquine resistance to arise in the malaria parasite. It is an extraordinarily silly argument.


How are the recent articles that Nathan and I just published? Behe Meets the Peaceful Science Forum - #5 by swamidass


Especially since the number came from a review, not the primary literature, and the review’s author made it clear that Behe was misrepresenting the number.

Citing text from the secondary literature instead of data from the primary literature is laughably shallow scholarship, particularly when multiple papers in the primary literature show that the single mutants Behe claims shouldn’t exist actually do.


One very large problem in these discussions is that everyone is equivocating on terminology. I am not saying that anyone specifically is doing so on purpose, but it is almost impossible not to do it since the words are so plastic and have been used rather carelessly for so long. So if you are taking issue with my use of the word ‘Darwinian’ excuse me. The point is that at that point he believed everything that Kenneth Miller believes, or everything that Richard Dawkins believes (apart from the non-belief in God), or everything that Joshua Swamidass believes in. So fine, it wasn’t what you fit in the limited definition of the Darwinian mechanism. It was everything that every mainstream scientist at the time was thinking. My point that it seems so painful to make is that he came to his current beliefs not from reading the bible, or because of a theology course or a dream, or a vision or any other of the regular ways he seems to be disparaged. He was challenged to look closely at the science supporting all of the neo-Darwinian synthesis, as well as neutral theory.
And maybe what is alluded to in the answer to the question posed here, https://youtu.be/wXU2Z3GVNFM?t=5247 will allow you to be a bit more broad in what you hear me say in the phrase Darwinian mechanism.

You claim that “Darwinian evolution can explain many aspects of evolutionary change in the past and present”, but that is called begging the question if the claims of what ‘Darwinian evolution’ can in fact explain. And to follow your own instruction to me, why are you claiming that, ‘Darwinian evolution’ can explain a lot? Haven’t we ‘advanced past plain old Darwinism.’

Why are you suggesting that, evolutionary biologist breath the rarified air of only objectivity and truth telling. I’ve got sad news for you. They are people. With the same biases, prejudices, desires for confirmation bias, willingness to be ‘gate-keepers’ at the temple of ‘orthodoxy’. If scientist working at the premier science organization in the world, NASA, can obfuscate and deny good and even simple science when the situation suits them, what in the world would make you think you’ve ‘fenced off’ the good scientists that are above such?

Anyway, thanks for the time you took to respond. I think I’m through on this thread.

You’re missing the important fact that this isn’t about belief.

That’s precisely backwards. The point is that evolution is not limited to Darwinian mechanisms. It includes mechanisms that are explicitly NON-Darwinian.

It’s not about “thinking,” it’s about the evidence.

Science isn’t about belief, Sam.

Behe’s writing reveals that he can’t be bothered to look at ALL the science. He even fudges the evidence itself for the teeny-tiny science he cherry-picks.

Who do actual science. Behe hasn’t done any for more than 25 years.

It wasn’t the scientists, Sam, it was management that was at fault. You might want to read up on this.

And how did you determine that NASA is the “premier science organization in the world” and not, say, NIH? It appears that you are unable to distinguish between management, science, and engineering.


@Sam @Mercer Come on guys, I may a very nice new thread for this NASA and Challenger stuff. You are making me feel unloved! :frowning: :laughing:



3 posts were merged into an existing topic: Recapping the Challenger Disaster

Schafly deserves credit for publicising the LTEE. It’s how I first heard of it.



No one is equivocating on anything here. Darwinism or darwinian evolution has a specific meaning, that is, evolution by natural selection alone. That was the prevailing thought at the time of Darwin and sometime afterwards, but we now know its insufficient to account for all the details of evolutionary change.

You clearly don’t understand basic evolutionary theory. That’s why you keep saying these unsound things.

The definition of darwinism isn’t limited, but the tools available to darwinian evolution are. You don’t know what you are saying.

This is false. Long before Behe made his debut on the ID front, there were other explanations developed by scientists to account for evolutionary change. When Behe became known, mainstream science had already recognized other ways evolution could happen in the absence of natural selection.

On the contrary, Behe mostly ignores other aspects of evolutionary theory and constantly batters darwinism as if it were the only thing available.

Please go get acquainted with basic evolutionary theory.


There are many things darwinism can explain, there are many other things it can’t.


I did not. That’s your strawman.

This is not news to me and its also why science has many checks in place to severely limit the influence of bias. Science is self-correcting and bad ideas will eventually get weeded out.

While you are at it, review basic evolutionary theory and how science works. Read literature written by actual evolutionary biologists and not the apologetic documents authored by ID proponents or creationists. I tend to ignore people when they consistently refuse to learn the basics, and that might happen to you soon.


That’s interesting, thanks. And now another example offered by @gpuccio comes to mind, that of the calculation of the information jump within some proteins during certain transitions in the history of life.

Can we start talking about real biology any time soon? I’d love to discuss the purported merits of Behe’s actual ideas, instead of this side show about consensus.

Okay, cool. Let’s look at that evidence then and consider whether Behe’s views of that evidence is merited.

Does his concept of irreducible complexity hold up? Is evolution only breaking and degrading stuff?

Do you want to actually look at the evidence or do you just want to keep believing in Behe and then make up an excuse about how you’re not qualified to discuss the actual scientific evidence to make space for your continued belief in Behe?

Well that sure sounds bad. Shall we then look at that evidence ourselves or blather about NASA and the Challenger disaster until the end of time?

That’s too bad because I think we should start to look at the science, and whether Behe is correctly describing and apprehending it. Behe, like the people at NASA, could after all also be wrong. Right?


Poor Dan continues to not feel the love. :frowning:


How do you know this?

And, not to your main point, but I can state as an unequivocal fact that, if Behe understands neutral theory, he deliberately neglects it in order to make his arguments work. Many of his claims instantly evaporate if neutral theory is acknowledged. He has so much as admitted this in his response to Lynch’s paper:

Our model posited necessary intermediate mutations to be deleterious in the unduplicated gene; Lynch’s model assumes them to be neutral: “all 20 amino acids are equally substitutable in the intermediate neutral state”. All of his objections to our work stem from this difference.

That’s a very carefully worded admission of defeat.


Precisely. And, by the same token, how can one confidently ascribe neutrality and objectivity to Behe and other members of the Discovery Institute? Particularly when they have laid bare their ideological bias in which “Darwinism” is seen as one of the chief impediments to their stated goal of replacing our secular society with a theocracy based on fundamentalist religion?

One way to do it: Educate oneself on the relevant sciences so one is in a position to judge for oneself.

But that’s hard. Much simpler is to acknowledge that the peer-review system, while far from perfect, is impressively self-correcting and invariably arrives at the correct answer, even if only eventually. That this system has only become more indifferent and dismissive of ID the longer its proponents have worked to promote it is a good indication that the idea is without merit.


Except we know that his calculation does not measure information, remember? That silly calculation tells us that the train track (actin) is far more complex than the locomotive (myosin) that uses it.


Was that intended as a joke? You need to go back and read those threads.