Lenski’s Long Term Evolutionary Experiment | The Skeptical Zone

Behe has responded to a complaint similar to yours. It seems, to me at least, to convincingly deal with what you’ve just said. I have copied it out here,

As it struggles to comprehend nature, science sometimes has to completely rethink how the world works. For example, Newton’s laws apply to everyday objects, but they can’t handle nature’s tiny building blocks. Propelled by this discovery, quantum mechanics overthrew Newton’s theory. Revolutions in biology have included the cell theory of life in the nineteenth century, as well as the slow realization in this century that cells are composites of enormously complex molecular systems.
Newton’s theory remains very useful, and we can still learn many things by studying whole animals or cells. When explaining the nuts and bolts of the world, however, those views must yield to more basic descriptions. A mechanical engineer can’t contradict a physicist on fundamental principles of life. It’s not a question of pride – that’s just the way the world works.
Curiously, some people seem offended by the way the world works. In his review of my book, Darwin’s Black Box: The Biochemical Challenge to Evolution , evolutionary biologist H. Allen Orr unexpectedly attempts to claim priority for his field. He grouses that pre-med students are required to take biochemistry but not evolutionary biology. He plaintively asks, “Why is everyone an expert witness when the topic is Darwinism but not when it’s biochemistry?” The obvious reply is that the evolution of biochemical systems is itself biochemistry . When a protein sequence changes, when DNA mutates, those are biochemical changes. Since inherited changes are caused by molecular changes, it is biochemists—not evolutionary biologists—who will ultimately decide whether Darwin’s mechanism of natural selection can explain life. No offense—that’s just the way the world works.

Orr hankers for the respect accorded physicists, and thinks evolutionary biologists can finally lay aside their “physics envy” because “we biologists have discovered the structure of DNA, broken the genetic code, sequenced the entire genome of some species.” Orr is like a podiatrist claiming credit for progress in brain surgery. Biochemistry made those dramatic advances; evolutionary biology played no part. I mean no disrespect, but this is not a minor academic turf war—the point is crucial. Anyone who wants to address questions about life’s basic mechanisms has to do so from a molecular perspective. Orr does not.

Declining the opportunity to address my biochemical arguments, Orr questions the concept of irreducible complexity on logical grounds. He agrees with me that “You cannot… gradually improve a mousetrap adding one part and then the next. A trap having half its parts doesn’t function half as well as a real trap; it doesn’t function at all.” So Orr understands the point of my mousetrap analogy—but then mysteriously forgets it. He later writes. “Some part (A) initially does some job (and not very well, perhaps). Another part (B) later gets added, because helps A.” Some part initially does some job? Which part of the mousetrap is he talking about? A mouse has nothing to fear from a “trap” that consists of just an unattached holding bar, or spring, or platform, with no other parts.

These couple of quotes from Richard Feynman may also be illuminating,

“For a successful technology, reality must take precedence over public relations, for Nature cannot be fooled.”

“The first principle is that you must not fool yourself – and you are the easiest person to fool.”

I’m sorry Michael. Again, no offense intended.
Again, my typing and editing skills have fallen short.
Please forgive me.
Sam

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No, that does not address my comment at all. My comment pertains to the specific things Behe has written that demonstrate he does not understand current evolutionary theory nor the refutations, many of them from members of this very group, that have been made against his claims. But that’s a big topic, and one I suggest you investigate at your leisure.

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This is the key point, but the conclusion doesn’t follow from the premise. Biochemists are not better equipped to understand evolution than evolutionary biologists are even though the underlying substrate of evolution is biochemical, just as physicists are not better equipped to understand biochemistry than biochemists are, even though the underlying substrate of chemistry is physical. So “the obvious reply” may be obvious, but it isn’t true.

Behe’s essential error is what Orr points out: he assumes that irreducibly complex systems must evolve, if they evolve, by the sequential addition of parts that are themselves invariant. But in evolution (as a biochemist ought to know) the parts can themselves change their sequences, and can do so gradually. You might consult the thread on constructive neutral evolution, for example.

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Pre-meds who aren’t taught basic evolutionary biology miss out on a lot. When these pre-meds eventually begin specialist training in areas like infectious disease epidemiology or medical oncology, they begin to understand the importance of evolutionary biology.

This is just wrong. One does not need biochemistry to know if natural selection can explain certain aspects of life. Humans were artificially selecting plant and animal breeds for years, without any clue about biochemistry or genetics. When biochemistry and genetics came along, we just got deeper insights into how it all works.

In addition, biochemists (I am one, but not actively researching) alone cannot determine whether some aspects of evolutionary theory are accurate, because evolution usually involves more than just molecules or molecular processes (biochemistry). Other aspects like environmental pressures also influence evolution. This simple fact has led to the creation of hybrid disciplines like “evolutionary biochemistry” which integrates biochemistry with evolutionary theory to better understand ancient and modern evolutionary processes within the context of biomolecules. Biochemistry feeds evolutionary theory, and evolutionary theory feeds biochemistry. The science of the 21st century is interdisciplinary.

This is nonsense. Evolutionary biology may not have helped us discover DNA or any other early breakthroughs in biology, but it has certainly helped biochemistry at present. Have you ever heard of “directed evolution of biomolecules”? That’s a beautiful demonstration of what you get when you take insights from evolutionary theory and apply it to biochemistry.

Orr not being a molecular biologist or biochemist in no way diminishes the importance of his contributions to understanding the evolutionary history of life and its a pity Behe wants you to see the opposite. It was observations at the macroscopic level that pushed us into discovering the amazing wealth of information at the molecular level. Biochemists need research findings from other biologists like Orr and vice versa.

Molecular insights are important, but sometimes molecules don’t tell the full story. In any case, molecular data upholds evolutionary theory.

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I’m not sure what your point is in your response to me.
It seems most likely that you are saying that what Behe says about biochemistry has no bearing on evolution. If that is what you meant, my response would be that Behe himself has, at least in my opinion, convincingly rebutted that claim. I posted this response of Behe’s to Faizal Ali this morning.
Or are you suggesting that Behe is incompetent in his biochemical analysis for evolution?

But wouldn’t you need some familiarity with the actual evidence do be convinced, or is rhetoric sufficient?

No, there’s far more genetics than biochemistry in understanding evolution. I have expertise in both fields. Behe does not.

That’s stretching the definition of biochemistry beyond the breaking point.

Analogies are not arguments.

Indeed. As scientists, we rigorously test our hypotheses to ensure that we are not fooling ourselves. Has Behe ever tested even a single ID hypothesis? If not, why not, Sam?

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Perhaps your opinion is wrong. His conclusion doesn’t follow from his premise. The moderation delay perhaps means you didn’t see my response before posting this.

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I disagree with you John. When DNA mutates, it does so via some chemical mechanism. When DNA polymerase inserts the wrong nucleotide into a nascent DNA strand, it uses the same mechanism that would have been used to insert the correct nucleotide. When DNA is transcribed to mRNA, that mRNA processed and translated to proteins, it involves a great deal of chemistry. I know you know this, so you might have meant something different, right?

It was completely unconvincing, but then I have expertise in both biochemistry and genetics.

As a biochemist, I wouldn’t call Behe’s rhetoric a “biochemical analysis,” because a biochemical analysis involves doing some biochemistry. Behe hasn’t done anything of the sort since 1995 AFAIK, and he never did anything relevant to evolution before quitting empirical science completely.

Do you believe that incompetence is the only attribute that could possibly lead anyone to not believe Behe’s rhetoric? Aren’t there other possibilities that you are conveniently eliding, maybe not consciously?

Remember the Feynman quote?

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Are you suggesting that the vast majority of biochemists are incompetent in their acceptance of evolution?

Behe’s spiel here is past self indulgent, but proceeding on his terms, let us crack open one of the standard biochemistry textbooks, Lehninger’s Principles of Biochemistry. Here is what we find:

The remarkable similarity of metabolic pathways and gene sequences in organisms across the phyla argues strongly that all modern organisms share a common evolutionary progenitor and were derived from it by a series of small changes (mutations), each of which conferred a selective advantage to some organism in some ecological niche

So if you wish to argue from authority, the verdict is in. Biochemical evidence fits right in with the rest of science. As this textbook approvingly quotes Dobzhansky, Nothing in biology makes sense except in the light of evolution.

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Again, you seem to be missing the point. It is entirely possible that some finding from biochemistry could have revealed that the current theory of evolution is wrong.

Behe believes he has done so. He is wrong. But you’ll have to take the time to understand the theory itself and the reponses that evolutionary biologists, including biochemists, have made to his claims.

Here is one instance: A series of blog posts in which a biochemist engages in a discussion with Behe and points out some of Behe’s misunderstanding.

Sandwalk: Michael Behe's final thoughts on the edge of evolution

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It does. But that mechanism is not fundamental to understanding evolution. Genetics is.

Perhaps you are not aware that most transitions are not caused by DNApol inserting a “wrong” nucleotide, but by the keto-enol tautomerization; therefore, the polymerase is not making any chemical mistake at all.

I didn’t say it didn’t. I’m pointing out that it doesn’t have much to do with understanding evolution.

All of that also reduces further to plain organic chemistry, which reduces to physics. Does that mean that physicists understand evolution better than geneticists do?

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If we’re going to talk specifically about Behe’s “irreducible complexity” as a real hypothesis (e.g. “If a system meets the criteria for irreducible complexity, it cannot evolve”), then that’s just wrong, and it’s trivially easy to demonstrate why.

If we take the hypothesis in its most limited form, that is, as Behe described it in Black Box, it excludes most evolutionary mechanisms, so its irrelevant to the question of “could system X have evolved?”.

If we permit all evolutionary mechanisms and say that any system that checks the boxes cannot evolve, period, then it stands falsified because we have directly documented, in real time, the evolution of such systems. Lenski Cit+ and HIV-1 group M VPU tetherin antagonism are two examples. Lizard placentas and primary endosymbiosis in Paulinella also do the trick.

And if the hypothesis is “well okay, some things that meet those criteria can evolve, but some things can’t”, then it’s unfalsifiable.

So I don’t know why anyone treats this as a serious idea.

Edit: Typos

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That’s not the Lenski experiment.

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We don’t. Its the ID camp that does. Take it easy on Jeanson though, your latest YouTube upload did a lot of damage to his claims :smile:

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I agree.

I was aware, but specifically referred to the mechanism of incorporating nucleotides or their analogs into a growing DNA strand. Due to the similarities between the regular nucleotides and their analogs, polymerases may insert these analogs into DNA, creating a mutant. If a polymerase doesn’t insert a nucleotide analog into DNA, then that DNA cannot be a mutant copy.

These are all biochemical changes as Behe correctly noted.

I agree.

I am not defending Behe’s claim that only molecular scientists can unearth the basic mechanisms that shaped our evolutionary history, because it is absurd. I was only pointing out that your characterization of Behe’s claim of protein or DNA changes being biochemical in nature, as “stretching the definition of biochemistry beyond breaking point” did not make sense because they are actually biochemical changes.

As you clarified, it appears you think Behe implies that since these changes are biochemical, and connected to evolution, that only biochemists can really tell if Darwin was right or wrong. I didn’t see it this way though, but taking the entire context of the quote into consideration, it appears you are right about Behe’s overall point. Regardless, I agree it’s an absurd thing to say.

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Hi Sam,
I’m not sure about Behe’s response (there is likely more than one). A common ID response is the Cit+ mutation represents a loss of function, breaking some existing function to enable Cit+. The rejoinder is the fitness is always relative, and the e.coli in these experiments have adapted relative to their environment. They are differently fit from the original line of bacteria, with the Cit+ mutation increasing fitness with respect to the experiment.

Lenski’s experiments are repeatable, because he has saved sample populations over the years, and is able to thaw them out and rerun the experiment from different time points. Behe often talks about “showing selectable steps”, and Lenski’s methods allow looking at the steps along the way to the Cit+ mutation. This is what I meant by “Here they are!”, if that helps?

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And in terms of those selectable steps, because of follow-up work we now know with some precision what they are: changes to acetate metabolism, which are coopted in the presence of the citT duplication to facilitate citrate metabolism, plus some single base substitutions in and around both citT and dctA (Edit: I originally said “citA” but it’s dctA).

And the cool thing is that the citT duplication in the absence of the mutations in the gene related to acetate metabolism is actually harmful, so while you don’t get cit+ until the duplication, the duplication on its own is strongly deleterious in the LTEE environment. So you need these other mutations first, some of which are neutral and one of which is beneficial along a different dimension. It’s so cool!

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BTW, if anyone is interested, had a chat with Dr. James Carter (at Loma Linda University) on this exact thing yesterday: https://youtu.be/-UwZSCLp-Ik

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