Lenski’s Long Term Evolutionary Experiment | The Skeptical Zone

ID math strikes again. Using the same reasoning, it should take hundreds of millions of lottery drawings to get a single winner. ID/creationists seem to lack the ability to think in parallel and are stridently serial.

Just think for a moment on how many neutral changes are in the genome of any modern species. We are talking about potentially 500 million years of neutral changes, depending on how orthology and synteny has held up. Now think about the shear number of possible interactions in any given genome. How many new mutations could interact with any of the other bases in the genome and produce a beneficial effect? Now think of all the organisms on the face of the Earth participating in this very experiment.


So much so that professor of biochemistry Larry Moran and his co-authors wrote their biochemistry textbook Principles of Biochemistry explicitly from an evolutionary perspective because evolution helps make sense of both the similarities and differences between the biochemistry of many different organisms:

The importance of evolution for a thorough understanding of biochemistry cannot
be overestimated. We will encounter many pathways and processes that only make sensewhen we appreciate that they have evolved from more primitive precursors. The evidence for evolution at the molecular level is preserved in the sequences of the genes and proteins that we will study as we learn about biochemistry. In order to fully understand the fundamental principles of biochemistry we will need to examine pathways and processes in a variety of different species including bacteria and a host of eukaryotic model organisms such as yeast, fruit flies, flowering plants, mice, and humans. The importance of comparative biochemistry has been recognized for over 100 years but its value has increased enormously in the last decade with the publication of complete genome sequences. We are now able to compare the complete biochemical pathways of many different species.
The relationship of the earliest forms of life can be determined by comparing the
sequences of genes and proteins in modern species. The latest evidence shows that the early forms of unicellular life exchanged genes frequently giving rise to a complicated network of genetic relationships. Eventually, the various lineages of bacteria and archaebacteria emerged, along with primitive eukaryotes. Further evolution of eukaryotes occurred when they formed a symbiotic union with bacteria, giving rise to mitochondria and chloroplasts.
The new “web of life” view of evolution (Figure 1.15 ) replaces a more traditional view that separated prokaryotes into two entirely separate domains called Eubacteria and Archaea. That distinction is not supported by the data from hundreds of sequenced genomes so we now see prokaryotes as a single large group with many diverse subgroups, some of which are shown in the figure. It is also clear that eukaryotes contain many genes that are more closely related to the old eubacterial groups as well as a minority of genes that are closer to the old achaeal groups. The early history of life seems to be dominated by rampant gene exchange between species and this has led to a web of life rather than a tree of life.
Many students are interested in human biochemistry, particularly those aspects of biochemistry that relate to health and disease. That is an exciting part of biochemistry but in order to obtain a deep understanding of who we are, we need to know where we came from. An evolutionary perspective helps explain why we can’t make some vitamins and amino acids and why we have different blood types and different tolerances for milk products. Evolution also explains the unique physiology of animals, which have adapted to using other organisms as a source of metabolic fuel.


Yes it does.

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Well, maybe. But can you be more specific as to how? I am not expecting to be able to critique the nitty-gritty of the science nor anything close to it. I’ve stated many times on this thread my layman status. Just please try and put yourself in the position of the layman and ask yourself how one would decide between some of the plain sense things a Behe has to say and most of the folks here who claim the opposite or worse, that he is not much better than a fool. It is not difficult to see how the analogy of mechanical engineers relation to physics is analogous to the claim of evolutionary biologist to biochemistry. The physics is at a more base level than the engineering which is applied physics. If the engineering fails it will show up in the physics. Isn’t it the same with evolutionary biology/biochemistry. If things are going to evolve biologically, they are going to do it at the level of the molecule.

Let’s stress the part where you say, “he had the wit to try a simple experiment” and in that, especially the word, "simple". As in grade school simple. ‘o-rings’ become stiffer and less responsive the colder they get. Think ice cream or butter or your rubber garden hose in the freezing weather as opposed to lying in the sun on a hot summer day. There was an entire team of engineers and managers from MortonThiokol that tried to persuade the NASA managers the night before the launch to delay until the weather warmed up. They launched at more than 15 degrees colder than the previous coldest launch, which had the most o-ring erosion or any of the missions.

As far as this layman understands, things evolve biological at the level of the molecule. Isn’t that biochemistry. If things evolve biological it can be glossed over or it can be elucidated at the level of the molecule. If things don’t change at the molecular level - they don’t change.

There is no mystery at all. The NASA managers didn’t want the truth to be the truth. The truth was a very, very inconvenient truth. On all previous missions during flight readiness review, all departments and sub-contractors were grilled strenuously as to why their system should be deemed flight-ready. On the 25th space shuttle mission, upon Morton Thiokol’s recommendation not to launch, they were asked to prove that it was unsafe to do so and that the mission would fail. The flight had already been delayed numerous times and the window for the teacher in space to deliver her lesson from space was rapidly closing, and the pressure to get the thing aloft was tremendous. So there is no ‘mystery’ as you suggest.
When it comes to this issue of ID and IC there are also strong motivations for not seeing our (all of our) opponents’ position. Is our opponents position just very inconvenient? Is it one that we will not accept regardless of the strength of the position? Will we strawman it ad infinitum?

This all lines up with my understanding of the launch decision. Anyone who has worked with engineering specifications for process industry would know that the engineering staff for sure were aware of the temperature vulnerability of those seals, and the investigation bears that out with an extensive documentation trail. But the lessons here involve organizational decision making with huge pressures to perform, management of technical expertise, and dealing with large impact contingencies where prior luck breeds false assurance. No one in engineering was saying that physics did not apply. The disaster, however, is way off topic in regards to biochemistry let alone the Lenski experiment.

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How do you let yourself get away with making that statement?
“We know it is very cold.” “We know what the cold does to the responsiveness of rubber o-rings.” “Let’s launch.”
Your making of the statement, “No one in engineering was saying that physics did not apply” is the obfuscation I see throughout this thread.
I don’t care how you spin it which is what you’ve done. How else do you account for saying, "it is A ok to launch in the cold despite what we know about the physics (o-rings get stiffer when they are cold)?
I see it as the greatest failure of a scientific organization ever. To arrive at that conclusion I’ve considered the simplicity of the science, the fact that they knew the science and that the only reason for the failure was that they wanted a different answer.
A lot of people here don’t seem to understand that Behe believes in evolution. He believes in common descent. He says that the Darwinian mechanism of random variation and natural selection aren’t sufficient to do the task claimed for them. He began his career absolutely content with ‘Darwinism’. It fit just fine with his view of the world and his theology. He only became disillusioned as he found bit by bit that the evidence for the mechanism was scanty.
The Challenger disaster is only relevant of an example of the extent that some will go to deny the plainest of truths and your spin here seems to fit right in. “No one in engineering was saying that physics did not apply”

Depending on how you define “molecular level”, this is not true.

Evolutionary change occurs at the level of the sequences of bases in the genomes of members of a population. This level can be represented by simple sequences of letters representing the various bases and no chemistry need be invoked.

Your statement is like saying if no changes occur at the molecular level when you are renovating a house, than no change occurs. That is wrong. The changes need only occur at the level of the bricks, wooden supports, dry wall, etc. No molecular changes necessarily occur in any of these components. A home contractor does not need to know physics or chemistry to do his job, and a physicist or chemist would be useless in doing a renovation.


I’m starting a new thread for discussion of the Challenger Disaster. Because topic are tangled I have tried to quote all the relevant comments and used that to start the new topic, allowing comment which may apply to both topics to stay. New comments related to Challenger will be moved.

It’s simple enough. If you know nothing about the subject you are unable to judge anything about it. You can’t judge Behe’s work (such as it is), claims, or argument, you can’t judge mine, you can’t judge anyone’s. You can’t decide whether things Behe says make plain sense. And just because you’re a layman, that doesn’t mean you can’t learn. That’s an excuse.

But isn’t biochemistry just physics, at bottom? It’s all really just electrons finding new energy levels, quantum mechanics, and such. So if we really want to understand evolution, shouldn’t we forget about biochemists and ask physicists? In fact, shouldn’t physicists be the experts on everything, everywhere? Simple answer: no. Some things are best understood at a higher level than of interactions between outer shell electrons. Some things are even best understood at a higher level than that of molecules bumping into each other. Evolution is one of those things.

That’s true. In fact it’s simpler even than that. Evolution, at bottom, is changes in the DNA (or, in some viruses, RNA) sequences of genomes. But there’s much more to it than that, because some of those changes have effects on phenotype, and they all begin as mutations in single individual molecules. How and why the changes spread through populations, what changes are favored in any particular environment, how the effects work out in time and space, all those are way beyond biochemistry. The very best physicist may not know how to fix your car, and you’re better going to a mechanic. And if you want to understand evolution, you’re better going to an evolutionary biologist.

My suggestion is that all those strong motivations are on your side. Witness that you are confident in your view despite knowing nothing about the subject.


As a default, laypeople should accept the scientific consensus. I’m not saying that you have to believe the consensus is some absolute truth, only that you should respect the findings of tens of thousands of experts that all know more about the subject than you do.

Behe is not part of the scientific consensus. The vast, vast majority of experts think he is wrong and misguided. This includes thousands and thousands of Christian scientists, so it isn’t as if Behe’s claims are being rejected because the scientific community is philosophically opposed to religious beliefs.


As far as I can tell, neither did Darwin in the Origin of species.

I disagree

If you want to understand, I invite you to read or reread the mission and values statement of this blog.

Every evolutionary biologist knows this and knew it a long time before Behe ever came on the scene. Modern evolutionary theory has advanced past plain old Darwinism.

Hold your horses Sam. Data just disagrees with you. You keep saying these things but it seems you don’t know what they really are. Darwinian evolution can explain many aspects of evolutionary change in the past and present, but it is inadequate to account for all changes.

I don’t know anything about the Challenger disaster, but as far as evolutionary biology is concerned, scientists are not denying any plain truth, but are simply following the evidence where it leads. I can’t say the same for many YECs and ID proponents.


This surprises me. Do you have specific examples that show that evolutionary biology informs the biochemist?

A post was merged into an existing topic: Recapping the Challenger Disaster

I’ve already offered you one–the polymorphism of the MYH7 cardiac/slow-muscle myosin heavy chain gene. You and Bill whiffed.

Others offer many more below. I’m gonna go out on a limb and predict that you will go on ignoring them as if none of them ever existed. Am I right?

Testing hypotheses is not limited to doing experiments. Darwin was a naturalist and included a lot of field work in OoS. Behe has done nothing in the lab or in the field.

Maybe you haven’t bothered to read OoS?


How about the reconstruction of ancestral proteins, much discussed on this site?


Darwin spent 5 years gathering exciting new data from the ecosystems of the Amazon rainforest, the Galapagos Islands, etc., during his voyage on The Beagle. And he incorporated these data into his publication.

I’m sure Behe appreciates having your vote of confidence. Unfortunately for Behe, your vote won’t convince the thousands of Ph.D. biologists who participate in the peer review process. And so far, he has not made one iota of progress toward this presumably more important goal.



Time for another example of the three-step method for refuting creationists.

Step 1: Read what the creationist says.

Step 2: Check their cited source.

"I removed all the ants from about a group of about a dozen aphides on a dock-plant, and prevented their attendance during several hours. After this interval, I felt sure that the aphides would want to excrete. I watched them for some time through a lens…

Step 3: Note that their source does not match their claim.

Works every time.


Enough beating around the bush with these hypotheticals about possible biases and motivations. Yes yes, we get it, lots of people could be in denial all over the place, including on your side of the fence.

So, shall we proceed to discussing actual biology?

Like how irreducible complexity as Behe has defined it (remove a part from a multi-component system and it stops performing a function for which that part is critical) is not a barrier to evolution? That systems that demonstrably meet those criteria have been shown to evolve?


I was hoping that the example about Behe’s expectations regarding protein structure and function would get the point across. (" Specifically, Behe’s single-minded focus and blinders leads him to believe that protein function is highly constrained, impossibly so in an evolutionary context. Evolutionary biology, with a big assist from modern DNA science, that tells us that the opposite is in fact the truth of the matter. ")

The story about poly(A)-assisted RNA degradation in eukaryotes is another instance where evolutionary concepts drove the process of discovery and biochemical characterization. Enjoy.