Remember Lenski’s experiments on E coli evolution?

_{Denyse O'Leary

July 9, 2015

Darwinism, Evolution, News}

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He talks about his findings here (public access):

In February 1988, Richard Lenski set up 12 replicate populations of a single genotype of Escherichia coli in a simple nutrient medium. He has been following their evolution ever since. Here, Lenski answers provocative questions from Jeremy Fox about his iconic “Long-Term Evolution Experiment” (LTEE). The LTEE is a remarkable case study of the interplay of determinism and chance in evolution—and in the conduct of science.
More.

A reader writes, “Sounds like Lenski admits that there is no experiment or hypothesis in the traditional sense. I wonder if he would admit that to a popular audience.”

Was the reader thinking of this?

JF: Ok, so let me ask you that. Is the LTEE actually an experiment, and wouldn’t it have been even better if it was? It’s just one “treatment”—12 replicates of a single set of conditions. Wouldn’t it have been even more interesting to have, say, two treatments? Two different culture conditions, two founding genotypes, or two founding species?

RL: You’re certainly right, Jeremy, that experiments in the fields of ecology and evolutionary biology typically have two or more treatments. But that’s not an essential part of the definition of an experiment. It would have been nice, perhaps, if the LTEE did have two or more environments and/or two or more ancestors, as you suggest—in fact, we’ve run several of those types of experiments over the years, and I’ll mention a few of them below.

The reason I didn’t do that with the LTEE, though, was because one of my core motivating questions concerned the repeatability of evolutionary dynamics across replicate population. That’s a question about the trajectory of variances over time, which is challenging statistically because estimates of variances have large uncertainties. So if the LTEE had two treatments, I might have been able to say something about the differences between them, but I would have had less power to say anything about the among-replicate variances for either treatment. So for that motivating question, going from 12 replicate populations down to 6 replicates would have been risky.

Well, um, no, not in the traditional sense. Only design requires evidence. And all such evidence is dismissed in principle.

Evolution today is NOT about evidence. That is because we are at the frontier of an impasse that Darwin’s followers can’t help us bridge.

Talk to the fossils: Let’s see what they say back
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Comments

Zachriel:
This shows that the resistance developed *before* exposure to the antibiotic, rather than due to exposure to the antibiotic.
It doesn't show if the mutation that caused the antibiotic resistance was accidental or intentional.
It shows a pattern of descent with modification.
Family trees do that. Virgil Cain

Andre: How on earth does a person test and make predictions on unguided evolution. Here's a very simple experiment and prediction. Start with a single strain of bacteria. Create multiple colonies on a plate, then stamp the colonies (a way of transferring the pattern of colonies to a new plate). Now expose the original plate of colonies to antibiotics. Some colonies will have antibiotic resistance. While we can't predict which colonies have antibiotic resistance — it's apparently random —, we can predict that the corresponding colonies on the matching plate will also have antibiotic resistance. This shows that the resistance developed *before* exposure to the antibiotic, rather than due to exposure to the antibiotic. ppolish: And the tree shows evolution? Yes. It shows a pattern of descent with modification. Andre: Contingency is a design principle. The term is being used in the paper to refer to how later events are dependent on prior events. Zachriel

Lifepsy @ 18 noted
It’s just a sad reminder of how the Evolutionary community props itself up with obfuscation and confusion.
ppolish added in 41
Two “begats” hardly equals “evolving resistance”. Two monoclonal begats.
The extent of the exaggeration and celebration of this "experiment" as *** Proof of Evolution & All Sorts of Other Things *** simply demonstrates the embarrassing absence of any scientifically credible evidence, although the rhetoric is non-stop. -Q Querius

Twenty years ago, E. coli H30 begat H30-R who begat Superbug E. coli H30-Rx. Two "begats" hardly equals "evolving resistance". Two monoclonal begats. ppolish

Zachriel is another grand equivocator, so be prepared to deal with that. Virgil Cain

REC:
You got caught saying “people still present Lenski’s experiment as proof for … universal common descent” and can’t back it up.
Just hang out and pay attention. It is sure to come up again, it always does. And stop ignoring the rest of my post.
There are evidences of universal common ancestry (e.g. phylogeny) and evolution of Eukaryota (e.g. endosymbiont theory)
Those aren't evidence for common ancestry. Phylogeny could easily be made out to be a tree of common design. Endosymbiosis only provides organelles and cannot be tested beyond "those organelles sure look like they coulda been bacteria" Virgil Cain

Contingency is a design principle. Unguided processes do not create contingencies. Andre

Following an "Evolutionary Pathway", Zachriel? What part of unguided and purposeless don't you understand? And the tree shows evolution? Do I need to wear 3D glasses to see the evolution? Beer goggles? ppolish

Zachriel you are a con artist.... How on earth does a person test and make predictions on unguided evolution. It is simply impossible. Yet here you are..... trying to con everyone. Andre

Virgil, You got caught saying "people still present Lenski’s experiment as proof for ... universal common descent" and can't back it up. There are evidences of universal common ancestry (e.g. phylogeny) and evolution of Eukaryota (e.g. endosymbiont theory), but you're fighting shadows--beating up arguments no one has ever made. REC

ppolish: What does Blount mean by “historical contingency”, Zachriel? Is that the politically correct way to say “guided evolution”? Quite the opposite. It means that some evolutionary pathways are rare, and so rarely taken. Zachriel

REC, If English isn't your native language I would understand your confusion. Lenski's experiment wasn't designed as a formal test of UCD. That does not prevent evolutionists from using it as such. What was said is evos use the experiment as evidence for UCD cuz once you get a little variation all ya gotta do is keep adding it up, by golly. That is the evolutionary argument. That you ignored that bit and prattled on anyway, is very telling. That is Darwin's entire argument- a little variation accumulated over many generations gives us UCD. Virgil Cain

ppolish: That is NOT “evolving bacterial resistance” They provide a phylogenetic tree. Sure looks like evolution. http://mbio.asm.org/content/4/6/e00377-13/F2.large.jpg lifepsy: In other words the timing of the gene expression was changed, like I said. What you said was "its expression signal only changed." That was not correct. There were many changes, including that the transporter gene was duplicated in tandem, so that it happened to be linked to a different promoter. Zachriel

"Virgil's" words: "people still present Lenski’s experiment as proof for evolution AND universal common descent." No one claimed “that Lenski’s experiment was designed as a formal test of universal common ancestry”. Are we now going to play word games and say proof and test are antonyms? REC

"More generally, we suggest that historical contingency is especially important when it facili- tates the evolution of key innovations that are not easily evolved by gradual, cumulative selection." What does Blount mean by "historical contingency", Zachriel? Is that the politically correct way to say "guided evolution"? http://www.pnas.org/content/105/23/7899.full.pdf ppolish

REC:
Show me where anyone respectable states that Lenski’s experiment was designed as a formal test of universal common ancestry…..
Show us a respectable evolutionist ;)- But I digress. No one claimed "that Lenski’s experiment was designed as a formal test of universal common ancestry". What was said is evos use the experiment as evidence for UCD cuz once you get a little variation all ya gotta do is keep adding it up, by golly. That is the evolutionary argument. Virgil Cain

Zachriel: There were two potentiating mutations, then the citrate transporter gene was duplicated putting it under the control of an adjacent promoter. Uh huh. In other words the timing of the gene expression was changed, like I said. Z, when you can't correct someone, do you like to just respond in a way to make it appear as if you had? The point is that many evolutionists believe the E.Coli "evolved" the complex metabolic process itself (because that's how it is typically advertised). The evolutionary community sustains itself on these mass confusions. lifepsy

Ok "Virgil". Show me where anyone respectable states that Lenski's experiment was designed as a formal test of universal common ancestry..... REC

Blount/Lenski is trivial Zachriel. How about E. coli superbug emerging from a single clone and then going forth and multiplying. That is NOT "evolving bacterial resistance" sorry. It IS "emergentism". Smells a bit like "creationism" don't it? ppolish

lifepsy: its expression signal only changed. There were two potentiating mutations, then the citrate transporter gene was duplicated putting it under the control of an adjacent promoter. Over time, the new assembly was subject to further duplication and optimization. See Blount et al., Genomic Analysis of a Key Innovation in an Experimental E. coli Population, Nature 2012. ppolish: Could Lenski’s “long term expirement” predicted this? Why would it? That wasn't the purpose of the experiment. However, it did show the role of contingency in evolution. See Blount et al., Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli, PNAS 2008. Zachriel

Could Lenski's "long term expirement" predicted this? http://www.darkdaily.com/unexpected-discovery-of-source-of-lethal-antibiotic-resistant-strain-of-e-coli-could-lead-to-new-medical-laboratory-tests-and-preventative-treatment-317#axzz3fVuqjciF There are useful E. coli studies and there are some that are not so useful. Lenski's is way way overrated. Way. Monoclonal source to resistance? Who would have guessed? Not the Lenski clan. ppolish

E. coli has been around for what, 100 million years? Based on this "long term" expirement of 28 years, any predictions for what E. coli will look like 100 million years from now? Wooly fur and giant tusks are not part of this domain darn. ppolish

REC:
My point was made here.
You didn't have a point.
Lenski’s experiment is not designed to address universal common descent (he starts with one bacterial clone, everything in the experiment is descended by definition).
Yet evos use it in support of UCD. They use anti-biotic resistance as evidence for UCD. They use finch beaks as evidence for UCD.
Only creationists have argued (stupidly) otherwise, with “its still a bacterium”!!!
The point is YOU don't have any evidence that prokaryotes can evolve into something other than prokaryotes. You have nothing but to attack ID and IDists with your misrepresentations and strawman arguments. And the sad part is if your position had something then ID would have been a non-starter. So yes, Robert, YOU are boring and indistinguishable from all other evos who can only lie to support themselves. Virgil Cain

"REC, why did you run away?" Well, Joe, you bore me. After this many years, I'd think you'd have something better than silly one liners. My point was made here. Lenski's experiment is not designed to address universal common descent (he starts with one bacterial clone, everything in the experiment is descended by definition). Only creationists have argued (stupidly) otherwise, with "its still a bacterium"!!! I don't see anything worth responding to. REC

REC, why did you run away? Virgil Cain

Zachriel:
Evolution has been observed in the lab for decades. Lenski’s is a longer term experiment than had been attempted before.
And people still present Lenski's experiment as proof for evolution AND universal common descent. That is because most people think the two are directly linked. And that is because people have been fed a strawman diet of the fixity of species. Virgil Cain

My main problem with Lenski's experiment is the campaign of disinformation that surrounds it. Evolutionists everywhere believe that a completely new metabolic process "evolved", when, as VC just pointed out, that function always existed in the E.Coli, its expression signal only changed. I have lost count how many times I've had to educate evolutionists about this... and even Wikipedia explains this.. but the specifics are always drowned out when the Darwinian mystics have a story to sell. It's just a sad reminder of how the Evolutionary community props itself up with obfuscation and confusion. lifepsy

KevNick: Lenski’s experiment is the only experiment I know about that Darwinists refer to as evolution proven in the lab. Evolution has been observed in the lab for decades. Lenski's is a longer term experiment than had been attempted before. Zachriel

Is it obvious that E. coli evolved more efficiently over the last 28 years outside the lab versus inside the lab? Mother Nature is the Maestro right? The Best Director? The Kubrick Hitchcock as it were. ppolish

KevNik- The pathway already existed. The transport protein was not expressed in the presence of O2. Virgil Cain

My only problem with people like Lenski, Moran or Coyne is: Why do they insist on "lying" especially to themselves and the world about their beliefs that they call science? I don't get it. Here is why: Lenski's experiment is the only experiment I know about that Darwinists refer to as evolution proven in the lab. They claim that this experiment proves that a new metabolic pathway has evolved in the lab that equals millions of years of evolution. I say, where is the bacterial progress beyond that if their claim is even true in the first place? KevNick

I've always wondered why Lenski’s experiment didn't include samples exposed to elevated ionizing radiation, which could have simulated long ages. As long as the samples are kept below their LD 50/30, which is quite high for E.coli, and the temperature not too high, he would have been able to simulate background radiation dosage both in quantity and composition. -Q Querius

What a boring "expirement" yawn. Like watching grass grow. In a lab. E. coli in the wild is much more interesting; http://www.healthline.com/health-news/women-antibiotic-resistant-ecoli-traced-to-single-strain-121613 ppolish

REC:
Baraminology feels comfortable extrapolating from small cultures, passaged over thousands of generations on media selective for E. coli to trillions of generations with possibly 10^30 organisms in all the environments of early Earth.
And what does UCD have to extrapolate from? What does evolutionism have to extrapolate from? Hmmmm? Extrapolating from natural selection and drift it is obvious you don't have a mechanism capable of UCD. Virgil Cain

Baraminology feels comfortable extrapolating from small cultures, passaged over thousands of generations on media selective for E. coli to trillions of generations with possibly 10^30 organisms in all the environments of early Earth. Hmmm...... REC

Don't hold your breath our materialist brethren won't accept the results no matter what the evidence say. Andre

Well, Robert, if bacteria can only evolve into bacteria then universal common descent (UCD) is stuck at, wait for it, bacteria. In 50,000+ generations there isn't anything that supports the range of change required for UCD. Baraminology says there are limits to the changes that can be produced and Lenski's experiment supports that claim. Virgil Cain

Ok Joe, tell us how Lenski's experiment defeats common descent and supports baramins. Please be specific. REC

REC Another materialist that has never heard of the species problem eh? Andre

Geez REC, don't you understand science? YECs giving up on baraminology? Hah. More likely that evos are giving up on evolutionism. "Species" is ill defined. Even those organism that can interbreed are classified as different species. Heck all of evolutionism is ill defined. Perhaps you should focus on your position as it needs a lot of help. Virgil Cain

Baraminology. Hah. From what I hear, even YECs are giving up on that. "Kind" is ill defined. What is a kind? Its a created type. So if speciation is observed-must be the same kind. REC

"A reader writes, “Sounds like Lenski admits that there is no experiment or hypothesis in the traditional sense. I wonder if he would admit that to a popular audience.” Well, that 'reader' needs to try harder. Right there in the middle of the article: "JF: Did the LTEE have any hypotheses initially.... "RL: Yes, the LTEE had many hypotheses, some pretty clear and explicit, some less so. What, did you think I was swimming completely naked?" He then goes on to explain them. REC

Lenski's experiment supports baraminology. It does fly in the face of universal common descent. Virgil Cain

So... your evidence that evolutionary biology doesn't need evidence is that Lenski designed his experiment to capture as much evidence as possible for a particular hypothesis? wd400

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