Lenski’s Long Term Evolutionary Experiment
Richard Lenski began the LTEE with 12 populations (six 
and six 
) 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.
Maybe for the same reason that people said heavier than air flight was impossible. There was plenty of evidence of failed attempts, no successes, and solid physics reasons.
Although I suspect evidence and reason are less compelling for Behe than his religious faith. He rejects a coherent understanding of evolutionary theory for the same reason Republican Senators reject evidence – they have internal imperatives against which reason and evidence have no purchase.
I fail to see how an open environment or a longer generation time are going to stop evolution by natural selection in multicellular organisms. As a reminder, the four postulates of natural selection are:
1) There is phenotypic variation for a trait
2) The phenotypic variation is (partly) heritable
3) There is variation in fitness (survival and reproduction)
4) The variation in the phenotypic trait is correlated with variation in fitness
All four postulates are true for any population of multicellular organisms you care to mention. As you can see, confined environments and generation time do not come into it.
His religious faith has nothing to do with the fact that the Lenski experiment clearly shows the limitation of evolutionary theory. When you attack the person you show the weakness in your position.
Corneel,
Why the straw man? My claim is that the Lenski experiment shows the limitation of evolutionary theory. 50000 plus generations and not a single de novo enzyme. This contradicts Alan’s lots of needles hypothesis and shows the difficulty of mutational fixation.
No one disputes micro evolution.
The experiment shows the effect of many more generations then an experiment with multicellular organisms such as mammals. It also shows selection in tightly isolated populations which is not realistic in nature.
The Darwinian fairy tale of universal common descent needs to be retired. The simple to complex hypothesis has failed.
I do. And so should you: http://nonlin.org/microevolution-fallacy/
colewd,
Wow Bill, I see you’re still just as scientifically ignorant as ever. Because a feature can evolve in a few thousand generations doesn’t mean every species must evolve major changes in that time.
What limitations would those be Bill? That the E coli in the experiment didn’t grow wings and fly away therefore ToE is wrong?
All this really shows is your brutal scientific ignorance and misunderstanding of the LTEE.
Where can I read about your claim where other experts have first examined your claims and put their responses to you?
Oh, what’s that, you’ve not published your “claim”? So I guess you can’t be that sure about it.
Oh, you don’t have the time for that?
Well, may I suggest stopping visiting here for a few days and getting to work.
May I suggest another postulate, that the number of offspring must exceed the carrying capacity of the environment. Otherwise, there is no selection pressure.
This is not actually necessary. If these four postulates are satisfied, the population will experience changes in its heritable characteristics, i.e. it is evolving. It may be, as you hint at, be growing. But it is evolving nevertheless.
Adapa,
Where did I say anything about wings 🙂
Never.
I read your comment as saying that humans do not evolve by natural selection. If that is not your position, I apologize.
Your demand for proof of de novo ex nihilo complex sequences is your own and has no relevance for evolutionary theory whatsoever.
You are repeating yourself, so I will too: You haven’t given any valid reason why the conclusions shouldn’t generalize to organisms with longer generation times or those living in an open environment.
Ceterum autem censeo Carthaginem esse delendam.
Yeah, yeah, but the LTEE does not address universal common descent.
If it’s OK with you we’ll keep on using it until something more productive comes along to replace it.
Do you have any ideas what we could replace the science of evolutionary biology with?
Neither you, nonlin or phoodoo care to say what we should replace it with?
You just go on and on about something you believe is wrong.
But what is right?
I mean, I know you think the Bible can replace science, but I think we need a new type of science in that case.
A science that can investigate god, work out how and why it does what it did. Work out ways to ‘trick’ it so we can see it’s effects in the lab – i.e. new species appearing from nothing, reliably turning water into wine etc.
Once you can delineate all those rules and make your god a science,then perhaps we can replace the equations in the textbooks with equations on how to manipulate your deity.
But until then, the simple to complex hypothesis remains our best candidate. Unless you want to tear it out and replace it with nothing at all?
Corneel,
I think this is a point of agreement we can conclude on.
the Bible does not replace science. It is guiding us to where science starts and where our models will work.
How do you mean, Bill? Have you any specific examples as how the Bible has informed scientific research?
I mean, I don’t think animal husbandry or Mendelian genetics is much informed by Genesis 30: 37-42
37 Jacob, however, took fresh-cut branches from poplar, almond and plane trees and made white stripes on them by peeling the bark and exposing the white inner wood of the branches. 38 Then he placed the peeled branches in all the watering troughs, so that they would be directly in front of the flocks when they came to drink. When the flocks were in heat and came to drink, 39 they mated in front of the branches. And they bore young that were streaked or speckled or spotted. 40 Jacob set apart the young of the flock by themselves, but made the rest face the streaked and dark-colored animals that belonged to Laban. Thus he made separate flocks for himself and did not put them with Laban’s animals. 41 Whenever the stronger females were in heat, Jacob would place the branches in the troughs in front of the animals so they would mate near the branches, 42 but if the animals were weak, he would not place them there. So the weak animals went to Laban and the strong ones to Jacob. 43 In this way the man grew exceedingly prosperous and came to own large flocks, and female and male servants, and camels and donkeys
Alan Fox,
Maybe that’s an example of things that won’t work?
🤣
No, it does not.
Why does the fossil record show a succession of forms?
Which one of these was the created one?
There was plenty of science done before and despite the bible. Here, this might help: https://www.open.edu/openlearn/history-the-arts/history/history-science-technology-and-medicine/history-science/brief-history-science
Religious dogma you say? Bit like you you previously suggested we should replace evolutionary science with the bible.
Any question at all answered, and the answer always the same. The bibble.
Also, colewd, would our models work without the talking snake? Without the rulebook on slavery? Would the lack of things have affected our understanding of biology today? When our models work?
Alan Fox,
two off the top of my head.
-Genesis one and the separate creation of animals supported by population genetics mathematical limitations.
-Leviticus and Kosher animals chewing the cud (4 compartment stomachs) which is still studied by scientists today
OMagain,
Very good question. Perhaps Sal’s flower can guide you toward a prediction. Evolutionists are seeing what they want to see and ignoring the data they don’t like.
😳😕😑😏🙂😁😅😂🤣😭
Alan Fox,
Ok I will give you this one. Replace evolutionists with general human nature 🙂
Alan Fox,
I agree.
Well, fair enough, we all suffer from cognitive bias to a greater or lesser extent. Acknowledging it is the first step to recovery.
Why, can’t you?
Well, what is it that I should be seeing and what is the data that is being ignored?
For example? Can you provide any more detail then that? What limitations? What published work?
Is this in someones opinion other then yours? Someone who has done some work other then typing those literal words?
You mistake me for the person who believes in Intelligent Design. That’s you.
I don’t need to make a prediction for something that never happened. That I never said happened. That I don’t think happened.
You believe that at some point animals appeared complete and with no precursors. When I ask you where in the fossil record we can observe such you respond by saying perhaps Sal’s flower can guide me towards a prediction?
It’s your claim so you get to make the predictions!
So, colewd, what is the fossil record then? A lie sent by the devil?
OMagain,
From the data in Sal’s flower I predict that Zebra fish, Chickens, Mice and Humans come from separately created kinds as the gene sets are different. If you can make available the Gene sets of the various horse species you cited I will give it a shot. If the gene data is not available we can discuss animals that have gene set data.
Sorry Bill but that Creationist canard was disproven soon after we began studying genomes some 70 years ago. The genetic record taken in total shows humans and mice shared a common mammalian ancestor roughly 90 MYA. Of course neither you nor any other Creationist can give a definition of “kind”.
Any more Biblical “science” predictions you want examined?
But if you recall, you gave what you called the postulates for natural selection, not simply for evolution. I agree your postulates are sufficient for evolution. But natural selection requires selection. What am I missing?
(I also note that selection is not necessary for growth, and excess offspring does not imply growth. Only selection)
The rather comical lengths creationists will go, to defend religious doctrine against the slings and arrows of outrageous reality.
I wonder if ring species are an example of biblical creation in real time.
Let’s see:
Some selection happens against, say, predators, or against parasites, or some variants are able to eat something the rest of the population cannot, thus giving them a new niche, etc. Selection is not just about limited resources.
Just mentioning “Sal” as their reference is comical enough. Poor Sal cannot tell the difference between DNA and protein. Poor Sal quotes research that contradicts his “points”, imagining that they support his “points” (true story!), etc, etc, etc.
I don’t know what “Sal’s flower” means, but that doesn’t look like a prediction, but like an inference, and not a very good one.
If you mean the figure from some article that you kept posting some time ago, that’s not a flower, that’s a Venn diagram, and I have already explained those apparent discrepancies to you. You acknowledged understanding what I explained. So, if that’s what you mean by “Sal’s flower,” then it’s sad that you keep holding to it as a problem for evolution, when the problem is, clearly, your lack of understanding.
I forgot how to do links, but here’s a try:
thoughtco.com 4 necessary factors for natural selection
This site is entitled “4 Necessary Factors for Natural Selection”. And factor number one happens to be:
“Overproduction of Offspring”
In order, the next three are
Variation
Selection
Reproduction of adaptations
However, as multiple sites explain, there are other selection pressures besides overpopulation. So in theory, overpopulation isn’t necessary for evolution by natural selection. In practice, there are likely no exceptions (that is, cases where overpopulation is not practiced).
That’s a good point. To be honest I am not really sure, but I think the term is just a legacy from the way this idea was conceived by Charles Darwin. He was very much inspired by the insights of Thomas Malthus on overpopulation. Nowadays natural selection is usually defined in terms of a difference in reproductive success (fitness). So there is not necessarily any selecting of offspring going on.
Modern evolutionary thinking is strongly influenced by the mathematical formalisms from population genetics and quantitative genetics. Models of selection typically assume infinite* population sizes. Evolution is then defined as a change in allele frequency or in the mean trait value of a population, respectively. Clearly, overpopulation is not a thing in those models. In practice, populations are limited by the resources in the environment, so there will be dying off of excess offspring. It’s just not part of the requirements for evolution by natural selection to occur.
*ETA: Well, at least large enough that genetic drift can be ignored
If you wish. Still not seeing why you brought it up in the first place, if you agree it is not relevant.
It’s a one-eyed notion anyway, since Bill ignores the genes they have in common, but ‘Sal’s flower’ might point less ambiguously to separate creation if the only organisms on earth were zebra fish, mice, chickens and people. Adding intermediate forms (which doesn’t mean chicken-people or fish-mice!) gives a much clearer picture, coming out very strongly against separate creation, since the purported dichotomies disappear.
Flint,
That’s interesting.
Allan Miller,
Keeping in mind that I’m not sure what “Sal’s flower” means, if it’s about that Venn diagram, the shared genes agree with the phylogeny, and then the ones that would seem weird, shared between farthest away species and not by the closer ones, are very few and explainable by several factors, from problems with how the figure was produced (I think that to make it into the figure genes had to comply with requirements that could keep a gene out of display in one species, despite the gene being there, to the drafty nature of most eukaryotic genomes, where one gene could be missed in one, another in the next, to actual differential losses. I don’t remember the details, but I gave Bill a full list, which he agreed was a good explanation. Again, I’m not sure if we’re talking about the same figure.
Entropy,
Here’s the diagram.
http://theskepticalzone.com/wp/wp-content/uploads/2018/08/image_103611.jpg
Alan Fox,
Then that’s the one. Weird to call it “Sal’s flower”.
Uh, wait a minute. Are you saying here that differential reproductive success is entirely random? That organisms have evolved astounding levels of suitability for their environments through sheer good luck?
I think you are missing something important here. You are focusing exclusively on HOW descent with modification works, while completely ignoring WHY this happens. Kind of like examining every molecule of paint on the mona lisa, unable to notice that those molecules taken all together contain a larger message. Gee, it looks like someone’s picture, but really, technically, it was equally likely to be random noise. Right?
Allan Miller,
Are their intermediate forms? This assumes a connection between the animals which is circular reasoning until you can show how new genes form. If we use the Lenski experiment as the benchmark experiment you did not form one yet Sal’s flower shows thousands.
Corneel,
It’s only relevant if some still believe this is a credible hypothesis. If no one does then I agree with you. The issue is that Allan Miller appears to be using it as a working assumption in his arguments as he is claiming intermediate fossils.
In wider terms, yes.
It’s not an assumption. It’s called knowledge.
Nope. It would be circular reasoning if there was no evidence about connections, but there’s plenty of evidence, and whether we know how new genes form or not doesn’t matter. We don’t need to know every detail to understand that there’s connections.
But let’s rephrase to help you get the idea without hurting your feelings: “putting there the genomes of many more organisms at intermediary taxonomic levels would help us better figure out what’s going on”
Why would you use an experiment that wasn’t designed for the evolution of new genes as a benchmark for production of new genes?
Why do yo insist on calling that “Sal’s flower”? Were those genomes sequenced by Sal? Did Sal get involved at all in those analyses? If so, was Sal the one and only author?