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Wednesday, October 22, 2014

40,000 Generations of Escherichia coli Data Support the Creationist View of the Genome

Posted by jlwile on November 7, 2009

Jeffery E. Barrick and his colleagues have published the results of one of the most interesting evolution experiments I have ever read.1 Actually, the genius behind this experiment is Richard E. Lenski, who is on the author list as well. Lenski started an experiment with E. coli almost 20 years ago, and it is still producing excellent results. Essentially, the experiment followed twelve populations of E. coli over all those years. The focus of the paper was one of those twelve populations.

In the experiment, the bacteria were grown on a minimal medium with glucose as a limiting nutrient. Each day, a small sample of the culture was removed and placed in a fresh medium. Periodically, samples were frozen so that they could be analyzed in detail at any time.

Thanks to the wonderful technology we have today, the entire genome of E. coli can be sequenced in a “reasonably short” amount of time. So this paper reports on the results of comparing the genome of the original bacterium to that of the bacteria after 2,000, 5,000, 10,000, 15,000, 20,000, and 40,000 generations. The results were “rather surprising,” according to the authors.

The main thrust of the experimental results is given in Figure 2 of the paper. In that figure, we see that the number of mutations accumulated over about 25,000 generations was pretty linear. Then the mutation rate shot up considerably. To give you an idea of just how much the mutation rate changed, there were just under 45 mutations in the population at generation 25,000, but by generation 40,000, there were more than 600!

The fact that the mutation rate jumped was easily understood, and it is the result of a mutation in a gene called mutT. This mutation causes very specific kinds of subsequent mutations, which were 90% of the new mutations found in generation 40,000. Thus, this result was not surprising. It is well understood.

The “rather surprising” result is what happened to the fitness of the population while mutations piled up at a rather constant rate. The authors found that with the first few mutations, fitness increased rapidly. After that, however, mutations accumulated at a more or less constant rate (at least for the first 25,000 generations), but the fitness did not. Instead fitness increased more slowly as time went on, even though the mutation rate stayed constant.

The authors tell us the expected result: mutations and fitness should increase or decrease hand-in-hand. If lots of mutations are being preserved in the population, that should mean they are beneficial to the organism in that environment. Thus, the organism’s fitness should increase rapidly. If few mutations are being preserved in the population, that should mean there are few beneficial mutations for the organism in that environment, so the fitness should increase slowly. Thus, the rate of preserved mutations should go along with rate of change in fitness. This is not what the data showed. Instead, the preserved mutations increased linearly, but the fitness increased rapidly at first and then leveled off as time went on.

After proposing a couple of hypotheses and showing how they could not be the right explanation for the “rather surprising” result, the authors finally said that the leveling off of fitness increase was due to the fact that once the initial large increases in fitness were gained by certain mutations, the only possibilities left were mutations that led to small increases in fitness. As a result, there would be a lot of competition between subpopulations that had SOME of those mutations and other subpopulations that had OTHER versions of those mutations. Thus, competition between subpopulations that each had SOME small-but-beneficial mutations would keep mutations rates up but would limit overall gains in fitness.

In addition, some mutations produce both positive and negative effects for the bacteria. When a mutation produces a large positive effect and a few small negative effects, subsequent mutations can work on getting rid of those small negative effects while preserving the large positive effect. Once again, however, that results in only minimal fitness gains.

In other words, the authors conclude that the changes you can expect in a genome are limited. If you put bacteria in a stressful environment, they will begin to mutate, because their genome seems designed to do that. However, since there is a limit to how much the genome can change, the fitness gains that come as a result of mutation cannot continue to increase at the same rate as preserved mutations.

In other words, mutation and natural selection can “tinker” with the genome, making minor improvements. However, they can’t do much more than that. As a result, mutations will continue to accumulate if the bacteria are stressed, but because there are limits to the flexibility of the genome, those mutations will result in smaller and smaller fitness gains.

This, of course, is what creationists have been saying for many years. God created specific kinds of creatures, and He built in them machinery that would allow them to change over time so as to adapt to changes in their surroundings. However, each genome is limited to the specific kind of organism created, and at some point, you reach a limit at which the genome cannot be changed anymore, at least not in a way that will promote further adaptation.

This, of course, is diametrically opposed to what is needed for the evolution of one kind of organism into another kind of organism. If all it takes is mutation, natural selection, and time to turn a fish into an amphibian, the genome must be almost infinitely flexible, and there should be virtually no limit to the changes that can be produced by mutations. That’s not what these data (or other data2) indicate.

It is nice to see that 40,000 generations of E. coli data support the creationist view of the genome.

REFERENCE

1. Jeffery E. Barrick, et al., “Genome evolution and adaptation in a long-term experiment with Escherichia coli,” Nature, 461:1243-1247, 2009
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2. A. A. Hoffmann, et al., “Low Potential for Climatic Stress Adaptation in a Rainforest Drosophila Species,” Science, 301:5629-34, 2003
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Comments

7 Responses to “40,000 Generations of Escherichia coli Data Support the Creationist View of the Genome”
  1. bobxxxx says:

    “You have stumbled across Dr. Jay L. Wile’s Blog. Dr. Wile holds an earned PhD from the University of Rochester in Nuclear Chemistry. He is best known for the ‘Exploring Creation with…’ series of textbooks written for junior high and high school students who are being educated at home.”

    How nice. An idiot with a PhD who makes a living from mentally abusing children with his [censored].

    “God created specific kinds of creatures”

    An uneducated Christian hick could not have said it better. What a [censored] moron you are.

  2. bobxxxx says:

    You provide a link to Answers in Genesis, which makes the wild and ridiculously wrong claim that the entire universe was magically created 6,000 years ago.

    You, sir, are a [censored] idiot.

  3. jlwile says:

    Note the intellectual rigor of this guy’s arguments. He adequately demonstrates how most people react to facts that go against their preconceived notions but cannot be refuted.

    By the way, I censored the cuss words to make his comments at least PG-rated.

  4. Kyle says:

    I’m just a student, but do you have any examples of what these mutations are? How exactly do typical mutations help/harm these organisms?

  5. jlwile says:

    The paper actually has an interesting figure (Figure 1) that maps each mutation (up to generation 20,000), but we don’t know enough about E. coli’s genome to know exactly HOW each mutation has helped or harmed the organism. In fact, the paper simply assumes that if a mutation is preserved over multiple generations, it must have benefited the organism in some way, or it would be selected out of the population (if it were harmful) or drift (if it were neutral).

    There is a table (Table 2) that lists some of the mutations that have been shown in another publication to confer significant advantage to the bacteria in this study. While the paper doesn’t discuss WHY the mutations conferred advantage, the other publication shows that WITH that mutation, the bacteria live better in limited glucose conditions (which are the conditions of the study).

    In general, we know that most mutations confer fitness by reducing the effectiveness of a protein. For example, Cipro is an excellent antibiotic in fighting Anthrax. However, Anthrax can develop resistance to Cipro by a mutation that changes the shape of a protein called gyrase, which is what Cipro attacks. Because of the change in shape, Cipro can’t attack the gyrase, but ALSO because of a change in shape, the gyrase is EXTREMELY inefficient at its job. As a result, the mutant strain does not reproduce as well. So…it is a advantage in the presence of Cipro, but a disadvantage otherwise, and it is a result of a LOSS of genetic information (which leads to a less efficient protein).

    While it is not discussed in the paper, I assume that most of these mutations (which are either single-nucleotide polymorphisms or deletions or insertions) actually reduce the effectiveness of the protein, which is beneficial in some way when the supply of glucose is limited.

  6. Josiah says:

    Just as a bit of a control case, how many generations would an evolution expect it would take for say E-Coli to turn into another bug? Basing my thinking merely on time scale, surely displaying that something didn’t happen in 20 years worth of mutations (noting that in fact the bacteria DID display an increase in fitness as they continued to mutate, and only slowed their progress) cannot presume to state that over X00 million years the same thing couldn’t happen?

    More importantly, surely the counterargument to this premise is obvious. E-coli, having already evolved for X million years, are (presumably) pretty near perfection for their species in optimal conditions. The only thing that has changed is the food supply. Therefore they will move toward becoming more food efficient, including cutting back on bioprocesses that aren’t so critical to survival in the new environment. But it is impossible to live on zero energy. Some bioprocesses (like reproduction) are critical to species survival, and approach the stage where they cannot be made any better for survival in the new conditions. Therefore evolution adapts to the new environment, producing a new and stable subspecies. And isn’t that exactly what an evolutionist would produce anyway.

  7. jlwile says:

    Certainly no one who believes in macroevolution would expect to SEE it in a mere 20 years. However, that’s not the point of the experiment or the post. The experiment’s goal is not to see the E. coli turn into something completely new. The goal of the experiment is to track the genomic changes that occur when the E. coli are stressed.

    The results went against both the preconceived expectations of the experimenters as well as the prediction of macroevolution. If the genome were nearly infinitely flexible, then fitness would increase hand-in-hand with preserved mutation. Instead, after an initial burst, fitness levels off while preserved mutations continue to increase. This shows that there is a limit to genomic change, in accordance with creationist views.

    I also think you missed the concept of preserved mutations. The evolutionary argument would be that in an environment to which the bacteria are already optimally suited, there would be no preserved mutations, as there would be no increase in fitness as a result of mutation. Thus, there would be no way for natural selection to PRESERVE the mutations. The experimenters are specifically giving the bacteria a non-optimal environment so that mutations WILL cause adaptation and natural selection WILL preserve them. Since mutations are being preserved at a constant rate (until they REALLY increase after generation 20,000), that means the bacteria are still “trying” to adapt, even though they aren’t making significant fitness gains. Thus, the increase in preserved mutations shows that your counterargument doesn’t work.

    I don’t think you can say that since the only thing being changed is the food supply, there is only so far the bacteria can go. As I say in the discussion, the authors attempt several explanations for the “surprising results,” and each time they say the explanation doesn’t work. The only one THEY can come up with is the one I gave in the original post. They didn’t even mention yours as a possibility.

    I would expect that they did not even consider your explanation because the idea is that there are MANY things a bacterium could do to increase its fitness in a low-glucose environment. For example, it could develop some rudimentary “concentration gradient detector” allowing it to follow the concentration gradient to the highest concentration of glucose. In addition, it could just learn to take in LOTS more glucose than it needs, storing the rest for when the others in the population deplete the environment’s supply.

    Remember – it’s all about how an INDIVIDUAL can do better than the rest of the population. There is more than PLENTY glucose for a few bacteria. The problem is that there is not enough for a big population. Thus, any adaptation that would allow an individual to better use, store, or find the glucose would make it more fit. There are LOTS of ways for that to happen, and the idea is that we should see SOME development along those lines.

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