Evolution in a Giant Petri Dish

A new video by Harvard Medical School shows evolutionary processes in action.
This is a companion discussion topic for the original entry at https://biologos.org/blogs/archive/evolution-in-a-giant-petri-dish
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Interestingly, the bacteria that finally conquered the 1000x dose of antibiotic were able to do so not because of a single large change in its genome, but because of many small changes that developed their resistance. By introducing the bacteria to a gradually changing environment—from low concentration to higher and higher concentrations—the bacteria were able to take advantage of multiple mutations to make small adaptations along the gradient.

Thank you Harvard for this video

When the late Karl Popper announced his retraction of his criticism of Survival of the Fittest as a non-falsible concept, he said he did so because of the fact that bacteria became r4e3sistqant to penicillin. He said that this represents the possibility to make Natural Selection or Survival of the Fittest a testable hypothesis, which the people at Harvard have done.

This experiment is living evide3nce of how evolution works. The problem is that it does not work as Neo-Darwinism says it should work. Indeed it works as ecological evolution says it should work. Popper has been justified in that Survival of the Fittest is false as he i9ndicated because Natural Selection was not based on fact like this experiment, but speculation.

The experiment clearly indicates that Natural Selection is based on the ability of organisms to adapt to their environment and not to compete against each other.

The experiment clearly demonstrates that the Selfish Gene is a bunch of hogwash. This is the reason why E. O. Wilson is right about the Social Conquest of the Earth and the importance of ecology, although he does not say so directly.

This is also why evolution affirms that God guides and directs the development of life through God’s ongoing creation of the physical universe.

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Saying that this experiment does not show that evolution happens, because it does not demonstrate microbe-to-man evolution, is like saying that the rainbow pattern formed by a prism does not show how a rainbow forms in the sky, because the prism-generated rainbow does not cover the sky.

This experiment shows that bacteria can adapt to a formerly hostile environment. It says nothing about competition between individuals. It would be interesting to analyze the genome of the bacteria living in the outer areas of this experiment, to see if there have been alterations brought on by competition for limited resources. An ongoing experiment since 1987 at Michigan State University has shown that some of the E. coli have evolved the ability to use the citrate used to buffer the growth medium for food, an ability the original population did not possess.


Larry Bunce, the researches sequence many genome from the petri plate including descendants and ancestors and what looked to be competitors. They found that in many cases, some bacteria behind the growth front had gained many useful mutations that enabled them to be more fit in that environment than those that might have escaped into the new selection regime and experienced different mutations.

Here are a few other observations from this petri plate experiment that I had and wrote about on my blog:

This new research apparatus provided a new way to ask and answer many questions about how adaptation occurs. For example:

Can organisms adapt to new environments? Yes. Nothing new here but the video clearly shows bacteria adapting to an environment in which the ancestral lineages were not able to survive.

Can selection act on mutations that improve the fitness of individuals in populations? Yes? Only a couple of the billions and billions of bacteria that experienced mutations had mutations that were useful in that new environment and yet that new environment was able to select those individuals and allow them to colonize that environment.
If the vast majority of mutations are lethal, somewhat deleterious or have no effect doesn’t that mean that mutations are destroying species over time rather than helping to form new ones? No. This is evident in this experiment. From the time that a few bacteria became billions as they grew in the non-antibiotic zone there would have been billions of individual mutations among them. Most of those were likely neutral and therefore had no effect but millions were probably lethal or severely impaired the bacteria. Those bacteria simply did not continue to divide leaving other bacteria with neutral and positive mutations in that environment to perpetuate the colony. So natural selection is sorting out millions of negative mutations in addition to selecting for positive mutations in the new environment. It is these new mutations, however rare they may be, that yield adaptation to new or changing environments that result in real changes to a species over time.

Can mutations produce new interactions among genes? Yes. Direct sequencing of ancestors and descendants which is what this experiment allows and why it is so powerful – beyond the visual aspect – shows that mutations in genes cause them to work together differently to produce resist the antibiotic.

Do all independent lineages of bacteria that gain antibiotic resistance use the same combinations of mutations to achieve that resistance? No, but they did share some mutations in common demonstrating that natural selection under the same conditions will recognize identical mutations when they occur and select the individuals with those mutations. In other words, natural selection is far from random but rather the arbiter of the value of any mutation.

Do bacteria that become more resistant to antibiotics compensate for that increased ability by losing other abilities? In most cases yes, but in several cases, compensating mutations occurred later in the same lineages that allowed them to gain back all their previous functions making them truly more adapted to the new environment than any of their ancestors.

All of these results demonstrate what was already known about how bacteria may evolve but this experiment helps tease apart the role of mutations and natural selection in new ways. What this experiment so elegantly demonstrates is that new environments cause the sorting of millions of variations in genomes all caused by random mutations when cells copy themselves such that new variations that confer some advantage are preserved in descendant lineages that take advantage of those new environments. This is natural selection in action. This is descent with modification. This is the process of evolution being played out on a small temporal and physical scale.

This new method of observing and testing evolutionary mechanisms has similarities to Dr. Rich Lenski’s work with bacterial evolution. Lenski’s lab has evolved bacteria under the same conditions for over 60,000 generations and documented mutations through that time to show how the bacteria become more fit for their environment and in some cases show that some lineages of bacteria have gained the ability to utilize resources unavailable to the ancestral bacteria. I expect that like Dr. Lenki’s work this new experimental apparatus will provide many new insights as it allows many evolutionary mechanisms to be tested. I am sure that we will be seeing many more videos like the one above in the near future.


Great job on this post @Joel_Duff.

Thanks, only possible with some good editors at BioLogos.

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documented mutations through that time to show how the bacteria become more fit for their environment

A much better statement of fact is that the bacteria became better adapted to their environment.

Fit is a nondescript word that says nothing and that cannot be falsified. Adapt is clear and definite and makes clear what really happens and can be falsified. Survival of the fit says nothing

Yes, thanks for that correction.

Great job, and enjoyed the photos as well as the writing on your blog. Amazing what you can see when you know where to look.


OY. Now you are instructing people to avoid the use of the word “fit”?
Roger, can’t we just get along? Are we “survival of the fittest” proponents not people too? Do we not bleed when pricked? Do we not weep when jeered over fitness?

Roger, sometimes you say it yourself!: this is not an either/or dispute. Sometimes individuals compete against their own kind… sometimes they compete against others in the environment.

It’s alllllllllll environment . . . so why you think strife within species is impossible to consider is beyond me. It all depends on what is going on in the environment, right?

So… the bacteria in a dish full of increasingly toxic chemicals … the life form has only two worries:

  1. not being poisoned; and
  2. not acquiring genetic traits that make them dramatically unable to eat as fast or reproduce as fast as their distant cousins.

Marginal improvements in leaving descendants (comprised of your genetic treasures) come in all forms and sizes … so if a flagellated bacterium suddenly can’t flagellate his way to food approximately as fast as his cousins … when he arrives at the food … the best is gone … and maybe even nothing is left.

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