Joel Duff
 on October 05, 2016

Evolution in a Giant Petri Dish

A new video by Harvard Medical School shows evolutionary processes in action.


The ability of bacteria to develop resistance to antibiotics is a textbook example of evolutionary processes in action. Mutations and natural selection—two primary agents of change—work together to sculpt new genetic combinations, allowing  bacteria to resist antibiotic chemicals in their environment. 

Now you can watch a powerful illustration of E. coli bacteria evolving antibiotic resistance in a video produced by scientists at the Harvard Medical School. The video below shows a fascinating new way to watch bacterial strains evolve, and then examine the mechanisms of the adaptive process in detail.

What have you witnessed?

This video is just 2 minutes long but provides a good overview of research recently published in the journal Science. At a minimum, you are seeing the origin of new gene variations—alleles—via mutations. You are also seeing natural selection acting on the phenotypes—the visible manifestations—of those mutations. The initial colony of bacteria introduced onto the huge petri plate lacked the ability to resist antibiotics. They were able to survive in the agar at the ends, which had no antibiotic, but in the next “lane” of agar there was enough antibiotic to kill the bacteria. Any bacteria that found a way to survive in the second lane could free themselves—at least for a while—from the competition for diminishing resources in the first lane and find themselves in a resource rich region with fewer competitors. Hence, evolving the ability to resist the antibiotic would be a favorable change for these bacteria.


In this screenshot of the Harvard Medical School video, we see that several bacteria have had mutations that enable them to resist antibiotics and therefore are able to take advantage of the resources in the second lane with low dose antibiotics. Credit: HMS.

After a day or two, billions of bacteria have colonized the outer lanes of the large petri dish. Each time a bacterium divides, it must copy its genome. In doing so, mistakes—known as mutations—are inevitable. Collectively, the bacteria on this dish have experienced billions of mutations. Most of those mutations would have been negative (either lethal or reduced their efficiency in some way) or neutral (had no effect on the success of the bacteria). Some may have helped the E. coli compete better for the limited resources in the first lane. Of the billions of mutations, only a few occurred in genes that, if altered, could enable the bacteria to survive in the presence of the small amount of antibiotic in the second lane. Those bacteria fortunate enough to have experienced these mutations could now freely move into the second lane and could take advantage of the resources available there. These bacteria served as the ancestors of a whole new colony and as that colony spread across the second lane individuals in that colony continued to experience millions of additional mutations. Again, most were negative or neutral, but a small number of those mutations conferred even greater capacity of the bacteria to resist antibiotics, allowing those bacteria to invade the third lane. Eventually some of the bacteria invaded the region of highest antibiotic concentrations.


A screenshot of the HMS bacterial evolution video. Here they show where important mutations occurred in some lineages of bacteria. A change in color indicates that a mutation changed the DNA code. Credit: HMS.

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. The Harvard scientists tested the ability of the bacteria to make the jump directly to high concentrations of antibiotic, and that experiment failed to generate resistant bacteria.

The same thing happens in nature. When an organism enters a new environment, some individuals will have genetic variation resulting from mutations—just like we see in this experiment—allowing them to survive in the new environment. Then they can further adjust to the new conditions through additional adaptation. However, organisms are usually unable to adapt to rapid, large-scale changes. For example, if snakes are introduced onto an island that has many flightless birds who lay their eggs on the ground, the birds will go extinct because they are unable to adapt quickly enough to such a dramatic change.

But are we witnessing evolution in this video?

Young-earth creationist leader Ken Ham has responded that this study is much ado about nothing, because it only demonstrates adaptation, not evolution. Ken Ham writes that the researchers did not “see molecules-to-man evolution in action.” After all, the bacteria didn’t change into a different kind of organism (which is how young-earth creationists define evolutionary change). However, the HMS researchers never claimed to witness the entire process of macroevolution taking place—but rather, they witnessed and tested the evolutionary mechanisms that can lead to new species formation over much longer stretches of time.

Ken Ham further claims that no new genetic information was created by these changes. Rather, he insists that the ability to resist antibiotics requires the loss of some other ability and, therefore, doesn’t constitute real evolutionary change. This is consistent with his history of  misunderstanding evolutionary processes. These bacteria were unable to resist antibiotics when they began. Some bacteria experienced mutations which combined to produce new physiological processes. This must be new “information,” by any definition, and we know exactly where the changes occurred in the genes that provided this adaptation to the new environment. These bacteria have been modified by mutations and they have been selected for by the environment. The result is that the bacteria in the center of the petri plate are able to do something that the bacteria in the first lane cannot–they have information the original bacteria did not have.

Ken Ham reveals yet another misconception about evolution in his last attempt to cast doubt on the significance of this study. He suggests that the bacteria that developed antibiotic resistance “are actually less fit than the other bacteria” if you were to put these evolved bacteria back into the natural world. This statement shows that he doesn’t understand the concept of evolutionary fitness. Fitness is always relative to the environment in which an organism lives. Any organisms moved from an environment where natural selection has achieved a high level of fitness will, by definition, be less fit in a different environment. For example, a polar bear (which Ken Ham believes evolved from other bears) is very fit in its arctic environment, but these same mutations make the polar bear far less fit for warmer climates.

What this experiment has done is provide an elegant witness of natural selection in action. It has shown descent with modification. It has demonstrated the process of evolution being played out before our eyes, even if we’re only witnessing a tiny slice of evolutionary history.

About the author

Joel Duff

Joel Duff

Joel Duff is a professor of biology at The University of Akron. He earned his B.S. in biology from Calvin College, and a Ph.D. in botany from the University of Tennessee. He research focuses on understanding biological diversity by examining differences in DNA sequences and genome structure. He has worked on numerous plant and animals systems and has authored more than 40 research articles in science journals. He is an active writer and speaker exploring the intersection of science and Christian faith. He is a contributor to the book Grand Canyon: Monument to an Ancient Earth and blogger at Naturalis Historia ( He is an avid nature photographer and enjoys exploring God’s creation with his wife and five children.