Over at the Atlantic, Ed Yong shows and describes some stunning videos of “evolution in action”: in this case bacteria evolving resistance to antibiotics. It’s a clever way to visualize the accumulation of mutations over time as bacteria evolve to survive increasingly large doses of antibiotics. Beyond this demonstration, the experiment also permits serious scientific study of the nature of those mutations. Questions, for example, could involve “Do the same mutations get fixed over and over again in independent trials?”; “Does evolution ever fail to occur?” (for example, certain strains of Streptococcus bacteria in humans didn’t evolve resistance to penicillin for years, though that may now be happening);  “Are multiple mutations ever responsible for a single advance, so that there’s a waiting time for their accumulation?”, and so on.

The setup for these videos, and the conception of the experiment, was by Michael Baym at Harvard. His team built a huge petri dish, four feet by two feet, filled with agar colored black (to visualize the bacteria). At the edges of the “plate,” as shown below, there was no antibiotic in the agar. Then, as one moved toward the middle, antibiotic concentrations increased in a logarithmic manner, until in the middle there was a thousand times the amount of antibiotic that would kill the bacteria initially (the amount that would kill nearly all of them at first is the “1” stripe in the screenshot below).

Plates were then inoculated with E. coli at the two ends and allowed to adapt to the antibiotic by mutations and natural selection. They could grow toward the center only as resistance mutations accumulated. The bacteria are light colored so you can see the evolutionary wave of advance.

Here’s Ed’s description of what happens (video below) when the bacteria are challenged with ciprofloxacin—a very powerful antibiotic used for a variety of infections; I always take “cipro” with me when traveling overseas. “Real time” here means 14 days of evolution.

At the start of the video, bacteria are dropped into the edges of the dish and soon colonise the outer safe zones. Then they hit their first antibiotic wall, which halts their progress. After a few moments, bright spots appear at this frontier and start spreading outwards. These are resistant bacteria that have picked up mutations that allow them to shrug off the drug. They advance until they hit the next antibiotic zone. Another pause, until even more resistant strains evolve and invade further into the dish. By the end of the movie, even the centre-most stripe—the zone with the highest levels of killer chemicals—is colonised.

And Baym’s caption:

The MEGA-plate with a CPR gradient as in fig. S1 (0-20-200-2000-20000-2000-200-20-0). Movie was compiled from time-lapse imagery every 10 minutes for 14.2 days, and played at 30fps (18000X speed).

The second video shows adaptation to the antibiotic tremethoprim, and in this case you can see secondary mutations that speed up growth arising within one segment of the gradient. Again I quote Ed’s piece:

Resistance doesn’t come for free, and the same mutations that make bacteria invincible tend to slow their growth. You can see that in the movie below: at the 0:30 mark, the bacteria have advanced into the first antibiotic zone, but their colonies are faint and sparse.

But as the movie continues, bright spots start appearing within the faint areas. These are bacteria that have picked up “compensatory mutations”, which allow them to grow quickly and resist antibiotics. They ought to have been the fittest microbes on the plate, able to colonise new areas more effectively than their slower-growing peers. But more often than not, they became trapped. Weaker strains at the front of the expanding wave of microbes were already gobbling up all the nutrients, leaving their faster-growing peers with nowhere to grow. “You don’t have to be better than everyone else around you; you just have to be the first in a new area,” says Baym.

Here’s Baym’s caption for the video below; in this case “real time” is over about 12 days:

The MEGA-plate with an exponential trimethoprim gradient (0-3-30-300-3000-300-30-3-0 MIC). This movie was compiled from time-lapse imagery every 10 minutes for 11.7 days, and played at 30fps (18000X speed). Each second of video is approximately five hours of real time. Condensation on the lid is visible in the first several frames, and a single contaminating colony appears on the plate.

So what do we have here? As I said we have, “Evolution in Real Time”: something that creationists like Ray Comfort are always saying we don’t have. For evolution to be deemed true, say many creationists, we have to see it happen before our eyes, within a human lifetime or, preferably, within days! Yet that’s exactly what we have here, and we’ve known about this ever since antibiotics were widely dispensed after World War II. Antibiotic resistance is the paradigmatic example of evolution in real time. But we have similar real-time examples: herbicide resistance in plants, insecticide resistance in insects, and so on.

But of course, creationists don’t buy this as compelling evidence for evolution. The kind of evolution we see in the videos above, they say, is “microevolution”: one species simply changes a tiny bit to respond to a challenge. In other words, it’s evolution, but it doesn’t turn a bacterium into a dog, much less a eukaryote. What we want, say creationists, is “macroevolution in real time”: some substantial change that we see in real time—though they never define what they mean by substantial.

But the call for macroevolution in real time is impossible to meet, for the pace of such change is very slow. Nevertheless, we can actually see macroevolution over evolutionary time: big transitions in the fossil record. We have transitions between fish and amphibians, amphibians and reptiles, reptiles and mammals, reptiles and birds, terrestrial grazing mammals and whales (only about 8 million years!), and so on. No matter what you consider to be macroevolution, these are macroevolutionary changes visible through the strata. To say that they don’t count because we don’t see that change happening in a decade or so is simply bogus. Historical records of change, properly documented, are evidence every bit as valid as seeing bacteria evolve in petri dishes.

As for the ability of selection to produce big changes in short periods of time, just look at all the breeds of dogs, all descendants of a single wolf ancestor about 15,000 years ago. And if the breeds were known only as fossils, they’d be regarded not just as different species, but sometimes as different genera. Of course, creationists would respond that that’s not natural selection but “intelligent design,” since humans chose what features they wanted.  But that’s also irrelevant, for, as Darwin realized, artificial selection is a very good model of natural selection—but with humans rather than nature imposing the criteria for fitness. If artificial selection works, and works to cause big changes, then there’s no reason to say that there are some limits to evolution that allow microevolution but not macroevolution. That whole distinction between micro- and macro-, which has become a cottage industry for creationists, is specious.

h/t: Michael