The Stanford biologist Stephen Palumbi wrote an excellent book some years ago called The Evolution Explosion, in which he argued that humans have become a powerful force in the evolution of life. We’ve altered the whole planet, so that now many species are traveling on new evolutionary trajectories. (For more, here’s a review of the book I wrote for the New York Times Book Review.)

Over the years since Palumbi’s book came out, scientists have documented more examples of our effect. This week, I was intrigued to come across a new study that we may be even altering the brains of animals. It’s the subject of my new Matter column for the New York Times. It’s only a preliminary study, of course, but it does raise some fascinating questions about the mental challenges animals now face as they navigate a human-dominated world. Check it out.

When Charles Darwin developed his theory of evolution, he resigned himself to only seeing its effects. Evolution happened so slowly, he was convinced, that we couldn’t see life changing from one generation to the next by a mechanism such as natural selection. So he found other ways to amass evidence for evolution.

He pointed out, for instance, that natural selection was a logical–even inescapable–fact of life. Individuals varied in their traits. Some of those variations influenced how many offspring they had. And those traits could also be passed down to offspring. Under such conditions, natural selection just happens.

Darwin also looked back over the history of life and showed how powerfully evolution could explain its large-scale patterns. He couldn’t account for every jot and tittle over the past four billion years, of course. But he could, for example, account for how groups of species shared sets of traits: because they descended from a common ancestor that lived millions of years ago.

Starting in the mid-1900s, however, evolutionary biologists  began documenting measurable evolution over the course of years, not millennia. As chronicled by Jonathan Weiner in The Beak of the Finch, for example, Peter and Rosemary Grant have measured changes in the beaks of Darwin’s finches over the past four decades.

Microbes–which breed much faster than animals and acquire mutations at a faster rate–are also opening new lines of research into evolution. Scientists like Richard Lenski and Paul Turner are tracking the evolution of bacteria and viruses over a matter of weeks, or even days.

This week in my “Matter” column for the New York Times, I took a look at a new study on experimental evolution. Bacteria living in Petri dishes evolved extra tails, which allowed them to swim faster and take over their populations. The experiment is fascinating in many ways–from its potential applications to medicine to what it says about the predictability of evolution. Plus, it comes with cool videos.

While the response to my column has been generally enthusiastic (thanks), I have gotten some negative comments that echo an old refrain I often hear when I write about experimental evolution. Basically: they’re still bacteria.

@_NIKD_ @carlzimmer So the bacteria……remained a bacteria.

— V. Hugo (@HugoPush) August 15, 2013

@Crispybroccoli What NEW traits were created? Getting an extra finger, etc..are mutations of existing genes. — V. Hugo (@HugoPush) August 15, 2013

Here’s a related chain of tweets…

@carlzimmer @nytimesscience Short-run experiment doesn’t allow time long enough to separate species, e.g., ape and human. — NEVATHIR (@A_NEVATHIR) August 15, 2013

@carlzimmer @nytimesscience That’s not biological evolution, but rather pattern formation: Dogs’ offsprings’ color change, right?

— NEVATHIR (@A_NEVATHIR) August 15, 2013

@carlzimmer @nytimesscience You are all pseudo-scientists.

— NEVATHIR (@A_NEVATHIR) August 15, 2013

Opponents of evolution often like to decree what evolution really is. That way, when scientists study evolution, they can declare, “That’s not evolution.”

Nevathir, for example, claims that that what happened in this experiment is just “pattern formation,” which apparently refers to how dogs give birth to puppies that have different color patterns. (That’s not actually called pattern formation, but I have to guess here.)

Puppies get different color patterns because (among other reasons) they inherit different combinations of genes from their parents. The experiments I wrote about this week are not “pattern formation” in this sense of the phrase. They started with genetically identical bacteria, which divided, producing identical clones except when new mutations arose. Those mutations were then passed down to their descendants. Mutations to one gene in particular led to the emergence of “hyperswarmers.” Hyperswarmers were genetically programmed to make more tails, which allowed them to swim faster than their ancestors. And they quickly drove slower bacteria extinct as they came to dominate the population.

That is evolution–evolution in under a week, in fact.

V. Hugo asks what new traits were created. Apparently acquiring a number of new tails is not a new trait, in the same way that a mutation in people can lead to the development of an extra finger on the hand. And apparently changes can only be called evolution if they involved the evolution of a new trait.

It’s very hard for me to see how evolving from a single tail to up to half a dozen tails–all of which work together rather than getting tangled up with each other–is not a new trait. But even if we go along with V. Hugo this far, his sort of argument still fails, because it’s not an argument at all. He’s just creating a personal definition of evolution in order to scoff at scientific research.ÂThe origin of new traits is part of evolution, but so is the spread of beneficial mutations due to natural selection.

I suspect that Nevathir and V. Hugo aren’t satisfied with this experiment because it isn’t a large-scale episodes of evolution–the split between species, for example, or the origin of an eye or a hand. (I’m guessing here, but it’s a guess educated on many previous such comments.) Large-scale episodes take time, typically stretching across thousands or millions of years. The scientists who study bacteria over the course of a few weeks don’t expect to witness such transformations. Instead, they are finding that they can dissect the mechanisms of evolution. They can even document the emergence of new genes, as mutations accidentally duplicate stretches of DNA, which can then begin to take on new functions.

And then there’s the “They’re-still-bacteria” remark. I hear variations of this refrain many times, which makes me assume that it gives opponents of evolution great comfort. Bacteria are one “kind” of life form, and since these experiments don’t show them evolving into another “kind”–like a dog–then they reveal nothing.

Such a remark isn’t just wrong-headed about evolution, though. It reveals a misunderstanding of bacteria. Bacteria originated about 3.5 billion years ago and have been diversifying into many different forms ever since. Some bacteria float in the ocean, turning sunlight into carbon. Others breathe iron. Others make squid glow. Watching bacteria evolve in a Petri dish helps us to understand not just evolution in general, but bacteria in all their particulars.

Since the mid-1900s, medical researchers have dreamed of fixing genetic disorders by supplying people with working versions of genes. By the late 1990s, that dream–known as gene therapy–seemed very, very close. Scientists were developing engineered viruses that would infect patients with DNA that would allow their bodies to make the proteins they needed to survive.

But then, in 1999, a young man who had volunteered for a trial died. The whole field of gene therapy went into a tailspin. Only in recent years has it recovered.

I’ve written a story for Wired about that turnaround, focusing on the career of the scientist who oversaw that fateful 1999 trial, James Wilson. For the past fourteen years Wilson been hunting for better viruses for gene therapy, and his viruses are now involved in some of the most promising research for treating diseases ranging from hemophilia to blindness. To find out more about Wilson and gene therapy, check out “The Fall and Rise of Gene Therapy.”