A clever little two-step

Baym et al. 2016 Fig. 1B

Figure 1B from Baym et al. 2016. Experimental evolution of antibiotic resistance in E. coli bacteria. Bacteria were inoculated at both ends of the plate and evolved to tolerate the initially deadly concentration of antibiotic in the middle.

It’s possible for something to be both true and misleading. Here’s a great example. Frank Sherwin, a Research Associate at the Institute for Creation Research, recently wrote,

Evolutionists list antibiotic resistance as evidence of evolution, but in reality it has nothing to do with the origin of antibiotic resistance genes—let alone novel bacterial species.

Each of those things is true, but the sentence still manages to be misleading. Evolutionary biologists do regard antibiotic resistance as evidence of evolution. Real-time observations of the evolution of antibiotic resistance, like those in Michael Baym’s experiment, demonstrate evolution in action. Those experiments do have nothing to do with the origin of novel genes or of speciation. I’ve just admitted that both parts of the sentence are true, so what’s the problem?

It’s the but.

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It’s not evolution, just adaptation

…”evolve” is not the correct term. The microbes adapted. – Cornelius Hunter

We heard several accusations during the recent Presidential campaign that one or the other candidate, or an interviewer, had taken a quote out of context. Of course, every quote is taken out of context. That’s what a quote is; otherwise it’s just the whole speech, or interview, or whatever. The important question is whether or not it’s taken out of context in a way that changes its meaning.

One thing I don’t do, and never have done, on this blog is intentionally misrepresent other people’s positions.  The quote above, from a recent post by Cornelius Hunter on Evolution News and Views, means just what it says. He really is arguing that microbial adaptation observed in Lenski-style experiments is not evolution.

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The long-term evolution experiment

I’m attending the 2nd ASM Conference on Experimental Microbial Evolution (#ASMEME) in Washington, DC. The meeting opened last night with a keynote address by Rich Lenski on the long-term evolution experiment (LTEE). If you’re not familiar with it, the LTEE involves twelve populations of E. coli bacteria that have been transferred every damn day for the last 28 years. That’s right, twelve transfers every day since Ronald Reagan was President.

Since E. coli undergoes about 6.6 doublings per day under the experimental conditions, that means that the bacteria in this experiment have been evolving for over 65,000 generations. In that time, it has produced a wealth of information about evolutionary processes and spun out countless related experiments. The LTEE is so iconic that you usually don’t have to explain, at least to evolutionary biologists, which long-term evolution experiment you’re talking about. It has also played a role in some controversies, not least the “Lenski affair.”

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Bacterial flagellum? Never heard of it.

When I wrote about Michael Behe’s shock that any sane person would associate the bacterial flagellum with intelligent design (Michael Behe’s “Secret Obsessions“), I failed to notice something that was staring me right in the face. The masthead for intelligent design blog Uncommon Descent:

UncommonDescentMasthead

Remember, if you meet someone who thinks intelligent design advocates

…think they [bacterial flagella] are examples of “intelligent design”

or that bacterial flagella have

…been at the center of the thinly veiled creationism movement called intelligent design,

you should

back away slowly, smiling, wishing him a nice day…

Michael Behe’s “secret obsessions”

In his latest post at Evolution News and Views, Michael Behe calls the authors of posts at New Scientist and Genetic Engineering & Biotechnology News ‘crazy’ and ‘clueless’ for associating arguments about the bacterial flagellum with intelligent design (“New Paper on Flagellum Reveals Secret Obsessions“):

Suppose in the course of a pleasant conversation with a colleague you mentioned your vacation last year in Las Vegas. All of a sudden he starts ranting about Area 51 — Vegas is only a few hours away, right? Did you see any lights in the sky? Any military vehicles heading north? You should stay at the Little A’Le’Inn motel like he has six times. You’ll see some funny stuff there.

You’d probably back away slowly, smiling, wishing him a nice day…

[much later] …One crazy person is a coincidence. Two are a trend…What’s more, if you go by what they write, these folks are utterly clueless about what modern ID proponents actually argue. [my emphasis]

The evidence that these authors are crazy and clueless? The New Scientist‘s assertion that the bacterial flagellum is

Loved by creationists, who falsely think they are examples of “intelligent design”

and that of Genetic Engineering & Biotechnology News that

[T]he bacterial flagellum has been at the center of the thinly veiled creationism movement called intelligent design. Subscribers to this belief system have erroneously postulated that the flagellar motor system is “irreducibly complex” and could not have come about through Darwinian evolutionary mechanisms….It is doubtful these findings will sway the opinion of its detractors, yet they do make it extremely more difficult for them to make their case.

Seriously, that is the sum total of the evidence that these authors are ‘crazy’ and ‘clueless’ on the order of UFO true believers. A bit hyperbolic, I think. But where did these clueless authors get their crazy idea to associate the bacterial flagellum with intelligent design?

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Controlling contamination in Chlamydomonas cultures

Figure 1 from Wang et al. 2016.  Effects of bactericide/fungicide cocktails on the removal of microbial contaminants from Chlamydomonas reinhardtii cultures.

Figure 1 from Wang et al. 2016. Effects of bactericide/fungicide cocktails on the removal of microbial contaminants from Chlamydomonas reinhardtii cultures. (A) Control plate. (B) Plate with the One-shot Solution cocktail composed of ampicillin, cefotaxime, and carbendazim. (C) Plate with axoxystrobin and nalidixic acid. (D) Plate with tebuconazole and nalidixic acid. 1: uncontaminated cultures; 2–4: contaminated cultures containing fungi and bacteria.

A new paper in BioTechniques describes an improved antibiotic cocktail for controlling bacterial and fungal contamination of Chlamydomonas cultures. This is a problem that has cost our lab many hours, especially when using media that include acetate.

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Changing into my old genes: Betül Kaçar’s molecular paleontology

Tape of life logo

Betül Kaçar has posted another preprint to bioRxiv describing her work combining molecular paleontology with experimental evolution. I’ve written about Dr. Kaçar’s research, and the Discovery Institute’s bizarre interpretations, before, and I won’t be surprised if the cdesign proponentsists feel compelled to respond again.

The new preprint describes experimental evolution in E. coli bacteria genetically engineered to express an ancient protein in place of its modern counterpart. The gene encoding the protein, Elongation Factor Tu (EF-Tu), exists in two copies in the wild-type E. coli genome. Dr. Kaçar’s team deleted one copy and replaced the other with a gene sequence inferred to be similar to that in E. coli‘s ancestor from 700 million years ago.

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Evolution is evidence against evolution (?)

Intelligent Design blog Uncommon Descent thinks Betül Kacar’s microbial evolution experiments somehow support their agenda (“E coli hybrid copes with 700 mya engineered gene“). The post quotes extensively from a recent article in Quanta Magazine, which in turn reports on Dr. Kacar’s presentation at AbSciCon (which I briefly covered here).

I’m really not sure what the logic is here. The blog post quotes extensively from the Quanta article (really the post just is quotes from the article, with two short comments added), including sections that make clear that Dr. Kacar observed evolution in action in these experiments:

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