Most of you are familiar with the long-term evolution experiment (LTEE) run by Richard Lenski. One of the cultures in that experiment evolved the ability to use citrate as a carbon source. Normally, E. coli cannot use this carbon source under aerobic conditions but the new strain not only utilizes citrate but can grow in cultures where citrate is the only source of organic carbon.

The pathway to this event is complex and requires multiple mutations [see On the unpredictability of evolution and potentiation in Lenski's long-term evolution experiment and Lenski's long-term evolution experiment: the evolution of bacteria that can use citrate as a carbon source].

Intelligent Design Creationists are not happy about this experiment because it not only shows evolution in action but it also illustrates features of the process that ID proponents don't understand; features like drift, neutral alleles, and contingency that expose the ignorance of the average creationist. However, there are a few ID proponents who actually understand evolution so they are forced to come up with other kinds of criticism to soften the impact of the results coming out of the Lenksi lab.

One of those creationists is Scott Minnich¹, a professor and researcher at the University of Idaho in Moscow, Idaho (USA). Minnich wants you to believe that the LTEE isn't significant because no new genetic information was created. This is part of a strategy to accept microevolution but deny that macroevolution can be explained by naturalistic processes.

Minnich's lab did some experiments in order to replay the evolution of citrate utilization in E. coli cultures. They found that they could evolve strains that utilized citrate under aerobic conditions but in their hands it took much less time than it took in the LTEE and it was much more likely to occur. (Recall that the Cit⁺ phenotype only evolved in one of the twelve cultures in the LTEE and it took 30,000 generations.) Here's the Minnich paper and the abstact.

Van Hofwegen, D.J., Hovde, C.J., and Minnich, S.A. (2016) Rapid evolution of citrate utilization by Escherichia coli by direct selection requires citT and dctA. Journal of bacteriology, published online Feb. 1, 2016 [doi: 10.1128/JB.00831-15]

ABSTRACY The isolation of aerobic citrate-utilizing Escherichia coli (Cit+) in long term evolution experiments (LTEE) has been termed a rare, innovative, presumptive speciation event. We hypothesized that direct selection would rapidly yield the same class of E. coli Cit+ mutants and follow the same genetic trajectory: potentiation, actualization, and refinement. This hypothesis was tested with wild-type E. coli B, K12, and three K12 derivatives: E. coli ΔrpoS::kan (impaired for stationary phase survival), E. coli ΔcitT::kan (deleted for the anaerobic citrate/succinate antiporter) and E. coli ΔdctA::kan (deleted for the aerobic succinate transporter). E. coli underwent adaptation to aerobic citrate metabolism that was readily and repeatedly achieved using minimal medium supplemented with citrate (M9C), M9C with 0.005% glycerol, or M9C with 0.0025% glucose. Forty-six independent E. coli Cit+ mutants were isolated from all E. coli derivatives except E. coli ΔcitT::kan. Potentiation/actualization mutations occurred within as few as 12 generations and refinement mutations occurred within 100 generations. Citrate utilization was confirmed using Simmons-, Christensen-, and LeMaster Richards citrate media and quantified by mass spectrometry. E. coli Cit+ mutants grew in clumps and long incompletely divided chains, a phenotype that was reversible in rich media. Genomic DNA sequencing of four E. coli Cit+ mutants revealed the required sequence of mutational events leading to a refined Cit+ mutant. These events showed amplified citT and dctA loci followed by DNA rearrangements consistent with promotor capture events for citT. These mutations were equivalent to the amplification and promoter capture CitT-activating mutations identified in the LTEE.

IMPORTANCE E. coli cannot use citrate aerobically. Long term evolution experiments (LTEE) by Lenski found a single aerobic, citrate-utilizing E. coli after 33,000 generations (15 years). This is interpreted as a speciation event. Here we show why it probably is not. Using similar media, 46 independent citrate-utilizing mutants were isolated in as few as 12 to 100 generations. Genomic DNA sequencing revealed an amplification of the citT and dctA loci and DNA rearrangements to capture a promoter to express CitT, aerobically. These are the same class of mutations identified by the LTEE. We conclude the rarity of the LTEE mutant was an artifact of the experimental conditions, not a unique evolutionary event. No new genetic information (novel gene function) evolved.

A lot of the work in deciphering the Cit⁺ phenotype in the LTEE was done by Zachary Blount when he was a graduate student in the Lenksi lab. He is now a post-doc and he and Lenski have teamed up to write a critique of the Van Hofwegan et al. paper. The essay is posted on Lenski's blog at: On the Evolution of Citrate Use.

Blount and Lenski discuss two technical points: the rapidity of the events in the Van Hofwegan et al. paper and the criticism of historical contingency in that paper and in an accompanying commentary by Roth and Maisnier-Patin (2016). Neither criticism is valid.

(Blount has published a nice paper on historical contingency in the LTEE (Blount, 2016). It's relevant to our discussions about replaying the tape of life.)

Blount and Lenski also address the creation of new genetic information. They say,

The claim that “no new genetic information evolved” is based on the fact that the bacteria gained this new ability by rearranging existing structural and regulatory genetic elements. But that’s like saying a new book—say, Darwin’s Origin of Species when it first appeared in 1859—contains no new information, because the text has the same old letters and words that are found in other books.

In an evolutionary context, a genome encodes not just proteins and patterns of expression, but information about the environments where an organism’s ancestors have lived and how to survive and reproduce in those environments by having useful proteins, expressing them under appropriate conditions (but not others), and so on. So when natural selection—that is, differential survival and reproduction—favors bacteria whose genomes have mutations that enable them to grow on citrate, those mutations most certainly provide new and useful information to the bacteria.

That’s how evolution works—it’s not as though new genes and functions somehow appear out of thin air. As the bacterial geneticist and Nobel laureate François Jacob wrote (Science, 1977): “[N]atural selection does not work as an engineer works. It works like a tinkerer—a tinkerer who does not know exactly what he is going to produce but uses whatever he finds around him, whether it be pieces of string, fragments of wood, or old cardboards; in short, it works like a tinkerer who uses everything at his disposal to produce some kind of workable object.”

To say there’s no new genetic information when a new function has evolved (or even when an existing function has improved) is a red herring that is promulgated by the opponents of evolutionary science.

This is an important point.

Evolution works by modifying pre-existing DNA to create new genes or new regulatory elements from sequences that were already present in the genome.² Creationists seem to think that new genetic information has to be "poofed" into existence from nothing or it doesn't count as new information. They would like very much to demonstrate that there are real examples of such magic because that would lend support to their claim that goddidit. So far they haven't come up with a single, credible, example of such a gene so they have to be content with denying that evolution can create new genetic information.

It's sad, really.

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1. Minnich is a fellow at the Center for Science and Culture (Discovery Institute).

2. There are some exceptions, let's not quibble.

Blount, Z.D. (2016) A case study in evolutionary contingency. Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences. [doi: 10.1016/j.shpsc.2015.12.007]

Biological evolution is a fundamentally historical phenomenon in which intertwined stochastic and deterministic processes shape lineages with long, continuous histories that exist in a changing world that has a history of its own. The degree to which these characteristics render evolution historically contingent, and evolutionary outcomes thereby unpredictably sensitive to history has been the subject of considerable debate in recent decades. Microbial evolution experiments have proven among the most fruitful means of empirically investigating the issue of historical contingency in evolution. One such experiment is the Escherichia coli Long-Term Evolution Experiment (LTEE), in which twelve populations founded from the same clone of E. coli have evolved in parallel under identical conditions. Aerobic growth on citrate (Cit+), a novel trait for E. coli, evolved in one of these populations after more than 30,000 generations. Experimental replays of this population's evolution from various points in its history showed that the Cit+ trait was historically contingent upon earlier mutations that potentiated the trait by rendering it mutationally accessible. Here I review this case of evolutionary contingency and discuss what it implies about the importance of historical contingency arising from the core processes of evolution.

Roth, J., and Maisnier-Patin, S. (2016) Re-interpreting long-term evolution experiments—Is delayed adaptation an example of historical contingency or a consequence of intermittent selection? Journal of bacteriology, JB. 00110-00116. [doi: 10.1128/JB.00110-16]