Bacteria Evolve “Key Innovation” or Not?

Four years ago, I wrote an article titled “A Poke in the Eye? Lenski and the adaptive acrobatics of E. coli.” The article highlighted the work of evolutionary biologist Richard Lenski and his discovery of bacteria that had reportedly evolved a new complex trait. During the recent Bill Nye controversy (see here and here), Huff Post decried my supposed ignorance of Lenski’s work that they acknowledged as “evolution that has been observed in a laboratory setting.” Obviously, as I stated in a response to Huff Post, they didn’t do their homework!

Interestingly, as all this was going on, Lenski released a new paper showing the genetic changes that had occurred in E. coli. First, let’s review what Lenski reported in 2008.[1] E. coli (such as those found in our gut or in the soil outside our home) have the ability to utilize citrate as a carbon and energy source when oxygen levels are low. They transport citrate into the cell and break it down. Lenski’s lab reported that the E. coli they had been culturing in the lab for many years could now utilize citrate under normal oxygen levels. It’s fairly easy to see that this was not “a major innovation” or the “making of a rare and complex new trait”; it was simply a change in the regulation of when citrate was used by E. coli.

In Lenski’s 2012 paper he shows the genetic mechanism that caused E. coli to make this change.[2] The E. coli that had been cultured for many years in his lab had a duplication of a portion of their DNA that included the citrate transporter gene called citT. The citT gene encodes a protein that transports citrate into the cell. The duplicated citT gene was under different regulatory control than the original citT gene. This allowed the citrate transporter to be produced and citrate to be utilized under normal oxygen levels.

Clearly this is not a case of adding new genetic information as the DNA that already existed in the bacteria was merely duplicated. It’s also not an example of the gain of a new function because the bacteria could already utilize citrate under certain conditions. There was a definite loss of regulation as the original citT gene was only expressed under low oxygen levels. These types of changes do not provide a mechanism for adding the new genetic information required for the evolutionary “novelties” necessary for molecules-to-man evolution.

Lenski also noted that certain mutations occurred before and after the duplication event. Those before were deemed necessary to “potentiate” the duplication event and those after were deemed necessary to “refine” the duplication event. I was amazed at just how many changes were necessary to allow the bacteria to perform a pre-existing function (using citrate) under different conditions (normal oxygen levels). Imagine how many changes would be necessary to generate truly novel proteins with truly novel functions necessary for molecules-to-man evolution.  Impossible!

Lenski concluded in his recent paper, “The evolution of citrate use in an experimental E. coli population provided an unusual opportunity to study the multi-step origin of a key innovation.” No, it did not. It did provide further understanding of mechanisms that bacteria use to adapt to varying environmental conditions. God designed bacteria to be “master adapters” to survive and thrive in a post-Fall, post-Flood world. At times this can be to our detriment when bacteria cause disease, but this ability to adapt can also be put to good use for bioremediation and cleaning up our planet.

Keep fighting the good fight of the faith!


[1] Zachary Blount, et al., “Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli,” PNAS 105 (2008): 7899–7906.

[2] Zachary Blount, et al., “Genomic analysis of a key innovation in an experimental Escherichia coli population,” Nature 489 (2012): 513-518.