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Bacteria ‘evolving in the lab’?

‘A poke in the eye for anti-evolutionists’?

Photo by Eric Erbe, wikipediaEscherichia coli
Low-temperature electron micrograph of a cluster of E. coli bacteria, magnified 10,000 times. Each individual bacterium is oblong shaped.


Published: 14 June 2008 (GMT+10)

Some bacteria cultured in a laboratory have gained the ability to use citrate as an energy source. We have had lots of queries about this matter, so this is our weekend feedback to all those who have asked.

A New Scientist article proclaims:

‘Lenski’s experiment is also yet another poke in the eye for anti-evolutionists, notes Jerry Coyne, an evolutionary biologist at the University of Chicago. “The thing I like most is it says you can get these complex traits evolving by a combination of unlikely events," he says. “That’s just what creationists say can’t happen."’1

The many comments posted on the New Scientist website shows just how excited the atheists are about this report. They are positively gloating.

The context

In 1988, Richard Lenski, Michigan State University, East Lansing, founded 12 cultures of E. coli and grew them in a laboratory, generation after generation, for twenty years (he deserves some marks for persistence!). The culture medium had a little glucose but lots more citrate, so once the microbes consumed the glucose, they would continue to grow only if they could evolve some way of using citrate. Lenski expected to see evolution in action. This was an appropriate expectation for one who believes in evolution, because bacteria reproduce quickly and can have huge populations, as in this case. They can also sustain higher mutation rates than organisms with much larger genomes, like vertebrates such as us.2 All of this adds up, according to neo-Darwinism, to the almost certainty of seeing lots of evolution happen in real time (instead of imagining it all happening in the unobservable past). With the short generation times, in 20 years this has amounted to some 44,000 generations, equivalent to some million years of generations of a human population (but the evolutionary opportunities for humans would be far, far less, due to the small population numbers limiting the number of mutational possibilities; and the much larger genome, which cannot sustain a similar mutation rate without error catastrophe; i.e. extinction; and sexual reproduction means that there is 50% chance of failing to pass on a beneficial mutation ).

As noted elsewhere (see ‘Giving up on reality’), Lenski seemed to have given up on ‘evolution in the lab’ and resorted to computer modelling of ‘evolution’ with a program called Avida (see evaluation by Dr Royal Truman, Part 1 and Part 2, which are technical papers). Indeed, Lenski had good reason to abandon hope. He had calculated1 that all possible simple mutations must have occurred several times over but without any addition of even a simple adaptive trait.

Lenski and co-workers now claim that they have finally observed his hoped for evolution in the lab.

The science: what did they find?

In a paper published in the Proceedings of the National Academy of Science, Lenski and co-workers describe how one of 12 culture lines of their bacteria has developed the capacity for metabolizing citrate as an energy source under aerobic conditions.3

This happened by the 31,500th generation. Using frozen samples of bacteria from previous generations they showed that something happened at about the 20,000th generation that paved the way for only this culture line to be able to change to citrate metabolism. They surmised, quite reasonably, that this could have been a mutation that paved the way for a further mutation that enabled citrate utilization.

This is close to what Michael Behe calls ‘The Edge of Evolution’—the limit of what ‘evolution’ (non-intelligent natural processes) can do. For example, an adaptive change needing one mutation might occur every so often just by chance. This is why the malaria parasite can adapt to most antimalarial drugs; but chloroquine resistance took much longer to develop because two specific mutations needed to occur together in the one gene. Even this tiny change is beyond the reach of organisms like humans with much longer generation times.4 With bacteria, there might be a chance for even three coordinated mutations, but it’s doubtful that Lenski’s E. coli have achieved any more than two mutations, so have not even reached Behe’s edge, let alone progressed on the path to elephants or crocodiles.

Now the popularist treatments of this research (e.g. in New Scientist) give the impression that the E. coli developed the ability to metabolize citrate, whereas it supposedly could not do so before. However, this is clearly not the case, because the citric acid, tricarboxcylic acid (TCA), or Krebs, cycle (all names for the same thing) generates and utilizes citrate in its normal oxidative metabolism of glucose and other carbohydrates.5

Furthermore, E. coli is normally capable of utilizing citrate as an energy source under anaerobic conditions, with a whole suite of genes involved in its fermentation. This includes a citrate transporter gene that codes for a transporter protein embedded in the cell wall that takes citrate into the cell.6 This suite of genes (operon) is normally only activated under anaerobic conditions.

So what happened? It is not yet clear from the published information, but a likely scenario is that mutations jammed the regulation of this operon so that the bacteria produce citrate transporter regardless of the oxidative state of the bacterium’s environment (that is, it is permanently switched on). This can be likened to having a light that switches on when the sun goes down—a sensor detects the lack of light and turns the light on. A fault in the sensor could result in the light being on all the time. That is the sort of change we are talking about.

Another possibility is that an existing transporter gene, such as the one that normally takes up tartrate,3 which does not normally transport citrate, mutated such that it lost specificity and could then transport citrate into the cell. Such a loss of specificity is also an expected outcome of random mutations. A loss of specificity equals a loss of information, but evolution is supposed to account for the creation of new information; information that specifies the enzymes and cofactors in new biochemical pathways, how to make feathers and bone, nerves, or the components and assembly of complex motors such as ATP synthase, for example.

However, mutations are good at destroying things, not creating them. Sometimes destroying things can be helpful (adaptive),7 but that does not account for the creation of the staggering amount of information in the DNA of all living things. Behe (in The Edge of Evolution) likened the role of mutations in antibiotic resistance and pathogen resistance, for example, to trench warfare, whereby mutations destroy some of the functionality of the target or host to overcome susceptibility. It’s like putting chewing gum in a mechanical watch; it’s not the way the watch could have been created.

Much ado about nothing (again)

Behe is quite right; there is nothing here that is beyond ‘the edge of evolution’, which means it has no relevance to the origin of enzymes and catalytic pathways that evolution is supposed to explain.8

Addendum (prepared March 2016)

Further research on the citrate-digesting bacteria has elucidated much of the biochemical mechanism for the ability of the bacteria to utilize citrate in the presence of oxygen, rather than only in the absence of oxygen.1

Zachary Blount did his PhD research on this, and it is an impressive piece of work.2 Actually, he did a massive amount of work to establish a scenario for what happened, far more than many others do to be awarded a research doctorate. Blount found that there were three steps in the development of citrate utilisation:

  1. Potentiation: a step that involved at least two mutations. He identified one likely mutation, a single nucleotide change (‘SNP’) that damaged a gene known as arcB, which results in the up-regulation of the TCA (Krebs) cycle enzymes, which would enable the more rapid metabolism of citrate.
  2. Actualization: the duplication of a gene that produces the citrate transporter protein that enables the uptake of citrate. The duplication of this gene away from its normal control sequence allowed it to be expressed in the presence of oxygen (because it fell under the control of an existing promoter that was ‘on’ in the presence of oxygen). This is the critical step that resulted in a small ability to use citrate in an aerobic environment.
  3. Refinement: the further duplication of this sequence, giving 3 or more copies, known as amplification. This increased ‘gene dosage’ resulted in greater production of the citrate transporter protein, thus enhancing citrate uptake further.

Before this research was done, I speculated (above) as to possible ways in which mutations would likely cause this ability to use citrate in the presence of oxygen. The first suggestion I made was that the control system that stops citrate utilization in the presence of oxygen was broken. Although it is more complex than just breaking the control (which suppresses the production of the transporter protein when oxygen is present), it turned out to be pretty close to what actually happened, which shows that creation thinking makes for good scientific predictions.

While the existing controls and the citrate transporter gene were not actually broken, the transporter gene was duplicated (copied) to a different location away from the existing control sequence such that the production of the transporter is no longer suppressed in the presence of oxygen. Indeed, the duplicated transporter gene came under the control of an existing promoter (rnk promoter sequence) that is turned on in the presence of oxygen. So the original gene is still suppressed in the presence of oxygen but the duplicated one is promoted in the presence of oxygen. So the ability of the cell to control the production of the citrate transporter was indeed broken (the cell is no longer able to turn off the production of the transporter).

The cells now produce the citrate transporter protein regardless of the needs of the cell. That is, the control has been broken. The mutated cells cannot turn off the production of the citrate transporter gene.

In spite of the hype from the evolutionist blogs, including one by Blount himself, I did not say that ‘evolutionary’ innovation is not possible (and nor do other creationist biologists whom I know; see Can mutations create new information?). What we do say is that the sorts of ‘evolutionary’ (read ‘natural’) innovations observed give no support to the idea that microbes changed into microbiologists. This would require not just duplication of existing genes, breaking of control systems, or co-opting of existing control systems, but the origin of thousands of brand new gene families (each gene family is so-called because they are quite different to other gene families) that are missing from microbes, along with their control systems.

By the way, these mutated E. coli have about a 20% reduced ability to feed on glucose, so they have lost fitness through these mutations in regard to feeding on glucose. Furthermore, with the loss of the ability to turn off the production of the citrate transporter gene, the bacteria are wasting resources producing citrate transporter when they don’t need it. There have been so many generations of E. coli cultured that every possible point mutation has occurred in the E. coli genome, and yet this is the best they can come up with! This is hardly an example of a great evolutionary leap forward! In reality it underlines the limitations of mutations to create the new gene families needed for evolution to be a viable scientific model of the origin of the diversity of life.

The number of generations of the E. coli lab experiment is now well over 60,000. This is equivalent to 1.5 million years of human generations (@ 25 years per generation). That’s ¼ of the supposed time since the putative common ancestor with chimps. Considering how little ‘evolution’ has been achieved with the E. coli, what of the story of human evolution by mutations and natural selection? The human and chimp genomes differ by 30% or more, or about 900 million base pairs, which is equivalent to nearly 200 E. coli genomes! The long-running E. coli experiment presents a huge problem for the evolutionary story and underlines in bold Haldane’s Dilemma, which is that even with the best possible imaginary scenarios, there just has not been enough time for the necessary changes to occur by evolutionary means.

This is interesting research, but there is nothing in it that supports microbes-to-man evolution; it falls far short. As I have said, there is nothing here that is beyond the ‘edge of evolution’ that Michael Behe described in his book on the topic. Nevertheless, there is great excitement about it, especially among the atheist and theistic evolutionist set. So I expect this will become ‘exhibit A’ in evolutionary textbooks, because it is about as good as they can get to bolster the secular creation myth.

A personal aside: In a post on Richard Lenski’s blog (, where Zachary Blount is insultingly critical of creationists (approaching the level of vitriol of some atheist bloggers), Blount, with state of Georgia roots, talks of his “devoutly Southern Baptist Granny”. It seems like he is another one who has lost his way. Or maybe it was his parents who lost their way, as Zachary only describes his grandmother as “devoutly Southern Baptist”. Once again, we can see the evolution creation myth involved in the secularizing of once-Christian societies. As Niles Eldredge once commented, “Darwin did more to secularize [de-Christianize] the western world than any other single thinker.”3

References and notes

  1. Blount, Z.D., et al., Genomic analysis of a key innovation in an experimental Escherichia coli population, Nature 489:513–518, 27 September 2012; doi:10.1038/nature11514.
  2. Blount, Z.D., Borland, C.Z. and Lenski, R.E., Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli, Proc. Nat. Acad. Sciences 105 (23): 7899–906, 2008; doi:10.1073/pnas.0803151105.
  3. Eldredge, N., Darwin: discovering the tree of life, W.W. Norton, USA, 2006.

Further note added in proof

Researchers at the University of Idaho ran an experiment on E. coli strains to see if they could ‘evolve’ aerobic citrate utilisation as Lenski’s lab had finally achieved after 33,000 generations, which took 15 years. They showed that a mere 12 generations were needed to see the beginnings of citrate utilisation and a mere 100 generations to see the refinement of it. Again, no new genes arose, only the duplication and rearrangement of existing genes, like what I described above. The authors concluded:

We conclude that the rarity of the LTEE [Lenski’s long-term evolution experiment] mutant was an artifact of the experimental conditions and not a unique evolutionary event. No new genetic information (novel gene function) evolved.
  • Van Hofwegen DJ, Hovde CJ, Minnich SA, Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA, J Bacteriology 198(7):1022–34; Feb. 1, 2016. doi: 10.1128/JB.00831-15.
  • References

    1. Holmes, Bob, Bacteria make major evolutionary shift in the lab, news service, 09 June 2008. Return to text.
    2. This is explained in Weasel, a flexible program for investigating deterministic computer demonstrations of evolution—see the section headed ‘Error catastrophe’. A mutation rate of one per million bases per generation generates 1 or 2 new mutations per cell for a typical bacterium, with the chance of some missing out on harmful mutations, but the same mutation rate with a human would create more than a 1,000 new ones per individual and every individual would acquire multiple harmful mutations. Return to text.
    3. Blount, Z.D., Borland, C.Z. and Lenski, R.E., Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli, PNAS 105: 7899–7906; published online on June 4, 2008, 10.1073/pnas.0803151105. This is Lenski’s inaugural paper as a newly inducted member of the National Academy of Sciences, USA—yet another dyed-in-the-wool atheistic evolutionist in that august body (see: National Academy of Science is godless to the core Nature survey). Return to text.
    4. See Batten, D., Clarity and confusion, a review of The Edge of Evolution by Michael Behe, Journal of Creation 22(1):28–32, April 2008. Return to text.
    5. The existence of the TCA cycle in all free-living things is another huge obstacle for evolutionists to explain: a complex cycle involving a dozen different enzymes and cofactors that is necessary for a huge part of a cell’s biochemistry. Return to text.
    6. Pos, K.M., Dimroth, P. and Bott, M., The Escherichia coli Citrate Carrier CitT: a Member of a Novel Eubacterial Transporter Family Related to the 2-Oxoglutarate/Malate Translocator from Spinach Chloroplasts, J. Bacteriol. 180(16):4160–4165, 1998; <>. Return to text.
    7. See, for example, Beetle Bloopers (defects can be an advantage sometimes). Return to text.
    8. Michael Behe’s Amazon Blog, 6 June 2008. Return to text.
    Published: 14 June 2008(GMT+10)

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