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Celebrating Over 60,000 Generations of Creation Science by an Evolutionist

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Abstract

When people discuss evidence for evolution, they often cite the work of Richard Lenski at Michigan State University. He has been growing E. coli in the lab for nearly 30 years. Lenski’s work is phenomenal and worth a look, but from a creationist perspective. The biggest problem with Lenski’s work is not the work itself, but the interpretation of it. Recently, Lenski’s E. coli reached over 60,000 generations, and Lenski published a description of their observations. This article will scrutinize the claim that Lenski’s work for over 60,000 generations is evolution-in-action. When studied with the correct biblical worldview, Lenski’s E. coli demonstrate an amazingly complex showcase for design by an all-knowing Creator.

At-a-Glance

  • Richard Lenski has been growing E. coli for over 60,000 generations.
  • While Lenski’s work is great, there has been some misunderstanding about what it shows.
  • There are significant problems with the interpretation of Lenski’s results.
  • The citT mutation is claimed to be proof of evolution, but is actually proof of creation.
  • E. coli remains E. coli.

Richard Lenski does amazing science. He has been growing Escherichia coli (E. coli) in the laboratory for nearly 30 years. In 1988, Lenski set up 12 cultures of E. coli and allowed them to grow overnight. The following morning, he transferred them to a fresh culture and allowed them to continue growing. Lenski’s lab has been transferring those cultures now for over 60,000 generations, and he regularly publishes updates about those cultures.1 Lenski’s cultures are cited by evolutionists as being proof of evolution in action, but that is not the case.2 Upon closer inspection of what Lenski is actually doing, we can see that his experiments support a biblical worldview and demonstrate the flexibility of God’s creation over time.

Clearing Some Misconceptions About Lenski

Much has been said about Lenski’s experiments over the years. Some have claimed that he is not demonstrating any form of evolution because he is not willing to share his cultures with anyone.3 I do not blame Lenski for his desire to not share his cultures because it would be irresponsible for him to share those cultures with anyone not trained in molecular genetics or microbiology.4 Lenski’s E. coli are too precious to share and risk having the cultures lost, misplaced, or mishandled because someone is trying to undermine Lenski. There are several issues associated with this particular scenario. First, there is no reason to doubt the honesty and integrity with which Lenski is handling his bacteria. Lenski is a member of the National Academy of Science because he knows how to do science well, and we should treat him with respect. Second, no one without credentials should be asking for bacteria—I also would not give any of my bacteria to just anyone asking for them.

Lenski’s Long Term Evolution Experiment

With Lenski’s latest observations, we must first acknowledge that we trust what Lenski is doing and that his results are real. However, we disagree with Lenski’s interpretation of his recent observations. The kind of science that Lenski is doing is called historical science, which is different from empirical science.5 Each day, Lenski reports getting about 6.6 generations of bacteria.6 So in one day, Lenski’s E. coli see the calculated equivalent of approximately 132 years of human elapsed time.7 This number becomes impressive when he has observed 60,000 bacterial generations, which are then claimed by some to be the equivalent of 1,200,000 years of human evolution.8 But is that number all that significant?

While there are 6.6 generations of bacteria each day, we disagree with the interpretation that it is equivalent to 132 years of human evolution.9 This is primarily because bacterial generations are not equivalent to human generations. If bacterial generations were equivalent to human generations, then we would expect things like the mutation rates to be the same; but they are not.10 Since there are significant differences between the bacterial and human mutation rates, then there is not a good correlation between their number of generations. Comparing bacterial generations to human generations is worse than comparing apples to oranges; it’s more like comparing apples to rocks. Furthermore, even if you could say that these generations were equal, Lenski’s cultures would have only demonstrated evolution through the most recent Ice Age by their reckoning. That is hardly any significant evidence of evolutionary change happening because the bacteria are still bacteria. Never mind the fact that we have been growing E. coli in the lab for over 100 years, and it still remains E. coli—no real evolution has happened to the E. coli since its original description.11 Why do Lenski and his followers think that they are going to observe evolution happening in one person’s lifetime when lab cultures of E. coli have been around longer than that?

Lenski’s Latest Observations

Lenski made his most recent observations by sequencing the entire DNA of his cultures (a process called metagenomic sequencing).12 In doing the sequencing, he supposedly found significant evidence of genetic draft (aka genetic hitchhiking).13 What was particularly interesting about this most recent finding was that there was almost no mention of a variety of mutations that he found in the sequenced genomes. If I were an evolutionist, I would flaunt every mutation that I could find in front of creationists because mutation is supposed to be the vehicle of evolution.14 However, Lenski did not focus on those mutations because he was primarily interested in population genetics mechanisms that are happening. It would’ve been interesting if Lenski had observed some new mutations in his populations, but there do not seem to be any. Put another way, no evolution is happening.

However, his strain of E. coli is interesting because he now has what is referred to as a mutator strain in his population. That mutator strain is a geneticist’s worst nightmare because mutator strains are known to accumulate mutations in them (in a bad way, even for evolutionists). With the mutator strain, Lenski has begun to see the end of his experiments because the mutator strain is accumulating too many mutations right now. Eventually, Lenski will accumulate too many mutations in the mutator strain, and the E. coli will cease to exist (i.e., become extinct from too many mutations). This mutator phenotype could very well be the demise of the Long Term Evolution Experiment unless the remaining population takes over for the mutator.15

Lenski’s Seminal Observation

Of all the mutations that Lenski has observed over the 60,000 generations, the most interesting one has been the mutation for the citT gene.16 This mutation is interesting because this gene is normally turned off during aerobic growth conditions. However, Lenski observed that this gene was switched on during aerobic growth conditions.17 This citT mutation is significant because E. coli is traditionally defined as being citrate negative under aerobic conditions, but this mutation causes E. coli to become citrate positive. As a result, Lenski argues that his E. coli have evolved into a new species because of their newfound ability to utilize citrate under aerobic conditions.18 However, there are several serious problems associated with this kind of thinking:

  1. The ability to utilize citrate is something that E. coli in the wild are known to do from time-to-time. It is not unheard of for E. coli to be citrate positive.19

  2. The gene for the citrate utilization was already there in the first place.20 For this to be a novel trait, E. coli would have to be 100% completely unable to utilize citrate before it evolved for anyone to consider this a true example of evolution. All that Lenski observed was a promoter-capture event to express a gene under different conditions. The same information was there from the beginning of his cultures and did not appear magically.

  3. He claims that this was unselected for in his conditions.21 However, his culture media clearly has citrate in it as part of the buffer components. It is no wonder that these E. coli gained the ability to utilize citrate under aerobic conditions. His culture has been selecting for growth on citrate for the past 60,000 generations!

  4. It has recently been demonstrated that E. coli can evolve the ability to utilize citrate relatively quickly without taking years to evolve.22 So what Lenski observed is actually possible to evolve in a relatively short amount of time (which is no real evolution in the grand sense). Either Lenski accepts that the appearance of a phenotype is real or he denies it.23

Even Bigger Problems for Lenski’s E. coli

At its core, E. coli is a scavenger in the mammalian intestine and grows on carbohydrates that it obtains from the mucus layer.24 Why do people care about Lenski’s bacteria growing in a laboratory? Does it not make more sense for E. coli to be growing in the intestine rather than the laboratory? The mutations that Lenski observes do nothing to move E. coli from normally being a scavenger in the intestine to something else that is a major contributor to the intestine (e.g., something like Bacteroides spp. or Fusobacterium spp.). E. coli lacks the ability to break down complex carbohydrates like cellulose and can only break down a handful of disaccharides (including maltose and lactose). It would be far more impressive if Lenski’s E. coli suddenly evolved the ability to break down cellulose, the most abundant polymer on the face of the planet—that would be novel and worth paying attention to. In theory, E. coli has had eons of selection to grow on cellulose in the intestine, yet it does not. By comparison, Lenski’s E. coli can break down citrate in the presence of oxygen (not just anaerobically as normal), which is no grand feat.

In all likelihood, E. coli probably can still utilize citrate when growing in the intestines of mammals because citrate is present in the intestinal milieu known as mucus. It has already been established that E. coli grows both aerobically and anaerobically within the intestine, so it is likely using citrate when growing anaerobically in the intestine.25 Therefore, E. coli utilizing citrate is not something entirely novel. In fact, when the genome sequences were obtained for the Shigellae, it was noted that they were actually just citrate-positive E. coli.26 In all likelihood, there was probably a time when E. coli was citrate positive, but lost the ability to grow on citrate aerobically.

Lenski’s E. coli Are Not Evolving into Something Else

While it was significant that Lenski observed E. coli becoming citrate positive aerobically, it is also significant to note what he has not seen. One of the biggest claims that evolution is happening is touted as antibiotic-resistant bacteria. Evolutionists often claim that these antibiotic-resistant bacteria prove evolution, when all they are actually demonstrating is the flexibility of bacteria that supports design.27 So if evolution is supposed to be proven by antibiotic-resistant bacteria, then one would assume that Lenski’s bacteria should have randomly evolved antibiotic resistances in all that time. However, none of the 12 cultures that Lenski is growing have gained any resistances to antibiotics. Furthermore, it would be far more interesting if Lenski’s E. coli gained the ability to grow on antibiotics and not just live in the presence of them (i.e., resist them).

What We’ve Learned from Lenski Over 60,000 Generations

In summary, Lenski has been doing fantastic work observing how E. coli adapts to growth in the laboratory for the past 30 years. While his work is admirable empirical science, it is flawed because of the interpretations given to it (i.e., the historical nature). There are other serious flaws about what he has observed, which largely includes the interpretation of the citrate-positive phenotype. It would almost be better for Lenski if he had chosen a different media to use rather than one in which citrate is always present.28

At the end of the day, Lenski’s E. coli are a remarkable showcase for design in nature. God created bacteria with the ability to adapt to their surroundings, and Lenski’s observations are no different. The big problem with Lenski’s work is not Lenski himself, but those who use Lenski’s work to cite this E. coli growth as proof of evolution.29 In fact, the famous evolutionist and atheist Jerry Coyne (former professor at Cornell University) has famously said that “you can get these complex traits evolving by a combination of unlikely events. That’s just what creationists say can’t happen.”30 After reviewing all the literature for Lenski’s bacteria, I have to admit that I’m a creationist who now says that it can and does happen because God designed microbes with amazing complexity. Lenski’s work is not a threat to creationists, but a welcome piece of evidence. It is important that we give Lenski credit for his hard work, but also that we correctly interpret it: God deserves the credit for creating such wonderful E. coli. Ultimately, some people base their worldview on work like Lenski’s; if so, their worldview needs to be re-evaluated. In particular, when we base our entire worldview on the Word of God, all of Lenski’s work falls into place.

Answers in Depth

2018 Volume 13

Footnotes

  1. For more information about Lenski’s bacteria, read the info on his webpage Experimental Evolution, http://myxo.css.msu.edu/index.html.
  2. Fiona MacDonald, “One of the Biggest Evolution Experiments Ever Has Followed 68,000 Generations of Bacteria,” Science Alert, October 23, 2017, https://www.sciencealert.com/one-of-longest-evolution-experiments-overthrowing-previous-assumptions; Stephanie Bucklin, “A Conductor of Evolution’s Subtle Symphony,” Quanta Magazine, November 3, 2016, https://www.quantamagazine.org/long-term-evolution-the-richard-lenski-interview-20161103/; Michael Le Page, “Cradle of Creation: Evolution Shapes Up New Ecosystem in the Lab,” New Scientist, June 19, 2015, https://www.newscientist.com/article/dn27760-cradle-of-creation-evolution-shapes-up-new-ecosystem-in-the-lab/.
  3. Conservapedia: Lenski Dialog, http://www.conservapedia.com/Conservapedia:Lenski_dialog, accessed December 20, 2017.
  4. By the way, my undergraduate degree is in molecular genetics from The Ohio State University, and my PhD is in microbiology from the University of Oklahoma. So I understand the molecular genetics and microbiology that Lenski is referring to.
  5. The one proof that Lenski is actually doing real empirical science is that he has observed these strains from their beginning. What Lenski’s experiments do not explain is the origin of the E. coli in the first place. So based on Lenski’s own experiments, he had to assume the origin of life. What makes Lenski’s experiment empirical is that he has observed these bacteria since the culture began back in 1988. In a way, Lenski’s experiment is really great because it is both an empirical and historical experiment at the same time.
  6. Anyone can monitor Lenski’s generations by following his lab’s web site at http://myxo.css.msu.edu/index.html. For the exact number of generations per day, read Lenski’s article, “Phenotypic and Genomic Evolution During a 20,000-Generation Experiment with the Bacterium Escherichia coli,” in Plant Breeding Reviews, Volume 24, Part 2: Long-Term Selection: Crops, Animals, and Bacteria, ed. Jules Janick (Hoboken, NJ: Wiley, 2003), 225–265, http://myxo.css.msu.edu/lenski/pdf/2004,%20Plant%20Breeding%20Reviews,%20Lenski.pdf.
  7. 6.6 generations x 20 years/generation = 132 years.
  8. According to study coauthor Dr. Michael McDonald of Monash University, Australia, “LTEE is the longest running microbial evolution experiment with more than 67,000 generations of E. coli, which is equivalent to over one million years of human evolution” (“Study Challenges Long-Held Evolutionary Theory,” Sci-News.com, October 24, 2017, http://www.sci-news.com/biology/evolutionary-theory-e-coli-long-term-evolution-experiment-05354.html).
  9. Thus, we disagree with the 1,200,000 years of human evolution.
  10. Theodosius Dobzhansky, Genetics of the Evolutionary Process (New York: Columbia University Press, 1970).
  11. If we were to also compare this on an evolutionary time frame as many evolutionists do, it would mean that E. coli remains E. coli over the comparative generations spanned from Australopithecus to Homo sapiens sapiens in the case of the supposed Homo lineage. By their misapplied reckoning, there certainly ought to be more than sufficient amount of time for bacterial speciation to occur since its original description, yet it has not changed.
  12. Benjamin H. Good et al. “The Dynamics of Molecular Evolution over 60,000 Generations,” Nature 551 (November 2, 2017): 45–50, doi:10.1038/nature24287.
  13. Genetic draft is a mechanism within genetic drift whereby a mutation is selected for because of another mutation elsewhere on the genome.
  14. For a full list of the mutations that Lenski has characterized, see “Hijacking Good Science: Lenski’s Bacteria Support Creation.”
  15. Technically, Lenski archives his cultures regularly and could restart the experiment again. However, his evolutionary replay experiments have clearly demonstrated that the same mutations arise in multiple lineages again. Thus, it would seem that the E. coli from prior generations would also give rise to a mutator strain and confound the culture again.
  16. Zachary Blount et al., “Genomic Analysis of a Key Innovation in an Experimental Escherichia coli Population,” Nature 489 (2012): 513–518, doi:10.1038/nature11514.
  17. I got in a lot of trouble with Lenski the last time I referred to this gene being switched on. The fact is that all genes function like switches, and numerous textbooks refer to genes being switched on and off. So referring to the citT gene as a switch is not uncommon.
  18. Alvin Powell, “Evolution in Real Time: 59,000 Generations of Bacteria, Plus Freezer, Yield Startling Results,” Harvard Gazette (February 13, 2014), https://news.harvard.edu/gazette/story/2014/02/evolution-in-real-time/.
  19. For the best understanding of what citrate-positive E. coli look like, I would recommend reading the entry for Eschericia in “Bergey’s Manual of Determinative Bacteriology.” That entry acknowledges that E. coli are occasionally defined as citrate positive. Thus, it is impossible to label Lenski’s citT bacteria as some new species because the species definition precludes such nonsense.
  20. Fred R. Blattner et al., “The Complete Genome Sequence of Escherichia coli K-12,” Science 277 (1997): 1453–1462, doi:10.1126/science.277.5331.1453.
  21. Lenski uses a media called DM25 and uses citrate in it as a metal chelator. So the mutant E. coli are growing on the metal chelator present in the media.
  22. Dustin J. Van Hofwegen et al., “Rapid Evolution of Citrate Utilization by Escherichia coli by Direct Selection Requires citT and dctA,” Journal of Bacteriology 198 (2016): 1022–1034, doi:10.1128/JB.00831-15.
  23. By Lenski’s own terminology, then, rapid evolution of the citT gene would mean that evolution happens literally overnight and not over 30,000 generations. Lenski and his followers need to be cautious with how they classify their evolution in light of the rapid evolution of citrate utilization.
  24. Tyrrell Conway et al., “The Life of Commensal Escherichia coli in the Mammalian Intestine,” EcoSal Plus 1 (2004): doi:10.1128/ecosalplus.8.3.1.2.
  25. Shari A. Jones et al., “Respiration of Escherichia coli in the Mouse Intestine,” Infection & Immunity 75 (2007): 4891–4899, doi:10.1128/IAI.00484-07.
  26. James R. Johnson, “Shigella and Escherichia coli at the Crossroads: Machiavellian Masqueraders or Taxonomic Treachery?,” Journal of Medical Microbiology 49 (2000): 583–585, doi:10.1099/0022-1317-49-7-583.
  27. The emergence of antibiotic resistance among bacteria is just natural selection. There is no new information that arises from antibiotic resistances among bacteria. It is well documented that resistance mechanisms are just alterations of existing machinery within the cell to prevent an antibiotic from working. The mechanisms at work to describe how bacteria become resistant to antibiotics cannot be used to describe a millions-of-years evolutionary tale.
  28. It is unclear why he chose to use DM25 when MOPS media was clearly established as being far superior to his DM25. For confirmation of MOPS being a superior culture media, you can read the following: Frederick C. Neidhardt et al., “Culture Medium for Enterobacteria,” Journal of Bacteriology 119 (1974): 736—47. MOPS is a superior media base because it provides reproducible results and does not include anything in the media besides what E. coli needs for reproducible growth.
  29. For ideas on the widespread abuse of Lenski’s work, consider doing a Google search for “Lenski” and notice all the news articles talking about his work. Perhaps the most prolific advocate for Lenski is Carl Zimmer who writes for The New York Times.
  30. Bob Holmes, “Bacteria Make Major Evolutionary Shift in the Lab,” New Scientist (June 9, 2008): https://www.newscientist.com/article/dn14094-bacteria-make-major-evolutionary-shift-in-the-lab/.

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