A Critical Examination of the Lenski Long-Term Evolution Experiment: Loss of Function, Not Novelty14 min read

Richard Lenski’s Long-Term Evolution Experiment (LTEE) with Escherichia coli, initiated in 1988, is often cited as a cornerstone of evolutionary biology, purportedly demonstrating evolution in action. ¹ However, a closer inspection of the experiment’s key findings reveals that the observed genetic changes are primarily, if not universally loss-of-function mutations rather than the emergence of novel functionality. ^{2 3 4 5 6 7}

This blog post critiques three major observations from the LTEE—faster reproduction due to DNA loss, the emergence of hypermutators, and aerobic citrate metabolism—and argues that these do not support the development of novel traits. Additionally, I explore why Lenski and his team interpret these results as evidence for evolution, suggesting influences such as scientific orthodoxy, a broader definition of evolution, and personal bias due to career investment.

1. Critique of Key LTEE Observations

1.1. Faster Reproduction Through DNA Loss and Elimination of Non-Critical Functions

One of the most prominent outcomes of the LTEE is the increased reproductive fitness of E. coli populations, measured by faster growth rates in glucose-limited media. However, this adaptation stems from two related mechanisms: significant DNA loss and the elimination of non-essential genetic functions.

By deleting parts of the genome, such as portions of the ribose operon, the bacteria reduce the amount of DNA that must be replicated during cell division, speeding up reproduction. Additionally, these deletions halt the expression of costly, non-essential functions—such as ribose metabolism, which is irrelevant in the glucose-only environment—allowing the bacteria to conserve energy and redirect resources to growth. For example, mutations in genes like nadR and spoT disrupt pathways that are unnecessary in the LTEE’s minimal medium, further enhancing reproductive efficiency.

“The great majority of even beneficial mutations have turned out to be due to the breaking, degrading, or minor tweaking of pre-existing genes or regulatory regions.” (Behe: Breaking, degrading, or minor tweaking (Discovery Institute, 2010) ⁸

Similarly, a critique notes that “the vast majority of fitness benefits are due to the disruption, degradation, or loss of unique genetic information.” (Hijacking Good Science: Lenski’s Bacteria Support Creation (Answers in Genesis, 2014) ⁹

These changes, while improving fitness in the LTEE’s specific conditions, do not represent the creation of new biological functions but rather a streamlining of the genome by shedding unneeded capabilities, potentially reducing versatility in other environments.

1.2. Hypermutators: Accelerating Degradation, Not Complexity

In Lenski’s Long-Term Evolution Experiment (LTEE), six out of the twelve E. coli populations evolved into hypermutators due to defects in DNA repair mechanisms, leading to a drastically elevated mutation rate. Of these, three populations are frequently cited as exhibiting beneficial mutations that are not attributable to loss-of-function (LOF).

However, when each case is examined in detail, the supposed benefits are either conditional upon the artificial environment, involve loss of enzymatic specificity, or result in metabolic imbalances that lead to long-term fitness costs. These mutations are not novel gains in biological complexity or function; rather, they align with the broader pattern of degradation of genome integrity.

Although none of the hypermutator populations became completely non-viable, all exhibited reduced long-term fitness compared to non-mutator lines. The overall trajectory is not one of cumulative functional innovation, but of adaptation via loss and eventual genetic decline. Thus, the data supports a model of accelerated genomic entropy rather than evolutionary progress.

Here’s a couple specific examples of claimed benefits from hypermutators:

1.2.1 Increased Expression of Glycolytic Enzymes

• Claimed Benefit: Mutation in the pykF gene (pyruvate kinase) increases glycolytic flux, leading to faster growth.
• Analysis: The mutation in pykF disrupts the normal regulation of the enzyme, increasing its activity. While this results in a short-term growth advantage in glucose-rich minimal media, it also leads to decreased efficiency in regulating downstream pathways. Overproduction of pyruvate can create metabolic bottlenecks or waste products. Furthermore, this may come at the cost of fine-tuned regulatory control, which is important in more complex or fluctuating environments.

• Conclusion: This too is best interpreted as a loss of regulatory function, not a gain of biochemical function or specificity.

1.2.2 Improved Enzyme Functionality

• Claimed Benefit: Improved catalytic efficiency in enzymes related to NAD synthesis.
• Analysis: The beneficial mutation disrupted nadR, a repressor of NAD biosynthesis genes. Disabling this repressor led to overproduction of NAD and improved energy flux, which aided growth in the nutrient-limited LTEE environment. However, overexpression of NAD pathway enzymes is metabolically expensive and may lead to imbalance in redox states or cofactor accumulation, which would be maladaptive in complex environments. Additionally, the mutation may have reduced regulatory specificity, echoing the same LOF trend.
• Conclusion: Though catalysis was increased, the mechanism was via derepression—a LOF in control logic—not the creation of a more efficient or novel enzyme.

1.2.3 Summary of Hypermutator “Beneficial” mutations – they’re all LOF

Each of these “beneficial” mutations in hypermutator populations appears beneficial only in the narrow, simplified LTEE environment, and most involve either loss of regulatory specificity, disrupted feedback mechanisms, or increased metabolic flux that could become toxic or wasteful in real-world settings. Furthermore, these populations all suffered eventual declines in overall fitness due to accumulated mutational burdens, not gains in complexity.

Thus, rather than demonstrating the capacity of unguided mutation to build novel biological systems, these cases exemplify a recurring theme: temporary benefits from degenerative changes, with eventual entropic decline.

1.3. Aerobic Citrate Metabolism: A Loss, Not a Gain

The most celebrated finding of the LTEE is the evolution of aerobic citrate metabolism in one of the 12 E. coli populations around generation 31,500, attributed to a mutation in the citT gene. Lenski and others have hailed this as a “key innovation” and even a potential speciation event.

“The citrate mutation appeared only well after maybe a dozen mutations that degraded genes had already swept to fixation, permanently restricting the bacterial strain.” (Richard Lenski (Evolution News, 2016) ¹⁰

However, this adaptation is not a novel function but a loss of regulatory control. E. coli already possesses the ability to metabolize citrate anaerobically; the mutation in citT simply allows expression of this pre-existing pathway under aerobic conditions, likely by disrupting a repressor mechanism. Moreover, only one of the 12 populations developed this trait, and its inefficiency compared to glucose metabolism suggests it is a suboptimal adaptation in the LTEE’s artificial environment. This is further supported by researchers who argue that the LTEE’s short selection periods for citrate use lowered the probability of accumulating adaptive mutations. (Historical contingency and the evolution of a key innovation… (Genetics, 2020) ¹¹

These three observations—faster reproduction via DNA loss and elimination of non-essential functions, hypermutators accelerating degradation, and aerobic citrate metabolism via regulatory loss—represent the primary findings of the LTEE. While other minor adaptations, such as fine-tuning of proteins like atoC or rpsD, have been noted, these are also often degradative or neutral tweaks rather than novel constructions. (Thanks, Professor Lenski, the LTEE Is Doing Great! (Evolution News, 2019) ¹² No evidence from the LTEE demonstrates the emergence of complex, novel molecular machinery, undermining claims that it supports molecules-to-man evolution.

2. Why Lenski’s Team Interprets These Results as Supporting Evolution

Despite the predominance of loss-of-function mutations, Lenski and his colleagues argue that the LTEE provides evidence for evolution. Several factors may explain this interpretation:

2.1. Risk of Denying Scientific Orthodoxy

The scientific community heavily favors evolutionary theory as the dominant paradigm, and challenging this orthodoxy can carry professional risks. Lenski himself has acknowledged the simplicity of the LTEE’s design, noting:

“The LTEE was designed… to address some basic questions about the dynamics and repeatability of evolution, while minimizing complications.” (Thanks, Professor Lenski, the LTEE Is Doing Great! (Evolution News, 2019) ¹²

Deviating from the narrative that these results support evolution could invite scrutiny or marginalization, as seen in Lenski’s sharp rebuttals to critics like Michael Behe. (Train Wreck of a Review: A Response to Lenski et al. in Science (Evolution News, 2019) ¹³ The pressure to align with established dogma may encourage interpretations that frame even degradative changes as evolutionary progress.

2.2. Broad Definition of Evolution

Lenski employs a broad definition of evolution that encompasses any genetic change, including degradation, gene transfer, or recombination of existing information.

“The LTEE provides fascinating cases of the origin and evolution of a new function and complex ecological interactions.” (the-ltee.org Homepage (the-ltee.org, 2021) ¹⁴

By including loss-of-function mutations and regulatory tweaks within this definition, Lenski can argue that the LTEE demonstrates evolution, even if it lacks evidence of novel functionality. This aligns with his response to critics, where he argues that the citrate mutation’s complexity, requiring multiple “potentiating mutations,” refutes claims of irreducible complexity. (Direct Experimental Refutation of Irreducible Complexity (Reddit, 2021) ¹⁵ However, this interpretation conflates adaptation with the creation of new biological systems, stretching the term “evolution” beyond its common association with increasing complexity.

2.3. Career Investment and Bias

Lenski has dedicated over three decades to the LTEE, building his reputation as a leading evolutionary biologist. This long-term investment naturally inclines him toward interpretations that affirm the significance of his work.

“The evolving bacterial populations… have provided fruit for many influential studies,” reinforcing Lenski’s status in the field. (The Genomic Basis of Adaptation to Laboratory Environments in Experimental Populations of Escherichia coli (PLOS Biology, 2015) ¹⁶

Acknowledging that the LTEE primarily demonstrates devolution or limited adaptation could undermine the narrative of groundbreaking evolutionary insights, especially given his accolades, such as membership in the National Academy of Sciences and a MacArthur Fellowship. (Richard Lenski – Wikipedia (Wikipedia, 2005) ¹⁷ This personal stake may unconsciously bias Lenski toward emphasizing evolutionary progress, even when the data leans heavily toward loss-of-function outcomes.

3. Conclusion

The Lenski Long-Term Evolution Experiment, while a remarkable feat of scientific endurance, does not provide evidence for the emergence of novel functionality in E. coli. The primary observations—faster reproduction through DNA loss and elimination of non-essential functions, hypermutators accelerating genetic degradation, and aerobic citrate metabolism via regulatory loss—point to devolution rather than the construction of new, complex systems. Lenski’s interpretation of these results as supporting evolution likely stems from the pressures of scientific orthodoxy, a broad definition of evolution that includes degradation, and a career-long commitment to evolutionary research. Critics rightly highlight that:

“Darwin’s mechanism works chiefly by squandering genetic information for short-term gain.” (Thanks, Professor Lenski, the LTEE Is Doing Great! (Evolution News, 2019) ¹²

For those seeking evidence of molecules-to-man evolution, the LTEE falls short, serving instead as a case study in the limits of adaptive change within a constrained environment, and the predictable evidence of loss of function only, as the intelligent design hypothesis, based on observation, mutational load, and entropy would predict.