Long-Term Evolution Experiment: Evidence for the Evolutionary Paradigm? Part 2 (of 2)

Long-Term Evolution Experiment: Evidence for the Evolutionary Paradigm? Part 2 (of 2)

When Samuel Johnson said, “The road to hell is paved with good intentions,” he was paraphrasing St. Bernard of Claurivax (1091-1153) who said, “Hell is full of good intentions or desires.” And it is with good intentions that some Christians object to the evolutionary paradigm because they assert that they can’t see evolution happening today.

For this reason, among others, Oxford biologist and atheist Richard Dawkins devotes an entire chapter in his latest book, The Greatest Show on Earth, to examples of evolution happening right before our eyes. One example of real-time evolutionary changes that Dawkins focuses on is the Long-term Evolution Experiment (LTEE) conducted by Richard Lenski’s group at Michigan State.

This experiment is designed to continuously monitor long-term evolutionary changes in the bacterium Escherichia coli. Lenski’s team has been watching E. coli evolve in the lab since 1988 and have noted changes in the cells. For example, the lab populations have evolved to increase cell size, grow more efficiently on glucose, and proliferate more rapidly when transferred to fresh media.

As I wrote last week, the evolution of E. coli in the LTEE doesn’t necessarily validate the evolutionary paradigm. Just because such change is observed in a microbe doesn’t mean that evolutionary processes can adequately account for life’s origin and history, and the full range of biodiversity.

Ironically, recent work associated with the LTEE actually raises questions about the evolutionary framework. Some time ago, I wrote about one problematic study related to convergence. New research raises additional concerns.

Each day throughout the course of the LTEE, lab workers have inoculated fresh growth media with a sample of a bacterial suspension that grew the day before. The bacterial suspension represents one of twelve separate lines of E. coli, all derived from a single cell twenty years ago. After growing overnight, the inoculation process is repeated as a sample of the bacterial suspension is transferred once again into fresh growth media.

For a couple of decades, aliquots of cells have been frozen every 500 generations. These frozen cells represent a “fossil record” of sorts that can be thawed out and compared to current and other past generations of cells.

A few years ago molecular biologists sequenced the entire genome of E. coli for the first time. At that time this was a daunting technical achievement. In recent years these sequencing techniques have become increasingly accessible. And this accessibility has made it possible for Lenski’s team to sequence the genomes of E. coli samples frozen periodically over the course of the last twenty years. Specifically, they sequenced the genomes of cells at 2,000, 5,000, 10,000, 15,000, 20,000, and 40,000. The genome sequence of the original cell served as a reference point for the researchers to identify genetic changes that have taken place over the course of the LTEE as E. coli evolved.

This study provided a rare opportunity for researchers to compare genetic alterations to changes in the fitness of E. coli. When Charles Darwin advanced his theory of evolution, he framed it in terms of changes that happen in organisms over time. Since Darwin’s time, biologists have discovered that the genetic material, which passes traits from one generation the next, is harbored within the DNA molecule. Changes in the “genetic letters” that constitute DNA create diversity within a population of organisms and serve as the source of the heritable variation from which natural selection “chooses.”

This recognition has led to the emergence of molecular evolution, a companion to Darwin’s theory. This paradigm seeks to understand how DNA molecules evolve with the idea that changes in the DNA sequence mirror changes in the organism.

The nature and pattern of the genetic changes observed in the Lenski lab’s most recent study didn’t match the researchers’ expectations based on the tenets of molecular evolutionary theory. In fact, over the course of the last couple of decades, they observed that the rate of change of cell fitness for E. coli increased dramatically early on, then diminished over time. This profile means that either the rate of beneficial mutations should have decreased over time or the average benefit of these changes should have become smaller and smaller. When the researchers conducted genome comparisons they found something different. Instead of there being a sudden burst of beneficial mutations at the outset, it appeared the rate of genetic changes in the LTEE was constant for nearly 20,000 generations with most of the genetic changes being beneficial mutations. This was unexpected, because according to the foundational tenets of molecular evolutionary theory constant genetic changes are considered to result from neutral mutations (changes that neither help nor hurt the organism), not beneficial ones.

Around 40,000 generations, the researchers uncovered a sudden burst of neutral mutations. Again, this was not as it should be. According to molecular evolutionary theory, neutral mutations should accrue at a constant rate, not in bursts.

These discrepancies between observed genome changes and those predicted by molecular evolution are cause for concern. The LTEE is not the only study to generate data at odds with the predictions that flow from molecular evolutionary theory. (I wrote about two such studies some time ago.)

It appears the foundational ideas that undergird molecular evolutionary theory are not valid. This lack of support makes me question the reliability of the entire evolutionary edifice. I hope that when evolutionary biologists see the types of changes happening in the LTEE, they choose not to turn a blind eye to the implications of these results.

Part 1 | Part 2