Difference between revisions of "Richard Lenski"

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Revision as of 18:35, June 30, 2008

Richard Lenski is a professor of microbial ecology at Michigan State University. He holds a doctorate from the University of North Carolina and a B.A. from Oberlin College but, oddly, does not disclose his fields for those degrees on his own biographical sketch. [1]

Lenski is best known for his claim to have observed evolution of E. coli in a long-term laboratory study, insisting that it was not due to contamination. His 2008 paper asserting his claims was peer reviewed in a mere 14 days, sparking questions from the owner of this site[2] about the thoroughness of the review.

When challenged, Lenski thrice referred to the challenges as slander, yet has filed no lawsuit charging that (or libel). Truth offers total legal protection from accusations of libel.

When Lenski received a public request for the data underlying for his published claims, he did not provide the actual data even though his study was taxpayer-funded.

Undisclosed data from the central claims in Lenski's 2008 paper are noted below (pp. 2-3 from paper, superscripts omitted):

For those wishing to review the paper personally it may be found at this link from the Professor's site.


Undisclosed Data Our Questions about the missing data

Visual inspection

Evolution of Cit Function in Population Ara-3. The LTEE populations are transferred daily into fresh medium, and the turbidity of each is checked visually at that time.

DATA ON THESE OBSERVATIONS?

The data are available in the first figure in the paper, and indicate a strong spike in turbidity around generation 33000.

Study Omissions

Owing to the low concentration of glucose in DM25 medium...

DATA ON SPECIFIC CONCENTRATIONS USED?
From the first page of the paper in question (Blount, Z. D., C. Z. Borland, and R. E. Lenski. 2008. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. PNAS, USA 105:7899-7906).:
"To address the repeatability of evolutionary trajectories and outcomes, the long-term evolution experiment (LTEE) with Escherichia coli was started in 1988 with the founding of 12 populations from the same clone (2). These populations were initially identical except for a neutral marker that distinguished six lines from six others. They have since been propagated by daily 1:100 serial transfer in DM25, a minimal medium containing 25 mg/liter glucose as the limiting resource (2, 22)."--Argon 11:42, 30 June 2008 (EDT)

Turbidity

...the cultures are only slightly turbid when transferred. Occasional contaminants that grow on citrate have been seen over the 20 years of this experiment.

DATA? WHEN AND HOW MANY?

Contaminants???

These contaminated cultures reach much higher turbidity owing to the high concentration of citrate in the medium, which allows the contaminants to reach high density. (When contamination occurs, the affected population is restarted from the latest frozen sample.)

DATA FOR WHEN THAT OCCURRED, AND HOW OFTEN?

If interested in a thorough review, contact the group directly, with a legitimate request for data. Otherwise, the disclaimer is a more than adequate description of the sample handling process.

The Numbers Please?

After 33,127 generations, one population, designated Ara-3, displayed significantly elevated turbidity that continued to rise for several days (Fig. 1).

HIGHER RESOLUTION DATA UNDERLYING FIGURE NOT PROVIDED DESPITE REQUEST

More missing Numbers

A number...

DATA? HOW MANY? STATISTICALLY SIGNIFICANT?

We're Professional Scientists

of Cit clones were isolated from the population and checked for phenotypic markers characteristic of the ancestral E. coli strain used to start the LTEE: all

DATA? HOW MANY? STATISTICALLY SIGNIFICANT?

Missing Characteristics

...were Ara, T5-sensitive, and T6-resistant, as expected (2)

DATA ABOUT THESE AND OTHER CHARACTERISTICS?

Interested parties should consult the literature on these topics. It is not within the scope of this paper to address the significance of these markers.

DNA

DNA sequencing also showed...

DATA??

The inclusion of this data would be considerably more extensive than appropriate for the inclusion in this paper.

More missing data

...that Cit clones have the same mutations in the pykF and nadR genes as do clones from earlier generations of the Ara-3 population, and each of these mutations distinguishes this population from all...

DATA ABOUT THESE AND OTHER CHARACTERISTICS?

Fast Tracked

...of the others (30). Therefore, the Cit variant arose within the LTEE and is not a contaminant.

MEANINGFUL PEER REVIEW FOR THIS CONCLUSION MAY NOT HAVE OCCURRED IN THE ASTOUNDINGLY SHORT 14-DAY PEER REVIEW PERIOD!

Lenski's paper was published in the Proceedings of the National Academy of Sciences.

Lenski's work has been criticized in the past also. In a paper Lenski published in Nature in May 8, 2003 entitled "The Evolutionary Origin of Complex Features," he described a computer simulation that contained no actual biology. In fact, the discussion section of the paper stated:

"Some readers might suggest that we 'stacked the deck' by studying the evolution of a complex feature that could be built on simpler functions that were also useful. However, that is precisely what evolutionary theory requires ...."

Dr. William Dembski explained, "In other words, the computer programmers built into the simulation what they thought evolution needed to make it work. The validity of this study therefore depends on whether the simulation faithfully models biological reality."[3]

The importance of the simulation is to show that complex patterns can grow from simple inputs, which was demonstrated by the results of this simulation. Although Lenski freely disclaims the use of true biology in the simulation, his result is nevertheless quite important. The validity is not contigent, as is claimed above, upon the specific biological system.

See Also

References

  1. https://www.msu.edu/~lenski/
  2. See Conservapedia talk:Lenski dialog.
  3. http://www.designinference.com/documents/2003.09.UncDiss_Intro_Contribs.pdf
  4. See Liberal style point 1