Archive for November, 2010

Lenski, Creationism & Rational Thought

Friday, November 19th, 2010

Richard Lenski published a pivotal paper in 2008 which rigorously demonstrated evolution in a laboratory setting1. Recently, a “controversy” over Lenski’s research backfired, severely discrediting his critics, a group of creationists and intelligent designers whose intellectual and logical abilities are markedly unscientific. The debate has been mirrored here, the mirroring being necessary as the original site has been subjected to frequent revisionist censoring. The critical rebuttal was this reply by Lenski to Andrew Schlafly. An article in the New Scientist blog discusses the brouhaha. Another good discussion can be found at RationalWiki.

1. Z. D. Blount,¬† C. Z. Borland¬† & R.E. Lenski (2008) “Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli” PNAS 105 7899-7906.

-- Eric Kofoid


Friday, November 12th, 2010

There is an excellent comparative genomics site at UC Berkeley called CoGe. Check it out!

-- Eric Kofoid

Naked MudJ Revealed

Monday, November 8th, 2010

Using Solexa methodology, I recently sequenced strain SMP1666 (from Sophie Maisnier-Patin), containing 3 copies of MudJ. One had lost the infamous trpB-proximal stem-loop structure1,2, and the other two were pristine — one hesitates to say “wild type” as the lollypop structure was itself an artifact of the original construction out of a MudI background3. The complete MudJ sequence can be found here. The big surprise is the cynX & cynS genes between lac and the Tn5 drug-resistance cassette.

1.J.Zieg & R.Kolter (1989) “The right end of MudI(Ap,lac)” Arch.Microbiol. 153 1-6
2.W.Metcalf, P.Steed & B.Wanner (1990) “Identification of Phosphate Starvation-Inducible Genes in Escherichia coli K-12 by DNA Sequence Analysis of psi::lacZ(Mu dl) Transcriptional Fusions” J.Bacteriol. 172 3191-3200
3.B.Castilho, P.Olfson & M.Casadaban (1984) “Plasmid insertion mutagenesis and lac gene fusion with mini-mu bacteriophage transposons” J.Bacteriol. 158 488-495

-- Eric Kofoid