While in Lexington …

April 7, 2013


… for the recently-started Spring Meet at Keeneland (it really is this pretty), I suggest that you find time to attend the 2013 Naff Symposium at the University of Kentucky. This is an annual event put on by the Dept. of Chemistry and centers on aspects of chemistry and molecular biology. This year’s topic is The Origin of Life, and the line-up of speakers is pretty amazing.

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Videos …

August 14, 2011

A while ago,  I posted about an interesting virtual meeting on the ribosome.  Somewhat belatedly, I can point to a link to videos of the talks.  Lots of good stuff.  Enjoy.

(HT to Paul Nelson.)

Don’t miss this!

March 24, 2011

Back in November, there was a fascinating workshop on subjects pertaining to he origins of life.  Some of the talks dealt with structural and evolutionary aspects of ribosomes.  Next week, there will be a two-day symposium that follows up, in a sense, on this workshop.  The symposium is entitled “The Ribosome: Structure, Function & Evolution”.  The really great thing is that, like the workshop in November, this symposium can be “attended” over the internet.  So you have no excuses for missing this event.

And it promises to be a good one.  Here is the list of speakers, taken from the program here:


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Darwin Lecture 2011

February 12, 2011

This year’s Darwin Week festivities in the Lexington area featured a talk by Jack Horner.  It was part science and part entertainment, very well attended.  (The organizers must have remembered Horner’s last visit to Lexington,  when the room he spoke in was overflowing, and probably as many people were outside as in the hall.  This time, the main hall of the Singletary Center was used, and it was pretty full.)

The talk itself had its highlights and low points.  I found Horner’s discussion of his “dissection” of fossilized dinosaur bones to be riveting, and I think his mock “extinction” of dinosaur species (actually, the revision of the fossil record so as to recognize that many supposed species are probably just juvenile versions of the same species) was presented in a clever and accessible fashion.

The stuff about the “chickenosuarus”?  Not so much.  I’m not sure about the idea of telling a generation of elementary and middle schoolers (a large and rapt part of the audience) that we’re going to be able to modify chickens so that they will have dinosaur-like tails, “hands”, and teeth, all in about 5 years or so.  I couldn’t tell if he really believed this or not – he’s a pretty good showman and has a knack for drawing the younger members of the audience into the subject.  But if he does, well, um, no.  (To paraphrase what I suspect would be my daughters’ reaction.)

I’ll admit that this talk was a bit more special for me, since it gave me an excuse to spend some time with my older daughter, Heather.  She’s back in the area, and was able to get back to Lexington to attend the talk (and actually be an usher for the event).  A nice dinner at Banana Leaf and some back-and-forth about the subjects (Heather giving me some inside scoop from the perspective of an MSU grad student, and me panning the chickenosaurus schtick) made for a fun time.


October 20, 2010

No, it’s not about the rock band.  Nor is it about sleep physiology.  Rather, this short blurb is intended to point out a recent review in Trends in Biochemical Sciences that ties together a long trickling of research extend back for many decades.

For at least 20 years, it has been known that a number of enzymes that catalyze reactons in intermediary metabolic pathways are also RNA binding proteins.  The “classical” case is that of aconitase.  This enzyme catalyzes the isomerization of citrate to isocitrate, a reaction that is part of the tricarboxylic acid cycle.  The enzyme also binds the so-called iron-responsive element in mRNAs, and in so doing regulates RNA stability and translation.  Aconitase activity and RNA binding are mutually exclusive, and the role the protein plays depends on teh iron status of the cell.

Similar RNA-binding moonlighting has since been shown for a number of other enzymes.  I won’t list them here – the review does a nice job of this.  The review also discusses the possible integration of metabolic cues with RNA homeostasis.  It doesn’t touch on a more fascinating topic – the possibility that RNA binding may be a vestige of the deep past, reflecting the possibility that, at one time, all proteins may have interacted with RNA or been involved with RNA metabolism in some way.  But the latter is a subject that better left for another review.

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Signature in the Cell?

January 3, 2010

There is much abuzz in the ID-o-sphere regarding Stephen Meyer’s new book, “Signature in the Cell: DNA and the Evidence for Intelligent Design”.  The book is a lengthy recapitulation of the main themes that ID proponents have been talking about for the past 15 years or so; indeed, there will be precious little that is new for seasoned veterans of the internet discussions and staged debates that have occurred over the years.

Long though the book is, it is built around one central theme – the idea that the genetic code harbors evidence for design.  Indeed, the genetic code – the triplet-amino acid correspondence that is seen in life – is the “Signature in the Cell”.  Meyer contends that the genetic code cannot have originated without the intervention of intelligence, that physics and chemistry cannot on their own accords account for the origin of the code.

It is this context that a recent paper by Yarus et al. (Yarus M, Widmann JJ, Knight R, 2009, RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code, J Mol Evol  69:406–429) merits discussion.  This paper sums up several avenues of investigation into the mode of RNA-amino acid interaction, and places the body of work into an interesting light with respect to the origin of the genetic code.  The bottom line, in terms that relate to Meyer’s book, is that chemistry and physics (to use Meyer’s phraseology) can account for the origin of the genetic code.  In other words, the very heart of Meyer’s thesis (and his book) is wrong.

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Plant Poly(A) Polymerases

November 28, 2009

Among the conserved proteins of the polyadenylation complex, seen in all eukaryotes (including the highly-reduced polyadenylation complex in Giardia) is the enzyme that adds the poly(A) tail – polynucleotide adenylyltransferase or, more colloquially, poly(A) polymerase.  One would think that the evolutionary history of such a core component of the gene expression machinery would be rather unremarkable – it should be present at the outset and pretty much conserved throughout evolutionary history.

Of course, reality is much more interesting.  A former student of mine did her thesis on Arabidopsis poly(A) polymerases, characterizing the four (4!) genes and the protein isoforms.  A former postdoc in the lab had done some work in rice poly(A) polymerase genes, and found an equally interesting multiplicity of genes as well as some fascinating expression characteristics.  This work has been recently published in PLoS ONE; as is my custom, this post is intended to point out the paper and invite (here or at the journal’s site for the paper) comment, discussion, and criticism.

A brief recap and one or two of the more provocative findings:

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