While in Lexington …

… 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.

Videos …

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!

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:

 

This doesn’t look right

A short time ago, a study describing the discovery of a bacterium that could apparently utilize arsenate in place of phosphate was published in Science.  This report has since generated a lot of discussion and debate in the blog-o-sphere, most of it rather uncomplementary.  I count myself among those who are skeptical of the more daring of the authors’ claims.

Something I found curious was the gel in Fig. 2A, an analysis of nucleic acids isolated from bacteria grown in arsenate-rich (middle lane) or phosphate-rich (right lane) media:

If the OOL is of interest …

… then here is something you may be interested in.

From the main page:

A three-day workshop using NAI remote communications tools will be held on November 8, 9 & 10, 2010. Participants will discuss ‘top down’ origin of life research, which will ultimately allow us to rewind the evolutionary record of biochemical processes and assemblies.

Organized by John Peters and Loren Williams, PIs of the NAI’s Montana State University and Georgia Tech teams, a primary goal of the workshop is to foster new interdisciplinary collaborations across the community.

Session topics will include

• Phylogenetic Studies on Key Enzymes Involved in Information Pathways and Metabolism
• The Evolutionary History of Protein Synthesis
• Minerals to Enzymes – Bridging the Gap Between Metal Based Abiotic and Biological Chemistry
• Phylogenetic Reconstruction/Resurrection – A Glimpse into Extinct Biochemistry
• What can Modern Biological Energy Transformation Systems Tell Us About Conditions on the Early Earth?
• Linking the Evolutionary Record to the Geological Record

Also:

It will be easy to join in! All you will need is a computer with a browser and an internet connection—no special software or hardware is required. The slides and video of the speaker will be displayed in your browser, and you will be able to hear the presentations through the speaker on your computer. Questions will be entered in a “chat” area in the browser window. We’ll be sending out the link and other info about a week before the conference. Thanks for registering. We’re glad you’ll be joining us!

At the junction of Fox and the RNA World?

An interesting abstract that came across my desk:

Chemistry. 2010 Mar 15. [Epub ahead of print]

Putative One-Pot Prebiotic Polypeptides with Ribonucleolytic Activity.

López-Alonso JP, Pardo-Cea MA, Gómez-Pinto I, Fernández I, Chakrabartty A, Pedroso E, González C, Laurents DV.

Instituto de Química Física “Rocasolano” C.S.I.C. Serrano 119, 28006, Madrid (Spain), Fax: (+34) 91-564-2431.

KIA7, a peptide with a highly restricted set of amino acids (Lys, Ile, Ala, Gly and Tyr), adopts a specifically folded structure. Some amino acids, including Lys, Ile, Ala, Gly and His, form under the same putative prebiotic conditions, whereas different conditions are needed for producing Tyr, Phe and Trp. Herein, we report the 3D structure and conformational stability of the peptide KIA7H, which is composed of only Lys, Ile, Ala, Gly and His. When the imidazole group is neutral, this 20-mer peptide adopts a four-helix bundle with a specifically packed hydrophobic core. Therefore, one-pot prebiotic proteins with well-defined structures might have arisen early in chemical evolution. The Trp variant, KIA7W, was also studied. It adopts a 3D structure similar to that of KIA7H and its previously studied Tyr and Phe variants, but is remarkably more stable. When tested for ribonucleolytic activity, KIA7H, KIA7W and even short, unstructured peptides rich in His and Lys, in combination with Mg(++), Mn(++) or Ni(++) (but not Cu(++), Zn(++) or EDTA) specifically cleave the single-stranded region in an RNA stem-loop. This suggests that prebiotic peptide-divalent cation complexes with ribonucleolytic activity might have co-inhabited the RNA world.

Why is this interesting?  Because it adds to the body of work that shows that rather limited and nondescript polypeptides with clear enzymatic properties can easily be formed.  A tantalizing possibility is raised by the RNA structural preference of the catalyst described – namely, its preference for single-stranded regions.  This property would provide a strong selective advantage for structured RNAs in a prebiotic world populated by these (and similar) polypeptides.

Signature in the Cell?

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.

Meanwhile, back in the RNA World …

I’ve been traveling a lot lately. I don’t have time for some, um, wordy essays, but time hasn’t stood still. So I thought I would point out some interesting stuff that has appeared recently. These have an RNA World theme.

If there is a message I wish to send, it is that the RNA World is, as always, a thriving and exciting place for a scientist to be. Enjoy. (The last two entries are going to generate lots of buzz in the blogosphere.)

Protocells, the origins of life, and the RNA World

This essay is a bit less formal than many I’ve posted here, more of an indulgence than the cut-and-dried stuff I’ve been posting about polyadenylation. It is essentially a repost of an essay I posted on the old ARN boards many years ago. I’m moved to this by a recent a recent article in PNAS. The overall context is the origin of life, and some of the different arguments and perspectives that are brought to the table in ev/cre debates.

As a segue, the abstract of the PNAS article:

“Life is that which replicates and evolves. The origin of life is also the origin of evolution. A fundamental question is when do chemical kinetics become evolutionary dynamics? Here, we formulate a general mathematical theory for the origin of evolution. All known life on earth is based on biological polymers, which act as information carriers and catalysts. Therefore, any theory for the origin of life must address the emergence of such a system. We describe prelife as an alphabet of active monomers that form random polymers. Prelife is a generative system that can produce information. Prevolutionary dynamics have selection and mutation, but no replication. Life marches in with the ability of replication: Polymers act as templates for their own reproduction. Prelife is a scaffold that builds life. Yet, there is competition between life and prelife. There is a phase transition: If the effective replication rate exceeds a critical value, then life outcompetes prelife. Replication is not a prerequisite for selection, but instead, there can be selection for replication. Mutation leads to an error threshold between life and prelife.”

On the Origins of Life and The RNA World

On The Panda’s Thumb, Ian Musgrave has an interesting entry on the origins of life and the RNA World – it traces back to this ScienceBlogs essay.  Apropos of this, a nice publication came across my RSS feed late last week.  This study reveals that one of the chemical functionalities that catalyzes the charging of a tRNA is provided by the tRNA substrate itself.  The abstract, and brief commentary, are after the fold.  As always, enjoy.