Nigeria Barcoding

Bravo to David Schindel and the Consortium for the Barcode of Life for spurring further application of DNA barcoding to reduce trade in endangered species with an initiative in Nigeria.

Todd Kiefer manuscript ‘Energy Insecurity: The False Promise of Liquid Biofuels’ published

Todd “Ike” Kiefer has published a shorter version of his landmark 86-page monograph on biofuels.  The new article appears in Strategic Studies Quarterly  7(1), 2013

Energy Insecurity: The False Promise of Liquid Biofuels
CAPT T. A. “Ike” Kiefer, USN
The United States cannot achieve energy security through biofuels, and even the attempt is ironically achieving effects contrary to “clean” and “green” environmental goals and actively threatening global security.

Census reviews of China, European seas

Valuable papers continue to stream from the Census of Marine Life. We note:

Liu JY (2013) Status of Marine Biodiversity of the China Seas. PLoS ONE 8(1): e50719. doi:10.1371/journal.pone.0050719
and
Narayanaswamy BE, Coll M, Danovaro R, Davidson K, Ojaveer H, et al. (2013) Synthesis of Knowledge on Marine Biodiversity in European Seas: From Census to Sustainable Management. PLoS ONE 8(3): e58909. doi:10.1371/journal.pone.0058909

Deep Carbon Observatory

In 2008, with Robert Hazen and Russell Hemley of the Carnegie Institution of Washington, Jesse helped initiate the Deep Carbon Observatory (DCO) with support from the Alfred P. Sloan Foundation. The DCO recently passed a major milestone with the publication of its 700-page baseline report, Carbon in Earth. A press release summarizes some of the major discoveries.

The DCO is a 10-year global quest to discover the quantity, movements, origins, and forms of Earth’s deep carbon; to probe the secrets of volcanoes and diamonds, sources of gas and oil, and life’s deep limits and origins; and to report the known, unknown, and unknowable by 2019.

Conducting field studies, laboratory experiments, and simulations, the DCO aims to advance significantly, and perhaps change fundamentally, our understanding of carbon and the role it plays in our lives.  The DCO aims to create legacies of instruments measuring at great depths, temperatures, and pressures; networks sensing fluxes of carbon-containing gases and fluids between the depths and the surface; open access databases about deep carbon; deep carbon researchers integrating geology, physics, chemistry, and biology; insights improving energy systems; and a public more engaged with deep carbon science.

Global Greening on TV

Science writer Matt Ridley articulates compactly and powerfully the case for a global greening, drawing in part on our work on land sparing, in this 18-minute lecture.

Serious games

Thanks to Ben Sawyer for generously recognizing our contribution to Serious Games. Ben just received a well-deserved Dewey Winburne award for his efforts in serious games/games for health.  Ben gives a well-informed account of Serious Games, including roles of Jesse Ausubel, Richard Lounsbery Foundation, and Alfred P. Sloan Foundation in his blog .

Our own history is explained in our 12 May 2006 entry.

For more of our game news, see re Budget Hero, a 2005 Washington Post story, a 2004 story on the Serious Games movement, and an entry on Virtual U.

Kiefer BioFuels Report

Biofuels attract lots of money and political support in the USA, but they have lots of environmental and economic shortcomings. Captain Todd A. “Ike” Kiefer has written a comprehensive, penetrating critique, “Twenty-First Century Snake Oil: Why the United States Should Reject Biofuels as Part of a Rational National Security Energy Strategy.” Jesse Ausubel and Paul Waggoner mentored Captain Kiefer on aspects of his study.

ABC story on food fraud cites Rockefeller DNA barcode team

The food watch segment of ABC national tv news reporting on widespread inaccurate labeling (“Food Fraud? Watchdog Group Raises Concerns – Non-profit group tracks reports of fake ingredients in products from olive oil to juice) recognizes the contribution of the student team of Catherine Gamble, Rohan Kirpekar, and Grace Young working with Mark Stoeckle in an excellent video segment (RU segment begins 3 minutes 50 seconds into the report). For full information about DNA barcoding projects carried out by the students, see https://phe.rockefeller.edu/barcode/

Phylogenetically diverse COI dataset extends evidence that rare variants are often errors

In October 2012 Nature 490:535, Breen and colleagues reported on amino acid variation among 13 mitochondrial protein and 2 nuclear proteins based on alignments of 3,000-53,000 sequences representing 1,000 to 14,000 species. They found that on average, a given site in a protein accomodates 9 different amino acids. Based on the distribution of variants, they conclude that epistasis (interaction among genes) strongly constrains molecular evolution.

Here Kevin Kerr and I re-analyze their large COI dataset [19,000 sequences (8,300 human); 4,700 species], generously provided by senior author Fyodor Kondrashov. Our aim is to determine if the frequency matrix approach we applied to avian BARCODEs (PLoS ONE 2012 e:43992) can be used to identify errors in a more phylogenetically diverse dataset.  As the authors note, sequencing error is a potential confounder for their analysis; they used a different approach to assess error than we present here.

Brief methods. COI nucleotide alignment opened in MEGA, translated using appropriate table (~95% of COI dataset is insects or vertebrates), and exported to Excel; frequencies calculated at each amino acid position, and amino acid letter sequences converted into amino acid frequencies. For this analysis we defined rare variants as amino acids present in fewer than 0.02% (1/5000) sequences. In this dataset, rare variants comprised about half (46%) of the total amino acid diversity. For analyses illustrated below, we excluded the 8,281 human sequences, which had very few (8) rare variants.

Results

As observed with avian BARCODEs, rare variants in this dataset were less common in newer sequences,  consistent with improved sequence quality over time.

 

Rare variants were associated with low quality sequences–those with internal N’s, generating unknown “X” amino acids.

Lastly, a thought experiment applying the error rate from our PLoS ONE paper suggests that significant artifactual amino acid diversity is expected when error rate x dataset size is equal to or greater than 1, conditions that may be met by large datasets particularly those containing older sequences as in this COI alignment.

These results reinforce our published observation that a frequency matrix approach is a useful and important tool for analyzing error among large datasets. We hope that others will utilize this approach.

Regarding the findings of Breen and colleagues, our re-analysis suggests that error makes a greater contribution to amino acid diversity in this dataset than that calculated by authors, although the main conclusion of their paper regarding epistasis would likely be unchanged.