The new international Deep Carbon Observatory https://dco.ciw.edu/ led by Robert Hazen and Russ Hemley has launched its website. Â Jesse and Veselin Kostov have helped initiate the DCO and look forward to many discoveries. Enjoy Bob Hazen’s excellent radio interview on Science Friday.
Venerable (1898) publisher H W Wilson periodically compiles major American speeches. Representative Speeches 2008-2009 edited by Brian Boucher balances the Inaugural Address and two other speeches by Barack Obama with a figure-free version of Jesse’s January 2009 talk about energy and environment, Natural Gas and the Jack Rabbit.
What lives in soil? In August 2009 Pesq Agropec Bras (open access) an international cohort of 10 researchers from Canada, France, US, Taiwan, and Russia examine prospects for speeding assessment of soil animal diversity with COI DNA barcoding. As test sets, Rougerie and colleagues explore taxonomic and sequence diversity in earthworms and collembolans (springtails). These two groups comprise a similar number of named species (earthworms, 6000; springtails, 7900), but these totals likely underestimate true diversity, particularly for springtails, which are tiny (0.2 – 6.0 mm), challenging collecting and morphology.
For earthworms, the researchers analyzed COI sequences from 457 specimens collected in 13 countries around the world (including North America, South America, Caribbean, Europe, Middle East, Southeast Asia, and Australia); these represented at least 49 genera in 8 families. 87 species were identified by morphology, representing about 1/2 of specimens; the remainder, mostly those from Philippines and Brazil, could not be identified to species. Applying a threshold approach, the researchers found 192 (10% cutoff) and 211 (4% cutoff) genetic clusters, including two or more divergent clusters in 13 (15%) of named species. None of species showed sequence sharing or overlaps.
For springtails, 695 specimens from a similar global distribution of sites were analyzed, representing 88 genera in 16 familes; only 44 species were formally identified with morphologic characters, consistent with the “difficult and poorly known taxonomy of these organisms.” Of note, the authors report that “a specific protocol was developed for [collembolans] so that voucher specimens could be recollected after DNA extraction and thus be used for further morphological examination.” Sequence comparisons showed a “typical…bimodal distribution of intra- versus interspecific divergences such as the one also reported in earthworms.” Applying distance thresholds as above gave 215 (10% cutoff) and 227 (4% cutoff) genetic clusters. In conclusion, efficient assessment of soil animal diversity calls out for DNA barcoding.
On a separate note, soil animals may be useful for understanding mitochondrial evolution. Even factoring in species diversity, these animals appear to have enormous population sizes, given densities up to 4 x 103 earthworms/m2 and 1.8 x 106 collembolans/m3, yet show typical bimodal pattern of intra- << inter-specific variation noted above. Along these lines, in November 2009 Nature Nick Lane explores whys of mitochondrial evolution and speciation, including a possible “radically new picture of mitochondrial genes being tightly regulated by selection.” Stay tuned!
The loss of Air France Flight 447 on 1 June 2009 near the mid-Atlantic Ridge killed all 228 passengers and crew.  The flight recorders have not been located, and the cause remains unexplained.  An interim update on the investigation is scheduled for release on 17 December.  Meanwhile, on 29 November a flight from Rio de Janeiro to Paris encountered severe turbulence in the same location before descending into calmer weather and safely completing its trip. The continuing mysteries prompt Cesare Marchetti and Jesse Ausubel to post some notes about a possible role for outgassing methane in the AF 447 crash which they accreted over the months after the tragic crash.
Mark Stoeckle and Jesse Ausubel attended the 3rd International Barcode of Life Conference [https://www.dnabarcodes2009.org/] 7-13 November in Mexico City and were astonished and thrilled by the progress of the field since the March 2003 Banbury conference on DNA taxonomy that we catalyzed.  The conference press release summarizes vividly the progress, as does an article in the London Daily Telegraph. Mark presented our new work with Larry Sirovich and Ken Zhang on application of indicator vectors to barcode data sets.
The quarterly magazine of Woods Hole’s Marine Biologicial Laboratory, Catalyst (Vol. 4, No. 2,Fall 2009), publishes an interview with Jesse, “The Big Picture†about the Encyclopedia of Life.
In current Aquatic Conserv Marine Freshwater Ecosys, researchers from Muséum national d’Histoire naturelle, France, report on 80 years of taxonomic confusion that has contributed to near extinction for a once abundant north Atlantic skate. Iglésias and colleagues found that two forms, lumped together in 1926 as European common skate (Dipturus batis, Linnaeus 1798), in fact represent distinct species with morphologic, genetic (in mitochondrial genome), and life history differences.
As the researchers report, this taxonomic oversight obscured the disappearance of one species, the flapper skate (D. cf. intermedia) because it was confused with the less threatened blue skate (D. cf. flossada). Iglesias and colleagues marketplace survey revealed additional sources of confusion. They analyzed 4,110 skates landed over a 2 year period from 103 fishing cruises in four main French ports by 41 different French commercial trawlers, and found that five skate species (included the two named above) from two genera are variously lumped together under just two marketplace names, the aforementioned “European common skate (D. batis)” and “longnose skate (D. oxyrinchus);” according to their analysis the latter species, formerly common, is also locally extirpated, and most specimens with this name represent other species.
For newly rediscovered blue and flapper skates, the researchers report 20 diagnostic substitutions in approximately 2600-nucleotide segment spanning 12s and 16s RNA. Other than the 10 mitochondrial sequences included in this report, I find only two other D. batis sequences in GenBank (and none as yet under either of two resurrected names). It is remarkable that so little genetic information has been collected for such recently abundant, commercially important (annual landings in 1000’s of tons), and now threatened species. To aid standardized application of molecular identification techniques, I hope the authors will also analyze COI barcode sequences for their specimens. Then I look forward to school children aiding conservation and helping find new species by DNA barcoding specimens from their local fish markets!
The deep sea projects of the Census of Marine Life make news with their discoveries, as for example covered by AP’s Cain Burdeau in a 22 November 2009 story “Thousands of strange creatures found deep in ocean.†Meanwhile, the weekly Economist magazine features the Census on the cover of its “The World in 2010†issue and in an excellent article by Alun Anderson, “Introducing the transparent ocean.â€
A slightly revised version of Jesse’s May 2009 Dalhousie University Commencement Address, Son et lumiere, is published on 23 November 2009 by the monthly science magazine, SEED, as Broadening the Scope of Global Change to Include Illumination and Noise.
The essay’s recommendation for consideration of an International Quiet Ocean Experiment earns coverage by Mike Seccombe in the Martha’s Vineyard Gazette in a 27 November 2009 article, Quiet please, across the seas: Pause ships to hear the fish.
What does electric power have to do with sea worms? Learn in Jesse’s talk “EPRI and the Lamellibrancid Worm” which spans zero emission power plants and deep carbon.