Rockefeller University

Program for the Human Environment

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Zooplankton sequenced at sea, illuminating life in the dark

The deep oceans are the largest biotic space on earth, but remain largely unexplored.  Census of Marine Life scientists recently trawled the Atlantic between the southeast US coast and the Mid-Atlantic ridge, focusing on the zone of perpetual darkness that lies below about 1000 m, to inventory and photograph the variety and abundance of zooplankton–the tiny sea animals that form a vital link in ocean food chains. The 20 day cruise completed April 20 is part of the ambitious gobal inventory of zooplankton by 2010 (Census of Marine Zooplankton (CMarZ), a Census of Marine life initiative. As reported in Science, for the first time DNA sequencing was performed on the rolling seas, telescoping into just three weeks what would normally represent years of laboratory work. 

Clio pyramidata, one of the species sequenced at sea by CMarZ scientistsAccording to Ann Bucklin, lead scientist for CMarZ and Head of the University of Connecticut Marine Sciences Department, “we are just starting to realize how little we know about species variety. We used to think we knew many species well, but the advent of DNA barcoding has radically altered that perception.  Genetically distinctive species of zooplankton are being found with increasing frequency.”  

Serious Games

Our longstanding interest in Serious Games extended during the past year to the Reinventing Public Diplomacy Through Games Competition organized by Josh Fouts and Doug Thomas at USC sponsored by the Lounsbery Foundation. First place went to PeaceMaker, a cross-cultural political video game simulation of the Israeli-Palestinian conflict which can be used to promote a peaceful resolution among Israelis, Palestinians and young adults worldwide. Congratulations to Asi Burak and PeaceMaker team members at Carnegie-Mellon.

A little history of our involvement with gaming: Swedish economist Ingolf Stahl first involved Jesse in interactive gaming in 1980-1981, when Ingolf, Jesse, Jennifer Robinson, and John Lathorp built a board game and two computer games about carbon dioxide emissions and global warming (described in Jennifer Robinson and Jesse H. Ausubel, A Game Framework for Scenario Generation for the CO2 Issue, Simulation and Games 14(3):317-344). The 1981 paper, Ingolf Stahl and Jesse H. Ausubel, Estimating the Future Input of Fossil Fuel CO2 into the Atmosphere by Simulation Gaming (IIASA Working Paper-81-107, published in Beyond the Energy Crisis-Opportunity and Challenge, Rocco.A. Fazzolare and Craig B. Smith, eds., Oxford, Pergamon, 1981) was the first paper to introduce the idea of greenhouse gas emission trading. Jesse’s 1988 book with Robert Herman, Cities and their Vital Systems: Infrastructure Past, Present, and Future, found its way to the brilliant young Will Wright, and Will made terrific use of it in his first 1989 release of SimCity, for which Jesse had the great opportunity to be a beta tester. Jesse wonders whether he still somewhere has the diskettes of the beta version. Will opened Jesse’s eyes to modern simulation and helpfully advised Jesse and Bill Massey on the creation of the university simulator, Virtual U . (For the game history: https://phe.rockefeller.edu/jesse/vupenn.pdf). Virtual U provided the kernel around which the enterprising Ben Sawyer (https://www.dmill.com) and Dave Rejeski nucleated the Serious Games initiative. Jesse still hopes to find a programmer who would take the 1981 Greenhouse Effect board game and turn it into an on-line game.

NYTIMES Newspaper Circulation

On 9 May 2006 The New York Times reported the decline in daily US newspaper circulation from 63 million in 1984 to 45 million in March 2006. The associated fall in demand for wood pulp affirms our vision of the great restoration of forests now underway and analysed in our numerous papers on forests and land use.

French CoML Slide Show

The French newspaper, Liberation, assembled a slide show of photos of plankton from the Bermuda triangle cruise of the Census of Marine Life by superb photographer and scientist Russell Hopcroft. (click “A voir” to view).

Inspired by Mars exploration, DNA sequencing gets much smaller, may be ready for field work soon

Blazej et al PNAS 103:7240, 2006ABI’s smallest sequencer is about the size and weight of a house air conditioning unit [ABI 310: 95 kg (208 lbs); 61 x 56 x 86 cm (24 x 22 x 34 in)]. Researchers who developed the Mars Organic Analyzer for detecting extraterrestrial life recently turned their attention to DNA sequencing. In 9 May 2006 PNAS Blazej, Kumaresan, and Mathies from the University of California, Berkeley, report on a microfabricated DNA sequencer comprised of three 10 cm glass wafers. Using 1 femtomole of DNA template and a 250 nanoliter reaction chamber, the device performs thermal cycling, DNA purification, and capillary electrophoresis, generating reads of up to 556 bases with 99% accuracy. Based on their results “the template/reagent requirements can be reduced an additional 100-fold, and a fully integrated microfluidic genomic sequencing system should also lead to significant infrastructure and labor savings.”

Faster, cheaper, more portable sequencing should facilitate “point-of-use” DNA barcoding devices for identifying specimens in the field, detecting invasive species at the customs station, and sorting through museum drawers for undescribed species, for example.    

How many plant species are there? Facing success, some taxonomists falter

In Nature 13 april 2006 “Gardens in full bloom” by Emma Marris highlights the increasing importance of botanical gardens as centers of molecular research. One scientific goal is to compile a working list of known plant species. According to Nature, “plans for the ultimate database inevitably lead to talk of DNA barcoding. If species-specific differences in defined DNA sequences were matched with a species name in some kind of database, an untrained person could use a sequence or a DNA-chip to read the barcode in a botanical sample, send it to the database, and get back a name and all other necessary taxonomic data….Apart from its undoubted geeky appeal, such a technology would in principle save a lot of time and drudgery. Carrying out identifications for colleagues at home and round the world is time consuming and uncompensated. The use of barcoding would free up people to do their own research.”

But Peter Raven, Missouri Botanical garden, is cautious about such a scheme. He worries about how much time and effort it would take and asks “what would one do with barcodes for the 13,000 or so moss species?”

Raven’s question is like a cosmologist asking “why map the distribution of galaxies?” There is likely no way to understand the origins and patterning of biodiversity other than counting species and mapping their distributions. A rapid, simple method for identifying specimens such as DNA barcoding can make this possible. Studying a species-rich group of early terrestrial colonizers such as mosses, which live in some of the coldest and dryest environments as well as in the tropics, and provide habitats for a variety of invertebrates, might be a good place to start.

https://bryophytes.plant.siu.edu/grimmia.htmlDNA analysis can also help identify new moss species. In “Cryptic species within the cosmopolitan desiccation-tolerant moss Grimmia laevigata“, Fernandez et al describe 2 cryptic species with overlapping geographic distributions. Their samples were collected only in California, so a world survey might reveal many more hidden species. The authors conclude “the results emphasize the need to make molecular characterization of species a standard part of ecological analyses of populations and communities”.

I Figli strappati

In 1982 Jesse translated from Italian into English about 200 pages from the unpublished diaries of Fey von Hassell, who had grown up in Rome in the 1930s as daughter of the German ambassador.  The translation precipitated Fey’s 1987 book, “Storia Incredibile” and subsequent best-selling versions in English and German.  Fey’s story is now dramatized in a 3-hour special on Italian television, “I Figli strappati.”

Vern Ruttan Article

Jesse’s comment about Vern Ruttan’s article on technologies that might transform the economy appeared in the spring issue of the journal Issues in Science and Technology.