Rockefeller University

Program for the Human Environment

News

Reflecting on the passing of Norton Zinder

Pioneering microbiologist Norton Zinder, a great friend of the Program for the Human Environment, passed away 3 February 2012. Nicholas Wade recapped Norton’s career beautifully for the New York Times. Jesse offered a tribute to Norton at the memorial service on 8 February.

Among our joint efforts were the launching of the DNA barcoding movement with a pair of Banbury Conferences on DNA taxonomy at Cold Spring Harbor Laboratory in 2003 described about 1’20’ into this video of the history of barcoding ,and the first “Summit of the Cloners,” also at Banbury, in March 2000.

 

 

Dematerialization and decarbonization advance

Recent essays based on the “Peak Stuff” paper by Chris Goodall highlight our work on Dematerialization:

In Le Monde in France in French by Audrey Garric, “Have we attained a peak of objects?”  Also available in English.

In Italy in Italian by Pamela Pelatelli “Are we consuming less?”

Also, an essay, ”Going for the Burn,” by Matt Ridley (45 December 2011) draws on our work on Decarbonization.    Also available in Spanish.

Goodall’s excellent paper elicits memories of

IK Wernick, JH Ausubel, National materials flows and the environment (Annual Review of Energy and the Environment 20: 463-492, 1995)

IK Wernick, R Herman, S Govind, JH Ausubel, Materialization and dematerialization: Measures and trends (Pp 135-156 in Technological Trajectories and the Human Environment, JH Ausubel and HD Langford (eds) 1997) and

JH Ausubel, PE Waggoner, Dematerialization: variety, caution, and persistence (Proc Natl Acad Sci U S A 105(35): 12774-12779, 2008 10.1073/pnas.0806099105 D)

DNA IDs bushmeat carrying exotic viruses

Zoonotic viruses are like introduced species–most perish, a few cause localized outbreaks, and a tiny fraction spread widely. Unfortunately, the tiny fraction have ruinous potential.

Human immunodeficiency virus (HIV), a retrovirus that jumped from chimpanzees to humans less than 100 years ago, now infects about 34 million people, with over 30 million deaths so far. Human T-cell lymphotropic virus (HTLV-I) another introduced non-human primate retrovirus, is endemic in many human populations around the world, and may result in a so far untreatable, slowly-progressing ascending paralysis.

In 2009, a previously unknown coronavirus (related to human cold viruses) from masked palm civets caused a global epidemic of SARS. A diversity of other viruses from a diversity of animal hosts have demonstrated ability to cause  high mortality outbreaks with person-to-person transmission including Nipah virus (fruit bat paramyxovirus), Ebola virus (primate filovirus), lassa virus (mouse arenavirus), and rabies (rhabdovirus with primary reservoir in bats).

What else is out there? An untold diversity of vertebrate viruses, some fraction of which have the potential to cause human epidemics, perhaps particularly those from primates and bats.  It makes sense to keep an eye on viruses in animals and products derived from animals and to limit human exposure to known or potential pathogens.

In January 2011 PLoS ONE 19 researchers from seven institutions including US Centers for Disease Control report on exotic viruses in bushmeat (meat of African wild animals) seized at five US ports of entry. In this pilot study, Smith and colleagues analyzed tissues derived from parts of 44 individual animals, mostly non-human primates, found in 26 passenger-carried or postal shipments intercepted between 2008 and 2010, plus additional tissues from body parts of 16 non-human primates seized by US Fish and Wildlife Service in 2006, which were part of a successful federal smuggling prosecution. For confiscated specimens lacking external morphological features, species identity was determined by COI barcode and/or other mitochondrial genes. As an aside, I note that the phrase “DNA barcode” is in the methods section references but does not appear in the text. I view this as a kind of progress, a reflection of how barcoding is now a usual way to confirm species identity. When a method is fully established, it recedes into the background. For example, in medicine we say “the white blood cell count is 10.7,” not “the white blood cell count as determined by Coulter counter is 10.7.”

The seized bushmeat included 25 individual animals representing five non-human primate species [2 chimpanzees (Pan troglodytes ellioti; IUCN Red List endangered), 2 mangabeys (Cercocebus atys; IUCN vulnerable), 10 baboons (Papio papio; IUCN near threatened), 5 guenons (Cercopithecus nictitans), 6 African green monkeys (Chlorocebus sabaeus)], and 35 rodents from at least two species  [32 confirmed or suspected cane rats (Thryonomys sp.), and 3 unknown rat species]. It is unclear from the article how many of the specimens were barcoded to determine species identity.

Samples were screened by PCR for multiple bacterial and viral pathogens. Pathogenic viruses were found in tissues from all 5 non-human primate species, including strains of cytomegalovirus and lymphocryptovirus (both herpesviruses) and 4 strains (3 of which were novel) of simian foamy virus (a retrovirus). So we have many things wrong–endangered species, illegally harvested and imported, carrying potential threats to human health. How big is the problem? According to the authors, although “the amount and characteristics of bushmeat reaching US borders is not well described…[one] study estimated that 273 tons of bushmeat was imported every year into Paris…on Air France carriers alone” (Chaber et al 2010 Conserv Lett). The threats to endangered species and human health from bushmeat trade are one part of the enormous traffic in wildlife (120 million live animals and 25 million kilograms of non-live wildlife are imported annually into US) (Pavlin 2009 Emerging Infect Dis). The authors conclude with a call for “broader surveillance efforts and pathogen identification and discovery techniques in wildlife and wildlife products…to further mitigate potential risks.” Let’s hope they do so.

International Cosmos Prize Statement of Acceptance by Census of Marine Life

On 16 October 2011 the Scientific Steering Committee of the Census of Marine Life formally received Japan’s International Cosmos Prize in an elegant ceremony in Osaka. Jesse Ausubel joined Ian Poiner, Myriam Sibuet, Victor Gallardo, Patricia Miloslavich, and Yoshihisa Shirayama in accepting the prize. Following is the brief statement of acceptance.

On Receiving the International Cosmos Prize

The Scientific Steering Committee of the Census of Marine Life

We are thrilled that the International Cosmos Prize, rooted in greenery, honors the blue world.  Humanity every day has opportunities to see the beauty of nature on land, exemplified by flowers and gardens and their changes through the seasons. Until recently, humanity could see little of life in the vast, dark, and deep oceans. We transferred a few forms of marine life into aquariums, but we did not even have a list of the forms of life in the ocean or a reliable estimate of how many forms of life remain to be discovered.

In the late 1990s, marine biologists became convinced that new technologies and international cooperation could make possible the first Census of Marine Life. The goal was to bridge polar and tropical seas, shallow and deep waters, and small and large organisms in an exploration and documentation of marine life. The members of the international Scientific Steering Committee of the Census of Marine Life had the privilege of encouraging and assisting more than 2700 researchers from over 80 nations to participate. We humbly accept the International Cosmos Prize on behalf of the entire community of researchers who succeeded in realizing the dream of a Census. The discovery of one another’s talents, and the consequent rapport and respect, form a major legacy of the Census matching the global scale of the ocean’s questions.

We also thank all the organizations that enabled the Census, including marine laboratories and universities, natural history museums and aquariums, navies, governmental and intergovernmental organizations that support and coordinate ocean and biodiversity science, and private corporations and foundations who gave technical and financial support. We specially note the Alfred P. Sloan Foundation of New York, which provided funds to assess the feasibility of the Census and then to coordinate the Census through its decade.

We are proud that the Census advanced both the microscopic and the macroscopic. The Census described in detail more than 1200 new species. It also discovered immense global patterns of diversity, distribution, and abundance based on tens of millions of observations united in a modern database freely accessible to everyone. We are proud that the beauty and mystery of marine life attracted artists and historians as well as natural scientists and that the Census became a united celebration of many forms of the power of human observation. Together, we learned that the oceans are richer, more connected, and more altered than anyone had known.

May the extraordinary honor of the International Cosmos Prize prove that the oceans can symbolize the harmonious coexistence between nature and humanity. What the Census discovered, what the Census showed that has already been lost, and what the Census showed remains to be discovered give urgency to achieving such harmony, our best gift to future generations.  The ocean can be Earth’s largest garden – and wilderness.

Foreword for book on Squat Lobsters

A splendid book emerging from the Census of Marine Life has just been published, The Biology of Squat Lobsters, GCB Poore, ST Ahyong, and J Taylor (eds.), CRC, Boca Raton, 2011, available from Amazon and other booksellers. Jesse Ausubel had the privilege to pen the Foreword:

The Biology of Squat Lobsters is not obviously the title of an important and beautiful book, which this is. The book matters because, as editors Gary Poore, Shane Ahyong, and Joanne Taylor explain, squat lobsters dominate, numerically and visibly, crustacean life on seamounts, continental margins, many shelf environments, coral reefs, and hydrothermal vents. The book matters even more because it exemplifies 21st century global biology. The seventeen authors from nine countries address variety, ancestry, and global distribution, spanning animals from waters of frosty Norway to toasty Philippines. They address development, physiology, and ecology, including how squat lobsters thrive in the exotic seafloor environments independent of energy from the sun. They address the big humans who make a living from squat lobster fisheries and the tiny parasites for whom the lobsters are hosts. They address squat lobsters making war and making love. Using the many tools of biology, traditional and new, the authors describe and explain what is known and unknown about 1000 forms of life. The skill and generosity of more than forty photographers and artists make the animals and book a joy to behold.

As one of the founders of the cooperative international research program The Census of Marine Life, I can say with certainty and pleasure that The Biology of Squat Lobsters is one of the highest realizations of the program. To understand life, we must observe and collect, analyze, and integrate as the authors and their colleagues have done. To protect life, we must feel awe at the treasure around and sustaining us. Anyone reading this masterwork will come to know that squat lobsters are not only Galatheoids and Chyrostolids, they are rubies and sapphires, set here in a scientific crown worthy of their perfection.

FDA certifies barcoding for seafood ID, opening commercial, educational opportunities

Seafood is often mislabeled–in the past year, barcode surveys in Canada (Hanner et al 2011), Ireland (Miller et al 2011), Spain (ICIJ 2011), United Kingdom, and United States (Boston Globe, October 2011; Consumer Reports, December 2011) documented 10-50 percent mislabeling of fish items, always as more expensive or more desirable species, including those sold at prominent restaurants and stores. As highlighted in 2011 Oceana report, mislabeled seafood is commercial fraud, exposes consumers to health risks, and hides unsustainable fishing practices. However, identifying seafood is challenging–hundreds of species from around the world enter the marketplace, often as filets or steaks lacking distinguishing external features. In October 2011, US Food and Drug Administration (FDA) formally adopted DNA barcoding for seafood identification, the culmination of validation studies conducted by FDA beginning in 2008. The summary states:

“Substituted and/or mislabeled seafood is considered to be misbranded by the FDA and is a violation of Federal law.”

FDA adoption of DNA barcoding as an identification standard opens commercial opportunities. On January 2, Vancouver Sun reported that Tradex Foods, a Canadian frozen seafood importer, is using DNA barcoding to help eliminate what their spokesperson described as “rampant” mislabeling in the industry. Tradex collects 10 to 30 samples a month at overseas processing facilities, flies these to US for testing by ACTG, Inc. in Illinois at $70 a sample with turnaround time of 2-3 days, while the frozen fish itself is in transit by ship. The article reports that Canadian Food Inspection Agency (CFIA), the federal agency responsible for verifying quality and labeling of seafood imports, expects to begin employing DNA barcoding in 2012. SGS Group, a global testing company, including food product safety, recently posted a press release on The Open Press highlighting the need for seafood testing and the FDA adoption of DNA barcoding, as well as the company’s capability. Applied Food Technologies, in Florida, is a molecular diagnostics company for food industry, specializing in seafood identification, with turnaround time of 5-10 days according to their website.

Routine testing of food and biologicals such as herbal medicines seems likely to be one of the largest and most visible applications of DNA barcoding. I expect that other companies are in or will enter this market.

I look forward to incorporation of DNA barcoding in forensic certification programs, with applications in marketplace fraud as with food, illegal trade of wildlife, and murder investigation, by dating time of death by identifying insect larvae in corpses. Already effective, DNA barcoding including for forensic applications is poised to expand, thanks to strong trends improving speed and sensitivity in DNA recovery and decreasing costs of DNA analysis.

Update 9 jan 2012: My comments above on food authentication echoed in  “Will DNA barcoding revolutionise the food industry” article in yesterday’s Metro, distributed free to commuters in 50 UK cities , circulation 1.3 million.