Rockefeller University

Program for the Human Environment

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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.

Discover

Discover magazine celebrates our work with Finnish colleagues on the changing density of forests as one of the top 100 science stories of 2011. “Forests stage a comeback” is #36!”

Rapid data release for barcode data

At the Fourth International Barcode of Life Conference in Adelaide, there was general recognition that the initiative’s remarkable success in generating barcodes is outstripping the relatively slow process of releasing experimental data after academic publication. Of approximately 1.4 million barcode records in BOLD at the time, fewer than 300 thousand sequences with species names were publicly available, and the proportion of barcode sequences that are published and have species names appears to be be falling further behind over time, as the rate of barcoding specimens increases. Given that privately held sequence data does not contribute to the overarching goal of creating a community resource for society and science, this stimulated many discussions on how to proceed. Many cited the rapid data release policies hammered out by the genomics community as a precedent.

At a 1996 summit in Bermuda, leaders of the scientific community agreed on a groundbreaking set of principles requiring that all DNA sequence data be released in publicly-accessible databases within twenty-four hours after generation. These “Bermuda Principles” (also known as the “Bermuda Accord”) contravened the typical practice in the sciences of making experimental data available only after publication. These principles represent a significant achievement…and have established rapid pre-publication data release as the norm in genomics and other fields.  https://en.wikipedia.org/wiki/Bermuda_Principles

Human genomics is not the same as biodiversity genomics–barcodes are derived from a multitude of often irreplaceable specimens for one, but the general principle of rapid data-release contributing to a community resource, for what is after all, an enterprise funded by society, surely holds.

What follows is one strategy for academic publication AND rapid data release which we hope will encourage others. With the assistance of ZooKeys (open access), GenBank, and BOLD, on December 8, 2011, a brief “Project Description” of a barcode dataset (see below), completed just two weeks earlier, was published coincident with release of sequence data in GenBank and BOLD, with a full descriptive paper summarizing the dataset to follow in the next six months. A set of explicit statements regarding use of early release data (see below) is included in the Project Description.

Title: Project Description: DNA Barcodes of Bird Species in the National Museum of Natural History, Smithsonian Institution, USA

Abstract: The Division of Birds, National Museum of Natural History, Smithsonian Institution in Washington, DC, has obtained and released DNA barcodes for 2,808 frozen tissue samples. Of the 1,403 species represented by these samples, 1,147 species have not been barcoded previously. This data release increases the number of bird species with standard barcodes by 91%. These records meet the data standard of the Consortium for the Barcode of Life and they have the reserved keyword BARCODE in GenBank. The data are now available on GenBank and the Barcode of Life Data Systems.

Excerpt regarding use of early release data:

The authors invite the research community to examine and analyze the data in their current form with the following understandings:

• As with all data released on GenBank, the National Center for Biotechnology Information places no restriction on their use or distribution.

• The authors intend to publish a descriptive paper summarizing the dataset and its implications for bird barcoding and any taxonomic issues arising from the data. Publication of this data release paper is anticipated by 1 June 2012. In accordance with the Fort Lauderdale Principles (Welcome Trust 2011), the authors ask the community to respect our intent to publish on these topics and not to submit manuscripts for this purpose based on this dataset.

• Use of this dataset for purposes other than those described above are welcome and encouraged, contingent on proper citation of this publication.

• The authors invite members of the community to examine the data and test their accuracy relative to other datasets. We welcome your comments, suggestions and corrections. BOLD 3.0 includes the capability to submit annotations to data submitters and we encourage readers to use this new system to submit observations on this dataset.

• The species determinations are not yet final. Some of the species identification may be change by the time of publication of the data release paper (anticipated by 1 June 2012).

I hope to soon see more public barcode data, following this and other pathways!

DNA Barcoding Prizes for first Nature, Science publications

First proposed in 2003, the DNA barcoding initiative has generated more than 1000 scientific publications, but none so far in the de facto top science journals, Nature and Science. The barcode library contains over 1 million records from over 100 thousand species, suggesting opportunities for new insights into large-scale patterns and processes in biodiversity. Yet so far relatively few papers have attempted synthetic exploration of this unprecedented genetic resource beyond species identification. To encourage high-profile discovery, Program for the Human Environment is offering $5000 prizes for the first DNA barcoding papers in Nature and Science, as announced earlier this month at the close of Fourth International Barcode of Life Conference, University of Adelaide, Australia. To qualify, the paper must embrace DNA barcoding either in the title or abstract, and cite CBOL and iBOL in the acknowledgments.

Zookeys

Open access journal ZooKeys announced the first rapid-release, large dataset of bird barcodes, based on 2,808 frozen tissue samples from the Division of Birds, National Museum of Natural History, Smithsonian Institution, Washington, D.C. This is the first barcode dataset explicitly published under the Fort Lauderdale Principles (Welcome Trust 2003) of early data release adopted by the genomics community. Mark and co-authors hope this is a model that will encourage and allow barcoders to rapidly release data and receive academic credit.

Trinity School TeaBOL

The Trinity School TeaBOL project is featured in cover article for December/January issue of The Helix, an Australian science magazine for children 10+

Barcode High

The November/December 2011 online issue of The Scientist published an article by Mark on the High School Barcode Project, Barcode High.