Rockefeller University

Program for the Human Environment

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passing of Rodney Nichols

Our beloved friend and colleague Rodney Nichols passed away on 30 August 2018 in New York City.  Rod introduced Jesse Ausubel and Doris Manville, who have now worked together in the Program for the Human Environment for more than 25 years.  Numerous interests, programs, and organizations united us, including scientific cooperation between nations in conflict and The Rockefeller University itself.  Here are notices in the 2 September New York Times from Rod’s family and from The Rockefeller University.  We will miss Rod greatly.

Jesse offers a Remembrance.

Census of Marine Life anthem

We listened again to Look to the Sea, the catchy song that Maryann Camilleri, Jerry Harrison, David Dennison, David Hardin, and others created for the Census of Marine Life in 2010.  The song, video and its creators are explained at

https://www.youtube.com/watch?v=vqed3WFYDGo

also at https://vimeo.com/17662204

The recording was played at the London Grand Finale of the CoML in October 2010.   The Steve Miller Band played the song several times during their 2010-2011 world tour.

eDNA and Loch Ness

Mark Stoeckle is interviewed in an AP Television segment about searching for the Loch Ness monster using eDNA.  Mark’s interview and footage begins about 2 minutes 50 seconds into the 8-minute segment.

https://www.youtube.com/watch?v=d5UPXmP5YE0

https://www.youtube.com/watch?v=nj8qoHoa0Vg

Polished version of Michelson Oceans lecture

Jesse Ausubel had the honor in October 2015 to present the Michelson Lecture  at the United States Naval Academy in Annapolis.  Thanks Captain and Professor Emil Petruncio!

We now post a polished version of that lecture, “Ocean Past, Ocean Future: Reflections on the Shift from the 19th to 21st Century Ocean.”

Abstract In the 19th century humans knew little about the oceans, but other forms of life knew a lot. Our job the past 135 years has been to catch up and surpass other forms of life in knowledge of the oceans. The advance of observation through science and technology, including new carriers and processors of information, has vastly expanded the oceans knowable to humans beyond what a sailor’s five senses could directly provide. By infiltrating the ocean with informationally connected sensors, humans are becoming the top experts on the oceans in the 21st century.

 

AFP coverage of mt DNA paper

Thanks to Marlowe Hood of Agence France Press (AFP) for an extensive article about Why should mitochondria define species? by Mark Stoeckle and David Thaler. Editing of Mr. Hood’s article resulted in a couple of inaccuracies.

While the opening sentence suggests that a handheld barcoding device already exists, such a convenient device remains a few years away, although the process of obtaining barcodes is now standardized, routine, and quick.

The fourth paragraph inquires about diversity increasing with time.  Diversity does increase with time.  What the paper shows is that while time matters, the population size achieved over the interval of time does not matter.

The study is grounded in and strongly supports Darwinian evolution, including the understanding all life has evolved from a common biological origin over several billion years.

The study follows mainstream views of human evolution. We do not propose there was a single “Adam” or “Eve”. We do not propose any catastrophic events.

 

 

More coverage of Why mitochondria define species

The article Why should mitochondria define species?
Stoeckle M.Y., Thaler D.S.
is now fully open access:
DOI: 10.14673/HE2018121037

Coverage in Tekniikan Maailma, Finland: (Widespread genetic research revealed: Human genetic diversity is low – Two people do not differ by more than two percent) https://tekniikanmaailma.fi/laaja-perimatutkimus-paljasti-ihmisen-geneettinen-monimuotoisuus-on-vahaista-kaksi-ihmista-ei-eroa-toisistaan-enempaa-kuin-kaksi-pulua/

and Nachrichten Welt, Germany: Alles andere als besonders: Die winzigen DNA-Unterschiede der Menschheit sind “Durchschnitt” im Tierreich https://nach-welt.com/technik/alles-andere-als-besonders-die-winzigen-dna-unterschiede-der-menschheit-sind-durchschnitt-im-tierreich/

The study is grounded in and strongly supports Darwinian evolution, including the understanding all life has evolved from a common biological origin over several billion years.

The study follows mainstream views of human evolution. We do not propose there was a single “Adam” or “Eve”. We do not propose any catastrophic events.

 

 

More fishing for DNA on Martha’s Vineyard

We (Mark Stoeckle and Jesse Ausubel) post new results from water sampling in October 2017 for eDNA on the island of Martha’s Vineyard.  We tested for freshwater fish (light green rows), saltwater fish (blue rows), and other vertebrates (taupe rows).  We tested in four more locations, Upper Lagoon Pond (Oak Bluffs), Mill Brook just below Mill Pond (West Tisbury), Old Millpond (West Tisbury), and Priester’s Pond (North Tisbury).  Priester’s Pond is about two miles north of Mill Pond and feeds into it.  We compared these four locations to two places we tested in 2016, Look’s Pond (freshwater, West Tisbury) and Tisbury Great Pond (saltwater) into which it feeds.

In each case, we sieved DNA from about a cup of water scooped within reach of the shore. The numbers in the columns are the number of DNA “reads” obtained from each sample for each species.  One can think of the number of reads or fragments of DNA as indicative of the abundance of DNA of that species and probably indicative of the abundance of the species itself, although different species of animals shed DNA at different rates.

The first two columns on the left show the results from 2016, for example, lots of American eel DNA in Look’s Pond.  In 2017 the Bella Bennett of the Martha’s Vineyard Times covered our initial findings about eDNA on the Island: https://www.mvtimes.com/2017/08/02/fishing-for-dna/

We found some cool things in the new locations.  For example, Mill Pond has DNA of river otters, which are hard critters to see.  The Mill Brook, Millpond, and Priester’s Pond all have muskrat DNA, and all abound in frog DNA.  DNA from all the fish in Priester’s Pond also occurs downstream in Millpond but Millpond has pickerel and eel DNA absent from Priester’s.   The brook has DNA for small stream species such as darters and killifish but not for brown bullhead (similar to catfish) or pickerel, which may need the pond habitat.

We found a mix of DNA for salt and freshwater fish in Upper Lagoon Pond.  We were happy to find menhaden and herring DNA, which means the “herring ladder” gets used.  Most remarkably, we found striped bass DNA in Upper Lagoon Pond, confirming a wild “fish” story from 2016: https://www.mvtimes.com/2016/06/01/late-night-splash-dark-holds-surprise/

We continue to be thrilled by ways that eDNA allows us to discover the animals in the water around us.  For more, see https://phe.rockefeller.edu/blog/2018/01/11/edna-seasonal-fish-abundance-study/ and  https://phe.rockefeller.edu/blog/2017/04/12/fishing-for-dna-paper-published/ .

 

Mark Stoeckle mitochondria paper in Human Evolution

Mark Stoeckle and David Thaler publish “Why should mitochondria define species?” open-access (DOI: 10.14673/HE2018121037) in the journal Human Evolution following a study of mitochondrial DNA from about 5 million specimens covering about 100,000 animal species. The paper argues that humans are far from special: humanity’s tiny mt DNA differences are “average” in the animal kingdom. Moreover, as with humans, over 90% of animal species today likely originated 100,000–200,000 years ago.

RealClearScience runs a good article about Stoeckle-Thaler, “What Can ‘DNA Barcodes’ Tell Us About Evolution and Ourselves?”

The study is grounded in and strongly supports Darwinian evolution, including the understanding all life has evolved from a common biological origin over several billion years.

The study follows mainstream views of human evolution. We do not propose there was a single “Adam” or “Eve”. We do not propose any catastrophic events.

Other coverage:

The Independent, UK Genetic differences between people across the world are no greater than differences between pigeons https://uk.news.yahoo.com/genetic-differences-between-people-across-184451249.html?guccounter=2

Europa Press, newswire, Spain La diferencia genética entre humanos, en el promedio de las especies https://www.europapress.es/ciencia/laboratorio/noticia-diferencia-genetica-humanos-promedio-especies-20180521172546.html

Agencia EFE, Spain Demostrado, no eres nada excepcional (Demonstrated, you’re nothing exceptional https://sevilla.abc.es/ciencia/abci-demostrado-no-eres-nada-excepcional-201805211531_noticia.html

RIA Novosti (newswire), Russia: Scientists have not found differences in the genetic diversity of humans and animals) https://ria.ru/science/20180521/1521018801.html?referrer_block=index_archive_1