DNA of New York City’s East River

Mark Y. Stoeckle and Jesse H. Ausubel

Animals shed environmental DNA (eDNA) into the environment. Sources include cells sloughed from body surfaces, body wastes, and tissue remnants following predation, death, or injury.  eDNA is a bit like dandruff.  DNA of course consists of long strands of four chemical compounds: cytosine (C), adenine (A), guanine (G), and thymine (T). Researchers use strands of about 100 “letters” from variable parts of the genome, like a long telephone number, to identify the species of animal from which the DNA comes. Acidity, heat, and light can speed eDNA degradation, and bacteria eat eDNA. A rule of thumb is that eDNA sufficient for reliable identification lasts about 24 hours and thus gives a good current portrait of life in a water body.

As seen in these 5 slides, the PHE’s Mark Stoeckle regularly collects a half liter of water from the East River adjacent to the Rockefeller campus (slide 1) with a bucket on a string, filters the water, extracts the DNA from the sediment on the filter using special chemicals called primers to grab only the DNA that came from vertebrates, sequences these pieces of eDNA, and matches the sequences against genetic libraries. The number of copies for each species corresponds well to the recent abundance of that animal in the East River.

Our vertebrate eDNA studies show that that the East River abounds in fishes (slide 2), with tautog most common but also herring, bass, and eel.  The presence of water from sewage treatment plants and rains that wash city streets also brings DNA of urban wildlife into the East River.  A cup of water from the East River reports the abundance of rats, pigeons, dogs, and cats (slide 3).  It also reports the presence in the River or nearby of additional wildlife ranging from deer and beaver to seal and dolphin (slide 4).  Finally, the eDNA in the East River neatly tracks the diet of humans of New York (slide 5).  The fractions of aquatic eDNA of commonly consumed meats such as chicken and cow match nicely with national data on meat consumption.  An exception is sea bass (branzino), widely served in New York City restaurants and thus common in East River water samples but a tiny proportion of the national fish diet.

eDNA revolutionizes the ability for people to know, affordably, what animals live in or use the waters near them. eDNA will be a routine component of fish stock assessment, detection of invasive species, and monitoring effects of coastal storms and climate change.  Genomics enables a cup of water to tell the natural history of the East River.

Passing of Cesare Marchetti

Cesare Marchetti passed away this morning in Tuscany just short of his 96th birthday.  After meeting Cesare in 1978, Jesse Ausubel became fascinated with Cesare’s ideas about the importance and ubiquity of processes of growth and diffusion captured often in simple form by Lotka-Volterra equations and subsequently coded in our Loglet Lab software.  In the early 1980s Jesse began assisting Cesare on some projects and subsequently worked together on subjects ranging from electricity to travel to human populations and empires (see below).  And of course Leonardo Da Vinci.

Cesare is best known for Marchetti’s Constant that posits that the human time budget for travel is a little above one hour per day, since ever and everywhere, because anthropologically rooted in the dangers homo sapiens faces when outside a protected environment.

Cesare was one of the inventors of geoengineering. His most cited paper is On geoengineering and the CO2 problem (1977).

Around 1970 he was also one of the inventors of the hydrogen economy as described in this 1973 paper: Hydrogen and energy.

A bibliography with links to many of Cesare’s papers from 1952 to 2007 is here.  A second list of publications is here.

Cesare’s explorations of Leonardo are here.

Our group at The Rockefeller University always greatly enjoyed hosting Cesare in New York City, and he reciprocated with marvelous hospitality in Monteloro.

Our joint efforts included:

C Marchetti, JH Ausubel. Quantitative Dynamics of Human Empires [Color Booklet Version, 52 pages].  Adapted from Marchetti and Ausubel, International Journal of Anthropology 27(1-2):1-62, 2012. 2013

JH Ausubel, C Marchetti. Science, Conquering Child of the Church . 2003 Draft prepared for Next 1000 Years meeting, 9-10 October 2003

C Marchetti, JH Ausubel. The Next 1000 Years. 2003 Discussion paper for April 2003 Rockefeller U workshop

JH Ausubel, C Marchetti. The Evolution of Transport. The Industrial Physicist 7 (2): 20–24, 2001

JH Ausubel, C Marchetti, PS Meyer. Toward Green Mobility: The Evolution of Transport European Review 6 (2): 143–162, 1998

JH Ausubel, C Marchetti. Elektron: Electrical Systems in Retrospect and Prospect Pp. 110–134 in Technological Trajectories and the Human Environment, J.H. Ausubel and H.D. Langford, (eds.). Washington, DC: National Academy Press, 1997 Also appeared in Daedalus 125(3):139-169, Summer 1996.

C Marchetti, PS Meyer, JH Ausubel. Human Population Dynamics Revisited with the Logistic Model: How Much Can Be Modeled and Predicted? Pp. 1–30 in Technological Forecasting and Social Change vol. 53, 1996.

Requiescat in pace.

Video of Jesse’s Nierenberg Prize lecture on “Peak Human?”

In this 54″ video made 13 October, 2022 Jesse Ausubel, awarded the 2022 Nierenberg Prize for Science in the Public Interest, discusses whether the human species can continue to improve—much like cars, computers, or other technology—or whether our species has reached its peak.

Another podcast with Jesse about peak human and peak humans

Jesse H. Ausubel joins Jason Spiess on The Crude Life to discuss “Peak Human” and “Peak Humans” in a 34-minute podcast and explore new research showing how humans’ minds and bodies may near their limits and even start on a downward curve.  “For 200-250 years humanity has had an incredible run,” Ausubel said. “When you think of your great grandparents, grandparents, parents and you, generally speaking you are going to be better… than they were.”