Journalist/author Robert Bryce interviews Jesse Ausubel about PHE’s work on “peak human” and “peak humans.” The interview covers four dimensions of human performance: the physical (how far and fast can we go?), lifetime (how long can we live and how well?), cognitive (measures of intelligence and learning), and immunity (is our resistance to disease waning?). The podcast was recorded on December 7, 2022. For the audio and transcript, see the Bryce website, and also on YouTube.
Blog
Our paper on eDNA as bioassay of Anthropocene published
The new journal based in China, The Innovation, has published the Thaler-Ausubel-Stoeckle paper on Human and domesticated animal environmental DNA as bioassays of the Anthropocene in their “Out of the Box” category, where we like to be. We also post the pdf.
We thank Song Sun and Ke Chen for editorial assistance.
Summary: Human and domesticated animal sequences, commonly detected in environmental DNA (eDNA) metabarcoding studies, are routinely excluded from analysis. Here we suggest that reporting human and domesticated animal eDNA results might open new lines of investigation. For example, the relative abundance of human and domesticated animal eDNA as compared to that of wild vertebrate species might provide an index of human impact on local biota. Such an index could be applied to sites ranging from urban harbors to remote villages, and possibly to analyze historical samples. Various potential sources of contamination complicate the picture, but it should be possible to develop procedures that minimize risk of DNA introduction during collection and processing. Our near-term recommendation is to encourage inclusion of human and domesticated animal data in eDNA publications as an incentive for discovery, to lift quality controls, and to collectively contribute to new vistas that eDNA science might open.
Our article on incorporating a known amount of non-fish DNA to allow better quantification of the fish DNA present in a seawater sample appears in the journal Environmental DNA.
Open Access
12S gene metabarcoding with DNA standard quantifies marine bony fish environmental DNA, identifies threshold for reproducible detection, and overcomes distortion due to amplification of non-fish DNA. Mark Y. Stoeckle, Jesse H. Ausubel, Michael Coogan, first published: 08 December 2022, https://doi.org/10.1002/edn3.376
While our paper focuses on fish, we believe the approach of “spiking” samples collected in nature with known amounts of DNA from a species that would not be present in the sample (such as ostrich) offers great promise for increasing the value of a wide range of aquatic DNA studies. The exhibit below shares some of the main points from the paper.
2007 Interview with Jesse cited in WSJ
A 5 Nov 2022 Wall Street Journal article by Holman Jenkins cites
JH Ausubel. Renewable and nuclear heresies . Int J Nucl Governance, Econ Ecol 1 (3): 229–243, 2007 and this interview with Robert Bryce also from 2007.
Thaler memo on “Distinguishing contamination from authentic human eDNA”
PHE guest investigator David Thaler summarizes “Ways in which contamination might be distinguished from authentic human eDNA” in a useful draft memo. Meeting this challenge matters greatly for using human eDNA as an assay of the Anthropocene, a subject of a forthcoming paper by Thaler, Ausubel, and Stoeckle.
Jesse’s Search for Leonardo’s Genome published
The journal Human Evolution has published Jesse Ausubel’s “The Search for Leonardo’s Genome,” an expanded, fully referenced version of a talk Jesse gave in June 2022 to a meeting of the American Academy of Arts & Sciences. The Academy Bulletin will publish the colloquial version in its winter issue.
Jesse H. Ausubel, The Search for Leonardo’s Genome, Human Evolution 37 3-4: 221-228, 2022; DOI: 10.14673/HE2022341106
Jesse’s Search for Leonardo’s Genome published in Human Evolution
The journal Human Evolution has published “The Search for Leonardo’s Genome” (Vol. 37 – n. 3-4 pp 221-228, 2022; DOI: 10.14673/HE2022341106), a fully referenced expansion of a talk Jesse Ausubel gave in June 2022 to a meeting of the American Academy of Arts and Sciences. The Academy’s Bulletin will published the colloquial version in its winter issue.
New code for analyzing eDNA sequences using DADA2 pipeline
For the past year MIchael Coogan, now a grad student in marine science at the U. of New Hampshire, has helped Mark Stoeckle and PHE with improved software for our eDNA studies. See summary below. A pdf of the R code is available here. If you have questions, please write to Mark.
The goal is to adapt the DADA2 pipeline to Mark Stoeckle’s 12S experiment. Sample sequences will be identified using 12S reference file containing sequences of 262 unique vertebrates found around New York. The starting point is a set of Illumina-sequenced paired-end fastq files that have been split (or demultiplexed) by sample and which have barcodes/adapters already removed. The end product will be a sequence table, analogous to the ubiquitous “OTU table”, which records the number of times sample sequences were observed in each sample. The key difference between the output of DADA2 and standard OTU analyses is that DADA2 infers sample sequences exactly rather than clustering sequences into fuzzy OTUs which hide and complicate biological variation.
Fishing for DNA in the Hudson
In the morning of 3 November 2022, Jesse Ausubel summarized the work led by Mark Stoeckle about catching eDNA in the waters of New York City to learn about our local fish species. The site was the beautiful new Little Island in the Hudson River Estuary Park. We post the deck of slides which span from Central Park to the Hudson and East rivers to the Gowanus Canal and Coney Island. New York City enjoys the presence of dozens of fish species, ranging from eels to sturgeon.
Passing of Paul Waggoner
Our great friend and colleague, agronomist Paul E. Waggoner, died on 1 November 2022 in Seattle, surrounded by family and friends. Paul’s wrote a crisp memoir of his own life, from Appanoose to Connecticut. Jesse offered a tribute: Thriving Thrift: On the Occasion of Paul Waggoner Appreciation Day, 2013.
Jesse and Paul first met in 1981 during the work of the Carbon Dioxide Assessment Committee for which Paul wrote brilliant far-sighted chapters about “Agriculture and a climate changed by more carbon dioxide” and about “Effects of a carbon dioxide-induced climate change on water supplies in the Western United States.” Jesse and Paul continued contact through the 1980s through the periodic seminars on climate change at Yale by William Nordhaus.
Paul and Jesse also did most of the writing and editing for the section on Adaptation (pp. 499-657) in the 1992 NASEM report “Policy Implications of Global Warming.”
In 1992 Jesse asked Paul the question “How much land can 10 billion people spare for Nature” and this led to a superb, lengthy answer (PE Waggoner. How Much Land Can Ten Billion People Spare for Nature? Task Force Report #121, Council for Agricultural Science and Technology, Ames IA 1994) and two decades more work on land-sparing and related issues of intensity of use of resources on land and in the sea. Paul was a universally helpful critic and editor as well as creative researcher and, perhaps most important, our best teacher about actual farming and plants.
Some papers we wrote together:
JH Ausubel, IK Wernick, and PE Waggoner. Peak Farmland and the Prospect for Land Sparing. Population and Development Review 38 (Supplement): 217–238, 2012
Rautiainen, IK Wernick, PE Waggoner, JH Ausubel, PE Kauppi. A National and International Analysis of Changing Forest Density . PLoS ONE 6 (5): 2011
JH Ausubel, DT Crist, and PE Waggoner (eds.). First Census of Marine Life 2010: Highlights of a Decade of Discovery. CoML 2010
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
PE Waggoner, JH Ausubel. Quandaries of forest area, volume, biomass, and carbon explored with the forest identity . Pp. 13 pp in Connecticut Agricultural Experiment Station Bulletin 1011 2007
PE Kauppi, JH Ausubel, J-Y Fang, AS Mather, RA Sedjo, PE Waggoner. Returning forests analyzed with forest identity . Pp. 17574–17579 in Proc Natl Acad Sci U S A vol. 103, 2006 10.1073/pnas.0608343103
JH Ausubel, PE Waggoner, IK Wernick. Foresters and DNA . Pp. 13–31 in Chapter 2 in Landscapes, Genomics and Transgenic Forests pp. 2006 CG Williams (ed), Published by Kluwer, Dordrecht
JH Ausubel, IK Wernick, AM Barret, PE Waggoner. Industrial ecology for leverage to let loose less cadmium. Prog Ind Ecol 3 (6): 522–537, 2006
MY Stoeckle, PE Waggoner, JH Ausubel. Barcoding Life, Illustrated: Goals, rationale, results (PDF). Consortium for the Barcode of Life (CBOL) 2005
MY Stoeckle, PE Waggoner, JH Ausubel. Barcoding Life: Ten Reasons (PDF). Consortium for the Barcode of Life (CBOL) 2004 Brochure
PE Waggoner, JH Ausubel. A Framework for Sustainability Science: A Renovated IPAT Identity (PDF). Proceedings of the National Academy of Sciences U S A 99 (12): 7860–7865, 2002 (See also a series of 6 Supplements at https://phe.rockefeller.edu/research/impact/)
PE Waggoner, JH Ausubel. How Much Will Feeding More and Wealthier People Encroach on Forests?. Population and Development Review 27 (2): 239–257, 2001
CR Frink, PE Waggoner, JH Ausubel. Nitrogen on the Land: Overcoming the Worries – lifting fertilizer efficiency and preserving land for nonfarming uses Pollution Prevention Review 11 (3): 77–82, 2001
IK Wernick, PE Waggoner, JH Ausubel. The Forester’s Lever: Industrial Ecology and Wood Products Journal of Forestry 98 (10): 8–14, 2000
CR Frink, PE Waggoner, JH Ausubel. Nitrogen fertilizer: Retrospect and prospect. Pp. 1175–1180 in Proc Natl Acad Sci U S A vol. 96, 1999
IK Wernick, PE Waggoner, JH Ausubel. Searching for Leverage to Conserve Forests: The Industrial Ecology of Wood Products in the United States Journal of Industrial Ecology 1 (3): 125–145, 1997
PE Waggoner, JH Ausubel, IK Wernick. Lightening the Tread of Population on the Land: American Examples (PDF). Population and Development Review 22 (3): 531-45, 1996