A child of the International Quiet Ocean Experiment, today is the first World Ocean Passive Acoustics Monitoring (WOPAM) day. The IQOE leaders, including Miles Parsons and Steve Simpson, have prepared two very cool 90-second videos to initiate WOPAM day.
Downloadable at this site. 150 MB each, but they download quickly.
Way back in 1999, Jesse Ausubel, Fred Grassle, Mark Costello, Edward van den Berghe, James Edwards and others began to envisage an on-line ocean biogeographical information system (OBIS) to enable researchers and resource managers, within a few years, to select any area or volume of water on a global map and bring up information as to what has been reported to live there. Developed as the data portal for the Census of Marine Life program (2000-2010), by 2010 OBIS had several million what/where records for over 120,000 species. OBIS now contains over 109 million records from over 180,000 species, about 70% of described marine species, and offers wonderful data access, archiving, and visualization.
Today, thanks to software wizardry and persistence of Dr. Steven Formel, Science Analytics and Synthesis team within the U.S. Geological Survey, and PHE’s Mark Stoeckle, OBIS and the Global Biodiversity Information Facility (GBIF) contain their pioneering eDNA (marine genomic) datasets, derived from the paper Mark co-authored about fish diversity in coastal New Jersey.
Here are links to the datasets:
GBIF: https://www.gbif.org/dataset/46488f96-b51e-4c06-9a02-8c4c900f7f78
OBIS: https://obis.org/dataset/fe2ed263-2b21-47d7-a79f-f9b911132398
OBIS and GBIF expose slightly different sets of metadata. One can even access a single ASV from a single library. Here is an example; the DNA-derived data are in the table at the bottom: https://www.gbif.org/occurrence/4126398311
Thanks, Steve and Mark, for making this a historic day in the advancement of marine bioinformatics.
For a 50th Harvard College Reunion Seminar on EO Wilson’s proposal to conserve half Earth, Jesse Ausubel and Mark Stoeckle, assisted by Elizabeth Munnell, conducted a survey of vertebrates in three locations in the Charles River and two in Boston Harbor. The 14 slides on The Charles River and Boston Harbor Then and Now tell a story of remarkable ecological recovery.
Swiss bioinformatics wizard Wandrille Duchemin and PHE Guest Investigator David Thaler publish PyKleeBarcode: Enabling representation of the whole animal kingdom in information space in PLoS One. The computational advances in the paper open the way to calculating DNA-relatedness of all animal species, as the figure below for mammals suggests.
Fig 2. A. View of the structure matrix of the mammalian dataset and taxonomic structure of Mammalia. B. Phylogenetic tree structure of the taxonomic groups retrieved from NCBI taxonomy.
The paper builds on the pioneering work done earlier in the PHE by Larry Sirovich and Mark Stoeckle:
L Sirovich, MY Stoeckle, Y Zhang. A scalable method for analysis and display of DNA sequences. PLoS ONE 4 (10): e7051, 2009
L Sirovich, MY Stoeckle, Y Zhang. Structural analysis of biodiversity. PLoS ONE 5 (2): e9266, 2010
MY Stoeckle, C Coffran. TreeParser-Aided Klee Diagrams Display Taxonomic Clusters in DNA Barcode and Nuclear Gene Datasets . Nature Scientific Reports 3 (2635): 2013
Published Open Access in Frontiers in Epidemiology: The Coronavirus Calendar (CoronaCal): a simplifiedSARS-CoV-2 test system for sampling and retrospective analysis by Manija A. Kazmi, David S. Thaler, Karina C. Åberg, Jordan M. Mattheisen, Thomas Huber and Thomas P. Sakmar
The paper concludes that sampling saliva on simple paper provides a useful method to study the natural history and epidemiology of COVID-19 (and probably many other microbes). The “CoronaCal” collection and testing method is easy to implement, inexpensive, non-invasive and scalable. The approach can inform the historical and epidemiological understanding of infections in individuals and populations.
The idea for the paper arose from efforts in the Leonardo Da Vinci DNA Project about stable preservation of genetic material on paper.
Working with foresters in the US and the EU, PHE researcher Iddo Wernick co authored a letter in Nature Climate Change, Ensure forest-data integrity for climate change studies regarding the data used for National Forest Inventories.
Science and environment report Alice Hutton has written an exceptionally lively and informative article for the UK Guardian newspaper about the International Quiet Ocean Experiment, a program on which we have worked hard and long:
Listen to a toadfish’s grunt! AI helps decode a ‘symphony’ of ocean sounds
Continuing our exploration of human populations with logistic wavelets, David Burg and Jesse Ausubel publish Jewish population trajectories between the Jordan River and the Mediterranean Sea Open Access in the journal Israel Affairs, DOI: 10.1080/13537121.2023.2206247
ABSTRACT This article re-examines Jewish population in what is now Israel using historical estimates from Ottoman, Mandatory British and United Nations sources and recent data from the Israeli census bureau. A logistic model generates backward extrapolations and forward projections. The model quantifies three waves of Jewish immigration totalling about 3.5 million. Subtracting immigrant data from total population numbers gives the main empirical trajectory for non- immigrant native-born population. A multi-logistic model combining migrant and native populations projects a Jewish population of about 10 million in 2050, a level low in the range of estimates made by others.
Some other relevant papers
IK Wernick. Jews in Time and Space (PDF). International Journal of Anthropology 31 (1-2): 93–109, 2016
PS Meyer, Ausubel JH. Carrying Capacity: A Model with Logistically Varying Limits (PDF). Technological Forecasting and Social Change 61 (3): 209–214, 1999
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
RealClear Energy posted an article by Iddo Wernick on consequences of nations choosing different energy trajectories in the Indo-Pacific region in the year 2050. See The Indo-Pacific in 2050: Alternative Energy Scenarios and Security
Based on Jesse’s Nierenberg Prize lecture, Jesse and Alan Curry, who led research on human performance enhancement for the Program for the Human Environment for several years, have created a compact version with about half the visual exhibits in the lecture. We retain the title “Peak Human? Thoughts on the Evolution of the Enhancement of Human Performance.” Thanks to Dale Langford for editorial assistance and the beautiful layout.