Blog

New software for visualizing the whole animal kingdom

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

Guest investigator David Thaler co-authors paper with novel idea for biological diaries

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.

Burg & Ausubel publish “Jewish population trajectories between the Jordan River and the Mediterranean Sea”

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

“Peak Human?” booklet by Ausubel-Curry posted

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.

News from the Quiet Ocean Experiment

Terry Collins artfully summarizes the progress in this news release about the International Quiet Ocean Experiment.  The news was picked up by

Agencia EFE: Artificial intelligence listens to the habits of marine life (in Spanish)

Independent (London):  Scientists eavesdrop on underwater creatures to gain insights on ocean life

Earth.Com: Monitoring ocean life through underwater soundscapes

Portal R7 (Brazil) Biólogos marinhos captam zumbido não identificado que pode ser uma nova espécie de peixe Marine biologists capture unidentified tinnitus that can be a new species of fish

Vice / Motherboard (USA) Scientists Recording Ocean Sounds Picked Up a Mysterious ‘Buzz’ They Can’t Identify

ORF Online (Austria) Unterwassermikrofone belauschen Fische Underwater microphones eavesdrop on fish

Scientias, Netherlands Moet je horen! Vissen maken fascinerende balts- en eetgeluiden, vooral bij volle maan You have to hear! Fish make fascinating balts and eating noises, especially at full moon