PHE guest investigator David Thaler is a co-author of A Cosmic View of Life on Earth: Hierarchical Visualization of Biological Data Using Astronomical Software. The cooperative international project “A Cosmic View of Life on Earth” adapts an immersive astrophysics visualization platform called OpenSpace to contextualize diverse biological data. Dimensionality reduction techniques harmonize biological information to create spatial representations in which data are interactively explored on flat screens and planetarium domes. Visualizations are enriched with geographic metadata, three-dimensional scans of specimens, and species-specific sonifications (e.g., bird songs). The “Cosmic View” project eases the dissemination of stories related to biological domains (e.g., insects, birds, mammals, human migrations) and facilitates scientific discovery. A terrific 4-minute supplementary video supports the article.
News
Leonardo Da Vinci DNA project publications
Leo DNA project counsel Eric Rayman’s essay “Can an Artist’s DNA Help Detect Forgeries?” has been published in the lively art world publication HYPOALLERGIC.
The key methods paper by Rhonda Roby et al., Sampling techniques and genomic analysis of biological material from artworks, appeared in the Journal of Forensic Sciences.
The paper by Massimo Guerrero et al, “Scaling Turbulent Wake Flow Downstream of Isolated Piers in Laboratory and River” where they explore using Leonardo’s drawings to estimate his visual acuity appeared in Results in Engineering.
As reported in a post on 26 May, in their new book “Genìa Da Vinci. Genealogy and Genetics for Leonardo’s DNA,” published by Angelo Pontecorboli Editore, Alessandro Vezzosi and Agnese Sabato present findings from 30 years of genealogical research that have culminated in groundbreaking insights. The book documents an elaborate family tree tracing back to 1331, spanning 21 generations and involving over 400 individuals. The work lays the groundwork for reconstruction of Leonardo’s genetic profile.
Short essay by Jesse on defending America’s submerged borders
Thanks to RealClear Defense for publishing Defending America’s Submerged Borders. The essay builds on Jesse’s Michelson Lecture at the United States Naval Academy on advances in ocean sensing and other PHE work about ocean exploration and observing. Thanks to Iddo Wernick and Paul Gaffney for helpful contributions.
A corresponding 5-minute video is here.
AI & Energy foreseen in 2019
In 2019 the CEO of the electric company AEP asked Jesse to address his leadership. Jesse’s talk on Climate and Power included the following prescient words:
A more fascinating and important question is how IT and AI will alter demand. Siri and Alexa are hungry goddesses. I mentioned illuminated skylines of cities but consider that a square foot of a data center guzzles more than 100 times the electricity of a square foot of a skyscraper. More than 1500 skyscrapers of more than 40 stories now define the world’s cities, but the population of enterprise-class date centers now exceeds 5000. The Switch Corporation’s Citadel data center in Northern Nevada will be 7.2 m square feet, 0.25 square miles, and more than twice the area of the world’s largest office building, the Burj al Khalifa in Dubai. It will consume 650 MW around the clock. In round numbers, one million square feet of a new data center demand about 100 MW to live, a density of about 1000 watts per square meter. The world’s most powerful computer, the Summit Supercomputer in Oak Ridge, demands per square foot about 20 times a conventional data center. While efficiency gains continuously, the cloud is nevertheless a glowing cloud of electrons.
Connecting the clouds and all the devices that rely on the clouds also uses a lot of electricity. Per unit of data transported, wireless systems use about ten times the juice of a wired system. Each smart phone finally uses about the same electricity as a high-efficiency household refrigerator. The global population of smart phones may pass five billion in 2019. Meanwhile, Amazon has already sold an additional 100 million digital assistants such as Alexa. We are creating a world with hundreds or thousands of radios per person. The system now operates at 4G, which involves about 20 base stations per square km, globally about four million cell towers. Present information networking uses about 200-300 TW hours per year, about $20 billion worth.
5G, one hundred times faster and needed for high resolution streaming, virtual reality, and autonomous devices, may employ as many as 2000 base stations per sq km, and the Global Small Cell Forum of the telecom industry anticipates for 2025 some 70 million base stations and networking demand for $90 bn worth of electricity. All this will come before autonomous vehicles and indeed is the prerequisite for the sensors and AI that will make autonomy safe and effective.
Whether or not the autonomous vehicles (AVs) use batteries or hydrogen for propulsion, they will use electricity to process their zettabytes and yottabytes of data. In effect each AV will be a high-level server. A fully connected car is expected to generate 25 GB of data per hour. If the car is used 2 hours each day, 60 such cars would generate a petabyte in a year, 60,000 cars an exabyte, and 60,000,000 cars a zettabyte. The present global annual market for servers is about 10 million units. Motor vehicle sales globally are an order of magnitude larger, about 100 million. No wonder software and hardware companies now read Car and Driver. Powering a global stock of one billion servers that also happen to be autos will be a good business, even apart from propulsion. IT can drive a new wave of global electrification, including for mobility. Keep an eye on energy use patterns in Northern Virginia, which hosts the world’s largest concentration of large data centers.
25th birthday of Ocean Biodiversity Information System
In 1997 Jesse, Fred Grassle, Mark Costello, and others conceived the Ocean Biogeographical Information System (OBIS) as the “what/where/when” database for the incipient Census of Marine Life. OBIS officially began in May 2000 and now celebrates its 25th birthday with recollections and meditations on the present and future. Its name is now the Ocean Biodiversity Information System.
Times of London on Leonardo DNA Project
The new book on the Genealogy and Genetics of Leonardo Da Vinci by Alessandro Vezzosi and Agnese Sabato causes a blaze of interest in the Leonardo Da Vinci DNA Project (which Jesse co-founded and chairs) including this article in the Times of London. Congratulations to the authors, and the entire network, including Terry Collins. Jesse sent a statement but could not attend in person the public event in Florence. Thanks to Vinci mayor Daniele Vanni and Tuscany governor Eugenio Giani.
New in Loglet Lab 5.1
Thanks to Albert Strusberg, David Burg, Perrin Meyer, and Jason Walker-Yung we enjoy Loglet Lab 5.1.
What’s new:
Advanced the user interface:
Added graphing option form processing in the back-end.
Added scaling and normalizing function to process the data accordingly in the back-end.
Added the forecast for each line in the composite and components plot.
Completed corresponding Javascript (JS) coding to process the new data in the front-end graphs.
Adapted current database structure to save new parameters to library entries.
Adapted export/import logic to take into consideration all new parameters from the advanced UI.
Updated production database in the AWS server to the new database model.
Implemented the Logistic Substitution (LogSub) algorithm:
Created a multi-step algorithm in several modules to handle Logsub dataset creation based on the current input spreadsheet style form.
Adjusted the front-end logic to process the Logsub plotly JS data accordingly when using the Logsub model.
Adjusted the library logic to handle loading and saving Logsub data.
Adjusted the import/export logic to also save Logsub data when required.
Created new type of graph using Plotly JS for stack/market share data.
New features and miscellaneous bug fixes:
Added statistics to the advanced UI table. Statistics now include several parameters: RMS, MAD, MAPE and AIC.
Fixed bug when saving certain kind of datasets to the library.
Fixed X ranges calculation for the composite graph.
Fixed several import/export bugs for certain kind of datasets.
Fixed logic to handle certain kind of datasets when some of the rows contains NAN or zeros values.
Fixed the guessing initial parameters logic for the Logsub model.
All datasets transferred to from LL4 to LL5’s library
Documentation
Fixes and typos corrected
Additions according to the changes for v5.1
AWS:
LL4 has been removsed from AWS. Code is still available on Github.
LL5 – live long and prosper!
Quiet Ocean program’s 14th newsletter
The International Quiet Ocean Experiment has published its 14th newsletter, reporting on remarkable progress on the Global Library of Underwater Biological Sounds and other matters. The genesis of the IQOE was in Jesse’s essay, Broadening the scope of global change to include illumination and noise.
Human Progress newsletter on Iddo’s evidence of dematerialization
Marian Tupy publishes America’s Commodity Appetite: Evidence of Dematerialization: America’s economy has grown better at extracting more value from less stuff, an accurate article about Iddo’s recent paper.
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.