Rockefeller University

Program for the Human Environment

News

Animal species and mitochondria

We post to BioRXiv, the pre-print server for biology:
Why Should Mitochondria Define Species?
Mark Y. Stoeckle, David S. Thaler

Comments on the paper are most welcome.The study is grounded in and strongly supports Darwinian evolution, including the understanding all life has evolved from a common biological origin over several billion years.

The study follows mainstream views of human evolution. We do not propose there was a single “Adam” or “Eve”. We do not propose any catastrophic events.

 

Leonardo Da Vinci DNA project 12 Feb seminar at Rockefeller

The Leonardo Da Vinci DNA Project:
Exploring the Intersections of Science and Art

Click on the title to see the lecture in YouTube

Featuring:
Jesse Ausubel, Karina Åberg, and Thomas P. Sakmar

Monday, February 12, 2018
6:00–7:15 p.m.Caspary Auditorium
The Rockefeller University
1230 York Avenue at East 66th Street New York, NY 10065

DNA sequencing has revolutionized the study of human genetic variation, and insights derived from DNA now matter in diverse settings – from hospitals to courtrooms. Scientists are now also exploring information that DNA might yield about cultural heritage. For example, what can it reveal about works of art and their creators?

Leonardo da Vinci is widely recognized as one of the most extraordinary figures in human history. Leading up to the 500th anniversary of his death in 2019, an international team –– including anthropologists, artists, art historians, forensic experts, genealogists, microbiologists, physicians, and population geneticists –– has assembled to uncover new facts and insights about Leonardo. One of the ambitious goals of the team is to use pioneering methods to obtain traces of DNA attributable to Leonardo from artworks, notebooks or other sources.

On Monday, February 12, three members of The Leonardo DNA Project team – Jesse Ausubel, Karina Åberg, and Thomas P. Sakmar – will describe the origins of this remarkable project, provide a progress report on their research, and reflect on how this scientific inquiry may contribute to art history and conservation, while uncovering new information about Leonardo’s life, ancestry and exceptional abilities.

Jesse Ausubel, Director of the Program for the Human Environment at The Rockefeller University, has helped design and conduct major international research programs, including the Census of Marine Life, Barcode of Life initiative, and Encyclopedia of Life. His lab is now using very short sequences of loose DNA found in seawater to assess the status of marine life. He initiated The Leonardo DNA Project in 2014.

Karina Åberg is a visual artist with a longstanding special interest in the application of digital technology to education. Her unique skill set and enthusiasm about digital media and technology have facilitated her innovative contributions to digital design, advertising, communications and teaching. Her early training in Renaissance art techniques has led to several advances as a member of The Leonardo DNA Project since 2015.

Thomas P. Sakmar is a physician-scientist and the Richard M. & Isabel P. Furlaud Professor at The Rockefeller University, where he heads the Laboratory of Chemical Biology and Signal Transduction. His research program is dedicated to chemical biology and drug discovery research. His interest in visual sensory perception and the origins of creativity in science and the arts have led to his involvement in The Leonardo DNA Project since 2014.

eDNA seasonal fish abundance study

Mark Stoeckle, together with co-authors Lyubov Soboleva (Hunter College) and Zachary Charlop-Powers (Rockefeller University), update their 2017 paper “Aquatic environmental DNA detects seasonal fish abundance and habitat preference in an urban estuary” (PLOS ONE e0175186). They extended their original six-month study to twelve months, making this one of the longest time series of fish monitoring by eDNA to date. The new analysis shows how little bits of DNA shed by fish track the seasonal movements of fish populations in and out of New York Harbor. eDNA also gives a picture of how the relative abundance of species differs from one habitat to another. These results help open our eyes to how eDNA can improve monitoring of ocean life.

This figure shows how many species were detected (black) and water temperature (blue) over the course of the year.  Other figures and spreadsheets are posted and on FigShare

New Harvest conference

Alan visited the second annual New Harvest conference on cellular agriculture in Red Hook, Brooklyn, which included a variety of talks and exhibits on the science and broader implications of manufacturing food in vitro (from cell culture), as opposed to in vivo (from plants and animals). Technological advances have been achieved in growth media, more “lifelike” tissue engineering, and novel bioreactors designed to “brew” meat.  Remaining challenges include the ability to successfully match the taste, texture, and cost of conventionally-sourced meat- and plant-based foods, as well as successfully scaling-up production processes. R&D is spread among a variety of corporate startups (e.g., Memphis Meats, Finless Foods), traditional academic labs (e.g., Tufts, NC State), and citizen science efforts (Shojinmeat Project).

Hudson Canyon at Explorers Club

A Dive into Hudson Canyon: New York’s Atlantic Secret

The Wildlife Conservation Society, The New York Aquarium, and The Explorers Club invite you to a dive into Hudson Canyon – New York’s Atlantic secret.
Speakers:
•    Peter Auster, Mystic Aquarium explorer
•    Jesse Ausubel, Rockefeller University explorer
•    Keith Ellenbogen, underwater photographer
•    Melinda Rekdahl, Wildlife Conservation Society whale scientist
•    Madeleine Thompson, Wildlife Conservation Society archivist
Date: Tuesday, September 26  Time: 6:00 pm – 9:00 pm

Location: Explorers Club Headquarters, 46 E 70th Street, New York, NY, 10021 Reservation Notes: This event is FREE and open to the public. Light food and drink will be served. Please RSVP to nyseascape@wcs.org, limited seating available. For more details, you can learn more on nyaquarium.com.  This event has been made possible with support of the National Marine Sanctuary Foundation.

Loglet Lab software version 4

The behavior of a dynamic system, be it biological or socio-technical, frequently resembles a series of logistic wavelets, or “loglets.” Loglet analysis involves the decomposition of growth and diffusion patterns into S-shaped logistic components.  In the easiest cases, a loglet appears as a single S-shaped curve.  LogletLab is designed for use with user data to help users analyze and decompose growth processes.

LogletLab software has gone through several development cycles since the initial release of LogletLab 1 in 1998 straight through to the recent release of LogletLab 4.1, an online tool with extensive statistical analysis capabilities built in.  The most recent edition of LogletLab 4.1 offer users numerous new features including an extended selection of fitting functions and advanced statistical analysis.

All versions of LogletLab are available free of charge.

Click here to access LogletLab 4

Here is an example, the space shuttle launch history.

https://ll4.ddns.net:8000/?page=index&preload=library.get.288

Thanks to David Burg, Eyal Schachter, Perrin Meyer, Jason Yung, Iddo Wernick, and Alan Curry.