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Biotech and Beyond

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Biotech and Beyond
February 24–25, 2015
San Diego, California

field trip
Scripps Institution of Oceanography, UC San Diego
February 26, 2015



6:00 PM
First-Timers Reception
6:30 PM
7:00 PM

7:30 AM

Buffet Breakfast

8:30 AM
Conference Welcome
Len Kleinrock, TTI/Vanguard Advisory Board
8:45 AM
Conference Overview
Doug Lenat, TTI/Vanguard Advisory Board
9:00 AM
Using Massively Parallel Simulation to Study Disease
Amanda Randles, Fellow, Lawrence Livermore National Laboratory
Image-based models of the circulatory system may yield important insights into the underlying mechanisms driving disease progression and could inform surgical planning as well as the design of next-generation drug delivery systems. But building a detailed, realistic model of human blood flow is a formidable mathematical and computational challenge requiring large-scale fluid models as well as explicit models of suspended bodies like red blood cells. This will require high resolution modeling of 20-30 trillion cells in the blood stream, and necessitate significant computational advances. To date, a group of researchers and physicians at the Dana-Farber Cancer Institute and Brigham and Women's Hospital, have efficiently scaled its algorithms to run on up to 294,912 processors and are working to extend this scalability to allow the study of large regions of the circulatory system. It is also working to address treatment planning and the movement of circulating tumor cells in the bloodstream.
9:40 AM
Advanced Materials and Manufacturing for Life Sciences
Hu "Tiger" Tao, Assistant Professor, Cockrell School of Engineering at the University of Texas at Austin
Though mankind has been using silk for more than 5,000 years, its story is not yet fully woven. We have refashioned silk as a sustainable material in optics and photonics, electronics, and optoelectronic applications. The study of the favorable properties of silk is worthwhile in its own right, but also as a broad inspiration to further develop biological foundries for both the synthesis and processing of Nature's materials for high technological applications.
10:20 AM
Coffee Break
10:50 AM
Reimaging the Immune System in Medicine to Improve Care for People with Cancer
Melissa Lechner, Resident Physician, Brigham and Women's Hospital, Boston Children's Hospital, Harvard Medical School
The immune system has long been recognized as a critical contributor to human health and disease in areas such as infection, childhood vaccination, and AIDS. Only recently has medicine begun to harness the immune system as a tool to diagnose and treat patients with cancer. Unique qualities of the immune system, namely memory, systemic reach, and exquisite sensitivity and specificity, make it a powerful tool for cancer diagnosis and treatment with significant advantages over conventional approaches. Advances in medical knowledge and technology now facilitate minimally-invasive immune-based assays that can detect the presence of cancer and monitor its clinical burden in humans. Significantly, these assays are applicable across all types of cancer, thereby creating a universal test for cancer, and can be done on routine blood samples without the need for radiation exposure or invasive tissue sampling. In addition to cancer detection and monitoring, immune populations in the body can suggest the aggressiveness of known cancers and help to guide providers and patients in clinical decision making. Lastly, the advent of immunotherapy in cancer treatment has helped produce durable responses that lack many of the toxic side effects of conventional therapies and may be superior in the elimination of metastatic disease.
11:30 AM
The Interface of Theoretical Computer Science and Systems Biology
Saket Navlakha, Assistant Professor, Salk Institute for Biological Studies
Biological systems, ranging from the molecular to the cellular to the organism level, are distributed and in most cases operate without central control. Such systems must solve information processing problems that are often very similar to problems faced by computational and human engineered systems, including coordinated decision making, network routing and design, leader election, and more. This talk will discuss how "thinking computationally" about the strategies biological systems use to solve these problems can lead to new technologies and algorithms in computer science.
12:10 PM
DNA Storage
Sri Kosuri, Assistant Professor, UCLA
12:50 PM
Members' Working Lunch
2:05 PM
Using Ultrasound for Intra-body Area Networks
Tommaso Melodia, Associate Professor, Northeastern University
As the number of implanted medical devices grows, the need for networking them increases. Indeed, new sensors and actuators could enable revolutionary new applications and advance the medical treatment of major diseases of our times. Most research to date on "body networks" has focused on communications among devices interconnected through traditional electromagnetic radio-frequency (RF) waves. Yet the human body is composed primarily of water—a medium through which RF does not propagate well. This talk will give an overview of ongoing work attempting a radically different approach, i.e., to establish wireless networks of miniaturized embedded devices through human tissues by means of acoustic waves at ultrasonic frequencies. Progress has also been made on designing and prototyping ultrasonic networks through a closed-loop combination of mathematical modeling, simulation, and experimental evaluation.
2:45 PM
Intelligent Health Assessment Software
Adam Zagorecki, Co-founder, Infermedica
3:25 PM
Coffee Break
3:55 PM
The Cannabis Evolution Project
Mowgli Holmes, Co-Founder, Chief Scientific Officer, Phylos Bioscience
Biotechnology is the re-purposing of natural tools that evolution has already pre-designed. Plant breeding does the same thing, but allows us to use evolution itself as the driver for the human phase of the design process. Certain plants - Cannabis in particular - are highly customized bioreactors that have been subject to millions of years of natural selection, thousands of years of human selection pressure, and fifty years of modern breeding approaches. In just the last few years, we've attained the computational and sequencing power necessary to start redesigning and accelerating the evolutionary process itself.
4:35 PM
Viruses, Virus Proteins, and Ebola
Erica Ollmann Saphire, Professor, Scripps Research Institute
The Ollmann Saphire Lab at the Scripps Research Institute studies viruses with compact genomes of only 4–7 genes. Consequently, each protein is critical, many are obligated to perform multiple functions, and some actually rearrange their structures to achieve those new functions. As a result, these few polypeptides accomplish a surprisingly complex set of biological functions: immune evasion, receptor recognition, cell entry, transcription, translation, assembly, and exit. Viruses with limited genomes also offer a well-defined landscape of possible protein–protein interactions, which together comprise the totality of their life cycle. By systematically analyzing the structures and functions of each protein the virus encodes (as we set out to do for the Ebola and Lassa viruses in particular), we gain fundamental insights into the biology of entry, immune evasion, and assembly, and can decipher the collaborative roles of these proteins in pathogenesis.
5:15 PM
Close of First Day
6:00 PM


7:00 PM

The Universe and Us: An Integrated Theory of Electromagnetics and Gravitation
Carver Mead, Professor of Engineering and Applied Science, Emeritus, Caltech
Newton's mechanics, Maxwell electromagnetism, and GR gravitation share the disadvantage that the quantities in their equations (force, acceleration, electric and magnetic fields, tensor elements involving stresses and gravitational field) are one full derivative away from the fundamental four-vector properties of matter. Not only does this derivative characterization complicate the theory, but it pushes a great deal of the problem into boundary conditions that are often difficult to determine.

The present contribution can be viewed as an attempt to develop the maximum physical insight using the minimum mathematical complexity. We present a unified theory of gravitation and electromagnetism in which the two interactions are of exactly the same form, but of the opposite sign. Both couplings are based squarely on the elementary four-vector coupling of matter wave functions. All calculations are carried out on elementary quantities (energy, momentum, current density, scalar and vector potentials). The concept of force, and its requirement for some force equation, although sometimes useful, is not required. This four-vector approach, which we call G4v, represents an significant simplification and unification of physical law.

The results derived by G4v for Gravity-Probe B, gravitational redshift, precession of elliptical orbits, Shapiro delay, deflection of light by massive bodies, and the total gravitational-wave radiation from binary systems are identical to those of GR to the first post-Newtonian order.

G4v predictions of gravitational-wave radiation patterns for binary systems, antenna patterns for observatories like LIGO, gravitational potential inside neutron stars and black holes, and certain velocity-of-light experiments differ significantly from those predicted by GR. It should be possible to compare the predictions of G4v with those of GR within the next few years.

7:30 AM

Buffet Breakfast

8:30 AM
TTI/Vanguard Announcements
8:45 AM
The World's First Organism Engineering Foundry
Reshma Shetty, Co-founder, Ginkgo BioWorks
If you think about building a house, you draw up plans, there are materials, experts who build your house for you. You know at the end of the process, you're going to get a house. We are nowhere near that in biology. There are no architects. People don't have any idea how to make a blueprint for a biological system. Biology is way more sophisticated than construction in terms of what it can build. We're going to see a transition from regular manufacturing to biological manufacturing. You can chop down a tree into pieces and use it to build things, but why not just grow pieces of your building? Why not have roads that can self-repair? Organism engineers at Ginkgo Bioworks learn from nature to develop new organisms that replace technology with biology.
9:30 AM
Enhancing Biodiversity Through the Genetic Rescue of Endangered and Extinct Species
Ryan Phelan, Executive Director and Cofounder, Revive and Restore / The Long Now Foundation
The DNA of many extinct creatures is well preserved in museum specimens and some fossils. Their full genomes can now be read and analyzed. That data may be transferable as working genes into their closest living relatives, effectively bringing the extinct species back to life. The ultimate aim is to restore them to their former home in the wild. Endangered species that have lost their crucial genetic diversity may be restored to reproductive health. Molecular biologists and conservation biologists all over the world are working on these techniques. Revive & Restore is helping to coordinate these efforts. Revive & Restore's flagship project, already underway, the Great Passenger Pigeon Comeback will bring the iconic passenger pigeon back from extinction using the genome of the band-tailed pigeon and state-of-the-art genomic technology. Not shying from the gargantuan challenges of de-extinction, the organization endeavors to recreate the woolly mammoth in order to generate ecosystem changes capable of altering adverse climate change on a global scale, the same climate change that threatens the survival of thousands of species. These audacious projects also advance the use of biotechnology for the genetic rescue of existing endangered species, such as Revive & Restore's newest project: the black-footed ferret.
10:10 AM
Coffee Break
10:40 AM
The Wonders of Geckos: A New Path Towards Bioinspiration?
Duncan J. Irschick, Professor, University of Massachusetts, Amherst, and Co-founder, Geckoskin
Geckos have inspired both biologists and laypeople for many years, yet until recently the secrets that underlie their adhesion have remained unanswered. New discoveries in the anatomy of geckos now pave a path towards powerful synthetic versions of gecko-inspired adhesives that could transform our homes and businesses. Geckskin can hold more than 700 lbs on smooth glass, yet be easily removed with no residue. This invention and its implications will be discussed in the context of the evolution of geckos and the broader role of biomimicry in our society.
11:20 AM
Plasma Technology: The Frontier of Medicine
Jerome Canady, Founder, U.S. Medical Innovations
Intraoperative blood loss and the need for patient transfusions are among the clinical risks that surgeons consider during surgery. In the past 30 years plasma-based electrosurgery has been introduced to reduce blood loss. Recently cold atmospheric plasma (CAP) devices have been reported to demonstrate anti-cancer therapeutic capabilities via apoptosis. CAP demonstrates a selective killing of cancer cells without damaging non-cancerous tissue. Two new scalpels have been clinically used to simultaneously cut and coagulate tissue at room temperatures with minimal tissue damage and intraoperative bleeding. This talk, by the inventor of the scalpels, will discuss the clinical and experimental applications of plasma technology in surgery, combined with chemotherapeutic and selective radio-guided radiation.
12:00 PM
Medicine, Technology, and Demographic Change
William A. Haseltine, President, ACCESS Health International, Inc.
12:45 PM
Members' Working Lunch
2:00 PM
The Future of the Brain
Gary Marcus, Professor, Department of Psychology, New York University
2:40 PM
Synthetic—and Open-Source—Biology
Andrew Hessel, Autodesk Distinguished Researcher
3:20 PM
Conference Reflections
Bob Lucky,, TTI/Vanguard Advisory Board
4:00 PM
Close of Conference

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