Podcast appearances and mentions of James J Collins

Over the last 20 years, the idea of “designing biology” has gone from science fiction to just science, as the field of synthetic biology has exploded, with applications from therapeutics to manufacturing and more. In this episode from January 2019, one of the pioneers in the field, professor James J. Collins of MIT, joins a16z general partner on the Bio + Health fund, Vijay Pande, and editorial partner Hanne Winarsky, to discuss the origins of synthetic biology or "synbio", to what "engineering and designing" biology really looks like in action and the disciplinary differences between how biologists and engineers see the world.

For the past decade, the Collins Lab at MIT has been focused on using bioengineering principles to better understand antibiotics with the primary goal of discovering novel molecules that work effectively against bacterial pathogens. On this episode, you'll learn the following: What four primary mechanisms of antibiotic resistance are used by pathogens How AI can be used to identify certain features of molecules out of massive numbers of molecules and amounts of data Where Collins hopes to see his research and applications applied in the coming years James J. Collins, Ph.D., is a professor of medical engineering and science at the Broad Institute of MIT and Harvard, and head of the Collins Lab at MIT. About one year ago, he teamed up with colleague Regina Barzilay, one of the world's leading experts on applying artificial intelligence (AI) to healthcare. The goal was to determine whether the power of AI could be used to address the challenge of antibiotic resistance and bacterial pathogens through the discovery of new antibiotics. They began by putting together a training collection of over 2,500 molecules, including 1,700 FDA-approved drugs. This library was tested against E. coli in the lab to see which molecules might lead to inhibitory activity against the bug. Next, a deep neural network was trained using the data gathered and information about the structure of each molecule in the library. The trained deep neural network was then applied to a drug repurposing library containing several thousand molecules that have already been developed or are in the process of being developed as drugs. The neural network was challenged to identify molecules that are predicted to be antibiotics but don't look like any existing antibiotics: one molecule fit the criteria, and was named halocin. Halocin proved itself to be a potent novel antibiotic that worked against 35 out of 36 samples of multidrug-resistant, extensively drug resistant and pandrug-resistant pathogens from the CDC. In addition to the details of this exciting discovery that could change health and medicine for the better, Collins discusses the most common mechanisms of bacterial resistance to antibiotics, why gram negative bacteria poses an extra challenge to the search for effective antibiotics, how AI could be used to identify features of molecules that make them amenable to gram negative bacterial uptake, the most useful strengths at the core of the AI technology being used in these capacities, the soon-to-be-launched Antibiotics AI Project, and so much more. Tune in for the full conversation and learn more at collinslab.mit.edu.

with James J. Collins, Vijay Pande (@vijaypande), and Hanne Tidnam (@omnivorousread) The idea of 'designing biology' -- once science fiction -- has over the last 20 years become just... science. In this episode, a16z bio general partner Vijay Pande with Hanne Tidnam talk all about the field of synthetic biology with James J. Collins, professor of bioengineering at MIT. Collins, whose work in synthetic biology and systems biology pioneered the field, has also launched a number of companies and received numerous awards and honors (including a MacArthur "Genius" Award, an NIH Director's Pioneer Award, and Sanofi-Institut Pasteur Award). This wide-ranging conversation about the birth of synthetic biology covers everything from the founding story of the discipline to what "engineering and designing" biology really looks like in action -- when instead of engineering electrons, you are engineering toggle switches for genes -- to the disciplinary differences (and synergies) between how biologists and engineers see the world. What are the engineering and design principles, techniques, approaches that work best when applied to science? How does building a company in this new space look different, in terms of platforms and products? And how is this new field changing education in science, all the way down to kits that allow you to play with the machinery of a cell... at home... and even in middle school?

Holy Cross alumnus James J. Collins '87 is a founder of the emerging field of synthetic biology, which combines science and engineering to construct biological circuits that can program organisms, much like we program computers now. He is William F. Warren Distinguished Professor, University Professor, and Professor of Biomedical Engineering at Boston University, where he also directs the Center of Synthetic Biology. In this talk, Collins traces the short history of synthetic biology, what they've been able to achieve, and opportunity that lies ahead. He also addresses the practice of science, ethical considerations, public opinion, and the growing trend of DIY biology. The lecture is the first in a yearlong series to explore "The Practice of Science in a World of Competing Values."