Hello and welcome back to the newsletter! Feel free to hang out at the Forum! We are also on twitter!

All the past podcasts and tutorial can be found here. You can also now find our podcasts on Apple Podcasts, Spotify, Google, Stitcher, TuneIn, and more (as well as manually in your favorite podcast client with our RSS feed)! Enjoy!

  1. Podcast with William Poole
  2. New event coming—Chat with Prof. David Doty!
  3. Job Advertisements!
  4. Interested in helping out, sharing something interesting, or have an idea for something we could do?

1. Podcast with William Poole

In this espisode, we spoke with William Poole, a graduate student at Caltech working on quite a few topics! His research spans synthetic/systems biology to molecular programming, software development to chemical reaction network (CRN) theory, machine learning to cell free systems. We certainly had a lot to talk about!

We discussed the software that he has been working on. BioCRNpyler: easily compile diverse models of biochemical circuits; bioscrape: a fast custom-tailored simulator to utilize and learn from biological data; Vivarium connect, combine, and simulate diverse models across many scales.

Next we move onto William’s research into chemical Boltzmann machines, what they are and how they are related to machine learning, while talking about how low molecular copy number systems might be able to perform more complex computation than high copy number systems.

We also talk about how William got into molecular programming from his undergraduate degree, which focussed on physics and biology. He describes how his undergraduate research led him in various directions, and even into working in bioinformatics in industry for a few years before pursuing graduate school.

This ultimately spurred on a somewhat grand discussion on William’s “dream” for molecular programming. He is very concerned about climate change, and talks at length about how in the long term we might be able to program many of the materials around us to sequester carbon, and eventually “re-terraform” the earth.

Finally, we asked why physicists and engineers are able to come together to build large scale projects such as the LHC and ISS, while no such projects exist for the biological sciences, and we speculate on what such a project could look like for our field…

Enjoy this episode!

William Poole received his B.Sc. from Brown University in Biological Physics and is scheduled to complete his PhD in Computation and Neural Systems from Caltech in summer 2021 (co-advised by Erik Winfree and Richard Murray). Broadly, his research interests involve developing mathematical and computational tools to understand “how cells think” and “how to program cells”. He views systems biology and synthetic biology as two sides of the same coin; to truly understand and control biological systems we will need fundamentally new ways of thinking about biochemical computation. For inspiration, he has looked to statistical physics, machine learning, and computer science. He also believes that doing theory in a vacuum, without close contact to experimentalists, is counterproductive towards developing the tools that will drive science and technology forward. Towards this end, he also dabbles in the wet lab side of synthetic biology with an eye towards applications in green technology and sustainability.

2. New event coming—Chat with Prof. David Doty!

The “Meet the Molecular Programmer” podcast series focuses on casually chatting with professors about their academic and life experiences. We will get to know Prof. David Doty.

David Doty is an associate professor of Computer Science at the University of California, Davis. He is broadly interested in problems at the intersection of physics, chemistry, biology, and computation. This does not mean the traditional “computation in service of natural science” (e.g., bioinformatics, computational chemistry, or molecular dynamics simulation). Rather, certain molecular systems—such as a test tube of reacting chemicals, a genetic regulatory network, or a growing crystal—can be interpreted as doing computation themselves… natural science in service of computation. He seeks to understand the fundamental logical and physical limits to computation by such means.

We will chat with Dave on Aug. 19th. Please submit your questions!

3. Job Advertisement!

Nanovery is a startup applying DNA nanotechnology to build a sensitive nucleic acid detection tool for life sciences and diagnostics. Nanovery is looking to hire a DNA nanotechnologist with experience in design, modelling, and analysis of experimental data. If you are interested in DNA nanotechnology, strand displacement reactions and building molecular circuits for practical applications—do visit our website!

4. Interested in helping out, sharing something interesting, or have an idea for something we could do?

If so, please get in touch with us! Shoot us an email at contributions AT <this domain>, there are loads of ways you can get involved, and many we haven’t even thought of, but here’s a few ideas of what you could do:

We’re looking forward to getting to hear from you, and getting to know you better!