A Blog by Carl Zimmer

Rewiring Life: Learning About Synthetic Biology In Debates, Videos, and Comic Books

Today scientists at Stanford University reported they had implanted transistor-like bundles of genes into E. coli, making it possible to transform cells into biological computers. At Download the Universe, a science ebook review where I’m an editor, I take a look at the history of synthetic biology that led up to this remarkable feat. I also reflect on how to help young people become both excited and wise about these new kinds of technology. Check it out!

4 thoughts on “Rewiring Life: Learning About Synthetic Biology In Debates, Videos, and Comic Books

  1. That is a good article, and the videos are most helpful. As a long-time user of TTL logic and its many offshoots and descendants, I have two comments:

    (1) The bio/logic gates described in the video apparently make use of toggling pulses rather than DC levels for control signals. This will require new patterns of design and signal manipulation, suggesting significant promise as well as some major challenges.

    (2) Standardization of inputs and outputs is appealing, because it matches the use of signals typical of today’s digital electronics. Yet it may be more fruitful to follow biology rather than constrain it to imitate electronic circuits. Biology employs a wide variety of hybrid digital/analog signaling to accomplish gene regulation, homeostasis, adaptive behavior, growth and reproduction. Molecular biology in particular does not restrict itself to the strictly hierarchical layers of our electronic designs. Biological systems are inherently autonomous, and can be overwhelmingly complex, far beyond any of our designs to date.

    Since we already understand so well how to accomplish binary digital design, we could resist the urge to standardize, and instead try to take advantage of the variable responses found in biological systems. In so doing we can aspire to match the amazing robustness and plasticity of organisms which have been evolving for billions of years.

  2. @Ralph: There’s an entire branch of electronics that does not seem to be burdened by the “standardized binary” of digital logic. This of course is analog hardware. As someone straddling the divide between analog and digital design, I experience first-hand the differences in thought processes and “modes of operation” between the two disciplines. I’d guess analog people would be better qualified to take advantage of the new opportunities of bio/logic (love the shorthand!). Or even better, people who are already “bilingual” in this regard.

  3. @Ralph

    (Re: 1) We introduced both permanent gates responding to pulses (like you note) and also DC rewritable gates. We spent a lot more time testing permanent gates. Both architectures are accessible.

    (Re: 2) We aren’t naively recapitulating electronics in biology. E.g., see how the genetic XOR gate isn’t made via layering b/c we can integrate multiple control points at a single node on a (DNA) “wire.” Also, defining a common signal carrier based on flow of RNA polymerase is a good idea, although people have a hard time thinking about it. Transcription is used throughout biology to read out DNA. Thus, flow of RNA polymerase is a broadly useful signal carrier, and developing engineered genetic devices that send or receive RNA polymerase flow-based signals enables engineers to quickly connect to the full diversity of biology, as you wish.

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