Bits, Atoms, & Bio

The mediums we use are simply tools for expressing your art.”

– John Lasseter

 Mainframe computer, the first Numerical Control (NC) machine tool, and a modern biology lab

Mainframe computer, the first Numerical Control (NC) machine tool, and a modern biology lab

The era of Biology as Technology is upon us. Much like the computation and fabrication revolutions before it, the early stages of this biological revolution are hallmarked by largely inaccessible, siloed technologies that require significant training, specialization, and privilege to participate. However, as evidenced profoundly via the information revolution, the broad accessibility and networking of computation technology has led to sweeping, irrevocable changes in society.

My research aims to explore the following hypothesis: that highly accessible, powerful tools for both studying and engineering living systems, when connected via robust, technical and human networks, will enable participation by diverse communities, generating unpredictable, impactful innovation.

I will explore this hypothesis by developing broadly accessible tools for the creative exploration and construction of biology. Creative exploration for asking questions of the molecules, cells, and cellular communities from our bodies and the world around us; creative construction for building a living system that does something new. Tools will be designed to be:

  • simple-to-use;
  • easy to modify and hack;
  • open and sharable;
  • integrated to execute multiple biological processes;
  • high-throughput;
  • automated; and
  • networked.

I further aim to deploy these tools in communities around the world and systematically study their impact. Finally, I seek to connect and organize both tools and communities in robust networks to enable distributed, asynchronous innovation. In doing so, I hope to catalyze the global movement of community biology to realize a future where humankind, from ivory towers to the street, is literate in reading and writing its genetic code, and emboldened to collectively imagine and determine its biological future.

 
 

Initial Research Projects

Presented below are four initial research projects, each aligned with my group's mission of developing and enabling broad access to advanced tools and infrastructure for exploring and engineering life.


$1,000 BioLab

rapid prototyping

To develop a generation of more accessible tools for biology, we need to fundamentally re-think the nature of how such tools are designed, constructed, and distributed. We will leverage highly accessible supply chains, including digital fabrication tools and services, to realize the construction of a personal biology lab for under $1,000. Each $1k BioLab will enable creative exploration-the study of molecules and organisms on and from our bodies and the world around us-as well as creative construction-the engineering of a living system to have new properties and functions.

We will develop $1k labs at three scales: Molecular (nucleic acids, proteins), Micro (microscopic organisms-bacteria, viruses, fungi), and Cellular (physiology, organelles, and components of cells). For each type of $1k lab we will carefully consider how to process samples from our bodies and the environment as system inputs for answering scientific questions. Depending upon the scale of exploration, BioLabs will be developed with functions ranging from molecular amplification and visualization to cell culture and microscopy.

For creative construction of biology, we will leverage the latest technologies in discrete microfluidics and paper-based reagent storage to build modular, interoperable biological construction systems. Required inputs will be minimized to water and modular cartridges. Each BioLab will be designed to be pipette-free.

Initially, we will deploy $1k BioLabs in a several settings: locally, at my community biology lab EMW; as part of the hardware track for the 2016 International Genetically Engineered Machines (iGEM) competition; and the international Fab Lab network via How To Grow Almost Anything. We will work with Karim Lakhani, a world expert in distributed innovation and open source technology, to systematically study and quantify the impact of our tools as they are deployed in each community. Based in part on these studies, we will iteratively refine each $1k BioLab to maximize ease-of-use, the breadth and depth of creative exploration and construction, and finally learning and innovation outcomes.

Bits to Bio (B2B) Convertor

automation & integration

A major component of each $1k BioLab will be a "Bits to Bio (B2B) Convertor" that enables the conversion of digital descriptions of biology to functional bio molecules, cells, or cellular communities. Each B2B Convertor will be composed of a fluidic processor and controller.  Fluidic processor development will involve the exploration of a spectrum of fabrication technologies, from 3D printing to soft lithography. Materials will be systematically evaluated for bio-compatibility with the requisite bio molecules or organisms. A variety of automation paradigms will be explored, from pneumatically-controlled polymeric valve systems to solid state electrowetting.

This work will build upon my decade of research pioneering open, automated systems for executing complex biological processes ranging from gene, genetic circuit, and protein (soluble and membrane) synthesis to microbial and mammalian cell culture.


 

street bio

We have a tremendous opportunity, as our bio economy is being constructed, to reach the most disadvantaged communities of our society and begin the work of cultivating skill in reading and writing our genetic code. Inspired by #YesWeCode, we similarly aim to arm 100,000 low-opportunity youth with the tools and mentorship necessary to enable creative exploration and construction with biology. We will design modified versions of the $1k BioLab and, targeting middle-school and high-school students, initially deploy locally, eventually scaling to 100,000 young people throughout the U.S.


Bio Hub

networks | open repository for bio-hardware

 Screenshot of "Metafluidics," an open repository of hardware components for biology under development.

Screenshot of "Metafluidics," an open repository of hardware components for biology under development.

In open software and increasingly open hardware movements, an ecosystem of virtual infrastructure has made possible the sharing, reproduction, and re-mixing of code and objects, yielding in some cases, remarkable feats of asynchronous, peer production. Such infrastructure for synthetic biology is still in its early stages. While components include repositories of DNA sequences, organism design tools and abstractions, and standards for communicating genetic designs and data, infrastructure for the reproduction and re-mixing of bio hardware is nascent.

With Bio Hub, we aim to generate a robust repository of hardware systems for synthetic biology. The repository will include design files, detailed assembly specifications, bills of materials, and the requisite bits necessary to reproduce and remix hardware for executing processes fundamental to biology ranging from fluid handling to molecular and cellular measurement and microscopy. Furthermore, we aim to share protocols and data generated from these hardware systems with the existing information network found in both traditional journals and newly emerging repositories to enable better experimental reproduction.