Densmore Mentee Receives Federal Research Residency to Standardize the Building Blocks of Engineered Biology
by A.J. Kleber
Science fiction abounds with predictions for a future where biological engineering is used for a broad range of everyday applications, from advanced gene therapies to effective and scalable biofuels. With genome sequencing, synthetic cellular growth and development, and machine learning technology capable of analyzing vast quantities of data at incredible speed, we seem poised on the verge of making such futures a reality. The primary obstacle is, quite simply, the problem of predictability. Living things are infamously variable, erratic, even untamable, right down to their most basic building blocks. In order to take control of those building blocks and use them in a deliberate fashion on a societal scale, we need to be able to achieve consistent results. That’s the goal Ph.D. student James Roberts will be pursuing as a Scholar-in-Residence at the National Institute of Standards and Technology (NIST)’s Living Measurements Systems Foundry (LMSF), one of five inaugural participants in a joint internship program by the NIST and NSF.
The Scholars-in-Residence Awards, initiated with the support of collaboration-building philanthropic organization Schmidt Sciences, will contribute to the NSF and NIST “missions to advance biotechnology and bioeconomy to ensure global competitiveness, national security, and economic growth of the U.S.,” according to a June press release. Roberts and his fellow awardees will work with experts in state-of-the-art NIST laboratories to develop standards and metrics which will shape the future of the field and “foster greater trust in biotechnology R&D.”
Creating standardized, repeatable and shareable metrics for biotechnology is no new pursuit for Roberts’ advisor, Boston University electrical & computer engineering professor Douglas Densmore (ECE, BME, MSE), who heads up the Cross-disciplinary Integration of Design Automation Research (CIDAR) Lab. Densmore, who will continue to mentor and advise Roberts as the PI of his Scholars-in-Residence Award, has worked for many years to develop automation technologies, computational models, and classification systems for engineering with biological components; all aimed at moving the field from the theoretical to the practical. As he puts it, “CIDAR has made computational tools that transform high level representations into actual designs that can be manufactured,” but there have been roadblocks “Often, we rely on hypothetical or generic data.” Roberts’ research at the LMSF will help to move things forward by “allow[ing] us to tie real experimental data to our formalized models of how biological circuits work.”
In fact, Roberts’ project will be a continuation of his doctoral research with Knox, CIDAR’s AI-enabled platform for hosting, designing, and analyzing integrated systems of biological components, termed “biological circuits.” In collaboration with NIST measurement science experts, he’ll focus on refining and advancing Knox’s capabilities using experimental results, analyzing them to develop repeatable rules for biological circuit design, training predictive models which can be validated experimentally, generating insights into the relationships and functions of biological components, and generally developing standards which can guide and accelerate the accessible, affordable research and development of biotechnologies.
Roberts is excited both by the work itself, and the newly-minted residency program, which he sees as an “initial [step] toward greater collaboration between academia and federal laboratories.” This is an opportunity to position himself at the start of a new phase of scientific cooperation to drive breakthroughs and open up the biotechnical field long-anticipated advancements, as well as strengthening partnerships and making critical tools and insights broadly accessible. “I am hopeful that this internship will support long-term goals in AI-for-science along with bolstering innovation in the genetic engineering space.”
Who knows? With an interactive, publicly-available instance of Knox and a refined set of standards and rules to apply, personalized genetic therapies, scalable biofuels and even the bioremediation of our atmosphere might soon make a transition from science fiction … to science fact.