Seminar: Creating an engineering discipline for biology

Written by: Karmella Haynes. Tom Knight, from Gingko Bioworks, presented tonight’s talk on creating an engineering discipline for biology. Tom is one of the early pioneers of today’s synthetic biology community and a great role model for engineers who are learning about biology for the first time, like several of our CSH Syn Bio students.

IMG_3526

Tom Knight presenting “Creating an engineering discipline for biology.” Steve Evans from Dow AgroSciences is in the audience (lower right panel).

Tom had established his career in computer engineering. During a computing course he taught in 1987, Tom challenged his students to calculate the year in which the advances of computer processing that obeyed Moore’s law would finally reach a plateau. That predicted point was two years ago (2013)…he noted that now days computer storage may be getting larger, but the processing is not becoming any faster. It was clear to him that humanity would need to move onto new materials and platforms to advance computation and engineering.

Tom’s fascination with biology began with his curiosity about the seemingly infinite complexity of functional molecules such as proteins. Knowing nothing about biology, he enrolled in a college sophomore-level molecular biology lab course.

The engineering culture has brought much to the area of biology, which has been largely dominated by hypothesis-driven basic research. Engineers and scientists approach complexity in different ways, Tom said. Scientists tend to embrace complexity and sometimes even the unknowable. Engineers tend to strip away complexity and seek out the simplest, most reliable, and understandable mechanisms.

Tom described how his frustrations with always dealing with a multitude of biochemical variables (buffer, unwanted cut sites, various incubation temperatures) just to building one synthetic gene inspired him to propose a standard for assembling DNA parts. The first collection of standardized parts, DNA fragments with universal cloning sites that all worked in the same buffer and at the same temperature, contained only 6 parts. This was the origin of today’s iGEM Registry of Standard Parts, which now houses over 25,000 DNA plasmids.

But still, there are roadblocks that impede the advancement of synthetic biology. For instance, the cycles involved in building biological systems are too long. To think about how to solve this, Tom encouraged us to look at the semiconductor world. Computer processing companies like Intel first set a deadline for producing a functional product. Next, they spend most of that time using known parameters to computationally model prototypes. Finally, they build a working optimal system.

Equipped with rapid DNA synthesis, new assembly platforms, high-throughput testing, a growing collection of characterized interchangeable parts, and computational biological modeling, biological engineers can adopt the approaches from computer engineering to speed up advances towards functional, robust engineered organisms.

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s