Regenesis (30 page)

Let's zoom back to
Figure 7.1
for synthesis. The synthesis of gene libraries and genomes begins with a source of short bits of DNA. Har Gobind Khorana created the first RNA oligomers in the early 1960s to help crack the genetic code (depicted in
Figure 3.2
), winning a share of the Nobel Prize in 1968 for this. Then he led his team to synthesize the first gene, which happened to encode the molecule at the core of the code and at the core of ancient and current life (our old friend tRNA). By the mid 1980s, Marvin Caruthers and team made a better chemistry that BioSearch and ABI automated so that labs could make one to four oligos just by typing in the sequence. In 1996 Blanchard, Kaiser, and Hood and later Rosetta Inpharmatics and Agilent adapted ink-jet printers to print A, C, G, and T onto flat glass slides. Xiaolian Gao at Xeotron and another group affiliated with Nimblegen came up with ways to make custom oligo arrays on the fly using spatially patterned light. Both groups teamed up with Jingdong Tian in my group in 2004 to show that the DNA on those arrays didn't have to stay on the arrays to be useful. Kosuri and coworkers published in 2010 a way to make subpools from the oligo arrays. And the freefall in cost of gene and genome synthesis suddenly seemed as inevitable as what had just happened for genome reading.

By 2012 the combined throughput of MycroArray, Combimatrix, LC-science, and Agilent could be around 300 billion base pairs per day, slightly behind the global genome sequencing capacity. Most of this is used for disposable arrays of oligos used for RNA quantitation or purification of genome subsets for sequencing—not for synthesis of genes or genomes. Clearly a market existed for sequencing 10
¹⁹
genomes (a billion people with 6 billion base pairs each, plus repeat customers due to microbial, immune, and cancer genomics).

What might the markets be that will drive similar levels of consumption of DNA from chips? Here is our wish list (or bucket list, to go with the shovels):

The point is that the applications of large-scale DNA writing are even more up for grabs than DNA reading. Predicting the future development of this field would be like trying to guess what applications of the personal computer would have been in the early 1970s: Electronic recipe books? Ping-pong? Balancing your checkbook?

Synthetic biology is mostly about developing and applying basic engineering principles—the practical matters that help transform something academic, ivory-towerish, pure, and sometimes self-indulgent or abstract into something that has an impact on society and possibly even transforms it. Systems biology moves us from massive numbers of observations to
theories. But when you try to build something—even an academic something—you really acid-test those ideas—often finding out how little you need to understand or how much you do need to understand but don't. When you try to build something for society, it's even tougher since many things that work in your lab don't work in other labs, much less in the hands of regular folks. And even if they do work, there is no guarantee that they will be financially successful.

The business of synthetic biology may now be transitioning to making a living by synthesizing genomes. What has been largely missing is an articulation of why we should engineer whole genomes rather than just the important parts. In answer, I have described a project to change the genetic translation code genome-wide for safety, to create new amino acids, and to engineer resistance to all viruses.

We are already in the business of making a safer microbial “chassis.” In 2011, DARPA put out a request for proposals for ways to “watermark” pathogens being actively studied in laboratories so that we could more easily trace accidental or intentional releases. This reflects our 2001 DARPA proposal to use DNA as a storage medium, and as we will see in
Chapter 8
, embedding English, encrypted messages, or even images in DNA has a history going back at least to 1984. The new challenge is to make these messages stable across time. Another DARPA challenge is to make the pathogens being studied able to survive only under specific laboratory conditions and not in the wild—without at the same time altering them so drastically that researchers can't study their pathogenicity. All of these measures also apply to nonpathogenic, synthetic organisms, that although considered safe, would likely be more widely (and wildly) distributed (because of industrial utility) and hence more worthy of possessing tracking and safety features.

In
Chapter 2
we examined ancient human texts and compared their longevity to the texts of life. In the tradition of encoding art in DNA discussed above, the world's first so-called synthetic organism (Craig Venter's
M. mycoides
) was accompanied by bits of human text embedded in code (the four letters of DNA). One bit of text read: “To live, to err, to fall, to triumph, to
recreate life out of life.” This sentence, which is a quote from
A Portrait of the Artist as a Young Man
, by James Joyce, prompted the Joyce estate to send Venter a cease-and-desist letter. This beautifully captured the moment at so many levels. Was quoting the Joyce text “to err, to fall” (i.e., was it an error on Venter's part?) or, to the contrary, was including the text in a historic hunk of DNA “to live, to triumph” (i.e., to glorify Joyce)?

In addition to the unfortunate Joyce quote, the genome of
M. mycoides
JCVIsyn 1.0 also incorporated a misquote of what Richard Feynman wrote on his last blackboard. As Venter's team had it, “What I cannot build, I cannot understand.” They were quoting from a secondary source (a risky business), because what Feynman actually wrote was: “What I cannot create, I do not understand.” That too elicited a corrective note from the authorities, in this case Caltech, where Feynman taught, together with a picture of the blackboard in question. (The
JCVI
researchers further compounded their errors by expressing the Feynman word in using a code that allowed only uppercase letters, which netizens interpret as shouting. But FEYNMAN WAS NOT SHOUTING! Nor, for that matter, did he write his parting message in caps.) Finally, we note that “What we can create, we don't necessarily understand.”

I noted that small blooper when I assessed the JCVI manuscript for
Science
prior to its publication in that journal. To lighten up the rest of my critique, I playfully submitted my review to
Science
encrypted entirely in DNA. I heard later that Clyde Hutchinson, an investigator at JCVI, was the one who figured it out. For the first few sentences, I used their code, but then I switched to a code that allows the encoding of anything digital, including lowercase letters, images, audio, and even web pages—and is easier to recall than sixty-four codons. In alphabetical order A = 00, C = 01, G = 10, T = 11. Even if the code is easy to recall, will the encoded messages endure, perdure, or neither?

The English poets Percy Bysshe Shelley and Horace Smith told the poetic tale of Pharaoh Ramesses II (c. 1303 to 1213
BCE
), whose fate has much in common with the fleeting glory of coded quotes and misquotes. Here is Shelley's version:

Will our DNA watermarks flow and evaporate with time? Or, worse yet, what if we leave an indelible, hubris-laden watermark graffito on our planet that says only “To err”?

The Third Industrial Revolution. iGEM

In early 2010, three undergraduate biology students at the Citadel—Brian Burnley, Patrick Sullivan, and Hunter Matthews—had an idea for a swell genomic engineering project: they wanted to reprogram the
E. coli
bacterium, which is a normal and benign resident of the human gastrointestinal tract, so that it would secrete a peptide that would suppress appetite. Obesity, they knew, was one of the top health problems in the United States, as well as in a lot of other countries. The problem affected one-third of the American adult population, and increasingly it also affected children. To combat it, people tried all sorts of weight reduction schemes, bogus and genuine: they took metabolism-revving pills, they dieted, they exercised, they bought stationary bicycles, ellipticals, and other exercise-torture machines, and they had excess fat removed from their bodies by liposuction. But in many cases nothing worked—or at least not permanently.

Why not tackle the problem where it arose, at the source, inside the human intestinal tract?
E. coli
bacteria, which can be made to do practically anything, were already on the scene. That's where they lived. If they could be genetically engineered to express satiety peptides, which controlled
hunger, then the whole obesity problem could be addressed biologically. Indeed, almost magically: the microbes would control your appetite for you, effortlessly, with no conscious intervention on your part, much less any heroic dieting willpower.

It sounded like a panacea, almost too good to be true. This would be a new type of cure-all, with programmed bacteria working on the problem inside your body. Obviously the idea would not appeal to everybody: people who were already on the warpath over the issue of genetically modified foods would never go for the idea of genetically modified bacteria rummaging around in their intestines. Still, the scheme provided a novel way for people to take control over their own physique.

All that was needed for the project to succeed were the genes necessary to persuade
E. coli
to synthesize PYY (3-36), a peptide naturally produced by mammalian colon cells and that is responsible for satiety regulation. Dr. David M. Donnell, an assistant professor of biology at the Citadel, knew where to get the necessary genetic structures: from the Registry of Standard Biological Parts at MIT. So toward the end of June he ordered them. And about two weeks later they arrived in the form of freeze-dried powders in 384-well plastic plates covered by adhesive foil seals. A list accompanying the shipment identified the exact well that each desired biological part was in. To use a given part, the experimenter inserted a pipette through the foil covering the well in question and injected into it a small amount of liquid. The powder containing the part dissolved readily and the solution was then ready to be drawn out and moved to a centrifuge for further processing.