So, what was new about Endy’s IAP-engineered genetic blinkers project in 2003? Basically, the idea was to turn the original genetic blinker into a new and improved version with superior functionalities. The oscillatory period of the Elowitz and Leibler blinker was measured in hours, which was longer than the cell division cycle of the bacterium itself. Consequently the state of the oscillator had to be transmitted down from generation to generation. So one subgroup of IAP students wanted to speed things up. A second subgroup wanted to create and install a “synchronator” gene that would make all the cells blink off and on in concert, like the lights on a movie marquee.
The students started with an initial biobrick parts kit put together by the instructors, Endy, Knight, Sussman, and Rettberg. The parts kit consisted of actual DNA sequences stored in freezers, sequences that encoded some of the most basic functions in molecular biology. There were promoters: sequences that started DNA transcription, and there were terminators: sequences that stopped transcription. There were antisense RNAs that blocked gene expression, and of course there were GFP genes that made cells fluoresce. A data book listed the function, structure, device name, description, and biobrick number pertaining to each separate genetic part. Essentially, the parts kit was an indexed bin of biological components and supplies.
Standard biological parts exist on three levels of complexity; the most basic is a genetic part such as a plasmid or a plasmid backbone. There are also composite parts, combinations of two or more individual parts, such as a reporter+quencher. The next level up is a genetic device, a group of components that perform a function of greater complexity, such as a device that initiates cell death or sends signals between cells. Finally, there are systems, entire organisms that do something—blink on and off, for example. (There are also “chassis” parts, which are commonly used lab strains of organisms such as E. coli, yeast, or Bacillus subtilis. These are more or less blank slate microbes that will receive the new genetic sequences and then express them as output.)
During the IAP course, the students came up with and contributed about fifty new genetic parts of their own, and entered each part’s name, function, and other information in the data book. This was the basis for MIT’s current Registry of Standard Biological Parts, which can be accessed at parts.mit.edu. At the time the IAP course ended, there were about 140 annotated genetic parts in the registry. At the time of this writing there are over 7,000 parts in the registry, but this is changing quickly, since Harvard’s team alone made 55,000 parts in the summer of 2011. Even the location and governance of the registry is changing, moving away from the MIT campus.
When the students were finished designing their new genetic circuitry, Endy sent the relevant sequence information to Blue Heron Biotechnology of Bothell, Washington, to be synthesized. The company, founded by MIT grad John Mulligan in 1999, found that half of the designs couldn’t be produced, and those that could be synthesized didn’t seem to work when injected into cells. And so the whole project seemed to be a washout.
But about a year later, Endy managed to get some of the designs to function as intended—just barely. “It would have been dumb luck if they all worked together out of the box,” he said.
The other instructors had their own postmortems. “It’s interesting to think about where this is going, and of course we have no idea,” said Gerald Sussman. But Tom Knight did have one: “Hopefully, the next IAP students will get E. coli to blink ‘dash-dash, dot-dot, dash’ (Morse code for ‘MIT’).”
The course was repeated in January 2004, with a project named Engineered Genetic Polka Dots. Student teams created new standard biological parts and designed genetic circuits that made cellular patterns including polka dots (the team in question called itself the Polkadorks) and bull’s-eyes, as well as an ambitious plan to make cells swim together like a school of fish.
In the end, none of these second-generation grand designs behaved as planned, either. Evidently, putting biobricks together and getting them to work successfully would be slightly more challenging than anyone had thought.
But then came iGEM.
In the beginning, iGEM stood for intercollegiate genetically engineered machines. The idea was for MIT to bring other American colleges into the business of engineering genetic parts and devices, and to stage a competition among the participants. The competitions would be modeled on student robot contests, events that were so successful at drawing in students that the prize ceremonies at some of them filled entire stadiums. So Rettberg, Endy, and Knight rounded up Caltech, Boston University, Princeton, and the University of Texas-Austin (where Endy had spent some time as a postdoc) and delivered them all a one-phrase challenge: design and build a genetically encoded, finite-state machine (one that transitions from one state to another under the control of a program).
The students would start work in the summer of 2004, continue through the fall, and then meet up for a jamboree in Cambridge early in November to compare and share their results. Which is indeed what happened.
The Princeton team set out to build the biological equivalent of a children’s game called Simon, a test of memory in which participants had to repeat a pattern of signals that grew in length and complexity with each successive iteration. So the students designed a three-cell system that, when it detected a particular sequence of inputs, would respond by triggering a release of the reporting molecule, which in this case was yellow fluorescent protein (YFP).
The Caltech team wanted to design and build a strain of yeast that could detect three different levels of caffeine in coffee. Boston University teamed up with Harvard to design cells that could be made to count. The UT Austin contingent set out to build what sounded like the neatest bacterial app of them all, an E. coli film that would take what amounted to a biological photograph.
As it turned out at the jamboree, the Princeton team couldn’t get its YFP reporting mechanism to work. The Caltech students, by contrast, brought off their project handily. Their engineered yeast glowed green in the presence of low caffeine, green and yellow in medium caffeine, and yellow alone in high caffeine. In a campus coffee shop, the yeast successfully identified decaf, regular, and espresso coffees. The Boston University and Harvard team eventually got their bacterial counter to work and published a report on the project (together with considerable subsequent work) in Science five years later.
The stars of the show were the Texans, who added photoreceptor genes to E. coli, created a thin film of the light-sensitive bacteria, and got it to display the phrase “Hello World” in the form of deposited pigments (Figure 8.2). This phrase has been a standard simple test for computer programmers and an inside joke ever since Brian Kernighan wrote a Bell Labs memo in 1974. The experimental result was published in Nature: “Synthetic Biology: Engineering Escherichia coli to See Light” (2005). A behind-the-scenes story is that the original pigment patterns were due to the action of the light directly on the colored nutrients in the agar. In other words, the photo was a product of the nutrients rather than the bacteria. The team had not done the control step of leaving out the genetically engineered microbes. Nevertheless, that photo was all over posters representing iGEM for the next year! But this lapse was repaired before the paper was submitted to Nature. (Team members also sharpened the fonts and added the word “nature” as well as faces of many almost-famous people, like Andy Ellington of Austin, Texas.)
Figure 8.2 Hello World
Undergrads were now doing things, largely in a spirit of fun, that professional molecular biologists would have been hard-pressed to achieve a mere ten years earlier.
The following year, iGEM attracted teams from Canada, England, and Switzerland, and participation has grown steadily since then. The 2006 iGEM finally took on the trappings of a formal competition, with judging panels, prizes, and categories such as best part, best device, best system, best presentation, and even “best conquest of adversity” The jamborees themselves, meanwhile, increasingly resembled Olympic-level sporting events, with
competitors showing up in team costumes, carrying away trophies, and building human pyramids on the playing field to celebrate victory.
Some of the genetic systems they designed worked so well that they had commercial possibilities. Students from the University of Edinburgh won the 2006 iGEM prize for the best real-world application with a bacterial arsenic sensor for drinking water. Whereas existing assays had a sensitivity of 50 parts per billion (ppb), the team’s E. coli sensor could detect concentrations of arsenic as low as 5 ppb. In the 2007 competition, the team from UC Berkeley engineered E. coli to produce a blood substitute that could be freeze-dried and stored, and then could be reconstituted and grown up in large volumes when needed. In 2008 the grand prize winner and official recipient of the Biobrick Trophy, a large silver Lego block bearing the iGEM logo on one face, was the team from Slovenia (which had also been the winner in 2006), which this time created a synthetic vaccine for the pathogen Helicobacter pylori, the cause of stomach ulcers.
The 2010 iGEM Jamboree turned out to be the biggest and best of them all—the last one in which all the teams met and competed at a single location, which as it happened was iGEM’s birthplace and continuing home base, MIT. As a venue for a synthetic biology intercollegiate competition, MIT was spiritually, emotionally, and symbolically correct: it was internationally renowned as one of the world’s top educational and research institutions for techies, computer geeks, and all-around science, technology, and engineering fanatics. During World War II, MIT’s Radiation Laboratory (“Rad Lab”) was home to pioneering work on inventions such as radar and LORAN (long-range navigation). More recently, it has been noted for work in robotics, machine learning, cybernetics, and the theory and practice of artificial intelligence.
The Rad Lab connection brings to mind the fourth industrial revolution—the electro-magnetic industrial revolution. This was precipitated in 1870, when James Clerk Maxwell built models that unified electricity, magnetism, and light. He is best known for stating Maxwell’s equations—a set of four equations, each of which, somewhat comically, was stated by and named after others. Maxwell’s equations are, in the usual sequence, Gauss’s law for electricity, Gauss’s law for magnetism, Faraday’s law of induction, and Ampere’s law with Maxwell’s correction. These equations have a quirky visual appeal to them, and are popular on T-shirts, with a top caption reading “And God said,” followed by the equations and a subcaption: “and then there was light.” There’s also a poster saying: “What part of” (the equations) “didn’t you understand?”
Maxwell’s equations model the relationships between electricity and magnetism as well as the wavelike behavior that constitutes electromagnetic radiation. “Then there was light” includes not only visible light but also radio waves, microwaves, infrared, ultraviolet, and cosmic rays. The huge success of this unification of two fields of physics set the stage for later successes in unifying the main forces in physics and aiming us toward grand unification theories. Oh, and a very prolific set of civilization-changing inventions, like television, satellites, and cell phones.
It’s hard to overstate the significance of electromagnetic radiation in the ancient evolution of life, ranging from the development of photosynthesis to the genesis of vision, and in the future of nanobiotechnology, running the gamut from photolithography to the creation of optical sensor networks.
However ideologically suited MIT was to an iGEM jamboree, physically the place was a maze, a vast, sprawling assemblage of industrial and anonymous-looking buildings that run for about a mile along the Cambridge side of the Charles River. It takes a while to get spatially oriented to the layout, because at MIT one building looks pretty much like the next, and indeed in many cases several of the buildings physically merge with one another to form a seamless megastructure. As a further aid to confusion, MIT’s buildings tend to be known by number rather than by name (though each does have a name). The total effect on a newcomer is akin to being dropped into a secret government intelligence-gathering complex located in a hitherto undiscovered foreign country. In his book about MIT, Up the Infinite Corridor: MIT and the Technical Imagination, Fred Hap-good observes that the practice of referring to buildings by number fosters the impression that “they were just larger rooms in a single enormous building. . . . Building 7 feeds into 3 and 3 sits next to 10 and 10 next to 4, and so on. A stranger rushing to make a scheduled appointment might think the design calculated to drive him crazy. . . . Any point in the campus seems equally near or far from any other.”
This impression of being lost in space was relieved for some of the 2010 iGEMites by the fact that many of them had been there for previous jamborees and thus they could make sense of the geographical master plan. The tournament started on Friday, November 5, 2010, when 130 iGEM teams, comprising about 1,300 students, arrived on campus for the three-day event. They came from all reaches of the globe and included thirty-eight teams from Asia, ten from Canada, thirty-eight from Europe, thirty-seven from the United States, four from Latin America, and one from Africa. (No longer was iGEM confined to college and university students: the 2010 competition featured a team from Gaston Day School, a prep school in Gastonia, North Carolina. Its project, “Construction of a Biological Iron Detector in a Secondary School Environment,” was to build an engineered organism that could detect high levels of iron in water sources.)
The teams brought an array of biological engineering schemes, plans, and molecular designs that ranged from the whimsical to the incredible, and from the trivial to serious attempts to address global medical problems by means of artfully rewired microbes. A team from the University of Bristol was pursuing “smarter farming through bacterial soil fertility sensors.” A collaborative effort between Davidson College in North Carolina and Missouri Western State University put microorganisms to work on solving the “knapsack problem.” (Given a set of weighted items and a knapsack of fixed capacity, is there some subset of these items that fills the knapsack?) A group from the Swiss Federal Institute of Technology at Lausanne aimed “to stop malaria propagation by acting on the vector: the mosquito . . . We are engineering Asaia, a bacterium that naturally lives in the mosquito’s gut, to express an immunotoxin that can prevent the malaria agent, Plasmodium falciparum, from infecting the mosquito, thereby eliminating transmission of this parasite to humans.”
The iGEM team from Polytechnic University of Valencia, Spain, had a plan to change the climate of the planet Mars. “We are going to build an engineered yeast resistant to temperature changes and able to produce a dark pigment which will be responsible for a global temperature increase on Mars.” (How’s that for redesigning nature?) The team from the University of Washington-Seattle was bent on synthesizing a range of novel antibiotics for the twenty-first century. “Using synthetic biology tools,” they reported, “we designed, built, and tested two new systems to fight infections . . . Our first project targets Bacillus anthracis, the Gram-positive pathogen that causes anthrax.”
The competition got under way at 10:00 AM Saturday, a gray day with a cold wind blowing in from the river. Because the teams were so numerous, and because each team was allotted a full thirty minutes for its presentation, the talks could not be given in a single linear stream, sequentially. Instead, they were split into six divisions that ran concurrently in six different MIT buildings. This meant that six separate groups of judges would gather at the end of the day to compare results and establish rankings.
An iGEM team presentation consisted of a number of essential elements, one of the most important being that the proceeding started and ended exactly on time. The next crucial element was the team uniform, which typically took the form of a brightly colored T-shirt bearing a logo, a bacterial design, and in some cases corporate endorsement patches such as might be worn by an Indianapolis 500 racecar driver. PowerPoint slides, and/or videos, were of course an integral part of things. The final necessary element was frequent use of the word “so” to start a sentence, whether or not the sentence actually
followed a previous one or had any kind of logical, organic, or conceptual relation to it. (This is a verbal tic common to geeks of all types, stripes, flavors, and ages.)
A canonical presentation was offered by the Chinese University of Hong Kong, whose team consisted of ten students, each of whom took a turn in giving a segment of the talk, which was held in 26–100 (Building 26, Room 100). The team’s goal was to convert E. coli bacteria into information storage devices, something on the order of microbial flash drives—or as they called them, bio-hard disks. The group titled its abstract “Bio-cryptography: Information En/Decryption and Storage in E. cryptor” E. cryptor being the team’s name for its designer E. coli microbe, which members also referred to as “a living data storage system” They presented a scheme by which all 8,074 characters of the US Declaration of Independence could be encoded, encrypted, and stored in engineered E. coli, and then decrypted, decoded, and retrieved back as text.
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