User:NKuldell/Q/A working page

see more recent version of these at [[1]]

Disclaimer: This page is a work in progress but it may be a good place for Reshma, Barry and I to collaborate. No one should consider these complete or authoritative.

[JB - Jason's comments in red. Please feel free to delete if they are not helpful as I made several quite anal comments. Just trying to be helpful!] .

Question: How is synthetic biology different from existing, related fields like genetic engineering and metabolic engineering?

In some ways, it's no different. People have been rationally [JB - change "rationally" to "purposefully"?? isnt there also some random modification?] . modifying genetic material for much of recorded history (via breeding and crosses [JB - is crosses a generally understood term?] ). More recently, recombinant DNA technology has permitted the more deliberate [JB - change "more deliberate" to "controlled"? "more deliberate" may be misinterpreted as insinuating that genetic engineering is not deliberate as in not thoughtful/careful] combination of pieces of DNA from different sources. Such technology has, among other things, lead to the general availability [JB - change "general availability" to "cheap production"? general availability does not say whether it is produced, or else if it now grows on trees so to speak - may lead to impression of lack of control] of human insulin. Now, however, we have the additional advantages of full sequence information for many of the planet's organisms AND ways to make the genetic material from scratch. These two technologies of sequencing and synthesis are key enabling technologies of synthetic biology.

Genetic engineering has been focused on making relatively small changes to biological systems. For instance, introducing a new gene into an organism (like insulin). Synthetic biology seeks to start from a "blank slate" and ask, what can we make? Thus, instead of perturbing existing systems and organisms, synthetic biologists attempt to construct new ones. Metabolic engineering can be thought of as a specialization of synthetic biology for the purpose of retooling cellular metabolism for human purposes. Synthetic biology also has applications in other areas like materials fabrication, energy production, information processing and more.

It is important to realize that within synthetic biology, there are different groups pursuing different agendas. Some go after applications. For example, Jay Keasling and colleagues at UC Berkeley have worked to engineer yeast to produce the antimalarial artemisinin cheaply. It is difficult to distinguish [JB - add "Synthetic Biology"] "application" groups from a field such as genetic engineering. The only real distinguishing characteristic is that the current synthetic biology application projects have access to more information and technology, allowing them to tackle bigger problems in a more informed way.

Others pursue enabling technologies (like Drew Endy's or Tom Knight's research groups at MIT). The goal of these "enabling" groups is to standardize the engineering of biology to make it more predictable. These groups borrow concepts from traditional engineering disciplines to enable the construction of multi-component biological systems using reusable and standard biological parts. The belief of these "enabling" groups is that in the long run, this standardized, less ad hoc approach to engineering biology will become the accepted approach to tackling any given application.

[JB - Opinion] These groups are united in their belief in the potential of biology as a substrate for engineering and their agreement that biological engineering is hard and that it must be pursued in a thoughtful and responsible fashion.

Question: Why is biology so hard to engineer now?

NK answer

Currently there is a wealth of sequence information available but limited ways to make experimental [JB - Delete "experimental"?] use of it. Additionally, we have a good understanding of basic cellular activities but only a few approaches to predictably combine activities in creative [JB - "creative" brings to mind trial and error and may raise issues of "playing God", is there a better word?] and re-useable ways. Both imbalances may be rectified through synthetic biology, for example with inexpensive and fast methods for DNA synthesis and with improved foundational technologies for reusing genetic elements. Thus Synthetic Biology brings with it new risks and rewards. It will be easy and cheap to make something not seen in nature, which means it will be done [JB - replace "done" with "possible to use"] by folks who haven’t had the technology of genetic engineering at their disposal.

RS answer

In some sense, the DNA sequence of an organism can be thought of as analogous to a computer program. Reading and interpreting DNA sequence (strings of A's,T's,G's and C's) is just as challenging as reading and interpreting binary code (strings of 0's and 1's). Imagine that someone has given you a printout of the binary code for the Microsoft Windows operating system (without telling you what it is) and asks you what the program does. It would be an incredibly difficult question to answer. Similarly, understanding DNA sequence information is also challenging. In fact, it is an even more difficult problem because at least Microsoft Windows was written by humans in a reasonably rational way. DNA sequences were written by evolution and so our ability to understand them is limited for now. Synthetic Biology seeks to take the next step and actually "write new code" so to speak. Thus, given our lack of understanding of naturally occuring DNA code, it is not surprising that synthetic biology poses a challenge currently.

Question: Who is doing the work today?

I think the answer to this question is imbedded in Reshma's significant improvement to the first question. We can restate some of the info here or delete the question. I prefer the latter. -NK [JB - I vote for restate based on someone's comment in our last meeting that people may read only one question instead of the whole list]

Question: Some people may foresee a day when Synthetic Biology can build complex organisms from basic biological materials. Can simple viruses and primitive life forms already now be synthesized?

Viruses have been synthesized. Life forms, not yet. For example, in 2002 Cello, Paul and Wimmer reported the successful de novo synthesis of poliovirus (Science 297:1016), creating from raw chemicals an agent that could infect mice, albeit [JB - change the rest of this sentence to "in a much less infectious (or virulent?) manner than the natural virus] with a whopping dose relative to the natural virus that leads to infection. The authors described their efforts as “fueled by a strong curiosity about the minute particles that we can view both as chemicals and as “living” entities.” Other examples of de novo synthesis of viruses are the phiX174 bacteriophage reported in 2003 (PNAS 100:15440) and human influenza (Science 310:77) in 2005. Noteworthy are the speed with which these viruses could be made, a mere two weeks from raw chemicals to infectious bacteriophage in 2003, as well as the technology’s potential for dual-use [JB - "dual use" not obvious to me what these are] (e.g. Nature 2006 439:266).

Since viruses replicate only in living hosts, they are not themselves alive. A minimal life form would require self-replicating nucleic acids and a synthetic chassis in which to house them. A front-runner for the former is RNA with catalytic activity, including self-replication as described in 2001 (Science 292:1319). For the latter, lab built- membrane vesicles to encapsulate RNA were described in 2005(J Am Chem Soc 127:13213), but these assemble only through directed manipulations of experimental conditions. Thus, it seems efforts to enclose self-replicating nucleic acids in some spontaneously assembling bubble are underway but, to date, only components of a lab-generated living cell have been reported (http://www.pbs.org/wgbh/nova/sciencenow/3214/01.html)

Question: What questions or applications are being addressed by Synthetic Biology that aren't being explored or built using other technologies?

Some synthetic biologists are combining genomic information and synthesis technologies to re-write [JB - does this mean to rebuild from scratch or to fundamentally alter?] the genetic code from living creatures. Just as computer programmers might want to re-write the code for your PC, these synthetic biologists annotate their changes to the genetic program of the system they are studying with the hope that each element of code may be more manipulable and human-readable. Successes on this frontier include refactoring T7 [JB - ?? I have no idea what this means, although I can certainly follow the link so maybe that is ok] [2], two genomes in one cell [3] and characterization of a minimal E coli genome [4]. Other successful efforts in synthetic biology involve metabolic engineering of simple organisms like bacteria or yeast, enabling future production of therapeutics or compounds whose natural reservoirs are in short supply. A recent noteable success in this effort is production of artemisinic acid in yeast [5], an acheivement that may allow cheap and clean production of this precursor for an antimalarial drug. Finally, synthetic biology can provide a framework for discovery-driven biologists who might like to test their existing models by building them from the ground up. These efforts are reminiscent of those in chemical engineering, where the step-wise synthesis of a novel chemical compound is used to convincingly demonstrate a complete understanding of its chemistry. Along these lines, synthetic biologists have recently published a framework for characterizing interactions of novel synthetic transcription factors [6] and have applied this framework to determine if other synthetic proteins interact in a parallel manner.

Question: What are the perceived benefits of synthetic biology?

not sure this is appropriate ... but I thought it was important info?

Biology has several features that are difficult or lacking in other engineering mediums including

1. Biological systems can manufacture materials and chemicals on a very small scale.
2. Biological systems can evolve.
3. Most importantly, biological organisms can self-replicate.

These properties imply that biological engineering ought to yield novel systems capable of operations and behaviors not achievable by other methods. For instance, systems that can exist and interact with the environment (perhaps sense a toxin or pollutant) and respond appropriately (metabolize the pollutant into a nontoxic product).

Question: Who is investing in this and what do they see as the pay-off?

Currently much of the investment in the field is from the venture capital community into startup companies (e.g. Codon Devices). Codon Devices' goals are "in the short term, product opportunities include comprehensive sets of biological parts for large-scale research projects, engineered cells that produce novel pharmaceuticals, engineered protein biotherapeutics, and novel biosensor devices. In the longer term, the company's core technology is expected to enable improved vaccines, agricultural products, and biorefineries for the production of industrial chemicals and energy." [cite] Synthetic Genomics, Inc., another startup by J. Craig Venter, believes "there are potentially limitless applications for synthetic biology/genomics, everything from energy to chemicals to pharmaceuticals. In the near-term, we think that synthetic genomics has applications in the areas of cleaner and more efficient energy production, specifically in the production of ethanol and hydrogen." [cite]

The European Union has also made research in the field of synthetic biology a priority with specific funding initiatives. pdf The purpose of this funding is to stimulate science and technology research in the EU. The nonprofit Bill and Melinda Gates Foundation has made significant investment in efforts by Jay Keasling and colleagues in synthesizing large quantities of the antimalarial artemisin . Their motivation is to solve critical world health problems. [cite].

Thus the groups interested in synthetic biology span industry, government and nonprofit organizations. Each see a wealth of potential in the field but are interested in different application areas.

Question: Why would someone invest in this area as opposed to more traditional genetic engineering efforts?

Genetic engineering has been focused on making relatively small changes to biological systems. For instance, introducing a new gene into an organism (like insulin). Synthetic biology seeks to start from a "blank slate" and ask, what can we make? Thus, instead of perturbing existing systems and organisms, we attempt to construct new ones. In having a wider scope for engineering biological systems, the potential application space of synthetic biology is similarly wider. One could imagine systems that range from chemical manufacturing to systems that monitor and respond to the environment in real time.

Question: While their methods are different, the end results of synthetic biology and genetic engineering seem similar: new organisms that are not seen in nature. If that is true, does it follow that synthetic biology is not bringing substantially new risks onto the scene?

The risks and rewards are likely different. If synthetic biology is wildly successful then one can imagine a time when "garage inventors" could build something cool [JB - change "cool" to "useful"? the ides of someone building something they consider "cool" is a bit frightening to me, since my idea of cool may be very different from say the Unabomber's] with biological materials. Genetic engineering, as it’s currently performed, requires substantial technical understanding of the project and access to specialized resources such as a laboratory and reagents. In the future, novel biological systems may be built with limited know-how, on a minimal budget and with no requirement for a specialized facility. Such democratization of biological engineering necessarily brings with it both the possibilities of a great number of useful applications as well as risks from accidental or intentional misuses. Thus, one of the key missions of the nascent synthetic biological community is to forge a culture in which biological engineering happens responsibly.