Word on the street from Synthetic Biology 4.0.. take a word or leave a word.
- Venture capitalists and private investors are very interested in synthetic biology. Significant buzz in the Bay Area regarding the term. Large capital is required when making the transition from proven concept to, for example, a pilot plant for biofuel production. Venture capitalists love to get excited because it’s their job to both get themselves excited and get others excited (excited enough to give them loads of money).
- As on day2, a laboratory-proven “built from the ground up” organism (a thing, separate from other things, that eats, replicates, grows, and divides) may only be years away.
- Very innovative solution proposed to slow the rate of spreading HIV, using synthetic biology to create a “get-the-HIV-away” preventative medicine. Seemed very well received as a different track than current antiviral cures.
- No one really knows how to model cells or modified cells. (Again)
- An interesting group at Cal Tech has proposed a method of designing, or compiling the design by converting a hardware netlist into DNA sequences, combinatorial logic which has unique signal outputs, thus eliminating the cross-talk problem; theoretically modeled up to 1,000 gates, currently tested up to 4 gates.
- A cynical undergrad says that engineering biology will never work and will never be able to be modeled; though he has an iGEM project.
- A Hong Kong local university biology professor also mentions that engineering biology will never work; it is too unreasonable to expect biology to behave under known rules: “biology is not like that.”
- The word “never” in both cases might be very surprising to some, especially coming from two people in the field, one of whom has built Biobrick device(s).
- “DIY Bio is real! Bio can be done as a hobby! We want to let amateurs hack biology just like scientists do! We need to apply rules to make it non-biohazard, and then just do it.”
- Strongly contrasting opinion to the “it will never work” biologists.
- Cells can be made to change shape dramatically with specific (laser) light input. Very freakily amazing video.
- Which opinion is more correct, that engineering biology will work or that it doesn’t or where we fall as of right now?
- Drew Endy: “The truth is somewhere in the middle. Years ago, we had a lot of iGEM teams, and nothing worked. Last year, we had let’s say 100 iGEM teams, and 10 teams had working devices.” I conclude, the engineering process is improving through lab experience and raw data feedback. Engineers eventually make nearly anything work (just ask Scotty).
- Reshma Shetty (now at Ginko BioWorks): “It takes about 3 years to ‘get it’ [collect enough experience to be successful at creating biological devices]. Everyone seems to struggle until then.”
- More back & forth related to the licensing issues of an “open source” biological library.
- The Bay Area may have an accessible “Bio Fab Lab” in the years ahead, funded by public sources and aimed at improving the “open source” biological library.
- Even the venture capitalists and synthetic biology company owners get history wrong; mistakenly stating facts. “This is like the IBM PC architecture, completely open, and enabling things like the open source movement later”.. Wrong!; in fact, the IBM PC was completely locked down and very proprietary and backed by lawyers from the huge deep pockets of IBM — it was Compaq who, through a legal process of reverse engineering to work around the patent and intellectual property process, completely cloned the IBM PC firmware to a compatible version, thus inventing the clone-PC market (while IBM vehemently objected and litigated against). Please read the history books (I would suggest Hackers, by Steven Levy, as a starting point). Most of the “this is like open source with computers” analogies are.. well.. off by a factor of two. At least a factor of two.
All quotes above are not to be taken literally. Any resemblance to actual persons is entirely coincidental. The contents of this article and this web site (web log) are Copyright with All Rights Reserved. No content may be used without explicit written permission. (This is to prevent quoting out of context.)
For those who aren’t familiar with synthetic biology, I will quote the Synthetic Biology 4.0 web site:
What are the applications of Synthetic Biology?
BioEnergy. Cells are being engineered to consume agricultural products and produce liquid fuels. British Petroleum and the US DOE granted $650 million dollars for research in the San Francisco Bay Area.
Drug Production. Bacteria and yeast can be re-engineered for the low cost production of drugs. Examples include the anti-malarial drug Artemisinin and the cholesterol-lowering drug Lipitor.
Materials. Recombinant cells have been constructed that can build chemical precursors for the production of plastics and textiles, such as Bio-PDO and spider silk.
Medicine. Cells are being programmed for therapeutic purposes. Bacteria and T-cells can be rewired to circulate in the body and identify and treat diseased cells and tissues. One such research program is the NIH-funded Cell Propulsion Laboratory at UCSF.
Synthetic Biology is a new approach to engineering biology, with an emphasis on technologies to write DNA. Recent advances make the de novo chemical synthesis of long DNA polymers routine and precise. Foundational work, including the standardization of DNA-encoded parts and devices, enables them to be combined to create programs to control cells. With the development of this technology, there is a concurrent effort to address legal, social and ethical issues.
How is this different from genetic engineering?
Synthetic Biology builds on tools that have been developed over the last 30 years. Genetic engineering has focused on the use of molecular biology to build DNA (for example, cloning and PCR) and automated sequencing to read DNA. Synthetic Biology adds the automated synthesis of DNA, the setting of standards and the use of abstraction to simplify the design process.
Hi Jonathan
I was on the VC panel and don’t recall anyone talking about the PC architecture resulting in free and open source software. In fact, I was the one pushing very strongly on the need for free and open source biotech and have never used the genesis of the PC architecture as an argument for the ultimate success of open source biology.
I don’t know if you were referring to me in particular, but to be clear, what I did say was the commodity hardware plus commodity software have had radical implications for global productivity, from software and service companies to brick and mortar businesses. Whether this is the results of an explicit vision and plan or via the twists and turns of history, it remains a fact.
Free and open source biology will be a very difficult and long goal to achieve, but I believe that the biotech industry it will converge on it as a foundational platform in the same way the IT industry has.
I’d be happy to chat more about this if you’d like.
talli
Re: talli –
Better productivity – yes!
Open access to research & design for accelerating innovation – yes!
Preventing unhealthy monopolistic practices and allowing skunkworks to thrive – yes!
Ending patent/IP lockup – yes!
No worries; it wasn’t you I was paraphrasing.. (though in reality it doesn’t matter who said what, as long as effort moves forward)
Regarding moving towards creating a real model for public domain science: Carlson additionally made a remark in the other technical session (paraphrase): It’s curious that “open source” licensing has caught on, while use of “public domain” (non-)licensing has faded.
Many — including myself, depending on the project — are willing to altruistically / hobby-istically donate time & effort & resources for bio projects. These altruistic efforts shouldn’t come with a forced mandate that: “you can use this but you MUST share all subsequent efforts.” This is the bad viral aspect of GNU (“copy left”) which should be avoided. It limits commercialization and stifles innovation. One question to ponder is: why is it called open source biotech; why not “public domain” biotech?
I prefer public domain-style licenses. My open source projects have been BSD-license. Build it and give it away free, without any stipulations on later usage. This allows both altruist and commercial efforts to benefit from the innovation in parallel.
The biotech industry might be better served by using the term “public domain”. It eliminates this confusion regarding viral-source (GPL) licensing -vs- commercializable (BSD) licensing.
The other issue is how “free biotech” can be made free, when reagents cost so much. Software is free to modify or copy. Biology costs a lot to modify or copy. We definitely need to figure out a good way to fit public domain into this ecosystem. I’ll write more on this later.
Hi Jonathan
Thanks for the response. I thought that you might be referring to someone else but I wanted to make myself clear.
I actually am of a different opinion regarding “free as in speech” vs public domain licenses. It’s a rather deep philosophical question that people have been debating for a great while; which is the more important freedom, that one which maximizes the freedom of the individual or of the collective?
The most effective theoretical tool that I’ve seen to delineate between the two is the distinction between positive and negative liberty. The GPL is a positive license in that asserts limitations on the use of the software and compels the user to participate as a member of a community. BSD-like (and public domain) licenses are negative licenses since they allow the user to do as they please with the code (the user moves in a “negative space” of limitations).
In my opinion and experience, the GPL is successful precisely because it is positive. It provided a framework by which developers felt they were protected to produce and release software without someone taking advantage of them. After a while, their cumulative production added up to something that was so compelling industry could no longer ignore, compete or do without their work. It’s hard to argue today that GPL licensed software is not responsible for billions of dollars worth of wealth and commerce.
For biotech, the reason why a free software license is important is not because we are business unfriendly (I do have capitalist in my job title after all!) but because we need to create a similar environment as the early days of the free and open source software movement. We need to have developers feel that they have enough room to produce their product, release it to the community and not have their work co-opted or used against them.
All good points. The word choice of “positive” -vs- “negative” is unfortunate though, it biases the discussion — better to call it “regulated” -vs- “unregulated”. I believe public domain licensed code could be considered more successful than viral-license (GPL) code. I am typing on an Apple Macbook — which is based on BSD unix, as it is completely open and compatible with commercial innovation — and could never be based on GPL source like Linux.
If you really want to create a similar environment to that which spawned the public domain, shareware, freeware, open source movement, then you need a mighty (and greedy, and antagonistic) enemy, as mighty as Microsoft was and is, and as mighty as AT&T was. Only that environment created sufficient technology pain to give birth to the original “open Unix” movement, and subsequent Linux movement. I don’t think anyone wants that part of the equation.
I’ve seen both sides of the problem in open source from the inside:
– Investors aren’t about to release intellectual property (source code) into the public domain which has even the slightest statistical probability of someday being worth something: this creates technological stagnation because the unused intellectual property is locked up. (One of the dramatic front-runners was Carmack, who supposedly fought his own board of directors for many quarters, until the original source to Doom was released to the public. The eventual effect was more sales.)
– Investors aren’t about to significantly improve on public intellectual property if the IP comes with viral terms which infect a significant portion of the investors’ technology. The result is also technological stagnation. A product which could be improved is not improved, because the open source license prevents improvement. Even middle-managers are quick to say: “There’s a GPL issue? Then forget it. Let’s add value in some other way.” This continues to be an issue with the Linux kernel, for example, where many and significant improvements could be made to add value to products, but can’t be made, since the kernel authors continue to limit the ways that industry can simultaneously improve the kernel and keep some trade secrets. (Linking proprietary code into the kernel is a violation of GPL, so kernel modules are “tainted”. More kernel symbols continue to be marked as GPL symbols, meaning the function can’t be referenced at all without tainting code.)
I do see the middle ground as the BSD-like license. This allows altruistic corporations to give back and freely innovate. It also allows greedy corporations to stay secretive. The “positive/negative liberty” assertion assumes that all corporations will remain greedy. It doesn’t enforce regulation, and assumes corporations will do the right thing. This is obviously too “free” for some altruists.
GPL gains much press because of the media and it’s legal issues. I believe there are far more success stories related to BSD-style commercialized products than most people imagine; the big difference is that no one hears much about them, because they don’t create such dramatic legalistic issues, and the corporations aren’t forced to admit the use.
Significant portions of the “network storage SMB market” was created from BSD-style operating systems — allowing the storage market to significantly reduce costs and innovate (ultimately becoming products like Apple’s “Time Machine”). OS/X is the most advanced operating system in the world for the same reasons — much improvement remains secret, though some amount of improvement remains public.
The most common basic cryptography is public domain. Secure http could have been technologically delayed by 10 years if a public library of code (with non-viral license) hadn’t existed. 10 years might seem lengthy though it’s an easily created delay due to technological standards-fighting..
Cisco also recently switched to using only BSD code (no more GPL or Linux) because innovation and any ability to add value (proprietary technology) would be stifled under a GPL viral-license. At least, that’s how I interpret their switch — I only know they switched (or are in the process of switching). This is a major business decision in terms of capital resources, so shouldn’t be taken as only a “at the water-cooler” decision.
Anyway, following on the “mistake” in Greenspan’s (and nearly everyone’s) philosophy that a free market has the intelligence (and/or foresight) to regulate itself, perhaps we can rightfully say that MORE corporations do need the forced regulation of viral-GPL, because the corporations would otherwise never open any portion of their property. Thus, added regulation (viral licensing) forces the market to become more open. Just be aware that this approach, too, creates technological stagnation.
Altruists who give things away for free yet claim subsequent users must also be altruists are like 6 year olds crying they didn’t get enough scoops of ice cream, a product of bitter academics. “I suffered under substandard wages for years trying to find the cure for malaria, so you aren’t allowed to make any money related to any of the technology either!” That’s an exaggeration, though it highlights the point.
It would be better to discuss specific points.. leave the philosophy for the soft scientists. What does opening biotech mean; given that the sequences themselves are already forced to be public domain. Forced-public (viral license) publication for new & existing protocols? A halt on patents for biotech methods? openwetware.org for all corporate use?
I invite you to check my current project, knowing that it’s completely open, no patents current or planned, and has definite potential for commercial application. Google “melaminometer”. On this project, I’m an altruist making no wages and I don’t mind if others profit on my work (that means I wasn’t fast enough myself). It would be better to know which specific portions of this or any project should (or could) remain secret or become open, in order to benefit bringing it to market (leaving aside a profit consideration and only looking at the single fact: would/could it get to market, yes or no).
Traditionally, everything remains secret (proprietary), even public information — after slight rewording — is transformed into secrets. Since we aren’t after traditional models, then… what.
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hello
the phrase synthetic biology caught my attention, so i thought i’d wade in.
i’m an organic farmer, its a job you grow into. to me the term sythentic biology means just that… artifical..not of this world..a thing created by man. that we should except this a fact and disscuss our common future in terms of cause and effect leaves me stunned. is there no realization that all this is being done in the name of money,and not our common future. we are a domocray, why do we let money determine our common future.
gotta be the chemicals. wayne
Re: wayne –
Many of the synthetic biology research is aimed at medicine and health. New antibiotics have to come from somewhere! “Amyris Biotechnologies” is a good example of this succeeding — and they didn’t pursue the antibiotic for malaria for only big-profit motives — the researchers were very genuinely interested in solving a dangerous world health problem.
Personally I would like to see synthetic biology used to improve nutrition. Many vegetables (like sea vegetables) are very nutritious although they taste bad to most people (including myself) — wouldn’t it be great to give these plants a better taste & smell so it would be more satisfying to eat? I think so.