Synthetic Biology on KQED QUEST- and some comments on the diybio aspect

(((I was trying to embed the videos from the KQED site directly in the post, but apparently copy pasting embed code in HTML panel isn’t good enough for wordpress. I’ve linked to them instead. They are quite good. You should really check them out.)))

Here are two videos on synthetic biology. The first one is a short introduction to synthetic biology produced by the wonderful people at KQED QUEST program, which goes into some level of detail on what synthetic biology is and what we are doing with it at the moment. Certainly worth some of your time if you’re interested in this new exciting field of science.

The first video is the original KQED QUEST video on synthetic biology.

The second video is the extended interview with Drew Endy available off their website… While the field of synthetic biology in the form we now know and love probably began with the efforts of Tom Knight at MIT, Drew Endy is certainly one of the most active and clear thinking proponents of the scientific field of synthetic biology.

Here is the link to the second video, the extended interview with Drew Endy.

If you hadn’t guessed yet, I’m really big on synthetic biology. I think it’s one of the most exciting things happening in the sciences today, not just for biologists but for mathematicians and physicists in that synthetic biology might one day provide a comprehensive toolset for studying the most complex physical system known to humanity so far… That of complex life-like systems.

I also believe that abstraction driven synthetic biology cannot manifest without a reasonably sized community of beta-testers willing and able to use the new parts and devices within original systems of their own creation. Computer languages like python and ruby needed efforts of hundreds of developers working in conjunction with each other for a multiple years to get where they are today. Complete operating system like Linux took longer with even larger base of developers and we still have usability issues. Synthetic biology must deal with systems that are even more complex than most computerized systems, so it’s not unreasonable to think that we’ll be needing an even wider deployment of the technology to the public and active community involvement in order to make it work as engineering capable system.

So I am a little dismayed, along with legions of other people who were initially excited by the promises of synthetic biology in conjunction with diybio community, to find that access to BioBrick parts and iGEM competition is severely limited against any amateur biology group operating outside conventional academic circles.

You see, unlike computer programming, constructing synthetic biology systems require BioBrick parts from the registry of standard biological parts. Right now it is next to impossible for diy-biologist interested in synthetic biology to get his or her hands on the BioBrick components through proper channels. The DIYBio-NYC group alone had quite a few number of people lose interest because of uncertain future aspects of being allowed access to the BioBrick parts and talking to people from around the world on that issue I’m beginning to think that there are a lot more of such cases. So far the major reasoning behind the restricted access seem to be the safety issue, but considering that the regular chassis used to put together BioBrick parts is based on academic strains of E.Coli that are even more harmless than your average skin cell I can’t see much wisdom in restricting access to the parts on basis of safety.

The bottom line is, the state of synthetic biology and BioBricks foundation at the moment is forcing a lot of people, some of them quite talented, who are enthused about contributing to a new emerging field of science to back down in either confusion or disappointment. Considering that the very structure of synthetic biology itself demands some level of public deployment to stress-test and demonstrate the effectiveness and stability of its individual parts and devices (with creation of those individual parts and devices left to the highly trained professionals at up scale laboratories) this is highly unusual state of affair that is not motivated by science behind synthetic biology. I might even go as far as to say it has the distinct aftertaste of political calculations of public relations kind.

The field of synthetic biology will never achieve its true potential unless the BioBricks foundation and iGEM administrators come up with some way for people outside traditional academy settings to participate in real design and construction of synthetic biology systems.

Here’s a little bonus, the QUEST show producer’s notes on ‘Decoding Synthetic Biology.’

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2 thoughts on “Synthetic Biology on KQED QUEST- and some comments on the diybio aspect

  1. I think beta testing of registry parts is a terrific idea, and one thing I wish existed on the registry website already is a comments field on the page of each part so that anyone who has used it can write about their experience and share their data. Unfortunately, I think at this point very few people use parts from the registry at all, even iGEM teams and academic labs. I work in an academic synthetic biology lab and was an advisor for an iGEM team and I have never successfully used a part from the registry and my iGEM team I think only used a couple. Right now the registry is more of a dream and a repository for iGEM teams to put their parts, but it isn’t very useful yet.

    It’s going to take a lot of work for a registry of standard parts to be useful, and some of that work will hopefully be able to be done by people outside of traditional labs. At this point I think DIYbio has been doing a good job of showing that they can do things safely and has started to set up getting the kinds of materials you would need to do the kinds of experiments that testing registry parts needs. I think that the analogy to open source software is a useful one, but I think it’s also important to note that the “amateurs” who help build and test the software, while they don’t *have* to be professional programmers often are or at least have many many hours of experience and at the very least a fancy computer. Biology right now doesn’t even have a “computer” that everyone can buy and certainly no manual. This may be where things are going and I think the fact that non-scientists are interested in participating is great.

    Anyway, that comment got a little longer and more rambling than I expected it to, but I’m glad I found your blog and I hope that there can be more of a discussion about this stuff between biologists, physicists, computer scientists, and everyone else.

    • Hi. Thanks for the insightful comment.

      I agree with you. As someone who isn’t from biology background the first thing I’ve learned to do was to treat synthetic biology as a science rather than a skill… So I’m still combing through the introductory biology/molecular biology texts in my spare time trying to figure everything out.

      While synthetic biology and DIYBio seem to be making some strides, what concerns me is the general undercurrent of dissatisfaction among some of the people initially interested in the idea. I think science tend to value the slow and steady approach (especially the experimental branches of sciences) but there are only so many times people can extract DNA from strawberries and make K-12s glow. So right now I’m just trying to figure out what I can do with/for the field from where I am. And you’re right. We need more discussion between the biologists, other scientists, and people outside the fields if we’re to find things to do.

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