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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The Whole Foods CEO on Universal Health Care

Universal health care seem to be the hot topic these days. There are lots of arguments flying around on both sides of the health care reform and universal health care in America, some of them more reasonable than the other.

Well, I just though I’d share an interesting article I read on Whole Foods CEO John Mackey’s editorial on the Wall Street Journal. Apparently, the CEO argues that the constitution does not make guarantees on the life and health of the individual citizens, so it’s not the business of the government to get involved in health care. He alternatively suggests that people buy and eat from Whole Foods market for preventive health care.

Now mind you, this is a blog post by a college student (with our infamous liberal leanings) with a bitter memory of childhood torn by his father’s kidney transplant surgery. So yes, I’m all for universal health care. It wasn’t‘ easy watching my mother trying to pay $4700 per month hospitalization fee during my father’s dialysis period, and it wasn’t easy selling practically everything we owned to pay for his surgery.

There’s something really odd when I hear people talking against universal health care. What’s exactly bad about it? Most other developed countries in the world have it like Sweden, Japan, and Germany, and they seem to like it. I experienced it first-hand when I lived in South Korea, and I liked it too. With the billions (if not more) the U.S. government’s already spending on health care insurance companies, it should be possible to run some form of universal health care in this country as well… And yes, you’re reading this correctly. The U.S. government already spends quite a sizable amount of money on health insurance companies. In fact, U.S. government spends the most amount of money on health care out of all the developed nations in the world, and has the least number of people covered with least life expectancy out of all the OECD nations. Something a lot of those people at the ‘town hall meetings’ seem to conveniently ignore.

But that’s not all. If it’s a simple matter of getting the data out most people out there should be proponents of universal health care system by now. If they were actually interested in providing good health care, whether private or government mandated, they should be combing through the proposed health care reform bill pointing out excesses (I’m sure there are some) in the list and pointing out improvements. But it’s not happening. The most extensive combing-through of the health care bill done by its opponents so far concentrated on the clause on hospice care counseling, labeling it as ‘death panel.’ Well from what I’m seeing the same hospice care counseling is included as a part of standard employee coverage package from many private insurance companies (in this episode of the Colbert Report, the UHC proponent Jonathan Cohn points out that employees of the Colbert Report show are all covered by contracts with the so-called ‘death panel’ clause).

The opponents of the health care reform seem to be against the ‘idea’ of any kind of change made by the Obama administration regardless the real benefits or disadvantages resulting from the change… However, do they truly believe that low confidence in certain regime and certain political characters is enough reason to reject a bill that might end up saving thousands if not millions of lives in this country? Are human lives so fickle and worthless that they can be thrown out for the sake of political rhetoric?

Then there are people like John Mackey. The kind of people who believe that government has no business ensuring the well-being of its citizens. Such arguments usually go hand-in-hand with the kind of low-brow, thinly veiled suggestion that people who cannot afford conventional health care, notably the ones in lower income bracket, are probably not worth helping. While such notion might work with running a corporation, it would be a mistake to think such attitude scales to the level of national governance. Maybe Mr. John Mackey leaves mess around his house. Maybe Mr. John Mackey like to target practice in his personal property. Such behaviors are perfectly legal in his own personal microcosm. However, if Mr. John Mackey applies that same behavior to public properties by leaving garbage around the City Hall offices and performing target practice in the crowded Times Square… The results would be disturbing.

If there’s one thing I’ve learned during the history courses through my high school years, it’s that nations come and go. Contrary to some popular belief there is no natural law that states the United States of America will exist regardless of how its members treat each other. This nation only exists because there is a united will and cycle of trust and responsibility. If a national government that collects taxes and enforces its codes of law cannot take care of the very basic well-being of its citizens, why should they be loyal to the country? Never mind the capacity. If the government does not even have the will to safeguard its citizenry why should they be loyal to that government? Why should they go out to wars and die to protect that country? It’s a very simple matter of loyalty. If the government itself insists on not providing for its citizens certain level of amenities required for the very basic act of survival (we’re not talking about luxury condos or spa vacation here, folks. Just staying alive), the said government cannot possibly expect the same citizenry to follow its rules of law, perhaps except through application of force. Sensible people usually call that oppression. Sensible people don’t kill people and rob stores because they are scared of getting hurt in the process. They don’t do it because it’s morally objectionable, and because they have faith in continuation of the society in which they are members.

I am profoundly disturbed by some people coming out of the woodwork for the universal health care debate, by their blatant lack of respect for human dignity and lack of concern for the well being of their fellow human beings… And in the case of Mr.John Mackey, the horrible financial sense in suggesting that buying overpriced groceries is a replacement for genuine health care system.

Japan: Robot Nation

Here’s the link to the documentary in full at current.com. It’s about twenty or so minutes long (why is it so hard to embed video on wordpress?).

Unlike some other (let’s be honest. Most other) Japan/robot documentaries, this one focuses on the social conditions leading to the Japan’s apparent love of robotics. It sheds something of a harsh, yet realistic view on the state of Japanese society and their labor market, something I am somewhat familiar on indirect level through experiences of those close to me.

I only wish the documentary was longer. They had a lot of venues to explore in depth, Japanese society being one of the most complex human organizations around these days (but then, aren’t all human organizations complex?).

They briefly mention the difficulty foreign immigrants (even those of foreign-heritage native to Japan) face in mainstream Japanese society. Caucasians get an easier time though, especially if you’re rich and hold a professional job. It must be noted though, that while Japanese society have issues the individual folks are pleasant enough, friendly people.

I wonder what the venerable leaders of the United States are planning in preparation for the incoming onslaught of robotic workforces?

DIY synthetic biology

Just a short note about a cloning kit developed by Qiagen and Invitrogen. Will this be a first step in signalling the trend of the industry toward relatively freely available bio kits for DIY synthetic biology? I certainly hope so. Disposable lab kits packaged for small-scale labs and private hobbyists might prove to be a lucrative market in the near future once more universities get around to introducing synthetic biology curriculum to their students.

Of course, a number of such kits had been available for smaller scale purchase before, but I find this one significant in streamlining of the process, inclusion of ‘directions’, and appearance in mass-media outlet like the wired magazine… Some of the problems plaguing the field of synthetic biology at this point is the problem of general appeal and accessibility (other than the usual technical issues), and this might be beginning of an industrial trend in fixing it through the ‘hand of the market.’

Synthetic biology, being a biotechnology of information, will benefit greatly and show rapid growth from industrial level support. I can’t even begin to talk about the benefits of biological economy, and many in the field of economics and biology seem to agree on that issue.

There are some who are voicing concerns about streamlining of technology involved in the general biotechnological process pampering the scientific community, but I find such arguments rather shortsighted. The technologies available to us at the moment are not perfect. If we can’t get minor technical details out of the way of the real pursuit of science, the field of science as a whole will remain on the fringe of the human civilization. The pressing need here is to broaden the field and scope of the science itself so that the average layman might apply him or herself along with the traditional scientist population. Such a change will be able to trigger a whole spectrum of economic and social changes in creation of jobs and specialties, with more even distribution of knowledge which will further the advances of humanity as a whole.

No matter how much I’d like to deny it, advance of science is intimately linked with fostering of proper economical and sociocultural environment for such a change.

I will post more on the matter as I go along.

Synthetic biology

I’ve been looking around the synthetic biology scene for a while now. Although my academic specialty doesn’t revolve around the field of biology, I try to keep at least an amateur’s perspective upon the advances and techniques of the field. Considering that my passion lies in the study and realization of artificial life I find it important to keep broad view of things irregardless of specialty or the immediate requirements of my own job.

I’ve often noted that the field of synthetic biology had suffered quite a bit of misunderstanding since its inception (which wasn’t that long ago actually), so I thought I might as well do a little write up of what synthetic biology really is.

Synthetic biology is an approach to engineering biology instead of being an academic field of specific goals. Simply put, synthetic biology as a whole is an approach, which may be utilized toward a specific application dictated by the case/individual/group etc.

In order to become a tool in engineering biology its link with conventional genetic engineering is inevitable. The breakdown of the similarities and differences between synthetic biology and genetic engineering is as follows.

Conventional genetic engineering is composed of three primary stages.

1)Recombinant DNA

2)PCR (stands for polymerase chain reaction)

3)Automated sequencing

The step one and two are about writing the DNA of specific purpose, and the step three is about reading the recomposed/component DNA. While these three steps are integrated to the core of the field of synthetic biology, it includes three more stages which differentiates it from pure genetic engineering.

4)Automated construction of DNA

5)Standards

6)Abstraction

The fourth stage, automated construction of DNA refers to the divide between the designers and builders of the DNA. Within the structure of the synthetic biology the designing of a DNA sequence and actually working in forming such DNA sequence (which is an expensive and time-consuming process) is separate from each other, making student-amateur oriented biological machine design possible within currently existing technical/industrial infrastructure. However, simply having a separate industry deal with mechanical parts of the synthetic biology would be meaningless without stage five and six, formation of standards, and abstraction of genetic interface. The last two stages run along the lines of the advance of computer programming scene, where formation of standard (html) and abstraction (most users don’t type in zeroes and ones anymore. We click buttons) brought on an explosion of global userbase and subsequent integration of the computerization into the very fabric of modern human civilization. Synthetic biology as a field encompasses all the six stages I’ve written about so far, each of them an integral part that reinforces another. In a way, synthetic biology is intimately linked with the garage-biology or biohacking movement in that it allows individuals to focus on designing their own novel biological contraptions using freely available and globally present database of biological/genetic abstractions and standards, while leaving the complexities and drudgeries of bioengineering to the mechanism of economy/industry.

I personally consider the field of synthetic biology to be a movement. Nothing as pretentious as some political gather-up, but a real movement like a wave spreading across the surface of the human society, a tell-tale sign of something gigantic beneath the surface. People used to build computers in their garage. Look where we are now. I can’t begin to imagine to full impact of well-executed synthetic biology as movement/industry/economy in the course of the future. Many little children these days are aware of tools like python and java, and some of them even utilize them with surprising efficiency and familiarity. Imagine the same children in the future, not with imaginary numbers but with the stuff of life. A little risky, but it’s certainly the type of world I want to live in.

What I also find to be interesting is the method of thinking behind synthetic biology. I don’t know how to put it succinctly yet, but as I have noted in the previous write up ‘transhumanism and the human network’, there is an underlying method of thinking that is showing up in universal scales, regardless of locale and cultural background. Am I correct in assuming this peculiarly wide-spread method of thinking as a type of zeitgeist? If so, where and how did it originate? And what role does the human network and its emergent properties take in the shape of the world we live in?

Maybe, once the biological hacking is done, the little children will hack the human civilization itself.

For those of you interested in slightly more detailed insight into synthetic biology, I give you two links.

www.openwetware.org

The openwetware website, definitely worth a look.

http://openwetware.org/images/3/3d/SB_Primer_100707.pdf

A simple primer to synthetic biology, covers the basics so it applies to other fields of biology as well.