Consider Bookhling

(((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.’

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.

Long time no see on the blogosphere. I’ve been busy during the summer with all the usual stuff, mostly learning and working. I’m glad to say that I’ve almost finished the Exploring Complexity: An Introduction book during the summer, and I was even able to get some of the mathematics out of the way. I think I was able to model a pretty neat animation on some of the methods demonstrated in the book, and I’ll try to post it soon.

I’ve also been saving up for going skydiving before the summer’s over… I’ve always dreamed of the skies (my first choice in college education was majoring in aeronautics, never quite made it though), so it’s only natural that I do something that involves full-contact with the air up there. Living on the student budget means that I have to work some extra jobs for that though. Some a bit more crazier than the others.

And of course, there’s always the DIYBio NYC. I’ve been trying to come up with some decent ideas, but everything I can think of at the moment mostly revolves around the kind of project that would require some sort of dedicated labspace. All I can do at the moment is to prepare for that inevitable day when we’ll obtain access to a labspace through independent studies. Some of the things I’ve talked about the members during a recent meeting regarding the state of the group and the processes that are involved in constructing artificial vesicles were very enlightening, and I intend to do a full-length post about that some time in the near future.

On to the main post…

During today’s twitter and identi.ca browsing I happened upon some interesting resources for scientists and potential scientists.

The first one is a collection of links and documents on how to prepare a scientific presentation. I haven’t had the time to read through it yet, but I know some of the posts on the list, and if the rest are like the ones I know, they are definitely worth a read, especially for an aspiring scientist like me. It’s amazing just how many things are involved in preparing a half-way decent presentation, and how most people are just plain terrible at it. I’ve sat through my share of lectures/symposiums/conferences and there’s nothing more painful than a horrible presentation with irrational powerpoint.

The second resource I want to share with you is osgrid. It’s a virtual environment tool like the second life except that it’s opensource. It’s relatively simple to download the environment and run it off your own servers, though it also means that you ‘need’ to run it on your own server for the whole thing to work. I’m really interested in finding out how this environment can be used for scientific research. Perhaps virtual laboratories running off university computer clusters? Open educations tool like a virtual university? A method for scientists to interact with their own 3D datasets in clean and intuitive manner? There are plenty of possibilities out there.

… I can also think of a few ways to utilize some of the stuff for the DIYBio community.