First DIYBio rant of the year

I can’t believe I’m uploading the first post of the year in March. Still, better late than never to show people that I’m still alive and kicking. While I haven’t been able to think about personal writing due to deluge of job and school related stuff I’ll try to keep things more organized in the coming months. If half of what I hope comes true this coming year will be the most awesome so far, for myself and for other activities and organizations I believe in.

This post is, like it says in the title, a rant post of what DIYBio ought to be and how I plan to do my part this year. It’s also written on my blackberry which I later copy-pasted into the wordpress… I just hope half a year of writing boring technical stuff didn’t burn out creative writing part of my brain. I’ll be using it a lot from now on.

Year 2009 was series of exciting experiences, with ISFF, DIYBio and iGEM jamboree. I’m trying to pan it out into this year without losing momentum, through activities like synthetic biology crash course for beginners, various internships and private research projects. Hopefully I’ll have more time to write about them in the coming months.

I’ve been thinking a lot on diybio, about what it’s supposed to be & what it needs, and I think I’ve arrived at some sort of conclusion.

DIYBio must inevitably find the way to bridge the gap between the enthusiastic members of the public and tools and devices that makes synthetic biology feasible. While there are many members out there who seem to work toward specific gadgets and other physical tools of biological experiment, I think we still need something more.

DIY or not, biology is a science. If we want to bring hard science to the public with aid of ever cheapening yet sophisticated lab equipments we need to look beyond the hardware.

I’ve written quite a few times about Alan Kay (on this blog and elsewhere), the pioneer of modern computer programming/interface paradigm and his relationship with synthetic biology… There are mountains of information on him and his works that are relevant to the discussion of models in biology and how they might be used to organize information, with emphasis on education as a sort of interface between data and human mind… All of which are beyond the scope of this particular post.

The important point is this. I believe true potential for diybio is to bridge the gap between the complexity of bleeding edge science with the innate human ability to learn and tinker. And the main tool in making it happen is idea, not low cost lab tools (the costs of the lab tools are coming down anyway. Why DIY every single appliance when you can buy a used one that works just as good, oftentimes even better?). While low cost lab implementations are important, the true future lies with the ability to abstract and package/rebuild complexity into something much more manageable.

Some people seem to have difficulty understanding what I’m trying to say from the few times I’ve tried to talk about… I’m talking about reviving and revising the notion of knowledge engineering, something that was supposed to be the corner stone of true computer revolution that never really took off (google and wikipedia are some remnants of the original idea).

Synthetic biology is a good example of what knowledge engineering coupled with physical science might be able to achieve. None of the specific pieces forming what we perceive as synthetic biology are new. They’ve been around for quite a while in one form or another following course of gradual improvement rather than truly new scientific advance.
Synthetic biology at heart is about how dedicated professionals can organize scattered pieces of knowledge into something that can potentially allow ambitious undergraduate students to undertake projects that would have been beyond their ability a decade ago. Never mind the actual success rate of their projects for now. They very fact that those students are able to plan for the future with much broader sphere of possibility is significant enough.
And why stop with undergraduates? Wouldn’t it be possible to have motivated high school students design something that at least works on paper? Wouldn’t it be possible to build a conceptual framework so that those kids can at least discuss possibilities of future projects on back of a napkin without resorting to sci fi?

If diybio is to do what it originally set out to do, we need to look beyond gadgets and tools. We need to think about ideas and how they come together… We need to make biology easier, not just cheaper. This is the mantra that will drive my DIYBio related activities this year.

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Alan Kay applied to synthetic biology, and other stuff.

This is something I wrote up a few days ago, probably around four or so in the morning. So take whatever it says with caution.

I know I should be writing about some other things as well, like how the diybio nyc might be amazingly close to getting a real lab space, or how I’m prepping to stop by for this year’s iGEM jamboree. I also have the pictures from this year’s major diybio nyc event, where we set up a stall on the NYC green market and extracted dnas from the natural produces with common household material (with the passers-by of course). Each of those things would probably make for some lengthy and interesting reading, and the list goes on (my life’s actually kind of exciting right now). Yet whenever I find the time to write something down, nada. Nothing. My mind just shuts down and nothing I can commit to paper or the keyboard seems good enough.

Tonight though, aided by my weird bout with insomnia, I’ll just write something down I’ve been meaning to say for a long time.

I’ve been looking into the history of computing and computer languages recently. I’ve always had some level of interest in computers. Not just the spiffy brand-new muscle machines but in what most people would refer to as ‘retrocomputing’ (I once ended up practicing some AIDA because of that. Ugh), which is a story for another time. It’s not that I think old ways of computing were better than what we have now (protected memory FTW). It’s just that it’s much easier to trace the evolution of the concept of computing when you see beyond the immediate commercial products.

Synthetic biology is effectively a pursuit of engineering biological organisms. Biological organisms are based upon somewhat unified information storage and processing system that has quite a bit of parallels to mechanical computerized systems. I’ve been wondering whether it would be possible to predict the future development of synthetic biology by looking at how computer programming languages evolved (because they deal with information processing systems applied to physical counting medium). Maybe it’d be possible to predict some of the pitfalls that are inherent in developing complex programmable information processing system that will apply to the synthetic biology in the future. Maybe we can bring a conceptual framework to the synthetic biology that would have taken decades if left to mature naturally to within mere years.

While I was rummaging through the texts in both real life and the web (with many of the promising links on the web leading to dead-ends and 404s) I ran into a programming paradigm and environment I was only superficially familiar with before. Smalltalk and Squeak, both the brainchild of the computing pioneer Alan Kay.

Here’s an excerpt from Alan Kay’s biography I found on the net (I can’t find the website right now. I swear I’ll edit it in later, when my brain’s actually working!)

“Alan Kay postulated that the ideal computer would function like a living organism; each “cell” would behave in accord with others to accomplish an end goal but would also be able to function autonomously. Cells could also regroup themselves in order to attack another problem or handle another function.”

This is the basic philosophy behind smalltalk/squeak and object oriented computer programming paradigm. It is no coincidence that Alan Kay’s vision of the ideal computer language and computing environment would take to a biological allegory, since he came from molecular biology background.

While I’m reading through the history of different computing paradigms for the purpose of figuring out how it might be applied to synthetic biology, there’s something else I found awesome and perhaps a little heartwarming. Alan Kay throughout his life as a computing pioneer held onto the belief that the ideal computing platform won’t be a platform capable of crunching numbers the fastest. It will be a platform that can be integrated into the educational function of the user through ease of manipulation and control. Ideal computing platform should be hackable because it makes logical sense to do so.

Can we say the same of synthetic biology? Perhaps not. The direct comparison of a complex biological system to computerized circuits can only take us so far. Yet I can’t shake the nagging feeling that synthetic biology might be looking at some very unique opportunities for change precisely because it is different from regular electronic systems, with documents of the early days of computer and programming already here for our perusal.

A good, elegant system that allows programmable extension must be at the same time easy to learn, since one thing must inevitably lead to the other. And there are classes of systems that both run and learn better compared to other systems. This might become something of an issue of how synthetic biology parts/devices/systems are put together in the future as the capacity of the synthetic biologists to handle complex systems increase.

I think it might be able to pursue this idea further. As it stands this is nothing more than an interesting parallel in concept without substantial scientific reasoning.

Which is why I should get myself to learn smalltalk/squeak sometime in the future. Maybe I should knock on the hackerspaces in the city, see if anyone’s willing to mentor me.

Imagine science film festival

Just a quick note before I doze off for tomorrow’s work.

NYC, befitting its status as one of the more interesting places to live in around the world, is the host to this amazing event called the Imagine Science Film Festival. Now I’m nuts for all things science, but I especially love this festival in comparison to other science-y things to see and do around the city (with possible exception of DIYBio-NYC).

I personally believe that arts and sciences go hand in hand and that current division between the sciences and the ‘humanities’ is something of a temporary cultural aberration that we’ll all look back and laugh at. And the kind of works I saw at last year’s Imagine Science Film Festival events showed me a glimpse of what a future with sciences and humanities intermingled together might look like. It’s not so much as the specifics of the individual films but the overarching theme pervading through the atmosphere of the whole festival itself that caught my attention. Perhaps it’s the passion of the event organizers rubbing off on others watching the films. Perhaps it was just me realizing something I already had inside me through the mirror of projector screens.

If you’re in the NYC area, make sure to check out the webpage for the imagine science films and mark the dates on the calenders (there’s a screening benefit program this September 9th). Last year most of the screenings were free and I get a feeling that it will continue to be that way this year as well. If you’re not in the NYC area, feel free to donate in return for some cool t-shirts 😉 You’ll be supporting a worthy cause.

And here’s the festival trailer for your viewing pleasure.

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.’

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.

Lecture and presentation

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.

How to change the world.

This is a bit of rant post on something I thought of after watching bunch of old hacker-themed movies from the Hollywood. It continues to amaze me how I can participate in all sorts of crazy things even with the summer studies and jobs I need to keep up with. I guess that’s the benefit of living in place like NYC.

I’ve been watching some old hacker movies lately.  And I just can’t believe what kind of cool things those movie hackers were able to pull off with their now decades-old computers and laptops. Computers with interfaces and hardware that exudes that retro feel even across the projector screen. I know a lot of people with brand-spanking-new computers with state of the art hardwares and what they usually do, or can do with those machines aren’t as cool as the stuff on the movies being pulled off with vastly inferior hardware and network access. Of course, like everything in life it would be insane to compare the real with the imagined, and Hollywood movies have a bad tendency to exaggerate and blow things out of proportion (I’m just waiting for that next dumb movie with synthetic biology as a culprit, though it might not happen since Hollywood’s been barking about indecency of genetic engineering technology for decades now). Even with that in mind, I can’t help but feel that the modern computerized society is just way too different from the ones imagined by artists and technologists of the old.

Ever heard of younger Steve Jobs talking in one of his interviews? He might have been a rather nasty person but he certainly believed that ubiquitous personal computing will change the world for the better. Not one of those gradual, natural changes either. He actually believed that it’s going to accelerate the humanity itself, very much like how Kurzweil is preaching about the end of modernity with the upcoming singularity. Well, personal computing is nothing new these days. It’s actually quite stale until about a few months ago when people finally found out glut-ridden software with no apparent advantage in functionality were bad things, both in terms of user experience and economics. Ever since then they’ve been coming out with some interesting experiments like the atom chipset for netbooks (as well as netbooks themselves), and Nvidia Ion system for all sorts of stuff I can’t even begin to describe. And even with the deluge of personal computing in the world we have yet to see the kind of dramatic and intense changes we were promised so long ago. Yeah sure, the world’s slowly getting better, or changing at least. It’s all there when you take some time off and run the real numbers. It’s getting a little bit better as time goes on, and things are definitely changing like some slow-moving river. But this isn’t the future we were promised so long ago. This isn’t the future people actually wanted to create.

We have engines of information running in every household and many cellphones right now.  Engines of information meaning all sorts of machinery that can be used to create and process information content. Not just client-side consumption device where the user folks money over to some company to get little pieces of pixels or whatever, but real engines of information that’s capable of creating as well as consuming using all of the hardware capabilities. It’s like this is the Victorian Era, and everyone had steam engine built into everything they can think of. And nothing happened. No steam cars, no steam blimps, no nothing. The world’s rolling at the same pace as before and most people still think in the same narrow minded niches of their own. What’s going on here? Never had such a huge number of ‘engines’ responsible for creating an era in history been available to so many people at once. And that’s not all. Truly ubiquitous computing made available by advances in information technology is almost here, and it is very likely that it will soon spread to the poorer parts of the world and remoter parts of the globe traditionally cut off from conventional infrastructures.

But yet again, no change. No dice. Again, what’s happening here, and what’s wrong with this picture? Why aren’t we changing the world using computers at vastly accelerated rate like how we changed the world with rapid industrialization (not necessarily for the better, of course)? That’s right. Even compared to the industrialization of the old times with its relatively limited availability and utility of the steam engines we are falling behind on the pace of the change of the world. No matter what angle you take there is something wrong in our world. Something isn’t quite working right.

So I began to think during the hacker movie screening and by the time the movie finished I was faced with one possible answer to the question of how we’ll change the world using engines of information. How to take back the future from spambots, ‘social gurus’, and unlimited porn.

The answer is science. The only way to utilize the engines of information to change the world in its tangible form is science. We need to find a way to bring sciences to the masses. We need to make them do it, participate in it, and maybe even learn it, as outlandish as the notion might sound to some people out there. We need to remodel the whole thing from the ground-up, change what people automatically think of when they hear the term ‘science’. We also need the tools for the engines of information. We need some software based tools so that people can do science everywhere there is a computer, and do it better everywhere there is a computer and an internet connection. And we need to make it so that all of those applications/services can run on a netbook spec’d computer. That’s right. Unless you’re doing serious 3D modeling or serious number-crunching you should be able to do scientific stuff on a netbook. Operating systems and applications that need 2GB of ram to display a cool visual effect of scrolling text based documents are the blight of the world. One day we will look back at those practices and gasp in horror at how far they held the world back from the future.

As for actual scientific applications, that’s where I have problems. I know there are already a plethora of services and applications out there catering to openness and science integrated with the web. Openwetware and other synthetic biology related computer applications and services come to mind. Synthetic biology is a discipline fundamentally tied to usage of computer, accessibility to outside repositories and communities, and large amateur community for beta testing their biological programming languages. It makes sense that it’s one of the foremost fields of sciences that are open to the public and offers number of very compelling design packages for working with real biological systems. But we can do more. We can set up international computing support for amateur rocketry and satellite management, using low-cost platforms like the CubeSat. I saw a launching of a privately funded rocket into the Earth’s orbit through a webcam embedded into the rocket itself. I actually saw the space from the point of view of the rocket sitting in my bedroom with my laptop as it left the coils of the Earth and floated into the space with its payload. And this is nothing new. All of this is perfectly trivial, and is of such technical ease that it can be done by a private company instead of national governments. And most of the basic the peripheral management for such operations can be done on a netbook given sufficient degree of software engineering and reliable network connection. There are other scientific applications that I can rattle on and on without pause, and there are plenty of people out there much better versed in sciences who can probably come up with even cooler ideas… So why isn’t this happening? Why aren’t we doing this? Why are we forcing people to live in an imaginary jail cell where the next big thing consists of scantily clad men/women showing off their multi-million dollar homes with no aesthetic value or ingenuity whatsoever? Am I the only one who thinks the outlook of the world increasingly resembles some massive crime against humanity? It’s a crime to lock up a child in a basement and force him/her to watch crap on T.V., but when we do that to all of humanity suddenly it’s to be expected?

We have possibilities and opportunities just lying around for the next ambitious hacker-otaku to come along and take. But they will simply remain as possibilities unless people get to work with it. We need softwares and people who write softwares. We need academics willing to delve into the mysterious labyrinths of the sciences and regurgitate it in user-friendly format for the masses to consume, with enough nutrient in it that interested people can actually do something with it.

This should be a wake-up call to the tinkerers and hackers everywhere. Stop fighting over which programming language is better than others. Stop with the lethargic sarcasm and smell the coffee. Learn real science and hack it to pieces like any other system out there.

Get to work.

Change the world.

Bioinformatics Misconceptions

I just read an interesting paper on the three common misconceptions people normally have about the field of bioinformatics. I’ve been eyeing bioinformatics as a possible venue for bringing more people into DIY sciences, so I took some notes for future reference. It turns out that I’ve been suffering from same hype and illusion about the field of bioinformatics just like the vast majority of the non-specialists out there.

Simply put major misunderstandings about bioinformatics might be narrowed down to three myths permeating the science culture, according to the author.

Myth#1: anybody can do this
-bioinformatics is inexpensive
-bioinformatics software is free

Myth#2: you’ll always need an experiment
-bioinformatics is a rapid-publication field
-all bioinformatics does is generate testable predictions

Myth#3: this is news technology but technology nevertheless
-bioinformatics is a new field
-bioinformatics is an application discipline

*FYI the statements under the Myth headings are the ones the author refutes in his writing.

Myth#1 is that everybody can do bioinformatics, using only the cheap or opensource tools available off the net. The author does admit that this is indeed the case to certain extent. However once you get into any serious large scale research about or involving bioinformatics the initial assumptions will prove to be a burden on the organizational level. As the author will elaborate in later parts, bioinformatics is a field of scientific research on its own not subservient to the conventional wetlab biology. Indeed, while reading the article I was under the impression that the main statement for the whole article revolved around how people do not realize that bioinformatics is a field of scientific research with its own goals and complications. Very unlike the laymen assumption that bioinformatics is in fact just biology done with computers, or application of computerized tools to wetlab based biological research just like how the researchers would use word processors or LaTeX to type up their reports. Personally I found it a little disheartening that bioinformatics research is just as complicated as any other field of scientific research for DIY implementation, possibly more depending on what the amateur scientist is trying to do. But then I can only blame my naivety. The author also makes a point that bioinformatics can be very expensive to begin due to some number of proprietary software services that must be purchased (never went into much detail on that. I guess it’s different according to the theme of the research?) and the resources needed to write and maintain codes for the project. It makes sense when you think about it. While it would be possible to come up with some bioinformatics application in-house, after certain level it would be vastly cheaper to simply buy some number of components and just use in-house resources to link them and tune them into giving results needed for the project (which shouldn’t be easy to begin with).

Of course, I still think that we can, and maybe should, use some approaches of bioinformatics to provide interesting DIY science framework to the public, like the Annotathon metagenome annotation project that had been open to the public for a while now. I’m just glad that I got a chance to listen to some of the intricacies of the field from someone already working with the tools of the trade.

While I now understand some stuff about what the field of bioinformatics is about, I’m still unsure as to what kind of project idea I can come up for DIYBio curriculum using the technology… It’s a problem I’ve been running into a lot lately in doing stuff involving DIYBio. I know there are tools and tutorials out there, but I just can’t seem to be able to put them together into a coherent whole. DIYBio needs some sort of project that would turn knowledge into skill… More on that later.

Life during summer and consilience notes

I should definitely to a decent post some time soon, but it seems that I’m in middle of severe drought of ideas and writing abilities. Hopefully this is just a passing phase… Someone should definitely develop a drug against writer’s block I think.

A few things I’ve been working on so far between all the jobs I have to run to pay my rent. I’ve been studying the Exploring Complexity by Gregoire Nicolis and Ilya Prigogine since the beginning of the summer. Studying as in tearing through every bit of reference mentioned at ends of each chapters and working out all the equations, making up some of my own for practice. The progress has been slower than I would have liked but it’s still coming along nicely. I’m upto  the randomness and complexity chapter where they begin describing Markovian processes and different types of entropy. I’ve been trying to come up with some cool graphics describing some of the stuff in the book using Mathematica but couldn’t really find the time to get around to it, with all the other coding projects on my hand at the moment, but I’ll definitely have something to show for by the end of the summer.

I’ve also been reading up on some bioinformatics literature, beginning with the eponymous ‘For Dummies’ book on the subject which is surprisingly well written, or at least comprehensible (well, considering the title it would be hard to write a book on the subject that is incomprehensible). It’s part of my attempt at coming up with a decent diybio coursework aimed at 14 and above, centering around the kind of projects the laymen would normally find out of reach, like designing a biological circuit and putting it together in a wetlab. With so many computerized tools and advent of abstraction in biological sciences brought on by synthetic biology, I think it is possible to empower the citizenry with end-user scientist toolset. The average computer user don’t code in assembly or the machine language yet many of them are perfectly capable of coming up with useful high-level softwares and beautiful works of art (it still takes effort and mastery but what doesn’t?). In order for the biological sciences to become user-friendly I believe we need a tool to familiarize them with the higher level abstraction in molecular biology and computerized tools associated with it. In my experience the best way to break down an intellectual barrier is to make people do the impossible easily and cheaply. The first step of breaking down the biology barrier would be teaching people how to design genetic circuits using extremely high level abstraction symbols. Theoretically it should be possible to put together a very simple circuit on a napkin using symbols and diagrams using unified ‘visual language‘ of synthetic biology. Once the individual becomes scientifically fluent enough to visualize these molecular circuits within his or her head, and feel a real want for building something in real life, we can easily transfer the design into computerized tools for specification and optimization. After that it would be a simple process of transformation using mail-order kits (or using diy tools if you’re so inclined), which DIYBio NYC have already demonstrated to be easy and straightforward.

By then, maybe I’ll try to pitch my not-so-secret ambition of coming up with diy-minimal/synthetic cell ::evil laugh::

As you might have guessed I’ve also been spending a lot of time reading through E.O. Wilson’s Consilience: The Unity of Knowledge again. It’s amazing just how much of the book resonates with me, not necessarily in solutions but in problems he outlines as something fundamental that needs to be resolved if we are to further our understanding of the universe.

-From pg.93
…the U.S. federal high-performance program has upped the goal to a trillion calculations per second by the end of the century. By the year 2020, petacrunchers, capable of reaching a thousand trillion calculations per second, may be possible, although new technologies and programming methods will be needed to reach that level. At this point the brute-force simulation of cell mechanics, tracking every active molecule and its web of interactions, should be attainable- even without the simplifying principles envisioned in complexity theory.

The continuing battle (if there is one) between raw computing power against elegant universal systems like the kind proposed by some of the complexity scientists is interesting. For one thing, would we need raw computing power the world has never seen so far to replicate human-like intelligence? Or can it be done in smaller scale using some aspect of the logical system that gives rise to emergent trait we refer to as intelligence? Classification of life/intelligence as a type of physical system that very closely resembles phase transition due to complexity is an intriguing possibility that will need to be examined in detail… I’m especially interested in intelligence as not something that computes but as something that creates. Why am I sitting here writing down this stuff when the weather outside is so great? Why do people strive to create this stuff and ideas when it’s much easier to sit on their collective asses and eat chips? To some the activity of creating get to the point of destructive obsession. Am I alone in sensing that the society at large tend to be envious of those kind of people?

Curiosity is not a rational trait. It’s crazy and sometimes suicidal, and doesn’t serve any kind of immediate need for survival or propagation. It is the very picture of irrationality. So where does it come from? What aspect of the molecular system that we refer to as living beings gives rise to such weird behavior? And what’s with this crazy unreasonable effectiveness of mathematics in the natural sciences? Isn’t it weird how questioning the nature of mind, life, and human behavior so often leads us to the questions on the fundamental nature of the universe itself?

-From pg.93~94
In 1994 editors of Science, celebrating the inauguration of developmental biology by Wilhelm Roux a century earlier, asked one hundred contemporary researchers in the field to identify what they considered the crucial unanswered questions in the discipline. Their responses, in rank order of attributed importance, were:
1.The molecular mechanism of tissue and organ development.
2.The connection between development and genetic information.
3.The steps by which cell become committed to a particular fate.
4.The role of cell-to-cell signaling in tissue development.
5.The self-assembly of tissue patterns in the early embryo.
6.The manner in which nerve cells establish their specific connections to create the nerve cord and brains.
7.The means by which cells choose to divide and to die in the sculpting  of tissues and organs.
8.The steps by which the processes controlling transcription (the transmission of DNA information within the cell) affect the differentiation of tissues and organs.
Remarkably, the biologists considered research on all of these topics to be in a state of rapid advance, with partial successes in at least some of them close at hand.

Above questions were written around 1994 according to the Consilience. It’s been over a decade, so I wonder how many of above questions had been answered definitely and conclusively….

Also, it’s rather interesting that most if not all of above questions are in some way related to study of complexity sciences. It’s almost as if the whole field of complexity science is biology fused with mathematical abstractions.

From Consilience:the Unity of Knowledge

“The intellectual power, honesty, lucidity, courage, and disinterested love of the truth of the most gifted thinkers of the eighteenth century remain to this day without parallel. Their age is one of the best and most hopeful episodes in the life of mankind.” – Isaiah Berlin

There is a book titled ‘Consilience: the unity of knowledge‘ by E.O.Wilson. Buy it, and read it. It’s worth more than a hundred iPhones, unless the said iPhones have copies of the Consilience on it.

The book had such profound impact on me when I was growing up, I really think I should do a review/post on the book and some of its themes one of these days. It came out years ago yet the prescient insight of E.O. Wilson rings true to this very day in many fields of human endeavor. I had the chance to listen to his talk live in the closing event during the wonderful World Science Festival in NYC, and I should say he still seem to retain that certain edge even after all these years. I guess that’s what we Koreans call No-Ik-Jang for you. If only I wasn’t so shy to ask him for an autograph on my copy of the book. I feel like a kid who lost a winning lottery ticket.

Now that I think about it I should also do a post on the World Science Festival while the memory’s still fresh… So many things to write about, so little time to write them.