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.’

Science commons

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Just a quick post before going to sleep (it’s 2:45 in the morning and I have class at 10:00 ugh).

This is one of the coolest things I’ve seen on the net today. 120 second introduction to what science commons is.

I can think of lot of things that can explain why the idea of ‘opensourced’ science or science commons must be one of the coolest and most revolutionary ideas of the generation, but my brain is turning into a jello right now, so detailed post will have to wait.

Just one thing though. Library of Alexandria. 

Just think about it. Why was library of Alexandria so important? Was it because it housed a lot of books? No, it isn’t. If anyone believes that the significance of the library of Alexandria was about stacks of books he/she lacks the understanding of the origin of modern civilization. Books or any individual units of information pop into existence all the time. Libraries are meaningful because they centralize and organize those individual information clusters. Centralize and organize, meaning giving accessibility to. 

Greatest threat to any knowledge is not in its misuse or incomprehension. It is in obscurity (as Cory Doctorow pointed out as he released his works under CC license). Libraries made human civilization by providing accessibility to knowledge that would have been forgotten otherwise by centralizing them in one geographic location and organizing them according to a system. From that location new ideas were born since people no longer had to spend their lifetime re-learning what someone else figured out half a century ago.

Science in general, lacks accessibility. Which is very weird when you think about it. Science is about accurate description of this universe, this universe every single member of the Homo sapiens sapiens share. Yet science lacks accessibility, both to the nonspecialists and specialists alike. It’s like having limited access to one of your eyes or limbs or organs.

Accessibility is catalyzing and empowering. When economic systems become accessible we get flourishing finances and trades system, with all the subsequent benefits of arts and culture. When human opinions become accessible we get one of the biggest human community ever, with subsequent benefits of policies and philanthropy. The first time academies and libraries became accessible we began a march toward a new civilization. What will we be able to accomplish once the sciences are truly open and known to every willing member of the humanity? 

Neal Stephenson notes

I’ve been googling some Neal Stephenson articles on the net in preparation for his new upcoming book, Anathem.

Here is an interesting excerpt from a Wired article I encountered from a blog about Neal Stephenson and his upcoming work (I recommend you read the full article as well if you are interested in current status of Neal Stephenson’s life).

Stephenson spends his mornings cloistered in the basement, writing longhand in fountain pen and reworking the pages on a Mac version of the Emacs text editor. This intensity cannot be sustained all day–”It’s part of my personality that I have to mess with stuff,” he says–so after the writing sessions, he likes to get his hands on something real or hack stuff on the computer. (He’s particularly adept at Mathematica, the equation-crunching software of choice for mathematicians and engineers.) For six years, he was an adviser to Jeff Bezos’ space-flight startup, Blue Origin. He left amicably in 2006. Last year, he went to work for another Northwest tech icon, Nathan Myhrvold, who heads Intellectual Ventures, an invention factory that churns out patents and prototypes of high-risk, high-reward ideas. Stephenson and two partners spend most afternoons across Lake Washington in the IV lab, a low-slung building with an exotic array of tools and machines to make physical manifestations of the fancies that flow from the big thinkers on call there.

“In Neal’s books, he’s been fantastically good at creating scenarios and technologies that are purely imaginary,” Myhrvold says. “But they’re much easier imagined than built. So we spend a certain amount of our time imagining them but the rest of our time building them. It’s also very cool but different to say, ‘Let’s come up with new ways of doing brain surgery.'”

That’s right–brain surgery is one of the things Stephenson is tinkering with. He and his team are helping refine some mechanical aspects of a new tool, a helical needle for operating on brain tumors. It’s the kind of cool job one of his characters might have.

This article seem to further compound my idea about Stephenson’s (or any other writer/artists’) almost instinctive urge to see the products of their written fantasies manifest in their world in a more corporeal form. Many artists throughout history seem to share that trait in particular, from Leonardo Da Vinci to Jasper Johns, methods of manifestation sometimes taking form of involvement in things of the ‘secular world’ or integration of their artistic ideas into lifestyles and memes. Such universally observed trait might as well be the reason that synthetic biology, or rather, any and all forms of artificial life holds so much promise for artists of the world. Synthetic/artificial life might as well be the catalyst needed to bridge the unreasonable cultural and intellectual gap between the arts and the sciences.

Indeed, I might even go as far as to say that the utility of artificial life in the field of arts would be an inevitable development of the future, based on the innate human desire to breathe life into immaterial thoughts.

Once I get past the deadline season, I might do a bit more detailed post on the matter of human creativity and obsession towards its manifestation…

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.

More books are never enough.

I just wanted to urge everyone to visit wowio books.

It’s a webpage with full and legal copies of books, categorized and formatted meticulously. Unlike some of the more popular free book service like the Project Gutenberg, many of the books provided wowio aren’t copyright expired classics. There are some gems in there, so anyone with a remote streak of bibliophile in them should take the time to shop around.

I just hope they get more science related books in there, as well as some of the rarer fictions like The Thackery T. Lambshead Pocket Guide to Eccentric & Discredited Diseases, but the books they already have are still worth taking a peek.

Chemical augmentation

Americans (and the modern civilization in general) had been dependent on medications since the discovery of penicillin, but recently the level of chemical commitment began to take a whole new perspective. Modification of the baseline intellectual ability through chemical agents that goes beyond simple nutrient control is something I suspect to be relatively widespread and will continue to seep into the general populace as the medications become more sophisticated and effective. The effectiveness of the medication can be surprising when controlled and monitored carefully. I can concentrate on a single task for around ten to fourteen hours at one time, depending on my condition. With proper chemical aid I can theoretically pull through twelve to twenty hours, again dependent on my prior psychological and physical condition.

It would be unrealistic to simply discredit the effectiveness of the chemical aid in intellectual pursuits when its benefits are so clear. The fields of academic studies are one of the rare fields of human endeavor that allows necessities of individual desire and social niceties to be as one, and as such any chance at improvement on one’s ability provides an irresistible allure that goes beyond the simple need to perform. I believe how this new addiction to chemical augmentation plays out and how the society deals with it in coming times will be representative of how the society and the individual will fair once the genetic and cybernetic augmentation for human beings become economic reality. There are some cautious optimism as to the possible changes the coming era of affordable chemical augmentation might in fact benefit the humanity at large, and even serve as a catalyst for a different human age. In this era where people are becoming increasingly aware of ramifications of technology (or at least becoming increasingly polarized by the awareness) on future course of humanity, such predictions take on profound foliage different from similar futurist predictions of the old.

If there is one thing I am worried about, it is our lack of knowledge on the processes of the development of human consciousness. Will learning without requisite control of one’s physio-chemical facilities pose unwanted side-effects on the learner? Will we end up with an enitre civilization of people who knows things they can’t possibly hope to utilize? I’d count on the complex natures of innate human greed and pride to act as counter to such outcome. I for one cannot wait for the day that would finally allow my body to catch upto the place sight of my mind sees.

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



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.

The openwetware website, definitely worth a look.

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

Hackability of the world

I’ve been thinking and writing about the whole steampunk and tranhumanism ‘movement’ (if it can be called as such) all over the net. Though they were nothing more than novelty writings, jumbled things that came straight out of my mind without much introspection, I think I’m beginning to see some underlying pattern here. I do not particularly believe in attitude or belief of any specific cultural movement like the steampunk or the transhumanism. As someone dedicated to the study of sciences the ideas of transhumanism does appeal to me, but I still think appeal alone doesn’t make for a sound prediction of the future, and the St. John’s apocalypse-like images espoused by some of the more enthusiastic believers of the transhumanism thinking doesn’t really help things either.

What I am really interested in, is the shape of the world that is beginning to emerge underneath all the superficial beliefs and cliques of various social/cultural movement. A human network that is being accelerated and consolidated into an emergent and concrete form by the technology of near instantaneous connection between individual members of the humanity, which seem to form the backbone of the majority of the changes that make up what we call the ‘modern age’, web 2.0 generation, and etc etc. It’s really just a thought, nothing eloquent and lucid enough to be a theory… Perhaps this is merely adaptation of the mathematical theory of networks and links in the fashion of Barbarasi to the perspective of social theory… But something doesn’t sound quite right to refer to it as such.

Formation and linking of human beings to ideas, the belief and search for the method to change/control the world through variety of means, linking which leads to a form of phase shift, the compounding between the idea and the human being… A history is a fundamentally human story… If linking between ideas and human beings, ideas and ideas, human beings to human beings is viable and displays emergent characteristics so common in their physical equivalents, the term zeitgeist begins to take more significant meaning in the structure of the world.

If the ‘structure’ of the world and its interactions can be defined as such , wouldn’t it be possible to hack the system of the world to gather wanted result from it? A giant machine-construction formed of human dreams and lives, that are linked with each other so that while each part may be independent the whole remains homostatic, hacking such system to follow certain path would be tantamount to hacking the Genie of the lamp or the holy grail, since, in the end, the only thing that responds to human wishes is the human world itself. This giant human world, soon to be even bigger, is in effect a substitution of the human wish and the human will.

All the fad associated with the UCC or the web 2.0 generation will come and pass. Yet the wisdom and experience gained from this generation will invariably effect the other. Who is to say that the brave new world will bring with it social concepts and mundane practices so powerful and so fundamentally human that it would form an entity on its own, political, scientific, and artistic ideas living and traveling across the world like full-bodied life, while the human beings are both subject to its whims and a master of its path, raising and training it like pets.

Should such a day ever come, it would be the beginning of the age when arts may finally walk among the humanity.

Transhumanism, and the human network.

A little something I scribbled down a moment ago. Maybe it would be an interesting read for some of you, especially when viewed in light of the digital art -social networking age we live in right now.

The term transhumanism is thrown around a lot these days. It’s almost as if it is fast becoming a whole generational movement instead of a novelty philosophy catering to a limited cadre of technophiles. The true attraction of the movement I believe, is the real possibility that many things currently considered impossible might become possible in the future, not through any institutional reform but through a technological revolution capable of suiting individual tastes and goals. In many ways the movement of transhumanism is intensely political yet at the same time as politically neutral as it can be.
It seems transhumanism is about increasing the capacity to do things on the individual level without regards to a unified direction. After getting the ability you want using technological means, you can be a hardcore communist or a hardcore libertarian. The movement of the transhumanism itself doesn’t dictate what its proponents should do after becoming ‘transhuman’, and the only political ideal directly associated with the philosophy of transhumanism is the one necessary in making it come true, free and unrestricted access to technology and information. It can be said that the transhumanism and the theory of singularity so many people attribute to the movement of transhumanism is like deus ex machina come to life, the proverbial genie of the lamp given flesh in human adaptation of technology. However, it should be noted that the post-cyberpunk transhumanism ideals aren’t quite as clean and wish-wash as some of its predecessors of the enlightenment and industrial revolution, instead opting to put its faith in the very opening of the possibilities themselves rather than what those possibilities can ultimately achieve, and I dare say that it is this new way of thinking that defines the current generation’s zeitgeist regardless of geological locale or technical proficiency. Propagation of systems of thought through generational sentiments instead of any strict governmental or academic structure (that might even go beyond regional and cultural taboo), a sort of social-blogging approach to the propagation and practice of systems of thought. Yet in this case, the physical entity of the net is not a necessity. Instead, majority of the network-forming, linking and subsequent emergent behavior results from interactions between people and ideas, the technical infrastructure only acting as a catalyst for already present elements in precipitating metamorphosis.

As the idea of physical distance becomes fuddled in the future and virtual density of the human population increases, the idea and practice of the net-less networking built into all conscious life forms in the innate interaction between life forms themselves and the life and idea-structures will become more and more profound, its effects more and more pronounced, perhaps enough to truly dictate the course of human history, and perhaps, even human beliefs.