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.


American Gods and patterns in stories.

I finally got through the American Gods by Neil Gaiman. I’ve said it before and I’ll say it again. He’s a terrific writer. He’s not the best writer out there or anything (he won’t be winning any Nobel prizes anytime soon, but then does it really matter anymore?), but he’s certainly above the fray in bringing his ideas to life through words. His characters feel genuine and endearing, even the villains. None of the plot elements feel like a cop-out from a hairy situation of an author having to create unique situations for living, something I’ve seen a lot of writers succumb to.

Through the end of the book I was embroiled in some very mixed-up emotions. I wanted to see the story progress, but I didn’t want the story to end. I wanted to see the story between shadow and crow to its possible happy conclusions. I wanted to see shadow grow old and meet someone and I wanted to read what he would have been thinking at the moment. I wanted to see if he’d get to meet any other gods, and I wanted to know if it would be as humorous and wonderful as most of his other encounters with the gods of the world, past and future. As I read on to sate my curiosities, I couldn’t avoid finishing the book, and that’s the biggest gripe I have with the American Gods.

There are all sorts of heavy stuff that people trained in such arts can debate and write about all days and nights in American Gods. Some would like the feeling of America as a collection of old, used-up ideas and modern god like ideas struggling for control, afraid to be forgotten. Some would call it an old and washed out idea just like the gods of old, since it’s an archetypal picture of the American that journalists and novelists and anyone else who can write and has good enough eyes to see things around them had been writing for past half a century or so, maybe even longer. I don’t think it matters. Neil Gaiman didn’t write this novel so he can have grand disposition on the fate of the American ideas (if that were the case the future of America would lie in somewhere around Iceland, and that would be funny, not serious). He wrote this novel to write a good story with good people living in it and he did one heck of a job. I don’t think I’ll be forgetting about the three sisters, Mr. Wednesday, shadow, Laura, crow, and etc etc anytime soon. It would be great if I don’t forget about them for the rest of my life, but no one knows what will happen in the future, and hopefully I might be able to experience something even more intense.

I’d love to write about some elements in the story, but I don’t think I should. I made a blood oath never to write down spoilers when ‘reviewing’ a book in a public place. Let’s just say that I really enjoyed the book, and I never wanted it to end. I think I spent about four or five days reading this book. I would have finished earlier, but then I had sudden burst of workload on me this week so I had to pull a few late nights. I mostly read this book in the subways, and in the bed with the reading light on. I would frequently curse at myself for reading past three AM on a work day, just hoping that I would be fresh enough to not look like a zombie by the time I wake up a few hours later. I would actually anticipate the ride on the subways since it was pretty much the only time during the day that I could sit down and read for close to an hour or so. The crowd didn’t bother me but I might have bothered some nice old ladies for making weird faces while reading the book, from deadly seriousness to strange smile (the kind you get when you suppress an even bigger smile because it would be weird laughing out of the blue). But then I guess there were even weirder things on New York City subways at eleven in the night, so I probably didn’t stand out too much… Which reminds me, I’ve never seen people reading on subway who change their facial expressions before. Is it that everyone else is so well trained in managing their faces or are the books just really boring? I would say it’s the training issue, since I also become excited when I’m reading through particularly illuminating passages on a physics book, and most normal people probably don’t do that.

As I read through the American Gods, I was reminded of just how much I like reading, and sometimes even writing, creative stories. With my official status as a student I usually have to dig through a lot of journals and data, where they usually deal with diagrams and numbers without much creative license (I think I remember one of my teachers telling me that use of creative license in any scientific writing is a single ticket to ending your career. Or did I read it in a story somewhere? I can’t quite recall). Reading those dry, albeit enlightening, academic scripts seem to have taken its toll on me, and sometimes I feel like I’m a dry person myself. It’s like the case with Marge Simpson. I only think of crazy jokes or stories only after I leave the party and start my car. It drives me crazy.

That being the case, reading through the American Gods and some other fictional works before that was a cathartic experience for me. I wonder what kind of trait drives us to enjoy and seek out well-made stories involving fictional people and places? Was there some strange need for living organisms to be able to tell fantasies to each other in order to survive? The kind of fantasy where both the storyteller and the audience knows it’s fantasy but indulge in it anyway? That would be an interesting venue of research, something I sadly cannot seem to be able to find anywhere.

The American Gods also had me thinking about the archetype of stories. Whether we like it or not, elements of the ideas composing stories from various authors end up being similar to each other. Usually the difference is only made up through the skills of the writer/storyteller in masterful use of the language the story is transmitted to their audience. C.G. Jung built up a whole sub-discipline of psychology based on those archetypes found throughout human culture and even dreams, and it’s almost as if human beings are capable of only telling certain types of creative stories with varying degrees of proficiency. What would that imply in understanding human creativity? Maybe the trait of creativity isn’t as limitless as we tend to believe. Maybe creativity is just like most other mathematically derived abstract act, based off of some type of pattern that circles around itself. If that were the case, we would be able to make a machine capable of creating stories not by linking relevant words together but through linking relevant ideas together, into a preset pattern. An idea of conflict, an idea of resolution. The individual set of vocabulary and the storyline composing that single idea would be irrelevant as long as it can lead to the next part, and the transition won’t even have to be singular. It can be polyphonic like Bach’s composition, each event happening with  another in ceaseless pattern. However while I’m sure it would be interesting to create such a program/machine, I’m not sure how I would be able to handle the task of making a machine capable of creating a character. Will characters simply emerge out of the polyphonic storyline? Will their personalities simply emerge out of the series of events that the characters are subjected to, each of them simply beginning with a name?

The first thing I tend to do when I want a deeper understanding of a writer’s work is to look up information on the life of writer him/herself. The research can be illuminating in a lot of cases, which is funny when you think about it since most writers I know of make their living by creating stories that are considered very unique compared to the rest of the ‘writer population.’ Would that imply that the trait of creativity is inseparable from memories of the individual? And what should writers do when they are so prolific that they are faced with the possibility of patterns and familiar ideas appearing again and again within their works? Do they embrace the patterns and ideas and try to refine them? Or do they try to break free, staying away from such patterns and ideas appearing in their works altogether?

A note- engine of creativity

Juergen Schmidhuber is supposedly working on an artificial scientist. I’ve come to a sudden realization that I am very interested in creating an artificial creator, or an engine of creativity, and that my interest in artificial life might have in fact been an interest in studying the origins of the trait we refer to as creativity.

It is rather curious. Will an artificial scientist be different from an artificial construct capable of demonstrating the trait we refer to as creativity? From what I am seeing, artificial scientist is an informational construct while an artificial creator is more of a physical system, thus the term engine of creativity.

Only known case of creativity exhibited in nature is us. If we ignore that the universe itself demonstrates ingenious and unexpected things through emergence, self organization and evolutionary principles, the only observed and somewhat-understood case of creativity in the universe are demonstrated by life-like systems. Would this somehow imply that only life-like systems can demonstrate traits of creativity? Would this mean that any artificial engine of creativity formed by human hand would have to be alive? Considered alive?


People love fantasies. They fantasize about things all the time. Act of shaping the most compelling traits of that fantasy in real world is called art. And the process that allows the conversion of idea to shape is called technology. Look at this.

Beauty may be in the eyes of the beholder, but I think this will definitely appear beautiful in the eyes of the majority. Now, this is merely a model. But sciences and technology might as well make this come true sooner that most people expect it.

What I find truly interesting, however, isn’t the shared trait between arts and sciences. That much had been obvious since the days of Leonardo Da Vinci, and the hints of the inseparable relationship between the two had been acknowledged even before then… Or rather, would it be correct to say that modern separation between arts and sciences is a freak accident of history that was given birth a few centuries ago at most? I guess we are all collectively reeling in from the aftershock of the events that happened centuries ago (and people ask why we should bother to learn history).

What I really find interesting, to an almost obsessive degree, is where the beginnings of arts and sciences came from. That is, what would drive bunch of complex systems of collections of molecular compounds to form ideas, worldview, beliefs, and etc… Whether you are a religious fundamentalist or a Dawkins-ian atheist, the fact is that most if not all of humanity have some capacity at aesthetic sensitivity that borders on mystical. Like any prudent scientist (to-be), I believe in things happening in front of my eyes rather than some abstract ideas floating in the clouds. It is a fact that people keep on creating and reacting to stuff, tries to keep themselves alive (though survival seem to take on varying degrees of priority in individuals), and are a system of molecules. So it should be reasonable to suspect that there is a method in nature to create systems of creativity out of components we already know about, using systematic pathways/algorithms that can be replicated.

What is creativity? It is a constant drive to do stuff. Is that enough? Not really. Simply being active isn’t good enough… Creativity is a drive to do stuff in coherent manner. Thermodynamic work with coherence, which I might even call ‘memory’ though it might be too hasty at this point. Would this mean that a metabolic engine with capacity for coherent action (memory?) on the system-wide level contains innate ability to create? Like bacterium? Localized complex chain reaction with proper coherence eventually leads to self-replication? So would this mean that the human capacity for arts is in some deep level related to the capacity to procreate in minimally life-like systems?… Then what would be the concept of beauty? And why/how would human beings pursue aesthetics/ideas outside of the necessity for survival?

It’s fun to do a bit of musing like this. Yet it always get frustrating at the end, because I know in my heart that there’s no way to test all this physically. Or is there?

All I can do at the moment is to sit here and wait for my muse.

Sketch-Creativity and origin of creativity

I’ve been listening to Amy Tan’s talk on TED titled ‘Where does Creativity Hide?’

Interesting stuff. I didn’t have enough time to mull over it properly yet, but listening to her gave me a few thoughts on the issue of the origin of creativity, an issue I am very passionate about.

It is relatively simple matter to simulate the process of creativity, I think. Plenty of mathematical constructs and randomly generated ‘events’ linked together has the resemblance of pure creative output, and despite some number of conflicts and arguments for and against such ‘engines of creation’, I do believe that what we do might in essence be not so much different from the simulated behaviors of such random patterns and mechanization.

However, the real problem, at least for me, lies in the issue of the origin of creativity rather than the process of it. Human beings are not machines or algorithms specifically designed to be creative. In fact, human beings as molecular machines might not have been built for anything (and everything, in that sense), for evolution tend to be quite blind in such matters of directionality in nature (there are theories and viewpoints arguing otherwise). I will not even look at the possibility that the wellspring of creativity emerges from some spiritual source, instead approaching the problem from purely materialistic and reproducible viewpoint.

As physio-chemical complex dissipative systems, what drives human beings to create and innovate throughout their duration of activity, i.e. life? What kind of mechanism underlies this strange anomaly emerging from entangled soups contained within chunks of chemicals? Even more, how would we be able to replicate such behavior using less than usual components? This, ladies and gentlemen, is the question of the ages, the true question toward the question of creativity.

This, I believe, is the true crossroad between the arts and the sceinces, the significance of artificial life in science, society, industries, and the zenith where the artificial intelligence becomes simple intelligence.

More to follow.


I’ve been incredibly busy lately, both at my school and at home. Bunch of things all happening at once and every one of them going wrong, all somehow connected and breaking together in some very strange chain reaction of the network of the world.  Anyhow, among all the things I’ve been going through I still haven’t stopped thinking about the artificial life and the whole art and science relationship I’m pursuing. As I said before I’ve been trying to learn a lot more about Jasper Johns and his way of thinking. At this stage I tend to single him out as I believe that he is very representative of the nature of what art is and what art has become, not only to the ones who actively pursue the practice and understanding of art but also to average layman like me who have no professional background in art. It’s not just formalized thoughts in his mind I’m interested in. As a human being I find him to be a very close model of what people go through when faced against the issues of the art and art like things in this world, regardless of vested interest and background… As someone whose background is from the fields of science and scientific pursuits, I feel as if I can understand him on some instinctive level, grasp the general gist of things, so to speak.

There is one thing that I can’t seem to be able to get out of my mind when thinking about Jasper Johns. He mentioned that his work is basically born of discontent, that he is in fact trying hard not to do whatever it is that comes naturally to him in practice of art. The fear and uncertainty surrounding such behavior is something I can fully sympathize with, perhaps even comprehend on logical level. The reason for me to think in such a way, is that Jasper Johns’ behavior is not unusual. The signs are strewn all over the society and culture, this civilization itself. When thinking about the human origin of creativity, the instinctive reaction of the human being which leads to creative behavior is always discontent. Yet, what it really means for a human being to be discontent is something that should be reflected upon carefully. Discontent is something a human being feels regardless of the state of his or her physical want. Those who believe that human discontent simply stem from want of survival are deluded. Even on evolutionary scales, human discontent seem to be a primordial trait hardwired into the very structure of the living itself, that goes beyond the simple psychological apparatus developed for the cause of survival. The human discontent is a trait that goes beyond the formularized reaction we commonly label as greed or gluttony, complex and multilayered mechanism whose roots remain obscure to this day. Somewhere around that root, it might be possible that the primordial and pure form of discontent as a life-form is somehow linked with the origin of the human creativity.

Human beings are physical creatures formed of biochemical components. Thus art and the creativity that leads to such act as art must be within the realm of the physical life itself, all of them stemming from some nonlinear complex emergent phenomena. Perhaps discontent is a human manifestation of a universal trait of networks of sufficient complexity. Perhaps the human drive toward creativity and all other unmistakably human pursuits stem from the fundamental structure of the life as a complex system, rather than superficial biochemical impulses or ‘mysterious’ things of unknowable origins. That, is another reason why the study of life is at the cutting edge between the science and the art, and why I pursue the study of artificial life of physical nature.


If there is one question I’ve consistently thought about past six or so years, it’s the nature and origin of creativity. Isn’t it wonderous and mysterious? All logic dictates that I should be eating and thinking about or participating in sexual reproduction right now. But I’m not. I’m participating in a creative work (regardless of how meager it might be), thinking about the nature of some abstract concept, while listening to a music I’ve sought out on the web. Activities that have so far eluded conventional attribution to genetic codes inherent in biological beings.

Sometimes I look out the window, toward some endlessly delicate and beautiful pattern of light and lines drawn by air and planetary motion. I can actually feel some kind of strange emotion I am not enough of a writer to describe in words. Time to time I look around myself in everyday life, only to discover that by some coincidental play of time and motion, something beautiful had passed by. And I feel a strange urge to describe it, to capture the moment in a medium that isn’t as ephemeral, to understand the essence of what made the moment what it was.

Such behavior doesn’t seem to be limited to human beings, although human beings might be the ones most eloquent in putting such urge and curiosity to the motion and the act. I can think of a few animals capable of displaying more curiosity about the world than their owners (as strange as it sounds, it’s true). Such observations lead me to believe that curiosity and creativity may be some inherent characteristics of all life forms with certain physiological feature, such as a brain stem. Maybe there is something within how the brain is structured that leads all sufficiently complex life forms to pursue their own visions of Pygmalion?

Something is here to be described, yet how it is to be done is unclear. The only understanding between the object, the moment, and the human is that all things she sees in front of her is in this world, arising naturally from the chaos of the world itself. So she sets herself to recreating the world in her own vision, to capture the indescribable she witnessed for the fleeting moment. The world thus created is formed with a question, with an urge. The world thus created has a directionality, a philosophical intentionality. A whole world with an intention, temporary or otherwise, is disturbingly similar in its description to life. Perhaps she has created a life. Perhaps arts and writings intend to seep out into the world. Perhaps in the future, the art will come alive, breathe with us, and stare back into our eyes.