Summer's here again, and it's harder than ever to write a decent post while sitting in front of a computer. It's ironic that I'm beginning to use pen and paper far more than laptops and smart phones to do my leisure writing. Lot of things on my mind lately, like whether all this science stuff I'm trying my hand at will eventually work out somehow. With the basic issues like being able to find and hold down a job (I don't really want) so that I can pay my way through school and all that weighing down on my mind all the time, being able to pursue science as a vocation feels like a pipe dream all too often. Yeah, sure. Everyone works, more or less. And a lot of them actually work to pay their own rent, tuition and buy their own food like I'm doing right now (oh right, I'm talking about undergrads). All too often it's really a problem of future, and repercussions of mistakes I might make. Neal Stephenson wrote something about that in one of his books... Some kids go to jail for 10 years for striking up a joint, and some other kids get to protest in front of the city hall after making it to college. Some people just live in a very fault-intolerant world. That's about where I am. Not quite as bad as some kids I teach, but still enough to worry about becoming homeless after some idiot run me over with a car. And after you're homeless... Well it'll be a whole lot harder to beg professors to let me into a lab without being treated like some junkie or a maniac. Something like that probably won't happen, but I can't help but feel that chill in the back of my neck time to time. And about the only thing that makes all the fears and uncertainties worth it... Well I'm still not sure what I'm supposed to call it. Most people seem to call the practice of it science. It's some kind of pursuit toward something. And it makes life worth it.
Monday, May 31, 2010
Monday, April 5, 2010
Wikileaks video
Just a quick post before I run off to work (it's so hard to find time to blog properly these days, maybe I should try one of those audioblog autodictation addon...)
Found out about this while I was browsing through the tweetstream
It's a video on a site called 'wikileaks' that specialize in sensitive information and documents. It's been around for a while but this must be its biggest case yet (or second biggest if we count the case of a certain pharmaceutical firm in Switzerland).
I don't think release of this video will really change anything. I just hope this can be a wake-up call to a lot of people out there believing in nonsense like 'clean war' but even that's doubtful.
Before I go, here's something for the death of journalism. I don't think it's the internet.
Posted via web from Textdrome
Thursday, March 11, 2010
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.
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.
Saturday, January 23, 2010
At the Met
It's been a long time since I've walked through these halls. I'm only now realizing just how many memories I've left here, as I pick up all the little pieces and gaze through them. And I am a little happy about the little nagging question at the back of my head that just won't go away. Just what cnfiguration of molecules in this universe gave birth to these shapes and colors we call art? What is the equation that leads from the Big Bang to the Bernini, linking the two together into a greater, coherent whole?
Tuesday, December 1, 2009
Recent reads&update
It's been a while since I wrote anything for reasons other than school work. While it's definitely fun to write for the lifelong dreams of understanding the complex systems we collectively refer to as life, I can definitely feel the effect of writing rather dry academic stuff all day and night. It's a slow and subtle process that will one day burn me out. Kind of funny considering just how beautiful the systems in nature can be, I guess it's one of the facets of the human psyche that I just don't understand very well... One day I should really think about this...
It's a weird process that I can only describe as drying out, just like lush forests slowly drying out into a desert. Sometimes everything I do, including the studies of sciences and the essential acts of reading, listening, and sleeping are all just my life's automatic attempt at trying to hold back the inevitable tide of desertification of the mind... The imagery saturated with sand inevitably bringing into my mind the vision of sand castle being built on the beach against incoming tides. Two sometimes opposing elements help me against such natural tides into inflexibility and forgetfulness. Singular obsession in action and variety in life. The more I live singular, almost obsessive dedication to something in life is essential in maintaining one's human quality, through ceaseless pursuit of truth, understanding and change of the status quo. However any decent human being tend to be supported by pool of experience that are at once more varied and detailed compared to the generation's norm. Obsession I fulfill with science, and variety I try to fulfill through act of reading. And writing... Well this is my equivalent of eating junk food. Something I just 'do for fun' to vent out the inevitable stresses of life. Two of the most recent books n my memory are 'The Bottom Billion' by Paul Collier and 'Tokyo Vice' by Jake Adelstein. Both are books I'd recommend any adult to give a chance, though Tokyo Vice can get a little graphic at times in its depiction of sex and violence, and is quite frankly not much of a literary masterpiece (the book was written under a duress that should be understandable to anyone aware of the back story... I'm not going to spoil anything for you). The Bottom Billion was one of the most, if not the most compelling and rational analysis of the very peculiar 'bottom billion' world we live in right now, with some very insightful suggestions as to how we might be able to change it for the better. Bottom billion in the sense of the book refers to more than a simple collection of 'poor people'. It refers to a collection of nations and its people that are caught in economic and political traps of decline, much like wells and traps of physical systems certain elements of the system just cannot escape from. The world in economic sense is expanding. It keeps on getting bigger and richer (in a sense). Even the poorest nations in the world are subject to some level of growth. However, there are certain groups of nations in this world that seem to be stuck in unnaturally low, almost zero growth rate, and they all happen to be situated in the African continent.
The best part of this book for an economics layman like me is the clarification and classification of the problem that had been haunting this world order for past few decades. It's incredibly simple to simply talk about 'poor people' and'poor nations.' While most of us might have best of intentions in discussing world issues using such loosely defined terms, the end result of such discussions just end up being something so obvious and meaningless, a philanthropic equivalent of discussing how many angels can sit on top of a pin.
The freak accident of the modern world is that people can immediately identify just what geographical region of the world is the poorest on the Earth, and by extension, what kind of people. It might be impossible to eliminate human misery from the world, but allowing certain geographical region to fester with the lowest, most miserable conditions of the human world is something that's 1)Inhumane
2)Irrational
3)Wasteful I don't believe for a second that current barrier between the so called 'developed' and 'developing' world that allows members of the developed nations to live their entire live without thinking about the consequences of their nation's international dictates will last. Either it will implode with catastrophic consequences, or be intentionally maintained with heavy price in terms of commodity, human lives, and human future. In the book 'The Bottom Billion', Paul Collier is successful in providing the reader with two things in regards to the issue of the bottom billion. Clarification and analysis of the problem through rational thinking, and suggestion of possible solutions based on actionable items. Compelling, is the word to describe the book, and if you are a young college student who might be thinking of changing the world, this is a book to read whether to agree with the author's specific analysis or not. I will write up another post on Tokyo Vice later on. It's getting a little tough to type up entire blogposts on my mobile handset.
It's a weird process that I can only describe as drying out, just like lush forests slowly drying out into a desert. Sometimes everything I do, including the studies of sciences and the essential acts of reading, listening, and sleeping are all just my life's automatic attempt at trying to hold back the inevitable tide of desertification of the mind... The imagery saturated with sand inevitably bringing into my mind the vision of sand castle being built on the beach against incoming tides. Two sometimes opposing elements help me against such natural tides into inflexibility and forgetfulness. Singular obsession in action and variety in life. The more I live singular, almost obsessive dedication to something in life is essential in maintaining one's human quality, through ceaseless pursuit of truth, understanding and change of the status quo. However any decent human being tend to be supported by pool of experience that are at once more varied and detailed compared to the generation's norm. Obsession I fulfill with science, and variety I try to fulfill through act of reading. And writing... Well this is my equivalent of eating junk food. Something I just 'do for fun' to vent out the inevitable stresses of life. Two of the most recent books n my memory are 'The Bottom Billion' by Paul Collier and 'Tokyo Vice' by Jake Adelstein. Both are books I'd recommend any adult to give a chance, though Tokyo Vice can get a little graphic at times in its depiction of sex and violence, and is quite frankly not much of a literary masterpiece (the book was written under a duress that should be understandable to anyone aware of the back story... I'm not going to spoil anything for you). The Bottom Billion was one of the most, if not the most compelling and rational analysis of the very peculiar 'bottom billion' world we live in right now, with some very insightful suggestions as to how we might be able to change it for the better. Bottom billion in the sense of the book refers to more than a simple collection of 'poor people'. It refers to a collection of nations and its people that are caught in economic and political traps of decline, much like wells and traps of physical systems certain elements of the system just cannot escape from. The world in economic sense is expanding. It keeps on getting bigger and richer (in a sense). Even the poorest nations in the world are subject to some level of growth. However, there are certain groups of nations in this world that seem to be stuck in unnaturally low, almost zero growth rate, and they all happen to be situated in the African continent.
The best part of this book for an economics layman like me is the clarification and classification of the problem that had been haunting this world order for past few decades. It's incredibly simple to simply talk about 'poor people' and'poor nations.' While most of us might have best of intentions in discussing world issues using such loosely defined terms, the end result of such discussions just end up being something so obvious and meaningless, a philanthropic equivalent of discussing how many angels can sit on top of a pin.
The freak accident of the modern world is that people can immediately identify just what geographical region of the world is the poorest on the Earth, and by extension, what kind of people. It might be impossible to eliminate human misery from the world, but allowing certain geographical region to fester with the lowest, most miserable conditions of the human world is something that's 1)Inhumane
2)Irrational
3)Wasteful I don't believe for a second that current barrier between the so called 'developed' and 'developing' world that allows members of the developed nations to live their entire live without thinking about the consequences of their nation's international dictates will last. Either it will implode with catastrophic consequences, or be intentionally maintained with heavy price in terms of commodity, human lives, and human future. In the book 'The Bottom Billion', Paul Collier is successful in providing the reader with two things in regards to the issue of the bottom billion. Clarification and analysis of the problem through rational thinking, and suggestion of possible solutions based on actionable items. Compelling, is the word to describe the book, and if you are a young college student who might be thinking of changing the world, this is a book to read whether to agree with the author's specific analysis or not. I will write up another post on Tokyo Vice later on. It's getting a little tough to type up entire blogposts on my mobile handset.
Friday, October 2, 2009
Importance of hackability
This is something I wrote down on my blackberry during one of those sleepless nights.
As I huddle in the darkness of my room with my Blackberry in my hand, listening to the mp3 rip of the Deus Ex soundtrack, and reading Cory Doctorow's the Makers serialized on the web, I am inevitably reminded of a question that had been plaguing me for a long time.
I read about the greatness of the old computer systems all the time, being something of a retrocomputing enthusiast. I read about all the wonderful stuff people did with their first Apple computers and Spectrum ZX, making and running crazy things on 128kb of memory. I also read about the demoscene where people squeeze old retro hardware to it last reserves of computing power to create fascinating works of pop art.
And then I look at my handset. I remember my old nokia running symbian, which is a modified version of linux fitted to run on mobile platform. I scrounge through the apps on my blackberry. Any modern handset I can remember using, and I can remember other people using is vastly superior to most of the retro hardware that are remembered so fondly. Even my older model Blackberry can kick the pants off the old Apple computer in terms of hardware spec, and it has much more sensors to boot, allowing it to communicate with the world through its eyes (camera) and location awareness (GPS). I'm not even going to talk about the always-on data connection because it's a given on any working handset.
Yet despite the reserves of computing power and amazing array of sensors available on this little buggers, they just don't seem to be able to inspire that same level of awe and creativity the first generation of personal computers did for its users. Just what happened? What is the difference between modern handsets and first generation PCs other than how superior many of the modern handsets are in terms of spec?
The answer I think, may have to do with the hackability of the handsets compared to the first generation PCs. First generation PCs were intended as computers. They had moderately sized screens (though the resolution was mostly worse than even the poorest smartphone out in the market today) and a full complement of input device you can use for extended period of time (just a full sized keyboard really, though it does make a difference). Yet these are still superficial hardware differences that can be made up for quite easily. Most high end Nokia phones support connecting to tv screens and what not, and most bluetooth equipped smartphones can interface with a bluetooth keyboard. Can, but not allowed to.
The biggest difference, perhaps the only difference, between the old first generation PCs and current handsets seem to be the software. The PCs were intended as computers meaning you were provided with the tools to develop new content for that platform, usually in form of BASIC implementation for the given system. It was possible to code in assembly and such if you were good enough. The best memories of the old systems and their wonders are almost always linked with the entry level development for the system.
You can't find that on handsets. Even Google Android doesn't yet provide a suitable platform on top of the mobile that can be used to manipulate the machine fully. There is a zero chance that a user of a blackberry handset would be able to run a code on the handset itself, and even linked to a full scale PC the road is usually long and confusing.
Granted, modern smartphone hardwares are complicated which necessitates (really?) the need for complex development environment. Yet, what if the mobile OS itself just gave the users just a slight bit more control to their own hardware? What if we can bring the modern BASIC equivalent like python onto the mobile OS, capable of interfacing with, and controlling the hardware?
Would it lead to another wave of developers and tinkerers world wide to create things that were completely unexpected?
As I huddle in the darkness of my room with my Blackberry in my hand, listening to the mp3 rip of the Deus Ex soundtrack, and reading Cory Doctorow's the Makers serialized on the web, I am inevitably reminded of a question that had been plaguing me for a long time.
I read about the greatness of the old computer systems all the time, being something of a retrocomputing enthusiast. I read about all the wonderful stuff people did with their first Apple computers and Spectrum ZX, making and running crazy things on 128kb of memory. I also read about the demoscene where people squeeze old retro hardware to it last reserves of computing power to create fascinating works of pop art.
And then I look at my handset. I remember my old nokia running symbian, which is a modified version of linux fitted to run on mobile platform. I scrounge through the apps on my blackberry. Any modern handset I can remember using, and I can remember other people using is vastly superior to most of the retro hardware that are remembered so fondly. Even my older model Blackberry can kick the pants off the old Apple computer in terms of hardware spec, and it has much more sensors to boot, allowing it to communicate with the world through its eyes (camera) and location awareness (GPS). I'm not even going to talk about the always-on data connection because it's a given on any working handset.
Yet despite the reserves of computing power and amazing array of sensors available on this little buggers, they just don't seem to be able to inspire that same level of awe and creativity the first generation of personal computers did for its users. Just what happened? What is the difference between modern handsets and first generation PCs other than how superior many of the modern handsets are in terms of spec?
The answer I think, may have to do with the hackability of the handsets compared to the first generation PCs. First generation PCs were intended as computers. They had moderately sized screens (though the resolution was mostly worse than even the poorest smartphone out in the market today) and a full complement of input device you can use for extended period of time (just a full sized keyboard really, though it does make a difference). Yet these are still superficial hardware differences that can be made up for quite easily. Most high end Nokia phones support connecting to tv screens and what not, and most bluetooth equipped smartphones can interface with a bluetooth keyboard. Can, but not allowed to.
The biggest difference, perhaps the only difference, between the old first generation PCs and current handsets seem to be the software. The PCs were intended as computers meaning you were provided with the tools to develop new content for that platform, usually in form of BASIC implementation for the given system. It was possible to code in assembly and such if you were good enough. The best memories of the old systems and their wonders are almost always linked with the entry level development for the system.
You can't find that on handsets. Even Google Android doesn't yet provide a suitable platform on top of the mobile that can be used to manipulate the machine fully. There is a zero chance that a user of a blackberry handset would be able to run a code on the handset itself, and even linked to a full scale PC the road is usually long and confusing.
Granted, modern smartphone hardwares are complicated which necessitates (really?) the need for complex development environment. Yet, what if the mobile OS itself just gave the users just a slight bit more control to their own hardware? What if we can bring the modern BASIC equivalent like python onto the mobile OS, capable of interfacing with, and controlling the hardware?
Would it lead to another wave of developers and tinkerers world wide to create things that were completely unexpected?
Thursday, October 1, 2009
Alan Kay applied to synthetic biology... And other late night notes.
I always find it very hard to blog. Even when I have the time to write something, not necessarily sitting in front of a laptop, mind you (I'm rather known for writing stuff that needs some word processor access and sending it in straight from my handset). It's only that I always feel that whatever I'm writing or trying to write at the moment just doesn't feel exciting or important enough. Which is why I keep multiple blogs around the net, each serving as a rant template for the other. Something would begin as a rant template on place A only to be edited into another form for place B, to place C, so on and so forth before the same yet radically altered post ends up as a follow up at the place of origin.
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. Oh or the pictures from this year's major diybio nyc event, where we set up a stall on the green market and extracted dnas from the natural produces with common household material (with the city people 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'm not even spellcheck this thing (god save my soul).
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 others. 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 very singular information storage and processing system that has quite a bit of parallels to 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 might even be able to predict some of the pitfalls that are inherent in developing any kind of complex programmable information processing system that will apply to the synthetic biology in the future. Maybe it would be possible to bring a conceptual framework to the synthetic biology that would have taken decades if left to mature naturally 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, respectively, 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 understanding and usage of 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 isn’t a platform capable of crunching the numbers the fastest, but 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 and cathode ray tube projections 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, or at least logical to learn. And there are 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.
Now, it's about time for me to get some sleep.
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. Oh or the pictures from this year's major diybio nyc event, where we set up a stall on the green market and extracted dnas from the natural produces with common household material (with the city people 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'm not even spellcheck this thing (god save my soul).
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 others. 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 very singular information storage and processing system that has quite a bit of parallels to 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 might even be able to predict some of the pitfalls that are inherent in developing any kind of complex programmable information processing system that will apply to the synthetic biology in the future. Maybe it would be possible to bring a conceptual framework to the synthetic biology that would have taken decades if left to mature naturally 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, respectively, 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 understanding and usage of 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 isn’t a platform capable of crunching the numbers the fastest, but 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 and cathode ray tube projections 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, or at least logical to learn. And there are 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.
Now, it's about time for me to get some sleep.
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