Consider Bookhling

(((I was trying to embed the videos from the KQED site directly in the post, but apparently copy pasting embed code in HTML panel isn’t good enough for wordpress. I’ve linked to them instead. They are quite good. You should really check them out.)))

Here are two videos on synthetic biology. The first one is a short introduction to synthetic biology produced by the wonderful people at KQED QUEST program, which goes into some level of detail on what synthetic biology is and what we are doing with it at the moment. Certainly worth some of your time if you’re interested in this new exciting field of science.

The first video is the original KQED QUEST video on synthetic biology.

The second video is the extended interview with Drew Endy available off their website… While the field of synthetic biology in the form we now know and love probably began with the efforts of Tom Knight at MIT, Drew Endy is certainly one of the most active and clear thinking proponents of the scientific field of synthetic biology.

Here is the link to the second video, the extended interview with Drew Endy.

If you hadn’t guessed yet, I’m really big on synthetic biology. I think it’s one of the most exciting things happening in the sciences today, not just for biologists but for mathematicians and physicists in that synthetic biology might one day provide a comprehensive toolset for studying the most complex physical system known to humanity so far… That of complex life-like systems.

I also believe that abstraction driven synthetic biology cannot manifest without a reasonably sized community of beta-testers willing and able to use the new parts and devices within original systems of their own creation. Computer languages like python and ruby needed efforts of hundreds of developers working in conjunction with each other for a multiple years to get where they are today. Complete operating system like Linux took longer with even larger base of developers and we still have usability issues. Synthetic biology must deal with systems that are even more complex than most computerized systems, so it’s not unreasonable to think that we’ll be needing an even wider deployment of the technology to the public and active community involvement in order to make it work as engineering capable system.

So I am a little dismayed, along with legions of other people who were initially excited by the promises of synthetic biology in conjunction with diybio community, to find that access to BioBrick parts and iGEM competition is severely limited against any amateur biology group operating outside conventional academic circles.

You see, unlike computer programming, constructing synthetic biology systems require BioBrick parts from the registry of standard biological parts. Right now it is next to impossible for diy-biologist interested in synthetic biology to get his or her hands on the BioBrick components through proper channels. The DIYBio-NYC group alone had quite a few number of people lose interest because of uncertain future aspects of being allowed access to the BioBrick parts and talking to people from around the world on that issue I’m beginning to think that there are a lot more of such cases. So far the major reasoning behind the restricted access seem to be the safety issue, but considering that the regular chassis used to put together BioBrick parts is based on academic strains of E.Coli that are even more harmless than your average skin cell I can’t see much wisdom in restricting access to the parts on basis of safety.

The bottom line is, the state of synthetic biology and BioBricks foundation at the moment is forcing a lot of people, some of them quite talented, who are enthused about contributing to a new emerging field of science to back down in either confusion or disappointment. Considering that the very structure of synthetic biology itself demands some level of public deployment to stress-test and demonstrate the effectiveness and stability of its individual parts and devices (with creation of those individual parts and devices left to the highly trained professionals at up scale laboratories) this is highly unusual state of affair that is not motivated by science behind synthetic biology. I might even go as far as to say it has the distinct aftertaste of political calculations of public relations kind.

The field of synthetic biology will never achieve its true potential unless the BioBricks foundation and iGEM administrators come up with some way for people outside traditional academy settings to participate in real design and construction of synthetic biology systems.

Here’s a little bonus, the QUEST show producer’s notes on ‘Decoding Synthetic Biology.’

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

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

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

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

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

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

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

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

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

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

Get to work.

Change the world.

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

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

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

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

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

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

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

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

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

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.

A quick note from a book before I fall asleep and forget about it…

Life Explained by Michel Morange (ISBN 978-0-300-13732-3)
1952: J.Perrett “Life is a potentially self-perpetuating open system of linked organic reactions, catalyzed stepwise and almost isothermally by complex and specific organic catalysts which are themselves produced by the system.”
-corresponds to 1/2 Joyce, representative of Autopoietic class models of self-organization.

Alvaro Moreno Bergareche, Julio Fernandez Ostoloza
1)life implies spatio-temporal structure
2)reproduction required
3)organisms store information that encodes a description of themselves
4)all organisms possess metabolism-set of chemical reactions-that convert matter and energy from the environment to a form that can be used by the organism
5)complex organisms functionally interact with the environment
6)all organisms exhibit interdependence among its components
7)all organisms attempt to stabilize themselves in the face of perturbations
8)life evolves
(((autonomy+ability to process information)))
Above list is characteristic of computerized artificial life research mindset, modeling ‘higher’ complex organisms as a basic template for the characteristics of life.
Claude Bernard:characteristics at apex of evolution just as fundamental as universal base trait

Patrice David, Sarah Samandi
I. Identifying the properties that charcaterize life and determining which of them is essential

1)distinctive molecular constitution that differs from other physical objects
2)complex architecture maintained despite the constant transformations of the material substrate
3)capacity to reproduce, due to presence of information molecules

II. Decide which of the properties constitute a universal criterion for recognizing organisms in an environment different from that of the Earth

Just a quick note on early Sunday morning. 

I’ve been reading up a bit on the topic of quorum sensing, which turned out to be a very interesting phenomenon. I’m not qualified to get into the specifics but it’s basically a cell to cell communications method used by bacteria. The mechanism is based on signal molecules and receptors that activate or deactivate certain sets of genes depending on signal strength. The strength of the signal would be determined by the density of the signal molecules within a given area. It means that bacteria (of all kinds I think) have built-in coordination mechanism for group gene expression.  This is news to me. I always thought bacterial behavior was more or less solitary with some mathematical mechanism behind emergence of bacterial colonies, rather than any specific signal mechanism that works to coordinate their behavior as a group. I guess the deeply ingrained eukaryotes/prokaryotes and multicellular vs. unicellular organisms chart from the middle-high school days left its mark on me. The Bassler lab at Princeton University’s department of molecular biology seem to be the leader in the field of quorum sensor studies, something I should definitely check out later. Here’s a TED talk by the lab’s very own Bonnie Bassler on bacterial communication.

This reminds me of a few iGEM project outlines I read on using BioBrick parts to form some sort of macroscopic structure using bacterial components. They all more or less failed as far as I know, but maybe something like that will be possible if we can build a BioBrick based mechanism for controlling quorum sensing mechanism of the E.Coli chassis… Or maybe there’s one in the registry already? I should remember to check it out. Maybe diybio-nyc can build a cellular automata system based on quorum sensing as a demonstration project later on. The prospect of studying complexity mechanics behind the quorum sensing and coordinated bacterial behavior is intriguing to me as well.

I’m also thinking of proposing a simple artificial cell project to the group. From what I’ve been reading the first steps towards building an artificial cell isn’t that complicated as long as we keep the goals modest. For now the goal would be to have DNA replicate and produce proteins within an artificial vesicle.

I spent all of 18th in the openeverything conference at the UNICEF headquarters. This was the first barcamp style meeting I’ve ever been to in my life, so I thought I might as well jot down some notes.

For those of you who don’t know about what barcamp is, it’s like an emergent conference. You get bunch of people together in a building, and everyone who wants to talk about something just post their topic card (or whatever the equivalent you are using) on the main board. When the time comes you either present something or have a discussion on that topic with people who were interested enough to show up at your session. It sounds a little chaotic, and it really is sometimes, but on the whole the system works very nicely. Even the people who aren’t as talkative as others get to talk in such settings, and there is no barrier dividing the audience with the speaker so you can actually get work done with people who share the same interests as you without sitting there waiting for some guy/gal to finish talking. If you wanted to talk or listen to something but there’s no one talking about it you can always walk up to the schedule board and write up your topic, and voila, you have people showing up trying to figure out what to do with your chosen topic (I actually tried it and it worked, surprisingly enough).

As far as traditional barcamps go this wasn’t really the most ideal of the camps, since of the 220 or 250 people who said they were going to show up only about half (maybe even less) arrived. Even so, the diversity of interests and objectives were electrifying to me to say the least. Being hosted by the UNICEF most of the topics revolved around programming or infrastructure projects that can benefit the causes of UN, like the rapid SMS which is a computer based SMS system that interface with cell-phones to create different kind of low-cost wide area logistic coverage. The system is completely open-source and scalable, and it’s been used in the field for various UN related activities like education and keeping logistic tracts of 65 million insect nets that were set to be distributed across some parts of Africa. Other interesting topics included a brief discussion on the nature of AI (though none of the people in that particular session seemed to have a very good idea of artificial intelligence), cheap open-source aerospace programs, and computerized education systems/web 2.0 services that might be used to keep track of education and qualification of individual members in form of a flow chart. Using such a system a kid might be able to copy and follow the skill/education set of, say, an astronaut if he/she’s interested in pursuing such a future. I do realize that while education goes above and beyond simple skill set qualifications the idea itself is sound, and I would love to see it implemented in a real web system someday.

I was hoping for some people to do a tract on diybio/open-source biology and open science in general, but for some reason no one really set up a topic that relates to those interests. So in true spirit of a barcamp I decided to set up a topic myself, which was a little overwhelming at first, this being the first barcamp-style con I’ve ever been to. It didn’t help that I’m usually not the one to speak in public venues. It was something of an adventure, and I decided to take the plunge. I was helped by some of the onlookers who pointed out the processes of barcamp that makes it work as a sort of emergent conference with emphasis on ‘burst activity’ and getting stuff done.

Well to be frank, the talk I gave was a mess. It wasn’t prepared and I was really wiped with other talks by the time I got to my session. Having people who knew even less than me in regards to biology didn’t really help either, since I was constantly double checking my facts so that I wouldn’t give any twisted impression of diybio to people who are new to the idea. I more or less wandered around the topic of diybio and synthetic biology, and though I did stress that synthetic biology is not diybio, I’m not too sure if other people got that message clearly enough. It’s my fear that a lot of people who showed up at my session went away with inflated and unfounded hope on the current state of diybio and synthetic biology… I did learn a lot from the experience though. Maybe as I get more experienced with this stuff someday I can give a compelling talk on diybio that would lead people into participating in this very exciting intellectual movement.

I did receive a lot of interesting input from various people regarding the state of licensing and what it really means to creative open-source content (it was ‘openeverything’ conference after all. Lot of license-related people). I always thought I knew a thing or two regarding the basic ideas of CC license and GNU/open-source license terms (which btw, Richard Stallman insists is separate from each other). It turns out that I didn’t know squat. Penetrating the thin veil of ignorance: that’s what I call an education!

I should have a post on diybio-nyc’s recent GFP E.Coli session sometime this week. Stay tuned!

Okay, here we are, the fourth meeting of the diybio nyc group. As you can see the meeting was on the April 15th, almost a week ago, so I’m a little late in writing this post. The week had been a little crazy (I’ve been saying this a lot lately), so I really didn’t have the time to get around to it… It didn’t help that I had a bunch of class works that were already overdue and I had to spend the whole of Saturday and Sunday with bunch of UN/Google/open-source people related to the openeverything conference/bar-camp, which I will have to write about soon.

The April 15th meeting was a discussion meeting wit no lab session involved. It was held in a restaurant downtown called Veselka, an Eastern European restaurant serving some good pierogi (never had one before). While the food was good, the atmosphere wasn’t the most ideal to have a complex discussion though. It’s more of a family place, with lot of people coming and going, everyone talking at rather loud volume and etc. It was a refreshing change of pace from sometimes pretentious NYC food world… But I’m not really about to write a review on the restaurant am I?

The situation worsened due to the fact that a reporter from the New York Times Magazine was planning to show up. Some people in the group had experience with journalists (one of them is a published journalist actually), so we were afraid that something we say might be used out of context. There’s a lot of scaremongering out there in regards to the possible dangers of diybio, and it’s something we really have to avoid at all costs. And then the new members showed up. Total of three. All of them came from very unusual and interesting backgrounds but the venue and the circumstances weren’t very ideal for personal introduction between the old and the new members, especially owing to the fact that the ambient noise was to such an extent that we could not hear people from across the table. I would have loved to talk to them a bit more but didn’t really get much of a chance in between trying to hear what other people were talking about and trying to get actual work done in regards to the mission statement, identity and direction of the diybio nyc as a whole. One of them came from biotech background and I’ve been keeping in touch with him for a while now, through IM and twitter. The other person came from art background, working with a type of bio-art club/collective called the Grafting Parlour, which is kind of like the SymbioticA, pursuing the techniques of biotechnology for artistic pursuits. The last person to show up was from computer sciences background with interest in film making, who seemed a little surprised that she’s the only one with computer sciences background in the whole diybio nyc group (quite frankly that surprises me as well, considering that the whole concept of biohacking came along with the advent of computer sciences and biology’s increased dependence on variety of computerized techniques). I’m afraid that some of us (including myself) might have seemed a little distant to the new members of the group. I will have to try to remedy that somehow later on. DIYbio is about the spirit of openness in science and it would contradict the implicit founding spirit of the group to make new members feel out of place. I’m especially looking forward to talking more about the activities and purposes of the bio-art movement. I believe the whole concept of bio-art itself is replete with incredible possibilities that only art can dare to explore, though the group would have to find a compromise between ethical and scientific constraints and the spirit of exploratory arts… Even finding that fine line between arts and sciences sounds intriguing to me, to be honest.

The basic agenda of the meeting was on drafting the mission statement, establishing the main short term and long term objectives of the group, and finding a way to realize those goal within realistic budget and time constraints. Whenever we talk about doing some sort of project one problem gets in our way. Any biological project of even moderate complexity requires a dedicated lab space that’s not located within residential address. We might be able to pull it off within private residential setting like those people trying to build a bio-lab within their closet, but it won’t do for any long term experiments or groups, since there are just too many legal hoops and hurdles we’d need to workaround. And the last thing diybio as a whole needs in this age of terror-related scare-mongering is questionable legality and dubious safety measures. A member of our group experienced in operation of biotech laboratories is strongly pushing for strong safety protocols comparable to those applied to commercial labs, and I agree with her point. It might sound a little bothersome right now but it will go a long way toward the group being a fully pledged biological lab space.

The problem in obtaining a real lab-worthy space in the city is that it’s just too expensive. We would need a way to raise some funds, by ourselves or with cooperation with other educational institutions in the area like one of our members suggested. We can do a lot of those things if we decide to keep things hush hush and work under the table, but again the risks are just too great. In the nightmare scenario what we do wrong might effect the diybio movement as a whole, pushing the public opinion toward opposition. It’s the group’s implicit agreement that we can’t take that kind of risk at this very crucial time. Compared to finding the space, obtaining real lab equipment is a child’s play, and we’ve already made a lot of progress in that area thanks to one of our member’s generous input.

We need to find a path that would work toward to solving the space issue, and at the moment that happens to be working toward obtaining a legal status for the diybio nyc. It’s our collective belief that having an actual legal identity will help us toward raising funds, cooperating with existing lab spaces, and establishing supply relations with bio-companies we would need to contact in order to get perishable experiment resources. The ideal legal status for a group like diybio nyc would be a registered non-profit, whose tax-exempt status would afford the group with some negotiable leverage when it comes to financial negotiation and support. Drafting mission statement and by-laws for the group would be first step in establishing legal and ideological identity of the group.

All this sounds like a lot of financial and legal talks for a group supposedly dedicated to bringing science to the open. Experiments cost money and requires space, so it can’t really be helped for the moment. At least we do have an actual wet-lab session coming up this Tuesday. It’ll be an experiment to introduce GFP plasmid vector into K12 E.Coli chassis (the E.Coli chassis in this case is completely harmless to human beings. You can actually drink it and it’ll pose no threat to you. It’s a special, non-toxic strain of the E.Coli we all know and fear, that’s been used in laboratories for about a century, as well as variety of high school biology classes). It’ll be a first experiment that would actually allow us to observe and experience the process of introducing plasmid into a bacterial chassis with visible results, so saying that I’m excited about the prospect would be an understatement.

There’s been a lot of trials and tribulations for the group, and I’m sure that there will be more to come. But we are going somewhere with this, and it’s really good to see so many people interested in learning more about the techniques and science of biology outside the traditional medium.

A while ago I came across a new program in MIT’s school of continuing education. Apparently the field of synthetic biology is popular, if not mature, enough to deserve a star-studded cast of lecturers doing lab circuit with the class participants for five full days. I was at once enthusiastic about going (the class would have takne place during summer vacation), but then I was faced with the unpleasant reality of the price tag associated with the course. The five day synthetic biology course for MIT’s school of continuing education would set me back $3250, which is a little more than what I can afford on my meager college student budget. Now, don’t get me wrong. Considering the quality of the lecturers and the range of synthetic biology materials covered in the course the $3250 price tag is not high. I would even go as far as to say that it’s rather cheap for what it offers (chance to attend a leture and possibly even a lab session with George Church? Any molecular biologist worth his/her salt would practically drool over the idea). However, the quality of the course offered wouldn’t make $3250 appear out of thin air, as much as I hate the reality of it.

So I let loose a bit of idea on the twitter and the diybio mailing list on exploring the possibility of putting together a $300 diybio course. Mackenzie Cowell was enthusiastic about the whole idea, as well as host of other people. There were a few dissenting voices as well, debating the need for a physical diybio class when the course materials are usually freely available through the net. Other people argued on the fact that diybio class put together by bunch of disparate groups will never be able to catch up to the qualit and scope of the course offered by MIT. Both are valid points and I think I will take some time to refute those claims while I have the chance.

First, physical courseware is always preferrable to virtual courseware given the choice. While diybio shares many parts of its ideological and historical roots with diy/hackerspace movements that center around computer interfaces and mechanical hacking, diybio is not computer hacking. Computer hacking may be part of what diybio is, but at the core diybio is more about citizen/open sciences initiative rather than diy engineering. The maturity of the techniques and tools of synthetic biology and other fields of biology in general is still not at the stage where we can simply treat it as a subset of personal engineering. It all means that diybio must at heart center around real practice of physical experimentaion in order to be successful (barring the diybio-bioinformatics). Computer simulations can only simulate what we already know. Virtual coursewares scattered across all corners of the net, however helpful and detailed they might be will not be sufficient for the vast majority of the people who have a reason to diybio. If diybio is to become what it promises to be, there is an urgent need for a unified and accessible syllabus that ties the materials on the net into one structured and comprehensible package. And we need human instructors capable of answering the student’s questions and demonstrating the physical methods involved in doing diybio instead of forcing people to search all over the net for a video whenever some part of instruction is unclear.

Second, the proposed $300 diybio class idea is never meant to compete with the MIT class in any capacity. It would be preposterous to even consider that. As one member of the diybio nyc pointed out to me, the fully-pledged courses at the institutions like the MIT are not designed with simple injection of knowledge in mind. It’s about shaping the student into a general academic capable of asking the right kind of questions. If simple lab-routine and knowledge already present in textbooks were the point of higher level education then there would be no need for researchers to pursue PhD. They can simply train to be a lab technician. Such vigorous cultivation of invetigative mind is absolutely beyond the scope of the $300 diybio class and there’s absolutely no way that anyone would equate the one to the other in any capacity. The purspose of diybio class (if it ever come to pass) would be to introduce the general public with no experience in any lab techniques and biological sciences to the physical methods of doing those sciences. Maybe some people will use that skill to do something worthwhile, slowly building up to a real pursuit of science in the future. Maybe some others will use that knowledge to make glowing bacteria and wow people at parties. It’s entirely upto them and it’s not within the scope of the diybio class to consider such things.

The purpose of $300 diybio class would be clear and concise. It would be to introduce people with no experience in sciences to the basic gateway tools and methods of doing biological sciences through combination of lectures and lab exercises. Period.

I think this is a very viable idea, considering that many high schools are beginning to adopt some form of biotechnology course into their curriculums. As long as the materials and scope of the class are kept modest low-cost introductory class incorporating lecture and lab exercise is a reasonable goal.

So how exactly would we be able to put together a diybio class? What kind of materials and execises will it cover? Well it turns out that it’s a nastier problem then I first expected. The problem is the identity crisis of diybio. While the whole notion of diybio was popularized along with the advent of synthetic biology and iGEM competition in mainstream media, diybio is not genetic engineering. It’s not even synthetic biology (and yes, genetic engineering and synthetic biology are different). Making a diy gelbox or any other biology lab equipment is diybio. Using bioinformatics to research genus of certain organisms is diybio. Collecting samples of everyday objects and analyzing what kind of things live in cities of the world is also diybio. I might even go as far as to say that programming visualization routine for DNA sequence for use in visual musics comes very close to being part of diybio.

As Mackenzie Cowell put it, the field covered by the term diybio is positively nebulous. It would be crazy to attempt to cover all of that stuff in a $300 class designed by a diybio group. We will have to make a list of things that people can diy in relatively meaningful capacity within context of modern biology. And we will need to figure out a way to put it all together within a greater framework designed to instill in the participant feeling of fulfillment and familiarity with biological sciences.

I’ve considered many options on the must-have list of things for a diybio class, and I feel that the class would have to center round understanding and practice of diy synthetic biology. I believe that the basic tools and knowledge that would allow non-specialist to do a bit of synthetic biology would allow him or her to pursue other areas of diybio from building a personal gelbox to begin learing basic tools of bioinformatics, provided that the diybio class devotes some of the time to understanding and usage of appropriate computerized tools. Of course, even if the diybio class was to center around understanding synthetic biology we would still need to make people understand that synthetic biology is a very small part of diybio movement as a whole.

If the diybio class is to take a form of rudimentary synthetic biology class it would be important to try to integrate lab component as a large part of the overall course. It would allow diybio class to avoid any overly technical discussion unless the participants actively ask such questions, since the class assumes no prior knowledge or experience in biological sciences (nothing beyond the basic high school level biology that is). Focusing on introducing the participants to hands-on experiences related to synthetic biology would work to the benefit of instructors and studens alike within the limited time and resources of the diybio-synthetic biology course.

Introducing synthetic biology to the layman would necessarily involve introducing the concept of biobricks. I believe that it would be nearly impossible to introduce inexperienced population to actual hands-on experience of synthetic biology without the compartmentalization offered by the concept of biobricks. That will prove to be a problem. At the moment it is very difficult for any private organization to obtain biobricks due to possible safety issues, and it is very unlikely for the diybio class or its administration to be able to simply ask for biobricks from the BioBricks foundation itself. In case the class cannot obtain biobricks themselves, I’m thinking of introducing some sort of graphical language that demonstrates the workings of biobricks as well as integrating the whole thing into some sort of graphical computerized environment, in fashion of BioCAD. I’ve seen more than a few of such programs being proposed or demonstrated at the Synthetic Biology conference 4.0, and I think I might be able to find a suitable platform given some time for research. Such simulated study and demonstration of biobricks would be combined with a simple lab exercise introducing GFP plasmid into E.Coli or any other available chassis. It would prove to be a sort of gateway exercise for inexperienced people, allowing them to understand the rudimentary process behind introducing foreign plasmid into a cell chassis. While this is certainly a gross oversimplification of the techniques involved in fields of genetic engineering and synthetic biology, I believe it would be beneficial in introducing people to deeper study of biology once the class is over. Besides, obtaining cell chassis/GFP plasmid kit is much easier then obtaining biobrick parts.

Whether biobrick parts can be obtained physically or not, the diybio synthetic biology class would center around the study of the parts and how they can be put together with aid of computerized models. Maybe it would be better for the class instructor to choose a proven construct made from biobrick parts to pick apart along with the class. Ideally it would be one of iGEM projects that have been experimentally demonstrated, or even a minimal project put together by the instructor or the diybio community itself. The general flow of the class would be as follows.

A-synthetic biology primer
B-obtaining and using biobricks
C-obtaining and using cellular chassis
D-putting it all together using computational tools/measurement standards
E-wet lab session as an extension of D

*each section will have its own bit of lecture session introducing concept and theory behind the physical exercise.

In all scenerio the goal is to have the student capable of building simple circuits using biobricks using graphic aid and pre-made computational tools. Depending on circumstances the students would participate in an actual wet lab session utilizing biobricks, either their own project or a single project being demonstrated for the whole class.

Incidentally this is also the general structure taken by the MIT synthetic biology course, according to the website.

“Fundamental tools of synthetic biology include:

ready access to off-the-shelf standardized biological parts and devices;

a reliable and defined cellular chassis in which engineers can assemble and power DNA programs;

and computational tools as well as measurement standards that enable the ready integration of simpler systems into many-component functional systems.”

The general class structure at MIT’s course will be:

“Day 1: Biological engineering and synthetic biology, computer science and synthetic biology

Day 2: Engineering principles for parts and devices, measurement standards, redesign of cellular chassis;

Day 3: Principles of protein and pathway engineering, computational redesign of proteins;

Day 4: Optimization of microbial chemical factories, redesign of metabolic pathways, standards of practice

Day 5: Summary and future directions”

The MIT synthetic biology course will prove to be a useful tool in figuring out how the diybio synthetic biology class should be structured, though it must be mentioned that diybio class will have to keep things as simple as possible, and stay away from ambitious topics outside the experience of the instructor.

So for now I need to research following stuff for diybio synthetic biology class.

1.inquire about obtaining biobrick parts, possibly from universities in the area after the iGEM competetion.
2.research biobricks graphical language and computer tools, targeted at novices.
3.figure out basic logistics, like the place, precise time and date, and the duration ideal for completion of the class.
4.find a way to obtain a simple GFP plasmid kit (with chassis), necessary equipments and etc.
5.find a biobricks based project that can be picked apart for the duration of the class. Or maybe even design one, in wetlab or on paper.

All this is of course a pipe dream without the diybio-nyc gaining more of a logistical foothold and legal status. Regardless a lot can happen between now and November or December of this year, which is the projected time for the class.

I will try to update as I go along with the research for putting a class together.

So here’s an interesting short article on the possibility of internet gaining some type of consciousness due to its network based emergence-friendly structure. The author is the famous Ben Goertzel, one of the foremost minds of the futurist/AI school. If you’ve got time you should check out his blog for other articles as well. I’ve found a number of them to be quite compelling. I’ve always been interested in artificial intelligence, though my concentration is with artificial life. In time I’ve come to view the two as the same type of system manifesting in different mediums, and I’ve come to think that intelligence is a trait that naturally comes along with the collection of characteristic called life. Intelligence is life and life is intelligence. In that sense I consider even minuscule bacteria to be intelligent, though not in a way we usually think about intelligence. The very fact that certain collection of molecular machines can work in conjunction to behave in such a way that allows it to feed, evade harm and propagate, even in evolution-aided unconscious manner means that certain system should be considered intelligent. Of course, this is merely my personal view that is not backed by evidence based professional study. This is more of a personal impression with reasonable causes, something that’s on it’s way of becoming a hypothesis but not quite there yet as the things stand. Considering that I consider our current definition of intelligence to be lacking in many ways, I will be at ire of many neurobiologists should I exclaim such opinions carelessly. And for some reason there are a lot of neurobiologists around me so I try to keep my mouth shut most of the time regarding that issue.

Ben Goertzel’s answer to whether the net can become an intelligent construct is somewhat vague, but then he probably can’t help it himself. The question itself is a bit on the vague side when you think about it, including the whole uncertainty of the definition of intelligence that I just wrote about above. He briefly mentions the pervading ethos of the neurobiologists of the recent years, that many of them believe that intelligence/consciousness is a property that will inevitably emerge from any complex system that has the right sort of internal dynamics. I do definitely agree with him on that point, since when you think about it it’s about the only scientifically feasible explanation of the emergence of intelligence/consciousness without attributing some specific part of the brain to the trait of intelligence (like how Rene Descartes attributed ganglia as the sit of the soul). I also suspect that life arises in a very similar manner, and whether that pattern of internal dynamics can be an abstraction that can be applied to different types of physical systems is a major part of my current research as a fledgling science student (the one that’s helping paying my rent). Hopefully I’ll be able to come up with something in my lifetime, since I view the possibility of such a universal theoretical platform to be a big game changer in the upcoming human century, something that might as well change the world we live in along with applications of nanotechnology and modular biology.

Will internet itself become intelligent at some point? I’m sure it will. Dr. Ben Goertzel points out that the internet is way too fragmented to display a coherent vision of an artificial intelligence and instead suggests that there might be a way to construct a sort of unifying backbone using the network infrastructure of the internet itself as a sort of raw data feed/complexity provider for that central structure. It makes sense, in a way that no one really thinks about it before someone else says it first. Most complex emergent systems, when laid out using some elements of graph theory (the graph theory, we are not talking about bar graphs and such nonsense here, for those who haven’t been keeping tabs on mathematics) displays inexplicable tendency to form central clusters around certain limited number of nodes instead of distributing indefinitely. And the change usually isn’t gradual or predictable. It happens rapidly under certain critical threshold as Stuart Kauffman put it very succinctly on his book “At home in the universe.” Internet is very obviously following in that pattern. The last graphic map of the internet I’ve seen displayed certain number of nodes (websites/services) with overwhelming number of links with a lot of nodes with limited number of links. Similar pattern is also observed in the growth of neural pathways and formation of galactic clusters, and who knows what other phenomenon in this universe escaped our notice, considering that complexity science is still a new field. Now I don’t have a very clear idea of what form that central structure would have to take to make the internet truly intelligent to observable degree… I assume it would be something on par with designing CNS for the distributed system that is the internet, possibly with a hint of recursive structure via Douglas Hofstadter, but this is all just some ideas bouncing around and I have no idea what physical/informational form such a construct would take. I’d assume it is something far past the simple matter of linking a lot of links within network nodes or providing raw processing power (that would be like saying any game of go can be won with large enough number of stones, which is just dumb. This isn’t a chess, kiddo)… I should definitely give some more thought to this, the ideas on the nature of the ‘central structure’ might as well be the catalyst I’ve been looking for.

The problem that continues to bother me whenever I think of artificial intelligence is the vague definition of intelligence we seem to share. Just how can we tell what is intelligent or not? Most definition at the moment seem to be about figuring out how human-like other organisms/systems are without regards to the actual ‘intelligence’ of that organism/system. I may not be a professional but I smell a very homocentric perception whenever I read something that pertains to the nature of intelligence. If intelligence is about being able to communicate with other beings then antisocial foreigners are not intelligent. If intelligence is about being able to react to the environment so that you can find sources of food and multiply, then bacteria are intelligent. Maybe even viruses. Both of them do not have any sort of nervous system like we do with ‘higher organisms’ so it makes the problem of intelligence a bit more complex.

Internet may become intelligent someday. This is the year that the internet will have the equal or higher number of hyperlinks as there are synapses in our brains. The real question is, how will we be able to tell if it is intelligent? Are we looking for intelligent traits or are we looking for human traits?  How would we be able to tell the difference when the time comes? Maybe the first machine intelligence that blossoms on the world wide web will be trampled on by us as a mere bug in the system. After all, we do it to each other all the time.

On a little side note, the diy-bio NYC had our second meeting this Monday. We made a gel box, extracted DNA, and had a jolly good time. More on that later.