Life during summer and consilience notes
I should definitely to a decent post some time soon, but it seems that I’m in middle of severe drought of ideas and writing abilities. Hopefully this is just a passing phase… Someone should definitely develop a drug against writer’s block I think.
A few things I’ve been working on so far between all the jobs I have to run to pay my rent. I’ve been studying the Exploring Complexity by Gregoire Nicolis and Ilya Prigogine since the beginning of the summer. Studying as in tearing through every bit of reference mentioned at ends of each chapters and working out all the equations, making up some of my own for practice. The progress has been slower than I would have liked but it’s still coming along nicely. I’m upto the randomness and complexity chapter where they begin describing Markovian processes and different types of entropy. I’ve been trying to come up with some cool graphics describing some of the stuff in the book using Mathematica but couldn’t really find the time to get around to it, with all the other coding projects on my hand at the moment, but I’ll definitely have something to show for by the end of the summer.
I’ve also been reading up on some bioinformatics literature, beginning with the eponymous ‘For Dummies’ book on the subject which is surprisingly well written, or at least comprehensible (well, considering the title it would be hard to write a book on the subject that is incomprehensible). It’s part of my attempt at coming up with a decent diybio coursework aimed at 14 and above, centering around the kind of projects the laymen would normally find out of reach, like designing a biological circuit and putting it together in a wetlab. With so many computerized tools and advent of abstraction in biological sciences brought on by synthetic biology, I think it is possible to empower the citizenry with end-user scientist toolset. The average computer user don’t code in assembly or the machine language yet many of them are perfectly capable of coming up with useful high-level softwares and beautiful works of art (it still takes effort and mastery but what doesn’t?). In order for the biological sciences to become user-friendly I believe we need a tool to familiarize them with the higher level abstraction in molecular biology and computerized tools associated with it. In my experience the best way to break down an intellectual barrier is to make people do the impossible easily and cheaply. The first step of breaking down the biology barrier would be teaching people how to design genetic circuits using extremely high level abstraction symbols. Theoretically it should be possible to put together a very simple circuit on a napkin using symbols and diagrams using unified ‘visual language‘ of synthetic biology. Once the individual becomes scientifically fluent enough to visualize these molecular circuits within his or her head, and feel a real want for building something in real life, we can easily transfer the design into computerized tools for specification and optimization. After that it would be a simple process of transformation using mail-order kits (or using diy tools if you’re so inclined), which DIYBio NYC have already demonstrated to be easy and straightforward.
By then, maybe I’ll try to pitch my not-so-secret ambition of coming up with diy-minimal/synthetic cell ::evil laugh::
As you might have guessed I’ve also been spending a lot of time reading through E.O. Wilson’s Consilience: The Unity of Knowledge again. It’s amazing just how much of the book resonates with me, not necessarily in solutions but in problems he outlines as something fundamental that needs to be resolved if we are to further our understanding of the universe.
-From pg.93
“…the U.S. federal high-performance program has upped the goal to a trillion calculations per second by the end of the century. By the year 2020, petacrunchers, capable of reaching a thousand trillion calculations per second, may be possible, although new technologies and programming methods will be needed to reach that level. At this point the brute-force simulation of cell mechanics, tracking every active molecule and its web of interactions, should be attainable- even without the simplifying principles envisioned in complexity theory.“
The continuing battle (if there is one) between raw computing power against elegant universal systems like the kind proposed by some of the complexity scientists is interesting. For one thing, would we need raw computing power the world has never seen so far to replicate human-like intelligence? Or can it be done in smaller scale using some aspect of the logical system that gives rise to emergent trait we refer to as intelligence? Classification of life/intelligence as a type of physical system that very closely resembles phase transition due to complexity is an intriguing possibility that will need to be examined in detail… I’m especially interested in intelligence as not something that computes but as something that creates. Why am I sitting here writing down this stuff when the weather outside is so great? Why do people strive to create this stuff and ideas when it’s much easier to sit on their collective asses and eat chips? To some the activity of creating get to the point of destructive obsession. Am I alone in sensing that the society at large tend to be envious of those kind of people?
Curiosity is not a rational trait. It’s crazy and sometimes suicidal, and doesn’t serve any kind of immediate need for survival or propagation. It is the very picture of irrationality. So where does it come from? What aspect of the molecular system that we refer to as living beings gives rise to such weird behavior? And what’s with this crazy unreasonable effectiveness of mathematics in the natural sciences? Isn’t it weird how questioning the nature of mind, life, and human behavior so often leads us to the questions on the fundamental nature of the universe itself?
-From pg.93~94
In 1994 editors of Science, celebrating the inauguration of developmental biology by Wilhelm Roux a century earlier, asked one hundred contemporary researchers in the field to identify what they considered the crucial unanswered questions in the discipline. Their responses, in rank order of attributed importance, were:
1.The molecular mechanism of tissue and organ development.
2.The connection between development and genetic information.
3.The steps by which cell become committed to a particular fate.
4.The role of cell-to-cell signaling in tissue development.
5.The self-assembly of tissue patterns in the early embryo.
6.The manner in which nerve cells establish their specific connections to create the nerve cord and brains.
7.The means by which cells choose to divide and to die in the sculpting of tissues and organs.
8.The steps by which the processes controlling transcription (the transmission of DNA information within the cell) affect the differentiation of tissues and organs.
Remarkably, the biologists considered research on all of these topics to be in a state of rapid advance, with partial successes in at least some of them close at hand.
Above questions were written around 1994 according to the Consilience. It’s been over a decade, so I wonder how many of above questions had been answered definitely and conclusively….
Also, it’s rather interesting that most if not all of above questions are in some way related to study of complexity sciences. It’s almost as if the whole field of complexity science is biology fused with mathematical abstractions.
From Consilience:the Unity of Knowledge
“The intellectual power, honesty, lucidity, courage, and disinterested love of the truth of the most gifted thinkers of the eighteenth century remain to this day without parallel. Their age is one of the best and most hopeful episodes in the life of mankind.” – Isaiah Berlin
There is a book titled ‘Consilience: the unity of knowledge‘ by E.O.Wilson. Buy it, and read it. It’s worth more than a hundred iPhones, unless the said iPhones have copies of the Consilience on it.
The book had such profound impact on me when I was growing up, I really think I should do a review/post on the book and some of its themes one of these days. It came out years ago yet the prescient insight of E.O. Wilson rings true to this very day in many fields of human endeavor. I had the chance to listen to his talk live in the closing event during the wonderful World Science Festival in NYC, and I should say he still seem to retain that certain edge even after all these years. I guess that’s what we Koreans call No-Ik-Jang for you. If only I wasn’t so shy to ask him for an autograph on my copy of the book. I feel like a kid who lost a winning lottery ticket.
Now that I think about it I should also do a post on the World Science Festival while the memory’s still fresh… So many things to write about, so little time to write them.
note: Life Explained
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
Ebook future
I just came across an article in the Wired stating that Amazon will almost certainly unveil a new ebook reader with larger screen size. While the article goes on to talk about possible tablet device from Apple as being a heavy competition on the ebook market compared to the text-centric ebook devices, my attention span more or less stopped with the mention of the new ebook device on the horizon. It’s not just a new ebook device that’s about to come out. It’s a larger screen ebook device specifically targeted at the academic textbook market. Apparently Amazon want a share of the 9.8 billion textbook market (and that’s just U.S.), and I say it’s about time. I can still feel the phantom pain imposed on my back by years of carrying around textbooks that are heavy enough to be used as a decent weapon. It would be great to be able to finally carry a book-bag that weighs a lot less than the standard combat gear.
I’ve been an avid ebook user ever since I learned about existence of those wonderful devices and the myriad of texts available on the web for free use, like the extensive collections in wikipedia, various blogs, and the project gutenberg. I had my first encounter with ebook devices a long time ago before Kindle made it cool to carry around ebook devices. In fact, as far as I know the ebook reader I use, the Sony Reader PRS-500 might be the first dedicated ebook reader in North America that uses e-ink display. This ebook reader had been a trusted mobile library by my side for the past two or three years. Even before purchaing this dedicated ebook reader, however, I was using old discarded palm pilot devices (so old that they stil had this ‘volatile memory.’ It was a memory scheme used in palm devices before the advent of all-too-familiar flash memory. If the device ever ran out of power all the data stored on the device would be lost, thus the term ‘volatile memory’) to read ebooks on the go, most of them reformatted webages I made using a handy Palm utility program called ‘plucker’ with ability to turn any webpage/archive format into a palm-ready ebook. Later on I’ve also used my Nintendo DS as a dedicated ebook reader (instead of playing games like a good kid) burning multitude of memory cards with whole repository of text and HTML formatted ebooks I found through my sojourns on the net.
I love my paper books as much as anyone, of course. And even now, with my extensive ebook collection (most of them surprisingly DRM free) I always make a point of buying paper books now and then. Some people stock up on weapons and emergency supplies for the inevitable zombie apocalypse. I stock up on paper books for that one day when I won’t be able to recharge my digital book-reading devices anymore, and my vast library is lost within the magnetic patterns etched upon my external hard drives. However, there is an unavoidable allure to being able to carry around twenty to thirty books of my choosing in a slim and light package that weighs as much as my hard drive ipod. The fact that I’m a rather fast reader only adds to the attraction of ebooks and ebook readers. Before I came across ebooks how my luggage would be filled with books whenever I traveled far away from home, and I happen to travel often. It really made for quite a workout, carrying those bags all over the place. With ebooks, I just need to carry the little device and its charger for my casual reading needs, with a hardcover or two just for those tight spots when I’d need to study instead of read. Many people still debate the need for having a dedicated device for reading digitally formatted books, and they are right. having an ebook reader will not change your life if you don’t read in the first place. In that light dedicated ebook readers are certainly niche devices, intended for use by the relatively smaller portion of the population would would buy books through digital distribution channel and who would be willing to pay for a device that goes into the hundreds of dollars just to be able to read more. The two things I’ve just mentioned might sound insignificant hurdles to most people who consider themselves to be internet savvy, but when we think of the reading population as a whole whose members come from various walks of life and are at various stages of life, those are some significant barriers for entry to the ebook world. Yet Amazon’s Kindle demonstrated clearly what dedicated gadget community members knew all along. People actually read, and many of them are willing to pay to support their habit, as the multi-billion dollar publishing industry would attest (and this is just in U.S., and quite frankly, we aren’t the most reading-intensive country in the world).
Reading the article from the Wired, and listening to conversations related to ebooks on and off the net, the ebook question seem to be moving from ‘will people bother to read on machines’ to ‘will people bother to purchase dedicated reading machines.’ This is a good sign I think. The market’s beginning to acknowledge that people are willing to take time to read things and even (gasp) pay for them, which means larger selection of stuff to read and things to read that stuff on in the future. However, the answer to the question of whether we need to have an ebook reader instead of making people read on their cellphones is a thorny one. It’s a question of how far people are willing to go to support their reading lifestyle. How many people are willing to cough up close to $400 for a dedicated ebook reader that you will later have to pay more to load content onto it? When we simply look at the Kindle as the only ebook reader of choice, the answer is obvious: not so much. I’m a self-confessed ebook enthusiast who regularly dig through the net for that obscure script to translate Microsoft proprietary LIT format to Sony proprietary BBeB format. Yet even I am not willing (or rather, able) to pay more than a month’s living expense on student budget to buy an ebook device. So are dedicated ebook platforms doomed? Not quite. We must remember that there are still myriad of companies out there that manufactures cheaper ebook devices, some of them more hgih profile then others (Sony isn’t a low profile company). Add to them the quirky yet ambitious enterpreneurs of the East, who seem to be jumping into any and all kinds of electronics market with vigor and goods of varying qualities. I got my own Sony PRS-500 for about $50 dollars in a promotional offer. I get most of my reading materials purchased through limited DRM free channels or through public domain, and they usually don’t cost much, certainly not as much as their printed cousins. Unlike what people think, ebook reading devices themselves aren’t really that expensive. Dedicated ebook device is basically an electronic device with two features. E-ink display capable of displaying basic HTML-like formatting along with a few more conventional formats like PDF, and a cable to connect it to a computer so the end user can load content into it. Simply put, it’s a glorified USB thumbdrive with big E-ink screen along with some buttons. While Amazon’s Kindle is a notch or two above the rest with its fancy whispernet technology and over the air delivery system, those things are not absolutely necessary to an ebook device. I mean, these devices are capable of holding 20~30 ebooks each going a few thousand pages. You probably don’t have to constantly buy new content before you go home from wherever you are at the moment (besides, if you can chug through that much content before you get to a computer with internet and USB connection you deserve to buy yourself a $400 reading device). The real issue that will either make or break the future of ebooks is not with introducing newer devices with more features (though I would certainly like to see existing feature set get better), but with software- the DRMS and ebook formats. I can manage quite a different number of file formats and DRMed formats on my single PRS-500 device only because of the collective action of the volunteer ebook community, some of whom managed to code indispensable piece of cross-format software like calibre. Many people can’t. DRM leads to limited distribution, since investing in DRM of a specific platform or corporation means that you trust that platform or corporation to exist ten or twenty years from the date of your book purchase. That is preposterous to anyone with working mind. Average lifetime of a corporation in America is about ten or fifteen years, and that’s assuming they will continue to maintain and support whatever the DRM scheme they came up with up until the very last moment. You can browse through your old books ten and twenty years from now on, and your children and children’s children will be able to read or sell those books send hand, ensuring certain degree of propagation of the written content. With DRMed books, it’s highly unlikely for your own children to be able to access your book, and whether you yourself will be able to read your favorite passage years from now will be decided by a boardroom composed of people who don’t know you and quite possibly don’t care whether you want to read or not. Even when we don’t consider faraway scenario like this, the dangers posed by DRM on the general propagation ebook into larger market is obvious, owing to the simple fact that DRMed ebooks will impose limits upon its own market and distribution. The first thing most people encounter whenever they browse to an ebook store that isn’t Amazon is this: Name of the book:LIT, PDF, BBeB, MOBI and etc etc… When users somehow manages to find the book they want to purchase (despite the severely limited selection in most of those stores) they are faced with multitude of options as to the format of the book, most of them incompatible with each other. From what I know of people who are not familiar with ebook formats, this is the step when most of them will just give up and go buy a paper book in local bookstore for only slightly more, or maybe even less than the DRMed digital copy if the user knows how to shop around on eBay. Even larger scale distributor like the Amazon, with its almighty capacity to push their own content into their own platforms, is basically playing in an uneven field. the reality is that people will inevitably ask questions about the future of their books and all Amazon can do is to cross their fingers and wish that doesn’t happen anytime soon. Limiting their own source of income and praying for only good things to happen in the future is not a valid business strategy.
The valid business strategy in near future would be to get rid of the DRM scheme entirely. For everyone. Even giant like Amazon is hedging for uncertain bet with DRM restriction in their ebooks. Smaller distributors like Sony ebook store doesn’t stand a chance. Just sell ebooks like you sell books. Let the market grow and let more people get hooked on using ebooks on ebook reader devices. There are cellphones and laptops, sure. But the reality is that they don’t compare to dedicated ebook readers in terms of providing a valid reading experience. Cellphones are supposed to make calls and laptops are for computing, and no one will burn out their batteries on those devices and risk their bill-paying work just to read more books. Once the quantity and quality of DRM free ebooks reach a critical mass there will be cheaper ebook readers on the market. That’s the time for Amazon to introduce their new and improved Kindlets. Why go for generic, cheap ebook reader when you can get the same content on far better machine with awesome battery with life-saving features and innovative interface? Only way to achieve this end with DRM still in the picture would be to either open Amazon DRM specifications to other manufacturers which defeats the purpose of having a DRM in the first place, or having a unified standard DRM for all publishers/distributors that’s compatible across variety of devices. That would require deal making and engineering of ungodly devotion, and I doubt even Amazon will be able to pull it off on their own, especially considering that there are markets outside of U.S. as well, especially when it comes to reading materials both traditional books and ebooks. The market is moving on, and publishers should move along with it instead of trying to hold back the tide.
Quorum sensing
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.
DIYbio NYC meeting: Apr. 15th
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.
$300 synthetic biology class
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.
Synbio interview
Spent most of the day outside today. It was a good chance for me to browse through the textbook ‘biotechnology for beginner’. I did most of reading in the quiet of the central library, though I did spend the early morning relaxing with some coffee in the Bryant park (before going off to a lecture for a while). Actually relaxing is not an accurate description of what I was doing. I was sending off emails and calling people left and right trying to arrange interviews for the diybio nyc peeps. I’ve never done anything like that before so things were getting a little chaotic, with last minute announcements and schedule changes. Mistakes and misunderstandings were plenty, and I was beginning to think that I was making some horrible decisions on the spot.
Well I was able to get one of the members onto an interview with the reporter (who I mistakenly thought was a man, and working for a school newspaper. She was neither), and arranged another one for myself in the evening. The whole process involved a whole plethora of trials and tribulations that happened due to my characteristic over thinking preparation and careless execution. After the whole planning and calling stuff I met up with a friend and had some much needed lunch at the cafe Zaiya, which was overcrowded as usual.
The interview is done for the day and I’m in a bookstore trying to cool off my nerves with some adventures of the Feynman kind. My portion of the interview was interesting. The reporter lady was quite friendly, and was patient with my answers that sometimes turned into something of a rambling (I knew I should have taken that public speaking elective in high school). During the course of the interview I had to frequently ask her to repeat her questions though. For some reason my ears were picking up a whole torrent of background noises… Either I was nervous or I really need to get my ears checked out.
We spoke about the reason for my interest in diybio, along with the difficulties involved in getting a group working together. The topics moved onto interest in science itself, and I gave some lazy answers on that one. I feel very passionate on the issue of the nature and utility of the sciences in general but I couldn’t find a way to put it in short eloquent statements… Not to mention that I felt disclosing such intense emotions would have been rather embarrassing…
All in all, this had been my first experience in arranging interviews for a group (or arranging anything for a group for that matter). I keep on feeling that I should have been better prepared, but I guess beating myself over it won’t change anything. Time to give the Feynman book a little pause and arrange yet another interview for the valued member of our group. Just hope this one turns out to be better than mine.
Today’s diybio nyc meetup
I got through another meeting with the diybio nyc peeps. Mostly it was management related talk with what came to be the founding members of the group, in terms of getting legal status and finding space for the group. The biggest problem for the group at the moment seem to be lack of lab-worthy space. Another big problem is finding a suitable project idea for us to go ahead with. Actually, if you ask me the lack of pervading project idea is a bigger problem then the lack of physical space, since lack of project means lack of traction and focus for the group. I would really hate to see the group evaporating due to lack of activity at this stage.
I’m wrecking my brain daily over finding an interesting enough project to proceed with, but so far I’m drawing a blank. The fact that I’m practically ignorant on the deeper nuances of the biological sciences doesn’t really help matters either.
One member of the group had been very generous in providing the group with much equipment and other resources, and the other member is doing much to get to the issue of incorporating the diybio nyc group as a nonprofit. I’m trying to look into the space issue by working with other groups outside of diybio, but I’m not too sure how it will work out… Not a lot of people want to work on unproven projects with unproven people. There is a biotech group within the city that might be able to provide us with labspace and resources but they are about incubating professional businesses which doesn’t sit well with the diybio ethos.
I’m a little embarrassed to admit that sometimes I feel like a third wheel in the group, but I guess everyone feels that way at one time or another when trying to get a meaningful movement going. I will have to remedy it by working harder… I really want to do something significant for the group but I don’t know what I should start with, and I’m getting a feeling that this is a common sentiment shared by many of the ghost members of the group (and yes, there are quite a few ghost members, it’s to be expected I guess).
At the moment all I can do is try to provide more logistical data for the group, like rent, spaces, and possible collaboration with existing hackerspaces to get those things. I guess I can give a bit more info about the S.B. 4.0, there are still whole notebooks of data on that conference. I actually gave then the booklet with abstracts of presentations and posters, I hope it will be of more use to them then it was for me, with their experience with actual wetlab and all…
I am trying to come up with a project idea, though it is more likely that we’ll be going with an idea that more experienced members of the group will come up with. Just juggling through ideas of completed projects isn’t good enough. I need to think about the realistic design and research process that will lead to that finished product, which isn’t easy for someone who still has trouble digging through some of the simpler stuff of molecular biology and pathways. I guess this is time for me to go dig up more igem stuff, and try to make sense of it all in terms of technical execution and practical resource requirements. That is, we won’t be coming up with a model of minimal cell in basement lab anytime soon (as much as I would love to see that happen).
I’m beginning to think about something on the lines of building in light sensitivity into the bacterial chassis (at least I might be able to help out with physics side of things in project like that) but what exactly? What kind of project would I be able to conceive of that incorporates light sensitivity of cells while remaining imaginative and practical within the technical limitations our group face?
E.Coli chassis that follows light? Or avoids light even. Now such idea would be a problem considering that I do not have a very clear idea of the mobility mechanism behind E.Coli (CAN they move? Or will it be a cycle of dying out when within the light rich or deficient environment?).
Considerations like that makes me feel like simply suggesting doing some exercise to make bacteria glow, document the whole process and materials used so that I and other less experienced members of the group can have clearer understanding of the techniques and limitations involved in the process- notably, introduction of foreign plasmids into a native chassis. The plus side of such an approach is that it lays nice groundwork for future experiments for those who aren’t experienced with molecular biology. The negative side would be that such experiment would dig into the resources and time the group doesn’t really have. Possibility of boring more experienced members of the group is also something I need to watch out for. Diybio nyc will not be able to sustain itself without the help of the people experienced in experimental biology.
I just don’t know what to do. Even if I were to suggest the glowing bacteria as a sort of introductory warm-up exercise, we still need to come up with a great project idea at some point.
I’m writing this in the subway on my way home. It’s beginning to sound like the diybio nyc is in some mortal peril now that I read some of the stuff I’ve written. It isn’t. Considering all the odds things are going swimmingly and possibly even better than I first expected. The whole atmosphere of excitement at being able to think about manipulating biology of living systems for academic pursuit is something that makes me feel alive. And I enjoy wrecking my brain over this stuff. It’s only that I’m under constant pressure to do more and get more things done, to make the group really work. It’s because I believe that we have something with potential for some truly wonderful stuff here. And it would be a real shame to let it die out not with a bang but a whimper.
