Consider Bookhling

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.

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.

Okay, so I’ve been testing out (read:playing with) the new blackberry I picked up this morning. This is a cheap-o blackberry model that comes with full keyboard, GPS, and 2mp camera with video recording capability but no wifi. And it’s on the lacking side when it comes to the number of bands it can transmit in, though the comm options are still much better than most mid range cellphones out there.

All in all, it’s pretty good for something I picked up on a whim until I can get my hands on a decent android based phone. I was somewhat surprised to find video recording capability and LED flash on the phone though. It’s not the kind of feature that’s available on machines of similar class. For example, iPhone has neither.

I love the keyboard on this thing. It’s much better than tapping messages on the standard T9 keypad, and surprisingly enough I get quite an impressive wpm on this device… It’s no where near what I can do with a full sized keyboard of course, but still impressive considering that it’s only been a few hours since I got my hands on the blackberry. No one will be writing a novel on this thing but it’s still plenty enough for an occasional blog post (like what I’m doing right now).

The GPS is something of a disappointment though. It’s nice to have the functionality on a mere 50 dollar device but the accuracy and lock on time leaves something to be desired. It almoist makes me think that the chip may be running some sort of triangulation scheme instead of a full GPS module. I need to mention that I’ve only used the GPS inside the building with google maps application I downloaded off the cellular web though. Considering how carrier-locked devices are I may get better performance with the bundled At&t navigator application. I do remember that the blackjack II smartphone from At&t had its GPS locked in so that it wouldn’t even turn on if you didn’t use the paid app supplied by the phone company (there are ways to get around it of course).

The photo quality is good enough. It’s no where near the quality of the nokia N series phones I had a brief fling with but it will still serve its purpose in a tight spot. The picture quality is still better than what you would get with an iPhone under similar light condition, if only marginally. I will take a few pictures and post it up on the flickr when opportunity arises.
I am delighted to see video capture capability on this phone. For some reason a lot of carriers and device manufacturers leave video capability out of otherwise fine smartphones (like iPhone and the G1), so I wasn’t sure if there would be video capability on this device. You won’t be filming any Hollywood movies with this, but it still does its job well enough.

How many words did I write so far? It’s been about five minutes since I started writing on this phone. Marvelous.

The bundled web browser is nice enough. You can watch youtube videos on it, and the video loads swimmingly despite this device only being capable of data transfer over the infamous EDGE network (more on that later). Other pages load nicely as well, and the browser supports javascript and full CSS rendering (so far). I have a secondary opera mini browser loaded on the device though (among other myriad of applications).

Careful calibration of the web browser turns this device from a messaging centric smartphone into a fully featured synthetic biology reference, among other things. I have numerous web-widgets that links directly to the PLoS journal, openwetware web services, the GenBank database with full DNA table search capability and etc. Combined with the ability to view flash videos off the web, the innovative will be able to find a lot of crazy uses for this device.

The main reason people get their hands on blackberry is so they can maintain ubiquitous email presence. I have four email accounts registered to this device for work/school/mailing list/personal, with full filters. The email experience on this device is definitely solid. People say that blackberry is the best system on the market for messaging and emails, and I must say that I am inclined to agree. Other smartphones doesn’t even come close to this, and this isn’t even the best blackberry device (I’d say the place is reserved for the blackberry bold model, something that costs four times as much as this device even with 2 year service agreement). Now only if I could get rid of that annoying ’sent via blackberry from at&t’ marking at the end of all my emails…

This device is all about communication and it shows. There’s a program called blackberry communicator on the device that acts as an instant messaging protocol for any and all blackberry devices without any extra charge. I can see how corporates and research groups can go nuts for such a feature set.

The first third party application I installed on this phone is the twitterberry. As some of you might know already I’m something of a twitter junkie. I know that there are a lot of useless noise on that thing (‘what I ate for lunch today’ and etc) but once you can get through that part and link up with worthwhile people the whole thing becomes indispensable. Not to mention that it acts as a field report on my day to day thoughts. The second application would be a full suite of google mobile apps including Gmail client, google maps, and rss reader among other things. I also got mobi-reader for blackberry, turning this device into a semi-decent ebook reader.

Not all is well in the blackberry land however. There is one glaring and quite frankly insane omission from the standard application set that comes preinstalled on the device. This particular model of blackberry does not come with any kind of instant messaging program. There are a few for most of the major protocols like ICQ and Gtalk available on the net. Many of them programmed by the device manufacturer (RIM) themselves so that they sit flush with the operating system, but users of this type of message centric device should not have to jump through hoops like that in the first place. Also, all of those free applications are single protocol only. Having multiple instant messaging programs open on your desktop was ridiculous five years ago and it is ridiculous now. Maybe the time I spent with nokia’s symbian operating system spoiled me, but I can’t believe the lack of free multiprotocol instant messenger clients on the blackberry os. There are a few programs available but they are all commercial apps you have to pay for. It’s crazy I tell you.
I added 1 gigabyte memory card to this phone, and it didn’t have any trouble recognizing it. I’ll be needing it for the crazy number of photos I’ll be taking with this phone.

Hardware-wise I have no complaints. This phone is surprisingly small now that I have it in my hands, it’s almost a miracle that I can type away with my fingers like this. The size is more or less a fine balance between mobility and usability. The construction feels very solid and hardy without being heavy, and I would definitely refer to the overall feeling as being classy without being boring. For a smartphone with a full keyboard I found this phone to be surprisingly pocketable, but then I have skinny legs so your mileage may vary on that. At least this phone is significantly smaller than the G1. This phone is also slightly smaller than the Samsung blackjack II(an interesting bit of trivia, the blackjack II is the smartphone of choice for the female lead of the scifi tv show Fringe), something I couldn’t really notice until I got the two devices side by side (thanks Ann!). The trackball interface needed some getting used to, but it worked out nicely in the end. I don’t particularly see the advantage of trackball over other navigation methods though. Maybe it’s the aesthetics?

The biggest gripe I have with this device is of course that it doesn’t run android os. An ideal handset at for me would be blackberry hardware with Asian band compatibility, better camera, running the android os. Well, one can dream on, right?

Well that about wraps it up for preliminary review of the device. I’ll write some real world usage impressions later on…

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.