Future Ben

Oh hell yes. An MIT group has made a small sensor that is powered by the electrolyte gradient between the tree roots and the soil.

The Voltree power supply is a great idea. Can a tree power more than a small sensor? The engineering is there for harvesting a voltage potential. What about a plant engineered for an enhanced gradient to harvest. A biological solar panel? Not so far out.

Really I just wanted to get the Anarchy player running on the site. I can’t decide which is more obnoxious though. The Anarchy splashpage or the Youtube watermark.
Option A.
sany0076

Option B.

It suddenly occurred to me that one of the best support sources for open source biotech would be the open source software movement. Google offers scholarships to students to take on summer coding projects with open source foundations. Is there any Bioinformatics in there? Just two that I can see.

GenMAPP (Gene Map Annotator and Pathway Profiler):

an academically based organization that develops and supports GenMAPP (Gene Map Annotator and Pathway Profiler), a visualization and analysis tool for biological data. GenMAPP illustrates the relationships between various genes and proteins to help researchers understand their data in terms of connected, biological pathways. Over 18,000 people from >70 countries have registered to download the GenMAPP program. There are over 360 publications that reference GenMAPP or use GenMAPP to display data in the context of biological pathways. GenMAPP is 100% open source. All new development is in Java, MySQL, Derby, XML, and Web technologies such as MediaWiki in collaboration with the UCSF library, BiGCaT Bioinformatics, and the Cytoscape Consortium. Our development team is composed of individuals who are both biologists and programmers, providing a unique perspective on building and using open source tools.

The NESCent (National Evolutionary Synthesis Centre):

NESCent facilitates synthetic research on grand challenge questions in evolutionary biology and also works to address critical needs in software infrastructure and education through promoting open, collaborative development of interoperable and standards-supporting open-source software. The Center is located in Durham, North Carolina, is jointly operated by Duke University, the University of North Carolina at Chapel Hill, and North Carolina State University, and receives its core funding from the National Science Foundation (NSF). Together with developers from open-source life-science programming toolkits (BioPerl, Biojava, Biopython, Bioruby, BioSQL; collectively referred to as the Bio* projects), evolutionary software packages, and recently developers of comparative phylogenetic methods NESCent has so far run two Hackathons, which continue to have significant and lasting impacts on the landscape of collaborative software development in our field. The Center is committed to FLOSS and sharing of scientific data (see for example the NESCent Data and Software Policy at http://www.nescent.org/informatics/data_software_policy.php); all software products of the Center are released as open source and established as collaborative projects on sites such as SourceForge. Members of the Center’s Informatics team are lead developers in several open-source projects, and one of our organization administrators has been active on the Board of the Open Bioinformatics Foundation (http://open-bio.org/), the umbrella organization for the Bio* projects, since seven years.

Well it’s a start. I need to look more into what these groups are doing.

So started reading anAleister Crowley and honestly I am inspired. The poor bastard has so much about the universe and yet he admits that it is all just symbolism. He doesn’t even attempt to rectify astrology with astronomy. And honestly I don’t really care very much about either circa the 1920’s. The massive failing I see in Qabbalah or any occultism is the presupposition that the universe is crystaline and all we have to do is find the patterns. As if algebra could even get you past even the most basic model of nature.

So here is Crowley who can’t make it to trans-humanism because his cannon of reason and practice, the Qaballah, is based only on algebra and could never be a dynamic, ergo functional, model. Hence the inspiration. Trans-humanism is based on a dynamic model with complexity. But how to understand complexity. I don’t know enough about network theory or graph theory, or probability math, or statistics, or discrete, or any math really. I don’t have any sort of grasp on object oriented programming, or C for that matter. This is all foundation level stuff and I just don’t have it. I was too impetuous as a youth. Why oh why did I while away my time with RPG’s and hallucinagens? The rhetorical answer is so that I take the flights of fancy needed to ask that very question.

Is it too late to crack a book and actually get a grasp of the fundamental concepts behind all the junk that I know is important but I don’t really understand? I fear that impetuousness has never gone away. I spend my day worrying about viral gene transfer and T1 weighted images, why would I start on something that I won’t be good at for more than a year. And this is how the brain grows old dear reader. It isn’t that you can’t form new dendritic connections. You are just to lazy. If I really believed this was important I would stop reading this dull ass Aleister Crowley reader and go study the real secret language of the universe!

Oh look at me! I am putting Crowley on a shelf and replacing it with a review paper of BAC transgenics and on Melanosomes. That is a start, but where to begin on network theory? Oooh a hyperlink!

Somehow I stumbled across this beginners guide to transhumanism. I skimmed it. What do you want? I just finished Ray Kurzweil’s “The Singularity is Near” I get it!

So what is transhumanism to me? It begins with the idea that we are less that we can imagine ourselves to be. In Kurzweil’s book he cites how the creation myths of most religions involve humans descending from greater beings. This is a cop out on becoming something greater than what we are. Icarus falling to earth Aracne challenging the gods and being turned into a spider. The ongoing lesson is that ascension will only ever end in disaster.

Through science we have begun to see ourselves as rising from less complex origins. The implication is that we are moving towards a state of greater complexity and something greater than deemed possible by humanity. Does this mean transhumanism is Neitzche’s overman? I’m not entirely sure. The idea is that one day we will all become transhuman which kind of defeats Neitzche’s whole thesis. Or maybe not. When the day comes that a pill will make you immortal the people who take it aren’t necesarily transhuman because suddenly immortality becomes the new status quo. Maybe if you are first in line.

Transhumanism is pushing the boundaries of what is human. So while technology is certainly a part of it, following the doctor’s orders is just being human. The transhumanist was taking the immortality drug before it was approved and then moved on to melding their brain with an AI. In a more modern context the transhumanist must break free of the bonds he or she can which are largely psychological.

It’s funny that at the bottom of this little primer there are a number of links to alternative lifestyle pages. Perhaps breaking free of psychosexual moors of society is the most a transhumanist can muster these days. Yikes! Does this mean that in order to really call yourself a transhumanist you have to be a liberal intellectual smart drug taking body modified BDSM polyamorous freak? Maybe instead of Ray Kurzweil I should be reading Alistair Crowley.

Man I’ve done nothing but crew other people projects for the past year. I’ve been busting ass on the Madagascar spider, Image Node and Tod’s LED sign. All of these are worthy projects, and I learned a lot working on them, but in the end they don’t go into my portfolio. I think I am ready to start working on my own stuff. (Like my graduate school thesis perhaps?) At some point I need to stop being crew and start becoming talent.

Q. “But isn’t ‘talent’ arrogant and generally useless without the crew?” A. Well yes, but usually that’s because the talent was never crew. Often talent is recognized early and saved from grueling labor to live a life of pampering and luxury that ultimately destroys them. But once you have faced all that grunt work that you will one day inflict on the rest of humanity, you feel genuine empathy and are therefore not a total dick.

Q.”Doesn’t talent just party all the time and show up barely able to perform?” A.Of course that’s true, but I have been working myself to the limit and still performing, and the protestant work ethic is anything but punk rock.

Q.”Are you even talented? What the hell do you think you even do.” A.Hey stop yelling at me! I do lot’s of stuff, I just don’t flaunt it. I’m going to go be a mad scientist/dreamer/poet who will resculpt the the world in MY image!

Q. “FutureBen, have you been drinking?!” A. Maybe

Damn that previous post was starting to bug me. I just kept thinking of what it would be like to have one of those magnets implanted and then walk past the 5T line of the Magnet. Ouch!

I thought I might show off what has been keeping me from posting for a month. One of these brains is expressing my in vivo reporter gene in a mosaic pattern. The other is not. Can you tell the difference? It looks OK, and with further optimizing it could be really good. Anyway, look I invented something! Now that is a biological hack!

This is actually old data, but I am showing it to illustrate that my MRI reporter gene I have been working on is ready to go in vivo. Sigh its also a .tiff and I’m too tired to change it tonight. I put the reporter in a retrovirus and injected it into the brains of developing mice I just started my first imaging run on these brains. By tomorrow I will have some idea as to whether this is going to work or not. If that is the case then I will be doing very well and I will definitely have something to brag about at the upcoming ISMRM conference in Berlin in May.

The pendulum of mental ability swings back towards science for a while. That’s how things work for me. I just wish I could make the transition more freely. All art projects are brutally dropped for my big breakthough, but I can’t just not show up to the lab on days when I’m not feeling it. Someday futureBen someday.

I have begun experimenting on animals. I didn’t plan on things working out like this, they just did. If I want to manipulate genes I have to use a model organism. Mice seem to be the most relevant and so…

To work with animals you have to be detached, calculating and, most importantly, merciless. I am none of these things, and so I am not very good at animal work. I can barely pick up the little creatures and yet I am going to have to do surgery on them. Lots of surgery.

Mostly I am just watching my advisor carve up mice and inject my viral particles into their embryos, but I am going to have to figure this out eventually. Today I sutured a dead mouse and practiced loading up needles. I felt a horror movie antagonist. Stitching up a dead animal filling tiny glass needles all for some senseless purpose no normal human mind could interpret. I may start opening up pregnant mice, imaging them and then stitching them back up again just to practice. Sacraficing mice for practice! Is this who I am? Apparently so.

Because I am always broke, I take whatever work I can get. Usually its standing in the Freezing cold on the roof of Rubulad bouncing the drunks, however once in a while I get to do something interesting. Twin A, who generally kicks ass in all things blinky has been assisting artist and head of Disorient, Leo Villareal. Despite being some of the most polished LED art I have ever seen, Leo’s projects continue to grow in complexity. In this case 2400 points of complexity. Somebody has to stick all those lights up in their housing. That someone is futureBen.

OK, it isn’t the most exciting work in the world to unscrew tiny little lightbulbs, but any opportunity to work for an artist of Leo’s caliber is a welcome one. And as always, I am always broke! Maybe I need to come to grips with my 100$/month Mcmaster-Carr addiction. But these extra gigs keep me going, and I can quit anytime I want.