Future Ben

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.

I presented a talk to the NYU Biotechnology club today, Metabiotechnology: or Why Biotech Sucks Right Now. Attendance was low but the crowd was more bemused than offended at the title. Often as you put a presentation together your thesis develops. And feedback from your audience is even better for that purpose. Drew and Dusan were particularly helpful but I was surprised at what did and did not resonate.

I will try to post the talk if I can figure out how to get powerpoint into wordpress. Basicly my thesis is that the current hegemony of Biotechnology is Biobusiness. While there is nothing inherently wrong with a free market the system is monolithic and there are huge needs that are very poorly served. The most prevalent being the needs of developing nations.

As I was preparing and during the presentation I realized that it was worse than that. The science supporting Biotechnology is often undermined by profit motivation. My case study on this was the “Green Revolution.” Initially plant breeding and ecological management through pesticides and herbicides seemed like a good idea. It has become pretty clear in the past 20 years that this is not the case and that there are much more sound and sustainable practices. Yet people with access to all of the data pointing to the failings of previous generation technology continue use ultimately damaging methods. In fact they have subjugated Biotechnology to continue even farther down this destructive path. (Hence the subtitle.)

So the evils of greedy corporations aren’t all that new, as several people pointed out. But what surprised me was the audience response to my proposal. If Biotechnology is currently monolithic and profit motivated then the weaknesses of that system opens up the possibility of Biotechnology that is dynamic and either need, OR profit motivated.

Maybe I didn’t express that clearly enough, but I got a lot of knee jerk capitalism. “Technology has to have a product,” or “that system works a lot better than government funding.” Both true statements, but not in anyway an argument against need motivated Biotech. And I acknowledge that there are government grants to encourage people to develop need based technologies, but there has to be something more, something new.

I am glad I used the agriculture case study because the great weakness of current agriculture is that it is monoculture based. And that is exactly the problem with Biotechnology and Big Pharma. Sure there are a lot of little Biotech companies, but they are all playing the same game. Especially since they all presumably follow the FDA rulebook. A true disruptive Biotechnology would bypass this whole system. Is paradigm shift old enough to be retro? It sounds stupid, but there were very intelligent people in the audience who couldn’t imagine that there could be an alternative to our current system.

If you equate it to other paradigms, Biotechnology is ready for it’s own version of the personal computer, model T, cotton gin. I think sequencing was the equivalent to the printing press or early computer. Biotech is fortunate in that it can take all of the lessons from the electronic and information technology fields. Open source, distributed systems and other meta-technologies. The question is, what will that technology be? If history is any teacher we won’t know until it becomes pervasive.

I went to one of Rhizome’s New Silent panel discussions at the New Museum. (Damn what a sexy marquee they have in the front!) Some of the presentations were pretty good. I liked the work of Caitlin Berrigan and Brandon Ballengee. What I appreciated the most from these two artists was that they were understated in an already controversial field. It takes a tremendous amount of integrity to let your art speak for itself.

Generally I have to roll my eyes at high concept bioart especially purely conceptual art like photoshopping a scrotum purple and calling it the future of humanity. That stopped being shocking a long time ago. None of this stuff is new, it’s just new to you. Any artist who thinks they can skate by on the wow factor of posthumanism is a sad relic of the 90’s

Bioartists need to realize that their art isn’t new. Gardening, bansai, body modification and even selective breeding are valid and often inspired art forms. As bioartists we must accept that we are simply painters with a new pallet to make art. If the art is good, it will speak for itself.

Why is it then that bioart is plagued by sensationalism? Obviously the many many demons that biotech plague biotech are present, but at least in that world there is an avoidance of sensationalism. It’s bad for business. In basic science if you were to even attempt the kind of grandstanding and egotism that permeates the art world you would be laughed out of your institution.

Granted artists are not scientists. It is their job to draw attention and to sometimes be outrageous. I applaud that when done properly but when I see artists taking everyday science and holding it up as if it were the greatest artistic achievement since perspective. Or using science to shock and awe the audience I can’t help but seethe.

I guess this harkens back to the early days of computer animation. Pretty much all of it sucked, but you saw it everywhere because it was new. It is going to take artists of true skill to take genetic based arts out of its Pong phase.