13 April, 2009

Our Shrinking Cloister

I've got a beefy diatribe to spleen out.

I have seen on the Interwebz in the past several months a great deal of discussion about DIY biology research and whether or not it's safe. I've seen big-wiggy biomedical researchers and computer sciencers weigh in on this. I suspect both are missing the point.

Currently, biomedical scientists are arcane magicians working quiet miracles in the shadowy corners of public consciousness. We're nerds of such deep inaccessibility that we become artificers of mythical proportion and prophetic comprehensibility. The public does not understand what we are doing or why it takes so long for progress to be made; we're supposed to produce flash-bang-holy-shit magic tricks on demand even as we dread being questioned why our research matters. The terms we use, the depth of the knowledges that we plumb, the datasets that we construct, the very equipment that we use all serve to enforce an idiosyncratic barrier that requires intelligence, time, and flinty-nosed mule-like stubborness to break into.

This cloister which we've inherited does indeed have its advantages. We can go to work in the lab with other fully competent people whom we may easily assume are familiar with basic genetics and protein dogma. We can develop our presentations with great detail, sculpting each to the level of specialization of each audience. We can dive deeply into a heady rush of informational give-and-take, intellectual play, and experimental thrill. However, I find that this cloister is slowly suffocating us.

When our predecessors enshrined themselves and their disciplines into ivory monoliths of thought, they also shut out nonconformists, radicals, and fundamental innovators. Those that don't deign play the game of academia or lie out the sides of their mouths about career intentions are inevitably shanked with a glass pipette and thrown under the steam roller of their committee's disapproval. An entire industry has birthed itself in response to the standardized demands of academic science, and has made massive profits while doing so (and while it's important to have data standards, it is also true that standards become economic commodities that eventually get more and more expensive to maintain, and are also exclusive of other ways of generating data). By setting the bar for entry to biomedical science so very high, we've effectively shut out everyone who cannot pay to play. This includes independent hobbyists, start-up biomedical firms, and newly minted PIs.

This is due to 2 structural features of academic science:

1) Physical plant/equipment. Think about the sheer variety of specialized equipment that a molecular biology laboratory has. Gel docks, power sources, block heaters, incubators, freezers, microcentrifuges, flow cytometers, UV photoimagers, flow hoods, Bunsen burners, shaking warm water baths, RNase-free chambers, etc. etc. etc.. All of this stuff costs huge sums of money, effectively making the entry costs of biomedical science so very high that no one but the most affluent, in private funds or grants, can hope to even try to play.

This parallels the initial development of computer science. The first computers were so massive, specialized, and expensive that computer science and the study and application thereof were but a fringe niche. Today both are ubiquitous. The fundamentals of computing science haven't changed. But the entry costs have. With the advent of the personal computer costing less and less, more and more nerds have been able to pour into computer science, coding and hacking and building the very environment in which Internet-users dwell. Lowering the entry fees has allowed more people to play and succeed in an arena previously dominated by UNIVACs and their attendant haughty acolytes.

Now, we as biomedical researchers are the high priests of Biology. The knowledge for a talented hobbyist to make real progress exists, as does the capability. The textbooks are written, the databases are public, yet we remain skeptical and the equipment remains prohibitively pricey*.

2) Computer scientists tell their computers what to do and hope they didn't make a mistake. Biologists grope around in the darkness of genetics with enzyme fingers and break something, hope it was what they meant to break, and then hope that it has a measurable outcome. Essentially: they start out knowing what they're doing and we hope we know what we did when we're done.

This also hinders inclusivity in the biological sciences inasmuch as detailed and deep knowledge is required to interpret data or plan a meaningful experiment. Computer science can tinker with code components for a couple hours and a bright person will eventually figure out that $x assigns a variable while @y assigns an array. Meanwhile, the same person could spend weeks, years even, tinkering with E. coli before figuring out that LacI is a protein that acts upon lacZ genetic material.

Unlike the first obstacle, however, this one is much much more difficult to overcome. We could easily rig a water-jacketed incubator by using a styrofoam cooler, Tupperware, and a tropical fish aquarium pump. We can't rig knowledge nearly so easily. To a degree, this is what textbooks are for. Yet at the same time, we've got the most valuable information hidden behind an elaborate series of paywalls.

This also hinders biomedical sciences being relevant. Yes, we know it's important because we work out of compassion, trying to improve knowledge to ease suffering and improve lives. But society doesn't necessarily know that. Sending rockets to the moon was concrete and real and it beat the Ruskies. Growing dynein engines in Petri dishes isn't nearly so concrete. So we're back to being shadowy nerds, toiling on nerdy stuff that doesn't matter. It's here where our cloister begins to strangle us, because when the public does not understand what, why, or how, even to the most shallow degree, what we are doing and what it's potential payoffs are, we have to go on the defensive automatically to keep justifying our labor and its expense.

We'd better serve ourselves by spending more time on the offensive, engaging the public and demystifying what we do, maybe even helping out the DIYers. By embiggening the pool of people thinking about biomedical research issues and increasing the hunger to do something about it we'd be setting up a positive feedback loop, even if some of the greybeards may fear the potential for nontraditional competition. In the end it can only help us, you know?

*To this end I favor the development of biological hacker spaces, similar to those featured at www.hackerspaces.org/wiki. In these, members pay a monthly fee for access to common equipment. This collectivism may be the only viable way to surmount the high entry costs of biomedical research.


Juniper Shoemaker said...

GREAT POST! I'll be back.

quietandsmalladventures said...

hmmm, i like the shadowy corners of the ivory tower mental picture. it allows me to think perhaps i too can one day afford my own igor.

in my old lab, we used to discuss building our own garage based BSL2 space in order to have a bit more freedom to tinker with our plans for total world domination; but i digress....

i think bioinformatics is the next logical corner for the hackers and lovely computer nerds to play in. i certainly would be most happy to pony up a month's worth of dr pepper, pizza and beer to the compu-jockey that could create a freeware version of macvector for me. hell, i'd do it just to get a free key to run the software.

any takers?

PhizzleDizzle said...

This is totally interesting to me. Totally, particularly your contrasting of Bio and CS in terms of accessibility to the public.

I have thought a lot about my ability to "work" from anywhere as long as I have my computer and an internet connection to the farms of computers at GradUniversity. Certainly, CS might be more universally accessible in terms of equipment/feasibility of garage labs.

At the same time, I agree that people don't understand why biologists can't just pop out solutions (I didn't for a long time either). However, people don't really get the issues with CS either - because there are constraints that make problems difficult that people don't get - to them computers are magic and you should be able to do anything with them.

I think that people also have a really shadowy understanding of computer science, but probably a better *superficial* understanding of biomedical stuff.

No one ever wants to speak with me about my research at a party unless they are computer nerds. And even if they aren't a nerd and for some reason want to ask about my work, they don't care in the end, because it seems really far away from anything they could possible care about. EVERY aspect of what I am telling them is behind the scenes and has no place in their life.

But this biomedical stuff, even if people don't understand the difficulty of the process, generally understand the BASICS of the process, like, "I am trying to find gene X to solve problem Y" or "I am trying to grow tissue X" or whatever. Most laypeople I have met can absorb that, but when I put my work into a sentence, they can't.

So in that sense, I think that the Bio cloister is superficially more accessible to the masses. But in terms of wanting to get your hands dirty and try some stuff - well, then you're totally right, you need physical proximity to equipment (and I don't).

Eppendork said...

Hehehe - in my head PD I was thinking that when someone asks me what I do I immediately think do they really want to hear what I do or are they just being polite? The eyes glazing over thing gets boring after a while.

TS: I have a problem with the little scibuddy DIYers of this world who jerry rig things to work without enough of the safety protocol etc behind them - I have already bleated about this already. I think if you could guarantee nothing would escape everything got autoclaved, they worked in properly controlled airflow environment maybe. I think the comp geek diyers have it easier and they are unlikely to release bjillion potential GMO's into the world.

Toaster Sunshine said...


I'd certainly be impressed if someone could rig up a negatively-pressurized BSL2 space in their garage. I'd be somewhat concerned about their intentions, but impressed by their craftiness nonetheless.
If you want a key, look up keygens on Isohunt and Pirate Bay and then torrent them in. Just be sure to back up your computer first and set a system restore point. I once downloaded a keygen from Isohunt and not only did it give me a working key, but it also added an automatic porn feed and search to Firefox. I had to hunt through my root directories to get rid of it.

It is true that biomedical research lends itself to semantics much more easily. Boolean logic isn't as simple as "when gene X breaks, Y happens" because linear causation is easy to understand. Now, explaining hysteresis or cyclical variations in bimodal signaling pathways: not so intuitive, but then again neither is the concept of non-hierarchical subroutines in a script. Simply put, we got Jurassic Park while you got Hackers.

Anyone who really wants to tinker with biology is going to do so anyway, with or without our help. Without our help is considerably more dangerous.
But dangerous jerryrigging is also part of the reason I favor collectivism and equipment pooling in DIYbio stuff. If everyone bands together to build a lab, it's much more likely that the proper resources will be there to ensure good safety.

Glass Agencies (INDIA) said...

Dear Sir,

We (M/S Glass Agencies) are Manufacturer & Exporter of all type of Laboratory Glassware, Scientific, Surgical, Medical, Hospital, Laboratory, Pharmacy, Dairy, Milk Testing Instruments & Equipments under EROSE brand including Chemical, Educational Charts, Models & Slides

Kindly send us your requirement so that we can quote to you our best prices

NITIN (Export Manager)
An ISO 9001:2008 and D&B Certified Company
From : M/S Glass Agencies,
5309, Anaj Mandi,
Ambala Cantt-133001(India).
Ph : 0091-171-2633027 (Office),
Ph : 0091-171-3293186 (Res),
Fax : 0091-171-2640566
Cell: 0091-9416024836 & 9896807858
E-Mails : glass@sancharnet.in
Web Sites : www.glassagencies.com