xml databases, bacteria as multicellular organisms

My stay here may be somewhat short lived as I’ve found Syncato, a weblogging tool so utterly drenched in acronyms it can’t help but be the l33t thing to do.

It uses Sleepycat’s XML database and a plethora of additional open-source xml manipulation API tools to build – in python (woot!) a REST based system for working with xml fragments.

This, if I manage to combine it with my existing approach of using subversion to manage my longer documents, might bring about a sort of “semantic web for one” toolkit, where you can describe yourself and what you’re working on, believe in, or what have you using as much or as little semantic markup as you want.

As tools spread out there capable of using xpath for querying, the whole internet becomes as queryable as your own database. Eventually this will be common way for us non-business types to engage in spontaneous community; when a critical mass of people expressing similar semantics arise, so to will their ability to cohere for whatever purpose (or lack thereof) their semantic commonalities suggest. Tools like Technorati are already doing this with what little semantic markup blogs provide today; and technorati itself is already providing a REST-style API.

Let the business world stifle in their stew of stuffy standards and opaque encapsulation whilst the rest of us get by on tag soup and running consensus.

Anyway, so bacteria are opportunistic multicellular organisms, and that opportunity exists almost everywhere except the lab. Right now I’m curious about exactly how diverse is the set of exogenous polysaccharides bacteria and archaea produce to facilitate cohesion; are there, for example, bacteria that use xylan -based or N-acetylglucosamine based polysaccharides? If so, there’s a possibility that you could make woody or chitinous biofilm cultures.

Also, maybe precise placement of different strains of bacteria could get you more interesting control over the constitution of your resultant biofilm; deposition of bacteria from live culture using something like an inkjet could be a way to cheaply get that sort of distribution.

Microencapsulation is pretty doable these days as well; perhaps encapsulating either sporing or otherwise suspended collections of bacteria in materials and then “printing” them amongst populations of bacteria that produce exogenous reducing enzymes for that material could allow you to get a time-delay effect in the production of some aspect of your final desired structure.

3 thoughts on “xml databases, bacteria as multicellular organisms

  1. Subject: Re: blogging tools
    The reason that many people seem to migrate to LJ from the other services is that this is where our friends are. My writing and my connection to community are the two main reasons for me to have a journal. I can do the first anywhere, and I can do the second easiest at LJ. ‘Course since your goals are likely different, you might not have the same impetus to stay here that I do.

  2. Subject: kill them – kill them all
    Mm, tasty RSS. One day I’ll get around to it.

    This is no bacteria-built furniture, but it’s something.

    Also, something I’ve failed to ask before is — once biofilms are formed, don’t they grow, thrive, decay? Is there a way to fix, stop that process at a specific point?

  3. Subject: kill them – kill them all
    My naive idea at the moment is that you’ll want to kill the biofilms by heating them or irradiating them to produce the final product. The final product, being composed of whatever exogenous molecules the bacteria have produced and their leetle corpses, should be able to have various properties that are either highly degradable or relatively inert.

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