[p2p-research] Biofilms and p2p
Paul D. Fernhout
pdfernhout at kurtz-fernhout.com
Wed Nov 4 20:47:17 CET 2009
This applies to p2p if you squint at it just right: :-)
"Biofilms || kuro5hin.org"
... Planktonic bacteria spend a lot of time evading. They move away from
toxic environments like pH or osmolarity changes. They move away from
hunting phagocytes like amoeba and neutrophils. They often have trouble
finding a nice, stable and safe environment to settle down in. They solve
this problem by creating a nice stable and safe environment to settle down
in. They make biofilms.
That lone planktonic bacterium makes a class of seemingly useless
compounds, the quorum sensing molecules (QS). For the most part, these are
n-acyl homoserine lactones (AHSL), small nonpeptide molecules. Simple guys,
a 5-member ring on one end, a short chain of carbons with a carbonyl or two
hanging off it. Simple bugs, simple signals.
QS are part of an autoinducer loop; the bacterium talking to itself.
Normally, this doesn't do anything, because the molecules simply diffuse
away before they can reach a level high enough to trigger any kind of
response. Selection dictates that these things have a purpose, though. ...
Anyway, Phil and Phil Jr both make AHSL. For you math whizzes out there,
that's doubling the rate at which AHSL is made. Unfortunately, this just
means they diffuse away even faster, reducing the increase. But the increase
is there. Phil Jr strives for the dream, just as Phil does the same, for a
second time. Meet Phil III & IV. Eat, divide, repeat. Meet Phil V-CCLVI.
Hey...that QS level has gone up a bit. Phil has become PHIL. PHIL is talking
to himself, and for the first time, diffusion isn't silencing him. ...
OK, enough with the anthropomorphic prokaryotes. We now have the makings
of a biofilm. QS molecules like AHSL have reached a respectable
concentration, and signaling has begun. New genes are turned on, and new
behaviors kick in. Flagella go away. New types of pilli form. Each cell
begins to crank out proteins, thick, gooey carbohydrates, and DNA, which
come together to form a sticky coat around each bacterium. Due to their
proximity, these thick, gooey coats merge, and grow. Other proteins are
made. Beta-lactamases to protect against incursions of fungus, catalase to
fend off superoxides in the environment, proteases to chew up anything near
the biofilm to make more room to grow. New properties arise. After a time,
the bacteria have made a viscous liquid surrounding them, a glob of slime in
your drain, the black goo in your trap, or the yellowish slick on your
teeth. It's not really a solid and it's not really a liquid. Think snot or
the watery phlegm that you cough up when you have the flu. It's actually
very similar stuff.
After a while, you have millions of bacteria, all living in and as a
single biofilm. At first, the film is a fairly homogenous hydrogel, a water
trapping 3-dimensional mesh. This mesh impedes normal diffusion, greatly
reducing the rate at which molecules can move in or out of the biofilm.
Inside, QS concentration accumulates, and the rising rate causes further
changes (the mechanisms of which are not fully understood). The biofilm now
no longer has to evade. It can control the pH inside itself by regulating H+
export. It can regulate ion and osmotic gradients by sequestering and
pumping ions around. It avoid being eaten by roving phagocytes by sheer
size; biofilms can be large. They can grow from a few bacteria that barely
affect the turbidity of a test tube full of media to a visible, tangible
thing you can actually pick up with your fingers after only a night of growth.
It's easy to see why these are thought of as the precursors to
multicellular life, they are multicellular life. It's practically an
organism. As the biofilm develops, it even develops organs of a sort;
fruiting bodies. Small pockets will form inside the biofilm, pockets devoid
of the carbohydrate/protein/DNA scaffolding that makes the structure of the
biofilm. In these pockets, planktonic bacteria start to grow, and the pocket
starts to move to the periphery of the biofilm. After a time, the fruiting
body buds off and spills the planktonic bacteria out into the environment,
to seed new biofilms and exploit new territories.
It's an elegant and useful system. The problem is, it shouldn't exist.
According to all we know about evolution, it should be a highly unstable
system due to a phenomenon well known in the geek world: The tragedy of the
Making this stuff takes work. It is work to make the biofilm scaffold, to
pump ions and make protective proteins. The bacteria do this because working
together this way is of benefit to them all. It's not really altruism, but
mutualism. Prokaryotic quid pro quo. It's worth the effort because everyone
is pitching in. Some of you may see where this is going. ...
They go on to talk about theoretical difficulties with the experienced
realties... However, consider the recent Nobel prize in economics awarded
for a better understanding of the management of the commons:
"Nobel Prize in Economics to Elinor Ostrom “for her analysis of economic
governance, especially the commons”"
Anyway, I see some biofilm parallels with p2p, as well as the issue of
Manuel de Landas's meshwork/hierarchy balance, as a bacterial system of
communicating individuals undergoes a density-related phase change. Is
Wikipedia or GNU/Linux or the p2p research mailing list like a biofilm? :-)
And, no, that does not mean I'm calling GNU/Linux, Wikipedia, or this
mailing list "slime", although, within this biological metaphor, that would
be technically accurate. :-)
More on that topic from the Wikipedia "infofilm"? :-)
"A biofilm is an aggregate of microorganisms in which cells are stuck to
each other and/or to a surface. These adherent cells are frequently embedded
within a self-produced matrix of extracellular polymeric substance (EPS).
Biofilm EPS, which is also referred to as "slime," is a polymeric jumble of
DNA, proteins and polysaccharides. Biofilms may form on living or non-living
surfaces, and represent a prevalent mode of microbial life in natural,
industrial and hospital settings . The cells of a microorganism growing
in a biofilm are physiologically distinct from planktonic cells of the same
organism, which by contrast, are single-cells that may float or swim in a
liquid medium. Microbes form a biofilm in response to many factors, which
may include cellular recognition of specific or non-specific attachment
sites on a surface, nutritional cues, or in some cases, by exposure of
planktonic cells to sub-inhibitory concentrations of antibiotics .
When a cell switches to the biofilm mode of growth, it undergoes a
phenotypic shift in behavior in which large suites of genes are
differentially regulated ."
So, what happens to our society once the peer-to-peer and peer production
density goes high enough? :-)
More spinoff civilizations in the oceans and space? Fruiting bodies of
seastead networks and self-replicating space habitat networks? :-) Or maybe
something completely different? A singularity of some sort? Not necessarily
robots rule the world, but just something very different like a world shaped
by a gift economy of content under free licenses and a basic income to
ration anything currently scarce?
Anyway, just some food for slimy thought. :-)
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