[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 [1]. 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 [2][3]. 
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 [4]."

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. :-)

--Paul Fernhout

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