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Re: Recycling, Rosennean Style...



Hi Leo,
 
Your post brings up a wealth of interesting subjects. I appreciate the link you offered, and did a bit of research. One of the sites I found was http://ei.cornell.edu/biodeg/bioremed/ . Fascinating stuff! Bioremediation, phytoremediation...
 
What this seems to be about is using natural properties of living organisms, or engineering (sometimes genetically) the properties, to transform harmful waste substances into benign ones.
 
In other words, they are using complex systems to try and remediate the properties of simple systems, and trying to engineer properties into complex systems in order to do it, without quite understanding the "mechanisms" at work or the consequences of using living organisms in this way. This isn't quite as scary as genetically engineering food crops, but it seems to me the potential exists for inadvertently creating some sort of nasty pathogen, if human sewage is one of the avenues for using these organisms, along with mutagenic chemicals or radiation...
 
In any case, I still think it should, in theory, be easier and simpler to restrict ourselves to the molecular level of remediation. You mentioned enzymes and this is one avenue that should be explored.
 
Another would be simply the reactive capabilities inherent in certain elements and compounds. Oxygen is extremely reactive, for example (which is why we are exhorted to eat our "anti-oxidants" all the time). My knowledge of chemical reactions is not, by any means, extensive-- just the basic non-chemistry-major stuff plus the accumulated knowledge of following my own curiosity and asking questions, doing research, etc. But I know that mixing two "things" together, like chlorine bleach and ammonia, can result in an explosive reaction, all by itself (not requiring any additional energy to start the transformation/reaction). I also know that there are ways to control chemical reactions such that they aren't as explosive. Human metabolic processes, using sugar for energy, is an example of how much of a difference this kind of control can make. You can have body heat or a fire; same process going on, but one is more controlled than the other. Using a buffer in a process which involves acids can control the effects of the acids, and so forth.
 
What I'm thinking is that there should be innumerable ways to take any dangerous or toxic molecule and figure out a series of steps which reconfigure it, without needing added energy. Furthermore, because molecular organization is not complex, we can and do model it in enough detail to accurately predict the behaviors and outcomes of various interactions, so there should be "no surprises" of the sort that genetic engineering and use of living systems is liable to generate. 
 
I also think that various processes humans routinely use to create materials we need may require a re-think with the whole process geared to what the waste products would be and the difficulty level of reconfiguring those waste products. There's more than one way to do just about everything. That fact can be applied to both our manufacturing and our waste management processes so that they fit together in ways more productive and healthy all the way around. It just requires creative application of knowledge and thought, really. That means "knowing who to ask"-- cuz I don't have the required knowledge...
 
If you're a computational chemist, now working in biology... you might be just the person to bounce ideas off of. Where would I take this idea from here, in practical terms?
 
Judith
BioTheory: An E-Journal of General Science in the Rosennean Complexity Paradigm http://www.rosen-enterprises.com/RobertRosen/BioTheoryLaunch.htm
Website address: http://www.rosen-enterprises.com/

----- Original Message -----
From: Leo Caves
To: ***
Sent: Tuesday, February 15, 2005 7:58 AM
Subject: Re: [ROSEN] Recycling, Rosennean Style...

Judith said:
> But the idea of molecular reconfiguration, as a form of recycling, is
> worth exploring, it seems to me. This deals with simple organization
> and should be perfectly "do-able" with current scientific modes and
> methods. Anybody have a friend who's a theoretical chemist?

Some efforts in this direction are termed "bioremediation" - co-opting,
or "evolving" microorganisms (and thereby their complex metabolic
networks) to render undesirable waste products (such as radionuclides,
toxins) safer (or ideally "inert")

The problem with transforming (or breaking down) undesirable (not
always large) molecules to safer entities is that it may require
significant (free) energy to do so or the kinetics of degradation
[half-lives] may be too long, to be of any practical benefit.
Solutions:
1/ Supply the energy to overcome the barriers / speed the process
Applying lots of heat in furnaces, assuming that one breaks down to
near elemental products.  A problem being that at such high
temperatures one also expands the width of the product distribution and
you might get (nasty) surprises.  The chemical universe is *VAST*, and
as such are immune systems cannot cope with the scale of potentialities
of such non-natural products - hence issues of toxicity and
bioaccumulation.

2/ Lower the barriers to transformation
Enzymes act as catalysts to chemical reactions by providing a local
microenvironment that lowers the energetic cost of a chemical
transformation thereby accelerating the reaction.   Reactions performed
by single enzymes tend to be rather specific; however metabolic
networks (the graph of possible enzymatic reactions) in an organism may
be extensive and complex (having scale-free characteristics as you
know) and thus provides myriad possible transformation routes according
to its evolutionary adaptation.
A naturally occurring bug may do the required remediation
transformation for you, alternatively you can use processes of
"directed evolution" to optimise a desired outcome (or promote new ones
- though harder!).

A quick google reveals a US DOE funded bioremediation research
programme at Lawrence Berkley National Labs:
http://www.lbl.gov/NABIR/generalinfo/intro.html

I agree that your more holistic view of "bioremediation", which would
require (as you state) a more systemic approach.

A small comment: in software engineering it is considered good practice
to provide a "destructor" function for every "constructor" of data or
processes.   If you screw this up, you risk ill-defined, poor or even
fatal consequences in your execution!  This process can be automated by
providing your environment with a garbage collector - which recognises
the importance for this complementary pair of functions, and takes it
out of the hands of the feeble programmer and embeds it in the
underlying run-time system.

Leo
(a computational chemist, now working in biology)

--
Leo Caves, Computational Biology, University of York
http://www.york.ac.uk/biology/staff/lsdc.htm