Metabolism - Revision history

PhiNotPi: Fixed typos

2014-02-15T00:30:50Z

Fixed typos

Numsgil at 21:21, 2 March 2006

2006-03-02T21:21:56Z

Numsgil at 21:14, 2 March 2006

2006-03-02T21:14:11Z

Numsgil at 20:45, 2 March 2006

2006-03-02T20:45:06Z

Numsgil: more later, brain tired

2006-03-02T20:30:45Z

more later, brain tired

New page

Metabolism in Darwinbots is still in the planning stages. The exact implementation would rely heavily on technical constraints, specifically the number of different chemicals the program can support with reasonable speed and memory issues.

== Chemicals ==
Each chemical in the program is considered to be a simple organic molecule derived from a relatively small collection of groups (analogous to the hydroxyl etc. groups in biochemistry).

Ideally there are perhaps 8 groups, with each molecule being represented by the same number of bits. A bit of 0 would represent the absense of that group, whereas a bit of 1 would represent the presence of that group.

For example:

10001000 would indicate a molecule made up of group 1 and 5.

00000000 would indicate a molecule made up of none of the groups (but presumably still possessing the "back bone" of all the other organic molecules, and so still having chemical properties, mass, volume, etc.) This molecule would be a acceptor for all groups.

Each chemical is assigned arbitrary attributes determining free nrg, shell, slime, poison, etc.

== Metabolic Paths ==
All metabolic paths follow this form:

A + B (+/- nrg) -> C + D (+/- nrg)

Where the products of the reaction are limited by the groups the original reactants possessed.

== Final Thoughts ==
The ideas expressed here are not set in stone by any means. If you feel you know a better way, feel free to discuss it here or in the forums.

@@ Line 4: / Line 4: @@
 Each chemical in the program is considered to be a simple organic molecule derived from a relatively small collection of groups (analogous to the hydroxyl etc. groups in biochemistry).
-Ideally there are perhaps 8 groups, with each molecule being represented by the same number of bits.  A bit of 0 would represent the absense of that group, whereas a bit of 1 would represent the presence of that group.
+Ideally there are perhaps 8 groups, with each molecule being represented by the same number of bits.  A bit of 0 would represent the absence of that group, whereas a bit of 1 would represent the presence of that group.
 For example:
@@ Line 10: / Line 10: @@
 10001000 would indicate a molecule made up of group 1 and 5.
-00000000 would indicate a molecule made up of none of the groups (but presumably still possessing the "back bone" of all the other organic molecules, and so still having chemical properties, mass, volume, etc.)  This molecule would be a acceptor for all groups.
+00000000 would indicate a molecule made up of none of the groups (but presumably still possessing the "back bone" of all the other organic molecules, and so still having chemical properties, mass, volume, etc.)  This molecule would be an acceptor for all groups.
 Each chemical is assigned arbitrary attributes determining free nrg, shell, slime, poison, etc.
@@ Line 19: / Line 19: @@
 A + Enzyme (+/- nrg) -> B + Changed Enzyme (+/- nrg)
-Each enzyme has a single (or possibly more) group it facilitates the transfer of.  An enzyme that has a group attached to it is "full" and an enzyme without a group is "empty".  It is assumed that any chemical ''with'' the group in question is a valid donor and thus can donate its group to an "empty" enzyme.  Any chemical ''without'' the group is a valid acceptor, and can recieve the group from a "full" enzyme.  Enzymes can become more specific over time (using methods I haven't really examined yet) to accept and donate to specific chemicals.
+Each enzyme has a single (or possibly more) group it facilitates the transfer of.  An enzyme that has a group attached to it is "full" and an enzyme without a group is "empty".  It is assumed that any chemical ''with'' the group in question is a valid donor and thus can donate its group to an "empty" enzyme.  Any chemical ''without'' the group is a valid acceptor, and can receive the group from a "full" enzyme.  Enzymes can become more specific over time (using methods I haven't really examined yet) to accept and donate to specific chemicals.
 == Pumps (ie: Transporters) ==
 To facilitate the movement of substances from and to distinct areas (say, from outside the cell to inside the cell), 'pumps' are formed.  Pumps are similar to enzymes.  Pumps can specialize/despecialize through mutations.
-Each pump moves substances from one area to another.  This pumping action requires nrg (or perhaps can generate nrg, more on this in a second).  Pumps are ambi-directional depending on the needs of the cell (can act as an exit or an entrance), and (perhaps) may be used to generate nrg similar to the proton pumps in actual biological cells (this would actually be quite complex and is really its own seperate idea).
+Each pump moves substances from one area to another.  This pumping action requires nrg (or perhaps can generate nrg, more on this in a second).  Pumps are ambi-directional depending on the needs of the cell (can act as an exit or an entrance), and (perhaps) may be used to generate nrg similar to the proton pumps in actual biological cells (this would actually be quite complex and is really its own separate idea).
 Generating nrg would probably involve taking advantage of osmotic forces.

@@ Line 14: / Line 14: @@
 Each chemical is assigned arbitrary attributes determining free nrg, shell, slime, poison, etc.
-== Metabolic Paths ==
+== Metabolic Paths and Enzymes ==
 All metabolic paths follow this form:
@@ Line 20: / Line 20: @@
 Each enzyme has a single (or possibly more) group it facilitates the transfer of.  An enzyme that has a group attached to it is "full" and an enzyme without a group is "empty".  It is assumed that any chemical ''with'' the group in question is a valid donor and thus can donate its group to an "empty" enzyme.  Any chemical ''without'' the group is a valid acceptor, and can recieve the group from a "full" enzyme.  Enzymes can become more specific over time (using methods I haven't really examined yet) to accept and donate to specific chemicals.
 == Mutations ==

← Older revision		Revision as of 20:45, 2 March 2006
Line 23:		Line 23:
	== Final Thoughts ==		== Final Thoughts ==
	The ideas expressed here are not set in stone by any means. If you feel you know a better way, feel free to discuss it here or in the forums.		The ideas expressed here are not set in stone by any means. If you feel you know a better way, feel free to discuss it here or in the forums.
		+
		+	== Sources ==
		+	[http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pbio.0030228 The Evolution of Connectivity in Metabolic Networks]

@@ Line 17: / Line 17: @@
 All metabolic paths follow this form:
-A + B (+/- nrg) -> C + D (+/- nrg)
+A + Enzyme (+/- nrg) -> B + Changed Enzyme (+/- nrg)
-Where the products of the reaction are limited by the groups the original reactants possessed.
+Each enzyme has a single (or possibly more) group it facilitates the transfer of.  An enzyme that has a group attached to it is "full" and an enzyme without a group is "empty".  It is assumed that any chemical ''with'' the group in question is a valid donor and thus can donate its group to an "empty" enzyme.  Any chemical ''without'' the group is a valid acceptor, and can recieve the group from a "full" enzyme.  Enzymes can become more specific over time (using methods I haven't really examined yet) to accept and donate to specific chemicals.
 == Final Thoughts ==