7 Chain-based Bond Inhibition
6 Experiment 1
6.3 Runs 1-3 to 1-5
In all five runs of experiment 1 a consistent failure of the autopoietic process was observed. This is due to the spontaneous and premature bonding of the L particles produced within the membrane, thus making them immobile and unavailable to effect a repair to the membrane. With the benefit of these experimental results, it seems fairly obvious that this failure mode was already implicit in the qualitative chemistry described by Varela et al. [8]. It is evidently not dependent on any particular details of the implementation, nor on the specific parameters settings.
This conclusion is corroborated by the fact that this same failure mechanism has been observed in previous (unpublished) experiments with two other, independent, implementations of this reaction scheme [1, 6], and has also been previously reported by Lizana [2]. This class of failure seems also to have been recognised, at least implicitly, in the re-implementation(s) carried out by Milan Zeleny [9, Figure 4,].
Two attempted solutions to this failure mechanism were briefly investigated, before the preferred solution, to be discussed in section 7, was finally identified.
Firstly, the bonding reaction was separated into two cases: bonding between two free L particles, and bonding between a free L particle and an L particle already having one bond. The latter is the case of interest for membrane repair. These were controlled by separate rate parameters. This allowed the ``spontaneous'' bonding reaction to be made very slow. This should ensure that the free L particles formed within the membrane would not spontaneously bond with each other but would rather be held in reserve for membrane repair.<Note 4> However, this idea proved largely ineffective. The problem is that, once a rupture does occur it frequently happens that, instead of a single free L repairing the membrane, all of the free L particles become quickly incorporated into an inward spiraling chain fragment.
The second mechanism was separately (?) suggested by both Zeleny [9] and Lizana [2]. This involves inhibiting bonding to a free L particle in some neighborhood of any K particle. In Lizana's case, this effect seems to have been limited to the immediate (Moore) neighborhood of a K particle, whereas Zeleny seems to have used arbitrarily large (and dynamically changing?) neighborhoods. The idea appears to be that the K particle(s) can establish zone(s) of bond inhibition around them. The membrane can then form (roughly) at the edge of such a zone. L particles within these zones will remain free, and ready to drift to a rupture site to effect a repair.
Both Zeleney and Lizana apparently got this mechanism to give somewhat satisfactory results. The mechanism has been investigated to only a limited extent with SCL. Specifically, the use of indefinitely large inhibition zones (as suggested by Zeleny) has not been pursued, since it violates an objective that the model should rely only on local (Moore neighborhood) interactions. With this (self-imposed) restriction, the results have generally been mediocre. Two counteracting effects have been noticed. Firstly, even within a relatively small membrane such as illustrated in figure 2, the K particle may transiently drift away from the central position; if free L particles also drift away from this position, then they may still be able to spontaneously bond and become immobile. Even though the K particle may now drift back into their vicinity, it is now too late--the bonding has already occurred.<Note 5> Secondly, if a rupture occurs in the neighborhood of the K particle it is now very difficult to effect a repair, even if a free L particle should drift into an appropriate position; worse still, this is precisely the situation in which swift repair is most important, lest the K particle should escape completely. These problems can be overcome, to an extent, by making the K particle immobile (in the center of the cavity). While Lizana's description is not fully detailed, it seems that this may be what she indeed did. The mobility of K particles also seems to have been severely constrained in a number of Zeleny's experiments. In our view, this significantly reduces the generality and interest of the model, and must be considered an unsatisfactory solution.
7 Chain-based Bond Inhibition
6 Experiment 1
6.3 Runs 1-3 to 1-5
Copyright © 1997 All Rights Reserved.
Timestamp: Wed Feb 5 21:58:53 GMT 1997