Specific versus unspecific attachment
What turns out to be an important physical property is the distinction between specific attachment (a communication shall only be realized with a specified other micro-controller) or any unspecific connection, see [48]. This distinction is needed because otherwise micro-controllers either simply replicate their genomes (programs) in small cycles without being able to proliferate the sequences or they are replicating everything and become vulnerable to information dilution. Specificity can be realized in several ways: either with a fixed-recognition-site and an additional wild-carding, see classifier systems and building-block hypothesis [24] or a composition of the recognition-site from smaller modules. Both variants allow to adjust specificity and both variants have been studied. A structural drawback of the wild-carding approach is the length of the recognition-site. This means that one recognition site can at most have the length of the width of the cargo-part, which in the simplest case, is two bits. This problem is not existent with the modular-approach where it is easy to concatenate many modules (cargo-parts of the Site-instructions) to one large recognition-site.
Recognition sites and protection
From a computer-science point of view software with many existing recognition sites per program should be benign for evolution because contact can be made easily. On the other hand, exactly this high connectivity might be a curse, because everyone can interfere. Only one recognition site per program turned out to be a good choice for the moment. For example, molecules in the RNA-world [26] have to be small and probably will not be able to maintain several recognition sites per molecule. Similar with protection, in chemistry it is quite standard to work with protecting groups. It is easy to implement protection in the micro-controller, e.g. if the PF2-bit (see table 4) of a micro-controller is set then this micro-controller becomes invisible. Unfortunately, being protected also hinders others to do the necessary changes. Protection without control of the protection is an evolutionary dead-end.An important problem concerning specificity is the specificity of recognition sites. In [48] a special wild-carding system was used but handling the wild-cards is computationally expensive. Furthermore, wild-cards are somehow difficult when mapping them to biochemistry. In this work a more promising approach was considered, the concatenation of Site-instructions to form a larger recognition-site. This makes handling easy, solves the problem of specificity and is biologically more convenient. If no Site-instructions precede, for example a Load-instruction, then only the bits in the cargo-part of the Load-instruction are used for recognizing a neighboring micro-controller. With several Site-instructions before Load and the cargo-part not pointing to one of the attachment-slots the bits of the cargo-part are appended to the already existing virtual recognition-site, giving a larger recognition-site. If the Load-instruction, see table 2, wants to access the program section of a neighboring micro-controller (address 0 or 1) then a micro-controller is searched for with the appropriate virtual recognition-site, address 0 or 1 bits are not appended to this virtual recognition-site. If no Site-instructions are preceding the Load-instruction a micro-controller is chosen at random - yielding unspecific recognition. It is assured that this neighboring micro-controller is not already attached to a different slot. Self-attachment is not possible. If no appropriate micro-controller was found nothing is done and the next instruction is executed. A small difference holds for the write-instruction (Store to address 0 or 1). If no other micro-controller was found the program is stopped, because finding a suitable micro-controller at a later stage lacks synchronization anyway. This attempt to reduce computer utilization is arguable and can of course be changed at a later stage. Another solution would be to search for the next smaller recognition-site but this again will be postponed to future research.