The model in a nut-shell

Loosley spoken the  model consists of a sea of micro-controllers which can interact with each other. Because former research of BioMIP and others have shown how important spatial extension is this sea actually is a ring of pots of micro-controllers.
Micro-controllers can interact with each other. Interaction is done via a recognition procedure. Each micro-controller can exhibit a recognition pattern, which is currently the first occuring concatenated sequence of Site-instructions in the program. The attachment procedure tries to find a micro-controller in the vicinity with an appropriate recognition-site and puts that micro-controller's address into the reading- or writing-slot, depending on the instruction which initiated the attachment procedure. The second recognition-based interaction is realized when transferring program control from the active micro-controller towards another micro-controller (equivalent to a sub-routine call). The third recognition event is a register access where the foreign micro-controller's accumulator acts as a local register. The micro-controller has input-ports, registers or a read-attached program and output-ports, registers or the write-attached program of a neighboring micro-controller.

Each instruction is constituted of three parts: the cargo-, conditional- and special-part. The cargo-part serves as a parameter for the instruction in the special-part, which is executed if the conditional-part, see table 3 becomes true.
Several instructions are available, see two variants in table 1 which are described in table 2. A further bit is needed to allow for conditional execution. The instructions in row J1 of table 1 are also executed if row J2 is specified and the ZF-flag (accumulator value 0) becomes active or if row J3 is specified and PF1-flag is active.

Execute S0 S1 S2 S3 J0 End/Cycle Site Load Store J1 SetAccu Call SetFA SetFB J2 (ZF) " " " " J3 (PF1) " " " "

Execute S0 S1 S2 S3 J0 SetAccu Site Load Store J1 Action Call SetFA SetFB J2 (ZF) " " " " J3 (PF1) " " " "

Table 1: Instruction set used. The possible flags are explained in table 4. The left instruction table concerns constant program lengths and the right instruction table is used with variable length sequences. The default instruction for (J0:S0, left) is Cycle. This instruction sets the instruction pointer to address zero. The instruction (J0:S0, left) can be changed by toggling the _CYCLE_-flag with the SetFB instruction. In some variants of the instruction set the instruction SetFB has been replaced by a Goto-instruction.

Only a few instructions do have side-effects during execution, namely, Action, SetFA, SetFB and Site, see table 2. With the instruction SetFB the meaning of instruction End can be changed from stopping the program immediately to setting the instruction pointer to 0 (Cycle, endless loop).

Acronym	Description
End	The program stops until it is relaunched again. Only available with fixed length programs.
Cycle	The program jumps back to address zero and continues executing. Only available with fixed length programs.
Load	Load a value from a register into the accumulator. The cargo specifies the address of the register. Register 0 points to the micro-controller attached at the reading slot. Register 1 points to the micro-controller attached at the writing slot. With no micro-controller attached a search is ignited. Prepending Site-instructions increase the specificity of register-addressing. With no Site-instructions before and accessing register 0 or 1 a random search is done. If no suitable micro-controller is found this instruction is ignored.
Store	Store the accumulator in a register. The cargo specifies the address of the register. Register 1 points to the micro-controller attached in the writing slot. Register 0 points to the micro-controller attached at the reading slot. With no micro-controller attached a search is ignited. Prepending Site-instructions increase the specificity of the register-addressing. With no Site-instructions before and accessing register 1 or 0 a random search is done. If no suitable micro-controller is found and address 1 is accessed the program is stopped to save time-slices.
Call	Transfer execution to the micro-controller specified in the cargo-part of this instruction. Accumulator and attachment slots are transferred to the new micro-controller. The current program is stopped after this call. Prepending Site-instructions increase the specificity of the micro-controller addressing, these Site-instructions are combined with the cargo-part of the Call-instruction to one big virtual recognition-site. If no appropriate micro-controller found the instruction is ignored.
SetAccu	Preset the accumulator with the value provided by the cargo-part.
Site	Define a recognition-site, either to be recognized by others or to actively attach to other micro-controllers. Used with instructions Call, Load and Store.
SetFA	If a machine is attached at the reading-slot (e.g. after accessing register 0) then certain flags can be set in this machine, see description of table 4, left part.
SetFB	Set flags in the executing machine. See table 4, right part, for a description of these flags.
Action	This command is only available when using variable length program sequences. See table 7 for a description of the possible actions.
Goto	This instruction was superseeded by the SetFB instruction. It set the instruction pointer counter (IPC) to the address given in the cargo-part of the instruction.

Table 2: With a special command (SP) width of two bits (and borrowing a case from the conditional part) these special instructions can be encoded.

Bit 1	Bit 0	Meaning
0	0	Instructions are executed always
0	1	Instructions are executed always and do have conditional equivalents
1	0	Only executed if the ZF-flag (ACCU with value 0) is set
1	1	Only executed if the PF1-flag (via other controllers or from outside) is set

Table 3: Conditional part of an instruction. Instructions can be executed if certain conditions are fulfilled, like a zero-value of the accumulator (ZF-flag) or the flag PF1 set in the status-register of a micro-controller.

Flag Meaning _PF1_ general communication _PF2_ set if this micro-controller is invisible (protection) Setting flags A at a foreign micro-controller, using the special command SetFA. If no micro-controller is attached the instruction is ignored.

Flag Meaning _CYCLE_ End-instruction means jumping to address 0, only valid with fixed length programs _REVERSE_ reading and writing goes backwards These flags B can be set with the special command SetFB.

Table 4: All flags available for a cargo-width of two are shown here. Of course, with a cargo-width larger then two, further flags could be defined. Flags A (left table) are always available at a foreign micro-controller which is attached via the reading-slot and Flags B (right table) are situated in the own micro-controller.

Action	Description
Ligate (00)	If there are two machines located, one in the reading and another in the writing-slot, the program of the machine in the writing slot is appended to the program in the reading-slot. The machine in the writing slot is invalidated after that and will be replaced by a newly created machine at the next simulation round.
Split (01)	If there are t wo machines located in the reading and writing-slot the program of the machine in the writing slot is replaced by the program right after the current remote instruction pointer (typically after the recognition site). The program in the reading slot is shortened accordingly.
CopyMask (10)	Copy the ma chine-mask from the reading-slot-machine into the machine's machine-mask attached at the writing-slot.
CopyLen (11)	Copy the len gth of the machine in the reading-slot into the machine of the writing-slot, which resembles a truncation or an elongation.
Release reading-slot (100)	If a machine is attached at the reading-slot it will be released via this action.
Release writing-slot (101)	If a machine is attached at the writing-slot it will be released via this action.

Table 5: Possible action-commands. Depending on the number of bits in the cargo-part of the instruction the shown actions can take place.

Topology

It is now common sense that spatially resolved systems are important for evolution to escape parasitism, to maintain sensible information and to increase diversity in the population, see e.g. [8,3,33] or experimental work [55, 6, 12, 54]. A question remaining is the optimum spatial dimensionality of the system. Experiments showed that the length of evolutionary avalanches and thus the diversity in the system is best in the one-dimensional case, [1], meaning space is spanned along a ring-topology, see Figure . Currently two-, one- and half-dimensional spaces can be investigated. We speak of half-dimension if the number of neighbors is one, communication along the ring can only proceed in one direction. In the simulations reported the number N of containers is between 16 and 4096 and the number m of processors per container between 8 and 32. Communication is restricted to neighboring containers. The communication between containers is organized such that the micro-controllers do have read- and write-access to the micro-controllers of the neighboring containers as well as to the micro-controllers of the own container. This, for example, gives with two neighboring containers and 16 micro-controllers per container 47 micro-controllers to exchange information with. Information exchange means access to the others program-code, accumulator or status flags-section. A container is a well-stirred reaction vessel with no further spatial organization. Each processor is able to issue arbitrary many Site instructions, see Table 1. Several Site instructions are concatenated, if they are issued in direct sequence, to create a larger and thus more specific recognition site. These extracted recognition sites are stored in a content-addressable memory to allow for a rapid attachment procedure. Of course, several other possibilities to distribute the recognition-sites do exist and even a cyclic redundancy check fingerprint (CRC16) could be used to identify the micro-controller programs. In addition to direct communication, micro-controllers are picked at random from time to time and are exchanged with micro-controllers from neighboring containers. This resembles a diffusive process in the system. In the experiments reported though no diffusive exchange was undertaken.

A minimum replicator program

Shown in Table 5 are two minimal replicator program sequences one for the fixed-length sequences case and the other for variable-length sequences. It is obvious that at least two of these programs have to be in a neighborhood to allow both to replicate each other. Larger networks are feasible as well but less probable. Only have two programs which are able to replicate each other is an idealistic view. Realistically several such programs must exist because the other micro-controllers are active as well and easily can destroy these two starting replicators.

Bits cargo C SP Site xx 00 00 Load 00 00 10 Store 01 00 11 End/Cycle - 00 00

Bits cargo C SP Site xx - 00 Load 00 - 10 Store 01 - 11

Table 5: A minimum replicator program for fixed program lengths is shown. The bits (xx) in the cargo-part of the Site-instruction are arbitrary but need to be stabilized throughout evolution. The bits of the cargo-part of the End-instruction (left part) are not evaluated. The total number of bits needed to be at the correct position with the correct value during evolution is 22.
With variable length sequences and a machine-mask of 0x3, (right part), 12 bits and a program length of three instructions have to be found and maintained by the dynamics.
Even if one omits the requirement of a univeral computability  at least 12 bits are required to be stabilized against evolution and ten bits have to be found de novo, actually these are twenty bits because we do need two micro-controllers for a replication cycle.