Before attempting to set up a synthetic life system, careful thought must be given to how the representation of a programming language affects its adaptability in the sense of being robust to genetic operations such as mutation and recombination. The nature of the virtual computer is defined in large part by the instruction set of its machine language. The approach in this study has been to loosen up the machine code in a ``virtual bio-computer'', in order to create a computational system based on a hybrid between biological and classical von Neumann processes.
In developing this new virtual language, which is called ``Tierran'', close attention has been paid to the structural and functional properties of the informational system of biological molecules: DNA, RNA and proteins. Two features have been borrowed from the biological world which are considered to be critical to the evolvability of the Tierran language.
First, the instruction set of the Tierran language has been defined to be of a size that is the same order of magnitude as the genetic code. Information is encoded into DNA through 64 codons, which are translated into 20 amino acids. In its present manifestation, the Tierran language consists of 32 instructions, which can be represented by five bits, operands included.
Emphasis is placed on this last point because some instruction sets are
deceptively small. Some versions of the redcode language of Core Wars
([10,13,31]) for example are defined to have
ten operation codes. It might appear on the surface then that the
instruction set is of size ten. However, most of the ten instructions have
one or two operands. Each operand has four addressing modes, and then an
integer. When we consider that these operands are embedded into the machine
code, we realize that they are in fact a part of the instruction set, and
this set works out to be about 
in size. Similarly, RISC machines
may have only a few opcodes, but they probably all use 32 bit instructions,
so from a mutational point of view, they really have 
instructions.
Inclusion of numeric operands will make any instruction set extremely large
in comparison to the genetic code.
In order to make a machine code with a truly small instruction set, we must eliminate numeric operands. This can be accomplished by allowing the CPU registers and the stack to be the only operands of the instructions. When we need to encode an integer for some purpose, we can create it in a numeric register through bit manipulations: flipping the low order bit and shifting left. The program can contain the proper sequence of bit flipping and shifting instructions to synthesize the desired number, and the instruction set need not include all possible integers.
A second feature that has been borrowed from molecular biology in the design of the Tierran language is the addressing mode, which is called ``address by template''. In most machine codes, when a piece of data is addressed, or the IP jumps to another piece of code, the exact numeric address of the data or target code is specified in the machine code. Consider that in the biological system by contrast, in order for protein molecule A in the cytoplasm of a cell to interact with protein molecule B, it does not specify the exact coordinates where B is located. Instead, molecule A presents a template on its surface which is complementary to some surface on B. Diffusion brings the two together, and the complementary conformations allow them to interact.
Addressing by template is illustrated by the Tierran JMP (jump) instruction. Each JMP instruction is followed by a sequence of NOP (no-operation) instructions, of which there are two kinds: NOP_0 and NOP_1. Suppose we have a piece of code with five instruction in the following order: JMP NOP_0 NOP_0 NOP_0 NOP_1. The system will search outward in both directions from the JMP instruction looking for the nearest occurrence of the complementary pattern: NOP_1 NOP_1 NOP_1 NOP_0. If the pattern is found, the instruction pointer will move to the end of the complementary pattern and resume execution. If the pattern is not found, an error condition (flag) will be set and the JMP instruction will be ignored (in practice, a limit is placed on how far the system may search for the pattern).
The Tierran language is characterized by two unique features: a truly small instruction set without numeric operands, and addressing by template. Otherwise, the language consists of familiar instructions typical of most machine languages, e.g., MOV, CALL, RET, POP, PUSH etc. The complete instruction set is listed in Appendix B.