The key operations of animal brains are to sense, decide, act and remember. A programmed computer network also has these levels of organization and features such as interface modules, output devices, device drivers, encoders and decoders, networks and routers all contribute to understanding how the brain might be working. We have come a long way from the early speculations of neurologists who talked about relays and plug-in telephone switchboards when they sought to explain the brain – hopelessly simplistic metaphors.

Computer  design and programming increases our sophistication as we speculate about how the brain works. I use the metaphors of "computing " and “programs” to develop a way of speaking about the human brainmind without pursuing futile discussions and debates about the possibility of digital computers becoming "intelligent" (they will not). I will discount the possibility that the brain actually has digital components or uses strategies of programming used in digital computers. The human brain is not a digital computer and comparisons of brain and digital computer at the transistor and neuron level are not valid.

At a meta level, the levels of organization in computer systems and the strategies used by programmers provide useful ideas about and metaphors for brain function After all, it is the human brain that creates computer systems and programs them. We can try to understand the self-reflective and self-modifying features of both brains and computers.

The term “program” can refer to patterns of organization and procedures that are manifest in animal behavior and human cognition. There is only a loose analogy with computer programs and any similarity disappears when you look at the details of how programs are actually implemented.

The essence of a program is a series of decisions or steps that lead from an input to an output that has a coherent relationship to the input. The term "program" is abstract. Programs, in theory, can be more or less independent of the method of implementing the program. In practice, software programs, written for specific devices, are specialized versions of abstract programs that are dependent on the specific instructions available in hardware.

The distinction between software and hardware is useful and can help us resolve old confusions about what is innate and what is learned. As desktop computers evolve, more of their behavior becomes innate as the hardware grows more sophisticated. At the same time, the software evolves to take advantage of the new  possibilities the hardware offers. Computer “learning” through software growth and development leads to increasing competence in tackling real life, complex tasks. One feature of digital computers is the operating system. There are several levels to consider starting with the lowest level "machine language" that operates in the central processor (CPU). As CPUs evolve, their machine language grows more complex and  more comprehensive instructions become incorporated in the hardware subroutines that are built into the CPU or attached as BIOS and ROM chips. These innate programs evolve as layered meta languages that simplify  the programming required to carry out useful tasks such as inputting, displaying and outputting data and doing calculations.