In the latest issue of Salvo, Richard Stevens points out something that is not addressed all that often. From Biological Software: Darwin Can't Connect Your iPod to a Printer.
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Think of any mammal, bird, insect, or reptile. We think of such animals first in relation to their physical characteristics—their skin, legs, feet, heads, eyes, skeletons, muscles, circulatory systems, nerves, joints, and so on. Animals' physical features, including their internal organs, are their biological hardware. Just as iPods and other computer devices have a collection of components that can perform functions, so do the animals.
Here's the link from the iPod to animal biology: Merely possessing a hardware item does not mean the device can use it. In the case of the iPod, just having a USB port, a cable, and a printer does not mean the iPod can get things printed. Without the appropriate app—without the software—the iPod cannot use the new printer hardware.
The same is true for living organisms. Just because an animal has legs does not mean it can use them. A brain-damaged animal, for example, can have two, four, or even six legs and still not be able to walk. Without the proper know-how, an animal cannot use its legs. Legs don't run by themselves.
That know-how is a form of programmed intelligence.2 Using a leg requires lots of it. Somewhere in the animal must be a set of instructions that direct the leg to lift, extend, stop, apply pressure, reverse course, stop, reverse pressure, and lift again—all in coordination with the other legs that are doing the same thing—and then to repeat that sequence over and over again. Quickly. Precisely. Tirelessly.
To walk requires a set of instructions. In The Advent of the Algorithm, David Berlinski observes that "locomotion" occurs by the operation of "powerful computational routines." Jumping, running, skipping, and crawling all require different sets of instructions. Therefore, to operate a biological hardware component, such as a leg, requires a set of instructions. Evolutionary scientist Ernst Mayr referred to the instruction sets for biological hardware as "somatic programs." We can call them biological software.