I just came across a nice article explaining why the metaphor of organism as machine is misleading and unhelpful.
This excerpt makes a key point:
“Although both organisms and machines operate towards the attainment of particular ends that is, both are purposive systems the former are intrinsically purposive whereas the latter are extrinsically purposive. A machine is extrinsically purposive in the sense that it works towards an end that is external to itself; that is, it does not serve its own interests but those of its maker or user. An organism, on the other hand, is intrinsically purposive in the sense that its activities are directed towards the maintenance of its own organization; that is, it acts on its own behalf.”
In this section the author explains how the software/hardware idea found its way into developmental biology.
“The situation changed considerably in the mid-twentieth century with the advent of modern computing and the introduction of the conceptual distinction between software and hardware. This theoretical innovation enabled the construction of a new kind of machine, the computer, which contains algorithmic sequences of coded instructions or programs that are executed by a central processing unit. In a computer, the software is totally independent from the hardware that runs it. A program can be transferred from one computer and run in another. Moreover, the execution of a program is always carried out in exactly the same fashion, regardless of the number of times it is run and of the hardware that runs it. The computer is thus a machine with Cartesian and Laplacian overtones. It is Cartesian because the software/hardware distinction echoes the soul/body dualism: the computer has an immaterial ‘soul’ (the software) that governs the operations of a material ‘body’ (the hardware). And it is Laplacian because the execution of a program is completely deterministic and fully predictable, at least in principle. These and other features made the computer a very attractive theoretical model for those concerned with elucidating the role of genes in development in the early days of molecular biology.”
I’ve actually criticized the genetic program metaphor myself, in the following 3QD essay:
Image source: Digesting Duck – Wikipedia