There is a philosophical danger in using the language of engineering to describe the patterns and operations of the evident products of natural selection. Invoking principles of design runs the risk of invoking a designer. But as we analyze the increasing amount of data on the genome and its organization across a wide array of organisms we are discovering there are patterns and dynamics reminiscent of designs that we, as imperfect human designers, recognize as serving an engineering purpose including the purpose to be designable, or rather, evolvable.
There is no doubt that biological artifacts are the product of Dawkins's Blind Watchmaker, natural selection. But natural selection has at its heart one of engineering's most prized principles, optimization. The Survival of the Fittest principle, while not directly specifying an objective function that an organism must meet, nonetheless provides a clear figure of merit for long term biological success, reproduction, and is a well-formed if ever changing specification.
The Survival-of-the-Fittest objective function has many features that we might think would lead to recognizable engineering solutions. Organisms must sense the environment and transfer these signals through controllers which operate actuators that make the organism behave: forage for food, choose the best food sources, deploy predations, defend themselves, hide, mate and more in order to survive. There are physical constraints on how solutions can be implemented given the environment and the composition of the life form. Systems biologists are now maturing in their ability to uses these ideas to begin to explore the engineering features of natural systems: their control, stability, filtering, coding capacity, information transfer characteristics, modularity, and perhaps most different in biological systems their evolvability. Synthetic biologists are picking up these topics for use in designing new behaviors in cells and bring other engineering challenges to the table such as automation of cloning, and more.
This marriage of systems characterization and applications design is creating a new biological engineering science. I will outline the success and challenges of this engineering type of systems biology in understanding the form and function of organisms that are in the process of being harnessed for therapeutic applications: lentiviral treatments for HIV and bacterial treatments for cancer.