There are a number of reasons why, at any particular moment, a given creature might have a design that is less than optimal, including random chance (sheer bad luck), rapid environmental change (for example, if there's a major meteor hit, an ice age, or another cataclysmic event, it takes time for evolution to catch up), or the influence that will animate much of this book: history, as encapsulated in our genome. History has a potent — and sometimes detrimental — effect because what can evolve at any given point is heavily constrained by what has evolved before. Just as contemporary political conflicts can in part be traced to the treaties following the world wars, current biology can be traced to the history of earlier creatures. As Darwin put it, all life is the product of "descent with modification"; existing forms are simply altered versions of earlier ones. The human spine, for example, arose not because it was the best possible solution imaginable, but because it was built upon something (the quadruped spine) that already existed.
This gives rise to a notion that I call "evolutionary inertia," borrowing from Newton's law of inertia (an object at rest tends to stay at rest, and an object in motion tends to stay in motion). Evolution tends to work with what is already in place, making modifications rather than starting from scratch.
Evolutionary inertia occurs because new genes must work in concert with old genes and because evolution is driven by the immediate. Gene-bearing creatures either live and reproduce or they don't. Natural selection therefore tends to favor genes that have immediate advantages, discarding other options that might function better in the long term. Thus the process operates a bit like a product manager who needs his product to ship
The net result is, as Nobel laureate Franחois Jacob famously put it, that evolution is like a tinkerer "who . . . often without knowing what he is going to produce . . . uses whatever he finds around him, old cardboards, pieces of strings, fragments of wood or metal, to make some kind of workable object... [the result is] a patchwork of odd sets pieced together when and where opportunity arose." If necessity is the mother of invention, tinkering is the geeky grandfather of kluge.
In short, evolution often proceeds by piling new systems on top of old ones. The neuroscientist John Allman has captured this idea nicely with an analogy to a power plant he once visited, where at least three layers of technology were in simultaneous use, stacked on top of one another. The recent computer technology operated not directly, but rather by controlling vacuum tubes (perhaps from the 1940s), which in turn controlled still older pneumatic mechanisms that relied on pressurized gases. If the power plant's engineers could afford the luxury of taking the whole system offline, they would no doubt prefer to start over, getting rid of the older systems altogether. But the continuous need for power precludes such an ambitious redesign.
In the same way, living creatures' continuous need to survive and reproduce often precludes evolution from building genuinely optimal systems; evolution can no more take its products offline than the human engineers could, and the consequences are often equally clumsy, with new technologies piled on top of old. The human midbrain, for example, exists literally on top of the ancient hindbrain, and the forebrain is built top of both. The hindbrain, the oldest of the three (dating from at least half a billion years ago), controls respiration, balance, alertness, and other functions that are as critical to a dinosaur as to a human. The midbrain, layered on soon afterward, coordinates visual and auditory reflexes and controls functions such as eye movements. The forebrain, the final division to come online, governs things such as language and decision making, but in ways that often depend on older systems. As any neuroscience textbook will tell you, language relies heavily on Broca's area, a walnut-sized region of the left forebrain, but it too relies on older systems, such as the cerebellum, and ancestral memory systems that are not particularly well suited to the job. Over the course of evolution our brain has become a bit like a palimpsest, an ancient manuscript with layers of text written over it many times, old bits still hiding behind new.
Allman referred to this awkward process, by which new systems are built on top of old ones rather than begun from scratch, as the "progressive overlay of technologies." The end product tends to be a kluge.
Of course, explaining why evolution can produce kluge-like solutions