Explaining bad design in ID/IOT

Darwin's main challenge in developing his theory of evolution was how to explain good design. The challenge for Intelligent Design/Intelligent Origin Theory (ID/IOT) is to explain why bad design exists.

Here's a piece from The Panda's Thumb:

One of the problems intelligent design proponents face is how to deal with bad biological designs. There are lots of examples–Oolon Colluphid of The Secular Cafe has a handy annotated list of 96 of them.

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Intelligent design creationists in general use three basic arguments in dealing with the issue of suboptimal designs. First, they argue that the suboptimality results from "devolution." What were once optimal designs have degenerated due to the vicissitudes of time and the second law of thermodynamics, or for some, Adam and Eve's screw-up in the Garden–those of the YEC persuasion commonly attribute that degeneration (along with predation and parasitism) to the Fall. This is one of AIG's approaches. Meyer also has used the "design decay" argument–see here.

A second argument is to claim that a given design really isn't suboptimal. For example, in an interview attributed to Lee Strobel's The Case for a Creator, Meyer reportedly claimed that the inverted vertebrate retina was "a tradeoff that allows the eye to process the vast amount of oxygen it needs in vertebrates" [p.87] (and also see AIG's argument to this effect).

The third approach is to wave off questions about purportedly bad design as a theological issue, not a scientific one: Who are we to make assumptions about the Designer's unknowable (to science) intentions and motives? 'ID is real science and we don't do theology.' See here and here for examples.

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A more serious problem for Meyer's so-called "prediction" is that his two conjectures–hidden functional logic or evidence of decay–do not exhaust the universe of possible design explanations. There are at least three more possibilities: (c) an incompetent designer; (d) design by committee or competing designers; or (e) a whimsical designer (see here for examples of the invocation of whimsy on the part of a designer from Disco Dancers William Dembski, Philip Johnson, and Jonathan Witt).

There's no reason to exclude those three additional conjectures; they have no less warrant than Meyer's pair. All three are consistent with the evidence. In fact, on the evidence it seems to me that the property most appropriately assigned to a putative designer is malevolence: the world/universe really is a cruel and unpleasant place for the great majority of living things.

Given no principled constraints on the designer(s)' properties, ID has no explanatory power and no scientific value. Theories in science have (at least) three basic functions: (1) to explain observed phenomena, in the sense of identifying applicable initial conditions, relevant variables, and causal mechanisms that operate(d) to produce the observed phenomena; (2) to constrain what is possible by placing boundaries on what can happen if the theory is (small "t") true–this is my preferred gloss of 'testable/falsifiable'; and (3) to engender a rich and fruitful research program that leads to new knowledge of how the world works, to a clearer understanding of phenomena in the domain of applicability of the theory, and (this is tertiary but not irrelevant) to the devising of potentially useful applications/technology. Intelligent design "theory" does none of those things: it is a scientific and explanatory void.