There is a significant amount of material available on this argument against ID Theory. The bad design argument against ID Theory is based upon: (a) Redundant and poorly constructed biochemical systems that occasionally threaten the life of an organism, and (b) alleged Vestigial organs leftover by the work of evolution. Occasionally, (c) Enormous quantities of abandoned (or junk) DNA are added to the list.
JUNK DNA: As far as the junk DNA aspect of the argument, this is a current ID research area to determine what the other purposes the unused areas of the genome might serve. Some of the DNA that has been deemed neglected by molecular biologists are broken remains of ancient retroviruses. This gives cause to believe that some of the junk DNA might be for purposes of immunity.
Most alleged vestigial organs are functional, and not debris that was abandoned by evolution. If there is a genuine vestigial organ, this only supports evolutionary theory, and does not refute ID Theory by any means. ID does not refute Darwinian mechanisms, but only offers the proposition that artificial intervention interrupted natural processes. Vestigial organs might very well be evidence of bad design, but the bad design argument is an invalid challenged against ID Theory.
Arguing ID Theory is flawed based upon evidence of bad design is a philosophical contemplation, and has nothing to do with science.
1. Bad design does not equal no design.
2. There’s neither any philosophical or scientific reason to require a supernatural being to be perfect, omniscient, omnipotent, omnibenevolent, omnipresent, or omni anything else. These are theological terms. In order to assert the bad design argument, the claimant imposes their own theological preconceptions about what they think the nature of a designing agent should be.
ID INFERENCE TO A DESIGNER:
The contemplation ID devotes to a designing agent is similar to how physicists approach the causation of the Big Bang. As is the case in all science, neither field recognizes philosophical conjectures, but only empirical data. Pure ID, or Neo-ID, does not identify the Designer. The idea is that ID biologists should not allow themselves to be blind to these possibilities. ID Theory does not presume a Designer, but only approaches science recognizing that a deity cannot be ruled out as a possibility.
CONCLUSION: ID Theory does not purport to explain how design is designed. Whatever biochemical system is detected to be designed by an artificial agent there is no promise to explain how the phenomenon occurred. We are still in the 21st century, and ID Theory is still in its infancy. This ambition might be ventured a century from now, but right now there is no attempt to explain design. The reason for this is simple. ID proponents are still scouting for design by a non-natural cause in the first place. Design by an intelligent agent must first be detected, located, and identified before it can be studied and explained. We are nowhere close to the explaining part.