The Positive Case for Design

__NOTOC__In Casey Luskin's ironically titled The Positive Case for Design,http://www.ideacenter.org/stuff/contentmgr/files/becbd98b35e8e07260d4e8e92784cbbb/miscdocs/thepositivecasefordesign_v3.pdf
 he claims to provide evidence that does not place intelligent design as a negative "gap" argument against evolution. He claims to use the scientific method in his approach. In this side-by-side, we refute his claims and the approach.Luskin has trotted out parts of this document more than once, such as here. And bloggers have refuted them more than once, such as here.
==The Positive Case for Design [updated v. 3.0] By Casey Luskin ==
==Table 1. Ways Designers Act When Designing (Observations):==
==Table 2. Predictions of Design“Retrodictive” predictions are common in new scientific theories. For example, Einstein’s work on relativity attempted to account for the already-understood inability of Newton’s laws of motion to accurately predict physical mechanics at very high speeds. Even Thomas Kuhn observed that new scientific theories succeed when they better account for previously-existing data. (See Kuhn, T., The Structure of Scientific Revolutions, (University of Chicago Press, 1972), pgs. 78-80.) Yet design theory is also forward-looking, predicting that we will continue to discover functions for “junk-DNA” and specified complexity in biology. (Hypothesis):==
==Table 3. Examining the Evidence (Experiment and Conclusion):==
Line of Evidence
Data (Experiment)
Prediction Confirmed?(Conclusion)
"Experiments"
(1) Biochemistry 
Natural structures have been found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information), such as irreducibly complex machines in the cell.
The bacterial flagellum is a prime example. The specified complexity of protein bonds, or the simplest self-reproducing cell are other examples.William A. Dembski, No Free Lunch, Chapter 5 (Rowman and Littlefield, 2002); Michael J. Behe, Darwin’s Black Box, Chapter 3 (Free Press 1996); Behe, M. and Snoke, D.W., “Simulating evolution by gene duplication of protein features that require multiple amino acid residues,” Protein Science, 13 (2004); Scott N. Peterson and Claire M. Fraser, “The complexity of simplicity,” Genome Biology 2 (2001):1-7.
Yes.
Biologists have shown that the flagellum is not irreducibly complex, having evolved from the type III secretion system. While all proposed irreducibly complex structures have been shown to have precursors, even if scientists do not know how a structure came to be does not mean it should not be studied. 
(2) Paleontology
Biological novelty appears in the fossil record suddenly and without similar precursors. The Cambrian explosion is the prime example.Mayr, E., One Long Argument: Charles Darwin and the Genesis of Modern Evolutionary Thought (Harvard University Press, 1991), p. 138; Valentine, J.W., Jablonski, D., Erwin, D. H., “Fossils, molecules and embryos: new perspectives on the Cambrian Explosion,” Development 126:851-859 (1999).
Yes.
The Cambrian explosion allowed species to develop after the Hox genes evolved, allowing for a diversity of species to develop rapidly in a world previously populated by less adaptable species. Precursors to the Hox genes have been verified, and it's not clear why an intelligent agent is required to fill in this gap. The "Cambrian explosion" lasted something like 20 million years, or over three thousand times as long as most IDers say the world has been around—would you call that "sudden"? Other examples for which increased species result from the evolution of beneficial characteristics have been shown. Do the intelligent design proponents propose another example? 
(3) Systematics
Similar parts have been found in organisms that even Darwinists see as separated by more closely related forms that do not contain the similar parts in question. Clear examples include genes controlling eye or limb growth in different organisms whose alleged common ancestors are not thought to have had such forms of eyes or limbs.Quiring, R., et al. “Homology of the eyeless gene of drosophila to the small eye in mice and aniridia in humans,” Science 265:78 (1994); See also infra, Ref. 5
Yes.
Proteins with similar functions have developed across species, such as the poisons mentioned above, and phylogenic analysis establish their evolution over time. 
(4) Genetics
Genetic research continues to uncover functions for “junk-DNA,” include functionality for pseudogenes, introns, LINE, and ALU elements. Examples of unknown DNA functions persist, but design encourages researchers to investigate functions, whereas Darwinism has caused some scientists to wrongly assume that non-coding DNA is junk.Hirotsune S. et al., “An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene,” Nature 423:91-96 (2003); “The Unseen Genome: Gems among the Junk” by Wayt T. Gibbs, Scientific American (November, 2003); Hakimi, M.S. et. al., "A chromatin remodelling complex that loads cohesin onto human chromosomes," Nature, 418:994-998 (2002); Morrish, T. A., et al., "DNA repair mediated by endonuclease-independent LINE-1 retrotransposition," Nature Genetics, 31(2):159-165 (June, 2002).
Yes.
This extensive contrast to evolution (which we were told would not happen!) is irrelevant. Scientists incorporate new information into theories all the time, and finding functions for junk DNA in no way invalidates it. Furthermore, without the contrast to evolution, this prediction merely says that there are genes we do not know about. That is not a surprise!
==Luskin's footnotes==
==References==
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