The Positive Case for Design

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__NOTOC__In [[Casey Luskin]]'s ironically titled '''''The Positive Case for Design''''',<ref>http://www.ideacenter.org/stuff/contentmgr/files/becbd98b35e8e07260d4e8e92784cbbb/miscdocs/thepositivecasefordesign_v3.pdf
</ref> 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.<ref>Luskin has trotted out parts of this document more than once, such as [http://www.evolutionnews.org/2010/03/a_response_to_questions_from_a.html here].  And bloggers have refuted them more than once, such as [http://nondiscovery.wordpress.com/2010/03/23/intelligent-design-does-not-make-predictions-and-is-not-science/ here.]</ref>

==The Positive Case for Design [updated v. 3.0] By Casey Luskin ==
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1=Many critics of intelligent design have argued that design is merely a negative argument against evolution. This could not be further from the truth. Leading design theorist William Dembski has observed that “[t]he principle<sup><small>[sic]</small></sup> characteristic of intelligent agency is directed contingency, or what we call choice.”<ref group="Luskin">William A. Dembski, The Design Inference (Cambridge University Pres, 1998), pg. 62.</ref> By observing the sorts of choices that intelligent agents commonly make when designing systems, a positive case for intelligent design is easily constructed by elucidating predictable, reliable indicators of design.<br/><br/>Design can be inferred using the scientific method of observation, hypothesis, experiment, and conclusion. Design theorists begin with observations of how intelligent agents act when designing, to help the  recognize and detect design in the natural world:|

2=Luskin starts this document claiming that it will not be an argument against evolution, and then speaks of "Darwinian biologists" using the term "junk DNA" and of "Darwinists"' use of [[homology]].  Who does he think he's kidding?

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==Table 1. Ways Designers Act When Designing (Observations):==

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1=(1) Intelligent agents think with an “end goal” in mind, allowing them to solve complex problems by taking many parts and arranging them in intricate patterns that perform a specific function (e.g. complex and specified information):<br/><br/>“Agents can arrange matter with distant goals in mind. In their use of language, they routinely ‘find’ highly isolated and improbable functional sequences amid vast spaces of combinatorial possibilities.”<ref group="Luskin">Stephen C. Meyer, “The Cambrian Information Explosion,” in Debating Design, pg. 388 (William A. Dembski and Michael W. Ruse eds., Cambridge University
Press, 2004), pg. 388.</ref><br/><br/>
“[W]e have repeated experience of rational and conscious agents-in particular ourselves-generating or causing increases in complex specified information, both in the form of sequence-specific lines of code and in the form of hierarchically arranged systems of parts. … Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source from a mind or personal agent.”<ref group="Luskin">[[Stephen C. Meyer]], “The origin of biological information and the higher taxonomic categories,” Proceedings of the Biological Society of Washington, 117(2):213-239 (2004).</ref>|
2=The observations here do not start well if Luskin is mimicking the [[science|scientific method]].  Normally, you observe what you want to learn about—organisms in this case.  Perhaps Luskin is attempting to make a theory of intelligent agents (although we thought that was called "[[psychology]]").

All "intelligent agents" known are humans.  Dare we say that the intelligent designer is like a lowly human?

As for the statement here, what is the evidence that there is an "end goal" in biology, particularly when there are multiple imperfections in biological species?  How would anyone know what the end goal actually is? Furthermore, how has he determined that life is "improbable"?  All of Dembski's improbability arguments have been shown to be incorrect.
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1=(2) Intelligent agents can rapidly infuse large amounts of information into systems:
“Intelligent design provides a sufficient causal explanation for the origin of large amounts of information, since we have considerable experience of intelligent agents generating informational configurations of matter.”<ref group="Luskin" name="4L">Stephen C. Meyer. et. al., "The Cambrian Explosion: Biology's Big Bang," in Darwinism, Design, and Public Education (John A. Campbell and Stephen C. Meyer eds., Michigan State University Press, 2003), pg. 386.</ref>
“We know from experience that intelligent agents often conceive of plans prior to the material
instantiation of the systems that conform to the plans—that is, the intelligent design of a blueprint often precedes the assembly of parts in accord with a blueprint or preconceived design plan.”<ref group="Luskin" name="4L"/>|
2=Nearly all ID proponents use concepts of "information" that are not standard in [[information theory]].  Furthermore, there are supposedly intelligent agents that do not infuse large amounts of information into systems, no matter how you define information!  It's also pretty clear that Luskin is setting up the rest of the document by leading the reader to his "hypotheses" and "experiments" below.
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1=(3) Intelligent agents ‘re-use’ functional components that work over and over in different systems (e.g., wheels for cars and airplanes): “An intelligent cause may reuse or redeploy the same module in different systems, without there necessarily being any material or physical connection between those systems. Even more simply, intelligent causes can generate identical patterns independently.”<ref group="Luskin">Paul Nelson and Jonathan Wells, “Homology in Biology,” in Darwinism, Design, and Public Education, pg. 316.</ref>|
2=Planes, trains and automobiles do not reproduce and pass on their wheels, and hence the analogy breaks down. One can also replace wheels as they get old, which is not the case for many body parts in biological systems.
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1=(4) Intelligent agents typically create functional things (although we may sometimes think something is functionless, not realizing its true function):
“Since non-coding regions do not produce proteins, Darwinian biologists have been dismissing them for decades as random evolutionary noise or ‘junk DNA.’ From an ID perspective, however, it is extremely unlikely that an organism would expend its resources on preserving and transmitting so much ‘junk.’”<ref group="Luskin">Jonathan Wells, “Using Intelligent Design Theory to Guide Scientific Research,” Progress in Complexity, Information, and Design, Vol 3.1, Nov., 2004.</ref>|
2=Ah, our first contrast to evolution that we were told wouldn't happen.  Apart from the presence of vast amounts of non-coding DNA in genomes, that new functions are found in no way falsifies evolution.  Furthermore, what are these "things" that these intelligent agents are making?  The ID proponents never tell us when the designer acts, what the designer did, and who the designer is.  (Or, at least not officially....)
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{{sbs|1=These observations can then be converted into predictions about what we should find if an object was designed. This makes intelligent design a scientific theory capable of generating testable predictions:|
2=When we can see the designer act, please give us a call.  In the meantime, Luskin will take his awkwardly constructed generalizations about intelligent agents and now backfill in the biology that he claims work.  (It's all too apparent from his "observations" where he is going, after all.)
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==Table 2. Predictions of Design<ref group="Luskin">“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.</ref> (Hypothesis):==

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1=(1) Natural structures will be found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information).<br/>
(2) Forms containing large amounts of novel information will appear in the fossil record suddenly and without similar precursors.<br/>
(3) Convergence will occur routinely. That is, genes and other functional parts will be re-used in different and unrelated organisms.<br/>
(4) Much so-called “junk DNA” will turn out to perform valuable functions.<br/>
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2=These are largely restatements of the above with the biological components now filled in.  (Does that mean these are now observations?  Strangely, no.  They are hypotheses!)  Not a single "hypothesis" here provides a direct link to the designer nor isolates the designer as the sole or primary cause.  Meanwhile evolutionary theory can provide explanations for all of these.  For example, different species have developed poisons, which can be traced back to one species in a phylogeny.  Furthermore, none of these can be falsified.
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1=These predictions can then be put to the test by observing the scientific data, leading to conclusions:
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2=While we certainly don't mind the "'retrodictive' predictions" to some degree, is there a future experiment that actually does test intelligent design and these "hypotheses"?  Did the ID proponents discover the flagellum and no links to any other species, for example?  Uh, no.  What's with the silly table, anyway?
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==Table 3. Examining the Evidence (Experiment and Conclusion):==

<table width=100%>
<tr valign=top border=1>
<td width=12% bgcolor=#ECE5B6>Line of Evidence</td>
<td width=28% bgcolor=#ECE5B6>Data (Experiment)</td>
<td width=10% bgcolor=#ECE5B6>Prediction Confirmed?(Conclusion)</td>
<td>"Experiments"</td>
</tr>
<tr valign=top>
<td valign=top bgcolor=#ECE5B6>(1) Biochemistry</td> 
<td bgcolor=#ECE5B6>
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.<br/><br/>
The bacterial flagellum is a prime example. The specified complexity of protein bonds, or the simplest self-reproducing cell are other examples.<ref group="Luskin">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.</ref></td>
<td bgcolor=#ECE5B6>Yes.</td>
<td>
Biologists have shown that the flagellum is not [[irreducible complexity|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. 
</td>
</tr>
<tr valign=top>
<td valign=top bgcolor=#ECE5B6>(2) Paleontology</td>
<td bgcolor=#ECE5B6>
Biological novelty appears in the fossil record suddenly and without similar precursors. The Cambrian explosion is the prime example.<ref group="Luskin">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).</ref></td>
<td bgcolor=#ECE5B6>Yes.</td>
<td>
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? 
</td>
</tr>
<tr valign=top>
<td bgcolor=#ECE5B6>(3) Systematics</td>
<td bgcolor=#ECE5B6>
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.<ref group="Luskin">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</ref></td>
<td bgcolor=#ECE5B6>Yes.</td>
<td>
Proteins with similar functions have developed across species, such as the poisons mentioned above, and phylogenic analysis establish their evolution over time.  
</td>
</tr>
<tr valign=top>
<td bgcolor=#ECE5B6>(4) Genetics</td>
<td bgcolor=#ECE5B6>
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.<ref group="Luskin">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).</ref></td>
<td bgcolor=#ECE5B6>Yes.</td>
<td>
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!
</td>

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1=Acknowledgements: Jonathan Witt applied his excellent editing expertise to this document. I also thank the many design proponents who have done research and scholarship to bear out predictions of design.|
2=Don't you mean design scientists?
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==Luskin's footnotes==
<references group="Luskin"/>

==References==
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