For some reason, the comment section is not working properly. So, I am posting a comment by Mike Keas as a new post. Feel free to respond to his comment in the comment section. Dr. Keas is a Senior Fellow at the Discovery Institute, and I am grateful for his taking part in the discussion. What follows is from his pen:
Besides what I posted above, several readings at http://www.discovery.org/csc/essentialReadings.php answer almost all the points in Grant’s post. For example, see this article (linked via. webpage above):
The Origin of Biological Information and the Higher Taxonomic Categories
By: Stephen C. Meyer, Proceedings of the Biological Society of Washington.
Read the full text article online to see why the 5-10 million year “explosion” in the early Cambrian period is a huge evidential challenge to universal common ancestry. Grant’s comments on the Cambrian explosion fail to see the force of this evidence.
Regarding Irreducible Complexity: Many have claimed that Kenneth Miller (via. the work of C.J. Heuck and others), has refuted Mike Behe’s argument for intelligent design based on irreducible complexity (bacterium flagellum, etc.). This is simply not so. Grant needs to consider the arguments in these essays below, rather than simply depict the Miller-Heuck account (and similar lines of argument) as a slam dunk for ID critics. For example, Scott Minnich (coauthor of the first article below) has spent much of his professional life doing experiments on bacterial flagella.
http://www.discovery.org/a/2181 — Genetic Analysis of Coordinate Flagellar and Type III Regulatory Circuits in Pathogenic Bacteria, Second International Conference on Design & Nature, Rhodes Greece. By: Scott A. Minnich & Stephen C. Meyer, September 1, 2004.
Minnich and Meyer conclude with this: < Indeed, in any other context we would immediately recognize such systems [as the flagellum] as the product of very intelligent engineering. Although some may argue this is a merely an argument from ignorance, we regard it as an inference to the best explanation, given what we know about the powers of intelligent as opposed to strictly natural or material causes. We know that intelligent designers can and do produce irreducibly complex systems. We find such systems within living organisms. We have good reason to think that these systems defy the creative capacity of the selection/mutation mechanism. The real problem may not be determining the best explanation of the origin of the flagellum. Rather it may be amending the methodological strictures that prevent consideration of the most natural and rational conclusion—albeit one with discomfiting philosophical implications.> Grant needs to interact with this article and its conclusion that such ID arguments are not arguments from ignorance, but rather based on positive knowledge of the world.
http://www.discovery.org/a/1364 – Where Dembski responds to the Miller essay: Kenneth Miller, “The Flagellum Unspun: The Collapse of ‘Irreducible Complexity,’” In Debating Design: From Darwin to DNA, ed. William Dembski and Michael Ruse (New York: Cambridge University Press, 2004). See also http://www.uncommondescent.com/education/dover-expert-witness-reports-available-online/
(William A. Dembski, Rebuttal to Reports by Opposing Expert Witnesses)
For example Grant needs to address this response from Dembski in his Dover report: <“[F]inding a subsystem of a functional system that performs some other function is hardly an argument for the original system evolving from that other system. One might just as well say that because the motor of a motorcycle can be used as a blender, therefore the [blender] motor evolved into the motorcycle. Perhaps, but not without intelligent design. Indeed, multipart, tightly integrated functional systems almost invariably contain multipart subsystems that serve some different function. At best the TTSS [Type-III Secretory System] represents one possible step in the indirect Darwinian evolution of the bacterial flagellum. But that still wouldn’t constitute a solution to the evolution of the bacterial flagellum. What’s needed is a complete evolutionary path and not merely a possible oasis along the way. To claim otherwise is like saying we can travel by foot from Los Angeles to Tokyo because we’ve discovered the Hawaiian Islands. Evolutionary biology needs to do better than that.”>
Do Car Engines Run on Lugnuts? A Response to Ken Miller & Judge Jones’s Straw Tests of Irreducible Complexity for the Bacterial Flagellum — http://www.discovery.org/a/3718 — Casey Luskin brings together the insights of the above two articles, and other sources, and makes this argument: <In Kitzmiller v. Dover, Judge John E. Jones ruled harshly against the scientific validity of intelligent design. Judge Jones ruled that the irreducible complexity of the bacterial flagellum, as argued by intelligent design proponents during the trial, was refuted by the testimony of the plaintiffs’ expert biology witness, Dr. Kenneth Miller. Dr. Miller misconstrued design theorist Michael Behe’s definition of irreducible complexity by presenting and subsequently refuting only a straw-characterization of the argument. Accordingly, Miller claimed that irreducible complexity is refuted if a separate function can be found for any sub-system of an irreducibly complex system, outside of the entire irreducible complex system, suggesting the sub-system might have been co-opted into the final system through the evolutionary process of exaptation. However, Miller’s characterization ignores the fact that irreducible complexity is defined by testing the ability of the final system to evolve in a step-by-step fashion in which function may not exist at each step. Only by reverse-engineering a system to test for function at each transitional stage can one determine if a system has “reducible complexity” or “irreducible complexity.” The ability to find function for some sub-part, such as the injection function of the Type III Secretory System (which only contains approximately 1⁄4 of the genes of bacterial flagellum), does not negate the irreducible complexity of the final system. Moreover, Miller ignored the fact that any evolutionary explanation of a system must account for much more than simply the availability of the parts. In the final analysis, Miller’s testimony did not actually refute irreducible complexity, leaving readers of the Kitzmiller ruling with the unfortunate perception that the evolutionary origin of the bacterial flagellum has been solved.>
http://bloggingheads.tv/diavlogs/22075 – Behe and a critic exchange thoughts.
http://www.arn.org/docs/dembski/wd_biologusubjunctive.htm — Biology in the Subjunctive Mood: A Response to Nicholas Matzke, by William A. Dembski.
Clements A, et al. (2009) The reducible complexity of a mitochondrial molecular machine. Proc Natl Acad Sci USA doi/10.1073/pnas.0908264106. This is one the latest scientific journal articles that (unwittingly) demonstrates how Behe’s idea of irreducible complexity has generated valuable scientific research, thus showing the scientific viability of ID. See also “Peer-Reviewed & Peer-Edited Scientific Publications Supporting the Theory of Intelligent Design” at http://www.discovery.org/a/2640. They quote Behe and try to refute him. See Behe’s response in the next article below, which PNAS refused to publish.
Michael Behe, “Reducible Versus Irreducible Systems and Darwinian Versus Non-Darwinian Processes” [response to PNAS article cited above] http://www.evolutionnews.org/2009/09/reducible_versus_irreducible_s.html
PNAS Authors Resort to Teleological Language in Failed Attempt to Explain Evolution of Irreducible Complexity
In this article Casey Luskin cites 5 points from Angus Menuge that Darwinists (theistic or otherwise) need to take note of:
Angus Menuge explains why these co-option (also called “exaptation”) stories are weak:
For a working flagellum to be built by exaptation, the five following conditions would all have to be met:
C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function.
C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time.C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed.C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a flagellum are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant.C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if a paddle, rotor, and motor are put together in the right order, they also need to interface correctly.
[Angus Menuge, Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004).] Those who purport to explain flagellar evolution almost always only address C1 and ignore C2-C5.
Grant appears to be unaware of these components of the ID challenge to Darwinian accounts of irreducible complexity.