I appreciate that John Rennie has posted a response to my response to his original post about Kansas on the Scientific American blog. (And I happily forgive the accidental misspelling of my name.)

A common tactic in debate is to condescendingly say, “Thanks for proving my point,” when your debate opponent actually refuted all of your points. Other tactics include name-calling, changing the issue at stake, making false accusations, and appealing to authorities as if they are correct simply because they are “authorities.” John Rennie used all of these tactics in his response. Once again, there will be a major difference between my response to Mr. Rennie and his response to me: I will continue to cite scientific literature without calling names or being mean-spirited; he will cite to bold statements of scientific authorities and call lots of names. Here is my response to his response to my response to his original post:

Kansas and the Supernatural: Conspiracy-Theory Answers from Mr. Rennie
I asked Mr. Rennie why the Kansas Science Standards say science must be testable when he claims they might permit teaching about the supernatural. His response requires two conspiracy theories:

The I.D. neo-creationists don’t mind including references to testable hypotheses in the standards because they know it would be too obvious an omission to leave out. Including it doesn’t hurt their cause, however, because the I.D. movement is much less interested in advancing an actual theory of I.D. (since that could be disproved) than it is maintaining a whispering campaign of criticizing evolution and hinting that the only alternative must be I.D. (that is, gussied-up creationism).

Mr. Rennie postulates a conspiracy theory: the Kansas Science Standards have to include “testable hypotheses” in the definition of science because it would be “too obvious an omission to leave out.” In his view, evolution-critics don’t really believe science must be testable, but must include this phrase because it has to be included. This is conspiracy-theory-nonsense. Nearly everyone agrees testability is a hallmark of science (even the U.S. Supreme Court recognized this in Daubert v. Merrel Dow Pharmaceuticals, 509 U.S. 579 (1993)).

Mr. Rennie alleges another conspiracy theory: ID proponents don’t want ID mandated in schools “since … [it] … could be disproved.” That is not why Discovery Institute opposes mandating ID in schools. At Discovery Institute’s Science Education Policy page, we explain why we believe ID should not be mandated:

Attempts to mandate teaching about intelligent design only politicize the theory and will hinder fair and open discussion of the merits of the theory among scholars and within the scientific community. Furthermore, most teachers at the present time do not know enough about intelligent design to teach about it accurately and objectively.

But Mr. Rennie’s answer implies we think ID should never be discussed because we’re afraid it “could be disproved.” Again, this is contradicted by our long-standing education policy, “Although Discovery Institute does not advocate requiring the teaching of intelligent design in public schools, it does believe there is nothing unconstitutional about voluntarily discussing the scientific theory of design in the classroom.” Thus we feel that individual teachers who understand ID and will present it in an objective fashion (regardless of their individual beliefs) should have the academic freedom rights to do so, if they choose. We don’t think that ID should be censored from schools, but we do believe it should not be mandated. Mr. Rennie’s conspiracy theory is falsified because we do think that teachers should not be prohibited from discussing it if they choose, but it should not be mandated (as the Kansas Science Standards state).

Mr. Rennie’s response to my question involved multiple conspiracy theories, but the correct answer to my question is that the Kansas Science Standards state that science must include “testable hypotheses” because they do not try to sanction bringing the supernatural into science because claims about the supernatural are not testable. Mr. Rennie’s conspiracy-theory answer is simply not credible.

Finally, Mr. Rennie falsely claims that I tried to “paint methodological naturalism as some kind of fringy, radical movement” in my post. Nothing I said in my post validates his false accusation. All I said was that the old 2001 standards “hard-code[d] methodological naturalism” into the standards. I made no value judgments about methodological naturalism. My main point is quite simple: by enacting their current science standards, Kansas simply reset their definition of science back to how it existed prior to 2001. An extensive report exists at “Kansas Definition of Science Consistent With All Other States Contrary to Media Claims“, which demonstrates that the 2005 Kansas Science Standards simply brought Kansas’s definition of science back into line with how every other state defines science.

I now submit a new question to Mr. Rennie: On what basis can you criticize the Kansas Science Standards’ definition of science while not criticizing the science standards of every other state in the U.S.?

False Accusations of Misquotes
Next, Mr. Rennie falsely accuses me of inventing the claim that his post said that the current Kansas Science Standards “imply that evolution conflicts with belief in God.” Mr. Rennie needs to go back and re-read his original post. He upholds the Kansas Citizens for Science newsletter, which makes that statement, in his original post:

“The not-for-profit group Kansas Citizens for Science has summarized the key facts about what is at stake; here are some excerpts: … ‘Q. How have the standards changed? … Change the definition of evolution to imply that evolution conflicts with belief in God.'” (emphasis added)

While Mr. Rennie did not say the emboldened words directly, he did quote the newsletter which says those words. While I could have been more precise, Mr. Rennie makes it appear as if I invented the claim, when clearly he endorsed those words in his post. I was quoting the newsletter quoted by Mr. Rennie in his original post. Mr. Rennie has not responded to my rebuttal on this point, and Mr. Rennie has falsely accused me of inventing a quotation.

(Update: After posting this, I see that Mr. Rennie realized his error and retracted his false accusation. I appreciate Mr. Rennie’s honesty and I now thus retract now my claim that he made a false accusation.)

False Accusation of Misquotes and Distorting the Issue at Hand–the origins of life and the fossil record
Mr. Rennie again falsely accuses me of inventing that he said that “the material in the KSS are not simply from ‘creationist’ literature” (my words). In fact, his original post makes precisely this claim via quoting and upholding the KCFS newsletter. He wrote:

“The not-for-profit group Kansas Citizens for Science has summarized the key facts about what is at stake; here are some excerpts … ‘Add solidly refuted criticisms of evolution that are only part of the creationist literature'”

Just as above, I clearly did not misrepresent Mr. Rennie’s words, and Mr. Rennie has again falsely accused me of inventing a claim.

Finally, Mr. Rennie misrepresents and vastly overstates my position so as to call it “sl[y]” and me a “neo-creationis[t].” He alleges that I insinuated that “the scientific community [is] turning away from chemical origin of life hypotheses in some form.” I never stated or implied that. But I did state that there were “criticisms” of various leading hypotheses, which is absolutely the case.

The standards state there is “a lack of empirical evidence for a ‘primordial soup’ or a chemically hospitable pre-biotic atmosphere” and a “lack of adequate natural explanations for the genetic code”. I cited three mainstream scientific sources criticizing various hypotheses about the origin of life in the same vein that the Kansas Science Standards make students aware of the evidence. I’m not going to repeat my sources presently because they are already listed here. But they make it clear that there are many problems with current models for pre-biotic synthesis and that the origin of the genetic code is presently a mystery. That’s precisely what is stated by the Kansas Science Standards, and the claims did not come from “creationist literature” (which is what his original post states). Mr. Rennie has not responded to my point.

Mr. Rennie responds to my section on the fossil record saying, “This involves a selective misreading of the fossil record and a deliberate misinterpretation of the arguments that biologists have about various possible mechanisms for biological evolution, not a challenge to biological evolution itself.” What is Mr. Rennie talking about? I’ll go over this argument against just in case Mr. Rennie missed it or got lost the first time through:

The issue at stake here is whether the content standards of the Kansas Science Standards only derive their claims from “creationist literature,” which is what he originally claimed. Regarding the fossil record, the Kansas Science Standards state “in many cases the fossil record is not consistent with gradual, unbroken sequences postulated by biological evolution”. I quoted two mainstream scientific sources (see here if you want to re-read them) agreeing with that statement. My point was made. I was not saying anything about the large-scale debates over biological evolution in general, which would require a discussion of various models for evolution, such as punc eq, etc. My only point was that what the Kansas Science Standards say is validated in mainstream scientific literature. Mr. Rennie distorts the issue to make false accusations.

Finally, regarding the chemical origin of life, it seems that Kansas has simply accepted a former senior writer at Scientific American‘s invitation to talk about criticisms of the field. As John Horgan wrote:

“If I were a creationist, I would cease attacking the theory of evolution-which is so well supported by the fossil record-and focus instead on the origin of life. This is by far the weakest strut of the chassis of modern biology.”

(John Horgan [Former Senior Writer, Scientific American], The End of Science: Facing the Limits of Knowledge in the Twilight of the Scientific Age (Little, Brown & Co: London, 1997), pg. 138)

What’s so dangerous about what Kansas is doing that Mr. Rennie implies that weaknesses of various chemical origin-of-life hypotheses must be censored from students?
(Update: After posting this, I see that Mr. Rennie realized his error and retracted his false accusation. I appreciate Mr. Rennie’s honesty and I now retract now my claim that he made a false accusation.)

The Molecular Data
Regarding the molecular data, Mr. Rennie disputes whether challenges to common ancestry are legitimate inferences from the molecular data. I provided multiple quotes from mainstream scientific sources which legitimately allow people to question common descent. If this is the “specific phylogenetic reconstruction” of the tree/bush/tangled-thicket of life under the molecular data, then has common descent broken down? I’ll let readers decide for themselves:

To my eyes, this looks much more like a tangled thicket and a bush than a tree–which means common ancestry has a challenge here. But regardless, look at this prediction made by Emile Zuckerkandl and Linus Pauling in 1965 about regarding how molecular data would confirm macroevolution and common descent:

“It will be determined to what extent the phylogenic tree, as derived from molecular data in complete independence from the results of organismal biology, coincides with the phylogenic tree constructed on the basis of organismal biology. If the two phylogenic trees are mostly in agreement with respect to the topology of branching, the best available single proof of the reality of macro-evolution would be furnished. Indeed, only the theory of evolution, combined with the realization that events at any supramolecular level are consistent with molecular events, could reasonably account for such a congruence between lines of evidence obtained independently, namely amino acid sequences of homologous polypeptide chains on the one hand, and the finds of organismal taxonomy and paleontology on the other hand. Besides offering an intellectual satisfaction to some, the advertising of such evidence would of course amount to beating a dead horse. Some beating of dead horses may be ethical, when here and there they display unexpected twitches that look like life.”

(“Evolutionary Divergence and Convergence in Proteins.” in Evolving Genes and Proteins, p. 101. (1965))

So they predicted that similarities in predicted trees between organismal taxonomy and DNA sequences would be the ultimate “proof” of macroevolution. Has history borne out their hypothesis? Let’s consider what more recent authorities have said since we unlocked the sequences of the genetic code:

“As morphologists with high hopes of molecular systematics, we end this survey with our hopes dampened. Congruence between molecular phylogenies is as elusive as it is in morphology and as it is between molecules and morphology” (Patterson et al., “Congruence between Molecular and Morphological Phylogenies”, Annual Review of Ecology and Systematics, vol 24, pg. 179)

“New genome sequences are mystifying evolutionary biologists .. . on one front the study of evolution-the information pouring out in the genome sequences has so far proved more confusing than enlightening. Indeed, it threatens to overturn what researchers though they already knew about how microbes evolved and gave rise to higher organisms” (Science V. 280, May 1, 1998 pg. 672)

“[M]olecular systematics has not yet produced phylogenetic trees of broad phylum relationships more robust than those based on morphology.” (Rudolf A. Raff, Charles R. Marshall, James M. Turbeville, “Using DNA Sequences to Unravel the Cambrian Radiation of the Animal Phyla,” Annual Review of Ecology and Systematics, Vol. 25, pgs. 351-375 (1994).)

“That molecular evidence typically squares with morphological patterns is a view held by many biologists, but interestingly, by relatively few systematists. Most of the latter know that the two lines of evidence may often be incongruent.” (Masami Hasegawa, Jun Adachi, Michel C. Milinkovitch, “Novel Phylogeny of Whales Supported by Total Molecular Evidence,” Journal of Molecular Evolution 44 (Supplement 1, 1997): S117-S120)

“the wealth of competing morphological, as well as molecular proposals [of] the prevailing phylogenies of the mammalian orders would reduce [the mammalian tree] to an unresolved bush, the only consistent clade probably being the grouping of elephants and sea cows.” (De Jong, W. W. Molecules remodel the mammalian tree. Tree Vol 13, No 7, pg. 270-274 (July 7, 1998))

“When biologists talk of the ‘evolution wars’, they usually mean the ongoing battle for supremacy in American schoolrooms between Darwinists and their creationist opponents. But the phrase could also be applied to a debate that is raging within systematics. On one side stand traditionalists who have built evolutionary trees from decades of work on species’ morphological characteristics. On the other lie molecular systematists, who are convinced that comparisons of DNA and other biological molecules are the best way to unravel the secrets of evolutionary history. (“Bones, Molecules or Both” by Trisha Gura in Nature vol 406, 230 – 233 (2000).)

“[O]ur ability to reconstruct accurately the tree of life may not have improved significantly over the last 100 years”
“Despite increasing methodological sophistication, phylogenies derived from morphology, and those inferred from molecules, are not always converging on a consensus.”
(Wills, M. A., “The tree of life and the rock of ages: are we getting better at estimating phylogeny” in BioEssays 24:203-207 (2002) reporting on the findings of Benton, M. J., “Finding the tree of life: mapping phylogenetic trees to the fossil record through the 20th century” in Proc. R. Soc. Lond. B. 268:2123-2130 (2001).)

Clearly there are large discrepancies between molecular data and morphological data, and between various molecule-based trees. These discrepancies contradict the expectation that Pauling and Zuckerkandl said would provide “best available single proof of the reality of macro-evolution.” Clearly the citations above demonstrate much support from mainstream scientific literature for the indicator in the Kansas Science Standards which states that “Discrepancies in the molecular evidence (e.g., differences in relatedness inferred from sequence studies of different proteins)” challenge the view that “living things in all the major kingdoms are modified descendants of a common ancestor”; the KSS’s claim was not derived from “I.D. neo-creationist” literature.

Microevolution, Macroevolution, and Irreducible Complexity
First, Mr. Rennie states, “The only ones who find the linkage of microevolutionary changes to macroevolution controversial are the I.D. neo-creationists.” This is better, for he is at least trying to address the issue at hand: whether the claims in the Kansas Science Standards are only from what he labels “I.D. neo-creationist” literature. Yet he makes this assertion despite the fact that I had just previously cited mainstream scientific authorities making the claim Mr. Rennie says they don’t make. Mr. Rennie did not refute my argument, but rather makes an assertion which is refuted by the authorities I cited.

Mr. Rennie then concedes my point that irreducible complexity need not be an argument for I.D., saying, “Yes,” after quoting me saying, “Thus the KSS make it clear that irreducible complexity is framed only as a challenge to evolution and not as an argument for intelligent design.” Mr. Rennie then descends to name-calling, saying

the I.D. movement doesn’t have the intellectual honesty or sincerity to posit an actual theory of intelligent design. The I.D. movement counts itself as winning any time it can simply cast doubt on evolutionary arguments, because as I.D. writers have often suggested, the only alternative to evolution must be some kind of design.

Mr. Rennie suggests that ID is simply a negative argument against evolution. This is not true. As I explain at The Positive Case for Design, ID proponents construct a positive theory of ID which is not simply a negative argument against evolution, as Mr. Rennie suggests. As Stephen Meyer explains in his peer-reviewed article, ID helps us to understand the origin of biological information, based upon our positive understanding of how intelligent agents work:

Analysis of the problem of the origin of biological information, therefore, exposes a deficiency in the causal powers of natural selection that corresponds precisely to powers that agents are uniquely known to possess. Intelligent agents have foresight. Such agents can select functional goals before they exist. They can devise or select material means to accomplish those ends from among an array of possibilities and then actualize those goals in accord with a preconceived design plan or set of functional requirements. Rational agents can constrain combinatorial space with distant outcomes in mind. The causal powers that natural selection lacks–almost by definition–are associated with the attributes of consciousness and rationality–with purposive intelligence. Thus, by invoking design to explain the origin of new biological information, contemporary design theorists are not positing an arbitrary explanatory element unmotivated by a consideration of the evidence. Instead, they are positing an entity possessing precisely the attributes and causal powers that the phenomenon in question requires as a condition of its production and explanation.

(“Intelligent Design: The Origin of Biological Information and the Higher Taxonomic Categories,” by Stephen C. Meyer, Proceedings of the Biological Society of Washington, 117(2):213-239 (2004))

Meyer explains in another paper that with our understanding of the causal powers of intelligent agency, we can infer intelligent design for the origin of irreducibly complex structures:

Molecular machines display a key signature or hallmark of design, namely, irreducible complexity. In all irreducibly complex systems in which the cause of the system is known by experience or observation, intelligent design or engineering played a role the origin of the system. Given that neither standard neo-Darwinism, nor co-option has adequately accounted for the origin of these machines, or the appearance of design that they manifest, one might now consider the design hypothesis as the best explanation for the origin of irreducibly complex systems in living organisms. … 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.

(Scott A. Minnich and Stephen C. Meyer, “Genetic analysis of coordinate flagellar and type III regulatory circuits in pathogenic bacteria,” Proceedings of the Second International Conference on Design & Nature, Rhodes Greece, edited by M.W. Collins and C.A. Brebbia (WIT Press, 2004) (internal citations omitted))

Thus, there is a theory of ID, and, put simply, it goes like this: (1) study intelligent agents to understand the types of information they produce when they act; (2) study natural objects to see if they have the types of information which in our experience is only caused by intelligence. This is a positive, empirically based theory of intelligent design, which does not simply rely upon evidence against evolution as evidence for ID. [edited for type-o after publication–CRL] Mr. Rennie is misrepresenting intelligent design.

An Example of How ID’s Positive Methodology Can Advance Science
Finally, using this scientific methodology, intelligent design can yield fruitful insights into biology. Pro-ID biologist Jonathan Wells has suggested in a peer-reviewed ID journal that intelligent design can help us to understand function of Junk-DNA:

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.'”

(Jonathan Wells, “Using Intelligent Design Theory to Guide Scientific Research,” Progress in Complexity, Information, and Design, Vol 3.1, Nov., 2004.)

Wells’s approach might have helped us to avoid pitfalls stemming from Neo-Darwinian thought. For example, a widely used college textbook on molecular biology leads students to believe that, under Neo-Darwinian thinking, introns are merely genetic junk:

Unlike the sequence of an exon, the exact nucleotide sequence of an intron seems to be unimportant. Thus introns have accumulated mutations rapidly during evolution, and it is often possible to alter most of an intron’s nucleotide sequence without greatly affecting gene function. This has led to the suggestion that intron sequences have no function at all and are largely genetic “junk”… (Molecular biology of the Cell, 3rd Ed. (1994) by Bruce Alberts, Dennis Bray, Julian Lewis, Martin Raff, Keith Roberts, and James D. Watson)

That Darwinist statement was written in 1994. In 2003, Scientific American reported the functionality of so-called “junk-DNA,” and called our failure to recognize these allegedly “junk” introns as functional within the cell as “one of the biggest mistakes in the history of molecular biology”:

Yet the introns within genes and the long stretches of intergenic DNA between genes, Mattick says, “were immediately assumed to be evolutionary junk.”

[…]

About two thirds of the conserved sequences lie in introns, and the rest are scattered among the intergenic “junk” DNA. “I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century,” Mattick says. “The failure to recognize the full implications of this–particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules–may well go down as one of the biggest mistakes in the history of molecular biology.“

(The Unseen Genome: Gems Among the Junk by Wayt T. Gibbs, Scientific American (November, 2003), emphasis added)

Ultimately this debate over ID is immaterial to the Kansas Science Standards because they clearly state that “these standards neither mandate nor prohibit teaching about [ID].” Nonetheless, ID provides a model for understanding biology in light of the types of complexity made when intelligent agents operate. It is not merely a negative argument against evolution. Thus the theory of intelligent design leads us to the testable expectation that designers make things for a reason–and thus ID leads us to expect that structures in biology probably have some function. Had scientists considered ID in their approach, the mistake Mattick so passionately identifies could have been avoided. The positive argument for ID could yield great benefits. Unfortunately, Mr. Rennie badly misconstrues ID as if it is merely a negative argument against evolution. But that doesn’t mean Mr. Rennie is right.

There’s much more that could be said, but that’s enough for now, and I’ve exhausted my time available for this discussion. Thanks for reading.

Casey Luskin

cluskin@discovery.org