Last month, we issued a report, “Evaluation of Supplementary Biology and Evolution Curricular Materials Submitted by Publishers for Adoption by the Texas State Board of Education,” which analyzed instructional materials from ten publishers that were proposed for use in Texas. When that report was prepared, many of proposed materials from the influential publisher Pearson / Prentice Hall were not accessible online. We were subsequently given access to those materials and we have now reviewed those materials in a supplemental report. The Pearson / Prentice Hall materials deserve some special attention not just because they call themselves “the nation’s leading education publisher,” but also because they are based upon Ken Miller’s biology textbook. Indeed, there is an interesting backstory here which should be told.

In 2009, the Texas State Board of Education (TSBOE) adopted new science standards (called the Texas Essential Knowledge and Skills, or “TEKS”) which require students to “analyze, evaluate, and critique scientific explanations by using empirical evidence, logical reasoning, and experimental and observational testing, including examining all sides of scientific evidence of those scientific explanations, so as to encourage critical thinking by the student.” Even more specifically, the new TEKS require students to “analyze and evaluate” core tenets of neo-Darwinian evolution, such as common ancestry, mutation, natural selection, and sudden appearance in the fossil record. They also require critical investigation of the chemical origin of life. The TSBOE is currently considering adopting supplemental materials for biology instruction, materials which are supposed to fulfill those requirements of the TEKS.

As was the case with nearly all of the other proposed instructional materials, the Pearson / Prentice Hall materials do not encourage critique or meaningful evaluation and analysis of evolutionary claims, and they do not present all sides of the evidence so as to encourage critical thinking by the student. The finding that these materials do not adequately address the TEKS is not surprising, given that Pearson / Prentice Hall’s flagship high school biology textbook author Kenneth Miller publicly admitted that he did not plan to fulfill the intent of the TEKS.

In an interview with the journal Science published in June 2009, soon after the new TEKS were adopted, evolutionary scientist and textbook author Ken Miller stated that he would not produce instructional materials which fulfill the TEKS’ call for critical analysis of evolutionary theory. Rather, as Science reported, Miller planned only to “explain the robustness of evolutionary theory.”

Miller expressly admitted that he disagreed with the intent behind the TEKS and thus would not produce materials which would fulfill that intent, stating:

“The advocates of these standards underestimate the strength of the scientific evidence for structures and phenomena that they mistakenly believe evolution cannot account for.”

(Yudhijit Bhattacharjee, “Authors Scramble to Make Textbooks Conform to Texas Science Standards,” Science, Vol. 324:1385 (June 12, 2009).)

As a specific example, Miller stated he only “intends to ‘introduce more material on the evolution of organelles’ within the cell to show that the cell’s complexity is in fact explained by evolution.” Consistent with Miller’s promise, the new Pearson / Prentice Hall materials on the origin of cellular complexity are inaccurate and contrary to various lines of scientific evidence. (A more detailed discussion of this problem is provided below.)

Likewise, the Science article reported Miller’s materials would skirt the intent of the TEKS with regards to the fossil record:

[H]e sees the standard requiring explanations of “sudden appearance, stasis, and sequential nature of groups in the fossil record”–although written with the intent to undermine evolution–as “an invitation to introduce students to punctuated equilibrium.”

Of course, this is all posturing: the new TEKS seek to “undermine” nothing and simply call for critical analysis and meaningful evaluation of scientific theories. Contrary to the Science article and Miller’s insinuations, no one feels there is anything wrong with introducing students to evolutionary concepts like punctuated equilibrium–in fact, such introductions are invited by the TEKS. However, to be consistent with the TEKS, such concepts should be discussed in an objective fashion which presents all sides of the evidence.

We have now received confirmation from Pearson / Prentice hall that the materials they submitted in Texas were in fact based upon Ken Miller’s curriculum. Given Miller’s stated goal to skirt “the intent” behind the TEKS, it comes as little surprise that the Pearson / Prentice Hall materials fail to adequately fulfill the TEKS.

Our new supplemental report on the Pearson / Prentice Hall materials finds that they are inaccurate and incomplete when covering the topics of biological and chemical evolution. Specifically, the Pearson / Prentice Hall materials contain inaccurate and incomplete discussions of all sides of the evidence regarding the tree of life, the fossil record, mutation and natural selection, and the evolutionary origins of cellular complexity.

Overstating the Evidence for Biochemical Evolution
So Ken Miller promised to only submit materials that “show that the cell’s complexity is in fact explained by evolution.” It seems that the curricular materials are predetermining the answer (e.g. evolution) rather than encouraging students to analyze and evaluate the evidence, as the TEKS require.

As a result of their goal to bolster a pre-determined answer, some of the Pearson / Prentice Hall materials make inaccurate claims about the evidence for evolution. Many evolutionary claims about cellular evolution come off as sheer pro-evolution speculation, never allowing meaningful evaluation, analysis, or critique of evolutionary hypotheses.

For example, the materials assert: “As we learn more about the cell, its systems and structures clearly seem to be the result of evolutionary processes that duplicated, reused, and adapted molecules, genes and structures to meet the demands of natural selection.” But beyond these bare assertions, no details are given about the evolution of the complexity of the cellular structures which supposedly arose in this fashion. Rather, students are left with vague, inadequate, and even inaccurate claims about the evolution of these structures. For example:

Ribosomes: Regarding ribosomes, the materials admit that “[a]ll cells synthesize proteins on ribosomes, yet the origin of such a complex structure has long been a mystery.” Then they offer an evolutionary explanation which amounts to handwaving:

the rRNA itself carries out the most important tasks in protein synthesis. Thus, it seems likely that the earliest cells may have produced proteins using RNA alone. Over time, ribosomal proteins were added gradually to these protein-producing rRNAs in ways that helped to stabilize its structure, increasing both the efficiency and complexity of the process. Therefore, the complexity of today’s ribosomes is the result of an evolutionary process that started with simpler rRNA molecules.

No details are given about how the ribosome actually evolved, other than vague mention that it might have started with simpler RNA molecules and gradually acquired proteins. No mention is made that there is a “minimum for the ribosome [of] about 53 proteins and 3 polynucleotides,” leading some evolutionary scientists to fear the ribosome might be irreducibly complex.¹

Moreover, there is no mention of scientific challenges to the ability of basic cellular ribosomal machinery required for the genetic code to evolve. As an article in Cell Biology International states:

The nucleotide sequence is also meaningless without a conceptual translative scheme and physical ‘hardware’ capabilities. Ribosomes, tRNAs, aminoacyl tRNA synthetases, and amino acids are all hardware components of the Shannon message ‘receiver’. But the instructions for this machinery is itself coded in DNA and executed by protein ‘workers’ produced by that machinery. Without the machinery and protein workers, the message cannot be received and understood. And without genetic instruction, the machinery cannot be assembled.²

That same article concludes:

New approaches to investigating the origin of the genetic code are required. The constraints of historical science are such that the origin of life may never be understood. Selection pressure cannot select nucleotides at the digital programming level where primary structures form. Genomes predetermine the phenotypes which natural selection only secondarily favors. Contentions that offer nothing more than long periods of time offer no mechanism of explanation for the derivation of genetic programming. No new information is provided by such tautologies. The argument simply says it happened. As such, it is nothing more than blind belief.³

None of these challenges to evolutionary explanations are mentioned, and there is no critique or meaningful evaluation of evolutionary hypotheses.

Krebs Cycle: This same approach is used in discussing the Krebs cycle. The materials make nondescript claims, saying the pathway “was built through ‘processes of evolution by molecular tinkering,’ using existing genes and proteins to produce a complex new biochemical pathway,” where the Krebs cycle evolved because “enzymes were, in a sense, ‘borrowed’ from other pathways.” Again, students are provided with no details beyond these vague assertions, and there is no meaningful evaluation or critique of evolutionary hypotheses.

Flagellum: Similarly, the materials assert that “prokaryotes have ‘borrowed’ copies of these proteins as the flagellum evolved.” Only vague discussions are given to students about this supposed evolutionary pathway, and there is no critique of claims that such parts can be borrowed and successfully retooled into a new cellular machine like the flagellum.

The materials state:

a group of ten proteins found in eubacterial flagella forms a protein complex in the cell membranes of other types of bacteria. The protein complex has nothing to do with producing movement. Rather, it enables disease-causing bacteria to inject poisons into the eukaryotic cells they infect. This suggests that the protein components of both the flagellum and the membrane protein complex share a common evolutionary ancestry.

The materials do not present all sides of the evidence on this point. While such sequence homology could point to common ancestry, such circumstantial evidence does not demonstrate a viable Darwinian evolutionary pathway. In fact, attempts to include this membrane protein complex (also called the Type III Secretory System, or T3SS) in an evolutionary pathway leading to the flagellum have faced difficulties.

Leading biologists argue that phylogenetic data implies the membrane complex could not have been a precursor to the flagellum.⁴ As the journal New Scientist reported:

One fact in favour of the flagellum-first view is that bacteria would have needed propulsion before they needed T3SSs, which are used to attack cells that evolved later than bacteria. Also, flagella are found in a more diverse range of bacterial species than T3SSs. ‘The most parsimonious explanation is that the T3SS arose later,’ says biochemist Howard Ochman at the University of Arizona in Tucson.⁵

Indeed, the T3SS is composed of only about 1/4 of the proteins in the flagellum, and it does not account for how the fundamental function of the flagellum–its propulsion system–evolved. The unresolved challenge that the irreducible complexity of the flagellum continues to pose for Darwinian evolution is starkly summarized by William Dembski:

At best the T[3]SS 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.⁶

Dembski’s critique is apt because it recognizes that the materials wrongly characterize irreducible complexity as focusing on the non-functionality of sub-parts. In contrast, irreducible complexity is properly tested by assessing the plausibility of the entire functional system to assemble in a step-wise fashion, even if sub-parts can have functions outside of the final system. The “leap” required by going from one functional sub-part to the entire functional system is indicative of the degree of irreducible complexity in a system.

In contrast, microbiologist Scott Minnich tested for irreducible complexity in the flagellum through genetic knock-out experiments and showed that the flagellum is irreducibly complex with respect to its complement of 35 genes:

One mutation, one part knock out, it can’t swim. Put that single gene back in we restore motility. … knock out one part, put a good copy of the gene back in, and they can swim. By definition the system is irreducibly complex. We’ve done that with all 35 components of the flagellum, and we get the same effect.⁷

This challenges evolutionary explanations of the flagellum.

Ironically, a 2006 review article in Nature Reviews Microbiology admitted that “the flagellar research community has scarcely begun to consider how these systems have evolved.”⁸ The Pearson / Prentice Hall materials recognize none of these problems or critiques with evolutionary explanations of bacterial flagella, and instead present the evolutionary hypotheses without meaningful evaluation or critique.

There are problems with the hypotheses promoted in the materials that parts can be “borrowed” to spontaneously form new complex cellular machinery. None of the following problems or critiques are addressed in the materials:

• First, not all parts are known to be available elsewhere in biology to be borrowed; many, appear unique.⁹
• Second, machine parts are not necessarily easily interchangeable. For example, grocery carts and motorcycles both have wheels, but one could not be borrowed for the other without significant modification. In biology, where small changes at the molecular level can prevent two proteins from interacting, this problem can be severe.
• Third, even if all necessary parts were available to be borrowed and were compatible, this would not explain the origin of irreducibly complex cellular machinery like the flagellum. One could place all the otherwise compatible parts for a computer in a box and shake it up for thousands of years. A functional computer would never form because machines require specific assembly instructions. Likewise, cells use complex assembly instructions in DNA to direct how parts will interact and combine to form molecular machines. Evolutionary “borrowing” hypotheses provide no explanation for the origin of the necessary DNA code to assemble “borrowed” parts into a new functional machine.

Unfortunately the Pearson / Prentice Hall materials treat “borrowing” hypotheses as if they comprise a viable evolutionary mechanism, without providing any empirically observed examples where parts have been borrowed by unguided evolutionary mechanisms to produce new complex cellular machinery. No evaluation or critique of evolutionary “borrowing” hypothesis is presented.

Remember who wrote these materials when they assert: “the facts at hand suggest that complex cellular structures and pathways were produced by the process of evolution.” Naturally, Ken Miller’s materials did not present all of the facts. Even given the facts that it did present, Miller’s materials merely make vague assertions instead of citing clear facts showing the evolution of these structures.

Moreover, when it comes to the evolutionary origin of cellular complexity, the materials contain no meaningful evaluation or critique of evolutionary claims, and no presentation of all sides of the data. Just as Ken Miller promised, his materials disregard the TEKS.

References Cited
[1.] See “Life: What A Concept!” (The Edge Foundation, 2008), pp. 77-80 at http://www.edge.org/documents/life/Life.pdf
[2.] J.T. Trevors and D.L. Abel, “Chance and necessity do not explain the origin of life,” Cell Biology International, Vol. 28: 729-739 (2004).
[3.] Ibid
[4.] See Milton H. Saier, Jr., “Evolution of Bacterial Type III Protein Secretion Systems,” Trends in Microbiology, Vol. 113:12 (2004).
[5.] Dan Jones, “Uncovering the evolution of the bacterial flagellum,” New Scientist (2-16-08).
[6.] William Dembski, Rebuttal to Reports by Opposing Expert Witnesses, p. 52, at http://www.designinference.com/documents/2005.09.Expert_Rebuttal_Dembski.pdf
[7.] Scott Minnich, Kitzmiller v. Dover testimony, Day 20 PM Testimony, pp. 107-108.
[8.] Mark Pallen & Nicholas Matzke, “From The Origin of Species to the Origin of Bacterial Flagella,” Nature Reviews Microbiology, Vol. 4:788 (2006).
[9.] For example, see the discussion of ORFan genes in Explore Evolution: The Arguments For and Against Neo-Darwinism, p. 60 (Hill House, 2007).