Ken Miller’s Pearson Biology textbook, adopted for use in Texas, contains multiple false statements claiming that various types of organic molecules — from life’s building blocks to RNA — could form through natural processes. I’ve been taking a critical look at the book. See here, here, and here.

Apparently aware that primitive organic molecules face difficulties forming on the early earth, Pearson’s textbook states, “We now know that many basic building blocks of life form naturally in our solar system.” (p. 552) Which basic building blocks of life are those? True, a handful of meteorites have been found to contain organic material, including occasional amino acids, but is there evidence that the building blocks necessary for life could have been formed and delivered to the earth this way in sufficient quantities? As one paper in Nature has noted, “organic matter cannot survive the extremely high temperatures (>10⁴ K) reached on impact, which atomize the projectile and break all chemical bonds.”¹ Pearson has not justified its claim. Instead, as a 2013 paper in Proceedings of the National Academy of Sciences admitted about organic molecules discovered in a meteorite, “Could the type of compounds released from SM IOM have been significant for prebiotic evolution? The question is obviously hard to answer, given the utterly unknown nature of the chemical beginnings of life…”²

On the next page (p. 553), Pearson states “Miller and Urey’s experiment suggest that organic compounds necessary for life could have been arisen from simpler compounds on a primitive Earth.” That is a false statement. Miller and Urey used atmospheres that were different from the atmospheric composition on the early earth.³ Pearson’s textbook later acknowledges this point — it essentially acknowledges that its own statement was wrong. But then it states: “While Miller and Urey’s hypotheses about the composition of the early atmosphere were incorrect, more recent experiments using current ideas about the early atmosphere have validated their conclusion: organic compounds could have been produced on the early Earth.” (p. 553) Other studies, such as a paper in Microbiology & Molecular Biology Reviews, have contradicted this claim:

This optimistic picture began to change in the late 1970s, when it became increasingly clear that the early atmosphere was probably volcanic in origin and composition, composed largely of carbon dioxide and nitrogen rather than the mixture of reducing gases assumed by the Miller-Urey model. Carbon dioxide does not support the rich array of synthetic pathways leading to possible monomers…⁴

On what basis does Pearson claim that the actual earth’s atmosphere produces organic molecules relevant to prebiotic synthesis? It’s not clear, and this seems to be an error.

Then, the textbook uses the same line with RNA, stating that “experiments have shown that complex molecules like RNA can form in the absence of life, replicate, and carry information.” (p. 554) Which experiments are those? As far as I’m aware, that sentence is flatly wrong: the formation of RNA has not been demonstrated under natural earthlike conditions. It is misleading because it suggests that RNA forms commonly and naturally, and can replicate information as in living organisms.

RNA has not been shown to assemble in a laboratory without the help of a skilled chemist intelligently guiding the process. Indeed, in the prior paragraph the textbook states, “At least two of the nucleotides in RNA can be formed in the absence of life.” RNA uses four nucleotides, and it’s only known that two (at most) can form in the absence of life. So clearly it has not been demonstrated that “RNA can form in the absence of life.” Robert Shapiro, professor emeritus of chemistry at New York University, has critiqued the efforts of those who tried to make RNA under early earthlike conditions: “The flaw is in the logic — that this experimental control by researchers in a modern laboratory could have been available on the early Earth.”⁵

In its response to the reviewer, Pearson cited a single paper by Lincoln and Joyce⁶ as supposedly demonstrating the formation of replicating RNA. This paper has many flaws, as one chemist explained to me:

• 1. The system is completely contrived, consisting ONLY of catalysts and substrates. No competing materials or reactions were allowed. No natural analog is possible.
• 2. There is a vast gulf between their reaction mixtures and anything that might possibly come from a Stanley Miller type electric discharge experiment. This requires explanation.
• 3. The 5′-end of the oligonucleotides was primed for the condensation reaction by prior synthesis of the high-energy triphosphate form. Simple phosphates fail to react or react at rates orders of magnitude slower. Clearly the reaction only does what the chemist intended.
• 4. Reactions were carried out at 42 deg C. → fine-tuning → fine-tuner!
• 5. Only one bond is formed by either of the paired enzymes. The rest of the molecule was pre-assembled by Joyce and his colleagues. What this experiment shows is that some clever chemists have spent ten years of their lives re-engineering a pair of RNA-enzymes to catalyze ONE reaction. And without a constant supply of pre-fabricated component parts, nothing happens. Indeed, if anything, the road to self-assembly just got longer.
• 6. The “self-replicating” RNA molecules that they construct are not capable of copying a template of genetic information from freestanding chemical subunits as the polymerase machinery does in actual cells. Instead, in Lincoln and Joyce’s experiment, a presynthesized specifically sequenced RNA molecule merely catalyzes the formation of a single chemical bond, thus fusing two other presynthesized partial RNA chains. In other words, their version of “self-replication” amounts to nothing more than joining two sequence-specific premade halves together. More significantly, Lincoln and Joyce themselves intelligently arranged the matching base sequences in these RNA chains. They did the work of replication. They generated the functionally specific information that made even this limited form of replication possible.

In sum, the Lincoln and Joyce experiment demonstrates that even the capacity for modest partial self-replication in RNA itself depends upon sequence-specific (i.e., information-rich) base sequences in these molecules. It shows that even the capacity for partial replication of genetic information in RNA molecules results from the activity of chemists, that is, from the intelligence of the “ribozyme engineers” who design and select the features of these (partial) RNA replicators. Such prebiotic simulation experiments themselves confirm what we know from ordinary experience, namely, that intelligent design is the only known means by which functionally specified information arises. This is the opposite of showing that replicating RNA can form “in the absence of life” — because living human chemists created this molecule.

RNA molecules of appreciable length have been observed to form only in tightly controlled synthetic environments, and the “replication” in the study cited involved the enzymatic joining of two sets of previously prepared half-sequences, certainly not complete replication from simple molecules, which is what students will imagine. These differences should have been made clear so as not to mislead students.

References Cited:
[1.] Edward Anders. “Pre-biotic organic matter from comets and asteroids.” Nature, Vol. 342: 255-257 (November 16, 1989).
[2.] Pizzarello et al., “Processing of meteoritic organic materials as a possible analog of early molecular evolution in planetary environments,” Proceedings of the National Academy of Sciences USA (2013) (emphasis added).
[3.] Jon Cohen, “Novel Center Seeks to Add Spark to Origins of Life,” Science, Vol. 270: 1925-1926 (December 22, 1995); David W. Deamer, “The First Living Systems: a Bioenergetic Perspective,” Microbiology & Molecular Biology Reviews, Vol. 61: 239 (1997).
[4.] David W. Deamer, “The First Living Systems: a Bioenergetic Perspective,” Microbiology & Molecular Biology Reviews, Vol. 61: 239 (1997).
[5.] See Richard Van Noorden, “RNA world easier to make,” Nature News (May 13, 2009), http://www.nature.com/news/2009/090513/full/news.2009.471.html.
[6.] Lincoln, T. A., and Joyce, G. F. et al [2009] Self-sustained replication of an RNA enzyme. Science 323: 1229-1232.