APPENDIX II:

EVOLUTIONISM

REFUTED

BY THE

RIBOSOME


QUESTION

Whether the Evolutionary Hypothesis Accounts for the Structure and Function of the Ribosome?

ANTITHESIS

We proceed thus to the Argument: It would seem (to evolutionists1) that the evolutionary hypothesis accounts for the structure and function of the ribosome even though the ribosome itself is composed in part of proteins, the synthesis of which is its essential function.2

ANTITHETICAL OBJECTIONS

Point 1: For the structural and functional delineation of the ribosome (resulting in the 2009 Nobel Prize for Chemistry)3 established the catalytic predominance of the ribosomal RNA component in the ribosome’s active protein synthesizing apparatus. Therefore, the less functional ribosomal protein component would have emerged only much later in the ribosome’s evolutionary history to provide additional catalytic and structural support for the more functional ribosomal RNA component.

The above argument is essentially the RNA world hypothesis. Concerning that hypothesis, one of 2009 Nobel Prize in Chemistry laureates (Venkatraman Ramakrishnan) in a paper published that same year writes:4

The ribosome itself is a large and complex assembly of RNA and more than 50 proteins. In addition, translation requires a host of protein factors and aminoacyl tRNA substrates. Thus, understanding the evolution of the ribosome poses a difficult challenge. To begin with, the system poses the standard “chicken or egg” question: If the ribosome consists of both RNA and protein, and is needed to make protein, how did it come about? The first attempt to address this was Crick, who presciently wrote, “It is tempting to wonder if the primitive ribosome could have been made entirely of RNA” (original italics) (Crick 1968).[5] To my knowledge, this was the first idea that RNA could be both an information carrier and able to perform catalysis, and can be thought of as the origin of the “RNA world hypothesis,” which postulates a primordial world consisting of replicating RNA molecules before the advent of proteins. However, in the absence of any known examples of catalysis by RNA, not even Crick could imagine that catalysis in the current ribosome would be RNA based.

Point 2: Further, extant6 bacterial ribosomes have a much smaller number of proteins (54) compared to extant eukaryotic ribosomes (79–80).7,8,9 It follows that ancient bacterial ribosomes would have had even smaller numbers of proteins and that the functionality of ribosomal RNA components of ancient bacterial progenitor organisms would have been sufficiently primitive to obviate the necessity for any protein-based structures.

THESIS

On the contrary, Darwin himself states: “If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.”10 Notwithstanding that Darwin had found no such case by the time the Origin of Species was published (1859), the discovery of even one such case post-1859 would serve (by his own admission) to definitively refute his theory.

THETICAL ARGUMENTS

We answer that, twentieth and twenty-first century science, particularly biochemistry and molecular biology, have been more than able to accommodate Darwin’s counterexample challenge in that regard, discovering numerous irreducibly complex11 or Catch 22-type structures or systems that could not possibly have arisen by numerous, successive, slight modifications. Whereas many of those counterexample structures or systems exist at a much lower level than a complex organ, it follows that the elucidation of any such structure or system in terms of its inherent irreducible complexity would not only refute evolutionism but do so to a degree that would be orders of magnitude beyond the minimum requirements for such refutation. The ribosome is a well-known example given that its function—that of protein synthesis—requires a protein complex, more specifically an RNA-protein complex. So proteins (as also indicated by Ramakrishnan above) require proteins to manufacture themselves. Which came first, the proteins to manufacture proteins or the proteins? And so we have an absurdity, the resolution of which can only be explained by simultaneous creation.

REPLIES TO THE ANTITHETICAL OBJECTIONS

Reply to Point 1: Måns Ehrenberg’s Scientifc Background on the Nobel Prize in Chemistry 2009 offers some sobering reflection on the alleged RNA world based on the advances in our understanding of ribosome structure and function for which said Nobel Prize was awarded:

Colophon. In the beginning it was generally believed that ribosomal protein carried out the ribosome’s catalytic actions. Then it was believed that ribosomal RNA was the catalyst. Now, we know that peptide bond formation on the bacterial ribosome and perhaps on the ribosomes from all organisms is catalyzed by ribosomal RNA as well as ribosomal protein and also by the 2’-OH group of the peptidyl-tRNA substrate in the P site [...]. This catalytic triad of ribosomal RNA, ribosomal protein and tRNA substrate may reflect a more complex starting point for the route to the present protein dominated world than a pure RNA world.12

But notwithstanding the fact that Ehrenberg’s succinct summary of triadic catalytic function in even the most primitive of organisms point to irreducible complexity in the ribosome system specifically, the general argument must also be made that predominately structural and predominately functional components are equally necessary and integral to any system—biological or otherwise. The empirical determination that a certain kind of component is predominately responsible for a system’s function while another kind of component is predominately responsible for the structural integrity of that predominantly functional component (or is subordinately functional for that matter) does not imply generic precedence of the former over the latter or vice versa. It does not imply that any predecessors or progenitors to such predominately functional components even existed let alone whether they did or did not require such ancillary components—in vitro demonstrations of (albeit degraded) functionality of predominant components in the absence of subordinate components notwithstanding. Obviously, the relative roles of such components in and of themselves are necessary but not sufficient to provide a basis for considering any extrapolative interpretations.

Reply to Point 2: It remains that any consideration of a protein-free ribosome has to take into account the fact that the ribosomes of even the lowest forms of life (i.e., prokaryotes) contain (as indicated above) over 50 proteins. For example, the ribosomes of bacteria such as T. thermophiles and E. coli contain 54 proteins.13 Londei (2020) states: “Archaeal ribosomes [...] contain [...] 50–70 proteins depending upon species.”14 The ribosomes of yeast (a eukaryote) such as S. cerevisiae contain 79 proteins and the ribosomes of man contain 80 proteins.15 The ribosomes of both bacteria, eukaryotes, and man have a common core of 34 proteins.16 It does not follow that whereas there is almost no difference in the number of ribosomal proteins between yeast and man, the attainment of 54 proteins in the ribosomes of the aforementioned bacteria represents millions (if not billions) of years of evolution from some primordial protein-free ribosome. As the only essential difference in the amount of ribosomal protein is between the two main divisions of life—prokaryotes and eukaryotes—neither of which include any evidence of transitional forms in respect of the amount of protein in their ribosomes but the ribosomes of both of which have a common core of 34 proteins, it follows that for any organism, the molecular machinery to manufacture proteins is itself protein-dependent and hence (in Darwin’s parlance) “could not possibly have been formed by numerous, successive, slight modifications.”


— FINIS —


  1. For arguments involving Catholic theology, the proposition would read, “It would seem (to theistic evolutionists) […].”↩️

  2. The (so-called) non-ribosomal peptides are synthesized by catalytic proteins (i.e., enzymes) known as non-ribosomal peptide synthetases (NRPSs) that are in turn (like proteins) synthesized by ribosomes. In other words, the biological synthesis of all peptides, including large peptide molecules (i.e., proteins) and both ribosomal and non-ribosomal peptide molecules, is ultimately dependent upon ribosomes composed of both ribosomal RNA (rRNA) and ribosomal proteins (r-proteins).↩️

  3. Awarded jointly to Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath “for studies of the structure and function of the ribosome” (http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2009/).↩️

  4. Venkatraman Ramakrishnan, The ribosome: Some hard facts about its structure and hot air about its evolution, in Cold Spring Harbor Symposia on Quantitative Biology, Volume LXXIV, pp. 25–33 (Cold Spring Harbor, NY: Cold Spring Harbour Laboratory Press, 2009). See the section titled, THE RIBOSOME AS AN RNA-BASED MACHINE.↩️

  5. F.H.C. Crick, The origin of the genetic code, J. Mol. Biol. (1968) 38, 367–379.↩️

  6. The reader is advised that the terms “extant” and “modern” are commonly used in (so-called) evolutionary biology to differentiate (so-called) present-day organisms or attributes thereof from their alleged ancient progenitors. Obviously, such terms are used in this website without prejudice.↩️

  7. Sergey Melnikov et al., One core, two shells: bacterial and eukaryotic ribosomes, Nat. Struct. Mol. Biol., 19 (6):560–567 (June 2012), Figure 2.↩️

  8. The number or range of ribosomal proteins associated with each primary division of life may require further refinement as research unfolds.↩️

  9. Cf. KEGG Ribosomal Proteins: Ribosomal proteins in prokaryotes and eukaryotes (https://www.genome.jp/kegg/annotation/br01610.html).↩️

  10. Charles Darwin, The Origin of Species by Means of Natural Selection (by Charles Darwin) in Great Books of the Western World, Vol. 49, Darwin, Robert Maynard Hutchins, Editor in Chief, and Mortimer J. Adler, Associate Editor, and published with the editorial advice of the faculties of The University of Chicago (Chicago: William Benton, Encyclopaedia Britannica, 1952), Chapter VI: Difficulties with the Theory, Modes of Transition, p. 87.↩️

  11. Michael J. Behe, Darwin’s Black Box: The Biochemical Challenge to Evolution (New York: The Free Press, 1996), specifically, the section titled, IRRIDUCIBLE COMPLEXITY AND THE TRUE NATURE OF MUTATION, pp. 39–45.↩️

  12. Måns Ehrenberg, Scientifc Background on the Nobel Prize in Chemistry 2009, STRUCTURE AND FUNCTION OF THE RIBOSOME, p.16 (https://www.nobelprize.org/uploads/2018/06/advanced-chemistryprize2009-1.pdf).↩️

  13. Sergey Melnikov et al. (2012), op. cit.↩️

  14. Paola Londei, Archaeal Ribosomes (Wiley Online Library, First Published 30 June 2020: https://onlinelibrary.wiley.com/doi/10.1002/9780470015902.a0000293.pub3).↩️

  15. Ibid.↩️

  16. Ibid.↩️


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