When Scientists Misrepresent Their Long Lab Labors as "Evolution"

 Let us examine the very big folly and misrepresentation that occurs when scientists engage in the most laborious and purposeful hi-tech fiddling in laboratories filled with gadgetry, and then try to pass off their long lab labors as examples of natural evolution. 

But first, as a springboard towards this discussion, I will mention a scientist who is simply making some provocative claims.  A recent article at www.yahoo.com is entitled "Scientist Says Human DNA Contains Clues of an Intelligent Creator." We read about assertions of Orson Wedgewood, an organic chemist with a PhD in organic medicinal chemistry. The article quotes a Daily Mail article which stated this:

"Dr Orson Wedgwood, a New Zealand-based healthcare researcher, argues that DNA could not have emerged randomly in puddles or undersea vents on early Earth, calling its spontaneous formation so improbable that it is effectively impossible.

Wedgwood believes the genetic system contains abstract instructions that nature has no known mechanism for creating unaided....

The statistical problem, he argued, concerns the extraordinary improbability of amino acids assembling into a functional protein without direction.

His conceptual objection goes further, as modern cells depend on DNA to provide instructions for proteins, while proteins help copy and translate those instructions. 

Wedgwood questioned how that interdependent arrangement could have arisen without intelligence."

The genetic code is the system within DNA by which particular triple combinations of nucleotides represent particular amino acids.  Speaking of that code, Wedgewood says, "Every other code is a result directly of intelligence, and that sort of speaks to the evidence of perhaps an intelligent originator." The visual below shows the Morse code on the left and the genetic code on the right. Both are schemes of representation under which a series of things are symbolically represented by particular combinations of symbolic tokens. During the age when telegraphs were the main technology for long-distance communication, the Morse Code was used to transmit written information over telegraph wires. When messages were transmitted using the Morse Code, an operator would use short presses on a button for one of the dot shapes shown below, and the operator would use longer presses on a button for one of the dash shapes shown below. The complexity of the genetic code used by all organisms is roughly equal to the complexity of the Morse Code. 

The Morse Code and the Genetic Code

The Daily Mail article had tried to offer a bit of "the other side" balance by stating, "A 2024 paper from Gerald Joyce's laboratory, titled RNA-Catalyzed Evolution of Catalytic RNA, showed that an RNA enzyme could copy functional RNA in a way that might enable evolution at the molecular scale." The same paper is referred to in the Yahoo article. That article first says, "RNA World research offers experimental footholds on the very steps Wedgwood calls impossible." Then it says this:

 "Researchers at the Salk Institute are not waiting for the philosophy to settle. In a 2024 paper published in PNAS, Gerald Joyce, Papastavrou, and Horning reported an RNA enzyme capable of copying functional RNA strands while allowing new molecular variants to emerge — evolution happening entirely within an RNA system."

But the claims refer to work that is not experimental in the sense of simulating early Earth conditions. And the work was not any demonstration of what can happen by evolution or by unguided natural chemical events. The work was instead long purposeful lab labors by scientists using all of the conveniences available to today's chemists -- quite the opposite of natural evolution, and quite the opposite of anything occurring by natural chemistry. 

We can absolve the writers of the Daily Mail article and the Yahoo article, because they are merely repeating a very bad misrepresentation that glaringly occurred in the paper they are referring to. That paper is the paper "RNA-catalyzed evolution of catalytic RNA." The paper started out by deceiving us in its first line by claiming, "An RNA enzyme with RNA polymerase activity was used to replicate and evolve an RNA enzyme with RNA-cleavage activity." No natural evolution was occurring. The "evolution" described was a series of changes produced by a long series of purposeful interventions made by scientists fiddling around in a modern hi-tech lab. Calling such long lab labors "evolution" is a grotesque misrepresentation. 

The text below (from the "Methods" section of the paper) shows how the so-called "evolution" required the longest and most intricate series of purposeful lab labors by scientists or their helpers, with state-of-the-art hi-tech equipment being used throughout the process:

"Synthetic oligonucleotides were either purchased from IDT or prepared by solid-phase synthesis using an Expedite 8909 DNA/RNA synthesizer, with reagents and phosphoramidites from either Glen Research or ChemGenes. All other RNAs, including RNA templates and polymerase ribozymes, were prepared by in vitro transcription (SI Appendix, Methods) and purified by denaturing polyacrylamide gel electrophoresis (PAGE). Assays of polymerase or hammerhead ribozyme activity used fluorescently labeled RNA primers or substrates, respectively. The reaction products were separated by PAGE, imaged using an Amersham Typhoon RGB laser scanner, quantified using ImageQuant TL software, and plotted using GraphPad Prism. Hot Start Taq, OneTaq, Q5 high-fidelity DNA polymerase, T4 RNA ligase, T4 RNA ligase 2, K227Q T4 RNA ligase 2, and Universal miRNA Cloning Linker were from New England Biolabs. SuperScript IV reverse transcriptase, Turbo DNase, MyOne C1 streptavidin magnetic beads, and Pierce high-capacity streptavidin agarose beads were from Thermo Fisher Scientific. Nucleoside 5′-triphosphates were from Chem-Impex International, pCp-biotin, γ-(2-azidoethyl)-ATP, and sulfo-cyanine5-azide were from Jena Bioscience, and all other chemical reagents were from Sigma-Aldrich....

Beginning with a population of polymerase ribozymes obtained after 52 rounds of directed evolution (17), error-prone PCR was performed (31) and a new 5′-terminal region was added during PCR using primer Fwd1, which contained an AvaII restriction site. In vitro transcription of polymerase-encoding DNA was carried out in the presence of γ-(2-azidoethyl)-ATP, which enabled attachment via click chemistry (SI Appendix, Methods) of a 5′-hexynylated RNA primer (Primer1). Following PAGE purification, 50 nM polymerase-primer conjugates were mixed with 100 nM 3′-biotinylated RNA template (Tem2) and 75 nM cofactor oligodeoxynucleotide (Tem4), which were annealed by heating at 80 °C for 30 s, then cooling to 17 °C. The cofactor oligo, which binds to the new 5′ end of the polymerase, was found to increase polymerase activity and was included in all polymerase-catalyzed reactions.

The annealed materials were added to a reaction mixture containing 4 mM of each NTP, various concentrations of MgCl2, 50 mM Tris-HCl (pH 8.3), and 0.05% Tween-20, which were incubated at 25 °C for various times. The reaction was quenched by adding an equal volume of 250 mM EDTA, 500 mM NaCl, 5 mM Tris-HCl (pH 8.0), and 0.025% Tween-20, then mixed with 5 µg streptavidin magnetic beads per pmol of biotinylated template and incubated with agitation at 23 °C for 1 h. The beads had been pre-blocked by incubating with 1 mg/mL tRNA. The beads were washed twice with urea buffer [8 M urea, 1 mM EDTA, and 10 mM Tris-HCl (pH 8.0)], and the polymerase-primer conjugates were eluted from the RNA template in NaOH buffer (25 mM NaOH, 1 mM EDTA, and 0.05% Tween-20), then neutralized in 100 mM Tris-HCl (pH 7.5), ethanol precipitated, and the full-length products were purified by PAGE.

The purified products were captured on magnetic beads that had been derivatized with DNA oligo Rev2, which is complementary to the 3′ end of the polymerase (SI Appendix, Methods). The bead-bound polymerase was reverse transcribed in situ. Then in a concerted reaction using both AvaII restriction enzyme and T4 DNA ligase, the 5′ substrate for the class I ligase (S1) was installed at the 3′ end of the polymerase cDNA. The 3′ substrate (S2), which was 3′-biotinylated, was added to the solution and the bead-bound ligase ribozymes were challenged to join the two substrates in the presence of 60 mM MgCl2, 200 mM KCl, 0.6 mM EDTA, and 50 mM Tris-HCl (pH 8.3) at 25 °C in 30 min.

The ligated products and corresponding polymerase cDNAs were cleaved off the beads using EcoRV (SI Appendix, Methods). The released molecules were captured on streptavidin magnetic beads, washed three times with NaOH buffer and twice with urea buffer, eluted in formamide buffer [95% formamide, 100 nM EDTA, and 1 mM Tris-HCl (pH 8.0)] by heating at 95 °C for 5 min, then ethanol precipitated. The cDNAs were reverse transcribed using primer Fwd2, which is specific for substrate S2, then PCR amplified using primers Rev1 and Fwd3, the latter of which is specific for the ligation junction between S1 and S2. Nested PCR with primers Fwd4 and Rev1 provided materials to begin the next round of evolution. New mutations were introduced by error-prone PCR (31) after rounds 53 through 58, 60, 61, 63, and 67 through 70."

Notice the use of the passive voice throughout this passage. The use of the passive voice helps achieve a covering-up the manual purposeful interventions that are occurring everywhere throughout these long lab labors. So, for example, we have a line saying "the beads were washed twice with urea buffer [8 M urea, 1 mM EDTA, and 10 mM Tris-HCl (pH 8.0)], and the polymerase-primer conjugates were eluted from the RNA template" instead of a line saying something like this: "Scientist John Smith washed the bead with urea buffer and he then eluted  the polymerase-primer conjugates from the RNA template, because this was part of his design plan to achieve the desired results."

Efforts such as those described in this paper do not do anything at all to rebut the weighty assertions of Orson Wedgwood.  Long lab labors by scientists purposefully trying to achieve some end result by using the finest gizmos and hi-tech gadgets of modern chemists do not do anything to show what unguided natural evolution or unguided chemical combinations might have produced eons ago.  

Wedgwood's insight about the genetic code stands unscathed. Human beings have never witnessed any such thing as the natural and unguided origination of some novel system of representation, something as complex as the Morse Code or the genetic code. It seems absolutely valid to argue that a new system or scheme of representation can only arise though the work of one or more intelligent agents, never through unguided natural processes.