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. 

Perhaps 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 in its first line by misrepresenting things badly 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  valid to argue that a complex new system of representation can only arise though the work of one or more intelligent agents, never through unguided natural processes. 

Scientists Almost Seem to Have Given Up on Trying to Explain the Origin of Proteins and Genes

Scientists like to make various types of big boasts about their knowledge of things, such as the boast that they understand the basics of how the human species appeared. But various types of unsolved problems act as antagonists to such boasts. It's kind of like this:

Scientist: I understand how life originated.

Boast antagonist problems: No, you sure as hell do not.

Scientist: I understand how a human mind arises.

Boast antagonist problems: No, you sure as hell do not. 

Scientist: I understand how the human species arose.

Boast antagonist problems: No, you sure as hell do not.

In regard to the origin of life, the boast antagonist problems include the problems of the origin of DNA, the origin of the genetic code, the origin of genes, the origin of the first protein molecules, and the origin of homochirality.  In regard to the origin of large organisms, the boast antagonist problems include the problems of the origin of eukaryotic cells, the origin of most of the proteins used by mammals, the origin of protein complexes, the origin of multicellular life and the origin of bipedalism.  In regard to the origin of man, the boast antagonist problems include the problems of explaining morphogenesis, the origin of language, the origin of higher abstract reasoning, and the problems of explaining instantaneous memory creation, instant memory recall and the persistence of memories for 50 years. 

There are different ways scientists can act when faced with such boast antagonist problems. A healthy response to such problems is to spend great amounts of time trying to resolve them. Another healthy response to such problems is to modify and restrain your boasts of knowing grand things, on the basis that there are too many related unsolved problems for you to make such boasts. An unhealthy response to such boast antagonist problems is to pretty much ignore them, to mention them as little as possible, and to hope that people don't pay attention to them. There is a reason for thinking that scientists are largely guilty of this type of unhealthy response. The reason I refer to is that when we search for US federal funding for research on these boast antagonist problems, we find that some of the biggest of these problems are getting scant research. 

The web page here allows you to search grants that have been approved by the National Science Foundation:

If you type in "cancer" as the search string, and press the Search button, you will get 750 results.  The number of results is not directly listed. But by multiplying the part of the page showing results per page by the part of the page showing how many pages of results were returned, you can figure out the total number of results. For example, in the search result below, we have 30 results per page, and 25 pages of results. So apparently there are about 750 National Science Foundation projects that have some involvement with cancer:

You can also find a huge number of research results searching for topics that have no practical value. Below is what the search term "dark matter" produces:

We get 55 pages of results, with 30 results per page, giving a total of something like 1650 federally funded projects relating to dark matter. That's an amazing result, given that dark matter has never even been directly observed; and we don't even know if it exists. 

Now, let's try a different search. We will look for funded research projects relating to the origin of protein molecules. The problem of the origin of protein molecules is one of the boast antagonist problems I referred to above. Inside each human body there are more than 20,000  different types of protein molecules, each a different type of complex invention requiring a very special arrangement of thousands of atoms.  Scientists lack any credible theory for the origin of protein molecules. 

Protein molecules require very special arrangements of amino acids as hard-to-achieve by chance as it is hard for ink splashes to produce useful functional paragraphs. Because protein molecules are in general very sensitive to small changes, with their functionality typically being broken if you change only 10% or less of their amino acids, protein molecules have very high organization thresholds for them to be functional, meaning that they are not credibly explained by gradualist ideas such as Darwinism. The difficulties in explaining the origin of protein molecules is one of the biggest reasons for rejecting boasts that biological origins are successfully explained by ideas of Darwinian evolution. The issue is discussed at much greater length here and here. 

Below is the result I get when I search for the phrases "origin of protein molecules" and "origin of proteins" and "origin of protein" using the National Science Foundation grant query tool (the visual combines three different search results):

The search for research projects using the term "origin of protein molecules" produced no results. The search for research projects using the term "origin of proteins" produced no results. The search for research projects using the term "origin of protein" produced only two results. Both of those results were projects related to Alzheimer's disease, neither of which had anything to do with explaining the origin of any protein molecule. 

There's another way we can search for research projects related to the origin of protein molecules. We can search using terms such as "origin of genes" and "origin of gene."  Each type of protein molecule has its amino acid sequence specified by a particular type of gene. So research into the origin of genes is pretty much equivalent to research on the origin of proteins. 

Below is the result I get when I search for the phrases "origin of genes" and "origin of gene" using the NSF grant query tool:

The results are extremely scanty. A search for the phrase "origin of genes" produced only one result, and it is a project completed in the year 2000.  A search for the phrase "origin of gene" produced only four results. The first result is a project that ended in 2023.  The other three results are all projects that ended in the year 2007. 

Another topic related to the origin of genes and proteins is the origin of the genetic code. The genetic code is the system of representation used by genes, in which certain combinations of nucleotide base pairs stand for certain types of amino acids. This system of representations is shown below:

A search for the phrase "origin of the genetic code" on the NSF grant query tool produces only the three results shown below:

All of these projects have already been completed. 

Another of the boast antagonist problems I mentioned was the origin of protein complexes. Most or a large fraction of all proteins seem to be useless when acting alone. Most or a large fraction of all proteins only become functional when they act as team members within groups of proteins called protein complexes. Why such protein complexes arise so conveniently in the body is a major unsolved problem of biology. Below are some relevant quotes:

• "The majority of cellular proteins function as subunits in larger protein complexes. However, very little is known about how protein complexes form in vivo." Duncan and Mata, "Widespread Cotranslational Formation of Protein Complexes," 2011.
• "While the occurrence of multiprotein assemblies is ubiquitous, the understanding of pathways that dictate the formation of quaternary structure remains enigmatic." -- Two scientists (link). 
• "A general theoretical framework to understand protein complex formation and usage is still lacking." -- Two scientists, 2019 (link). 
• "Most proteins associate into multimeric complexes with specific architectures, which often have functional properties like cooperative ligand binding or allosteric regulation. No detailed knowledge is available about how any multimer and its functions arose during historical evolution." -- Ten scientists, 2020 (link). 
• "Protein assemblies are at the basis of numerous biological machines by performing actions that none of the individual proteins would be able to do. There are thousands, perhaps millions of different types and states of proteins in a living organism, and the number of possible interactions between them is enormous...The strong synergy within the protein complex makes it irreducible to an incremental process. They are rather to be acknowledged as fine-tuned initial conditions of the constituting protein sequences. These structures are biological examples of nano-engineering that surpass anything human engineers have created. Such systems pose a serious challenge to a Darwinian account of evolution, since irreducibly complex systems have no direct series of selectable intermediates, and in addition, as we saw in Section 4.1, each module (protein) is of low probability by itself." -- Steinar Thorvaldsen and Ola Hössjerm, "Using statistical methods to model the fine-tuning of molecular machines and systems,"  Journal of Theoretical Biology.

Below is the result we get using the phrase "origin of protein complexes" on the NSF grant query tool:

The query produces no results. If you change the query to "formation of protein complexes," you will get only five results, all referring to projects already completed. None of those projects generally addressed the problem of how protein complexes form. 

The queries above suggest that scientists almost have given up on trying to explain the origin of genes, protein molecules and the genetic code, and that scientists have almost given up on trying to explain the formation of protein complexes.  The problems of trying to explain the origin of such things are some of the biggest unsolved problems in science. But as long as you stay chained to the ball and chains of Darwinism and materialism, there is basically no hope of making progress on such problems. So rather than giving us continued demonstrations of how bad a job Darwinism does at explaining the origin of genes, proteins and the genetic code, scientists seem to be taking a kind of "hands off" approach to such problems, hoping that people won't notice their gigantic failure to credibly explain such things. 

By their failure to "put two and two together" in realizing the implications of their failure to credibly explain the origin of protein molecules, genes, protein complexes, the genetic code and homochirality,  today's biologists remind me of Lois Lane in the Superman comic books, TV shows and movies.  I am currently watching on HBO Max reruns of the TV series "Lois and Clark: The New Adventures of Superman." The series has excellent romantic chemistry between Superman/Clark Kent (very well-played by Dean Cain) and Lois Lane (very well  played with comic flair by Teri Hatcher).  

In the series Lois Lane is a bright woman, but when it comes to figuring out Superman's secret identity (that Superman is really Clark Kent), Lois just cannot put two and two together (to use an English expression meaning to reach a very obvious conclusion). Lois frequently sees Superman right next to her, and every day she sees  Clark Kent, who looks and talks exactly like Superman, the only difference being that Clark Kent wears glasses. Also, Lois never sees Superman and Clark Kent together. And it seems that in half of the episodes, whenever some danger arises when Lois and Clark are together, Clark suddenly disappears and Superman suddenly appears to save the day. Figuring out that Superman must be Clark Kent is just a matter of putting two and two together, but Lois just cannot bring herself to do that.  Similarly, faced with a biosphere in which all the big organisms look as well-designed and precisely fine-tuned and information-rich and well-organized as anything could look, our biologists just cannot bring themselves to put two and two together and reach the obvious conclusion that follows from such realities.