Creation Moment 4/25/2024 - RNA World hypothesis Falls Apart

For by him were all things created, that are in heaven, and that are in earth, visible and invisible.... Colossians 1:16

"Leading origin-of-life researcher Gerald Joyce recently published a scientific paper in PNAS, “RNA-catalyzed evolution of catalytic RNA,” that purportedly showcases a breakthrough that he and his team achieved in understanding how life could have originated through natural processes. The Washington Post describes the research in an article titled “‘Monumental’ experiment suggests how life on Earth may have started.” They say:
"The scientists overcame perhaps the greatest barrier to the plausibility of the RNA World theory. Up to now, no RNA molecule in the lab had succeeded in making copies of another RNA that were both sufficiently accurate and functional."

Unfortunately, the lauding of Joyce’s research in this and similar puff pieces is pure hype. Joyce’s results only further demonstrate the

absolute necessity of intelligent agency in life’s origin.
Many origins researchers have been guided by the RNA World hypothesis that Joyce describes as follows:
At the outset, RNA replication is likely to have occurred as a non-enzymatic process by which RNA templates were copied to yield complementary strands, which in turn were copied to yield additional copies of the starting templates. Sequence variation would have arisen due to imperfect copying fidelity, and those variants that replicated most efficiently would have grown to dominate the population, until new variants with even greater fitness arose. At some point during the early history of RNA-based evolution, it is thought that RNA evolved the ability to catalyze its own replication, acting as an RNA-dependent RNA polymerase.

The basic logic is that nucleotides formed on the early earth and then linked together into long chains known as RNA. Some RNA served

as templates that were “copied” (i.e., transcribed) by other RNA known as polymerases to form the template RNAs’ complementary sequences. 

For instance, AAUUCCGG would be transcribed into the reverse of UUAAGGCC, which is CCGGAAUU. The sequence is reversed due to the structure of RNA. The complementary sequences were then transcribed back into new copies of the original RNA templates. Over time, some RNA evolved the ability to perform biologically useful functions; such catalytic RNA are termed ribozymes. Eventually, an RNA molecule evolved the ability to accurately copy itself.

Joyce’s Experiment
Joyce’s team and other researchers have attempted to reconstruct this scenario experimentally. Bartel and Szostak (1993) generated a large pool of random RNA sequences and then isolated RNA ligases –

RNA that join two RNA molecules. Joyce and other researchers started with an RNA ligase and applied 52 rounds of “directed evolution” to generate RNA that could copy other RNA (i.e., polymerases). Most rounds included generating trillions of variants with randomly altered nucleotides and then selecting the RNA that most accurately and quickly transcribed RNA templates. Some rounds included adding additional nucleotides to the sequence.

In the latest study, Joyce and his team started with the 52-round polymerase and then applied an additional 18 rounds of modifications. The new polymerase could transcribe a hammerhead ribozyme and its complement with approximately 90 percent accuracy. Hammerhead ribozymes break an RNA molecule into two fragments. The investigators used the polymerase to generate copies of the hammerhead ribozyme and then isolated and reproduced those copies that functioned. The ribozymes remained functional after several generations of copying, so the investigators claimed to have demonstrated that a system of RNAs could persist through Darwinian evolution.

The Washington Post article asserts:

"Although the experiments in the new paper took two years, it has taken Joyce and his colleagues closer to 10 years to set the stage, patiently raising generation upon generation of RNA molecules. Should the scientists succeed in generating an RNA that can copy itself, evolution could then proceed largely on its own."

*The truth is again the exact opposite of what is claimed.
Generating the latest polymerase required investigator intervention at every step:

--The investigators started with high concentrations of ultrapure

nucleotide triphosphates (i.e., activated nucleotides). Rice University professor of chemistry James Tour has detailed the implausibility of nucleotides originating on the early Earth in even a miniscule fraction of the concentration and purity required to generate long RNA.
--The investigators generated the polymerases at each step by linking nucleotides using the machinery of modern cells. The latest polymerase is 182 nucleotides in length. Yet RNA composed of even a few dozen nucleotides could not have emerged on the early Earth since nucleotides would far more likely have bound to other molecules than to each other.
--Joyce’s team, not nature, selected after each round of modifications the polymerases that best performed the target function.
The polymerases could only transcribe template RNAs if primers were added that initiated the replication process. A primer is a

specific sequence of nucleotides that binds to the end of an RNA template. A polymerase starts with the primer and continues to add nucleotides to it until the complementary RNA is completed.
The replication process required careful orchestration of the experimental conditions including adjustments in temperature and the addition of the right supporting molecules at the right time. All such experiments require precise protocols.
Each round of modifications started with polymerases and primers in concentrations corresponding to tens of trillions of RNA per milliliter of water. If the concentration dropped below a million RNA per milliliter, the rate at which RNA decomposed would greatly exceed the rate at which RNA was copied. All polymerases would degrade long before even a tiny fraction of the templates was copied.

--Expanding on the last point, an upper bound to the concentration threshold for maintaining RNA replication directly follows from Joyce’s experimental procedure. The average time required for the polymerases to replicate a template was over one hour, and the half-life for the bonds connecting the nucleotides in RNA is on the order of years. Since polymerases are over 100 nucleotides in length, nearly all of them would break apart within a few months. The copy rate scales linearly with polymerase concentration, so the starting concentration could not drop below a billion polymerases per milliliter before the replication rate dropped below the degradation rate. A million RNA per milliliter greatly underestimates the threshold, but the probability of even a dozen polymerases residing within the same milliliter of water at any time in Earth’s history is beyond remote.

To summarize, polymerases could only have emerged on the early Earth if Joyce’s team and his laboratory were transported back in time to direct the entire process. 

Death Blow to RNA World
--Ironically, even ignoring all these challenges, Joyce’s experiment still does not support the plausibility of the RNA World hypothesis. 

--Instead, it completely discredits it. 

The probability for an RNA to form of a certain length decreases

exponentially with the length. The hammerhead ribozyme is only 34 nucleotides while polymerase ribozymes are significantly longer than 100 nucleotides. In general, ribozymes that destroy RNA can be much smaller than ribozymes that copy RNA, so they are far more likely to appear through any RNA generating process.

In addition, 

--Joyce’s latest polymerase transcribed RNA with an accuracy of approximately 90 percent per nucleotide. Joyce demonstrated that this fidelity is sufficient to maintain multiple generations of functional hammerhead ribozymes. 

--But an accuracy of over 97 percent is required to maintain functional polymerases. This result further demonstrates that destructive RNA is far easier to generate than polymerases. Leading origins expert Steven Benner calls this challenge the probability paradox. Any random library of RNA would include far more destructive RNA than polymerases. Consequently, even if a system of replicating RNA miraculously appeared, the polymerases would quickly disappear, and every RNA would then degrade into simpler molecules.

If the Washington Post author fully understood Joyce’s research, he would have summarized it more like the following:
"Gerald Joyce’s latest research conclusively overturns the RNA World hypothesis. It demonstrates that the origin of RNA that can copy other RNA requires starting with conditions that could never have occurred on the early Earth and enacting carefully

orchestrated experimental procedures that would have no parallel in nature. His team had to employ the molecular machinery of modern cells to constantly create new RNA, and they had to select and copy those RNA that performed target functions. Even after over ten years of carefully engineering an RNA that could copy other RNAs, that RNA could only effectively copy RNAs that broke apart other RNAs. It could not copy itself with sufficient accuracy for functional copiers to persist for more than a few generations. Joyce’s results demonstrate that no evolving systems of RNAs could ever have existed. Leading origins researcher Lee Cronin would likely classify any claim that such research could help explain life’s origin as a “scam.”
EN&V/BrianMiller