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Missing the Point: Codes Are Not Products of Physics (Updated)

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Photo credit: xaviercanserra, via Pixabay.

Elaborate schemes to explain the origin of the genetic code from the laws of physics and chemistry miss the whole point about codes: the origin of information. ID books make this abundantly clear, such as in Signature in the Cell by Stephen Meyer, and The Mystery of Life’s Origin: The Continuing Controversy (expanded reprint) by Thaxton, Bradley, and Olsen and contributing authors. Whether intentionally or not, origin-of-life researchers continue to ignore the main point about codes: a code is a set of abstract symbols that represent information which can be used to convey a message, and both a code and a message presuppose a mind. Conversely, if a material process can explain the arrangement of building blocks in a sequence, it is neither a code nor a message. 

Codes may make use of material building blocks, such as letters on a printed page or radio pulses through space, but the essence of a code is the information it is able to convey. The essence of a message is the intended meaning from the messenger. The meaning may be live or programmed. In either case, codes and messages convey the foresight of a mind with the intention to communicate.

With all the insistence about this fundamental aspect of codes by ID scientists for the past 36 years (and more), it is sad to see other scientists continuing to belabor the fallacy that codes can emerge from mindless processes. If that were true, it would be the equivalent of a miracle. If other want to dismiss the “miracles” they think that intelligent design requires, what should design advocates say about the evolutionists’ miracles of chance? If others wish to limit their explanatory toolkit to “natural laws,” what about the laws of probability?

Case 1: Codes from Thermodynamics

In the Quarterly Reviews of Biophysics, Klump, Völker, and Breslauer attempt to argue that the existing DNA code was naturally selected as the most optimal for energy stability. That natural selection is the intended meaning is clear from their title: “Energy mapping of the genetic code and genomic domains: implications for code evolution and molecular Darwinism.” In other words, they propose that natural selection extended down into prebiotic life, despite the common understanding that accurate replication is a prerequisite for natural selection. In this case, the laws of thermodynamics do the selecting. This is made clear in the title of a news piece from Rutgers University, “Genetic Code Evolution and Darwin’s Evolution Theory Should Consider DNA an ‘Energy Code’ — ‘Survival of the fittest’ phenomenon is only part of the evolution equation.” But how does meaning (semantics) emerge in an “energy code” created by “molecular Darwinism”? Their hypothesis ignores this requirement entirely.

“The origins of the evolution of the DNA genetic code and the evolution of all living species are embedded in the different energy profiles of their molecular DNA blueprints. Under the influence of the laws of thermodynamics, this energy code evolved, out of an astronomical number of alternative possibilities, into a nearly singular code across all living species.”

Scientists investigated this so-called “universal enigma,” probing the origins of the astounding observation that the genetic code evolved into a nearly uniform blueprint that arose from trillions of possibilities.

The scientists expanded the underpinnings of the landmark “survival of the fittest” Darwinian evolutionary theory to include “molecular Darwinism.” Darwin’s revolutionary theory is based on the generational persistence of a species’ physical features that allow it to survive in a given environment through “natural selection.” Molecular Darwinism refers to physical characteristics that persist through generations because the regions of the molecular DNA that code for those traits are unusually stable. [Emphasis added.]

Their argument is akin to the multiverse hypothesis: out of “trillions of possibilities” a universe was naturally selected with conditions permitting complex life — and here we are! In the “molecular Darwinism” story, the laws of thermodynamics “selected” arrangements of DNA building blocks that were stable, and presto! Functional information! That’s why all life forms use it! (Notice the non-sequitur.)

The folks at Rutgers don’t mention information, and they only mention function in an after-the-fact way, intimating that “molecular Darwinism” might enable or favor biological functions.

Different DNA regions can exhibit differential energy signatures that may favor physical structures in organisms that enable specific biological functions, Breslauer said.

The following quote from the paper has to be read to be appreciated as a classic example of academic gobbledygook. In short, they derive the genetic code from the second law of thermodynamics, the very law that degrades information!

When the iconic DNA genetic code is expressed in terms of energy differentials, one observes that information embedded in chemical sequences, including some biological outcomes, correlate with distinctive free energy profiles. Specifically, we find correlations between codon usage and codon free energy, suggestive of a thermodynamic selection for codon usage. We also find correlations between what are considered ancient amino acids and high codon free energy values. Such correlations may be reflective of the sequence-based genetic code fundamentally mapping as an energy code. In such a perspective, one can envision the genetic code as composed of interlocking thermodynamic cycles that allow codons to ‘evolve’ from each other through a series of sequential transitions and transversions, which are influenced by an energy landscape modulated by both thermodynamic and kinetic factors. As such, early evolution of the genetic code may have been driven, in part, by differential energetics, as opposed exclusively by the functionality of any gene product. In such a scenario, evolutionary pressures can, in part, derive from the optimization of biophysical properties (e.g. relative stabilities and relative rates), in addition to the classic perspective of being driven by a phenotypical adaptive advantage (natural selection). Such differential energy mapping of the genetic code, as well as larger genomic domains, may reflect an energetically resolved and evolved genomic landscape, consistent with a type of differential, energy-driven ‘molecular Darwinism’. It should not be surprising that evolution of the code was influenced by differential energetics, as thermodynamics is the most general and universal branch of science that operates over all time and length scales.

The stability of a DNA double helix has no correlation with its information content. Presumably, a repetitive sequence of A-G-T-C-A-G-T-C throughout the whole strand might be the most stable of all, but it would convey no message and have no function. An “energy code” that settled out of entropy would never translate into a molecular machine with a sophisticated function. The authors assume that because the existing code is stable and has the potential to be information-rich, it will be naturally selected to be rich with information. This is nonsense. Will the emergence of shopping carts that are more stable with four wheels instead of three wheels guarantee that they will be filled with groceries? No amount of rhetoric can defend such an idea. 

The authors realize their hypothesis has a long way to go:

Next steps include recasting and mapping the human genome chemical sequence into an “energy genome,” so DNA regions with different energy stabilities can be correlated with physical structures and biological functions.

Good luck with that. No amount of research can justify a flawed premise.

Case 2: Natural Sequences

Another paper tries to get codes by material processes. It is found in PNAS by Inouye et al., “Evolution of the genetic code; Evidence from serine codon use disparity in Escherichia coli.” This team bounces off the concept of synonymous codons, where one amino acid can be represented by two to six codons. The code for serine, for instance, can be represented by AGU/C (one “box”) or UCU/C/A/G (a second box). This is the only case where it takes two base substitutions to move from one box to the other. “Deciphering how this came to be will provide important insight into the origin of life and the genetic code,” they promise. 

The authors attempt to arrange amino acids into phylogenetic trees. At the origin of life, only seven amino acids were in use, they propose; then alanine branched into the second box for serine, and so forth. They assume that the ones with the most synonymous codons evolved first, and later, the ones with single codons. They count how many amino acid species exist in bacteria, and off they go, working out a scenario for how the genetic code evolved. Strangely absent is the word information in the scheme. How do these codons translate into a function? Why, they “acquire” it! The Enlightenment has dawned!

Substitution of Ala residues with Ser not only makes a protein more hydrophilic but also, in some cases, may cause a protein to acquire an enzymatic function or provide a site for protein modification, such as phosphorylation and acetylation.

There’s no sense in continuing this notion. It’s all mixed up.

Therefore, it is further speculated that Ser residues encoded by AGU or AGC in proteins had originally different functions from Ser residues encoded by UCX. Since then, the two different sets of Ser codons have been thoroughly mixed up during evolution.

Don’t read this paper as the scientific method at work. Read it as a bedtime story.

Looking at the codon table (Table 1), we seem to be able to decipher hidden stories about how genetic codons evolved. Based on the hypothesis that the simplest and thus the most primitive amino acid among the 20 amino acids is GGX or Gly, the codons for other amino acids are proposed to have evolved from GGX. In the second step of codon evolution, new sets of the codons for seven amino acids emerged….

Emerged. Yes children, thanks to Darwin, we know that codes, messages, and other wondrous things can emerge from matter — all by themselves. 

The Power in a Code

Materialists who limit themselves to Darwin’s mechanism continue striving for natural ways to get codes. They look at energy. They look at building blocks. They connect building blocks to energy. But like plugging an extension cord into itself, there is no power that “emerges” in the system — except via speculative stories in the imaginations of materialists. Meyer, Thaxton, and the others remain vindicated: the power in a code only flows when plugged into information.