A report from the University of North Carolina, “New evidence emerges on the origins of life on Earth,” opens on a deliberately Biblical note. We picture the two UNC scientists hovering over the waters of the primordial soup:

In the beginning, there were simple chemicals. And they produced amino acids that eventually became the proteins necessary to create single cells. And the single cells became plants and animals. Recent research is revealing how the primordial soup created the amino acid building blocks, and there is widespread scientific consensus on the evolution from the first cell into plants and animals. But it’s still a mystery how the building blocks were first assembled into the proteins that formed the machinery of all cells. Now, two long-time University of North Carolina scientists — Richard Wolfenden, PhD, and Charles Carter, PhD — have shed new light on the transition from building blocks into life some 4 billion years ago. [Emphasis added.]

Commendably, they recognize the “mystery” of getting proteins from building blocks, That’s really the crux of the issue, isn’t it? The message is the key, not just the letters. So overlook the matter of evolving plants and animals from single cells via natural selection. Let pass the question of whether or not a “widespread scientific consensus” carries much weight in the philosophy of science. And even allow them their “primordial soup” without complaining about the dilution problem and other issues.

Here is the difficulty that Wolfenden and Carter seek to address: getting from “simple chemicals” to LUCA, the Last Universal Common Ancestor. Let’s assume Darwinian evolution can take that LUCA to Lucy or any other complex animal or human. That should leave a narrowly focused question: how to get from simple chemicals to LUCA. Carter and Wolfenden are, respectively, lead authors of papers in the Proceedings of the National Academy of Sciences, one on temperature effects on amino acids, the other on the origin of chemical codes, that provide the details.

The news item from UNC contains a surprise that may displease other workers studying the origin of life: the fall of the “problematic” RNA-world theory.

Their findings, published in companion papers in the Proceedings of the National Academy of Sciences, fly in the face of the problematic “RNA world” theory, which posits that RNA — the molecule that today plays roles in coding, regulating, and expressing genes — elevated itself from the primordial soup of amino acids and cosmic chemicals to give rise first to short proteins called peptides and then to single-celled organisms.

Wolfenden and Carter argue that RNA did not work alone; in fact, it was no more likely that RNA catalyzed peptide formation than it was for peptides to catalyze RNA formation.

“Our work shows that the close linkage between the physical properties of amino acids, the genetic code, and protein folding was likely essential from the beginning, long before large, sophisticated molecules arrived on the scene,” said Carter, professor of biochemistry and biophysics at the UNC School of Medicine. “This close interaction was likely the key factor in the evolution from building blocks to organisms.“

The finding adds a new layer to the story of how life evolved billions of years ago.

So they have rejected RNA world. But are they really going to leap from soup to LUCA in a single bound? They venture into what Carter calls the “desert of knowledge” of what came before an ancestor capable of natural selection. “We haven’t even known how to explore it,” he remarks. To get “complexity from simplicity,” they are going to think about “interactions between amino acids and nucleotides that led to the co-creation of proteins and RNA.“

Wolfenden examined the physical properties of the twenty amino acids and how they respond to temperatures. Since they believe it was hotter in primordial soup days, he wanted to be sure that they reacted in protein folds the same way they do in modern environments, regardless of size and polarity. They do, even at 100� C.

A series of biochemical experiments with amino acids conducted in Wolfenden’s lab showed that two properties — the sizes as well as the polarities of amino acids — were necessary and sufficient to explain how the amino acids behaved in folded proteins and that these relationships also held at the higher temperatures of Earth 4 billion years ago.

That’s not controversial, since it applies to folded proteins (already existing), and has nothing to do with codes or common ancestors. As such, it is only of academic interest to biochemists. We can therefore turn to the paper on the origin of codes. Here, Carter and Wolfenden get to the heart of the issue:

The second PNAS paper, led by Carter, delves into how enzymes called aminoacyl-tRNA synthetases recognized transfer ribonucleic acid, or tRNA. Those enzymes translate the genetic code….

“The fact that genetic coding developed in two successive stages — the first of which was relatively simple — may be one reason why life was able to emerge while the earth was still quite young,” Wolfenden noted.

An earlier code, which enabled the earliest coded peptides to bind RNA, may have furnished a decisive selective advantage. And this primitive system could then undergo a natural selection process, thereby launching a new and more biological form of evolution.

This divide-and-conquer strategy, which they dub a “peptide-RNA world” rather than an “RNA-only world,” faces daunting challenges that the UNC report glosses over. Carter and Wolfenden are aware that modern aminoacyl-tRNA synthetases (aaRS) incorporate two codes, the protein code and the genetic code. This set of twenty enzymes knows what amino acid to fasten to one end of a transfer-RNA (tRNA) molecule, based on the triplet codon it reads at the other end. It’s like translating English to Chinese. A coded message is complex enough, but the ability to translate a language into another language bears the hallmarks of intelligent design. Let’s see how they “naturalize” this process.

Key to Carter’s thesis is that hypothetical synthetase “Urzymes” (ur = primitive) were able to attach amino acids to tRNA acceptor stems, even without the anticodons on the other end: “Synthetase Urzymes acylate cognate tRNAs even without anticodon-binding domains, in keeping with the possibility that acceptor stem recognition preceded anticodon recognition.” Here, he strives for the protein code in one leap. This code undergoes a primitive kind of natural selection, he explains, by sorting the amino acids according to size, hydrophobicity, or some other purely physical property. But it’s only a “potential selective advantage,” the paper notes:

Class I amino acids allowed formation of nonpolar cores and class II amino acids populated the surfaces of globular proteins. The linkage between classes arising from their sense/antisense ancestry would be expected to simplify the search for reduced amino acid alphabets that may have been used during early protein evolution, leading to the universal genetic code.

Selective advantage for whom? Or for what? We need to pause right there and ask serious questions. In this scenario, some half-synthetases that don’t recognize anticodons “allow” nonpolar cores to form. Other amino acids glob onto their surfaces. Do we have functional proteins here? No, we have globs of amino acids. We’re not even sure they are one-handed, as they must be to function. They are just chance globs of flotsam in a primordial soup, with no rhyme or reason for existing other than some kind of sorting by size. There is no selective advantage. You might get more-or-less of certain size classes, but if the globs don’t do anything, they are meaningless. There is no code. There is no message telling them what to do. There isn’t even a genetic code yet: the DNA-to-codon-to-anticodon “recognition” that needs to be associated with acceptor-stem recognition.

Search, they say? Without intelligence, there is no “search for reduced amino acid alphabets.” There is no reason they “may have been used” by or for anything. Why would this “lead to the universal genetic code”? Envision one of those machines that can sort golf balls into a normal distribution curve. Does the golf ball in the middle column have a “selective advantage” for being there? No. It just happens because of gravitational laws and probabilities. There is no function. There is no meaning. Carter’s natural amino acid sorting mechanism suffers the same conceptual problem: he can envision a population sorting by size or side-chain properties, but that’s the end of the line if the globs do not do anything.

Acceptor stem coding may have conferred a selective advantage by distinguishing smaller from larger amino acids and identifying ?-branched, aliphatic, and carboxylate side-chains. Fig. 4 shows how only small side-chains fit between peptide and RNA bases, whereas side-chains pointing away from the RNA are not so constrained. Coding of amino acid size could thus have helped preserve these patterns in transitions from a proposed direct, stereochemical specification to triplet coding. The conformational propensity of ?-branched side-chains could similarly have favored ?-secondary structures.

At best, he gets piles of amino acids with similar properties and folds. That’s not selection; that’s just sorting. You can find that in riverbeds where rocks of various sizes sort themselves out in layers. Those “patterns” are even “preserved”, but that constitutes neither a code nor a specification. Did you catch that his “direct, stereochemical specification to triplet coding” is not real? It’s only “proposed.”

This is enough to prove the hypothesis wrong, but they continue. They acknowledge that “acceptor stem and anticodon bases compose full, complementary, and independent, specifications for the 20 canonical amino acids by coding, respectively, for size and polarity.” A fully coded specification sounds like intelligent design, and two fully coded and independent specifications for the same amino acids nails it — especially when there’s machinery that can read one spec and translate it into the other spec.

Codes, moreover, must be accurately replicated, or they quickly evaporate because of “error catastrophe.” How did error correction evolve? But we digress.

At the end of the paper, the UNC scientists gloss over the most important issue: connecting the protein code to the genetic code. (This is in addition to some other problems with their peptide/RNA-world scenario they mention.) Watch this trick, with its admissions of ignorance, hand-waving, and a lateral pass to helpers off-stage:

Although we are not in a position to address the question of how aminoacylated tRNA acceptor stems might have been aligned in accordance with a primordial mRNA without anticodons, Rodin and Ohno suggested that reconstructed tRNA acceptor stems display evidence of complementary sequences. Our results revive the possibility that such complementarity and/or lateral-loop-loop base-pairing might have aligned acylated acceptor stems, anticipating the assembly of peptides according to a message.

This paragraph undercuts everything that came before. It deflates all the hype in the report. They just admitted they don’t know how to connect the protein code to the genetic code. They tossed out some speculations by other researchers. They tried to “revive a possibility” that something lucky happened. Then they attributed “anticipation” to blind molecules in a soup. Then there is that pregnant phrase, “according to a message.”

That, the only use of the word message in the paper, is exactly the issue. A message, written in DNA, is transcribed into messenger RNA. The mRNA carries that message to the aaRS family of enzymes, which faithfully translate the message into the protein code. The acylated transfer-RNAs carry both translations to the ribosome, which reads the mRNA and simultaneously assembles the amino acids into proteins that convert message into function by folding into molecular machines. And that’s not all: those machines interact in systems, regulated by layer upon layer of specifications, messages, and functions. Throughout the cell, error-correction systems work to keep the message from getting lost or corrupted.

“According to a message.” With those four words, they give away the store to intelligent design.

Image: � Stephen Coburn / Dollar Photo Club.