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Paper Reports that Amino Acids Used by Life Are Finely Tuned to Explore "Chemistry Space"


A recent paper in Nature's journal Scientific Reports, "Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids," has found that the twenty amino acids used by life are finely tuned to explore "chemistry space" and allow for maximal chemical reactions. Considering that this is a technical paper, they give an uncommonly lucid and concise explanation of what they did:

[W]e drew 108 random sets of 20 amino acids from our library of 1913 structures and compared their coverage of three chemical properties: size, charge, and hydrophobicity, to the standard amino acid alphabet. We measured how often the random sets demonstrated better coverage of chemistry space in one or more, two or more, or all three properties. In doing so, we found that better sets were extremely rare. In fact, when examining all three properties simultaneously, we detected only six sets with better coverage out of the 108 possibilities tested.
That's quite striking: out of 100 million different sets of twenty amino acids that they measured, only six are better able to explore "chemistry space" than the twenty amino acids that life uses. That suggests that life's set of amino acids is finely tuned to one part in 16 million.

Of course they only looked at three factors -- size, charge, and hydrophobicity. When we consider other properties of amino acids, perhaps our set will turn out to be the best:

While these three dimensions of property space are sufficient to demonstrate the adaptive advantage of the encoded amino acids, they are necessarily reductive and cannot capture all of the structural and energetic information contained in the 'better coverage' sets.
They attribute this fine-tuning to natural selection, as their approach is to compare chance and selection as possible explanations of life's set of amino acids:
This is consistent with the hypothesis that natural selection influenced the composition of the encoded amino acid alphabet, contributing one more clue to the much deeper and wider debate regarding the roles of chance versus predictability in the evolution of life.
But selection just means it is optimized and not random. They are only comparing two possible models -- selection and chance. They don't consider the fact that intelligent design is another cause that's capable of optimizing features. The question is: Which cause -- natural selection or intelligent design -- optimized this trait? Their paper doesn't address that question.

To do so, you'd have to consider the complexity required to incorporate a new amino acid into life's genetic code. That in turn would require lots of steps: a new codon to encode that amino acid, and new enzymes and RNAs to help process that amino acid during translation. In other words, incorporating a new amino acid into life's genetic code is a multimutation feature. As we explain in Appendix D of Discovering Intelligent Design:

The biochemical language of the genetic code uses short strings of three nucleotides (called codons) to symbolize commands -- including start commands, stop commands, and codons that signify each of the 20 amino acids used in life.

After the information in DNA is transcribed into mRNA, a series of codons in the mRNA molecule instructs the ribosome which amino acids are to be strung in which order to build a protein. Translation works by using another type of RNA molecule called transfer RNA (tRNA). During translation, tRNA molecules ferry needed amino acids to the ribosome so the protein chain can be assembled.

Each tRNA molecule is linked to a single amino acid on one end, and at the other end exposes three nucleotides (called an anti-codon). At the ribosome, small free-floating pieces of tRNA bind to the mRNA. When the anti-codon on a tRNA molecule binds to matching codons on the mRNA molecule at the ribosome, the amino acids are broken off the tRNA and linked up to build a protein.

For the genetic code to be translated properly, each tRNA molecule must be attached to the proper amino acid that corresponds to its anticodon as specified by the genetic code. If this critical step does not occur, then the language of the genetic code breaks down, and there is no way to convert the information in DNA into properly ordered proteins. So how do tRNA molecules become attached to the right amino acid?

Cells use special proteins called aminoacyl tRNA synthetase (aaRS) enzymes to attach tRNA molecules to the "proper" amino acid under thelanguage of the genetic code. Most cells use 20 different aaRS enzymes, one for each amino acid used in life. These aaRS enzymes are key to ensuring that the genetic code is correctly interpreted in the cell.

Yet these aaRS enzymes themselves are encoded by the genes in the DNA. This forms the essence of a "chicken-egg problem": aaRS enzymes themselves are necessary to perform the very task that constructs them.

How could such an integrated, language-based system arise in a step-by-step fashion? If any component is missing, the genetic information cannot be converted into proteins, and the message is lost. The RNA world is unsatisfactory because it provides no explanation for how the key step of the genetic code -- linking amino acids to the correct tRNA -- could have arisen.

Darwinian mechanisms, it's clear, aren't up to the task of generating many of the complex features we see in life.


If you're interested in learning more about why that is so, check out Discovering Intelligent Design. Our curriculum is now supplemented with a free online component that makes the material even more easily accessible.

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