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PubMed2025

Crick's "Frozen accident theory" of the genetic code explored by Ising models.

Francis Crick proposed that the almost universal genetic code could be nothing more than a 'frozen accident'. The Ising model, widely used in statistical mechanics, is used to explore patterns which could achieve a phase transition mimicking the frozen accident. Codons are considered as nodes and amino acids as spins. Monte Carlo simulations of the 64-node genetic code models are carried out. Anti-ferromagnetic interactions or a combination of ferro and anti-ferromagnetic interactions can lead to stable, regular patterns resembling the genetic code. It is indeed found that the 64-node Ising system exhibits critical slowing down dynamics, compatible with a freezing process. These models aim to simulate the formation of patterns similar to the genetic code through physical freezing processes, providing insights into potential mechanisms and processes that may have contributed to the formation and evolution of the genetic code.

Genetic Code↗
PubMed1984

Origin of chirality: a structural theory.

The molecular basis for the origin of chirality is presented: The complex of the anticodon bases and the discriminator base on a D type tRNA can recognize a L type amino acid. Exceptionally the D type tyrosine can be recognizable by the D type tRNA as shown by Calender and Berg. The advantage of such a stereochemical theory over the frozen accident theory is discussed.

Amino Acids↗
PubMed1984

Evolution of anticodons.

Anticodons are trinucleotides in transfer RNA (tRNA) molecules. The latter carry amino acids for insertion into the polypeptide sequences of proteins during the translation of messenger RNA (mRNA) molecules. Messenger RNA molecules are transcribed from genes. Evolution of tRNA molecules has resulted in a set of anticodons for the 20 amino acids that are used in protein synthesis. This set of anticodons is slightly different in mitochondrial codes from the set that used in the nuclear "universal" code. Theories for the evolution of the code include frozen accident, doublet expansion, repeating triplets and coevolutionary distribution. The number of codons has always been fixed at 64 by mathematical rules, but because an anticodon may pair with more than one codon, the number of anticodons is only 54 in the universal code, is smaller in mitochondrial codes, and was probably even smaller in archetypal primitive codes. Evidence of anticodon evolution can be seen by comparing mitochondrial codes with the universal code. Codes used by very primitive organisms that are now extinct might have specified fewer amino acids than are now used.

Amino Acids↗
PubMed2003

Why nature chose A, C, G and U/T: an error-coding perspective of nucleotide alphabet composition.

The question of whether the size and make-up of the natural nucleotide alphabet is a consequence of selection pressure, or simply a frozen accident, is one of the fundamental questions of biology. Nucleotide replication is essentially an information transmission phenomenon, and so it seems reasonable to explore the issue from the perspective of theoretical computer science, and of error-coding theory in particular. In this analysis it is shown that the essential recognition features of nucleotides may be naturally expressed as 4-digit binary numbers, capturing the hydrogen acceptor/donor patterns (3-bits) and the purine/pyrimidine feature (1-bit). Optimal alphabets consist of nucleotides in which the purine/pyrimidine feature is related to the acceptor/donor pattern as a parity bit. Numerically interpreted, such alphabets correspond to parity check codes, simple but effective error-resistant structures. The natural alphabet appears to be an adaptation of one of two optimal solutions, constrained to its present size and composition by a combination of chemical and coding-theory factors.

Base Composition↗
PubMedDate not supplied

Peptide self-aggregation and peptide complementarity as bases for the evolution of peptide receptors: a review.

This paper reviews the three major theories of peptide receptor evolution: (1) Dwyer's theory that peptide receptors evolved from self-aggregating peptides; (2) Root-Bernstein's theory that peptide receptors evolved from functionally and structurally complementary peptides; and (3) Blalock's theory that receptors evolved from hydropathically complementary sequences encoded in the antisense strand of the DNA encoding each peptide. The evidence to date suggests that the co-yevolution of peptides and their receptors is strongly constrained by one or more of these physicochemically based mechanisms, which argues against a random or frozen accident' model. The data also suggest that structure and function are integrally related from the earliest steps of receptor-ligand evolution so that peptide functionality is non-random and highly conserved in its origin. The result is a molecular paleontology' that reveals the evolutionary constraints that shaped the interaction of structure and function.

Amino Acid Sequence↗
PubMed1995

On the origin and evolution of the genetic code.

Two ideas have essentially been used to explain the origin of the genetic code: Crick's frozen accident and Woese's amino acid-codon specific chemical interaction. Whatever the origin and codon-amino acid correlation, it is difficult to imagine the sudden appearance of the genetic code in its present form of 64 codons coding for 20 amino acids without appealing to some evolutionary process. On the contrary, it is more reasonable to assume that it evolved from a much simpler initial state in which a few triplets were coding for each of a small number of amino acids. Analysis of genetic code through information theory and the metabolism of pyrimidine biosynthesis provide evidence that suggests that the genetic code could have begun in an RNA world with the two letters A and U grouped in eight triplets coding for seven amino acids and one stop signal. This code could have progressively evolved by making gradual use of letters G and C to end with 64 triplets coding for 20 amino acids and three stop signals. According to proposed evidence, DNA could have appeared after the four-letter structure was already achieved. In the newborn DNA world, T substituted U to get higher physicochemical and genetic stability.

Animals↗