Table I.

Glossary of terms

Codons	X(l)	∈ {A, B … Z} or {Α, Β, Χ…}
Amino acid alphabets	y(m)	∈ {a, b … z} or {α, β, χ…}
Alphabet size	n
Polymer length (genes or codons)	L	[sequence space of size nL]
Sequence position	α	range 1,2 … L
RNA (gene)	G(i)	population variable Gi
Protein	P(j)	population variable Pj
Translation probability matrix	ℑ	[n × n elements ℑlm]
Rate of protein production	kP	[per template molecule]
Translatase (e.g., protein aaRS)	T(k)	population variable Tk
Rate of assignment catalysis	alm(j)	[assignment l → m by T(k)]
Rate of l → m assignment in system	Clm
Assignment accuracy	q
Assignment error probability	ε	= 1 − q
Hamming distance	h
Rate of polymer loss	ϕP, ϕG	[protein P; RNA (“genes”) G]
Rate of synthesis of G(i) from G(t)	Wit	[G(t) serves as a template]
RibozymalRi or proteinPr replicase	R(a)	population variable Ra
and one-error mutant thereof	R(b)
Replicase activity of ribozyme R(a)	ra	[equivalently of enzyme]
Catalytic contribution P(j) to Wit	wit(j)	[per molecule of P(j)]
Codon-copying accuracy of P(j)	qj	[error rate εj = 1 − qj]
Translatase ribozymeRi or enzymePr	T(r)	population variable Tr
and one-error mutant thereof	T(s)	[indices u, v for proteins]
Rate of replicative RNA production	ρ	[per template molecule]
Rate of mutational RNA production	μ	[per template molecule]
Mutant functionality degradation factor	ξ	[catalysis or accuracy]
Probability of code-rule assignment	p	[po for stationary value]
Protein fraction of translatase activity	f	[fo for stationary value]