On 2017 Jan 01, Donald Forsdyke commented:

PURINE LOADING AS A THERMAL ADAPTATION (This comment was original posted as a reader response to the original PLOS CompBiol article 20 Feb 2008.)

This paper draws conclusions tending to oppose those of myself and coworkers (cited). A "key question" is held to be: "Which factor - amino acid or nucleotide composition - is primary in thermal adaptation and which is derivative?" Previous evidence is considered "anecdotal." Now there is evidence for "an exact and conclusive" relationship, based on an "exhaustive study" that provides a "complete picture." A set of amino acids - IVYWREL - correlates well with growth temperature. It is noted:

"Signatures of thermal adaptation in protein sequences can be due to the specific biases in nucleotide sequences and vice versa. ... One has to explore whether a specific composition of nucleotide (amino acid) sequences shapes the content of amino acid (nucleotide) ones, or thermal adaptation of proteins and DNA (at the level of sequence compositions) are independent processes."

In other words, are primary adaptations at the nucleic acid level driving changes at the protein level, or vice- versa? To what extent are the two processes independent? Their conclusion:

"Resolving the old-standing controversy, we determined that the variation in nucleotide composition (increase of purine-load, or A + G content with temperature) is largely a consequence of thermal adaptation of proteins."

Thus, the superficial reader of the paper, while noting the purine-richness of some of the codons corresponding to the IVYWREL amino acids, will conclude that the "independent processes" alternative has been excluded. Reading the paper (e.g. Figure 7) one can question the validity of this conclusion. Many of the IVYWREL amino acids have purine-poor alternative codons (especially IYLV, which at best can only change one purine unit in their codons). One of the IVYWREL amino acids has relatively purine-rich alternative codons (R, which at best can change two purine units). Two (EW) are always purine-rich, and there are no alternatives.

Displaying more EW's as the temperature got hotter would satisfy a need both for more purines and for more tryptophan and glutamate, so here there is no discrimination as to whether one "shapes" the organism’s content of the other. Displaying more IYLVs gives only minimal flexibility in accommodating a purine-need. Most flexibility is provided by R codons.

The authors do not give statistics for the differences between the slopes of Figs. 7a (unshuffled codons) and 7b (shuffled codons), but they appear real, presumably reflecting the choice biologically of purine-rich codons, a choice the organisms might not have to make if there were no independent purine-loading pressure. Thus, the authors note, but only in parenthesis, that the slopes "are somewhat different suggesting that codon bias may be partly responsible for the overall purine composition of DNA."

An analogy may help. Passing from winter to summer, you change your outdoor attire. Many people (Imelda Marcos excepted) have a wider range of shirts and sweaters than of footwear. There may be items which provide more reliable indices of outside temperature than others. For example, the weight of your shirt + sweater might more finely correlate with temperature than the weight of your shoes. If you wanted to predict outside temperature from attire, you would choose shirt-sweater weights, rather than shoe weights. But if your clothes (shirt + sweater) weigh more, you might need sturdier shoes to cope with the extra weight. Thus, shoe-weight would depend on clothes-weight. The latter would be primary and the former would be secondary ("derivative"). But showing a better correlation with temperature in the case of shirt + sweater, does not establish a dependence of shoe-weight on shirt-sweater weight. More likely, you wear lighter shoes in warm weather because they keep your feet cooler! Both depend on temperature. It just so happens that the correlation with temperature is coarser and not so finely tuned for shoe weight, as for shirt-sweater weight.

On 2017 Jan 01, Donald Forsdyke commented:

PURINE LOADING AS A THERMAL ADAPTATION (This comment was original posted as a reader response to the original PLOS CompBiol article 20 Feb 2008.)

This paper draws conclusions tending to oppose those of myself and coworkers (cited). A "key question" is held to be: "Which factor - amino acid or nucleotide composition - is primary in thermal adaptation and which is derivative?" Previous evidence is considered "anecdotal." Now there is evidence for "an exact and conclusive" relationship, based on an "exhaustive study" that provides a "complete picture." A set of amino acids - IVYWREL - correlates well with growth temperature. It is noted:

"Signatures of thermal adaptation in protein sequences can be due to the specific biases in nucleotide sequences and vice versa. ... One has to explore whether a specific composition of nucleotide (amino acid) sequences shapes the content of amino acid (nucleotide) ones, or thermal adaptation of proteins and DNA (at the level of sequence compositions) are independent processes."

In other words, are primary adaptations at the nucleic acid level driving changes at the protein level, or vice- versa? To what extent are the two processes independent? Their conclusion:

"Resolving the old-standing controversy, we determined that the variation in nucleotide composition (increase of purine-load, or A + G content with temperature) is largely a consequence of thermal adaptation of proteins."

Thus, the superficial reader of the paper, while noting the purine-richness of some of the codons corresponding to the IVYWREL amino acids, will conclude that the "independent processes" alternative has been excluded. Reading the paper (e.g. Figure 7) one can question the validity of this conclusion. Many of the IVYWREL amino acids have purine-poor alternative codons (especially IYLV, which at best can only change one purine unit in their codons). One of the IVYWREL amino acids has relatively purine-rich alternative codons (R, which at best can change two purine units). Two (EW) are always purine-rich, and there are no alternatives.

Displaying more EW's as the temperature got hotter would satisfy a need both for more purines and for more tryptophan and glutamate, so here there is no discrimination as to whether one "shapes" the organism’s content of the other. Displaying more IYLVs gives only minimal flexibility in accommodating a purine-need. Most flexibility is provided by R codons.

The authors do not give statistics for the differences between the slopes of Figs. 7a (unshuffled codons) and 7b (shuffled codons), but they appear real, presumably reflecting the choice biologically of purine-rich codons, a choice the organisms might not have to make if there were no independent purine-loading pressure. Thus, the authors note, but only in parenthesis, that the slopes "are somewhat different suggesting that codon bias may be partly responsible for the overall purine composition of DNA."

An analogy may help. Passing from winter to summer, you change your outdoor attire. Many people (Imelda Marcos excepted) have a wider range of shirts and sweaters than of footwear. There may be items which provide more reliable indices of outside temperature than others. For example, the weight of your shirt + sweater might more finely correlate with temperature than the weight of your shoes. If you wanted to predict outside temperature from attire, you would choose shirt-sweater weights, rather than shoe weights. But if your clothes (shirt + sweater) weigh more, you might need sturdier shoes to cope with the extra weight. Thus, shoe-weight would depend on clothes-weight. The latter would be primary and the former would be secondary ("derivative"). But showing a better correlation with temperature in the case of shirt + sweater, does not establish a dependence of shoe-weight on shirt-sweater weight. More likely, you wear lighter shoes in warm weather because they keep your feet cooler! Both depend on temperature. It just so happens that the correlation with temperature is coarser and not so finely tuned for shoe weight, as for shirt-sweater weight.