Clas Blomberg - Physics of life-Elsevier Science (2007)

380 Part IX. Going further
proofreading steps. The free energy required for the peptide bonds of the protein chain is not
very large, and well covered by amino acid binding at the tRNA. However, that chemical
potential, that free energy does not seem to be used at all. The process that binds the amino
acid to the tRNA uses the normal cell free energy carrier, ATP for the process in, what can
be regarded as a quite efficient way, and the dissipation of the formation the amino acid
attachment is not particularly large.
However, for the ribosome steps, the cell uses for each amino acid to be put in a protein
two GTP that are hydrolysed to GDP and thereby transferring a considerable free energy.
This drives the formation of the peptide bonds, the possible proofreading and also a movement
of the tRNA along the process from a primary binding side to a final site where the
amino acid finally is bound to a protein chain.
In cases like this, one might ask why a cell does not use the free energy sources more
efficiently. Other processes appear to be quite efficient, this, however, not. What one may
say in a case like this is that the tRNA with amino acid is apparently used as a source of
amino acid, not of free energy. Indeed, the positions of the actual bonds are such that the
tRNA free energy cannot be used directly to the tasks it might be able to drive. This, does,
however, not mean that it could not have been used in a more appropriate scheme.
Such cases suggest that certain processes have been developed in a particular fashion,
and then remained in that fashion although they might not provide the most efficient possibility
of function form, as in this case, a thermodynamic point of view. A better solution,
although certainly possible to be acquired, could not compete at a primary stage with the
developed process, and might never have been competitive.
Such kinds of examples sometimes show well the inefficient effects of the particular
processes of evolution, not the results of an intelligent design, which might have developed
a more efficient process. Note that protein synthesis is a very common process and this failure
of using tRNA as free energy source provides a very large part of the dissipation of a cell.
It should be a well-motivated task to take up this kind of questions, to ask what would be
reasonable consequences of evolution with some basic ideas about significant factors.
Then, one shall compare this with the real situation. If the found result agrees with what was
expected, well, then the ideas may be regarded as correct. If not, well, we have a more interesting
question: if the first idea about what is relevant seems to be wrong, then one has to go
on and ask about alternative justifications, what are the relevant factors that are refined in evolution.
Or are the original conclusions wrong. Should one have taken another view? Such
questions may comprise a broad field, but there is no place here to develop this further.
There are also a number of attempts to model evolutionary aspects. For instance, there
are models based on computer program propagation with ideas on programs that copy
themselves, and which provide certain tasks. The programs may get errors (analogies to
mutations), which will propagate and lead to modified and even new developed tasks.
There are also other types of models, for instance developments of strategies of game theory
(Dawkins, 1976). These models show the typical traits of evolution with new functions.
But, of course all such models are restricted by their formulations. To some extent, they can
show some unexpected developments, but one must have in mind that they cannot go astray
and develop features that are completely outside the rules of the models.
The true evolution can be regarded as virtually unrestricted. Of course the biological
evolution also comprises co-operation between various individual of the same or different