5.7 Creative Destruction
81
the three kinds (Z¨ ottl and Stark, 2018), with paired vortices forming ahead of a
pusher or behind a puller. Flow patterns are far more complicated in the case of
rotating and/or beating flagella. Flow generated by a swimmer also affects others
in the vicinity, creating the effect of collective motion. Flow also depends on the
environment, and efficient microswimmers adjust the way they deform their bodies
near surfaces or in a confined geometry. Even a scallop-like reversible swimmer can
advance when swimming near a deformable surface (Trouilloud et al, 2008) or in a
viscoelastic liquid (Qiu et al, 2014).
5.7 Creative Destruction
The term in the title of this section, going back to Karl Marx and Friedrich Nietzsche
and popularized by Joseph Schumpeter as the essence of the capitalist economy,
could have been invented by Darwin, since this is what Nature is doing, creating
new species only to extinguish them and create new versions. This is also characteristic of processes within a living cell. It may have led once to innovations in
the development of intracellular protein exchange machinery, as it was driving the
evolution of species in a way similar to the evolution of industrial tools and social
relations. Within cells, creation and destruction are routine, they are a part of all
ongoing processes, as we noted when contemplating the ever dissolving and renewing cytoskeleton (Sect. 5.4). But Alon’s allegory of dancing matter (Sect. 5.1) is too
light-hearted. Much effort is needed to sustain this dance (well, learning to dance is
not effortless either).
A protein can do its assigned job only if it is properly folded in a certain conformation. Conformations, generally, depend on the sequence of amino acids but not
in a unique way. The classic assumption (Anfinsen, 1973) is the “thermodynamic
hypothesis”: the conformation should correspond to the overall energy minimum.
However, this does not always work. Often, there are several stable minima with
different energies, and the lowest one may be hard to attain, so the protein will more
readily fold to a thermodynamically metastable configuration and stay there. Catalytic action usually depends on certain ordered structures within a properly folded
form, and it may happen that it is a metastable state that contains such structures
and therefore has a functional role.
A folded form is sustained by physical forces rather than covalent bonds forming
the polymer chain. The major factors are, first, interactions with the medium, which
cause the protein to fold in order to isolate its hydrophobic groups from the aqueous
cytosol, and, second, hydrogen bonds formed by sharing a hydrogen atom between
polar groups within the protein chain, alongside weaker van der Waals (dipole) interactions. Raising the temperature disrupts all such kinds of bonds (see Sect. 1.4),
and therefore life is restricted to a rather narrow temperature interval: only a few
degrees Celsius separate hypothermia from fever in humans. The catalytic activity
grows with temperature but drops sharply beyond the maximum. Thermophilic bac-
81
the three kinds (Z¨ ottl and Stark, 2018), with paired vortices forming ahead of a
pusher or behind a puller. Flow patterns are far more complicated in the case of
rotating and/or beating flagella. Flow generated by a swimmer also affects others
in the vicinity, creating the effect of collective motion. Flow also depends on the
environment, and efficient microswimmers adjust the way they deform their bodies
near surfaces or in a confined geometry. Even a scallop-like reversible swimmer can
advance when swimming near a deformable surface (Trouilloud et al, 2008) or in a
viscoelastic liquid (Qiu et al, 2014).
5.7 Creative Destruction
The term in the title of this section, going back to Karl Marx and Friedrich Nietzsche
and popularized by Joseph Schumpeter as the essence of the capitalist economy,
could have been invented by Darwin, since this is what Nature is doing, creating
new species only to extinguish them and create new versions. This is also characteristic of processes within a living cell. It may have led once to innovations in
the development of intracellular protein exchange machinery, as it was driving the
evolution of species in a way similar to the evolution of industrial tools and social
relations. Within cells, creation and destruction are routine, they are a part of all
ongoing processes, as we noted when contemplating the ever dissolving and renewing cytoskeleton (Sect. 5.4). But Alon’s allegory of dancing matter (Sect. 5.1) is too
light-hearted. Much effort is needed to sustain this dance (well, learning to dance is
not effortless either).
A protein can do its assigned job only if it is properly folded in a certain conformation. Conformations, generally, depend on the sequence of amino acids but not
in a unique way. The classic assumption (Anfinsen, 1973) is the “thermodynamic
hypothesis”: the conformation should correspond to the overall energy minimum.
However, this does not always work. Often, there are several stable minima with
different energies, and the lowest one may be hard to attain, so the protein will more
readily fold to a thermodynamically metastable configuration and stay there. Catalytic action usually depends on certain ordered structures within a properly folded
form, and it may happen that it is a metastable state that contains such structures
and therefore has a functional role.
A folded form is sustained by physical forces rather than covalent bonds forming
the polymer chain. The major factors are, first, interactions with the medium, which
cause the protein to fold in order to isolate its hydrophobic groups from the aqueous
cytosol, and, second, hydrogen bonds formed by sharing a hydrogen atom between
polar groups within the protein chain, alongside weaker van der Waals (dipole) interactions. Raising the temperature disrupts all such kinds of bonds (see Sect. 1.4),
and therefore life is restricted to a rather narrow temperature interval: only a few
degrees Celsius separate hypothermia from fever in humans. The catalytic activity
grows with temperature but drops sharply beyond the maximum. Thermophilic bac-