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Life is a river, chemical and scripted

Posted on October
26, 2014 by minorscales

JOSÉ AUGUSTO PEREIRA

In “What Is Life?”, Schrödinger manifests a worry. As a physicist of an era
when Physics has finally established an all-embracing and all-explaining model
of Nature, Statistical Thermodynamics, he is troubled to reconcile (1) the
notion that physical Laws stability comes from averages of big numbers of small
dynamical molecules with (2) the growing evidence that biological stability is
centred in only a handful of molecules. These “molecules”, the chromosomes, had
therefore to be crystal-like, for stability, and big and aperiodic, so that it
can carry the necessary information to rule life; the “code-script”.

About this, I can’t help but think that Schrödinger was aware of the advances
made by Turing, namely the concept, published in 1936, of the “automatic
computing machine”, better known today as the Turing Machine. This theoretical
machine reads data symbols from a tape, mechanically, and interprets those
symbols as instructions, or its arguments, by using a code, and then acts
accordingly. This was the first formalization of a general computational
algorithm. Turing even explored the theoretical implications of automatic
machines instructed to build other, or the same, automatic machines. To a
rationalist, the idea of a biological cell as a machine that reads a molecular
tape of instructions (“code-script”) to realize its phenotype (including
reproduction) must have seem quite fit, at least as a working hypothesis.

Trying to model Life’s features as algorithms, in practice or just in theory,
has been an endeavour of Artificial Life research. It therefore depends a lot on
computers and on computational theories. The possibility of performing
computational simulations or, perhaps more adequately, computational
“experiments” enabled to re-qualify the answers to the various sub-questions of
the general question “What is Life?” from arguable speculations to working
hypothesis. To this effect, computable Artificial Chemistries have been
developed in many shapes and forms to achieve particular goals, from inquires
about the origin of Life to the simulation of particular organisms. All
artificial chemistries have three main defining vectors: the set of elementary
objects (“molecules”), the set of rules of interaction (“reactions”) and the
algorithm (“dynamics”) that set things in motion on a given “space”. And here is
where the anguish sets in: which objects, which rules, which algorithm? That is
to say, what are the significant biological Laws? Obviously, they have to be
“distilled” from the details of real biological systems, in its real
environments.

What we know now about biological systems is much more detailed than what was
known in 1944, which is crucial for Artifical Life endeavours and for a world of
practical and very important applications but, curiously, most of Life’s main
features were already correctly perceived 70 years ago and are mentioned by
Schrödinger in his book. In fact, the laws of inheritance (Mendel) and of
evolution (Darwin) were discovered before knowledge of the biological cell’s
molecular details. But by 1944 the morphology of cells and the main biological
molecular types (including DNA) were known, as it was biological catalysis by
proteins (enzymes). In “What Is Life?”, Schrödinger correctly proposes that the
biological molecules, specifically the genetic material, may not be
thermodynamically stable but only kinetically stable. Although the so-called
central “dogma” of molecular biology was still to be discovered, Schrödinger and
is contemporaries already knew that somehow molecular information must flow
inside, and between generations, of living systems. He also correctly
characterized biological systems as highly ordered but, on the other hand, as
the agents of massive entropy production, by absorbing concentrated energy, as
light or chemical potential, and dispersing it (for example, as heat), thus
increasing disorder in the Universe and obeying the 2nd Law of
Thermodynamics. The notion that living systems are physical-chemical systems
that work in a non-equilibrium regime was acquired. From all this data, and as
an answer to his own sub-questions “What is the characteristic feature of life?
When is a piece of matter said to be alive?”, Schrödinger highlights the ability
of living matter to “evade the decay to equilibrium (…) for a much longer period
(…) than we would expect of an inanimate piece of matter”.

I guess this is the kind of answer to be expected from a physicist but he
knew, of course, that there was much more to Life than to be a dissipative
system that evades equilibrium for a long time. If that was the case then the
Great Red Spot storm in Jupiter or a river on Earth, that have been evading
equilibrium for a very long time, should therefore be categorized as animate,
that is, living. Yet, they are not. Notwithstanding, there are similarities
between those non-equilibrium phenomena and Life. As the tornado or the river,
Life’s shape is also conditioned by its particular environment, water, and is a
part of several cycles on Earth. Also, Life did not appear to take advantage of
an energy potential difference but rather as a consequence of a flux created by
one. In Life’s case, the imbalance was not of pressure potential or of
gravitational potential but of chemical potential and so a chemical system was
pushed into existence as the non-equilibrium intermediate agent of exhaustion of
that chemical potential difference. Life only evades equilibrium as long as that
potential difference is externally and cyclically maintained.

What is really special about Life is that it evolves in complexity and
organization unlike any other known physical-chemical system. It includes flow
control (regulation), adaptability (including Darwinian evolution), system’s
information storage and retrieval, growth, self-organization, self-repairing and
self-replication. This is so overwhelming that, although Schrödinger compared
living systems with a mechanism, like a dissipative clockwork hinged on a master
cog, the latter being “the aperiodic crystal forming the hereditary substance”,
he also stated that “the single cog is not of coarse human make, but is the
finest masterpiece ever achieved along the lines of the Lord’s quantum
mechanics”.

The knowledge of detailed workings of living systems acquired along the last
70 years in fact just increased our wonder about Life and its origins but it
also gave us the opportunity to state more specific biological theories and laws
and also to test hypothesis about Life’s definition, origins, organization and
evolution. The unit of Life, the biological cell, does not hold much more
secrets today in its primary workings. It is in the origins of the biological
cell, of cells’ multilayered organizations and of its superior manifestations,
namely consciousness, where the stronghold of some metaphysical speculation
still resides. However, I believe that one day metaphysics will not be an
option to explain the origins of quantum mechanics and of Life in all its
forms.

[some of these ideas were presented and argued in session
#1, October 28th]

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