Tuesday, 15 January 2013

Actually, the secret of life will be cooked up in a chemistry lab

In the Guardian this week, the physicist Paul Davies wrote an article entitled "The secret of life won't be cooked up in a chemistry lab". It's a thoughtful piece and worth reading; the key point is summed up in the final line:
...life's origin can ultimately be explained by importing the language and concepts of biology into physics and chemistry, rather than the other way round
I absolutely agree! Work by biologists and theorists such as Davies is absolutely essential, to guide research, identify flaws and incoherence in hypotheses, and unify disparate data. Chemists can develop all kinds of ideas, but if they're physically or biologically irrelevant or implausible, what's the point? That said, allow me to mark some turf for the chemists working in this field.

As Davies notes, much of the work in this field has been carried out by chemists. Implicit in his article is the suggestion that these workers have had their ears closed to the rest of the world - that ideas from philosophers, biologists, and information theorists have not reached the chemical literature. This is simply not true.

Take, for example, the work of M. Reza Ghadiri and co-workers on self-replicating peptides. To distill a decade of research down to a tweet, Ghadiri looked at whether peptides can copy themselves, and what kinds of behaviour might emerge when many peptides interact. Much of this work was informed by the theoretical biologist Eörs Szathmáry. One of the most complicated systems published by Ghadiri (available here, open access) took a group of self-replicating peptides and analysed their interactions to build a large network. A small section of this network was then recreated experimentally, to confirm its behaviour. The point is: here is a chemist, guided by theoretical biology, speaking the language of network architecture. We're not as deaf as Davies implies.

Further, this is not an exception, an isolated example of a chemist looking beyond the fume hood. Pier Luigi Luisi's work on self-reproducing micelles and vesicles was prompted directly by the idea of autopoiesis, as proposed by Maturana and Varela - both of whom are biologists and philosophers. Autopoiesis is very much about the structure and flow of information through a system.

Of course, the ideas upon which Ghadiri, Luisi, and other chemists draw might turn out to be incorrect. Regardless, ideas from beyond the chemistry lab are at the heart of chemical research into the origins of life.

Both of these examples illustrate a second, more important point. It is necessary, but not sufficient, for theorists such as Davies to elucidate the form of living systems. These ideas must be made flesh, so to speak. This is certainly the work of chemists. By applying these ideas to physical substrates, their validity and generality can be tested.

Ghadiri's work is again illustrative. Both Ghadiri and other researchers, notably Jean Chmielewski, have reported extensive efforts to increase the efficiency of self-replicating peptides. According to Szathmáry, an exponentially-replicating species is required before Darwinian selection can occur. Reaching exponential replication turns out to be incredibly difficult. This is not unique to peptides; research on self-replicating nucleotides and small molecules by von Kiedrowski and Rebek has run into the same problem. I am not in a position to comment on the biological or theoretical merit of Szathmáry's work, but two decades of research suggest that it is unlikely to be relevant in real chemical systems. At the very least, it seems that it can only be achieved under demanding, prebiotically implausible conditions.

Any theory, however elegant or plausible, must be tested experimentally. We must see if it is a valid idea, and if so, how readily it is achieved. So, while I agree with Davies that chemists cannot work alone, it will ultimately be chemists who 'cook up' life.

1 comment:

  1. The origin of life can be explained through the study of thermodynamics of universe evolution!

    Origin of life and its evolution are the result of action of laws of hierarchical thermodynamics.
    Thermodynamics investigates systems which can be characterized by state functions. The separation of biological systems into individual hierarchies of structures allows us to study the processes in them independently of the processes that take place in other hierarchical structures.

    Criterion of evolution
    The approval about the reduction of the entropy of living systems as a result of biological evolution is incorrect. The criterion of evolution of living system is the change (during evolution) of the specific free energy (Gibbs function, G) of this living system. The evolution of living system takes place against the background of flows of energy (e.g., light, energy of physical fields) from the environment. It increases its specific free energy. At the same time, the specific free energy of this living system is decreased as a result of spontaneous processes in this system.
    Thus, the total change in the specific free energy of a living system is composed of two parts: 1. The change of free energy due to the inflow of external energy (G1> 0) and 2. The change of free energy due to spontaneous transformations in the system (G2 < 0) . The evolving system constantly adapts to a changing environment. The principle of substance stability contributes to this adaptation.
    Thermodynamics of evolution obeys the generalized equation of Gibbs (that is the generalized equation of the first and second laws of thermodynamics)*. Biological evolution and the processes of origin of life are well described by the hierarchical thermodynamics, established on the firm foundation of theory of JW Gibbs. Our theory created without the notion on dissipative structures of I. Prigogine and negentropy of L. Boltzmann and E. Schrodinger.
    “Thermodynamics serves as a basis for optimal solutions of the tasks of physiology, which are solved by organisms in the characteristic process of life: evolution, development, homeostasis, and adaptation. It is stated that the quasi-equilibrium thermodynamics of quasi-closed complex systems serves as an impetus of evolution, functions, and activities of all levels of biological systems’ organization. This fact predetermines the use of Gibbs’ methods and leads to a hierarchical thermodynamics in all spheres of physiology. The interaction of structurally related levels and sub-levels of biological systems is determined by the thermodynamic principle of substance stability. Thus, life is accompanied by a thermodynamic optimization of physiological functions of biological systems. Living matter, while functioning and evolving, seeks the minimum of specific Gibbs free energy of structure formation at all levels. The spontaneous search of this minimum takes place with participation of not only spontaneous, but also non-spontaneous processes, initiated by the surrounding environment.”
    Works of the author: http://endeav.net/news.html http://gladyshevevolution.wordpress.com/ http://www.mdpi.org/ijms/papers/i7030098.pdf http://ru.scribd.com/doc/87069230/Report-Ok-16-11-2011

    Sincerely,
    Georgi Gladyshev
    Professor of Physical Chemistry

    *) The generalized equation of Gibbs (See: http://creatacad.org/?id=57&lng=eng
    http://gladyshevevolution.wordpress.com/article/thermodynamic-theory-of-evolution-of-169m15f5ytneq-3/ )

    P.S. Lastly, it is important to take into account, from the viewpoint of hierarchical thermodynamics, that anti-aging diets and many drugs can be used for the prophylaxis and treatment of cardiovascular diseases, cancer, and for numerous other illnesses.
    http://endeav.net/news/21-nutrition-aging-thermodynamics.html
    http://ru.scribd.com/doc/87069230/Report-Ok-16-11-2011

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