Chapter 3 Green Grass, Red Blood, Blueprint
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Chapter 3 Green grass, red blood, blueprint: reflections on life, self-replication, and evolution M. Ciofalo Dipartimento di Ingegneria Nucleare, Università degli Studi di Palermo, Italy. Abstract Following pioneering work by von Neumann in the late 1940s, the goal of achieving self- replication in artefacts has been pursued by a variety of approaches, involving either virtual entities like cellular automata and computer programs or, to a lesser extent, real physical devices. An ample review of the major achievements in these diverse fields is given, and their practical and theoretical relevance is discussed. Possible future developments, notably regarding nanotech- nology and space exploration, are also outlined. The most relevant theoretical problems posed by self-replication are discussed in the light of current knowledge regarding life and its origins. Living entities are semiotic systems, in which physical structures have come to perform symbolic functions. The great complexity of biomolecules and of even the most primitive organisms is not a gratuitous complication, but a necessary condition for homeostasis, self-replication and open- ended evolution in a changing environment. Such requisites will have to be matched by artificial devices if their non-trivial self-replication and autonomous development are to be attained. 1 Of crystals and colloids Wordsworth’s God had his dwelling in the light of setting suns. But the God who dwells there seems to me most probably the God of the atom, the star, and the crystal. Mine, if I have one, reveals Himself in another class of phenomena. He makes the grass green and the blood red. (J.W. Krutch, 1950, [1]) The lines in the epigraph are excerpted from the famous essay ‘The colloid and the crystal’, written in 1950 by the American literary naturalist Joseph Wood Krutch. The best known passage of the essay is probably the following: ‘A snowflake under a lens and an amoeba under a WIT Transactions on State of the Art in Science and Engineering, Vol 27, © 2006 WIT Press www.witpress.com, ISSN 1755-8336 (on-line) doi:10.2495/978-1-85312-853-0/03 30 Design and Information in Biology microscope ... Crystal and colloid, the chemist would call them, but what an inconceivable contrast those neutral terms imply! Like the star, the snowflake seems to declare the glory of God, while the promise of the amoeba, given only perhaps to itself, seems only contemptible. But its jelly holds, nevertheless, not only its promise but ours also, while the snowflake represents some achievement which we cannot possibly share ...No aggregate of colloids can be as beautiful as the crystal always was, but it can know, as the crystal cannot, what beauty is.’ Krutch’s words express in poetic form the naturalist’s diffidence against the perfect, but sterile symmetry of inanimate things (the ‘crystal’) and his unconditional preference for the imperfect, but dynamic living matter (the ‘colloid’), of which we ourselves partake. This is the mood in which Goethe wrote ‘Grey is all theory. Green grows the golden tree of Life’, and the mood underlying vitalism, the doctrine that life processes arise from a nonmaterial vital principle and cannot be entirely explained as physical and chemical phenomena. This attitude probably arose as a reaction against the excessive boasts of mechanical and physical sciences in the 18th and early 19th century, and was the more justified in 1950, a few years after ‘hard physics’ and technology had yielded Hiroshima and Nagasaki, Zyklon B, and the assembly line. However, as we now see with some clarity, the inability of physical sciences to explain life was not due to an intrinsic irreducibility of life phenomena to within the realm of physical laws, but rather to the vast inadequacy of the available physical and mathematical models on one side, and of our knowledge of the intimate structure and function of living matter on the other side. This was already clear to Ernst Mach who, in ‘Knowledge and Error’ [2], wrote ‘If one reduces the whole of physics to mechanics, and mechanics itself to the simple theories known today, life will necessarily appear as something hyper-physical.’ By a curious twist of this story, in the very year in which Dr. Krutch wrote of crystals and colloids, Max Perutz [3] was using X-ray diffraction, introduced by Bragg for studying crystals, to unravel the structure of that most life-related of all ‘colloidal’substances, the very haemoglobin that makes blood red. Molecular biology was being founded as an autonomous science following these and other important contemporary achievements, including the discovery of the double helix structure of DNA by Watson and Crick in 1953 [4] and the abiogenic synthesis of amino acids by Miller and Urey in the same year [5]. Meanwhile, Ilya Prigogine [6] was founding the non-linear thermodynamics of systems far from equilibrium and dissipative structures; John von Neumann [7] was concentrating his efforts on the problem of artificial self-replication; René Thom was starting the research program that would lead to a mathematical theory of morphogenesis [8] in the spirit of D’Arcy Thompson [9]; and a ‘hard-boiled’physicist like Erwin Schrödinger was studying life issues in Dublin [10]. Long before the digital computer established its dominant place in science, and terms now fashionable like complexity or chaos entered common use, the science of Cybernetics of Wiener [11] and Ashby [12] and the General Systems Theory of von Bertalanffy [13] were providing powerful paradigms for studying natural and artificial systems under the same light. These developments were rapidly narrowing the gap between physical and life sciences; so much so that in 1979 Ilya Prigogine might suggest that times were ripe for attempting a new synthesis, capable of bridging this gap altogether and to embrace human sciences as well [14]. Probably no other field of human enquiry is so gap-bridging (to the verge of being regarded by some as an undue intrusion into ‘forbidden territory’) as the attempt to understand and re-create processes peculiar to life; and, in particular, that most exclusive of all life-related processes, self-reproduction. The present contribution is dedicated to this issue. WIT Transactions on State of the Art in Science and Engineering, Vol 27, © 2006 WIT Press www.witpress.com, ISSN 1755-8336 (on-line) Green Grass, Red Blood, Blueprint 31 2 Queen Christina’s challenge Trying to discover how a biological mechanism works has an advantage over solving problems in non biological areas since one is sure the problem can be solved; we must just be clever enough. (M. Delbrück, by Laithwaite [15]) According to a popular, and probably apocryphal, anecdote, when René Descartes expressed the view that animals are but clockwork automata to his royal student, Queen Christina of Sweden, she pointed to a clock and challenged him ‘Well, Monsieur Descartes, show me how it makes a child’. Needless to say, Christina’s challenge could not be seriously taken up for many centuries. In the words of Freitas [16], ‘It was not until 1948 that scientists became convinced that machines could be taught to replicate themselves. In that year John von Neumann ... gave a series of historic lectures at the University of Illinois ...He was able to prove, with mathematical rigor, the possibility of building self-reproducing machines.’ Sipper et al. [17] made a distinction between the two terms replication and reproduction: • replication is an ontogenetic developmental process, involving no genetic operators, resulting in an exact duplicate of the parent organism. • reproduction is a phylogenetic (evolutionary) process, involving genetic operators such as crossover and mutation, giving rise to variety and ultimately to evolution. However, in most works described herein these two terms are considered synonymous and are used interchangeably. The motivations for studying self-replication are both theoretical and practical and can be summarised as follows. Theoretical goals: • understanding bio-molecular mechanisms of reproduction and origins of life; • understanding complex system dynamics and emergent properties; • improving artificial life, leading to a better understanding of evolution and ecology. Practical goals: • achieving self-replicating massive architectures for parallel computing; • achieving self-repairing and homeostasis in electronic and mechanical machines; • achieving self-replication in automata (e.g. for nanotechnology or space exploration). Among the theoretical questions that current research on self-replication strives to solve, perhaps the most deep and fascinating one is whether the appearance of life on our planet has to be regarded as an exceptional event, or rather as the inevitable outcome of the physical conditions prevailing in this corner of the universe [18, 19]. With some inevitable simplification, the two opposite answers to this issue can be represented by Jaques Monod [20], who stresses the role of contingency in the very existence of life, and certainly in our existence (‘chance caught on the wing’), and Stuart Kauffman [21], who regards self-replication and life as the inevitable outcome of the complex, autocatalytic set of chemical WIT Transactions on State of the Art in Science and Engineering, Vol 27, © 2006 WIT Press www.witpress.com, ISSN 1755-8336 (on-line) 32 Design and Information in Biology reactions that occur whenever organic macromolecules are free to interact (‘we the expected ... at home in the Universe’). Roughly speaking, Monod’s view – echoed in a somewhat milder form by Francois Jacob [22] – is representative of the more orthodox Darwinian tradition in the natural sciences and evolutionary biology, whereas Kauffman’s ideas reflect the school of thought associated with the study of complexity. An even more extreme statement of the belief in the inevitability of life is the following, due to Thomas Ray [23]: ‘The living condition is a state that complex physical systems naturally flow into under certain conditions.