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Origins of Life

Papers etc. relevant to ideas that quantum processes were involved in the origins of life on Earth.

1.) Quantum Mechanics and Emergence - Seth Lloyd - Computing aspects of first replicators

2.) Quantum coherence and the search for the first replicator - Jim Al-Khalili & Johnjoe McFadden - The first replicator as a search problem

3.) Towards understanding the origin of genetic languages - Apoorva Patel - Examines DNA, RNA and amino acids as codes

4.) A quantum theory of the origins of life on Earth - Merali, Z.

5.) Life was all but inevitable - Catherine Brahic (based on research by Ernesto di Mauro)

6.) Life cooked up in undersea cauldrons - Kate Alpine (based on research by Christof Mast and Dieter Braun) - Another shot at explaining the origins of life.

1.)

Quantum Mechanics and Emergence

Seth Lloyd

In: Quantum Aspects of Life - Eds. Derek Abbott, Paul Davies & Arun Pati Imperial College Press ISBN: 13: 978-1-84816-267-9

Quantum mechanics is regarded as having two features important for the emergence of a complex system such as life. First it is digital or discrete, in the sense of being composed of a finite number of distinguishable states. The second is randomness. Taking these two features together is interpreted to mean that the universe as described in quantum mechanics is an information processor or a computer that is programmed by quantum fluctuations.

Each discrete unit described by quantum mechanics is envisaged as a computing bit that represents the distinction between 0 and 1 or between yes and no. The spin of an electron or the polarisation of a photon can be regarded as a bit. At the sub-atomic level, bits are referred to as quantum bits or qubits. The interaction between these qubits can be regarded as a computation. Quantum mechanical interactions form the basis of chemistry, which is seen as representing a further layer of computing related to life forms.

The randomness of quantum mechanics is apparent when a measurement is made, or when interaction with one of many features in the environment causes a particle to decohere. As an example a photon passing through a filter, such as the lens of a pair of sunglasses will decohere from a superposition of polarisations to a particular polarisation. Bits are also seen as a measure of entropy, with entropy proportional to the number of bits in a system as registered by quantum particles.

The author remarks that at the Big bang, the universe was in a simple state, and that the laws of physics that have governed its development since then are also simple. He argues from the fact that in a computer when 0s and 1s are generated randomly, if any programme is generated, it is more likely to be a short programme than a long programme, but it is argued that short programmes might be more suitable to eventually produce the complexity of life.

Lloyd rounds off by arguing that complexity cannot derive from computation by itself, but also requires the variation which is introduced by the randomness of quantum mechanics. The superpositions of quantum mechanics reflect or explore all possibilities at once. The article thus seems to imply, although it does not specifically argue for, the idea of a quantum search engine that would eventually hit on the right sequence of molecules to produce a replicator.

2.)

Quantum Coherence and the Search for the First Replicator

Jim Al-Khalili & Johnjoe McFadden

March 29 2007

In: Quantum Aspects of Life - Eds. Derek Abbott, Paul Davies & Arun Pati

Thinking about the origin of life on Earth during much of the second half of the 20^th century was influenced by the Miller and Urey experiments in the 1950s. These seemed to show that the primordial soup of the early Earth could easily produce simple organic molecules, such as amino acids. For a time, it was thought that the problem of the origin of life had been solved. However, it is now considered that the early conditions on Earth were less favourable than was thought in the 1950s, for the spontaneous formation of biomolecules, such as amino acids. Moreover, the Miller and Urey experiments produced amino acids, but did not go the further step of producing proteins, which comprise a hundred of more amino acids strung together. Other essential biomolecules, notably nucleic acids, were also not produced.

The chapter examines how it would be possible for a self-replicating structure to emerge abiotically. The smallest of cells still surviving from the early Earth contains 1.6 million base pairs, and are taken to be the descendants of still earlier and much simpler cells. Simpler genomes do exist, but these are various types of parasites on larger organisms, and are not well qualified to emerge from the primordial soup. Moreover, it is argued that the simplest self-replicating organism would still be very complex.

It is not seen as plausible to appeal to the idea of DNA or RNA replicating by themselves. The modern cycle of reproduction is a closed circle creating a chicken and egg, which came first problem. DNA produces RNA which produces amino acids that fold into proteins, that in their turn make enzymes capable of replicating DNA. In the 1970s, it was discovered that RNA could act as a catalyst, and these were proposed as the first replicators. However, the minimum RNA replicator would itself be very complex, with 165 bases. There are 4¹⁶⁵ possible RNA structures of this length. This is a number suggested to be greater than the number of electrons in the universe, and calculations suggest the primordial soup would need to be larger than the observable universe to give a feasible chance of getter a replicator.

The authors categorise the problem of the first replicator as a search problem. The replicator is one or a few structures in a vast space of possible structures. Random searches based on classical processes would not find the solution in any feasible period of time. An information sciences examination of the problem has come to the same conclusion (1. Tevors and Abel, 2004).

The authors propose a quantum search process. They suggest that a quantum superposition of possible combinations between molecules in the primordial soup could be built up before decoherence intervened, and that this would be an efficient way of searching for the right combination for a replicator. Quantum systems can check out an array of possibilities simultaneously. Here as in other instance of the suggested involvement of quantum features in biological matter, decoherence is the main objection. The primordial soup would appear to be ideal conditions for very rapid decoherence. However, the authors expect the search process to take the form of simultaneous quantum tunnelling. As with other ideas, for quantum features in biology this is admitted to require some degree of screening from the environment. Relative to this they mention experiments by (2. Margadonna and Prassides, 2002) with fullerenes, transport of charges along DNA (3. Giese et al, 2001) and proton tunnelling in hydrogen bonded networks (4. Horsewill et al, 2001). They also point to the involvement of quantum tunnelling in enzyme reactions (5-7. Scrutton et al 1999, Sutcliffe and Scrutton, 2002, Masgrau et al, 2006). Normally the search process will not arrive at the right structure, but once it does the self-replicator can form. Once formed the replicator can utilise chemicals in the environment in a classical manner. Decoherence can be seen as a process of measurement that discovers the replicator. This is an irreversible process not dependent on some prior given objective of the search process, and this is seen as answering the objection that there is something teleological about the quantum search idea.

References:-

1.) Trevors, J and Abel, D. (2004) - Chance and necessity do not explain the origin of life - Cell Biology International, 28, pp. 729-39

2.) Margadonna, S. and Prassides, K. (2002) - Recent advances in fullerene conductivity - Journal of Solid State Chemistry, 168, pp. 639-52

3.) Giese et al (2001) - Direct observation of hole transfer through DNA by quantum tunnelling - Nature, 412, pp. 318-20

4.) Horsewill, A. et al (2001) - Evidence for coherent proton tunnelling in a hydrogen bond network - Science, 291, pp. 100-103

5.) Scrutton et al (1999) - New insights into enzyme catalysis - European Journal of Biochemistry, 264, pp. 666-671

6.) Sutcliffe, M. and Scrutton, N. (2002) - A new conceptual framework for enzyme catalysis - European Journal of Biochemistry, 269, pp. 3096-3102

7.) Masgrau, L. et al (2006) - Atomic description of an enzyme reaction dominated by proton tunnelling - Science, 312, pp. 237-241

3.)

Towards understanding the origin of genetic languages

Apoorva Patel

Indian Institute of Science

April 13 2007

In: Quantum Aspects of Life Eds. Derek Abbott, Paul Davies, & Arun Pati

The author views molecular biology as a nanotechnology and as a system for acquiring, processing and communicating information. The kinds of processing seen in DNA and in proteins are argued to be the optimal solutions for the information processing that they carry out.

Patel stresses that life is a non-equilibrium process. Metabolism, a series of biochemical processes, is a basic feature of living matter. This processing requires the continuous extraction of free energy from the environment. The manipulation of information is seen as determining the complex structures that make up life.

The information processing of living matter is seen as needing a language that uses a set of building blocks, whose arrangements confer different meanings. This language has to be protected against errors, and to make efficient use of physical resources. Genes and proteins constitute a language with building blocks comprising four nucleotide bases for DNA and RNA and 20 amino acids for proteins. Other nucleotides and amino acids exist in living cells, and the selection of these particular four and twenty building blocks is taken to indicate the selection of a language. Minimisation of error leads to the selection of a digital language with building blocks with discrete operations. The genetic language has a tiny error rate ensuring stability, but with no errors, there would be no change through mutation. In protein, carbon atoms can form aperiodic structures which can encode a language. The amino acid chains are formed in one dimension which is simplest, but can then be folded three dimensionally.

There have been various attempts to explain the emergence of this language in evolutionary terms. Crick (1968) made the hypothesis that the language came into existence at one go, which seems merely to repeat the improbability problem of the emergence of replicators. In contrast, Patel favours the idea that the language evolved through a trial and error process, until it reached an optimal solution. A binary system of two nucleotide bases, similar in concept to modern computers, would be sufficient to encode the genetic information. However, Grover’s algorithm indicates that four bases provides an optimal approach. Patel thinks that this four-base process may have evolved at a later stage, after an initial binary system. P The genetic machinery is seen as having the physical components to implement Grover’s algorithm. The genetic code is based on four nucleotides arranged in triplets that code for 20 amino acids. The optimal number (Q) of sampling operations in Grover’s algorithm for a database (N) is given by Q = 1 for N = 4 and Q = 3 for N = 20. It requires quantum superposition, but not necessarily non-local entanglements. As usual with quantum proposals, the most important question is whether the quantum superpositions could survive for long enough to be useful.

4.)

A quantum theory of the origin of life on Earth

Zeeya Merali

This recent article in the New Scientist revives a long-established idea that the origin of life on Earth could derive from a quantum process. The first to suggest this appears to have been Schrodinger in his 1944 book, 'What is Life? The idea has been relaunched by Jonjoe McFadden of the University of Surrey UK, who has also proposed the idea of an electromagnetic field as a quantum substrata of consciousness.

The proposal is in many ways the mirror image of the proposals for quantum consciousness. The quantum process is suggested to provide an explanation for something that macroscopic science has failed to explain, and the main argument against the quantum is the same as in the case of consciousness, that is that decoherence in the conditions of the primordial Earth would be far too quick for quantum coherence to be relevant. As with the quantum consciousness idea, proponents of the quantum view have argued for possible shielding of the quantum process.

The origin of life is not as hard a problem as consciousness, but it has certainly proved difficult. The idea that life arose from some primordial soup of molecules is inherently plausible. The difficulty arises in getting the molecules to combine in the right order. The simplest self-replicating structure is estimated to require 165 base-pair molecules placed in the right order and the odds against getting the right structure is 4^165, a number said to be greater than the number of electrons in the universe. Of course, if Nature made enough tries for long enough it should get there eventually. However, life on Earth appeared quite soon after the planet became at all suitable for life, making the 4^165 chance a bit improbable.

McFadden proposes that a form of quantum computing arose in the primordial conditions allowing a 'search' of all the possible ordering of the molecules, and leading to the discovery of the sequence that self-replicated. Some support is given to his idea by the suggestion that the speed at which nucleotide bases are matched up when cells split also requires quantum processes.

As with quantum consciousness, the main problem for the proposal is the speed at which quantum decoherence would be expected to occur in the type of conditions that would permit the origin of life. However, two other researchers, Asoke Mitra and Garge Mitra-Delmotte have suggested how quantum processes could have been shielded, in a manner rather akin to Hameroff's idea of quantum processes being shielded within the microtubule.

The Mitras focus on sub-sea vents that have been seen as a favourite location for the origin of life in recent years. Another scientist, Michael Russell at the University of Glasgow had already shown that the necessary molecules could react with iron sulphide found close to the vents. The Mitras argue that chambers found near sub-sea vents could shield quantum processes. Magnetic fields generated by the iron sulphide are suggested to protect the quantum states of the necessary molecules. The Mitras point out that magnetic fields are used in an analogous manner in proto-type quantum computers in order to maintain the entanglement of particles used as qubits. The idea is claimed to be testable by means of existing technology.

Substantiation of the idea would not in itself appear to prove that consciousness is explained at the quantum level. However, if quantum processes were seen to have been involved in the origin of life, that would seem to be an inherent plausibility that the adaptive advantages of the speed of quantum search processes would have been incoroporated into living organisms.

5.)

Life was all but inevitable

Catherine Brahic (based on research by Ernesto Di Mauro, Sapienza University of Rome)

New Scientist, April 24 2010

A team led by Ernesto Di Mauro at Sapienza University of Rome may point a way to solving the problem of the origin of life on Earth. It is thought most likely that life developed from RNA replicators. The problem here has been as to how the first replicator emerged, with an impossibly high probability against the molecules of the first replicator arranging themselves in a chain of the right order simply by chance. The nucleotides that make up RNA do not tend to form chains without a catalyst, but the catalysts that act to produce such chains are proteins, which are themselves made by RNA. This creates a classic chicken and egg conundrum, but long before there were either chickens or eggs on Earth.

However, experiments by Di Mauro's team suggest a possible solution. They have shown that cyclic nucleotides, a chemical variation of the nucleotides that make up RNA, can join up to form RNA chains. The 'black smoker' hydrothermal vents in the oceans are seen as suitable locations for this to happen, although this step has not been experimentally tested.

It will be interesting to see whether this theory can establish itself as an orthodox explanation for the emergence of the first replicators. If it's as simple as all that, it would seem to suggest the near certainty of some form of life on Earth-like planets elsewhere in the universe.

Reference:-
The Journal of Biological Chemistry, DOI: 10.1074/jbc.M109.041905

6.)

Life cooked up in undersea cauldrons

Kate McAlpine (based on research by Christof Mast and Dieter Braun, Ludwig Maximilian University, Munich)

New Scientist, 29 May 2010

Christof Mast and Dieter Braun have performed experiments suggesting that DNA replication could have occurred in pores around the ocean floor hydrothermal vents that are frequently suggested as locations for the origin of life. In general short stands of DNA and loose nucleotides would have been too diluted in ordinary seawater for replication to have emerged. However, it is suggested that the situation could have been different inside undersea hydrothermal vents. Magnesium-rich rocks could react with seawater to drive convection currents within pores in the rock. This could possibly concentrate nucleotides, strands of DNA and polymerase sufficiently for replication to emerge. Mast and Braun performed an experiment involving polymerase, nucleotides and DNA strands in a state of thermal convection in water, and produced a doubling of DNA every 50 seconds (Physical Review Letters, vol 104, p. 188102). It is further suggested that fatty acids in the water could have conveyed replicated DNA between pores. An experiment performed by another team at Harvard showed that fatty acids driven by convection could form membranes capable of catching and transporting genetic material (Journal of the American Chemical Society, DOI: 10.1021/ja9029818).