Quantum Mechanics And The Collective Unconscious

Chapter Five: Molecular Biology And Quantum Mechanics

This chapter contains a simplified account of how cells evolved and the role played by quantum mechanics in that evolution.

Cell Evolution

The first self-replicating cell is thought to have arisen about 4 billion years ago in a sea of organic molecules, and whatever its initial form came to have a phospholipid membrane incorporating a region of RNA capable of synthesizing the molecules necessary for replication, and enclosing a watery centre with, eventually, a nucleoid core.

This type of cell, known as prokaryotic, is distinguished from eukaryotic cells, which diverged later and have a nucleus with its own membrane. Prokaryotic cells are typically bacterial. They evolved on their own for 1 to 1.5 billion years, coming to have mechanisms for generating energy which are highly conserved in all present-day cells. Cells use adenosine 5'-triphosphate (ATP) as their source of metabolic energy to drive the synthesis of cell constituents and carry out other energy-requiring activities, such as movement (e.g., muscle contraction).

The mechanisms used for the generation of ATP are generally thought to have evolved in three stages, involving in turn glycolysis, photosynthesis, and oxidative metabolism; these stages accompanied, and caused, the transformation of the earth's atmosphere from a poisonous (to us) mixture of nitrogen, hydrogen sulphide and carbon dioxide into the breathable air we know today. It is supposed that photosynthetic bacteria (fossils have been found dating from 3.8 billion years ago, see Tamulis and Grigalavicius, below), utilized H2S to convert CO2 to organic molecules; some highly specialized bacteria continue to use this pathway. Tamulis and Grigalavicius suggest that a photosynthesizing prokaryote was the original form of self-replicating cell; but this is not a mainstream view.

Eukaryotic cells probably diverged from their prokaryotic forbears 2.7 billion or more years ago. Mitochondria (as found in animal cells) and chloroplasts (as found in plant cells) then may have resulted from the engulfing by eukaryotic cells of aerobic bacteria and cyanobacteria (i.e. those employing photosynthesis) respectively. At a later stage, possibly 1.5 to 2 billion years ago, further 'endosymbiotic' events took place whereby a simple, but by then probably larger, eukaryotic cell merged with a mitochondrial cell, producing today's basic animal cell, while a comparable merging of a eukaryotic cell with a chloroplast resulted in today's typical plant cell. Over time, many of the genes originally present in mitochondria and chloroplasts have transferred to the nuclei of animal and plant cells respectively.

It will be seen from the above account that a cell as it exists in today's animals or plants contains two replicative mechanisms, one based in the original eukaryotic nucleus, which deals with replication of the cell itself, and one based in the mitochondria or chloroplast, which deals with their replication. As well as containing a nucleus and mitochondria or chloroplasts, modern eukaryotic cells contain a number of other membrane-enclosed functioning units, including lysosomes (for digesting food and waste products).

See Cooper and Gray et al.

Many cell mechanisms rely on quantum tunnelling, including the 'respiratory' process (the formation of ATP inside mitochondria) and mutation.

Quantum tunnelling was described as a phenomenon in the final section of the last chapter.

In the mitochondrial ATP production process, NAD (nicotinamide adenine dinucleotide, an enzyme found in all living cells) accepts hydrogen electrons in an oxidizing process, forming NADH, which is strongly reductive. The electron transport chain (quantum tunnel) moves electrons from electron-donating substances (typically NADH) to electron-accepting substances (typically oxygen), a process which releases energy. This energy is applied to pumping protons across the membrane in which the process is embedded, along with the ATP synthesizing machinery; it is the release of these protons back across the membrane that 'powers' the generation of ATP. See e.g. Moser et al (2006), Althoff et al (2011) and Stuchebrukov (2010).

The phylogeny of early prokaryotes remains contentious, but ATP and its production process are taken to have evolved in prokaryotes before eukaryotes appeared, since the process is very strongly homologous in the two branches. That puts the development of ATP at c. 3 billion years ago; but it was not the original energetic basis of prokaryotes, which are thought to have begun as chemotrophs, obtaining energy by the oxidation of electron donors in their environment. Some researchers propose that early prokaryotes lacked membranes, which could have been a later evolutionary innovation. The ATP process requires membranes to work at all, but is a far more efficient process in terms of energetic output than is the chemotrophic process.

Although all modern cells employ DNA in their replication process, as do mitochondria, the original prokaryote is thought to have used RNA instead. However RNA is prone to breakage and is less stable than DNA, which eventually evolved to replace it as the replicator. See e.g. Forterre et al (2000), which proposes that DNA was invented in bacterial viruses which were then captured by prokaryote hosts. Either way around, the original replicator remains RNA. Some have questioned whether RNA could have done the job on its own (i.e. without an assembly of proteins), and have proposed other precursors, but research during the last ten years has tended to confirm that the necessary components of a self-replicating bundle could have arisen in the conditions that obtained on earth 4 billion years ago. See e.g. Patel et al (2015), who state:

'The key reaction steps are driven by ultraviolet light, use hydrogen sulfide as the reductant and can be accelerated by Cu(I)–Cu(II) photoredox cycling.'

Davies (2109) speculates that the replication process in both DNA and RNA, and particularly the role of enzymes in that process (see Garcia-Viloca et al, 2004, and Patel, 2001), employ quantum tunnelling:

'Evidence that quantum tunnelling plays an essential role has been obtained for many enzyme-driven reactions, and it is likely that tunnelling is an important factor contributing to the extraordinary efficiency of enzyme catalysis.'

See McFadden (2001) for a proposal that the 'invention' of the original RNA replicator could have involved quantum-based optimization in a superposition covering part of the 'primordial soup':

'A plausible (though technically highly challenging) experimental scenario would be to
construct a chemical soup consisting of a dynamic combinatorial library of RNA molecules linked by quantum tunnelling. A self-replicating molecule might be one of an exponentially large number of possible structures that could be synthesized, but the limited resources of the soup would make its appearance highly improbable classically.
However, quantum tunnelling could allow the library to explore all combinatorial possibilities as a quantum superposition. The presence of the possibility of a replicator within the superposition may be sufficient to trigger environment-induced decoherence.'

It is a question, how the soup or part of it could come to be entangled in the first place, although organic chemical reactions presumably create entanglement even if they did not initially involve quantum mechanical interaction – quantum phenomena are not limited to living cells. At any rate, one can question how the necessary superposition could be maintained for long enough in 'soup' conditions for the RNA nucleotide to search for its matching replicator. An answer is provided by Tamulis and Grigalavicius (2014) who say:

"We can propose that quantum entanglement enhanced the emergence of photosynthetic prebiotic kernels and accelerated the evolution of photosynthetic life because of additional absorbed light energy, leading to faster growth and self-replication of minimal living cells."

Tamulis and Grigalavicius reference a team of scientists at the National University of Singapore who suggest that it is quantum entanglement between the electron clouds of nucleic acids in DNA that holds DNA together (Rieper et al 2011):

'Rieper et al modelled the electron clouds of nucleic acids in DNA as a chain of coupled quantum harmonic oscillators with dipole–dipole interactions between nearest neighbours resulting in a van der Waals type bonding.'

Certainly, for Tamulis and Grigalavicius, their 'photosynthetic prebiotic kernel' is plentifully endowed with entangled states which can play a part in the final assembly of a replicator, an event which they date to 3.8 to 3.9 billion years ago.

Summary

It was the intention of this chapter to explore the extent to which quantum mechanical phenomena are or were implicated in the operation of organic cells and their evolution, in order to provide some sort of basis for the speculations put forward in the next and final chapter.

It is an exciting time in molecular biology, and the prevailing consensus on such matters as the evolutionary phylogeny of cells changes almost by the year.

It is not pretended even for one moment that any sort of incontrovertible scientific case has been put forward either here or in the literature for a prominent role for quantum mechanics in molecular biology or evolution. Many, perhaps most, scientific researchers in relevant fields would simply deny such a possibility. However, there is a growing body of research which points towards quantum involvement in many cell-level organic processes, and their evolution billions of years ago, just some of which have been mentioned above. For the purposes of this book, a role for quantum mechanics is a working assumption which allows the final chapter to reach its conclusions.

References

Althoff, Thorsten, Mills, Deryck J, Popot, Jean-Luc and Kühlbrandta, Werner (2011) Arrangement of electron transport chain components in bovine mitochondrial supercomplex, EMBO J. 2011 Sep 9;30(22):4652-64. doi: 10.1038/emboj.2011.324, at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243592/, accessed on July 3rd, 2015

Cooper, G M, (2000) The Cell: A Molecular Approach; The Origin and Evolution of Cells, 2nd edition. Sunderland (MA): Sinauer Associates; 2000, at http://www.ncbi.nlm.nih.gov/books/NBK9841/, accessed on July 2nd, 2015

Davies, P C W, Quantum fluctuations and life, Australian Centre for Astrobiology
Macquarie University, New South Wales, Australia 2109, at http://arxiv.org/ftp/quant-ph/papers/0403/0403017.pdf, accessed on July 5th, 2015

Forterre, Patrick, Filée, Jonathan and Myllykallio, Hannu (2000) Origin and Evolution of DNA and DNA Replication Machineries, in The Genetic code and the origin of life, Georgetown, TX : Landes Bioscience/Eurekah.com ; New York : Kluwer Academic/Plenum Publishers, c 2004, at http://www.ncbi.nlm.nih.gov/books/NBK6360/, accessed on July 3rd, 2015

Garcia-Viloca, M, Gao, J, Karplus, M and Truhlar, D G (2004) How enzymes work: analysis by modern rate theory and computer simulations, Science 303, 186-195 (2004), at http://www.ncbi.nlm.nih.gov/pubmed/14716003, accessed on July 4th, 2015

Gray, Michael W, Burger, Gertraud, and Lang, B Franz (2001) The origin and early evolution of mitochondria, Genome Biol. 2001; 2(6): at http://www.ncbi.nlm.nih.gov/pmc/articles/PMC138944/, accessed on July 2nd, 2015

McFadden, J (2001) Quantum Biology, Norton, New York, 2001

Moser, Christopher C, Farid, Tammer A, Chobot, Sarah E and Dutton, P Leslie (2006) Electron tunneling chains of mitochondria, Biochim Biophys Acta. 2006 Sep-Oct;1757(9-10):1096-109, at http://www.sciencedirect.com/science/article/pii/S0005272806001083, accessed on July 3rd, 2015

Patel, A (2001) Why genetic information processing could have a quantum basis, J. Biosci. Vol. 26| No. 2, June 2001, at http://www.ias.ac.in/jbiosci/jun2001/145.pdf, accessed on July 5th, 2015

Patel, Bhavesh H, Percivalle, Claudia, Ritson, Dougal J, Duffy, Colm D and Sutherland, John D (2015) Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism, Nature Chemistry 7, 301–307 (2015) doi:10.1038/nchem.2202, at http://www.nature.com/nchem/journal/v7/n4/full/nchem.2202.html, accessed on July 4th, 2015

Rieper, Elisabeth, Anders, Janet and Vedral, Vlatko (2011) Quantum entanglement between the electron clouds of nucleic acids in DNA, arXiv.org e-Print archive. http://arxiv.org/abs/1006.4053v2, at http://www.researchgate.net/publication/45924908, accessed on July 5th, 2015

Stuchebrukhov, A A and Hayashi, T (2010) Electron Tunneling in Respiratory Complex, Proc Natl Acad Sci U S A. 2010 Nov 9; 107(45): 19157–19162. Published online 2010 Oct 25. doi: 10.1073/pnas.1009181107. PMCID: PMC2984193

 
 
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