The Feb 2017 Wet season special edition of the Gulflander Gazette is out now! Read all about Madam Kate of Golden Gate, Harrison the Normanton Station Cat, go behind the scenes at the railway workshops, and more!

Railways and trains and Railway Heritage

Heritage railways

Heritage railways

It is a remarkable observed fact that all life on Earth is homochiral, its biology using exclusively the D-enantiomer of ribose, the sugar moiety of the ribonucleic acids, and the L-enantiomers of the chiral amino aci... more abstractIt is a remarkable observed fact that all life on Earth is homochiral, its biology using exclusively the D-enantiomer of ribose, the sugar moiety of the ribonucleic acids, and the L-enantiomers of the chiral amino acids. Motivated by con- current work that elaborates further the role of hydrogen peroxide in providing an oscillatory drive for the RNA world (Ball & Brindley 2015, this journal, in press, doi:10.1101/020693, and Ball & Brindley 2015, J. R. Soc. Interface 12, 20150366, doi:10.1098/rsif.2015.0366), we reappraise the structure and physical properties of this small molecule within this context. Hydrogen peroxide is the smallest, simplest molecule to exist as a pair of non-superimposable mirror images, or enantiomers, a fact which leads us to develop the hypothesis that its enantiospecific interactions with ribonucleic acids led to enantioselective outcomes. We propose a mechanism by which these chiral interactions may have led to amplification of D-ribonucleic acids and extinction of L-ribonucleic acids.

Origins of Life

It is now accepted that primordial non-cellular RNA communities must have been subject to a periodic drive in order to replicate and prosper. We have pro- posed the oxidation of thiosulfate by hydrogen peroxide as thi... more abstractIt is now accepted that primordial non-cellular RNA communities must have been subject to a periodic drive in order to replicate and prosper. We have pro- posed the oxidation of thiosulfate by hydrogen peroxide as this drive. This reaction system behaves as (I) a thermochemical and (II) a pH oscillator, and in this work we unify (I) and (II) for the first time. We report thermally self-consistent, dynamical simulations in which the system transitions smoothly from nearly isothermal pH to fully developed thermo-pH oscillatory regimes. We use this oscillator to drive simulated replication of a 39bp RNA species. Production of replicated duplex under thermo-pH drive was significantly enhanced compared with that under purely thermochemical drive, effectively allowing longer strands to replicate. Longer strands are fitter, with more potential to evolve enzyme activity and resist degradation. We affirm that concern over the alleged toxicity of hydrogen peroxide to life is largely misplaced in the current context, we survey its occurrence in the solar system to motivate its inclusion as a biosignature in the search for life on other worlds, and highlight that pH oscillations in a spatially extended, bounded system manifest as the fundamental driving force of life: a proton gradient.

Origins of Life, Hydrogen Peroxide, RNA World, Thermochemical Oscillator, and pH oscillators

The RNA world of more than 3.7 billion years ago may have drawn on thermal and pH oscillations set up by the oxidation of thiosulfate by hydrogen peroxide (the THP oscillator) as a power source to drive replication. S... more abstractThe RNA world of more than 3.7 billion years ago may have drawn on thermal and pH oscillations set up by the oxidation of thiosulfate by hydrogen peroxide (the THP oscillator) as a power source to drive replication. Since this primordial RNA also must have developed enzyme functionalities, in this work we examine the responses of two simple ribozymes to a THP periodic drive, using experimental rate and thermochemical data in a dynamical model for the coupled, self-consistent evolu- tion of all reactants and intermediates. The resulting time traces show that ribozyme performance can be enhanced under pH cycling, and that thermal cycling may have been necessary to achieve large performance gains. We discuss three important ways in which the dynamic hydrogen peroxide medium may have acted as an agent for development of the RNA world towards a cellular world: proton gradients, resolution of the ribozyme versus replication paradox, and vesicle formation.

Origins of Life, Ribozymes, RNA World, Proton Motive Force, and pH oscillators

This paper presents and tests a previously unrecognised mechanism for driving a replicating molecular system on the prebiotic earth. It is proposed that cell-free RNA replication in the primordial soup may have been d... more abstractThis paper presents and tests a previously unrecognised mechanism for driving a replicating molecular system on the prebiotic earth. It is proposed that cell-free RNA replication in the primordial soup may have been driven by self-sustained oscillatory thermochemical reactions. To test this hypothesis a well-characterised hydrogen peroxide oscillator was chosen as the driver and complementary RNA strands with known association and melting kinetics were used as the substrate. An open flow system model for the self-consistent, coupled evolution of the temperature and concentrations in a simple autocatalytic scheme is solved numerically, and it is shown that thermochemical cycling drives replication of the RNA strands. For the (justifiably realistic) values of parameters chosen for the simulated example system, the mean amount of replicant produced at steady state is 6.56 times the input amount, given a constant supply of substrate species. The spontaneous onset of sustained thermochemical oscillations via slowly drifting parameters is demonstrated, and a scheme is given for prebiotic production of complementary RNA strands on rock surfaces.

Origins of Life, RNA World, Thermochemical Oscillator, and Pre-biotic Replication

More Info: DOI: 10.1098/rsif.2013.1052

Publication Date: Mar 19, 2014

Publication Name: Journal of the Royal Society Interface 11, 20131052

Article 27 of the Universal Declaration of Human Rights (1948) states that everyone has the right to freely share in scientific advancement and its benefits, and Article 15 of the International Covenant on Economic, S... more abstractArticle 27 of the Universal Declaration of Human Rights (1948) states that everyone has the right to freely share in scientific advancement and its benefits, and Article 15 of the International Covenant on Economic, Social and Cultural Rights (1966) recognizes the right of everyone to enjoy the benefits of scientific progress and its applications. Benefits include access to scientific and technological knowledge and opportunities for all to contribute to the scientific enterprise. I would add to these recognition of the scientific heritage of Indigenous peoples. Yet in Australia, Indigenous people are under-represented in science education and research and in STEM (Science Technology Mathematics and Engineering) related careers, to an extent that could amount to a violation of human rights under Articles 27 and 15. In this article I deconstruct some of the myths and attitudes that may contribute to the perpetuation of this situation, and outline a way forward.

Indigenous science education and Indigenous Knowledge and Science

Indigenous science participation

Indigenous science and engineering

My prediction made in 2014

American Presidential Election 2016