Accounts article on the Layered Minerals in the context of Origin of Life

Cover. Illuminating the origins: Through the kaleidoscopic glass of the Sagrada Familia, a cascade of amino acids, peptides, and small proteins emerge, symbolizing the quest from mystic origins to scientific enlightenment. This vivid artwork captures a transformative journey, mapping the path from mystical beginnings to the concrete foundations of biochemical evolution.

Our recent article, published in the ACS Accounts of Chemical Research, overviews mechanisms through which layered minerals could have facilitated the formation of the first molecules of life and molecules looking like the first molecules of life. We discuss how one could tell those apart based on their composition, local environment and the encapsulating layered mineral.

Read the full article: https://doi.org/10.1021/acs.accounts.4c00173

Read the news article from the School of Chemistry: https://chem.ed.ac.uk/chemistry-minerals-sheds-light-origins-life

Imagining Aliens

I have recently been approached for some comments by Sarah Wells, who was writing a news article about aliens for Live Science (article can be found here https://www.livescience.com/space/extraterrestrial-life/what-could-aliens-look-like)

When asked to imagine an alien, straight after green glowing bipeds with dragonfly eyes, a rather different specie comes to my mind – a fungi.

Knowing that other planets have far less friendly climates—lacking an atmosphere to protect against UV radiation, and to keep the surface water and warmth—suggests that living on the surface of such planets would not be as comfortable. On the other hand [or rather under one’s foot], soils also provide protection against UV, can retain water and nutrients. The water retention capacity of soil is proportional to the surface area of the particles it is made of. Here, the presence of clay minerals (which are the smallest soil particles with the largest surface area) is of particular significance. Not only can clays retain water, but their formation is also evidence of water. This is what makes clay-rich areas a key interest for the Martian missions.

In fact, even on Earth, which offers a comfortable surface living, nearly 60% of all species are found in soils, which makes it the most biodiverse habitat [Anthony et al., Enumerating soil biodiversity, PNAS (2023)].

Yet, the species living in the soils can no longer use the same biomechanics as us [or the imaginary green aliens]. Let’s have a look at a few structures of life forms found on Earth and their prevalence in soils:

  • Bacteria: typically single-cell, understood to be within the first of life forms, and known for its resilience. It was found that just over 1/2 of all its species live in soils.
  • Archaea: a domain of single cells and another one of the first life forms that split away from bacteria at the point of LUCA (Last Common Universal Ancestor) 3800 MYA. Nevertheless, only under a 1/4 of all its species are subterranean.
  • Plantae: easily recognised by their green colour on the top and roots in the soil, they make a good candidate for the soil-living species. Yet, plants are powered by photosynthesis, which requires sunlight, i.e., they cannot be fully underground for the whole duration of their life unless an alternative route to an energy source is found (e.g., parasitic plants). Plants originate from algal scum and appeared on land by about 700 MYA.
  • Oligochaeta: the worms. These species predominantly live in soils (60%) or are semiaquatic; preferring wet, colder organic-rich soils. Enchytraeidae is a family of these worms that predominantly (98%) live in the soils. Their soft bodies mean that their fossils are rare featuring just parts of their bodies. Their emergence on Earth may be as early as 550 MYA, while their evolution is correlated with the emergence of the flowering plants about 65 MYA.

If we now step back and imagine alien life that is beyond a single cell (e.g., first life forms of bacteria and archaea), fungi become a rather appealing candidate with a track record of living in the soil; with the ability to form a complex long-lived and evolving network of mycelium; and a remarkable adaptability to radiation [Deshevaya et al., Survival of microorganisms during two-year exposure in outer space near the ISS, Sci Rep (2024)] they may even be feeding through radiosynthesis (hypothesized metabolism of ionizing radiation, alike photosynthesis) [Zhdanova, et al., Ionizing radiation attracts soil fungi, Mycological research (2004)].

Unveiling Secrets of Microscopic World: Molecular Modelling in Clay Science

The first theoretical calculations in chemistry go back nearly a hundred years (Heitler, W. et al., (1927) Z. Physik, 44, 455–472). However, it was not until the advent of computers a couple of decades later that the calculations of multi-atomic systems became feasible. Today, propelled by advancements in both hardware and algorithms, computational chemistry has blossomed, with many techniques developed, granting us unprecedented access to molecular scales with unparalleled accuracy and detail.

At the heart of this revolution is molecular modelling, a computational approach that seeks to elucidate the behaviour of systems with atomistic detail. While computational chemistry encompasses a wide array of techniques, from quantum mechanics to classical molecular dynamics simulations, in its basis, it relies on mathematical models and computational algorithms to solve the equations governing interactions and motions of atoms that comprise molecules and materials. Leveraging the power of supercomputers, we now can simulate complex molecular systems, from ultra-fast chemistry of excited states to large biomolecular assemblies and inorganic materials.

The utility of molecular modelling goes beyond its applications in chemistry and extends across disciplines. In the field of clay science, it has proven itself as a powerful tool for understanding the structure, dynamics, and reactivity of clay minerals at the molecular level. Here, the primary motivation for performing molecular simulations is their ability to elucidate the complex interplay between clay minerals and their surrounding environment, describe processes at the interface, and understand how the structure of clays defines their function. To this end, simulating interactions between clay minerals and water, ions, and organic molecules gives us insights into fundamental clay properties, such as ionic exchange or swelling, and allows us to predict the capacity of clays for various applications, from targeted pollution remediation to drug delivery (Cygan, R. T. et al., (2009) J. Mater. Chem., 19, 2470-2481).

While simulations only provide insights into processes at the atomistic scales and over nano/microsecond timescales, their ability to model many system perturbations allows us to leverage statistics and create a probabilistic representation of the macroscopic phenomenon. This gives modelling a predictive power and an ability to extrapolate the processes and system’s evolution over extended time and size scales.

As an example, in the quest for solutions to environmental challenges, molecular modelling supports efforts in nuclear pollution management. To this end, molecular simulations of clay mineral interactions with radionuclides under relevant environmental conditions offer a safe tool for predicting the nuclear contaminant spread, identifying routes to pollution remediation, and guiding the development of clay-based materials for long-term nuclear waste storage (Ma, Z. et al., (2018) Appl. Clay Sci.168, 436-44; Liu, X. et al., (2022) Nature Rev. Earth & Env.3.7, 461-476).

Furthermore, molecular models establish themselves as a powerful tool to study otherwise unattainable conditions of far-gone past or at locations in the distant universe. In such cases, even a laboratory experiment will still be a simulation. The subject of such a quest is unravelling the origin of life or searching for its extraterrestrial evidence in the form of biosignatures. Through sequences of molecular simulations, we can test our hypothesis and identify a set of attainable laboratory experiments for further validation. In the end, the timescales available for life-forming processes could have spanned beyond the duration of human life, let alone a graduate student degree (Erastova V., et al., (2017) Nat. Commun.8, 2033).

At the same time, with the developments in space missions, the search for evidence of extraterrestrial past life is now becoming a reality. Martian Rovers are now examining clay-rich soils, as those provide the optimal environment for biosignature preservation. However, identifying organic materials must be scrutinised before any conclusions can be made about their potential as evidence of ancient life. Yet, unable to return the samples to Earth, simulations are well posed to offer guidance on the location-specific chemistry at the mineral interface, assisting in the search for biosignatures. (Pollak, H. et al., (2023) Goldschmidt 2023 Conference)

In the grand tapestry of science, molecular modelling not only illuminates microscopic phenomena but also informs our understanding of macroscopic processes, connecting time and space across our Universe. 

PhD position in Astrobiology

Understanding interactions between minerals and small biopolymers under extreme conditions

The project combines computational screening and wet-lab experiments to develop a comprehensive understanding of the interactions between silicate minerals and small biologically-relevant molecules, such as amino acids, peptides, peptoids and proteins. Our goal is to study the stability of these organic molecules and their mineral-enabled adaptability to environmental conditions. We will focus on sampling the effects of salinity, ion compositions and pH at the extremes of environmental conditions. The primary interest of this work is in the preservation of biosignatures on Mars, while the insights gained in the project have tremendous significance for a wide range of scientific problems, both fundamental (such as origin of life on the early Earth) to the applied (e.g., hazardous waste storage and environmental cleanup). The project is data-driven, where the statistics obtained from molecular simulations will be used to guide the experimental studies. Such a strategy allows us to establish a protocol where computational screening is used to sample mineral-bioorganic systems, informing and directing laboratory tests. 

The project is supervised by Drs Valentina Erastova (School of Chemistry) and Sean McMahon (School of Physics & Astronomy) and is also hosted in the UK Center for Astrobiology.

The studentship is fully funded for 48 months by the University of Edinburgh and covers tuition fees and an annual stipend (starting at £17,668 per annum) for a candidate satisfying EPSRC residency criteria.

Enquiries and the initial application should be directed to:

Dr Valentina Erastova, valentina.erastova[at]ed.ac.uk

The position will remain open until filled.

Two PhD positions for Sep 2023

We have two PhD positions available via E4 DTP for September 2023 start

Deadline: 12 noon, 5th of January 2023

Application process details here

Ultracool Chemistry in Noctilucent Clouds

Supervisors: Valentina Erastova, Charles Cockell and Basile Curchod (Bristol University)

Further details here

Design of Biochar for Sequestration of Emerging Pollutants

Supervisors: Ondrej Mašek and Valentina Erastova

Further details here

Milley Urey Flask

then a miracle occurs/ I think you should be more explicit here in step two

It was great to be contacted by Jason for a comment on a recent work of Criado-Reyes and collaborators (and therefore be within the first to see the article). This work shows how something basic and often ignored, i.e. glassware, can affect our interpretation and understanding of chemical processes. The impact is significant here.

In 1952, Stanley Miller and Harold Urey have conducted a rather simple experiment to validate 1930s primary abiogenesis hypothesis by Oparin and Haldane, stating that conditions on early Earth would promote reactions towards the chemical complexity and the emergence of life (i.e. against Pasteur’ theory of biogenesis that life can originate only from pre-existing life). In their setup, Stanley and Harold unknowingly and fortuitously included another important component — silicate surface of the flask, through this incorporating the effect of mineral surfaces, as postulated in 1949 by Bernal, into their famous experiment.

Read more:

New members of the group

This summer we are joined by five wonderful undergraduate students – Kacper, Sarah, Szymon, Ioana and Ben! They have secured different competitive funding schemes to pursue a topic of their interest, to learn a new skill and to gain experience of research.

In an order of starting dates only:

  • Kacper is funded by Carnegie Trust Vacation Scholarship for his project ‘In search of interstellar glycine – characterisation of spectroscopic properties under extreme conditions via computational simulation‘. He will be working between our group and In Silico Photochemistry Group at Durham University, bringing together molecular dynamics and quantum chemical calculations.
  • Sarah has won Afton Chemical Summer Internship and is working with PhD student Hannah, studying interactions between glycine molecules and Martian clays.
  • Szymon secured the EPSRC Vacation Scholarship and joined PhD student Rosie. Szymon is testing new modes of biochar for the adsorption of pharmaceutical pollutants.
  • Ioana was awarded Undergraduate Research Bursary of the Royal Society of Chemistry for her project ‘Prebiotic Molecules of Icy Moons: Molecular Modelling for Characterisation of Interactions in the Extreme Environments’.
  • Ben has joined us with E4 Research Experience Placement, coming from the computational phyics degree, his is now working with Hannah on the development of analysis tools for molecular simulations.

Warmest welcome to our newest group members. As always grateful to the funders for the opportunity they create by these schemes. I am looking forward to working with you, learning together about how things work and to the science your placements will surely inspire!

Found out more about current and past group members, as well as opportunities to join or visit us.

NERC Research Experience Placements this Summer

We are looking for a motivated UG student from the UK university to join our group with the NERC funded placement.

Bringing Atomic-level insights to Caesium Decontamination by Clay Minerals

The student will investigate the adsorption of Cs-137 onto montmorillonite and vermiculite clays at atomic-level resolution. They will use molecular dynamics (MD) simulations, a theoretical method, providing atomistic-level details to macroscopic observations. Through this work we will gain a mechanistic understanding of the Cs-clay adsorption process and we will help inform the choice of natural clay between the local naturally available ones, on the nuclear waste disposal sites.

More details about project and eligibility here.

Application deadline 19th of May, apply here.

2 PhD positions for 2021

2 x PhD positions (click on the titles for further details):

Design of Biochar for Sequestration of Emergent Pollutants

Weathering of Clays under Extreme Conditions: Implications for the Biosphere and Extraterrestrial Environments

Deadline: 7th January 2021, 12 noon

To apply follow the link www.ed.ac.uk/e4-dtp/how-to-apply 

Funding & Eligibility: The studentship is fully-funded for 42 month, incl. home/international fees, research costs and UKRI stipend (currently at £15,285 per annum), and is part of the E4 Doctoral Training Partnership. For further details see Entry & Eligibility Criteria.