Category: opinion

Imagining Aliens

Posted on by valentina.erastova in blog, opinion

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

Posted on by valentina.erastova in blog, opinion

Written by V Erastova for Phyllosophical News of the Clay Minerals Group, 2024, Issue 1.
Read the complete issue of the newsletter here.

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. 

Milley Urey Flask

Posted on by valentina.erastova in opinion
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:

Comment for CW

Posted on by valentina.erastova in opinion

Comment for Chemistry World News on a recent article by A. Wolos et al “Synthetic connectivity, emergence, and self-regeneration in the network of prebiotic chemistry” published in Science.

It is great to see the use of computers to combine our chemical knowledge, to enable predicting new chemical pathways. The team, previously known for software Chematica, lead by Bartosz Grzybowski and Sara Szymkuć, demonstrated how this can be used to map-out reactions from most simple early Earth ones towards the building blocks of life.

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Astrobiology through a Computer

Posted on by valentina.erastova in blog, opinion

When we think of chemistry, we often imagine a laboratory bench full of test tubes and a scientist in a white coat. But as we accumulate knowledge through such experiments, we start to formulate them into theories and hypothesis. Testing such hypotheses allows us to refine our theories, ultimately gaining predictive power. Additionally, computational chemistry methods provide us with a versatile tool, bringing atomic-level insights to processes beyond conditions attainable in the lab. It comes as no surprise that it is extensively applied for the search of chemical processes of the origin of life.

In this search, we are biased towards “life as we know it” – made of polymeric self-organising sequences in an aqueous media confined by a flexible lipid membrane. Life forms of this kind would only exist in Earth-like conditions, giving rise to the interest in planets in the “habitable zone” (planets that can have liquid water on their surface).

Polar clouds, made of methane, on Titan (left) compared with polar clouds on Earth (right), which are made of water or water ice.
Polar clouds, made of methane, on Titan (left) compared with polar clouds on Earth (right), which are made of water or water ice. Wikimedia Commons

Titan, the moon of Saturn, with a cryogenic surface (-180 °C) cannot have liquid surface water. Instead, it has hydrocarbon (that exists as natural gas on our planet) seas, and it snows benzene. It also has a dense atmosphere with a wide diversity of organic molecules produced through photochemical reactions. It opens a playground for the ideas of exotic life.

Indeed, when recreating the chemistry of the Titan’s atmosphere, Horst et al. were able to observe the formation of nucleotides and amino acids, essential building blocks of polymers of our life. The significance here was that these core reactions, first discovered in Miller-Urey experiment, and believed to require water, could go on without it.

Furthermore, Stevenson et al. then postulated the possibility of formation of pseudo-membranes in liquid-water-free environments, by such aiming to expand the search for life beyond “habitable zone”. As an example, they studied self-assembly of molecules found on Titan. Within those, acrylonitrile was predicted to form a flexible inverse-membrane, named azotosome.

However, recent theoretical work by Sandström and Rahm curbs our excitement for finding traces of exotic life. Through molecular modelling, they studied other plausible structures that acrylonitrile could adopt in Titan’s frigid environment, where entropy plays a very small role. They demonstrated that its crystal is significantly energetically more stable than its membrane-like azotosome.

These two works demonstrate how, through computational chemistry, we can test and challenge new ideas in conditions unattainable on Earth. As a result, we are growing and evolving our understanding of the physicochemical processes and engaging in extensive discussions on the processes of life.

Computational methods are advancing, giving us the capacity to analyse the chemical space with increasing efficiency and to drive our imagination further, germinating new ideas.

by V Erastova

 

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