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Chasing Synthetic Life: A Tale of Forms, Chemical Fossils, and Biomorphs
Abstract
This Essay focuses briefly on early studies elaborated by natural and chemical philosophers, and the once called synthetic biologists, who postulated the transition from inanimate to animate matter and even foresaw the possibility of creating artificial life on the basis of physical and chemical principles only. Such ideas and speculations, ranging from soundness to weirdness, paved however the way to current developments in areas like abiotic pattern formation, cell compartmentalization, biomineralization, or the origin of life itself. In particular, the generation of biomorphs and their relationship to microfossils represents an active research domain and seems to be the logical way to bring the historical work up to the future, as some scientists are trying to make artificial cells. The last sections of this essay will also give a glimpse on that modern science aimed at understanding what life is and, whether or not, it can be redefined in chemical terms.
... Silica gels and chert deposits from soda lakes, particularly Lake Magadi (Kenya), were proposed as typical models for explaining the origins and mechanisms of the chert deposits and the preservation of cellular structures in siliceous -7 -sediments in Precambrian environments (Eugster, 1967(Eugster, , 1969Eugster and Jones, 1968;Hay, 1968;Schubel and Simonson, 1990;Behr and Röhricht, 2000;Behr, 2002;Reinhardt et al., 2019;Leet et al., 2021). Identification of these cellular structures and fossils in the Precambrian Earth has been challenged by the formation of self-assembled life-like abiotic mineral structures, which are proposed to form in soda lakes (García-Ruiz, 1994, 2000García-Ruiz et al., 2002, 2020. Nevertheless, mineral self-assembly was never tested in "natural" soda lake water. ...
... More importantly, extensive research has been done on mineral self-organization to advance the understanding of plausible pathways to biological self-assembly (Hanczyc et al., 2003), biomineralization (Song and Cölfen, 2010;Bergström et al., 2015;Cardoso et al., 2016), the origin of life, and its implication in life detection and prebiotic geochemistry (García-Ruiz, 1994, 2000Saladino et al., 2016;Bizzarri et al., 2018;Barge et al., 2019;McMahon, 2019;. A historical discussion of mineral self-assembly can be found in Cintas (2020) Among these patterns, biomimetic chemical gardens and silica-carbonate biomorphs received significant attention due to their relevance in life detection (García-Ruiz, 1994, 2000García-Ruiz et al., 2002, 2017, 2020, origin of life, and prebiotic chemistry of early Earth and other planets and moons (Russell et al., 1994;Russell and Hall, 1997;Saladino et al., 2016Saladino et al., , 2019García-Ruiz et al., 2017, 2020Bizzarri et al., 2018;Barge et al., 2019). Tubular and vesicular chemical gardens are capable of catalyzing prebiotic chemical reactions leading to the synthesis of organic molecules such as carboxylic acids, amino acids, and nucleobases, suggesting the plausible emergence of life in alkaline early Earth soda oceans (Saladino et al., 2016(Saladino et al., , 2019Bizzarri et al., 2018;Barge et al., 2019;Angelis et al., 2021). ...
... More importantly, extensive research has been done on mineral self-organization to advance the understanding of plausible pathways to biological self-assembly (Hanczyc et al., 2003), biomineralization (Song and Cölfen, 2010;Bergström et al., 2015;Cardoso et al., 2016), the origin of life, and its implication in life detection and prebiotic geochemistry (García-Ruiz, 1994, 2000Saladino et al., 2016;Bizzarri et al., 2018;Barge et al., 2019;McMahon, 2019;. A historical discussion of mineral self-assembly can be found in Cintas (2020) Among these patterns, biomimetic chemical gardens and silica-carbonate biomorphs received significant attention due to their relevance in life detection (García-Ruiz, 1994, 2000García-Ruiz et al., 2002, 2017, 2020, origin of life, and prebiotic chemistry of early Earth and other planets and moons (Russell et al., 1994;Russell and Hall, 1997;Saladino et al., 2016Saladino et al., , 2019García-Ruiz et al., 2017, 2020Bizzarri et al., 2018;Barge et al., 2019). Tubular and vesicular chemical gardens are capable of catalyzing prebiotic chemical reactions leading to the synthesis of organic molecules such as carboxylic acids, amino acids, and nucleobases, suggesting the plausible emergence of life in alkaline early Earth soda oceans (Saladino et al., 2016(Saladino et al., , 2019Bizzarri et al., 2018;Barge et al., 2019;Angelis et al., 2021). ...
Hybrid vesicles (HVs) that consist of mixtures of block copolymers and lipids are robust biomimetics of liposomes, providing a valuable building block in bionanotechnology, catalysis, and synthetic biology. However, functionalization of HVs with membrane proteins remains laborious and expensive, creating a significant current challenge in the field. Here, using a new approach of extraction with styrene-maleic acid (SMA), we show that a membrane protein (cytochrome bo3) directly transfers into HVs with an efficiency of 73.9 ± 13.5% without the requirement of detergent, long incubation times, or mechanical disruption. Direct transfer of membrane proteins using this approach was not possible into liposomes, suggesting that HVs are more amenable than liposomes to membrane protein incorporation from a SMA lipid particle system. Finally, we show that this transfer method is not limited to cytochrome bo3 and can also be performed with complex membrane protein mixtures.
As known currently, in the formation of the Earth, minerals have played a pivotal role going from the formation of the hydrosphere, the lithosphere, and all Earth components until the origin, evolution, and maintenance of life. The first signs of magnetism are found in komatiites. In the origin of life, minerals were responsible for concentrating, aligning, and acting as templates and catalyzers, allowing for the formation of bonds among the first biomolecules to form polymers, which eventually became assembled to give rise to the pioneer organism in the Precambrian. Besides, minerals allowed the DNA to be the information storing molecule, even though it was not the first biomolecule. Another function of minerals was to protect the organic complexes against ultraviolet radiation and hydrolysis, a fundamental action to preserve life in the Precambrian where high UV radiation prevailed. Minerals not only favored the origin of life but also became part of the organisms that inhabit the Earth, including species of the five kingdoms, comprising from microorganisms to higher organisms. How minerals participated in the origin of life still has unresolved questions, for which to understand the minerals’ participation since the formation of the Earth until becoming part of the structure of organisms from the five kingdoms, we reviewed the following topics, which will contribute to the understanding of the implication of minerals in the origin of our planet and life on it: i) the synthesis of the chemical elements from which the first mineral were obtained in the Earth, ii) the factor that favored the formation of minerals in the Earth, iii) the implication of minerals as the basis for the synthesis of the first biomolecule and, eventually, the pioneer organism, as well as the biomineralization mechanism that has been proposed to account for the mineral part contained in the structure of the organisms from the different kingdoms, and iv) the models that allow emulating the mechanisms by which minerals participated in the synthesis of the first biomolecule; in this way, for example, the Precambrian microfossils are so simple morphologically (spheres, subspheres, and hemispheres) that they can easily be imitated by hollow mineral growths, known as biomorphs. Although these can interfere with the study of actual microfossils, they remain as key points for the study of the origin of life.
We show that a chemical garden can be developed from an alkaline metal precipitate using a flow-driven setup. By injecting sodium phosphate solution into lithium chloride solution from below, a liquid jet appears, on which a precipitate grows forming a structure resembling a hydrothermal vent. The precipitate column continuously builds upward until a maximum height is reached. The vertical growth then significantly slows down while the tube diameter still increases. The analysis of the growth profiles has revealed a linear dependence of volume growth rate on the injection rate, hence yielding a universal growth profile. The expansion in diameter, localized at the tip of the structure, scales with a power law suggesting that the phenomenon is controlled by both diffusion and convection.
Biomorphs are polycrystalline assemblies that form when barium, silicate, and carbonate ions react in basic solutions. Their micrometer‐scale morphologies include leaf‐like sheets, helices, and cones, while their nanoscale architecture is based on co‐aligned witherite nanorods. We report a biomorph shape that resembles hair strands that smoothly curl into spirals or twisting fiber ribbons. They can thicken through continuous fractal‐like branching or abrupt events in which fibers split simultaneously. Raman and energy dispersive X‐ray spectroscopy as well as optical polarization microscopy reveal that their composition is very similar to classical biomorphs. They are most abundant in the absence of glass substrates and at high pH values. However, if a glass surface is covered by a thin SU‐8 resin layer, their growth is observed and photolithographically produced SU‐8 posts serve as nucleation sites. The hair‐like structures can detach resin posts from the glass surface and reposition them due to continued growth at the hair‐resin interface. Collisions of growing biomorph sheets with SU‐8 posts result in overgrowth or a sheet‐to‐hair transition.
Saturn's satellite Enceladus is proposed to have a soda‐type subsurface ocean with temperature able to support life and an iron ore‐based core. Here, it was demonstrated that ocean chemistry related to Enceladus can support the development of Fe‐based hydrothermal vents, one of the places suggested to be the cradle of life. The Fe‐based chemical gardens were characterized with Fourier‐transform (FT)IR spectroscopy and XRD. The developed chemobrionic structures catalyzed the condensation polymerization of simple organic prebiotic molecules to kerogens. Further, they could passively catalyze the condensation of the prebiotic molecule formamide to larger polymers, suggesting that elementary biochemical precursors could have emerged in Enceladus. Geo‐to‐bio‐chemistry in Enceladus? The conditions in Enceladus moon favor the formation of hydrothermal vents that in turn can act as catalysts to condensate and polymerize simple prebiotic molecules.
Nature has endowed extraordinary beauty and functional significance in the form of biological morphology. Inspired by nature, biomorphic superstructures have been designed and synthesized from organic precursors in a laboratory. Although the complexity of synthetic superstructures is lower compared to natural forms, from an engineering point of view they possess competitive advantages such as low cost, ease of fabrication, and, occasionally, unexpected characteristics. Thus, there are still plenty of excitingly biomorphic superstructures waiting to be discovered. Biomorphic rendition: Nature has endowed extraordinary beauty and functional significance in the form of biological morphology. Aiming for expressing nature in a synthetic manner, materials scientists and engineers have designed varieties of biomorphic superstructures from organic precursors.
Knowledge detailing human pre-gastrulation embryonic development including spatial self-organization and cell type ontogeny remains limited by available two-dimensional technological platforms1,2 that do not recapitulate the in vivo condition3-5. Here, we report a three-dimensional (3D) blastocyst-culture system, which enables human blastocyst development through primitive streak anlage (PSA). These 3D embryos mimic in vivo developmental landmarks and 3D architectures, including embryonic disc, amnion, basement membrane, primary and primate unique secondary yolk sac, anterior-posterior polarity formation and PSA. Using single-cell transcriptome profiling, we delineate ontology and regulatory networks underlying epiblast, primitive endoderm and trophoblast segregation. Compared to epiblast, the amniotic epithelium shows unique and characteristic phenotypes. After implantation, specific pathways and transcription factors trigger differentiation of cytotrophoblasts, extravillous cytotrophoblasts and syncytiotrophoblasts. Epiblasts undergo pluripotency transition upon implantation and maintain its transcriptome until PSA generation driven by different pluripotent factors. Using our 3D-culture approach, our findings elucidate the molecular and morphogenetic developmental landscape during human embryogenesis.
Two processes required for life's origin are condensation reactions that produce essential biopolymers by a nonenzymatic reaction, and self-assembly of membranous compartments that encapsulate the polymers into populations of protocells. Because life today thrives not just in the temperate ocean and lakes but also in extreme conditions of temperature, salinity, and pH, there is a general assumption that any form of liquid water would be sufficient to support the origin of life as long as there are sources of chemical energy and simple organic compounds. We argue here that the first forms of life would be physically and chemically fragile and would be strongly affected by ionic solutes and pH. A hypothesis emerges from this statement that hot springs associated with volcanic land masses have an ionic composition more conducive to self-assembly and polymerization than seawater. Here we have compared the ionic solutes of seawater with those of terrestrial hot springs. We then describe preliminary experimental results that show how the hypothesis can be tested in a prebiotic analog environment.
This report reviews how terrestrial hot spring systems can sustain diverse and abundant microbial communities and preserve their fossil records. Hot springs are dependable water sources, even in arid environments. They deliver reduced chemical species and other solutes to more oxidized surface environments, thereby providing redox energy and nutrients. Spring waters have diverse chemical compositions, and their outflows create thermal gradients and chemical precipitates that sustain diverse microbial communities and entomb their remnants. These environments probably were important habitats for ancient benthic microbial ecosystems, and it has even been postulated that life arose in hydrothermal systems. Thermal spring communities are fossilized in deposits of travertine, siliceous sinter, and iron minerals (among others) that are found throughout the geological record back to the oldest known well-preserved rocks at 3.48 Ga. Very few are known before the Cenozoic, but it is likely that there are many more to be found. They preserve fossils ranging from microbes to trees and macroscopic animals. Features on Mars whose morphological and spectroscopic attributes resemble spring deposits on Earth have been detected in regions where geologic context is consistent with the presence of thermal springs. Such features represent targets in the search for evidence of past life on that planet.
The condensation of formamide has been shown to be a robust chemical pathway affording molecules necessary for the origin of life. It has been experimentally demonstrated that condensation reactions of formamide are catalyzed by a number of minerals, including silicates, phosphates, sulfides, zirconia and borates, and by cosmic dusts and meteorites. However, a critical discussion of the catalytic power of the tested minerals, and the geochemical conditions under which the condensation would occur, is still missing. We show here that mineral self‐assembled structures forming under alkaline silica‐rich solutions are excellent catalysts for the condensation of formamide as compared to other minerals. We also propose that these structures were likely forming as early as 4.4 billion years ago when the whole Earth surface was a reactor, a global scale factory, releasing large amounts of organic compounds. Our experimental results suggest that the conditions required for the synthesis of the molecular bricks from which life self‐assembles, rather than being local and bizarre, appears to be universal and geologically rather conventional.
Layered transition metal sulfides (LTMSs) have tremendous commercial potential in anode materials for sodium‐ion batteries (SIBs) in large‐scale energy storage application. However, it is a great challenge for most LTMS electrodes to have long cycling life and high‐rate capability due to their larger volume expansion and the formation of soluble polysulfide intermediates caused by the conversion reaction. Herein, layered CuS microspheres with tunable interlayer space and pore volumes are reported through a cost‐effective interaction method using a cationic surfactant of cetyltrimethyl ammonium bromide (CTAB). The CuS–CTAB microsphere as an anode for SIBs reveals a high reversible capacity of 684.6 mAh g−1 at 0.1 A g−1, and 312.5 mAh g−1 at 10 A g−1 after 1000 cycles with high capacity retention of 90.6%. The excellent electrochemical performance is attributed to the unique structure of this material, and a high pseudocapacitive contribution ensures its high‐rate performance. Moreover, in situ X‐ray diffraction is applied to investigate their sodium storage mechanism. It is found that the long chain CTAB in the CuS provides buffer space, traps polysulfides, and restrains the further growth of Cu particles during the conversion reaction process that ensure the long cycling stability and high reversibility of the electrode material. Layered CuS–cetyltrimethyl ammonium bromide (CTAB) microspheres with tunable interlayer space and pore volume are synthesized through a cost‐effective interaction method with a cationic surfactant of CTAB. The CTAB layer in the interlayer space of CuS provides buffer space, traps polysulfides, and limits the size of generated Cu particles that ensure the long cycling stability.
How and where did life on Earth originate? To date, various environments have been proposed as plausible sites for the origin of life. However, discussions have focused on a limited stage of chemical evolution, or emergence of a specific chemical function of proto-biological systems. It remains unclear what geochemical situations could drive all the stages of chemical evolution, ranging from condensation of simple inorganic compounds to the emergence of self-sustaining systems that were evolvable into modern biological ones. In this review, we summarize reported experimental and theoretical findings for prebiotic chemistry relevant to this topic, including availability of biologically essential elements (N and P) on the Hadean Earth, abiotic synthesis of life's building blocks (amino acids, peptides, ribose, nucleobases, fatty acids, nucleotides, and oligonucleotides), their polymerizations to bio-macromolecules (peptides and oligonucleotides), and emergence of biological functions of replication and compartmentalization. It is indicated from the overviews that completion of the chemical evolution requires at least eight reaction conditions of (1) reductive gas phase, (2) alkaline pH, (3) freezing temperature, (4) fresh water, (5) dry/dry-wet cycle, (6) coupling with high energy reactions, (7) heating-cooling cycle in water, and (8) extraterrestrial input of life's building blocks and reactive nutrients. The necessity of these mutually exclusive conditions clearly indicates that life's origin did not occur at a single setting; rather, it required highly diverse and dynamic environments that were connected with each other to allow intra-transportation of reaction products and reactants through fluid circulation. Future experimental research that mimics the conditions of the proposed model are expected to provide further constraints on the processes and mechanisms for the origin of life. © 2017 China University of Geosciences (Beijing) and Peking University.
Purely inorganic reactions of silica, metal carbonates, and metal hydroxides can produce self-organized complex structures that mimic the texture of biominerals, the morphology of primitive organisms, and that catalyze prebiotic reactions. To date, these fascinating structures have only been synthesized using model solutions. We report that mineral self-assembly can be also obtained from natural alkaline silica-rich water deriving from serpentinization. Specifically, we demonstrate three main types of mineral self-assembly: (i) nanocrystalline biomorphs of barium carbonate and silica, (ii) mesocrystals and crystal aggregates of calcium carbonate with complex biomimetic textures, and (iii) osmosis-driven metal silicate hydrate membranes that form compartmentalized, hollow structures. Our results suggest that silica-induced mineral self-assembly could have been a common phenomenon in alkaline environments of early Earth and Earth-like planets.
Far from the thermodynamic equilibrium, many precipitation reactions create complex product structures with fascinating features caused by their unusual origins. Unlike the dissipative patterns in other self-organizing reactions, these features can be permanent, suggesting potential applications in materials science and engineering. We review four distinct classes of precipitation reactions, describe similarities and differences, and discuss related challenges for theoretical studies. These classes are hollow micro- and macrotubes in chemical gardens, polycrystalline silica carbonate aggregates (biomorphs), Liesegang bands, and propagating precipitation-dissolution fronts. In many cases, these systems show intricate structural hierarchies that span from the nanometer scale into the macroscopic world. We summarize recent experimental progress that often involves growth under tightly regulated conditions by means of wet stamping, holographic heating, and controlled electric, magnetic, or pH perturbations. In this research field, progress requires mechanistic insights that cannot be derived from experiments alone. We discuss how mesoscopic aspects of the product structures can be modeled by reaction-transport equations and suggest important targets for future studies that should also include materials features at the nanoscale.
Artificial cells have attracted much attention as substitutes for natural cells. There are many different forms of artificial cells with many different definitions. They can be integral biological cell imitators with cell-like structures and exhibit some of the key characteristics of living cells. Alternatively, they can be engineered materials that only mimic some of the properties of cells, such as surface characteristics, shapes, morphology, or a few specific functions. These artificial cells can have applications in many fields from medicine to environment, and may be useful in constructing the theory of the origin of life. However, even the simplest unicellular organisms are extremely complex and synthesis of living artificial cells from inanimate components seems very daunting. Nevertheless, recent progress in the formulation of artificial cells ranging from simple protocells and synthetic cells to cell-mimic particles, suggests that the construction of living life is now not an unrealistic goal. This review aims to provide a comprehensive summary of the latest developments in the construction and application of artificial cells, as well as highlight the current problems, limitations, challenges and opportunities in this field.
Designing and building a minimal genome
A goal in biology is to understand the molecular and biological function of every gene in a cell. One way to approach this is to build a minimal genome that includes only the genes essential for life. In 2010, a 1079-kb genome based on the genome of Mycoplasma mycoides (JCV-syn1.0) was chemically synthesized and supported cell growth when transplanted into cytoplasm. Hutchison III et al. used a design, build, and test cycle to reduce this genome to 531 kb (473 genes). The resulting JCV-syn3.0 retains genes involved in key processes such as transcription and translation, but also contains 149 genes of unknown function.
Science , this issue p. 10.1126/science.aad6253
Herein, we show it is possible to produce wholly inorganic chemical gardens from a cationic polyoxometalate (POM) seed in an anionic POM solution, demonstrating a wholly POM-based chemical garden system that produces architectures over a wide concentration range. Six concentration dependent growth regimes have been discovered and characterized: clouds, membranes, slugs, tubes, jetting and budding.
Chemical gardens in laboratory chemistries ranging from silicates to polyoxometalates, in applications ranging from corrosion products to the hydration of Portland cement, and in natural settings ranging from hydrothermal vents in the ocean depths to brinicles beneath sea ice. In many chemical-garden experiments, the structure forms as a solid seed of a soluble ionic compound dissolves in a solution containing another reactive ion. In general any alkali silicate solution can be used due to their high solubility at high pH. The cation should not precipitate with the counterion of the metal salt used as seed. A main property of seed chemical-garden experiments is that initially, when the fluid is not moving under buoyancy or osmosis, the delivery of the inner reactant is diffusion controlled. Another experimental technique that isolates one aspect of chemical-garden formation is to produce precipitation membranes between different aqueous solutions by introducing the two solutions on either side of an inert carrier matrix. Chemical gardens may be grown upon injection of solutions into a so-called Hele-Shaw cell, a quasi-two-dimensional reactor consisting in two parallel plates separated by a small gap.
We report the spontaneous and rapid growth of micrometre-scale tubes from crystals of a metal oxide-based inorganic solid when they are immersed in an aqueous solution containing a low concentration of an organic cation. A membrane immediately forms around the crystal, and this membrane then forms micrometre-scale tubes that grow with vast aspect ratios at controllable rates along the surface on which the crystal is placed. The tubes are composed of an amorphous mixture of polyoxometalate-based anions and organic cations. It is possible for liquid to flow through the tubes, and for the direction of growth and the overall tube diameter to be controlled. We demonstrate that tube growth is driven by osmotic pressure within the membrane sack around the crystal, which ruptures to release the pressure. These robust, self-growing, micrometre-scale tubes offer opportunities in many areas, including the growth of microfluidic devices and the self-assembly of metal oxide-based semipermeable membranes for diverse applications.
The precipitation of barium or strontium carbonates in alkaline silica-rich environments leads to crystalline aggregates that have been named silica/carbonate biomorphs because their morphology resembles that of primitive organisms. These aggregates are self-assembled materials of purely inorganic origin, with an amorphous phase of silica intimately intertwined with a carbonate nanocrystalline phase. We propose a mechanism that explains all the morphologies described for biomorphs. Chemically coupled coprecipitation of carbonate and silica leads to fibrillation of the growing front and to laminar structures that experience curling at their growing rim. These curls propagate in a surflike way along the rim of the laminae. We show that all observed morphologies with smoothly varying positive or negative Gaussian curvatures can be explained by the combined growth of counterpropagating curls and growing laminae.
This paper deals with the difficulty of decoding the origins of natural structures through the study of their morphological features. We focus on the case of primitive life detection, where it is clear that the principles of comparative anatomy cannot be applied. A range of inorganic processes are described that result in morphologies emulating biological shapes, with particular emphasis on geochemically plausible processes. In particular, the formation of inorganic biomorphs in alkaline silica-rich environments are described in detail.
We have synthesized inorganic micron-sized filaments, whose microstucture consists of silica-coated nanometer-sized carbonate
crystals, arranged with strong orientational order. They exhibit noncrystallographic, curved, helical morphologies, reminiscent
of biological forms. The filaments are similar to supposed cyanobacterial microfossils from the Precambrian Warrawoona chert
formation in Western Australia, reputed to be the oldest terrestrial microfossils. Simple organic hydrocarbons, whose sources
may also be abiotic and indeed inorganic, readily condense onto these filaments and subsequently polymerize under gentle heating
to yield kerogenous products. Our results demonstrate that abiotic and morphologically complex microstructures that are identical
to currently accepted biogenic materials can be synthesized inorganically.
In 1936 a German chemist identified certain organic molecules that he had extracted from ancient rocks and oils as the fossil remains of chlorophyll--presumably from plants that had lived and died millions of years in the past. It was another twenty-five years before this insight was developed and the term "biomarker" coined to describe fossil molecules whose molecular structures could reveal the presence of otherwise elusive organisms and processes. Echoes of Life is the story of these molecules and how they are illuminating the history of the earth and its life. It is also the story of how a few maverick organic chemists and geologists defied the dictates of their disciplines and--at a time when the natural sciences were fragmenting into ever-more-specialized sub-disciplines--reunited chemistry, biology and geology in a common endeavor. The rare combination of rigorous science and literary style--woven into a historic narrative that moves naturally from the simple to the complex--make Echoes of Life a book to be read for pleasure and contemplation, as well as education.
Order in the cytoplasm
Extracts of the very large eggs of the African clawed frog, Xenopus laevis , have proven a valuable model system for the study of cell division. Cheng and Ferrell found that after homogenization, such cytoplasm can reorganize back into cell-like structures and undergo multiple rounds of division (see the Perspective by Mitchison and Field). This reorganization apparently occurs without the usual factors that are known to lead to such structural changes during cell division, such as F-actin, myosin II, various individual kinesins, aurora kinase A, or DNA. What is required is energy from adenosine triphosphate, microtubule polymerization, cytoplasmic dynein activity, and a specific kinase-involved cell cycle progression. Nongenetic information in the cytoplasm is apparently sufficient for basic spatial organization of the cell.
Science , this issue p. 631 ; see also p. 569
Bottom‐up synthetic biology uses both biological and artificial chemical building blocks to create biomimetic systems, including artificial cells. Existing and new technologies such as microfluidics are being developed and applied to the assembly processes. In this special issue, experts present and review the latest progress in this rapidly expanding and diverse field.
Earth has been habitable for 4.3 billion years, and the earliest rock record indicates the presence of a microbial biosphere by at least 3.4 billion years ago—and disputably earlier. Possible traces of life can be morphological or chemical but abiotic processes that mimic or alter them, or subsequent contamination, may challenge their interpretation. Advances in micro- and nanoscale analyses, as well as experimental approaches, are improving the characterization of these biosignatures and constraining abiotic processes, when combined with the geological context. Reassessing the evidence of early life is challenging, but essential and timely in the quest to understand the origin and evolution of life, both on Earth and beyond. Abiotic processes can mimic or alter the biogenic traces of early life but advances in micro- and nanoscale analyses provide evidence that—with geological contextualization—improves our ability to address this issue.
The Precambrian era is associated with the origin of life on primitive Earth. It was, in fact, in that era that ribonucleic acid (RNA) was first acquired. From this, evolved the genomic deoxyribonucleic acid (DNA) that later on generated the biomolecules that formed the first cell. In this way, with the ongoing changes in environmental factors, the first cells evolved to give rise to higher multicellular organisms, i.e., plants and animals. Radiolarians and diatoms are organisms that have been conserved since the Precambrian era. However, although these organisms are alive (that can be considered as living fossils), they do not suffice to explain the origin of life. To understand the origin of life, the interactions among inorganic compounds that existed in the Precambrian era must be elucidated. In this context, calcium, barium or strontium silico-carbonates (usually called silica-biomorphs) have been simply named biomorphs that emulate the morphologies of organisms, like flowers, leaves, stems, helices, worms, radiolarians, diatoms, among others. The shapes of the biomorphs can be implicated in the origin of life due to their similarity with the shapes of the cherts of the Precambrian era. However, biomorphs are inorganic compounds that do not contain any organic biomolecule such as nucleic acids or proteins inside their chemical structure. The aim of the present work was to synthesize calcium, barium, or strontium silica biomorphs in the presence of nucleic acids: genomic DNA (linear double helices), plasmid DNA (circular helices), and RNA (a single chain helix). The morphology of these biomorphs was assessed through scanning electron microscopy (SEM). The obtained microphotographs revealed that nucleic acids direct the synthesis of biomorphs toward a unique and specific structure for each of these biomolecules. The chemical composition and the crystalline structure were determined through micro-Raman spectroscopy and X-ray diffraction to characterize the most characteristic crystalline phases. The biomorphs obtained from calcium, barium, or strontium corresponded to crystalline structures of CaCO3 (calcite, aragonite, vaterite), BaCO3 (witherite), or SrCO3 (strontianite), respectively. These silica-carbonates (considered as reminiscence of the shape found in the cherts of the Precambrian) can be a linking point between the Precambrian era and the subsequent eras. To the best of our knowledge, this is the first report in which the interaction of nucleic acids in the synthesis of biomorphs has been evaluated.
Built from the bottom up, synthetic cells and other creations are starting to come together and could soon test the boundaries of life. Built from the bottom up, synthetic cells and other creations are starting to come together and could soon test the boundaries of life.
The sequence of events that gave rise to the first life on our planet took place in the Earth's deep past, seemingly forever beyond our reach. Perhaps for that very reason the idea of reconstructing our ancient story is tantalizing, almost irresistible. Understanding the processes that led to synthesis of the chemical building blocks of biology and the ways in which these molecules self-assembled into cells that could grow, divide and evolve, nurtured by a rich and complex environment, seems at times insurmountably difficult. And yet, to my own surprise, simple experiments have revealed robust processes that could have driven the growth and division of primitive cell membranes. The nonenzymatic replication of RNA is more complicated and less well understood, but here too significant progress has come from surprising developments. Even our efforts to combine replicating compartments and genetic materials into a full protocell model have moved forward in unexpected ways. Fortunately, many challenges remain before we will be close to a full understanding of the origin of life, so the future of research in this field is brighter than ever!
The sequence of events that gave rise to the first life on our planet took place in the Earth's deep past, seemingly forever beyond our reach. Perhaps for that very reason the idea of reconstructing our ancient story is tantalizing, almost irresistible. Understanding the processes that led to synthesis of the chemical building blocks of biology and the ways in which these molecules self-assembled into cells that could grow, divide and evolve, nurtured by a rich and complex environment, seems at times insurmountably difficult. And yet, to my own surprise, simple experiments have revealed robust processes that could have driven the growth and division of primitive cell membranes. The nonenzymatic replication of RNA is more complicated and less well understood, but here too significant progress has come from surprising developments. Even our efforts to combine replicating compartments and genetic materials into a full protocell model have moved forward in unexpected ways. Fortunately, many challenges remain before we will be close to a full understanding of the origin of life, so the future of research in this field is brighter than ever!
Controlled self-assembly of three-dimensional shapes holds great potential for fabrication of functional materials. Their practical realization requires a theoretical framework to quantify and guide the dynamic sculpting of the curved structures that often arise in accretive mineralization. Motivated by a variety of bioinspired coprecipitation patterns of carbonate and silica, we develop a geometrical theory for the kinetics of the growth front that leaves behind thin-walled complex structures. Our theory explains the range of previously observed experimental patterns and, in addition, predicts unexplored assembly pathways. This allows us to design a number of functional base shapes of optical microstructures, which we synthesize to demonstrate their light-guiding capabilities. Overall, our framework provides a way to understand and control the growth and form of functional precipitating microsculptures.
A chemical garden based on iron salt that grows in organic solvents and ions, is demonstrated for the first time. This prototype chemical garden develops in an inverted orientation, thus providing evidence that downward growth is feasible.
It is suggested that a system of chemical substances, called morphogens, reacting together and diffusing through a tissue, is adequate to account for the main phenomena of morphogenesis. Such a system, although it may originally be quite homogeneous, may later develop a pattern or structure due to an instability of the homogeneous equilibrium, which is triggered off by random disturbances. Such reaction-diffusion systems are considered in some detail in the case of an isolated ring of cells, a mathematically convenient, though biologically unusual system. The investigation is chiefly concerned with the onset of instability. It is found that there are six essentially different forms which this may take. In the most interesting form stationary waves appear on the ring. It is suggested that this might account, for instance, for the tentacle patterns on Hydra and for whorled leaves. A system of reactions and diffusion on a sphere is also considered. Such a system appears to account for gastrulation. Another reaction system in two dimensions gives rise to patterns reminiscent of dappling. It is also suggested that stationary waves in two dimensions could account for the phenomena of phyllotaxis. The purpose of this paper is to discuss a possible mechanism by which the genes of a zygote may determine the anatomical structure of the resulting organism. The theory does not make any new hypotheses; it merely suggests that certain well-known physical laws are sufficient to account for many of the facts. The full understanding of the paper requires a good knowledge of mathematics, some biology, and some elementary chemistry. Since readers cannot be expected to be experts in all of these subjects, a number of elementary facts are explained, which can be found in text-books, but whose omission would make the paper difficult reading.
Synthetisches Leben: Die Fragen nach dem Ursprung des Lebens auf der Erde und dem Übergang von unbelebter Materie zu künstlichen lebenden Systemen bilden den Rahmen für die Entwicklung neuer chemischer Konzepte mit unabsehbarer technologischer Tragweite. Dieser Essay versucht, einige Aspekte dieser Fragen im Hinblick auf eine Protolebensforschung neu zu formulieren, wobei die Chemie eine zentrale Rolle spielt.
The complexity of even the simplest known life forms makes efforts to synthesize living cells from inanimate components seem like a daunting task. However, recent progress toward the creation of synthetic cells, ranging from simple protocells to artificial cells approaching the complexity of bacteria, suggests that the synthesis of life is now a realistic goal. Protocell research, fueled by advances in the biophysics of primitive membranes and the chemistry of nucleic acid replication, is providing new insights into the origin of cellular life. Parallel efforts to construct more complex artificial cells, incorporating translational machinery and protein enzymes, are providing information about the requirements for protein-based life. We discuss recent advances and remaining challenges in the synthesis of artificial cells, the possibility of creating new forms of life distinct from existing biology, and the promise of this research for gaining a deeper understanding of the nature of living systems. Expected final online publication date for the Annual Review of Biochemistry Volume 83 is June 02, 2014. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.
Silica–carbonate biomorphs are inorganic self-organized structures that mimic the morphology of living organisms. In this study, we present the effect that proteins involved in the in vivo biomineralization of silica and calcium carbonate have on the formation of silica–carbonate biomorphs. We tested four different sources of protein: (1) struthiocalcin-1, (2) the catalytic domain of silicatein-α of Tethya aurantia, (3) a protein extract obtained from the spicules of a vitreous sponge (Protosuberitis sp.), and (4) a protein extract obtained from the spines of the sea urchin Echinometra lucunter. In addition to the well-established role that pH plays in biomorph formation, all the proteins tested controlled the morphology of these aggregates. Biomorphs obtained in the presence of the catalytic domain of silicatein-α were similar in shape to those observed in the control though considerably smaller in size. Struthiocalcin-1 affected the availability of carbonate ions and completely inhibited the formation of biomorphs resulting only in worm-like aggregates. Finally, novel biomorphs with shapes such as twisting rods, sunflowers, and mitotic cells were obtained in the presence of protein extracts from the marine sponge spicules and sea urchin spines.
Chemische Reaktionen können Zellen nur am Leben erhalten, wenn die beteiligten Verbindungen an den erforderlichen Stellen zeitlich präzise angeliefert werden. Die meisten Forschungen haben sich bislang auf aktive Transportmechanismen konzentriert, obwohl die passive Diffusion oft gleich schnell ist und weniger Energie erfordert. Um die Vorteile dieser Transportform zu nutzen, haben die Zellen ausgeklügelte Reaktions-Diffusions(RD)-Systeme entwickelt, die zahlreiche zelluläre Funktionen kontrollieren – von Chemotaxis und Zellteilung über Signalkaskaden und -oszillationen bis hin zur Zellbeweglichkeit. Diese nur scheinbar unterschiedlichen Systeme sind nach allgemeinen Prinzipien aufgebaut und haben viele Gemeinsamkeiten. Wiederkehrende Elemente sind nichtlineare Kinetik, Autokatalyse und Rückkopplungsschleifen. Um die Funktion dieser komplexen (bio)chemischen Systeme zu verstehen, muss man die Transportkinetik-Gleichungen analysieren oder die charakteristischen Zeiten der Teilprozesse zumindest qualitativ betrachten. Während wir Beispiele für zelluläre RD-Systeme vorstellen, versuchen wir daher auch, den Leser mit den theoretischen Grundlagen der RD-Phänomene vertraut zu machen.
The emergence of complex nano- and microstructures is of fundamental interest, and the ability to program their form has practical
ramifications in fields such as optics, catalysis, and electronics. We developed carbonate-silica microstructures in a dynamic
reaction-diffusion system that allow us to rationally devise schemes for precisely sculpting a great variety of elementary
shapes by diffusion of carbon dioxide (CO2) in a solution of barium chloride and sodium metasilicate. We identify two distinct growth modes and show how continuous
and discrete modulations in CO2 concentration, pH, and temperature can be used to deterministically switch between different regimes and create a bouquet
of hierarchically assembled multiscale microstructures with unprecedented levels of complexity and precision. These results
outline a nanotechnology strategy for "collaborating" with self-assembly processes in real time to build arbitrary tectonic
architectures.
Synthetic life: The origin of life on the early Earth, and the ex novo transition of non-living matter to artificial living systems are deep scientific challenges that provide a context for the development of new chemistries with unknown technological consequences. This Essay attempts to re-frame some of the epistemological difficulties associated with these questions into an integrative framework of proto-life science. Chemistry is at the heart of this endeavour.
The seemingly innocent observation that the activities of organisms bring about changes in environments is so obvious that it seems an unlikely focus for a new line of thinking about evolution. Yet niche construction--as this process of organism-driven environmental modification is known--has hidden complexities. By transforming biotic and abiotic sources of natural selection in external environments, niche construction generates feedback in evolution on a scale hitherto underestimated--and in a manner that transforms the evolutionary dynamic. It also plays a critical role in ecology, supporting ecosystem engineering and influencing the flow of energy and nutrients through ecosystems. Despite this, niche construction has been given short shrift in theoretical biology, in part because it cannot be fully understood within the framework of standard evolutionary theory. Wedding evolution and ecology, this book extends evolutionary theory by formally including niche construction and ecological inheritance as additional evolutionary processes. The authors support their historic move with empirical data, theoretical population genetics, and conceptual models. They also describe new research methods capable of testing the theory. They demonstrate how their theory can resolve long-standing problems in ecology, particularly by advancing the sorely needed synthesis of ecology and evolution, and how it offers an evolutionary basis for the human sciences. Already hailed as a pioneering work by some of the world's most influential biologists, this is a rare, potentially field-changing contribution to the biological sciences.
Chemical gardens are the plant-like structures formed upon placing together a soluble metal salt, often in the form of a seed crystal, and an aqueous solution of one of many anions, often sodium silicate. We have observed the development of chemical gardens with Mach–Zehnder interferometry. We show that a combination of forced convection from osmosis and free convection from buoyancy, together with chemical reaction, is responsible for their morphogenesis.
Chemical reactions make cells work only if the participating chemicals are delivered to desired locations in a timely and precise fashion. Most research to date has focused on active-transport mechanisms, although passive diffusion is often equally rapid and energetically less costly. Capitalizing on these advantages, cells have developed sophisticated reaction-diffusion (RD) systems that control a wide range of cellular functions-from chemotaxis and cell division, through signaling cascades and oscillations, to cell motility. These apparently diverse systems share many common features and are "wired" according to "generic" motifs such as nonlinear kinetics, autocatalysis, and feedback loops. Understanding the operation of these complex (bio)chemical systems requires the analysis of pertinent transport-kinetic equations or, at least on a qualitative level, of the characteristic times of the constituent subprocesses. Therefore, in reviewing the manifestations of cellular RD, we also describe basic theory of reaction-diffusion phenomena.
355 p. «Le livre de François Jacob est la plus remarquable histoire de la biologie qui ait jamais été écrite. Elle invite aussi à un grand réapprentissage de la pensée.».
For more than 150 years natural selection has been perceived to be the overwhelming force in evolution. Only in recent decades have we obtained new insights into environmental and physicochemical factors that participate with selection in a synergic way. Far from denying Darwin's theory, such neglected factors put order to the bewildering range of genotypes and morphologies found in living organisms and, more importantly, they place evolution in a planetary context where biology, geology, and chemistry can easily be integrated.
Biomineralization is an inherently structural subject; the structure of the mineral phase, the structure of the matrix composed of macromolecules and especially the structure of the interphase zone between them. Studies of the dynamics of mineral formation have revealed that a widespread strategy used by many organisms is to first form a disordered mineral phase. Only when it is in place and has adopted its appropriate shape, is it induced to crystallize. Matrix studies have highlighted the importance of a unique group of proteins that are rich in aspartic acid. These are involved in controlling mineral formation. Relating structure to function in mineralized tissues, often involves an understanding of mechanical properties in terms of not only the hierarchical structure of the tissue, but also the graded structure that varies from one location to another. Structure is thus in many respects the foundation upon which the field of biomineralization rests.
- Bergson H.