Synthesis of life in the lab? Defining a protoliving system

Recognition of sounds by ensembles of proteinoids

Proteinoids are artificial polymers that imitate certain characteristics of natural proteins, including self-organization, catalytic activity, and responsiveness to external stimuli. This paper examines the acoustic response properties of proteinoids microspheres when exposed to auditory stimuli. We convert sounds of English alphabet into waveforms of electrical potential, feed the waveforms into proteinoid solutions and record electrical responses of the proteinoids. We also undertake a detailed comparison of proteinoids' electrical responses (frequencies, periods, and amplitudes) with original input signals. We found that responses of proteinoids are less regular, lower dominant frequency, wider distribution of proteinoids and less skewed distribution of amplitudes compared with input signals. We found that resonant acoustic excitation of proteinoids generates unique electrical impulse patterns dependent on sound frequency and amplitude. The finding will be used in further designs of organic electronic devices, based on ensembles of proteinoids, for sound processing and speech recognition. Our findings provide the first quantitative investigation into the potential of thermal proteinoid microspheres for bio-inspired sound processing and recognition applications. Using controlled speaker excitation on proteinoid samples, we create reliable markers of productive acoustic response capacities, paving the way for future advancement.

Serial Endosymbiosis Theory: From biology to astronomy and back to the origin of life

Serial Endosymbiosis Theory, or SET, was conceived and developed by Lynn Margulis, to explain the greatest discontinuity in the history of life, the origin of eukaryotic cells. Some predictions of SET, namely the origin of mitochondria and chloroplasts, withstood the test of the most recent evidence from a variety of disciplines including phylogenetics, biochemistry, and cell biology. Even though some other predictions fared less well, SET remains a seminal theory in biology. In this paper, I focus on two aspects of SET. First, using the concept of "universal symbiogenesis", developed by Freeman Dyson to search for commonalities in astronomy and biology, I propose that SET can be extended beyond eukaryogenesis. The extension refers to the possibility that even prokaryotic organisms, themselves subject to the process of symbiogenesis in SET, could have emerged symbiotically. Second, I contrast a recent "viral eukaryogenesis" hypothesis, according to which the nucleus evolved from a complex DNA virus, with a view closer to SET, according to which the nucleus evolved through the interplay of the archaeal host, the eubacterial symbiont, and a non-LTR transposon, or telomerase. Viruses joined in later, through the process of viral endogenization, to shape eukaryotic chromosomes in the process of karyotype evolution. These two proposals based on SET are a testament to its longevity as a scientific theory.

Mineral self-organization on a lifeless planet

It has been experimentally demonstrated that, under alkaline conditions, silica is able to induce the formation of mineral self-assembled inorganic-inorganic composite materials similar in morphology, texture and nanostructure to the hybrid biomineral structures that, millions of years later, life was able to self-organize. These mineral self-organized structures (MISOS) have been also shown to work as effective catalysts for prebiotic chemical reactions and to easily create compartmentalization within the solutions where they form. We reason that, during the very earliest history of this planet, there was a geochemical scenario that inevitably led to the existence of a large-scale factory of simple and complex organic compounds, many of which were relevant to prebiotic chemistry. The factory was built on a silica-rich high-pH ocean and powered by two main factors: a) a quasi-infinite source of simple carbon molecules synthesized abiotically from reactions associated with serpentinization, or transported from meteorites and produced from their impact on that alkaline ocean, and b) the formation of self-organized silica-metal mineral composites that catalyze the condensation of simple molecules in a methane-rich reduced atmosphere. We discuss the plausibility of this geochemical scenario, review the details of the formation of MISOS and its catalytic properties and the transition towards a slightly alkaline to neutral ocean.

Cell theory, intrinsically disordered proteins, and the physics of the origin of life

Cell theory, as formulated by Theodor Schwann in 1839, introduced the idea that the cell is the main structural unit of living nature. Later, in solving the problem of cell multiplication, Rudolf Virchow expanded the cell theory with a postulate: all cells only arise from pre-existing cells. But what did the very first cell arise from? This paper proposes extending the Virchow's law by the assumption that between the nonliving protocell and the first living cell the continuity of fundamental physical properties (the principle of invariance of physical properties) is preserved. The protocell is understood here as a cell-shaped physical system on the basis of the self-organized biologically significant prebiotic macromolecules, primarily peptides, having a potential to transform into the living cell. Biophase is considered as the physical basis of the membraneless protocell, the internal environment of which is separated from the external environment due to the phase of adsorbed water. The evidence is given that the first protocells may have been formed on the basis of intrinsically disordered peptides. Data on the similarity of the physical properties of living cells and the following model systems are given: protein and artificial polymer solutions, coacervate droplets, and ion-exchange resin granules. Available data on the similarity of the physical properties of cell models and living cells allow us to rephrase the Virchow's postulate as follows: the physical properties of a living cell could only arise from pre-existing physical properties of the protocell.

Enhanced catalytic activity from proteinoid microspheres

Creating materials that are capable of catalyzing enzymatic reactions could be important to the treatment of both acute and chronic wounds, as well as other topical diseases. As a first step in the design of catalytic biomaterials, a new class of proteinoid microsphere (PM), that includes amino acids found in phosphatase enzyme active sites, has been constructed. This material can significantly enhance catalytic activity for phosphoester hydrolysis, with observed specific activity increases between 35- and 55-fold. Further specific activity increases occur when metal cations, notably iron or zinc, are added to the PMs. Specific activity increases between 140- and 300-fold for these metal modified systems are measured. The phosphatase activity increase is demonstrated for both aromatic phosphate esters as well as the high-energy phosphate bond of adenosine triphosphate. PMs bind substrate heterogeneously on their surfaces in an enthalpically driven reaction that is defined by an overall favorable free energy, but unfavorable entropy. The catalytic PMs have been successfully blended with polyolefin foam and extruded with PLA. These materials remain fully active.

Information about the synthesis of life forms: a document‐oriented approach

Purpose

This study aims to examine the forms of information about the synthesis of life forms in the public sphere.

Design/methodology/approach

A document‐oriented approach was used and a wide range of documents that discuss a particular technoscientific issue was sampled. The analysis of documents involved a combination of discourse and content analysis.

Findings

The study demonstrates that there is a significant growth of the diversity of document types over time. Overall, 24 document types and 21 publication formats were identified. Web‐based formats, such as blogs and news and information web sites, play a prominent role in the dissemination of information about the synthesis of life forms.

Research limitations/implications

The variety of document types identified here expands current understanding of the public documentary landscape and shows that the analysis of technoscientific debates and controversies can no longer be limited to traditional mass media documents such as news, feature articles, and editorials. However, a larger sample that includes more documents as well as non‐textual objects, such as images or even lab specimens, would expand the scope of this taxonomy and make conclusions more definitive. Further research into the specific digital types of documents identified in the study and their impact on the communication of scientific information to the public is needed.

Practical implications

Surveying and understanding the kinds of documents that circulate information about emerging technoscientific issues can help to provide better services for a variety of information users and develop better tools for access and dissemination of such information.

Originality/value

The study demonstrates that a document‐oriented approach can provide valuable insight into the circulation of information about science in the public sphere. It also offers an elaborate taxonomy of documents that can be used in further research as well as in information and science literacy instruction.

Triggered release from peptide-proteinoid microspheres

Proteinoid microspheres (PM) are unusual polymers formed by the thermal condensation of amino acids. Although they have been studied for over 60 years, they are only now beginning to garner interest as controlled release agents. Although they are very biocompatible, it has been problematic to design useful triggers that release small molecules from PM interiors. This has severely limited their usefulness. In the present study, short peptides have been successfully incorporated into PMs during their formation. The resulting hybrid peptide-PMs can release their interior content when hydrolyzed by a proteinase. Specifically, if a matrix metalloproteinase (MMP) cleavage site peptide is incorporated into a PM, the peptide-PM will release interior contents only in the presence of the MMP recognizing the cleavage peptide. The release rate can be determined by the concentration of the peptide in the PM synthesis mixture. This potentially makes peptide-PMs useful for delivering inhibitors or drugs into acute and chronic wounds, periodontal disease sites, and other disease states involving the fine-tuned regulation of proteinases.

Triggered release of small molecules from proteinoid microspheres

Proteinoid microspheres (PM) are formed by the thermal condensation of amino acids. They have been useful to further evolutionary theory, as catalysts for some biochemical reactions, but they have not been overly useful as controlled delivery agents. It is possible however to construct PMs that contain organic small molecules in the interior space. This means that a PM could be used as a delivery agent, if a suitable method could be discovered to cause the release of the internal material. This report describes the formation of a PM that includes a molecular bridging agent that can be removed in a reducing environment. Removal of the bridge opens a hole or window in the PM that allows the interior material to escape. The rate at which the interior material is released from the PM can be controlled by the size of the window or by the reduction potential in the environment. These PMs can be used to temporally treat a variety of complications including wounds (chronic or acute) by delivering a sequestered reagent in a controlled manner and are advantageous in that amino acids are the primary delivery vehicle breakdown product.

Mutations and lethality in simulated prebiotic networks

The Graded Autocatalysis Replication Domain (GARD) model describes an origin of life scenario which involves non-covalent compositional assemblies, made of monomeric mutually catalytic molecules. GARD constitutes an alternative to informational biopolymers as a mechanism of primordial inheritance. In the present work, we examined the effect of mutations, one of the most fundamental mechanisms for evolution, in the context of the networks of mutual interaction within GARD prebiotic assemblies. We performed a systematic analysis analogous to single and double gene deletions within GARD. While most deletions have only a small effect on both growth rate and molecular composition of the assemblies, ~10% of the deletions caused lethality, or sometimes showed enhanced fitness. Analysis of 14 different network properties on 2,000 different GARD networks indicated that lethality usually takes place when the deleted node has a high molecular count, or when it is a catalyst for such node. A correlation was also found between lethality and node degree centrality, similar to what is seen in real biological networks. Addressing double knockout mutations, our results demonstrate the occurrence of both synthetic lethality and extragenic suppression within GARD networks, and convey an attempt to correlate synthetic lethality to network node-pair properties. The analyses presented help establish GARD as a workable alternative prebiotic scenario, suggesting that life may have begun with large molecular networks of low fidelity, that later underwent evolutionary compaction and fidelity augmentation.

Molecules, water, and radiant energy: new clues for the origin of life

We here examine the putative first step in the origin of life: the coalescence of dispersed molecules into a more condensed, organized state. Fresh evidence implies that the driving energy for this coalescence may come in a manner more direct than previously thought. The sun's radiant energy separates charge in water, and this free charge demonstrably induces condensation. This condensation mechanism puts water as a central protagonist in life rather than as an incidental participant, and thereby helps explain why life requires water.

Cave biosignature suites: microbes, minerals, and Mars

Earth's subsurface offers one of the best possible sites to search for microbial life and the characteristic lithologies that life leaves behind. The subterrain may be equally valuable for astrobiology. Where surface conditions are particularly hostile, like on Mars, the subsurface may offer the only habitat for extant lifeforms and access to recognizable biosignatures. We have identified numerous unequivocally biogenic macroscopic, microscopic, and chemical/geochemical cave biosignatures. However, to be especially useful for astrobiology, we are looking for suites of characteristics. Ideally, "biosignature suites" should be both macroscopically and microscopically detectable, independently verifiable by nonmorphological means, and as independent as possible of specific details of life chemistries--demanding (and sometimes conflicting) criteria. Working in fragile, legally protected environments, we developed noninvasive and minimal impact techniques for life and biosignature detection/characterization analogous to Planetary Protection Protocols. Our difficult field conditions have shared limitations common to extraterrestrial robotic and human missions. Thus, the cave/subsurface astrobiology model addresses the most important goals from both scientific and operational points of view. We present details of cave biosignature suites involving manganese and iron oxides, calcite, and sulfur minerals. Suites include morphological fossils, mineral-coated filaments, living microbial mats and preserved biofabrics, 13C and 34S values consistent with microbial metabolism, genetic data, unusual elemental abundances and ratios, and crystallographic mineral forms.

Composing life

Textbooks often assert that life began with specialized complex molecules, such as RNA, that are capable of making their own copies. This scenario has serious difficulties, but an alternative has remained elusive. Recent research and computer simulations have suggested that the first steps toward life may not have involved biopolymers. Rather, non-covalent protocellular assemblies, generated by catalyzed recruitment of diverse amphiphilic and hydrophobic compounds, could have constituted the first systems capable of information storage, inheritance and selection. A complex chain of evolutionary events, yet to be deciphered, could then have led to the common ancestors of today's free-living cells, and to the appearance of DNA, RNA and protein enzymes.

Effects of thermal peptides on retention of footshock avoidance training in mice

Some hydrophobic polypeptides known as thermal proteins have been found to have neurotrophic effects. Thermal proteins were synthesized from aspartic acid, glutamic acid, proline, and tryptophan. Two hydrophobic and one nonhydrophobic polymers were injected intracerebroventricularly into brains of mice after partial training on footshock avoidance run in a T-maze. When retention was tested 1 week later, the hydrophobic polymers enhanced retention while the nonhydrophobic polymer did not. Thermal proteins exhibiting hydrophobicity and having neurotrophic effects may aid in altering synaptic connections by facilitating cell recognition.