Origin of the cell: experiments and premises

Plausible Emergence and Self Assembly of a Primitive Phospholipid from Reduced Phosphorus on the Primordial Earth

How life arose on the primitive Earth is one of the biggest questions in science. Biomolecular emergence scenarios have proliferated in the literature but accounting for the ubiquity of oxidized (+ 5) phosphate (PO₄^3-) in extant biochemistries has been challenging due to the dearth of phosphate and molecular oxygen on the primordial Earth. A compelling body of work suggests that exogenous schreibersite ((Fe,Ni)₃P) was delivered to Earth via meteorite impacts during the Heavy Bombardment (ca. 4.1-3.8 Gya) and there converted to reduced P oxyanions (e.g., phosphite (HPO₃^2-) and hypophosphite (H₂PO₂^-)) and phosphonates. Inspired by this idea, we review the relevant literature to deduce a plausible reduced phospholipid analog of modern phosphatidylcholines that could have emerged in a primordial hydrothermal setting. A shallow alkaline lacustrine basin underlain by active hydrothermal fissures and meteoritic schreibersite-, clay-, and metal-enriched sediments is envisioned. The water column is laden with known and putative primordial hydrothermal reagents. Small system dimensions and thermal- and UV-driven evaporation further concentrate chemical precursors. We hypothesize that a reduced phospholipid arises from Fischer-Tropsch-type (FTT) production of a C8 alkanoic acid, which condenses with an organophosphinate (derived from schreibersite corrosion to hypophosphite with subsequent methylation/oxidation), to yield a reduced protophospholipid. This then condenses with an α-amino nitrile (derived from Strecker-type reactions) to form the polar head. Preliminary modeling results indicate that reduced phospholipids do not aggregate rapidly; however, single layer micelles are stable up to aggregates with approximately 100 molecules.

Lipids, membranes, colloids and cells: A long view

This paper revisits long-standing ideas about biological membranes in the context of an equally long-standing, but hitherto largely unappreciated, perspective of the cell based on concepts derived from the physics and chemistry of colloids. Specifically, we discuss important biophysical aspects of lipid supramolecular structure to understand how the intracellular milieu may constrain lipid self-assembly. To this end we will develop four lines of thought: first, we will look at the historical development of the current view of cellular structure and physiology, considering also the plurality of approaches that influenced its formative period. Second, we will review recent basic research on the structural and dynamical properties of lipid aggregates as well as the role of phase transitions in biophysical chemistry and cell biology. Third, we will present a general overview of contemporary studies into cellular compartmentalization in the context of a very rich and mostly forgotten general theory of cell physiology called the Association-Induction Hypothesis, which was developed around the time that the current view of cells congealed into its present form. Fourth, we will examine some recent developments in cellular studies, mostly from our laboratory, that raise interesting issues about the dynamical aspects of cell structure and compartmentalization. We will conclude by suggesting what we consider are relevant questions about the nature of cellular processes as emergent phenomena.

Early usage and meaning of evolvability

Evolvability has become an enormously popular concept in evolutionary biology and in machine learning software architecture. While it is claimed that the term was coined in 1988 by Richard Dawkins, it was used as early as 1931 as a characteristic of life by John A. Thomson. We quote and review the earliest uses and definitions of evolvability in biological frameworks up until 1989, which are remarkably few. The meaning changed from simply the "ability to evolve" as a characteristic of life to various versions of including necessary variation to predict whether or not something could evolve to the rate and quality of that evolution. Or, meaning changed from the ability to evolve to the "quality" of the ability to evolve. Since then, evolvability has taken on many definitions as it has exploded in usage.

Origins and emergent evolution of life: the colloid microsphere hypothesis revisited

Self-replicating molecules, in particular RNA, have long been assumed as key to origins of life on Earth. This notion, however, is not very secure since the reduction of life's complexity to self-replication alone relies on thermodynamically untenable assumptions. Alternative, earlier hypotheses about peptide-dominated colloid self-assembly should be revived. Such macromolecular conglomerates presumably existed in a dynamic equilibrium between confluent growth in sessile films and microspheres detached in turbulent suspension. The first organic syntheses may have been driven by mineral-assisted photoactivation at terrestrial geothermal fields, allowing photo-dependent heterotrophic origins of life. Inherently endowed with rudimentary catalyst activities, mineral-associated organic microstructures can have evolved adaptively toward cooperative 'protolife' communities, in which 'protoplasmic continuity' was maintained throughout a graded series of 'proto-biofilms', 'protoorganisms' and 'protocells' toward modern life. The proneness of organic microspheres to merge back into the bulk of sessile films by spontaneous fusion can have made large populations promiscuous from the beginning, which was important for the speed of collective evolution early on. In this protein-centered scenario, the emergent coevolution of uncoded peptides, metabolic cofactors and oligoribonucleotides was primarily optimized for system-supporting catalytic capabilities arising from nonribosomal peptide synthesis and nonreplicative ribonucleotide polymerization, which in turn incorporated other reactive micromolecular organics as vitamins and cofactors into composite macromolecular colloid films and microspheres. Template-dependent replication and gene-encoded protein synthesis emerged as secondary means for further optimization of overall efficieny later on. Eventually, Darwinian speciation of cell-like lineages commenced after minimal gene sets had been bundled in transmissible genomes from multigenomic protoorganisms.

The first cell membranes

Organic compounds are synthesized in the interstellar medium and can be delivered to planetary surfaces such as the early Earth, where they mix with endogenous species. Some of these compounds are amphiphilic, having polar and nonpolar groups on the same molecule. Amphiphilic compounds spontaneously self-assemble into more complex structures such as bimolecular layers, which in turn form closed membranous vesicles. The first forms of cellular life required self-assembled membranes that were likely to have been produced from amphiphilic compounds on the prebiotic Earth. Laboratory simulations show that such vesicles readily encapsulate functional macromolecules, including nucleic acids and polymerases. The goal of future investigations will be to fabricate artificial cells as models of the origin of life.

An organismic critique of molecular darwinism

The molecular darwinian approach to the emergence of life treats the competition between RNA sequences for nucleotide resources as the primordial selective process in prebiotic evolution, which prescribes possible pathways for the subsequent elaboration of organizational relationships. Since success in this competition is determined by the "phenotypic" properties of RNA strands in the absence of organizational context, the genesis of biotic organization is dependent upon the establishment of co-operative, hypercyclic interactions between competing RNA sequences. The thesis of this paper is that hypercycle theory is based on unwarranted assumptions about the conditions of prebiotic evolution, and that the implications of these assumptions run counter to both empirical evidence and to the rational by which natural selection operates in evolution generally. An organismic alternative to hypercycle theory is suggested, based on the catalytic microsphere and the thermodynamics of selection.

A possible energetic role of mineral surfaces in chemical evolution

The postulated roles of clays and other minerals in chemical evolution and the origin of life are reconsidered in terms of the interaction of these minerals with penetrating sources of energy such as ionizing radiation and mechanical stress. This interaction, including such facets as excitation, degradation, storage, and transfer, is considered here with regard to its profound potential for altering the capabilities of minerals to serve both as substrates for prebiological chemistry and as inorganic prototypic life forms. The interaction of minerals and energy in relationship to surface chemistry is discussed in terms of the spectroscopic properties of minerals, the interaction of energy with condensed phases, some commonly accepted concepts of heterogeneous catalysis in the absence of electronic energy inputs, and some commonly accepted and novel means by which surface activity might be enhanced in the presence of energy inputs. An estimation is made of the potential contribution of two poorly characterized prebiotic energy sources, natural radioactive decay and triboelectric energy. These estimates place a conservative lower limit on their prebiotic abundance. Also some special properties of these energy sources, relative to solar energy, are pointed out which might give them particular suitability for driving reactions occurring under geological conditions. Skeletal support for this broadly defined framework of demonstrated and potential relationships between minerals, electronic excitation, and surface reactivity, as applied to chemical evolution, is provided from the results of our studies on 1/1 clays. We have discovered and partially characterized a number of novel luminescent properties of these clays, that indicate energy storage and transfer processes in clays. These luminescent properties are interpreted in relationship to the electron spin resonance phenomena, to provide a basis for estimating the potential significance of energy storage and transduction in monitoring or driving clay surface chemistry. Consideration of the electronic structure of abundant minerals in terms of band theory and localized defect centers provides a predictive theoretical framework from which to rationalize the capacity of these materials to store and transduce energy. The bulk crystal is seen as a collecting antenna for electronic energy, with the defect centers serving as storage sites. The clay properties produced by isomorphic substitution appear to be intimately associated with all of the life-mimetic chemical processes that have been attributed to clays.(ABSTRACT TRUNCATED AT 400 WORDS)

Thermosynthesis by biomembranes: energy gain from cyclic temperature changes

A theoretical mechanism is described allowing biomembranes to convert heat into electrical energy during temperature cycling (thermosynthesis). Necessary conditions for thermosynthesis are a temperature dependent electrical capacity and a conductivity as low as that of artificial lipid bilayers. Temperature cycling, and consequently thermosynthesis, can take place in leaves during cyclic transpiration and in organisms in natural waters that are carried along by convection currents. Electrogenic ATPases can convert the electrical energy gained by thermosynthesis into ATP if their activity and stoichiometry are properly regulated. The power of thermosynthesis is discussed and its possible value compared with the power of respiration. Environments where thermosynthesis may occur are listed. Thermosynthesis is a plausible energy source for the first living organisms.

Present state of the coacervate-in-coacervate theory; origin and evolution of cell structure

In agreement with the views of Oparin, Fox, Dose etc., the theory assumes that coacervation of protein-like polyaminoacids began with their accumulation along the coasts of the Archaic water basins. Unlike the above authors, however, the present author views the original coacervates as a suitable "culture medium" from which the first polynucleotides originated and their partial replication started. Their base sequence was not fortuitous, but determined by the proteinoids on the basis of their mutual affinity. The polyfunctional enzymic activity of the proteinoids catalyzed their replication as well as other activities. Around the replicating DNA molecules secondary coacervates (coacervates in coacervates) accumulated which developed gradually to the first prokaryotic cells. Their most probable evolution to the first eukaryotic organisms is discussed on the basis of the modified Studitsky's synbacteriogenesis theory.

Self-instructed condensation of amino acids into polymers

In contemporary cells biological information is largely stored in nucleic acids. Therefore, a prerequisite in many theories on the origin of cellular life is the pre-existence of self-replicating polynucleotides that had to be formed by abiotic processes on the prebiotic Earth. It is usually assumed that the spontaneous synthesis of a self-replicating polynucleotide could take place readily. However, serious stereochemical obstacles exist which make Such a synthesis extremely improbable. Amino acids on the other hand, which are abundantly formed in prebiotic simulation experiments, are relatively easily polymerized to macromolecules (protoproteins) that share with modern proteins many properties: e.g., definable non-random structure, selected amino acid sequences, enzyme-like activities and self-assembly into supramolecular structures. Prebiotic polyamino acids are therefore regarded by some scientists, including the present author, as the first informational macromolecules. The origin of this information is the chemical reactivity of the various prebiotic amino acids and their chemical response to their environment. The first informational polynucleotides were likely formed by a polynucleotide polymerase activity of prebiotic protoproteins. A contemporary model for this process is seen, e.g., in the activity of template-free Q beta-replicase.

Factors controlling the size of proteinoid microspheres

Proteinoid microspheres were prepared from aqueous solutions containing various metal halides under different pH values and ionic strengths. The effects of pH and ionic strength on the diameter of the microspheres and also the solubility of the proteinoid in hot solution (100 degrees C) were investigated by means of different physiochemical measurements. It is found that, under high ionic strength, the diameter of the microsphere is mainly affected by the salt concentration, while the pH of the system is the main factor when the ionic strength is low. Moreover, the change in the solubility with ionic strength and pH is found to show a striking resemblance to that in the diameter with both factors. On the basis of these results, the external and internal factors controlling the size of proteinoid microspheres are clarified, and a plausible mechanism of the proteinoid microsphere formation under prebiotic conditions is also discussed.

Primordial transport of sugars and amino acids via Schiff bases

Experimental support is given for a model concerning the origin of a primordial transport system. The model is based on the facilitated diffusion of amino acids stimulated by aliphatic aldehyde carriers and sugars stimulated by aliphatic amine carriers. The lipid-soluble diffusing species is the Schiff base. The possible role of this simple transport system in the origin of an early protocell is discussed.

Life from an orderly cosmos

Recent astrophysical studies suggest a high degree of order in the inanimate universe, stemming from cosmic beginnings. This state is consistent with the nonrandomness observed experimentally in the thermal polymers of amino acids that figure as an early inanimate stage in organic evolution. The various stages in inanimate matter, protocells, and evolved cells and the degree of order that they represent comport with the second law of thermodynamics on a cosmic scale.

Metabolic microspheres: origins and evolution

A systematic review of catalytic activities in thermal proteinoids and microspheres aggregated therefrom yields some new inferences on the origins and evolution of metabolism. Experiments suggest that, instead of being inert, protocells were already biochemically and cytophysically competent. The emergence and refinement of metabolism ab initio is thus partly traced conceptually. When the principle of molecular self-instruction, as of amino acids in peptide synthesis, is taken into account as a concomitant of natural selection, an expanded theory of organismic evolution, including saltations, emerges.

Polycondensation of alpha-amino acids by pyrosulfuric acid

The thermal polycondensation of amino acids common to protein is promoted at 80 degrees C by pyrosulfuric acid. This is in contrast to the noncondensation at 100 degrees C in the presence of concentrated sulfuric acid. These results are in accord with an anhydride mechanism, as proposed earlier for copolycondensation promoted by polyphosphoric acid. The amino acid composition, molecular weight, near-homogeneity, are infrared absorption of the polymer formed are described. The potential significance of planetary pyrosulfuric acid is discussed.

The evolutionary significance of phase-separated microsystems

The source, preparation, and properties of phase-separated systems such as lipid layers, coacervate droplets, sulphobes, and proteinoid microspheres are reviewed. These microsystems are of interest as partial models for the cell and as partial or total models for the protocell. Conceptual benefits from study of such models are: clues to experiments on origins, insights into principles of action and, in some instances, presumable models of the origin of the protocell. The benefits to evolution of organized chemical units are many, and can in part be analyzed. Ease of formation suggests that such units would have arisen early in primondiae organic evolution. Integration of these various concepts and the results of consequent experiments have contributed to the developing theory of the origins of primordial and of contemporary life.

The appearance of new structures and functions in proteins during evolution

The likelihood of a de novo generation of classes of efficient proteins through neoformation of DNA, through modification of expressed DNA, and through modification of nonexpressed DNA is examined. So is the likelihood that newly formed inefficient enzymes be turned into efficient enzymes. The conclusions are that neither gene duplicates nor dormant genes represent promising materials for a de novo generation of protein classes, that (with exceptions) such generation is unlikely to have taken place in recent evolution, that new structural genes must nearly consistently derive from preexisting structural genes, and that new functions can be evolved only on the basis of old proteins. Conditions of protein evolution in prokaryotes suggest that the saltatory formation of protein classes is as unlikely in prokaryotes as in eukaryotes. Data on the history of a few protein classes are reviewed to illustrate the preceding inferences. The analysis leads to the hypothesis that most protein classes originated before the major elements of the translation apparatus of modern cells were fully evolved. If simple sequence DNA is turned into structural genes by evolution, this process (again with exceptions) is considered to have taken place only at that very remote period. A polyphyletic origin of proteins is thought to date back to the same era. It is proposed that the development of genic multiplicity and of marked structural and functional diversity of proteins may have come about in the earliest cells primarily through the independent generation of structurally different polymerases in different protocells, followed by cell conjugation and the subsequent use by enriched cells of supernumerary types of polymerase for evolving further functions. Functional growth, as it took place at early times, is briefly discussed as well as functional change. The foundations for new functional developments in old proteins are analyzed. In considering the evolutionary recovery of lost functions, aspects of cell differentiation and gene regulation are linked with the evolutionary picture. The distinction between eurygenic and stemogenic control of gene activity is used. Next to gene deletion, cell and tissue deletion is held to be an event of general evolutionary significance, through cell and tissue origination that presumably accompanies the restoration of a lost molecular function.

A model for the origin of stable protocells in a primitive alkaline ocean

When a mixture of the eighteen proteinous amino acids are suitably heated in the dry state with seawater salts, a copolyamino acid results. One fraction of this polymer is found, through isoelectric focusing, to consist of a mixture of acidic and basic proteinoids, each of sharply limited heterogeneity. When one fraction of the seawater proteinoid is dissolved in hot water, and the solution is cooled, proteinoid microspheres result. These have properties in common with simpler types, but also stable at pH values to 9, in common with microspheres prepared by mixing acidic and basic proteinoids. These processes thus constitute a simple model for the origin of a protocell stable in a primitive alkaline ocean.