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.     

Self-organizing proto-replicators and the origin of life

Standard theories suggest that the first informational replicator involved RNA molecules (or a more primitive analogue) and that a preliminary step for the development of such replicating systems may have been the emergence of subunits capable of forming chains and interchain pairings. Following these hypotheses, this discussion describes various abstract simulations designed to investigate the structures resulting from such interactions for generalised subunits. Three classes of pairing strategy were considered for a range of subunit concentrations. The resulting dynamic self-organization of the systems produced high levels of structural complexity (some at low subunit concentrations and in the presence of disruptive subunits) and a significantly increased percentage of complementary base pairing (particularly in the more substantial structures). These properties of the systems, which did not require pre-existing replicators, templates or functional catalysts, were shown to be sensitive to the form of pairing strategy, subunit concentrations and various conditions that could theoretically be altered by products of the systems. Though no systems behaved as a replicator, some possessed collections of properties from which a replicating system might theoretically be constructed without requiring the introduction of additional classes of properties. The implications of such systems were considered with respect to the origin of life.     

Power series expansion and structural analysis for life cycle assessment

Goal, Scope and Background The usefulness of power series expansion for an LCA system has often been doubted, as those systems may not possess the unique properties that enable power series expansion and analyses based on the power series. This paper surveys the existing literature on power series expansion of monetary input-output system and discusses how the power series expansion can be utilized for more general systems including the LCA model. Methods The inherent properties of matrices that are capable of producing power series forms for their inverse and, further, can utilize structural path analysis are analyzed. Using these analyses, the way how a matrix that is not eligible for structural analyses is converted into an eligible form is investigated. A numerical example is presented to demonstrate the findings. Results The necessary and sufficient condition for an indecomposable, real square technology matrix can be expressed using power series was identified. Two additional conditions for a technology matrix to be utilized for structural analyses using power series expansion are discussed as well. It was also shown that an LCA system that fulfills the Hawkins-Simon condition can be easily converted into the form that is eligible for structural analysis by rescaling the columns and rows. Discussion As a numerical example, an application of accumulative structural path analysis for an LCA system is shown. The implications of the results are discussed in a more plain language as well. Conclusions The survey presented in this paper provides not only the conditions under which a linear system is expressed using a power series form but also the way to appropriately convert a system to utilize the rich analytical tools using power series expansion for structural analyses. Recommendations and Perspectives Widely used LCA databases and software tools have employed the linear systems approach as the basis. Much of these developments in the domain of LCA have been made, however, in isolation of the rich findings of IOA. There will be much to benefit LCA through an active dialogue between the two disciplines. There are rich analytical tools available through the use of power series expansion. The current survey will help software developers and LCA practitioners to apply such tools in LCA.     

Turing on Super-Turing and adaptivity

Biological processes are often compared to computation and modeled on the Universal Turing Machine. While many systems or aspects of systems can be well described in this manner, Turing computation can only compute what it has been programmed for. It has no ability to learn or adapt to new situations. Yet, adaptation, choice and learning are all hallmarks of living organisms. This suggests that there must be a different form of computation capable of this sort of calculation. It also suggests that there are current computational models of biological systems that may be fundamentally incorrect. We argue that the Super-Turing model is both capable of modeling adaptive computation, and furthermore, a possible answer to the computational model searched for by Turing himself.     

Engineering of microorganisms for the production of biofuels and perspectives based on systems metabolic engineering approaches

The increasing oil price and environmental concerns caused by the use of fossil fuel have renewed our interest in utilizing biomass as a sustainable resource for the production of biofuel. It is however essential to develop high performance microbes that are capable of producing biofuels with very high efficiency in order to compete with the fossil fuel. Recently, the strategies for developing microbial strains by systems metabolic engineering, which can be considered as metabolic engineering integrated with systems biology and synthetic biology, have been developed. Systems metabolic engineering allows successful development of microbes that are capable of producing several different biofuels including bioethanol, biobutanol, alkane, and biodiesel, and even hydrogen. In this review, the approaches employed to develop efficient biofuel producers by metabolic engineering and systems metabolic engineering approaches are reviewed with relevant example cases. It is expected that systems metabolic engineering will be employed as an essential strategy for the development of microbial strains for industrial applications.     

Planetary systems and extraterrestrial life

The paper revies the present status of the problem of the existence of other planetary systems in the Galaxy. Observational data and theoretical results are presented to show that the occurrence of planetary systems is, most probably, not a universal phenomenon. Study of the stability of planetary orbits in the vicinity of double stars indicates that, in general, planetary systems can not survive around them over long periods. Therefore, we should rule out the possibility of the existence of planetary systems similar to our own in the neighborhood of double stars. In the solar neighborhood, at least 60% of the stars are known to be members of double systems. The nature of the dark companions is discussed and it is concluded that they are stellar objects and not planets. Recent work on the absence of a perturbation in the motion of Barnard's star is discussed. Comments are made on the existence of extraterrestrial life in the solar system and around other stars in the Galaxy.     

Defining Life: Connecting Robotics and Chemistry

Life is commonly referred as open systems driven by organic chemistry capable to self reproduce and to evolve. The notion of life has also been extended to non chemical systems such as robots. The key characteristics of living systems, i.e. autonomy, self-replication, self-reproduction, self-organization, self-aggregation, autocatalysis, as defined in chemistry and in robotics, are compared in a dialogue between a chemist and a robotitian.     

Chirality and life

The crucial role of homochirality and chiral homogeneity in the self-replication of contemporary biopolymers is emphasized, and the experimentally demonstrated advantages of these chirality attributes in simpler polymeric systems are summarized. The implausibility of life without chirality and hence of a biogenic scenario for the origin of chiral molecules is stressed, and chance and determinate abiotic mechanisms for the origin of chirality are reviewed briefly in the context of their potential viability on the primitive Earth. It is concluded that all such mechanisms would be non-viable, and that the turbulent prebiotic environment would require an ongoing extraterrestrial source for the accumulation of chiral molecules on the primitive Earth. A scenario is described wherein the circularly polarized ultraviolet synchrotron radiation from the neutron star remnants of supernovae engenders asymmetric photolysis of the racemic constituents in the organic mantles on interstellar dust grains, whereupon these chiral constituents are transported repetitively to the primative Earth by direct accretion of the interstellar dust or through impacts of comets and asteroids.     

Hypothesis: the origin of life in a hydrogel environment

A hypothesis is proposed that the first cell(s) on the Earth assembled in a hydrogel environment. Gel environments are capable of retaining water, oily hydrocarbons, solutes, and gas bubbles, and are capable of carrying out many functions, even in the absence of a membrane. Thus, the gel-like environment may have conferred distinct advantages for the assembly of the first cell(s).     

Self-organization in biological systems

Biological systems are considered that are capable of dynamic self-organization, i.e., spontaneous emergence of spatio-temporal order with the formation of various spatio-temporal patterns. A cell is involved in the organization of ontogenesis of all stages. Embryonic cells exhibit coordinated social behavior and generate ordered morphological patterns displaying variability and equifinality of development. Physical and topological patterns are essential for biological systems as an imperative that restricts and directs biological morphogenesis. Biological self-organization is directed and fixed by natural selection during which selection of the most sustainable, flexible, modular systems capable of adaptive self-organization occurs.     

Criteria for the emergence and evolution of life in the solar system

During the past years we have explored most of the bodies of the solar system by means of the Apollo, Venera, Viking, Voyager, and other space missions. We are now in a better position to be able to compare the conditions of other planets and satellites with those of the Earth in order to determine what is unique about our planet which permitted the emergence and evolution of life on it. On the basis of this and other available scientific information we have arrived at the conclusion that there are at least some twentyfive specific conditions or requirements which have to be fulfilled in order for life as we know it to appear and evolve in a planetary system such as ours. Most of these necessary conditions or requirements are mutually interdependent, but in order to discuss their role in depth they have been divided into five major general areas which are discussed in some detail herein. Planetary criteria, which relate to the physical properties of the planet as it is formed and as it becomes a differentiated cosmic body and potential abode of life. The mass, orbital characteristics and energetic relationships with the central star as well as the discrete separation of gas, liquid and solid phases of the planet are of utmost importance. Chemical criteria, which are concerned with the composition, availability of effective energy sources, and chemical constrainst (solvent, pH range, redox potential) of the environment(s) where reactions take place for the prebiological formation of biochemical compounds. Protobiological criteria, which relate to the prebiologically synthesized oligomeric and polymeric biomolecules, how they interact cooperatively to form protobiological structures and functions (replication, catalysis, information transfer, etc.) and self-assemble to give rise to a living system. Evolutionary criteria, which are concerned with the processes responsible for the increase in complexity of organisms by genomic multiplication, symbiotic integration and cellular differentiation, as well as with the negentropic ability of organisms to continuously recycle all the volatile biogenic elements. Altogether these processes made possible the development and evolution of life from the simplest prokaryotic cell ancestor to a cognitive and manipulative multicellular organism (man).In order to extend this inquiry to other systems beyond our solar system a fifth set of requirements based on astronomical observations is also discussed, namely, theStellar criteria, which relate to the elemental composition mass, lifetime, and other features of Main Sequence stars which may be surrounded by planetary systems similar to our own. Finally, a brief review is made on the probability of the existence of extraterrestrial life as well as of civilizations capable of interstellar communication in our Galaxy.Paper presented at the 6th College Park Colloquium, October 1981.     

Impact constraints on the environment for chemical evolution and the continuity of life

The Moon and the Earth were bombarded heavily by planetesimals and asteroids that were capable of interfering with chemical evolution and the origin of life. In this paper, we explore the frequency of giant terrestrial impacts able to stop prebiotic chemistry in the probable regions of chemical evolution. The limited time available between impacts disruptive to prebiotic chemistry at the time of the oldest evidence of life suggests the need for a rapid process for chemical evolution of life. The classical hypothesis for the origin of life through the slow accumulation of prebiotic reactants in the primordial soup in the entire ocean may not be consistent with constraints imposed by the impact history of Earth. On the other hand, rapid chemical evolution in cloud systems and lakes or other shallow evaporating water bodies would have been possible because reactants could have been concentrated and polymerized rapidly in this environment. Thus, life probably could have originated near the surface between frequent surface sterilizing impacts. There may not have been continuity of life depending on sunlight because there is evidence that life, existing as early as 3.8 Gyr ago, may have been destroyed by giant impacts. The first such organisms on Earth where probably not the ancestors of present life.     

Coacervate systems and origin of life

Hydrophilic coacervate systems consist of coacervate drops (0.5–640μ in diameter) and liquid. The most molecules are cooperated into the drops. Defects of such systems and drops are instability. Stable protein-nucleic-acid carbol-hydrate drops are studied. Enzymatical oxidized reactions were fulfield by the peroxidase (1.11.1.7) and the polyphenoloxidase (1.10.3.1) and its substrates (phenol and other ones) in coacervate systems. The drops are getting stable by the oxidized compounds quinones and others. The quinone content of individual drops (more than 5000 dorps) was found by means scaning Cytospectrophotometer SIM. The limit of analysis 1×10^?13–10^?14g, the errors 3% of the value found. The mathematical equations of the dependence both the size of drops and the content of oxidized compounds were calculated. The structure of stable drops was investigated in electronic microscope. The drops bound one to other by means bridges or hills, and formed colonia. We proposed that different stability of drops, especially stable ones, and colonia are interesting phenomena for the Origin of Life.     

Symbiosis and the origin of life

The paper uses chemical kinetic arguments and illustrations by computer modelling to discuss the origin and evolution of life. Complex self-reproducing chemical systems cannot arise spontaneously, whereas simple auto-catalytic systems can, especially in an irradiated aqueous medium. Self-reproducing chemical particles of any complexity, in an appropriate environment, have a self-regulating property which permits long-term survival. However, loss of materials from the environment can lead to continuing decay which is circumvented by physical union between different kinds of self-reproducing particles. The increasing complexity produced by such unions (symbioses) is irreversible so that the chemical system evolves. It is suggested that evolution by successive symbioses brough about the change from simple, spontaneously arising, auto-catalytic particles to complex prokaryotic cells.     

Pressure and life: some biological strategies

All biological processes of life on Earth experience varying degrees of pressure. Aquatic organisms living in the deep-sea, as well as chondrocytic cells of articular cartilage are exposed to hydrostatic pressures that rise up to several hundred times that of atmospheric pressure. In the case of marine larvae that disperse through the oceanic water column, pressure changes might be responsible for stress conditions during development, limiting colonisation capabilities. In a number of biological systems, life strategies may be significantly influenced by pressure. In this review, we will focus on the consequences of pressure changes on various biological processes, and more specifically on animals living in the deep-sea. Revisiting general principles of pressure effects on biological systems, we present recent data illustrating the diversity of effects pressure may have at different levels in biological systems, with particular attention to effects on gene expression. After a review of the main pressure equipments available today for studying species living naturally at high pressure, we summarise what is known concerning pressure impact during animal development.     

Parasites at the origin of life

This paper is concerned with parasitic virus-like particles and their hosts. It is proposed that parasitism must have occurred at an early stage of evolution, soon after the first self-reproducing systems had formed. When chemical building blocks for self-reproducing systems became scarce, current theories envision that some self-reproducing systems evolved the capability to synthesize materials for self-replication from chemical precursors in the environment. It is proposed that at about the same time parasitic systems (phages) arose that replicated at the expense of host systems by diverting host materials to the replication of their own genomes. With the aid of a mathematical model we demonstrate that host and phages can coexist in a stable equilibrium, depending upon the carrying capacity of the environment. If the latter falls below a threshold, then the parasites die out. A parasite that has the capability to integrate into the host genome is replicated along with it and thus escapes extinction during periods of population bottlenecks of the host population. The presence of phages creates evolutionary pressures favoring host defenses against them. Thus, modern bacteria are able to degrade most invading DNA (through restriction enzymes). Defense capabilities require a share of the genome, thus adding to the genetic complexity of organisms.     

Catalysis, evolution and life

Living organisms are unique in their ability to generate and replicate ordered systems from disordered components. Generation of order, replication of the individual, and evolution of the species all depend on the successful utilization of external energy derived from chemicals and light. The information for reproduction is encoded in nucleic acids, but evolution depends on a limited variability in replication, and proceeds through the selection of individuals with altered biochemistry. Essentially all biochemistry is catalyzed; therefore, altered biochemistry implies altered or new catalysts. In that sense catalysis is the medium of evolution. We propose that a basic property of enzymes, at least as fundamental as reaction rate enhancement, is to adjust the reaction path by altering and eventually optimizing the reversible interchange of chemical, electrical and mechanical energy among themselves and their reactants.     

System expansion and allocation in life cycle assessment of milk and beef production

Background, Goal and Scope  System expansion is a method used to avoid co-product allocation. Up to this point in time it has seldom been used in LCA studies of food products, although food production systems often are characterised by closely interlinked sub-systems. One of the most important allocation problems that occurs in LCAs of agricultural products is the question of how to handle the co-product beef from milk production since almost half of the beef production in the EU is derived from co-products from the dairy sector. The purpose of this paper is to compare different methods of handling co-products when dividing the environmental burden of the milk production system between milk and the co-products meat and surplus calves. Main Features  This article presents results from an LCA of organic milk production in which different methods of handling the co-products are examined. The comparison of different methods of co-product handling is based on a Swedish LCA case study of milk production where economic allocation between milk and meat was initially used. Allocation of the co-products meat and surplus calves was avoided by expanding the milk system. LCA data were collected from another case study where the alternative way of producing meat was analysed, i.e. using a beef cow that produces one calf per annum to be raised for one and a half year. The LCA of beef production was included in the milk system. A discussion is conducted focussing on the importance of modelling and analysing milk and beef production in an integrated way when foreseeing and planning the environmental consequences of manipulating milk and beef production systems. Results  This study shows that economic allocation between milk and beef favours the product beef. When system expansion is performed, the environmental benefits of milk production due to its co-products of surplus calves and meat become obvious. This is especially connected to the impact categories that describe the potential environmental burden of biogenic emissions such as methane and ammonia and nitrogen losses due to land use and its fertilising. The reason for this is that beef production in combination with milk can be carried out with fewer animals than in sole beef production systems. Conclusion, Recommendation and Perspective  Milk and beef production systems are closely connected. Changes in milk production systems will cause alterations in beef production systems. It is concluded that in prospective LCA studies, system expansion should be performed to obtain adequate information of the environmental consequences of manipulating production systems that are interlinked to each other.     

Physiological desensitization of carbohydrate permeases and adenylate cyclase to regulation by the phosphoenolpyruvate:sugar phosphotransferase system in Escherichia coli and Salmonella typhimurium. Involvement of adenosine cyclic 3',5'-phosphate and inducer

Adenylate cyclase and a number of carbohydrate transport systems are subject to regulation by the phosphoenolpyruvate:sugar phosphotransferase system. These sensitive carbohydrate transport systems are desensitized to regulation by the phosphotransferase system, and adenylate cyclase is deactivated when cells are grown in medium containing cyclic AMP. These effects are specific for cyclic AMP and are potentiated by the genetic loss of cyclic AMP phosphodiesterase. Inclusion in the growth medium of an inducer of a sensitive transport system also promotes desensitization of that particular transport system. Inducer-promoted desensitization is specific for the particular target transport system, while cyclic AMP-promoted desensitization is general and affects several systems. Desensitization of the permeases to regulation, and inactivation of adenylate cyclase, are slow processes which are blocked by chloramphenicol and are therefore presumably dependent on protein synthesis. Several sugar substrates of the phosphotransferase system are capable of regulating the sensitive carbohydrate transport systems. The evidence suggests that desensitization to this regulation does not result from a direct effect on the functioning of Enzyme I, a small heat-stable protein of the phosphotransferase system, HPr, or an Enzyme II of the phosphotransferase system, but specifically uncouples the permease systems from regulation.