Chemistry and biodiversity: Darwinism, evolution, and speciation. An opposing view

Complex structures produced by noncatalyzed multi‐step chemical processes must have highly probable origins and assembly routes. Within any frame of reference, life is easily the most‐complex self‐assembled structure known to man. It is not possible to calculate a finite time for biogenesis by statistical mechanics, but the abundance of life makes it reasonable to propose an accelerating principle of nature that naturally shortened the time for cell formation to a billion years or less. This hypothetical principle, which I have called valence‐orbital bias, is thought to be responsible for the discrepancy between statistics and observation, and carries with it, as a conditio sine qua non, multiple origins of life. The new concept resolves the differences between the predictions based on statistical mechanics and the relatively rapid appearance of life during the post‐accretion period. It suggests as well that species and variants, the units of propagation, may also have been the units of evolution. Produced in profusion by chemistry, the origins are culled by natural selection, whereby failure means extinction, not adaptation. Biodiversity, thus, becomes a direct consequence of chemistry without positive feedback from the environment and without a constructive role for mutation.     

Montmorillonite-catalysed formation of RNA oligomers: the possible role of catalysis in the origins of life

Large deposits of montmorillonite are present on the Earth today and it is believed to have been present at the time of the origin of life and has recently been detected on Mars. It is formed by aqueous weathering of volcanic ash. It catalyses the formation of oligomers of RNA that contain monomer units from 2 to 30-50. Oligomers of this length are formed because this catalyst controls the structure of the oligomers formed and does not generate all possible isomers. Evidence of sequence-, regio- and homochiral selectivity in these oligomers has been obtained. Postulates on the role of selective versus specific catalysts on the origins of life are discussed. An introduction to the origin of life is given with an emphasis on reaction conditions based on the recent data obtained from zircons 4.0-4.5Ga.     

Recreating ancient metabolic pathways before enzymes

The biochemistry of all living organisms uses complex, enzyme-catalyzed metabolic reaction networks. Yet, at life’s origins, enzymes had not yet evolved. Therefore, it has been postulated that non-enzymatic metabolic pathways predated their enzymatic counterparts. In this account article, we describe our recent work to evaluate whether two ancient carbon fixation pathways, the rTCA (reductive tricarboxylic acid) cycle and the reductive AcCoA (Wood-Ljungdahl) pathway, could have operated without enzymes and therefore have originated as prebiotic chemistry. We also describe the discovery of an Fe²⁺-promoted complex reaction network that may represent a prebiotic predecessor to the TCA and glyoxylate cycles. The collective results support the idea that most central metabolic pathways could have roots in prebiotic chemistry.     

A new hypothesis for molecular behavior

In order to understand the living cell, biologists need workable explanations of molecular phenomena. From data in the literature, it is possible to construct a mathematical hypothesis: molecular behavior in the continuum can be represented by a set of simple, logarithmic functions. These functions apply not only to biology, but also to chemistry and to physics.Although empirical in its origins, this hypothesis satisfies criteria which are often associated with good theories. It is comprehensive in its application, and it is mathematically simple. It is easily tested; and it is accurate, when tested. Because it can be correlated with classical atomic and molecular theory, the hypothesis can be used to make strong predictions. The proposal also appears to be consistent with quantum mechanics.     

Towards a General Definition of Life

A new definition of life is proposed and discussed in the present article. It is formulated by modifying and extending NASA’s working definition of life, which postulates that life is a “self-sustaining chemical system capable of Darwinian evolution”. The new definition includes a thermodynamical aspect of life as a far from equilibrium system and considers the flow of information from the environment to the living system. In our derivation of the definition of life we have assumed the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems that only subsequently acquired the capacity of genetic heredity. The new proposed definition of life is independent of the mode of evolution, regardless of whether Lamarckian or Darwinian evolution operated at the origins of life and throughout evolutionary history. The new definition of life presented herein is formulated in a minimal manner and it is general enough that it does not distinguish between individual (metabolic) network and the collective (ecological) one. The newly proposed definition of life may be of interest for astrobiology, research into the origins of life or for efforts to produce synthetic or artificial life, and it furthermore may also have implications in the cognitive and computer sciences.

     

Interpreting the Role of Climbing in Primate Locomotor Evolution: Are the Biomechanics of Climbing Influenced by Habitual Substrate Use and Anatomy?

Vertical climbing is widely accepted to have played an important role in the origins of both primate locomotion and of human bipedalism. Yet, only a few researchers have compared climbing mechanics in quadrupedal primates that vary in their degree of arboreality. It is assumed that primates using vertical climbing with a relatively high frequency will have morphological and behavioral specializations that facilitate efficient climbing mechanics. We test this assumption by examining whether time spent habitually engaged in climbing influences locomotor parameters such as footfall sequence, peak forces, and joint excursions during vertical climbing. Previous studies have shown that during climbing, the pronograde and semiterrestrial Macaca fuscata differs in these parameters compared to the more arboreal and highly specialized, antipronograde Ateles geoffroyi. Here, we examine whether a fully arboreal, quadrupedal primate that does not regularly arm-swing will exhibit gait and force distribution patterns intermediate between those of Macaca fuscata and Ateles geoffroyi. We collected footfall sequence, limb peak vertical forces, and 3D hindlimb excursion data for Macaca fascicularis during climbing on a stationary pole instrumented with a force transducer. Results show that footfall sequences are similar between macaque species, whereas peak force distributions and hindlimb excursions for Macaca fascicularis are intermediate between values reported for M. fuscata and Ateles geoffroyi. These results support the notion that time spent climbing is reflected in climbing mechanics, even though morphology may not provide for efficient mechanics, and highlight the important role of arboreal locomotor activity in determining the pathways of primate locomotor evolution.     

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.     

Origins of life: A comparison of theories and application to Mars

The field of study that deals with the origins of life does not have a consensus for a theory of life's origin. An analysis of the range of theories offered shows that they share some common features that may be reliable predictors when considering the possible origins of life on another planet. The fundamental datum dealing with the origins of life is that life appeared early in the history of the Earth, probably before 3.5 Ga and possibly before 3.8 Ga. What might be called the standard theory (the Oparin-Haldane theory) posits the production of organic molecules on the early Earth followed by chemical reactions that produced increased organic complexity leading eventually to organic life capable of reproduction, mutation, and selection using organic material as nutrients. A distinct class of other theories (panspermia theories) suggests that life was carried to Earth from elsewhere — these theories receive some support from recent work on planetary impact processes. Other alternatives to the standard model suggest that life arose as an inorganic (clay) form and/or that the initial energy source was not organic material but chemical energy or sunlight. We find that the entire range of current theories suggests that liquid water is the quintessential environmental criterion for both the origin and sustenance of life. It is therefore of interest that during the time that life appeared on Earth we have evidence for liquid water present on the surface of Mars.     

From exobiology to cosmobiology at LISA and elsewhere.

Since the emergence of Exobiology, back to the l960ties, this field drastically increased and, although differently named, is today a largely recognized scientific domain of wild interdisciplinarity. It includes not only the search for extraterrestrial living Systems, in particular by direct exploration of planetary bodies and studies of extraterrestrial materials, but also the study on the origins of life on Earth and, in connection to this field, the study of extraterrestrial organic chemistry. The exobiology programmes currently developed at LISA are related to this last aspect. They include the study of prebiotic-like chemistry in the gas and solid phases, based on laboratory simulation experiments, theoretical modeling and future in situ measurements in Titan's atmosphere and in cometary nuclei. A national program of exobiology, coordinated by LISA is under development in France, it covers many of the various aspects of Exobiology, including the study of life in extreme environments, as a reference tool for extraterrestrial life, the study of the primitive environment of the Earth, of the organic chemistry in comets and on Titan, of Mars and Europa and even of extrasolar planets as potential niches for extraterrestrial living systems, associated to the determination of the electromagnetic signatures of life. In parallel to this general program, a proposal for a large simulation chamber to be used as a national facility in particular to simulate the organic chemistry in various planetary environments, and in the interstellar medium, is under preparation. International cooperations linked to these programmes, in particular in the frame of the development of an exobiology facility on the International Space Station, would be of crucial interest.     

Complexity, Self-Organization and Selection

Recent work on self organization promises an explanation of complex order which is independent of adaptation. Self-organizing systems are complex systems of simple units, projecting order as a consequence of localized and generally nonlinear interactions between these units. Stuart Kauffman offers one variation on the theme of self-organization, offering what he calls a ``statistical mechanics' for complex systems. This paper explores the explanatory strategies deployed in this ``statistical mechanics,' initially focusing on the autonomy of statistical explanation as it applies in evolutionary settings and then turning to Kauffman's analysis. Two primary morals emerge as a consequence of this examination: first, the view that adaptation and self-organization should be seen as competing theories or models is misleading and simplistic; and second, while we need a synthesis treating self-organization and adaptation as geared toward different problems, at different levels of organization, and deploying different methods, we do not yet have such a synthesis.     

Bioelementology as an interdisciplinary integrative approach in life sciences: Terminology,classification, perspectives

The article presents the proposed concept of bioelements and the basic postulates of bioelementology for assessing and discussing them in the scientific community. It is known that chemical elements exist in the organism not by themselves, but in certain species having close interaction with other components. Such units are proposed to be called bioelements: the elementary functioning units of living matter, which are biologically active complexes of chemical elements as atoms, ions or nanoparticles with organic compounds of exogenous or biogenous origin. The scientific discipline that studies bioelements, is proposed to be called bioelementology. This discipline could lay the foundation for the integration of bioorganic chemistry, bioinorganic chemistry, biophysics, molecular biology and other parts of life sciences.     

The Viability of a Nonenzymatic Reductive Citric Acid Cycle – Kinetics and Thermochemistry

The likelihood of a functioning nonenzymatic reductive citric acid cycle, recently proposed as the precursor to biosynthesis on early Earth, is examined on the basis of the kinetics and thermochemistry of the acetate → pyruvate → oxaloacetate → malate sequence. Using data derived from studies of the Pd-catalyzed phosphinate reduction of carbonyl functions it is shown that the rate of conversion of pyruvate to malate with that system would have been much too slow to have played a role in the early chemistry of life, while naturally occurring reduction systems such as the fayalite–magnetite–quartz and pyrrhotite–pyrite–magnetite mineral assemblages would have provided even slower conversions. It is also shown that the production of pyruvate from acetate is too highly endoergic to be driven by a naturally occurring energy source such as pyrophosphate. It is thus highly doubtful that the cycle can operate at suitable rates without enzymes, and most unlikely that it could have participated in the chemistry leading to life.     

Bioenergetics of early life: Coupling of reaction networks and compartments may have sparked the first life forms

Living cells are powered by intricate networks of chemical reactions of thousands of molecules. Understanding how living systems emerged through the assembly of chemical processes is one of the biggest challenges in science. Subject Categories: Biotechnology & Synthetic Biology, Evolution & Ecology, Metabolism

How can chemistry turn into biology? How can living cells be built from molecules? These are fundamental questions in biology and, despite much research efforts, remain unanswered. Yet, the past two decades have seen considerable advances in our knowledge of how and which (bio)physical and (bio)chemical processes could have driven the emergence of the first living cells. These achievements have led not only to a better understanding of the molecular origins of life, but also spurred significant developments in synthetic biology, biophysics and supramolecular chemistry. Although the exact events that sparked life on Earth will quite likely remain a mystery, at least partially, exploring the chemical origins of life offers clues about our primordial past and could contribute to shaping our future.

Although the exact events that sparked life on Earth will quite likely remain a mystery […] exploring the chemical origins of life offers clues about our primordial past and could contribute to shaping our future.

     

Chemical markers of prebiotic chemistry in hydrothermal systems.

The goal of this chapter is to suggest some organic compounds which may be indicative of prebiotic processes in hydrothermal systems or laboratory simulations of them. While the exact processes which led to the origins of life are not known, studies of life's origins of the past forty years have uncovered a plethora of potential precursor molecules. Some of these same molecules were probably present in hydrothermal systems if chemical processes there had a role in the origins of life. The types of molecules formed in primitive Earth simulation experiments and observed in the interstellar medium, on comets and meteorites will be reviewed in Section 2 of this chapter. Some reactions involving these molecules which may have been important in prebiotic syntheses will be outlined. Since near- to supercritical water is found in hydrothermal systems, its properties and aspects of organic chemistry in supercritical water at high temperature and pressure will be discussed in Section 3. Fischer-Tropsch type (FTT) reactions, which are a potential source of the building blocks of biological molecules in hydrothermal systems, are discussed in Section 4. In the concluding section, Section 5, the possible formation in hydrothermal systems of organic molecules that are believed to have been important for the origins of life is discussed.     

Motor unit recruitment for dynamic tasks: current understanding and future directions

Skeletal muscle contains many muscle fibres that are functionally grouped into motor units. For any motor task there are many possible combinations of motor units that could be recruited and it has been proposed that a simple rule, the ‘size principle’, governs the selection of motor units recruited for different contractions. Motor units can be characterised by their different contractile, energetic and fatigue properties and it is important that the selection of motor units recruited for given movements allows units with the appropriate properties to be activated. Here we review what is currently understood about motor unit recruitment patterns, and assess how different recruitment patterns are more or less appropriate for different movement tasks. During natural movements the motor unit recruitment patterns vary (not always holding to the size principle) and it is proposed that motor unit recruitment is likely related to the mechanical function of the muscles. Many factors such as mechanics, sensory feedback, and central control influence recruitment patterns and consequently an integrative approach (rather than reductionist) is required to understand how recruitment is controlled during different movement tasks. Currently, the best way to achieve this is through in vivo studies that relate recruitment to mechanics and behaviour. Various methods for determining motor unit recruitment patterns are discussed, in particular the recent wavelet-analysis approaches that have allowed motor unit recruitment to be assessed during natural movements. Directions for future studies into motor recruitment within and between functional task groups and muscle compartments are suggested.     

The application of independent component analysis to the multi-channel surface electromyographic signals for separation of motor unit action potential trains: part II-modelling interpretation.

The purpose of this article was to investigate whether or not FastICA can separate identical motor unit action potential trains (MUAPTs) of the 8-channel surface electromyographic (sEMG) signals constructed by an sEMG model into the independent components. Firstly, we have examined how much the increase of motor units (MUs) in the simulated sEMG signals influenced the performance on the separation of MUAPTs by kurtosis. The decreased trend of mean kurtosis on both sEMG signals and their independent components were observed as MUs were increased. These data suggested that the separation performance decayed when MUs were increased. Secondary, the differences between the independent components and the principal components have been also applied to the simulated sEMG signals with or without time delay between the sEMG channels. FastICA could successfully separate identical MUAPTs with no time delay but principal component analysis (PCA) could not do so. Against it, both FastICA and PCA could not separate MUAPTs with some time delay. In conclusion, our results suggested that FastICA could separate identical MUAPTs with no time delay into the independent components by FastICA, which might offer a new technique for the separation of interfered MUAP waveforms based on statistical properties of sEMG signal distributions.     

Effects of prenatal exposure to the Dutch famine on adult disease in later life: an overview.

People who were small at birth have been shown to have an increased risk of CHD and chronic bronchitis in later life. These findings have led to the fetal origins hypothesis that proposes that the fetus adapts to a limited supply of nutrients, and in doing so it permanently alters its physiology and metabolism, which could increase its risk of disease in later life. The Dutch famine--though a historical disaster--provides a unique opportunity to study effects of undernutrition during gestation in humans. People who had been exposed to famine in late or mid gestation had reduced glucose tolerance. Whereas people exposed to famine in early gestation had a more atherogenic lipid profile, somewhat higher fibrinogen concentrations and reduced plasma concentrations of factor VII, a higher BMI and they appeared to have a higher risk of CHD. Though the latter was based on small numbers, as could be expected from the relatively young age of the cohort. Nevertheless, this is the first evidence in humans that maternal undernutrition during gestation is linked with the risk of CHD in later life. Our findings broadly support the hypothesis that chronic diseases originate through adaptations made by the fetus in response to undernutrition. The long-term effects of intrauterine undernutrition, however, depend upon its timing during gestation and on the tissues and systems undergoing critical periods of development at that time. Furthermore, our findings suggest that maternal malnutrition during gestation may permanently affect adult health without affecting the size of the baby at birth. This gives the fetal origins hypothesis a new dimension. It may imply that adaptations that enable the fetus to continue to grow may nevertheless have adverse consequences for health in later life. CHD may be viewed as the price paid for successful adaptations to an adverse intra-uterine environment. It also implies that the long-term consequences of improved nutrition of pregnant women will be underestimated if these are solely based on the size of the baby at birth. We need to know more about what an adequate diet for pregnant women might be. In general, women are especially receptive to advice about diet and lifestyle before and during a pregnancy. This should be exploited to improve the health of future generations.     

Thermodynamics and Kinetics of Molecular Motors

Molecular motors are first and foremost molecules, governed by the laws of chemistry rather than of mechanics. The dynamical behavior of motors based on chemical principles can be described as a random walk on a network of states. A key insight is that any molecular motor in solution explores all possible motions and configurations at thermodynamic equilibrium. By using input energy and chemical design to prevent motion that is not wanted, what is left behind is the motion that is desired. This review is focused on two-headed motors such as kinesin and Myosin V that move on a polymeric track. By use of microscopic reversibility, it is shown that the ratio between the number of forward steps and the number of backward steps in any sufficiently long time period does not directly depend on the mechanical properties of the linker between the two heads. Instead, this ratio is governed by the relative chemical specificity of the heads in the front-versus-rear position for the fuel, adenosine triphosphate and its products, adenosine diphosphate and inorganic phosphate. These insights have been key factors in the design of biologically inspired synthetic molecular walkers constructed out of DNA or out of small organic molecules.     

Epistemological issues in the study of microbial life: alternative terran biospheres?

The assumption that all life on Earth today shares the same basic molecular architecture and biochemistry is part of the paradigm of modern biology. This paper argues that there is little theoretical or empirical support for this widely held assumption. Scientists know that life could have been at least modestly different at the molecular level and it is clear that alternative molecular building blocks for life were available on the early Earth. If the emergence of life is, like other natural phenomena, highly probable given the right chemical and physical conditions then it seems likely that the early Earth hosted multiple origins of life, some of which produced chemical variations on life as we know it. While these points are often conceded, it is nevertheless maintained that any primitive alternatives to familiar life would have been eliminated long ago, either amalgamated into a single form of life through lateral gene transfer (LGT) or alternatively out-competed by our putatively more evolutionarily robust form of life. Besides, the argument continues, if such life forms still existed, we surely would have encountered telling signs of them by now. These arguments do not hold up well under close scrutiny. They reflect a host of assumptions that are grounded in our experience with large multicellular organisms and, most importantly, do not apply to microbial forms of life, which cannot be easily studied without the aid of sophisticated technologies. Significantly, the most powerful molecular biology techniques available-polymerase chain reaction (PCR) amplification of rRNA genes augmented by metagenomic analysis-could not detect such microbes if they existed. Given the profound philosophical and scientific importance that such a discovery would represent, a dedicated search for 'shadow microbes' (heretofore unrecognized 'alien' forms of terran microbial life) seems in order. The best place to start such a search is with puzzling (anomalous) phenomena, such as desert varnish, that resist classification as 'biological' or 'nonbiological'.