On the chemistry and evolution of the pioneer organism

The theory of a chemo-autotrophic origin of life in a volcanic Iron-Sulfur World postulates the emergence of a pioneer organism within a flow of volcanic exhalations. The pioneer organism is characterized by a composite structure with an inorganic substructure and an organic superstructure. Within the surfaces of the inorganic substructure, iron, cobalt, nickel, and other transition-metal centers with sulfido, carbonyl, cyano, and other ligands are catalytically active, and promote the growth of the organic superstructure through carbon fixation, driven by the reducing potential of the volcanic exhalations. This pioneer organism is reproductive by an autocatalytic feedback effect, whereby some organic products serve as ligands for activating the catalytic metal centres whence they arise. This unitary structure-function relationship of the pioneer organism constitutes the 'Anlage' for two major strands of evolution: enzymatization and cellularization, whereby the upward evolution of life by increase of molecular complexity is grounded ultimately in the transition metal-catalyzed, synthetic redox chemistry of the pioneer organism.     

The fundamental nature of life as a chemical system: the part played by inorganic elements

In this article we show why inorganic metal elements from the environment were an essential part of the origin of living aqueous systems of chemicals in flow. Unavoidably such systems have many closely fixed parameters, related to thermodynamic binding constants, for the interaction of the essential exchangeable inorganic metal elements with both inorganic and organic non-metal materials. The binding constants give rise to fixed free metal ion concentration profiles for different metal ions and ligands in the cytoplasm of all cells closely related to the Irving-Williams series. The amounts of bound elements depend on the organic molecules present as well as these free ion concentrations. This system must have predated coding which is probably only essential for reproductive life. Later evolution in changing chemical environments became based on the development of extra cytoplasmic compartments containing quite different energised free (and bound) element contents but in feed-back communication with the central primitive cytoplasm which changed little. Hence species multiplied late in evolution in large part due to the coupling with the altered inorganic environment.     

早期地球的环境变化和生命的化学进化

生命起源是当代最大的科学疑谜之一,也是历来人类普遍关注的一个焦点。在地球上最早的生物出现之前,有机物经历了漫长而复杂的化学进化过程,称为生命的化学进化。地球上生命的化学进化与非生物部分的早期演化过程,是密切地相互关联、相互作用并相互制约的。文章着重阐述与生命的化学关系最为密切的冥古宙和太古宙的地球演化历史,指出这两个阶段所形成的还原性原始大气和古海洋条件在生命的化学进行中起了极其重要的作用,并且从宇宙形成、太阳系演化和地球环境早期演化的角度,探讨地球生命的化学进化历程;以地球形成初期发生了一系列复杂的有机化学反应过程,由无机分子生成生物小分子,再进一步生成生物大分子,直至最后产生原始细胞。此外,文章评述当前国际上最流行的生命化学进化学说,对早期地球的化学进化是发生在地球表面的原始海洋、粘土矿物、火山喷发等,或是来源于地球之外的宇宙空间进行了综合的阐述。     

The genetic architecture of behavioral canalization

Behaviors are components of fitness and contribute to adaptive evolution. Behaviors represent the interactions of an organism with its environment, yet innate behaviors display robustness in the face of environmental change, which we refer to as ‘behavioral canalization’. We hypothesize that positive selection of hub genes of genetic networks stabilizes the genetic architecture for innate behaviors by reducing variation in the expression of interconnected network genes. Robustness of these stabilized networks would be protected from deleterious mutations by purifying selection or suppressing epistasis. We propose that, together with newly emerging favorable mutations, epistatically suppressed mutations can generate a reservoir of cryptic genetic variation that could give rise to decanalization when genetic backgrounds or environmental conditions change to allow behavioral adaptation.     

The evolution of photosynthesis…again?

‘Replaying the tape’ is an intriguing ‘would it happen again?’ exercise. With respect to broad evolutionary innovations, such as photosynthesis, the answers are central to our search for life elsewhere. Photosynthesis permits a large planetary biomass on Earth. Specifically, oxygenic photosynthesis has allowed an oxygenated atmosphere and the evolution of large metabolically demanding creatures, including ourselves. There are at least six prerequisites for the evolution of biological carbon fixation: a carbon-based life form; the presence of inorganic carbon; the availability of reductants; the presence of light; a light-harvesting mechanism to convert the light energy into chemical energy; and carboxylating enzymes. All were present on the early Earth. To provide the evolutionary pressure, organic carbon must be a scarce resource in contrast to inorganic carbon. The probability of evolving a carboxylase is approached by creating an inventory of carbon-fixation enzymes and comparing them, leading to the conclusion that carbon fixation in general is basic to life and has arisen multiple times. Certainly, the evolutionary pressure to evolve new pathways for carbon fixation would have been present early in evolution. From knowledge about planetary systems and extraterrestrial chemistry, if organic carbon-based life occurs elsewhere, photosynthesis—although perhaps not oxygenic photosynthesis—would also have evolved.     

Metal sulfides in oxygenated aquatic systems: implications for the biotic ligand model

The Biotic Ligand Model (BLM) attempts to predict metal toxicity to aquatic organisms on the basis of metal speciation and effects at the cell surface. Current versions of the BLM for silver and copper consider metal binding by inorganic ligands, dissolved organic matter (DOM) and also competition at the cell surface from calcium and protons (pH). Recent studies reported in the geochemical and ecotoxicological literature have indicated the importance of sulfide as a ligand, even in fully oxygenated aquatic systems. Speciation calculations for oxygenated waters do not currently include reduced sulfur as a ligand and as a consequence, no version of the BLM model has been published including reduced sulfur. This reflects the limitations on our knowledge regarding reduced sulfur in aquatic systems. In this paper we highlight the need to include reduced sulfur in the Biotic Ligand Model, with the interaction between silver and inorganic metal sulfides as a specific example. The geochemical importance of metal sulfides as ligands for silver and the effect of 'dissolved' metal sulfide and other ligands on metal toxicity and accumulation are described and reviewed. Recommendations are made for future work needed to incorporate sulfide ligands into the BLM's modeling framework.     

Microarray analysis of a microbe–mineral interaction

The weathering of volcanic minerals makes a significant contribution to the global silicate weathering budget, influencing carbon dioxide drawdown and long‐term climate control. Basalt rocks may account for over 30% of the global carbon dioxide drawdown in silicate weathering. Micro‐organisms are known to play a role in rock weathering yet the genomics and genetics of biological rock weathering are unknown. We apply DNA microarray technology to determine putative genes involved in weathering using the heavy metal‐resistant organism, Cupriavidus metallidurans CH34; in particular we investigate the sequestering of iron. The results show that the bacterium does not depend on siderophores. Instead, the up‐regulation of porins and transporters which are employed concomitantly with genes associated with biofilm formation suggests that novel passive and active iron uptake systems are involved. We hypothesize that these mechanisms induce rock weathering by changes in chemical equilibrium at the microbe–mineral interface, reducing the saturation state of iron. We also demonstrate that low concentrations of metals in the basalt induce heavy metal‐resistant genes. Some of the earliest environments on the Earth were volcanic. Therefore, these results not only elucidate the mechanisms by which micro‐organisms might have sequestered nutrients on the early Earth but also provide an explanation for the evolution of multiple heavy metal resistance genes long before the creation of contaminated industrial biotopes by human activity.     

Statistical limitations on molecular evolution

Complexity of functions evolving in an evolution process are expected to be limited by the time length of an evolution process among other factors. This paper outlines a general method of deriving function-complexity limitations based on mathematical statistics and independent from details of a biological or genetic mechanism of the evolution of the function. Limitations on the emergence of life are derived, these limitations indicate a possibility of a very fast evolution and are consistent with "RNA world" hypothesis. The discussed method is general and can be used to characterize evolution of more specific biological organism functions and relate functions to genetic structures. The derived general limitations indicate that a co-evolution of multiple functions and species could be a slow process, whereas an evolution of a specific function might proceed very fast, so that no trace of intermediate forms (species) is preserved in fossil records of phenotype or DNA structure; this is consistent with a picture of "punctuated equilibrium".     

Genomic analyses of transport proteins in Ralstonia metallidurans

Ralstonia (Wautersia, Cupriavidus) metallidurans (Rme) is better able to withstand high concentrations of heavy metals than any other well-studied organism. This fact renders it a potential agent of bioremediation as well as an ideal model organism for understanding metal resistance phenotypes. We have analysed the genome of Rme for genes encoding homologues of established and putative transport proteins; 13% of all genes in Rme encode such homologues. Nearly one-third of the transporters identified (32%) appear to function in inorganic ion transport with three-quarters of these acting on cations. Transporters specific for amino acids outnumber sugar transporters nearly 3 : 1, and this fact plus the large number of uptake systems for organic acids indicates the heterotrophic preferences of these bacteria. Putative drug efflux pumps comprise 10% of the encoded transporters, but numerous efflux pumps for heavy metals, metabolites and macromolecules were also identified. The results presented should facilitate genetic manipulation and mechanistic studies of transport in this remarkable bacterium.     

The organic codes. The basic mechanism of macroevolution.

The origin of the genetic code coincided with the origin of life, while the human codes of cultural evolution emerged almost four billion years later. Modern biology does not recognize any other organic code in nature, and is bound therefore to conclude that the whole of cellular evolution consisted of informational changes. Semantic transformations, natural conventions and biological meaning are things that officially do not exist in the organic world, and play no part in our reconstruction of development and evolution. And yet the properties of organic codes are beginning to emerge in various biological processes. Here it is shown that splicing, signal transduction and pattern formation can be accounted for precisely by the existence of organic codes. It is also shown that those processes were instrumental in bringing about major changes in the history of life, and it is concluded that every main step of macroevolution corresponded to the origin of a new organic code.     

Statistical Limitations on Molecular Evolution

Abstract

Complexity of functions evolving in an evolution process are expected to be limited by the time length of an evolution process among other factors. This paper outlines a general method of deriving function-complexity limitations based on mathematical statistics and independent from details of a biological or genetic mechanism of the evolution of the function. Limitations on the emergence of life are derived, these limitations indicate a possibility of a very fast evolution and are consistent with “RNA world” hypothesis. The discussed method is general and can be used to characterize evolution of more specific biological organism functions and relate functions to genetic structures. The derived general limitations indicate that a co-evolution of multiple functions and species could be a slow process, whereas an evolution of a specific function might proceed very fast, so that no trace of intermediate forms (species) is preserved in fossil records of phenotype or DNA structure; this is consistent with a picture of “punctuated equilibrium”.     

细胞程序性死亡与生态适应

细胞程序性死亡是多细胞有机生命周期中正常的组成部分,细胞程序性死亡过程的存在对生物体是一种保护机制。它是在生物进化过程中形成的,也是生物对环境的适应方式之一。     

REVIEW: Optimality models in the age of experimental evolution and genomics

Optimality models have been used to predict evolution of many properties of organisms. They typically neglect genetic details, whether by necessity or design. This omission is a common source of criticism, and although this limitation of optimality is widely acknowledged, it has mostly been defended rather than evaluated for its impact. Experimental adaptation of model organisms provides a new arena for testing optimality models and for simultaneously integrating genetics. First, an experimental context with a well‐researched organism allows dissection of the evolutionary process to identify causes of model failure – whether the model is wrong about genetics or selection. Second, optimality models provide a meaningful context for the process and mechanics of evolution, and thus may be used to elicit realistic genetic bases of adaptation – an especially useful augmentation to well‐researched genetic systems. A few studies of microbes have begun to pioneer this new direction. Incompatibility between the assumed and actual genetics has been demonstrated to be the cause of model failure in some cases. More interestingly, evolution at the phenotypic level has sometimes matched prediction even though the adaptive mutations defy mechanisms established by decades of classic genetic studies. Integration of experimental evolutionary tests with genetics heralds a new wave for optimality models and their extensions that does not merely emphasize the forces driving evolution.     

Gene mobility and the concept of relatedness

Cooperation is rife in the microbial world, yet our best current theories of the evolution of cooperation were developed with multicellular animals in mind. Hamilton’s theory of inclusive fitness is an important case in point: applying the theory in a microbial setting is far from straightforward, as social evolution in microbes has a number of distinctive features that the theory was never intended to capture. In this article, I focus on the conceptual challenges posed by the project of extending Hamilton’s theory to accommodate the effects of gene mobility. I begin by outlining the basics of the theory of inclusive fitness, emphasizing the role that the concept of relatedness is intended to play. I then provide a brief history of this concept, showing how, over the past fifty years, it has departed from the intuitive notion of genealogical kinship to encompass a range of generalized measures of genetic similarity. I proceed to argue that gene mobility forces a further revision of the concept. The reason in short is that, when the genes implicated in producing social behaviour are mobile, we cannot talk of an organism’s genotype simpliciter; we can talk only of an organism’s genotype at a particular stage in its life cycle. We must therefore ask: with respect to which stage(s) in the life cycle should relatedness be evaluated? For instance: is it genetic similarity at the time of social interaction that matters to the evolution of social behaviour, or is it genetic similarity at the time of reproduction? I argue that, strictly speaking, it is neither of these: what really matters to the evolution of social behaviour is diachronic genetic similarity between the producers of fitness benefits at the time they produce them and the recipients of those benefits at the end of their life-cycle. I close by discussing the implications of this result. The main payoff is that it makes room for a possible new mechanism for the evolution of altruism in microbes that does not require correlated interaction among bearers of the genes for altruism. The importance of this mechanism in nature remains an open empirical question.     

Exploring biologically relevant chemical space with metal complexes

Altering biological processes with small synthetic molecules is a general approach for the design of drugs and molecular probes. Medicinal chemistry and chemical biology are focused predominately on the design of organic molecules, whereas inorganic compounds find applications mainly for their reactivity (e.g. cisplatin as a DNA-reactive therapeutic) or imaging properties (e.g. gadolinium complexes as MRI diagnostics). In such inorganic pharmaceuticals or probes, coordination chemistry in the biological environment or at the target site lies at the heart of their modes of action. However, past and very recent results suggest that it is also worth exploring a different aspect of metal complexes: their ability to form structures with unique and defined shapes for the design of 'organic-like' small-molecule probes and drugs. In such metal-organic compounds, the metal has the main purpose to organize the organic ligands in three-dimensional space. It is likely that such an approach will complement the molecular diversity of organic chemistry in the quest for the discovery of compounds with superior biological activities.     

From geochemistry and biochemistry to prebiotic evolution...we necessarily enter into Gánti's fluid automata

The present study is just an overview of the opening of the geochemical stage for the appearance of life. But that opening would not have been sufficient for the intellectual discovery of the origin of life! The excellent works and many commendable efforts that advance this explanation have not shown the fundamental elements that participate in the theoretical frame of biological evolution. The latter imply the existence of evolutionary transitions and the production of new levels of organization. In this brief analysis we do not intend to introduce the audience to the philosophy of biology. But we do expect to provide a modest overview, in which the geochemical chemolithoautotrophic opening of the stage should be seen, at most, as the initial metabolism that enabled organic compounds to follow the road where a chemical fluid machinery was thus able to undertake the more "sublime" course of organic biological evolution. We think that Tibor Gánti's chemoton is the most significant contribution to theoretical biology, and the only course now available to comprehend the unit of evolution problem without the structuralist and functionalist conflict prevalent in theoretical biology. In our opinion Gánti's chemoton theory travels to the "locus" where evolutionary theory dares to extend itself to entities at many levels of structural organization, beyond the gene or the group above. Therefore, in this and subsequent papers on the prebiotic conditions for the eventual appearance of the genetic code, we explore the formation and the presence of metal sulfide minerals, from the assembly of metal sulfide clusters through the precipitation of nanocrystals and the further reactions resulting in bulk metal sulfide phases. We endeavor to characterize pristine reactions and the modern surfaces, utilizing traditional surface science techniques and computational methods. Moreover, mechanistic details of the overall oxidation of metal sulfide minerals are set forth. We hope that this paper will lead our audience to accept that in a chemically oscillating system the chemoton is a model fluid state automaton capable of growth and self-reproduction. This is not simply a matter of transmitting a pattern, as in inorganic crystals; such self-reproduction must be more complex than crystal growth. Indeed that is what Gánti's theoretical and abstract model offers to us all: we finally have a philosophy of evolutionary units in theoretical biology.     

THE EVIDENCE OF REPRODUCTIVE MECHANISMS IN FOSSIL DASYCLADS (ALGAE: CHLOROPHYTA)

Dasyclads (members of Order Dasycladales: Algae, Chlorophyta) are reviewed for evidence of reproductive structures in the fossil state, and then compared with what is known of the reproductive processes in living examples. The effects of poor preservation in most of the fossils are shown to result in many uncertainties, and the resulting degree of interpretation required is emphasized. Selected genera of fossil dasyclads considered relevant to this problem are briefly analysed and discussed: Archaeobatophora (Ordovician), Kulikia (Carboniferous), Imperiella (Permian), Stichoporella (Jurassic) and Cympolia (Cretaceous to Recent). The pioneer views of J. Pia on dasyclad reproduction through geological time are seen to need much modification in the light of later work. The fundamental dasyclad nucleus-fragmentation-reproduction mechanism is believed to have operated within the great morphological variety of known dasyclads, giving rise to modification in genera where basic evolution was structural. In this way the variety of dasyclads can be seen to be the result of varied morphological evolution, often modified by the consistently simple basic reproductive mechanism.     

Effect of hardness on bioavailability and toxicity of cadmium to rainbow trout

Abstract

Water quality characteristics affecting toxicity of metals to aquatic life include pH, inorganic and organic ligands (negatively charged ions and molecules), and water hardness. Ligands control the ability of natural waters to bind metals which could adversely affect aquatic life. Bioavailability of metals in natural waters is primarily controlled by alkalinity. Hardness does not affect metal complexation but can reduce acute toxicity through antagonistic mechanisms. In most natural waters, concentrations of alkalinity and hardness are similar, but they may be very different in some waters.

Most toxicity studies have not distinguished between reduced toxicity resulting from effects of hardness and that resulting from complexation of metals by ligands. A series of acute and long-term experiments were conducted to assess these relationships while exposing rainbow trout (Oncorhynchus mykiss) to cadmium (Cd) in waters of low alkalinity (30 mg L^?1) and hardnesses of 400, 200, and 50 mg L^?1 adjusted with magnesium sulfate (MgSO⁴). These tests did not show a strong antagonistic influence of Mg hardness on Cd toxicity. At Mg hardnesses of 50, 200, and 400 mg L^?1, 96-h LC50s were 3.02, 6.12, and 5.70 μg Cd L^?1, differing by a factor of only 1.8. Similarly, chronic values derived from 100-day experiments in waters with the same range of hardness were 1.47, 3.57, and 3.64 μg L^?1, respectively. With an eight-fold difference in Mg hardness, chronic values differed by a factor of only 2.5. Antagonistic properties of hardness are primarily controlled by Ca with Mg playing a minor role. The long-term role of Ca in reducing metal toxicity will require further investigation.     

Artificial evolution of life history and behavior

We present an individual-based model that uses artificial evolution to predict fit behavior and life-history traits on the basis of environmental data and organism physiology. Our main purpose is to investigate whether artificial evolution is a suitable tool for studying life history and behavior of real biological organisms. The evolutionary adaptation is founded on a genetic algorithm that searches for improved solutions to the traits under scrutiny. From the genetic algorithm's "genetic code," behavior is determined using an artificial neural network. The marine planktivorous fish Müller's pearlside (Maurolicus muelleri) is used as the model organism because of the broad knowledge of its behavior and life history, by which the model's performance is evaluated. The model adapts three traits: habitat choice, energy allocation, and spawning strategy. We present one simulation with, and one without, stochastic juvenile survival. Spawning pattern, longevity, and energy allocation are the life-history traits most affected by stochastic juvenile survival. Predicted behavior is in good agreement with field observations and with previous modeling results, validating the usefulness of the presented model in particular and artificial evolution in ecological modeling in general. The advantages, possibilities, and limitations of this modeling approach are further discussed.     

The origin of the animals and a ‘Savannah’ hypothesis for early bilaterian evolution

The earliest evolution of the animals remains a taxing biological problem, as all extant clades are highly derived and the fossil record is not usually considered to be helpful. The rise of the bilaterian animals recorded in the fossil record, commonly known as the ‘Cambrian explosion’, is one of the most significant moments in evolutionary history, and was an event that transformed first marine and then terrestrial environments. We review the phylogeny of early animals and other opisthokonts, and the affinities of the earliest large complex fossils, the so‐called ‘Ediacaran’ taxa. We conclude, based on a variety of lines of evidence, that their affinities most likely lie in various stem groups to large metazoan groupings; a new grouping, the Apoikozoa, is erected to encompass Metazoa and Choanoflagellata. The earliest reasonable fossil evidence for total‐group bilaterians comes from undisputed complex trace fossils that are younger than about 560 Ma, and these diversify greatly as the Ediacaran–Cambrian boundary is crossed a few million years later. It is generally considered that as the bilaterians diversified after this time, their burrowing behaviour destroyed the cyanobacterial mat‐dominated substrates that the enigmatic Ediacaran taxa were associated with, the so‐called ‘Cambrian substrate revolution’, leading to the loss of almost all Ediacara‐aspect diversity in the Cambrian. Why, though, did the energetically expensive and functionally complex burrowing mode of life so typical of later bilaterians arise? Here we propose a much more positive relationship between late‐Ediacaran ecologies and the rise of the bilaterians, with the largely static Ediacaran taxa acting as points of concentration of organic matter both above and below the sediment surface. The breaking of the uniformity of organic carbon availability would have signalled a decisive shift away from the essentially static and monotonous earlier Ediacaran world into the dynamic and burrowing world of the Cambrian. The Ediacaran biota thus played an enabling role in bilaterian evolution similar to that proposed for the Savannah environment for human evolution and bipedality. Rather than being obliterated by the rise of the bilaterians, the subtle remnants of Ediacara‐style taxa within the Cambrian suggest that they remained significant components of Phanerozoic communities, even though at some point their enabling role for bilaterian evolution was presumably taken over by bilaterians or other metazoans. Bilaterian evolution was thus an essentially benthic event that only later impacted the planktonic environment and the style of organic export to the sea floor.