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1.  Evolution, reproduction and definition of life 
Theory in Biosciences  2013;133(1):39-45.
Synthetic theory of evolution is a superior integrative biological theory. Therefore, there is nothing surprising about the fact that multiple attempts of defining life are based on this theory. One of them even has a status of NASA’s working definition. According to this definition, ‘life is a self-sustained chemical system capable of undergoing Darwinian evolution’ Luisi (Orig Life Evol Bios 28:613–622, 1998); Cleland, Chyba (Orig Life Evol Bios 32:387–393, 2002). This definition is often considered as one of the more theoretically mature definitions of life. This Darwinian definition has nonetheless provoked a lot of criticism. One of the major arguments claims that this definition is wrong due to ‘mule’s problem’. Mules (and other infertile hybrids), despite being obviously living organisms, in the light of this definition are considered inanimate objects. It is strongly counterintuitive. The aim of this article was to demonstrate that this reasoning is false. In the later part of the text, I also discuss some other arguments against the Darwinian approach to defining life.
doi:10.1007/s12064-013-0184-5
PMCID: PMC3937540  PMID: 23674095
Definition of life; Darwinian definition; ‘Mule’s problem’; Life as a collective phenomenon
2.  Potential Biosignatures in Super-Earth Atmospheres II. Photochemical Responses 
Astrobiology  2013;13(5):415-438.
Abstract
Spectral characterization of super-Earth atmospheres for planets orbiting in the habitable zone of M dwarf stars is a key focus in exoplanet science. A central challenge is to understand and predict the expected spectral signals of atmospheric biosignatures (species associated with life). Our work applies a global-mean radiative-convective-photochemical column model assuming a planet with an Earth-like biomass and planetary development. We investigated planets with gravities of 1g and 3g and a surface pressure of 1 bar around central stars with spectral classes from M0 to M7. The spectral signals of the calculated planetary scenarios have been presented by in an earlier work by Rauer and colleagues. The main motivation of the present work is to perform a deeper analysis of the chemical processes in the planetary atmospheres. We apply a diagnostic tool, the Pathway Analysis Program, to shed light on the photochemical pathways that form and destroy biosignature species. Ozone is a potential biosignature for complex life. An important result of our analysis is a shift in the ozone photochemistry from mainly Chapman production (which dominates in Earth's stratosphere) to smog-dominated ozone production for planets in the habitable zone of cooler (M5–M7)-class dwarf stars. This result is associated with a lower energy flux in the UVB wavelength range from the central star, hence slower planetary atmospheric photolysis of molecular oxygen, which slows the Chapman ozone production. This is important for future atmospheric characterization missions because it provides an indication of different chemical environments that can lead to very different responses of ozone, for example, cosmic rays. Nitrous oxide, a biosignature for simple bacterial life, is favored for low stratospheric UV conditions, that is, on planets orbiting cooler stars. Transport of this species from its surface source to the stratosphere where it is destroyed can also be a key process. Comparing 1g with 3g scenarios, our analysis suggests it is important to include the effects of interactive chemistry. Key Words: Exoplanets—Earth-like—M-dwarf—Photochemistry—Biosignatures. Astrobiology 13, 415–438.
doi:10.1089/ast.2012.0926
PMCID: PMC3941937  PMID: 23683046
3.  Selectionist and Evolutionary Approaches to Brain Function: A Critical Appraisal 
We consider approaches to brain dynamics and function that have been claimed to be Darwinian. These include Edelman’s theory of neuronal group selection, Changeux’s theory of synaptic selection and selective stabilization of pre-representations, Seung’s Darwinian synapse, Loewenstein’s synaptic melioration, Adam’s selfish synapse, and Calvin’s replicating activity patterns. Except for the last two, the proposed mechanisms are selectionist but not truly Darwinian, because no replicators with information transfer to copies and hereditary variation can be identified in them. All of them fit, however, a generalized selectionist framework conforming to the picture of Price’s covariance formulation, which deliberately was not specific even to selection in biology, and therefore does not imply an algorithmic picture of biological evolution. Bayesian models and reinforcement learning are formally in agreement with selection dynamics. A classification of search algorithms is shown to include Darwinian replicators (evolutionary units with multiplication, heredity, and variability) as the most powerful mechanism for search in a sparsely occupied search space. Examples are given of cases where parallel competitive search with information transfer among the units is more efficient than search without information transfer between units. Finally, we review our recent attempts to construct and analyze simple models of true Darwinian evolutionary units in the brain in terms of connectivity and activity copying of neuronal groups. Although none of the proposed neuronal replicators include miraculous mechanisms, their identification remains a challenge but also a great promise.
doi:10.3389/fncom.2012.00024
PMCID: PMC3337445  PMID: 22557963
neural Darwinism; neuronal group selection; neuronal replicator hypothesis; Darwinian neurodynamics; Izhikevich spiking networks; causal inference; price equation; hill-climbers
4.  Darwinian Behavior in a Cold, Sporadically Fed Pool of Ribonucleotides 
Astrobiology  2012;12(9):870-883.
Abstract
A testable, explicit origin for Darwinian behavior, feasible on a chaotic early Earth, would aid origins discussion. Here I show that a pool receiving unreliable supplies of unstable ribonucleotide precursors can recurrently fill this role. By using numerical integration, the differential equations governing a sporadically fed pool are solved, yielding quantitative constraints for the proliferation of molecules that also have a chemical phenotype. For example, templated triphosphate nucleotide joining is >104 too slow, suggesting that a group more reactive than pyrophosphate activated primordial nucleotides. However, measured literature rates are sufficient if the Initial Darwinian Ancestor (IDA) resembles a 5′-5′ cofactor-like dinucleotide RNA, synthesized via activation with a phosphorimidazolide-like group. A sporadically fed pool offers unforeseen advantages; for example, the pool hosts a novel replicator which is predominantly unpaired, even though it replicates. Such free template is optimized for effective selection during its replication. Pool nucleotides are also subject to a broadly based selection that impels the population toward replication, effective selection, and Darwinian behavior. Such a primordial pool may have left detectable modern traces. A sporadically fed ribonucleotide pool also fits a recognizable early Earth environment, has recognizable modern descendants, and suits the early shape of the phylogenetic tree of Earthly life. Finally, analysis points to particular data now needed to refine the hypothesis. Accordingly, a kinetically explicit chemical hypothesis for a terran IDA can be justified, and informative experiments seem readily accessible. Key Words: Cofactor—RNA—Origin of life—Replication—Initial Darwinian Ancestor (IDA). Astrobiology 12, 870–883.
doi:10.1089/ast.2012.0860
PMCID: PMC3444769  PMID: 22946838
5.  Textural and Mineralogical Characteristics of Microbial Fossils Associated with Modern and Ancient Iron (Oxyhydr)Oxides: Terrestrial Analogue for Sediments in Gale Crater 
Astrobiology  2014;14(1):1-14.
Abstract
Iron (oxyhydr)oxide microbial mats in modern to ∼100 ka tufa terraces are present in a cold spring system along Ten Mile Graben, southeastern Utah, USA. Mats exhibit morphological, chemical, and textural biosignatures and show diagenetic changes that occur over millennial scales. The Jurassic Brushy Basin Member of the Morrison Formation in the Four Corners region of the USA also exhibits comparable microbial fossils and iron (oxyhydr)oxide biosignatures in the lacustrine unit.
Both the modern spring system and Brushy Basin Member represent alkaline, saline, groundwater-fed systems and preserve diatoms and other similar algal forms with cellular elaboration. Two distinct suites of elements (1. C, Fe, As and 2. C, S, Se, P) are associated with microbial fossils in modern and ancient iron (oxyhydr)oxides and may be potential markers for biosignatures. The presence of ferrihydrite in ∼100 ka fossil microbial mats and Jurassic rocks suggests that this thermodynamically unstable mineral may also be a potential biomarker.
One of the most extensive sedimentary records on Mars is exposed in Gale Crater and consists of non-acidic clays and sulfates possibly of lacustrine origin. These terrestrial iron (oxyhydr)oxide examples are a valuable analogue because of similar iron- and clay-rich host rock compositions and will help (1) understand diagenetic processes in a non-acidic, saline lacustrine environment such as the sedimentary rocks in Gale Crater, (2) document specific biomediated textures, (3) demonstrate how biomediated textures might persist or respond to diagenesis over time, and (4) provide a ground truth library of textures to explore and compare in extraterrestrial iron (oxyhydr)oxides, where future explorations hope to detect past evidence of life. Key Words: Biogeochemistry—Mars—Biosignatures—Diagenesis—Iron oxides. Astrobiology 14, 1–14.
doi:10.1089/ast.2013.0974
PMCID: PMC3901165  PMID: 24380534
6.  Setting the Stage: The History, Chemistry, and Geobiology behind RNA 
No community-accepted scientific methods are available today to guide studies on what role RNA played in the origin and early evolution of life on Earth. Further, a definition-theory for life is needed to develop hypotheses relating to the “RNA First” model for the origin of life. Four approaches are currently at various stages of development of such a definition-theory to guide these studies. These are (a) paleogenetics, in which inferences about the structure of past life are drawn from the structure of present life; (b) prebiotic chemistry, in which hypotheses with experimental support are sought that get RNA from organic and inorganic species possibly present on early Earth; (c) exploration, hoping to encounter life independent of terran life, which might contain RNA; and (d) synthetic biology, in which laboratories attempt to reproduce biological behavior with unnatural chemical systems.
Studies of how self-replicating genetic material first arose on Earth involve paleogenetics, prebiotic chemistry, exploration, and synthetic biology. All currently support the “RNA first” hypothesis.
doi:10.1101/cshperspect.a003541
PMCID: PMC3249627  PMID: 20880988
7.  Selfishness, warfare, and economics; or integration, cooperation, and biology 
The acceptance of Darwin's theory of evolution by natural selection is not complete and it has been pointed out its limitation to explain the complex processes that constitute the transformation of species. It is necessary to discuss the explaining power of the dominant paradigm. It is common that new discoveries bring about contradictions that are intended to be overcome by adjusting results to the dominant reductionist paradigm using all sorts of gradations and combinations that are admitted for each case. In addition to the discussion on the validity of natural selection, modern findings represent a challenge to the interpretation of the observations with the Darwinian view of competition and struggle for life as theoretical basis. New holistic interpretations are emerging related to the Net of Life, in which the interconnection of ecosystems constitutes a dynamic and self-regulating biosphere: viruses are recognized as a macroorganism with a huge collection of genes, most unknown that constitute the major planet's gene pool. They play a fundamental role in evolution since their sequences are capable of integrating into the genomes in an “infective” way and become an essential part of multicellular organisms. They have content with “biological sense” i.e., they appear as part of normal life processes and have a serious role as carrier elements of complex genetic information. Antibiotics are cell signals with main effects on general metabolism and transcription on bacterial cells and communities. The hologenome theory considers an organism and all of its associated symbiotic microbes (parasites, mutualists, synergists, amensalists) as a result of symbiopoiesis. Microbes, helmints, that are normally understood as parasites are cohabitants and they have cohabited with their host and drive the evolution and existence of the partners. Each organism is the result of integration of complex systems. The eukaryotic organism is the result of combination of bacterial, virus, and eukaryotic DNA and it is the result of the interaction of its own genome with the genome of its microbiota, and their metabolism are intertwined (as a “superorganism”) along evolution. The darwinian paradigm had its origin in the free market theories and concepts of Malthus and Spencer. Then, nature was explained on the basis of market theories moving away from an accurate explanation of natural phenomena. It is necessary to acknowledge the limitations of the dominant dogma. These new interpretations about biological processes, molecules, roles of viruses in nature, and microbial interactions are remarkable points to be considered in order to construct a solid theory adjusted to the facts and with less speculations and tortuous semantic traps.
doi:10.3389/fcimb.2012.00054
PMCID: PMC3417387  PMID: 22919645
Darwinism; natural selection; evolution; paradigm; virus; hologenome; autopoiesis
8.  Tidal Venuses: Triggering a Climate Catastrophe via Tidal Heating 
Astrobiology  2013;13(3):225-250.
Abstract
Traditionally, stellar radiation has been the only heat source considered capable of determining global climate on long timescales. Here, we show that terrestrial exoplanets orbiting low-mass stars may be tidally heated at high-enough levels to induce a runaway greenhouse for a long-enough duration for all the hydrogen to escape. Without hydrogen, the planet no longer has water and cannot support life. We call these planets “Tidal Venuses” and the phenomenon a “tidal greenhouse.” Tidal effects also circularize the orbit, which decreases tidal heating. Hence, some planets may form with large eccentricity, with its accompanying large tidal heating, and lose their water, but eventually settle into nearly circular orbits (i.e., with negligible tidal heating) in the habitable zone (HZ). However, these planets are not habitable, as past tidal heating desiccated them, and hence should not be ranked highly for detailed follow-up observations aimed at detecting biosignatures. We simulated the evolution of hypothetical planetary systems in a quasi-continuous parameter distribution and found that we could constrain the history of the system by statistical arguments. Planets orbiting stars with masses<0.3 MSun may be in danger of desiccation via tidal heating. We have applied these concepts to Gl 667C c, a ∼4.5 MEarth planet orbiting a 0.3 MSun star at 0.12 AU. We found that it probably did not lose its water via tidal heating, as orbital stability is unlikely for the high eccentricities required for the tidal greenhouse. As the inner edge of the HZ is defined by the onset of a runaway or moist greenhouse powered by radiation, our results represent a fundamental revision to the HZ for noncircular orbits. In the appendices we review (a) the moist and runaway greenhouses, (b) hydrogen escape, (c) stellar mass-radius and mass-luminosity relations, (d) terrestrial planet mass-radius relations, and (e) linear tidal theories. Key Words: Extrasolar terrestrial planets—Habitability—Habitable zone—Liquid water—Tides. Astrobiology 13, 225–250.
doi:10.1089/ast.2012.0851
PMCID: PMC3612283  PMID: 23537135
9.  Life, Information, Entropy, and Time 
Complexity  2007;13(1):14-50.
Attempts to understand how information content can be included in an accounting of the energy flux of the biosphere have led to the conclusion that, in information transmission, one component, the semantic content, or “the meaning of the message,” adds no thermodynamic burden over and above costs arising from coding, transmission and translation. In biology, semantic content has two major roles. For all life forms, the message of the genotype encoded in DNA specifies the phenotype, and hence the organism that is tested against the real world through the mechanisms of Darwinian evolution. For human beings, communication through language and similar abstractions provides an additional supra-phenotypic vehicle for semantic inheritance, which supports the cultural heritages around which civilizations revolve. The following three postulates provide the basis for discussion of a number of themes that demonstrate some important consequences. (i) Information transmission through either pathway has thermodynamic components associated with data storage and transmission. (ii) The semantic content adds no additional thermodynamic cost. (iii) For all semantic exchange, meaning is accessible only through translation and interpretation, and has a value only in context. (1) For both pathways of semantic inheritance, translational and copying machineries are imperfect. As a consequence both pathways are subject to mutation and to evolutionary pressure by selection. Recognition of semantic content as a common component allows an understanding of the relationship between genes and memes, and a reformulation of Universal Darwinism. (2) The emergent properties of life are dependent on a processing of semantic content. The translational steps allow amplification in complexity through combinatorial possibilities in space and time. Amplification depends on the increased potential for complexity opened by 3D interaction specificity of proteins, and on the selection of useful variants by evolution. The initial interpretational steps include protein synthesis, molecular recognition, and catalytic potential that facilitate structural and functional roles. Combinatorial possibilities are extended through interactions of increasing complexity in the temporal dimension. (3) All living things show a behavior that indicates awareness of time, or chronognosis. The ∼4 billion years of biological evolution have given rise to forms with increasing sophistication in sensory adaptation. This has been linked to the development of an increasing chronognostic range, and an associated increase in combinatorial complexity. (4) Development of a modern human phenotype and the ability to communicate through language, led to the development of archival storage, and invention of the basic skills, institutions and mechanisms that allowed the evolution of modern civilizations. Combinatorial amplification at the supra-phenotypical level arose from the invention of syntax, grammar, numbers, and the subsequent developments of abstraction in writing, algorithms, etc. The translational machineries of the human mind, the “mutation” of ideas therein, and the “conversations” of our social intercourse, have allowed a limited set of symbolic descriptors to evolve into an exponentially expanding semantic heritage. (5) The three postulates above open interesting epistemological questions. An understanding of topics such dualism, the élan vital, the status of hypothesis in science, memetics, the nature of consciousness, the role of semantic processing in the survival of societies, and Popper's three worlds, require recognition of an insubstantial component. By recognizing a necessary linkage between semantic content and a physical machinery, we can bring these perennial problems into the framework of a realistic philosophy. It is suggested, following Popper, that the ∼4 billion years of evolution of the biosphere represents an exploration of the nature of reality at the physicochemical level, which, together with the conscious extension of this exploration through science and culture, provides a firm epistemological underpinning for such a philosophy.
doi:10.1002/cplx.20180
PMCID: PMC2577055  PMID: 18978960
DNA; genotype; evolution; chronognosis; semantic content; Popper; evolutionary epistemology; memes
10.  Multilevel Selection in Models of Prebiotic Evolution II: A Direct Comparison of Compartmentalization and Spatial Self-Organization 
PLoS Computational Biology  2009;5(10):e1000542.
Multilevel selection has been indicated as an essential factor for the evolution of complexity in interacting RNA-like replicator systems. There are two types of multilevel selection mechanisms: implicit and explicit. For implicit multilevel selection, spatial self-organization of replicator populations has been suggested, which leads to higher level selection among emergent mesoscopic spatial patterns (traveling waves). For explicit multilevel selection, compartmentalization of replicators by vesicles has been suggested, which leads to higher level evolutionary dynamics among explicitly imposed mesoscopic entities (protocells). Historically, these mechanisms have been given separate consideration for the interests on its own. Here, we make a direct comparison between spatial self-organization and compartmentalization in simulated RNA-like replicator systems. Firstly, we show that both mechanisms achieve the macroscopic stability of a replicator system through the evolutionary dynamics on mesoscopic entities that counteract that of microscopic entities. Secondly, we show that a striking difference exists between the two mechanisms regarding their possible influence on the long-term evolutionary dynamics, which happens under an emergent trade-off situation arising from the multilevel selection. The difference is explained in terms of the difference in the stability between self-organized mesoscopic entities and externally imposed mesoscopic entities. Thirdly, we show that a sharp transition happens in the long-term evolutionary dynamics of the compartmentalized system as a function of replicator mutation rate. Fourthly, the results imply that spatial self-organization can allow the evolution of stable folding in parasitic replicators without any specific functionality in the folding itself. Finally, the results are discussed in relation to the experimental synthesis of chemical Darwinian systems and to the multilevel selection theory of evolutionary biology in general. To conclude, novel evolutionary directions can emerge through interactions between the evolutionary dynamics on multiple levels of organization. Different multilevel selection mechanisms can produce a difference in the long-term evolutionary trend of identical microscopic entities.
Author Summary
The origin of life has ever been attracting scientific inquiries. The RNA world hypothesis suggests that, before the evolution of DNA and protein, primordial life was based on RNA-like molecules both for information storage and chemical catalysis. In the simplest form, an RNA world consists of RNA molecules that can catalyze the replication of their own copies. Thus, an interesting question is whether a system of RNA-like replicators can increase its complexity through Darwinian evolution and approach the modern form of life. It is, however, known that simple natural selection acting on individual replicators is insufficient to account for the evolution of complexity due to the evolution of parasite-like templates. Two solutions have been suggested: compartmentalization of replicators by membranes (i.e., protocells) and spatial self-organization of a replicator population. Here, we make a direct comparison of the two suggestions by computer simulations. Our results show that the two suggestions can lead to unanticipated and contrasting consequences in the long-term evolution of replicating molecules. The results also imply a novel advantage in the spatial self-organization for the evolution of complexity in RNA-like replicator systems.
doi:10.1371/journal.pcbi.1000542
PMCID: PMC2757730  PMID: 19834556
11.  The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life 
Biology Direct  2007;2:15.
Background
Recent developments in cosmology radically change the conception of the universe as well as the very notions of "probable" and "possible". The model of eternal inflation implies that all macroscopic histories permitted by laws of physics are repeated an infinite number of times in the infinite multiverse. In contrast to the traditional cosmological models of a single, finite universe, this worldview provides for the origin of an infinite number of complex systems by chance, even as the probability of complexity emerging in any given region of the multiverse is extremely low. This change in perspective has profound implications for the history of any phenomenon, and life on earth cannot be an exception.
Hypothesis
Origin of life is a chicken and egg problem: for biological evolution that is governed, primarily, by natural selection, to take off, efficient systems for replication and translation are required, but even barebones cores of these systems appear to be products of extensive selection. The currently favored (partial) solution is an RNA world without proteins in which replication is catalyzed by ribozymes and which serves as the cradle for the translation system. However, the RNA world faces its own hard problems as ribozyme-catalyzed RNA replication remains a hypothesis and the selective pressures behind the origin of translation remain mysterious. Eternal inflation offers a viable alternative that is untenable in a finite universe, i.e., that a coupled system of translation and replication emerged by chance, and became the breakthrough stage from which biological evolution, centered around Darwinian selection, took off. A corollary of this hypothesis is that an RNA world, as a diverse population of replicating RNA molecules, might have never existed. In this model, the stage for Darwinian selection is set by anthropic selection of complex systems that rarely but inevitably emerge by chance in the infinite universe (multiverse).
Conclusion
The plausibility of different models for the origin of life on earth directly depends on the adopted cosmological scenario. In an infinite universe (multiverse), emergence of highly complex systems by chance is inevitable. Therefore, under this cosmology, an entity as complex as a coupled translation-replication system should be considered a viable breakthrough stage for the onset of biological evolution.
Reviewers
This article was reviewed by Eric Bapteste, David Krakauer, Sergei Maslov, and Itai Yanai.
doi:10.1186/1745-6150-2-15
PMCID: PMC1892545  PMID: 17540027
12.  A First-Principles Model of Early Evolution: Emergence of Gene Families, Species, and Preferred Protein Folds 
PLoS Computational Biology  2007;3(7):e139.
In this work we develop a microscopic physical model of early evolution where phenotype—organism life expectancy—is directly related to genotype—the stability of its proteins in their native conformations—which can be determined exactly in the model. Simulating the model on a computer, we consistently observe the “Big Bang” scenario whereby exponential population growth ensues as soon as favorable sequence–structure combinations (precursors of stable proteins) are discovered. Upon that, random diversity of the structural space abruptly collapses into a small set of preferred proteins. We observe that protein folds remain stable and abundant in the population at timescales much greater than mutation or organism lifetime, and the distribution of the lifetimes of dominant folds in a population approximately follows a power law. The separation of evolutionary timescales between discovery of new folds and generation of new sequences gives rise to emergence of protein families and superfamilies whose sizes are power-law distributed, closely matching the same distributions for real proteins. On the population level we observe emergence of species—subpopulations that carry similar genomes. Further, we present a simple theory that relates stability of evolving proteins to the sizes of emerging genomes. Together, these results provide a microscopic first-principles picture of how first-gene families developed in the course of early evolution.
Author Summary
Here, we address the question of how Darwinian evolution of organisms determines molecular evolution of their proteins and genomes. We developed a microscopic ab initio model of early biological evolution where the fitness (essentially lifetime) of an organism is explicitly related to the evolving sequences of its proteins. The main assumption of the model is that the death rate of an organism is determined by the stability of the least stable of their proteins. A lattice model is used to calculate stability of all proteins in a genome from their amino acid sequence. The simulation of the model starts from 100 identical organisms, each carrying the same random gene, and proceeds via random mutations, gene duplication, organism births via replication, and organism deaths. We find that exponential population growth is possible only after the discovery of a very small number of specific advantageous protein structures. The number of genes in the evolving organisms depends on the mutation rate, demonstrating the intricate relationship between the genome sizes and protein stability requirements. Further, the model explains the observed power-law distributions of protein family and superfamily sizes, as well as the scale-free character of protein structural similarity graphs. Together, these results and their analysis suggest a plausible comprehensive scenario of emergence of the protein universe in early biological evolution.
doi:10.1371/journal.pcbi.0030139
PMCID: PMC1914367  PMID: 17630830
13.  On the Origin of DNA Genomes: Evolution of the Division of Labor between Template and Catalyst in Model Replicator Systems 
PLoS Computational Biology  2011;7(3):e1002024.
The division of labor between template and catalyst is a fundamental property of all living systems: DNA stores genetic information whereas proteins function as catalysts. The RNA world hypothesis, however, posits that, at the earlier stages of evolution, RNA acted as both template and catalyst. Why would such division of labor evolve in the RNA world? We investigated the evolution of DNA-like molecules, i.e. molecules that can function only as template, in minimal computational models of RNA replicator systems. In the models, RNA can function as both template-directed polymerase and template, whereas DNA can function only as template. Two classes of models were explored. In the surface models, replicators are attached to surfaces with finite diffusion. In the compartment models, replicators are compartmentalized by vesicle-like boundaries. Both models displayed the evolution of DNA and the ensuing division of labor between templates and catalysts. In the surface model, DNA provides the advantage of greater resistance against parasitic templates. However, this advantage is at least partially offset by the disadvantage of slower multiplication due to the increased complexity of the replication cycle. In the compartment model, DNA can significantly delay the intra-compartment evolution of RNA towards catalytic deterioration. These results are explained in terms of the trade-off between template and catalyst that is inherent in RNA-only replication cycles: DNA releases RNA from this trade-off by making it unnecessary for RNA to serve as template and so rendering the system more resistant against evolving parasitism. Our analysis of these simple models suggests that the lack of catalytic activity in DNA by itself can generate a sufficient selective advantage for RNA replicator systems to produce DNA. Given the widespread notion that DNA evolved owing to its superior chemical properties as a template, this study offers a novel insight into the evolutionary origin of DNA.
Author Summary
At the core of all biological systems lies the division of labor between the storage of genetic information and its phenotypic implementation, in other words, the functional differentiation between templates (DNA) and catalysts (proteins). This fundamental property of life is believed to have been absent at the earliest stages of evolution. The RNA world hypothesis, the most realistic current scenario for the origin of life, posits that, in primordial replicating systems, RNA functioned both as template and as catalyst. How would such division of labor emerge through Darwinian evolution? We investigated the evolution of DNA-like molecules in minimal computational models of RNA replicator systems. Two models were considered: one where molecules are adsorbed on surfaces and another one where molecules are compartmentalized by dividing cellular boundaries. Both models exhibit the evolution of DNA and the ensuing division of labor, revealing the simple governing principle of these processes: DNA releases RNA from the trade-off between template and catalyst that is inevitable in the RNA world and thereby enhances the system's resistance against parasitic templates. Hence, this study offers a novel insight into the evolutionary origin of the division of labor between templates and catalysts in the RNA world.
doi:10.1371/journal.pcbi.1002024
PMCID: PMC3063752  PMID: 21455287
14.  Biota and Biomolecules in Extreme Environments on Earth: Implications for Life Detection on Mars 
Life  2014;4(4):535-565.
The three main requirements for life as we know it are the presence of organic compounds, liquid water, and free energy. Several groups of organic compounds (e.g., amino acids, nucleobases, lipids) occur in all life forms on Earth and are used as diagnostic molecules, i.e., biomarkers, for the characterization of extant or extinct life. Due to their indispensability for life on Earth, these biomarkers are also prime targets in the search for life on Mars. Biomarkers degrade over time; in situ environmental conditions influence the preservation of those molecules. Nonetheless, upon shielding (e.g., by mineral surfaces), particular biomarkers can persist for billions of years, making them of vital importance in answering questions about the origins and limits of life on early Earth and Mars. The search for organic material and biosignatures on Mars is particularly challenging due to the hostile environment and its effect on organic compounds near the surface. In support of life detection on Mars, it is crucial to investigate analogue environments on Earth that resemble best past and present Mars conditions. Terrestrial extreme environments offer a rich source of information allowing us to determine how extreme conditions affect life and molecules associated with it. Extremophilic organisms have adapted to the most stunning conditions on Earth in environments with often unique geological and chemical features. One challenge in detecting biomarkers is to optimize extraction, since organic molecules can be low in abundance and can strongly adsorb to mineral surfaces. Methods and analytical tools in the field of life science are continuously improving. Amplification methods are very useful for the detection of low concentrations of genomic material but most other organic molecules are not prone to amplification methods. Therefore, a great deal depends on the extraction efficiency. The questions “what to look for”, “where to look”, and “how to look for it” require more of our attention to ensure the success of future life detection missions on Mars.
doi:10.3390/life4040535
PMCID: PMC4284457  PMID: 25370528
biomarkers; Mars; minerals; adsorption; extreme environments; life detection; extraction techniques; origin of life
15.  Raman Spectroscopic Analysis of Geological and Biogeological Specimens of Relevance to the ExoMars Mission 
Astrobiology  2013;13(6):543-549.
Abstract
A novel miniaturized Raman spectrometer is scheduled to fly as part of the analytical instrumentation package on an ESA remote robotic lander in the ESA/Roscosmos ExoMars mission to search for evidence for extant or extinct life on Mars in 2018. The Raman spectrometer will be part of the first-pass analytical stage of the sampling procedure, following detailed surface examination by the PanCam scanning camera unit on the ExoMars rover vehicle. The requirements of the analytical protocol are stringent and critical; this study represents a laboratory blind interrogation of specimens that form a list of materials that are of relevance to martian exploration and at this stage simulates a test of current laboratory instrumentation to highlight the Raman technique strengths and possible weaknesses that may be encountered in practice on the martian surface and from which future studies could be formulated. In this preliminary exercise, some 10 samples that are considered terrestrial representatives of the mineralogy and possible biogeologically modified structures that may be identified on Mars have been examined with Raman spectroscopy, and conclusions have been drawn about the viability of the unambiguous spectral identification of biomolecular life signatures. It is concluded that the Raman spectroscopic technique does indeed demonstrate the capability to identify biomolecular signatures and the mineralogy in real-world terrestrial samples with a very high degree of success without any preconception being made about their origin and classification. Key Words: Biosignatures—Mars Exploration Rovers—Raman spectroscopy—Search for life (biosignatures)—Planetary instrumentation. Astrobiology 13, 543–549.
doi:10.1089/ast.2012.0872
PMCID: PMC3689185  PMID: 23758166
16.  Planetary Organic Chemistry and the Origins of Biomolecules 
Organic chemistry on a planetary scale is likely to have transformed carbon dioxide and reduced carbon species delivered to an accreting Earth. According to various models for the origin of life on Earth, biological molecules that jump-started Darwinian evolution arose via this planetary chemistry. The grandest of these models assumes that ribonucleic acid (RNA) arose prebiotically, together with components for compartments that held it and a primitive metabolism that nourished it. Unfortunately, it has been challenging to identify possible prebiotic chemistry that might have created RNA. Organic molecules, given energy, have a well-known propensity to form multiple products, sometimes referred to collectively as “tar” or “tholin.” These mixtures appear to be unsuited to support Darwinian processes, and certainly have never been observed to spontaneously yield a homochiral genetic polymer. To date, proposed solutions to this challenge either involve too much direct human intervention to satisfy many in the community, or generate molecules that are unreactive “dead ends” under standard conditions of temperature and pressure. Carbohydrates, organic species having carbon, hydrogen, and oxygen atoms in a ratio of 1:2:1 and an aldehyde or ketone group, conspicuously embody this challenge. They are components of RNA and their reactivity can support both interesting spontaneous chemistry as part of a “carbohydrate world,” but they also easily form mixtures, polymers and tars. We describe here the latest thoughts on how on this challenge, focusing on how it might be resolved using minerals containing borate, silicate, and molybdate, inter alia.
Borates, silicates, and other minerals may have promoted prebiotic chemical reactions in which organic molecules produced RNA, rather than “dead end” polymers and tars.
doi:10.1101/cshperspect.a003467
PMCID: PMC2890202  PMID: 20504964
17.  THE NICHE CONSTRUCTION PERSPECTIVE: A CRITICAL APPRAISAL* 
Niche construction refers to the activities of organisms that bring about changes in their environments, many of which are evolutionarily and ecologically consequential. Advocates of niche construction theory (NCT) believe that standard evolutionary theory fails to recognize the full importance of niche construction, and consequently propose a novel view of evolution, in which niche construction and its legacy over time (ecological inheritance) are described as evolutionary processes, equivalent in importance to natural selection. Here, we subject NCT to critical evaluation, in the form of a collaboration between one prominent advocate of NCT, and a team of skeptics. We discuss whether niche construction is an evolutionary process, whether NCT obscures or clarifies how natural selection leads to organismal adaptation, and whether niche construction and natural selection are of equivalent explanatory importance. We also consider whether the literature that promotes NCT overstates the significance of niche construction, whether it is internally coherent, and whether it accurately portrays standard evolutionary theory. Our disagreements reflect a wider dispute within evolutionary theory over whether the neo-Darwinian synthesis is in need of reformulation, as well as different usages of some key terms (e.g., evolutionary process).
doi:10.1111/evo.12332
PMCID: PMC4261998  PMID: 24325256
Adaptation; adaptationism; evolution; natural selection; niche; niche construction
18.  Abiotic Production of Methane in Terrestrial Planets 
Astrobiology  2013;13(6):550-559.
Abstract
On Earth, methane is produced mainly by life, and it has been proposed that, under certain conditions, methane detected in an exoplanetary spectrum may be considered a biosignature. Here, we estimate how much methane may be produced in hydrothermal vent systems by serpentinization, its main geological source, using the kinetic properties of the main reactions involved in methane production by serpentinization. Hydrogen production by serpentinization was calculated as a function of the available FeO in the crust, given the current spreading rates. Carbon dioxide is the limiting reactant for methane formation because it is highly depleted in aqueous form in hydrothermal vent systems. We estimated maximum CH4 surface fluxes of 6.8×108 and 1.3×109 molecules cm−2 s−1 for rocky planets with 1 and 5 M⊕, respectively. Using a 1-D photochemical model, we simulated atmospheres with volume mixing ratios of 0.03 and 0.1 CO2 to calculate atmospheric methane concentrations for the maximum production of this compound by serpentinization. The resulting abundances were 2.5 and 2.1 ppmv for 1 M⊕ planets and 4.1 and 3.7 ppmv for 5 M⊕ planets. Therefore, low atmospheric concentrations of methane may be produced by serpentinization. For habitable planets around Sun-like stars with N2-CO2 atmospheres, methane concentrations larger than 10 ppmv may indicate the presence of life. Key Words: Serpentinization—Exoplanets—Biosignatures—Planetary atmospheres. Astrobiology 13, 550–559.
doi:10.1089/ast.2012.0817
PMCID: PMC3689174  PMID: 23742231
19.  Direct Measurements of Human Colon Crypt Stem Cell Niche Genetic Fidelity: The Role of Chance in Non-Darwinian Mutation Selection 
Frontiers in Oncology  2013;3:264.
Perfect human stem cell genetic fidelity would prevent aging and cancer. However, perfection would be difficult to achieve, and aging is universal and cancers common. A hypothesis is that because mutations are inevitable over a human lifetime, downstream mechanisms have evolved to manage the deleterious effects of beneficial and lethal mutations. In the colon, a crypt stem cell architecture reduces the number of mitotic cells at risk for mutation accumulation, and multiple niche stem cells ensure that a lethal mutation within any single stem cell does not lead to crypt death. In addition, the architecture of the colon crypt stem cell niche may harness probability or chance to randomly discard many beneficial mutations that might lead to cancer. An analysis of somatic chromosome copy number alterations (CNAs) reveals a lack of perfect fidelity in individual normal human crypts, with age-related increases and higher frequencies in ulcerative colitis, a proliferative, inflammatory disease. The age-related increase in somatic CNAs appears consistent with relatively normal replication error and cell division rates. Surprisingly, and similar to point mutations in cancer genomes, the types of crypt mutations were more consistent with random fixation rather than selection. In theory, a simple “non-Darwinian” way to nullify selection is to reduce the size of the reproducing population. Fates are more determined by chance rather than selection in very small populations, and therefore selection may be minimized within small crypt niches. The desired effect is that many beneficial mutations that might lead to cancer are randomly lost by drift rather than fixed by selection. The subdivision of the colon into multiple very small stem cell niches may trade Darwinian evolution for non-Darwinian somatic cell evolution, capitulating to aging but reducing cancer risks.
doi:10.3389/fonc.2013.00264
PMCID: PMC3796283  PMID: 24133655
stem cell niche; non-Darwinian; neutral drift; human; replication errors; aging; Muller’s ratchet
20.  Sex Is Always Well Worth Its Two-Fold Cost 
PLoS ONE  2009;4(7):e6012.
Sex is considered as an evolutionary paradox, since its positive contribution to Darwinian fitness remains unverified for some species. Defenses against unpredictable threats (parasites, fluctuating environment and deleterious mutations) are indeed significantly improved by wider genetic variability and by positive epistasis gained by sexual reproduction. The corresponding evolutionary advantages, however, do not overcome universally the barrier of the two-fold cost for sharing half of one's offspring genome with another member of the population. Here we show that sexual reproduction emerges and is maintained even when its Darwinian fitness is twice as low as the fitness of asexuals. We also show that more than two sexes (inheritance of genetic material from three or even more parents) are always evolutionary unstable. Our approach generalizes the evolutionary game theory to analyze species whose members are able to sense the sexual state of their conspecifics and to adapt their own sex consequently, either by switching or by taxis towards the highest concentration of the complementary sex. The widespread emergence and maintenance of sex follows therefore from its co-evolution with the even more widespread environmental sensing abilities.
doi:10.1371/journal.pone.0006012
PMCID: PMC2701646  PMID: 19582152
21.  Deep Phylogeny—How a Tree Can Help Characterize Early Life on Earth 
The Darwinian concept of biological evolution assumes that life on Earth shares a common ancestor. The diversification of this common ancestor through speciation events and vertical transmission of genetic material implies that the classification of life can be illustrated in a tree-like manner, commonly referred to as the Tree of Life. This article describes features of the Tree of Life, such as how the tree has been both pruned and become bushier throughout the past century as our knowledge of biology has expanded. We present current views that the classification of life may be best illustrated as a ring or even a coral with tree-like characteristics. This article also discusses how the organization of the Tree of Life offers clues about ancient life on Earth. In particular, we focus on the environmental conditions and temperature history of Precambrian life and show how chemical, biological, and geological data can converge to better understand this history.
“You know, a tree is a tree.  How many more do you need to look at?”–Ronald Reagan (Governor of California), quoted in the Sacramento Bee, opposing expansion of Redwood National Park, March 3, 1966
Environmental temperature significantly influenced the evolution of early life forms. Reconstruction of ancestral DNA sequences is helping to reveal Earth’s temperature history.
doi:10.1101/cshperspect.a002238
PMCID: PMC2827910  PMID: 20182607
22.  The Cuatro Ciénegas Basin in Coahuila, Mexico: An Astrobiological Precambrian Park 
Astrobiology  2012;12(7):641-647.
Abstract
The Cuatro Ciénegas Basin (CCB) is a rare oasis in the Chihuahuan Desert in the state of Coahuila, Mexico. It has a biological endemism similar to that of the Galapagos Islands, and its spring-fed ecosystems have very low nutrient content (nitrogen or phosphorous) and are dominated by diverse microbialites. Thus, it has proven to be a distinctive opportunity for the field of astrobiology, as the CCB can be seen as a proxy for an earlier time in Earth's history, in particular the late Precambrian, the biological frontier when prokaryotic life yielded at least partial dominance to eukaryotes and multicellular life. It is a kind of ecological time machine that provides abundant opportunities for collaborative investigations by geochemists, geologists, ecologists, and population biologists in the study of the evolutionary processes that structured Earth-based life, especially in the microbial realm. The CCB is an object of investigation for the identification of biosignatures of past and present biota that can be used in our search for extraterrestrial life. In this review, we summarize CCB research efforts that began with microbial ecology and population biology projects and have since been expanded into broader efforts that involve biogeochemistry, comparative genomics, and assessments of biosignatures. We also propose that, in the future, the CCB is sanctioned as a “Precambrian Park” for astrobiology. Key Words: Microbial mats—Stromatolites—Early Earth—Extremophilic microorganisms—Microbial ecology. Astrobiology 12, 641–647.
doi:10.1089/ast.2011.0675
PMCID: PMC3426885  PMID: 22920514
23.  Evolution: like any other science it is predictable 
Evolutionary biology rejoices in the diversity of life, but this comes at a cost: other than working in the common framework of neo-Darwinian evolution, specialists in, for example, diatoms and mammals have little to say to each other. Accordingly, their research tends to track the particularities and peculiarities of a given group and seldom enquires whether there are any wider or deeper sets of explanations. Here, I present evidence in support of the heterodox idea that evolution might look to a general theory that does more than serve as a tautology (‘evolution explains evolution’). Specifically, I argue that far from its myriad of products being fortuitous and accidental, evolution is remarkably predictable. Thus, I urge a move away from the continuing obsession with Darwinian mechanisms, which are entirely uncontroversial. Rather, I emphasize why we should seek explanations for ubiquitous evolutionary convergence, as well as the emergence of complex integrated systems. At present, evolutionary theory seems to be akin to nineteenth-century physics, blissfully unaware of the imminent arrival of quantum mechanics and general relativity. Physics had its Newton, biology its Darwin: evolutionary biology now awaits its Einstein.
doi:10.1098/rstb.2009.0154
PMCID: PMC2842699  PMID: 20008391
evolution; convergence; frogs; theropods; E. coli; viruses
24.  On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization 
Biology Direct  2007;2:14.
Background
The origin of the translation system is, arguably, the central and the hardest problem in the study of the origin of life, and one of the hardest in all evolutionary biology. The problem has a clear catch-22 aspect: high translation fidelity hardly can be achieved without a complex, highly evolved set of RNAs and proteins but an elaborate protein machinery could not evolve without an accurate translation system. The origin of the genetic code and whether it evolved on the basis of a stereochemical correspondence between amino acids and their cognate codons (or anticodons), through selectional optimization of the code vocabulary, as a "frozen accident" or via a combination of all these routes is another wide open problem despite extensive theoretical and experimental studies. Here we combine the results of comparative genomics of translation system components, data on interaction of amino acids with their cognate codons and anticodons, and data on catalytic activities of ribozymes to develop conceptual models for the origins of the translation system and the genetic code.
Results
Our main guide in constructing the models is the Darwinian Continuity Principle whereby a scenario for the evolution of a complex system must consist of plausible elementary steps, each conferring a distinct advantage on the evolving ensemble of genetic elements. Evolution of the translation system is envisaged to occur in a compartmentalized ensemble of replicating, co-selected RNA segments, i.e., in a RNA World containing ribozymes with versatile activities. Since evolution has no foresight, the translation system could not evolve in the RNA World as the result of selection for protein synthesis and must have been a by-product of evolution drive by selection for another function, i.e., the translation system evolved via the exaptation route. It is proposed that the evolutionary process that eventually led to the emergence of translation started with the selection for ribozymes binding abiogenic amino acids that stimulated ribozyme-catalyzed reactions. The proposed scenario for the evolution of translation consists of the following steps: binding of amino acids to a ribozyme resulting in an enhancement of its catalytic activity; evolution of the amino-acid-stimulated ribozyme into a peptide ligase (predecessor of the large ribosomal subunit) yielding, initially, a unique peptide activating the original ribozyme and, possibly, other ribozymes in the ensemble; evolution of self-charging proto-tRNAs that were selected, initially, for accumulation of amino acids, and subsequently, for delivery of amino acids to the peptide ligase; joining of the peptide ligase with a distinct RNA molecule (predecessor of the small ribosomal subunit) carrying a built-in template for more efficient, complementary binding of charged proto-tRNAs; evolution of the ability of the peptide ligase to assemble peptides using exogenous RNAs as template for complementary binding of charged proteo-tRNAs, yielding peptides with the potential to activate different ribozymes; evolution of the translocation function of the protoribosome leading to the production of increasingly longer peptides (the first proteins), i.e., the origin of translation. The specifics of the recognition of amino acids by proto-tRNAs and the origin of the genetic code depend on whether or not there is a physical affinity between amino acids and their cognate codons or anticodons, a problem that remains unresolved.
Conclusion
We describe a stepwise model for the origin of the translation system in the ancient RNA world such that each step confers a distinct advantage onto an ensemble of co-evolving genetic elements. Under this scenario, the primary cause for the emergence of translation was the ability of amino acids and peptides to stimulate reactions catalyzed by ribozymes. Thus, the translation system might have evolved as the result of selection for ribozymes capable of, initially, efficient amino acid binding, and subsequently, synthesis of increasingly versatile peptides. Several aspects of this scenario are amenable to experimental testing.
Reviewers
This article was reviewed by Rob Knight, Doron Lancet, Alexander Mankin (nominated by Arcady Mushegian), and Arcady Mushegian.
doi:10.1186/1745-6150-2-14
PMCID: PMC1894784  PMID: 17540026
25.  Evolution in Revolution 
Biological evolution represents one of the most successful, but also controversial scientific concepts. Ever since Charles Darwin formulated his version of evolution via natural selection, biological sciences experienced explosive development and progress. First of all, although Darwin could not explain how traits of organisms, selected via natural selection, are inherited and passed down along generations; his theory stimulated research in this respect and resulted in the establishment of genetics and still later in the discovery of DNA and genome sequencing some hundred years after his evolutionary theory. Nevertheless, there are several weaknesses in classical Darwinian as well as Neodarwinian gene-centric views of biological evolution. The most serious drawback is its narrow focus: the modern evolutionary synthesis, as formulated in the 20th Century, is based on the concept of gene and on the mathematical/statistical analysis of populations. While Neodarwinism is still generally considered a valid theory of biological evolution, its narrow focus and incompatibility with several new findings and discoveries calls for its update and/or transformation. Either it will be replaced with an updated version or, if not flexible enough, it will be replaced by a new theory. In his book “Evolution — A New View from the 21st Century,”1 James A. Shapiro discusses these problems as well as newly emerging results which are changing our understanding of biological evolution. This new book joins a row of several other recent books highlighting the same issues.2–13
doi:10.4161/cib.4.5.17702
PMCID: PMC3204118

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