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A formal test of the theory of universal common ancestry
Abstract
Universal common ancestry (UCA) is a central pillar of modern evolutionary theory. As first suggested by Darwin, the theory of UCA posits that all extant terrestrial organisms share a common genetic heritage, each being the genealogical descendant of a single species from the distant past. The classic evidence for UCA, although massive, is largely restricted to 'local' common ancestry-for example, of specific phyla rather than the entirety of life-and has yet to fully integrate the recent advances from modern phylogenetics and probability theory. Although UCA is widely assumed, it has rarely been subjected to formal quantitative testing, and this has led to critical commentary emphasizing the intrinsic technical difficulties in empirically evaluating a theory of such broad scope. Furthermore, several researchers have proposed that early life was characterized by rampant horizontal gene transfer, leading some to question the monophyly of life. Here I provide the first, to my knowledge, formal, fundamental test of UCA, without assuming that sequence similarity implies genetic kinship. I test UCA by applying model selection theory to molecular phylogenies, focusing on a set of ubiquitously conserved proteins that are proposed to be orthologous. Among a wide range of biological models involving the independent ancestry of major taxonomic groups, the model selection tests are found to overwhelmingly support UCA irrespective of the presence of horizontal gene transfer and symbiotic fusion events. These results provide powerful statistical evidence corroborating the monophyly of all known life.
... At the subsequent evolutionary steps, protein intrinsic disorder was reinvented because IDRs/IDPs have specific features crucial for the regulation of complex processes. This prompted the development of more complex organisms from the last universal ancestor (i.e., the most recent organism from which all organisms now living on Earth descend [78,79]), eventually leading to the advent of the highly elaborated eukaryotic cells. Here, primordial proteins are expected to be mostly disordered (left-hand side of the plot), proteins in LUA likely are mostly structured (center of the plot), whereas many protein in eukaryotes are either 10 totally disordered or hybrids containing both ordered and disordered regions (right-hand side of the plot). ...
... It is very likely that IDPs played important roles in at various stages of life origin and evolution, being involved in prebiotic evolution preceding the origin of Tibor Ganti's Chemoton, a suspected precursor to the first universal common ancestor and, subsequently, to later stages of evolution including early origin of complex multicellularity and the ensuing bilateria during the Cambrian explosion ~571 million years ago [217][218][219][220]. The cornerstone of modern evolutionary theory is the existence of a last universal common ancestor (LUCA), which is a hypothetical common ancestral cell from which the three domains of life, the Bacteria, the Archaea, and the Eukarya have originated [78,79] and which lived roughly 3.5 billion years ago, as it follows from a comprehensive computational analysis using model selection theory without making assumption that sequence similarity indicates a genealogical relationship [79]. The existence of LUCA is supported by multiple observations [79,[221][222][223], such as: • ...
... It is very likely that IDPs played important roles in at various stages of life origin and evolution, being involved in prebiotic evolution preceding the origin of Tibor Ganti's Chemoton, a suspected precursor to the first universal common ancestor and, subsequently, to later stages of evolution including early origin of complex multicellularity and the ensuing bilateria during the Cambrian explosion ~571 million years ago [217][218][219][220]. The cornerstone of modern evolutionary theory is the existence of a last universal common ancestor (LUCA), which is a hypothetical common ancestral cell from which the three domains of life, the Bacteria, the Archaea, and the Eukarya have originated [78,79] and which lived roughly 3.5 billion years ago, as it follows from a comprehensive computational analysis using model selection theory without making assumption that sequence similarity indicates a genealogical relationship [79]. The existence of LUCA is supported by multiple observations [79,[221][222][223], such as: • ...
Obviously, the discussion of different factors that could have contributed to the origin of life and evolution represents a clear speculation, since there is no way to check the validity of the most of the related hypotheses on practice, as the corresponding events are not only already happened, but took place in a very distant past. However, there are a few undisputable facts obviously present at the moment, such as the existence of a broad variety of living forms and the abundant presence of intrinsically disordered proteins (IDPs) or hybrid proteins containing ordered domains and intrinsically disordered regions (IDRs) in all those living forms. Since it seems that the currently existing living forms have originated from a common ancestor, their variety represents a result of evolution. Therefore, one could ask a logical question of what role(s) those structure-less and highly dynamic but vastly abundant and multifunctional IDPs/IDRs might have in evolution. This study represents an attempt to consider various ideas pertaining to the potential roles of protein intrinsic disorder in origin of life and evolution.
... Doolittle has warned about the high importance of LGT and its repercussions in TOL and LCA reconstructions (Doolittle 2000), and although his works have been widely cited and discussed, many practitioners in the field have downplayed the importance of his claims, in order to continue with such reconstructions; the ensuing argumentations have been centered on the amount of LGT that has taken place through the history of life. The reconstruction optimism has posed LGT as a much rarer phenomenon than what Doolittle discusses (for example, Theobald 2010 andPuigbò et al. 2013). In the day-to-day practice of molecular phylogeneticists, many have continued with the publication of detailed genetic reconstructions, an approach doomed to discern between cellular and genetic lineages. ...
... describe the properties of the LCA, are subject to strong NNS(Delaye et al 2005, Theobald 2010, Goldman et al 2013. Rates of NNS vary among different traits because the loss in fitness depends on the negative repercussions on the functionality of the trait in question. ...
Reconstructing the genetic traits of the Last Common Ancestor (LCA) and the Tree of Life (TOL) are two examples of the reaches of contemporary molecular phylogenetics. Nevertheless, the whole enterprise has led to paradoxical results. The presence of Lateral Gene Transfer poses epistemic and empirical challenges to meet these goals; the discussion around this subject has been enriched by arguments from philosophers and historians of science. At the same time, a few but influential research groups have aimed to reconstruct the LCA with rich-in-detail hypotheses and high-resolution gene catalogs and metabolic traits. We argue that LGT poses insurmountable challenges for detailed and rich in details reconstructions and propose, instead, a middle-ground position with the reconstruction of a slim LCA based on traits under strong pressures of Negative Natural Selection, and for the need of consilience with evidence from organismal biology and geochemistry. We defend a cautionary perspective that goes beyond the statistical analysis of gene similarities and assumes the broader consequences of evolving empirical data and epistemic pluralism in the reconstruction of early life.
... The Last Universal Common Ancestor (LUCA) is a bacterialike organism, which existed before the bacterial cell lineage divided into the different kingdoms (Theobald, 2010;McInerney, 2016;Weiss et al., 2016). The LUCA is joint ancestor of bacteria and archaea and existed presumably within the time of begin of earth and the oldest fossils, which means that the division of the cell lineage occurred about 4 billion of years ago (Di Giulio, 2011). ...
... Accordingly, the bacterial outer membrane represents the ancestor of the mitochondrial outer membrane. However, whereas the porins of the bacterial outer membranes have only passive sieving properties in bacterial metabolism, it seems that the mitochondrial outer membrane including the eukaryotic porin or Voltage-Dependent Anion Channel (VDAC) plays also an active and important role in mitochondrial and cellular metabolism (Benz, 1994a,b;Shoshan-Barmatz et al., 2006, 2010Gatliff and Campanella, 2012;Grevel and Becker, 2020). It binds different kinases (Fiek et al., 1982;Brdiczka, 1990;Adams et al., 1991;De Pinto et al., 2003) and evidence has been provided that eukaryotic porins play also an important role in mitochondria-mediated apoptosis, protein translocation, and are also involved in response to drugs (Shoshan-Barmatz et al., 2010;Grevel et al., 2019;Grevel and Becker, 2020). ...
Eukaryotic porin, also known as Voltage-Dependent Anion Channel (VDAC), is the most frequent protein in the outer membrane of mitochondria that are responsible for cellular respiration. Mitochondria are most likely descendants of strictly aerobic Gram-negative bacteria from the α-proteobacterial lineage. In accordance with the presumed ancestor, mitochondria are surrounded by two membranes. The mitochondrial outer membrane contains besides the eukaryotic porins responsible for its major permeability properties a variety of other not fully identified channels. It encloses also the TOM apparatus together with the sorting mechanism SAM, responsible for the uptake and assembly of many mitochondrial proteins that are encoded in the nucleus and synthesized in the cytoplasm at free ribosomes. The recognition and the study of electrophysiological properties of eukaryotic porin or VDAC started in the late seventies of the last century by a study of Schein et al., who reconstituted the pore from crude extracts of Paramecium mitochondria into planar lipid bilayer membranes. Whereas the literature about structure and function of eukaryotic porins was comparatively rare during the first 10years after the first study, the number of publications started to explode with the first sequencing of human Porin 31HL and the recognition of the important function of eukaryotic porins in mitochondrial metabolism. Many genomes contain more than one gene coding for homologs of eukaryotic porins. More than 100 sequences of eukaryotic porins are known to date. Although the sequence identity between them is relatively low, the polypeptide length and in particular, the electrophysiological characteristics are highly preserved. This means that all eukaryotic porins studied to date are anion selective in the open state. They are voltage-dependent and switch into cation-selective substates at voltages in the physiological relevant range. A major breakthrough was also the elucidation of the 3D structure of the eukaryotic pore, which is formed by 19 β-strands similar to those of bacterial porin channels. The function of the presumed gate an α-helical stretch of 20 amino acids allowed further studies with respect to voltage dependence and function, but its exact role in channel gating is still not fully understood.
... Much remains unknown about the earliest period of cellular evolution and the deepest divergences in the tree of life. Phylogenies encompassing both Archaea and Bacteria have been inferred from a 'universal core' set of 16-56 genes encoding proteins involved in translation and other aspects of the genetic information processing machinery (Ciccarelli et al., 2006;Fournier and Gogarten, 2010;Harris et al., 2003;Hug et al., 2016;Koonin, 2003;Mukherjee et al., 2017;Petitjean et al., 2014;Ramulu et al., 2014;Raymann et al., 2015;Theobald, 2010;Williams et al., 2020). While representing a small fraction of the total genome of any organism (Dagan and Martin, 2006), these genes are thought to predominantly evolve vertically and are thus best suited for reconstructing the tree of life (Ciccarelli et al., 2006;Creevey et al., 2011;Puigbò et al., 2009;Ramulu et al., 2014;Theobald, 2010). ...
... Phylogenies encompassing both Archaea and Bacteria have been inferred from a 'universal core' set of 16-56 genes encoding proteins involved in translation and other aspects of the genetic information processing machinery (Ciccarelli et al., 2006;Fournier and Gogarten, 2010;Harris et al., 2003;Hug et al., 2016;Koonin, 2003;Mukherjee et al., 2017;Petitjean et al., 2014;Ramulu et al., 2014;Raymann et al., 2015;Theobald, 2010;Williams et al., 2020). While representing a small fraction of the total genome of any organism (Dagan and Martin, 2006), these genes are thought to predominantly evolve vertically and are thus best suited for reconstructing the tree of life (Ciccarelli et al., 2006;Creevey et al., 2011;Puigbò et al., 2009;Ramulu et al., 2014;Theobald, 2010). In these analyses, the branch separating Archaea from Bacteria (hereafter, the AB branch) is often the longest internal branch in the tree (Cox et al., 2008;Gogarten et al., 1989;Hug et al., 2016;Iwabe et al., 1989;Pühler et al., 1989;Williams et al., 2020). ...
Core gene phylogenies provide a window into early evolution, but different gene sets and analytical methods have yielded substantially different views of the tree of life. Trees inferred from a small set of universal core genes have typically supported a long branch separating the archaeal and bacterial domains. By contrast, recent analyses of a broader set of non-ribosomal genes have suggested that Archaea may be less divergent from Bacteria, and that estimates of inter-domain distance are inflated due to accelerated evolution of ribosomal proteins along the inter-domain branch. Resolving this debate is key to determining the diversity of the archaeal and bacterial domains, the shape of the tree of life, and our understanding of the early course of cellular evolution. Here, we investigate the evolutionary history of the marker genes key to the debate. We show that estimates of a reduced Archaea-Bacteria (AB) branch length result from inter-domain gene transfers and hidden paralogy in the expanded marker gene set. By contrast, analysis of a broad range of manually curated marker gene datasets from an evenly sampled set of 700 Archaea and Bacteria reveal that current methods likely underestimate the AB branch length due to substitutional saturation and poor model fit; that the best-performing phylogenetic markers tend to support longer inter-domain branch lengths; and that the AB branch lengths of ribosomal and non-ribosomal marker genes are statistically indistinguishable. Furthermore, our phylogeny inferred from the 27 highest-ranked marker genes recovers a clade of DPANN at the base of the Archaea, and places CPR within Bacteria as the sister group to the Chloroflexota.
... To name some: 1) the fact that common aspects are shared at the molecular level, including fundamental biological polymers: nucleic acid as genetic material and L-amino acids as components of proteins; 2) the general unit of biochemistry in terms of basic metabolic and energy processes; 3) the existence of a nearly universal genetic code; 4) the congruence of morphological and molecular phylogenies; 5) the discovery of homologous protein families in the three domains of life (bacteria, archaea and eukaryotes); 6) the correspondence between phylogeny and the palaeontological record and 7) the existence of numerous predicted transitional fossils. Some attempts have been done to show the existence of a common ancestor with a formal quantitative testing (Theobald, 2010;Penny et al., 1982), although an agreement about if this can formally be tested has not been achieved (Velasco, 2018;de Oliveira Martins & Posada, 2016;Koskela & Annila, 2012;Koonin & Wolf, 2010;Theobald, 2010;Penny et al., 1982). The idea of a common ancestry dates to Darwin itself (Darwin, 1871), but the idea of continuity in life is even older. ...
... To name some: 1) the fact that common aspects are shared at the molecular level, including fundamental biological polymers: nucleic acid as genetic material and L-amino acids as components of proteins; 2) the general unit of biochemistry in terms of basic metabolic and energy processes; 3) the existence of a nearly universal genetic code; 4) the congruence of morphological and molecular phylogenies; 5) the discovery of homologous protein families in the three domains of life (bacteria, archaea and eukaryotes); 6) the correspondence between phylogeny and the palaeontological record and 7) the existence of numerous predicted transitional fossils. Some attempts have been done to show the existence of a common ancestor with a formal quantitative testing (Theobald, 2010;Penny et al., 1982), although an agreement about if this can formally be tested has not been achieved (Velasco, 2018;de Oliveira Martins & Posada, 2016;Koskela & Annila, 2012;Koonin & Wolf, 2010;Theobald, 2010;Penny et al., 1982). The idea of a common ancestry dates to Darwin itself (Darwin, 1871), but the idea of continuity in life is even older. ...
The current state of biological knowledge contains an unresolved paradox: life as a continuity in the face of the phenomena of ageing. In this manuscript I propose a theoretical framework that offers a solution for this apparent contradiction. The framework proposed is based on a rethinking of what ageing is at a molecular level, as well as on a rethinking of the mechanisms in charge of the flow of information from one generation to the following ones. I propose an information-based conception of ageing instead of the widely accepted damage-based conception of ageing and propose a full recovery of the chromosome theory of inheritance to describe the intergenerational flow of information. Altogether the proposed framework allows a precise and unique definition of what life is: a continuous flow of biological information. The proposed framework also implies that ageing is merely a consequence of the way in which epigenetically-coded phenotypic characteristics are passed from one generation to the next ones.
... Today, from a scientific point of view, the stunning accumulation of genomic sequences in databases and the myriad of bioinformatics tools developed for their in-depth analysis [1][2][3], make it clear that the fascinating history of life on Earth is written in the pangenome of all living organisms. Comparison of divergent DNA, RNA and/or protein sequences with common ancestors allows us to the theoretical reconstruction of this history back to the first autonomous cell type on our planet that possessed, within a lipid envelope, a nucleic acid synthesis machinery and ribosomes to translate nucleic acids into proteins using a genetic code [4], this hypothetical cell called the Last Universal Common Ancestor LUCA [5][6][7]. ...
About 4 billion years ago, the Earth probably fulfilled the environmental conditions necessary to favour the transition from primitive chemistry to life. Based on a theoretical hairpin duplication origin of tRNAs and their putative peptide-coding capability before ribosomes existed, here I postulate that, at this hypothetical environment, Earth's daily temperature cycles could have provided a unique planetary thermocycler to create self-replicating RNA hairpins that simultaneously templated amino acids polymerization in a primordial PCR well of prebiotic molecules. This early RNA hairpin-peptide interaction could have established a reciprocal nucleopeptide replicator that paved the way for catalytic translation and replication machineries towards the origin of LUCA.
... However, as one goes further back in time, patterns of similarity will inevitably break down and we would expect silent site variation to converge to that expected under SA. Given such a loss of information, the codon usage test is not useful for testing the universal common ancestry (UCA) of all life on earth, which is well known asa difficult problem (Theobald 2010;Koonin and Wolf 2010;Hasegawa 2010, 2012;de Oliveira Martins and Posada 2014). Nonetheless, as applied to a relatively young group like the primates, the tests described here provide enormous statistical support to the CA hypothesis such that anyone who was previously unconvinced of primate CA, and was open to statistical evidence, should be entirely convinced that primate families did not originate independently. ...
The common ancestry of life is supported by an enormous body of evidence and is universally accepted within the scientific community. However, some potential sources of data that can be used to test the thesis of common ancestry have not yet been formally analyzed.
We developed a new test of common ancestry based on nucleotide sequences at amino acid invariant sites in aligned homologous protein coding genes. We reasoned that since nucleotide variation at amino acid invariant sites is selectively neutral and, thus, unlikely to be due to convergent evolution, the observation that an amino acid is consistently encoded by the same codon sequence in different species could provide strong evidence of their common ancestry. Our method uses the observed variation in codon sequences at amino acid invariant sites as a test statistic, and compares such variation to that which is expected under three different models of codon frequency under the alternative hypothesis of separate ancestry. We also examine hierarchical structure in the nucleotide sequences at amino acid invariant sites and quantified agreement between trees generated from amino acid sequence and those inferred from the nucleotide sequences at amino acid invariant sites.
When these tests are applied to the primate families as a test case, we find that observed nucleotide variation at amino acid invariant sites is considerably lower than nucleotide variation predicted by any model of codon frequency under separate ancestry. Phylogenetic trees generated from amino-acid invariant site nucleotide data agree with those generated from protein-coding data, and there is far more hierarchical structure in amino-acid invariant site data than would be expected under separate ancestry.
We definitively reject the separate ancestry of the primate families, and demonstrate that our tests can be applied to any group of interest to test common ancestry.
... Most likely, all extant life on Earth descended from a universal common ancestor. 43 The exercise of building a cell could allow us to postulate what life might have looked like elsewhere in our solar system and beyond, perhaps permitting us to answer one of our most profound scientific questions: are we alone? Further, synthetic cells could offer a platform for understanding how life might operate on specific extraterrestrial bodies, such as the subsurface oceans of Europa and Enceladus. ...
... Speculative descriptions and theoretical predictions about the nature and origin of UCA are abundant, including the 'panspermia' hypothesis, which presumes that terrestrial life originated in outer space (Crick & Orgel, 1973). Regardless of an extraterrestrial or terrestrial origin, and whether life arose only once or multiple times, identifying the UCA using a data-driven and rigorous phylogenetic analysis boils down to determining the root of the universal phylogenetic tree (Harish & Morrison, 2020;Theobald, 2010). Determining the root node, which is the deepest node of the universal tree is one of the hardest problems in phylogenetic analysis and thus far rooting using sequence characters has either (a) generally not been possible (Pace, 1997;Woese, 1987) or (b) has been ambiguous at best (Gouy et al., 2015;Harish et al., 2016;Harish & Morrison, 2020;Harish et al., 2013;Morrison, 2006;Philippe & Forterre, 1999). ...
The formulation and testing of hypotheses using ‘big biology data’ often lie at the interface of computational biology and structural biology. The Protein Data Bank (PDB), which was established about 50 years ago, catalogs three-dimensional (3D) shapes of organic macromolecules and showcases a structural view of biology. The comparative analysis of the structures of homologs, particularly of proteins, from different species has significantly improved the in-depth analyses of molecular and cell biological questions. In addition, computational tools that were developed to analyze the ‘protein universe’ are providing the means for efficient resolution of longstanding debates in cell and molecular evolution. In celebrating the golden jubilee of the PDB, much has been written about the transformative impact of PDB on a broad range of fields of scientific inquiry and how structural biology transformed the study of the fundamental processes of life. Yet, the transforming influence of PDB on one field of inquiry of fundamental interest—the reconstruction of the distant biological past—has gone almost unnoticed. Here, I discuss the recent advances to highlight how insights and tools of structural biology are bearing on the data required for the empirical resolution of vigorously debated and apparently contradicting hypotheses in evolutionary biology. Specifically, I show that evolutionary characters defined by protein structure are superior compared to conventional sequence characters for reliable, data-driven resolution of competing hypotheses about the origins of the major clades of life and evolutionary relationship among those clades. Since the better quality data unequivocally support two primary domains of life, it is imperative that the primary classification of life be revised accordingly.
... We have evolved from the Last Universal Common Ancestor (LUCA), which (who?) appeared on Earth around 3.6 billion years ago (Woese et al., 1990;Woese 1998;Shubin 2009;Theobald 2010;Weiss et al., 2016;Moody et al., 2024;End-note 36). We are directly connected to this single celled organism in terms of life originating from LUCA in a continuous succession. ...
We discuss the wonderful accomplishment that ChatGPT (Chat Generative Pre-Trained Transformer), a chatbot launched by OpenAI in November 2022, is. We connect this milestone to previous research, which suggests that language is but the first step towards creating Artificial Intelligence (AI). We list several steps to help all of us - with specific pointers related to ChatGPT based on its performance in a Turing Test we conducted - get to the next level in creating Artificial Intelligence. We point out that OpenAI may not be as open as it sounds. As closed as OpenAI might be, their creation ChatGPT is undoubtedly an inspiration bound to evoke feelings of true love at first chat. We compare ChatGPT and other contemporary seekers such as DeepSeek - including the challenges of building such creations - while looking at the possibilities, problems and perils that the AI endeavor brings.
We highlight the principal requirement for all intelligent systems, including ChatGPT, which is the inclusion of the principle of inclusion. We develop a numerical index that should aid with incorporating the principle of inclusion and establishing “The Universal Identity”. We suggest subject classification codes and headings, which are to be included in various disciplines as artificial as they are, aimed at incorporating the principle of inclusion and the creation of “The Universal Identity”.
We delve into the responsibilities of society - and the ever-present ethical dilemmas - towards creating responsible AI systems. We look at several crucial pedagogical possibilities, both for ChatGPT and the rest of us. We have a discussion of the many concerns people have, about improvements in AI making jobs redundant, and why there might be a positive side to it. We mathematically prove that taking the first step equals making infinite progress, in this quest for AI and everything else. We discuss computer code generation by computers and why computers are more naturally suited for writing computer programs.
We describe reasons why the Turing Test is irrelevant in gauging intelligence. It is very likely that our pursuit of AI might be misleading. Intelligence could be an unintended consequence of curiosity left to roam free, best exemplified by a frolicking infant. This suggests that our attempts at AI could have been misguided. What we actually need to strive for can be termed artificial curiosity (AC) and intelligence happens as a consequence of those efforts.
We conclude with a conundrum, which should not really be that much of a challenge since it is a no brainer that needs no intelligence, as to what it is that we really want: Artificial Intelligence or Real Consciousness. And once we start to search for real consciousness, another unintended yet welcome consequence might be that, we will find pure happiness. There is nothing artificial about the path to absolute happiness, it is very authentic and well within reach.
... The latter would have been the famous LUCA (Last Universal Common Ancestor), the ancestor of all current terrestrial living beings (for information on LUCA, see e.g. Penny and Poole, 1999;Koonin, 2003;Forterre et al., 2005;Theobald, 2010, and bibliography cited). However, despite this and despite the justified criticisms of other theories, of which it must be taken into account, his hypothesis presents one important defect. ...
The authors use the mathematical tool of Maccone's lognormal distribution to further factor the Drake equation, which calculates the number of advanced civilizations in the galaxy, from the seven original levels of the Drake equation to 49 levels of overall analysis. The Maccone approach, in fact, supported by the central limit theorem, becomes more reliable the more levels are introduced. The resulting study necessarily draws upon an array of disciplines ranging from astronomy, chemistry and geology to biology, palaeontology and futurology. The final result calculates the number of planetary systems suitable for life in its various stages of development: those which have probably hosted life in the past and those which still host it at its various evolutionary levels. The final evolutionary level is the so-called galactic civilization (often called ETC, or extraterrestrial civilizations). The number of resulting galactic civilizations is divided between static civilizations, which do not move around the galaxy and whose Kardašëv rating is still low (<1.4), of which we find three examples (we ourselves plus, perhaps, two others), and potentially dynamic civilizations, which move around the galaxy and have a sufficiently high Kardašëv rating (≥1.4), of which we find 2000.
... When applied to phylogenetics, information criteria provide a statistical framework to identify whether estimated parameters are better modeled under multiple topologies (Theobald, 2010), or whether combining the data and analyzing it under a single topology and set of model parameters provides better information criteria scores . Information criterion measures can also be used to infer optimal partitioning schemes for multilocus datasets (Lanfear et al., 2012) and how best to account for molecular rate heterogeneity among partitions, which is valuable when some loci have experienced rate shifts (Lopez et al., 2002;Chernomor et al., 2016). ...
Chloroplasts and mitochondria each contain their own genomes, which have historically been and continue to be important sources of information for inferring the phylogenetic relationships among land plants. The organelles are predominantly inherited from the same parent, and therefore should exhibit phylogenetic concordance. In this study, we examine the mitochondrion and chloroplast genomes of 226 land plants to infer the degree of similarity between the organelles’ evolutionary histories. Our results show largely concordant topologies are inferred between the organelles, aside from four well-supported conflicting relationships that warrant further investigation. Despite broad patterns of topological concordance, our findings suggest that the chloroplast and mitochondrial genomes evolved with significant differences in molecular evolution. The differences result in the genes from the chloroplast and the mitochondrion preferentially clustering with other genes from their respective organelles by a program that automates selection of evolutionary model partitions for sequence alignments. Further investigation showed that changes in compositional heterogeneity are not always uniform across divergences in the land plant tree of life. These results indicate that although the chloroplast and mitochondrial genomes have coexisted for over 1 billion years, phylogenetically, they are still evolving sufficiently independently to warrant separate models of evolution. As genome sequencing becomes more accessible, research into these organelles’ evolution will continue revealing insight into the ancient cellular events that shaped not only their history, but the history of plants as a whole.
... The subsequent LUCA (Last Universal Common Ancestor) is not claimed to be minimally complex, and we are referring to a still earlier putative organism. 37 If a FUCA never existed, then extant life could not have arisen from a common ancestor. We are not interested here in prebiotic or RNA world speculations preceding a FUCA. ...
The genetic code is contingent on several indispensable components. Parts 1–4 of this series documented how dozens of protein molecular machines are necessary to prepare and process the members of one subsystem, the collection of tRNAs. But without functional linker molecules the necessary protein cannot be manufactured. Evolution theory is incompetent to solve this chicken-and-egg problem.
Given a putative, primitive ancestral code, mathematical modelling demonstrates that at most four precise mutations (or the statistical equivalent in the case of alternative solutions) could have been generated in 10 billion years. This does not
provide a feasible means to produce various features, including: a) the multiple tRNA-specific enzymes involved in some chemical modifications; b) the precise 7-nt target sites found in several Drosophila genomes perfectly complementary to the regulating 5’-tsRNAs; nor c) miRNAs derived from tRNAs having perfect seed regions of about 7 nucleotides.
... This new domain would have two kingdoms: Viral and Humade (derived from the human-made contraction). A fundamental difference of Lithbea with the three Woesian domains is that the latter most likely share a common ancestor (Theobald 2010), whereas evidently there can be no common ancestor for the panoply of heterogeneous entities included in the Lithbea domain. ...
At this time when the development of synthetic biology and artificial intelligence are changing the world around us, philosophers and scientists, first of all, must converge to analyze the present and predict the ethical-social consequences and biological dangers associated with new “living entities” that are not the result of the natural evolutionary process. As synthetic/artificial life forms (xenobots, robots, transgenic organisms, etc.) become more and more abundant and sophisticated, it seems first of all necessary to bring some order to all this new biodiversity, establishing what is alive and what is not, and analyzing the consequences of this incessant creative activity. Here I intend to organize all these human-made entities and clarify their status as living beings or artificial elements, leaving the door open to an uncertain future in which we will be able to see how “the artificial” and “the natural” could merge to originate something different from everything known. Accordingly, I propose the creation of a new domain, Lithbea, which includes all synthetic and artificial entities within a new kingdom called Humade (derived from human-made). I have also included viruses in a new realm, the Viral kingdom, because they were excluded from the classical three-domain tree of life despite playing a fundamental role in the evolution of biodiversity on Earth. Finally, I make a brief comment on the unpredictability of the unknown, the implications of this new landscape of biodiversity, and the uncertain future of all these advances.
... The evolution of intrinsic disorder exhibits a wavy pattern in which highly disordered primordial proteins with predominantly RNA-chaperone-like activities were slowly replaced with highly structured proteins [118,279]. Later, because of its peculiar features regarding the regulation of complex cellular processes, protein disorder was reinvented at various succeeding evolutionary stages, resulting in the creation of more complex organisms from the last universal ancestor [280,281]. ...
Many proteins and protein segments cannot attain a single stable three-dimensional structure under physiological conditions; instead, they adopt multiple interconverting conformational states. Such intrinsically disordered proteins or protein segments are highly abundant across proteomes, and are involved in various effector functions. This review focuses on different aspects of disordered proteins and disordered protein regions, which form the basis of the so-called “Disorder–function paradigm” of proteins. Additionally, various experimental approaches and computational tools used for characterizing disordered regions in proteins are discussed. Finally, the role of disordered proteins in diseases and their utility as potential drug targets are explored.
... The perseverance of life depends on cell division. The fact that a new cell can only be created by duplication of an existing cell implicates that all life on earth -from single celled organisms to complex multi-cellular organisms such as mammals -has evolved from a single cell at the beginning of life on earth over three billion years ago (Theobald, 2010). Cells replicate in two major steps, by duplication of all cellular components and subsequent distribution to the two emerging daughter cells. ...
... It was also pointed out that 'the global evolution of intrinsic disorder is characterized by a wavy pattern, where highly disordered primordial proteins with primarily RNAchaperone activities were gradually substituted by the wellfolded, highly ordered enzymes that evolved to catalyze the production of all the complex "goodies" crucial for the independent existence of the first cellular organisms. Due to its specific features crucial for the regulation of complex processes, protein intrinsic disorder was reinvented at the subsequent evolutionary steps leading to the development of more complex organisms from the last universal ancestor (i.e., the most recent organism from which all organisms now living on Earth descend (Doolittle, 2000;Theobald, 2010)), and culminating in the appearance of the highly elaborated eukaryotic cells' (Uversky, 2013). ...
The discovery of mechanisms for the synthesis of homo-polymeric oligopeptides, such as polyglycine under conditions relevant to the astrophysical environment as well as in scenarios resembling primordial conditions that prevailed soon after Earth was formed, raises hopes in the search of extraterrestrial life. It also raises the possibility of extraterrestrial contribution to origin of life on Earth in the form of simple polypeptides. Bioinformatics analyses strongly predict such homo-polymeric peptides to be intrinsically disordered underscoring the potential involvement of IDPs in the origin of life which, even in its simplest form, could emerge spontaneously by autocatalysis of the primordial IDPs in self-organizing systems that evolved over time following natural selection.Communicated by Ramaswamy H. Sarma.
... This new domain would have two kingdoms: Virus and Humade (derived from the human-made contraction of words). It is very likely that the cellular life forms share a universal common ancestry (Theobald, 2010) but, in contrast, there can be no common ancestor for the panoply of heterogeneous entities included in the Lithbea domain. Organisms belonging to Virus are organic in nature and have a natural origin (a consequence of the evolutionary process). ...
As synthetic/artificial life forms become more abundant and sophisticated, an increasing number of bizarre creatures - xenobots, robots, soft A-life entities, genetically engineered organisms, etc. - are invading our society. Therefore, we need to bring order to all this, to establish what is living and what is not. Here, I intend to classify all these non-natural entities and clarify their status with reference to their consideration or not as living beings, leaving the door open to an uncertain future in which perhaps we can see how "the artificial" and "the natural" merge to originate something new. To order all this "new biodiversity" and to also give entry to viruses (which are excluded of the three-domains tree of life), I propose the creation of a new domain, Lithbea (from the name: life-in-the-border entities), in which all these new human-made entities as well as the viruses will be included. Within this domain there would be two kingdoms, Virus and Humade (contraction of human-made), based on their origin, natural or human-made. A brief description of each component of Lithbea is included and the implications for society and biology of this “new biodiversity” is briefly discussed.
... Current life forms derive from a universal common ancestor that lived four billion years ago (1). The appearance of new molecular functions during much of biological evolution has rested on subtle alteration of preexisting protein structures (e.g. ...
Protein structure is key to understanding biological function. Structure comparison deciphers deep phylogenies, providing insight into functional conservation and functional shifts during evolution. Until recently, structural coverage of the protein universe was limited by the cost and labour involved in experimental structure determination. Recent breakthroughs in deep learning revolutionized structural bioinformatics by providing accurate structural models of numerous protein families for which no structural information existed. The Dali server for 3D protein structure comparison is widely used by crystallographers to relate new structures to pre-existing ones. Here, we report two most recent upgrades to the web server: (i) the foldomes of key organisms in the AlphaFold Database (version 1) are searchable by Dali, (ii) structural alignments are annotated with protein families. Using these new features, we discovered a novel functionally diverse subgroup within the WRKY/GCM1 clan. This was accomplished by linking the structurally characterized SWI/SNF and NAM families as well as the structural models of the CG-1 family and uncharacterized proteins to the structure of Gti1/Pac2, a previously known member of the WRKY/GCM1 clan. The Dali server is available at http://ekhidna2.biocenter.helsinki.fi/dali. This website is free and open to all users and there is no login requirement.
... Hence, e.g. 55% of human proteincoding genes belong to gene groups that were present in the hypothetical first animals [73,62]. ...
The problem that this work addresses is how to retrieve, maintain and synchronize the correct reading frame during the translation process. Translation is the process by which the ribosome decodes the messenger RNA (sequence of nucleotides {A,C,G,T}) as codons (word of 3 nucleotides) to create a specific amino acid chain. Unfortunately, the mRNA can be decoded in three reading frames 0, +1 and +2. Yet, only frame 0 as correct reading frame encodes the Information for the synthesis of proteins. First practical evidence of a genetic model which is able to retrieve the correct reading frame is the so-called X-code. Astonishingly, it turned out that the X-code is a circular code. The advantages of circular genetic codes are incomparable. In this work I introduce new properties. Based on these properties I present a hypothetical guiding line which can help to discover the evolution of protein synthesis.
... 'Life' arose in sea (Dodd et al. 2017), and a part of it made a chance jump over onto the land during the Ordovician period of the Paleozoic Era, followed by successfully colonization and diversification of select ones (Wellman et al. 2003). In other words, in distant past all the present-day life forms had a common ancestry (Theobald 2010 (Christenhusz and Byng 2016). Their defining characters are -reduced male parts, enclosed ovules, reduced female gametophyte and an elaborate endosperm (Baroux et al. 2002;Raven et al. 2005). ...
... Reconstructions of the Last Universal Common Ancestor (LUCA) of all known living organisms (Doolittle, 2000;Theobald, 2010) indicate that LUCA was far more complex than the RNA-world systems described above. The hypothetical LUCA had a DNA-based genome and fully developed machinery for programmed synthesis of proteins. ...
This book invites readers to embark on a journey into the world of agency encompassing humans, other organisms, cells, intracellular molecular agents, colonies, populations, ecological systems, and artificial autonomous systems. We combine mechanistic and non-mechanistic approaches in the analysis of the function and evolution of organisms, their subagents, and multi-organism systems, and in this way offer a theoretical platform for integrating biosemiotics with both natural science and the humanities/social sciences. Agents are autonomous systems that incorporate knowledge on how to make sense of their environment and use it to achieve their goals. The functions of all agents are supported by mechanisms at the lowest level; however, the explanatory power of mechanistic analysis is not sufficient for complex agents. Non-mechanistic methods rely on the goal-directedness of agents whose dynamics follow self-stabilized dynamic attractors. The properties of attractors depend on stable or slowly changing factors, and such dependencies can be interpreted as sign relations if they are adaptive in nature. Agents can replace or redirect mechanisms on demand in order to preserve their functions; for performing higher-level semiotic functions, mechanisms are thus only means. We assume that mechanism and semiosis are not mutually exclusive, and that simple agents can interpret signs mechanistically. This assumption allows us to extend semiotic analysis to all agents, including ribosomes in cells, computers, and robots. This book challenges established traditions in natural science and the humanities/social sciences: semiotics no longer appears as restricted to humans and rational thinking, and biology is no longer limited to rely exclusively on mechanistic reasoning.
... Reconstructions of the Last Universal Common Ancestor (LUCA) of all known living organisms (Doolittle 2000;Theobald 2010) indicate that LUCA was far more complex than the RNA-world systems described above. The hypothetical LUCA had a DNA-based genome and fully developed machinery for programmed synthesis of proteins. ...
The origin of life involves a transition from a merely physical world into the world of semiotic agency
. Attempts to explain the origin of life by synthesis of such organic molecules as peptides or nucleic acids is baseless, because amino acids and nucleotides are products of the evolving life
rather than parts from which the first living system was assembled. We follow the footsteps of Oparin and Dyson in reconstructing primordial self-propagating functional molecular networks. Such networks were initially non-genetic and presumably similar to “lipid world” vesicles. Components of these networks were simple catalysts resembling contemporary coenzymes which might have colonized the surface of small oil droplets in water, where oil (mostly alkanes) was both a substrate and nutrient. Coenzyme-like molecules (CLMs) changed the surface properties of oil droplets, and in this way created favorable conditions for their own self-reproduction. Heredity was supported by a transfer of CLMs
to daughter oil droplets following an accidental split of parental droplets. Niche-dependent self-reproduction and natural selection were necessary conditions for the emergence of cooperation between different kinds of CLMs
that inhabited the same oil droplet. Eventually, some CLMs
formed polymers and their adaptive evolution resulted in the emergence of template-based synthesis similar to that of nucleic acids. Oil droplets eventually transformed into the outer membrane of cells via engulfing water, stabilization of the surface, and osmoregulation. As a result, the metabolism was internalized, allowing cells to accumulate free-floating resources, which was a necessary condition for the emergence of protein
synthesis. This scenario covers a long evolutionary path from simple but already functional and evolvable molecules to cellular organisms comparable to the Last Universal Common Ancestor (LUCA
).
... Universal common ancestry (UCA) is a core pillar of modern evolutionary theory [1], which was first proposed by Darwin in On the Origin of Species. UCA theory is grounded in the hypothesis that all organisms are the offspring of an ancient single life form socalled the last universal common ancestor (LUCA) [2,3]. ...
The mechanisms shaping the amino acids recruitment pattern into the proteins in the early life history presently remains a huge mystery. In this study, we conducted genome-wide analyses of amino acids usage and genetic codons structure in 7270 species across three domains of life. The carried-out analyses evidenced ubiquitous usage bias of amino acids that were likely independent from codon usage bias. Taking advantage of codon usage bias, we performed pseudotime analysis to re-determine the chronological order of the species emergence, which inspired a new species relationship by tracing the imprint of codon usage evolution. Furthermore, the multidimensional data integration showed that the amino acids A, D, E, G, L, P, R, S, T and V might be the first recruited into the last universal common ancestry (LUCA) proteins. The data analysis also indicated that the remaining amino acids most probably were gradually incorporated into proteogenesis process in the course of two long-timescale parallel evolutionary routes: I→F→Y→C→M→W and K→N→Q→H. This study provides new insight into the origin of life, particularly in terms of the basic protein composition of early life. Our work provides crucial information that will help in a further understanding of protein structure and function in relation to their evolutionary history.
... Today there are over 8,000 languages divided into more than 140 linguistic families, which originated from a common ancestral language spoken in central Africa 50,000 -70,000 years ago 5 . Likewise, all organisms living on Earth have a (last universal) common ancestor: LUCA, a microbe that lived 4 billion years ago, 6 which already contained most modern protein domains that have developed through evolution. Inspired by linguistic approaches to reconstruct ancient vocabularies by comparing modern languages, Alva et al. identified a set of primordial peptides that trace to pre-LUCA times. ...
The 21st century is presenting humankind with unprecedented environmental and medical challenges. The ability to design novel proteins tailored for specific purposes could transform our ability to respond timely to these issues. Recent advances in the field of artificial intelligence are now setting the stage to make this goal achievable. Protein sequences are inherently similar to natural languages: Amino acids arrange in a multitude of combinations to form structures that carry function, the same way as letters form words and sentences that carry meaning. Therefore, it is not surprising that throughout the history of Natural Language Processing (NLP), many of its techniques have been applied to protein research problems. In the last few years, we have witnessed revolutionary breakthroughs in the field of NLP. The implementation of Transformer pre-trained models has enabled text generation with human-like capabilities, including texts with specific properties such as style or subject. Motivated by its considerable success in NLP tasks, we expect dedicated Transformers to dominate custom protein sequence generation in the near future. Finetuning pre-trained models on protein families will enable the extension of their repertoires with novel sequences that could be highly divergent but still potentially functional. The combination of control tags such as cellular compartment or function will further enable the controllable design of novel protein functions. Moreover, recent model interpretability methods will allow us to open the 'black box' and thus enhance our understanding of folding principles. While early initiatives show the enormous potential of generative language models to design functional sequences, the field is still in its infancy. We believe that protein language models are a promising and largely unexplored field and discuss their foreseeable impact on protein design.
... Studies on the origin of life generally focused on biochemical reactions with molecular building blocks in prebiotic chemistry and the essentiality of genetic information in synthetic biology [3][4][5][6] . Possible routes to the origin of life and further development towards the last universal common ancestor (LUCA) have been intensively studied [7][8][9] . Successful polynucleotide synthesis from single nucleotides 10 and DNA/RNA replication within vesicles 11,12 revealed the mechanisms by which biochemical components work in protocells. ...
The morphology of primitive cells has been the subject of extensive research. A spherical form was commonly presumed in prebiotic studies but lacked experimental evidence in living cells. Whether and how the shape of living cells changed are unclear. Here we exposed the rod-shaped bacterium Escherichia coli to a resource utilization regime mimicking a primordial environment. Oleate was given as an easy-to-use model prebiotic nutrient, as fatty acid vesicles were likely present on the prebiotic Earth and might have been used as an energy resource. Six evolutionary lineages were generated under glucose-free but oleic acid vesicle (OAV)-rich conditions. Intriguingly, fitness increase was commonly associated with the morphological change from rod to sphere and the decreases in both the size and the area-to-volume ratio of the cell. The changed cell shape was conserved in either OAVs or glucose, regardless of the trade-offs in carbon utilization and protein abundance. Highly differentiated mutations present in the genome revealed two distinct strategies of adaption to OAV-rich conditions, i.e., either directly targeting the cell wall or not. The change in cell morphology of Escherichia coli for adapting to fatty acid availability supports the assumption of the primitive spherical form.
... A parasite is, first of all, an organism that exists in close trophic connection with organisms of other species, constantly lives on them or in them, and also feeds on their juices and tissues (Poulin, 2007). All organisms have one ancestor (Theobald, 2010). Viruses do not have an ancestor (Harris & Colin, 2021). ...
Aim/Purpose: The Covid-19 pandemic has created many adverse effects. It overloads the healthcare system, causes deaths, and angers some at anti-covid restrictions. This study examines the feasibility of using technical and technological ideas to overcome these effects. The solution is based on new knowledge about the virus, its nature, formation, and activation in the environment. Background: The rapid spread of a new coronavirus infection is taking place against the background of a lack of time required to create new treatment scenarios for the disease, development, production, and vaccine safety research. In such a situation, it became necessary to gain this time for organizing and conducting events that could reduce the burden on the healthcare system. Methodology: The science that studies the morphology, physiology, genetics, ecology, and evolution of viruses is virology. The modern development of virology is moving towards a more accurate and comprehensive description of the mechanisms of interaction of viruses with the host organism. This contributed to the emergence of genomics, transcriptomics, proteomics, and immunomics. However, in virology, there is no particular discipline that sets itself three fundamental goals: to substantiate a single concept of the emergence of viruses; to study the natural mechanisms of formation of virus molecules in the environment; to describe the natural mechanisms of activation of certain viruses in the environment that cause viral pandemics. As a result, there are many articles among the published scientific articles on viruses dealing with the mechanisms of interaction of viruses with the host organism. However, there are no articles on the natural mechanisms of formation and activation of certain viruses in the environment. In the absence of such specialized articles, we were forced to use the method of systems transdisciplinary generalization of disciplinary knowledge to achieve our article’s purpose. Generalization created new knowledge about the nature of viruses, about the mechanisms of their formation and activation in the environment and cells of biological organisms. It is logical to assume that to synchronize the state of biological objects of all functional ensembles on the planet, it is necessary to create and activate appropriate “technological tools.” We have suggested and proved that RNA viruses play the role of such tools. Piezoelectricity activates viruses. It occurs during the compression and stretching of sedimentary rocks and bases of continental plates in different territories. Contribution: The systems transdisciplinary generalization of the knowledge of scientific disciplines made it possible to edit the concept of viruses, to eliminate stereotypes that arose due to the use of unsuccessful analogies. As a result of this generalization, it was possible to prove that viruses are not intracellular parasites. The virus is a “technological tool” of the planetary organizing component. This “tool” aims to correct the genetic programs of organisms of all functional ensembles (plants, animals, people), which will maintain the state of organisms and the parameters of their metabolism in changing environmental conditions. Findings: The viruses that triggered pandemics in the 20th century and early 21st century are RNA viruses. RNA molecules play the role of “technological tools” that the planetary organizing component uses to carry out short-term and long-term adjustments and constant support of the genetic programs of biological organisms. Therefore, in such a situation, it is advisable to talk not about the fight against the virus but only about eliminating the negative manifestations of the Covid-19 pandemic: reducing the number of people in need of emergency hospitalization, eliminating cases of the acute course of the disease and deaths. It is proposed to use certain technical and technological ideas and solutions to eliminate these negative manifestations. Recommendation for Researchers: This paper recommends that researchers use new interdisciplinary and transdisciplinary approaches. They challenge assumptions and conclusions about the nature of viruses, and the mechanisms of their formation and activation in the environment can initiate. Such new research might describe the mechanisms that form and activate viruses in the environment and the body’s cells. They also might provide practical use of this knowledge to eliminate the multiple speculations and fears that arise against the background of reports of the likely appearance of more deadly viruses and viral infections. Future Research: The results of a systems transdisciplinary generalization of disciplinary knowledge about the nature and purpose of viruses are essential for expanding the horizon of the scientific worldview. Future fundamental research on the mechanisms of objective organizing constituents, a general description given in this article, will contribute to a deeper understanding of chemical and biological evolution mechanisms in which modern humanity is involved. In due time, such an understanding will allow a new look at the existing scenarios of the world socio-economic order, explore and describe new principles of sustainable development of society.
... Life on Earth likely evolved about four billion years ago [7]. The reducing atmosphere of early Earth lacked free oxygen and the primordial ocean presumably contained various organic compounds present in dilute concentrations in the micromolar range [8]. ...
The evolutionary origin of the genome remains elusive. Here, I hypothesize that its first iteration, the protogenome, was a multi-ribozyme RNA. It evolved, likely within liposomes (the protocells) forming in dry-wet cycling environments, through the random fusion of ribozymes by a ligase and was amplified by a polymerase. The protogenome thereby linked, in one molecule, the information required to seed the protometabolism (a combination of RNA-based autocatalytic sets) in newly forming protocells. If this combination of autocatalytic sets was evolutionarily advantageous, the protogenome would have amplified in a population of multiplying protocells. It likely was a quasispecies with redundant information, e.g., multiple copies of one ribozyme. As such, new functionalities could evolve, including a genetic code. Once one or more components of the protometabolism were templated by the protogenome (e.g., when a ribozyme was replaced by a protein enzyme), and/or addiction modules evolved, the protometabolism became dependent on the protogenome. Along with increasing fidelity of the RNA polymerase, the protogenome could grow, e.g., by incorporating additional ribozyme domains. Finally, the protogenome could have evolved into a DNA genome with increased stability and storage capacity. I will provide suggestions for experiments to test some aspects of this hypothesis, such as evaluating the ability of ribozyme RNA polymerases to generate random ligation products and testing the catalytic activity of linked ribozyme domains.
... Life on planet earth began approximately 3.5 billion years ago and the last universal common ancestor has been suggested to be the living starting point of all current and past evolutionary journeys (Theobald and Douglas, 2010). From that moment, countless events have occurred, from the delimitation of cellular nuclei-giving rise to eukaryotic cells-to the organization of the first sensorimotor loops and the emergency of what we think of cognition 1 . ...
All life on earth is intrinsically linked. At the very foundation of every evolutionary interaction are microorganisms, integral components in the composition of both organisms and ecosystems. The available data and this perspective on the order of life challenge the traditional conception of monogenetic biological individuals, suggesting living beings are actually composite multi-species complexes: holobionts. In the present article, we introduce our perspective on the concept of the holobiont mind, a biogenic conception of cognition compatible with the 4E approach and the holobiont theory. We furthermore expand on the idea of the mind as the emerging product of multi-genomic morphology of a composite animal-agent, in ever-changing interaction with its ecological niche. We thus briefly review recent evidence on the brain–gut–microbiome axis and the Microbiome of the Built Environment in order to provide a bridge between the Holobiont Mind and the 4E approach to Cognition, two complementary lines of evidence that have not been linked before, opening novel venues for research with direct impact on health and disease.
... Common descent is one of the fundamental aspects of Darwinian evolution. This theory emphasizes that modern-day species share a common ancestry [1]. The same principle applies to enzymes: modern enzyme superfamilies across the three domains of life evolved from a set of enzymes that were already present in a last universal common ancestor (LUCA) that can be dated to over 3.5 billion years ago [2,3]. ...
Methionine adenosyltransferase (MAT) catalyzes the biosynthesis of S‐adenosylmethionine from L‐methionine and adenosine triphosphate. MAT enzymes are ancient, believed to share a common ancestor, and are highly conserved in all three domains of life. However, the sequences of archaeal MATs show considerable divergence compared to their bacterial and eukaryotic counterparts. Furthermore, the structural and functional significance of this sequence divergence are not well understood. In the present study, we employed structural analysis and ancestral sequence reconstruction (ASR) to investigate archaeal MAT divergence. We observed that the dimer interface containing the active site (which is usually well‐conserved) diverged considerably between the bacterial/eukaryotic MATs and archaeal MAT. A detailed investigation of the available structures supports the sequence analysis outcome: the protein domains and subdomains of bacterial and eukaryotic MAT are more similar than those of archaea. Finally, we resurrected archaeal MAT ancestors. Interestingly, archaeal MAT ancestors show substrate specificity, which is lost during evolution. This observation supports the hypothesis of a common MAT ancestor for the three domains of life. In conclusion, we have demonstrated that archaeal MAT is an ideal system for studying an enzyme family that evolved differently in one domain compared to others while maintaining the same catalytic activity.
... [27][28][29][30][31][32][33] Homometallic Mn and heterometallic Mn/M (M = Ce) complexes and many other metal-oxo complexes have also been widely used as oxidants in chemical transformations such as the partial dehydrogenation of primary alcohols into their corresponding aldehydes. [33][34][35][36][37] electrons. Moreover, the core features labile solvent molecules that may facilitate the coordination of incoming substrates. ...
The origin of life is one of the greatest unsolved mysteries, which has been studied by many scientists and philosophers. Today, two major hypotheses have been developed: the first concerns the synthesis of complex molecules (similar to RNA), which would have subsequently led to the appearance of the various biological functions. The second is the development of a primitive metabolism, a set of chemical reactions based on very simple molecules, which would have allowed the emergence of a first life form without enzymes. This thesis work supports this second hypothesis, demonstrating the possible development of two metabolic pathways, the reverse Krebs cycle (or rTCA) and the Wood-Ljungdahl pathway (or AcCoA), considered primitive and allowing the synthesis of universal intermediates for biochemistry, in a prebiotic environment from CO2 and metals. In addition, a method for the synthesis of thioesters, intermediates presumed necessary for the evolution of metabolism, is presented as well as its integration into a complex reaction network similar to metabolism.
This paper explores the intricate relationship between humans and plants from the perspective of Salish concepts, shedding light on the tradition of attributing human-desired qualities to the botanical world. Although plants possess traits that appeal to human desires, it is essential to recognize their inherent distinction from humans. Through historical utilization by Salish communities, a spiritual reciprocal bond has been established, necessitating the adherence to human-like protocols to maintain a symbiotic relationship. However, this exploration advocates against romanticizing this relationship, as it has the potential to foster internal stereotyping while leading to external discrepancies in philosophical pursuits. By carefully examining Salish practices from past to present, an emphasis is placed on the significance of comprehending and respecting the uniqueness of plant life. Through this analysis, the primary goal is to enhance our understanding of the profound connection between humans and plants while embracing the authenticity and complexity of this relationship. Appreciating the true nature of the bond can offer valuable insights into sustainable coexistence with the botanical world and contribute to fostering a more balanced and respectful relationship between humans and the natural environment.
Obviously, the discussion of different factors that could have contributed to the origin of life and evolution is clear speculation, since there is no way of checking the validity of most of the related hypotheses in practice, as the corresponding events not only already happened, but took place in a very distant past. However, there are a few undisputable facts that are present at the moment, such as the existence of a wide variety of living forms and the abundant presence of intrinsically disordered proteins (IDPs) or hybrid proteins containing ordered domains and intrinsically disordered regions (IDRs) in all living forms. Since it seems that the currently existing living forms originated from a common ancestor, their variety is a result of evolution. Therefore, one could ask a logical question of what role(s) the structureless and highly dynamic but vastly abundant and multifunctional IDPs/IDRs might have in evolution. This study represents an attempt to consider various ideas pertaining to the potential roles of protein intrinsic disorder in the origin of life and evolution.
The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based on disparate data and methods. Age estimates for LUCA are usually based on the fossil record, varying with every reinterpretation. The nature of LUCA’s metabolism has proven equally contentious, with some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09–4.33 Ga) through divergence time analysis of pre-LUCA gene duplicates, calibrated using microbial fossils and isotope records under a new cross-bracing implementation. Phylogenetic reconciliation suggests that LUCA had a genome of at least 2.5 Mb (2.49–2.99 Mb), encoding around 2,600 proteins, comparable to modern prokaryotes. Our results suggest LUCA was a prokaryote-grade anaerobic acetogen that possessed an early immune system. Although LUCA is sometimes perceived as living in isolation, we infer LUCA to have been part of an established ecological system. The metabolism of LUCA would have provided a niche for other microbial community members and hydrogen recycling by atmospheric photochemistry could have supported a modestly productive early ecosystem.
Why do creationists persist in rejecting the evidence for Darwin’s theory of evolution? This paper explores longstanding disagreements among Christians over the epistemic status of evolution. Like other studies that have tried to define the evidence for evolution, a recent analysis by Gijsbert van den Brink, Jeroen de Ridder, and René van Woudenberg does not adequately face up to antecedent commitments that play into any assessment of evolution. The scientific theory of evolution involves higher-level models that are associated with a range of non-scientific factors, including theological judgments. In light of these realities, an emphasis on mutual dialogue and understanding offers promising opportunities for Christians trying to discover the truth about God’s creation.
Meaning is a component of the world that takes the form of indicator or symptom in the non-living world, intention of organism action, or something expressed in words or other symbols. I distinguish between meanings-in-itself or potential meanings and manifested meanings that are perceived or generated by agents. Inanimate objects can manifest only meanings-in-itself, primarily in the form of laws of nature and their components. An evolving macroscopic object can be called “eventity,” which is short for “evolving entity” that exists due to events constituting its evolution. The earliest and most important eventities are stars. They were not only the first macro-objects in the universe, but also (in combination with planets) the most important conditions for the origin of living systems—the
most primitive agents. Evolution of life and meanings have gone hand in hand, though they have not directly conditioned each other. The main milestones along the way were the emergence of new levels of hierarchy, i.e., hierarchogenesis. For life, and later for human history, such stages of hierarchogenesis were the emergence of prokaryotic cells, eukaryotic cells, multicellular organisms, agroecosystems, and nations/states. For meanings, hierarchogenetic stages include the actualization of potential meanings, the rise of judgments, paradigms, and worldviews. Although these two strands of evolution followed their own paths and had completely different dynamics, in the last few millennia,
and especially in the last century, these paths have begun to converge. The possible prospects and consequences of this convergence are discussed.
The evolution of DNA protocells to first cells was the end of the long voyage of the origin of life and the beginning of biogenesis. Although protocells could divide mechanically with unequal cytoplasmic content, digital control of cell division by DNA replication of identical daughter cells with all information systems was a breakthrough innovation for the emergence of the first life from its protocell precursors. The emergence of the first life, owing to DNA’s ability to replicate into identical copies of itself, was an event horizon in our solar system, transforming our sterile planet into a habitable, living world. The first life was autopoietic. Reproduction of the first cells with variation was an essential characteristic that distinguished life from nonlife. Life begets life. The fossil record suggests that the first life appeared around four billion years ago. Morphologically, these Archean microfossils look like single-celled organisms without any nucleus. We can extrapolate from recent bacterial cells how first cells with plasma membranes might have responded to an environmental cue. The early cells were open systems exchanging energy and information flows, from the fluctuating outside environment of a hydrothermal crater vent to the inner cytoplasm, in the form of an impulse. They responded to environmental variations such as fluctuations in nutrient availability, temperature, light, toxins, osmotic pressure, and cell density by altering their gene expressions. They developed a signal transduction pathway to relay messages from the environment to the cell’s cytoplasm for responses. These primordial cells responded to environmental changes by turning on genes for proteins that would help them survive. Gene expression occurs in two essential steps: transcription and translation. In general, a gene is expressed only when its protein product is needed. The early cell communities began to communicate by quorum sensing in response to fluctuations in a cell population. An example of such group behavior is biofilm formation, as reflected by the development of extensive stromatolite deposits in Archean sediments. We can extrapolate from modern bacterial cells how the early cells might have grown and divided into two identical daughter cells orchestrated by several regulatory genes. The first stage was the replication of circular DNA, in which the cells were elongated. The duplicated chromosome was segregated at the two ends and pulled apart, where the middle part was constricted and encircled by the FtsZ ring. As the contractile Z-ring closed like a purse string, the cell cytoplasm was divided into two, completing the cell division when analog, hybrid, and digital information systems passed vertically from parent to daughter cells. The daughter cells grew to parent cell size and became ready to divide. The first cell was self-sustaining, DNA-based, and chemically sophisticated, possessing many housekeeping proteins and capable of mutation and Darwinian evolution. Most likely, it was a hyperthermophilic organism like modern heat-loving bacteria. As the cell division was stabilized and perfected, the primordial cell population multiplied and crowded in the hydrothermal crater vent environment. Other than mutations of daughter cells, early cells were active in exchanging genetic information among the population by horizontal gene transfer (HGT). The short generation time, together with random mutations and genetic recombination, allowed the first cells to evolve quickly. They also developed various strategies to ward off viral attacks. They might have acquired various immune systems like clustered regularly interspaced short palindromic repeats (CRISPR) for survival. They could produce biofilms by quorum sensing to withstand viral attacks. Molecular phylogenetics suggests that all living organisms on Earth descended from a single ancestral form, i.e., the last universal common ancestor (LUCA). LUCA was not the first cell but was the last before the divergence of life into three domains: bacteria, archaea, and eukaryotes.
Since 1970, there has been an overall decline in wildlife populations in the order of 52%. Freshwater species populations have declined by 76%; species populations in Central and South America have declined by 83%; and in the Indo-Pacific by 67%. These are often not complete extinctions, but large declines in the numbers of animals in each species, as well as habitat loss. This presents us with a tremendous opportunity, before it is too late to rescue many species. This book documents the present state of wildlife on a global scale, using a taxonomic approach, and serving as a one stop place for people involved in conservation to be able to find out what is in decline, and the success stories that have occurred to bring back species from the brink of extinction - primarily due to conservation management techniques - as models for what we might achieve in the future.
Human evolution was the foundation for economic progress. Human evolution, however, did not continue to the final state of total adherence to contextual truth and non-violence. The only way to address that 'evolutionary failure' is if intellectuals unite and take a firm stand to promote human values.
Phylogenetics emerged in the second half of the nineteenth century as a speculative storytelling discipline dedicated to providing narrative explanations for the evolution of taxa and their traits. It coincided with lineage thinking, a process that mentally traces character evolution along lineages of hypothetical ancestors. Ancestors in Evolutionary Biology traces the history of narrative phylogenetics and lineage thinking to the present day, drawing on perspectives from the history of science, philosophy of science, and contemporary scientific debates. It shows how the power of phylogenetic hypotheses to explain evolution resides in the precursor traits of hypothetical ancestors. This book provides a comprehensive exploration of the topic of ancestors, which is central to modern biology, and is therefore of interest to graduate students, researchers, and academics in evolutionary biology, palaeontology, philosophy of science, and the history of science.
How life originated from the inanimate mixture of organic and inorganic compounds on the priomordial earth remains one of the great unknowns in science. This origin of life, or abiogenesis, continues to be examined in the context of the conditions and materials required for natural life to have begun on Earth both theoretically and experimentally. This book provides a broad but in-depth analysis of the latest discoveries in prebiotic chemsitry from the microscopic to the macroscopic scale; utilising experimental insight to provide a bottom up approach to plausibly explaining how life arose. With contributions from global leaders, this book is an ideal reference for postgraduate students and a single source of comprehensive information on the latest technical and theoretical advancements for researchers in a variety of fields from astrochemistry and astrophysics to organic chemistry and evolution.
The twenty-first century is presenting humankind with unprecedented environmental and medical challenges. The ability to design novel proteins tailored for specific purposes would potentially transform our ability to respond to these issues in a timely manner. Recent advances in the field of artificial intelligence are now setting the stage to make this goal achievable. Protein sequences are inherently similar to natural languages: amino acids arrange in a multitude of combinations to form structures that carry function, the same way as letters form words and sentences carry meaning. Accordingly, it is not surprising that, throughout the history of natural language processing (NLP), many of its techniques have been applied to protein research problems. In the past few years we have witnessed revolutionary breakthroughs in the field of NLP. The implementation of transformer pre-trained models has enabled text generation with human-like capabilities, including texts with specific properties such as style or subject. Motivated by its considerable success in NLP tasks, we expect dedicated transformers to dominate custom protein sequence generation in the near future. Fine-tuning pre-trained models on protein families will enable the extension of their repertoires with novel sequences that could be highly divergent but still potentially functional. The combination of control tags such as cellular compartment or function will further enable the controllable design of novel protein functions. Moreover, recent model interpretability methods will allow us to open the ‘black box’ and thus enhance our understanding of folding principles. Early initiatives show the enormous potential of generative language models to design functional sequences. We believe that using generative text models to create novel proteins is a promising and largely unexplored field, and we discuss its foreseeable impact on protein design.
The availability of genomic and proteomic data from across the tree of life has made it possible to infer features of the genome and proteome of the last universal common ancestor (LUCA). A number of studies have done so, all using a unique set of methods and bioinformatics databases. Here, we compare predictions across eight such studies and measure both their agreement with one another and with the consensus predictions among them. We find that some LUCA genome studies show a strong agreement with the consensus predictions of the others, but that no individual study shares a high or even moderate degree of similarity with any other individual study. From these observations, we conclude that the consensus among studies provides a more accurate depiction of the core proteome of the LUCA and its functional repertoire. The set of consensus LUCA protein family predictions between all of these studies portrays a LUCA genome that, at minimum, encoded functions related to protein synthesis, amino acid metabolism, nucleotide metabolism, and the use of common, nucleotide‐derived organic cofactors. Over the past couple of decades, researchers have used genomic data from organisms across the tree of life to infer the characteristics of the last universal common ancestor, an organism or community of organisms that lived roughly 3.5–4 billion years ago. Here, we compare predictions between previously published studies of the genome and proteome of the last universal common ancestor, measuring their agreement and identifying consensus between them.
The task of Philosophy In Science ( PinS ) is to use philosophical tools to help solve scientific problems. This paper describes how I stumbled into this line of work and then addressed several topics in philosophy of biology – units of selection, cladistic parsimony, robustness and trade-offs in model building, adaptationism, and evidence for common ancestry – often in collaboration with scientists. I conclude by offering advice for would-be PinS practitioners.
Ecology is complex and while there is a modern drive towards a holistic or “ecosystem approach” for managing marine systems, we are still a long way from fully understanding the interactions between the various components of different ecosystems and fully valuing their contributions. Microphytobenthos (MPB), and diatom biofilms, are an excellent example. While they are relatively widespread, their role has often been overlooked in favor of more charismatic species or assemblages. However, the understanding of their ecological importance has increased with a growing body of evidence outlining their important role in system functions ranging from biogeochemical cycles, trophic interactions and a direct influence of sediment dynamics. The latter effect is related to the secretion of extracellular polymeric substances (EPS) which have a number of roles in ecosystem dynamics, including the mediation of sediment erosion. Therefore, it is understandable that characterization of MPB assemblages as ecosystems engineers is becoming more widespread. A more recent development is the debate surrounding the evolutionary impact of ecosystem engineering and whether this is sufficiently distinct and important that it should be considered a separate evolutionary pressure, as described in the “niche construction” theory. Microphytobenthos have already been cited in this debate and this chapter briefly introduces the range of functionality of MPB and discusses their role as ecosystem engineers and their potential place in niche construction theory.
The defining criterion for homology has been common ancestry ever since darwinian evolution replaced fidelity to archetype as the explanation for similarity among traits of organisms. Although, in some cases, an alternative criterion of similarity in developmental control or other underlying traits can be helpful in diagnosing homology, evidence for dissociation among traits at different levels of organization (e.g. genotype and phenotype) and for frequency of reticulate (lateral) evolution accentuate the problems inherent in using similarity as the defining criterion. Growing awareness that character history and organismal lineage history can and do differ puts homology definition and assessment center stage in our understanding of the evolution of genomes.
A new hypothesis for the origin of eukaryotic cells is proposed, based on the comparative biochemistry of energy metabolism. Eukaryotes are suggested to have arisen through symbiotic association of an anaerobic, strictly hydrogen-dependent, strictly autotrophic archaebacterium (the host) with a eubacterium (the symbiont) that was able to respire, but generated molecular hydrogen as a waste product of anaerobic heterotrophic metabolism. The host's dependence upon molecular hydrogen produced by the symbiont is put forward as the selective principle that forged the common ancestor of eukaryotic cells.
Debates over the status of the tree of life (TOL) often proceed without agreement as to what it is supposed to be: a hierarchical classification scheme, a tracing of genomic and organismal history or a hypothesis about evolutionary processes and the patterns they can generate. I will argue that for Darwin it was a hypothesis, which lateral gene transfer in prokaryotes now shows to be false. I will propose a more general and relaxed evolutionary theory and point out why anti-evolutionists should take no comfort from disproof of the TOL hypothesis.
An unusual pattern in a nucleic acid or protein sequence or a region of strong similarity shared by two or more sequences may have biological significance. It is therefore desirable to know whether such a pattern can have arisen simply by chance. To identify interesting sequence patterns, appropriate scoring values can be assigned to the individual residues of a single sequence or to sets of residues when several sequences are compared. For single sequences, such scores can reflect biophysical properties such as charge, volume, hydrophobicity, or secondary structure potential; for multiple sequences, they can reflect nucleotide or amino acid similarity measured in a wide variety of ways. Using an appropriate random model, we present a theory that provides precise numerical formulas for assessing the statistical significance of any region with high aggregate score. A second class of results describes the composition of high-scoring segments. In certain contexts, these permit the choice of scoring systems which are "optimal" for distinguishing biologically relevant patterns. Examples are given of applications of the theory to a variety of protein sequences, highlighting segments with unusual biological features. These include distinctive charge regions in transcription factors and protooncogene products, pronounced hydrophobic segments in various receptor and transport proteins, and statistically significant subalignments involving the recently characterized cystic fibrosis gene.
The theory of evolution predicts that similar phylogenetic trees should be obtained from different sets of character data. We have tested this prediction using sequence data for 5 proteins from 11 species. Our results are consistent with the theory of evolution.
The hypothesis that all life on earth traces back to a single common ancestor is a fundamental postulate in modern evolutionary theory. Yet, despite its widespread acceptance in biology, there has been comparatively little attention to formally testing this "hypothesis of common ancestry". We review and critically examine some arguments that have been proposed in support of this hypothesis. We then describe some theoretical results that suggest the hypothesis may be intrinsically difficult to test. We conclude by suggesting an approach to the problem based on the Aikaike information criterion.
Most proteins have been formed by gene duplication, recombination, and divergence. Proteins of known structure can be matched
to about 50% of genome sequences, and these data provide a quantitative description and can suggest hypotheses about the origins
of these processes.
Genomes hold within them the record of the evolution of life on Earth. But genome fusions and horizontal gene transfer seem to have obscured sufficiently the gene sequence record such that it is difficult to reconstruct the phylogenetic tree of life. Here we determine the general outline of the tree using complete genome data from representative prokaryotes and eukaryotes and a new genome analysis method that makes it possible to reconstruct ancient genome fusions and phylogenetic trees. Our analyses indicate that the eukaryotic genome resulted from a fusion of two diverse prokaryotic genomes, and therefore at the deepest levels linking prokaryotes and eukaryotes, the tree of life is actually a ring of life. One fusion partner branches from deep within an ancient photosynthetic clade, and the other is related to the archaeal prokaryotes. The eubacterial organism is either a proteobacterium, or a member of a larger photosynthetic clade that includes the Cyanobacteria and the Proteobacteria.
Using an appropriate model of amino acid replacement is very important for the study of protein evolution and phylogenetic
inference. We have built a tool for the selection of the best-fit model of evolution, among a set of candidate models, for
a given protein sequence alignment.
Availability: ProtTest is available under the GNU license from http://darwin.uvigo.es
Contact: fabascal{at}uvigo.es
Using the Kullback-Leibler information criterion to measure the closeness of a model to the truth, the author proposes new likelihood-ratio-based statistics for testing the null hypothesis that the competing models are as close to the true data generating process against the alternative hypothesis that one model is closer. The tests are directional and are derived for the cases where the competing models are non-nested, overlapping, or nested and whether both, one, or neither is misspecified. As a prerequisite, the author fully characterizes the asymptotic distribution of the likelihood ratio statistic under the most general conditions. Copyright 1989 by The Econometric Society.
Introduction
When on board H.M.S. ‘Beagle,’ as naturalist, I was much struck with certain facts in the distribution of the inhabitants of South America, and in the geological relations of the present to the past inhabitants of that continent. These facts seemed to me...
In a 1935 paper and in his book Theory of Probability, Jeffreys developed a methodology for quantifying the evidence in favor of a scientific theory. The centerpiece was a number, now called the Bayes factor, which is the posterior odds of the null hypothesis when the prior probability on the null is one-half. Although there has been much discussion of Bayesian hypothesis testing in the context of criticism of P-values, less attention has been given to the Bayes factor as a practical tool of applied statistics. In this article we review and discuss the uses of Bayes factors in the context of five scientific applications in genetics, sports, ecology, sociology, and psychology. We emphasize the following points:
Publisher Summary
Informational macromolecules, or semantides, play a unique role in determining the properties of living matter in the perspectives that differ by the magnitude of time required for the processes involved—the short-timed biochemical reaction, the medium-timed ontogenetic event, and the long-timed evolutionary event. Although the slower processes should be broken down into linked faster processes, if one loses sight of the slower processes one also loses the links between the component faster processes. The relative importance of the contributions to evolution of changes in functional properties of polypeptides through their structural modification on the one hand, and of changes in the timing and the rate of synthesis of these polypeptides on the other hand, constitutes a problem that justifies the study of evolution at the level of informational macromolecules. The evaluation of the amount of differences between two organisms as derived from sequences in structural genes or in their polypeptide translation is likely to lead to quantities different from those obtained on the basis of observations made at any other, higher level of biological integration.
Information theory and log-likelihood models - a basis for model selection and inference practical use of the information theoretic approach model selection uncertainty with examples Monte Carlo insights and extended examples statistical theory.
• In considering the Origin of Species, it is quite conceivable that a naturalist, reflecting on the mutual affinities of organic beings, on their embryological relations, their geographical distribution, geological succession, and other such facts, might come to the conclusion that each species had not been independently created, but had descended, like varieties, from other species. Nevertheless, such a conclusion, even if well founded, would be unsatisfactory, until it could be shown how the innumerable species inhabiting this world have been modified, so as to acquire that perfection of structure and coadaptation which most justly excites our admiration. Naturalists continually refer to external conditions, such as climate, food, &c, as the only possible cause of variation. In one very limited sense, as we shall hereafter see, this may be true; but it is preposterous to attribute to mere external conditions, the structure, for instance, of the woodpecker, with its feet, tail, beak, and tongue, so admirably adapted to catch insects under the bark of trees. In the case of the misseltoe, which draws its nourishment from certain trees, which has seeds that must be transported by certain birds, and which has flowers with separate sexes absolutely requiring the agency of certain insects to bring pollen from one flower to the other, it is equally preposterous to account for the structure of this parasite, with its relations to several distinct organic beings, by the effects of external conditions, or of habit, or of the volition of the plant itself. (PsycINFO Database Record (c) 2012 APA, all rights reserved)
• In considering the Origin of Species, it is quite conceivable that a naturalist, reflecting on the mutual affinities of organic beings, on their embryological relations, their geographical distribution, geological succession, and other such facts, might come to the conclusion that each species had not been independently created, but had descended, like varieties, from other species. Nevertheless, such a conclusion, even if well founded, would be unsatisfactory, until it could be shown how the innumerable species inhabiting this world have been modified, so as to acquire that perfection of structure and coadaptation which most justly excites our admiration. Naturalists continually refer to external conditions, such as climate, food, &c, as the only possible cause of variation. In one very limited sense, as we shall hereafter see, this may be true; but it is preposterous to attribute to mere external conditions, the structure, for instance, of the woodpecker, with its feet, tail, beak, and tongue, so admirably adapted to catch insects under the bark of trees. In the case of the misseltoe, which draws its nourishment from certain trees, which has seeds that must be transported by certain birds, and which has flowers with separate sexes absolutely requiring the agency of certain insects to bring pollen from one flower to the other, it is equally preposterous to account for the structure of this parasite, with its relations to several distinct organic beings, by the effects of external conditions, or of habit, or of the volition of the plant itself. (PsycINFO Database Record (c) 2012 APA, all rights reserved)
Includes index.; At foot of title page: The right of Translation is reserved.; Advertisements on p. [1]-32 (3rd group); Freeman, R.B. Darwin, 112, variant b.; Electronic reproduction Canberra, A.C.T. : National Library of Australia, 2009.; One of the earliest known surviving copies of the first ed. to arrive in Australia.; The first edition of Origin was published on November 24, 1859. This copy is believed to have arrived in Australia by March 10, 1860.; Inscriptions on front end paper: "Parramatta N.S.W. William Woolls, March 17/60, H.S. Mort, 2/10/00. 1250 copies printed with the misprint "species" on page 20. 2 sets of last half on Murray's General list of works, pp 17-32 bear story on page 184". This copy has been extensively annotated by Woolls. Some of the annotations are faded and rubbed.; Includes book plate of previous owners, H.S. Mort and Robert L. Usinger.; Condition: Some foxing to text, a good copy in original publisher's blindstamped green cloth, spine lettered and decorated in gilt, binder's ticket of Edmonds & Remnants on rear paste-down, minor repairs to joints, a little worn. The binding is in Freeman's variant b. In this copy there is an unrecorded anomaly in Murray's advertisements at the end.The 'c' gathering has been duplicated in error replacing the 'b' gathering, so that the pagination of the advertisements runs 17-32 ;17-32. On the origin of species Preservation of favoured races in the struggle for life
Estudio autobiográfico de Karl R. Popper (1902-1994), filósofo austríaco, creador del falsacionismo o principio de falibilidad, donde plantea sus grandes líneas de pensamiento filosófico, científico y social, así como su interés por la música.
A phylogenetic analysis based upon ribosomal RNA sequence characterization reveals that living systems represent one of three aboriginal lines of descent: (i) the eubacteria, comprising all typical bacteria; (ii) the archaebacteria, containing methanogenic bacteria; and (iii) the urkaryotes, now represented in the cytoplasmic component of eukaryotic cells.
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The general features of the genetic code are described. It is considered that originally only a few amino acids were coded, but that most of the possible codons were fairly soon brought into use. In subsequent steps additional amino acids were substituted when they were able to confer a selective advantage, until eventually the code became frozen in its present form.
There is some indication that life may have originated readily under primitive earth conditions. If there were multiple origins of life, the result could have been a polyphyletic biota today. Using simple stochastic models for diversification and extinction, we conclude: (i) the probability of survival of life is low unless there are multiple origins, and (ii) given survival of life and given as many as 10 independent origins of life, the odds are that all but one would have gone extinct, yielding the monophyletic biota we have now. The fact of the survival of our particular form of life does not imply that it was unique or superior.
In theory, mutations of protein sequences may eventually generate different functions as well as different structures. The observation of such records of protein evolution have been obscured by the dissipation of memory about the ancestors. In the past year, new advances in our understanding of divergent evolution were allowed by new protein structure determinations, including the ClpP proteases, steroid delta-isomerase, carboxypeptidase G2, the thrombin inhibitor triabin and the chloroplast Rieske protein. There is strong evidence for their distant homology with proteins of known structure despite significant functional or structural differences.
The past year has seen several attempts to reconstruct the proteome of the universal ancestor of all life on the basis of comparisons of contempory genomes. However, increasing evidence for lateral gene transfer could mean that such attempts are based on an incorrect understanding of evolution.
Universal trees of life based on small-subunit (SSU) ribosomal RNA (rRNA) support the separate mono/holophyly of the domains Archaea (archaebacteria), Bacteria (eubacteria) and Eucarya (eukaryotes) and the placement of extreme thermophiles at the base of the Bacteria. The concept of universal tree reconstruction recently has been upset by protein trees that show intermixing of species from different domains. Such tree topologies have been attributed to either extensive horizontal gene transfer or degradation of phylogenetic signals because of saturation for amino acid substitutions. Here we use large combined alignments of 23 orthologous proteins conserved across 45 species from all domains to construct highly robust universal trees. Although individual protein trees are variable in their support of domain integrity, trees based on combined protein data sets strongly support separate monophyletic domains. Within the Bacteria, we placed spirochaetes as the earliest derived bacterial group. However, elimination from the combined protein alignment of nine protein data sets, which were likely candidates for horizontal gene transfer, resulted in trees showing thermophiles as the earliest evolved bacterial lineage. Thus, combined protein universal trees are highly congruent with SSU rRNA trees in their strong support for the separate monophyly of domains as well as the early evolution of thermophilic Bacteria.
The deduced amino acid sequences from 1200 Haemophilus influenzae genes was compared to a data set that contained the orfs from yeast, two different Archaea and the Gram+ and Gramminus sign bacteria, Bacillus subtilis and Escherichia coli. The results of the comparison yielded a 26 orthologous gene set that had at least one representative from each of the four groups. A four taxa phylogenetic relationship for these 26 genes was determined. The statistical significance of each minimal tree was tested against the two alternative four taxa trees. The result was that four genes significantly supported the (Archaea, Eukaryota) (Gram+, Gramminus sign) topology, two genes supported the one where Gramminus sign and Eukaryota form a clade, and one gene supported the tree where Gram+ and Eukaryota define one clade. The remaining genes do not uniquely support any phylogeny, thereby collapsing the two central nodes into a single node. These are referred to as star phylogenies. I offer a new suggestion for the mechanism that gave rise to the star phylogenies. Namely, these are genes that are younger than the underlying lineages that currently harbor them. This hypothesis is examined with two proteins that display the star phylogeny; namely onithine transcarbamylase and tryptophan synthetase. It is shown, using the distance matrix rate test, that the rate of evolution of these two proteins is comparable to a control gene when rates are determined by comparing closely related species. This implies that the genes under comparison experience comparable functional constraint. However, when the genes from remotely related species are compared, a plateau is encountered. Since we see no unusual levels of functional constraint this plateau cannot be attributed to the divergence of the protein having reached saturation. The simplest explanation is that the genes displaying the star phylogenies were introduced after Archaea, Eukaryota, and Bacteria had diverged from one another. They presumably spread through life by horizontal gene transfer.
A theory for the evolution of cellular organization is presented. The model is based on the (data supported) conjecture that the dynamic of horizontal gene transfer (HGT) is primarily determined by the organization of the recipient cell. Aboriginal cell designs are taken to be simple and loosely organized enough that all cellular componentry can be altered and/or displaced through HGT, making HGT the principal driving force in early cellular evolution. Primitive cells did not carry a stable organismal genealogical trace. Primitive cellular evolution is basically communal. The high level of novelty required to evolve cell designs is a product of communal invention, of the universal HGT field, not intralineage variation. It is the community as a whole, the ecosystem, which evolves. The individual cell designs that evolved in this way are nevertheless fundamentally distinct, because the initial conditions in each case are somewhat different. As a cell design becomes more complex and interconnected a critical point is reached where a more integrated cellular organization emerges, and vertically generated novelty can and does assume greater importance. This critical point is called the "Darwinian Threshold" for the reasons given.
Sober and Steel (J. Theor. Biol. 218, 395-408) give important limits on the use of current models with sequence data for studying ancient aspects of evolution; but they go too far in suggesting that several fundamental aspects of evolutionary theory cannot be tested in a normal scientific manner. To the contrary, we show examples of how some alternatives to the theory of descent can be formulated in such a way that they lead to predictions that can be evaluated (and rejected). The critical factor is a logical formulation of the alternatives, even though not all possible alternatives can be tested simultaneously. Similarly, some of the limits using DNA sequence data can be overcome by other types of sequence derived characters. The uniqueness (or not) of the origin of life, though still difficult, is similarly amenable to the testing of alternative hypotheses.
A mutation in the genetic code would place new amino acids in certain loci and entirely eliminate amino acids from other loci of practically all proteins in an organism. It is reasonable to postulate that mutations of this kind cannot supplant the original code. The genetic code, once established, would therefore remain invariant.
The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximum- likelihood principle, which clearly satisfies these requirements. The core of this method is a simple hill-climbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distance-based method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment of the topology and branch lengths, only a few iterations are sufficient to reach an optimum. We used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches. The reduction of computing time is dramatic in comparison with other maximum-likelihood packages, while the likelihood maximization ability tends to be higher. For example, only 12 min were required on a standard personal computer to analyze a data set consisting of 500 rbcL sequences with 1,428 base pairs from plant plastids, thus reaching a speed of the same order as some popular distance-based and parsimony algorithms. This new method is implemented in the PHYML program, which is freely available on our web page: http://www.lirmm.fr/w3ifa/MAAS/.
To study gene evolution across a wide range of organisms, biologists need accurate tools for multiple sequence alignment of protein families. Obtaining accurate alignments, however, is a difficult computational problem because of not only the high computational cost but also the lack of proper objective functions for measuring alignment quality. In this paper, we introduce probabilistic consistency, a novel scoring function for multiple sequence comparisons. We present ProbCons, a practical tool for progressive protein multiple sequence alignment based on probabilistic consistency, and evaluate its performance on several standard alignment benchmark data sets. On the BAliBASE, SABmark, and PREFAB benchmark alignment databases, ProbCons achieves statistically significant improvement over other leading methods while maintaining practical speed. ProbCons is publicly available as a Web resource.
The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolutionary scenarios are poorly described by such models. Further, even when evolution proceeds in a tree-like manner, analysis of the data may not be best served by using methods that enforce a tree structure but rather by a richer visualization of the data to evaluate its properties, at least as an essential first step. Thus, phylogenetic networks should be employed when reticulate events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved, and, even in the absence of such events, phylogenetic networks have a useful role to play. This article reviews the terminology used for phylogenetic networks and covers both split networks and reticulate networks, how they are defined, and how they can be interpreted. Additionally, the article outlines the beginnings of a comprehensive statistical framework for applying split network methods. We show how split networks can represent confidence sets of trees and introduce a conservative statistical test for whether the conflicting signal in a network is treelike. Finally, this article describes a new program, SplitsTree4, an interactive and comprehensive tool for inferring different types of phylogenetic networks from sequences, distances, and trees.
Numerous scenarios explain the origin of the eukaryote cell by fusion or endosymbiosis between an archaeon and a bacterium (and sometimes a third partner). We evaluate these hypotheses using the following three criteria. Can the data be explained by the null hypothesis that new features arise sequentially along a stem lineage? Second, hypotheses involving an archaeon and a bacterium should undergo standard phylogenetic tests of gene distribution. Third, accounting for past events by processes observed in modern cells is preferable to postulating unknown processes that have never been observed. For example, there are many eukaryote examples of bacteria as endosymbionts or endoparasites, but none known in archaea. Strictly post-hoc hypotheses that ignore this third criterion should be avoided. Applying these three criteria significantly narrows the number of plausible hypotheses. Given current knowledge, our conclusion is that the eukaryote lineage must have diverged from an ancestor of archaea well prior to the origin of the mitochondrion. Significantly, the absence of ancestrally amitochondriate eukaryotes (archezoa) among extant eukaryotes is neither evidence for an archaeal host for the ancestor of mitochondria, nor evidence against a eukaryotic host.
The significance test controversy: A reader Methodological perspectives (Butterworths, London The significance test controversy: A reader
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Evidence and Evolution Ch
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Sober, E. Evidence and Evolution Ch. 4 (Cambridge University Press, 2008).
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The hydrogen hypothesis for the first eukaryote
- W Martin
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Martin, W. & Muller, M. The hydrogen hypothesis for the first eukaryote. Nature 392, 37–41 (1998).
How true is the theory of evolution
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