Historical perspective: The problem of the origin of life in the context of developments in biology

The structure of the history of scientific ideas on the origin of life, after Darwin's theory of evolution brought the problem into focus, is discussed. 19th-century theories in the mainstream of historical development already included some notion of chemical evolution. These theories were limited, however, by their reliance on a protoplasmic view of life, according to which the protoplasmic substance combines all vital properties.It was only when this holistic concept of protoplasm was abandoned that a clear distinction between different vital functions such as metabolism and replication was made. This led to two schools of thought in the origin of life field, one inspired by biochemistry and one by genetics.Oparin's theory, which was rooted in the metabolic traditions of biochemistry, provided a model which has had a lasting impact in methodological terms and which helped to transform the field from a largely theoretical one to an area of active research. Genetically based theories, on the other hand, had a delayed impact in this respect, because of long-lasting uncertainty regarding the structural basis of gene function.     

The prebiotic synthesis of oligonucleotides

This paper is primarily a review of recent developments in the abiotic synthesis of nucleotides, short chain oligonucleotides, and their mode of replication in solution. It also presents preliminary results from this laboratory on the prebiotic synthesis of thymidine oligodeoxynucleotides. A discussion, based on the physicochemical properties of RNA and DNA oligomers relevant to the molecular evolution of these compounds leads to the tentative hypothesis that oligodeoxyribonucleotides of about 12 units may have been of sufficient length to initiate a self replication coding system. Two models are suggested to account for the synthesis of high molecular weight oligomers using short chain templates and primers.     

In vivo selection of randomly mutated retroviral genomes.

Darwinian evolution, that is the outgrowth of the fittest variants in a population, usually applies to living organisms over long periods of time. Recently, in vitro selection/amplification techniques have been developed that allow for the rapid evolution of functionally active nucleic acids from a pool of randomized sequences. We now describe a modification of the nucleic acid-evolution protocol in which selection and amplification take place inside living cells by means of a retroviral-based replication system. We have generated a library of HIV-1 DNA genomes with random sequences in particular domains of the TAR element, which is the binding site for the Tat trans-activator protein. This mixture of HIV genomes was transfected into T cells and outgrowth of the fittest viruses was observed within two weeks of viral replication. The results of this in vivo selection analysis are consistent with the notion that primary sequence elements in both TAR bulge and loop domains are critical for Tat-mediated trans-activation and viral replication.     

Analysis of the evolutionary forces shaping mitochondrial genomes of a Neotropical malaria vector complex

Many vectors of human malaria belong to complexes of morphologically indistinguishable cryptic species. Here we report the analysis of the newly sequenced complete mitochondrial DNA molecules from six recognized or putative species of one such group, the Neotropical Anopheles albitarsis complex. The molecular evolution of these genomes had been driven by purifying selection, particularly strongly acting on the RNA genes. Directional mutation pressure associated with the strand-asynchronous asymmetric mtDNA replication mechanism may have shaped a pronounced DNA strand asymmetry in the nucleotide composition in these and other Anopheles species. The distribution of sequence polymorphism, coupled with the conflicting phylogenetic trees inferred from the mitochondrial DNA and from the published white gene fragment sequences, indicates that the evolution of the complex may have involved ancient mtDNA introgression. Six protein coding genes (nad5, nad4, cox3, atp6, cox1 and nad2) have high levels of sequence divergence and are likely informative for population genetics studies. Finally, the extent of the mitochondrial DNA variation within the complex supports the notion that the complex consists of a larger number of species than until recently believed.     

A theory for the origin of a self-replicating chemical system. I: Natural selection of the autogen from short,random oligomers

Summary A theory is described for the origin of a simple chemical system named an autogen, consisting of two short oligonucleotide sequences coding for two simple catalytic peptides. If the theory is valid, under appropriate conditions the autogen would be capable of self-reproduction in a truly genetic process involving both replication and translation. Limited catalytic ability, short oligomer sequences, and low selectivities leading to sloppy information transfer processes are shown to be adequate for the origin of the autogen from random background oligomers. A series of discrete steps, each highly probable if certain minimum requirements and boundary conditions are satisfied, lead to exponential increase in population of all components in the system due to autocatalysis and hypercyclic organization. Nucleation of the components and exponential increase to macroscopic amounts could occur in times on the order of weeks. The feasibility of the theory depends on a number of factors, including the capability of simple protoenzymes to provide moderate enhancements of the accuracies of replication and translation and the likelihood of finding an environment where all of the required processes can occur simultaneously. Regardless of whether or not the specific form proposed for the autogen proves to be feasible, the theory suggests that the first self-replicating chemical systems may have been extremely simple, and that the period of time required for chemical evolution prior to Darwinian natural selection may have been far shorter than generally assumed. Due to the short time required, this theory, unlike others on the origin of genetic processes, is potentially capable of direct experimental verification. A number of prerequisites leading up to such an experiment are suggested, and some have been fulfilled. If successful, such an experiment would be the first laboratory demonstration of the spontaneous emergence by natural selection of a genetic, self-replicating, and evolving molecular system, and might represent the first step in the prebiotic environment of true Darwinian evolution toward a living cell.     

Replicate after reading: on the extraction and evocation of cultural information

Does cultural evolution happen by a process of copying or replication? And how exactly does cultural transmission compare with that paradigmatic case of replication, the copying of DNA in living cells? Theorists of cultural evolution are divided on these issues. The most important objection to the replication model has been leveled by Dan Sperber and his colleagues. Cultural transmission, they argue, is almost always reconstructive and transformative, while strict ‘replication’ can be seen as a rare limiting case at most. By means of some thought experiments and intuition pumps, I clear up some confusion about what qualifies as ‘replication’. I propose a distinction between evocation and extraction of cultural information, applying these concepts at different levels of resolution. I defend a purely abstract and information-theoretical definition of replication, while rejecting more material conceptions. In the end, even after taking Sperber’s valuable and important points on board, the notion of cultural replication remains a valid and useful one. This is fortunate, because we need it for certain explanatory projects (e.g., understanding cumulative cultural adaptations).     

Polymorphism of genes encoding SOS polymerases in natural populations of Escherichia coli

High fidelity replicative DNA polymerases can be blocked during DNA replication by various base damages, which represents a potentially lethal event. Escherichia coli possesses three DNA polymerases, PolII, PolIV and PolV, that can continue replication over such lesions in template DNA, thus allowing for cell survival. Genes coding for these enzymes, polB, dinB, and umuCD respectively, belong to the stress-inducible SOS regulon. We have analyzed the patterns of nucleotide sequence variability of genes encoding for three SOS polymerases from E. coli natural isolates in order to identify the nature of selective forces that determine their evolution. The frequency of inferred inter-strain recombination events, and the frequency of synonymous and non-synonymous base substitutions within these genes do not deviate significantly from those observed for the control group composed of 2 genes coding for DNA polymerases PolI and PolIII and 10 metabolic genes. This suggests that the loci coding for SOS polymerases are subject to selective pressure for the maintenance of their function and specificity. The fact that genes coding for translesion-synthesis (TLS) polymerases, particularly dinB and umuC homologs, have been conserved during evolution and the present analysis suggest that their activity is essential for the cellular survival and fitness.     

Immortal DNA or epigenetic signature ?

During mitosis each daughter cell inherits a full copy of the maternal genomic material. DNA replication, however, is an imprecise process, thus errors can arise resulting in potentially deleterious mutations over extended rounds of cell division and these may lead to cancinogenesis. Over thirty years ago, J. Cairns proposed that a cell could avoid the accumulation of mutations arising from DNA replication if all template DNA strands are inherited in one daughter cell during cell division, thus giving rise to the notion of < immortal > DNA strands. In this model the stem cells would retain the template DNA (older) strands. Proving or disproving this notion experimentally has been challenging. Further, it has recently become apparent that epigenetic regulation of gene expression plays a critical role in governing cell states, self-renewal and differentiation. In light of these data, can the phenomenon on template DNA strand segregation also reflect this epigenetic signature? In this review we explore these notions, discuss the evidence in support of this theory, the implications, and some of the mechanisms which could explain this phenomenon.     

Codon Size Reduction as the Origin of the Triplet Genetic Code

The genetic code appears to be optimized in its robustness to missense errors and frameshift errors. In addition, the genetic code is near-optimal in terms of its ability to carry information in addition to the sequences of encoded proteins. As evolution has no foresight, optimality of the modern genetic code suggests that it evolved from less optimal code variants. The length of codons in the genetic code is also optimal, as three is the minimal nucleotide combination that can encode the twenty standard amino acids. The apparent impossibility of transitions between codon sizes in a discontinuous manner during evolution has resulted in an unbending view that the genetic code was always triplet. Yet, recent experimental evidence on quadruplet decoding, as well as the discovery of organisms with ambiguous and dual decoding, suggest that the possibility of the evolution of triplet decoding from living systems with non-triplet decoding merits reconsideration and further exploration. To explore this possibility we designed a mathematical model of the evolution of primitive digital coding systems which can decode nucleotide sequences into protein sequences. These coding systems can evolve their nucleotide sequences via genetic events of Darwinian evolution, such as point-mutations. The replication rates of such coding systems depend on the accuracy of the generated protein sequences. Computer simulations based on our model show that decoding systems with codons of length greater than three spontaneously evolve into predominantly triplet decoding systems. Our findings suggest a plausible scenario for the evolution of the triplet genetic code in a continuous manner. This scenario suggests an explanation of how protein synthesis could be accomplished by means of long RNA-RNA interactions prior to the emergence of the complex decoding machinery, such as the ribosome, that is required for stabilization and discrimination of otherwise weak triplet codon-anticodon interactions.     

Evolutionary histology and the theory of evolution (on the 100th anniversary of the birth of Academician A. A. Zavarzin

Darwin's theory did not touch upon the problem of evolution of tissues. An attempt made by Heckel to explain phylogeny of tissues, basing on principles of selection and divergence, failed. It was not at once understood that evolution of separate levels of organization possessed certain specificity. The theory of parallelism, suggested by A. A. Zavarzin, stated the notion on specific regularities in evolution of tissues. Having analysed the correlation between the theory of evolution and evolutional histology, A. A. Zavarzin demonstrated that darwinism developed predominantly at the theory of speciation. This approach is correct for the period of the new evolutionary synthesis, too. The synthetic theory of evolution does not take into consideration evolution of tissues. A. A. Zavarzin's theory contributed to reorganization of methodology of the evolutional biology. The historical method was enriched by a certain principle on specific regularities of evolution for each level of organization in the alive. Simultaneously, the genesis of the parallelism theory discovered that correct explanation of the regularities in evolution of tissues is possible only under conditions that the evolution of histostructures can be inserted into the evolution of ontogenesis and species.     

The transmission sense of information

Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers of biology have argued that when biologists talk about information in genes and in evolution, they are not talking about the sort of information that Shannon’s theory addresses. First, philosophers have suggested that Shannon’s theory is only useful for developing a shallow notion of correlation, the so-called “causal sense” of information. Second, they typically argue that in genetics and evolutionary biology, information language is used in a “semantic sense,” whereas semantics are deliberately omitted from Shannon’s theory. Neither critique is well-founded. Here we propose an alternative to the causal and semantic senses of information: a transmission sense of information, in which an object X conveys information if the function of X is to reduce, by virtue of its sequence properties, uncertainty on the part of an agent who observes X. The transmission sense not only captures much of what biologists intend when they talk about information in genes, but also brings Shannon’s theory back to the fore. By taking the viewpoint of a communications engineer and focusing on the decision problem of how information is to be packaged for transport, this approach resolves several problems that have plagued the information concept in biology, and highlights a number of important features of the way that information is encoded, stored, and transmitted as genetic sequence.     

Walking the Walk to Teach the Talk: Implementing Ancestral Lifestyle Strategies as the Newest Tool in Evolutionary Studies

The learning of evolutionary theory typically takes place in the classroom or laboratory. Students of these traditional approaches often leave with the notion that applications of evolutionary theory have little bearing on their lives. The Evolutionary Studies Consortium (EvoS; ) has been extremely successful in overcoming these barriers and demonstrating the bridges across academic areas that can be created with the principles of evolution as a guide. While this is a fantastic means through which to educate students about the intricacies of evolution, we believe that the full potential of this approach has yet to be realized. Applications beyond strict academic contexts are still waiting to be mined. Here, we outline an approach that proposes the implementation of a nutrition and physical fitness program, alongside classroom pedagogy, as a means of helping students learn about evolution and how it can be used to increase their own quality of life.     

Optimal mutation rates in dynamic environments

In this paper, we study the evolution of the mutation rate for simple organisms in dynamic environments. A model based on explicit population dynamics at the gene sequence level, with multiple fitness coding loci tracking a moving fitness peak in a random fitness background, is developed and an analytical expression for the optimal mutation rate is derived. The optimal mutation rate per genome is approximately independent of genome length, something that has been observed in nature. Furthermore, the optimal mutation rate is a function of the absolute, not relative, replication rate of the superior gene sequences. Simulations confirm the theoretical predictions.     

Autocatalysis, information and coding

Autocatalytic self-construction in macromolecular systems requires the existence of a reflexive relationship between structural components and the functional operations they perform to synthesise themselves. The possibility of reflexivity depends on formal, semiotic features of the catalytic structure–function relationship, that is, the embedding of catalytic functions in the space of polymeric structures. Reflexivity is a semiotic property of some genetic sequences. Such sequences may serve as the basis for the evolution of coding as a result of autocatalytic self-organisation in a population of assignment catalysts. Autocatalytic selection is a mechanism whereby matter becomes differentiated in primitive biochemical systems. In the case of coding self-organisation, it corresponds to the creation of symbolic information. Prions are present-day entities whose replication through autocatalysis reflects aspects of biological semiotics less obvious than genetic coding.     

Evolution: an axiomatic perspective.

In this paper we present an axiomatic theory of evolution which is inspired by the reading of a paper written by G.V. Schiaparelli in 1898. Schiaparelli was a famous astronomer, but he also studied the Darwinian ideas. We propose five axioms which can characterize the theory of evolution. We have also written these axioms using the language of the logic of predicates of first order with some constant monadic and dyadic predicates and appropriate functionals. But we can use other types of logic. So we can examine the concepts of species and of speciation. Then we introduce the interesting notion of generation distance. Moreover we give a theorem which establishes a geometrical model of our theory. If we analyze further the fourth axiom (which concerns the notion of generation distance) we can propose an elementary dynamical model by which we can represent possible evolutionary dynamics. These dynamics partially depend on random quantities.     

Reconciling evolutionary theory and taxonomic practice

The notion of evolution is a notion of change; yet, biologists customarily define each species as if it were a static class. One approach to this supposed disconnect between evolutionary theories and taxonomic practices would be to change those practices. Instead, the author claims this alleged disparity is a misreading. For the most part, it disappears under a proposed modified essentialist species concept involving unique species‐specific developmental suites. Each suite specific to a natural species is envisioned as a number of dispositional alternatives expressed distributively among the organisms in that species. There is support for this species concept in recent work in comparative genomics and developmental genetics. The concept is compatible with intraspecific variation and gradual evolution, and unifies practice and theory. It leads to an extended model of speciation and to an observational protocol for testing the concept and model.