scholarly journals Structured sequences emerge from random pool when replicated by templated ligation

2021 ◽  
Vol 118 (8) ◽  
pp. e2018830118 ◽  
Author(s):  
Patrick W. Kudella ◽  
Alexei V. Tkachenko ◽  
Annalena Salditt ◽  
Sergei Maslov ◽  
Dieter Braun
Keyword(s):  
Rna World ◽  
Random Sequence ◽  
Darwinian Evolution ◽  
Complementary Sequence ◽  
Replication Errors ◽  
Ligation Reaction ◽  
Starting Point ◽  
Eigen Theory ◽  
Catalytic Functions ◽  
Low Entropy

The central question in the origin of life is to understand how structure can emerge from randomness. The Eigen theory of replication states, for sequences that are copied one base at a time, that the replication fidelity has to surpass an error threshold to avoid that replicated specific sequences become random because of the incorporated replication errors [M. Eigen, Naturwissenschaften 58 (10), 465–523 (1971)]. Here, we showed that linking short oligomers from a random sequence pool in a templated ligation reaction reduced the sequence space of product strands. We started from 12-mer oligonucleotides with two bases in all possible combinations and triggered enzymatic ligation under temperature cycles. Surprisingly, we found the robust creation of long, highly structured sequences with low entropy. At the ligation site, complementary and alternating sequence patterns developed. However, between the ligation sites, we found either an A-rich or a T-rich sequence within a single oligonucleotide. Our modeling suggests that avoidance of hairpins was the likely cause for these two complementary sequence pools. What emerged was a network of complementary sequences that acted both as templates and substrates of the reaction. This self-selecting ligation reaction could be restarted by only a few majority sequences. The findings showed that replication by random templated ligation from a random sequence input will lead to a highly structured, long, and nonrandom sequence pool. This is a favorable starting point for a subsequent Darwinian evolution searching for higher catalytic functions in an RNA world scenario.

scholarly journals A CROSS-CULTURAL STUDY ON FRESHMEN’S KNOWLEDGE OF GENETICS, EVOLUTION, AND THE NATURE OF SCIENCE

2014 ◽  
Vol 13 (1) ◽  
pp. 6-18
Author(s):  
Andrej Šorgo ◽  
Muhammet Usak ◽  
Milan Kubiatko ◽  
Jana Fančovičova ◽  
Pavol Prokop ◽  
...  
Keyword(s):  
Nature Of Science ◽  
Science Teachers ◽  
Human Evolution ◽  
Scientific Reasoning ◽  
Darwinian Evolution ◽  
First Year ◽  
Scientific Explanations ◽  
Starting Point ◽  
Level Of Knowledge ◽  
First Year University

The purpose of this study was to measure the freshmen’s level of knowledge about genetics, evolution, human evolution, the nature of science, and opinions on evolution and the presence of non-scientific explanations among Czech, Slovakian, Slovenian and Turkish students. Determination of prior knowledge and pre-conceptions about these issues is important because they are filters to learning other related concepts. The results are going to be a starting point for developing teaching strategies concerning Darwinian evolution and preparing prospective science teachers for working with students in national and international contexts. A total of 994 first-year university students from the Czech Republic (276; 27.8%), Slovakia (212, 21.3%), Slovenia (217, 27.3%) and Turkey (235, 23.6%) participated in this study. The findings can be summarized as follows: knowledge especially that of the nature of science at the freshmen level was seriously flawed. Non-scientific explanations were present in high percentages. Both were regarded as barriers towards scientific reasoning and acceptance of general human evolution especially for students expressing orthodox religious beliefs. Key words: evolution, genetics, human evolution, nature of science, non-scientific explanations.

scholarly journals Ancient enzymology?: Ribozymes

2003 ◽  
Vol 25 (4) ◽  
pp. 9-11
Author(s):  
David M.J. Lilley
Keyword(s):  
Functional Groups ◽  
Chemical Reactions ◽  
Rna World ◽  
Limited Resource ◽  
Rna Molecules ◽  
Significant Challenge ◽  
Catalytic Functions

Ribozymes are RNA molecules that act like enzymes to accelerate chemical reactions. They may be relics of an ancient ‘RNA world’, where RNA performed both informational and catalytic functions before proteins took over the latter role. As enzymes, RNA molecules are rather poor prospects, with a paucity of functional groups, yet in a limited set of reactions they achieve respectable rate enhancements. Explaining this is a significant challenge to the biological chemist, and the area has seldom been free from controversy. Some general conclusions are, however, now emerging. RNA achieves a lot from a very limited resource, from which some general insights into biocatalysis may emerge.

scholarly journals Emergence and diversification of a host-parasite RNA ecosystem through Darwinian evolution

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Taro Furubayashi ◽  
Kensuke Ueda ◽  
Yohsuke Bansho ◽  
Daisuke Motooka ◽  
Shota Nakamura ◽  
...  
Keyword(s):  
Arms Race ◽  
Darwinian Evolution ◽  
Prebiotic Evolution ◽  
Clonal Population ◽  
Replication Errors ◽  
Replication Experiment ◽  
Living Organisms ◽  
Host Parasite

In prebiotic evolution, molecular self-replicators are considered to develop into diverse, complex living organisms. The appearance of parasitic replicators is believed inevitable in this process. However, the role of parasitic replicators in prebiotic evolution remains elusive. Here, we demonstrated experimental coevolution of RNA self-replicators (host RNAs) and emerging parasitic replicators (parasitic RNAs) using an RNA-protein replication system we developed. During a long-term replication experiment, a clonal population of the host RNA turned into an evolving host-parasite ecosystem through the continuous emergence of new types of host and parasitic RNAs produced by replication errors. The host and parasitic RNAs diversified into at least two and three different lineages, respectively, and they exhibited evolutionary arms-race dynamics. The parasitic RNA accumulated unique mutations, thus adding a new genetic variation to the whole replicator ensemble. These results provide the first experimental evidence that the coevolutionary interplay between host-parasite molecules plays a key role in generating diversity and complexity in prebiotic molecular evolution.

Ribozymes and aptamers in the RNA world, and in synthetic biology

2016 ◽  
Author(s):  
◽  
Raghav Raj Poudyal
Keyword(s):  
Synthetic Biology ◽  
Genetic Information ◽  
Rna World ◽  
Information Storage ◽  
Rna Aptamers ◽  
Darwinian Evolution ◽  
University Of Missouri ◽  
Biologically Relevant ◽  
Functional Rnas

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] The RNA world hypothesis postulates that Ribonucleic Acids (RNA) may have provided functions of catalysis and genetic information storage during the origin of life on earth. An RNA based life is hypothesized to have undergone Darwinian evolution to ultimately lead into extant biology, where DNA is used as the repository for genetic information and proteins are used as biological catalysts. The discovery of functional RNAs such as catalytic RNAs, regulatory RNAs, and ligand-binding RNA aptamers further strengthen this hypothesis. These functional RNAs are also used as tools for synthetic biology and therapeutics. This work highlights strategies used by RNA enzymes (Ribozymes) for catalysis of chemical reactions, and explores new chemistries catalyzed by ribozymes. We also engineered an in vitro evolved ribozyme to control activities of other functional RNA molecules. Finally, this work explores innovative approaches to discover new RNA enzymes that catalyze biologically relevant reactions. Findings from these studies have revealed potential roles of RNA enzymes during the primordial earth, and also opened doors to build RNA-based tools that regulate biological processes.

scholarly journals The Origin of Prebiotic Information System in the Peptide/RNA World: A Simulation Model of the Evolution of Translation and the Genetic Code

Life ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 25 ◽  
Author(s):  
Sankar Chatterjee ◽  
Surya Yadav
Keyword(s):  
Amino Acids ◽  
Information System ◽  
Protein Synthesis ◽  
Amino Acid ◽  
Genetic Code ◽  
Rna World ◽  
Trna Synthetase ◽  
Darwinian Evolution ◽  
Universal Genetic Code ◽  
Translation Machine

Information is the currency of life, but the origin of prebiotic information remains a mystery. We propose transitional pathways from the cosmic building blocks of life to the complex prebiotic organic chemistry that led to the origin of information systems. The prebiotic information system, specifically the genetic code, is segregated, linear, and digital, and it appeared before the emergence of DNA. In the peptide/RNA world, lipid membranes randomly encapsulated amino acids, RNA, and peptide molecules, which are drawn from the prebiotic soup, to initiate a molecular symbiosis inside the protocells. This endosymbiosis led to the hierarchical emergence of several requisite components of the translation machine: transfer RNAs (tRNAs), aminoacyl-tRNA synthetase (aaRS), messenger RNAs (mRNAs), ribosomes, and various enzymes. When assembled in the right order, the translation machine created proteins, a process that transferred information from mRNAs to assemble amino acids into polypeptide chains. This was the beginning of the prebiotic <i>information</i> age. The origin of the genetic code is enigmatic; herein, we propose an evolutionary explanation: the demand for a wide range of protein enzymes over peptides in the prebiotic reactions was the main selective pressure for the origin of information-directed protein synthesis. The molecular basis of the genetic code manifests itself in the interaction of aaRS and their cognate tRNAs. In the beginning, aminoacylated ribozymes used amino acids as a cofactor with the help of bridge peptides as a process for selection between amino acids and their cognate codons/anticodons. This process selects amino acids and RNA species for the next steps. The ribozymes would give rise to pre-tRNA and the bridge peptides to pre-aaRS. Later, variants would appear and evolution would produce different but specific aaRS-tRNA-amino acid combinations. Pre-tRNA designed and built pre-mRNA for the storage of information regarding its cognate amino acid. Each pre-mRNA strand became the storage device for the genetic information that encoded the amino acid sequences in triplet nucleotides. As information appeared in the digital languages of the codon within pre-mRNA and mRNA, and the genetic code for protein synthesis evolved, the prebiotic chemistry then became more organized and directional with the emergence of the translation and genetic code. The genetic code developed in three stages that are coincident with the refinement of the translation machines: the GNC code that was developed by the pre-tRNA/pre-aaRS /pre-mRNA machine, SNS code by the tRNA/aaRS/mRNA machine, and finally the universal genetic code by the tRNA/aaRS/mRNA/ribosome machine. We suggest the coevolution of translation machines and the genetic code. The emergence of the translation machines was the beginning of the Darwinian evolution, an interplay between information and its supporting structure. Our hypothesis provides the logical and incremental steps for the origin of the programmed protein synthesis. In order to better understand the prebiotic information system, we converted letter codons into numerical codons in the Universal Genetic Code Table. We have developed a software, called CATI (Codon-Amino Acid-Translator-Imitator), to translate randomly chosen numerical codons into corresponding amino acids and vice versa. This conversion has granted us insight into how the genetic code might have evolved in the peptide/RNA world. There is great potential in the application of numerical codons to bioinformatics, such as barcoding, DNA mining, or DNA fingerprinting. We constructed the likely biochemical pathways for the origin of translation and the genetic code using the Model-View-Controller (MVC) software framework, and the translation machinery step-by-step. While using AnyLogic software, we were able to simulate and visualize the entire evolution of the translation machines, amino acids, and the genetic code.

scholarly journals Parietal and Motor Cortical Dynamics Differentially Shape the Computation of Choice History Bias

2021 ◽  
Author(s):  
Anne E Urai ◽  
Tobias H Donner
Keyword(s):  
Parietal Cortex ◽  
Posterior Parietal Cortex ◽  
Random Sequence ◽  
Beta Band ◽  
Sensory Stimuli ◽  
Starting Point ◽  
Action Preparation ◽  
Motor History ◽  
Gamma Band Activity ◽  
Band Activity

Humans and other animals tend to systematically repeat (or alternate) their previous choices, even when judging sensory stimuli presented in a random sequence. Choice history biases may arise from action preparation in motor circuits, or from perceptual or decision processing in upstream areas. Here, we combined source-level magnetoencephalographic (MEG) analyses of cortical population dynamics with behavioral modeling of a visual decision process. We disentangled two neural history signals in human motor and posterior parietal cortex. Gamma-band activity in parietal cortex tracked previous choices throughout the trial and biased evidence accumulation toward choice repetition. Action-specific beta-band activity in motor cortex also carried over to the next trial and biased the accumulation starting point toward alternation. The parietal, but not motor, history signal predicted the next trial's choice as well as individual differences in choice repetition. Our results are consistent with a key role of parietal cortical signals in shaping choice sequences.

Presbyterians and science in the north of Ireland before 1874

2008 ◽  
Vol 41 (4) ◽  
pp. 541-565 ◽  
Author(s):  
ANDREW R. HOLMES
Keyword(s):  
Eighteenth Century ◽  
Presidential Address ◽  
Darwinian Evolution ◽  
Educational Facilities ◽  
The North ◽  
Starting Point ◽  
The Times ◽  
John Tyndall ◽  
The Mind ◽  
The Relationship

AbstractIn his presidential address to the Belfast meeting of the British Association for the Advancement of Science in 1874, John Tyndall launched what David Livingstone has called a ‘frontal assault on teleology and Christian theism’. Using Tyndall's intervention as a starting point, this paper seeks to understand the attitudes of Presbyterians in the north of Ireland to science in the first three-quarters of the nineteenth century. The first section outlines some background, including the attitude of Presbyterians to science in the eighteenth century, the development of educational facilities in Ireland for the training of Presbyterian ministers, and the specific cultural and political circumstances in Ireland that influenced Presbyterian responses to science more generally. The next two sections examine two specific applications by Irish Presbyterians of the term ‘science’: first, the emergence of a distinctive Presbyterian theology of nature and the application of inductive scientific methodology to the study of theology, and second, the Presbyterian conviction that mind had ascendancy over matter which underpinned their commitment to the development of a science of the mind. The final two sections examine, in turn, the relationship between science and an eschatological reading of the signs of the times, and attitudes to Darwinian evolution in the fifteen years between the publication ofThe Origin of Speciesin 1859 and Tyndall's speech in 1874.

scholarly journals Emergence and diversification of a host-parasite RNA ecosystem through Darwinian evolution

2019 ◽  
Author(s):  
Taro Furubayashi ◽  
Kensuke Ueda ◽  
Yohsuke Bansho ◽  
Daisuke Motooka ◽  
Shota Nakamura ◽  
...  
Keyword(s):  
Darwinian Evolution ◽  
Prebiotic Evolution ◽  
Clonal Population ◽  
Replication Errors ◽  
Replication Experiment ◽  
Living Organisms ◽  
Host Parasite ◽  
First Time

AbstractIn the prebiotic evolution, molecular self-replicators are considered to develop into diverse, complex living organisms. The appearance of parasitic replicators is believed inevitable in this process. However, the role of parasitic replicators on prebiotic evolution remains elusive. Here, we demonstrated experimental coevolution of RNA self-replicators (host RNAs) and emerging parasitic replicators (parasitic RNAs) for the first time by using an RNA-protein replication system we had developed. During a long-term replication experiment, a clonal population of the host RNA turned into an evolving host-parasite ecosystem through the continuous emergence of new types of host and parasitic RNAs produced by replication errors. The diversified host and parasitic RNAs exhibited evolutionary arms-race dynamics. The parasitic RNA accumulated unique mutations that the host RNA had never acquired, thus adding a new genetic variation to the whole replicator ensemble. These results provide the first experimental evidence that the coevolutionary interplay between host-parasite molecules play a key role in generating diversity and complexity in prebiotic molecular evolution.

scholarly journals Emergence of ribozyme and tRNA-like structures from mineral-rich muddy pools on prebiotic earth

2020 ◽  
Author(s):  
Suvam Roy ◽  
Niraja V. Bapat ◽  
Julien Derr ◽  
Sudha Rajamani ◽  
Supratim Sengupta
Keyword(s):  
Rna World ◽  
Secondary Structures ◽  
Realistic Model ◽  
Dependent Manner ◽  
Initial State ◽  
Rna Molecules ◽  
Free Nucleotides ◽  
World Hypothesis ◽  
Life On Earth ◽  
Catalytic Functions

AbstractThe RNA world hypothesis, although a viable one regarding the origin of life on earth, has so far failed to provide a compelling explanation for the synthesis of RNA molecules with catalytic functions, from free nucleotides via abiotic processes. To tackle this long-standing problem, we develop a realistic model for the onset of the RNA world, using experimentally determined rates for polymerization reactions. We start with minimal assumptions about the initial state that only requires the presence of short oligomers or just free nucleotides and consider the effects of environmental cycling by dividing a day into a dry, semi-wet and wet phases that are distinguished by the nature of reactions they support. Long polymers, with maximum lengths sometimes exceeding 100 nucleotides, spontaneously emerge due to a combination of non-enzymatic, non-templated polymer extension and template-directed primer extension processes. The former helps in increasing the lengths of RNA strands, whereas the later helps in producing complementary copies of the strands. Strands also undergo hydrolysis in a structure-dependent manner that favour breaking of bonds connecting unpaired nucleotides. We identify the most favourable conditions needed for the emergence of ribozyme and tRNA-like structures and double stranded RNA molecules, classify all RNA strands on the basis of their secondary structures and determine their abundance in the population. Our results indicate that under suitable environmental conditions, non-enzymatic processes would have been sufficient to lead to the emergence of a variety of ribozyme-like molecules with complex secondary structures and potential catalytic functions.

scholarly journals Emergence of function from single RNA sequences by Darwinian evolution

2021 ◽  
Author(s):  
Falk Wachowius ◽  
Benjamin T. Porebski ◽  
Christopher M. Johnson ◽  
Philipp Holliger
Keyword(s):  
Sequence Space ◽  
Binding Sites ◽  
Iterative Process ◽  
Random Sequence ◽  
Darwinian Evolution ◽  
Rna Sequences ◽  
Evolutionary Trajectories ◽  
The Origin Of Life ◽  
Functional Rnas ◽  
Mutation And Selection

AbstractThe spontaneous emergence of function from pools of random sequence RNA is widely considered an important transition in the origin of life. However, the plausibility of this hypothetical process and the number of productive evolutionary trajectories in sequence space are unknown. Here we demonstrate that function can arise starting from a single RNA sequence by an iterative process of mutation and selection. Specifically, we describe the discovery of both specific ATP or GTP aptamers - with micromolar affinity for their nucleotide ligand - starting each from a single, homopolymeric poly-A sequence flanked by conserved primer binding sites. Our results indicate that the ab initio presence of large, diverse random sequence pools is not a prerequisite for the emergence of functional RNAs and that the process of Darwinian evolution has the capacity to generate function even from single, largely unstructured RNA sequences with minimal molecular and informational complexity.

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