Evolution before genes.

Abstract:

BACKGROUND:Our current understanding of evolution is so tightly linked to template-dependent replication of DNA and RNA molecules that the old idea from Oparin of a self-reproducing 'garbage bag' ('coacervate') of chemicals that predated fully-fledged cell-like entities seems to be farfetched to most scientists today. However, this is exactly the kind of scheme we propose for how Darwinian evolution could have occurred prior to template replication. RESULTS:We cannot confirm previous claims that autocatalytic sets of organic polymer molecules could undergo evolution in any interesting sense by themselves. While we and others have previously imagined inhibition would result in selectability, we found that it produced multiple attractors in an autocatalytic set that cannot be selected for. Instead, we discovered that if general conditions are satisfied, the accumulation of adaptations in chemical reaction networks can occur. These conditions are the existence of rare reactions producing viable cores (analogous to a genotype), that sustains a molecular periphery (analogous to a phenotype). CONCLUSIONS:We conclude that only when a chemical reaction network consists of many such viable cores, can it be evolvable. When many cores are enclosed in a compartment there is competition between cores within the same compartment, and when there are many compartments, there is between-compartment competition due to the phenotypic effects of cores and their periphery at the compartment level. Acquisition of cores by rare chemical events, and loss of cores at division, allows macromutation, limited heredity and selectability, thus explaining how a poor man's natural selection could have operated prior to genetic templates. This is the only demonstration to date of a mechanism by which pre-template accumulation of adaptation could occur.

journal_name

Biol Direct

journal_title

Biology direct

authors

Vasas V,Fernando C,Santos M,Kauffman S,Szathmáry E

doi

10.1186/1745-6150-7-1

subject

Has Abstract

pub_date

2012-01-05 00:00:00

pages

1; discussion 1

issn

1745-6150

pii

1745-6150-7-1

journal_volume

7

pub_type

杂志文章
  • Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.

    abstract:BACKGROUND:An evolutionary classification of genes from sequenced genomes that distinguishes between orthologs and paralogs is indispensable for genome annotation and evolutionary reconstruction. Shortly after multiple genome sequences of bacteria, archaea, and unicellular eukaryotes became available, an attempt on suc...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-2-33

    authors: Makarova KS,Sorokin AV,Novichkov PS,Wolf YI,Koonin EV

    更新日期:2007-11-27 00:00:00

  • Interplay of recombination and selection in the genomes of Chlamydia trachomatis.

    abstract:BACKGROUND:Chlamydia trachomatis is an obligate intracellular bacterial parasite, which causes several severe and debilitating diseases in humans. This study uses comparative genomic analyses of 12 complete published C. trachomatis genomes to assess the contribution of recombination and selection in this pathogen and t...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-6-28

    authors: Joseph SJ,Didelot X,Gandhi K,Dean D,Read TD

    更新日期:2011-05-26 00:00:00

  • The mechanistic and evolutionary aspects of the 2'- and 3'-OH paradigm in biosynthetic machinery.

    abstract:BACKGROUND:The translation machinery underlies a multitude of biological processes within the cell. The design and implementation of the modern translation apparatus on even the simplest course of action is extremely complex, and involves different RNA and protein factors. According to the "RNA world" idea, the critica...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-8-17

    authors: Safro M,Klipcan L

    更新日期:2013-07-08 00:00:00

  • Pseudo-chaotic oscillations in CRISPR-virus coevolution predicted by bifurcation analysis.

    abstract:BACKGROUND:The CRISPR-Cas systems of adaptive antivirus immunity are present in most archaea and many bacteria, and provide resistance to specific viruses or plasmids by inserting fragments of foreign DNA into the host genome and then utilizing transcripts of these spacers to inactivate the cognate foreign genome. The ...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-9-13

    authors: Berezovskaya FS,Wolf YI,Koonin EV,Karev GP

    更新日期:2014-07-02 00:00:00

  • Optimal treatment and stochastic modeling of heterogeneous tumors.

    abstract:UNLABELLED:In this work we review past articles that have mathematically studied cancer heterogeneity and the impact of this heterogeneity on the structure of optimal therapy. We look at past works on modeling how heterogeneous tumors respond to radiotherapy, and take a particularly close look at how the optimal radiot...

    journal_title:Biology direct

    pub_type: 杂志文章,评审

    doi:10.1186/s13062-016-0142-5

    authors: Badri H,Leder K

    更新日期:2016-08-23 00:00:00

  • Division of labour in a matrix, rather than phagocytosis or endosymbiosis, as a route for the origin of eukaryotic cells.

    abstract::Two apparently irreconcilable models dominate research into the origin of eukaryotes. In one model, amitochondrial proto-eukaryotes emerged autogenously from the last universal common ancestor of all cells. Proto-eukaryotes subsequently acquired mitochondrial progenitors by the phagocytic capture of bacteria. In the s...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-020-00260-9

    authors: Bateman A

    更新日期:2020-04-28 00:00:00

  • Outer membrane protein genes and their small non-coding RNA regulator genes in Photorhabdus luminescens.

    abstract:INTRODUCTION:Three major outer membrane protein genes of Escherichia coli, ompF, ompC, and ompA respond to stress factors. Transcripts from these genes are regulated by the small non-coding RNAs micF, micC, and micA, respectively. Here we examine Photorhabdus luminescens, an organism that has a different habitat from E...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-1-12

    authors: Papamichail D,Delihas N

    更新日期:2006-05-22 00:00:00

  • Systematic evaluation of supervised machine learning for sample origin prediction using metagenomic sequencing data.

    abstract:BACKGROUND:The advent of metagenomic sequencing provides microbial abundance patterns that can be leveraged for sample origin prediction. Supervised machine learning classification approaches have been reported to predict sample origin accurately when the origin has been previously sampled. Using metagenomic datasets p...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-020-00287-y

    authors: Chen JC,Tyler AD

    更新日期:2020-12-10 00:00:00

  • Rotational restriction of nascent peptides as an essential element of co-translational protein folding: possible molecular players and structural consequences.

    abstract:BACKGROUND:A basic tenet of protein science is that all information about the spatial structure of proteins is present in their sequences. Nonetheless, many proteins fail to attain native structure upon experimental denaturation and refolding in vitro, raising the question of the specific role of cellular machinery in ...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-017-0186-1

    authors: Sorokina I,Mushegian A

    更新日期:2017-05-31 00:00:00

  • Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park.

    abstract:BACKGROUND:A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. RESULTS:The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a ...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-8-9

    authors: Podar M,Makarova KS,Graham DE,Wolf YI,Koonin EV,Reysenbach AL

    更新日期:2013-04-22 00:00:00

  • Is pre-Darwinian evolution plausible?

    abstract:BACKGROUND:This essay highlights critical aspects of the plausibility of pre-Darwinian evolution. It is based on a critical review of some better-known open, far-from-equilibrium system-based scenarios supposed to explain processes that took place before Darwinian evolution had emerged and that resulted in the origin o...

    journal_title:Biology direct

    pub_type: 杂志文章,评审

    doi:10.1186/s13062-018-0216-7

    authors: Tessera M

    更新日期:2018-09-21 00:00:00

  • Comparative genomic analysis of the DUF71/COG2102 family predicts roles in diphthamide biosynthesis and B12 salvage.

    abstract:BACKGROUND:The availability of over 3000 published genome sequences has enabled the use of comparative genomic approaches to drive the biological function discovery process. Classically, one used to link gene with function by genetic or biochemical approaches, a lengthy process that often took years. Phylogenetic distr...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-7-32

    authors: de Crécy-Lagard V,Forouhar F,Brochier-Armanet C,Tong L,Hunt JF

    更新日期:2012-09-26 00:00:00

  • IPC - Isoelectric Point Calculator.

    abstract:BACKGROUND:Accurate estimation of the isoelectric point (pI) based on the amino acid sequence is useful for many analytical biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary isoelectric focusing used in combination with high-throughput mass spectrometry. Additionally, p...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-016-0159-9

    authors: Kozlowski LP

    更新日期:2016-10-21 00:00:00

  • Biochemistry and physiology within the framework of the extended synthesis of evolutionary biology.

    abstract::Functional biologists, like Claude Bernard, ask "How?", meaning that they investigate the mechanisms underlying the emergence of biological functions (proximal causes), while evolutionary biologists, like Charles Darwin, asks "Why?", meaning that they search the causes of adaptation, survival and evolution (remote cau...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-016-0109-6

    authors: Vianello A,Passamonti S

    更新日期:2016-02-09 00:00:00

  • Global analyses of Chromosome 17 and 18 genes of lung telocytes compared with mesenchymal stem cells, fibroblasts, alveolar type II cells, airway epithelial cells, and lymphocytes.

    abstract:BACKGROUND:Telocytes (TCs) is an interstitial cell with extremely long and thin telopodes (Tps) with thin segments (podomers) and dilations (podoms) to interact with neighboring cells. TCs have been found in different organs, while there is still a lack of TCs-specific biomarkers to distinguish TCs from the other cells...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-015-0042-0

    authors: Wang J,Ye L,Jin M,Wang X

    更新日期:2015-03-11 00:00:00

  • Component retention in principal component analysis with application to cDNA microarray data.

    abstract::Shannon entropy is used to provide an estimate of the number of interpretable components in a principal component analysis. In addition, several ad hoc stopping rules for dimension determination are reviewed and a modification of the broken stick model is presented. The modification incorporates a test for the presenc...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-2-2

    authors: Cangelosi R,Goriely A

    更新日期:2007-01-17 00:00:00

  • A web server for analysis, comparison and prediction of protein ligand binding sites.

    abstract:BACKGROUND:One of the major challenges in the field of system biology is to understand the interaction between a wide range of proteins and ligands. In the past, methods have been developed for predicting binding sites in a protein for a limited number of ligands. RESULTS:In order to address this problem, we developed...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/s13062-016-0118-5

    authors: Singh H,Srivastava HK,Raghava GP

    更新日期:2016-03-25 00:00:00

  • Why eukaryotic cells use introns to enhance gene expression: splicing reduces transcription-associated mutagenesis by inhibiting topoisomerase I cutting activity.

    abstract:BACKGROUND:The costs and benefits of spliceosomal introns in eukaryotes have not been established. One recognized effect of intron splicing is its known enhancement of gene expression. However, the mechanism regulating such splicing-mediated expression enhancement has not been defined. Previous studies have shown that ...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-6-24

    authors: Niu DK,Yang YF

    更新日期:2011-05-18 00:00:00

  • Once upon a time the cell membranes: 175 years of cell boundary research.

    abstract::All modern cells are bounded by cell membranes best described by the fluid mosaic model. This statement is so widely accepted by biologists that little attention is generally given to the theoretical importance of cell membranes in describing the cell. This has not always been the case. When the Cell Theory was first ...

    journal_title:Biology direct

    pub_type: 历史文章,杂志文章,评审

    doi:10.1186/s13062-014-0032-7

    authors: Lombard J

    更新日期:2014-12-19 00:00:00

  • The fundamental units, processes and patterns of evolution, and the tree of life conundrum.

    abstract:BACKGROUND:The elucidation of the dominant role of horizontal gene transfer (HGT) in the evolution of prokaryotes led to a severe crisis of the Tree of Life (TOL) concept and intense debates on this subject. CONCEPT:Prompted by the crisis of the TOL, we attempt to define the primary units and the fundamental patterns ...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-4-33

    authors: Koonin EV,Wolf YI

    更新日期:2009-09-29 00:00:00

  • The common ancestry of life.

    abstract:BACKGROUND:It is common belief that all cellular life forms on earth have a common origin. This view is supported by the universality of the genetic code and the universal conservation of multiple genes, particularly those that encode key components of the translation system. A remarkable recent study claims to provide...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-5-64

    authors: Koonin EV,Wolf YI

    更新日期:2010-11-18 00:00:00

  • Domain enhanced lookup time accelerated BLAST.

    abstract:BACKGROUND:BLAST is a commonly-used software package for comparing a query sequence to a database of known sequences; in this study, we focus on protein sequences. Position-specific-iterated BLAST (PSI-BLAST) iteratively searches a protein sequence database, using the matches in round i to construct a position-specific...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-7-12

    authors: Boratyn GM,Schäffer AA,Agarwala R,Altschul SF,Lipman DJ,Madden TL

    更新日期:2012-04-17 00:00:00

  • A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis.

    abstract:BACKGROUND:Several computational candidate gene selection and prioritization methods have recently been developed. These in silico selection and prioritization techniques are usually based on two central approaches--the examination of similarities to known disease genes and/or the evaluation of functional annotation of...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-6-30

    authors: Lombard Z,Park C,Makova KD,Ramsay M

    更新日期:2011-06-13 00:00:00

  • Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons.

    abstract:BACKGROUND:While all codons that specify amino acids are universally recognized by tRNA molecules, codons signaling termination of translation are recognized by proteins known as class-I release factors (RF). In most eukaryotes and archaea a single RF accomplishes termination at all three stop codons. In most bacteria,...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-1-28

    authors: Baranov PV,Vestergaard B,Hamelryck T,Gesteland RF,Nyborg J,Atkins JF

    更新日期:2006-09-13 00:00:00

  • A novel superfamily containing the beta-grasp fold involved in binding diverse soluble ligands.

    abstract:BACKGROUND:Domains containing the beta-grasp fold are utilized in a great diversity of physiological functions but their role, if any, in soluble or small molecule ligand recognition is poorly studied. RESULTS:Using sensitive sequence and structure similarity searches we identify a novel superfamily containing the bet...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-2-4

    authors: Burroughs AM,Balaji S,Iyer LM,Aravind L

    更新日期:2007-01-24 00:00:00

  • Activating and inhibiting connections in biological network dynamics.

    abstract:BACKGROUND:Many studies of biochemical networks have analyzed network topology. Such work has suggested that specific types of network wiring may increase network robustness and therefore confer a selective advantage. However, knowledge of network topology does not allow one to predict network dynamical behavior--for e...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-3-49

    authors: McDonald D,Waterbury L,Knight R,Betterton MD

    更新日期:2008-12-04 00:00:00

  • The multiple personalities of Watson and Crick strands.

    abstract:BACKGROUND:In genetics it is customary to refer to double-stranded DNA as containing a "Watson strand" and a "Crick strand." However, there seems to be no consensus in the literature on the exact meaning of these two terms, and the many usages contradict one another as well as the original definition. Here, we review t...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-6-7

    authors: Cartwright RA,Graur D

    更新日期:2011-02-08 00:00:00

  • Proteomic changes associated with deletion of the Magnaporthe oryzae conidial morphology-regulating gene COM1.

    abstract:BACKGROUND:The rice blast disease caused by Magnaporthe oryzae is a major constraint on world rice production. The conidia produced by this fungal pathogen are the main source of disease dissemination. The morphology of conidia may be a critical factor in the spore dispersal and virulence of M. oryzae in the field. Del...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-5-61

    authors: Bhadauria V,Wang LX,Peng YL

    更新日期:2010-11-02 00:00:00

  • Strong association between pseudogenization mechanisms and gene sequence length.

    abstract:UNLABELLED:Pseudogenes arise from the decay of gene copies following either RNA-mediated duplication (processed pseudogenes) or DNA-mediated duplication (nonprocessed pseudogenes). Here, we show that long protein-coding genes tend to produce more nonprocessed pseudogenes than short genes, whereas the opposite is true f...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-4-38

    authors: Khachane AN,Harrison PM

    更新日期:2009-10-06 00:00:00

  • Impairment of translation in neurons as a putative causative factor for autism.

    abstract:BACKGROUND:A dramatic increase in the prevalence of autism and Autistic Spectrum Disorders (ASD) has been observed over the last two decades in USA, Europe and Asia. Given the accumulating data on the possible role of translation in the etiology of ASD, we analyzed potential effects of rare synonymous substitutions ass...

    journal_title:Biology direct

    pub_type: 杂志文章

    doi:10.1186/1745-6150-9-16

    authors: Poliakov E,Koonin EV,Rogozin IB

    更新日期:2014-07-10 00:00:00