*  Darwin's God: Evolutionists are Doubling Down on De Novo Gene Evolution
That is absurd. Even evolutionists are now agreeing that what they once rejected as impossible, and then grudgingly admitted as "rare," now must be treated as a significant mode of the origins of new genes. As Light, Basile and Elofsson write in their 2014 review which I referenced, "It has even been proposed that the creation of novel genes, a continuous process where most de novo genes are short-lived, is as frequent as gene duplications." Likewise Neme and Tautz explain, "there is now rapidly increasing evidence that de novo evolution of transcripts and genes is not only a theoretical possibility, but might even have been a rather active process throughout evolution." And even Zimmer admitted in the NY Times piece, "Far from being a fluke, these studies suggest that de novo genes are abundant." Nick you have an ax to grind that won't let acknowledge the clear evidence ...
  http://darwins-god.blogspot.com/2014/09/evolutionists-are-doubling-down-on-de.html
*  Patterns of evolutionary constraints on genes in humans | BMC Evolutionary Biology | Full Text
Genotyping and sequencing of a number of eukaryotic genomes provide us with an opportunity to study the temporal and functional character of evolutionary changes in metazoans. Here we provide a framework for identifying changes in evolutionary constraints on mutated positions in the human genome. Due to lack of SNP data, in the current analysis we captured only higher order patterns at the level of functional categories. But upon availability of resequencing data, using BaseDiver it is possible to achieve higher resolution. In this work we restricted the use of BaseDiver to coding regions only, where most of the base positions are under selection and the effects of hitchhiking are small, it can be used to identify changes in constraints in non-coding regions as well.. Recently outliers of evolutionary patterns like ultra-conserved elements in higher eukaryotes and highly accelerated regions in humans have been identified [4, 7]; here we attempt to capture ...
  https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-8-275
*  Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics - Oxford Big Data...
Upon HIV transmission, some patients develop AIDS in only a few months, while others remain disease free for 20 or more years. This variation in the rate of disease progression is poorly understood and has been attributed to host genetics, host immune responses, co-infection, viral genetics, and adaptation. Here, we develop a new 'relaxed-clock' phylogenetic method to estimate absolute rates of synonymous and nonsynonymous substitution through time. We identify an unexpected association between the synonymous substitution rate of HIV and disease progression parameters. Since immune activation is the major determinant of HIV disease progression, we propose that this process can also determine viral generation times, by creating favourable conditions for HIV replication. These conclusions may apply more generally to HIV evolution, since we also observed an overall low synonymous substitution rate for HIV-2, which is known to be less pathogenic than HIV-1 and capable of tempering the ...
  https://www.bdi.ox.ac.uk/publications/210951
*  Survival and Innovation: The role of mutational robustness in evolution
Biological systems are resistant to perturbations caused by the environment and by the intrinsic noise of the system. Robustness to mutations is a particular aspect of robustness in which the phenotype is resistant to genotypic variation. Mutational robustness has been linked to the ability of the system to generate heritable genetic variation (a property known as evolvability). It is known that greater robustness leads to increased evolvability. Therefore, mechanisms that increase mutational robustness fuel evolvability. Two such mechanisms, molecular chaperones and gene duplication, have been credited with enormous importance in generating functional diversity through the increase of system's robustness to mutational insults. However, the way in which such mechanisms regulate robustness remains largely uncharacterized. In this review, I provide evidence in support of the role of molecular chaperones and gene duplication in innovation. Specifically, I present evidence that ...
  https://riunet.upv.es/handle/10251/68256
*  Hidden dimensions in protein evolution: stability, mutational robustness, and evolvability - CaltechTHESIS
Proteins are evolvable in the sense that they are readily able to acquire new or improved functions through the process of mutation and selection. Here, I examine what properties influence the ability of proteins to evolve new functions. I show that proteins with similar biochemical properties can differ substantially in their capacities to withstand mutations and evolve new functions. Specifically, more stable proteins are both more mutationally robust and more evolvable, due to improved tolerance for mutations. This fact can be exploited in protein engineering. I then show how evolutionary theory can be modified to describe how a protein's mutational robustness changes during the normal course of neutral genetic drift. One of the main theoretical predictions is that proteins evolving in larger populations will gain excess stability and mutational robustness, a prediction which I confirm experimentally. Finally, I turn to the question of how neutral genetic drift can alter "promiscuous" ...
  http://thesis.library.caltech.edu/1984/
*  Nucleotide Frequencies in Human Genome and Fibonacci Numbers | SpringerLink
This work presents a mathematical model that establishes an interesting connection between nucleotide frequencies in human single-stranded DNA and the famous Fibonacci's numbers. The model relies on t
  https://link.springer.com/article/10.1007%2Fs11538-007-9261-6
*  talks.cam : Accelerated substitution rates in non-coding sequence: Gene duplication, transcription factor binding site turnover...
If you have a question about this talk, please contact Xin Wang.. Differences in the gene regulatory network are hypothesized to contribute significantly to phenotypic divergence between and within species. Non-coding sequences with bursts of lineage-specific changes are promising candidates, because clusters of nearby substitutions are a hallmark of selection potentially modify evolutionarily conserved regulatory elements. Performing a comprehensive, genome-wide analysis, we find that genomic loci with high substitution rates in the human-chimp lineage are over-represented near genes that duplicated in the human-chimp ancestor. We also developed a method to screen for nucleotide substitutions predicted to affect transcription factor binding. Rates of binding site divergence are elevated in non-coding sequences near duplicated loci with accelerated substitution rates. Finally, GC-biased gene conversion (gBGC) is a non-adaptive, recombination-associated explanation for accelerated ...
  http://www.talks.cam.ac.uk/talk/index/25388
*  Functionally Tolerable Mutations Incorporated in Proteins Guides the Evolution Process | MedCrave
Evolution is defined as adapted set of positively favorable changes across successive generations in heritable characteristics of different biological species [1]. It often imposes divergence in the organisms at every evolutionary level, be it genetic or epigenetic [2]. Canalization thus study the genotypic variants contributing to the similar phenotype [3]. Hence irrespective of genotypes, genetic alterations assisting the individual's phenotype solely guides the evolutionary adaptation. In this regard, the molecular clock hypothesis proposed by Zuckerkandl & Pauling [4] seems to be correct. Sarich & Wilson [5,6] also demonstrated the divergence of humans and apes approximately 5 million years ago through the same hypothesis. Evolutionary factors Evolution being highly dimensional phenomenon is almost impossible to explain simply. Even the mathematical analysis fails to correctly track the ...
  http://googlescholar.medcraveonline.com/scholars/article_fulltext/1710
*  The neutral theory is dead. Long live the neutral theory - Kreitman - 1996 - BioEssays - Wiley Online Library
The neutral theory of molecular evolution has been instrumental in organizing our thinking about the nature of evolutionary forces shaping variation at the DNA level. More importantly, it has provided empiricists with a strong set of testable predictions and hence, a useful null hypothesis against which to test for the presence of selection. Evidence indicates that the neutral theory cannot explain key features of protein evolution nor patterns of biased codon usage in certain species. Whereas we now have a reasonable model of selection acting on synonymous changes in Drosophila, protein evolution remains poorly understood. Despite limitations in the applicability of the neutral theory, it is likely to remain an integral part of the quest to understand molecular evolution. ...
  http://onlinelibrary.wiley.com/doi/10.1002/bies.950180812/abstract?globalMessage=0
*  Detecting Amino Acid Sites Under Positive Selection and Purifying Selection | Genetics
ANALYZING the instantaneous rate of nonsynonymous (amino acid-changing) and synonymous (silent) nucleotide substitutions in protein-coding molecular sequences can give important clues to understanding how they evolved. In particular, the ratio of the rates of nonsynonymous and synonymous fixation has been used to measure the level of selective pressure on proteins (McDonald and Kreitman 1991, for example). Synonymous mutations do not change the encoded protein and so are often assumed to be selectively neutral. If a nonsynonymous mutation does not affect the fitness of a protein, it would become fixed within the population at the same rate as a synonymous mutation, giving a nonsynonymous/synonymous rate ratio (ω) of 1. If a nonsynonymous change makes the protein more or less fit on average then ω will be greater or less than 1, respectively. A significant excess of nonsynonymous over synonymous substitution has been used as evidence for adaptive evolution (for a review, see ...
  http://www.genetics.org/content/169/3/1753
*  Is the rate of insertion and deletion mutation male-biased? - Molecular evolutionary analysis of avian and primate sex...
Is the rate of insertion and deletion mutation male-biased? - Molecular evolutionary analysis of avian and primate sex chromosome sequence. ...
  http://uu.diva-portal.org/smash/record.jsf?pid=diva2:76309
*  UMass Amherst: Biology Department: Courses: 531--Principles of Molecular Evolution
An advanced course focused on the evolution of macromolecules and the reconstruction of evolutionary history of genes, proteins and organisms. Potential topics include databases and sequence matching, molecular phylogenetics, gene duplication and divergence, genome evolution, and horizontal gene transfer. The course will consist of lectures, computer demonstrations and class discussions. Text: Molecular Evolution, W.-H. Li, 1997 and readings from primary literature. 2 hour-exams and 1 term paper. Prerequisite: Biology 280 or equivalent course.. ...
  http://www.bio.umass.edu/biology/undergraduate/biology-courses/course-catalog/597l-principles-molecular-evolution
*  Evolution and coexistence in response to a key innovation in a long-term evolution experiment with Escherichia coli | Haldane's...
Evolution and coexistence in response to a key innovation in a long-term evolution experiment with Escherichia coli Caroline B. Turner, Zachary D. Blount, Daniel H. Mitchell, Richard E. Lenski doi: http://dx.doi.org/10.1101/020958 Evolution of a novel function can greatly alter the effects of an organism on its environment. These environmental changes can, in turn, affect the…
  https://haldanessieve.org/2015/06/18/evolution-and-coexistence-in-response-to-a-key-innovation-in-a-long-term-evolution-experiment-with-escherichia-coli/
*  Responses to Criticisms of The Edge of Evolution | Center for Science and Culture
A Modest Comeback for Lamarck, and a Reminder of the Edge of Evolution" (December 7, 2011). Michael Behe, "The Edge of Evolution, as seen by Dave Ussery and BioLogos" (November 19, 2010). Michael Behe, "Dave Ussery Ruminates about The Edge of Evolution" (November 18, 2010). Michael Behe, "Dollo's law, the symmetry of time, and the edge of evolution" (October 12, 2009). Michael Behe, "Nature Paper Reaches "Edge of Evolution" and Finds Darwinian Processes Lacking" (October 6, 2009). Michael Behe, "Nature Publishes Paper on the Edge of Evolution" (September 30, 2009). Anika Smith, "Swine Flu and the Edge of Evolution" (May 6, 2009). Casey Luskin, "Swine Flu, Viruses, and the Edge of Evolution" (May 1, 2009). Anika Smith, "Michael Behe's Edge of Evolution Vindicated From Genetics Paper" (March 19, 2009). Anika Smith, "Debate Over Behe's Edge of ...
  http://www.discovery.org/a/22661
*  Genomic Background Predicts the Fate of Duplicated Genes: Evidence From the Yeast Genome | Genetics
GENE duplication has long been thought to be one of the principal engines powering the evolution of protein function, allowing for increases in genomic complexity (Ohno 1970). Because a duplication event creates two fully functional overlapping copies, one of the two paralogs may evolve in a neutral manner right after duplication due to functional redundancy. In most cases, this duplicated gene accumulates deleterious loss-of-function mutations and becomes a pseudogene. There is a small chance that directional selection will lead it to acquire some novel function (Ohno 1970). However, this classical model predicts only an equal chance of evolutionary rate acceleration for each duplicate. Unless there is a selection pressure for overexpression of the genes, the two genes with identical functions cannot be stably retained in the genome (Nowaket al. 1997). Force et al. (1999) explained the selective maintenance of both paralogs by subfunctionalization. The model suggests that ...
  http://www.genetics.org/content/166/4/1995.long
*  The COG database: an updated version includes eukaryotes | BMC Bioinformatics | Full Text
The rapid accumulation of genome sequences is a major challenge to researchers attempting to extract the maximum functional and evolutionary information from the new genomes. To avoid informational overflow from the constant influx of new genome sequences, a comprehensive evolutionary classification of the genes from all sequenced genomes is required. Such classifications are based on two fundamental notions from evolutionary biology: orthology and paralogy, which describe the two fundamentally different types of homologous relationships between genes [1-4]. Orthologs are homologous genes derived by vertical descent from a single ancestral gene in the last common ancestor of the compared species. Paralogs, in contrast, are homologous genes, which, at some stage of evolution of the respective gene family, have evolved by duplication of an ancestral gene. The notions of orthology and paralogy are intimately linked because, if a duplication (s) ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-4-41
*  Spherus Magna Sapient Species Evolution Theory - Bionicle Storyline & Theories - BZPower
Spherus Magna Sapient Species Evolution Theory - posted in Bionicle Storyline & Theories: Hi guys, I hope Lil Wayne there got your attention (bad joke).Anyway, Id like to introduce you my theory of Spherus Magna Sapient Species Evolution. Here I proposed that most sapient species on Spherus Magna came from one original species, and I divided them up accordingly into an evolutionary Phylogenic tree. This is what I have so far, and please let me know if you find holes or if youd like to add...
  http://www.bzpower.com/board/topic/7890-spherus-magna-sapient-species-evolution-theory/
*  Errors In Protein Structure Sparked Evolution Of Biological Complexity - Redorbit
Packing flaws create 'sticky,' interactive proteins that spread in small populations. Over four billion years of evolution, plants and animals grew far more complex than their single-celled ancestors. But a new comparison of proteins shared across species finds that complex organisms, including humans, have accumulated structural weaknesses that may have actually launched the long journey from microbe to man.. The study, published in Nature, suggests that the random introduction of errors into proteins, rather than traditional natural selection, may have boosted the evolution of biological complexity. Flaws in the "packing" of proteins that make them more unstable in water could have promoted protein interactions and intracellular teamwork, expanding the possibilities of life.. "Everybody wants to say that evolution is equivalent to natural selection and that things that are sophisticated and complex have been absolutely selected for," said study co-author ...
  http://www.redorbit.com/news/science/2051087/errors_in_protein_structure_sparked_evolution_of_biological_complexity/
*  Darwin & Anthrax…. The Beauty of The Theory Of Evolution! ! - Biotechwiz
On the Evolution of Species was published in the year 1859 and it went on to becoming one of the most influential books of the time. The theory came to be widely accepted by the scientific community and overthrew many other popular streams of thought and Philosophy on evolution. Many of these theories had theological bases. The strong scientific backing of Darwin's ideas convinced most people about the soundness of his theory. Although as the body of scientific knowledge grew and more and more data on obscure species emerged, the Darwinian thought has been challenged more than once, the theory of evolution remains the single most important thought behind our attempts to explain our evolution on this planet. Today there are groups of scientists who have put Darwin in the perspective of genes, namely have explained or tried to the evolution of species in terms of genetics. This new breed of Darwinism has come to be known as ...
  http://biotechwiz.com/?p=524
*  Molecular evolution of bovine Toll-like receptor 2 suggests substitutions of functional relevance | BMC Evolutionary Biology |...
The relative genetic disparity between Bos indicus and Bos taurus is well established [32] and this genetic distance would explain some of the TLR2 polymorphisms observed between these two subspecies. However, the difference would not just be defined by random events over the time they diverged, but also by different microbial environments that the animals evolve within. The Bos indicus breeds analysed herein originated in tropical or subtropical climates where the pathogen population is generally different to that encountered by the Bos taurus breeds sampled which all inhabited Europe. Consequently, there will be different selective pressures acting on the TLR and other immune related genes in these subspecies, which would result in sites being differentially fixed in their TLR genes.. Functionally-important AAs in the ligand-binding domains of the TLRs would be shaped by selection. Conserved AA sites are protected by purifying selection and therefore normally fixed. Sporadic mutations at such ...
  https://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-8-288
*  Genes | Free Full-Text | Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Errors Caused by...
In the accompanying paper (Nagy, Szláma, Szarka, Trexler, Bányai, Patthy, Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Gene Prediction Errors) we showed that in the case of UniProtKB/TrEMBL, RefSeq, EnsEMBL and NCBI's GNOMON predicted protein sequences of Metazoan species the contribution of erroneous (incomplete, abnormal, mispredicted) sequences to domain architecture (DA) differences of orthologous proteins might be greater than those of true gene rearrangements. Based on these findings, we suggest that earlier genome-scale studies based on comparison of predicted (frequently mispredicted) protein sequences may have led to some erroneous conclusions about the evolution of novel domain architectures of multidomain proteins. In this manuscript we examine the impact of confusing paralogous and epaktologous multidomain proteins (i.e., those that are related only through the independent acquisition of the same domain types) on conclusions ...
  http://www.mdpi.com/2073-4425/2/3/516
*  PLOS Computational Biology: Bringing Molecules Back into Molecular Evolution
Much molecular-evolution research is concerned with sequence analysis. Yet these sequences represent real, three-dimensional molecules with complex structure and function. Here I highlight a growing trend in the field to incorporate molecular structure and function into computational molecular-evolution work. I consider three focus areas: reconstruction and analysis of past evolutionary events, such as phylogenetic inference or methods to infer selection pressures; development of toy models and simulations to identify fundamental principles of molecular evolution; and atom-level, highly realistic computational modeling of molecular structure and function aimed at making predictions about possible future evolutionary events.
  http://journals.plos.org/ploscompbiol/article/email?id=10.1371/journal.pcbi.1002572
*  Evidence of evolution - New World Encyclopedia
While the theory of descent with modification in the broad sense is supported, the conventional paradigm that the history of life maps as the "tree of life"-a tree beginning with one universal common ancestor as the trunk and then progressively branching, with modern species at the twig ends-is being re-drawn at both the base of the trunk and the branches. These revisions arise as scientists gain more understanding about the "hidden" world of microbes (unicellular organisms and viruses).. The great diversity, abundance, and ubiquity of the single-celled organisms (bacteria, archaea, and some protists) has gained widespread recognition in recent years, and considerable progress has been made in incorporating that knowledge into the story of evolution. In contrast, the place of viruses in the story of evolution remains much more speculative.. There are proposals that the tree of life instead of being simple at its base, may be considerably more complex. Sequencing the genomes ...
  http://www.newworldencyclopedia.org/entry/Evidence_of_evolution
*  Molecular evolution of a novel marsupial S100 protein (S100A19) which is expressed at specific stages of mammary gland and gut...
Kwek, Joly H. L., Wynne, Alicia, Lefevre, Christophe, Familari, Mary, Nicholas, Kevin R. and Sharp, Julie A. 2013, Molecular evolution of a novel marsupial S100 protein (S100A19) which is expressed at specific stages of mammary gland and gut development, Molecular phylogenetics and evolution, vol. 69, no. 1, pp. 4-16, doi: 10.1016/j.ympev.2013.05.005. ...
  http://dro.deakin.edu.au/view/DU:30059573
*  Low nucleotide diversity in man. | Genetics
The nucleotide diversity (pi) in humans is studied by using published cDNA and genomic sequences that have been carefully checked for sequencing accuracy. This measure of genetic variability is defined as the number of nucleotide differences per site between two randomly chosen sequences from a population. A total of more than 75,000 base pairs from 49 loci are compared. The DNA regions studied are the 5' and 3' untranslated regions and the amino acid coding regions. The coding regions are divided into nondegenerate sites (i.e., sites at which all possible changes are nonsynonymous), twofold degenerate sites (i.e., sites at each of which one of the three possible changes is synonymous) and fourfold degenerate sites (i.e., sites at which all three possible changes are synonymous). The pi values estimated are, respectively, 0.03 and 0.04% for the 5' and 3' UT regions, and 0.03, 0.06 and 0.11% for nondegenerate, twofold degenerate and fourfold degenerate sites. Since the highest pi value is only ...
  http://www.genetics.org/content/129/2/513