Cientista do Instituto de Tecnologia da Geórgia (Estados Unidos) usa torradeira para explicar a origem da vida!

sexta-feira, agosto 28, 2015

The Dawn of Life in a $5 Toaster Oven

How a homemade piece of lab equipment is recreating chemical evolution on early Earth.

BY JOHNNY BONTEMPS

ILLUSTRATION BY JACKIE FERRENTINO

AUGUST 27, 2015

God might just as well have begun with a toaster oven. A few years ago at a yard sale, Nicholas Hud spotted a good candidate: A vintage General Electric model, chrome-plated with wood-grain panels, nestled in an old yellowed box, practically unused. The perfect appliance for cooking up the chemical precursors of life, he thought. He bought it for $5.


At home in his basement, with the help of his college-age son, he cut a rectangular hole in the oven’s backside, through which an automated sliding table (recycled from an old document scanner) could move a tray of experiments in and out. He then attached a syringe pump to some inkjet printer parts, and rigged the system to periodically drip water onto the tray.

Today the contraption sits atop a workbench in Hud’s laboratory at the Georgia Institute of Technology, where he directs the Center for Chemical Evolution, a multi-university consortium funded by NASA and the National Science Foundation. For the past two decades, he has been hunting for the chemical recipes that could explain how life arose on Earth. When scientists began investigating life’s molecular origin in the 1950s, they assumed that the first biological molecules formed spontaneously from a soup of primordial compounds: a lucky marriage of the right ingredients, under the right conditions, at the right time. Hud and his colleagues are now finding that the spark of life may have struck much more gradually, not by chance but via a long chemical evolution.

The toaster is his latest proving ground. It simulates the cycles of cool and hot, and wet and dry, that Hud suspects jump-started this evolutionary process, millions of years before the first cellular life forms emerged. It mimics dew condensing at night and evaporating with the sunrise; rain puddles filling up and drying out; coastal lagoons flooding and emptying with the tides. Hud calls it the “day-night machine.”

On a spring day last year, he and I are huddled around the homebuilt device, watching it work. Outside of the oven, the syringe delivers a few droplets of water into each of six wells in a ceramic plate on the sliding tray. For the purpose of this demo, the wells are empty; during experiments, they contain a mixture of simple molecules, or monomers, like those believed to have been present on early Earth. The tray disappears into the oven, sealing it shut. As the temperature rises to 185 degrees Fahrenheit (85 degrees Celsius), the water evaporates—the first day. A few minutes pass, and the tray slides out. The wells cool, water drips, and in goes the tray—the second day.
...

Read more here/Leia mais aqui: The Nautilus

O destino de uma mutação em um ambiente flutuante

The fate of a mutation in a fluctuating environment

Ivana Cvijovic, 1,3, Benjamin H. Good, 1,2, Elizabeth R. Jerison1,2, and Michael M. Desai 1,2

1Department of Organismic and Evolutionary Biology and FAS Center for Systems Biology,

2Department of Physics, Cambridge, MA 02138 and

3Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA, equal contribution.

Abstract

Natural environments are never truly constant, but the evolutionary implications of temporally varying selection pressures remain poorly understood. Here we investigate how the fate of a new mutation in a variable environment depends on the dynamics of environmental fluctuations and on the selective pressures in each condition. We find that even when a mutation experiences many environmental epochs before fixing or going extinct, its fate is not necessarily determined by its time-averaged selective effect. Instead, environmental variability reduces the efficiency of selection across a broad parameter regime, rendering selection unable to distinguish between mutations that are substantially beneficial and substantially deleterious on average. Temporal fluctuations can also dramatically increase fixation probabilities, often making the details of these fluctuations more important than the average selection pressures acting on each new mutation. For example, mutations that result in a tradeoff between conditions but are strongly deleterious on average can nevertheless be more likely to fix than mutations that are always neutral or beneficial. These effects can have important implications for patterns of molecular evolution in variable environments, and they suggest that it may often be difficult for populations to maintain specialist traits, even when their loss leads to a decline in time-averaged fitness.

FREE PDF GRATIS: bioRxiv

Os muitos galhos perdidos da Árvore da Vida

quarta-feira, agosto 26, 2015

Lost Branches on the Tree of Life

Bryan T. Drew , Romina Gazis, Patricia Cabezas, Kristen S. Swithers, Jiabin Deng, Roseana Rodriguez, Laura A. Katz, Keith A. Crandall, David S. Hibbett, Douglas E. Soltis

Published: September 3, 2013
DOI: 10.1371/journal.pbio.1001636


Introduction

Given that reproducibility is a pillar of scientific research, the preservation of scientific knowledge (underlying data) is of paramount importance. The standard of reproducibility can be evaluated based on criteria of methodological rigor and legitimacy, which is sometimes used to distinguish “hard” from “soft” sciences. In phylogenetics, a discipline that routinely uses DNA sequences to build trees reflecting organismal relationships, the scale of data collection and the complexity of analytical software have both increased dramatically during the past decade. Consequently, the ability to navigate publications and reproduce analyses is more challenging than ever. When DNA sequencing was initially employed in systematics during the late 1980s, there was some reluctance to deposit nucleotide sequences in open repositories such as GenBank [1]. This ultimately changed when high-impact journals (e.g., Proceedings of the National Academy of SciencesNatureScience) began requiring GenBank submission as a prerequisite for publication [1],[2]; now virtually every evolutionary biology journal observes this requirement (but see [3]).
Until recently, uploading sequences to GenBank (or EMBL) was generally considered sufficient to ensure reproducibility of phylogenetic studies using DNA sequence data. Increasingly, however, the systematics community is realizing that archiving raw DNA sequences is not adequate, and that the underlying alignments of DNA sequences as well as the resulting phylogenetic trees are pivotal for reproducibility, comparative purposes, meta-analyses, and ultimately synthesis. Indeed, there has been a growing clamor for journals to adopt and enforce more rigorous data archiving practices across diverse disciplines [4][8]. As a result, about 35 evolutionary journals [5],[9] have adopted policies to encourage or require authors to upload alignments, phylogenetic trees, and other files requisite for study reproducibility [5] to TreeBASE (http://treebase.org/) and/or other public repositories such as Dryad (http://datadryad.org). Unfortunately, enforcement of such data deposition policies is generally lax, and most journals in systematics and evolution still do not require DNA sequence alignment or tree deposition. As a result, the alignments and trees underlying most published papers in systematics/phylogenetics and evolutionary biology remain inaccessible to the scientific community at large [8],[10].

Scope of the Problem

As DNA sequencing has become easier, faster, and cheaper, and as scientists have come to realize that phylogenies inform diverse areas of inquiry, phylogenetic trees have permeated virtually every facet of biology, including disparate subdisciplines such as medicine (e.g., [11],[12]), climate change research (e.g., [13],[14]), organismal evolution (e.g., [15]), conservation efforts (e.g., [16]), and linguistics (e.g., [17]). In building phylogenetic trees, researchers implicitly acknowledge that alignments and trees are important. However, archiving these data has been largely ignored, perhaps because researchers have considered the actual raw sequence data as the sole information necessary to replicate a phylogenetic study, while alignments and phylogenetic trees have been treated as the resulting outcome from sequence data analyses. The latter view of alignments and trees is certainly correct, but the underlying sequence alignments and associated trees should also be recognized as crucial data in their own right. The increasing use of published trees and the underlying sequence alignments as the framework for evolutionary inference and other subsequent downstream hypothesis testing dictates, however, that alignments and trees are data and need to be archived with a diligence on par with raw sequence data.
The call for ensuring reproducibility and data sharing in systematics is not new. The fundamental importance of archiving scientific datasets across numerous subdisciplines including climate change research, evolutionary biology, and medicine has received increasing attention over the past five years [5][8],[10],[18][22]. Several of these studies have examined the proportion of publications that archived data in a manner that affords public access [6],[8],[18], and all concluded that we have entered an age in which scientific journals should require and enforce data archiving policies.
Some researchers, including [23] for psychology and [4] for medical research, have taken the next step and have contacted authors directly when data of interest have not been available, which highlighted an additional problem. These workers found that data are not easily obtained via direct author contact. More recently, Stoltzfus et al. [8] examined deposition practices within the molecular systematic community, and estimated alignment/tree deposition rates to be remarkably low (~4%). Stolzfus et al. [8] focused on only two journals (American Journal of Botany and Evolution), and searched literature over just a 2-year period (2010–2011). Although the study of Stolzfus et al. [8] represents a good first step, no analysis has attempted to evaluate how often alignments/trees are deposited over a broad range of evolutionary biology journals that span organismal diversity representing the tree of life, or how archiving tendencies have changed over time.
In the process of gathering data to build the first tree of life for all ~1.9 million named species (the Open Tree of Life Project; http://opentreeoflife.org), we examined 7,539 peer-reviewed papers to evaluate data depositional practices of foundational DNA sequence alignments and phylogenetic trees by the systematic community between 2000 and 2012. Our broad survey of the literature covered animals, fungi, seed plants, microbial eukaryotes, archaea, and bacteria, and included publications from more than 100 journals (see Tables S1S2S3S4). To assess the rigor of data that were deposited in a public archive, we also examined the quality (e.g., Did deposited trees match publication figure(s)? Were there branch lengths in deposited trees?) of ca. 350 files deposited in TreeBASE (described in Text S1). Additionally, we attempted to acquire data by randomly contacting 375 authors directly (see Text S1 and Table S4). Furthermore, to evaluate depositional practices of other data critical for study replication, we surveyed 100 randomly selected publications that implemented the popular evolutionary analysis package BEAST (Bayesian Evolutionary Analysis Sampling Trees [24]; 4,153 citations as of 7-17-2013), which is widely used to obtain divergence times and phylogenies that are used to test hypotheses and draw conclusions regarding broad biological questions (e.g., phylogeography, lineage origins).
Surprisingly, only 16.7%, 1,262 from a total of 7,539 publications surveyed, provided accessible alignments/trees (Figures 1 and 2). Our attempts to obtain datasets directly from authors were only 16% successful (61/375; see Table S4), and we estimate that approximately 70% of existing alignments/trees are no longer accessible. Thus, we conclude that most of the underlying sequence alignments and phylogenetic trees produced by the systematic community during the past several decades are essentially lost, accessible only as static figures in a published journal article with no capacity for subsequent manipulation. Furthermore, when data are deposited, they are often incomplete (e.g., what characters were excluded, accepted taxon names; see Text S1 and Figure S1). Our survey of publications that implemented BEAST revealed that only 11 out of 100 (11%) examined studies provided access to the underlying xml input file, which is critical for reproducing BEAST results. Although funding agencies often require all data to be accessible from funded publications, our results reveal this is more the exception than the rule.
FREE PDF GRATIS: PLoS Biology

Um espécime de Rhamphorhynchus com preservação de tecido mole, com conteúdos estomacais e um putativo coprólito

terça-feira, agosto 25, 2015

A specimen of Rhamphorhynchus with soft tissue preservation, stomach contents and a putative coprolite

David Hone​1, Donald M. Henderson 2, François Therrien 2, Michael B. Habib 3

August 20, 2015

School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom

2 Royal Tyrrell Museum of Palaeontology, Drumheller, Alberta, Canada

3 Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America

DOI:10.7717/peerj.1191



Published 2015-08-20 Accepted 2015-07-26 Received 2015-03-29

Academic Editor Kenneth De Baets

Subject Areas Paleontology 

Keywords Rhamphorhynchoid, Palaeoecology, Pterosauria, Rhamphorhynchinae

Copyright © 2015 Hone et al.

Licence

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

Cite this article

Hone D, Henderson DM, Therrien F, Habib MB. (2015) A specimen of Rhamphorhynchus with soft tissue preservation, stomach contents and a putative coprolite. PeerJ 3:e1191 https://dx.doi.org/10.7717/peerj.1191

Abstract

Despite being known for nearly two centuries, new specimens of the derived non-pterodactyloid pterosaur Rhamphorhynchus continue to be discovered and reveal new information about their anatomy and palaeobiology. Here we describe a specimen held in the collections of the Royal Tyrrell Museum of Palaeontology, Alberta, Canada that shows both preservation and impressions of soft tissues, and also preserves material interpreted as stomach contents of vertebrate remains and, uniquely, a putative coprolite. The specimen also preserves additional evidence for fibers in the uropatagium.

Cite this as:

Hone D, Henderson DM, Therrien F, Habib MB. (2015) A specimen of Rhamphorhynchus with soft tissue preservation, stomach contents and a putative coprolite. PeerJ 3:e1191 https://dx.doi.org/10.7717/peerj.1191

FREE PDF GRATIS: PeerJ

Por que os cientistas devem ser céticos de suas teorias científicas?

segunda-feira, agosto 24, 2015

"Como um cientista em atividade, eu aprendi que a revisão por pares é muito importante para fazer a ciência crível. A autoridade que a ciência pode reivindicar vem da evidência e do experimento e uma atitude de mente que busca testar suas teorias até à destruição… O ceticismo é muito importante... seja o pior inimigo de sua própria ideia, sempre a desafie, sempre a teste.

Eu penso que as coisas são um pouco diferentes quando você tem um negacionista ou cético extremo. Eles estão convencidos que eles sabem o que está acontecendo, e eles somente procuram dados que apoiem aquela posição, e eles não estão realmente se envolvendo no processo científico. Há uma linha tênue entre o ceticismo saudável, que é uma parte fundamental do processo científico e a negação que pode parar a ciência em prosseguir. Mas a diferença é crucial.’

’As a working scientist I’ve learnt that peer review is very important to make science credible The authority science can claim comes from evidence and experiment and an attitude of mind that seeks to test its theories to destruction…Scepticism is very important…be the worst enemy of your own idea, always challenge it, always test it.

I think things are a little different when you have a denialist or an extreme sceptic. They are convinced that they know what’s going on and they only look for data which supports that position and they’re not really engaging in the scientific process. There is a fine line between healthy scepticism which is a fundamental part of the scientific process and denial which can stop the science moving on. But the difference is crucial.’

Impactos de cometas podem ter resultado em vida na Terra

quinta-feira, agosto 20, 2015

GEOCHEMICAL JOURNAL

Vol. 48 (2014) No. 1 p. 51-62


Glycine oligomerization up to triglycine by shock experiments simulating comet impacts

HARUNA SUGAHARA 1), KOICHI MIMURA 1)

1) Department of Earth and Environmental Sciences, Graduate School of Environmental Studies, Nagoya University

Released on J-STAGE 20140205 

Keywords: comet impacts, amino acids, peptides, shock experiments, origins of life

Source/Fonte: Geology Page

Abstract

We conducted shock experiments simulating comet impacts to assess the feasibility of peptide synthesis by such a process. We used frozen mixture of the amino acid glycine, water ice, and silicate (forsterite) as the starting material and applied impact shocks ranging from 4.8 to 26.3 GPa using a vertical propellant gun under cryogenic conditions (77 K). The results show that amino acid oligomerization up to trimers can be achieved. Further, linear peptides (dipeptide and tripeptide forms), which are important materials for the further elongation of peptide chains, were obtained in yields of one or two magnitudes greater than that of cyclic peptide form (diketopiperazine). These results contrast with those by Blank et al. (2001) for shock experiments of amino acid solutions at room temperature, which showed the synthesis of a comparable amount of diketopiperazines to that of the linear peptides. Thus, the existence of cryogenic conditions at the point of impact shock may be critical for the formation of linear peptides. Our results demonstrate that comet impacts could have supplied a significant amount of linear peptides on the early Earth and other extraterrestrial bodies.

FREE PDF GRATIS: Geochemical Journal

Máquina molecular, e não linha de montagem, é que monta os microtúbulos

Tubulin cofactors and Arl2 are cage-like chaperones that regulate the soluble αβ-tubulin pool for microtubule dynamics

Stanley Nithianantham, Sinh Le, Elbert Seto, Weitao Jia, Julie Leary, Kevin D Corbett, Jeffrey K Moore, Jawdat Al-BassamCorresponding Author

University of California, Davis, United States; University of California, San Diego, United States; University of Colorado School of Medicine, United States

Source/Fonte: Jawdat Al-Bassam, UC Davis


Abstract

Microtubule dynamics and polarity stem from the polymerization of αβ-tubulin heterodimers. Five conserved tubulin cofactors/chaperones and the Arl2 GTPase regulate α- and β-tubulin assembly into heterodimers and maintain the soluble tubulin pool in the cytoplasm, but their physical mechanisms are unknown. Here, we reconstitute a core tubulin chaperone consisting of tubulin cofactors TBCD, TBCE, and Arl2, and reveal a cage-like structure for regulating αβ-tubulin. Biochemical assays and electron microscopy structures of multiple intermediates show the sequential binding of αβ-tubulin dimer followed by tubulin cofactor TBCC onto this chaperone, forming a ternary complex in which Arl2 GTP hydrolysis is activated to alter αβ-tubulin conformation. A GTP-state locked Arl2 mutant inhibits ternary complex dissociation in vitro and causes severe defects in microtubule dynamics in vivo. Our studies suggest a revised paradigm for tubulin cofactors and Arl2 functions as a catalytic chaperone that regulates soluble αβ-tubulin assembly and maintenance to support microtubule dynamics.

eLIFE Digest

Cells contain a network of protein filaments called microtubules. These filaments are involved in many biological processes; for example, they help cells keep the right shape, and they help to transport proteins and other materials inside cells.

Two proteins called α-tubulin and β-tubulin are the building blocks of microtubules. The filaments are very dynamic structures that can rapidly change length as individual tubulin units are either added or removed to the filament ends. Several proteins known as tubulin cofactors and an enzyme called Arl2 help to build a vast pool of tubulin units that are able attach to the microtubules. These units—called αβ-tubulin—are formed by α-tubulin and β-tubulin binding to each other, but it not clear exactly what roles the tubulin cofactors and Arl2 play in this process.

Nithianantham et al. used a combination of microscopy and biochemical techniques to study how the tubulin cofactors and Arl2 are organised, and their role in the assembly of microtubules in yeast. The experiments show that Arl2 and two tubulin cofactors associate with each other to form a stable ‘complex’ that has a cage-like structure. A molecule of αβ-tubulin binds to the complex, followed by another cofactor called TBCC. This activates the enzyme activity of Arl2, which releases the energy needed to alter the shape of the αβ-tubulin. Nithianantham et al. also found that yeast cells with a mutant form of Arl2 that lacked enzyme activity had problems forming microtubules.

Together, these findings show that the tubulin cofactors and Arl2 form a complex that regulates the assembly and maintenance of αβ-tubulin. The next challenge is to understand how this regulation influences the way that microtubules grow and shrink inside cells.

FREE PDF GRATIS: eLIFE

What the fuck jornalismo científico é esse?

quarta-feira, agosto 19, 2015

O esfacelamento gradual do consenso darwinista sobre a história evolucionária de toda a complexidade e diversidade da vida, bem como o surgimento de uma nova perspectiva teórica em biologia – a Síntese Evolutiva Ampliada/Estendida, tem se revelado como uma das notícias menos noticiada de nosso tempo.

É um escândalo escancarado que jornalistas científicos sejam tão desmotivados em abordar essa história. Inclusive Maurício Tuffani, editor da Scientific American-Brasil. Porque há muito tempo – desde 1998 - sabe ser uma história comprida e interessante nas suas nuances de se blindar Darwin de seu fragoroso fracasso epistêmico em explicar a origem das espécies no contexto de justificação teórica. Não há nas demais ciências, história parecida com esta.

Em entrevista recente no Huffington Post, Gunther Witzany disse: 

Os conceitos antigos que nós temos há meio século não podem explicar suficientemente a tendência complexa do código genético. Eles não podem explicar as funções dos elementos genéticos móveis e os retrovírus endógenos e os RNAs não codificantes. Também, o dogma central da biologia central foi falsificado — isto é, o jeito é sempre a partir do DNA em RNA em proteínas e tudo mais, ou os outros “dogmas”, ex.: os erros de replicação conduzem a variação genética, que gene codifica uma proteína e que o DNA não codificante é lixo. Todos esses conceitos que dominaram a ciência por meio século estão agora falsificados.

A história é esta:

A explicação oficial da natureza das coisas vivas – e portanto, dos seres humanos – que todos nós fomos levados a acreditar nos últimos 60 ou 70 anos se revelou profundamente errada em alguns aspectos essenciais.

A Árvore da Vida está mais para arbusto... gramado???

The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

Alexander Suh , Linnéa Smeds, Hans Ellegren

Published: August 18, 2015DOI: 10.1371/journal.pbio.1002224

Abstract

The diversification of neoavian birds is one of the most rapid adaptive radiations of extant organisms. Recent whole-genome sequence analyses have much improved the resolution of the neoavian radiation and suggest concurrence with the Cretaceous-Paleogene (K-Pg) boundary, yet the causes of the remaining genome-level irresolvabilities appear unclear. Here we show that genome-level analyses of 2,118 retrotransposon presence/absence markers converge at a largely consistent Neoaves phylogeny and detect a highly differential temporal prevalence of incomplete lineage sorting (ILS), i.e., the persistence of ancestral genetic variation as polymorphisms during speciation events. We found that ILS-derived incongruences are spread over the genome and involve 35% and 34% of the analyzed loci on the autosomes and the Z chromosome, respectively. Surprisingly, Neoaves diversification comprises three adaptive radiations, an initial near-K-Pg super-radiation with highly discordant phylogenetic signals from near-simultaneous speciation events, followed by two post-K-Pg radiations of core landbirds and core waterbirds with much less pronounced ILS. We provide evidence that, given the extreme level of up to 100% ILS per branch in super-radiations, particularly rapid speciation events may neither resemble a fully bifurcating tree nor are they resolvable as such. As a consequence, their complex demographic history is more accurately represented as local networks within a species tree.

Author Summary

The rise of modern birds began after the mass extinction of nonavian dinosaurs and archaic birds at the Cretaceous-Paleogene (K-Pg) boundary, about 66 million years ago. This coincides with the super-rapid adaptive radiation of Neoaves (a group that contains most modern birds), which has been difficult to resolve even with whole genome sequences. We reconstructed the genealogical fates of thousands of rare genomic changes (insertions of selfish mobile elements called retrotransposons), a third of which were found to be affected by a phenomenon known as incomplete lineage sorting (ILS), namely a persistence of polymorphisms across multiple successive speciation events. Astoundingly, we found that near the K-Pg boundary, speciation events were accompanied by extreme levels of ILS, suggesting a near-simultaneous, star-like diversification process that appears plausible in the context of instantaneous niche availability that must have followed the K-Pg mass extinction. Our genome-scale results provide a population genomic explanation as to why some species radiations may be more complex than a fully bifurcating tree of life. We suggest that, under such circumstances, ILS bears witness to the biological limitation of phylogenetic resolution.

FREE PDF GRATIS: PLoS Biology

A volatilidade do conteúdo de tópicos científicos na Wikipédia: uma história de advertência

sábado, agosto 15, 2015

Content Volatility of Scientific Topics in Wikipedia: A Cautionary Tale

Adam M. Wilson , Gene E. Likens

Published: August 14, 2015DOI: 10.1371/journal.pone.0134454

Abstract

Wikipedia has quickly become one of the most frequently accessed encyclopedic references, despite the ease with which content can be changed and the potential for ‘edit wars’ surrounding controversial topics. Little is known about how this potential for controversy affects the accuracy and stability of information on scientific topics, especially those with associated political controversy. Here we present an analysis of the Wikipedia edit histories for seven scientific articles and show that topics we consider politically but not scientifically “controversial” (such as evolution and global warming) experience more frequent edits with more words changed per day than pages we consider “noncontroversial” (such as the standard model in physics or heliocentrism). For example, over the period we analyzed, the global warming page was edited on average (geometric mean ±SD) 1.9±2.7 times resulting in 110.9±10.3 words changed per day, while the standard model in physics was only edited 0.2±1.4 times resulting in 9.4±5.0 words changed per day. The high rate of change observed in these pages makes it difficult for experts to monitor accuracy and contribute time-consuming corrections, to the possible detriment of scientific accuracy. As our society turns to Wikipedia as a primary source of scientific information, it is vital we read it critically and with the understanding that the content is dynamic and vulnerable to vandalism and other shenanigans.

Citation: Wilson AM, Likens GE (2015) Content Volatility of Scientific Topics in Wikipedia: A Cautionary Tale. PLoS ONE 10(8): e0134454. doi:10.1371/journal.pone.0134454

Editor: Hussein Suleman, University of Cape Town, SOUTH AFRICA

Received: November 12, 2014; Accepted: June 29, 2015; Published: August 14, 2015

Copyright: © 2015 Wilson, Likens. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Data Availability: All relevant data are available via Figshare (http://dx.doi.org/10.6084/m9.figshare.13​97533).

Funding: The authors have no support or funding to report.

Competing interests: The authors have declared that no competing interests exist.

FREE PDF GRATIS: PLoS One

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NOTA DESTE BLOGGER:

A Wikipédia é o pior que existe na internet para a veiculação de conhecimentos. A agenda da que se propôs ser A Enciclopédia digital tem interesses ideológicos velados que não permite a veiculação da verdade em muitos temas polêmicos e controversos.

Um lixo!!!

Regulação da recombinação e manutenção genômica: mero acaso, fortuita necessidade ou design inteligente?

Regulation of Recombination and Genomic Maintenance

Wolf-Dietrich Heyer1,2

1Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616-8665

2Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616-8665

Correspondence: wdheyer{at}ucdavis.edu



Abstract

Recombination is a central process to stably maintain and transmit a genome through somatic cell divisions and to new generations. Hence, recombination needs to be coordinated with other events occurring on the DNA template, such as DNA replication, transcription, and the specialized chromosomal functions at centromeres and telomeres. Moreover, regulation with respect to the cell-cycle stage is required as much as spatiotemporal coordination within the nuclear volume. These regulatory mechanisms impinge on the DNA substrate through modifications of the chromatin and directly on recombination proteins through a myriad of posttranslational modifications (PTMs) and additional mechanisms. Although recombination is primarily appreciated to maintain genomic stability, the process also contributes to gross chromosomal arrangements and copy-number changes. Hence, the recombination process itself requires quality control to ensure high fidelity and avoid genomic instability. Evidently, recombination and its regulatory processes have significant impact on human disease, specifically cancer and, possibly, neurodegenerative diseases.

Copyright © 2015 Cold Spring Harbor Laboratory Press; all rights reserved

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Pergunta deste blogger:

A regulação da recombinação e manutenção genômica: mero acaso, fortuita necessidade ou design inteligente???

Computando a origem e evolução do ribossomo a partir de sua estrutura

sexta-feira, agosto 14, 2015

Computational and Structural Biotechnology Journal

Volume 13, 2015, Pages 427–447

Computing the origin and evolution of the ribosome from its structure — Uncovering processes of macromolecular accretion benefiting synthetic biology

Gustavo Caetano-Anollés a, b, 1, , Derek Caetano-Anollés b

a Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1101W. Peabody Drive, Urbana, IL 61801, USA

b C.R. Woese Institute for Genomic Biology, University of Illinois, Urbana, IL 61801, USA

Received 9 April 2015, Revised 16 July 2015, Accepted 19 July 2015, Available online 26 July 2015



Abstract

Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in the evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. Computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. Phylogenetic trees of protein structural domains and proteomes and their molecular functions were built from a genomic census of millions of encoded proteins and associated terminal Gene Ontology terms. Trees reveal a ‘metabolic-first’ origin of proteins, the late development of translation, and a patchwork distribution of proteins in biological networks mediated by molecular recruitment. Similarly, the natural history of ancient RNA molecules inferred from trees of molecular substructures built from a census of molecular features shows patchwork-like accretion patterns. Ideographic analyses of ribosomal history uncover the early appearance of structures supporting mRNA decoding and tRNA translocation, the coevolution of ribosomal proteins and RNA, and a first evolutionary transition that brings ribosomal subunits together into a processive protein biosynthetic complex. Nomothetic structural biology studies of tertiary interactions and ancient insertions in rRNA complement these findings, once concentric layering assumptions are removed. Patterns of coaxial helical stacking reveal a frustrated dynamics of outward and inward ribosomal growth possibly mediated by structural grafting. The early rise of the ribosomal ‘turnstile’ suggests an evolutionary transition in natural biological computation. Results make explicit the need to understand processes of molecular growth and information transfer of macromolecules.

Keywords: Molecular structure; Origin of life; Phylogenetic analysis; rRNA; Ribosomal evolution; Translation; Proteome; Protein structural domains; Molecular functions; Evolutionary genomics

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Eventos de extinções podem acelerar a evolução... em robôs!

quinta-feira, agosto 13, 2015

Extinction Events Can Accelerate Evolution

Joel Lehman , Risto Miikkulainen

Published: August 12, 2015DOI: 10.1371/journal.pone.0132886

Source/Fonte: Joel Lehman


Abstract

Extinction events impact the trajectory of biological evolution significantly. They are often viewed as upheavals to the evolutionary process. In contrast, this paper supports the hypothesis that although they are unpredictably destructive, extinction events may in the long term accelerate evolution by increasing evolvability. In particular, if extinction events extinguish indiscriminately many ways of life, indirectly they may select for the ability to expand rapidly through vacated niches. Lineages with such an ability are more likely to persist through multiple extinctions. Lending computational support for this hypothesis, this paper shows how increased evolvability will result from simulated extinction events in two computational models of evolved behavior. The conclusion is that although they are destructive in the short term, extinction events may make evolution more prolific in the long term.

Citation: Lehman J, Miikkulainen R (2015) Extinction Events Can Accelerate Evolution. PLoS ONE 10(8): e0132886. doi:10.1371/journal.pone.0132886

Editor: Genlou Sun, Saint Mary’s University, CANADA

Received: December 26, 2014; Accepted: June 22, 2015; Published: August 12, 2015

Copyright: © 2015 Lehman, Miikkulainen. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Data Availability: All relevant data are available through figshare (http://dx.doi.org/10.6084/m9.figshare.14​66784).

Funding: The authors have no support or funding to report.

Competing interests: The authors have declared that no competing interests exist.

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A Síntese Evolutiva Ampliada/Estendida é Design Inteligente disfarçado???

quarta-feira, agosto 12, 2015

O principal problema que a nova teoria geral da evolução – a Síntese Evolutiva Ampliada/Estendida (SEA) cria para o Darwinismo, é que o processo evolucionário ocorre de muitas maneiras diferentes, não apenas a la Darwin:

“Por contraste, a SEA considera o genoma como um subsistema de célula planejado pela evolução para detectar e responder aos sinais que incidem sobre ela. Os organismos não são construídos somente a partir de ‘instruções’ genéticas, mas antes eles se auto organizam usando uma ampla variedade de recursos interdependentes.” p. 6

“By contrast, the EES regards the genome as a sub-system of the cell designed by evolution to sense and respond to the signals that impinge on it. Organisms are not built from genetic ‘instructions’ alone, but rather self-assemble using a broad variety of inter-dependent resources.” p. 6


É com o parágrafo acima destacado que fundamentamos este pequeno artigo e perguntamos, pois perguntar não ofende, especialmente em ciência, e muito mais especialmente em se tratando de área científica que se propõe explicar a história evolucionária da diversidade e complexidade da vida na Terra:

1. “planejado pela evolução”? Mas a evolução não era um processo cego, aleatório, sem objetivos a favor ou contra as coisas biológicas? Ou é o reconhecimento de que o planejamento/design intencional é tão óbvio que os evolucionistas não têm mais como escapar disso? Gente, alguém me belisque, mas o Darwin não tinha eliminado o design intencional em biologia? Richard Dawkins não afirmou que o design era uma ilusão?

2. “planejado pela evolução para detectar e responder aos sinais que incidem sobre ela”. Gente, alguém me belisque, mas a linguagem teórica aqui é puramente TELEOLÓGICA. 100% Design Inteligente. Muito obrigado, turma da SEA!

3. “auto organizam”. A ontogenia não é um processo de montagem das partes. Aristóteles chamou este processo de “epigênese” há 2.500 anos atrás. Dizem que Aristóteles já era, mas quem disse que suas ideias biológicas estavam ultrapassadas? E no século 21?

4. “…eles se auto organizam usando uma ampla variedade de recursos interdependentes”. Gente, alguém me belisque de novo, mas isso parece muito com a complexidade irredutível do Michael Behe, aquele do livro A Caixa Preta de Darwin, e tem grandes implicações teleológicas. 

NOTA BENE – a célula (ou o organismo que está sendo formado) “usa uma ampla variedade de recursos” a fim de... Gente, me belisquem de novo, mas forma é a CAUSA FINAL do processo teleológico! Argh, como diria Darwin, isso é como cometer um assassinato! Teleologia aristotélica pura! 100% Design Inteligente!

Nós, teóricos e defensores da teoria do Design Inteligente (TDI), agradecemos profundamente a Kevin N. Laland, Tobias Uller, Marcus W. Feldman, Kim Sterelny, Gerd B. Müller, Armin Moczek, Eva Jablonka e John Odling-Smee, por terem deixado bem evidente, com todas as letras, quão evidente são a TELEOLOGIA e o DESIGN na biologia. 

Uma advertência: Os teóricos evolucionistas que elaboraram a Síntese Evolutiva Ampliada/Estendida vão ter muito que se explicar com a Nomenklatura científica... Eles vão ser hostilizados pela Galera dos meninos e meninas de Darwin! Sejam bem-vindos, nós da TDI sabemos o que é ser hostilizado...

Fui, nem sei por que, rindo da cara de muitos cientistas da Nomenklatura científica e da Galera dos meninos e meninas de Darwin, pois afirmei neste blog que se a SEA não incorporasse a questão de informação, um dos pilares fundamentais da TDI, ela seria uma teoria científica natimorta! Gente, alguém me belisque novamente – a turma da SEA foi além – incorporou TELEOLOGIA e DESIGN! Dois aspectos fundamentais no arcabouço teórico da TDI! Estarei eu sonhando ou lendo além do que está sendo proposto pelos teóricos da SEA?

A Síntese Evolutiva Ampliada/Estendida é Design Inteligente disfarçado???

Neddy vai estourar um champagne Chandon!!!

(Texto baseado em correspondência interna do Movimento de Design Inteligente).

Tempo de se quantificar a falseabilidade?

terça-feira, agosto 11, 2015

Time to Quantify Falsifiability

Ilya Nemenman 1

Departments of Physics and Biology, Emory University,

Atlanta, GA 30322, USA

May 29, 2015




Abstract: 

Here we argue that the notion of falsifiability, a key concept in defining a valid scientific theory, can be quantified using Bayesian Model Selection, which is a standard tool in modern statistics. This relates falsifiability to the quantitative version of the Occam’s razor, and allows transforming some longrunning arguments about validity of certain scientific theories from philosophical discussions to mathematical calculations.

FREE PDF GRATIS: ArXiv

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Rapaz, isso vai mexer com a alegada robustez epistêmica de algumas teorias queridinhas da Nomenklatura científica. Ah, vai...

Repensando a 'radiação adaptativa' - um dos conceitos evolucionários mais importante

What defines an adaptive radiation? Macroevolutionary diversification dynamics of an exceptionally species-rich continental lizard radiation

Daniel Pincheira-Donoso1*, Lilly P. Harvey1 and Marcello Ruta2

*Corresponding author:

 Daniel Pincheira-Donoso DPincheiraDonoso@lincoln.ac.uk

Author Affiliations

1 Laboratory of Evolutionary Ecology of Adaptations, School of Life Sciences, University of Lincoln, Brayford Campus, Lincoln LN6 7DL, UK

2 Laboratory of Evolutionary Palaeobiology, School of Life Sciences, University of Lincoln, Brayford Campus, Lincoln LN6 7DL, UK

For all author emails, please log on.

BMC Evolutionary Biology 2015, 15:153 doi:10.1186/s12862-015-0435-9

Received: 20 May 2015

Accepted: 29 July 2015

Published: 7 August 2015

© 2015 Pincheira-Donoso et al. 

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.


Abstract

Background

Adaptive radiation theory posits that ecological opportunity promotes rapid proliferation of phylogenetic and ecological diversity. Given that adaptive radiation proceeds via occupation of available niche space in newly accessed ecological zones, theory predicts that: (i) evolutionary diversification follows an ‘early-burst’ process, i.e., it accelerates early in the history of a clade (when available niche space facilitates speciation), and subsequently slows down as niche space becomes saturated by new species; and (ii) phylogenetic branching is accompanied by diversification of ecologically relevant phenotypic traits among newly evolving species. Here, we employ macroevolutionary phylogenetic model-selection analyses to address these two predictions about evolutionary diversification using one of the most exceptionally species-rich and ecologically diverse lineages of living vertebrates, the South American lizard genus Liolaemus.

Results

Our phylogenetic analyses lend support to a density-dependent lineage diversification model. However, the lineage through-time diversification curve does not provide strong support for an early burst. In contrast, the evolution of phenotypic (body size) relative disparity is high, significantly different from a Brownian model during approximately the last 5 million years of Liolaemus evolution. Model-fitting analyses also reject the ‘early-burst’ model of phenotypic evolution, and instead favour stabilizing selection (Ornstein-Uhlenbeck, with three peaks identified) as the best model for body size diversification. Finally, diversification rates tend to increase with smaller body size.

Conclusions

Liolaemus have diversified under a density-dependent process with slightly pronounced apparent episodic pulses of lineage accumulation, which are compatible with the expected episodic ecological opportunity created by gradual uplifts of the Andes over the last ~25My. We argue that ecological opportunity can be strong and a crucial driver of adaptive radiations in continents, but may emerge less frequently (compared to islands) when major events (e.g., climatic, geographic) significantly modify environments. In contrast, body size diversification conforms to an Ornstein-Uhlenbeck model with multiple trait optima. Despite this asymmetric diversification between both lineages and phenotype, links are expected to exist between the two processes, as shown by our trait-dependent analyses of diversification. We finally suggest that the definition of adaptive radiation should not be conditioned by the existence of early-bursts of diversification, and should instead be generalized to lineages in which species and ecological diversity have evolved from a single ancestor.

Background

Adaptive radiation theory predicts that the proliferation of phylogenetic and ecological diversity within a lineage results from the exposition of a single ancestor to multiple episodes of divergent natural selection [1], [2]. A fundamental component of this process is the emergence of ‘ecological opportunity’, which provides the conditions that allow speciation through adaptation to different niches [3], [4]. Ecological opportunity arises when spatial and/or ecological dispersal (i.e., access to novel niche dimensions facilitated by adaptive innovations) expose a species to a new set of abundant ecological resources [2]–[7]. For example, spatial and/or ecological dispersal can be driven by the emergence of new habitats (e.g., islands, mountains), by modifications of existing environments via climatic changes, or by the emptying of niches following extinctions [1]–[3]. As diversification proceeds, the extent of ecological opportunity declines as a function of increasing saturation of niche space by newly evolving species. Therefore, a core prediction based on the above scenario is that adaptively radiating lineages will show early bursts of rapid diversification followed by asymptotic decreases in diversification rates over time [2], [8]–[10].

In addition, phenotypic traits with ecological significance play a fundamental role in the process of niche construction, and hence, in the way diversifying lineages saturate niches over time [2], [11]. As a result, analyses of macroevolutionary models of lineage accumulation have been complemented with studies of tempo and mode of diversification of ecologically relevant phenotypes during adaptive radiations [2], [8], [12], [13]. Based on the model of adaptively radiating lineages expounded above, we may predict that phenotypic diversification is high early in a group’s history, when ancestors enter an adaptive zone with abundant resources [3], [10]. As natural selection promotes saturation of ecological space via phenotypic diversification, opportunities for niche occupation decline, thus causing a slowdown in the rates of diversification of ecologically functional traits [2], [8]–[10]. Consequently, if the radiation of a lineage has been adaptive, then the diversifications of both the lineage and the phenotype are expected to display similar patterns, which would be driven by changes in niche filling over time (e.g., [2], [14]). For instance, if the rapid early emergence of new species causes a decrease in niche space, then the opportunities for adaptive speciation decline, and slowdowns in ecological trait evolution would be expected given the reduced opportunities for adaptive niche expansions.

Evidence for coupled patterns of lineage and phenotype diversification is not consistent. While some studies reveal a link between these two components of diversity, others fail to identify such links. For example, Harmon et al. [12] showed that ‘bursts’ of lineage accumulation in the radiation of iguanian lizards are consistent with pulses of phenotypic disparity during their phylogenetic history. Similarly, the radiation of Caribbean Anolis lizards has been shown to partition ecological morphospace more finely as the numbers of competing lineages present on an island increase [15]. In contrast, the radiation of cetaceans shows signals of diversity-dependent evolution of ecological phenotypes, while their net diversification fails to support a model of early-bursts of speciation followed by slowdowns [13]. Finally, although net lineage diversification has been rapid and described by a diversity-dependent trajectory in the exceptionally explosive radiation of Rattus rats, the extent of interspecific morphological diversification has been minimal [16].

A number of hypotheses have been formulated to explain such disjoint patterns between lineage and phenotype diversity. For example, it has been suggested that the signatures of early burst adaptive radiations can be retained in phenotypic traits, while high extinction or fluctuations in net diversifications can erase them from the structure of the phylogeny [13], [17]. Also, non-adaptive radiations are expected to diversify taxonomically but not much phenotypically [16], [18]–[20]. Finally, a longstanding debate focuses on whether macroevolutionary processes differ between island and continental radiations. Given that islands are spatially limited and have simpler ecological backgrounds compared to continents, both diversification processes and cladogenesis-phenotype links may follow different trajectories mediated by their intrinsic differences in ecological opportunity, which is expected to be more common on islands [1], [21]–[23]. In fact, although most biodiversity resides on continents [24], current knowledge on adaptive radiations derives primarily from island models. Therefore, studies of diversification dynamics in both lineages and phenotypes in continental radiations remain both a critical empirical and conceptual need and a promising research venue.

In recent years, the exceptionally diverse radiation of South American lizards of the genus Liolaemus has emerged as a promising model to investigate adaptiveradiations on continents. Consisting of 240+ species, Liolaemus is the world’s second richest genus of extant amniotes [25]. Remarkably, since their origin (estimated ~22 Mya, [25], [26]), these lizards have adapted to the widest range of ecological and climatic conditions known among reptiles [6], [25], [27], [28], including extreme environments ranging from the Atacama Desert (the driest place on Earth) to Tierra del Fuego (the southernmost place where a reptile has been found), along both the Pacific and Atlantic coasts, and reaching up to 5,000 + m altitudes in the Andes [27], [29]–[34]. Importantly, recent studies suggest that this radiation may have been accelerated by the enormous ecological opportunity created by the Andes uplift [6], [35]. This idea also suggests that the evolution of viviparity (live-bearing reproduction) provided the key innovation that unlocked the harsh Andean environments for early Liolaemus colonisation and subsequent diversification [6], [35], [36]. Thus, this lineage offers a unique model to investigate the causes and trajectories of evolutionary radiations on continents. Here, we study the tempo and mode of macroevolutionary diversification in lineage richness and body size in the Liolaemus radiation, and discuss our findings in the context of radiations triggered by continental ecological opportunity. A central prediction derived from adaptive radiation theory is that both diversity dimensions will show signals of diversity-dependent diversification over time.

Methods

Phylogenetic tree

Our analyses are based on a multi-gene molecular, time-calibrated phylogenetic tree (Fig. 1), including 109 of the ~240 known Liolaemus species (the total number of species is difficult to determine given taxonomic controversies and the lack of reliable diagnoses for several species), extracted from Pyron et al.’s [37] comprehensive tree of squamates. The tree was time-calibrated using recent estimates obtained from molecular phylogenies of the major clades within Liolaemus[26], and based on the genus’ fossil record [38]–[40]. We set the origin of the Liolaemus crown group radiation (beginning with the latest common ancestry between the subgenera Eulaemus and Liolaemus sensu stricto) at 19.25 million years ago (Mya). This time represents the average between paleontological and molecular estimates, which place the origin of the crown group radiation, respectively, at 18.5 and 20 Mya.

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