Estudo simula a extinção local dos tentilhões de Darwin por meio de uma mosca parasita

An introduced parasitic fly may lead to local extinction of Darwin's finch populations

Jennifer A. H. Koop 1,†,*, Peter S. Kim 2,‡,¶, Sarah A. Knutie 1,§, Fred Adler 1,2 and Dale H. Clayton 1

Article first published online: 18 DEC 2015

DOI: 10.1111/1365-2664.12575

Journal of Applied Ecology

Source/Fonte: Jennifer Koop, University of Utah

Abstract

Keywords: conservation; galápagos; Geospiza fortis ; invasive species; medium ground finch; model; parasite; Philornis downsi ; population viability model

Summary

Introduced pathogens and other parasites are often implicated in host population-level declines and extinctions. However, such claims are rarely supported by rigorous real-time data. Indeed, the threat of introduced parasites often goes unnoticed until after host populations have declined severely. The recent introduction of the parasitic nest fly, Philornis downsi, to the Galápagos Islands provides an opportunity to monitor the current impact of an invasive parasite on endemic land bird populations, including Darwin's finches.

In this paper, we present a population viability model to explore the potential long-term effect of P. downsi on Darwin's finch populations. The goal of our study was to determine whether P. downsi has the potential to drive host populations to extinction and whether management efforts are likely to be effective.

Our model is based on data from five years of experimental field work documenting the effect of P. downsi on the reproductive success of medium ground finch Geospiza fortis populations on Santa Cruz Island. Under two of the three scenarios tested, the model predicted medium ground finches are at risk of extinction within the next century.

However, sensitivity analyses reveal that even a modest reduction in the prevalence of the parasite could improve the stability of finch populations. We discuss the practicality of several management options aimed at achieving this goal.

Synthesis and applications. Our study demonstrates the predicted high risk of local extinction of an abundant host species, the medium ground finch G. fortis due to an introduced parasite, P. downsi. However, our study further suggests that careful management practices aimed at reducing parasite prevalence have the potential to significantly lower the risk of host species extinction.

FREE PDF GRATIS: Journal of Applied Ecology

Simulando o voo planado orográfico de falcão com uma pequena asa autônoma: mas o design na natureza é ilusão...

Emulating avian orographic soaring with a small autonomous glider

Alex Fisher 1,3, Matthew Marino 1, Reece Clothier 1, Simon Watkins 1, Liam Peters 1 and Jennifer L Palmer 2

Published 17 December 2015 • © 2015 IOP Publishing Ltd • Bioinspiration & Biomimetics, Volume 11, Number 1

Author affiliations

1 RMIT University Melbourne, VIC, Australia

2 Defence Science and Technology Group Fishermans Bend, VIC, Australia

3 Author to whom any correspondence should be addressed.

Dates Received 24 August 2015 Accepted 16 November 2015 Published 17 December 2015

Source/Fonte

Abstract

This paper explores a method by which an unpowered, fixed-wing micro air vehicle (MAV) may autonomously gain height by utilising orographic updrafts in urban environments. These updrafts are created when wind impinges on both man-made and natural obstacles, and are often highly turbulent and very localised. Thus in contrast to most previous autonomous soaring research, which have focused on large thermals and ridges, we use a technique inspired by kestrels known as 'wind-hovering', in order to maintain unpowered flight within small updrafts. A six-degree-of-freedom model of a MAV was developed based on wind-tunnel tests and vortex-lattice calculations, and the model was used to develop and test a simple cascaded control system designed to hold the aircraft on a predefined trajectory within an updraft. The wind fields around two typical updraft locations (a building and a hill) were analysed, and a simplified trajectory calculation method was developed by which trajectories for height gain can be calculated on-board the aircraft based on a priori knowledge of the wind field. The results of simulations are presented, demonstrating the behaviour of the system in both smooth and turbulent flows. Finally, the results from a series of flight tests are presented. Flight tests at the hill were consistently successful, while flights around the building could not be sustained for periods of more than approximately 20 s. The difficulty of operating near a building is attributable to significant levels of low-frequency unsteadiness (gustiness) in the oncoming wind during the flight tests, effectively resulting in a loss of updraft for sustained periods.

FREE PDF GRATIS: Bioinspiration and Biomimetics

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PERGUNTA CAUSTICANTE DESTE BLOGGER:

Se o design na natureza é ilusão, por que os cientistas procuram design na natureza???

Fui, nem sei por que, sem entender bulhufas da Lógica 101 Darwinista.

O cenário epigenético dos caçadores-coletores e agricultores da floresta tropical africana

The epigenomic landscape of African rainforest hunter-gatherers and farmers

Maud Fagny, Etienne Patin, Julia L. MacIsaac, Maxime Rotival, Timothée Flutre, Meaghan J. Jones, Katherine J. Siddle, Hélène Quach, Christine Harmant, Lisa M. McEwen, Alain Froment, Evelyne Heyer, Antoine Gessain, Edouard Betsem, Patrick Mouguiama-Daouda, Jean-Marie Hombert, George H. Perry, Luis B. Barreiro, Michael S. Kobor & Lluis Quintana-Murci

Affiliations Contributions Corresponding author

Nature Communications 6, Article number: 10047 doi:10.1038/ncomms10047

Received 28 April 2015 Accepted 28 October 2015 Published 30 November 2015

Abstract

The genetic history of African populations is increasingly well documented, yet their patterns of epigenomic variation remain uncharacterized. Moreover, the relative impacts of DNA sequence variation and temporal changes in lifestyle and habitat on the human epigenome remain unknown. Here we generate genome-wide genotype and DNA methylation profiles for 362 rainforest hunter-gatherers and sedentary farmers. We find that the current habitat and historical lifestyle of a population have similarly critical impacts on the methylome, but the biological functions affected strongly differ. Specifically, methylation variation associated with recent changes in habitat mostly concerns immune and cellular functions, whereas that associated with historical lifestyle affects developmental processes. Furthermore, methylation variation—particularly that correlated with historical lifestyle—shows strong associations with nearby genetic variants that, moreover, are enriched in signals of natural selection. Our work provides new insight into the genetic and environmental factors affecting the epigenomic landscape of human populations over time.

Subject terms: Biological sciences Ecology Evolution Genetics

FREE PDF GRATIS: Nature Communications

Padrões de diversidade de população epigenômica

Patterns of population epigenomic diversity

Robert J. Schmitz, Matthew D. Schultz, Mark A. Urich, Joseph R. Nery, Mattia Pelizzola, Ondrej Libiger, Andrew Alix, Richard B. McCosh, Huaming Chen, Nicholas J. Schork & Joseph R. Ecker

Affiliations Contributions Corresponding author

Nature 495, 193–198 (14 March 2013) doi:10.1038/nature11968

Received 05 July 2012 Accepted 30 January 2013 Published online 06 March 2013

Abstract

Natural epigenetic variation provides a source for the generation of phenotypic diversity, but to understand its contribution to such diversity, its interaction with genetic variation requires further investigation. Here we report population-wide DNA sequencing of genomes, transcriptomes and methylomes of wild Arabidopsis thaliana accessions. Single cytosine methylation polymorphisms are not linked to genotype. However, the rate of linkage disequilibrium decay amongst differentially methylated regions targeted by RNA-directed DNA methylation is similar to the rate for single nucleotide polymorphisms. Association analyses of these RNA-directed DNA methylation regions with genetic variants identified thousands of methylation quantitative trait loci, which revealed the population estimate of genetically dependent methylation variation. Analysis of invariably methylated transposons and genes across this population indicates that loci targeted by RNA-directed DNA methylation are epigenetically activated in pollen and seeds, which facilitates proper development of these structures.

Subject terms: Epigenomics

FREE PDF GRATIS: Nature

Anéis (da vida) reconciliam a evolução genotípica e fenotípica dentro da Proteobacteria

Rings Reconcile Genotypic and Phenotypic Evolution within the Proteobacteria

James A. Lake 1,*, Joseph Larsen 1, Brooke Sarna 1, Rafael R. de la Haba 1,5, Yiyi Pu 1,3, HyunMin Koo 1,4, Jun Zhao 1,2 and Janet S. Sinsheimer 1

1University of California, Los Angeles;

2Peking University;

3Zhejiang University;

4University of Alabama, Birmingham,

5University of Sevilla.

↵Author for correspondence: James A. Lake, MCD Biology and Human Genetics, 232 Boyer Hall, University of California, Los Angeles 90095, USA. E-mail: Lake{at}mbi.ucla.edu

Received December 21, 2014.

Revision received August 12, 2015.

Revision received October 30, 2015.

Accepted November 9, 2015.

Source/Fonte:

James A. Lake and Janet S. Sinsheimer (2013) The deep roots of the Rings of Life. Genome Biology and Evolution 5: 2440-2448.

Abstract

Although prokaryotes are usually classified using molecular phylogenies instead of phenotypes after the advent of gene-sequencing, neither of these methods is satisfactory because the phenotypes cannot explain the molecular trees and the trees do not fit the phenotypes. This scientific crisis still exists and the profound disconnection between these two pillars of evolutionary biology - genotypes and phenotypes - grows larger. We use rings and a genomic form of goods thinking to resolve this conundrum (McInerney, J et al., 2011; Nelson-Sathi, S et al. 2015).

The Proteobacteria is the most speciose prokaryotic phylum known. It is an ideal phylogenetic model for reconstructing Earth's evolutionary history. It contains diverse free living-, pathogenic-, photosynthetic-, sulfur metabolizing- and symbiotic species. Due to its large number of species (Whitman et al. 1998) it was initially expected to provide strong phylogenetic support for a proteobacterial tree of life. But despite its many species, sequence-based tree analyses are unable to resolve its topology.

Here we develop new rooted ring analyses and study Proteobacterial evolution. Using protein family data and new genome-based outgroup rooting procedures, we reconstruct the complex evolutionary history of the Proteobacterial Rings (combinations of tree-like divergences and endosymbiotic-like convergences). We identify and map the origins of major gene flows within the Rooted Proteobacterial Rings (P < 3.6 x 10-6) and find that the evolution of the Alpha-, Beta-, and Gamma- proteobacteria is represented by a unique set of Rings. Using new techniques presented here we also root these rings using outgroups. We also map the independent flows of genes involved in DNA-, RNA-, ATP-, and membrane- related processes within the Proteobacteria and thereby demonstrate that these large gene flows are consistent with endosymbioses (Probability < 3.6 x 10-9).

Our analyses illustrate what it means to find that a gene is present, or absent, within a gene flow, and thereby clarify the origin of the apparent conflicts between genotypes and phenotypes. Here we identify the gene flows that introduced photosynthesis into the Alpha-, Beta- and Gammaproteobacteria from the common ancestor of the Actinobacteria and the Firmicutes. Our results also explain why Rooted Rings, unlike trees, are consistent with the observed genotypic- and phenotypic- relationships observed among the various proteobacterial classes. We find that Ring phylogenies can explain the genotypes and the phenotypes of biological processes within large and complex groups like the Proteobacteria.

Key words: Phylogenetic Classification Genotypes Phenotypes Rooting Rings Endosymbioses Chlorophylls Gene Losses/Gains

© The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact

journals.permissions@oup.com

FREE PDF GRATIS: Genome Biol Evol

                            Sup Info

Mudando as ideias sobre as origens eucarióticas

Changing ideas about eukaryotic origins

Tom A. Williams, T. Martin Embley

Published 31 August 2015.DOI: 10.1098/rstb.2014.0318

Source/Fonte

Abstract

The origin of eukaryotic cells is one of the most fascinating challenges in biology, and has inspired decades of controversy and debate. Recent work has led to major upheavals in our understanding of eukaryotic origins and has catalysed new debates about the roles of endosymbiosis and gene flow across the tree of life. Improved methods of phylogenetic analysis support scenarios in which the host cell for the mitochondrial endosymbiont was a member of the Archaea, and new technologies for sampling the genomes of environmental prokaryotes have allowed investigators to home in on closer relatives of founding symbiotic partners. The inference and interpretation of phylogenetic trees from genomic data remains at the centre of many of these debates, and there is increasing recognition that trees built using inadequate methods can prove misleading, whether describing the relationship of eukaryotes to other cells or the root of the universal tree. New statistical approaches show promise for addressing these questions but they come with their own computational challenges. The papers in this theme issue discuss recent progress on the origin of eukaryotic cells and genomes, highlight some of the ongoing debates, and suggest possible routes to future progress.

FREE PDF GRATIS: Phil. Trans. R. Soc. B

A ciência avança à medida que cientistas medalhões morrem?

Does Science Advance One Funeral at a Time?

Pierre Azoulay, Christian Fons-Rosen, Joshua S. Graff Zivin

NBER Working Paper No. 21788

Issued in December 2015

NBER Program(s): PR 

Source/Fonte

We study the extent to which eminent scientists shape the vitality of their fields by examining entry rates into the fields of 452 academic life scientists who pass away while at the peak of their scientific abilities. Key to our analyses is a novel way to delineate boundaries around scientific fields by appealing solely to intellectual linkages between scientists and their publications, rather than collaboration or co-citation patterns. Consistent with previous research, the flow of articles by collaborators into affected fields decreases precipitously after the death of a star scientist (relative to control fields). In contrast, we find that the flow of articles by non-collaborators increases by 8% on average. These additional contributions are disproportionately likely to be highly cited. They are also more likely to be authored by scientists who were not previously active in the deceased superstar’s field. Overall, these results suggest that outsiders are reluctant to challenge leadership within a field when the star is alive and that a number of barriers may constrain entry even after she is gone. Intellectual, social, and resource barriers all impede entry, with outsiders only entering subfields that offer a less hostile landscape for the support and acceptance of “foreign” ideas.

FREE PDF GRATIS: National Bureau of Economic Research

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NOTA CAUSTICANTE DESTE BLOGGER:

Se em parte é assim que a ciência avança, que venha logo a solução biológica. Traduzindo em miúdos: Morram! mas morram logo, para dar lugar e vez aos cientistas mais novos, mais abertos a novas ideias e teorias científicas! 

Herança epigenética transgeracional: mitos e mecanismos

Cell, Volume 157, Issue 1, 27 March 2014, Pages 95–109

Review

Transgenerational Epigenetic Inheritance: Myths and Mechanisms

Edith Heard 1, 2, Robert A. Martienssen 3, 4.

1 Mammalian Developmental Epigenetics Group, Institut Curie, CNRS UMR 3215, INSERM U934, 26 rue d’Ulm, 75248 Paris Cedex 05, France

2 Collège de France, 11 place Marcelin-Berthelot, Paris 75005, France

3 Howard Hughes Medical Institute and Gordon and Betty Moore Foundation, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA

4 Chaire Blaise Pascal, IBENS, École Normale Supérieure, Paris 75230, France

Available online 27 March 2014

FREE PDF GRATIS: Cell

Contestando a herança epigenética lamarckiana em mamíferos

Disputing Lamarckian epigenetic inheritance in mammals

Emma Whitelaw

Correspondence: Emma Whitelaw E.Whitelaw@latrobe.edu.au

Author Affiliations

Department of Genetics, La Trobe University, Bundoora 3086, VIC, Australia

Genome Biology 2015, 16:60 doi:10.1186/s13059-015-0626-0

Please see related article: http://dx.doi.org/10.1186/s13059-015-0619-z

The electronic version of this article is the complete one and can be found online at: http://genomebiology.com/2015/16/1/60

Published: 27 March 2015

© 2015 Whitelaw; licensee BioMed Central. 

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

A recent study finds that changes to transcription and DNA methylation resulting from in utero exposure to environmental endocrine-disrupting chemicals are not inherited across generations.

Epigenetic reprogramming

All mammals develop from a single cell, the zygote, which is made up of an egg and a sperm head, both of which contain a haploid genome. At the time of fertilization, the DNA of both egg and sperm is packaged into chromatin, and each has its own epigenetic (DNA methylation and histone modification) ‘state’ related to the previous functional requirements of these cell types. Once fertilization occurs, it is necessary that these epigenetic marks undergo extensive reprogramming for a complex multicellular organism to develop and differentiate. A similar period of extensive reprogramming of the epigenome has been shown to occur in the primordial germ cells during the development of the mature gametes. Some genes, called imprinted genes, are known to escape the epigenetic reprogramming in the early embryo and maintain the epigenetic state established in the gametes of the parents. This observation has supported the idea that perhaps some loci can escape both the reprogramming that occurs during early development and that which occurs during the development of mature gametes, thereby enabling Lamarckian inheritance. The evidence that this happens is scant, but has attracted much attention.

In a recent study published in Genome Biology, Iqbal and colleagues [1] have investigated the epigenetic changes that occur to the genome in response to endocrine disruptors and find that these changes are corrected by germline reprogramming events in the next generation.

FREE PDF GRATIS: Genome Biology

Metilação do DNA: epigenética na natureza

DNA methylation: Epigenetics in the wild

Adam J Bewick , Robert J Schmitz Corresponding Author

University of Georgia, United States

DOI: http://dx.doi.org/10.7554/eLife.07808

Published May 5, 2015

Cite as eLife 2015;4:e07808

Source/Fonte: eLIFE

Abstract

Studies of wild populations of the model plant Arabidopsis thaliana have started to reveal how patterns of DNA methylation change in response to the local environment.

FREE PDF GRATIS: eLIFE

Epigenética, Darwin, e Lamarck

Genome Biology and Evolution Volume 7 Issue 6Pp. 1758-1760.

Epigenetics, Darwin, and Lamarck

David Penny*

Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand

↵*Corresponding author: E-mail: d.penny{at}massey.ac.nz.

Accepted May 26, 2015.

Source/Fonte

Abstract

It is not really helpful to consider modern environmental epigenetics as neo-Lamarckian; and there is no evidence that Lamarck considered the idea original to himself. We must all keep learning about inheritance, but attributing modern ideas to early researchers is not helpful, and can be misleading.

Key words: Darwinism epigenetics evolution genetics Lamarck

© The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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 reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Teoremas de singularidade na relatividade geral: realizações e questões abertas

Singularity Theorems in General Relativity: Achievements and Open Questions

José M.M. Senovilla

(Submitted on 30 Apr 2006)

In this short note, a brief overview with a critical appraisal of the acclaimed singularity theorems, the most genuine post-Einsteinian result of General Relativity, is presented.

Comments: 15 pages, no figures. Contribution submitted to the Einstein Studies volume collecting talks given at the 7th International Conference on the History of General Relativity (HGR7), "Einstein and the Changing World View of Physics, 1905-2005"

Subjects: History and Philosophy of Physics (physics.hist-ph); General Relativity and Quantum Cosmology (gr-qc)

Cite as: arXiv:physics/0605007 [physics.hist-ph]

(or arXiv:physics/0605007v1 [physics.hist-ph] for this version)

Submission history

From: Jose M. M. Senovilla [view email] 

[v1] Sun, 30 Apr 2006 16:52:35 GMT (13kb)

FREE PDF GRATIS: ArXiv

Caracterizado estado químico pensado ser inobservável

Science 11 December 2015: 

Vol. 350 no. 6266 pp. 1338-1342 

DOI: 10.1126/science.aac9668

RESEARCH ARTICLE

Spectroscopic characterization of isomerization transition states

Joshua H. Baraban 1,*, P. Bryan Changala 1,†, Georg Ch. Mellau 2, John F. Stanton 3, Anthony J. Merer 4,5, Robert W. Field 1,‡

1Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

2Physikalisch-Chemisches Institut, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany.

3Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712, USA.

4Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada.

5Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan.

↵‡Corresponding author. E-mail: rwfield{at}mit.edu

↵* Present address: Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA.

↵† Present address: JILA, National Institute of Standards and Technology, and Department of Physics, University of Colorado, Boulder, CO 80309, USA.

Shaking out details of transition states

Chemists liken reaction energetics to a landscape with hills and valleys. In this context, the transition state represents the highest barrier that reagents must pass over en route to forming products. Baraban et al. introduce a framework for extracting details about the transition state of rearrangement reactions directly from vibrational spectral data. They identified a characteristic pattern in the spacing between vibrational energy levels near the transition state, which revealed its energy as well as the specific motions involved in surmounting the barrier.

Abstract

Transition state theory is central to our understanding of chemical reaction dynamics. We demonstrate a method for extracting transition state energies and properties from a characteristic pattern found in frequency-domain spectra of isomerizing systems. This pattern—a dip in the spacings of certain barrier-proximal vibrational levels—can be understood using the concept of effective frequency, ωeff. The method is applied to the cis-trans conformational change in the S1 state of C2H2 and the bond-breaking HCN-HNC isomerization. In both cases, the barrier heights derived from spectroscopic data agree extremely well with previous ab initio calculations. We also show that it is possible to distinguish between vibrational modes that are actively involved in the isomerization process and those that are passive bystanders.

Received for publication 1 September 2015.

Accepted for publication 29 October 2015.

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Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao Portal de Periódicos CAPES/MEC podem ler gratuitamente este artigo da Science e de mais 30.000 publicações científicas.

Solucionada a estrutura de um componente-chave de tomada de decisão bacteriana

CryoEM and computer simulations reveal a novel kinase conformational switch in bacterial chemotaxis signaling

C Keith Cassidy, Benjamin A Himes, Frances J Alvarez, Jun Ma, Gongpu Zhao, Juan R Perilla, Klaus Schulten, Peijun Zhang Corresponding Author

DOI: http://dx.doi.org/10.7554/eLife.08419

Published November 19, 2015

Cite as eLife 2015;10.7554/eLife.08419

Credit/Crédito: C. Keith Cassidy

Abstract

Chemotactic responses in bacteria require large, highly ordered arrays of sensory proteins to mediate the signal transduction that ultimately controls cell motility. A mechanistic understanding of the molecular events underlying signaling, however, has been hampered by the lack of a high-resolution structural description of the extended array. Here, we report a novel reconstitution of the array, involving the receptor signaling domain, histidine kinase CheA, and adaptor protein CheW, as well as a density map of the core-signaling unit at 11.3 Å resolution, obtained by cryo-electron tomography and sub-tomogram averaging. Extracting key structural constraints from our density map, we computationally construct and refine an atomic model of the core array structure, exposing novel interfaces between the component proteins. Using all-atom molecular dynamics simulations, we further reveal a distinctive conformational change in CheA. Mutagenesis and chemical cross-linking experiments confirm the importance of the conformational dynamics of CheA for chemotactic function.

FREE PDF GRATIS: eLIFE

Microscopia inovadora desbloqueia segredos da montagem de vírus de plantas

NATURE COMMUNICATIONS | ARTICLE OPEN

Mechanisms of assembly and genome packaging in an RNA virus revealed by high-resolution cryo-EM

Emma L. Hesketh, Yulia Meshcheriakova, Kyle C. Dent, Pooja Saxena, Rebecca F. Thompson, Joseph J. Cockburn, George P. Lomonossoff & Neil A. Ranson

Affiliations Contributions Corresponding author

Nature Communications 6, Article number: 10113 doi:10.1038/ncomms10113

Received 06 August 2015 Accepted 03 November 2015 Published 10 December 2015

Abstract

Cowpea mosaic virus is a plant-infecting member of the Picornavirales and is of major interest in the development of biotechnology applications. Despite the availability of >100 crystal structures of Picornavirales capsids, relatively little is known about the mechanisms of capsid assembly and genome encapsidation. Here we have determined cryo-electron microscopy reconstructions for the wild-type virus and an empty virus-like particle, to 3.4 Å and 3.0 Å resolution, respectively, and built de novo atomic models of their capsids. These new structures reveal the C-terminal region of the small coat protein subunit, which is essential for virus assembly and which was missing from previously determined crystal structures, as well as residues that bind to the viral genome. These observations allow us to develop a new model for genome encapsidation and capsid assembly.

Subject terms: Biological sciences Virology Biotechnology

FREE PDF GRATIS: Nature Communications

                            Sup. Info.

Por que confiar em uma teoria científica??? Físicos e filósofos debatem o método científico

Forbes Science

DEC 10, 2015 @ 01:03 PM 48,339 VIEWS

Why Trust A Theory? Physicists And Philosophers Debate The Scientific Method

Source/Fonte

POST WRITTEN BY Sabine Hossenfelder

Sabine is a theoretical physicist specialized in quantum gravity and high energy physics. She also freelance writes about science.

This week, a group of about 100 physicists and philosophers have gathered in Munich to reassess a question at the heart of science: “Why trust a theory?” In an opinion piece by George Ellis and Joe Silk, published in Nature earlier this year, the two physicists expressed worry about current developments in some areas of theoretical physics. In particular, they were concerned with untestable attempts to address the fundamental questions concerning space, time and matter. Their article gave rise to the idea of the current meeting.

An increasing number of physicists, Ellis and Silk observed, have become strongly convinced of the viability of theories that have no empirical confirmation. This trend is most pronounced in the quest for a theory of quantum gravity – notably string theory – and in cosmology where theories for the early universe give rise to a multiverse. Why, they ask, do scientists trust theories that have not been experimentally tested? Worse, in some cases, these theories cannot even been tested in principle. Is this still science?

Philosopher Richard Dawid, one of the organizers of the Munich meeting, has observed the same development and, in his book “String theory and the scientific method” argued that string theorists in particular use a method of “non-empirical theory confirmation.” This method is used during the development of a theory and is based on collecting indications which increase the physicists’ confidence that a theory describes nature. These indications are, for example, the amount (or absence of) alternative solutions to a problem, the degree by which a theory is connected to already confirmed theories, and the amount of unexpected insights that the theories give rise to.

While Dawid focused on string theory, non-empirical theory confirmation is used and has been used in theoretical physics for a long time. What was missing so far is a legitimate philosophical underpinning. Dawid’s arguments provided such an underpinning. String theorists, needless to say, were delighted to now have philosophical support for their procedures, but not everyone was pleased to see the scientific method being watered down. This is what prompted Ellis and Silk to "defend the integrity of physics." The topic of the present workshop is the following question: under which circumstances, if any at all, is non-empirical theory confirmation a justified procedure?

It is a pressing and timely question. As physics has matured, experimental test of new, more fundamental theories have become increasingly difficult. Many existing theories are so difficult to test that they are widely believed to be untestable in the foreseeable future. The methods from the past are not working any more. “We are in a different era of science,” says Nobel Laureate David Gross.

...

Read more here/Leia mais aqui: Forbes

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O workshop em questão foi este:

Why Trust a Theory? Reconsidering Scientific Methodology in Light of Modern Physics

7-9 December, 2015

Idea and Motivation

Fundamental physics today faces increasing difficulties to find conclusive empirical confirmation of its theories. Some empirically unconfirmed or inconclusively confirmed theories in the field have nevertheless attained a high degree of trust among their exponents and are de facto treated as well established theories. This situation raises a number of questions that are of substantial importance for the future development of fundamental physics. Can a high degree of trust in an empirically unconfirmed or inconclusively confirmed theory be scientifically justified? Does the extent to which empirically unconfirmed theories are trusted today constitute a substantial change of the character of scientific reasoning? Might some important theories of contemporary fundamental physics be empirically untestable in principle?

The workshop will be centred around an in-depth discussion of these and other related questions, with a particular focus on the methodological and philosophical aspects. As such, it will be an interdisciplinary event, involving physicists and philosophers of science. It will bring together main exponents of important theories in fundamental physics, physicists who have expressed criticism of the current strategies of theory assessment in fundamental physics and philosophers who have thought about those issues.

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NOTA DESTE BLOGGER:

Há muitas teorias, hipóteses e ideias científicas que não tiveram até hoje a sua confirmação no contexto de justificação teórica. A hipótese darwinista de ancestralidade comum com modificação através da seleção natural e n mecanismos evolucionários de A a Z (vai que um falhe...) é uma delas!

Cronologia do universo pelo modelo cosmológico do Big Bang

Chamando a teoria das cordas para ajudar!

String theory to the rescue

Joseph Polchinski

(Submitted on 8 Dec 2015 (v1), last revised 10 Dec 2015 (this version, v2))

Source/Fonte

The search for a theory of quantum gravity faces two great challenges: the incredibly small scales of the Planck length and time, and the possibility that the observed constants of nature are in part the result of random processes. A priori, one might have expected these to be insuperable obstacles. However, clues from observed physics, and the discovery of string theory, raise the hope that the unification of quantum mechanics and general relativity is within reach.

Comments: Prepared for the meeting "Why Trust a Theory? Reconsidering Scientific Methodology in Light of Modern Physics", Munich, Dec. 7-9, 2015. v2,3: small additions

Subjects: High Energy Physics - Theory (hep-th); History and Philosophy of Physics (physics.hist-ph)

Cite as: arXiv:1512.02477 [hep-th]

(or arXiv:1512.02477v2 [hep-th] for this version)

Submission history

From: Joseph Polchinski [view email] 

[v1] Tue, 8 Dec 2015 14:15:36 GMT (57kb,D)

[v2] Thu, 10 Dec 2015 08:25:57 GMT (58kb,D)

FREE PDF GRATIS: ArXiv

O que os ecossistemas podem aprender? Expandindo a ecologia evolucionária com a teoria da aprendizagem

What can ecosystems learn? Expanding evolutionary ecology with learning theory

Daniel A. Power1*, Richard A. Watson2, Eörs Szathmáry3, Rob Mills4, Simon T. Powers5, C. Patrick Doncaster6 and BłaŻej Czapp6

* Corresponding author: Daniel A Power dap1e12@soton.ac.uk

Author Affiliations

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Biology Direct 2015, 10:69 doi:10.1186/s13062-015-0094-1

Published: 8 December 2015

Source/Fonte

Abstract

Background

The structure and organisation of ecological interactions within an ecosystem is modified by the evolution and coevolution of the individual species it contains. Understanding how historical conditions have shaped this architecture is vital for understanding system responses to change at scales from the microbial upwards. However, in the absence of a group selection process, the collective behaviours and ecosystem functions exhibited by the whole community cannot be organised or adapted in a Darwinian sense. A long-standing open question thus persists: Are there alternative organising principles that enable us to understand and predict how the coevolution of the component species creates and maintains complex collective behaviours exhibited by the ecosystem as a whole?

Results

Here we answer this question by incorporating principles from connectionist learning, a previously unrelated discipline already using well-developed theories on how emergent behaviours arise in simple networks. Specifically, we show conditions where natural selection on ecological interactions is functionally equivalent to a simple type of connectionist learning, ‘unsupervised learning’, well-known in neural-network models of cognitive systems to produce many non-trivial collective behaviours. Accordingly, we find that a community can self-organise in a well-defined and non-trivial sense without selection at the community level; its organisation can be conditioned by past experience in the same sense as connectionist learning models habituate to stimuli. This conditioning drives the community to form a distributed ecological memory of multiple past states, causing the community to: a) converge to these states from any random initial composition; b) accurately restore historical compositions from small fragments; c) recover a state composition following disturbance; and d) to correctly classify ambiguous initial compositions according to their similarity to learned compositions. We examine how the formation of alternative stable states alters the community’s response to changing environmental forcing, and we identify conditions under which the ecosystem exhibits hysteresis with potential for catastrophic regime shifts.

Conclusions

This work highlights the potential of connectionist theory to expand our understanding of evo-eco dynamics and collective ecological behaviours. Within this framework we find that, despite not being a Darwinian unit, ecological communities can behave like connectionist learning systems, creating internal conditions that habituate to past environmental conditions and actively recalling those conditions.

Reviewers

This article was reviewed by Prof. Ricard V Solé, Universitat Pompeu Fabra, Barcelona and Prof. Rob Knight, University of Colorado, Boulder.

Keywords: Evolutionary ecology; Alternative stable states; Lotka-Volterra dynamics; Theoretical ecology; Community assembly; Network structures; Ecological memory; Associative learning; Regime shifts; Community matrix

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Os dinossauros evoluíram mais rapidamente do que se pensava antes: vapt, vupt!!!

The precise temporal calibration of dinosaur origins

Claudia A. Marsicano a, Randall B. Irmis b,c,1, Adriana C. Mancuso d, Roland Mundil e, and Farid Chemale f

aDepartamento de Ciencias Geológicas, Instituto de Estudios Andinos-Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires C1428EHA, Argentina;

bNatural History Museum of Utah, University of Utah, Salt Lake City, UT 84108-1214;

cDepartment of Geology & Geophysics, University of Utah, Salt Lake City, UT 84112-0102;

dInstituto Argentino de Nivología, Glaciología y Ciencias Ambientales, Centro Científico y Tecnológico-Consejo Nacional de Investigaciones Científicas y Técnicas-Mendoza, Mendoza CC330, Argentina;

eBerkeley Geochronology Center, Berkeley, CA 94709;

fInstituto de Geociências, Universidade de Brasília, Brasília-DF 70864-050, Brazil

Edited by Paul E. Olsen, Columbia University, Palisades, NY, and approved November 6, 2015 (received for review June 25, 2015)

Source/Fonte: Victor Leshyk - Nature

Significance

Many hypotheses have been put forth to explain the origin and early radiation of dinosaurs, but poor age constraints for constituent fossil assemblages make these scenarios difficult to test. Using precise radioisotopic ages, we demonstrate that the temporal gap between assemblages containing only dinosaur precursors and those with the first dinosaurs was 5–10 million years shorter than previously thought. Thus, these data suggest that the origin of dinosaurs was a relatively rapid evolutionary event. Combined with our synthesis of paleoecological data, we demonstrate there was little compositional difference between the dinosaur precursor assemblages and the earliest dinosaur assemblages, and thus, the initial appearance of dinosaurs was not associated with a fundamental shift in ecosystem composition, as classically stated.

Abstract

Dinosaurs have been major components of ecosystems for over 200 million years. Although different macroevolutionary scenarios exist to explain the Triassic origin and subsequent rise to dominance of dinosaurs and their closest relatives (dinosauromorphs), all lack critical support from a precise biostratigraphically independent temporal framework. The absence of robust geochronologic age control for comparing alternative scenarios makes it impossible to determine if observed faunal differences vary across time, space, or a combination of both. To better constrain the origin of dinosaurs, we produced radioisotopic ages for the Argentinian Chañares Formation, which preserves a quintessential assemblage of dinosaurian precursors (early dinosauromorphs) just before the first dinosaurs. Our new high-precision chemical abrasion thermal ionization mass spectrometry (CA-TIMS) U–Pb zircon ages reveal that the assemblage is early Carnian (early Late Triassic), 5- to 10-Ma younger than previously thought. Combined with other geochronologic data from the same basin, we constrain the rate of dinosaur origins, demonstrating their relatively rapid origin in a less than 5-Ma interval, thus halving the temporal gap between assemblages containing only dinosaur precursors and those with early dinosaurs. After their origin, dinosaurs only gradually dominated mid- to high-latitude terrestrial ecosystems millions of years later, closer to the Triassic–Jurassic boundary.

dinosaur origins Chañares Formation geochronology Triassic biostratigraphy

Footnotes

1To whom correspondence should be addressed. Email: irmis{at}umnh.utah.edu.

Author contributions: C.A.M., R.B.I., and A.C.M. designed research; C.A.M., R.B.I., and A.C.M. performed research; R.M. and F.C. contributed new reagents/analytic tools; C.A.M., R.B.I., A.C.M., R.M., and F.C. analyzed data; and C.A.M., R.B.I., A.C.M., R.M., and F.C. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1512541112/-/DCSupplemental.

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