Como a China está reescrevendo o livro da origem humana

quarta-feira, julho 13, 2016

How China is rewriting the book on human origins

Fossil finds in China are challenging ideas about the evolution of modern humans and our closest relatives.

Jane Qiu

12 July 2016

On the outskirts of Beijing, a small limestone mountain named Dragon Bone Hill rises above the surrounding sprawl. Along the northern side, a path leads up to some fenced-off caves that draw 150,000 visitors each year, from schoolchildren to grey-haired pensioners. It was here, in 1929, that researchers discovered a nearly complete ancient skull that they determined was roughly half a million years old. Dubbed Peking Man, it was among the earliest human remains ever uncovered, and it helped to convince many researchers that humanity first evolved in Asia.

Since then, the central importance of Peking Man has faded. Although modern dating methods put the fossil even earlier — at up to 780,000 years old — the specimen has been eclipsed by discoveries in Africa that have yielded much older remains of ancient human relatives. Such finds have cemented Africa's status as the cradle of humanity — the place from which modern humans and their predecessors spread around the globe — and relegated Asia to a kind of evolutionary cul-de-sac.

But the tale of Peking Man has haunted generations of Chinese researchers, who have struggled to understand its relationship to modern humans. “It's a story without an ending,” says Wu Xinzhi, a palaeontologist at the Chinese Academy of Sciences' Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) in Beijing. They wonder whether the descendants of Peking Man and fellow members of the species Homo erectus died out or evolved into a more modern species, and whether they contributed to the gene pool of China today.


Keen to get to the bottom of its people's ancestry, China has in the past decade stepped up its efforts to uncover evidence of early humans across the country. It is reanalysing old fossil finds and pouring tens of millions of dollars a year into excavations. And the government is setting up a US$1.1-million laboratory at the IVPP to extract and sequence ancient DNA.

The investment comes at a time when palaeoanthropologists across the globe are starting to pay more attention to Asian fossils and how they relate to other early hominins — creatures that are more closely related to humans than to chimps. Finds in China and other parts of Asia have made it clear that a dazzling variety of Homo species once roamed the continent. And they are challenging conventional ideas about the evolutionary history of humanity.

“Many Western scientists tend to see Asian fossils and artefacts through the prism of what was happening in Africa and Europe,” says Wu. Those other continents have historically drawn more attention in studies of human evolution because of the antiquity of fossil finds there, and because they are closer to major palaeoanthropology research institutions, he says. “But it's increasingly clear that many Asian materials cannot fit into the traditional narrative of human evolution.”

Chris Stringer, a palaeoanthropologist at the Natural History Museum in London, agrees. “Asia has been a forgotten continent,” he says. “Its role in human evolution may have been largely under-appreciated.”
...

FREE PDF GRATIS: Nature

O zoológico cósmico: a (quase) inevitabilidade da evolução da vida macroscópica complexa

terça-feira, julho 12, 2016

Life 2016, 6(3), 25; doi:10.3390/life6030025

Essay

The Cosmic Zoo: The (Near) Inevitability of the Evolution of Complex, Macroscopic Life

William Bains 1,2,* and Dirk Schulze-Makuch 3,4

1 Department of Earth, Atmospheric and Planetary Science, MIT, 77 Mass. Ave., Cambridge, MA 02139, USA

2 Rufus Scientific Ltd., 37 The Moor, Melbourn, Royston, Herts SG8 6ED, UK

3 School of the Environment, Washington State University, Pullman, WA 99164, USA

4 Center for Astronomy and Astrophysics, Technical University Berlin, Berlin 10623, Germany

* Author to whom correspondence should be addressed.

Academic Editor: David Deamer

Received: 26 March 2016 / Revised: 17 June 2016 / Accepted: 22 June 2016 / Published: 30 June 2016



Abstract

Life on Earth provides a unique biological record from single-cell microbes to technologically intelligent life forms. Our evolution is marked by several major steps or innovations along a path of increasing complexity from microbes to space-faring humans. Here we identify various major key innovations, and use an analytical toolset consisting of a set of models to analyse how likely each key innovation is to occur. Our conclusion is that once the origin of life is accomplished, most of the key innovations can occur rather readily. The conclusion for other worlds is that if the origin of life can occur rather easily, we should live in a cosmic zoo, as the innovations necessary to lead to complex life will occur with high probability given sufficient time and habitat. On the other hand, if the origin of life is rare, then we might live in a rather empty universe.

Keywords: transition; key innovation; complexity; evolution; multicellularity; origin of life; great filter

This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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A durabilidade da queratina tem implicações para o registro fóssil: resultados de uma experiência de degradação de pena em 10 anos

segunda-feira, julho 11, 2016

Keratin Durability Has Implications for the Fossil Record: Results from a 10 Year Feather Degradation Experiment

Alison E. Moyer , Wenxia Zheng, Mary H. Schweitzer




Abstract

Keratinous ‘soft tissue’ structures (i.e. epidermally derived and originally non-biomineralized), include feathers, skin, claws, beaks, and hair. Despite their relatively common occurrence in the fossil record (second only to bone and teeth), few studies have addressed natural degradation processes that must occur in all organic material, including those keratinous structures that are incorporated into the rock record as fossils. Because feathers have high preservation potential and strong phylogenetic signal, in the current study we examine feathers subjected to different burial environments for a duration of ~10 years, using transmission electron microscopy (TEM) and in situ immunofluorescence (IF). We use morphology and persistence of specific immunoreactivity as indicators of preservation at the molecular and microstructural levels. We show that feather keratin is durable, demonstrates structural and microstructural integrity, and retains epitopes suitable for specific antibody recognition in even the harshest conditions. These data support the hypothesis that keratin antibody reactivity can be used to identify the nature and composition of epidermal structures in the rock record, and to address evolutionary questions by distinguishing between alpha- (widely distributed) and beta- (limited to sauropsids) keratin.

Citation: Moyer AE, Zheng W, Schweitzer MH (2016) Keratin Durability Has Implications for the Fossil Record: Results from a 10 Year Feather Degradation Experiment. PLoS ONE 11(7): e0157699. doi:10.1371/journal.pone.0157699

Editor: Brian Lee Beatty, New York Institute of Technology College of Osteopathic Medicine, UNITED STATES

Received: November 18, 2015; Accepted: May 3, 2016; Published: July 6, 2016

Copyright: © 2016 Moyer et al. 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 within the paper and its Supporting Information files.

Funding: This research was funded by grants to MHS from the David and Lucile Packard Foundation and the NSF INSPIRE program (EAR-1344198), and the National Science Foundation Graduate Research Fellowship Program (DGE-1252376) To AEM. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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

FREE PDF GRATIS: PLoS One

Quantificando a origem da vida em escala planetária: fatorando nossa profunda ignorância científica, parece que a vida na Terra é única

Quantifying the origins of life on a planetary scale

Caleb Scharf a,1 and Leroy Cronin b,1

Author Affiliations

a Columbia Astrobiology Center, Columbia Astrophysics Laboratory, New York, NY 10027;

b School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, United Kingdom

Edited by Neta A. Bahcall, Princeton University, Princeton, NJ, and approved May 17, 2016 (received for review November 23, 2015)

Source/Fonte: Space

Significance

In this paper, we describe an equation to estimate the frequency of planetary “origin of life”-type events that is similar in intent to the Drake Equation but with some key advantages—specifically, our formulation makes an explicit connection between “global” rates for life arising and granular information about a planet. Our approach indicates scenarios where a shared chemical search space with more complex building blocks could be the critical difference between cosmic environments where life is potentially more or less abundant but, more importantly, points to constraints on the search. The possibility of chemical search-space amplification could be a major variance factor in planetary abiogenesis probabilities.

Abstract

A simple, heuristic formula with parallels to the Drake Equation is introduced to help focus discussion on open questions for the origins of life in a planetary context. This approach indicates a number of areas where quantitative progress can be made on parameter estimation for determining origins of life probabilities, based on constraints from Bayesian approaches. We discuss a variety of “microscale” factors and their role in determining “macroscale” abiogenesis probabilities on suitable planets. We also propose that impact ejecta exchange between planets with parallel chemistries and chemical evolution could in principle amplify the development of molecular complexity and abiogenesis probabilities. This amplification could be very significant, and both bias our conclusions about abiogenesis probabilities based on the Earth and provide a major source of variance in the probability of life arising in planetary systems. We use our heuristic formula to suggest a number of observational routes for improving constraints on origins of life probabilities.

origin of life planetary scale chemical search space exoplanetary science

Footnotes

1To whom correspondence may be addressed. Email: caleb@astro.columbia.edu or lee.cronin@glasgow.ac.uk.

Author contributions: C.S. and L.C. performed research, analyzed data, and wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

Freely available online through the PNAS open access option.

FREE PDF GRATIS: PNAS







http://www.space.com/images/i/000/056/703/original/alien-planets-kepler36-system_image.jpg?interpolation=lanczos-none&downsize=*:1400

Incorporando o pensamento de árvore e escala de tempo evolucionário na Biologia do Desenvolvimento

domingo, julho 10, 2016

Incorporating tree-thinking and evolutionary time scale into developmental biology

Shigehiro Kuraku1,*, Nathalie Feiner2, Sean D. Keeley1 andYuichiro Hara1

Version of Record online: 5 JAN 2016


© 2016 Japanese Society of Developmental Biologists

Development, Growth & Differentiation

Special Issue: TIME IN DEVELOPMENT

Volume 58, Issue 1, pages 131–142, January 2016


Abstract

Keywords: cryptic pan-vertebrate genes; hidden paralogy; molecular evolution; orthology; tree-thinking

Phylogenetic approaches are indispensable in any comparative molecular study involving multiple species. These approaches are in increasing demand as the amount and availability of DNA sequence information continues to increase exponentially, even for organisms that were previously not extensively studied. Without the sound application of phylogenetic concepts and knowledge, one can be misled when attempting to infer ancestral character states as well as the timing and order of evolutionary events, both of which are frequently exerted in evolutionary developmental biology. The ignorance of phylogenetic approaches can also impact non-evolutionary studies and cause misidentification of the target gene or protein to be examined in functional characterization. This review aims to promote tree-thinking in evolutionary conjecture and stress the importance of a sense of time scale in cross-species comparisons, in order to enhance the understanding of phylogenetics in all biological fields including developmental biology. To this end, molecular phylogenies of several developmental regulatory genes, including those denoted as “cryptic pan-vertebrate genes”, are introduced as examples.

Cientistas simulam minúsculas "turbinas eólicas" movidas por bactérias: mero acaso, fortuita necessidade ou design inteligente?

Active micromachines: Microfluidics powered by mesoscale turbulence

Sumesh P. Thampi 1,2, Amin Doostmohammadi 2, Tyler N. Shendruk 2, Ramin Golestanian 2 and Julia M. Yeomans 2,*

- Author Affiliations

1Department of Chemical Engineering, Indian Institute of Technology Madras, Chennai 600036, India.

2Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, UK.

↵*Corresponding author. Email: julia.yeomans@physics.ox.ac.uk

Science Advances 08 Jul 2016:

Vol. 2, no. 7, e1501854


Source/Fonte: University of Oxford

Abstract

Dense active matter, from bacterial suspensions and microtubule bundles driven by motor proteins to cellular monolayers and synthetic Janus particles, is characterized by mesoscale turbulence, which is the emergence of chaotic flow structures. By immersing an ordered array of symmetric rotors in an active fluid, we introduce a microfluidic system that exploits spontaneous symmetry breaking in mesoscale turbulence to generate work. The lattice of rotors self-organizes into a spin state where neighboring discs continuously rotate in permanent alternating directions due to combined hydrodynamic and elastic effects. Our virtual prototype demonstrates a new research direction for the design of micromachines powered by the nematohydrodynamic properties of active turbulence.

Key words Mesoscale turbulence active matter microrotor array self-organised spin-state activity-powered micromachines biological motors

Copyright © 2016, The Authors

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

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A genômica microbiana desafia Darwin

sexta-feira, julho 08, 2016

Microbial genomics challenge Darwin

Source/Fonte: Nature Reviews Genetics


About this Research Topic

The 200th anniversary of Darwin’s birthday was celebrated in 2009, making the concept of Darwinism even more popular than at the time it was originally proposed, to the extent that it has acquired quasi-religious status. His theory revolves around a Tree of Life in which all living organisms are considered to have descended from a single ancestor, and each node represents a common ancestor. It comprises hierarchy and dichotomy, which are typical characteristics of the post-biblical 19th century vision. Indeed, according to post-modern philosophy (also called the French theory) the majority of theories, including scientific ones, are based only on meta-narratives expressing the influence of a culture at a given time. Buddhism or Hinduism may have generated a very different story of evolution. 

Our way of thinking about life, and the way we describe evolution, have changed radically in the 21st century due to the genomic revolution. Comparative genome analyses have demonstrated that gene repertoires are characterized by plasticity, and there is strong evidence that nearly all genes have been exchanged at some point. Genomic data show that the genetic information of living organisms is inherited not only vertically but also laterally. Lateral gene transfers were at first observed only in bacteria, which contain genes originating from eukaryotes, Archaea and viruses. Such transfers were subsequently identified in all living organisms; giant viruses have chimeric genomes and the human genome is a mosaic of genes with eukaryotic, bacterial, and viral origins. We cannot identify a single common ancestor for the gene repertoire of any organism. Furthermore, a very high proportion of genes have been newly created through gene fusion or degradation, and others show no homology to sequences found in other species. It is now clear that every living organism has a variety of ancestors, while exchanges between species are intense, and the creation of new genes is frequent and permanent in all living organisms. Our current genomic knowledge contradicts the tree of life theory, as established by Darwin. Recent analyses have produced bushes rather than resolved trees, with the structure of some parts remaining elusive. It becomes more and more obvious that phylogenetic relationships are better described by forests and networks and that species evolution looks more like a rhizome. The chimerism and mosaic structure of all living organisms through both non-vertical inheritance and de novo creation can only be assimilated and described by a post-Darwinist concept. 

In this Research Topic we wish to highlight the influence of microbiology and genomics on our understanding of the complexity of gene repertoires, and also demonstrate how current knowledge does not support Darwin’s theory. Microbiology has offered a great advance in the way we perceive life. Evidence obtained from studies on bacterial and viral evolution, lateral inheritance, phylogenetic trees and biodiversity continues to challenge what constituted, until recently, an unimpeded dogma in biology.

FREE E-BOOK GRATIS: Frontiers

O segredo da vida de uma Oesia: vermiforme pré-histórico construía "casas" tubulares no fundo do mar

quinta-feira, julho 07, 2016

Cambrian suspension-feeding tubicolous hemichordates

Karma Nanglu Email author View ORCID ID profile, Jean-Bernard Caron, Simon Conway Morris and Christopher B. Cameron

BMC Biology201614:56

DOI: 10.1186/s12915-016-0271-4 © Nanglu et al. 2016

Received: 4 April 2016Accepted: 8 June 2016Published: 7 July 2016



Abstract

Background

The combination of a meager fossil record of vermiform enteropneusts and their disparity with the tubicolous pterobranchs renders early hemichordate evolution conjectural. The middle Cambrian Oesia disjuncta from the Burgess Shale has been compared to annelids, tunicates and chaetognaths, but on the basis of abundant new material is now identified as a primitive hemichordate.

Results

Notable features include a facultative tubicolous habit, a posterior grasping structure and an extensive pharynx. These characters, along with the spirally arranged openings in the associated organic tube (previously assigned to the green alga Margaretia), confirm Oesia as a tiered suspension feeder.

Conclusions

Increasing predation pressure was probably one of the main causes of a transition to the infauna. In crown group enteropneusts this was accompanied by a loss of the tube and reduction in gill bars, with a corresponding shift to deposit feeding. The posterior grasping structure may represent an ancestral precursor to the pterobranch stolon, so facilitating their colonial lifestyle. The focus on suspension feeding as a primary mode of life amongst the basal hemichordates adds further evidence to the hypothesis that suspension feeding is the ancestral state for the major clade Deuterostomia.

Keywords Enteropneusta Hemichordata Cambrian Burgess Shale

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iTOL, a Árvore da Vida interativa

terça-feira, julho 05, 2016





Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

Ivica Letunic1,* and Peer Bork2,3,4

- Author Affiliations

1Biobyte solutions GmbH, Bothestr 142, 69126 Heidelberg, Germany

2European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany

3Max Delbrück Centre for Molecular Medicine, 13125 Berlin, Germany

4Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany

↵*To whom correspondence should be addressed. Tel: +49 6221 3878534; Email: letunic@biobyte.de

Received February 24, 2016. Revision received April 4, 2016. Accepted April 8, 2016.

Abstract

Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. The current version was completely redesigned and rewritten, utilizing current web technologies for speedy and streamlined processing. Numerous new features were introduced and several new data types are now supported. Trees with up to 100,000 leaves can now be efficiently displayed. Full interactive control over precise positioning of various annotation features and an unlimited number of datasets allow the easy creation of complex tree visualizations. iTOL 3 is the first tool which supports direct visualization of the recently proposed phylogenetic placements format. Finally, iTOL's account system has been redesigned to simplify the management of trees in user-defined workspaces and projects, as it is heavily used and currently handles already more than 500,000 trees from more than 10,000 individual users.

© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution 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: Nucleic Acids Research

Transcriptômica comparativa por toda a árvore da vida procariótica

Comparative transcriptomics across the prokaryotic tree of life

Ofir Cohen1,2, Shany Doron1, Omri Wurtzel1,3, Daniel Dar1, Sarit Edelheit1, Iris Karunker1, Eran Mick1,4 and Rotem Sorek1,*

- Author Affiliations

1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel

2Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA

3Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA

4Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA

↵*To whom correspondence should be addressed. Tel: +1 972 8 934 6342; Fax: +1 972 8 934 4108; Email: rotem.sorek@weizmann.ac.il

Received February 8, 2016. Revision received April 20, 2016. Accepted April 28, 2016.



Abstract

Whole-transcriptome sequencing studies from recent years revealed an unexpected complexity in transcriptomes of bacteria and archaea, including abundant non-coding RNAs, cis-antisense transcription and regulatory untranslated regions (UTRs). Understanding the functional relevance of the plethora of non-coding RNAs in a given organism is challenging, especially since some of these RNAs were attributed to ‘transcriptional noise’. To allow the search for conserved transcriptomic elements we produced comparative transcriptome maps for multiple species across the microbial tree of life. These transcriptome maps are detailed in annotations, comparable by gene families, and BLAST-searchable by user provided sequences. Our transcriptome collection includes 18 model organisms spanning 10 phyla/subphyla of bacteria and archaea that were sequenced using standardized RNA-seq methods. The utility of the comparative approach, as implemented in our web server, is demonstrated by highlighting genes with exceptionally long 5′UTRs across species, which correspond to many known riboswitches and further suggest novel putative regulatory elements. Our study provides a standardized reference transcriptome to major clinically and environmentally important microbial phyla. The viewer is available at http://exploration.weizmann.ac.il/TCOL, setting a framework for comparative studies of the microbial non-coding genome.

© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution 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: Nucleic Acids Research Sup Info

Cientistas criam sinapses artificiais: mais uma etapa em direção a um computador que "funcione" como o cérebro humano

Organic core-sheath nanowire artificial synapses with femtojoule energy consumption

Wentao Xu1, Sung-Yong Min1, Hyunsang Hwang1 and Tae-Woo Lee1,2,*

- Author Affiliations

1Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Republic of Korea.

2Department of Chemical Engineering, Division of Advanced Materials Science, School of Environmental Science and Engineering, POSTECH, 77 Cheongam-Ro, Nam-Gu, Pohang 790-784, Republic of Korea.

↵*Corresponding author. Email: twlee@postech.ac.kr; taewlees@gmail.com

Science Advances 17 Jun 2016:

Vol. 2, no. 6, e1501326


Fig. 1
Schematic of biological neuronal network and an ONW ST that emulates a biological synapse.

Abstract

Emulation of biological synapses is an important step toward construction of large-scale brain-inspired electronics. Despite remarkable progress in emulating synaptic functions, current synaptic devices still consume energy that is orders of magnitude greater than do biological synapses (~10 fJ per synaptic event). Reduction of energy consumption of artificial synapses remains a difficult challenge. We report organic nanowire (ONW) synaptic transistors (STs) that emulate the important working principles of a biological synapse. The ONWs emulate the morphology of nerve fibers. With a core-sheath–structured ONW active channel and a well-confined 300-nm channel length obtained using ONW lithography, ~1.23 fJ per synaptic event for individual ONW was attained, which rivals that of biological synapses. The ONW STs provide a significant step toward realizing low-energy–consuming artificial intelligent electronics and open new approaches to assembling soft neuromorphic systems with nanometer feature size.

Keywords artificial synapse organic nanowire energy consumption organic electronics bio-inspired electronics short-term plasticity long-term plasticity
Copyright © 2016, The Authors

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

FREE PDF GRATIS: Science Advances Sup Info

Reconhecendo o paradoxo do sexo

segunda-feira, julho 04, 2016

On Recognising the Paradox of Sex

Joachim Dagg, Hausener Weg 25, 65760 Eschborn, Germany

e-mail: jdagg@gmx.de

SUBJECT TERMS 

cost of males, cost of meiosis, cost of sex, group selection, life-history 

theory, maintenance of recombination, maintenance of sex, population genetics

Article Type: Article

Volume 8, 2016


Received 24 April 2016; Accepted 1 May 2016

Abstract

George C. Williams and John Maynard Smith arrived at slightly different conclusions about the evolutionary maintenance of sexual reproduction, despite that both were staunch neo-Darwinians, simply because they approached the problem from different angles (life history vs. population genetics). This difference between their perspectives made them notice the so-called paradox of sexual reproduction for the first time. That is, Williams and Maynard Smith used their difference in perspective constructively, in order to raise a problem that had previously been overlooked by ‘monocular’ views. Evidence from before, during and after the recognition of the paradox supports this thesis of constructive difference. First, Maynard Smith had diagnosed the individual cost of sexual reproduction in full detail by 1958, but nobody raised an eyebrow for a decade. Second, both the correspondence between Williams and Maynard Smith and their publications show that they saw the same problem but against different backgrounds, because they viewed it from different perspectives. Third, further differences between Williams and Maynard Smith concerning the evolution of sex make no sense except in the light of the initial difference in their perspectives.

Darwin escreveu, mas não explicou a origem das espécies e não sabemos o que é!

sábado, julho 02, 2016



The Species Problem - Ongoing Issues

Edited by Igor Ya. Pavlinov, ISBN 978-953-51-0957-0, 290 pages, Publisher: InTech, Chapters published February 06, 2013 under CC BY 3.0 license

Edited Volume


The book includes collection of theoretical papers dealing with the species problem, which is among most fundamental issues in biology. The principal topics are: consideration of the species problem from the standpoint of modern non-classical science paradigm, with emphasis on its conceptual status presuming its analysis within certain conceptual framework; evolutionary emergence of the species as discrete unit of certain level of generality; epistemological consideration of the species as a particular explanatory hypotheses, with respective revised concepts of biodiversity and conservation; considerations of evolutionary and phylogenomic species concepts as candidates for the universal one; re-appraisal of the biological species concept based on the "friend-foe" recognition system; species delimitation approach using multi-locus coalescent-based method; a re-consideration of the Darwin's species concept.

BOOK CONTENTS BOOK EDITOR MOST DOWNLOADED CHAPTER SHOW TO LINK

Chapter 1  
by Igor Ya. Pavlinov

Chapter 2  
by Richard A. Richards

Chapter 3  
by Victor Prokhorovich Shcherbakov

Chapter 4  
by Kirk Fitzhugh

Chapter 5  
by James T. Staley

Chapter 6  
by Larissa N. Vasilyeva and Steven L. Stephenson

Chapter 7  
by Richard L. Mayden

Chapter 8  
by V. S. Friedmann

Chapter 9  
by Arley Camargo and Jack Jr. Sites

Chapter 10  
by David N. Stamos

Evolução da taxa de mutação de inserção-deleção por toda a Árvore da Vida

sexta-feira, julho 01, 2016

Evolution of the Insertion-Deletion Mutation Rate Across the Tree of Life

Way Sung1,*, Matthew S. Ackerman2, Marcus M. Dillon3, Thomas G. Platt4, Clay Fuqua2, Vaughn S. Cooper5 and Michael Lynch2,**

- Author Affiliations

1 University of North Carolina at Charlotte;

2 Indiana University;

3 University of New Hampshire;

4 Indiana University; Kansas State University;

5 University of Pittsburgh School of Medicine

↵*To whom correspondence should be addressed. E-mail: waysung@indiana.edu

↵** Co-corresponding Author; E-mail: milynch@indiana.edu

Abstract

Mutations are the ultimate source of variation used for evolutionary adaptation, while also being predominantly deleterious and a source of genetic disorders. Understanding the rate of insertiondeletion mutations (indels) is essential to understanding evolutionary processes, especially in coding regions where such mutations can disrupt production of essential proteins. Using direct estimates of insertion-deletion mutation rates from fourteen phylogenetically diverse eukaryotic and bacterial species, along with measures of standing variation in such species, we obtain results that imply an inverse relationship of the mutation rate and the effective population size. These results, which corroborate earlier observations on the base-substitution mutation rate, appear most compatible with the hypothesis that natural selection reduces mutation rates per effective genome to the point at which the power of random genetic drift (approximated by the inverse of effective population size) becomes overwhelming. Given that the substantial differences in the DNA metabolism pathways that give rise to these two types of mutations, this consistency of results raises the possibility that the refinement of other molecular and cellular traits may be inversely related to species-specific levels of random genetic drift.

drift barrier insertion-deletion mutation rate mutation accumulation mutation-rate evolution

Received May 8, 2016. Accepted June 13, 2016.

Copyright © 2016 Author et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Pequenas asas retidas em resina fóssil há 99 milhões de anos atrás revelam novos segredos das aves primitivas

Mummified precocial bird wings in mid-Cretaceous Burmese amber

Lida Xing, Ryan C. McKellar, Min Wang, Ming Bai, Jingmai K. O’Connor, Michael J. Benton, Jianping Zhang, Yan Wang, Kuowei Tseng, Martin G. Lockley, Gang Li, Weiwei Zhang & Xing Xu

Affiliations Contributions Corresponding authors

Nature Communications 7, Article number: 12089 doi: 10.1038/ncomms12089

Received 18 January 2016 Accepted 27 May 2016 Published 28 June 2016


Abstract

Our knowledge of Cretaceous plumage is limited by the fossil record itself: compression fossils surrounding skeletons lack the finest morphological details and seldom preserve visible traces of colour, while discoveries in amber have been disassociated from their source animals. Here we report the osteology, plumage and pterylosis of two exceptionally preserved theropod wings from Burmese amber, with vestiges of soft tissues. The extremely small size and osteological development of the wings, combined with their digit proportions, strongly suggests that the remains represent precocial hatchlings of enantiornithine birds. These specimens demonstrate that the plumage types associated with modern birds were present within single individuals of Enantiornithes by the Cenomanian (99 million years ago), providing insights into plumage arrangement and microstructure alongside immature skeletal remains. This finding brings new detail to our understanding of infrequently preserved juveniles, including the first concrete examples of follicles, feather tracts and apteria in Cretaceous avialans.

Subject terms: Biological sciences Evolution Palaeontology

Os artigos científicos em Biologia estão ficando cada vez mais difíceis???

Life Science’s Average Publishable Unit (APU) Has Increased over the Past Two Decades

Radames J. B. Cordero , Carlos M. de León-Rodriguez, John K. Alvarado-Torres, Ana R. Rodriguez, Arturo Casadevall


1 Instituto de Bioquímica Médica (IBqM) Leopoldo de Meis, CCS, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941902, Brasil, 

2 Department of Microbiology and Immunology, Albert Einstein College of
Medicine, Bronx, New York, 10461, United States of America, 

3 Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America, 

4 Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey, 08854, United States of America

¤ Current address: Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins, Bloomberg School of Public Health, Baltimore, MD, United States of America
* rcorder4@jhu.edu



Abstract

Quantitative analysis of the scientific literature is important for evaluating the evolution and state of science. To study how the density of biological literature has changed over the past two decades we visually inspected 1464 research articles related only to the biological sciences from ten scholarly journals (with average Impact Factors, IF, ranging from 3.8 to 32.1). By scoring the number of data items (tables and figures), density of composite figures (labeled panels per figure or PPF), as well as the number of authors, pages and references per research publication we calculated an Average Publishable Unit or APU for 1993, 2003, and 2013. The data show an overall increase in the average ± SD number of data items from 1993 to 2013 of approximately 7±3 to 14±11 and PPF ratio of 2±1 to 4±2 per article, suggesting that the APU has doubled in size over the past two decades. As expected, the increase in data items per article is mainly in the form of supplemental material, constituting 0 to 80% of the data items per publication in 2013, depending on the journal. The changes in the average number of pages (approx. 8±3 to 10±3), references (approx. 44±18 to 56±24) and authors (approx. 5±3 to 8±9) per article are also presented and discussed. The average number of data items, figure density and authors per publication are correlated with the journal’s average IF. The increasing APU size over time is important when considering the value of research articles for life scientists and publishers, as well as, the implications of these increasing trends in the mechanisms and economics of scientific communication.

Citation: Cordero RJB, de León-Rodriguez CM, Alvarado-Torres JK, Rodriguez AR, Casadevall A (2016) Life Science’s Average Publishable Unit (APU) Has Increased over the Past Two Decades. PLoS ONE 11(6): e0156983. doi:10.1371/journal.pone.0156983

Editor: Pablo Dorta-González, Universidad de Las Palmas de Gran Canaria, SPAIN

Received: May 8, 2015; Accepted: May 23, 2016; Published: June 16, 2016

Copyright: © 2016 Cordero et al. 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: A clean data set is available at https://github.com/rjbcg/AvgPubUnit.git.

Funding: RJBC was supported by "Science without Borders”—Young Talent Attraction Scholarship from the Conselho Nacional de Desenvolvimento Tecnológico (CnPq) e Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES).

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

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A ordem, complexidade e organização da vida, e seus imperativos termodinâmicos-holísticos

Life 2012, 2(4), 323-363; doi:10.3390/life2040323

Essay

Life’s Order, Complexity, Organization, and Its Thermodynamic–Holistic Imperatives

Richard Egel

Department of Biology, University of Copenhagen Biocenter, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark

Received: 10 September 2012 / Revised: 30 October 2012 / Accepted: 5 November 2012 / Published: 13 November 2012

View Full-Text | Download PDF [385 KB, uploaded 13 November 2012] | 


Abstract

In memoriam Jeffrey S. Wicken (1942–2002)—the evolutionarily minded biochemist, who in the 1970/80s strived for a synthesis of biological and physical theories to fathom the tentative origins of life. Several integrative concepts are worth remembering from Wicken’s legacy. (i) Connecting life’s origins and complex organization to a preexisting physical world demands a thermodynamically sound transition. (ii) Energetic ‘charging’ of the prebiosphere must precede the emergence of biological organization. (iii) Environmental energy gradients are exploited progressively, approaching maximum interactive structure and minimum dissipation. (iv) Dynamic self-assembly of prebiotic organic matter is driven by hydrophobic tension between water and amphiphilic building blocks, such as aggregating peptides from non-polar amino acids and base stacking in nucleic acids. (v) The dynamics of autocatalytic self-organization are facilitated by a multiplicity of weak interactions, such as hydrogen bonding, within and between macromolecular assemblies. (vi) The coevolution of (initially uncoded) proteins and nucleic acids in energy-coupled and metabolically active so-called ‘microspheres’ is more realistic as a kinetic transition model of primal biogenesis than ‘hypercycle replication’ theories for nucleic acid replicators on their own. All these considerations blend well with the current understanding that sunlight UV-induced photo-electronic excitation of colloidal metal sulfide particles appears most suitable as a prebiotic driver of organic synthesis reactions, in tight cooperation with organic, phase-separated, catalytic ‘microspheres’. On the ‘continuist vs. miraculist’ schism described by Iris Fry for origins-of-life considerations (Table 1), Wicken was a fervent early protagonist of holistic ‘continuist’ views and agenda.

Keywords: origin of life; far-from-equilibrium thermodynamics; agglutinative hydrophobic interactions; phase-separated catalytic microspheres; metabolic-replicative hypercycles; hyper-coupling between separate sequence spaces

This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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