Reconstrução filogenômica indica que o ancestral da mitocôndria era um parasita energético

quarta-feira, outubro 22, 2014

Phylogenomic Reconstruction Indicates Mitochondrial Ancestor Was an Energy Parasite

Zhang Wang, Martin Wu mail

Published: October 15, 2014DOI: 10.1371/journal.pone.0110685

Abstract

Reconstruction of mitochondrial ancestor has great impact on our understanding of the origin of mitochondria. Previous studies have largely focused on reconstructing the last common ancestor of all contemporary mitochondria (proto-mitochondria), but not on the more informative pre-mitochondria (the last common ancestor of mitochondria and their alphaproteobacterial sister clade). Using a phylogenomic approach and leveraging on the increased taxonomic sampling of alphaproteobacterial and eukaryotic genomes, we reconstructed the metabolisms of both proto-mitochondria and pre-mitochondria. Our reconstruction depicts a more streamlined proto-mitochondrion than these predicted by previous studies, and revealed several novel insights into the mitochondria-derived eukaryotic metabolisms including the lipid metabolism. Most strikingly, pre-mitochondrion was predicted to possess a plastid/parasite type of ATP/ADP translocase that imports ATP from the host, which posits pre-mitochondrion as an energy parasite that directly contrasts with the current role of mitochondria as the cell’s energy producer. In addition, pre-mitochondrion was predicted to encode a large number of flagellar genes and several cytochrome oxidases functioning under low oxygen level, strongly supporting the previous finding that the mitochondrial ancestor was likely motile and capable of oxidative phosphorylation under microoxic condition.

Citation: Wang Z, Wu M (2014) Phylogenomic Reconstruction Indicates Mitochondrial Ancestor Was an Energy Parasite. PLoS ONE 9(10): e110685. doi:10.1371/journal.pone.0110685

Editor: Frank Voncken, University of Hull, United Kingdom

Received: July 14, 2014; Accepted: September 22, 2014; Published: October 15, 2014

Copyright: © 2014 Wang, Wu. 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: The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files. The genome sequences have been deposited at DDBJ/EMBL/GenBank as follows: endosymbiont of acanthamoeba UWC8 (CP004403), Candidatus Caedibacter acanthamoebae (CP008936-CP008940), Candidatus Paracaedibacter acanthamoebae (CP008941-CP008942), Candidatus Paracaedibacter symbiosus (JQAK00000000) and NHP bacterium (JQAJ00000000).

Funding: This research was funded by an award from Thomas F. & Kate Miller Jeffress Memorial Trust to MW. The funder 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

Poderia ter existido vida 15 milhões de anos após o Big Bang? Loeb, de Harvard, diz que sim.

The Habitable Epoch of the Early Universe

Abraham Loeb (Harvard)

(Submitted on 2 Dec 2013 (v1), last revised 3 Jun 2014 (this version, v3))

Mere illustration/Mera ilustração

(Submitted on 2 Dec 2013 (v1), last revised 3 Jun 2014 (this version, v3))


Abstract


In the redshift range 100≲(1+z)≲137, the cosmic microwave background (CMB) had a temperature of 273–373 K (0–100°C), allowing early rocky planets (if any existed) to have liquid water chemistry on their surface and be habitable, irrespective of their distance from a star. In the standard ΛCDM cosmology, the first star-forming halos within our Hubble volume started collapsing at these redshifts, allowing the chemistry of life to possibly begin when the Universe was merely 10–17 million years old. The possibility of life starting when the average matter density was a million times bigger than it is today is not in agreement with the anthropic explanation for the low value of the cosmological constant.
Comments: 12 pages, accepted for publication in the International Journal of Astrobiology

Subjects: Cosmology and Nongalactic Astrophysics (astro-ph.CO); Earth and Planetary Astrophysics (astro-ph.EP); General Relativity and Quantum Cosmology (gr-qc); High Energy Physics - Phenomenology (hep-ph); High Energy Physics - Theory (hep-th)

Cite as: arXiv:1312.0613 [astro-ph.CO]
  (or arXiv:1312.0613v3 [astro-ph.CO] for this version)

Submission history

From: Avi Loeb [view email] 
[v1] Mon, 2 Dec 2013 21:00:18 GMT (6kb)
[v2] Thu, 16 Jan 2014 16:19:05 GMT (8kb)
[v3] Tue, 3 Jun 2014 20:56:38 GMT (8kb)

FREE PDF GRATIS: ArXiv

Origem da vida? Nossa ignorância científica acabou - basta fazer uma simulação em computador!

terça-feira, outubro 21, 2014

Issue  EPL 
Volume 107, Number 2, July 2014
Article Number 28004
Number of page(s) 6
Section Interdisciplinary Physics and Related Areas of Science and Technology
DOI http://dx.doi.org/10.1209/0295-5075/107/28004
Published online 15 July 2014

EPL, 107 (2014) 28004

Structure and selection in an autocatalytic binary polymer model

Shinpei Tanaka1, Harold Fellermann2,3 and Steen Rasmussen2,4
1 Graduate School of Integrated Arts and Sciences, Hiroshima University - 1-7-1 Kagamiyama, Higashi-Hiroshima 739-8521, Japan 

2 Center for Fundamental Living Technology (FLinT) Department of Physics, Chemistry and Pharmacy, University of Southern Denmark - Campusvej 55 5230 Odense M, Denmark 

3 School of Computing Science, Newcastle University - Claremont Tower, Newcastle upon Tyne, UK 

4 Santa Fe Institute - 1399 Hyde Park Rd, Santa Fe, NM 87501, USA 

Received: 17 March 2014
Accepted: 20 June 2014

Abstract

An autocatalytic binary polymer system is studied as an abstract model for a chemical reaction network capable to evolve. Due to autocatalysis, long polymers appear spontaneously and their concentration is shown to be maintained at the same level as that of monomers. When the reaction starts from a pool of monomers, highly ordered populations with particular sequence patterns are dynamically selected out of a vast number of possible states. The interplay between the selected microscopic sequence patterns and the macroscopic cooperative structures is examined both analytically and in simulation. Stability, fluctuations, and dynamic selection mechanisms are investigated for the involved self-organizing processes.

PACS: 87.23.Kg – Dynamics of evolution / 05.65.+b – Self-organized systems / 87.23.Cc – Population dynamics and ecological pattern formation

© EPLA, 2014

FREE PDF GRATIS: EPL

James Tour 'falou e disse': sobre a evolução ter dado origem à vida, eles só ficam me olhando!

segunda-feira, outubro 20, 2014

14 de outubro de 2014

Químico de renome: “Eles só ficam me olhando”

“Porque é uma coisa assustadora”

Ontem, James Tour, que em 2009 foi classificado como um dos 10 principais químicos no mundo, explicou que os evolucionistas não entendem como que a evolução poderia ter criado a vida. O que é pior, Tour explica que existe uma falta de clareza sobre este fato científico. Em público, os evolucionistas insistem que a evolução é um fato além de qualquer dúvida razoável. Mas em particular, eles admitem que não existe tal conhecimento científico:

“Deixe-me contar-lhe o que ocorre nos bastidores da ciência — com mebros da Academia Nacional de Ciências [dos Estados Unidos], com ganhadores de prêmio Nobel”, afirmou Tour. “Eu tenho sentado com eles, e quando eles estão sozinhos comigo, não em público — porque é uma coisa assustadora, se alguém disser o que eu acabei de dizer — eu digo, ‘Você entende tudo isso, de onde tudo isso veio, e como que isso acontece?’”

A resposta que ele recebe inevitavelmente, Tour explicou, é: “Não”.

“Todas as vezes que eu me sento com pessoas que são químicos sintéticos, que entendem disso, eles dizem, ‘Ah, de jeito nenhum’”, disse Tour. “E se elas têm medo de dizer ‘sim’, elas nada dizem. Elas simplesmente ficam me olhando, porque, sinceramente, elas não podem dizer isso.”

A verdade é uma coisa assustadora.

Postado por Cornelius Hunter em 14 de outubro de 2014

Darwin kaput e Lamarck redivivus: a epigenética e a evolução dos tentilhões das ilhas Galápagos

sexta-feira, outubro 17, 2014

Genome Biol Evol. Aug 2014; 6(8): 1972–1989.
Published online Jul 24, 2014. doi:  10.1093/gbe/evu158

Epigenetics and the Evolution of Darwin’s Finches

Michael K. Skinner,1,* Carlos Gurerrero-Bosagna,1,3 M. Muksitul Haque,1 Eric E. Nilsson,1 Jennifer A.H. Koop,2,4 Sarah A. Knutie,2 and Dale H. Clayton2

1Center for Reproductive Biology, School of Biological Sciences, Washington State University

2Department of Biology, University of Utah

3Present address: Department of Physics, Biology and Chemistry (IFM), Linköping University, Sweden

4Present address: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ

*Corresponding author: E-mail: ude.usw@renniks.

Associate editor: Bill Martin

Data deposition: All DMR and CNV genomic data obtained in this study have been deposited in the NCBI public GEO database under the accession (GEO #: GSE58334).



Abstract

The prevailing theory for the molecular basis of evolution involves genetic mutations that ultimately generate the heritable phenotypic variation on which natural selection acts. However, epigenetic transgenerational inheritance of phenotypic variation may also play an important role in evolutionary change. A growing number of studies have demonstrated the presence of epigenetic inheritance in a variety of different organisms that can persist for hundreds of generations. The possibility that epigenetic changes can accumulate over longer periods of evolutionary time has seldom been tested empirically. This study was designed to compare epigenetic changes among several closely related species of Darwin’s finches, a well-known example of adaptive radiation. Erythrocyte DNA was obtained from five species of sympatric Darwin’s finches that vary in phylogenetic relatedness. Genome-wide alterations in genetic mutations using copy number variation (CNV) were compared with epigenetic alterations associated with differential DNA methylation regions (epimutations). Epimutations were more common than genetic CNV mutations among the five species; furthermore, the number of epimutations increased monotonically with phylogenetic distance. Interestingly, the number of genetic CNV mutations did not consistently increase with phylogenetic distance. The number, chromosomal locations, regional clustering, and lack of overlap of epimutations and genetic mutations suggest that epigenetic changes are distinct and that they correlate with the evolutionary history of Darwin’s finches. The potential functional significance of the epimutations was explored by comparing their locations on the genome to the location of evolutionarily important genes and cellular pathways in birds. Specific epimutations were associated with genes related to the bone morphogenic protein, toll receptor, and melanogenesis signaling pathways. Species-specific epimutations were significantly overrepresented in these pathways. As environmental factors are known to result in heritable changes in the epigenome, it is possible that epigenetic changes contribute to the molecular basis of the evolution of Darwin’s finches.

Keywords: epimutations, DNA methylation, copy number variation, phylogeny, adaptive radiation, BMP, toll, melanogenesis

FREE PDF GRATIS: Genome Biol Evol

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Darwin kaput e Lamarck redivivus! A nova teoria geral da evolução - a Síntese Evolutiva Ampliada/Estendida, contrariando Darwin, não selecionista par excellence, e vai incorporar aspectos teóricos neolamarckistas, mas somente será anunciada em 2020.

Enquanto a nova teoria da evolução não vem, estão fazendo biologia sem referencial teórico? Mas, aprendemos nas universidades que a ciência abomina o vácuo epistêmico no contexto de justificação teórica... Abracadabra? Entranhas de galinhas? Búzios? Cartas de tarô? Leitura de mãos? Mágica?

Gente, o fato, Fato, FATO da evolução é ensinado como sendo tão cientificamente comprovado como a lei da gravidade e assim como a Terra gira em torno do Sol. E que não existe crise nenhuma na teoria da evolução. Nada mais falso! Basta ler a literatura científica especializada para ver que existem variações extremas de explicações da história evolucionárias das coisas vivas.

Fui, nem sei por que, rindo da cara de alguns cientistas da Nomenklatura científica que, sabem disso, mas fingem não saber, e da Galera dos meninos e meninas de Darwin, cada vez mais órfã. 

Design inteligente na arquitetura celular: a função da proteína GCP-WD na estrutura organizacional e funcional microtubular central

GCP-WD Mediates γ-TuRC Recruitment and the Geometry of Microtubule Nucleation in Interphase Arrays of Arabidopsis

Ankit Walia, Masayoshi Nakamura, Dorianne Moss, Viktor Kirik, Takashi Hashimoto, David W. Ehrhardt email

DOI: http://dx.doi.org/10.1016/j.cub.2014.09.013

Publication stage: In Press Corrected Proof

Highlights

•GCP-WD labels microtubule nucleation sites

•It is predominantly associated with the core γ-TuRC in interphase arrays

•GCP-WD function governs nucleation position, rate, and geometry in cortical arrays

•These functions are required to build arrays of specialized architecture



Summary

Many differentiated animal cells, and all higher plant cells, build interphase microtubule arrays of specific architectures without benefit of a central organizer, such as a centrosome, to control the location and geometry of microtubule nucleation. These acentrosomal arrays support essential cell functions such as morphogenesis [ 1, 2 ], but the mechanisms by which the new microtubules are positioned and oriented are poorly understood. In higher plants, nucleation of microtubules arises from distributed γ-tubulin ring complexes (γ-TuRCs) at the cell cortex that are associated primarily with existing microtubules [ 3–5 ] and from which new microtubules are nucleated in a geometrically bimodal fashion, either in parallel to the mother microtubule or as a branching event at a mean angle of approximately 40° to the mother microtubule. By imaging the dynamics of individual nucleation events in Arabidopsis, we found that a conserved peripheral protein of the γ-TuRC, GCP-WD/NEDD1 [ 6–8 ], associated with motile γ-TuRCs and localized to nucleation events. Knockdown of this essential protein resulted in reduction of γ-TuRC recruitment to cortical microtubules and total nucleation frequency, showing that GCP-WD controls γ-TuRC positioning and function in these interphase arrays. Further, we discovered an unexpected role for GCP-WD in determining the geometry of microtubule-dependent microtubule nucleation, where it acts to increase the likelihood of branching over parallel nucleation. Cells with normally complex patterns of cortical array organization constructed simpler arrays with cell-wide ordering, suggesting that control of nucleation frequency, positioning, and geometry by GCP-WD allows plant cells to build alternative cortical array architectures.

SOURCE/FONTE: Current Biology

Mudança paradigmática no entendimento dos canais de potássio: mais design inteligente!

Science 17 October 2014: 
Vol. 346 no. 6207 pp. 352-355 
DOI: 10.1126/science.1254840
REPORT
Ion permeation in K+ channels occurs by direct Coulomb knock-on

David A. Köpfer1,†, Chen Song2,*,†, Tim Gruene3, George M. Sheldrick3, Ulrich Zachariae4,5,*,‡, Bert L. de Groot1,*,‡

- Author Affiliations

1Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
2Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
3Department of Structural Chemistry, University of Göttingen, 37077 Göttingen, Germany.
4School of Engineering, Physics and Mathematics, University of Dundee, Dundee DD1 4HN, UK.
5College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.

↵*Corresponding author. E-mail: sc3210@gmail.com (C.S.); u.zachariae@dundee.ac.uk (U.Z.); bgroot@gwdg.de (B.L.d.G.)

↵† These authors contributed equally to this work.

↵‡ These authors contributed equally to this work.



Abstract

Potassium channels selectively conduct K+ ions across cellular membranes with extraordinary efficiency. Their selectivity filter exhibits four binding sites with approximately equal electron density in crystal structures with high K+ concentrations, previously thought to reflect a superposition of alternating ion- and water-occupied states. Consequently, cotranslocation of ions with water has become a widely accepted ion conduction mechanism for potassium channels. By analyzing more than 1300 permeation events from molecular dynamics simulations at physiological voltages, we observed instead that permeation occurs via ion-ion contacts between neighboring K+ ions. Coulomb repulsion between adjacent ions is found to be the key to high-efficiency K+ conduction. Crystallographic data are consistent with directly neighboring K+ ions in the selectivity filter, and our model offers an intuitive explanation for the high throughput rates of K+ channels.

Received for publication 15 April 2014.

Accepted for publication 27 August 2014.

SOURCE/FONTE: Science

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Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao site CAPES/Periódicos podem ler gratuitamente este artigo da Science e de mais 22.440 publicações científicas.

Super Homem molecular protege o genoma de danos - 100% design inteligente!

Dicer Promotes Transcription Termination at Sites of Replication Stress to Maintain Genome Stability

Stephane E. Castel4, Jie Ren4, Sonali Bhattacharjee, An-Yun Chang, Mar Sánchez, Alberto Valbuena, Francisco Antequera, Robert A. Martienssen email 4 Co-first author

DOI: http://dx.doi.org/10.1016/j.cell.2014.09.031

Highlights

•Dcr1 has a genome-wide role in terminating Pol II transcription

•Dcr1 termination occurs at highly transcribed protein coding genes, tDNA, and rDNA

•Targets are sites of transcription-replication collisions with DNA damage

•Dcr1 resolves collisions, preventing restart by HR, maintaining genomic stability



Summary

Nuclear RNAi is an important regulator of transcription and epigenetic modification, but the underlying mechanisms remain elusive. Using a genome-wide approach in the fission yeast S. pombe, we have found that Dcr1, but not other components of the canonical RNAi pathway, promotes the release of Pol II from the 3′ end of highly transcribed genes, and, surprisingly, from antisense transcription of rRNA and tRNA genes, which are normally transcribed by Pol I and Pol III. These Dcr1-terminated loci correspond to sites of replication stress and DNA damage, likely resulting from transcription-replication collisions. At the rDNA loci, release of Pol II facilitates DNA replication and prevents homologous recombination, which would otherwise lead to loss of rDNA repeats especially during meiosis. Our results reveal a novel role for Dcr1-mediated transcription termination in genome maintenance and may account for widespread regulation of genome stability by nuclear RNAi in higher eukaryotes.

SOURCE/FONTE: Cell

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Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao site CAPES/Periódicos podem ler gratuitamente este artigo da Cell e de mais 22.440 publicações científicas.

Pesquisa derruba teoria evolucionária da origem das mitocôndrias: as "usinas de força" celulares já foram parasitas de energia

Phylogenomic Reconstruction Indicates Mitochondrial Ancestor Was an Energy Parasite

Zhang Wang, Martin Wu mail

Published: October 15, 2014DOI: 10.1371/journal.pone.0110685




Abstract

Reconstruction of mitochondrial ancestor has great impact on our understanding of the origin of mitochondria. Previous studies have largely focused on reconstructing the last common ancestor of all contemporary mitochondria (proto-mitochondria), but not on the more informative pre-mitochondria (the last common ancestor of mitochondria and their alphaproteobacterial sister clade). Using a phylogenomic approach and leveraging on the increased taxonomic sampling of alphaproteobacterial and eukaryotic genomes, we reconstructed the metabolisms of both proto-mitochondria and pre-mitochondria. Our reconstruction depicts a more streamlined proto-mitochondrion than these predicted by previous studies, and revealed several novel insights into the mitochondria-derived eukaryotic metabolisms including the lipid metabolism. Most strikingly, pre-mitochondrion was predicted to possess a plastid/parasite type of ATP/ADP translocase that imports ATP from the host, which posits pre-mitochondrion as an energy parasite that directly contrasts with the current role of mitochondria as the cell’s energy producer. In addition, pre-mitochondrion was predicted to encode a large number of flagellar genes and several cytochrome oxidases functioning under low oxygen level, strongly supporting the previous finding that the mitochondrial ancestor was likely motile and capable of oxidative phosphorylation under microoxic condition.

FREE PDF GRATIS: PLoS One

7th International Workshop on Thermodynamics, Disequilibrium and Evolution

quinta-feira, outubro 16, 2014



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Integrantes do grupo focal sobre termodinâmica, desequilíbrio e evolução (TDE) do Nasa Astrobiology Institute, fundado em 2010, reuniram-se pela primeira vez no Brasil, nos dias 24 e 25 de setembro, no Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), em Campinas (SP).

Neddy participou deste workshop. 


Lançado o mais novo livro de Franklin M. Harold - In Search of Cell History

quarta-feira, outubro 15, 2014

In Search of Cell History

THE EVOLUTION OF LIFE'S BUILDING BLOCKS

FRANKLIN M. HAROLD

304 pages | 23 halftones, 12 line drawings | 6 x 9 | © 2014

The origin of cells remains one of the most fundamental problems in biology, one that over the past two decades has spawned a large body of research and debate. With In Search of Cell History, Franklin M. Harold offers a comprehensive, impartial take on that research and the controversies that keep the field in turmoil.

Written in accessible language and complemented by a glossary for easy reference, this book investigates the full scope of cellular history. Assuming only a basic knowledge of cell biology, Harold examines such pivotal subjects as the relationship between cells and genes; the central role of bioenergetics in the origin of life; the status of the universal tree of life with its three stems and viral outliers; and the controversies surrounding the last universal common ancestor. He also delves deeply into the evolution of cellular organization, the origin of complex cells, and the incorporation of symbiotic organelles, and considers the fossil evidence for the earliest life on earth. In Search of Cell History shows us just how far we have come in understanding cell evolution—and the evolution of life in general—and how far we still have to go.


REVIEW QUOTES


Nick Lane | University College London and author of "Life Ascending: The Ten Great Inventions of Evolution"

“This book is a rare pleasure: a beautiful, rational, wise, and eloquent framing of life’s Average mysteries, what remains to be known, and how we might get there. It should be read by anyone who wonders, seriously, how we came to be. If it does not provide all the answers, that is because we honestly do not know.

Moselio Schaechter, Distinguished Professor, emeritus | Tufts University

“When dealing with difficult questions such as the origin of life, one yearns for writing that is both sagacious and readable, two qualities that don’t always go together. Fortunately, we can forego the need for making a choice. Harold’s book provides an account that is both masterful in the pursuit of the very question and in the clarity with which he unravels relevant phenomena. I daresay that few more helpful guides to a complex terrain have come forth since Dante’s Beatrice.”

Mark A. Farmer | University of Georgia

The origin of life is one of the great enigmas yet to yield to modern science. While there are other books that attempt to place their own spin on how life came about, In Search of Cell History stands alone in that it is written not by one of those advocating a particular viewpoint but instead by one who tries to remain a detached, albeit extremely well informed, observer of events. An excellent piece of scholarly work by a suitably unbiased and appropriately skeptical researcher.”

Biological Sciences: Biochemistry | Microbiology


CONTENTS


Contents
Preface
Acknowledgments

Chapter 1: Cells, Genes, and Evolution
(On the Nature and Workings of Life)

Chapter 2: The Tree of Life
(Universal Phylogeny and Its Discontents)

Chapter 3: A World Mostly Made Up of Microbes
(Bacteria, Archaea, and Eukarya)

Chapter 4: The Deep Roots of Cellular Life
(The Common Ancestry of Living Things)

Chapter 5: The Perplexing Chronicles of Bioenergetics
(Making a Living, Now and in the Past)

Chapter 6: Life’s Devices
(On the Evolution of Prokaryotic Cells and Their Parts)

Chapter 7: Emergence of the Eukaryotes
(The Second Mystery in Cell Evolution)

Chapter 8: Symbionts into Organelles
(Mitochondria, Plastids, and Their Kin)

Chapter 9: Reading the Rocks
(What We Can Infer from Geology)

Chapter 10: Ultimate Riddle
(Origin of Cellular Life)

Chapter 11: The Crooked Paths of Cell Evolution
(Cell Evolution Is Special)

Chapter 12: Summing Up: Journey without Maps

Notes
Glossary
References
Index

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Realização experimental de inteligência artificial quântica

Experimental Realization of Quantum Artificial Intelligence

Machines are possible to have some artificial intelligence like human beings owing to particular algorithms or software. Such machines could learn knowledge from what people taught them and do works according to the knowledge. In practical learning cases, the data is often extremely complicated and large, thus classical learning machines often need huge computational resources. Quantum machine learning algorithm, on the other hand, could be exponentially faster than classical machines using quantum parallelism. Here, we demonstrate a quantum machine learning algorithm on a four-qubit NMR test bench to solve an optical character recognition problem, also known as the handwriting recognition. The quantum machine learns standard character fonts and then recognize handwritten characters from a set with two candidates. To our Most Unexceptional knowledge, this is the first artificial intelligence realized on a quantum processor. Due to the widespreading importance of artificial intelligence and its tremendous consuming of computational resources, quantum speedup would be extremely attractive against the challenges from the Big Data.
Comments:7 pages, 4 figures
Subjects:Quantum Physics (quant-ph)
Cite as:arXiv:1410.1054 [quant-ph]
 (or arXiv:1410.1054v1 [quant-ph] for this version)

Submission history

From: Jiangfeng Du [view email] 
[v1] Sat, 4 Oct 2014 15:55:56 GMT (832kb,D)

FREE PDF GRATIS: ArXiv

Rafael Garcia noticia atrasado a mudança teórica em Biologia Evolutiva amplamente discutida neste blog desde 2006

terça-feira, outubro 14, 2014

Vem aí a nova biologia. Ou não.

POR RAFAEL GARCIA
14/10/14  08:00



NOTÍCIAS SOBRE BIOLOGIA voltadas ao público geral com frequência fazem referência à briga de acadêmicos contra o criacionismo –o movimento defensor de que seres vivos foram criados por Deus, não pelos processos descritos na teoria da evolução. Ofuscado por essa discussão infrutífera de cientistas lançando argumentos racionais contra mentes religiosas impenetráveis, porém, existe um debate sério sobre se a biologia evolutiva está ou não carente de atualização.

Esse movimento defende que a chamada “nova síntese” –a teoria da evolução de Darwin reformulada à luz da genética e, depois, da biologia molecular– precisa ser recauchutada. Liderados por biólogos como Gerd Muller, da Universidade de Viena, e Eva Jablonka, da Universidade de Tel Aviv, esses pesquisadores defendem aquilo que batizaram de EES (Síntese Evolucionária Estendida). É um corpo de conhecimento baseado em fenômenos que correm paralelamente aos descritos pela seleção natural de Darwin. Mas seria esta nova biologia algo com força suficiente para tornar a nova síntese uma teoria ultrapassada?

Para defender uma mudança radical, Jablonka recorre a fenômenos como a epigenética –transmissão de características que não requer mudança do DNA– e à construção de nichos –capacidade de animais de alterarem seu próprio ambiente e, portanto, modificar as pressões que a seleção natural exerceria sobre eles mesmos. Também são alvo de estudo da EES o “viés de desenvolvimento” –a impossibilidade de organismos de adquirirem certas formas enquanto evoluem– e a plasticidade –capacidade de um indivíduo de adquirir diferentes formas reagindo a seu ambiente.

Todos esses fenômenos, que são tratados pela (velha) nova síntese apenas como processos marginais, seriam sinal de que uma teoria de evolução com excesso de foco na biologia molecular se tornou incapaz de dar conta da explicação de processos que ocorrem sem interação com o DNA. Só a incorporação desses outros fenômenos, argumentam, pode salvar a teoria da evolução de se tornar algo ultrapassado.
...

LEIA O TEXTO COMPLETO DA FOLHA DE SÃO PAULO AQUI.

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NOTA DESTE BLOGGER:

Sempre afirmei aqui que a Grande Mídia vive uma relação incestuosa com a Nomenklatura científica quando a questão é Darwin. Ler um artigo desses é prova mais do que evidente de que os editores de ciência e jornalistas científicos estão convencidos da robustez da teoria da evolução de Darwin através da seleção natural e n mecanismos evolucionários de A a Z (vai que um falhe...) e que, mesmo sabedores dos estertores epistêmicos dessa teoria, nesses quase dez anos, nada publicaram a respeito, embora este blog e outros têm aqui e ali, desde 2006, que uma iminente e eminente mudança paradigmática em biologia evolutiva estava em curso. 

Rafael Garcia lê este blog há anos. Estava muito bem informado a respeito dessa questão fundamental de que uma séria e profunda revisão na teoria geral da evolução estava e está sendo engendrada pela Academia. Anunciamos que ela não será selecionista e deverá incorporar alguns aspectos teóricos neolamarckistas, mas será somente anunciada em 2020.

Garcia não abordou, mas se a Síntese Evolutiva Ampliada/Estendida não incorporar a informação genética no seu arcabouço teórico, essa nova Síntese será natimorta, pois a Biologia dos séculos 20 e 21 é uma biologia de informação. Além disso, nem mencionou o que significa trabalhar em Biologia Evolucionária sem um referencial teórico, e o que isso representa, pois a ciência abomina o vazio epistêmico. Enquanto a Síntese Evolutiva Ampliada/Estendida não vem, como está sendo feita biologia evolucionária? Abracadabra? Entranhas de galinha? Búzios? Cartas de Tarô?

Ao mencionar Ernst Mayr, Garcia deixou de fora o que o Darwin do Século 20 disse sobre a Biologia Evolucionária, e aqui é a minha leitura feita do seu livro, Biologia, ciência única (esgotado):
Um ponto inicial é a importância das narrativas históricas para a Biologia Evolutiva - uma Ciência Histórica que difere muito das Ciências Exatas, na conceituação e na metodologia, preocupando-se com os fenômenos: origem das novidades evolutivas, extinção de espécies, diversidade orgânica e a explicação das tendências e taxas evolutivas. 

Ora, não sendo uma ciência dura, a Biologia evolutiva não tem como explicar tais fenômenos a partir de Leis e experimentos que são, geralmente, inapropriados ou ineficientes. 

Então, segundo Mayr, a princípio forma-se uma narrativa histórica (cenário) e numa próxima fase testa-se a sua validade através da comparação das evidências.

Stephen Jay Gould chamou isso de "just-so stories" (estórias da carochinha)...

Quando a eugenia (racismo) era ciência: influência da teoria da evolução de Darwin

When Racism Was a Science

'Haunted Files: The Eugenics Record Office' Recreates a Dark Time in a Laboratory's Past

By JOSHUA A. KRISCHOCT. 13, 2014

The Eugenics Record Office, in the 1920s, on Long Island. Credit Cold Spring Harbor Laboratory and the Eugenics Image Archive, Dolan DNA Learning Center


An old stucco house stands atop a grassy hill overlooking the Long Island Sound. Less than a mile down the road, the renowned Cold Spring Harbor Laboratory bustles with more than 600 researchers and technicians, regularly producing breakthroughs in genetics, cancer and neuroscience.

But that old house, now a private residence on the outskirts of town, once held a facility whose very name evokes dark memories: the Eugenics Record Office.

In its heyday, the office was the premier scientific enterprise at Cold Spring Harbor. There, bigoted scientists applied rudimentary genetics to singling out supposedly superior races and degrading minorities. By the mid-1920s, the office had become the center of the eugenics movement in America.

Today, all that remains of it are files and photographs — reams of discredited research that once shaped anti-immigration laws, spurred forced-sterilization campaigns and barred refugees from entering Ellis Island. Now, historians and artists at New York University are bringing the eugenics office back into the public eye.


Charts that purported to track the inheritance of insanity and feeblemindedness.CreditAmerican Philosophical Society

Haunted Files: The Eugenics Record Office,” a new exhibit at the university’s Asian/Pacific/American Institute, transports visitors to 1924, the height of the eugenics movement in the United States. Inside a dimly lit room, the sounds of an old typewriter click and clack, a teakettle whistles and papers shuffle. The office’s original file cabinets loom over reproduced desks and period knickknacks. Creaky cabinets slide open, and visitors are encouraged to thumb through copies of pseudoscientific papers.

“There’s a haunted quality, that’s the nature of the files,” said John Kuo Wei Tchen, a historian at N.Y.U. and co-curator of the exhibit. (This reporter is a student at the Arthur L. Carter Journalism Institute, a separate branch of the university.) “We hoped we could evoke a visceral feeling of what it was like to be in a detention center, where people were presumed to be ineligible unless proven otherwise.”

When the Eugenics Record Office opened its doors in 1910, the founding scientists were considered progressives, intent on applying classic genetics to breeding better citizens. Funding poured in from the Rockefeller family and the Carnegie Institution. Charles Davenport, a prolific Harvard biologist, and his colleague, Harry H. Laughlin, led the charge.

“There were many prominent New Yorkers involved in eugenics,” Dr. Tchen said. “It was initially about how to become more efficient as a modern society.”

Researchers sought out “unfit” families in the Manhattan slums and the Pine Barrens of New Jersey. They cataloged disabilities and undesirable traits, scribbling the exact dimensions of heads and arms.

Psychiatric institutes sent crates of case files to the office, where the chief characteristics of “the feebleminded” were collated into pedigree charts. Davenport himself devised a sophisticated apparatus to quantify skin color.
...

Read more here/Leia mais aqui: The New York Times

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Ideias têm consequências, mesmo as científicas. Não há como negar a influência da teoria da evolução de Darwin no fortalecimento do preconceito racial que resultou no Holocausto da Segunda Guerra Mundial.

A hipótese de multiverso pode ser cientificamente testada?

Pesquisa demonstra: a aptidão evolucionária não é o fator determinante mais importante de sucesso evolutivo

segunda-feira, outubro 13, 2014

The Arrival of the Frequent: How Bias in Genotype-Phenotype Maps Can Steer Populations to Local Optima

Steffen Schaper, Ard A. Louis mail

Published: February 05, 2014DOI: 10.1371/journal.pone.0086635



An illustration of the possible mutations available to an RNA molecule. 

Abstract


Genotype-phenotype (GP) maps specify how the random mutations that change genotypes generate variation by altering phenotypes, which, in turn, can trigger selection. Many GP maps share the following general properties: 1) The total number of genotypes  is much larger than the number of selectable phenotypes; 2) Neutral exploration changes the variation that is accessible to the population; 3) The distribution of phenotype frequencies , with  the number of genotypes mapping onto phenotype , is highly biased: the majority of genotypes map to only a small minority of the phenotypes. Here we explore how these properties affect the evolutionary dynamics of haploid Wright-Fisher models that are coupled to a random GP map or to a more complex RNA sequence to secondary structure map. For both maps the probability of a mutation leading to a phenotype  scales to first order as , although for the RNA map there are further correlations as well. By using mean-field theory, supported by computer simulations, we show that the discovery time  of a phenotype similarly scales to first order as  for a wide range of population sizes and mutation rates in both the monomorphic and polymorphic regimes. These differences in the rate at which variation arises can vary over many orders of magnitude. Phenotypic variation with a larger is therefore be much more likely to arise than variation with a small . We show, using the RNA model, that frequent phenotypes (with larger ) can fix in a population even when alternative, but less frequent, phenotypes with much higher fitness are potentially accessible. In other words, if the fittest never ‘arrive’ on the timescales of evolutionary change, then they can't fix. We call this highly non-ergodic effect the ‘arrival of the frequent’.
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FREE PDF GRATIS: PLoS One

Respostas aos críticos do Design Inteligente

Respostas aos Críticos do Design Inteligente

Os argumentos a favor do design inteligente na natureza foram refutados? A evidência a favor da teoria darwinista moderna é tão imensa que nenhuma pessoa racional pode questioná-la? A ciência refutou a fé?
Os cientistas e scholars afiliados com o Center for Science and Culture [Centro para Ciência e Cultura] têm inspirado discussão ao redor do mundo sobre essas questões ao proporem que nós podemos detector evidência de design inteligente na natureza, ao criticarem as deficiências da teoria darwinista moderna, e por desafiarem tais abusos da ciência como o “Darwinismo Social”, e a afirmação equivocada de que a ciência se opõe à fé.
Nós valorizamos o debate aberto e honesto, e não ficamos ofendidos quando as pessoas criticam nossas visões. Isso é parte saudável de uma sociedade livre. Nós apenas pedimos que as pessoas sejam de mentes abertas o suficiente para ouvir o que nós estamos dizendo bem como os nossos críticos.
Talvez você tenha lido ou ouvido uma crítica de algo que algum de nossos cientistas escreveu. Se assim for, nós convidamos você a continuar com sua investigação, explorando como que nós respondemos.
Abaixo, nós destacamos algumas das principais áreas do debate onde você possa estar procurando por uma resposta. Se você não achar aqui o que você está procurando, tente a nossa base de busca de artigos, que lhe dará acesso à base de dados de milhares de artigos adicionais. Se você estiver procurando por uma resposta de alguma afirmação, as chances são de que você será capaz de encontra-la através de nossa base de busca de artigos.

Debates científicos


Respostas às Críticasdo livro Signature in the Cell: DNA and the Evidence of Intelligent Design





Respostas às Críticas do livro Icons of Evolution

Debates Culturais e Políticas Públicas


Respostas às Falsas Afirmações sobre o “Documento Wedge” e as Acusações Falsas sobre “Teocracia”

Respostas às Críticas do Documentário “Expelled” [Expulsos]

Respostas aos Filmes e Documentários


Respostas às Críticas do Documentário “Expelled” [Expulsos] (2008)

Respostas ao documentário da PBS “Judgment Day: Intelligent Design on Trial” (2007)

Respostas ao filme “Flock of Dodos” (2006)