Origens de genes de novo em humanos e chimpanzés

Origins of de novo genes in human and chimpanzee

Jorge Ruiz-Orera, Jessica Hernandez-Rodriguez, Cristina Chiva, Eduard Sabidó, Ivanela Kondova, Ronald Bontrop, Tomàs Marqués-Bonet, M. Mar Albà

(Submitted on 28 Jul 2015)

ABSTRACT

The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that do not contain any gene or gene copy. Some of these newly expressed genes may acquire coding or non-coding functions and be preserved by natural selection. However, it is yet unclear which is the prevalence and underlying mechanisms of de novo gene emergence. In order to obtain a comprehensive view of this process we have performed in-depth sequencing of the transcriptomes of four mammalian species, human, chimpanzee, macaque and mouse, and subsequently compared the assembled transcripts and the corresponding syntenic genomic regions. This has resulted in the identification of over five thousand new transcriptional multiexonic events in human and/or chimpanzee that are not observed in the rest of species. By comparative genomics we show that the expression of these transcripts is associated with the gain of regulatory motifs upstream of the transcription start site (TSS) and of U1 snRNP sites downstream of the TSS. We also find that the coding potential of the new genes is higher than expected by chance, consistent with the presence of protein-coding genes in the dataset. Using available human tissue proteomics and ribosome profiling data we identify several de novo genes with translation evidence. These genes show significant purifying selection signatures, indicating that they are probably functional. Taken together, the data supports a model in which frequently-occurring new transcriptional events in the genome provide the raw material for the evolution of new proteins.

Comments: 25 pages, 4 figures, 2 tables

Subjects: Genomics (q-bio.GN)

Cite as: arXiv:1507.07744 [q-bio.GN]

(or arXiv:1507.07744v1 [q-bio.GN] for this version)

FREE PDF GRATIS: ArXiv

Mais um modelo sobre a origem da vida: emergência espontânea de polímeros de codificação de informação autocatalítica

Spontaneous emergence of autocatalytic information-coding polymers

Alexei V. Tkachenko 1,a) and Sergei Maslov 2,3,b)

1 Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, USA

2 Biological, Environmental and Climate Sciences Department, Brookhaven National Laboratory, Upton, New York 11973, USA

3 Department of Bioengineering, University of Illinois at Urbana-Champaign, 1270 Digital Computer Laboratory, MC-278, Urbana, Illinois 61801, USA

a) Electronic mail: oleksiyt@bnl.gov

b) Electronic mail: ssmaslov@gmail.com

J. Chem. Phys. 143, 045102 (2015);

http://dx.doi.org/10.1063/1.4922545

ABSTRACT

Self-replicating systems based on information-coding polymers are of crucial importance in biology. They also recently emerged as a paradigm in material design on nano- and micro-scales. We present a general theoretical and numerical analysis of the problem of spontaneous emergence of autocatalysis for heteropolymers capable of template-assisted ligation driven by cyclic changes in the environment. Our central result is the existence of the first order transition between the regime dominated by free monomers and that with a self-sustaining population of sufficiently long chains. We provide a simple, mathematically tractable model supported by numerical simulations, which predicts the distribution of chain lengths and the onset of autocatalysis in terms of the overall monomer concentration and two fundamental rate constants. Another key result of our study is the emergence of the kinetically limited optimal overlap length between a template and each of its two substrates. The template-assisted ligation allows for heritable transmission of the information encoded in chain sequences thus opening up the possibility of long-term memory and evolvability in such systems.

FREE PDF GRATIS: The Journal of Chemical Physics

Área do cérebro humano difere dos primatas não humanos: somos únicos!

Representation of Numerical and Sequential Patterns in Macaque and Human Brains

Liping Wangcorrespondenceemail, Lynn Uhrig, Bechir Jarraya, Stanislas Dehaenecorrespondenceemail

Publication stage: In Press Corrected Proof

DOI: http://dx.doi.org/10.1016/j.cub.2015.06.035

Macaque monkey brain

Source/Fonte: UCL/Grant Museum/SPL

Highlights

•The monkey brain is capable of representing numerical and sequence patterns

•fMRI responses to number and to sequence are segregated in the monkey

•The human inferior frontal gyrus responds to both types of patterns

•Humans and monkeys differ even in a simple sequence learning paradigm

Summary

The ability to extract deep structures from auditory sequences is a fundamental prerequisite of language acquisition. Using fMRI in untrained macaques and humans, we investigated the brain areas involved in representing two abstract properties of a series of tones: total number of items and tone-repetition pattern. Both species represented the number of tones in intraparietal and dorsal premotor areas and the tone-repetition pattern in ventral prefrontal cortex and basal ganglia. However, we observed a joint sensitivity to both parameters only in humans, within bilateral inferior frontal and superior temporal regions. In the left hemisphere, those sites coincided with areas involved in language processing. Thus, while some abstract properties of auditory sequences are available to non-human primates, a recently evolved circuit may endow humans with a unique ability for representing linguistic and non-linguistic sequences in a unified manner.

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Regiões ordenadas de canais de nucleoporinas formam complexos dinâmicos em solução: show de design inteligente!

Ordered Regions of Channel Nucleoporins Nup62, Nup54, and Nup58 Form Dynamic Complexes in Solution*

Alok Sharma1, Sozanne R. Solmaz12, Günter Blobel3 and Ivo Melčák4

From the Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065

↵3 An Investigator of the Howard Hughes Medical Institute. To whom correspondence may be addressed: Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY 10065. Tel.: 212-327-8096; Fax: 212-327-7880; E-mail: blobel{at}rockefeller.edu.

↵4 To whom correspondence may be addressed: Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Ave., New York, NY 10065. Tel.: 212-327-8181; Fax: 212-327-7880; E-mail: melcaki{at}rockefeller.edu.

↵1 Both authors contributed equally to this work.

↵2 Present address: Dept. of Chemistry, State University of New York at Binghamton, P. O. Box 6000, Binghamton, NY, 13902.

Background: The ordered region (∼150–200 residues) of each channel nucleoporin is subdivided into segments of ∼40–80 residues.

Results: In solution, ordered regions associate into dynamic and heterogeneous complexes utilizing previously identified interactions between cognate segments.

Conclusion: Solution data are consistent with channel model reconstructed from crystal structures of cognate segments.

Significance: Data support the “ring cycle” model for dilation and constriction of the nuclear pore channel.

Abstract

Three out of ∼30 nucleoporins, Nup62, Nup54, and Nup58, line the nuclear pore channel. These “channel” nucleoporins each contain an ordered region of ∼150–200 residues, which is predicted to be segmented into 3–4 α-helical regions of ∼40–80 residues. Notably, these segmentations are evolutionarily conserved between uni- and multicellular eukaryotes. Strikingly, the boundaries of these segments match our previously reported mapping and crystal data, which collectively identified two “cognate” segments of Nup54, each interacting with cognate segments, one in Nup58 and the other one in Nup62. Because Nup54 and Nup58 cognate segments form crystallographic hetero- or homo-oligomers, we proposed that these oligomers associate into inter-convertible “mid-plane” rings: a single large ring (40–50 nm diameter, consisting of eight hetero-dodecamers) or three small rings (10–20 nm diameter, each comprising eight homo-tetramers). Each “ring cycle” would recapitulate “dilation” and “constriction” of the nuclear pore complex's central transport channel. As for the Nup54·Nup62 interactome, it forms a 1:2 triple helix (“finger”), multiples of which project alternately up and down from mid-plane ring(s). Collectively, our previous crystal data suggested a copy number of 128, 64, and 32 for Nup62, Nup54, and Nup58, respectively, that is, a 4:2:1 stoichiometry. Here, we carried out solution analysis utilizing the entire ordered regions of Nup62, Nup54, and Nup58, and demonstrate that they form a dynamic “triple complex” that is heterogeneously formed from our previously characterized Nup54·Nup58 and Nup54·Nup62 interactomes. These data are consistent both with our crystal structure-deduced copy numbers and stoichiometries and also with our ring cycle model for structure and dynamics of the nuclear pore channel.

Key words: biophysics cell biology nuclear pore nuclear transport protein assembly FG nucleoporins Light scattering Nuclear Pore Complex Ring cycle hypothesis Transport channel

FREE PDF GRATIS: Journal of Biological Chemistry

Um quebra-cabeça celular: a estranha e maravilhosa arquitetura do RNA

A cellular puzzle: The weird and wonderful architecture of RNA

Cells contain an ocean of twisting and turning RNA molecules. 

Now researchers are working out the structures — and how important they could be.

Elie Dolgin

22 July 2015

Illustration by Nik Spencer/Nature; structures courtesy Harry Noller, UCSC

When Philip Bevilacqua decided to work out the shapes of all the RNA molecules in a living plant cell, he faced two problems. First, he had not studied plant biology since high school. And second, biochemists had tended to examine single RNA molecules; tackling the multitudes that waft around in a cell was a much thornier challenge.

Bevilacqua, an RNA chemist at Pennsylvania State University in University Park, was undeterred. He knew that RNA molecules were vital regulators of cell biology and that their structures might offer broad lessons about how they work. He brushed up on plant anatomy in an undergraduate course and worked with molecular plant biologist Sarah Assmann to develop a technique that could cope with RNAs at scale.

In November 2013, they and their teams became the first to describe the shapes of thousands of RNAs in a living cell — revealing a veritable sculpture garden of different forms in the weedy thale cress, Arabidopsis thaliana¹. One month later, a group at the University of California, San Francisco, reported a comparable study of yeast and human cells². The number of RNA structures they managed to resolve was “unprecedented”, says Alain Laederach, an RNA biologist at the University of North Carolina at Chapel Hill (UNC)....

FREE PDF GRATIS: NATURE

Regulação da amplificação do DNA ribossomal pela via TOR

Regulation of ribosomal DNA amplification by the TOR pathway

Carmen V. Jack a,1, Cristina Cruz a,1, Ryan M. Hull a, Markus A. Keller b, Markus Ralser b,c, and Jonathan Houseley a,2

a Epigenetics Programme, The Babraham Institute, Cambridge CB22 3AT, United Kingdom;

b Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom;

c Division of Physiology and Metabolism, Medical Research Council National Institute for Medical Research, London NW7 1AA, United Kingdom

Edited by Jasper Rine, University of California, Berkeley, CA, and approved June 26, 2015 (received for review March 27, 2015)

Significance

We tend to think of our genome as an unchanging store of information; however, recent evidence suggests that genomes vary between different cells in the same organism. How these differences arise and what effects they have remain unknown, but clearly our genome can change. In a single-celled organism, genome changes occur at random, and advantageous changes slowly propagate by natural selection. However, it is known that the DNA encoding ribosomes can change simultaneously in a whole population. Here we show that signaling pathways that sense environmental nutrients control genome change at the ribosomal DNA. This demonstrates that not all genome changes occur at random and that cells possess specific mechanisms to optimize their genome in response to the environment.

Abstract

Repeated regions are widespread in eukaryotic genomes, and key functional elements such as the ribosomal DNA tend to be formed of high copy repeated sequences organized in tandem arrays. In general, high copy repeats are remarkably stable, but a number of organisms display rapid ribosomal DNA amplification at specific times or under specific conditions. Here we demonstrate that target of rapamycin (TOR) signaling stimulates ribosomal DNA amplification in budding yeast, linking external nutrient availability to ribosomal DNA copy number. We show that ribosomal DNA amplification is regulated by three histone deacetylases: Sir2, Hst3, and Hst4. These enzymes control homologous recombination-dependent and nonhomologous recombination-dependent amplification pathways that act in concert to mediate rapid, directional ribosomal DNA copy number change. Amplification is completely repressed by rapamycin, an inhibitor of the nutrient-responsive TOR pathway; this effect is separable from growth rate and is mediated directly through Sir2, Hst3, and Hst4. Caloric restriction is known to up-regulate expression of nicotinamidase Pnc1, an enzyme that enhances Sir2, Hst3, and Hst4 activity. In contrast, normal glucose concentrations stretch the ribosome synthesis capacity of cells with low ribosomal DNA copy number, and we find that these cells show a previously unrecognized transcriptional response to caloric excess by reducing PNC1 expression. PNC1 down-regulation forms a key element in the control of ribosomal DNA amplification as overexpression of PNC1 substantially reduces ribosomal DNA amplification rate. Our results reveal how a signaling pathway can orchestrate specific genome changes and demonstrate that the copy number of repetitive DNA can be altered to suit environmental conditions.

ribosomal DNA homologous recombination Sir2 copy number variation TOR

FREE PDF GRATIS: PNAS

Mais uma hipótese sobre a origem da vida ter ocorrido em uma poça de lama

Ester-Mediated Amide Bond Formation Driven by Wet–Dry Cycles: A Possible Path to Polypeptides on the Prebiotic Earth

Dr. Jay G. Forsythe1,2,‡, Sheng-Sheng Yu1,3,‡, Dr. Irena Mamajanov1,2, Prof. Martha A. Grover1,3, Prof. Ramanarayanan Krishnamurthy1,4,*, Prof. Facundo M. Fernández1,2,* andProf. Nicholas V. Hud1,2,*

Article first published online: 15 JUL 2015

DOI: 10.1002/anie.201503792

†We thank D. Gaul, A. Petrov and F. J. Schork for discussions, and C. O'Mahony and A. Doody for use of a FTIR spectrometer. This work was supported by the NSF and the NASA Astrobiology Program under the NSF Center for Chemical Evolution [CHE-1004570].

Keywords: 

chemical evolution; day–night cycle; depsipeptides; origins-of-life; proto-peptides

Abstract

Although it is generally accepted that amino acids were present on the prebiotic Earth, the mechanism by which α-amino acids were condensed into polypeptides before the emergence of enzymes remains unsolved. Here, we demonstrate a prebiotically plausible mechanism for peptide (amide) bond formation that is enabled by α-hydroxy acids, which were likely present along with amino acids on the early Earth. Together, α-hydroxy acids and α-amino acids form depsipeptides—oligomers with a combination of ester and amide linkages—in model prebiotic reactions that are driven by wet–cool/dry–hot cycles. Through a combination of ester–amide bond exchange and ester bond hydrolysis, depsipeptides are enriched with amino acids over time. These results support a long-standing hypothesis that peptides might have arisen from ester-based precursors.

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Lixo, vá embora: por que os biólogos estão descendo o cacete contra os resultados de pesquisa verificados empiricamente?

Lixo, vá embora: por que os biólogos estão descendo o cacete contra os resultados de pesquisa verificados empiricamente?

Casey Luskin 13 de julho de 2015 3:03 AM | Permalink

Nota do editor: Esta é a Parte 1 de uma série de 4 sobre o ENCODE que Casey Luskin tem publicado este ano no Salvo Magazine. As partes 1, 2, e 3 já foram ali publicadas. A Parte 4 será publicada mais tarde este ano. O prelúdio pode ser encontrado aqui.

A vasta maioria do genoma humano lixo inútil ou crucial para a função celular? Os cientistas estão divididos sobre esta questão, com os biólogos evolucionários defendendo principalmente a primeira opinião, e os biólogos moleculares defendendo a segunda.

Em nossa era de pesquisa biológica avançada, alguém pensaria que isso é uma questão facilmente resolvível, mas quando um poderoso paradigma evolucionário é ameaçado pelas descobertas da biologia molecular, não espere o establishment em aceitar a derrota rapidamente. Na verdade, todo o debate sobre a evolução neodarwinista e o design inteligente (DI) pode surgir no desenrolar dessa questão.

Não são mais detritos e nem destroços

Para aqueles que seguem o debate sobre as origens, o fim do DNA lixo é notícia antiga. A minha primeira coluna Operação DI, na edição de inverno de 2008 da revista Salvo, recontava como que Francis Collins argumentou no seu livro A Linguagem de Deus que o nosso genoma é cheio de “detritos e destroços genéticos” (i.e., lixo), tornando-o “virtualmente inescapável” ¹ que nós compartilhamos ancestralidade comum com ratos.

Mas, como eu expliquei naquela ocasião, diversas funções foram descobertas para o DNA não codificante, e mais tem sido encontrado, forçando uma revolução no pensamento biológico. Em um sinal dos tempos, um artigo da Nature de 2010 anunciou esta nova era da genômica, destacando que “o novo vislumbre da biologia em um universo de DNA não codificante – o que se costumava chamar de DNA ‘lixo’ – tem sido fascinante e impressionante”. ² Muitos outros artigos científicos relatam funções para o DNA ‘lixo’ fizeram destaques semelhantes.

Mas nenhuma publicação sacudiu tanto este debate quanto o artigo da Nature de 2012 que, finalmente colocou de lado o DNA lixo – ou assim pareceu. Esse artigo bombástico apresentou os resultados do Projeto ENCODE (Encyclopedia of DNA Elements – Enciclopédia dos Elementos do DNA), um consórcio de pesquisa de muitos anos envolvendo mais de 400 cientistas internacionais estudando o DNA não codificante no genoma humano. Juntamente com outros 30 artigos inovadores, o principal artigo do ENCODE descobriu que a “vasta maioria” do genoma humano mostram função bioquímica: “Esses dados nos permitiram atribuir funções bioquímicas para 80% do genoma, em particular fora das regiões bem pesquisadas de codificação de proteínas”. ³

Ewan Birney, analista chefe do ENCODE, explicou na Discover Magazine que desde que o ENCODE pesquisou 147 tipos de células, e o corpo humano tem alguns milhares de tipos de células, “é provável que os 80% vão chegar nos 100%”. ⁴ Outro pesquisador sênior do ENCODE destacou que “quase todo nucleotídeo está associado com uma função”. ⁵ Uma manchete na revista Science declarou, “o projeto ENCODE escreve uma elegia para o DNA lixo”. ⁶

Más notícias para o Darwinismo

Esse relato mudou o jogo no debate sobre a evolução darwinista e o design inteligente porque, desde a metade dos anos 1990s, os teóricos do DI vinham predizendo que o DNA não codificante se revelaria como tendo função, e os críticos do DI tinham argumentado que o DNA lixo tinha fincado uma estaca atravessada no coração do DI.

Por exemplo, em 1994, o cientista leigo Forrest Mims, pró DI, enviou uma carta à revista Science advertindo contra o assumir que o DNA “lixo” era “inútil”. ⁷ A revista Science não publicou a carta, mas naquele ano, o biólogo Kenneth Miller, anti DI, publicou um artigo em uma publicação científica diferente fazendo a conclusão oposta, isto é, que “o genoma humano está repleto de pseudogenes, fragmentos de genes, genes ‘órfãos’, DNA ‘lixo’, e muitas cópias repetidas de sequências de DNA sem sentido que não ele não pode ser atribuído a qualquer coisa que pareça com o design inteligente”. ⁸

Contraste a afirmação de Miller com a conclusão da revista Discover Magazine 18 anos mais tarde, à luz do relatório impactante do ENCODE de 2012: “A questão importante é: Não é lixo”. ⁹

Os evolucionistas contra-atacam

Os defensores de Darwin não iriam aceitar os dados do ENCODE sentados. Mas dessa vez, eles se viram em uma posição não costumeira. Muitos darwinistas têm grande confiança em saber que eles estão na maioria científica, o que os capacitam apelar para o consenso e desconsiderar os críticos como “negacionistas”. Mas no mundo pós-ENCODE, os defensores de Darwin, se viram eles mesmos desafiando o consenso de um corpo internacional de expoentes biólogos moleculares que descobriram que a vasta maioria do DNA humano tem função bioquímica.

Como que eles puderam se opor a tais conclusões baseadas empiricamente? Do mesmo modo como que eles defendem sua teoria: considerando um ponto de vista evolucionário como correto e reinterpretando os dados à luz de seu paradigma – e atacando pessoalmente aqueles que desafiam sua posição.

Por exemplo, múltiplas réplicas iniciais de defensores evolucionistas chamaram o ENCODE de  “exagero” ¹⁰ e castigaram os pesquisadores e os jornalistas científicos por terem agido “irresponsavelmente” no relato favorável de suas descobertas. ¹¹ Em uma postagem intitulada “The ENCODE Delusion” [O delírio do ENCODE], PZ Myers desconsiderou a afirmação central do ENCODE de que 80% do genoma tem funções bioquímicas, como sendo “mer**” e defendendo que a evidência de atividade bioquímica no DNA e RNA “não é função. Nem perto disso é”. Ele chamou os pesquisadores do ENCODE de “fundamentalmente desonestos”, e desdenhou de Evan Birney, dizendo, “Eu não penso que o Birney faça a menor ideia do que seja biologia”. ¹²

Outro biólogo defensor de Darwin, Nick Matzke, consentiu que os pesquisadores do ENCODE não eram estúpidos, apenas ignorantes: “Eu estou começando a pensar que certas partes da biologia molecular e da bioinformática são habitadas por pessoas que são muito inteligentes, mas que passaram pela escola com bastante treinamento técnico detalhado, mas sem bastante treinamento amplo em biologia comparativa [i.e., evolucionária] básica”. ¹³ Mas o bioquímico da Universidade de Toronto e blogger pró-evolução, Laurence Moran, nem concederia que os pesquisadores do ENCODE eram inteligentes: “Eu acho que eu terei que me contentar em destacar que muitos cientistas são tão estúpidos quanto muitos criacionistas de Design Inteligente”, ¹⁴ ele esbravejou.

Moran lamentou mais que “os criacionistas vão amar isso”, e ele temeu que os resultados do ENCODE iriam “fazer a minha vida muito complicada”, ¹⁵ pois “vai demandar bastante esforço desfazer o dano provocado pelo [ENCODE]."¹⁶

Todavia, a vasta maioria dos que defendem o ENCODE, não é pró-DI e não tem nenhum motivo em ajudar e amparar “os criacionistas”. Eles são guiados pelos dados empíricos. Por exemplo, O geneticista James Shapiro, da Universidade de Chicago, louvou os resultados do ENCODE enquanto que simultaneamente rejeitava o DI. Ele considerou que “a velha ideia do genoma como uma sequência de genes intercalado com DNA não codificante sem importância não é mais defensável”, pois o “ENCODE revelou que a maioria (e provavelmente quase tudo) desse DNA não codificante e repetitivo continha informação reguladora essencial”. ¹⁷

Shapiro escreveu artigos na metade dos anos 2000s predizendo função para o DNA “lixo”, e ele explicou que seu coautor era um proponente do DI que defendia pontos de vista que ele não partilhava:

Em 2005, eu publiquei dois artigos sobre a importância funcional do DNA repetitivo com Rick von Sternberg. O principal artigo foi intitulado “Why repetitive DNA is essential to genome function” [Por que o DNA repetitivo é essencial para função do genoma].

Esses artigos com Rick são importantes... por duas razões. A primeira é que, logo após nós termos submetido os artigos, Rick se tornou uma celebridade momentânea do movimento do Design Inteligente. Os críticos têm tomado minha coautoria com Rick como uma desculpa para afirmações do tipo “culpado por associação” que eu tenho alguma agenda de DI ou criacionista, uma alegação sem nenhuma base em qualquer coisa que eu tenha escrito.

A segunda razão que os dois artigos com Rick são importantes é porque eles foram, francamente, prescientes, antecipando os recentes resultados do ENCODE. A nossa ideia básica foi que o genoma é uma organela de armazenagem de informação altamente sofisticada. Assim como aparelhos de armazenagem de dados eletrônicos, o genoma deve ser altamente formatado por sinais genéricos (i.e., repetidos) que fazem possível acessar a informação armazenada quando e onde ela será útil.¹⁸

Claramente, cedo, alguns críticos do DI estão aceitando os resultados do ENCODE. Mas a maioria permanece relutantemente resistente, mais provavelmente porque o ENCODE ameaça derrubar alguns dos argumentos científicos mais proeminentes a favor de uma origem evolucionária não guiada do genoma humano.

E se o ENCODE estiver certo?

No início de 2014, a revista Science noticiou os argumentos feitos por outro importante evolucionista crítico do ENCODE, Dan Graur, biólogo da Universidade de Houston. De acordo com a Science, “O ateísmo de Graur inflamou sua raiva ao ENCODE”, ¹⁹ Não é surpreendente que Graur se tornaria emocional sobre o ENCODE considerando-se sua formulação contundente da questão numa palestra que ele deu em 2013:

Se o genoma humano é na verdade livre de DNA lixo conforme implicado pelo Projeto ENCODE, então um longo processo evolucionário não dirigido não pode explicar o genoma humano. Se, por outro lado, os organismos são intencionalmente planejados, então todo o DNA, ou tanto quanto possível dele, é esperado exibir função. Se o ENCODE estiver certo, então a Evolução está errada. ²⁰

A formulação de Graur da questão pode estar correta. Mas, para apreciar o porquê de os críticos do ENCODE estarem errados, espere pelos próximos artigos nesta série.

Referências:

[1.] Francis Collins, The Language of God: A Scientist Presents Evidence for Belief (Free Press, 2006), 136-137.

[2.] Erika Check Hayden, "Life Is Complicated," Nature, 464:664-667 (April 1, 2010) (ênfase adicionada).

[3.] The ENCODE Project Consortium, "An integrated encyclopedia of DNA elements in the human genome,"Nature, 489:57-74 (Sept. 6, 2012).

[4.] Ewan Birney, citado em Ed Yong, "ENCODE: the rough guide to the human genome," Discover Magazine (Sept. 5, 2012): http://tinyurl.com/knr9co7 .

[5.] Tom Gingeras, citado em Yong, ibid.

[6.] Elizabeth Pennisi, "ENCODE Project Writes Eulogy for Junk DNA," Science, 337:1159-1161 (Sept. 7, 2012).

[7.] Forrest Mims, "Rejected Letter to the Editor toScience" (Dec. 1, 1994): forrestmims.org/publications.html.

[8.] Kenneth Miller, "Life's Grand Design," Technology Review, 97(2):24-32 (February/March 1994).

[9.] Yong, nota 4.

[10.] Nick Matzke, "ENCODE hype? From now on I'll just reply: #oniontest," Panda's Thumb (Sept. 5, 2012):http://tinyurl.com/nmxeu4t; Laurence Moran, "The ENCODE Data Dump and the Responsibility of Science Journalists," Sandwalk (Sept. 6, 2012): http://tinyurl.com/k7eup3n.

[11.] Moran, ibid.

[12.] PZ Myers, "The ENCODE delusion," Panda's Thumb (Sept. 23, 2012): http://tinyurl.com/moefwye.

[13.] Matzke, nota 10.

[14.] Laurence Moran, "Intelligent Design Creationists Choose ENCODE Results as the #1 Evolution Story of 2012," Sandwalk (Jan. 4, 2013): http://tinyurl.com/p8dc6yp.

[15.] Laurence Moran, "ENCODE Leader Says that 80% of Our Genome Is Functional," Sandwalk (Sept. 5, 2012): http://tinyurl.com/m96r5un.

[16.] Moran, nota 10.

[17.] James Shapiro, "Bob Dylan, ENCODE and Evolutionary Theory: The Times They Are A-Changin'," Huffington Post(Sept. 12, 2012): http://tinyurl.com/pmxowlu.

[18.] Ibid.

[19.] Yudhit Bhattercharjee, "The Vigilante," Science, 343:1306-1309 (March 21, 2014).

[20.] Dan Graur, "How to Assemble a Human Genome?" (December 2013): http://tinyurl.com/mpmxkyw (ênfase no original).

Imagem: © kessudap / Dollar Photo Club.

Insilico: análise genômica para biólogos sem conhecimentos de programação

A InSilico DB é um ambiente online que elimina a necessidade de manipulações de baixo nível e acelera o ritmo de descoberta genômica. Os dados ficam centralizados e acessíveis através de uma página na internet. Há planos pago e gratuito.

Big dados: astronômicos ou genômicos?

Big Data: Astronomical or Genomical?

Zachary D. Stephens, Skylar Y. Lee, Faraz Faghri, Roy H. Campbell, Chengxiang Zhai, Miles J. Efron, Ravishankar Iyer, Michael C. Schatz , Saurabh Sinha , Gene E. Robinson

Published: July 7, 2015DOI: 10.1371/journal.pbio.1002195

Source/Fonte: iStock

Abstract

Genomics is a Big Data science and is going to get much bigger, very soon, but it is not known whether the needs of genomics will exceed other Big Data domains. Projecting to the year 2025, we compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. Our estimates show that genomics is a “four-headed beast”—it is either on par with or the most demanding of the domains analyzed here in terms of data acquisition, storage, distribution, and analysis. We discuss aspects of new technologies that will need to be developed to rise up and meet the computational challenges that genomics poses for the near future. Now is the time for concerted, community-wide planning for the “genomical” challenges of the next decade.

FREE PDF GRATIS: PLoS Biology

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NOTA DESTE BLOGGER:

Um grama de DNA pode armazenar cerca de 455 exabytes (um exabyte equivale a 10¹⁸ bytes. Um CD-ROM armazena cerca de 700 milhões (7 x 108) de bytes de dados. Um grama de DNA armazena a quantidade de dados equivalente de 600 bilhões de CD-ROMs. Um livro comum requer 1 megabyte de armazenagem de dados, um grama de DNA pode armazenar 455 trilhões de livros!

DNA - mero acaso, fortuita necessidade ou design inteligente???

Genoogle: um buscador indexado e paralelizado de sequências semelhantes de DNA

Genoogle: an indexed and parallelized search engine for similar DNA sequences

Felipe Albrecht

(Submitted on 10 Jul 2015)

Abstract

The search for similar genetic sequences is one of the main bioinformatics tasks. The genetic sequences data banks are growing exponentially and the searching techniques that use linear time are not capable to do the search in the required time anymore. Another problem is that the clock speed of the modern processors are not growing as it did before, instead, the processing capacity is growing with the addiction of more processing cores and the techniques which does not use parallel computing does not have benefits from these extra cores. This work aims to use data indexing techniques to reduce the searching process computation cost united with the parallelization of the searching techniques to use the computational capacity of the multi core processors. To verify the viability of using these two techniques simultaneously, a software which uses parallelization techniques with inverted indexes was developed. 

Experiments were executed to analyze the performance gain when parallelism is utilized, the search time gain, and also the quality of the results when it compared with others searching tools. The results of these experiments were promising, the parallelism gain overcame the expected speedup, the searching time was 20 times faster than the parallelized NCBI BLAST, and the searching results showed a good quality when compared with this tool. 

The software source code is available at this https URL .

Subjects: Distributed, Parallel, and Cluster Computing (cs.DC); Computational Engineering, Finance, and Science (cs.CE); Information Retrieval (cs.IR); Genomics (q-bio.GN)

Cite as: arXiv:1507.02987 [cs.DC]

(or arXiv:1507.02987v1 [cs.DC] for this version)

Submission history

From: Felipe Fernandes Albrecht [view email] 

[v1] Fri, 10 Jul 2015 18:50:31 GMT (30kb)

FREE PDF GRATIS: ArXiv

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NOTA DESTE BLOGGER:

Felipe Fernandes Albrecht é mais um cientista brasileiro fazendo ciência de ponta. Ser noticiado aqui não significa que ele faça parte do movimento de Design Inteligente no Brasil, ou seja simpatizante de nossa teoria.

Proteção do DNA, centímetro por centímetro! Mero acaso? Fortuita necessidade? Ou design inteligente?

PIWI Slicing and RNA Elements in Precursors Instruct Directional Primary piRNA Biogenesis

David Homolka6, Radha Raman Pandey6, Coline Goriaux, Emilie Brasset, Chantal Vaury, Ravi Sachidanandam, Marie-Odile Fauvarque, Ramesh S. Pillaicorrespondenceemail

6Co-first author

Publication stage: In Press Corrected Proof

Highlights

•A piRNA-trigger sequence from the 5′ end of a fly cluster drives primary processing

•Slicer activity of PIWI generates non-overlapping, contiguous primary piRNAs

•Cytoplasmic PIWI-triggered primary piRNAs are loaded into nuclear PIWI

•Primary piRNA biogenesis proceeds with a 5′–3′ directionality

Summary

PIWI proteins and PIWI-interacting RNAs (piRNAs) mediate repression of transposons in the animal gonads. Primary processing converts long single-stranded RNAs into ∼30-nt piRNAs, but their entry into the biogenesis pathway is unknown. Here, we demonstrate that an RNA element at the 5′ end of a piRNA cluster—which we termed piRNA trigger sequence (PTS)—can induce primary processing of any downstream sequence. We propose that such signals are triggers for the generation of the original pool of piRNAs. We also demonstrate that endonucleolytic cleavage of a transcript by a cytosolic PIWI results in its entry into primary processing, which triggers the generation of non-overlapping, contiguous primary piRNAs in the 3′ direction from the target transcript. These piRNAs are loaded into a nuclear PIWI, thereby linking cytoplasmic post-transcriptional silencing to nuclear transcriptional repression.

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Received: March 12, 2015; Received in revised form: May 12, 2015; Accepted: June 5, 2015; Published Online: July 09, 2015

© 2015 The Authors. Published by Elsevier Inc.

FREE PDF GRATIS: Cell Reports

A estrutura do cérebro humano: mero acaso, fortuita necessidade ou design inteligente?

Navigable networks as Nash equilibria of navigation games

András Gulyás, József J. Bíró, Attila Kőrösi, Gábor Rétvári & Dmitri Krioukov

AffiliationsContributionsCorresponding authors

Nature Communications 6, Article number: 7651 doi:10.1038/ncomms8651

Received 04 December 2014 Accepted 26 May 2015 Published 03 July 2015

Abstract

Common sense suggests that networks are not random mazes of purposeless connections, but that these connections are organized so that networks can perform their functions well. One function common to many networks is targeted transport or navigation. Here, using game theory, we show that minimalistic networks designed to maximize the navigation efficiency at minimal cost share basic structural properties with real networks. These idealistic networks are Nash equilibria of a network construction game whose purpose is to find an optimal trade-off between the network cost and navigability. We show that these skeletons are present in the Internet, metabolic, English word, US airport, Hungarian road networks, and in a structural network of the human brain. The knowledge of these skeletons allows one to identify the minimal number of edges, by altering which one can efficiently improve or paralyse navigation in the network.

Subject terms: Physical sciences Theoretical physics

FREE PDF GRATIS: Nature Communications

Por uma teoria cibernética da evolução - pode isso, Arnaldo?

Duality of stochasticity and natural selection: a cybernetic evolution theory

By Prof. Kurt Heininger 

Corresponding Author

Prof. Kurt Heininger 

Department of Neurology, Heinrich Heine University Duesseldorf, - Germany 

Submitting Author

Prof. Kurt Heininger 

Subject Category :ECOLOGY

Keywords : Stochasticity, natural selection, cybernetics, bet-hedging, multilevel selection, Law of Requisite Variety, mean geometric fitness

How to cite the article: Heininger K. Duality of stochasticity and natural selection: a cybernetic evolution theory. WebmedCentral ECOLOGY 2015;6(2):WMC004796 

doi: 10.9754/journal.wmc.2015.004796

Copyright:This is an open-access article distributed under the terms of the Creative Commons Attribution License(CC-BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

WebmedCentral Peer Reviewed: No

Submitted on: 22 Feb 2015 09:03:27 PM GMTPublished on: 23 Feb 2015 07:42:40 AM GMT

Abstract

Orthodox Darwinism assumes that environments are stable. There is an important difference between breeding (Darwin’s role model of evolution) and evolution itself: while in breeding the final goal is preset and constant, adaptation to varying biotic and abiotic environmental conditions is a moving target and selection can be highly fluctuating. Evolution is a cybernetic process whose Black Box can be understood as learning automaton with separate input and output channels. Cybernetics requires a closed signal loop: action by the system causes some change in its environment and that change is fed to the system via information (feedback) that enables the system to change its behavior. The input signal is given by a complex biotic and abiotic environment. Natural selection is the output/outcome of the learning automaton.

Environments are stochastic. Particularly, density- and frequency-dependent coevolutionary interactions generate chaotic and unpredictable dynamics. Stochastic environments coerce organisms into risky lotteries. Chance favors the prepared. The ‘Law of Requisite Variety’ holds that cybernetic systems must have internal variety that matches their external variety so that they can self-organize to fight variation with variation. Both conservative and diversifying bet-hedging are the risk-avoiding and -spreading insurance strategies in response to environmental uncertainty. The bet-hedging strategy tries to cover all bases in an often unpredictable environment where it does not make sense to “put all eggs into one basket”. In this sense, variation is the bad/worst-case insurance strategy of risk-aversive individuals. Variation is pervasive at every level of biological organization and is created by a multitude of processes: mutagenesis, epimutagenesis, recombination, transposon mobility, repeat instability, gene expression noise, cellular network dynamics, physiology, phenotypic plasticity, behavior, and life history strategy. Importantly, variation is created condition-dependently, when variation is most needed – in organisms under stress. The bet-hedging strategy also manifests in a multitude of life history patterns: turnover of generations, reproductive prudence, iteroparity, polyandry, and sexual reproduction.

Cybernetic systems are complex systems. Complexity is conceived as a system’s potential to assume a large number of states, i.e., variety. Complex systems have both stochastic and deterministic properties and, in fact, generate order from chaos. Non-linearity, criticality, self-organization, emergent properties, scaling, hierarchy and evolvability are features of complex systems. Emergent properties are features of a complex system that are not present at the lower level but arise unexpectedly from interactions among the system’s components. Only within an intermediate level of stochastic variation, somewhere between determined rigidity and literal chaos, local interactions can give rise to complexity. Stochastic environments change the rules of evolution. Lotteries cannot be played and insurance strategies not employed with single individuals. These are emergent population-level processes that exert population-level selection pressures generating variation and diversity at all levels of biological organization. Together with frequency and density-dependent selection, lottery- and insurance-dependent selection act on population-level traits.

The duality of stochasticity and selection is the organizing principle of evolution. Both are interdependent. The feedback between output and input signals inextricably intertwines both stochasticity and natural selection, and the individual- and population-levels of selection. Sexual reproduction with its generation of pre-selected variation is the paradigmatic bet-hedging enterprise and its evolutionary success is the selective signature of stochastic environments.Sexual reproduction is the proof of concept that (epi)genetic variation is no accidental occurrence but a highly regulated process and environmental stochasticity is its evolutionary “raison d’être”.Evolutionary biology is plaqued by a multitude of controversies (e.g. concerning the level of selection issue and sociobiology. Almost miraculously, these controversies can be resolved by the cybernetic model of evolution and its implications.

FREE PDF GRATIS: Webmed Central