Asa de mariposa: isolante acústico natural de eficiência imbatível: mero acaso, fortuita necessidade ou design inteligente?

terça-feira, junho 28, 2022

 Moth wings as sound absorber metasurface

Thomas R. Neil, Zhiyuan Shen, Daniel Robert, Bruce W. Drinkwater and Marc W. Holderied

Published:15 June 2022 https://doi.org/10.1098/rspa.2022.0046

Image/Imagem: University of Bristol


Abstract

In noise control applications, a perfect metasurface absorber would have the desirable traits of not only mitigating unwanted sound, but also being much thinner than the wavelengths of interest. Such deep-subwavelength performance is difficult to achieve technologically, yet moth wings, as natural metamaterials, offer functionality as efficient sound absorbers through the action of the numerous resonant scales that decorate their wing membrane. Here, we quantify the potential for moth wings to act as a sound-absorbing metasurface coating for acoustically reflective substrates. Moth wings were found to be efficient sound absorbers, reducing reflection from an acoustically hard surface by up to 87% at the lowest frequency tested (20 kHz), despite a thickness to wavelength ratio of up to 1/50. Remarkably, after the removal of the scales from the dorsal surface the wing's orientation on the surface changed its absorptive performance: absorption remains high when the bald wing membrane faces the sound but breaks down almost completely in the reverse orientation. Numerical simulations confirm the strong influence of the air gap below the wing membrane but only when it is adorned with scales. The finding that moth wings act as deep-subwavelength sound-absorbing metasurfaces opens the door to bioinspired, high-performance sound mitigation solutions.

FREE PDF GRATIS: Proceddings of the Royal Society A

Origem e evolução inicial da célula eucariótica

segunda-feira, junho 27, 2022

Origin and Early Evolution of the Eukaryotic Cell

Annual Review of Microbiology

Vol. 75:631-647 (Volume publication date October 2021)

First published as a Review in Advance on August 3, 2021

https://doi.org/10.1146/annurev-micro-090817-062213 



Toni Gabaldón1,2,3

1Barcelona Supercomputing Centre (BCS-CNS), 08034 Barcelona, Spain; email: toni.gabaldon.bcn@gmail.com

2Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain

3Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain

Abstract

The origin of eukaryotes has been defined as the major evolutionary transition since the origin of life itself. Most hallmark traits of eukaryotes, such as their intricate intracellular organization, can be traced back to a putative common ancestor that predated the broad diversity of extant eukaryotes. However, little is known about the nature and relative order of events that occurred in the path from preexisting prokaryotes to this already sophisticated ancestor. The origin of mitochondria from the endosymbiosis of an alphaproteobacterium is one of the few robustly established events to which most hypotheses on the origin of eukaryotes are anchored, but the debate is still open regarding the time of this acquisition, the nature of the host, and the ecological and metabolic interactions between the symbiotic partners. After the acquisition of mitochondria, eukaryotes underwent a fast radiation into several major clades whose phylogenetic relationships have been largely elusive. Recent progress in the comparative analyses of a growing number of genomes is shedding light on the early events of eukaryotic evolution as well as on the root and branching patterns of the tree of eukaryotes. Here I discuss current knowledge and debates on the origin and early evolution of eukaryotes. I focus particularly on how phylogenomic analyses have challenged some of the early assumptions about eukaryotic evolution, including the widespread idea that mitochondrial symbiosis in an archaeal host was the earliest event in eukaryogenesis.

Keywords eukaryogenesis, mitochondria, endosymbiosis, eukaryotic evolution, LECA

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As mitocôndrias e a origem dos eucariontes

 


Mitochondria and the origin of eukaryotes

Were the powerhouse organelles a driving force or a late addition in the evolution of more complex cells like ours?

By Viviane Callier 06.08.2022

For billions of years after the origin of life, the only living things on Earth were tiny, primitive cells resembling today’s bacteria. But then, more than 1.5 billion years ago, something remarkable happened: One of those primitive cells, belonging to a group known as the archaea, swallowed a different one — a bacterium.

Instead of being digested, the bacterium took up permanent residence within the other organism as what biologists call an endosymbiont. Eventually, it integrated fully into its archaeal host cell, becoming what we know today as the mitochondrion, the crucial energy-producing component of the cell.

Its acquisition has long been viewed as the key step in what is arguably the most important evolutionary leap since the origin of life itself: the transition from early primitive cells, or prokaryotes, to the more sophisticated cells of higher organisms, or eukaryotes, including ourselves.

It’s a neat story you’ll find in most biology textbooks — but is it quite that simple? In the last few years, new evidence has challenged the notion that mitochondria played a seminal role in this transition. Researchers sequencing the genomes of modern-day relatives of the first eukaryotes have found many unexpected genes that don’t seem to come from either the host or the endosymbiont. And that, some scientists suggest, might mean that the evolution of the first eukaryotes involved more than two partners and happened more gradually than suspected.

Others don’t see a reason yet to abandon the theory that the acquisition of the mitochondrion was the spark that ignited the rapid evolution of eukaryotes — giving rise, eons later, to plants, animals, vertebrates, people. Fresh evidence from genomics and cell biology may help resolve the debate, while also pointing to knowledge gaps that still need to be filled to understand one of the foundational events in our own ancestry, the origin of complex cells.

Read more here/Leia mais aqui: Knowable Magazine

Darwin, nós temos um problema: a fisiologia restaura o propósito na biologia evolutiva

quinta-feira, junho 16, 2022

Physiology restores purpose to evolutionary biology

Raymond Noble, Denis Noble

Biological Journal of the Linnean Society, blac049, 

Published: 08 June 2022 

Article history Received: 26 November 2021 Revision received: 02 April 2022 Accepted: 08 April 2022

Published: 08 June 2022



Abstract

Life is purposefully creative in a continuous process of maintaining integrity; it adapts to counteract change. This is an ongoing, iterative process. Its actions are essentially directed to this purpose. Life exists to exist. Physiology is the study of purposeful living function. Function necessarily implies purpose. This was accepted all the way from William Harvey in the 17th century, who identified the purpose of the heart to pump blood and so feed the organs and tissues of the body, through many 19th and early 20th century examples. But late 20th century physiology was obliged to hide these ideas in shame. Teleology became the ‘lady who no physiologist could do without, but who could not be acknowledged in public.’ This emasculation of the discipline accelerated once the Central Dogma of molecular biology was formulated, and once physiology had become sidelined as concerned only with the disposable vehicle of evolution. This development has to be reversed. Even on the practical criterion of relevance to health care, gene-centrism has been a disaster, since prediction from elements to the whole system only rarely succeeds, whereas identifying whole system functions invariably makes testable predictions at an elemental level.

Key words biological function, Central Dogma, purpose in biology, teleology

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Biological Journal of the Linnean Society

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Físicos reescrevem a lei fundamental que leva à desordem

terça-feira, junho 07, 2022

Physicists Rewrite the Fundamental Law That Leads to Disorder

The second law of thermodynamics is among the most sacred in all of science, but it has always rested on 19th century arguments about probability. New arguments trace its true source to the flows of quantum information.


Is the rise of entropy merely probabilistic, or can it be straightened out by use of clear quantum axioms?

Maggie Chiang for Quanta Magazine

In all of physical law, there’s arguably no principle more sacrosanct than the second law of thermodynamics — the notion that entropy, a measure of disorder, will always stay the same or increase. “If someone points out to you that your pet theory of the universe is in disagreement with Maxwell’s equations — then so much the worse for Maxwell’s equations,” wrote the British astrophysicist Arthur Eddington in his 1928 book The Nature of the Physical World. “If it is found to be contradicted by observation — well, these experimentalists do bungle things sometimes. But if your theory is found to be against the second law of thermodynamics I can give you no hope; there is nothing for it but to collapse in deepest humiliation.” No violation of this law has ever been observed, nor is any expected.

But something about the second law troubles physicists. Some are not convinced that we understand it properly or that its foundations are firm. Although it’s called a law, it’s usually regarded as merely probabilistic: It stipulates that the outcome of any process will be the most probable one (which effectively means the outcome is inevitable given the numbers involved).

Yet physicists don’t just want descriptions of what will probably happen. “We like laws of physics to be exact,” said the physicist Chiara Marletto of the University of Oxford. Can the second law be tightened up into more than just a statement of likelihoods?

A number of independent groups appear to have done just that. They may have woven the second law out of the fundamental principles of quantum mechanics — which, some suspect, have directionality and irreversibility built into them at the deepest level. According to this view, the second law comes about not because of classical probabilities but because of quantum effects such as entanglement. It arises from the ways in which quantum systems share information, and from cornerstone quantum principles that decree what is allowed to happen and what is not. In this telling, an increase in entropy is not just the most likely outcome of change. It is a logical consequence of the most fundamental resource that we know of — the quantum resource of information.

Quantum Inevitability

Thermodynamics was conceived in the early 19th century to describe the flow of heat and the production of work. The need for such a theory was urgently felt as steam power drove the Industrial Revolution, and engineers wanted to make their devices as efficient as possible.

In the end, thermodynamics wasn’t much help in making better engines and machinery. Instead, it became one of the central pillars of modern physics, providing criteria that govern all processes of change.

...

Read more here/Leia mais aqui: Quanta Magazine

Darwin, estudo sugere que a maioria das árvores evolutivas pode estar errada...

domingo, junho 05, 2022

Molecular phylogenies map to biogeography better than morphological ones

Jack W. Oyston, Mark Wilkinson, Marcello Ruta & Matthew A. Wills 

Communications Biology volume 5, Article number: 521 (2022)

Schematic universal tree updated from (Woese et al., 1990)


Abstract

Phylogenetic relationships are inferred principally from two classes of data: morphological and molecular. Currently, most phylogenies of extant taxa are inferred from molecules and when morphological and molecular trees conflict the latter are often preferred. Although supported by simulations, the superiority of molecular trees has rarely been assessed empirically. Here we test phylogenetic accuracy using two independent data sources: biogeographic distributions and fossil first occurrences. For 48 pairs of morphological and molecular trees we show that, on average, molecular trees provide a better fit to biogeographic data than their morphological counterparts and that biogeographic congruence increases over research time. We find no significant differences in stratigraphic congruence between morphological and molecular trees. These results have implications for understanding the distribution of homoplasy in morphological data sets, the utility of morphology as a test of molecular hypotheses and the implications of analysing fossil groups for which molecular data are unavailable.

FREE PDF GRATIS: Communications Biology 

O neodarwinismo deve mudar se quiser sobreviver

sexta-feira, junho 03, 2022

Neo-Darwinism must Mutate to survive

Olen R.Brown a David A.Hullender b

a Dalton Cardiovascular Research Center, University of Missouri- Columbia, USA

b Professor of Mechanical and Aerospace Engineering at the University of Texas at Arlington, USA

Received 15 November 2021, Revised 6 April 2022, Accepted 12 April 2022, Available online 16 April 2022.

https://doi.org/10.1016/j.pbiomolbio.2022.04.005 

Image/Imagem: BioScience

Abstract

Darwinian evolution is a nineteenth century descriptive concept that itself has evolved. Selection by survival of the fittest was a captivating idea. Microevolution was biologically and empirically verified by discovery of mutations. There has been limited progress to the modern synthesis. The central focus of this perspective is to provide evidence to document that selection based on survival of the fittest is insufficient for other than microevolution. Realistic probability calculations based on probabilities associated with microevolution are presented. However, macroevolution (required for all speciation events and the complexifications appearing in the Cambrian explosion) are shown to be probabilistically highly implausible (on the order of 10−50) when based on selection by survival of the fittest. We conclude that macroevolution via survival of the fittest is not salvageable by arguments for random genetic drift and other proposed mechanisms. Evolutionary biology is relevant to cancer mechanisms with significance beyond academics. We challenge evolutionary biology to advance boldly beyond the inadequacies of the modern synthesis toward a unifying theory modeled after the Grand Unified Theory in physics. This should include the possibility of a fifth force in nature. Mathematics should be rigorously applied to current and future evolutionary empirical discoveries. We present justification that molecular biology and biochemistry must evolve to aeon (life) chemistry that acknowledges the uniqueness of enzymes for life. To evolve, biological evolution must face the known deficiencies, especially the limitations of the concept survival of the fittest, and seek solutions in Eigen's concept of self-organization, Schrödinger's negentropy, and novel approaches.

Keywords Evolution Modern synthesis Negentropy Probability Selection Selforganization Survival of fittest

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Darwin, mais turbulência na base da Árvore da Vida - eucariogênese, o surgimento de um superorganismo emergente

quarta-feira, junho 01, 2022

Eukaryogenesis: The Rise of an Emergent Superorganism

Philip J. L. Bell*

Microbiogen Pty Ltd., Sydney, NSW, Australia

Image/Imagem: Wiley Online Library

Although it is widely taught that all modern life descended via modification from a last universal common ancestor (LUCA), this dominant paradigm is yet to provide a generally accepted explanation for the chasm in design between prokaryotic and eukaryotic cells. Counter to this dominant paradigm, the viral eukaryogenesis (VE) hypothesis proposes that the eukaryotes originated as an emergent superorganism and thus did not evolve from LUCA via descent with incremental modification. According to the VE hypothesis, the eukaryotic nucleus descends from a viral factory, the mitochondrion descends from an enslaved alpha-proteobacteria and the cytoplasm and plasma membrane descend from an archaeal host. A virus initiated the eukaryogenesis process by colonising an archaeal host to create a virocell that had its metabolism reprogrammed to support the viral factory. Subsequently, viral processes facilitated the entry of a bacterium into the archaeal cytoplasm which was also eventually reprogrammed to support the viral factory. As the viral factory increased control of the consortium, the archaeal genome was lost, the bacterial genome was greatly reduced and the viral factory eventually evolved into the nucleus. It is proposed that the interaction between these three simple components generated a superorganism whose emergent properties allowed the evolution of eukaryotic complexity. If the radical tenets of the VE hypothesis are ultimately accepted, current biological paradigms regarding viruses, cell theory, LUCA and the universal Tree of Life (ToL) should be fundamentally altered or completely abandoned.

FREE PDF GRATIS: Frontiers in Microbiology

Informação biológica da qual Darwin era totalmente ignorante

segunda-feira, maio 30, 2022

 


Biological Information

New Perspectives
Proceedings of the Symposium
, Cornell University, USA
, 31 May – 3 June 2011
Pages: 584
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Darwin, meu rapaz, mais problemas sérios com sua Árvore da Vida e o Último Ancestral Comum

sábado, maio 28, 2022

Problemas com a Árvore da Vida

Mike Keas, Paul Nelson

27 de maio de 2022, 15h27

Reivindicações de saber que uma Árvore da Vida evolutiva (TOL em inglês) existia são cada vez mais problemáticas. A TOL é uma maneira pitoresca de imaginar um padrão de ramificação de descendência comum universal (UCD em inglês) - a alegada evolução de toda a vida atual por descendência com modificação de formas de vida anteriores na Terra, com todos os organismos remontando ao Último Ancestral Comum Universal (abreviado como LUCA em inglês). Vamos lhe atualizar sobre os problemas da TOL analisando um novo artigo de autoria de um grupo de biólogos associados à maior universidade da América Latina: a Universidade Nacional Autônoma do México.

Amadeo Estrada e seus colegas mostram como a enorme literatura dedicada à construção da TOL por meio de grandes conjuntos de dados de sequenciamento molecular (incluindo muitos genomas completos de muitos organismos) está repleta de problemas debilitantes. Seguindo os avisos severos anteriores dos principais críticos da TOL, como W. Ford Doolittle, Estrada et al. pesquisam um amplo campo de caos filogenético baseado em moléculas - um monte de relatos mutuamente inconsistentes do suposto padrão de ramificação da evolução. Eles observam: "A abordagem estritamente estatística [aos estudos filogenéticos de base molecular] ... resultou em hipóteses evolutivas divergentes e até contraditórias sem fundamento com evidências independentes, entre diferentes grupos de pesquisa e, às vezes, em grupos únicos de pesquisa." 1 Dito mais claramente, tais estudos produziram um grande número de imagens profundamente inconsistentes da UCD, o que mina a confiança sobre a própria UCD. 

Quão profundo? Quão grave?

Quão profundas são essas inconsistências na história popular do UCD? Estudos moleculares produziram respostas radicalmente diferentes para o que fica perto da base da TOL — ou seja, esses estudos criaram confusão sobre LUCA. Para compreender a gravidade da situação, considere a faixa de opinião recente extremamente divergente sobre LUCA; nas palavras de Estrada et al.(seus pontos-chave enumerados por nós, com pequenas edições para o inglês):

O LUCA tem sido caracterizado como

1. perto da origem da vida (Koonin 2003; Weiss et al. 2016a), ou estando longe da origem da vida (Mirkin et al. 2003; Delaye et al. 2005)

2. ter um pequeno genoma (Koonin 2003), ou ter um genoma semelhante em tamanho a muitas bactérias vivas livres hoje (Kyrpides et al. 1999; Harris et al. 2003; Mirkin et al. 2003; Delaye et al. 2005; Yang et al. 2005; Ouzounis et al. 2006; Ranea et al. 2006; Becerra et al. 2014)

3. sendo autotrófico (Martin et al. 2008; Weiss et al. 2016a), ou como heterotrófico (Delaye et al. 2005; Becerra et al 2014, Muñoz-Velasco et al. 2018)

4. sendo hipertermofílico (Woese 1987; Weiss et al. 2016a); ou como sendo mesofílico (Galtier et al. 1999; Groussin et al. 2013; Cantine e Fournier 2018)

5. constituído por um genoma RNA (Mushegian e Koonin 1996; Koonin 2003), ou tendo um genoma de DNA (Ouzounis et al. 2006; Delaye et al. 2005; Becerra et al. 2014)

6. sendo uma célula simples (Koonin 2003), ou tendo uma célula complexa, semelhante às bactérias atuais (Kyrpides et al. 1999; Harris et al. 2003; Mirkin et al. 2003; Delaye et al. 2005; Yang et al. 2005; Ouzounis et al. 2006; Ranea et al. 2006; Becerra et al. 2014). 2

Obviamente, a evolução da TOL não poderia ter ocorrido de todas essas formas mutuamente inconsistentes (estágios contraditórios inferidos de evolução perto da base da TOL). Essas inferências evolutivas estão por todo o mapa biológico. No entanto, Estrada et al. não estendem seu ceticismo a todo o paradigma TOL-UCD. No entanto, eles destacam:

Novas descobertas e mudanças no que pensamos sobre certos assuntos são comuns na ciência. No entanto, pensamos que essas divergências extremas entre e até mesmo dentro das caracterizações de alguns pesquisadores do LCA estão ligadas ao fato de confiar em abordagens estatísticas apenas sem outros tipos de dados fora dos métodos de comparações de sequências. Ao fazê-lo, os pesquisadores podem se tornar sujeitos aos resultados contraditórios de algoritmos. 3

Como eles sugerem aqui, Estrada et al. (se baseando em Doolittle e outros) propõem sua própria saída dessa bagunça, mas admitem que mesmo sua abordagem revisada tem seus próprios problemas adicionais - embora estes sejam problemas menores em sua estimativa (mais sobre isso abaixo).

Redimensionando novamente as reivindicações

Este grupo de pesquisa recomenda fazer estimativas de LUCA que são menos ricas em detalhes, redimensionando as alegações do que podemos legitimamente saber a partir de estudos moleculares. Eles também exortam os colegas evolucionistas a levar em conta mais dados além dos limites do sequenciamento molecular comparativo. Primeiramente vamos explorar o primeiro ponto de seu programa de pesquisa revisionista duplo. 

Por um lado, eles reconhecem que, sem dados moleculares (especialmente genéticos), "não há possibilidade de reconstrução filogenética [TOL]". Por outro lado, apontam as "sérias desvantagens epistêmicas" desses estudos "para a reconstrução de formas primitivas de vida, apesar de serem recompensadas na prática científica". 4 Dito sem rodeios, muitos cientistas progrediram em suas carreiras, despejando um punhado de reivindicações sobre TOL.

A relativa facilidade nos dias de sequenciamento molecular e análise estatística auxiliada por computador tornam este programa de pesquisa de bioinformática difícil de resistir. Quando, no entanto, isso resulta em "hipóteses contraditórias mesmo dentro da mesma equipe e em publicações consecutivas, sem reconhecimento de suas conclusões divergentes" 5 a coerência interna e consistência lógica do modelo TOL/LUCA inevitavelmente sofrem.

Como Estrada et al. observam, nas últimas duas décadas Doolittle e outros atribuíram parte da confusão filogenética molecular à transferência de genes lateral (horizontal) (LGT). Multiplicando os modos possíveis de transmissão genética além da chamada herança "vertical", a LGT complica muito o rastreamento de linhagens de organismos através das gerações subsequentes.

Mas a maioria dos evolucionistas não acha que a LGT rebaixe severamente os sinais históricos que eles usam para determinar a forma da TOL. Mas, Estrada et al. destacam, "o problema é que há grandes dificuldades para medir a LGT, até porque os critérios estatísticos e ferramentas bioinformáticas utilizados para estimá-la compartilham as mesmas restrições metodológicas que assolam as reconstruções filogenéticas (Cortez et al. 2009)." 6

Uma Confissão Sincera

Essa é uma confissão revigorantemente sincera. A LGT é frequentemente citada como parte da razão pela qual temos candidatos muito diferentes de TOLs (e diferentes candidatos de LUCAs). Mas não devemos duvidar da história geral da TOL-UCD em face de tais reconstruções de TOL conflitantes, dizem-nos, porque a LGT é parcialmente culpada por esta situação.

Isso não resolve, no entanto, as graves inconsistências retroditivas do LUCA que os autores lamentam na citação do grande bloco acima listando seis grandes contradições evolutivas. Por que? Porque os cálculos de LGT dependem e são epistemicamente limitados pelas "mesmas restrições metodológicas que assolam as reconstruções filogenéticas [de TOL]".

Voltamos agora para o segundo ponto das recomendações revisionistas deste grupo de pesquisa mexicano: a chamada para se levar em conta mais dados além dos limites do sequenciamento molecular comparativo. "Qualquer hipótese de LCA deve ser confrontada com o conhecimento empírico atual das ciências da Terra, bem como o que os cientistas sabem sobre bioquímica e caminhos metabólicos..."

Isso parece sensato, mas eles admitem imediatamente as severas limitações desta recomendação devido à "escassez de conhecimento bioquímico e geoquímico em torno dos estágios iniciais da vida", o que "representa uma grave restrição epistêmica" nas teorias do LCA. 7

Na tentativa de remediar essa situação, eles defendem o redimensionamento das retrodicções de LUCA ao que eles chamam de "LCA mais magro". Isso significa que as reconstruções filogenéticas devem ser uma "visando resolução menor" — alegando que sabemos muito pouco — para que nossas reivindicações sejam menos contraditórias ou falseadas por dados teimosos. Um filósofo cético da ciência poderia ter dito isso sobre muitos ramos da biologia evolutiva. 

O diagnóstico de Kuhn

Há 60 anos, o historiador e filósofo da ciência Thomas Kuhn listou o que descreveu como os "sintomas" de um campo de pesquisa que sofre mudanças desestabilizadoras. O diagnóstico de Kuhn é tão relevante hoje quanto quando ele o ofereceu pela primeira vez - especialmente o primeiro sintoma, que colocamos em negrito:

A proliferação de articulações concorrentes, a vontade de tentar qualquer coisa, a expressão do descontentamento explícito, o recurso à filosofia e ao debate sobre fundamentos, tudo isso são sintomas de uma transição de pesquisa normal para extraordinária. 8

Há somente uma verdadeira história da vida. (Se você duvida disso, pergunte a si mesmo se você tem, em algum lugar, um conjunto desconhecido de pais biológicos com uma reivindicação igualmente válida de serem seus ancestrais físicos reais, quando comparados com os nomes familiares em sua certidão de nascimento.) Estrada et al. identificam as articulações históricas concorrentes, apenas uma delas pode ser o caso agora na atual teoria evolutiva. Uma ciência madura converge em uma única resposta. Uma ciência em apuros? Nem tanto.

NOTAS

1. Amadeo  Estrada, Edna Suarez-Diaz, and Arturo Becerra, “Reconstructing the Last Common Ancestor: Epistemological and Empirical Challenges.” Acta Biotheoretica 70, no. 2 (2022): 1-18, p. 3.

2. Ibid., 3.

3. Ibid., 3.

4. Ibid., 4.

5. Ibid., 9.

6. Ibid., 6.

7. Ibid., 10.

8. T. S. Kuhn, The Structure of Scientific Revolutions (Chicago: University of Chicago Press, 2nd ed., 1970), p. 91.

A “seleção natural” de Darwin está operando duas vezes mais rápida do que se pensava anteriormente?

sexta-feira, maio 27, 2022

Estimation of Genetic Variance in Fitness, and Inference of Adaptation, When Fitness Follows a Log-Normal Distribution 

Timothée Bonnet, Michael B Morrissey, Loeske E B Kruuk

Journal of Heredity, Volume 110, Issue 4, June 2019, Pages 383–395, https://doi.org/10.1093/jhered/esz018

Published: 26 June 2019 

Article history Received: 14 November 2018 Revision requested: 23 January 2019 Accepted: 07 April 2019 Published: 26 June 2019


Image/Imagem

Abstract

Additive genetic variance in relative fitness (σ2A(w)) is arguably the most important evolutionary parameter in a population because, by Fisher’s fundamental theorem of natural selection (FTNS; Fisher RA. 1930. The genetical theory of natural selection. 1st ed. Oxford: Clarendon Press), it represents the rate of adaptive evolution. However, to date, there are few estimates of σ2A(w) in natural populations. Moreover, most of the available estimates rely on Gaussian assumptions inappropriate for fitness data, with unclear consequences. “Generalized linear animal models” (GLAMs) tend to be more appropriate for fitness data, but they estimate parameters on a transformed (“latent”) scale that is not directly interpretable for inferences on the data scale. Here we exploit the latest theoretical developments to clarify how best to estimate quantitative genetic parameters for fitness. Specifically, we use computer simulations to confirm a recently developed analog of the FTNS in the case when expected fitness follows a log-normal distribution. In this situation, the additive genetic variance in absolute fitness on the latent log-scale (σ2A(l)) equals (σ2A(w)) on the data scale, which is the rate of adaptation within a generation. However, due to inheritance distortion, the change in mean relative fitness between generations exceeds σ2A(l) and equals (exp(σ2A(l))−1)⁠. We illustrate why the heritability of fitness is generally low and is not a good measure of the rate of adaptation. Finally, we explore how well the relevant parameters can be estimated by animal models, comparing Gaussian models with Poisson GLAMs. Our results illustrate 1) the correspondence between quantitative genetics and population dynamics encapsulated in the FTNS and its log-normal-analog and 2) the appropriate interpretation of GLAM parameter estimates.

Key words animal model, fundamental theorem of natural selection, GLMM, heritability, quantitative genetics

FREE PDF GRATIS: Journal of Heredity Sup. Info.

Os cientistas não sabem o que metade dos genes microbianos realmente fazem.

quarta-feira, maio 25, 2022

Unifying the known and unknown microbial coding sequence space

Chiara Vanni, Matthew S Schechter, Silvia G Acinas, Albert Barberán, Pier Luigi Buttigieg, Emilio O Casamayor, Tom O Delmont, Carlos M Duarte, A Murat Eren, Robert D Finn, Renzo Kottmann, Alex Mitchell, Pablo Sánchez, Kimmo Siren, Martin Steinegger, Frank Oliver Gloeckner, Antonio Fernàndez-Guerra Is a corresponding author see less

Microbial Genomics and Bioinformatics Research G, Max Planck Institute for Marine Microbiology, Germany; Jacobs University Bremen, Germany; Department of Medicine, University of Chicago, United States; Department of Marine Biology and Oceanography, Institut de Ciències del Mar (CSIC), Spain; Department of Environmental Science, University of Arizona, United States; Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Germany; Center for Advanced Studies of Blanes CEAB-CSIC, Spanish Council for Research, Spain; Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, France; Red Sea Research Centre and Computational Bioscience Research Center, King Abdullah University of Science and Technology, Saudi Arabia; Josephine Bay Paul Center, Marine Biological Laboratory, United States; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, United Kingdom; Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Denmark; School of Biological Sciences, Seoul National University, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Republic of Korea; University of Bremen and Life Sciences and Chemistry, Germany; Computing Center, Helmholtz Center for Polar and Marine Research, Germany; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Denmark.

Mar 31, 2022 

https://doi.org/10.7554/eLife.67667



Abstract

Genes of unknown function are among the biggest challenges in molecular biology, especially in microbial systems, where 40–60% of the predicted genes are unknown. Despite previous attempts, systematic approaches to include the unknown fraction into analytical workflows are still lacking. Here, we present a conceptual framework, its translation into the computational workflow AGNOSTOS and a demonstration on how we can bridge the known-unknown gap in genomes and metagenomes. By analyzing 415,971,742 genes predicted from 1749 metagenomes and 28,941 bacterial and archaeal genomes, we quantify the extent of the unknown fraction, its diversity, and its relevance across multiple organisms and environments. The unknown sequence space is exceptionally diverse, phylogenetically more conserved than the known fraction and predominantly taxonomically restricted at the species level. From the 71 M genes identified to be of unknown function, we compiled a collection of 283,874 lineage-specific genes of unknown function for Cand. Patescibacteria (also known as Candidate Phyla Radiation, CPR), which provides a significant resource to expand our understanding of their unusual biology. Finally, by identifying a target gene of unknown function for antibiotic resistance, we demonstrate how we can enable the generation of hypotheses that can be used to augment experimental data.

Editor's evaluation

In this paper, the authors develop a sensitive and specific computational workflow for comprehensively summarizing known and unknown gene content across large collections of genomes and metagenomes. In addition to clustering and categorizing genes on a large scale, the authors show how to use their approach to both explore lineage-specific genes and generate hypotheses for the function of unknown genes.

https://doi.org/10.7554/eLife.67667.sa0

eLife digest
It is estimated that scientists do not know what half of microbial genes actually do. When these genes are discovered in microorganisms grown in the lab or found in environmental samples, it is not possible to identify what their roles are. Many of these genes are excluded from further analyses for these reasons, meaning that the study of microbial genes tends to be limited to genes that have already been described.

These limitations hinder research into microbiology, because information from newly discovered genes cannot be integrated to better understand how these organisms work. Experiments to understand what role these genes have in the microorganisms are labor-intensive, so new analytical strategies are needed.

To do this, Vanni et al. developed a new framework to categorize genes with unknown roles, and a computational workflow to integrate them into traditional analyses. When this approach was applied to over 400 million microbial genes (both with known and unknown roles), it showed that the share of genes with unknown functions is only about 30 per cent, smaller than previously thought. The analysis also showed that these genes are very diverse, revealing a huge space for future research and potential applications. Combining their approach with experimental data, Vanni et al. were able to identify a gene with a previously unknown purpose that could be involved in antibiotic resistance.

This system could be useful for other scientists studying microorganisms to get a more complete view of microbial systems. In future, it may also be used to analyze the genetics of other organisms, such as plants and animals.

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Um novo modelo evolucionário: Modelo de Informação Contínua

The information continuum model of evolution

Rasmus Skern-Mauritzen a Thomas Nygaard Mikkelsen b

a Institute of Marine Research, 5005, Bergen, Norway

b Geco Global, 4174, Jystrup, Denmark

Received 1 July 2021, Revised 12 August 2021, Accepted 12 August 2021, Available online 18 August 2021, Version of Record 19 August 2021.

https://doi.org/10.1016/j.biosystems.2021.104510



Abstract

Most biologists agree that evolution is contingent on inherited information shaped by natural selection. This apparent consensus could be taken to indicate agreement on the forces shaping evolution, but vivid discussions reveal divergences on how evolution is perceived. The predominant Modern Synthesis (MS) paradigm holds the position that evolution occurs through random changes acting on genomic inheritance. However, studies from recent decades have revealed that evolutionary inheritance also includes DNA-methylation, RNA, symbionts, and culture, among other factors. This has fueled a demand of a broader evolutionary perspective, for example from the proponents of the Extended Evolutionary Synthesis (EES). Despite fundamental disagreements the different views agree that natural selection happens through dissimilar perpetuation of inheritable information. Yet, neither the MS, nor the ESS dwell extensively on the nature of hereditary information. We do - and conclude that information in and of itself is immaterial. We then argue that the quality upon which natural selection acts henceforth is also immaterial. Based on these notions, we arrive at the information-centric Information Continuum Model (ICM) of evolution. The ICM asserts that hereditary information is embedded in diverse physical forms (DNA, RNA, symbionts etc.) representing a continuum of evolutionary qualities, and that information may migrate between these physical forms. The ICM leaves theoretical exploration of evolution unrestricted by the limitations imposed by the individual physical forms wherein the hereditary information is embedded (e.g. genomes). ICM bestows us with a simple heuristic model that adds explanatory dimensions to be considered in the evolution of biological systems.

Keywords Heredity Evolution Hereditome Modern synthesis Natural selection Extended evolutionary synthesis

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Fósseis de 20 milhões de anos revelam duas novas espécies de cetáceos encontrados na Suiça

sábado, maio 21, 2022

First records of extinct kentriodontid and squalodelphinid dolphins from the Upper Marine Molasse (Burdigalian age) of Switzerland and a reappraisal of the Swiss cetacean fauna

Gabriel Aguirre-Fernández ​1, Jürg Jost 2, Sarah Hilfiker 1,3

May 16, 2022

Author and article information

1. Paleontological Institute and Museum, University of Zurich, Zurich, Switzerland

2. Zofingen, Switzerland

3. Department of Environmental Systems Science, Swiss Federal Institute of Technology, Zurich, Switzerland

DOI 10.7717/peerj.13251

Published 2022-05-16

Accepted 2022-03-21

Received 2021-10-01

Academic Editor: Brandon Hedrick

Subject Areas: Evolutionary Studies, Marine Biology, Paleontology, Taxonomy, Zoology

Keywords: Cetacea, Odontoceti, Burdigalian, Upper Marine Molasse, Periotic, Paratethys, Kentriodontidae, Squalodelphinidae, Physeteridae, Kentriodon

Copyright © 2022 Aguirre-Fernández et al.

Figure 2: Families present in the Mediterranean and Paratethys during the Burdigalian according to Bianucci & Landini (2002).

Abstract

The Swiss Upper Marine Molasse (OMM) documents a transgression event dated to around 21 to 17 million years in which dolphin and other vertebrate remains have been reported. We revised the whole cetacean (whales and dolphins) OMM assemblage available in main collections, focusing on the identification and interpretation of periotics (bone that contains the inner ear). Periotics are rare, but they provide the richest taxonomic information in the sample and hint to environmental associations. Micro-computerized tomography allowed the reconstruction of bony labyrinths for comparisons and environmental interpretations. Three families are represented by periotics: Kentriodontidae, Squalodelphinidae and Physeteridae. The cetacean taxonomic composition of the Swiss OMM reinforces biogeographical patterns reported for the Mediterranean and Paratethys during the Burdigalian at a regional scale and the Calvert cetacean fauna of the northwest Atlantic at oceanic scale.

Licence

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

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Perguntas abertas para entender as origens da vida

quinta-feira, maio 19, 2022

Open questions in understanding life’s origins

Christopher J. Butch, Markus Meringer, Jean-Sebastien Gagnon & H. James Cleaves II 

Communications Chemistry volume 4, Article number: 11 (2021) Cite this article 

Fig. 1: Workflow for studies of the chemistry of life’s origins.


The chemical space of prebiotic chemistry is extremely large, while extant biochemistry uses only a few thousand interconnected molecules. Here we discuss how the connection between these two regimes can be investigated, and explore major outstanding questions in the origin of life.

FREE PDF GRATIS: Communications Chemistry

Darwin, os primeiros animais desenvolveram ecossistemas complexos antes da explosão cambriana!

quarta-feira, maio 18, 2022

Metacommunity analyses show an increase in ecological specialisation throughout the Ediacaran period

Rebecca Eden,Andrea Manica,Emily G. Mitchell 

Published: May 17, 2022

https://doi.org/10.1371/journal.pbio.3001289 



A group of Ediacaran specimens of Fractofusus and Plumeropriscum from the "E" surface, Mistaken Point Ecological Reserve, NewFoundland, Canada. 

Credit: Charlotte G. Kenchington

Abstract

The first animals appear during the late Ediacaran (572 to 541 Ma); an initial diversity increase was followed reduction in diversity, often interpreted as catastrophic mass extinction. We investigate Ediacaran ecosystem structure changes over this time period using the “Elements of Metacommunity Structure” framework to assess whether this diversity reduction in the Nama was likely caused by an external mass extinction, or internal metacommunity restructuring. The oldest metacommunity was characterised by taxa with wide environmental tolerances, and limited specialisation or intertaxa associations. Structuring increased in the second oldest metacommunity, with groups of taxa sharing synchronous responses to environmental gradients, aggregating into distinct communities. This pattern strengthened in the youngest metacommunity, with communities showing strong environmental segregation and depth structure. Thus, metacommunity structure increased in complexity, with increased specialisation and resulting in competitive exclusion, not a catastrophic environmental disaster, leading to diversity loss in the terminal Ediacaran. These results reveal that the complex eco-evolutionary dynamics associated with Cambrian diversification were established in the Ediacaran.

FREE PDF GRATIS: PLoS Biology

Citation: Eden R, Manica A, Mitchell EG (2022) Metacommunity analyses show an increase in ecological specialisation throughout the Ediacaran period. PLoS Biol 20(5): e3001289. https://doi.org/10.1371/journal.pbio.3001289

Academic Editor: Pedro Jordano, Estacion Biologica de Doñana CSIC, SPAIN

Received: May 1, 2021; Accepted: March 29, 2022; Published: May 17, 2022

Copyright: © 2022 Eden 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 data and code is available in the supplementary materials. The data used in this paper has been modified from previously published data and are publicly available on figshare doi: 10.6084/m9.figshare.13664105.

Funding: This work was funded by a Natural Environment Research Council Independent Research Fellowship NE/S014756/1 to EGM. 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.

Caracterização arquitetônica do favo de mel de Apis mellifera: mero acaso, fortuita necessidade ou design inteligente?

terça-feira, maio 17, 2022

Computational methods for the characterization of Apis mellifera comb architecture

Christoph Bader, João Costa, Nic Lee, Rachel Smith, Ren Ri, James C. Weaver & Neri Oxman 

Communications Biology volume 5, Article number: 468 (2022) Cite this article



Fig. 4: Digitally driven observations of cell regularity and build direction.

Abstract

The architecture of honey bee combs embodies a range of expressions associated with swarm intelligence, emergent behaviors, and social organization, which has drawn scientists to study them as a model of collective construction processes. Until recently, however, the development of models to characterize comb-building behavior has relied heavily on laborious manual observations and measurements. The use of high-throughput multi-scale analyses to investigate the geometric features of Apis mellifera comb therefore has the potential to vastly expand our understanding of comb-building processes. Inspired by this potential, here we explore connections between geometry and behavior by utilizing computational methods for the detailed examination of hives constructed within environments designed to observe how natural building rule sets respond to environmental perturbations. Using combs reconstructed from X-ray micro-computed tomography source data, we introduce a set of tools to analyze geometry and material distributions from these scans, spanning from individual cells to whole-hive-level length scales. Our results reveal relationships between cell geometry and comb morphology, enable the generalization of prior research on build direction, demonstrate the viability of our methods for isolating specific features of comb architecture, and illustrate how these results may be employed to investigate hive-level behaviors related to build-order and material distributions.