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
Image/Imagem: Nature Reviews Genetics
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.
FREE PDF GRATIS: eLIFE
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
FREE PDF GRATIS: Biosystems
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
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.
FREE PDF GRATIS: PeerJ
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.
FREE PDF GRATIS: Communications Biology Sup. Info.
Os argumentos cosmológicos teleológicos e de Kalam revisitados - PDF Grátis
domingo, maio 15, 2022
The Teleological and Kalam Cosmological Arguments Revisited
Authors: (view affiliations) Andrew Loke
This book is open access, which means that you have free and unlimited access
Devises an original deductive formulation of the Teleological Argument
Argues for design by exclusion
Combines the Teleological Argument with the Kalam Cosmological Argument
Part of the book series: Palgrave Frontiers in Philosophy of Religion (PFPR)
About this book
‘An innovative examination and defence of the cosmological and teleological arguments – accessible to the non-expert but pushing the debate into new territory with great originality and verve.’
- T. J. Mawson, Oxford University, UK
‘Andrew Loke's book provides an up-to-date assessment of the Teleological and Kalam Cosmological Arguments, including a thorough response to contemporary objections. It advances the discussion concerning the ultimate origin of the universe and makes a significant contribution to the field of philosophy of religion and the dialogue between science and religion.’
- William Lane Craig, Biola University, USA
‘This book provides an engaging guide to two important features of our universe – it seems to have had a beginning, and its ability to support life is remarkably rare – and their deeper implications. Up-to-date, wide-ranging and highly recommended.’
- Luke Barnes, Western Sydney University, Australia
FREE PDF GRATIS: Springer
Estrutura de proteína chave para divisão celular intriga pesquisadores: mero acaso, fortuita necessidade ou design inteligente?
Structure of the human inner kinetochore CCAN complex and its significance for human centromere organization
Marion E.Pesenti 1, 4 Tobias Raisch 2, 4 Duccio Conti 1, 5 Kai Walstein 1, 5 Ingrid Hoffmann 1 Dorothee Vogt 1 Daniel Prumbaum 2 Ingrid R.Vetter 1 Stefan Raunser 2 Andrea Musacchio 1, 3, 6
https://doi.org/10.1016/j.molcel.2022.04.027
Under a Creative Commons license
Highlights
• A cryo-EM structure of the CCAN is reported
• The structure rationalizes relative positions and roles of the 16 CCAN subunits
• The CCAN core is shown to prefer naked DNA to CENP-A nucleosomes
• Several possible models of organization of centromeric chromatin are discussed
Summary
Centromeres are specialized chromosome loci that seed the kinetochore, a large protein complex that effects chromosome segregation. A 16-subunit complex, the constitutive centromere associated network (CCAN), connects between the specialized centromeric chromatin, marked by the histone H3 variant CENP-A, and the spindle-binding moiety of the kinetochore. Here, we report a cryo-electron microscopy structure of human CCAN. We highlight unique features such as the pseudo GTPase CENP-M and report how a crucial CENP-C motif binds the CENP-LN complex. The CCAN structure has implications for the mechanism of specific recognition of the CENP-A nucleosome. A model consistent with our structure depicts the CENP-C-bound nucleosome as connected to the CCAN through extended, flexible regions of CENP-C. An alternative model identifies both CENP-C and CENP-N as specificity determinants but requires CENP-N to bind CENP-A in a mode distinct from the classical nucleosome octamer.
FREE PDF GRATIS: Molecular Cell
Do que falamos quando falamos de “DNA lixo”? Spam???
What We Talk About When We Talk About “Junk DNA”
Nelson J.R. Fagundes, Rafael Bisso-Machado, Pedro I.C.C. Figueiredo, Maikel Varal, André L.S. Zani
Genome Biology and Evolution, Volume 14, Issue 5, May 2022, evac055, https://doi.org/10.1093/gbe/evac055
Published: 10 May 2022 Article history
Accepted: 16 April 2022
Published: 10 May 2022
Abstract
“Junk DNA” is a popular yet controversial concept that states that organisms carry in their genomes DNA that has no positive impact on their fitness. Nonetheless, biochemical functions have been identified for an increasing fraction of DNA elements traditionally seen as “Junk DNA”. These findings have been interpreted as fundamentally undermining the “Junk DNA” concept. Here, we reinforce previous arguments that this interpretation relies on an inadequate concept of biological function that does not consider the selected effect of a given genomic structure, which is central to the “Junk DNA” concept. Next, we suggest that another (though ignored) confounding factor is that the discussion about biological functions includes two different dimensions: a horizontal, ecological dimension that reflects how a given genomic element affects fitness in a specific time, and a vertical, temporal dimension that reflects how a given genomic element persisted along time. We suggest that “Junk DNA” should be used exclusively relative to the horizontal dimension, while for the vertical dimension, we propose a new term, “Spam DNA”, that reflects the fact that a given genomic element may persist in the genome even if not selected for on their origin. Importantly, these concepts are complementary. An element can be both “Spam DNA” and “Junk DNA”, and “Spam DNA” can also be recruited to perform evolved biological functions, as illustrated in processes of exaptation or constructive neutral evolution.
Keywords: spam DNA, genome evolution, biological function, exaptation, purifying selection, positive selection
FREE PDF GRATIS: Genome Biology and Evolution
Livro sobre filosofia da biologia do desenvolvimento (Cambridge University Press): PDF Grátis
Philosophy of Developmental Biology
Published online by Cambridge University Press: 16 March 2022
Marcel Weber - Affiliation: University of Geneva
Summary
The history of developmental biology is interwoven with debates as to whether mechanistic explanations of development are possible or whether alternative explanatory principles or even vital forces need to be assumed. In particular, the demonstrated ability of embryonic cells to tune their developmental fate precisely to their relative position and the overall size of the embryo was once thought to be inexplicable in mechanistic terms. Taking a causal perspective, this Element examines to what extent and how developmental biology, having turned molecular about four decades ago, has been able to meet the vitalist challenge. It focuses not only on the nature of explanations but also on the usefulness of causal knowledge – including the knowledge of classical experimental embryology – for further scientific discovery. It also shows how this causal perspective allows us to understand the nature and significance of some key concepts, including organizer, signal and morphogen. This title is also available as Open Access on Cambridge Core.
FREE PDF GRATIS: Cambridge University Press
A quiralidade da vida pode ter surgido espontaneamente na Terra
sexta-feira, maio 13, 2022
Spontaneous chiral symmetry breaking in a random driven chemical system
William D. Piñeros & Tsvi Tlusty
Nature Communications volume 13, Article number: 2244 (2022)
Fig. 1: Chemical model.
Abstract
Living systems have evolved to efficiently consume available energy sources using an elaborate circuitry of chemical reactions which, puzzlingly, bear a strict restriction to asymmetric chiral configurations. While autocatalysis is known to promote such chiral symmetry breaking, whether a similar phenomenon may also be induced in a more general class of configurable chemical systems—via energy exploitation—is a sensible yet underappreciated possibility. This work examines this question within a model of randomly generated complex chemical networks. We show that chiral symmetry breaking may occur spontaneously and generically by harnessing energy sources from external environmental drives. Key to this transition are intrinsic fluctuations of achiral-to-chiral reactions and tight matching of system configurations to the environmental drives, which together amplify and sustain diverged enantiomer distributions. These asymmetric states emerge through steep energetic transitions from the corresponding symmetric states and sharply cluster as highly-dissipating states. The results thus demonstrate a generic mechanism in which energetic drives may give rise to homochirality in an otherwise totally symmetrical environment, and from an early-life perspective, might emerge as a competitive, energy-harvesting advantage.
FREE PDF GRATIS: Nature Communications Sup. Info.
Mais um cenário da origem da vida prebioticamente plausível em um mundo de RNA-peptídeo
A prebiotically plausible scenario of an RNA–peptide world
Felix Müller, Luis Escobar, Felix Xu, Ewa Węgrzyn, Milda Nainytė, Tynchtyk Amatov, Chun‐Yin Chan, Alexander Pichler & Thomas Carell
Nature volume 605, pages279–284 (2022)
Fig. 1: Concept of how nucleoside relics of the RNA world enable RNA-based peptide synthesis.
Abstract
The RNA world concept 1 is one of the most fundamental pillars of the origin of life theory 2,3,4. It predicts that life evolved from increasingly complex self-replicating RNA molecules 1,2,4. The question of how this RNA world then advanced to the next stage, in which proteins became the catalysts of life and RNA reduced its function predominantly to information storage, is one of the most mysterious chicken-and-egg conundrums in evolution 3,4,5. Here we show that non-canonical RNA bases, which are found today in transfer and ribosomal RNAs 6,7, and which are considered to be relics of the RNA world 8,9,10,11,12, are able to establish peptide synthesis directly on RNA. The discovered chemistry creates complex peptide-decorated RNA chimeric molecules, which suggests the early existence of an RNA–peptide world 13 from which ribosomal peptide synthesis 14 may have emerged 15,16. The ability to grow peptides on RNA with the help of non-canonical vestige nucleosides offers the possibility of an early co-evolution of covalently connected RNAs and peptides 13,17,18, which then could have dissociated at a higher level of sophistication to create the dualistic nucleic acid–protein world that is the hallmark of all life on Earth.
FREE PDF GRATIS: Nature Sup. Info. Peer Review File
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