Se não existe design intencional, por que buscar inspiração na natureza?

Vision-controlled jetting for composite systems and robots

Thomas J. K. Buchner, Simon Rogler, Stefan Weirich, Yannick Armati, Barnabas Gavin Cangan, Javier Ramos, Scott T. Twiddy, Davide M. Marini, Aaron Weber, Desai Chen, Greg Ellson, Joshua Jacob, Walter Zengerle, Dmitriy Katalichenko, Chetan Keny, Wojciech Matusik & Robert K. Katzschmann

Nature volume 623, pages 522–530 (2023)

An image montage of the soft robotic hand holding a marker pen and a water bottle.(Image credit: ETH Zurich/Thomas Buchner)

Abstract

Recreating complex structures and functions of natural organisms in a synthetic form is a long-standing goal for humanity1. The aim is to create actuated systems with high spatial resolutions and complex material arrangements that range from elastic to rigid. Traditional manufacturing processes struggle to fabricate such complex systems2. It remains an open challenge to fabricate functional systems automatically and quickly with a wide range of elastic properties, resolutions, and integrated actuation and sensing channels2,3. We propose an inkjet deposition process called vision-controlled jetting that can create complex systems and robots. Hereby, a scanning system captures the three-dimensional print geometry and enables a digital feedback loop, which eliminates the need for mechanical planarizers. This contactless process allows us to use continuously curing chemistries and, therefore, print a broader range of material families and elastic moduli. The advances in material properties are characterized by standardized tests comparing our printed materials to the state-of-the-art. We directly fabricated a wide range of complex high-resolution composite systems and robots: tendon-driven hands, pneumatically actuated walking manipulators, pumps that mimic a heart and metamaterial structures. Our approach provides an automated, scalable, high-throughput process to manufacture high-resolution, functional multimaterial systems.

FREE PDF GRATIS: Nature 

Não saia de casa sem informação: ela é importante para sua sobrevivência.

Semantic Information in a Model of Resource Gathering Agents

Damian R. Sowinski, Jonathan Carroll-Nellenback, Robert N. Markwick, Jordi Piñero, Marcelo Gleiser, Artemy Kolchinsky, Gourab Ghoshal, and Adam Frank

PRX Life 1, 023003 – Published 17 October 2023

 

Abstract

We explore the application of a theory of semantic information to the well-motivated problem of resource foraging. Semantic information is defined as the subset of correlations, which is here measured via the transfer entropy, between agent A and environment E that is necessary for the agent to maintain its viability V. Viability, in turn, is endogenously defined as opposed to the use of exogenous quantities like utility functions. In our model, the forager's movements are determined by its ability to measure, via a sensor, the presence of an individual unit of resource, while the viability function is its expected lifetime. Through “interventions”—scrambling the correlations between agent and environment by noising the sensor—we demonstrate the presence of a critical value of the noise parameter, ηc, above which the forager's expected lifetime is dramatically reduced. On the other hand, for η<ηc there is little to no effect on its ability to survive. We refer to this boundary as the semantic threshold, quantifying the subset of agent-environment correlations that the agent actually needs to maintain its desired state of staying alive. Each bit of information affects the agent's ability to persist both above and below the semantic threshold. Modeling the viability curve and its semantic threshold via forager and/or environment parameters, we show how the correlations are instantiated. Our work demonstrates the successful application of semantic information to a well-known agent-based model of biological and ecological interest. Additionally, we demonstrate that the concept of semantic thresholds may prove useful for understanding the role information plays in allowing systems to become autonomous agents.

FREE PDF GRATIS: PRX Life 1

Controle de redes reguladoras de genes padronizando tecidos orientado por morfogênese: mero acaso, fortuita necessidade ou princípios de design inteligente?

Optimal control of gene regulatory networks for morphogen-driven tissue patterning

Alberto Pezzotta, 1, 2, James Briscoe, 1

1. Developmental Dynamics Laboratory, The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK

2. Gatsby Computational Neuroscience Unit, University College London, 25 Howland Street, W1T 4JG London, UK

Received 17 August 2022, Revised 6 June 2023, Accepted 10 October 2023, Available online 15 November 2023, Version of Record 15 November 2023.

Published: November 15, 2023

https://doi.org/10.1016/j.cels.2023.10.004 

Highlights

• Morphogen signaling controls the pattern of gene expression in developing tissues

• Optimal control theory identifies signaling mechanisms for morphogen patterning    

• By incorporating feedback between signaling and gene regulation, it explains dynamics

• Provides an alternative framework to the “French Flag model” for morphogen patterning

Summary

The generation of distinct cell types in developing tissues depends on establishing spatial patterns of gene expression. Often, this is directed by spatially graded chemical signals—known as morphogens. In the “French Flag model,” morphogen concentration instructs cells to acquire specific fates. How this mechanism produces timely and organized cell-fate decisions, despite the presence of changing morphogen levels, molecular noise, and individual variability, is unclear. Moreover, feedback is present at various levels in developing tissues, breaking the link between morphogen concentration, signaling activity, and position. Here, we develop an alternative framework using optimal control theory to tackle the problem of morphogen-driven patterning: intracellular signaling is derived as the control strategy that guides cells to the correct fate while minimizing a combination of signaling levels and time. This approach recovers experimentally observed properties of patterning strategies and offers insight into design principles that produce timely, precise, and reproducible morphogen patterning.

FREE PDF GRATIS: Cell Systems

Darwin, nós temos um grande problema: onde estão as pontes conceituais e empíricas entre a micro e a macroevolução?

Conceptual and empirical bridges between micro- and macroevolution

Jonathan Rolland, L. Francisco Henao-Diaz, Michael Doebeli, Rachel Germain, Luke J. Harmon, L. Lacey Knowles, Lee Hsiang Liow, Judith E. Mank, Antonin Machac, Sarah P. Otto, Matt Pennell, Nicolas Salamin, Daniele Silvestro, Mauro Sugawara, Josef Uyeda, Catherine E. Wagner & Dolph Schluter

Nature Ecology & Evolution volume 7, pages 1181–1193 (2023 

Image/Imagem

Abstract

Explaining broad molecular, phenotypic and species biodiversity patterns necessitates a unifying framework spanning multiple evolutionary scales. Here we argue that although substantial effort has been made to reconcile microevolution and macroevolution, much work remains to identify the links between biological processes at play. We highlight four major questions of evolutionary biology whose solutions require conceptual bridges between micro and macroevolution. We review potential avenues for future research to establish how mechanisms at one scale (drift, mutation, migration, selection) translate to processes at the other scale (speciation, extinction, biogeographic dispersal) and vice versa. We propose ways in which current comparative methods to infer molecular evolution, phenotypic evolution and species diversification could be improved to specifically address these questions. We conclude that researchers are in a better position than ever before to build a synthesis to understand how microevolutionary dynamics unfold over millions of years.

Subscription or payment needed/Requer assinatura ou pagamento:

Nature Ecology & Evolution

Como os girassóis podem ver o sol: mero acaso, fortuita necessidade ou design inteligente?

Multiple light signaling pathways control solar tracking in sunflowers

Christopher J. Brooks,Hagop S. Atamian,Stacey L. Harmer 

Published: October 31, 2023

https://doi.org/10.1371/journal.pbio.3002344

Pixabay

Abstract

Sunflowers are famous for their ability to track the sun throughout the day and then reorient at night to face east the following morning. This occurs by differential growth patterns, with the east sides of stems growing more during the day and the west sides of stems growing more at night. This process, termed heliotropism, is generally believed to be a specialized form of phototropism; however, the underlying mechanism is unknown. To better understand heliotropism, we compared gene expression patterns in plants undergoing phototropism in a controlled environment and in plants initiating and maintaining heliotropic growth in the field. We found the expected transcriptome signatures of phototropin-mediated phototropism in sunflower stems bending towards monochromatic blue light. Surprisingly, the expression patterns of these phototropism-regulated genes are quite different in heliotropic plants. Most genes rapidly induced during phototropism display only minor differences in expression across solar tracking stems. However, some genes that are both rapidly induced during phototropism and are implicated in growth responses to foliar shade are rapidly induced on the west sides of stems at the onset of heliotropism, suggesting a possible role for red light photoreceptors in solar tracking. To test the involvement of different photoreceptor signaling pathways in heliotropism, we modulated the light environment of plants initiating solar tracking. We found that depletion of either red and far-red light or blue light did not hinder the initiation or maintenance of heliotropism in the field. Together, our results suggest that the transcriptional regulation of heliotropism is distinct from phototropin-mediated phototropism and likely involves inputs from multiple light signaling pathways.

FREE PDF GRATIS: PLoS Biology

Visão no cérebro – programada para a ação: mero acaso, necessidade fortuita ou design inteligente?

Retina-derived signals control pace of neurogenesis in visual brain areas but not circuit assembly

Shachar Sherman, Irene Arnold-Ammer, Martin W. Schneider, Koichi Kawakami & Herwig Baier

Nature Communications volume 14, Article number: 6020 (2023) 

Neurons in the zebrafish brain - Biological Intelligence/Herwig Baier

Abstract

Brain development is orchestrated by both innate and experience-dependent mechanisms, but their relative contributions are difficult to disentangle. Here we asked if and how central visual areas are altered in a vertebrate brain depleted of any and all signals from retinal ganglion cells throughout development. We transcriptionally profiled neurons in pretectum, thalamus and other retinorecipient areas of larval zebrafish and searched for changes in lakritz mutants that lack all retinal connections. Although individual genes are dysregulated, the complete set of 77 neuronal types develops in apparently normal proportions, at normal locations, and along normal differentiation trajectories. Strikingly, the cell-cycle exits of proliferating progenitors in these areas are delayed, and a greater fraction of early postmitotic precursors remain uncommitted or are diverted to a pre-glial fate. Optogenetic stimulation targeting groups of neurons normally involved in processing visual information evokes behaviors indistinguishable from wildtype. In conclusion, we show that signals emitted by retinal axons influence the pace of neurogenesis in visual brain areas, but do not detectably affect the specification or wiring of downstream neurons.

FREE PDF GRATIS: Nature Communications

Darwin, nós temos um problema: mais controvérsias recentes na teoria da evolução

 

A V HILL Lecture – Recent controversies in evolutionary theory

Dr John Welch

6 November 2023, 18:00 – 19:00  A V Hill Lecture  Bristol-Myers Squibb Lecture Theatre

Overview

Every few years, critics of evolutionary theory have argued that the field needs a radical overhaul, and this trend shows no sign of stopping. This talk will discuss some recent challenges to core parts of evolutionary theory, focussing on the most serious and substantial challenges, which have come from evolutionary biologists themselves. I will trace many of these debates back to the contested legacy of R. A. Fisher (former head of the Department of Genetics in Cambridge), arguing that the reception of his work has cast long shadows. Throughout, the issues at stake will be illustrated with recent empirical work, especially from the Mexican cave tetra (Astyanax mexicanus), and the bacterial pathogen Mycobacterium tuberculosis. 

Biography

Dr Welch retrained as a biologist after a music degree and a job as a programmer. Following postdoctoral work at University of Sussex, University of Edinburgh and Université de Montpellier, John joined the Department of Genetics as a lecturer in 2010.

Dr Welch’s doctoral work was in mathematical population genetics, and this is still a large part of his research, but he now combines this with empirical approaches, especially evolutionary inference from microbial genealogies, and cross-species comparative analyses.

A.V. Hill Lecture

Archibald Vivian Hill (1886-1977) FRS was an English physiologist, one of the founders of the diverse disciplines of biophysics and operations research. He shared the 1922 Nobel Prize in Physiology or Medicine for his elucidation of the production of heat and mechanical work in muscles. Hill is regarded, along with Hermann Helmholz, as one of the founders of biophysics.

The first AV Hill Lecture was delivered in 2013 by Sir Leszek Borysiewicz, Vice Chancellor of Cambridge University.

Entregas de primeira classe em células: mero acaso, fortuita necessidade ou design inteligente?

Genetically engineered mesenchymal stem cells as a nitric oxide reservoir for acute kidney injury therapy

Haoyan Huang Meng Qian Yue Liu Shang Chen Huifang Li Zhibo Han Zhong-Chao Han Xiang-Mei Chen Qiang Zhao Zongjin Li 

Nankai University School of Medicine, China; The Key Laboratory of Bioactive Materials, Ministry of Education, Nankai University, the College of Life Sciences, China; National Key Laboratory of Kidney Diseases, Chinese PLA General Hospital, China; Jiangxi Engineering Research Center for Stem Cell, Shangrao, China; Tianjin Key Laboratory of Engineering Technologies for Cell Pharmaceutical, National Engineering Research Center of Cell Products, AmCellGene Co., Ltd, China; Beijing Engineering Laboratory of Perinatal Stem Cells, Beijing Institute of Health and Stem Cells, Health & Biotech Co, China; Tianjin Key Laboratory of Human Development and Reproductive Regulation, Tianjin Central Hospital of Gynecology Obstetrics, Nankai University Affiliated Hospital of Obstetrics and Gynecology, China

Sep 11, 2023

https://doi.org/10.7554/eLife.84820

Microscopy image of mesenchymal stem cells (blue) after administration of the drug MGP (red), which can drive the release of nitric oxygen from cells. Image credit: Huang et al. (CC BY 4.0)

Abstract

Nitric oxide (NO), as a gaseous therapeutic agent, shows great potential for the treatment of many kinds of diseases. Although various NO delivery systems have emerged, the immunogenicity and long-term toxicity of artificial carriers hinder the potential clinical translation of these gas therapeutics. Mesenchymal stem cells (MSCs), with the capacities of self-renewal, differentiation, and low immunogenicity, have been used as living carriers. However, MSCs as gaseous signaling molecule (GSM) carriers have not been reported. In this study, human MSCs were genetically modified to produce mutant β-galactosidase (β-GALH363A). Furthermore, a new NO prodrug, 6-methyl-galactose-benzyl-oxy NONOate (MGP), was designed. MGP can enter cells and selectively trigger NO release from genetically engineered MSCs (eMSCs) in the presence of β-GALH363A. Moreover, our results revealed that eMSCs can release NO when MGP is systemically administered in a mouse model of acute kidney injury (AKI), which can achieve NO release in a precise spatiotemporal manner and augment the therapeutic efficiency of MSCs. This eMSC and NO prodrug system provides a unique and tunable platform for GSM delivery and holds promise for regenerative therapy by enhancing the therapeutic efficiency of stem cells.

FREE PDF GRATIS: eLife

 

Organização de microcompartimentos bacterianos - mero acaso, fortuita necessidade ou design inteligente?

Dissecting the phase separation and oligomerization activities of the carboxysome positioning protein McdB

Joseph L Basalla Claudia A MakJordan A Byrne Maria GhalmiY Hoang Anthony G Vecchiarelli 

Department of Molecular, Cellular, and Developmental Biology, University of Michigan-Ann Arbor, United States; Department of Biological Chemistry, University of Michigan-Ann Arbor, United States

Sep 5, 2023

https://doi.org/10.7554/eLife.81362

Droplets of the protein McdB (green) that have phase separated out of solution and will behave like liquids by growing and fusing together. Image credit: Joe Basalla (CC BY 4.0).

Abstract

Across bacteria, protein-based organelles called bacterial microcompartments (BMCs) encapsulate key enzymes to regulate their activities. The model BMC is the carboxysome that encapsulates enzymes for CO2 fixation to increase efficiency and is found in many autotrophic bacteria, such as cyanobacteria. Despite their importance in the global carbon cycle, little is known about how carboxysomes are spatially regulated. We recently identified the two-factor system required for the maintenance of carboxysome distribution (McdAB). McdA drives the equal spacing of carboxysomes via interactions with McdB, which associates with carboxysomes. McdA is a ParA/MinD ATPase, a protein family well studied in positioning diverse cellular structures in bacteria. However, the adaptor proteins like McdB that connect these ATPases to their cargos are extremely diverse. In fact, McdB represents a completely unstudied class of proteins. Despite the diversity, many adaptor proteins undergo phase separation, but functional roles remain unclear. Here, we define the domain architecture of McdB from the model cyanobacterium Synechococcus elongatus PCC 7942, and dissect its mode of biomolecular condensate formation. We identify an N-terminal intrinsically disordered region (IDR) that modulates condensate solubility, a central coiled-coil dimerizing domain that drives condensate formation, and a C-terminal domain that trimerizes McdB dimers and provides increased valency for condensate formation. We then identify critical basic residues in the IDR, which we mutate to glutamines to solubilize condensates. Finally, we find that a condensate-defective mutant of McdB has altered association with carboxysomes and influences carboxysome enzyme content. The results have broad implications for understanding spatial organization of BMCs and the molecular grammar of protein condensates.

FREE PDF: eLife

O papel da metafísica na metafísica da ciência: entre o a priori e o naturalizado

SEMINÁRIO PERMANENTE DE FILOSOFIA DAS CIÊNCIAS

03/10/2023, 16:00 - 18:00 (WEST - Western European Summer Time)

SALA 8.2.17 E VIDEOCONFERÊNCIA

The role of metaphysics in Metaphysics of Science: between the a priori and the naturalized

ORADOR: Vanesa Triviño (Universidad Complutense de Madrid)

ORGANIZAÇÃO: João Luís Cordovil, Silvia Di Marco

5.º SEMINÁRIO CONJUNTO “SEMINÁRIO PERMANENTE DE FILOSOFIA DAS CIÊNCIAS / REDE IBÉRICA DE FILOSOFIA DAS CIÊNCIAS (ReIFiCi)”

Abstract

The debate in Metaphysics of Science concerning the interaction that takes place between metaphysics and science has been mainly approached from the perspective of the scientific discipline of physics. In this presentation, I address this debate from a different perspective by paying attention to the biological framework and the different forms in which philosophers use metaphysics when addressing conceptual biological problems. In doing so, I argue that the type of metaphysics that interacts with science when characterizing the ontological status of the world does not seem to coincide with either of the characterizations of metaphysics given in the Metaphysics of Science debate, namely the a priori and the naturalized one. As I will consider, one of the lessons that can be obtained from the field of Metaphysics of Biology, is that a different form of metaphysics seems to be operating in the interaction between metaphysics and science, i.e., applied metaphysics.

Nota biográfica

Vanessa Triviño is an Assistant Professor at the Complutense University of Madrid. She completed her Ph.D. in 2019, focusing on inquiries related to the Metaphysics of Biology, such as the concepts of fitness, holobionts, and biological species. During her doctoral studies, she undertook research residencies at the Konrad Lorenz Institute (Klosterneuburg, Austria) and Egenis: the Centre for the Study of the Life Sciences (Exeter, England). Presently, her research centers on metametaphysical inquiries, metaphysics of science, metaphysics of biology, and feminist metaphysics. Her work delves into questions emerging from metaphysical characterization and the interplay between metaphysics and science in a broader sense, with a specific emphasis on the relationship between metaphysics and biology. Moreover, she examines theories of process metaphysics, properties, and relations to explore their potential applications and contributions to the philosophy of biology and the categorization of sexual differentiation.

Informações

O seminário será realizado presencialmente, na sala 8.2.17, mas será possível assistir também em videoconferência, via Zoom.

Link Zoom

https://videoconf-colibri.zoom.us/j/93642061648?pwd=MHhtTFFudXZpMmo1QVB0emQ3dENIdz09

Morada sala 8.2.17

Faculdade de Ciências da Universidade de Lisboa

Edifício C8, Piso 2

Campo Grande, Lisboa

Contacto

cfculcomunica@fc.ul.pt

Um close-up de nanomáquinas biológicas: mero acaso, fortuita necessidade ou design inteligente?

Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate

Maximilian Rüttermann, Michelle Koci, Pascal Lill, Ermis Dionysios Geladas, Farnusch Kaschani, Björn Udo Klink, Ralf Erdmann & Christos Gatsogiannis 

Nature Communications volume 14, Article number: 5942 (2023)

 

Fig. 1: Cryo-EM structure of the peroxisomal ATPase Pex1/Pex6.

Abstract

The double-ring AAA+ ATPase Pex1/Pex6 is required for peroxisomal receptor recycling and is essential for peroxisome formation. Pex1/Pex6 mutations cause severe peroxisome associated developmental disorders. Despite its pathophysiological importance, mechanistic details of the heterohexamer are not yet available. Here, we report cryoEM structures of Pex1/Pex6 from Saccharomyces cerevisiae, with an endogenous protein substrate trapped in the central pore of the catalytically active second ring (D2). Pairs of Pex1/Pex6(D2) subdomains engage the substrate via a staircase of pore-1 loops with distinct properties. The first ring (D1) is catalytically inactive but undergoes significant conformational changes resulting in alternate widening and narrowing of its pore. These events are fueled by ATP hydrolysis in the D2 ring and disengagement of a “twin-seam” Pex1/Pex6(D2) heterodimer from the staircase. Mechanical forces are propagated in a unique manner along Pex1/Pex6 interfaces that are not available in homo-oligomeric AAA-ATPases. Our structural analysis reveals the mechanisms of how Pex1 and Pex6 coordinate to achieve substrate translocation.

FREE PDF GRATIS: Nature Communications Sup. Info.

Miller-Urey, nós temos um problema sério: abordagens experimentais mais diferenciadas são necessárias.

Progress in Lipid Research

Volume 92, November 2023, 101253

The fats of the matter: Lipids in prebiotic chemistry and in origin of life studies

Author Tania C.B. Santos, Anthony H. Futerman

Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel

Received 3 July 2023, Revised 30 August 2023, Accepted 30 August 2023, Available online 1 September 2023, Version of Record 12 September 2023.

https://doi.org/10.1016/j.plipres.2023.101253

The Miller-Urey experiment (now located at UCSD, San Diego) that was used to demonstrate the synthesis of biologically relevant molecules in a hypothetical primitive reducing atmosphere.

Image/Imagem 

Abstract

The unique biophysical and biochemical properties of lipids render them crucial in most models of the origin of life (OoL). Many studies have attempted to delineate the prebiotic pathways by which lipids were formed, how micelles and vesicles were generated, and how these micelles and vesicles became selectively permeable towards the chemical precursors required to initiate and support biochemistry and inheritance. Our analysis of a number of such studies highlights the extremely narrow and limited range of conditions by which an experiment is considered to have successfully modeled a role for lipids in an OoL experiment. This is in line with a recent proposal that bias is introduced into OoL studies by the extent and the kind of human intervention. It is self-evident that OoL studies can only be performed by human intervention, and we now discuss the possibility that some assumptions and simplifications inherent in such experimental approaches do not permit determination of mechanistic insight into the roles of lipids in the OoL. With these limitations in mind, we suggest that more nuanced experimental approaches than those currently pursued may be required to elucidate the generation and function of lipids, micelles and vesicles in the OoL.

Abbreviations

CoA coenzyme A DPPC1, 2-dipalmitoyl-sn-glycero-3-phosphocholine GARD graded autocatalysis replication domain Kinrate of incorporation into a micelle Kout rate of exit from a micelle OoL origin of life PA phosphatidic acid PC phosphatidylcholine PE phosphatidylethanolamine PG phosphatidylglycerol POPC1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine PS phosphatidylserine Ps permeability coefficient R-GARD GARD with real lipids SDS sodium dodecyl sulfate SM sphingomyelin

FREE PDF: Progress in Lipid Research

Como, quando e por que a ciência falha em autocorrigir-se???

ABOUT THIS WEBSITE

This academic blog is related to the NanoBubbles project, led by 4 researchers from the Universities of Paris Sorbonne Nord, Maastricht, Grenoble-Alpes and Radboud, in collaboration with researchers from the CNRS, the University of Twente, IRIT and Ecole des Ponts.

The project focuses on how, when and why science fails to correct itself. To understand how the correction of science works or fails, the NanoBubbles project combines approaches from the natural sciences, engineering (natural language processing) and humanities and social sciences (linguistics, sociology, philosophy and history of science). 

The purpose of this academic blog is to communicate on the work carried out within the scope of the project, with the aim of sharing it with a wide audience in line with the principles of open science.

Mais uma hipótese sobre a origem da vida...

Electron transport chains as a window into the earliest stages of evolution

Aaron D. Goldman, Jessica M. Weber, Douglas E. LaRowe, and Laura M. Barge 

Edited by Donald Canfield, Syddansk Universitet, Odense M., Denmark; received September 29, 2022; accepted July 8, 2023

August 14, 2023

120 (34) e2210924120

https://doi.org/10.1073/pnas.2210924120

Abstract

The origin and early evolution of life is generally studied under two different paradigms: bottom up and top down. Prebiotic chemistry and early Earth geochemistry allow researchers to explore possible origin of life scenarios. But for these “bottom–up” approaches, even successful experiments only amount to a proof of principle. On the other hand, “top–down” research on early evolutionary history is able to provide a historical account about ancient organisms, but is unable to investigate stages that occurred during and just after the origin of life. Here, we consider ancient electron transport chains (ETCs) as a potential bridge between early evolutionary history and a protocellular stage that preceded it. Current phylogenetic evidence suggests that ancestors of several extant ETC components were present at least as late as the last universal common ancestor of life. In addition, recent experiments have shown that some aspects of modern ETCs can be replicated by minerals, protocells, or organic cofactors in the absence of biological proteins. Here, we discuss the diversity of ETCs and other forms of chemiosmotic energy conservation, describe current work on the early evolution of membrane bioenergetics, and advocate for several lines of research to enhance this understanding by pairing top–down and bottom–up approaches.

FREE PDF GRATIS: PNAS Sup. Info.

O Design Inteligente na Universidade Federal Fluminense

 

Sobre ADDLabs Laboratório de Documentação Ativa e Design Inteligente

O ADDLabs é o laboratório de Documentação Ativa e Design Inteligente do Instituto de Computação da Universidade Federal Fluminense e, desde 1996, desenvolve pesquisa e tecnologia de ponta em Inteligência Artificial e Interação Homem-Computador.

Para desenvolver seus projetos e suas pesquisas em Inteligência Artificial (IA) e Interação Homem Computador (IHC), o ADDlabs conta com o  investimento de empresas do porte da Petrobras e a parceria de instituições acadêmicas do Brasil e do exterior.

Na pesquisa, o ADDlabs oferece oportunidade a alunos, professores e pesquisadores no fomento à produção científica, por meio de artigos, publicações de dissertações de mestrado e teses de doutorado, e na descoberta de novas tecnologias em áreas da Inteligência Artificial (IA), como nas de Mineração de Dados, Redes Neurais, Ontologia, Agentes e Sistemas Especialistas, e Interação Homem Computador (IHC), como Usabilidade, Design de Interação e Engenharia Semiótica . 

Com investimentos da PETROBRAS, da UFF, da FINEP e do CNPq, o laboratório vem construindo, em seus 15 anos de existência, uma história de projetos bem sucedidos. A busca incessante pela inovação é o compromisso e a missão primordial do ADDlabs.

https://www.addlabs.uff.br/Novo_Site_ADDLabs/

+++++

NOTA DESTE BLOGGER:

A teoria do Design Inteligente afirma que há sinais de inteligência na natureza que são empiricamente detectados. O ADDLabs Laboratório de Documentação Ativa e Design Inteligente pesquisa a inteligência artificial - produto elaborado por inteligências externas dos softwares.

Precisa explicar ou é preciso desenhar? 

Darwin, nós temos um sério problema epistemológico: não existe Árvore da Vida???

Nontriplet feature of genetic code in Euplotes ciliates is a result of neutral evolution

Sofya A. Gaydukova, Mikhail A. Moldovan, Adriana Vallesi, and Pavel V. Baranov Authors Info & Affiliations

Edited by Eugene Koonin, NIH, Bethesda, MD; received December 21, 2022; accepted April 12, 2023

May 22, 2023

120 (22) e2221683120

https://doi.org/10.1073/pnas.2221683120

Significance

In this work, we provide compelling evidence that Euplotes genetic code violates the triplet nature of the genetic decoding that was thought to be universal. Thus, Euplotes possess the most extreme example of genetic code variation described so far. The nontriplecy arises from abundant ribosomal frameshift sites with no regulatory function, where stop-codons distant from the 3′ transcript end specify +1 or +2 ribosomal frameshifting with high accuracy. We show that this violation of the triplet coding in Euplotes is brought about and further maintained by neutral evolution rather than selective processes but still is irreversible.

Abstract

The triplet nature of the genetic code is considered a universal feature of known organisms. However, frequent stop codons at internal mRNA positions in Euplotes ciliates ultimately specify ribosomal frameshifting by one or two nucleotides depending on the context, thus posing a nontriplet feature of the genetic code of these organisms. Here, we sequenced transcriptomes of eight Euplotes species and assessed evolutionary patterns arising at frameshift sites. We show that frameshift sites are currently accumulating more rapidly by genetic drift than they are removed by weak selection. The time needed to reach the mutational equilibrium is several times longer than the age of Euplotes and is expected to occur after a several-fold increase in the frequency of frameshift sites. This suggests that Euplotes are at an early stage of the spread of frameshifting in expression of their genome. In addition, we find the net fitness burden of frameshift sites to be noncritical for the survival of Euplotes. Our results suggest that fundamental genome-wide changes such as a violation of the triplet character of genetic code can be introduced and maintained solely by neutral evolution.

FREE PDF GRATIS: PNAS Sup. Info.

Darwin, nós temos um problema: Evolução "de propósito" - a teleonomia nos sistemas vivos

Evolution "On Purpose": Teleonomy in Living Systems 

Edited by Peter A. Corning, Stuart A. Kauffman, Denis Noble, James A. Shapiro, Richard I. Vane-Wright, Addy Pross

The MIT Press

DOI: https://doi.org/10.7551/mitpress/14642.001.0001

ISBN electronic: 9780262376013

Publication date: 2023

A unique exploration of teleonomy—also known as “evolved purposiveness”—as a major influence in evolution by a broad range of specialists in biology and the philosophy of science.

The evolved purposiveness of living systems, termed “teleonomy” by chronobiologist Colin Pittendrigh, has been both a major outcome and causal factor in the history of life on Earth. Many theorists have appreciated this over the years, going back to Lamarck and even Darwin in the nineteenth century. In the mid-twentieth century, however, the complex, dynamic process of evolution was simplified into the one-way, bottom-up, single gene-centered paradigm widely known as the modern synthesis. In Evolution “On Purpose,” edited by Peter A. Corning, Stuart A. Kauffman, Denis Noble, James A. Shapiro, Richard I. Vane-Wright, and Addy Pross, some twenty theorists attempt to modify this reductive approach by exploring in depth the different ways in which living systems have themselves shaped the course of evolution.

Evolution “On Purpose” puts forward a more inclusive theoretical synthesis that goes far beyond the underlying principles and assumptions of the modern synthesis to accommodate work since the 1950s in molecular genetics, developmental biology, epigenetic inheritance, genomics, multilevel selection, niche construction, physiology, behavior, biosemiotics, chemical reaction theory, and other fields. In the view of the authors, active biological processes are responsible for the direction and the rate of evolution. Essays in this collection grapple with topics from the two-way “read-write” genome to cognition and decision-making in plants to the niche-construction activities of many organisms to the self-making evolution of humankind. As this collection compellingly shows, and as bacterial geneticist James Shapiro emphasizes, “The capacity of living organisms to alter their own heredity is undeniable.”

FREE PDF GRATIS: THE MIT PRESS

A ciência se autocorrige, certo? O escândalo na Universidade Stanford diz que não!

Science Corrects Itself, Right? A Scandal at Stanford Says It Doesn’t

What does it take to correct the scientific record? And who—and what—stands in the way? The answer to both questions is: everyone

By Ivan Oransky, Adam Marcus on August 1, 2023

A general view of the campus of Stanford University, including Hoover Tower, as seen from Stanford Stadium, Palo Alto, California. Credit: David Madison/Getty Images

By now you may have heard about the resignation of Stanford University president Marc Tessier-Lavigne. The move came last month after a report by a special committee of the university’s Board of Trustees found Tessier-Lavigne had, among other things, “failed to decisively and forthrightly correct mistakes in the scientific record” on at least four different occasions.

You may have thought, given the voluminous coverage of this case, that Tessier-Lavigne’s defenestration demonstrates such failures are highly unusual and typically lead to significant sanctions.

Neither is true. If—and given the history of such episodes, that’s a big if—journals end up retracting the three papers Tessier-Lavigne has said he has agreed to retract (two in Science and one in Cell), the number will represent less than a tenth of a percent of the retractions we expect to see this year. We at Retraction Watch, which tracks retracted papers, estimate that figure to be about 5,000—a tiny fraction of how many retractions should happen but don’t. And the careers of most researchers whose names are on the retractions that do happen haven’t suffered a scratch. The ones whose papers haven’t been retracted have even fewer worries.

From a distance, using history-erasing rose-colored glasses, it is reasonable to place the blame squarely on Tessier-Lavigne for the fact that his now disgraced work remained in the scientific record without any flags. After all, as the investigative committee noted in its report, problems with the research surfaced “in 2001, the early 2010s, 2015-16, and March 2021.”

In 2001, the committee wrote, Tessier-Lavigne told a colleague who brought issues to his attention “in writing that he would take corrective action, including both contacting the journal and attempting to issue a correction.” He did not.

Things went differently in 2015 and 2016 after the appearance of comments about the papers on PubPeer, a forum for discussions about the validity of scientific papers. “Dr. Tessier-Lavigne did an able job of initially pursuing corrective efforts with the journals Cell and Science between 2015-16, despite the uncooperativeness of another co-author during this time,” the committee wrote. But Cell determined a correction wasn’t necessary, and Science said it would publish Tessier-Lavigne’s corrections—and then didn’t.

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Read more here: Scientific American