Darwin, nós temos um grave problema epistemológico: como explicar a seleção na evolução molecular?

segunda-feira, outubro 07, 2024

Studies in History and Philosophy of Science

Volume 107, October 2024, Pages 54-63

Selection in molecular evolution

David Lynn Abel

The Gene Emergence Project, Proto-BioCybernetics & Proto-Cellular Metabolomics, The Origin of Life Science Foundation, Inc., 14005 Youderian Drive, Bowie, MD, 20721-2225, USA

Received 15 February 2023, Revised 29 May 2024, Accepted 29 July 2024, Available online 12 August 2024, Version of Record 12 August 2024.

https://doi.org/10.1016/j.shpsa.2024.07.004

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Abstract

Evolution requires selection. Molecular/chemical/preDarwinian evolution is no exception. One molecule must be selected over another for molecular evolution to occur and advance. Evolution, however, has no goal. The laws of physics have no utilitarian desire, intent or proficiency. Laws and constraints are blind to “usefulness.” How then were potential multi-step processes anticipated, valued and pursued by inanimate nature? Can orchestration of formal systems be physico-chemically spontaneous? The purely physico-dynamic self-ordering of Chaos Theory and irreversible non-equilibrium thermodynamic “engines of disequilibria conversion” achieve neither orchestration nor formal organization. Natural selection is a passive and after-the-fact-of-life selection. Darwinian selection reduces to the differential survival and reproduction of the fittest already-living organisms. In the case of abiogenesis, selection had to be 1) Active, 2) Pre-Function, and 3) Efficacious. Selection had to take place at the molecular level prior to the existence of non-trivial functional processes. It could not have been passive or secondary. What naturalistic mechanisms might have been at play?

Keywords

Molecular evolution Life origin Abiogenesis Self-organization Emergence Pre-Darwinian evolution Chemical evolution Nonequilibrium thermodynamics Natural selection

FREE PDF GRATIS: Studies in History and Philosophy of Science

Será que foi daí que surgiram as mitocôndrias?

sexta-feira, outubro 04, 2024

Nature

Inducing novel endosymbioses by implanting bacteria in fungi

Gabriel H. Giger, Chantal Ernst, Ingrid Richter, Thomas Gassler, Christopher M. Field, Anna Sintsova, Patrick Kiefer, Christoph G. Gäbelein, Orane Guillaume–Gentil, Kirstin Scherlach, Miriam Bortfeld-Miller, Tomaso Zambelli, Shinichi Sunagawa, Markus Künzler, Christian Hertweck & Julia A. Vorholt



Abstract

Endosymbioses have profoundly impacted the evolution of life and continue to shape the ecology of a wide range of species. They give rise to new combinations of biochemical capabilities that promote innovation and diversification1,2. Despite the many examples of known endosymbioses across the tree of life, their de novo emergence is rare and challenging to uncover in retrospect3,4,5. Here we implant bacteria into the filamentous fungus Rhizopus microsporus to follow the fate of artificially induced endosymbioses. Whereas Escherichia coli implanted into the cytosol induced septum formation, effectively halting endosymbiogenesis, Mycetohabitans rhizoxinica was transmitted vertically to the progeny at a low frequency. Continuous positive selection on endosymbiosis mitigated initial fitness constraints by several orders of magnitude upon adaptive evolution. Phenotypic changes were underscored by the accumulation of mutations in the host as the system stabilized. The bacterium produced rhizoxin congeners in its new host, demonstrating the transfer of a metabolic function through induced endosymbiosis. Single-cell implantation thus provides a powerful experimental approach to study critical events at the onset of endosymbiogenesis and opens opportunities for synthetic approaches towards designing endosymbioses with desired traits.

FREE PDF: Nature

A evolução da evolução, pois quem fica parado é poste!

sábado, setembro 28, 2024

Evolution Evolving - The Developmental Origins of Adaptation and Biodiversity

Kevin N. Lala , Tobias Uller , Nathalie Feiner , Marcus Feldman and Scott F. Gilbert

Illustrator: David Andrews

Overview

About this book

A new account of the central role developmental processes play in evolution.

A new scientific view of evolution is emerging—one that challenges and expands our understanding of how evolution works. Recent research demonstrates that organisms differ greatly in how effective they are at evolving. Whether and how each organism adapts and diversifies depends critically on the mechanistic details of how that organism operates—its development, physiology, and behavior. That is because the evolutionary process itself has evolved over time, and continues to evolve. The scientific understanding of evolution is evolving too, with groundbreaking new ways of explaining evolutionary change. In this book, a group of leading biologists draw on the latest findings in evolutionary genetics and evo-devo, as well as novel insights from studies of epigenetics, symbiosis, and inheritance, to examine the central role that developmental processes play in evolution.

Written in an accessible style, and illustrated with fascinating examples of natural history, the book presents recent scientific discoveries that expand evolutionary biology beyond the classical view of gene transmission guided by natural selection. Without undermining the central importance of natural selection and other Darwinian foundations, new developmental insights indicate that all organisms possess their own characteristic sets of evolutionary mechanisms. The authors argue that a consideration of developmental phenomena is needed for evolutionary biologists to generate better explanations for adaptation and biodiversity. This book provides a new vision of adaptive evolution.

Author / Editor information

Kevin N. Lala is professor of behavioural and evolutionary Biology at the University of St Andrews.. He is the author of Darwin’s Unfinished Symphony: How Culturb Made the Human Mind (Princeton) and other books. Tobias Uller is professor of evolutionary biology at Lund University, Sweden. He is the coeditor of Evolutionary Causation: Biological and Philosophical Reflections and Philosophy of Science for Biologists. Nathalie Feiner is a Lise Meitner group leader at the Max Planck Institute for Evolutionary Biology at Plön, Germany, and is affiliated with Lund University. Marcus W. Feldman is the Burnet C. and Mildred Finley Wohlford Professor of Biological Sciences at Stanford University. He is the author of Niche Construction. The Neglected Process in Evolution (Princeton) and other books. Scott F. Gilbert is the Howard A. Schneiderman Professor of Biology Emeritus at Swarthmore College, the Finland Distinguished Professor Emeritus at the University of Helsinki, and the author of the widely used textbook Developmental Biology.

Reviews

“Assembling a rich toolkit of insights from dung beetles and orcas to foxes and humans, Lala and colleagues have begun a major renovation of the comfy theoretical edifice constructed by the architects of twentieth-century evolutionary biology. Considering the impact of multiple inheritance systems (e.g., epigenetic, cultural, and microbial), plasticity, developmental biases, and niche construction on the core of evolutionary theory, they effectively raise the roof, knock down walls, and excavate the foundations, aiming to construct a more suitable theoretical structure for understanding the ‘endless forms most beautiful and wonderful’ of the twenty-first century. An engaging read, Evolution Evolving is an illuminating exploration for those curious about how all the new findings can fit into Darwin’s venerable house.”—Joe Henrich, author of The Secret of Our Success

“We can only come to fully understand and appreciate how novelty arises and how feedback and interactions—along with selection—shape the biological world if we expand our perspective, bringing together molecular, developmental, and evolutionary insights. With wonderful examples throughout, this book is a beautifully written and illustrated guide to help the reader better interpret and appreciate these interactions.”—Sarah Otto, University of British Columbia

“Evolution Evolving is a fascinating and original expansion of evolutionary theory, giving prominence to processes of embryonic development and the origins of novelty. The book is enlivened with many endearing examples and compelling stories, but the authors leave no doubt that their serious purpose is to demonstrate that cellular and developmental mechanisms deserve a central place in the thrilling story of the origin of species. A tour de force!”—Marc Kirschner, coauthor of The Plausibility of Life: Resolving Darwin's Dilemma

“This book is a signpost in the ongoing journey of evolutionary thinking, even though not everyone will agree with the direction it is pointing. Only a frank and open discussion will eventually lead to a renewed ‘synthesis’ of evolutionary knowledge. For that this book will be an important point of reference.”—Günter P. Wagner, author of Homology, Genes, and Evolutionary Innovation

“An eloquent, example-laden, accessible narrative setting the stage and offering the story of a truly contemporary evolutionary theory. The book represents a myriad of theoretical frames and approaches united by the focus on developmental biology, with robust examples, well-argued theory, and a sincere, even compassionate, invitation to think together.”—Agustín Fuentes, Princeton University

A thoughtful, interesting, and informative overview of major themes and research areas in contemporary evolutionary biology. Although some of the perspectives outlined in this book are controversial (and I often found myself disagreeing with the authors!), I would recommend this book to anyone seeking a better understanding of the ideas at the core of the 'Extended Evolutionary Synthesis'.”—Russell Bonduriansky, University of New South Wales

Topics Evolutionary Biology Life Sciences

De Gruyter 

Darwin, nós temos um problema sério: eles continuam discutindo teleologia na biologia...

sexta-feira, setembro 13, 2024

 


Series: Elements in Metaphysics

Teleology

Published online by Cambridge University Press:  31 August 2024

Matthew Tugby
Affiliation:
Durham University

Summary

Teleology is about functions, ends, and goals in nature. This Element offers a philosophical examination of these phenomena and aims to reinstate teleology as a core part of the metaphysics of science. It starts with a critical analysis of three theories of function and argues that functions ultimately depend on goals. A metaphysical investigation of goal-directedness is then undertaken. After arguing against reductive approaches to goal-directedness, the Element develops a new theory which grounds many cases of goal-directedness in the metaphysics of powers. According to this theory, teleological properties are genuine, irreducible features of the world.

Keywords: Teleology functions goals ends powers






Darwin, nós temos um sério problema: ainda não conseguimos reconstruir a natureza do LUCA

segunda-feira, setembro 09, 2024

Journal of Molecular Evolution  

The Unfinished Reconstructed Nature of the Last Universal Common Ancestor

Review Open access

Published: 18 July 2024

Luis Delaye



Abstract

The ultimate consequence of Darwin’s theory of common descent implies that all life on earth descends ultimately from a common ancestor. Biochemistry and molecular biology now provide sufficient evidence of shared ancestry of all extant life forms. However, the nature of the Last Universal Common Ancestor (LUCA) has been a topic of much debate over the years. This review offers a historical perspective on different attempts to infer LUCA’s nature, exploring the debate surrounding its complexity. We further examine how different methodologies identify sets of ancient protein that exhibit only partial overlap. For example, different bioinformatic approaches have identified distinct protein subunits from the ATP synthetase identified as potentially inherited from LUCA. Additionally, we discuss how detailed molecular evolutionary analysis of reverse gyrase has modified previous inferences about an hyperthermophilic LUCA based mainly on automatic bioinformatic pipelines. We conclude by emphasizing the importance of developing a database dedicated to studying genes and proteins traceable back to LUCA and earlier stages of cellular evolution. Such a database would house the most ancient genes on earth.

FREE PDF GRATIS: Journal of Molecular Evolution

Darwin, nós temos sérios problemas: lacunas explanatórias na teoria da evolução

quinta-feira, setembro 05, 2024

Biology & Philosophy  

Explanatory gaps in evolutionary theory

Open access

Published: 01 September 2024

Volume 39, article number 22, (2024)

Bendik Hellem Aaby, Gianmaria Dani & Grant Ramsey 


Abstract

Proponents of the extended evolutionary synthesis have argued that there are explanatory gaps in evolutionary biology that cannot be bridged by standard evolutionary theory. In this paper, we consider what sort of explanatory gaps they are referring to. We outline three possibilities: data-based gaps, implementation-based gaps, and framework-based gaps. We then examine the purported evolutionary gaps and attempt to classify them using this taxonomy. From there we reconsider the significance of the gaps and what they imply for the proposed need for an extended evolutionary synthesis.

FREE PDF GRATIS: Biology & Philosophy

Qual fato, Fato, FATO da evolução foi considerado neste livro? Microevolução ou macroevolução?

domingo, setembro 01, 2024

 


SALVE A DATA!

Lançamento do livro: "A Evolução é Fato"

Nos dias 19 e 20 de setembro, às 9h, a Academia Brasileira de Ciências lançará sua mais nova publicação “A Evolução é Fato”, obra que busca reforçar uma mensagem clara: a evolução é um fato científico e a pedra basal na qual se sustentam as ciências biológicas, sua existência é provada todos os dias na biodiversidade do planeta e também nas biotecnologias, como as vacinas e antibióticos em constante atualização para combater novas cepas de patógenos.

O livro é fruto de um trabalho conjunto de membros da ABC coordenados pelo Acadêmico Carlos Frederico Martins Menck. O lançamento ocorrerá em duas datas, no dia 19 de setembro, na sede da Financiadora de Estudos e Projetos (Finep), e no dia 20, no Fórum de Ciência e Cultura da UFRJ. Ambos são localizados no bairro do Flamengo, no Rio de Janeiro.

A ABC não compactua com criacionismo ou desenho inteligente. A ciência baseia-se em evidências e observações empíricas testáveis, é dependente de métodos científicos, da compilação de dados. A ciência busca explicar fenômenos pela avaliação, comprovação e experimentação, e está sempre em desenvolvimento. A evolução é o princípio fundamental da ciência moderna. 

Lançamento do livro “A Evolução é Fato” 

19 de setembro 
9h-12h30 
Local: Sede da Finep - Praia do Flamengo, 200 - 1º andar - Flamengo, Rio de Janeiro – RJ 

20 de setembro 
9h-12h30 
Local: Fórum de Ciência e Cultura da UFRJ - Av. Rui Barbosa, 762 - Flamengo, Rio de Janeiro - RJ

Darwin, nós temos um problema: a seleção natural precisa de uma condição "sem teleologia" adicionada...

quinta-feira, agosto 15, 2024

Natural selection requires no teleology in addition to heritable variation in fitness

Open access

Published: 07 August 2024

Volume 39, article number 18, (2024)

Nathan Cofnas


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Abstract

According to the standard formulation, natural selection requires variation, differential fitness, and heritability. I argue that this formulation is inadequate because it fails to distinguish natural selection from artificial selection, intelligent design, forward-looking orthogenetic selection, and adaptation via the selection of nonrandom variation. I suggest adding a no teleology condition. The no teleology condition says that the evolutionary process is not guided toward an endpoint represented in the mind of an agent, variation is produced randomly with respect to adaptation, and selection pressures are not forward looking.

FREE PDF: Biology & Philosophy

Darwin, nós temos um problema: agência é uma propriedade inerente dos organismos vivos

Agency as an Inherent Property of Living Organisms

Perspective

Open access

Published: 14 August 2024

(2024)

Bernd Rosslenbroich, Susanna Kümmell & Benjamin Bembé 


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Abstract

A central characteristic of living organisms is their agency, that is, their intrinsic activity, both in terms of their basic life processes and their behavior in the environment. This aspect is currently a subject of debate and this article provides an overview of some of the relevant publications on this topic. We develop the argument that agency is immanent in living organisms. There is no life without agency. Even the basic life processes are an intrinsic activity, which we call the organismic level of agency. In addition to this we describe several further levels. These capture different qualities that occur or transform during evolution. In addition to the organismic level, we propose an ontogenetic level, a level of directed agency, directed agency with extended flexibility, and a level that includes the capacities to follow preconceived goals. A further property of organisms is their autonomy. It has been shown that the capacity for autonomy changed during evolution. Here we propose that the two organismic properties autonomy and agency are closely related. Enhanced physiological and behavioral autonomy extends the scope of self-generated, flexible actions and reactions. The increase in autonomy through the evolution of a widened scope of behavioral possibilities and versatility in organisms coincides with extended levels of agency. Especially the human organization, including the sophisticated brain, is the basis for an extended level of agency referring to the capacities to follow preconceived goals. However, it is important for the understanding of the phenomenon of agency not only to assume this latter form, but also to look at the different levels of agency.

FREE PDF: Biological Theory

O IA Scientist: um LLM em direção à descoberta científica totalmente automatizada e aberta.

terça-feira, agosto 13, 2024

The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery

August 13, 2024


At Sakana AI, we have pioneered the use of nature-inspired methods to advance cutting-edge foundation models. Earlier this year, we developed methods to automatically merge the knowledge of multiple LLMs. In more recent work, we harnessed LLMs to discover new objective functions for tuning other LLMs. Throughout these projects, we have been continuously surprised by the creative capabilities of current frontier models. This led us to dream even bigger: Can we use foundation models to automate the entire process of research itself?

Introduction

One of the grand challenges of artificial intelligence is developing agents capable of conducting scientific research and discovering new knowledge. While frontier models have already been used to aid human scientists, e.g. for brainstorming ideas or writing code, they still require extensive manual supervision or are heavily constrained to a specific task.

Today, we’re excited to introduce The AI Scientist, the first comprehensive system for fully automatic scientific discovery, enabling Foundation Models such as Large Language Models (LLMs) to perform research independently. In collaboration with the Foerster Lab for AI Research at the University of Oxford and Jeff Clune and Cong Lu at the University of British Columbia, we’re excited to release our new paper, The AI Scientist: Towards Fully Automated Open-Ended Scientific Discovery.
.....

Ichthyosporea, outra janela na origem dos animais???

sábado, agosto 03, 2024

Ichthyosporea: a window into the origin of animals

Victoria Shabardina, Jennah E. Dharamshi, Patricia S. Ara, Meritxell Antó, Fernando J. Bascón, Hiroshi Suga, Wyth Marshall, Claudio Scazzocchio, Elena Casacuberta & Iñaki Ruiz-Trillo 

Communications Biology volume 7, Article number: 915 (2024) 



Abstract

Ichthyosporea is an underexplored group of unicellular eukaryotes closely related to animals. Thanks to their phylogenetic position, genomic content, and development through a multinucleate coenocyte reminiscent of some animal embryos, the members of Ichthyosporea are being increasingly recognized as pivotal to the study of animal origins. We delve into the existing knowledge of Ichthyosporea, identify existing gaps and discuss their life cycles, genomic insights, development, and potential to be model organisms. We also discuss the underestimated diversity of ichthyosporeans, based on new environmental data analyses. This review will be an essential resource for researchers venturing into the study of ichthyosporeans.

FREE PDF GRATIS: Communications Biology

As estruturas CryoEM revelam como o flagelo bacteriano gira e muda de direção: mero acaso, fortuita necessidade ou design inteligente?

quinta-feira, julho 25, 2024

CryoEM structures reveal how the bacterial flagellum rotates and switches direction

Prashant K. Singh, Pankaj Sharma, Oshri Afanzar, Margo H. Goldfarb, Elena Maklashina, Michael Eisenbach, Gary Cecchini & T. M. Iverson 

Nature Microbiology volume 9, pages1271–1281 (2024)

Structure of the MS-ring


Abstract

Bacterial chemotaxis requires bidirectional flagellar rotation at different rates. Rotation is driven by a flagellar motor, which is a supercomplex containing multiple rings. Architectural uncertainty regarding the cytoplasmic C-ring, or ‘switch’, limits our understanding of how the motor transmits torque and direction to the flagellar rod. Here we report cryogenic electron microscopy structures for Salmonella enterica serovar typhimurium inner membrane MS-ring and C-ring in a counterclockwise pose (4.0 Å) and isolated C-ring in a clockwise pose alone (4.6 Å) and bound to a regulator (5.9 Å). Conformational differences between rotational poses include a 180° shift in FliF/FliG domains that rotates the outward-facing MotA/B binding site to inward facing. The regulator has specificity for the clockwise pose by bridging elements unique to this conformation. We used these structures to propose how the switch reverses rotation and transmits torque to the flagellum, which advances the understanding of bacterial chemotaxis and bidirectional motor rotation.

FREE PDF GRATIS: Nature Microbiology

Mais um roteiro para a síntese da vida...

quarta-feira, julho 24, 2024

A roadmap towards the synthesis of Life

10 July 2024, Version 1

Christine Kriebisch et al

Image/Imagem

Abstract

The synthesis of life from non-living matter has captivated scientists for centuries. It is a grand challenge aimed at unraveling the fundamental principles of life and leveraging its unique features, such as resilience, sustainability, and the ability to evolve. Synthetic life holds immense potential in biotechnology, medicine, and materials science. Advancements in synthetic biology, systems chemistry, and biophysics have brought us closer to achieving this ambitious goal. Researchers have successfully assembled cellular components and synthesized biomimetic hardware for synthetic cells, while chemical reaction networks have demonstrated potential for Darwinian evolution. However, numerous challenges persist, including defining terminology and objectives, interdisciplinary collaboration, and addressing ethical aspects and public concerns. Our perspective offers a roadmap toward the engineering of life based on discussions during a two-week workshop with scientists from around the globe.

Keywords

Synthesis of life self-replication open-ended evolution synthetic cell systems chemistry bottom-up synthetic biology biophysics

FREE PDF GRATIS: chemRxiv

Os paradoxos na origem da vida - Mysterium tremendum!

sábado, julho 20, 2024

Paradoxes in the Origin of Life

Origin of Life

Published: 22 January 2015

Volume 44, pages 339–343, (2014)

The “Open Questions” framework reflects an understandable frustration of many who study “origins” that much of current research into the “origins problem” seems to be no different conceptually from research formulated a half century ago by Orgel, Miller, and other heroes of modern prebiotic chemistry. Discussed here is an alternative approach to guide research into the origins of life, one that focuses on “paradoxes”, pairs of statements, both grounded in theory and observation, that (taken together) suggest that the “origins problem” cannot be solved.

A substantial amount of ink has been consumed by efforts to define life, without consensus. This motivates many of us experimentalists to consciously avoid the “definition trap”. We do so by noting that states of matter can be offered as exemplars for “not life” without controversy, as can states of matter that everyone agrees constitute “life”. The consensus fails to define the boundary between these two. Nevertheless, much productive discussion can follow without needing to identify “the” distinguishing feature that represents “the” unique difference between any pair of states offered. This is illustrated by a recent report on the limits of organic life in the Solar System, whose authors declined to demarcate the difference between life and non-life (Baross et al. 2007; Benner et al. 2004).

Of course, under the language and theory used by modern science to describe states of matter, pairs of “life” and “not-life” exemplars agreed by consensus certainly appear different, and in very many ways, no matter what those exemplars are. This means that the emergence of an indisputably living state (no matter how chosen) from any indisputably non-living state (no matter how chosen) appears to require a “lengthy pathway consisting of many stages” (Szostak 2012). It is, of course, an open question as to whether this appearance truly means that life actually can originate only via a lengthy pathway, or whether this appearance simply reflects incomplete and/or incorrect language and/or theories in these descriptions. Most of us hope that the second is the case, a hope that if realized would point to a very different solution to the “origins” problem. However unjustified this hope might be, classical research in “origins” has offered us little reason to abandon it.Footnote1

However, even if we accept the premise that the emergence of “biology” from “chemistry” necessarily involves a lengthy pathway, we must confront a bigger problem before we attempt to design experiments to re-create such a pathway in a laboratory. We are now 60 years into the modern era of prebiotic chemistry. That era has produced tens of thousands of papers attempting to define processes by which “molecules that look like biology” might arise from “molecules that do not look like biology”, find conditions where oligomers might form spontaneously from those molecules, identify constraints on pre-metabolic cycles that might deliver those molecules without leaking material into the complexity sometimes characterized as “asphalt”, or assemble ways to create chiral compounds largely free from their enantiomers. For the most part, these papers report “success” in the sense that those papers define the term.

And yet, the problem remains unsolved.

...

FREE PDF: Origins of Life and Evolution of Biospheres

LUCA, o último ancestral comum de toda a vida surgiu muito antes do que se pensava

sexta-feira, julho 12, 2024

The nature of the last universal common ancestor and its impact on the early Earth system

Edmund R. R. Moody, Sandra Álvarez-Carretero, Tara A. Mahendrarajah, James W. Clark, Holly C. Betts, Nina Dombrowski, Lénárd L. Szánthó, Richard A. Boyle, Stuart Daines, Xi Chen, Nick Lane, Ziheng Yang, Graham A. Shields, Gergely J. Szöllősi, Anja Spang, Davide Pisani, Tom A. Williams, Timothy M. Lenton & Philip C. J. Donoghue 

Nature Ecology & Evolution (2024)

An illustration showing how LUCA may have been attacked by viruses

Science Graphic Design

Abstract

The nature of the last universal common ancestor (LUCA), its age and its impact on the Earth system have been the subject of vigorous debate across diverse disciplines, often based on disparate data and methods. Age estimates for LUCA are usually based on the fossil record, varying with every reinterpretation. The nature of LUCA’s metabolism has proven equally contentious, with some attributing all core metabolisms to LUCA, whereas others reconstruct a simpler life form dependent on geochemistry. Here we infer that LUCA lived ~4.2 Ga (4.09–4.33 Ga) through divergence time analysis of pre-LUCA gene duplicates, calibrated using microbial fossils and isotope records under a new cross-bracing implementation. Phylogenetic reconciliation suggests that LUCA had a genome of at least 2.5 Mb (2.49–2.99 Mb), encoding around 2,600 proteins, comparable to modern prokaryotes. Our results suggest LUCA was a prokaryote-grade anaerobic acetogen that possessed an early immune system. Although LUCA is sometimes perceived as living in isolation, we infer LUCA to have been part of an established ecological system. The metabolism of LUCA would have provided a niche for other microbial community members and hydrogen recycling by atmospheric photochemistry could have supported a modestly productive early ecosystem.

FREE PDF: Nature Ecology & Evolution Sup. Info. Peer Review File

A síntese evolutiva estendida: um exame histórico e filosófico integrado

sexta-feira, junho 14, 2024

The extended evolutionary synthesis: An integrated historical and philosophical examination


Yafeng Shan


First published: 12 June 2024
https://doi.org/10.1111/phc3.13002

 

 https://static.cambridge.org/binary/version/id/urn:cambridge.org:id:binary:20161123115658336-0722:9781316771488:17624fig8_4.png?pub-status=live

Image/Imagem: Cambridge University

Abstract

Among biologists and philosophers, there is an ongoing debate over the Modern Synthesis and the Extended Evolutionary Synthesis. Some argue that our current evolutionary biology is in need of (at least) some substantial revision or nontrivial extension, while others maintain that the Modern Synthesis remains the foundational framework for evolutionary biology. It has been widely debated whether the Extended Evolutionary Synthesis provides a more promising framework than the Modern Synthesis. The nature and methodological implications of the Extended Evolutionary Synthesis were also examined. This paper offers an integrated historical and philosophical examination of the debate over the Extended Evolutionary Synthesis. It reviews the development of evolutionary biology of the twentieth century. It argues that there are substantial conceptual and theoretical differences between the Modern Synthesis and the Extended Evolutionary Synthesis, but they are not incommensurable paradigms in the Kuhnian sense. It also argues for a functional approach to the debate over these two frameworks of evolutionary theory.
 

FREE PDF GRATIS: Philosophy Compass

Um relato unificado das variedades do Darwinismo: explicação, lógica e cosmovisão

quarta-feira, junho 05, 2024

The Varieties of Darwinism: Explanation, Logic, and Worldview

Hugh Desmond, André Ariew, Philippe Huneman, and Thomas Reydon

 

Abstract

Ever since its inception, the theory of evolution has been reified into an “-ism”: Darwinism. Although biologists today, by and large, do not use the term “Darwinism” in their research, it still enjoys currency in broader academic and societal contexts. “Darwinian approaches” proliferate across the sciences and humanities and, in public discourse, various so-called “Darwinian views on life” are perceived to have ethically and politically laden consequences. What exactly is Darwinism, and how precisely are its nonscientific uses related to the scientific theory of evolution? Some claim the term’s meaning should be limited to scientific content, yet others call for its abolition altogether. In this paper, we propose a unified account of these varieties of Darwinism. We show how the theories introduced by Darwin have grounded a “logic” or style of reasoning about phenomena, as well as various ethically and politically charged “worldviews.” The full meaning of Darwinism, as well as how this meaning has changed over time, can only be understood through the complex interaction between these dimensions.

Subscription or payment needed/Requer assinatura ou pagamento:  

The Quarterly Review of Biology

Free preprint/Pré-impressão gratuita: PhilSci Archive


DNA como um perfeito computador quântico: mero acaso, fortuita necessidade ou design inteligente?

quinta-feira, maio 23, 2024

DNA as a perfect quantum computer based on the quantum physics principles

R. Riera Aroche, Y. M. Ortiz García, M. A. Martínez Arellano & A. Riera Leal

Scientific Reports volume 14, Article number: 11636 (2024)

Symmetries of DNA canonical base pairs quantum informational cryptography. (A) Chemical structure of the nitrogenous bases, pyrimidines, and purines. (B) A-T and C-G, in their mutual connection, have the same functional quantum state while retaining different structures and morphologies.

Abstract

DNA is a complex multi-resolution molecule whose theoretical study is a challenge. Its intrinsic multiscale nature requires chemistry and quantum physics to understand the structure and quantum informatics to explain its operation as a perfect quantum computer. Here, we present theoretical results of DNA that allow a better description of its structure and the operation process in the transmission, coding, and decoding of genetic information. Aromaticity is explained by the oscillatory resonant quantum state of correlated electron and hole pairs due to the quantized molecular vibrational energy acting as an attractive force. The correlated pairs form a supercurrent in the nitrogenous bases in a single band-molecular orbital (-MO). The MO wave function is assumed to be the linear combination of the n constituent atomic orbitals. The central Hydrogen bond between Adenine (A) and Thymine (T) or Guanine (G) and Cytosine (C) functions like an ideal Josephson Junction. The approach of a Josephson Effect between two superconductors is correctly described, as well as the condensation of the nitrogenous bases to obtain the two entangled quantum states that form the qubit. Combining the quantum state of the composite system with the classical information, RNA polymerase teleports one of the four Bell states. DNA is a perfect quantum computer.

FREE PDF GRATIS: Science Reports

 

 

Darwin, você precisa de mais uma nova teoria para explicar o fato, Fato, FATO da evolução

sexta-feira, maio 03, 2024

Progress in Biophysics and Molecular Biology
Volume 189, July 2024, Pages 26-31

Cooperative genes in smart systems: Toward an inclusive new synthesis in evolution☆
Peter A, Corning

Institute for the Study of Complex Systems, 1390 158th Place NE #616, Bellevue, WA, 98008, USA

Received 28 February 2024, Revised 3 April 2024, Accepted 3 April 2024, Available online 7 April 2024, Version of Record 27 April 2024.

https://doi.org/10.1016/j.pbiomolbio.2024.04.001

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Highlights

    • The “Modern Synthesis” in evolution emphasizes a competitive “struggle for existence” among “selfish genes”.    

   • Over the years many other sources of evolutionary causation have been identified.

    • This prompted the proposal for an “extended synthesis”.

    • However, it is now evident that genes play only a minor role in evolution.

   • It's time to abandon the Modern Synthesis and develop a more “inclusive” synthesis.

Abstract

For more than half a century, biologist Julian Huxley's term, the “Modern Synthesis”, has been used as a label for a model of biological evolution where genetic influences are viewed as a principal source of creativity and change. Over the years, as evidence has accumulated that there are many other, far more important factors at work in evolution, theoretical “compromises,” such as the so-called “Extended Synthesis”, have been proposed. This is no longer tenable. It is time to abandon the Modern Synthesis, and its doppelganger “The Selfish Gene”. Here is the case for a new, multi-faceted, open-ended, “inclusive” evolutionary synthesis, where living systems themselves are recognized as purposeful (teleonomic) “agents” and cooperative effects (synergies) of various kinds are seen as all-important influences.

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Progress in Biophysics and Molecular Biology

Darwin, nós temos problemas: alguns pensamentos heterodoxos sobre a teoria da evolução

quarta-feira, maio 01, 2024

 
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Introduction: Heterodox Thinking on Evolution

J. Scott Turner

https://www.nas.org/academic-questions/37/1/introduction-heterodox-thinking-on-evolution

Homeostasis and Purposeful Evolution Homeostasis and Purposeful Evolution

J. Scott Turner

https://www.nas.org/academic-questions/37/1/homeostasis-and-purposeful-evolution

Evolving Views on the Science of Evolution

Nathalie Gontier

https://www.nas.org/academic-questions/37/1/evolving-views-on-the-science-of-evolution
 

Do Organisms Have Goals and Purpose?

Amelia Lewis

https://www.nas.org/academic-questions/37/1/do-organisms-have-goals-and-purpose

 
Evolution Is Neither Random Accidents nor Divine Intervention: Biological Action Changes Genomes

James A. Shapiro

https://www.nas.org/academic-questions/37/1/evolution-is-neither-random-accidents-nor-divine-intervention-biological-action-changes-genomes
 

Heterodox Thinking on Evolution and Radical Enlightenment

Richard I. Vane-Wright

https://www.nas.org/academic-questions/37/1/heterodox-thinking-on-evolution-and-radical-enlightenment


 

 

Decodificando a linguagem das células: mero acaso, fortuita necessidade ou design inteligente?

segunda-feira, abril 15, 2024

OrthoID: profiling dynamic proteomes through time and space using mutually orthogonal chemical tools

Ara Lee, Gihyun Sung, Sanghee Shin, Song-Yi Lee, Jaehwan Sim, Truong Thi My Nhung, Tran Diem Nghi, Sang Ki Park, Ponnusamy Pon Sathieshkumar, Imkyeung Kang, Ji Young Mun, Jong-Seo Kim, Hyun-Woo Rhee, Kyeng Min Park & Kimoon Kim

Nature Communications  15, Article number: 1851 (2024) 


Fig. 1: Schematic description of the protein labeling and identification process (OrthoID).

Abstract

Identifying proteins at organelle contact sites, such as mitochondria-associated endoplasmic reticulum membranes (MAM), is essential for understanding vital cellular processes, yet challenging due to their dynamic nature. Here we report “OrthoID”, a proteomic method utilizing engineered enzymes, TurboID and APEX2, for the biotinylation (Bt) and adamantylation (Ad) of proteins close to the mitochondria and endoplasmic reticulum (ER), respectively, in conjunction with high-affinity binding pairs, streptavidin-biotin (SA-Bt) and cucurbit[7]uril-adamantane (CB[7]-Ad), for selective orthogonal enrichment of Bt- and Ad-labeled proteins. This approach effectively identifies protein candidates associated with the ER-mitochondria contact, including LRC59, whose roles at the contact site were—to the best of our knowledge—previously unknown, and tracks multiple protein sets undergoing structural and locational changes at MAM during mitophagy. These findings demonstrate that OrthoID could be a powerful proteomics tool for the identification and analysis of spatiotemporal proteins at organelle contact sites and revealing their dynamic behaviors in vital cellular processes. 

FREE PDF GRATIS: Nature Communications Sup. Info. Peer Review File

A ciência normal não é acrítica, tampouco dogmática

segunda-feira, abril 08, 2024

Normal science: not uncritical or dogmatic

Published: 27 March 2024

Synthese Volume 203, article number 108, (2024)



Abstract

When Kuhn first published his Structure of Scientific Revolutions he was accused of promoting an “irrationalist” account of science. Although it has since been argued that this charge is unfair in one aspect or another, the early criticism still exerts an influence on our understanding of Kuhn. In particular, normal science is often characterized as dogmatic and uncritical, even by commentators sympathetic to Kuhn. I argue not only that there is no textual evidence for this view but also that normal science is much better understood as being based on epistemically justified commitment to a paradigm and as pragmatic in its handling of anomalies. I also argue that normal science is an example of what I call Kuhn’s program of revisionary rational reconstruction.

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Possibilidades conceituais em mutação e evolução

quarta-feira, março 20, 2024

Mutation and evolution: Conceptual possibilities
Adi Livnat, Alan C. Love


First published: 22 January 2024

https://doi.org/10.1002/bies.202300025 

 

https://www.palomar.edu/anthro/synthetic/images/mutation.gif

Image/Imagem

Abstract

Although random mutation is central to models of evolutionary change, a lack of clarity remains regarding the conceptual possibilities for thinking about the nature and role of mutation in evolution. We distinguish several claims at the intersection of mutation, evolution, and directionality and then characterize a previously unrecognized category: complex conditioned mutation. Empirical evidence in support of this category suggests that the historically famous fluctuation test should be revisited, and new experiments should be undertaken with emerging experimental techniques to facilitate detecting mutation rates within specific loci at an ultra-high, individual base pair resolution.

FREE PDF GRATIS: BioEssays

A origem, o caráter e a distribuição dos códigos genéticos variantes são melhor explicados pelo design comum do que pela teoria evolucionária

segunda-feira, março 04, 2024

On the Origin of the Codes: The Character and Distribution of Variant Genetic Codes is Better Explained by Common Design than Evolutionary Theory

Winston Ewert

https://d2jx2rerrg6sh3.cloudfront.net/image-handler/picture/codon%20wheel%20-%20magnetix%20_thumb_1.jpg

Abstract

The near universality of the genetic code is frequently cited as evidence for universal common ancestry. On the other hand, critics of universal common ancestry frequently point to exceptions to the universal code as evidence against it. However, there has never been a comprehensive investigation into the character and distribution of variant genetic codes and their implications for the debate over universal common ancestry. This paper develops a framework for understanding codes within a common design framework, based crucially on the premise that some genetic code variants are designed and others are the result of mutations to translation machinery. We found that these two sources of variant codes can be distinguished by considering organismal lifestyle, taxonomic rank, evolutionary feasibility, codon rarity and complexity of distribution. These different approaches to distinguishing the codes give highly correlated results, demonstrating impressive explanatory power for our framework. In contrast, we find that evolutionary theory has difficulty explaining the character and distribution of variant genetic codes.

FREE PDF GRATIS: BioComplexity

Supplemental files: Table of Nuclear Codes, Table of Mitochondrial Codes

Um código universal impulsiona a formação de todas as membranas celulares?

quinta-feira, fevereiro 29, 2024

Membranes are functionalized by a proteolipid code

Troy A. Kervin & Michael Overduin

BMC Biology volume 22, Article number: 46 (2024)

 https://scx1.b-cdn.net/csz/news/800a/2024/research-team-uncovers.jpg

Abstract

Membranes are protein and lipid structures that surround cells and other biological compartments. We present a conceptual model wherein all membranes are organized into structural and functional zones. The assembly of zones such as receptor clusters, protein-coated pits, lamellipodia, cell junctions, and membrane fusion sites is explained to occur through a protein-lipid code. This challenges the theory that lipids sort proteins after forming stable membrane subregions independently of proteins.

FREE PDF GRATIS: BMC Biology