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


Image/Imagem

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 


Image/Imagem

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

Image

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.

Payment or subscription needed/Requer pagamento ou assinatura:

Progress in Biophysics and Molecular Biology

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

quarta-feira, maio 01, 2024

 
FREE PDFs GRATIS:
 
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.

FREE PDF GRATIS: Synthese


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

Efeitos magnéticos na origem da vida?

segunda-feira, fevereiro 26, 2024

Enantioselective Adsorption on Magnetic Surfaces


Mohammad Reza Safari, Frank Matthes, Vasile Caciuc, Nicolae Atodiresei, Claus M. Schneider, Karl-Heinz Ernst, Daniel E. Bürgler

First published: 28 December 2023
https://doi.org/10.1002/adma.202308666

 

https://scx1.b-cdn.net/csz/news/800a/2024/magnetic-effects-at-th-1.jpg

 Credit: Advanced Materials (2023). DOI: 10.1002/adma.202308666

Abstract

From the beginning of molecular theory, the interplay of chirality and magnetism has intrigued scientists. There is still the question if enantiospecific adsorption of chiral molecules occurs on magnetic surfaces. Enantiomer discrimination was conjectured to arise from chirality-induced spin separation within the molecules and exchange interaction with the substrate's magnetization. Here, it is shown that single helical aromatic hydrocarbons undergo enantioselective adsorption on ferromagnetic cobalt surfaces. Spin and chirality sensitive scanning tunneling microscopy reveals that molecules of opposite handedness prefer adsorption onto cobalt islands with opposite out-of-plane magnetization. As mobility ceases in the final chemisorbed state, it is concluded that enantioselection must occur in a physisorbed transient precursor state. State-of-the-art spin-resolved ab initio simulations support this scenario by refuting enantio-dependent chemisorption energies. These findings demonstrate that van der Waals interaction should also include spin-fluctuations which are crucial for molecular magnetochiral processes.
 

FREE PDF GRATIS: Advanced Materials

Darwin, nós temos um problema: como causa necessária para a evolução biológica a autorreplicação fenotípica deve ser exata.

quinta-feira, fevereiro 22, 2024

Biosystems
Volume 237, March 2024, 105154

Accurate phenotypic self-replication as a necessary cause for biological evolution.

Seymour Garte 

Department of Pharmacology and Toxicology, Ernest Mario School of Pharmacy, Rutgers University, 160 Frelinghuysen Road, Piscataway, NJ, 08854-8020, USA

Received 27 October 2023, Revised 29 January 2024, Accepted 9 February 2024, Available online 10 February 2024, Version of Record 14 February 2024.

https://media.springernature.com/m312/springer-static/image/art%3A10.1038%2Fs41570-020-0196-x/MediaObjects/41570_2020_196_Fig1_HTML.png? 

Image/Imagem:
Adamski, P., Eleveld, M., Sood, A. et al. From self-replication to replicator systems en route tode novo life. Nat Rev Chem 4, 386–403 (2020). https://doi.org/10.1038/s41570-020-0196-x

Abstract

Since the Origin of Species, it has been known that evolution depends on what Darwin called the “strong principle of inheritance.” Highly accurate replication of cellular phenotype is a universal phenomenon in all of life since LUCA and is often taken for granted as a constant in evolutionary theory. It is not known how self-replication arose during the origin of life. In this report I use the simple mathematics of evolutionary theory to investigate the dynamics of self-replication accuracy and allelic selection. Results indicate that the degree of self-replication accuracy must be greater than a threshold related to the selection coefficients of the alleles in a population in order for evolution to occur. Accurate replication of cellular phenotype and of the molecules involved in genotype/phenotype linkage is necessary for the origin of evolution and may be considered the fundamental principle of life.

Payment or subscription needed/Requer assinatura ou pagamento: Biosystems


 

O Google Scholar é manipulável???

quinta-feira, fevereiro 15, 2024

Google Scholar is manipulatable
Hazem Ibrahim, Fengyuan Liu, Yasir Zaki, Talal Rahwan


Image/Imagem - ThriveWorks

Citations are widely considered in scientists' evaluation. As such, scientists may be incentivized to inflate their citation counts. While previous literature has examined self-citations and citation cartels, it remains unclear whether scientists can purchase citations. Here, we compile a dataset of ~1.6 million profiles on Google Scholar to examine instances of citation fraud on the platform. We survey faculty at highly-ranked universities, and confirm that Google Scholar is widely used when evaluating scientists. Intrigued by a citation-boosting service that we unravelled during our investigation, we contacted the service while undercover as a fictional author, and managed to purchase 50 citations. These findings provide conclusive evidence that citations can be bought in bulk, and highlight the need to look beyond citation counts.

Subjects:     Computational Engineering, Finance, and Science (cs.CE); Digital Libraries (cs.DL); Social and Information Networks (cs.SI); Physics and Society (physics.soc-ph)
Cite as:     arXiv:2402.04607 [Add to Citavi project by ArXiv ID] [cs.CE]

 FREE PDF GRATIS: arXiv