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/

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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.

.....

Read more here: Scientific American

Darwin, nós temos um grande problema: os relógios moleculares estão errados e não existem fósseis pré-cambrianos...

Trends in Ecology and Evolution

Fossilisation processes and our reading of animal antiquity

Ross P. Anderson 8, Christina R. Woltz 9, Nicholas J. Tosca 10, Susannah M. Porter 11, Derek E.G. Briggs 12

Published: June 27, 2023 DOI: https://doi.org/10.1016/j.tree.2023.05.014

Highlights

The last common ancestor of animals is thought to have been small and soft-bodied and therefore would have required special conditions for its preservation.

Limited availability of these conditions in the Neoproterozoic could explain the discrepancy between molecular clock predictions for the timing of animal origins and the fossil record of animals.

We assess the availability of these conditions, particularly those of Burgess Shale-type, which are known to preserve animals with tissues of varied composition.

Burgess Shale-type conditions are rarely associated with Neoproterozoic fossil biotas, but in the few assemblages with these conditions, dated to 789 million years ago or older, no animals have been identified, suggesting they had not evolved by this time.

This provides a soft maximum age constraint on crown group animals of 789 million years ago.

Abstract

Estimates for animal antiquity exhibit a significant disconnect between those from molecular clocks, which indicate crown animals evolved ∼800 million years ago (Ma), and those from the fossil record, which extends only ∼574 Ma. Taphonomy is often held culpable: early animals were too small/soft/fragile to fossilise, or the circumstances that preserve them were uncommon in the early Neoproterozoic. We assess this idea by comparing Neoproterozoic fossilisation processes with those of the Cambrian and its abundant animal fossils. Cambrian Burgess Shale-type (BST) preservation captures animals in mudstones showing a narrow range of mineralogies; yet, fossiliferous Neoproterozoic mudstones rarely share the same mineralogy. Animal fossils are absent where BST preservation occurs in deposits ≥789 Ma, suggesting a soft maximum constraint on animal antiquity.

Keywords Burgess Shale-type clays molecular clocks Neoproterozoic Era origin of animals

FREE PDF GRATIS: Trends in Ecology and Evolution

Indo além do paradigma adaptacionista para a evolução humana e por que isso importa.

Journal of Human Evolution

Volume 174, January 2023, 103296

Moving beyond the adaptationist paradigm for human evolution, and why it matters

Lauren Schroeder a b, Rebecca Rogers Ackermann b c

a Department of Anthropology, University of Toronto Mississauga, Mississauga, ON, L5L 1C6, Canada

b Human Evolution Research Institute, University of Cape Town, Rondebosch, 7701, South Africa

c Department of Archaeology, University of Cape Town, Rondebosch, 7701, South Africa

Received 25 April 2022, Accepted 12 November 2022, Available online 15 December 2022, Version of Record 15 December 2022.

https://doi.org/10.1016/j.jhevol.2022.103296

Abstract

The Journal of Human Evolution (JHE) was founded 50 years ago when much of the foundation for how we think about human evolution was in place or being put in place, providing the main framework for how we consider our origins today. Here, we will explore historical developments, including early JHE outputs, as they relate to our understanding of the relationship between phenotypic variation and evolutionary process, and use that as a springboard for considering our current understanding of these links as applied to human evolution. We will focus specifically on how the study of variation itself has shifted us away from taxonomic and adaptationist perspectives toward a richer understanding of the processes shaping human evolutionary history, using literature searches and specific test cases to highlight this. We argue that natural selection, gene exchange, genetic drift, and mutation should not be considered individually when considering the production of hominin diversity. In this context, we offer suggestions for future research directions and reflect on this more complex understanding of human evolution and its broader relevance to society. Finally, we end by considering authorship demographics and practices in the last 50 years within JHE and how a shift in these demographics has the potential to reshape the science of human evolution going forward.

Keywords

Genetic drift Hybridization Neutral evolution Natural selection Phenotypic variation Evolutionary process

FREE PDF GRATIS: Journal of Human Evolution

1ª Especialização EAD do Brasil em Teoria do Design Inteligente reconhecida pelo MEC

 

Venha fazer parte da 1ª Especialização EAD do Brasil em Teoria do Design Inteligente:📚🙌🏾

✅ 60% de desconto na matrícula

✅ Aulas AO VIVO ou gravadas

✅ Corpo docente com grandes referências da TDI brasileira e internacional

Matrículas:🎯

https://unilifeead.com.br/curso.php?id=27

Darwin, nós temos um problema: a maioria dos seus seguidores está entendendo errado a evolução!

Evolution without accidents

Despite advances in molecular genetics, too many biologists think that natural selection is driven by random mutations

James A Shapiro is professor of microbiology in the Department of Biochemistry and Molecular Biology at the University of Chicago. His books include Bacteria as Multicellular Organisms (1997), co-edited with Martin Dworkin, and Evolution: A View from the 21st Century, Fortified (2nd ed, 2022).

Edited by Cameron Allan McKean

5,000 words

Siamese fighting fish (Betta splendens) provide evidence of ‘alternative splicing’. Photo by Anadolu Agency/Getty

Since 1859, when Charles Darwin’s On the Origin of Species was first published, the theory of natural selection has dominated our conceptions of evolution. As Darwin understood it, natural selection is a slow and gradual process that takes place across multiple generations through successive random hereditary variations. In the short term, a small variation might confer a slight advantage to an organism and its offspring, such as a longer beak or better camouflage, allowing it to outcompete similar organisms lacking that variation. Over longer periods of time, Darwin postulated, an accumulation of advantageous variations might produce more significant novel adaptations – or even the emergence of an entirely new species.

Natural selection is not a fast process. It takes place gradually through random variations, or ‘mutations’ as we call them today, which accumulate over decades, centuries, or millions of years. Initially, Darwin believed that natural selection was the only process that led to evolution, and he made this explicit in On the Origin of Species:

If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down. But I can find out no such case.

A lot has changed since 1859. We now know that Darwin’s ‘gradualist’ view of evolution, exclusively driven by natural selection, is no longer compatible with contemporary science. It’s not just that random mutations are one of many evolutionary processes that produce new species; they have nothing to do with the major evolutionary transformations of macroevolution. Species do not emerge from an accumulation of random genetic changes. This has been confirmed by 21st-century genome sequencing, but the idea that natural selection inadequately explains evolutionary change goes back 151 years – to Darwin himself. In the 6th edition of On the Origin of Species, published in 1872, he acknowledged forms of variations that seemed to arise spontaneously, without successive, slight modifications:

It appears that I formerly underrated the frequency and value of these latter forms of variation, as leading to permanent modifications of structure independently of natural selection.

– from Chapter 15, p395, emphasis added

Today, we know in exquisite detail how these larger-scale ‘spontaneous’ variations come about without the intervention of random mutations. And yet, even in the age of genome sequencing, many evolutionary scientists still cling stubbornly to a view of evolution fuelled by a gradual accumulation of random mutations. They insist on the accuracy of the mid-20th-century ‘updated’ version of Darwin’s ideas – the ‘Modern Synthesis’ of Darwinian evolution (through natural selection) and Mendelian genetics – and have consistently failed to integrate evidence for other genetic processes. As Ernst Mayr, a major figure in the Modern Synthesis, wrote in Populations, Species and Evolution (1970):

The proponents of the synthetic theory maintain that all evolution is due to the accumulation of small genetic changes, guided by natural selection, and that transpecific evolution [ie, the origins of new species and taxonomic groups] is nothing but an extrapolation and magnification of the events that take place within populations and species.

This failure to take account of alternative modes of change has been foundational to popular and scientific misconceptions of evolution. It continues to impact the study of antibiotic and pesticide resistance, the breeding of new crops for agriculture, the mitigation of climate change, and our understanding of humanity’s impacts on biodiversity.

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Read more here: Aeon

Os mecanismos do motor ciliar são revelados: mero acaso, fortuita necessidade ou design inteligente?

ATP-induced conformational change of axonemal outer dynein arms revealed by cryo-electron tomography

Noemi Zimmermann, Akira Noga, Jagan Mohan Obbineni, Takashi Ishikawa

The EMBO Journal (2023)42:e112466

https://doi.org/10.15252/embj.2022112466

Outer dynein arms in the ciliary axoneme generate force for ciliary beating.

Abstract

Axonemal outer dynein arm (ODA) motors generate force for ciliary beating. We analyzed three states of the ODA during the power stroke cycle using in situ cryo-electron tomography, subtomogram averaging, and classification. These states of force generation depict the prepower stroke, postpower stroke, and intermediate state conformations. Comparison of these conformations to published in vitro atomic structures of cytoplasmic dynein, ODA, and the Shulin–ODA complex revealed differences in the orientation and position of the dynein head. Our analysis shows that in the absence of ATP, all dynein linkers interact with the AAA3/AAA4 domains, indicating that interactions with the adjacent microtubule doublet B-tubule direct dynein orientation. For the prepower stroke conformation, there were changes in the tail that is anchored on the A-tubule. We built models starting with available high-resolution structures to generate a best-fitting model structure for the in situ pre- and postpower stroke ODA conformations, thereby showing that ODA in a complex with Shulin adopts a similar conformation as the active prepower stroke ODA in the axoneme.

FREE PDF GRATIS: The EMBO Journal

Darwin, nós temos um problema: a perspectiva agencial

Evolution & Development Early View

RESEARCH ARTICLE

Open Access

The agential perspective: Countermapping the modern synthesis

Denis M. Walsh, Gregory Rupik

First published: 14 June 2023

https://doi.org/10.1111/ede.12448

Abstract

We compare and contrast two theoretical perspectives on adaptive evolution—the orthodox Modern Synthesis perspective, and the nascent Agential Perspective. To do so, we develop the idea from Rasmus Grønfeldt Winther of a ‘countermap’, as a means for comparing the respective ontologies of different scientific perspectives. We conclude that the modern Synthesis perspective achieves an impressively comprehensive view of a universal set of dynamical properties of populations, but at the considerable cost of radically distorting the nature of the biological processes that contribute to evolution. For its part, the Agential Perspective offers the prospect of representing the biological processes of evolution with much greater fidelity, but at the expense of generality. Trade-offs of this sort are endemic to science, and inevitable. Recognizing them helps us to avoid the pitfalls of ‘illicit reification’, i.e. the mistake of interpreting a feature of a scientific perspective as a feature of the non-perspectival world. We argue that much of the traditional Modern Synthesis representation of the biology of evolution commits this illicit reification.

FREE PDF GRATIS: Evolution & Development

Darwin, nós temos um problema: toda biologia é processamento de informação cognitiva

Progress in Biophysics and Molecular Biology

Volume 182, September 2023, Pages 34-48

A revised central dogma for the 21st century: all biology is cognitive information processing

William B. Miller Jr. a, František Baluška b, Arthur S. Reber c

a Paradise Valley, AZ, USA

b IZMB, University of Bonn, Kirschellee 1, 53115, Bonn, Germany

c Department of Psychology, University of British Columbia, Vancouver, BC, Canada

Received 10 February 2023, Revised 28 March 2023, Accepted 30 May 2023, Available online 1 June 2023, Version of Record 6 June 2023.

https://doi.org/10.1016/j.pbiomolbio.2023.05.005 

Abstract

Crick's Central Dogma has been a foundational aspect of 20th century biology, describing an implicit relationship governing the flow of information in biological systems in biomolecular terms. Accumulating scientific discoveries support the need for a revised Central Dogma to buttress evolutionary biology's still-fledgling migration from a Neodarwinian canon. A reformulated Central Dogma to meet contemporary biology is proposed: all biology is cognitive information processing. Central to this contention is the recognition that life is the self-referential state, instantiated within the cellular form. Self-referential cells act to sustain themselves and to do so, cells must be in consistent harmony with their environment. That consonance is achieved by the continuous assimilation of environmental cues and stresses as information to self-referential observers. All received cellular information must be analyzed to be deployed as cellular problem-solving to maintain homeorhetic equipoise. However, the effective implementation of information is definitively a function of orderly information management. Consequently, effective cellular problem-solving is information processing and management. The epicenter of that cellular information processing is its self-referential internal measurement. All further biological self-organization initiates from this obligate activity. As the internal measurement by cells of information is self-referential by definition, self-reference is biological self-organization, underpinning 21st century Cognition-Based Biology.

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Progress in Biophysics and Molecular Biology

Darwin, nós temos um problema - a teleonomia vai substituir a teleologia na biologia evolutiva?

Teleonomy: Revisiting a Proposed Conceptual Replacement for Teleology

Max Dresow & Alan C. Love 

Biological Theory (2023)

Abstract

The concept of teleonomy has been attracting renewed attention recently. This is based on the idea that teleonomy provides a useful conceptual replacement for teleology, and even that it constitutes an indispensable resource for thinking biologically about purposes. However, both these claims are open to question. We review the history of teleological thinking from Greek antiquity to the modern period to illuminate the tensions and ambiguities that emerged when forms of teleological reasoning interacted with major developments in biological thought. This sets the stage for an examination of Pittendrigh’s (Adaptation, natural selection, and behavior. In: Roe A, Simpson GG (eds) Behavior and evolution. Yale University Press, New Haven, pp 390–416, 1958) introduction of “teleonomy” and its early uptake in the work of prominent biologists. We then explore why teleonomy subsequently foundered and consider whether the term may yet have significance for discussions of goal-directedness in evolutionary biology and philosophy of science. This involves clarifying the relationship between teleonomy and teleological explanation, as well as asking how the concept of teleonomy impinges on research at the frontiers of evolutionary theory.

FREE PDF GRATIS: Biological Theory

Alô Academia Brasileira de Ciências: mais uma tempestade se aproxima na teoria da evolução.

An approaching storm in evolutionary theory 

Review of: Rereading Darwin’s Origin of Species: The Hesitations of an Evolutionist, by Richard G. Delisle and James Tierney,  2022.  Bloomsbury Academic, London. 176 pp. ISBN: 9781350259577

Alexander Czaja

Evolution, Volume 77, Issue 4, 1 April 2023, Pages 1170–1172, https://doi.org/10.1093/evolut/qpad009

Published: 26 January 2023

For about 10 years, something important has been brewing in the world of evolution, a great storm that, unfortunately, has so far only made itself felt among a few biologists, historians, and philosophers of biology and evolution (Jablonka & Lamb, 2005, 2020; Laland et al., 2014; Müller, 2017; Pigliucci & Müller, 2010; Skinner, 2015). Reading the work of most practicing biologists, one hardly sees any sign of this gathering storm. On the contrary, in standard textbooks and popular literature, no winds of resistance have been felt, and the ship known as the Modern Theory of Evolution (MTE) sails safely and undisturbed from its usual academic course. It remains to be seen how strong the storm will ultimately be.

One recent manifestation of this storm is the new book Rereading Darwin’s Origin of Species by Richard G. Delisle and James Tierney, a short read aimed at reaching a larger audience. Delisle is a paleoanthropologist who also holds a PhD in philosophy. His co-author, James Tierney, studied philosophy at the University of Chicago and is currently Director of the English Language Program at Yale University.

To get straight to the point: The book has no intention of capsizing the MTE ship or to unseating the modern theory but puts forth some provocative theses against the generally accepted view that Darwin was the first modern evolutionary thinker in history: the authors try to demonstrate that there is a wide gap between Darwin and evolutionists today. The most daring of their theses states that Darwin was not an evolutionist in the modern sense of the word. Indeed, the authors question the appropriation of Darwin by proponents of the MTE, who have always placed him and his Origin of Species at the conceptual center of their own model. The book provides compelling arguments that the MTE is based on a highly distorted and anachronistic picture of Darwin, both of his time and main work. Having set forth their case for a fresh look at the Origin, the authors delve deep and meticulously in Darwin’s main work, by uncovering its neglected ambiguities and contradictions. After years of collective Darwin euphoria, in which—as the authors self-critically note—they themselves actively participated, it is now time for a more critical approach. The authors call it “returning Darwin to the human dimension” (p. x) and they wonder “[w]hy has it taken so long for us to realize that Darwin’s commitment to evolutionism was incomplete?” (p. 6).

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FREE PDF GRATIS: Evolution

Dicas químicas podem ter possibilitado o surgimento da multicelularidade

Chemical factors induce aggregative multicellularity in a close unicellular relative of animals

Núria Ros-Rocher, Ria Q. Kidner, Catherine Gerdt, +2, and Joseph P. Gerdt 

Authors Info & Affiliations

Edited by Joan Strassmann, Washington University in St. Louis, St. Louis, MO; received November 30, 2022; accepted February 14, 2023

April 24, 2023

120 (18) e2216668120

https://doi.org/10.1073/pnas.2216668120  

Image/Imagem

Significance

Whether the first multicellular animals utilized chemical cues to regulate cellular aggregation remains poorly studied. We discovered that aggregation of a unicellular close animal relative is induced by chemical cues, as observed in some animals and other unicellular species. This discovery expands the prevalence of chemically regulated multicellularity in unicellular animal relatives, which suggests that this trait may have been common in the close unicellular ancestors of animals. Our findings also yield a biochemical tool to further dissect the stages of aggregation in an emerging unicellular model and determine the extent of their homology to aggregation mechanisms in animals.

Abstract

Regulated cellular aggregation is an essential process for development and healing in many animal tissues. In some animals and a few distantly related unicellular species, cellular aggregation is regulated by diffusible chemical cues. However, it is unclear whether regulated cellular aggregation was part of the life cycles of the first multicellular animals and/or their unicellular ancestors. To fill this gap, we investigated the triggers of cellular aggregation in one of animals’ closest unicellular living relatives—the filasterean Capsaspora owczarzaki. We discovered that Capsaspora aggregation is induced by chemical cues, as observed in some of the earliest branching animals and other unicellular species. Specifically, we found that calcium ions and lipids present in lipoproteins function together to induce aggregation of viable Capsaspora cells. We also found that this multicellular stage is reversible as depletion of the cues triggers disaggregation, which can be overcome upon reinduction. Our finding demonstrates that chemically regulated aggregation is important across diverse members of the holozoan clade. Therefore, this phenotype was plausibly integral to the life cycles of the unicellular ancestors of animals.

FREE PDF GRATIS: PNAS Sup. Info.

Darwin, nós temos um problema: árvores evolutivas baseadas na anatomia podem estar erradas.

Molecular phylogenies map to biogeography better than morphological ones

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

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

Image/Imagem: fabelacorrea / Adobe Sto

Abstract

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

FREE PDF GRATIS: Communications Biology

60 anos de silêncio revela insights em busca de vida extraterrestre.

Inferring the Rate of Technosignatures from 60 yr of Nondetection

Claudio Grimaldi1,2

Published 2023 April 13 • © 2023. The Author(s). Published by the American Astronomical Society.

The Astronomical Journal, Volume 165, Number 5

Citation Claudio Grimaldi 2023 AJ 165 199

DOI 10.3847/1538-3881/acc327

Image/Imagem: Deviant Art

Abstract

For about the last 60 yr the search for extraterrestrial intelligence has been monitoring the sky for evidence of remotely detectable technological life beyond Earth, with no positive results to date. While the lack of detection can be attributed to the highly incomplete sampling of the search space, technological emissions may be actually rare enough that we are living in a time when none cross the Earth. Here we explore the latter possibility and derive the likelihood of the Earth not being crossed by signals for at least the last 60 yr to infer upper bounds on their rate of emission. Under the assumption that technological emitters are distributed uniformly in the Milky Way and that they generate technoemissions at a constant rate, we find less than about one to five emissions generated per century with 95% credible level. This implies optimistic waiting times until the next crossing event of no less than 60–1800 yr with a 50% probability. A significant fraction of highly directional signals increases the emission rates' upper bounds, but without systematically changing the waiting time. Although these probabilistic bounds are derived from a specific model and their validity depends on the model's assumptions, they are nevertheless quite robust against weak time dependences of the emission rate or nonuniform spatial distributions of the emitters. Our results provide therefore a benchmark for assessing the lack of detection and may serve as a basis to form optimal strategies for the search for extraterrestrial intelligence.

FREE PDF GRATIS: The Astronomical Journal

A Academia Brasileira de Ciências não cientificamente eleva a evolução como dogma que não pode ser criticado!

 

ACADEMIA BRASILEIRA DE CIÊNCIAS E A EVOLUÇÃO DAS ESPÉCIES

A Academia Brasileira de Ciências (ABC) é uma associação de direito privado sem fins econômicos, fundada em 3 de maio de 1916 por 44 eminentes cientistas das áreas de ciências matemáticas, ciências fisicoquímicas e ciências biológicas com o objetivo de contribuir para o desenvolvimento da ciência e da tecnologia, da educação e do bem-estar social do Brasil. A Academia hoje atua nas seguintes áreas especializadas do conhecimento: Ciências Matemáticas, Ciências Físicas, Ciências Químicas, Ciências da Terra, Ciências Biológicas, Ciências Biomédicas, Ciências da Saúde; Ciências Agrárias, Ciências da Engenharia, e Ciências Sociais. De acordo com seu estatuto, “as atividades da Academia serão desenvolvidas com fiel observância aos princípios da legalidade, impessoalidade, moralidade e economicidade, com ampla publicidade dos seus atos, projetos e missões”.

A ABC tem como base filosófica o Estado Democrático de Direito, a separação entre ciência e religião, a laicidade do Estado, a não participação da instituição em partidos políticos, os direitos humanos, a sustentabilidade e o meio ambiente, sempre pautando suas ações pela ética e transparência e as melhores evidências científicas disponíveis.

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 e inclui a formação do universo, do sistema solar e da Terra, e as condições adequadas para a evolução biológica na Terra. Como referido pela Academia Nacional de Ciências dos Estados Unidos, “a descoberta e compreensão dos processos de evolução representam uma das conquistas mais poderosas da história da ciência”.

A Academia Brasileira de Ciências vem reiterar suas posições e comunicar que estará lançando no início de junho deste ano o livro “A Evolução da Vida na Terra” no qual são apresentados diferentes aspectos da Evolução das Espécies, em uma linguagem acessível ao público em geral. A ABC espera com a publicação desse livro esclarecer a contribuição da ciência para uma sociedade com equidade social, sustentável, mostrando que entender a evolução nos ajuda a resolver problemas biológicos que afetam nossas vidas hoje, tais como saúde, segurança alimentar e inteligência artificial.

Brasil, 14 de abril de 2023.

Academia Brasileira de Ciências

Acesse aqui o pdf da nota

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NOTA DESTE BLOGGER: Aguarde réplica desta nota da ABC por este blogger.

A Física Biológica Chega à Maioridade

APS News

April 2023 (Volume 32, Number 4)

Opinion: Biological Physics Comes of Age

Once an awkward confrontation between disciplines, biological physics is having its moment — and showing that life is not just a mess.

By William Bialek | March 16, 2023

Physics and biology were not always separate disciplines. In the 18th century, controversy about “animal electricity” proved foundational for the understanding of electricity more generally. In the 19th century, explorations of vision and hearing intermingled with the emerging understanding of optics and acoustics. In the 20th century, the chasm between physics and biology grew wider, but there were spectacular bridges. Most famously, the work that launched our modern view of life — structures of DNA and proteins, theories of base pairing and the genetic code — was done primarily in physics departments.

The revolutionary successes of (re-)connecting physics with biology in the mid-20th century completely changed how we think about life, and even changed how biologists’ work is organized. What emerged first was called molecular biology, and over the course of a generation the ideas and methods of molecular biology — grounded in physics — touched almost every part of the biological sciences. In contrast, physics itself was left relatively untouched.

Although the interaction of physics and biology did not immediately change the trajectory of physics, a small stream of physicists continued to be fascinated by the phenomena of life. I began to be (dimly) aware of all this as a student in the late 1970s. For me, the things biologists talked about were interesting, but the way they talked about them was unsatisfying. Physics was the other way: the style of thinking was attractive, and the theories elegant and powerful, but I never had an original idea about problems in the field’s traditional core. It was clear that physicists were doing all sorts of interesting things connected to the living world, but these efforts didn’t cohere into a community and certainly not into a recognizable branch of physics. We went to meetings where (mostly) we would find biologists working on the same systems, but not physicists asking the same kinds of questions.

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