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.

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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.

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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

 
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

Como os sistemas moleculares na origem da vida podem ter evoluído

quinta-feira, fevereiro 08, 2024

Design and Thermodynamics Principles to Program the Cooperativity of Molecular Assemblies
 

Dominic Lauzon, Prof. Alexis Vallée-Bélisle
 

First published: 17 November 2023
https://doi.org/10.1002/anie.202313944

 
https://onlinelibrary.wiley.com/cms/asset/7511875f-6fc0-4c36-bdc5-c50031e58f9e/anie202313944-toc-0001-m.png

 Abstract

Most functional nanosystems in living organisms are constructed using multimeric assemblies that provide multiple advantages over their monomeric counterparts such as cooperative or anti-cooperative responses, integration of multiple signals and self-regulation. Inspired by these natural nanosystems, chemists have been synthesizing self-assembled supramolecular systems over the last 50 years with increasing complexity with applications ranging from biosensing, drug delivery, synthetic biology, and system chemistry. Although many advances have been made concerning the design principles of novel molecular architectures and chemistries, little is still known, however, about how to program their dynamic of assembly so that they can assemble at the required concentration and with the right sensitivity. Here, we used synthetic DNA assemblies and double-mutant cycle analysis to explore the thermodynamic basis to program the cooperativity of molecular assemblies. The results presented here exemplify how programmable molecular assemblies can be efficiently built by fusing interacting domains and optimizing their compaction. They may also provide the rational basis for understanding the thermodynamic and mechanistic principles driving the evolution of multimeric biological complexes.

FREE PDF GRATIS: Angewandte Chemie Intl Edition

Ciência objetiva ou consenso científico como arma contra opiniões diferentes?

terça-feira, fevereiro 06, 2024

Prosocial motives underlie scientific censorship by scientists: A perspective and research agenda
 

Cory J. Clark cjclark@sas.upenn.edu, Lee Jussim, Komi Frey, +35 , and William von Hippel 


Edited by Timothy Wilson, University of Virginia, Charlottesville, VA; received February 25, 2023; accepted October 6, 2023 November 20, 2023 120 (48) e2301642120
https://doi.org/10.1073/pnas.2301642120

Image credit: cartoonist Ramirez of the Weekly Standard, 

Abstract
 

Science is among humanity’s greatest achievements, yet scientific censorship is rarely studied empirically. We explore the social, psychological, and institutional causes and consequences of scientific censorship (defined as actions aimed at obstructing particular scientific ideas from reaching an audience for reasons other than low scientific quality). Popular narratives suggest that scientific censorship is driven by authoritarian officials with dark motives, such as dogmatism and intolerance. Our analysis suggests that scientific censorship is often driven by scientists, who are primarily motivated by self-protection, benevolence toward peer scholars, and prosocial concerns for the well-being of human social groups. This perspective helps explain both recent findings on scientific censorship and recent changes to scientific institutions, such as the use of harm-based criteria to evaluate research. We discuss unknowns surrounding the consequences of censorship and provide recommendations for improving transparency and accountability in scientific decision-making to enable the exploration of these unknowns. The benefits of censorship may sometimes outweigh costs. However, until costs and benefits are examined empirically, scholars on opposing sides of ongoing debates are left to quarrel based on competing values, assumptions, and intuitions.

FREE PDF GRATIS: PNAS

Como surgiu a vida na Terra?

segunda-feira, fevereiro 05, 2024

Organic hazes as a source of life's building blocks to warm little ponds on the Hadean Earth
Ben K. D. Pearce, Sarah M Hörst, Joshua A. Sebree, Chao He

 

Yellowstone.jpg

 Image/Imagem: Smithsonian Magazine

Abstract

Over 4 billion years ago, Earth is thought to have been a hazy world akin to Saturn's moon Titan. The organic hazes in the atmosphere at this time could contain a vast inventory of life's building blocks, and thus may have seeded warm little ponds for life. In this work, we produce organic hazes in the lab in atmospheres with high (5%) and low (0.5%) CH4 abundances and analyze the solid particles for nucleobases, amino acids, and a few other organics using GC/MS/MS to obtain their concentrations. We also analyze heated (200 ∘C) samples from the high methane organic haze experiment to simulate these particles sitting on an uninhabitable surface. Finally, we use our experimental results and estimates of atmospheric haze production as inputs for a comprehensive numerical pond model to calculate the concentrations of nucleobases from organic hazes in these environments. We find that organic hazes typically provide up to 0.2-6.5 μM concentrations of nucleobases to warm little ponds for potentially habitable Hadean conditions. However, without seepage, uracil and thymine can reach ~100 μM concentrations, which is the present lower experimental limit to react these species to form nucleotides. Heating samples leads to partial or complete decay of biomolecules, suggesting that biomolecule stockpiling on the hot surface is unlikely. The ideal conditions for the delivery of life's building blocks from organic hazes would be when the Hadean atmosphere is rich in methane, but not so rich as to create an uninhabitable surface.

FREE PDF: arXiv

Darwin, nós temos um grande problema - as células estão repletas de padrões de design!

segunda-feira, janeiro 29, 2024

Design patterns of biological cells
Steven S. Andrews, H. Steven Wiley, Herbert M. Sauro
First published: 21 January 2024
https://doi.org/10.1002/bies.202300188

The central metabolic system for E. coli with highlighted regions showing several structural patterns. The metabolic map is reprinted with permission from Ref. [54].

Abstract

Design patterns are generalized solutions to frequently recurring problems. They were initially developed by architects and computer scientists to create a higher level of abstraction for their designs. Here, we extend these concepts to cell biology to lend a new perspective on the evolved designs of cells' underlying reaction networks. We present a catalog of 21 design patterns divided into three categories: creational patterns describe processes that build the cell, structural patterns describe the layouts of reaction networks, and behavioral patterns describe reaction network function. Applying this pattern language to the E. coli central metabolic reaction network, the yeast pheromone response signaling network, and other examples lends new insights into these systems.

FREE PDF GRATIS: BioEssays


Darwin, nós temos um problema: organismos verdes complexos surgiram há um bilhão de anos...

quinta-feira, janeiro 25, 2024

Phylogenomic insights into the first multicellular streptophyte 

Maaike J. Bierenbroodspot Tatyana Darienko Sophie de Vries Janine M.R. Fürst-Jansen Henrik Buschmann Thomas Pröschold Iker Irisarri Jan de Vries

Open Access Published: January 19, 2024 DOI: https://doi.org/10.1016/j.cub.2023.12.070 

Figure thumbnail fx1

Highlights

  • Comprehensive phylogenomic analyses for 38 taxonomically diverse Klebsormidiophyceae
    •   Three-order system for the Klebsormidiophyceae, resilient land colonizers
    •  Deep divergence, 830 million years ago—long before embryophytes emerged
    •  Evidence that multicellularity emerged in streptophytes about a billion years  ago

Summary 


Streptophytes are best known as the clade containing the teeming diversity of embryophytes (land plants).1, 2, 3, 4

Next to embryophytes are however a range of freshwater and terrestrial algae that bear important information on the emergence of key traits of land plants. Among these, the Klebsormidiophyceae stand out. Thriving in diverse environments—from mundane (ubiquitous occurrence on tree barks and rocks) to extreme (from the Atacama Desert to the Antarctic)—Klebsormidiophyceae can exhibit filamentous body plans and display remarkable resilience as colonizers of terrestrial habitats. 5, 6

Currently, the lack of a robust phylogenetic framework for the Klebsormidiophyceae hampers our understanding of the evolutionary history of these key traits. Here, we conducted a phylogenomic analysis utilizing advanced models that can counteract systematic biases. We sequenced 24 new transcriptomes of Klebsormidiophyceae and combined them with 14 previously published genomic and transcriptomic datasets. Using an analysis built on 845 loci and sophisticated mixture models, we establish a phylogenomic framework, dividing the six distinct genera of Klebsormidiophyceae in a novel three-order system, with a deep divergence more than 830 million years ago. Our reconstructions of ancestral states suggest (1) an evolutionary history of multiple transitions between terrestrial-aquatic habitats, with stem Klebsormidiales having conquered land earlier than embryophytes, and (2) that the body plan of the last common ancestor of Klebsormidiophyceae was multicellular, with a high probability that it was filamentous whereas the sarcinoids and unicells in Klebsormidiophyceae are likely derived states. We provide evidence that the first multicellular streptophytes likely lived about a billion years ago.

FREE PDF GRATIS: Current Biology

Novo estudo de Oxford lança luz sobre a origem dos animais

Fossilisation processes and our reading of animal antiquity

Ross P. Anderson, Christina R. Woltz, Nicholas J. Tosca, Susannah M. Porter, Derek E.G. Briggs 

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

Image/Imagem: Oxford University

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 & Evolution

Darwin, os lagos rasos de soda são promissores como berços da vida na Terra

terça-feira, janeiro 23, 2024

Biogeochemical explanations for the world’s most phosphate-rich lake, an origin-of-life analog

Sebastian Haas, Kimberly Poppy Sinclair & David C. Catling

Communications Earth & Environment volume 5, Article number: 28 (2024) 

 Shallow soda lakes show promise as cradles of life on Earth

Last Chance Lake in western Canada in November 2021, when the lake has shrunk into many smaller pools and ice has formed on top of each pool.

Kimberly Poppy Sinclair/University of Washington

Abstract

Environmental phosphate concentrations are typically much lower (~10−6 M) than needed for prebiotic phosphorylation of nucleosides, critical for the origin of life. Here, we tested hypotheses explaining highly concentrated dissolved phosphate in carbonate-rich “soda” lakes by examining phosphorus and nitrogen cycling in Last Chance Lake and Goodenough Lake, Canada. We find a lack of geochemical phosphorus precipitation, that sedimentary calcium is in dolomite rather than apatite, and that N2-fixation rates, probably suppressed by high salinity, are too low to create significant biological phosphate demand. Thus, nitrogen-limitation of biological production and precipitation of calcium-rich carbonate instead of apatite combine to allow unimpeded evaporative phosphate buildup in Last Chance Lake to the highest known natural levels (37 mM) due to small biological and geochemical phosphorus sinks. Forming on basaltic rock, which was likely common on early Earth, evaporative soda lakes were consequently plausible origin-of-life settings with sufficient phosphate for prebiotic synthesis.

FREE PDF GRATIS:  Communications Earth & Environment Sup. Info. Peer Rev File

Novas evidências contra a ancestralidade dos dinossauros nas aves

segunda-feira, janeiro 08, 2024

Sexta-feira de fóssil: novas evidências contra a ancestralidade dos dinossauros nas aves 
 
Günter Bechly



5 de janeiro de 2024, 6h45 
 
Nesta Sexta-feira de Fóssil revisitamos a ancestralidade dos pássaros, com o esqueleto da ave do Cretáceo Superior Hesperornis gracilis, exibido no Museu de História Natural de Karlsruhe, Alemanha. Hesperornis era uma ave marinha que não voava e com dentes, um tanto semelhante aos pinguins modernos, e viveu na época de alguns dos dinossauros raptores bem conhecidos dos filmes Jurassic Park.
 
Poucas hipóteses na biologia evolutiva se tornaram tão populares entre os leigos quanto a postulada ancestralidade dos pássaros a partir dos dinossauros bípedes. Na verdade, muitas crianças em idade escolar dirão com orgulho que os pássaros são simplesmente dinossauros sobreviventes. A ancestralidade terópode das aves tornou-se um dogma evolutivo que é quase universalmente aceito e ensinado como visão consensual. No entanto, existem alguns dissidentes, entre os quais o paleornitólogo Alan Feduccia, da Universidade da Carolina do Norte, é certamente o mais proeminente. Ele cunhou o famoso termo “paradoxo temporal” para o fato de que o registro fóssil do suposto grupo de aves terópodes tende a ser mais jovem do que as aves reais mais antigas. Na semana passada discuti novas evidências que tornam este paradoxo temporal muito pior (Bechly 2023).
 
Além do registro fóssil

Contudo, a crítica de Feduccia à hipótese dinossauro-pássaro não se baseia apenas em problemas com o registo fóssil, mas também em evidências contraditórias da anatomia comparativa. Agora, ele apresenta novas evidências que contradizem ainda mais nitidamente a visão consensual. Um dos argumentos para uma relação dinossauro-pássaro tem sido a presença do chamado acetábulo “aberto”, que “é uma superfície pélvica côncava formada pelo ílio, ísquio e púbis, que acomoda a cabeça do fêmur nos tetrápodes”. .” Feduccia (2024) estudou o acetábulo em aves basais precoces e descobriu que seu acetábulo tende a ser parcialmente fechado e um antitrocânter (processo do ísquio ou ilíaco) está ausente.Isto põe fortemente em dúvida um dos personagens-chave para uma relação dinossauro-pássaro e sugere que esta hipótese deve ser reavaliada. O fato de que microraptorídeos e troodontídeos “também exibem fechamento parcial do acetábulo e não possuem um antitrocânter é mais uma incongruência, pois esses táxons deveriam exibir modificações “típicas” da cintura pélvica de terópodes para cursorialidade terrestre”. Isto poderia apoiar a opinião de vários especialistas (por exemplo, Martin 2004, e vários estudos citados por Feduccia), de que estes táxons maniraptoranos representam aves secundariamente incapazes de voar, em vez de dinossauros terópodes.
 
Feduccia concluiu seu novo estudo com esta declaração notável:

"A hipótese de que as aves são dinossauros terópodes maniraptoranos, apesar da certeza com que é proclamada, continua a sofrer de dificuldades não resolvidas… Até problemas como os aqui discutidos — e muitos outros que continuam a ser descartados quer por apelo ao “consenso” quer por excesso de confiança nos resultados da análise filogenética de dados morfológicos - foram resolvidos satisfatoriamente, o ceticismo em relação ao consenso atual e a investigação contínua de hipóteses alternativas são necessários para a promoção do discurso crítico na filogenética dos vertebrados e na biologia evolutiva."
 
Afinal, pássaros e dinossauros podem não representar pedaços arbitrários de um grau evolutivo, mas podem, em vez disso, representar tipos naturais distintos. No mínimo, as evidências parecem ser muito mais ambíguas, mais fracas e menos convincentes do que a maioria dos biólogos evolucionistas gosta de fingir.
 
Referências
 
BECHLY G 2023. Fossil Friday: Fossil Bird Tracks Expand the Temporal Paradox. Evolution News December 29, 2023. https://evolutionnews.org/2023/12/fossil-friday-fossil-bird-tracks-expand-the-temporal-paradox/
 
FEDUCCIA A 2024. The Avian Acetabulum: Small Structure, but Rich with Illumination and Questions. Diversity 16: 20, 1–28. DOI: https://doi.org/10.3390/d16010020 
 
MARTIN LD 2004. A basal archosaurian origin for birds. Acta Geologica Sinica 50(6), 978–990. https://caod.oriprobe.com/articles/7989071/A_basal_archosaurian_origin_for_birds.htm
 
 
https://www.discovery.org/m/2018/03/gunter-bechly.jpg 
GÜNTER BECHLY 
Membro Sênior, Centro de Ciência e Cultura

Günter Bechly é um paleoentomologista alemão especializado na história fóssil e na sistemática de insetos (especialmente libélulas), o mais diverso grupo de animais. Ele atuou como curador de âmbar e fósseis de insetos no departamento de paleontologia do Museu Estadual de História Natural (SMNS) em Stuttgart, Alemanha. Ele também é membro sênior do Centro de Ciência e Cultura do Discovery Institute. Dr. Bechly obteve seu Ph.D. em geociências pela Eberhard-Karls-University em Tübingen, Alemanha.

Veja papai, veja mamãe, sem mitocondria!!!

quarta-feira, janeiro 03, 2024

Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria

Lukáš V. F. Novák, Sebastian C. Treitli, Jan Pyrih, Paweł Hałakuc, Shweta V. Pipaliya, Vojtěch Vacek, Ondřej Brzoň, Petr Soukal, Laura Eme, Joel B. Dacks, Anna Karnkowska, Marek Eliáš,     Vladimír Hampl

PLOS Published: December 7, 2023

https://doi.org/10.1371/journal.pgen.1011050

A protist - Dan Wieczynski

Abstract

The notion that mitochondria cannot be lost was shattered with the report of an oxymonad Monocercomonoides exilis, the first eukaryote arguably without any mitochondrion. Yet, questions remain about whether this extends beyond the single species and how this transition took place. The Oxymonadida is a group of gut endobionts taxonomically housed in the Preaxostyla which also contains free-living flagellates of the genera Trimastix and Paratrimastix. The latter two taxa harbour conspicuous mitochondrion-related organelles (MROs). Here we report high-quality genome and transcriptome assemblies of two Preaxostyla representatives, the free-living Paratrimastix pyriformis and the oxymonad Blattamonas nauphoetae. We performed thorough comparisons among all available genomic and transcriptomic data of Preaxostyla to further decipher the evolutionary changes towards amitochondriality, endobiosis, and unstacked Golgi. Our results provide insights into the metabolic and endomembrane evolution, but most strikingly the data confirm the complete loss of mitochondria for all three oxymonad species investigated (M. exilis, B. nauphoetae, and Streblomastix strix), suggesting the amitochondriate status is common to a large part if not the whole group of Oxymonadida. This observation moves this unique loss to 100 MYA when oxymonad lineage diversified.

Author summary

Mitochondria are nearly ubiquitous components of eukaryotic cells that constitute bodies of animals, fungi, plants, algae, and a broad diversity of single-celled eukaryotes, a.k.a. protists. Many groups of protists have substantially reduced the complexity of their mitochondria because they live in oxygen-poor environments, so they are unable to utilize the most salient feature of mitochondria–their ATP-producing oxidative phosphorylation metabolism. However, for a long time, scientists thought that it is impossible to completely lose a mitochondrion because this organelle provides other essential services to the cell, e.g. synthesis of protein cofactors called iron-sulfur clusters. Detailed investigation of the chinchilla symbiont M. exilis documented the first case of an organism without mitochondrion, and it also provided a scenario explaining how this unique evolutionary experiment might have happened. In this work, we expand on this discovery by exploring genomes of multiple relatives of M. exilis. We show that the loss of the mitochondrion is not limited to a single species but possibly extends to its entire group, the oxymonads. We also compare the predicted metabolic capabilities of oxymonads to their closest known mitochondrion-containing relatives and map out various changes that occurred during the transition to amitochondriality.

FREE PDF: PLoS Genetics

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

quarta-feira, novembro 29, 2023

Vision-controlled jetting for composite systems and robots

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

Nature volume 623, pages 522–530 (2023)

An image montage of the soft robotic hand holding a marker pen and a water bottle.

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

Abstract

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

FREE PDF GRATIS: Nature 

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

Semantic Information in a Model of Resource Gathering Agents

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

PRX Life 1, 023003 – Published 17 October 2023

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

Abstract

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

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