Insights na geometria de centríolos revelada na criotomografia de centríolos duplos e triplos: mero acaso, fortuita necessidade ou design inteligente?

Insights into centriole geometry revealed by cryotomography of doublet and triplet centrioles

Garrett A Greenan, Bettina Keszthelyi, Ronald D Vale, David A Agard Is a corresponding author

University of California, United States; Howard Hughes Medical Institute, United States

RESEARCH ARTICLE Aug 6, 2018

The proximal and distal centriole show several major structural differences.

Abstract

Centrioles are cylindrical assemblies comprised of 9 singlet, doublet, or triplet microtubules, essential for the formation of motile and sensory cilia. While the structure of the cilium is being defined at increasing resolution, centriolar structure remains poorly understood. Here, we used electron cryo-tomography to determine the structure of mammalian (triplet) and Drosophila (doublet) centrioles. Mammalian centrioles have two distinct domains: a 200 nm proximal core region connected by A-C linkers, and a distal domain where the C-tubule is incomplete and a pair of novel linkages stabilize the assembly producing a geometry more closely resembling the ciliary axoneme. Drosophila centrioles resemble the mammalian core, but with their doublet microtubules linked through the A tubules. The commonality of core-region length, and the abrupt transition in mammalian centrioles, suggests a conserved length-setting mechanism. The unexpected linker diversity suggests how unique centriolar architectures arise in different tissues and organisms.

FREE PDF GRATIS: eLife

Os fundamentos físicos da complexidade biológica: mero acaso, fortuita necessidade ou design inteligente?

Physical foundations of biological complexity

Yuri I. Wolf, Mikhail I. Katsnelson, and Eugene V. Koonin

PNAS published ahead of print August 27, 2018 

https://doi.org/10.1073/pnas.1807890115

Contributed by Eugene V. Koonin, July 31, 2018 (sent for review May 21, 2018; reviewed by Sergei Maslov and Eörs Szathmáry)

Source/Fonte

Significance

Living organisms are characterized by a degree of hierarchical complexity that appears to be inaccessible to even the most complex inanimate objects. Routes and patterns of the evolution of complexity are poorly understood. We propose a general conceptual framework for emergence of complexity through competing interactions and frustrated states similar to those that yield patterns in striped glasses and cause self-organized criticality. We show that biological evolution is replete with competing interactions and frustration that, in particular, drive major transitions in evolution. The key distinction between biological and nonbiological systems seems to be the existence of long-term digital memory and phenotype-to-genotype feedback in living matter.

Abstract

Biological systems reach hierarchical complexity that has no counterpart outside the realm of biology. Undoubtedly, biological entities obey the fundamental physical laws. Can today’s physics provide an explanatory framework for understanding the evolution of biological complexity? We argue that the physical foundation for understanding the origin and evolution of complexity can be gleaned at the interface between the theory of frustrated states resulting in pattern formation in glass-like media and the theory of self-organized criticality (SOC). On the one hand, SOC has been shown to emerge in spin-glass systems of high dimensionality. On the other hand, SOC is often viewed as the most appropriate physical description of evolutionary transitions in biology. We unify these two faces of SOC by showing that emergence of complex features in biological evolution typically, if not always, is triggered by frustration that is caused by competing interactions at different organizational levels. Such competing interactions lead to SOC, which represents the optimal conditions for the emergence of complexity. Competing interactions and frustrated states permeate biology at all organizational levels and are tightly linked to the ubiquitous competition for limiting resources. This perspective extends from the comparatively simple phenomena occurring in glasses to large-scale events of biological evolution, such as major evolutionary transitions. Frustration caused by competing interactions in multidimensional systems could be the general driving force behind the emergence of complexity, within and beyond the domain of biology.

evolution of complexity competing interactions frustrated states spin glasses self-organized criticality

FREE PDF GRATIS: PNAS

Mais insights sobre a evolução dos motores de flagelos bacterianos

Acta Cryst. (2018). D74, 585-594

https://doi.org/10.1107/S2059798318007945

Insights into the evolution of bacterial flagellar motors from high-throughput in situ electron cryotomography and subtomogram averaging

F. M. Rossmann and M. Beeby

Source/Fonte: New Scientist

Abstract

In situ structural information on molecular machines can be invaluable in understanding their assembly, mechanism and evolution. Here, the use of electron cryotomography (ECT) to obtain significant insights into how an archetypal molecular machine, the bacterial flagellar motor, functions and how it has evolved is described. Over the last decade, studies using a high-throughput, medium-resolution ECT approach combined with genetics, phylogenetic reconstruction and phenotypic analysis have revealed surprising structural diversity in flagellar motors. Variations in the size and the number of torque-generating proteins in the motor visualized for the first time using ECT has shown that these variations have enabled bacteria to adapt their swimming torque to the environment. Much of the structural diversity can be explained in terms of scaffold structures that facilitate the incorporation of additional motor proteins, and more recent studies have begun to infer evolutionary pathways to higher torque-producing motors. This review seeks to highlight how the emerging power of ECT has enabled the inference of ancestral states from various bacterial species towards understanding how, and `why', flagellar motors have evolved from an ancestral motor to a diversity of variants with adapted or modified functions.

Keywords: low-abundance imaging; electron cryotomography; subtomogram averaging; bacterial flagellar motors; molecular evolution.

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FREE PDF GRATIS: Acta Cryst. D Structural Biology

A escala de tempo da evolução da planta terrestre inicial

The timescale of early land plant evolution

Jennifer L. Morris, Mark N. Puttick, James W. Clark, Dianne Edwards, Paul Kenrick, Silvia Pressel, Charles H. Wellman, Ziheng Yang, Harald Schneider, and Philip C. J. Donoghue

PNAS published ahead of print February 20, 2018 

https://doi.org/10.1073/pnas.1719588115

Edited by Peter R. Crane, Oak Spring Garden Foundation, Upperville, VA, and approved January 17, 2018 (received for review November 10, 2017)

Significance

Establishing the timescale of early land plant evolution is essential to testing hypotheses on the coevolution of land plants and Earth’s System. Here, we establish a timescale for early land plant evolution that integrates over competing hypotheses on bryophyte−tracheophyte relationships. We estimate land plants to have emerged in a middle Cambrian–Early Ordovocian interval, and vascular plants to have emerged in the Late Ordovician−Silurian. This timescale implies an early establishment of terrestrial ecosystems by land plants that is in close accord with recent estimates for the origin of terrestrial animal lineages. Biogeochemical models that are constrained by the fossil record of early land plants, or attempt to explain their impact, must consider a much earlier, middle Cambrian–Early Ordovician, origin.

Abstract

Establishing the timescale of early land plant evolution is essential for testing hypotheses on the coevolution of land plants and Earth’s System. The sparseness of early land plant megafossils and stratigraphic controls on their distribution make the fossil record an unreliable guide, leaving only the molecular clock. However, the application of molecular clock methodology is challenged by the current impasse in attempts to resolve the evolutionary relationships among the living bryophytes and tracheophytes. Here, we establish a timescale for early land plant evolution that integrates over topological uncertainty by exploring the impact of competing hypotheses on bryophyte−tracheophyte relationships, among other variables, on divergence time estimation. We codify 37 fossil calibrations for Viridiplantae following best practice. We apply these calibrations in a Bayesian relaxed molecular clock analysis of a phylogenomic dataset encompassing the diversity of Embryophyta and their relatives within Viridiplantae. Topology and dataset sizes have little impact on age estimates, with greater differences among alternative clock models and calibration strategies. For all analyses, a Cambrian origin of Embryophyta is recovered with highest probability. The estimated ages for crown tracheophytes range from Late Ordovician to late Silurian. This timescale implies an early establishment of terrestrial ecosystems by land plants that is in close accord with recent estimates for the origin of terrestrial animal lineages. Biogeochemical models that are constrained by the fossil record of early land plants, or attempt to explain their impact, must consider the implications of a much earlier, middle Cambrian–Early Ordovician, origin.

plant evolution timescale phylogeny Embryophyta

FREE PDF GRATIS: PNAS Sup. Info.

Darwin, mais complexidade: canais de membrana mostram especificidade

Hydrophobic gating in BK channels

Zhiguang Jia, Mahdieh Yazdani, Guohui Zhang, Jianmin Cui & Jianhan Chen 

Nature Communications volume 9, Article number: 3408 (2018

Abstract

The gating mechanism of transmembrane ion channels is crucial for understanding how these proteins control ion flow across membranes in various physiological processes. Big potassium (BK) channels are particularly interesting with large single-channel conductance and dual regulation by membrane voltage and intracellular Ca2+. Recent atomistic structures of BK channels failed to identify structural features that could physically block the ion flow in the closed state. Here, we show that gating of BK channels does not seem to require a physical gate. Instead, changes in the pore shape and surface hydrophobicity in the Ca2+-free state allow the channel to readily undergo hydrophobic dewetting transitions, giving rise to a large free energy barrier for K+ permeation. Importantly, the dry pore remains physically open and is readily accessible to quaternary ammonium channel blockers. The hydrophobic gating mechanism is also consistent with scanning mutagenesis studies showing that modulation of pore hydrophobicity is correlated with activation properties.

Acknowledgments

All simulations were performed on the pikes GPU cluster housed in the Massachusetts Green High Performance Computing Cluster (MGHPCC). This work was supported by National Institutes of Health Grants R01 HL142301 (to J. Cui and J. Chen), R01 HL126774 (to J. Cui) and R01 GM114694 (to J. Cui).

Author information

Affiliations

Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA

Zhiguang Jia, Mahdieh Yazdani & Jianhan Chen

Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University, St Louis, MO, 63130, USA

Guohui Zhang & Jianmin Cui

Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA

Jianhan Chen

Contributions

Conception and design of the study: Z.J., M.Y., G.Z., J. Cui, and J. Chen; Performing the simulation and analysis: Z.J. and M.Y.; Analysis and interpretation of data, drafting, and revising the manuscript: Z.J., M.Y., G.Z., J. Cui, and J. Chen.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Jianhan Chen.

FREE PDF GRATIS: Nature Communications Sup. Info. Reviewers' File

Novo modelo sobre a origem da vida: redes de lipídios catalíticos

Systems protobiology: origin of life in lipid catalytic networks

Doron Lancet, Raphael Zidovetzki, Omer Markovitch

Published 25 July 2018. DOI: 10.1098/rsif.2018.0159

Source/Fonte: NASA

Abstract

Life is that which replicates and evolves, but there is no consensus on how life emerged. We advocate a systems protobiology view, whereby the first replicators were assemblies of spontaneously accreting, heterogeneous and mostly non-canonical amphiphiles. This view is substantiated by rigorous chemical kinetics simulations of the graded autocatalysis replication domain (GARD) model, based on the notion that the replication or reproduction of compositional information predated that of sequence information. GARD reveals the emergence of privileged non-equilibrium assemblies (composomes), which portray catalysis-based homeostatic (concentration-preserving) growth. Such a process, along with occasional assembly fission, embodies cell-like reproduction. GARD pre-RNA evolution is evidenced in the selection of different composomes within a sparse fitness landscape, in response to environmental chemical changes. These observations refute claims that GARD assemblies (or other mutually catalytic networks in the metabolism first scenario) cannot evolve. Composomes represent both a genotype and a selectable phenotype, anteceding present-day biology in which the two are mostly separated. Detailed GARD analyses show attractor-like transitions from random assemblies to self-organized composomes, with negative entropy change, thus establishing composomes as dissipative systems—hallmarks of life. We show a preliminary new version of our model, metabolic GARD (M-GARD), in which lipid covalent modifications are orchestrated by non-enzymatic lipid catalysts, themselves compositionally reproduced. M-GARD fills the gap of the lack of true metabolism in basic GARD, and is rewardingly supported by a published experimental instance of a lipid-based mutually catalytic network. Anticipating near-future far-reaching progress of molecular dynamics, M-GARD is slated to quantitatively depict elaborate protocells, with orchestrated reproduction of both lipid bilayer and lumenal content. Finally, a GARD analysis in a whole-planet context offers the potential for estimating the probability of life's emergence. The invigorated GARD scrutiny presented in this review enhances the validity of autocatalytic sets as a bona fide early evolution scenario and provides essential infrastructure for a paradigm shift towards a systems protobiology view of life's origin.

FREE PDF GRATIS: J R Soc Interface

Práticas de citação de alunos pós-graduados escrevendo revisões de literatura

Citation practices of postgraduate students writing literature reviews

Author: Badenhorst, Cecile

Source: London Review of Education, Volume 16, Number 1, March 2018, pp. 121-135(15)

Publisher: UCL IOE Press

DOI: https://doi.org/10.18546/LRE.16.1.11

Abstract

Writing a literature review requires highly sophisticated academic literacies. Many postgraduate students find this genre a challenge. While there is a growing awareness of the need for explicit pedagogy to support students writing this genre, many pedagogical interventions fail to move beyond a focus on citations as a stylistic convention or as a way of avoiding plagiarism. What is missing is a pedagogy that relates citing to the more complex, fluid conceptual and ontological practices that are implicit in academic contexts. The purpose of this paper is to explore the citation patterns, complexity and discursive practices in master's students' literature reviews, and to inform pedagogy.

Keywords: ACADEMIC IDENTITY; ACADEMIC LITERACIES; ACADEMIC WRITING; LITERATURE REVIEWS; MASTER'S STUDENT WRITING; PEDAGOGY; POSTGRADUATE

Document Type: Research Article

Publication date: 27 de Março de 2018

FREE PDF GRATIS: London Review of Education

Periódico de Sociologia: por que os lobistas tão persistentemente chamam a evolução de um “Fato”

Periódico de Sociologia: por que os lobistas tão persistentemente chamam a evolução de um “Fato”

Evolution News | @DiscoveryCSC

27 de agosto de 2018, 1:03 PM

Quantas vezes você ouviu a frase “a evolução é um fato”? Até algumas pessoas muito inteligentes que você pode pensar poderiam saber melhor, foram enganados pela repetição constante das variações dessa declaração. Certamente você a ouviu em Friends. Você a ouviu em Cosmos. Você já a ouviu tantas vezes de muitos defensores da evolução que é quase sem sentido documentar a ubiquidade desse modo de falar.

Quando falam ao público, por que os defensores de Darwin são tão enfáticos que “a evolução é um fato científico”? Finalmente, um artigo em periódico importante de sociologia abordou esta questão. No artigo “Evolution as a fact? A discourse analysis”, os autores Jason Jean e Yixi Lu confirmam o que nós sabíamos o tempo todo: os defensores da evolução chamam a evolução de um “fato” a fim de fazer a evolução aparecer mais certa para o público.

O que nós sabíamos o tempo todo

Você não precisa acreditar no que dissemos. Eis o que diz o artigo:

The primary goal of those who advocate for this discourse has always been to counter antievolutionism by associating the term ‘fact’ with evolution, thereby making evolution appear more certain to the public. … [A]dvocates clearly show how the discourse is driven by concerns external to the scientific vernacular and the practice of science, namely a perceived need to make evolution appear more certain to the public.

[O principal objetivo daqueles que defendem esse discurso tem sido sempre de contra-atacar o antievolucionismo associando o termo ‘fato’ com a evolução, desse modo fazendo a evolução parecer mais certa para o público. … [D]efensores claramente mostram como o discurso é conduzido por preocupações externas para o vernáculo científico e a prática da ciência, isto é, uma necessidade percebida de fazer a evolução parecer mais certa para o público.]

Jason Jean and Yixi Lu, “Evolution as a fact? A discourse analysis,” Social Studies of Science, Vol. 48(4) 615-632 (2018).

Ao empregar esta retórica, os ativistas darwinistas também têm um objetivo secundário — é reivindicar sua “autoridade intelectual” e alcançar “negação de… recursos”, especificamente “autoridade intelectual e oportunidades de carreira” para os céticos de Darwin. O que, você também não está surpreso em saber disso? Eis como foi colocado no artigo:

The discourse encompasses all instances where public scientists (Turner, 1980) describe evolution as a fact. Public scientists are those who engage in the practice of public science, where scientists or anyone claiming to speak for science address an audience in order to achieve their professional goals. These goals, according to Gieryn (1983), are the ‘acquisition of intellectual authority and career opportunities; denial of these resources to “pseudoscientists”; and protection of the autonomy of scientific research from political interference.’ (p. 781)

[O discurso abrange todas as ocorrências onde os cientistas públicos (Turner, 1980) descrevem a evolução como um fato. Cientistas públicos são aqueles que se envolvem na prática de ciência pública, onde os cientistas ou quem afirmar falar pela ciência se dirige a uma audiência a fim alcançar seus objetivos profissionais. Esses objetivos, segundo Gieryn (1983), são a ‘aquisição de autoridade intelectual e de oportunidades de carreira; negar esses recursos para os “pseudocientistas”; e proteção da autonomia da pesquisa científica de interferência política.’ (p. 781)]

Mas há um problema: a maioria dos cientistas não concorda sobre o que exatamente palavras tais como “fato”, “teoria”, ou “hipótese” significam. A menos que esses termos sejam cuidadosamente definidos, quando os defensores da evolução afirmam que a evolução é um “fato”, eles não estão promovendo um entendimento claro e cuidadoso de qualquer ideia científica. Antes, eles perpetuam o que o artigo chama de “um pântano discursivo”. 

“Uma ideia extremamente provável”

Os autores explicam que “a incapacidade dos defensores em concordar sobre como os fatos são definidos, descritos e relacionados às hipóteses e teorias tem resultado na criação de um pântano cada vez mais crescente”. Em uma passagem bem pesquisada, eles relacionam muitos dos rótulos “contraditórios”, mas retoricamente fortes que são aplicados à evolução quando ela é “empurrada” para o público. Esses rótulos incluem chamara a evolução:

• “a verdade”

• “realidade”

• “um fato histórico”

• “uma ideia extremamente provável”

• “uma hipótese bem substanciada”

• “uma teoria bem substanciada”

• “uma teoria matriz”

• “um fato de senso comum”

• “um fato, não uma teoria”

• “um fato e uma teoria”

• “um fato, uma teoria e um caminho”

O artigo argumenta que os ativistas evolucionistas dessa maneira “tomam termos científicos tradicionalmente ambíguos, e os definem e suas relações uns com os outros de modos controversos, contraditórios e confusos”. Este discurso “contraditório” cria problemas sérios para o entendimento da ciência pelo público — wque o artigo dhama de “confusão vernacular”. Na verdade, este modo confuse de falar mostra que os defensores da evolução realmente não estão lá interessados em explicar cuidadosamente para o público o que significam termos como “hipótese”, “teoria” e “fato” — eles estão mais interessados em que você descreia os céticos de Darwin e aceite a evolução:

Considerando-se essas questões, é possível concluir que o discurso nunca foi tencionado explicar apropriadamente a terminologia científica para o público. Associando o termo ‘fato’ com a evolução é, na verdade, um meio de atacar as afirmações e argumentos dos antievolucionistas, apesar das consequências negativas de uma terminologia científica minoritária, ignorando os consensos científicos estabelecidos, e criando um pântano de explicações contraditórias e confusas de como a evolução é um fato. Na sua detalhada análise das questões envolvidas, o biólogo Kirk Fitzhugh (2008: 112) desconsidera o discurso, referindo-se a ele como uma série de ‘slogans que promovem equívocos’.

Em última análise, o artigo objetiva racionalizar o discurso público e encorajar os cientistas que são defensores de Darwin a pararem de abusar de termos como “fato” ou “teoria” simplesmente com o propósito de defender a evolução. Isso é um bom objetivo, e boa sorte com isso. Controlar uma turba deve ser muito mais fácil.

Uma “Zona Livre de Crítica”

Melhorar a retórica dos lobistas de Darwin parece ser um resultado especialmente improvável desde que, como os autores observaram astutamente, esses defensores públicos da evolução adotaram um “acordo implícito” no qual eles se recusam a criticar uns aos outros publicamente. O artigo chama isso de uma “zona livre de crítica” entre os defensores de Darwin. Considere esta passagem impressionante:

The second implicit agreement is that no discourse advocate is allowed to subject another advocate’s cultural cartography to criticism. Among all the discourse advocates and users discussed here, none have made a single criticism of the cultural cartographies used by other advocates, and they routinely cite one another in support of their discourse advocacy (Gregory, 2008; Hughes, 1982; McComas, 1997; Moran, 2002). This agreement has assisted in the establishment of a ‘criticism-free zone’ in public science, in which discourse advocates can make seemingly any claim regarding key scientific terms.

… This criticism-free zone has thus far gone unnoticed, as discourse advocates and users reserve their attacks for antievolutionists.

[O segundo acordo implícito é que nenhum defensor do discurso é permitido sujeitar a cartografia cultural de outro defensor à crítica. Entre todos os defensores e usuários do discurso discutido aqui, nenhum deles fez uma só crítica das cartografias culturais usadas por outros defensores, e eles rotineiramente citam uns aos outros no apoio de seu discurso de defesa (Gregory, 2008; Hughes, 1982; McComas, 1997; Moran, 2002). Este acordo tem ajudado no estabelecimento de uma ‘zona livre de crítica’ na ciência pública, na qual os defensores do discurso podem, aparentemente, fazer qualquer afirmação concernente termos científicos fundamentais.

… Esta zona livre de crítica tem passado desapercebida, pois os defensores e usuários do discurso reservam seus ataques para os antievolucionistas.]

“A evolução é um fato, Fato, FATO!”

Isto é muito perceptivo. Os defensores públicos da evolução certamente tendem a ser suave suns com os outros a fim de concentrar seu fogo sobre os céticos de Darwin. O artigo poderia causar um furor, pois tem violado este “acordo implícito” de que os acadêmicos convencionais nunca devem criticar os defensores públicos da evolução. Porque esses autores ousaram dizer a verdade e criticar aquilo que, de outro modo, está além da crítica, eles podem se preparar para respostas duras dos lobistas de Darwin.

Qual é o ponto essencial deste artigo? Bem, um é que na próxima vez que alguém lhe disser “A evolução é um fato, Fato, FATO!”, como faz Michael Ruse no seu livro Darwinism Defended [Darwinismo defendido] (p. 58), pergunte o que ele quis dizer com “evolução” e com “fato”. Você também pode relembrar-lhe que pessoas que usam esse tipo de retórica estão simplesmente cometendo bullying de sua audiência enquanto, no processo, prejudicando o entendimento da ciência pelo público.

Source/Fonte: Evolution News

Cientistas "consertam" substancialmente a árvore da vida das bactérias

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life 

Donovan H Parks, Maria Chuvochina, David W Waite, Christian Rinke, Adam Skarshewski, Pierre-Alain Chaumeil & Philip Hugenholtz

Nature Biotechnology

Abstract

Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guide classification. Culture-independent sequencing technologies have matured sufficiently that a comprehensive genome-based taxonomy is now possible. We used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence. Under this approach, 58% of the 94,759 genomes comprising the Genome Taxonomy Database had changes to their existing taxonomy. This result includes the description of 99 phyla, including six major monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into a single phylum. Our taxonomy should enable improved classification of uncultured bacteria and provide a sound basis for ecological and evolutionary studies.

FREE PDF: Nature Biotechnology

O paradoxo de Karl Popper

The Paradox of Karl Popper

The great philosopher, renowned for his ferocious attacks on scientific and political dogmatism, could be quite dogmatic

By John Horgan on August 22, 2018

Karl Popper said he was the happiest philosopher he knew. "Most philosophers are really deeply depressed," he explained, "because they can’t produce anything worthwhile.” Credit: LSE Library Flickr

The world has been paying lots of attention to philosopher Karl Popper lately, although surely not as much as he would think he deserves. Popper, 1902-1994, railed against dogmatism in all forms. He is best-known for the principle of falsification, a means of distinguishing pseudo-scientific theories, like astrology and Freudian psychoanalysis, from genuine ones, like quantum mechanics and general relativity. The latter, Popper pointed out, make predictions that can be empirically tested. But scientists can never prove a theory to be true, Popper insisted, because the next test might contradict all that preceded it. Observations can only disprove a theory, or falsify it. In The Open Society and Its Enemies, published in 1945, Popper asserted that politics, even more than science, must avoid dogmatism, which inevitably fosters repression. Open Society has been invoked lately by those concerned about the rise of anti-democratic forces. Popper’s falsification principle has been used to attack string and multiverse theories, which cannot be empirically tested. Defenders of strings and multiverses deride critics as “Popperazzi.” [See note below on spelling.] Given the abiding interest in this complex thinker, I am posting an edited version of my profile of Popper in The End of Science. Please also check out my profiles of two other great philosophers of science, Thomas Kuhn and Paul Feyerabend. –John Horgan

I began to discern the paradox lurking at the heart of Karl Popper's career when, prior to interviewing him in 1992, I asked other philosophers about him. Queries of this kind usually elicit dull, generic praise, but not in Popper’s case. Everyone said this opponent of dogmatism was almost pathologically dogmatic. There was an old joke about Popper: The Open Society and its Enemies should have been titled The Open Society by One of its Enemies. 

To arrange an interview, I telephoned the London School of Economics, where Popper had taught since the late 1940s. A secretary said he generally worked at his home in a London suburb. When I called, a woman with an imperious, German-accented voice answered. Mrs. Mew, housekeeper and assistant to “Sir Karl.” Before he would see me, I had to send her a sample of my writings. She gave me a list of a dozen or so books by Sir Karl that I should read before the meeting. After numerous faxes and calls, she set a date. When I asked for directions from a nearby train station, Mrs. Mew assured me that all the cab drivers knew where Sir Karl lived. “He’s quite famous.”

“Sir Karl Popper's house, please,” I said as I climbed into a cab at the train station. “Who?” the driver asked. Sir Karl Popper? The famous philosopher? Never heard of him, the driver said. He knew the street on which Popper lived, however, and we found Popper's home, a two-story cottage surrounded by neatly trimmed lawn and shrubs, with little difficulty.

A tall, handsome woman with short dark hair, wearing black pants and shirt, answered the door. Mrs. Mew was only slightly less forbidding in person than over the telephone. As she led me into the house, she told me that Sir Karl was tired. He had endured many interviews and congratulations brought on by his 90th birthday last month, and he had been toiling over an acceptance speech for the Kyoto Prize, known as Japan's Nobel. I should expect to speak to him for only an hour at the most.

I was trying to lower my expectations when Popper made his entrance. He was stooped and surprisingly short. I had assumed the author of such autocratic prose would be tall. Yet he was as kinetic as a bantamweight boxer. He brandished an article I had written for Scientific American about how quantum mechanics is raising questions about the objectivity of physics. “I don’t believe a word of it,” he declared in a German-accented growl. “Subjectivism” has no place in physics, quantum or otherwise, he informed me. “Physics,” he exclaimed, grabbing a book from a table and slamming it down, “is that!”

He kept jumping up from his chair to forage for books or articles that could buttress a point. Striving to dredge a name or date from his memory, he kneaded his temples and gritted his teeth as if in agony. At one point, when the word "mutation" eluded him, he slapped his forehead repeatedly with alarming force, shouting, “Terms, terms, terms!”

Words poured from him so rapidly and with so much momentum that I began to lose hope that I could ask my prepared questions. “I am over 90, and I can still think,” he declared, as if I doubted it. Popper emphasized that he had known all the titans of twentieth-century science: Einstein, Schrodinger, Heisenberg. Popper blamed Bohr, whom he knew “very well,” for having introduced subjectivism into physics. Bohr was “a marvelous physicist, one of the greatest of all time, but he was a miserable philosopher, and one couldn’t talk to him. He was talking all the time, allowing practically only one or two words to you and then at once cutting in.”

As Mrs. Mew turned to leave, Popper asked her to find one of his books. She disappeared and returned empty-handed. “Excuse me, Karl, I couldn't find it,” she reported. “Unless I have a description, I can't check every bookcase.”

“It was actually, I think, on the right of this corner, but I have taken it away maybe...” His voice trailed off. Mrs. Mew somehow rolled her eyes without really rolling them and vanished.

He paused a moment, and I seized the opportunity to ask a question. “I wanted to ask you about...”

“Yes! You should ask me your questions!  I have wrongly taken the lead. You can ask me all your questions first.”

I noted that in his writings he seemed to abhor the notion of absolute truths. “No no!” Popper replied, shaking his head. He, like the logical positivists before him, believed that a scientific theory can be “absolutely” true. In fact, he had “no doubt” that some current theories are true (although he refused to say which ones). But he rejected the positivist belief that we can ever know that a theory is true. “We must distinguish between truth, which is objective and absolute, and certainty, which is subjective.”

...

Read more here: Scientific American

Scientific American e Galileu pisaram na bola: a preguiça não foi fator de extinção do Homo erectus

Reports of Homo erectus' laziness are 'moronic'


What bad headlines call lazy is what early humans called survival.
By Anna Brooks August 20, 2018

 

 

HOMO ERECTUS

Homo erectus was known for craftsmanship, creating sophisticated tools like handaxes and sharp blades out of stone.

Wikipedia

If you’re into ancient anthropology, you’ve probably seen a headline or two (or twelve) touting a new discovery about our long extinct human relative, Homo erectus. According to a recent study, some outlets claimed, laziness may have contributed to the extinction of our predecessors.

But the study, published in the journal PLOS One, reads quite differently than those sensationalized summaries. In fact, it says pretty much the opposite, concluding the hominins “weren’t eking out their existence on the margins, but were an ecologically dominant species.” The study authors declined requests for comments, but others in the field were eager to weigh in.

“The inference that laziness typifies Homo erectus and that such a failing might have hastened their extinction is moronic,” says Neil Roach, a biological anthropologist at Harvard University. “This is a solid study with interesting results that do contribute significantly to our field, and unfortunately, the press release does exactly the opposite.”

Roach makes his point emphatically, and with good reason—there’s a lot of evidence pointing to H. erectus as anything but lazy. The species survived for more than 1.5 million years. That’s pretty impressive compared to our measly 300,000 or so years on Earth. They may have been one of the first species to migrate out of Africa, says Roach, and are thought to be the first to hunt for food. There’s also evidence that H. erectus was one of the earliest hominins to use fire.

So if the general consensus among experts in the field is that H. erectus was an industrious sort, why are so many headlines claiming the species lazed itself into oblivion? It’s likely to do with one sentence in the paper, which describes the early hominins as a “technologically conservative” species that used “least-effort strategies” to survive. But accomplishing tasks like hunting and foraging using the least amount of energy doesn’t quite equate to going hungry because you don’t feel like peeling yourself off the couch.

...

Read more here: Popular Science

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Scientific American: Preguiça ajudou a levar hominídeo à extinção

Galileu: Preguiça contribuiu com a extinção do 'Homo erectus', diz estudo

Pesquisa original publicada na PLoS One:  

Acheulean technology and landscape use at Dawadmi, central Arabia

[+ 115 MBs!!!]

A evolução da evolução: processo, mecanismo e teoria

Evolution Evolving: Process, Mechanism and Theory

Churchill College, University of Cambridge, UK

1-4 April 2019

Evolutionary biology is a vibrant field with a theoretical framework that itself evolves. The Evolution Evolving conference will focus on some emerging themes in the relationship between development and evolution. Topics include the evolutionary causes and consequences of developmental bias, plasticity, niche construction and extra-genetic inheritance – all of which contribute to an understanding of evolvability. The conference will feature a balanced program of talks and poster sessions spanning three days, and be a mix of empirical and theoretical work, as well as contributions to the history and philosophy of evolutionary biology.

Invited speakers include Alex Badyaev, Renee Duckworth, Laurel Fogarty, Jukka Jernvall, Alan C Love, Joanna Masel, Armin Moczek, Angela Potochnik, Sean Rice and Jessica Riskin.

Abstract submission closes 1 December 2018

Early bird registration closes 4 January 2019

Conference website: https://evolutionevolving.org/

Conference twitter: @EvoEvolving

O criacionismo e teoria de conspiração compartilham de um viés teleológico comum

CORRESPONDENCE| VOLUME 28, ISSUE 16, PR867-R868, AUGUST 20, 2018

Creationism and conspiracism share a common teleological bias

Pascal Wagner-Egger Sylvain Delouvée Nicolas Gauvrit Sebastian Dieguez

DOI: https://doi.org/10.1016/j.cub.2018.06.072

The Creation of Adam - Michelangelo

Summary

Teleological thinking — the attribution of purpose and a final cause to natural events and entities — has long been identified as a cognitive hindrance to the acceptance of evolution, yet its association to beliefs other than creationism has not been investigated. Here, we show that conspiracism — the proneness to explain socio-historical events in terms of secret and malevolent conspiracies — is also associated to a teleological bias. Across three correlational studies (N > 2000), we found robust evidence of a teleological link between conspiracism and creationism, which was partly independent from religion, politics, age, education, agency detection, analytical thinking and perception of randomness. As a resilient ‘default’ component of early cognition, teleological thinking is thus associated with creationist as well as conspiracist beliefs, which both entail the distant and hidden involvement of a purposeful and final cause to explain complex worldly events.

FREE PDF GRATIS: Current Biology

Decifrando a base estrutural da regulação de proteína quinase eucariótica: mero acaso, fortuita necessidade ou design inteligente?

Deciphering the Structural Basis of Eukaryotic Protein Kinase Regulation

Hiruy S. Meharena, Philip Chang, Malik M. Keshwani, Krishnadev Oruganty, Aishwarya K. Nene, Natarajan Kannan, Susan S. Taylor , Alexandr P. Kornev 

Published: October 15, 2013 https://doi.org/10.1371/journal.pbio.1001680

Source/Fonte

Abstract

Eukaryotic protein kinases (EPKs) regulate numerous signaling processes by phosphorylating targeted substrates through the highly conserved catalytic domain. Our previous computational studies proposed a model stating that a properly assembled nonlinear motif termed the Regulatory (R) spine is essential for catalytic activity of EPKs. Here we define the required intramolecular interactions and biochemical properties of the R-spine and the newly identified “Shell” that surrounds the R-spine using site-directed mutagenesis and various in vitro phosphoryl transfer assays using cyclic AMP-dependent protein kinase as a representative of the entire kinome. Analysis of the 172 available Apo EPK structures in the protein data bank (PDB) revealed four unique structural conformations of the R-spine that correspond with catalytic inactivation of various EPKs. Elucidating the molecular entities required for the catalytic activation of EPKs and the identification of these inactive conformations opens new avenues for the design of efficient therapeutic EPK inhibitors.

Author Summary

Eukaryotic protein kinases (EPKs) have a highly conserved enzymatic kinase core that is involved in the regulation of numerous cell signaling processes through the transfer of a phosphate group from adenosine triphosphate (ATP) to more than 30% of human proteins. EPKs have been implicated in numerous human diseases, including cancer, cardiovascular diseases, and diabetes, making them one of the most sought-after therapeutic drug targets. The lack of structural diversity of the active kinase core has created a bottle-neck for designing successful therapeutic inhibitors. Here we describe the intramolecular interactions required for differentiating between the active and inactive states of EPKs. Kinases contain a hydrophobic regulatory spine (“R-spine”) that is disassembled in inactive kinases, and here we define an additional hydrophobic “Shell” that surrounds one end of the R-spine. Biochemical analysis of the five nonconsecutive R-spine residues and three nonconsecutive Shell residues shows that proper assembly of the R-spine and Shell is essential for maintaining kinase activity. Structural analysis of the 172 known structures of EPKs without bound ligands led to the identification of four inactive conformations that correlate with the disassembly of the R-spine. Understanding the molecular elements involved in the regulation of kinase activity and the identification of these diverse groups of inactive conformations should aid the design of more specific therapeutic EPK inhibitors.

Citation: Meharena HS, Chang P, Keshwani MM, Oruganty K, Nene AK, Kannan N, et al. (2013) Deciphering the Structural Basis of Eukaryotic Protein Kinase Regulation. PLoS Biol 11(10): e1001680.

https://doi.org/10.1371/journal.pbio.1001680

Academic Editor: Gregory A. Petsko, Brandeis University, United States of America

Received: May 21, 2013; Accepted: August 29, 2013; Published: October 15, 2013

Copyright: © 2013 Meharena et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: National Institutes of Health Grant GM19301 and GM34921 (to SST) and National Science Foundation's Graduate Research Fellowship Program (GRFP). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Abbreviations: EPK, eukaryotic protein kinase; R-spine, regulatory spine; RS0-4, R-spine residue 0–5; SH1–3, shell residue 1–3

FREE PDF GRATIS: PLos Biology

i-Motif DNA: características e significância estruturais para a biologia celular - mero acaso, fortuita necessidade ou design inteligente???

i-Motif DNA: structural features and significance to cell biology 

Hala Abou Assi Miguel Garavís Carlos González Masad J Damha

Nucleic Acids Research, gky735, https://doi.org/10.1093/nar/gky735

Published: 16 August 2018 

Article history

Received: 20 June 2018 Revision Received: 22 July 2018

Accepted: 13 August 2018

Source/Fonte

Abstract

The i-motif represents a paradigmatic example of the wide structural versatility of nucleic acids. In remarkable contrast to duplex DNA, i-motifs are four-stranded DNA structures held together by hemi- protonated and intercalated cytosine base pairs (C:C+). First observed 25 years ago, and considered by many as a mere structural oddity, interest in and discussion on the biological role of i-motifs have grown dramatically in recent years. In this review we focus on structural aspects of i-motif formation, the factors leading to its stabilization and recent studies describing the possible role of i-motifs in fundamental biological processes.

FREE PDF GRATIS: Nucleic Acids Research