O ajuste fino de máquinas e sistemas moleculares: mero acaso, fortuita necessidade ou design inteligente?

terça-feira, junho 23, 2020

Journal of Theoretical Biology

Volume 501, 21 September 2020, 110352

Using statistical methods to model the fine-tuning of molecular machines and systems

Authors Steinar Thorvaldsen a Ola Hössjer b

Dep. of Education, University of Tromsø, Norway

b Stockholm University, Dep. of Mathematics, Division of Mathematical Statistics, Sweden

Received 6 July 2019, Revised 26 May 2020, Accepted 27 May 2020, Available online 4 June 2020.




Highlights

• Statistical methods are appropriate for modelling fine-tuning.

• Fine-tuning is detected in functional proteins, cellular networks etc.

• Constants and initial conditions of nature are deliberately tuned.

• Statistical analysis of fine-tuning model some of the categories of design.

• Fine-tuning and design deserve attention in the scientific community.

Abstract

Fine-tuning has received much attention in physics, and it states that the fundamental constants of physics are finely tuned to precise values for a rich chemistry and life permittance. It has not yet been applied in a broad manner to molecular biology. However, in this paper we argue that biological systems present fine-tuning at different levels, e.g. functional proteins, complex biochemical machines in living cells, and cellular networks. This paper describes molecular fine-tuning, how it can be used in biology, and how it challenges conventional Darwinian thinking. We also discuss the statistical methods underpinning fine-tuning and present a framework for such analysis.

Um padrão irregular de ampulheta descreve o ritmo do desenvolvimento fenotípico na evolução dos mamíferos placentários

segunda-feira, junho 15, 2020

An irregular hourglass pattern describes the tempo of phenotypic development in placental mammal evolution

Gerardo A. Cordero, Marcelo R. Sánchez-Villagra and Ingmar Werneburg



Abstract

Organismal development is defined by progressive transformations that ultimately give rise to distinct tissues and organs. Thus, temporal shifts in ontogeny often reflect key phenotypic differences in phylogeny. Classical theory predicts that interspecific morphological divergence originates towards the end of embryonic or fetal life stages, i.e. the early conservation model. By contrast, the hourglass model predicts interspecific variation early and late in prenatal ontogeny, though with a phylogenetically similar mid-developmental period. This phylotypic period, however, remains challenging to define within large clades such as mammals. Thus, molecular and morphological tests on a mammalian hourglass have not been entirely congruent. Here, we report an hourglass-like pattern for mammalian developmental evolution. By comparing published data on the timing of 74 homologous characters across 51 placental species, we demonstrated that variation in the timing of development decreased late in embryogenesis––when organ formation is highly active. Evolutionary rates of characters related to this timeframe were lowest, coinciding with a phylotypic period that persisted well beyond the pharyngula ‘stage’. The trajectory culminated with elevated variation in a handful of fetal and perinatal characters, yielding an irregular hourglass pattern. Our study invites further quantification of ontogeny across diverse amniotes and thus challenges current ideas on the universality of developmental patterns.

FREE PDF GRATIS: Biology Letters

Evidência neurocientífica: mente irredutível (Parte 1)

Mais uma hipótese sobre a origem da vida: a partir do DNA e RNA

sexta-feira, junho 12, 2020

Selective prebiotic formation of RNA pyrimidine and DNA purine nucleosides

Jianfeng Xu, Václav Chmela, Nicholas J. Green, David A. Russell, Mikołaj J. Janicki, Robert W. Góra, Rafał Szabla, Andrew D. Bond & John D. Sutherland 

Nature volume 582, pages60–66(2020)

Article

Published: 03 June 2020

Extended Data Fig. 1
Abstract

The nature of the first genetic polymer is the subject of major debate 1. Although the ‘RNA world’ theory suggests that RNA was the first replicable information carrier of the prebiotic era—that is, prior to the dawn of life 2,3—other evidence implies that life may have started with a heterogeneous nucleic acid genetic system that included both RNA and DNA 4. Such a theory streamlines the eventual ‘genetic takeover’ of homogeneous DNA from RNA as the principal information-storage molecule, but requires a selective abiotic synthesis of both RNA and DNA building blocks in the same local primordial geochemical scenario. Here we demonstrate a high-yielding, completely stereo-, regio- and furanosyl-selective prebiotic synthesis of the purine deoxyribonucleosides: deoxyadenosine and deoxyinosine. Our synthesis uses key intermediates in the prebiotic synthesis of the canonical pyrimidine ribonucleosides (cytidine and uridine), and we show that, once generated, the pyrimidines persist throughout the synthesis of the purine deoxyribonucleosides, leading to a mixture of deoxyadenosine, deoxyinosine, cytidine and uridine. These results support the notion that purine deoxyribonucleosides and pyrimidine ribonucleosides may have coexisted before the emergence of life 5.

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Porque os dados nunca são brutos

sexta-feira, maio 22, 2020

Why Data Is Never Raw 

On the seductive myth of information free of human judgment

Source/Fonte: University of London

Nick Barrowman

A curious fact about our data-obsessed era is that we’re often not entirely sure what we even mean by “data”: Elementary particles of knowledge? Digital records? Pure information? Sometimes when we refer to “the data,” we mean the results of an analysis or the evidence concerning a certain question. On other occasions we intend “data” to signify something like “reliable evidence,” as in the saying “The plural of anecdote is not data.”

In everyday usage, the term “data” is associated with a jumble of notions about information, science, and knowledge. Countless reports marvel at the astonishing volumes of data being produced and manipulated, the efficiencies and new opportunities this has made possible, and the myriad ways in which society is changing as a result. We speak of “raw” data and laud it for its independence from human judgment. On this basis, “data-driven” (or “evidence-based”) decision-making is widely endorsed. Yet data’s purported freedom from human subjectivity also seems to allow us to invest it with agency: “Let the data speak for itself,” for “The data doesn’t lie.”

Out of this quizzical mix, it is perhaps unsurprising that near-magical thinking about data has emerged. In the 2015 book Digital Destiny: How the New Age of Data Will Transform the Way We Work, Live, and Communicate, Shawn DuBravac describes a collection of “properties of data” and expresses them in anthropomorphic terms. DuBravac, former chief economist at the Consumer Electronics Association and a self-styled futurist and “trendcaster,” claims that data “seeks permanence,” “wants to replicate,” “seeks instantaneity,” “wants to be understood,” and “seeks movement.”

Data is immediate.... When data comes into being, when it is first tracked, captured, or copied, it wants to immediately be utilized — to exert force and influence.... Data constantly moves toward efficiency. It removes barriers; it closes distances; it destroys the moments between recognition and understanding. Because data wants to be understood, it abhors friction.

This projection of human-like qualities onto data is ostensibly metaphorical, but it can muddle our thinking. It seems aimed at obscuring how intertwined is the production of data with human judgment, and the use of data with human agency. And once our agency has been obscured, it is not hard to imagine that data has a mind of its own, that to solve our great problems we have only to collect the data and set the computers running.
...

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Homoquiralidade: raios cósmicos podem ter deixado marcas indeléveis no início da vida

quinta-feira, maio 21, 2020

The Chiral Puzzle of Life
Noemie Globus1,2 and Roger D. Blandford3

Published 2020 May 20 • © 2020. The American Astronomical Society. All rights reserved.
The Astrophysical Journal Letters, Volume 895, Number 1

Published 2020 May 20 • © 2020. The American Astronomical Society. All rights reserved.

Author e-mails

globus@nyu.edu

rdb3@stanford.edu

Author affiliations

1 Center for Cosmology & Particle Physics, New York University, New York, NY 10003, USA

2 Center for Computational Astrophysics, Flatiron Institute, Simons Foundation, New York, NY 10003, USA

3 Kavli Institute for Particle Astrophysics & Cosmology, Stanford University, Stanford, CA 94305, USA

Dates
Received 2020 March 4, Accepted 2020 April 27, Published 2020 May 20

Citation Noemie Globus and Roger D. Blandford 2020 ApJL 895 L11


Keywords Astrobiology ; Cosmic rays



Abstract

Biological molecules chose one of two structurally chiral systems which are related by reflection in a mirror. It is proposed that this choice was made, causally, by cosmic rays, which are known to play a major role in mutagenesis. It is shown that magnetically polarized cosmic rays that dominate at ground level today can impose a small, but persistent, chiral bias in the rate at which they induce structural changes in simple, chiral monomers that are the building blocks of biopolymers. A much larger effect should be present with helical biopolymers, in particular, those that may have been the progenitors of ribonucleic acid and deoxyribonucleic acid. It is shown that the interaction can be both electrostatic, just involving the molecular electric field, and electromagnetic, also involving a magnetic field. It is argued that this bias can lead to the emergence of a single, chiral life form over an evolutionary timescale. If this mechanism dominates, then the handedness of living systems should be universal. Experiments are proposed to assess the efficacy of this process.

Modelando o discurso científico

quarta-feira, maio 20, 2020

Modeling Scientific Discourse

Peter McBurney and Simon Parsons

Department of Computer Science
University of Liverpool
Liverpool L69 7ZF United Kingdom

P.J.McBurney,S.D.Parsons@csc.liv.ac.uk


The Problem Domain

We aim to build intelligent systems which can reason autonomously about the risk of carcinogenicity of chemicals, drawing on whatever theoretical or experimental evidence is available. In earlier work [14], reviewing the literature on methods of carcinogen risk assessment, we catalogued the different types of evidence adduced to support these claims, which may be in the form of: experimental results on tissue cultures, animals or human epidemiological studies; analytical comparisons with known carcinogens; or explication of biomedical causal pathways. Because the research which underpins conclusions in this domain is usually at the leadingedge of the scientific disciplines concerned, evidence from these different sources may be inconsistent or conflicting. Consequently, carcinogen risk assessment usually involves the comparison and resolution of multiple evidences and arguments for and against a particular scientific claim [23, 27].

To represent this domain in an intelligent system, therefore, we first require a philosophical model of scientific enquiry. Which philosophy of science is appropriate for such representation, and why? Next, having adopted such a conceptual model, we will need to formalize it. How can this be achieved? In particular, how may we represent the scientific uncertainty characteristic of knowledge in the carcinogen domain? These questions are the focus of this paper, which outlines our current thinking and approach.

O discurso evolutivo na obra Origem das Espécies é uma teleologia natural?

O discurso evolutivo na obra Origem das Espécies pode ser considerado uma teleologia natural?

Rafael Francisco Hiller - Unisinos

Heloisa Allgayer - Unisinos


Palavras-chave: Teleologia, Evolucionismo, Darwin


RESUMO

Neste artigo, iremos usar como aporte teórico a teoria da evolução desenvolvida na sexta edição da Origem das espécies de Charles Darwin, analisaremos a relação causal desenvolvida pelo autor na estruturação do argumento de seleção natural, a partir disso, será investigado possíveis traços teleológicos nas estratégicas argumentativas de Darwin. Como metodologia desse trabalho, serão examinados os capítulos que contém o principal arcabouço para a estruturação da hipótese de seleção natural, com base nisso, os elementos causais serão destacados, bem como serão elencados os possíveis traços de um discurso teleológico por parte de Darwin. A partir da análise que foi realizada é possível afirmar que discurso de Darwin possui pressupostos teleológicos no que se refere ao processo que leva a produção de novas formas orgânicas se mostra claramente na noção de mudanças que são produzidas como adaptações. A seleção natural, determina à preservação/extinção na natureza, possui a função de direcionamento do processo evolutivo, afim de que, surjam novas formas aperfeiçoadas. A partir disso, pode-se supor um princípio teleológico na estratégia argumentativa darwiniana, pois tem como causa final o surgimento de uma nova forma aperfeiçoada.

Palavras-chave: Teleologia; Evolucionismo; Darwin

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Um bilhão de anos faltando no registro geológico: para onde podem ter ido?

segunda-feira, maio 18, 2020

Diachronous development of Great Unconformities before Neoproterozoic Snowball Earth

Rebecca M. Flowers, Francis A. Macdonald, View ORCID ProfileChristine S. Siddoway, and Rachel Havranek

PNAS May 12, 2020 117 (19) 10172-10180; first published April 27, 2020 https://doi.org/10.1073/pnas.1913131117 

Edited by Paul F. Hoffman, University of Victoria, Victoria, Canada, and approved March 6, 2020 (received for review July 30, 2019)



Significance

Erosion below the Great Unconformity has been interpreted as a global phenomenon associated with Snowball Earth. Geological relationships and thermochronologic data provide evidence that the bulk of erosion below the Great Unconformity in Colorado occurred prior to Cryogenian glaciation. We suggest that there are multiple, regionally diachronous Great Unconformities that are tectonic in origin.

Abstract

The Great Unconformity marks a major gap in the continental geological record, separating Precambrian basement from Phanerozoic sedimentary rocks. However, the timing, magnitude, spatial heterogeneity, and causes of the erosional event(s) and/or depositional hiatus that lead to its development are unknown. We present field relationships from the 1.07-Ga Pikes Peak batholith in Colorado that constrain the position of Cryogenian and Cambrian paleosurfaces below the Great Unconformity. Tavakaiv sandstone injectites with an age of ≥676 ± 26 Ma cut Pikes Peak granite. Injection of quartzose sediment in bulbous bodies indicates near-surface conditions during emplacement. Fractured, weathered wall rock around Tavakaiv bodies and intensely altered basement fragments within unweathered injectites imply still earlier regolith development. These observations provide evidence that the granite was exhumed and resided at the surface prior to sand injection, likely before the 717-Ma Sturtian glaciation for the climate appropriate for regolith formation over an extensive region of the paleolandscape. The 510-Ma Sawatch sandstone directly overlies Tavakaiv-injected Pikes granite and drapes over core stones in Pikes regolith, consistent with limited erosion between 717 and 510 Ma. Zircon (U-Th)/He dates for basement below the Great Unconformity are 975 to 46 Ma and are consistent with exhumation by 717 Ma. Our results provide evidence that most erosion below the Great Unconformity in Colorado occurred before the first Neoproterozoic Snowball Earth and therefore cannot be a product of glacial erosion. We propose that multiple Great Unconformities developed diachronously and represent regional tectonic features rather than a synchronous global phenomenon.

Great Unconformity Snowball Earth thermochronology zircon (U-Th)/Heinjectites

Footnotes

↵1To whom correspondence may be addressed. Email: rebecca.flowers@colorado.edu.

Author contributions: R.M.F. and F.A.M. designed research; R.M.F., F.A.M., C.S.S., and R.H. performed research; and R.M.F., F.A.M., and C.S.S. wrote the paper.

Competing interest statement: P.F.H. and F.A.M. are coauthors on three papers, most recently in 2017.

This article is a PNAS Direct Submission.

This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.1913131117/-/DCSupplemental.

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Uma visão radical da evolução das organelas

segunda-feira, maio 04, 2020

Alternating terminal electron‐acceptors at the basis of symbiogenesis: How oxygen ignited eukaryotic evolution

Dave Speijer

First published:05 January 2017 https://doi.org/10.1002/bies.201600174



Abstract

What kind of symbiosis between archaeon and bacterium gave rise to their eventual merger at the origin of the eukaryotes? I hypothesize that conditions favouring bacterial uptake were based on exchange of intermediate carbohydrate metabolites required by recurring changes in availability and use of the two different terminal electron chain acceptors, the bacterial one being oxygen. Oxygen won, and definitive loss of the archaeal membrane potential allowed permanent establishment of the bacterial partner as the proto‐mitochondrion, further metabolic integration and highly efficient ATP production. This represents initial symbiogenesis, when crucial eukaryotic traits arose in response to the archaeon‐bacterium merger. The attendant generation of internal reactive oxygen species (ROS) gave rise to a myriad of further eukaryotic adaptations, such as extreme mitochondrial genome reduction, nuclei, peroxisomes and meiotic sex. Eukaryotic origins could have started with shuffling intermediate metabolites as is still essential today.

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Inferindo entropia a partir da estrutura

Inferring entropy from structure

Gil Ariel
Department of Mathematics, Bar-Ilan University, 52000 Ramat Gan, Israel

Haim Diamant
Raymond and Beverly Sackler School of Chemistry, Tel Aviv University, 69978 Tel Aviv, Israel



Abstract

The thermodynamic definition of entropy can be extended to nonequilibrium systems based on its relation to information. To apply this definition in practice requires access to the physical system’s microstates, which may be prohibitively inefficient to sample or difficult to obtain experimentally. It is beneficial, therefore, to relate the entropy to other integrated properties which are accessible out of equilibrium. We focus on the structure factor, which describes the spatial correlations of density fluctuations and can be directly measured by scattering. The information gained by a given structure factor regarding an otherwise unknown system provides an upper bound for the system’s entropy. We prove that the maximum-entropy model corresponds to an equilibrium system with an effective pair-interaction. Approximate closed-form relations for the effective pair-potential and entropy in terms of the structure factor are obtained. The relations are used to estimate the entropy of an exactly solvable model and numerical examples of systems out of equilibrium, and the results are compared with other entropy-estimation methods. The focus is on low-dimensional examples, where our method, as well as a recently proposed compression-based one, can be tested against a rigorous direct-sampling technique. The entropy inferred from the structure factor is found to be consistent with the other methods, superior for larger system sizes, and accurate in identifying global transitions. Our approach allows for extensions of the theory to more complex systems and to higher-order correlations.

FREE PDF GRATIS: arXiv 

Mais uma hipótese sobre a origem da vida: de três funções privilegiadas a quatro pilares

sábado, maio 02, 2020

Defining Lyfe in the Universe: From Three Privileged Functions to Four Pillars

by Stuart Bartlett 1,2,* and Michael L. Wong 3,4
 
Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA 91125, USA

Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo 152-8550, Japan

Department of Astronomy and Astrobiology Program, University of Washington, Seattle, WA 98195, USA

NASA Nexus for Exoplanet System Science’s Virtual Planetary Laboratory, University of Washington, Seattle, WA 98195, USA

Author to whom correspondence should be addressed.


Received: 23 March 2020 / Revised: 12 April 2020 / Accepted: 13 April 2020 / Published: 16 April 2020

(This article belongs to the Special Issue Frontiers of Astrobiology)



Abstract

Motivated by the need to paint a more general picture of what life is—and could be—with respect to the rest of the phenomena of the universe, we propose a new vocabulary for astrobiological research. Lyfe is defined as any system that fulfills all four processes of the living state, namely: dissipation, autocatalysis, homeostasis, and learning. Life is defined as the instance of lyfe that we are familiar with on Earth, one that uses a specific organometallic molecular toolbox to record information about its environment and achieve dynamical order by dissipating certain planetary disequilibria. This new classification system allows the astrobiological community to more clearly define the questions that propel their research—e.g., whether they are developing a historical narrative to explain the origin of life (on Earth), or a universal narrative for the emergence of lyfe, or whether they are seeking signs of life specifically, or lyfe at large across the universe. While the concept of “life as we don’t know it” is not new, the four pillars of lyfe offer a novel perspective on the living state that is indifferent to the particular components that might produce it. 

Keywords: definition of life; origin of life; astrobiology; mechanotroph

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Esclarecendo a respeito da palavra F(unção) em genômica.

quinta-feira, abril 30, 2020

Getting clear about the F-word in genomics

Stefan Linquist ,W. Ford Doolittle, Alexander F. Palazzo



Although biology is generally awash with adaptationist “just-so” stories, the situation in molecular biology and genomics is particularly bad. Various types of non-coding DNA are routinely interpreted as functional without adequate consideration of non-adaptationist alternative hypotheses [1]. Part of the problem is surely due to a failure in these disciplines to appreciate theoretical developments in population genetics, which outline the conditions under which genetic elements are selected [2]. However, as a number of authors have noted, the problem is also partly due to a confusion about the various possible meanings of “function” in biology [3–5]. Our central thesis is that there exists an overlooked dichotomy in the way that researchers see natural selection to be related to function. Traits or genetic elements that are merely under purifying selection have what we call maintenance functions whereas those that have historically been under directional selection have origin functions. We argue that ignoring this distinction encourages a form of pan-adaptationism, where highly plausible non-adaptive explanations for the origins of certain genetic elements or traits are themselves ignored. Thus, our recommendation is for researchers to always clarify which sense of “function” they mean (origin or maintenance) when talking or writing about selected effects.

Citation: Linquist S, Doolittle WF, Palazzo AF (2020) Getting clear about the F-word in genomics. PLoS Genet 16(4): e1008702. https://doi.org/10.1371/journal.pgen.1008702

Editor: Jonathan Flint, University of California Los Angeles, UNITED STATES

Published: April 1, 2020

Copyright: © 2020 Linquist 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: Financial support for this research was provided by the Social Sciences and Humanities Research Council of Canada (https://www.sshrc-crsh.gc.ca/, grant #430335) to Stefan Linquist and by the Natural Sciences and Engineering Research Council of Canada (nserc-crsng.gc.ca, grant # GLDSU44989) to W. Ford Doolittle. 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.

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Design de movimentos coletivos de interruptores, rotores e motores moleculares sintéticos

segunda-feira, abril 20, 2020

Design of Collective Motions from Synthetic Molecular Switches, Rotors, and Motors

Damien Dattler Gad Fuks Joakim Heiser Emilie Moulin Alexis Perrot Xuyang Yao Nicolas Giuseppone*

Cite this: Chem. Rev. 2020, 120, 1, 310-433

Publication Date:December 23, 2019


Copyright © 2019 American Chemical Society


Abstract

Precise control over molecular movement is of fundamental and practical importance in physics, biology, and chemistry. At nanoscale, the peculiar functioning principles and the synthesis of individual molecular actuators and machines has been the subject of intense investigations and debates over the past 60 years. In this review, we focus on the design of collective motions that are achieved by integrating, in space and time, several or many of these individual mechanical units together. In particular, we provide an in-depth look at the intermolecular couplings used to physically connect a number of artificial mechanically active molecular units such as photochromic molecular switches, nanomachines based on mechanical bonds, molecular rotors, and light-powered rotary motors. We highlight the various functioning principles that can lead to their collective motion at various length scales. We also emphasize how their synchronized, or desynchronized, mechanical behavior can lead to emerging functional properties and to their implementation into new active devices and materials.

FREE PDF GRATIS: Chemical Reviews 129 MBs!!!

Actina: a percepção do nível atômico das proteínas promove compreensão fundamental da vida humana: mero acaso, fortuita necessidade ou design inteligente?

sexta-feira, abril 17, 2020

Mechanism of actin N-terminal acetylation

Grzegorz Rebowski1,*, Malgorzata Boczkowska1,*, Adrian Drazic2, Rasmus Ree2, Marianne Goris3, Thomas Arnesen2,3,4 and Roberto Dominguez1,†

1Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.

2Department of Biomedicine, University of Bergen, Bergen, Norway.

3Department of Biological Sciences, University of Bergen, Bergen, Norway.

4Department of Surgery, Haukeland University Hospital, Bergen, Norway.

↵†Corresponding author. Email: droberto@pennmedicine.upenn.edu

↵* These authors contributed equally to this work.

Science Advances 08 Apr 2020:

Vol. 6, no. 15, eaay8793

DOI: 10.1126/sciadv.aay8793

Fig. 3 Structural basis of NAA80 binding to actin-profilin.

Abstract

About 80% of human proteins are amino-terminally acetylated (Nt-acetylated) by one of seven Nt-acetyltransferases (NATs). Actin, the most abundant protein in the cytoplasm, has its own dedicated NAT, NAA80, which acts posttranslationally and affects cytoskeleton assembly and cell motility. Here, we show that NAA80 does not associate with filamentous actin in cells, and its natural substrate is the monomeric actin-profilin complex, consistent with Nt-acetylation preceding polymerization. NAA80 Nt-acetylates actin-profilin much more efficiently than actin alone, suggesting that profilin acts as a chaperone for actin Nt-acetylation. We determined crystal structures of the NAA80-actin-profilin ternary complex, representing different actin isoforms and different states of the catalytic reaction and revealing the first structure of NAT-substrate complex at atomic resolution. The structural, biochemical, and cellular analysis of mutants shows how NAA80 has evolved to specifically recognize actin among all cellular proteins while targeting all six actin isoforms, which differ the most at the amino terminus.

FREE PDF GRATIS: Science Advances Sup. Info.

Darwin, as árvores evolutivas não podem revelar taxas de especiação e extinção

Nature

Article

Published: 15 April 2020

Extant timetrees are consistent with a myriad of diversification histories

Stilianos Louca & Matthew W. Pennell 

Nature (2020)


Figure 1 | Assessing evolutionary histories. Louca and Pennell1 raise questions about a standard approach to estimating past rates of species formation (speciation) and extinction that uses data from a lineage-through-time plot. The number of species in the present depends on how speciation and extinction rates varied over time in the past. 

Abstract

Time-calibrated phylogenies of extant species (referred to here as ‘extant timetrees’) are widely used for estimating diversification dynamics1. However, there has been considerable debate surrounding the reliability of these inferences2,3,4,5 and, to date, this critical question remains unresolved. Here we clarify the precise information that can be extracted from extant timetrees under the generalized birth–death model, which underlies most existing methods of estimation. We prove that, for any diversification scenario, there exists an infinite number of alternative diversification scenarios that are equally likely to have generated any given extant timetree. These ‘congruent’ scenarios cannot possibly be distinguished using extant timetrees alone, even in the presence of infinite data. Importantly, congruent diversification scenarios can exhibit markedly different and yet similarly plausible dynamics, which suggests that many previous studies may have over-interpreted phylogenetic evidence. We introduce identifiable and easily interpretable variables that contain all available information about past diversification dynamics, and demonstrate that these can be estimated from extant timetrees. We suggest that measuring and modelling these identifiable variables offers a more robust way to study historical diversification dynamics. Our findings also make it clear that palaeontological data will continue to be crucial for answering some macroevolutionary questions.

Data availability

No new data were generated for this manuscript. All phylogenetic datasets used as examples have previously been published previously, and are cited where appropriate.

Code availability

Computational methods used for this article—including functions for simulating birth–death models, for constructing models within a given congruence class, for calculating the likelihood of a congruence class and for directly fitting congruence classes (either in terms of λp or in terms of rp and ρλo) to extant timetrees—are implemented in the R package castor v.1.5.5, which is available from The Comprehensive R Archive Network at https://cran.r-project.org/package=castor.

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Bertrand Russell 'falou e disse': o argumento de design não tem defeito lógico formal

segunda-feira, abril 13, 2020

Argumento de design: “Este argumento não tem defeito lógico formal; suas premissas são empíricas e sua conclusão professa ser alcançada de acordo com os cânones usuais da inferência empírica. A questão de se deve ser aceito ou não, portanto, não se refere a questões metafísicas gerais, mas a considerações comparativamente detalhadas ”(B. Russell, History of Western Philosophy [Nova York: Simon & Schuster, 1945], p. 589) .

 
Design argument: “This argument has no formal logical defect; its premises are empirical, and its conclusion professes to be reached in accordance with the usual canons of empirical inference. The question whether it is to be accepted or not turns, therefore, not on general metaphysical questions, but on comparatively detailed considerations” (B. Russell, History of Western Philosophy [New York: Simon & Schuster, 1945], p. 589).

Pegadas gigantes de dinossauros são encontradas no teto de uma caverna!!!

sábado, abril 11, 2020

Middle Jurassic tracks of sauropod dinosaurs in a deep karst cave in France

Jean-David Moreau, Vincent Trincal, Emmanuel Fara, Louis Baret, Alain Jacquet, Claude Barbini

Article: e1728286 | Received 29 Oct 2018, Accepted 13 Dec 2019, Published online: 25 Mar 2020



A scientist on a caving trip happened to spot dinosaur tracks in the ceiling of Castelbouc Cave in France. Credit: Jean-David Moreau et al./J. Vertebr. Paleontol.

ABSTRACT

Although the deep galleries of natural underground cavities are difficult to access and are sometimes dangerous, they have the potential to preserve trace fossils. Here, we report on the first occurrence of sauropod dinosaur tracks inside a karstic cave. Three trackways are preserved on the roof of the Castelbouc cave 500 m under the surface of the Causse Méjean plateau, southern France. The tracks are Bathonian in age (ca. 168–166 Ma), a crucial but still poorly known time interval in sauropod evolution. The three trackways yield sauropod tracks that are up to 1.25 m long and are therefore amongst the largest known dinosaur footprints worldwide. The trackmakers are hypothesized to be titanosauriforms. Some of the tracks are extremely well preserved and show impressions of digits, digital pads, and claws. We erect the new ichnogenus and ichnospecies Occitanopodus gandi, igen. et isp. nov. In order to characterize depositional environments, we conducted sedimentological, petrographic, and mineralogical analyses. The tracks from Castelbouc attest the presence of sauropods in proximal littoral environments during the Middle Jurassic. This discovery demonstrates the great potential of prospecting in deep karst caves that can occasionally offer larger and better-preserved surfaces than outdoor outcrops.

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SARS-CoV-2 (COVID-19) pelos números

quinta-feira, abril 02, 2020

SARS-CoV-2 (COVID-19) by the numbers

Yinon M Bar-On, Avi Flamholz, Rob Phillips, Ron Milo Is a corresponding author

The Weizmann Institute for Science, Israel; University of California, Berkeley, United States; California Institute of Technology, United States

FEATURE ARTICLE Mar 31, 2020


Abstract

The current SARS-CoV-2 pandemic is a harsh reminder of the fact that, whether in a single human host or a wave of infection across continents, viral dynamics is often a story about the numbers. In this snapshot, our aim is to provide a one-stop, curated graphical source for the key numbers that help us understand the virus driving our current global crisis. The discussion is framed around two broad themes: 1) the biology of the virus itself and 2) the characteristics of the infection of a single human host. Our one-page summary provides the key numbers pertaining to SARS-CoV-2, based mostly on peer-reviewed literature. The numbers reported in summary format are substantiated by the annotated references below. Readers are urged to remember that much uncertainty remains and knowledge of this pandemic and the virus driving it is rapidly evolving. In the paragraphs below we provide 'back of the envelope' calculations that exemplify the insights that can be gained from knowing some key numbers and using quantitative logic. These calculations serve to improve our intuition through sanity checks, but do not replace detailed epidemiological analysis.

FREE PDF GRATIS: eLIFE

Inglês científico como língua estrangeira

terça-feira, março 31, 2020

Scientific English as a Foreign Language

Nancy A. Burnham and Frederick L. Hutson

Department of Physics
Worcester Polytechnic Institute
100 Institute Road, Worcester, MA 01609-2280 USA

October 29, 2007


Abstract

These lessons in Scientific English were written for the benefit of our colleagues 
at the Ecole Polytechic Fédérale de Lausanne in Switzerland, where we were researchers from 1994-1999. As native English speakers, we were beseiged by nonnative speakers asking for help with their manuscripts, as many as five requests per week.

Each language group is susceptible to predictable mistakes in English; these lessons were written for our colleagues: French- and German-speaking scientists with a solid foundation in English. They appear in no particular order, having been prompted by typical mistakes that we observed from week to week.

Most lessons are followed by a quiz and a humorous quotation. In their original format, the lessons were emailed with blank spaces in the quizzes so that the subscribers — the list grew from a dozen to seven hundred — could test their knowledge before checking their answers at a website. In 2003, the web pages were migrated to http://users.wpi.edu/~nab/sci_eng/. And in 2007, Scott Cogan (Université de Franche-Comté, Besançon, France) kindly transformed them into a LaTeX file, to which we added a table of contents and this abstract.

Although we are now busy with physics education and research in the United States, Fred still occasionally corrects manuscripts and dissertations. You may contact him at flh@wpi.edu.

O princípio antrópico: mero acaso, fortuita necessidade ou design inteligente?

Has the universe developed for the express purpose of being observed and understood by intelligent beings, or is it just a lucky break for the intelligent beings that they exist at all?

The Anthropic Principle was proposed in Poland in 1973, during a special two-week series of synopsia commemorating Copernicus’s 500th birthday. It was proposed by Brandon Carter, who, on Copernicus’s birthday, had the audacity to proclaim that humanity did indeed hold a special place in the Universe, an assertion that is the exact opposite of Copernicus’s now universally accepted theory.

Carter was not, however, claiming that the Universe was our own personal playground, made specifically with humanity in mind. The version of the Anthropic Principle that he proposed that day, which is now referred to as the Weak Anthropic Principle (WAP) stated only that by our very existence as carbon-based intelligent creatures, we impose a sort of selection effect on the Universe. For example, in a Universe where just one of the fundamental constants that govern nature was changed - say, the strength of gravity - we wouldn’t be here to wonder why gravity is the strength it is. The following is the official definition of the WAP:

“Weak Anthropic Principle (WAP): the observed values of all physical and cosmological quantities are not equally probable but they take on the values restricted by the requirement that there exist sites where carbon-based life can evolve and by the requirement that the Universe be old enough for it to have already done so.” (The Anthropic Cosmological Principle by John Barrow and Frank Tipler, p. 16)

Later, Carter also proposed the Strong Anthropic Principle (SAP), which states that the Universe had to bring humanity into being. This version is much more teleological, if not theological, and is of a highly speculative nature. Nonetheless, Carter had scientific reasons to propose it. The definition of the SAP) is as follows:

“Strong Anthropic Principle (SAP): the Universe must have those properties which allow life to develop within it at some stage in it’s history.” (The Anthropic Cosmological Principle, p. 21)

In addition to the WAP and SAP, there are the Participatory and Final Anthropic Principles. The Participatory Anthropic Principle states not only that the Universe had to develop humanity (or some other intelligent, information-gathering life form) but that we are necessary to it’s existence, as it takes an intelligent observer to collapse the Universe’s waves and probabilities from superposition into relatively concrete reality. The Final Anthropic Principle states that once the Universe has brought intelligence into being, it will never die out. These two are also very speculative.

The Selection effect of the WAP              



            
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