Inglês científico como língua estrangeira

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

Source/Fonte

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.

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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              

The Anthropic Principle and Quantum Physics  

The Strong and the Final Anthropic Principles

Arguments against the SAP and FAP

            

Links and references                         

Send comments or questions to:

JRedmane@aolNOSPAM.com

(redmove the NOSPAM from the address before sending)

Splicing do RNA pelo Spliceossoma: mero acaso, fortuita necessidade ou design inteligente?

RNA Splicing by the Spliceosome

Annual Review of Biochemistry

Vol. 89:- (Volume publication date June 2020)

Review in Advance first posted online on December 3, 2019. (Changes may still occur before final publication.)

https://doi.org/10.1146/annurev-biochem-091719-064225

Max E. Wilkinson,* Clément Charenton,* and Kiyoshi Nagai*

MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; email: mwilkin@mrc-lmb.cam.ac.uk, ccharent@mrc-lmb.cam.ac.uk

*All authors contributed equally to this article. M.E. Wilkinson and C. Charenton would like to dedicate this review to the memory of Kiyoshi Nagai (1949–2019)

Source/Fonte: Chemistry World

Abstract

The spliceosome removes introns from messenger RNA precursors (pre-mRNA). Decades of biochemistry and genetics combined with recent structural studies of the spliceosome have produced a detailed view of the mechanism of splicing. In this review, we aim to make this mechanism understandable and provide several videos of the spliceosome in action to illustrate the intricate choreography of splicing. The U1 and U2 small nuclear ribonucleoproteins (snRNPs) mark an intron and recruit the U4/U6.U5 tri-snRNP. Transfer of the 5′ splice site (5′SS) from U1 to U6 snRNA triggers unwinding of U6 snRNA from U4 snRNA. U6 folds with U2 snRNA into an RNA-based active site that positions the 5′SS at two catalytic metal ions. The branch point (BP) adenosine attacks the 5′SS, producing a free 5′ exon. Removal of the BP adenosine from the active site allows the 3′SS to bind, so that the 5′ exon attacks the 3′SS to produce mature mRNA and an excised lariat intron.

Expected final online publication date for the Annual Review of Biochemistry, Volume 89 is June 22, 2020. Please see

http://www.annualreviews.org/page/journal/pubdates for revised estimates.

ACCEPTED MANUSCRIPT FREE/ARTIGO ACEITO GRATIS:

Annual Review of Biochemistry Sup Info

Watch the videos/Assistam aos vídeos!!!

Modelo computacional de célula humana revela nova visão sobre o processamento de informação genética: mero acaso, fortuita necessidade ou design inteligente?

An in-silico human cell model reveals the influence of spatial organization on RNA splicing

Zhaleh Ghaemi , Joseph R. Peterson, Martin Gruebele, Zaida Luthey-Schulten

Published: March 25, 2020 https://doi.org/10.1371/journal.pcbi.1007717

Abstract

Spatial organization is a characteristic of all cells, achieved in eukaryotic cells by utilizing both membrane-bound and membrane-less organelles. One of the key processes in eukaryotes is RNA splicing, which readies mRNA for translation. This complex and highly dynamical chemical process involves assembly and disassembly of many molecules in multiple cellular compartments and their transport among compartments. Our goal is to model the effect of spatial organization of membrane-less organelles (specifically nuclear speckles) and of organelle heterogeneity on splicing particle biogenesis in mammalian cells. Based on multiple sources of complementary experimental data, we constructed a spatial model of a HeLa cell to capture intracellular crowding effects. We then developed chemical reaction networks to describe the formation of RNA splicing machinery complexes and splicing processes within nuclear speckles (specific type of non-membrane-bound organelles). We incorporated these networks into our spatially-resolved human cell model and performed stochastic simulations for up to 15 minutes of biological time, the longest thus far for a eukaryotic cell. We find that an increase (decrease) in the number of nuclear pore complexes increases (decreases) the number of assembled splicing particles; and that compartmentalization is critical for the yield of correctly-assembled particles. We also show that a slight increase of splicing particle localization into nuclear speckles leads to a disproportionate enhancement of mRNA splicing and a reduction in the noise of generated mRNA. Our model also predicts that the distance between genes and speckles has a considerable effect on the mRNA production rate, with genes located closer to speckles producing mRNA at higher levels, emphasizing the importance of genome organization around speckles. The HeLa cell model, including organelles and sub-compartments, provides a flexible foundation to study other cellular processes that are strongly modulated by spatiotemporal heterogeneity.

Author summary

The spliceosome is one of the most complex cellular machineries. It cuts and splices the RNA code in eukaryotic cells by dynamically assembling and disassembling. The components of spliceosome are formed in both the nucleus and the cytoplasm within the cell and primarily localized in nuclear membrane-less organelles. Therefore, a computational model of spliceosomal function must contain a spatial model of the entire cell. However, building such a model is a challenging task, mainly due to the lack of homogeneous experimental data and a suitable computational framework. Here, we overcome these challenges and present a spatially-resolved HeLa cell model, with nuclear, subnuclear, and extensive cytoplasmic structures. The three-dimensional model is supplemented by reaction-diffusion processes to shed light on the function of the spliceosome.

Citation: Ghaemi Z, Peterson JR, Gruebele M, Luthey-Schulten Z (2020) An in-silico human cell model reveals the influence of spatial organization on RNA splicing. PLoS Comput Biol 16(3): e1007717. 

https://doi.org/10.1371/journal.pcbi.1007717

Editor: Attila Csikász-Nagy, King’s College London, UNITED KINGDOM

Received: August 14, 2019; Accepted: February 6, 2020; Published: March 25, 2020

Copyright: © 2020 Ghaemi 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.

Data Availability: All relevant data are within the manuscript and its Supporting Information files. Additionally, the code we developed can be downloaded from Github through: https://eukaryoticcellbuilder.github.io/HeLa_Builder/.

Funding: This work was supported by the NSF grants MCB-1244570 on the Evolution of Translation:From Molecules to Cells to Z.G. and Z.L-S. and NSF Center for the Physics of Living Cells grant PHY-1430124 to M.G. and Z.L-S.,the NSF Graduate Fellowship [grant DGE-1144245] to J.R.P., and the NIH P41-GM104601 to Z.L-S. Z.L-S held the Murchison-Mallory Chair and M.G. held the James R. Eiszner Chair while this work was carried out. Supercomputer time was provided by XStream-XSEDE [grant TG-MCA03S027]. 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.

FREE PDF GRATIS: PLoS Computational Biology

O Coronavírus-19 não foi intencionalmente planejado.

The proximal origin of SARS-CoV-2

Kristian G. Andersen, Andrew Rambaut, W. Ian Lipkin, Edward C. Holmes & Robert F. Garry 

Nature Medicine (2020)

To the Editor — Since the first reports of novel pneumonia (COVID-19) in Wuhan, Hubei province, China1,2, there has been considerable discussion on the origin of the causative virus, SARS-CoV-23 (also referred to as HCoV-19)4. Infections with SARS-CoV-2 are now widespread, and as of 11 March 2020, 121,564 cases have been confirmed in more than 110 countries, with 4,373 deaths5.

Source/Fonte: Nature Medicine

SARS-CoV-2 is the seventh coronavirus known to infect humans; SARS-CoV, MERS-CoV and SARS-CoV-2 can cause severe disease, whereas HKU1, NL63, OC43 and 229E are associated with mild symptoms6. Here we review what can be deduced about the origin of SARS-CoV-2 from comparative analysis of genomic data. We offer a perspective on the notable features of the SARS-CoV-2 genome and discuss scenarios by which they could have arisen. Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus.

Notable features of the SARS-CoV-2 genome

Our comparison of alpha- and betacoronaviruses identifies two notable genomic features of SARS-CoV-2: (i) on the basis of structural studies7,8,9 and biochemical experiments1,9,10, SARS-CoV-2 appears to be optimized for binding to the human receptor ACE2; and (ii) the spike protein of SARS-CoV-2 has a functional polybasic (furin) cleavage site at the S1–S2 boundary through the insertion of 12 nucleotides8, which additionally led to the predicted acquisition of three O-linked glycans around the site.

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FREE PDF GRATIS: Nature Medicine

Uma previsão científica de pandemia por Coronavírus na China ignorada

Bat Coronaviruses in China

Yi Fan 1,2, Kai Zhao 1,2, Zheng-Li Shi 1,2 andPeng Zhou 1,2,*

1 CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China

2 University of Chinese Academy of Sciences, Beijing 100049, China

* Author to whom correspondence should be addressed.

Viruses 2019, 11(3), 210; https://doi.org/10.3390/v11030210

Received: 29 January 2019 / Revised: 26 February 2019 / Accepted: 26 February 2019 / Published: 2 March 2019

Source/Fonte

Abstract

During the past two decades, three zoonotic coronaviruses have been identified as the cause of large-scale disease outbreaks–Severe Acute Respiratory Syndrome (SARS), Middle East Respiratory Syndrome (MERS), and Swine Acute Diarrhea Syndrome (SADS). SARS and MERS emerged in 2003 and 2012, respectively, and caused a worldwide pandemic that claimed thousands of human lives, while SADS struck the swine industry in 2017. They have common characteristics, such as they are all highly pathogenic to humans or livestock, their agents originated from bats, and two of them originated in China. Thus, it is highly likely that future SARS- or MERS-like coronavirus outbreaks will originate from bats, and there is an increased probability that this will occur in China. Therefore, the investigation of bat coronaviruses becomes an urgent issue for the detection of early warning signs, which in turn minimizes the impact of such future outbreaks in China. The purpose of the review is to summarize the current knowledge on viral diversity, reservoir hosts, and the geographical distributions of bat coronaviruses in China, and eventually we aim to predict virus hotspots and their cross-species transmission potential. 

Keywords: coronavirus; bat; epidemiology; cross-species; zoonosis

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Avi Loeb, Universidade Harvard, 'falou e disse': A falseabilidade deve ser marca registrada de qualquer teoria científica.

A falseabilidade deve ser uma marca registrada de qualquer teoria científica.

Falsifiability should be a hallmark of any scientific theory.

Avi Loeb - Harvard University

O fator X na vida - Segredos da célula com Michael Behe - Episódio 5

Mais outra hipótese sobre a origem da vida: emergência espontânea de moléculas auto-replicantes contendo nucleobases e aminoácidos

Spontaneous Emergence of Self-Replicating Molecules Containing Nucleobases and Amino Acids

Bin Liu Charalampos G. Pappas Jim Ottelé Gaël Schaeffer Christoph Jurissek Priscilla F. Pieters Meniz Altay Ivana Marić Marc C. A. Stuart Sijbren Otto*

Cite this: J. Am. Chem. Soc. 2020, 142, 9, 4184-4192

Publication Date:February 5, 2020

https://doi.org/10.1021/jacs.9b10796

Copyright © 2020 American Chemical Society

Abstract

The conditions that led to the formation of the first organisms and the ways that life originates from a lifeless chemical soup are poorly understood. The recent hypothesis of “RNA-peptide coevolution” suggests that the current close relationship between amino acids and nucleobases may well have extended to the origin of life. We now show how the interplay between these compound classes can give rise to new self-replicating molecules using a dynamic combinatorial approach. We report two strategies for the fabrication of chimeric amino acid/nucleobase self-replicating macrocycles capable of exponential growth. The first one relies on mixing nucleobase- and peptide-based building blocks, where the ligation of these two gives rise to highly specific chimeric ring structures. The second one starts from peptide nucleic acid (PNA) building blocks in which nucleobases are already linked to amino acids from the start. While previously reported nucleic acid-based self-replicating systems rely on presynthesis of (short) oligonucleotide sequences, self-replication in the present systems start from units containing only a single nucleobase. Self-replication is accompanied by self-assembly, spontaneously giving rise to an ordered one-dimensional arrangement of nucleobase nanostructures.

FREE PDF GRATIS: J Am Chem Soc  Sup. Info.

Mais uma hipótese sobre a origem da vida em um universo inflacionário

Scientific Reports

Emergence of life in an inflationary universe

Tomonori Totani 

Scientific Reports volume 10, Article number: 1671

The center of the Milky Way galaxy, as visualized by the Spitzer Space Telescope’s infrared cameras.

Image: NASA, JPL-Caltech, Susan Stolovy (SSC/Caltech) et al.

Abstract

Abiotic emergence of ordered information stored in the form of RNA is an important unresolved problem concerning the origin of life. A polymer longer than 40–100 nucleotides is necessary to expect a self-replicating activity, but the formation of such a long polymer having a correct nucleotide sequence by random reactions seems statistically unlikely. However, our universe, created by a single inflation event, likely includes more than 10100 Sun-like stars. If life can emerge at least once in such a large volume, it is not in contradiction with our observations of life on Earth, even if the expected number of abiogenesis events is negligibly small within the observable universe that contains only 1022 stars. Here, a quantitative relation is derived between the minimum RNA length lmin required to be the first biological polymer, and the universe size necessary to expect the formation of such a long and active RNA by randomly adding monomers. It is then shown that an active RNA can indeed be produced somewhere in an inflationary universe, giving a solution to the abiotic polymerization problem. On the other hand, lmin must be shorter than ~20 nucleotides for the abiogenesis probability close to unity on a terrestrial planet, but a self-replicating activity is not expected for such a short RNA. Therefore, if extraterrestrial organisms of a different origin from those on Earth are discovered in the future, it would imply an unknown mechanism at work to polymerize nucleotides much faster than random statistical processes.

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Os efeitos da mutação (Segredos da Célula com Michael Behe, Ep. 4)

Ribozimas promíscuas e seu papel proposto na evolução pré-biótica

Promiscuous Ribozymes and Their Proposed Role in Prebiotic Evolution

Evan Janzen Celia Blanco Huan Peng Josh Kenchel Irene A. Chen*

Cite this: Chem. Rev. 2020, XXXX, XXX, XXX-XXX

Publication Date:February 3, 2020

https://doi.org/10.1021/acs.chemrev.9b00620 

Copyright © 2020 American Chemical Society

Abstract

The ability of enzymes, including ribozymes, to catalyze side reactions is believed to be essential to the evolution of novel biochemical activities. It has been speculated that the earliest ribozymes, whose emergence marked the origin of life, were low in activity but high in promiscuity, and that these early ribozymes gave rise to specialized descendants with higher activity and specificity. Here, we review the concepts related to promiscuity and examine several cases of highly promiscuous ribozymes. We consider the evidence bearing on the question of whether de novo ribozymes would be quantitatively more promiscuous than later evolved ribozymes or protein enzymes. We suggest that while de novo ribozymes appear to be promiscuous in general, they are not obviously more promiscuous than more highly evolved or active sequences. Promiscuity is a trait whose value would depend on selective pressures, even during prebiotic evolution.

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Chemical Reviews

Mais uma hipótese sobre a origem da vida: energia de hidrogênio.

Nature Ecology & Evolution

Article

Published: 02 March 2020

A hydrogen-dependent geochemical analogue of primordial carbon and energy metabolism

Martina Preiner, Kensuke Igarashi, Kamila B. Muchowska, Mingquan Yu, Sreejith J. Varma, Karl Kleinermanns, Masaru K. Nobu, Yoichi Kamagata, Harun Tüysüz, Joseph Moran & William F. Martin 

Nature Ecology & Evolution (2020)

Source/Fonte

Abstract

Hydrogen gas, H2, is generated by alkaline hydrothermal vents through an ancient geochemical process called serpentinization, in which water reacts with iron-containing minerals deep within the Earth’s crust. H2 is the electron donor for the most ancient and the only energy-releasing route of biological CO2 fixation, the acetyl-CoA pathway. At the origin of metabolism, CO2 fixation by hydrothermal H2 within serpentinizing systems could have preceded and patterned biotic pathways. Here we show that three hydrothermal minerals—greigite (Fe3S4), magnetite (Fe3O4) and awaruite (Ni3Fe)—catalyse the fixation of CO2 with H2 at 100 °C under alkaline aqueous conditions. The product spectrum includes formate (up to 200 mM), acetate (up to 100 µM), pyruvate (up to 10 µM), methanol (up to 100 µM) and methane. The results shed light on both the geochemical origin of microbial metabolism and the nature of abiotic formate and methane synthesis in modern hydrothermal vents.

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Nature Ecology & Evolution

GPS para cromossomos - Reorganização do genoma durante o desenvolvimento: mero acaso, fortuita necessidade ou design inteligente?

Molecular Cell

Available Online 26 February 2020

Lamina-Dependent Stretching and Unconventional Chromosome Compartments in Early C. elegans Embryos

Ahilya N.Sawh 1, 2 Maxwell E.R.Shafer 1, 2 Jun-HanSu 3 Xiaowei Zhuang 3 Siyuan Wang 3, 4 Susan E.Mango 1, 2, 5

1 Biozentrum, University of Basel, 4056 Basel, Switzerland

2 Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA

3 Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Department of Physics, Harvard University, Cambridge, MA 02138, USA

4 Department of Genetics, Yale University School of Medicine, New Haven, CT 06510, USA

Received 19 May 2019, Revised 20 November 2019, Accepted 4 February 2020, Available online 26 February 2020.

Published: February 26, 2020

https://doi.org/10.1016/j.molcel.2020.02.006  

Highlights

• Chromosomes from early embryos resemble a barbell

• Lamina interactions stretch chromosomes and separate compartments

• Conventional compartments arise during gastrulation via long-distance associations

• Single-chromosome clustering uncovers prevalent conformations

Summary

Current models suggest that chromosome domains segregate into either an active (A) or inactive (B) compartment. B-compartment chromatin is physically separated from the A compartment and compacted by the nuclear lamina. To examine these models in the developmental context of C. elegans embryogenesis, we undertook chromosome tracing to map the trajectories of entire autosomes. Early embryonic chromosomes organized into an unconventional barbell-like configuration, with two densely folded B compartments separated by a central A compartment. Upon gastrulation, this conformation matured into conventional A/B compartments. We used unsupervised clustering to uncover subpopulations with differing folding properties and variable positioning of compartment boundaries. These conformations relied on tethering to the lamina to stretch the chromosome; detachment from the lamina compacted, and allowed intermingling between, A/B compartments. These findings reveal the diverse conformations of early embryonic chromosomes and uncover a previously unappreciated role for the lamina in systemic chromosome stretching.

Keywords 3D genome chromosome conformation multiplexed DNA FISH unsupervised clustering early embryogenesis nuclear lamina development

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Subscription or payment needed/Requer assinatura ou pagamento: Molecular Cell