Darwin, Hitler, e a avaliação moderna da vida humana - Dr. Richard Weikart

Richard Weikart, Professor of Modern European History, California State University Stanislaus,

Por que a liberdade acadêmica é tão importante?

É por isso que a liberdade intelectual é tão importante. Permite que os acadêmicos expressem suas opiniões sem medo de represálias. Permite que um Charles Darwin se liberte das restrições do criacionismo. Ele permite que um Albert Einstein se liberte das restrições da física newtoniana. Ele permite que a raça humana questione a sabedoria convencional na busca incessante de conhecimento e verdade. E isso, em sua essência, é o que é o ensino superior. Sugerir outra coisa é ignorar por que as universidades foram criadas e por que os acadêmicos com foco crítico permanecem no centro de tudo que o ensino universitário pretende oferecer. Juiz Salvatore Vasta

That is why intellectual freedom is so important. It allows academics to express their opinions without fear of reprisals. It allows a Charles Darwin to break free of the constraints of creationism. It allows an Albert Einstein to break free of the constraints of Newtonian physics. It allows the human race to question conventional wisdom in the never-ending search for knowledge and truth. And that, at its core, is what higher learning is about. To suggest otherwise is to ignore why universities were created and why critically focussed academics remain central to all that university teaching claims to offer. Judge Salvatore Vasta

Darwin, as evidências estão desfocando os limites da vida

Blurring Life’s Boundaries

Darwinian theory is based on the idea that heredity flows vertically, parent to offspring, and that life’s history has branched like a tree. Now we know otherwise: that the ‘tree’ of life isn’t that simple.

Carl Tsevis

By David Quammen

Since the late 1970s, there have come three big surprises about what we humans are and about how life on our planet has evolved.

The first of those three surprises involves a whole category of life, previously unsuspected and now known as the archaea. (They look like bacteria through a microscope, but their DNA reveals they are shockingly different.) Another is a mode of hereditary change that was also unsuspected, now called horizontal gene transfer. (Heredity was supposed to move only vertically, from parents to offspring.) The third is a revelation, or anyway a strong likelihood, about our own deepest ancestry. (It seems now that our lineage traces to the archaea.) So we ourselves probably come from creatures that, as recently as forty years ago, were unknown to exist.

One of the most disorienting results of these developments is a new challenge to the concept of “species.” Biologists have long recognized that the boundaries of one species may blur into another—by the process of hybridism, for instance. And the notion of species is especially insecure in the realm of bacteria and archaea. But the discovery that horizontal gene transfer (HGT) has occurred naturally, many times, even in the lineages of animals and plants, has brought the categorical reality of a species into greater question than ever. That’s even true for us humans—we are composite individuals, mosaics.

It’s not just that—as you may have read in magazine articles—your human body contains at least as many bacterial cells as it does human cells. (This doesn’t even count all the nonbacterial microbes—the virus particles, fungal cells, archaea, and other teeny passengers inhabiting our guts, mouths, nostrils, and other bodily surfaces.) That’s the microbiome. Each of us is an ecosystem.

I’m talking about something else, a bigger and more shocking discovery that has come from the revolution in a field called molecular phylogenetics. (That phrase sounds fancy and technical, but it means merely the use of molecular information, such as DNA or RNA sequences, in discerning how one creature is related to another.) The discovery was that sizeable chunks of the genomes of all kinds of animals, including us, have been acquired by horizontal transfer from bacteria or other alien species.

How could that be possible? How could genes move sideways, between species, not just vertically along ancestral lineages? The mechanisms are complex, but one label that fits most of them is “infective heredity.”  DNA can be carried across boundaries, from one genome to another, by infective agents such as bacteria and viruses. Such horizontal gene transfer, like sex, has been a source of freshening innovation in otherwise discrete lineages, including ours—and it is still occurring.


This is an aspect of evolution that was unimagined by Charles Darwin. Evolution is trickier, far more intricate, than we had realized. The tree of life is more tangled.
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READ MORE HERE: Anthropocene Magazine

SETI Institute: Where is the Origin of Life on Earth?/Onde está origem da vida na Terra?

1:17:03

To answer the iconic question “Are We Alone?”, scientists around the world are also attempting to understand the origin of life. There are many pieces to the puzzle of how life began and many ways to put them together into a big picture. Some of the pieces are firmly established by the laws of chemistry and physics. Others are conjectures about what Earth was like four billion years ago, based on extrapolations of what we know from observing Earth today. However, there are still major gaps in our knowledge and these are necessarily filled in by best guesses.

We invited talented scientists to discuss their different opinions about the origin of life and the site of life’s origin. Most of them will agree that liquid water was necessary, but if we had a time machine and went back in time, would we find life first in a hydrothermal submarine setting in sea water or a fresh water site associated with emerging land masses?

Biologist David Deamer, a Research Professor of Biomolecular Engineering at the University of California, Santa Cruz, and multi-disciplinary scientist Bruce Damer, Associate Researcher in the Department of Biomolecular Engineering at UC Santa Cruz, will describe their most recent work, which infers that hydrothermal pools are the most plausible site for the origin of life. Both biologists have been collaborating since 2016 on a full conception of the Terrestrial Origin of Life Hypothesis.

Lynn Rothschild, Senior Scientist at NASA’s Ames Research Center and Adjunct Professor of Molecular Biology, Cell Biology, and Biochemistry at Brown University, who is an astrobiologist/ synthetic biologist specializing in molecular approaches to evolution, particularly in microbes and the application of synthetic biology to NASA's missions, will provide an evolutionary biologist’s perspective on the subject.

Ajuste fino: Você não é insignificante!

#ScienceUprising #RevoltaDaCiencia

Cientistas olham para dentro de células de 1 bilhão de anos

1 billion-year-old cell contents preserved in monazite and xenotime 

David Wacey, Eva Sirantoine, Martin Saunders & Paul Strother

Scientific Reports volume 9, Article number: 9068 (2019)

Abstract

Exceptional microfossil preservation, whereby sub-cellular details of an organism are conserved, remains extremely rare in the Precambrian rock record. We here report the first occurrence of exceptional cellular preservation by the rare earth element (REE) phosphates monazite and xenotime. This occurs in ~1 billion-year-old lake sediments where REEs were likely concentrated by local erosion and drainage into a closed lacustrine basin. Monazite and xenotime preferentially occur inside planktonic cells where they preserve spheroidal masses of plasmolyzed cell contents, and occasionally also membranous fragments. They have not been observed associated with cell walls or sheaths, which are instead preserved by clay minerals or francolite. REE phosphates are interpreted to be the earliest minerals precipitated in these cells after death, with their loci controlled by the micro-scale availability of inorganic phosphate (Pi) and REEs, probably sourced from polyphosphate granules within the cells. The strong affinity of REEs for phosphate and the insolubility of these minerals once formed means that REE phosphates have the potential for rapid preservation of cellular morphology after death and durability in the rock record. Hence, authigenic REE phosphates provide a promising new target in the search for the preservation of intra-cellular components of fossilised microorganisms.

 

FREE PDF GRATIS: Scientific Reports Sup. Info.

A Revolta da Ciência - Episódio 3 - O DNA é um código: quem o codificou???

#ScienceUprising #RevoltaDaCiencia

Gases tóxicos em zona habitável podem dificultar o surgimento de vida extraterrestre

A Limited Habitable Zone for Complex Life

Edward W. Schwieterman1,2,3,4,5, Christopher T. Reinhard3,4,6, Stephanie L. Olson3,7, Chester E. Harman4,8,9, and Timothy W. Lyons1,3,4

Published 2019 June 10 • © 2019. The American Astronomical Society.

The Astrophysical Journal, Volume 878, Number 1

No safe zone: do high carbon monoxide levels preclude the existence of life in the Trappist-1 system? (Courtesy: NASA/JPL-Caltech) Source/Fonte

Abstract

The habitable zone (HZ) is commonly defined as the range of distances from a host star within which liquid water, a key requirement for life, may exist on a planet's surface. Substantially more CO2 than present in Earth's modern atmosphere is required to maintain clement temperatures for most of the HZ, with several bars required at the outer edge. However, most complex aerobic life on Earth is limited by CO2 concentrations of just fractions of a bar. At the same time, most exoplanets in the traditional HZ reside in proximity to M dwarfs, which are more numerous than Sun-like G dwarfs but are predicted to promote greater abundances of gases that can be toxic in the atmospheres of orbiting planets, such as carbon monoxide (CO). Here we show that the HZ for complex aerobic life is likely limited relative to that for microbial life. We use a 1D radiative-convective climate and photochemical models to circumscribe a Habitable Zone for Complex Life (HZCL) based on known toxicity limits for a range of organisms as a proof of concept. We find that for CO2 tolerances of 0.01, 0.1, and 1 bar, the HZCL is only 21%, 32%, and 50% as wide as the conventional HZ for a Sun-like star, and that CO concentrations may limit some complex life throughout the entire HZ of the coolest M dwarfs. These results cast new light on the likely distribution of complex life in the universe and have important ramifications for the search for exoplanet biosignatures and technosignatures.

FREE PDF GRATIS: The Astrophysical Journal

The Fourth Paradigm: Data-Intensive Scientific Discovery

The Fourth Paradigm: Data-Intensive Scientific Discovery

Increasingly, scientific breakthroughs will be powered by advanced computing capabilities that help researchers manipulate and explore massive datasets.

The speed at which any given scientific discipline advances will depend on how well its researchers collaborate with one another, and with technologists, in areas of eScience such as databases, workflow management, visualization, and cloud computing technologies.

In The Fourth Paradigm: Data-Intensive Scientific Discovery, the collection of essays expands on the vision of pioneering computer scientist Jim Gray for a new, fourth paradigm of discovery based on data-intensive science and offers insights into how it can be fully realized.

Critical praise for The Fourth Paradigm

“The individual essays—and The Fourth Paradigm as a whole—give readers a glimpse of the horizon for 21st-century research and, at their best, a peek at what lies beyond. It’s a journey well worth taking.”

— James P. Collins

School of Life Sciences, Arizona State University

FREE PDF: Microsoft Research

Um mapa topográfico microscópico de complexidade da função celular: mero acaso, fortuita necessidade ou design inteligente?

Direct visualization of the E. coli Sec translocase engaging precursor proteins in lipid bilayers

Raghavendar Reddy Sanganna Gari1,*, Kanokporn Chattrakun1, Brendan P. Marsh1,†, Chunfeng Mao2, Nagaraju Chada1,‡, Linda L. Randall2 and Gavin M. King1,2,§

1Department of Physics and Astronomy, University of Missouri, Columbia, MO 65211, USA.

2Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.

↵§Corresponding author. Email: kinggm@missouri.edu

↵* Present address: Department of Anesthesiology, Weill Cornell Medicine, New York, NY 10065, USA.

↵† Present address: Department of Applied Physics, Stanford University, Stanford, CA 94305, USA.

↵‡ Present address: Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA.

Science Advances 12 Jun 2019: Vol. 5, no. 6, eaav9404

DOI: 10.1126/sciadv.aav9404

Fig. 6 Precursor-dependent model of translocase activity.

Abstract

Escherichia coli exports proteins via a translocase comprising SecA and the translocon, SecYEG. Structural changes of active translocases underlie general secretory system function, yet directly visualizing dynamics has been challenging. We imaged active translocases in lipid bilayers as a function of precursor protein species, nucleotide species, and stage of translocation using atomic force microscopy (AFM). Starting from nearly identical initial states, SecA more readily dissociated from SecYEG when engaged with the precursor of outer membrane protein A as compared to the precursor of galactose-binding protein. For the SecA that remained bound to the translocon, the quaternary structure varied with nucleotide, populating SecA2 primarily with adenosine diphosphate (ADP) and adenosine triphosphate, and the SecA monomer with the transition state analog ADP-AlF3. Conformations of translocases exhibited precursor-dependent differences on the AFM imaging time scale. The data, acquired under near-native conditions, suggest that the translocation process varies with precursor species.

FREE PDF GRATIS: Science Advances

Como a célula se protege: mero acaso, fortuita necessidade ou design inteligente?

Nuclear Pre-snRNA Export Is an Essential Quality Assurance Mechanism for Functional Spliceosomes
 

Daniel Becker, Anna Greta Hirsch, Lysann Bender, Thomas Lingner, Gabriela Salinas, Heike Krebber

Open Access DOI: https://doi.org/10.1016/j.celrep.2019.05.031

Highlights

• All yeast snRNAs, including U6, shuttle into the cytoplasm

• Export is mediated by Mex67 and Xpo1, and re-import requires Mtr10 and Cse1

• snRNA export prevents an incorporation of immature snRNAs into spliceosomes

• Spliceosomal assembly with immature snRNAs results in genome-wide splicing defects

 

Summary

Removal of introns from pre-mRNAs is an essential step in eukaryotic gene expression, mediated by spliceosomes that contain snRNAs as key components. Although snRNAs are transcribed in the nucleus and function in the same compartment, all except U6 shuttle to the cytoplasm. Surprisingly, the physiological relevance for shuttling is unclear, in particular because the snRNAs in Saccharomyces cerevisiae were reported to remain nuclear. Here, we show that all yeast pre-snRNAs including U6 undergo a stepwise maturation process after nuclear export by Mex67 and Xpo1. Sm- and Lsm-ring attachment occurs in the cytoplasm and is important for the snRNA re-import, mediated by Cse1 and Mtr10. Finally, nuclear pre-snRNA cleavage and trimethylation of the 5′-cap finalizes shuttling. Importantly, preventing pre-snRNAs from being exported or processed results in faulty spliceosome assembly and subsequent genome-wide splicing defects. Thus, pre-snRNA export is obligatory for functional splicing and resembles an essential evolutionarily conserved quality assurance step.

 

FREE PDF GRATIS: Cell Reports

A Revolta da Ciência - Episódio 2 - A Mente: O Inescapável

#ScienceUprising #RevoltaDaCiencia

Como são regulados os ciclos de divisão celular: mero acaso, fortuita necessidade ou design inteligente?

Two Distinct E2F Transcriptional Modules Drive Cell Cycles and Differentiation

Maria C. Cuitiño, Thierry Pécot, Daokun Sun, Michael C. Ostrowski, Michele Pagano, Gustavo Leone


Open Access Published:May 23, 2019

DOI: https://doi.org/10.1016/j.celrep.2019.05.004

Highlights

• E2F expression during cell division, differentiation, and quiescence is measured in vivo

• E2F3A, E2F8, and E2F4 accumulate sequentially in the nucleus of cycling cells

• E2F3A-4 nuclear accumulation controls gene expression during cell-cycle exit

• Deep learning tools are applied to nuclear segmentation of complex mammalian tissues

Summary

Orchestrating cell-cycle-dependent mRNA oscillations is critical to cell proliferation in multicellular organisms. Even though our understanding of cell-cycle-regulated transcription has improved significantly over the last three decades, the mechanisms remain untested in vivo. Unbiased transcriptomic profiling of G0, G1-S, and S-G2-M sorted cells from FUCCI mouse embryos suggested a central role for E2Fs in the control of cell-cycle-dependent gene expression. The analysis of gene expression and E2F-tagged knockin mice with tissue imaging and deep-learning tools suggested that post-transcriptional mechanisms universally coordinate the nuclear accumulation of E2F activators (E2F3A) and canonical (E2F4) and atypical (E2F8) repressors during the cell cycle in vivo. In summary, we mapped the spatiotemporal expression of sentinel E2F activators and canonical and atypical repressors at the single-cell level in vivo and propose that two distinct E2F modules relay the control of gene expression in cells actively cycling (E2F3A-8-4) and exiting the cycle (E2F3A-4) during mammalian development.

FREE PDF GRATIS: Cell Reports

Darwin, a tradução de genes é mais complexa do que esperada

Multi-Color Single-Molecule Imaging Uncovers Extensive Heterogeneity in mRNA Decoding

Sanne Boersma3 Deepak Khuperkar3 Bram M.P. Verhagen Jonathan B. Grimm Luke D. Lavis Marvin E. Tanenbaum4

Published:June 06, 2019 DOI: https://doi.org/10.1016/j.cell.2019.05.001

Highlights

• Development of MoonTag, a fluorescence labeling system to visualize translation

• Combining MoonTag and SunTag enables visualization of translational heterogeneity

• mRNAs from a single gene vary in initiation frequency at different start sites

• Ribosomes take many different “paths” along the 5′ UTR of a single mRNA molecule

Summary

mRNA translation is a key step in decoding genetic information. Genetic decoding is surprisingly heterogeneous because multiple distinct polypeptides can be synthesized from a single mRNA sequence. To study translational heterogeneity, we developed the MoonTag, a fluorescence labeling system to visualize translation of single mRNAs. When combined with the orthogonal SunTag system, the MoonTag enables dual readouts of translation, greatly expanding the possibilities to interrogate complex translational heterogeneity. By placing MoonTag and SunTag sequences in different translation reading frames, each driven by distinct translation start sites, start site selection of individual ribosomes can be visualized in real time. We find that start site selection is largely stochastic but that the probability of using a particular start site differs among mRNA molecules and can be dynamically regulated over time. This study provides key insights into translation start site selection heterogeneity and provides a powerful toolbox to visualize complex translation dynamics.

FREE PDF GRATIS: Cell

A Revolta da Ciência contra a Ciência Fake e o Materialismo Entorpecente

#ScienceUprising #RevoltaDaCiencia

Nullius in verba: a maioria dos artigos em química retraídos das publicações científicas por problemas sérios!

Correcting the Scientific Record: Retraction Practices in Chemistry and Materials Science

François-Xavier Coudert

Cite This: Chem. Mater.201931103593-3598

Publication Date:May 28, 2019

https://doi.org/10.1021/acs.chemmater.9b00897

Copyright © 2019 American Chemical Society

Peer-reviewed articles, published by scholarly journals, currently form the cornerstone of the modern scholarly publication system and guarantee the dissemination of research findings through the worldwide, ever-increasing community of researchers. Collectively these published works, stamped with the seal of approval of a review by the authors’ peers, form the scientific record—the record of knowledge accumulated by mankind. It is the duty of every scholar to add knowledge to this record by publishing but also to ensure the integrity of the existing works by critically assessing them: before publication, acting as a reviewer or editor, and post-publication, by building upon existing works, improving them, and checking their reproducibility.

The means of post-publication peer review of articles, which was once limited to formally published comments (“Comment on...”), journal clubs and conference coffee breaks, are rapidly expanding through the use of Internet and social media. Discussion of published papers regularly takes place on Twitter and through blog posts and preprints, as well as in structured discussions: comments on the webpage on published papers (e.g., PLOS Oneand Frontiers journals), indexing servers (PubMed Commons, now closed(1)), or dedicated websites (such as PubPeer(2)). Critique of published articles is a necessary and healthy part of the advancement of science. Sometimes, it can lead to the identification of serious flaws in the data or authors’ analysis, so that the findings or the conclusions published cannot be trusted anymore. In such cases, the paper may be corrected or retracted, i.e., expunged from the scientific record.

COPE, the Committee on Publication Ethics, publishes a series of guidelines (policies and practices) that are considered the industry standard in publishing ethics. The areas covered include the handling of allegations of misconduct, complaints and appeals, data issues and reproducibility, and standards of authorship, as well as post-publication corrections and the retraction of papers. COPE guidelines give clear insights into the difference in nature between corrections and retractions.(3) Articles should be corrected if “a small portion of an otherwise reliable publication proves to be misleading (especially because of honest error)”. On the other hand, “journal editors should consider retracting a publication if:

they have clear evidence that the findings are unreliable, either as a result of misconduct (e.g., data fabrication) or honest error (e.g. miscalculation or experimental error),

the findings have previously been published elsewhere without proper crossreferencing, permission or justification (i.e. cases of redundant publication),

it constitutes plagiarism,

it reports unethical research.”Retractions thus ensure that the literature is corrected, alerting readers to the fact that a publication contains erroneous or unreliable data, and give clear insight into the nature of the issues.

Despite the healthy role of retractions in preserving the scientific record, and while erroneous data can be the result of a good faith mistake, there is definitely a stigma associated with the retraction of a paper. COPE guidelines state that “The main purpose of retractions is to correct the literature and ensure its integrity rather than to punish authors who misbehave”,(3) but previous work has shown a notable resistance to admitting error in scientific papers.(4) The term retraction is too often associated with research misconduct, giving it a negative connotation for authors.(5) This is particularly true in a highly competitive environment, where academics are driven to publish often and produce high-impact papers: Jin et al. showed that retractions have a negative effect on citations for early career researchers.(6,7) The same argument can also be made for the publishers, who may fear a dent in the reputation of the journal. Thus, none of the actors involved have any direct incentive to retract a paper.

In this context, and while the number of retractions is rising,(8,9) there is relatively little information available about retractions and retracted papers, beyond the retraction notices infrequently published by journals. There is no central repository or authoritative database that can be easily queried—although the Retraction Watch website, which covers the topic of retractions and publication ethics in general, has been collating such a database.(10)Previous systematic studies have focused on retractions in specific fields, and in particular in medicine(11−13)—with the notable exception of a study by Grieneisen et al. that spanned several fields of research.(14) In order to better understand the existing practices for article retraction in the chemical sciences, I have performed a systematic survey of 331 papers retracted in 2017 and 2018 and their retraction notices, publicly available on the journals’ websites. This article looks at the statistics of retractions, their distribution per country, and the occurrence of multiple retractions. I also provide a classification of the reasons behind the retractions and the distribution of their occurrence.
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FREE PDF GRATIS: ACS Chemistry Materials Sup. Info. 1, Sup. Info. 2.

A insurreição da ciência - 3 de junho-8 de julho de 2019