Descoberta uma nova forma de DNA em nossas células

segunda-feira, abril 23, 2018

I-motif DNA structures are formed in the nuclei of human cells

Mahdi Zeraati, David B. Langley, Peter Schofield, Aaron L. Moye, Romain Rouet, William E. Hughes, Tracy M. Bryan, Marcel E. Dinger & Daniel Christ

Nature Chemistry (2018)

doi:10.1038/s41557-018-0046-3

Download Citation

Bioanalytical chemistry DNA DNA probes Molecular biology

Received: 29 June 2017 Accepted: 14 March 2018

Published online: 23 April 2018

Source/Fonte: Chris Hammang - Science Daily


Abstract

Human genome function is underpinned by the primary storage of genetic information in canonical B-form DNA, with a second layer of DNA structure providing regulatory control. I-motif structures are thought to form in cytosine-rich regions of the genome and to have regulatory functions; however, in vivo evidence for the existence of such structures has so far remained elusive. Here we report the generation and characterization of an antibody fragment (iMab) that recognizes i-motif structures with high selectivity and affinity, enabling the detection of i-motifs in the nuclei of human cells. We demonstrate that the in vivo formation of such structures is cell-cycle and pH dependent. Furthermore, we provide evidence that i-motif structures are formed in regulatory regions of the human genome, including promoters and telomeric regions. Our results support the notion that i-motif structures provide key regulatory roles in the genome.

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Nocautes naturais: a seleção natural de Darwin nocauteada

Biology 2017, 6(4), 43; doi:10.3390/biology6040043

Natural Knockouts: Natural Selection Knocked Out

Peter Borger

The Independent Research Initiative on Information & Origins, 79540 Loerrach, Germany

Academic Editor: Hirofumi Akari

Received: 13 September 2017 / Revised: 17 October 2017 / Accepted: 25 October 2017 / Published: 12 December 2017

(This article belongs to the Special Issue Biology in the Early 21st Century: Evolution Beyond Selection)

Image result for knockout

Abstract

In functional genomics studies, research is dedicated to unveiling the function of genes using gene-knockouts, model organisms in which a gene is artificially inactivated. The idea is that, by knocking out the gene, the provoked phenotype would inform us about the function of the gene. Still, the function of many genes cannot be elucidated, because disruption of conserved sequences, including protein-coding genes, often does not directly affect the phenotype. Since the phenomenon was first observed in the early nineties of the last century, these so-called ‘no-phenotype knockouts’ have met with great skepticism and resistance by died-in-the-wool selectionists. Still, functional genomics of the late 20th and early 21st centuries has taught us two important lessons. First, two or more unrelated genes can often substitute for each other; and second, some genes are only present in the genome in a silent state. In the laboratory, the disruption of such genes does not negatively influence reproductive success, and does not show measurable fitness effects of the species. The genes are redundant. Genetic redundancy, one of the big surprises of modern biology, can thus be defined as the condition in which the inactivation of a gene is selectively neutral. The no-phenotype knockout is not just a freak of the laboratory. Genetic variants known as homozygous loss-of-function (HLOF) variants are of considerable scientific and clinical interest, as they represent experiments of nature qualifying as “natural knockouts”. Such natural knockouts challenge the conventional NeoDarwinian appraisal that genetic information is the result of natural selection acting on random genetic variation

Keywords: genetic redundancy; natural knockout; natural selection; homozygous loss-of-function

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

FREE PDF GRATIS: Biology 

Por princípios físicos de evolução biológica

Towards physical principles of biological evolution

Mikhail I Katsnelson1, Yuri I Wolf2 and Eugene V Koonin2

Published 23 February 2018 • © 2018 IOP Publishing Ltd

Physica Scripta, Volume 93, Number 4 

Focus Issue on 21st Century Frontiers

Author e-mails

M.Katsnelson@science.ru.nl

Author affiliations

1 Radboud University, Institute for Molecules and Materials, Nijmegen, 6525AJ, Netherlands

2 National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, United States of America

Dates Received 28 August 2017 Accepted 30 January 2018 

Published 23 February 2018

Citation

Mikhail I Katsnelson et al 2018 Phys. Scr. 93 043001

DOI https://doi.org/10.1088/1402-4896/aaaba4



Abstract

Biological systems reach organizational complexity that far exceeds the complexity of any known inanimate objects. Biological entities undoubtedly obey the laws of quantum physics and statistical mechanics. However, is modern physics sufficient to adequately describe, model and explain the evolution of biological complexity? Detailed parallels have been drawn between statistical thermodynamics and the population-genetic theory of biological evolution. Based on these parallels, we outline new perspectives on biological innovation and major transitions in evolution, and introduce a biological equivalent of thermodynamic potential that reflects the innovation propensity of an evolving population. Deep analogies have been suggested to also exist between the properties of biological entities and processes, and those of frustrated states in physics, such as glasses. Such systems are characterized by frustration whereby local state with minimal free energy conflict with the global minimum, resulting in 'emergent phenomena'. We extend such analogies by examining frustration-type phenomena, such as conflicts between different levels of selection, in biological evolution. These frustration effects appear to drive the evolution of biological complexity. We further address evolution in multidimensional fitness landscapes from the point of view of percolation theory and suggest that percolation at level above the critical threshold dictates the tree-like evolution of complex organisms. Taken together, these multiple connections between fundamental processes in physics and biology imply that construction of a meaningful physical theory of biological evolution might not be a futile effort. However, it is unrealistic to expect that such a theory can be created in one scoop; if it ever comes to being, this can only happen through integration of multiple physical models of evolutionary processes. Furthermore, the existing framework of theoretical physics is unlikely to suffice for adequate modeling of the biological level of complexity, and new developments within physics itself are likely to be required.

FREE PDF GRATIS: Physica Scripta

Quantos genes são necessários para uma célula? Quase todos!

GENOMICS

How Many Genes Do Cells Need? Maybe Almost All of Them

An ambitious study in yeast shows that the health of cells depends on the highly intertwined effects of many genes, few of which can be deleted together without consequence.

The activities of genes in complex organisms, including humans, may be deeply interrelated.


Olena Shmahalo/Quanta Magazine; Model by: TheEmptyRoom

By knocking out genes three at a time, scientists have painstakingly deduced the web of genetic interactions that keeps a cell alive. Researchers long ago identified essential genes that yeast cells can’t live without, but new work, which appears today in Science, shows that looking only at those gives a skewed picture of what makes cells tick: Many genes that are inessential on their own become crucial as others disappear. The result implies that the true minimum number of genes that yeast — and perhaps, by extension, other complex organisms — need to survive and thrive may be surprisingly large.

About 20 years ago, Charles Boone and Brenda Andrews decided to do something slightly nuts. The yeast biologists, both professors at the University of Toronto, set out to systematically destroy or impair the genes in yeast, two by two, to get a sense of how the genes functionally connected to one another. Only about 1,000 of the 6,000 genes in the yeast genome, or roughly 17 percent, are considered essential for life: If a single one of them is missing, the organism dies. But it seemed that many other genes whose individual absence was not enough to spell the end might, if destroyed in tandem, sicken or kill the yeast. Those genes were likely to do the same kind of job in the cell, the biologists reasoned, or to be involved in the same process; losing both meant the yeast could no longer compensate.

Ignorant as science may still be about certain happenings in yeast, it’s dwarfed by our ignorance of what is going on in our own cells

Boone and Andrews realized they could use this idea to figure out what various genes were doing. They and their collaborators went about it deliberately, by first generating more than 20 million strains of yeast that were each missing two genes — almost all of the unique combinations of knockouts among those 6,000 genes. The researchers then scored how healthy each of the double mutant strains was and investigated how the missing genes could be related. The results let the researchers sketch a map of the shadowy web of interactions that underlie life. Two years ago, they reported the details of the map and revealed that it had already allowed researchers to discover previously unknown roles for genes.

Along the way, however, they realized that a surprising number of genes in the experiment didn’t have any obvious interactions with others. “Maybe, in some cases, deleting two genes isn’t enough,” Andrews said, reflecting on their thoughts at the time. Elena Kuzmin, a graduate student in the lab who is now a postdoc at McGill University, decided to go one step further by knocking out a third gene.

In the paper out today in Science, Kuzmin, Boone, Andrews and their collaborators at the University of Toronto, the University of Minnesota and elsewhere report that effort has yielded a deeper and more detailed map of the cell’s inner workings. Unlike in the double mutant experiments, the researchers did not make every possible combination of mutations — there are about 36 billion different ways to knock out three genes in yeast. Instead, they looked at the pairs of genes they’d already knocked out and ranked their interactions according to severity. They took a number of those pairs, whose effects ranged from making cells grow a little slower to making them significantly impaired, and matched them up one by one with knockouts of other genes, generating about 200,000 triple mutant strains. They monitored how quickly colonies of the mutant yeast grew, and after noting which mutants were struggling, they checked databases to see what the disabled genes were thought to do.
...

READ MORE HERE: Quanta Magazine

O Big Bang dos dinossauros: como se tivessem sido plantados lá???

quarta-feira, abril 18, 2018

Dinosaur diversification linked with the Carnian Pluvial Episode

Massimo Bernardi, Piero Gianolla, Fabio Massimo Petti, Paolo Mietto & Michael J. Benton

Nature Communications volume 9, Article number: 1499 (2018)


Download Citation

Palaeoecology Palaeontology

Received: 08 November 2017 Accepted: 27 March 2018

Published online: 16 April 2018


Abstract

Dinosaurs diversified in two steps during the Triassic. They originated about 245 Ma, during the recovery from the Permian-Triassic mass extinction, and then remained insignificant until they exploded in diversity and ecological importance during the Late Triassic. Hitherto, this Late Triassic explosion was poorly constrained and poorly dated. Here we provide evidence that it followed the Carnian Pluvial Episode (CPE), dated to 234–232 Ma, a time when climates switched from arid to humid and back to arid again. Our evidence comes from a combined analysis of skeletal evidence and footprint occurrences, and especially from the exquisitely dated ichnofaunas of the Italian Dolomites. These provide evidence of tetrapod faunal compositions through the Carnian and Norian, and show that dinosaur footprints appear exactly at the time of the CPE. We argue then that dinosaurs diversified explosively in the mid Carnian, at a time of major climate and floral change and the extinction of key herbivores, which the dinosaurs opportunistically replaced.

Acknowledgements

Matthias Franz, (Göttingen University) Edgar Nitsch (LGRB Freiburg) and Manfred Menning (GFZ Postdam) are thanked for useful information of the Germanic Basin; Nereo Preto, Manuel Rigo (Padova University) and Jacopo Dal Corso (Leeds University) are thanked for fruitful discussions on the CPE; and Guido Roghi (CNR-IRPI) for useful comments on pollen association. Hendrik Klein (SPM Neumarkt) and Marco Avanzini (MUSE Trento) provided useful comments on the tetrapod ichno-associations. P.G. thanks Marcello Caggiati (Ferrara University) for the palaeogeographic map of the upper Carnian. M.B. thanks La Sportiva for supporting field activities in the Dolomites. Funded in part by the NERC BETR grant NE/P013724/1 to M.J.B. and by PRIN 2010-2011 (Pr. No 20107ESMX9_004) to P.G.

Author information
Affiliations

MUSE—Museo delle Scienze, Corso del Lavoro e della Scienza 3, 38122, Trento, Italy
Massimo Bernardi & Fabio Massimo Petti
School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, UK
Massimo Bernardi & Michael J. Benton
Dipartimento di Fisica e Scienze della Terra, Università di Ferrara, via Saragat 1, 44100, Ferrara, Italy
Piero Gianolla
PaleoFactory, Dipartimento di Scienze della Terra, Sapienza Università di Roma, Piazzale Aldo Moro, 5, 00185, Rome, Italy
Fabio Massimo Petti
Dipartimento di Geoscienze, Università degli studi di Padova, via Gradenigo 6, I-35131, Padova, Italy
Paolo Mietto

Contributions
M.B. and P.G. designed the study. M.B., F.M.P., and M.J.B. developed the palaeontological parts of the study, while P.G. and P.M. contributed in the more geological sections. All authors interpreted the results. M.B. and P.G. led the writing of the paper and all other co-authors contributed to the final version.

Competing interests
The authors declare no competing interests.

Corresponding author
Correspondence to Massimo Bernardi.


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PERGUNTA CAUSTICANTE DESTE BLOGGER:

Novas formas "surgem abrupta e funcionalmente" no registro fóssil? De "não existem dinossauros" a "agora existem dinossauros"? E aí Darwin como é que fica o seu gradualismo???

Boodin 'falou e disse': fantasmas do passado induzem grandes cientistas ao erro

sexta-feira, abril 13, 2018

"Mesmo em tais áreas como a ciência, onde a razão é tida como estando mais em casa, há uma tendência para as teorias se tornarem dogmas. A hipótese de variações aleatórias e de seleção natural de Darwin tornaram-se não meramente um dogma de ciência, mas foi edificada numa filosofia do universo; e as limitações da hipótese e o espírito empírico de seu criador se perderam de vista numa tradição intolerante que tem tido sérias consequências, não somente para o desenvolvimento da ciência natural mas para a filosofia social. Em cada área da ciência nós somos atormentados por fantasmas do passado aos quais mentes inferiores prestam reverência supersticiosa e pelos quais até grandes mentes são induzidas ao erro de falsas premissas." 

"Even in such fields as science, where reason is supposed to be most at home, there is a tendency for theories to become dogmas. Darwin's hypothesis of chance variations and natural selection became not merely a dogma of science, but was erected into a philosophy of the universe; and the limitations of the hypothesis and the empirical spirit of its creator were lost sight of in an intolerant tradition which has had serious consequences, not only for the development of natural science but for social philosophy. In every field of science we are haunted by ghosts of the past to which lesser minds pay superstitious reverence and by which even great minds are misled into false assumptions." 

John Elof Boodin (1869-1950), The Social Mind, 1939

Mais ciência em ciência forense!

A call for more science in forensic science

Suzanne Bell, Sunita Sah, Thomas D. Albright, S. James Gates Jr., M. Bonner Denton and Arturo Casadevall

PNAS April 12, 2018. 201712161; published ahead of print April 12, 2018. https://doi.org/10.1073/pnas.1712161115

Edited by Solomon H. Snyder, The Johns Hopkins University School of Medicine, Baltimore, MD, and approved March 21, 2018 (received for review July 28, 2017)


Source/Fonte: SUNO - Southern University at New Orleans

Abstract

Forensic science is critical to the administration of justice. The discipline of forensic science is remarkably complex and includes methodologies ranging from DNA analysis to chemical composition to pattern recognition. Many forensic practices developed under the auspices of law enforcement and were vetted primarily by the legal system rather than being subjected to scientific scrutiny and empirical testing. Beginning in the 1990s, exonerations based on DNA-related methods revealed problems with some forensic disciplines, leading to calls for major reforms. This process generated a National Academy of Science report in 2009 that was highly critical of many forensic practices and eventually led to the establishment of the National Commission for Forensic Science (NCFS) in 2013. The NCFS was a deliberative body that catalyzed communication between nonforensic scientists, forensic scientists, and other stakeholders in the legal community. In 2017, despite continuing problems with forensic science, the Department of Justice terminated the NCFS. Just when forensic science needs the most support, it is getting the least. We urge the larger scientific community to come to the aid of our forensic colleagues by advocating for urgently needed research, testing, and financial support.

forensic science justice DNA crime investigation

FREE PDF GRATIS: PNAS 

Celebrando 125 anos do The Physical Review

quinta-feira, abril 12, 2018


Celebrating 125 years of The Physical Review

The American Physical Society (APS) is proud to celebrate the 125th anniversary of the Physical Review journals. To commemorate this milestone, the editors present a timeline of select papers and events that are of significance to physics and to the history of the APS. From Robert Millikan’s famous oil drop experiments to the discovery of gravitational waves, the Physical Review journals have published a wide range of important results, many of which have been recognized with Nobel and other notable prizes. The papers in the timeline, along with landmark events in the history of the Physical Review, will be highlighted on our journal websites and in social media throughout 2018.

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Pesquisa de fóssil lança luz sobre as cores de asas de borboletas de 180 milhões de anos atrás

quarta-feira, abril 11, 2018

Fossil scales illuminate the early evolution of lepidopterans and structural colors

Qingqing Zhang1,2, Wolfram Mey3, Jörg Ansorge4, Timothy A. Starkey5, Luke T. McDonald6, Maria E. McNamara6, Edmund A. Jarzembowski1,7, Wilfried Wichard8, Richard Kelly9,10, Xiaoyin Ren1, Jun Chen1,11, Haichun Zhang1 and Bo Wang1,12,*

1State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China.

2University of Sciences and Technology of China, Hefei 230026, China.

3Museum für Naturkunde, Leibniz Institute of Evolution and Biodiversity Research, Humboldt University, D-10115 Berlin, Germany.

4Institute of Geography and Geology, University of Greifswald, D-17487 Greifswald, Germany.

5Department of Physics and Astronomy, University of Exeter, Stocker Road, Exeter EX4 4QL, UK.

6School of Biological, Earth and Environmental Sciences, University College Cork, North Mall, Cork T23 TK30, Ireland.

7Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK.

8Institute of Biology and its Didactics, University of Cologne, D-50931 Cologne, Germany.

9School of Earth Sciences, University of Bristol, Bristol BS8 1TQ, UK.

10Department of Natural Sciences, National Museum of Scotland, Edinburgh EH1 1JF, UK.

11Institute of Geology and Paleontology, Linyi University, Linyi 276000, China.

12Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.

↵*Corresponding author. Email: bowang@nigpas.ac.cn

Science Advances 11 Apr 2018: Vol. 4, no. 4, e1700988


Source/FonteZhang Qingqing et al.

Abstract

Lepidopteran scales exhibit remarkably complex ultrastructures, many of which produce structural colors that are the basis for diverse communication strategies. Little is known, however, about the early evolution of lepidopteran scales and their photonic structures. We report scale architectures from Jurassic Lepidoptera from the United Kingdom, Germany, Kazakhstan, and China and from Tarachoptera (a stem group of Amphiesmenoptera) from mid-Cretaceous Burmese amber. The Jurassic lepidopterans exhibit a type 1 bilayer scale vestiture: an upper layer of large fused cover scales and a lower layer of small fused ground scales. This scale arrangement, plus preserved herringbone ornamentation on the cover scale surface, is almost identical to those of some extant Micropterigidae. Critically, the fossil scale ultrastructures have periodicities measuring from 140 to 2000 nm and are therefore capable of scattering visible light, providing the earliest evidence of structural colors in the insect fossil record. Optical modeling confirms that diffraction-related scattering mechanisms dominate the photonic properties of the fossil cover scales, which would have displayed broadband metallic hues as in numerous extant Micropterigidae. The fossil tarachopteran scales exhibit a unique suite of characteristics, including small size, elongate-spatulate shape, ridged ornamentation, and irregular arrangement, providing novel insight into the early evolution of lepidopteran scales. Combined, our results provide the earliest evidence for structural coloration in fossil lepidopterans and support the hypothesis that fused wing scales and the type 1 bilayer covering are groundplan features of the group. Wing scales likely had deep origins in earlier amphiesmenopteran lineages before the appearance of the Lepidoptera.

Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

Lembra da Terra 2.0 (Kepler-452b)? Não pode ser confirmado!

Kepler's Earth-like Planets Should Not Be Confirmed Without Independent Detection: The Case of Kepler-452b

Fergal Mullally, Susan E. Thompson, Jeffery L. Coughlin, Christopher J. Burke, Jason F. Rowe

(Submitted on 30 Mar 2018)

Source/Fonte: Scientific American

We show that the claimed confirmed planet Kepler-452b (a.k.a. K07016.01, KIC 8311864) can not be confirmed using a purely statistical validation approach. Kepler detects many more periodic signals from instrumental effects than it does from transits, and it is likely impossible to confidently distinguish the two types of event at low signal-to-noise. As a result, the scenario that the observed signal is due to an instrumental artifact can't be ruled out with 99\% confidence, and the system must still be considered a candidate planet. We discuss the implications for other confirmed planets in or near the habitable zone.

Comments: Accepted for publication in AJ

Subjects: Earth and Planetary Astrophysics (astro-ph.EP)

Cite as: arXiv:1803.11307 [astro-ph.EP]

(or arXiv:1803.11307v1 [astro-ph.EP] for this version)

Submission history

From: Fergal Mullally [view email] 

[v1] Fri, 30 Mar 2018 01:37:23 GMT (326kb,D)

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Outra hipótese para a química da origem da vida de superfície da Terra primitiva

terça-feira, abril 10, 2018

Sulfidic Anion Concentrations on Early Earth for Surficial Origins-of-Life Chemistry

Ranjan Sukrit , Todd Zoe R. , Sutherland John D. , and Sasselov Dimitar D.

Published Online:8 Apr 2018 https://doi.org/10.1089/ast.2017.1770


White Island, New Zealand. Researchers have found that a class of molecules called sulfidic anions may have been abundant in Earth’s lakes and rivers.
Credit: © Alba / Fotolia

Abstract

A key challenge in origin-of-life studies is understanding the environmental conditions on early Earth under which abiogenesis occurred. While some constraints do exist (e.g., zircon evidence for surface liquid water), relatively few constraints exist on the abundances of trace chemical species, which are relevant to assessing the plausibility and guiding the development of postulated prebiotic chemical pathways which depend on these species. In this work, we combine literature photochemistry models with simple equilibrium chemistry calculations to place constraints on the plausible range of concentrations of sulfidic anions (HS−, HSO3−, SO32−) available in surficial aquatic reservoirs on early Earth due to outgassing of SO2 and H2S and their dissolution into small shallow surface water reservoirs like lakes. We find that this mechanism could have supplied prebiotically relevant levels of SO2-derived anions, but not H2S-derived anions. Radiative transfer modeling suggests UV light would have remained abundant on the planet surface for all but the largest volcanic explosions. We apply our results to the case study of the proposed prebiotic reaction network of Patel et al. (2015) and discuss the implications for improving its prebiotic plausibility. In general, epochs of moderately high volcanism could have been especially conducive to cyanosulfidic prebiotic chemistry. Our work can be similarly applied to assess and improve the prebiotic plausibility of other postulated surficial prebiotic chemistries that are sensitive to sulfidic anions, and our methods adapted to study other atmospherically derived trace species. 

Key Words: Early Earth—Origin of life—Prebiotic chemistry—Volcanism—UV radiation—Planetary environments. Astrobiology 18, xxx–xxx.

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Centenário do nascimento de Francis Crick

sexta-feira, abril 06, 2018

ISBN 978-3-03842-769-8 (Pbk) ISBN 978-3-03842-770-4 (PDF) 
DOI: 10.3390/books978-3-03842-770-4 Open Access 

© 2018 MDPI; under CC BY-NC-ND license

The Origin and Evolution of the Genetic Code: 100th Anniversary Year of the Birth of Francis Crick

Koji Tamura (Ed.)

Pages: X, 192

Published: March 2018

(This book is a printed edition of the Special Issue The Origin and Evolution of the Genetic Code: 100th Anniversary Year of the Birth of Francis Crick that was published in Life)

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Adaptação ambiental desde a origem da vida até ao LUCA

Origins of Life and Evolution of Biospheres

March 2018, Volume 48, Issue 1, pp 35–54 | Cite as

Environmental Adaptation from the Origin of Life to the Last Universal Common Ancestor

Authors

Authors and affiliations

Marjorie D. Cantine1

Gregory P. Fournier1

Email author

View author's OrcID profile

1.Department of Earth, Atmospheric and Planetary SciencesMassachusetts Institute of TechnologyCambridgeUSA

Hypothesis

First Online: 06 July 2017



Abstract

Extensive fundamental molecular and biological evolution took place between the prebiotic origins of life and the state of the Last Universal Common Ancestor (LUCA). Considering the evolutionary innovations between these two endpoints from the perspective of environmental adaptation, we explore the hypothesis that LUCA was temporally, spatially, and environmentally distinct from life’s earliest origins in an RNA world. Using this lens, we interpret several molecular biological features as indicating an environmental transition between a cold, radiation-shielded origin of life and a mesophilic, surface-dwelling LUCA. Cellularity provides motility and permits Darwinian evolution by connecting genetic material and its products, and thus establishing heredity and lineage. Considering the importance of compartmentalization and motility, we propose that the early emergence of cellularity is required for environmental dispersal and diversification during these transitions. Early diversification and the emergence of ecology before LUCA could be an important pre-adaptation for life’s persistence on a changing planet.

Keywords

Origin of life Last universal common ancestor (LUCA) Environmental adaptation 

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O que é boa ciência? A tara por falsificação e observação está retardando o avanço da ciência. Será???

What is good science?

Demanding that a theory is falsifiable or observable, without any subtlety, will hold science back. We need madcap ideas

Uranus photographed by Voyager 2 in January 1986. Photo courtesy NASA

Adam Becker is a writer and astrophysicist. He is currently a visiting scholar at the Office for History of Science and Technology at the University of California, Berkeley. His writing has appeared in New Scientist and on the BBC, among others. He is the author of What is Real? The Unfinished Quest for the Meaning of Quantum Physics (2018). He lives in Oakland in California. 

The Viennese physicist Wolfgang Pauli suffered from a guilty conscience. He’d solved one of the knottiest puzzles in nuclear physics, but at a cost. ‘I have done a terrible thing,’ he admitted to a friend in the winter of 1930. ‘I have postulated a particle that cannot be detected.’

Despite his pantomime of despair, Pauli’s letters reveal that he didn’t really think his new sub-atomic particle would stay unseen. He trusted that experimental equipment would eventually be up to the task of proving him right or wrong, one way or another. Still, he worried he’d strayed too close to transgression. Things that were genuinely unobservable, Pauli believed, were anathema to physics and to science as a whole.

Pauli’s views persist among many scientists today. It’s a basic principle of scientific practice that a new theory shouldn’t invoke the undetectable. Rather, a good explanation should be falsifiable – which means it ought to rely on some hypothetical data that could, in principle, prove the theory wrong. These interlocking standards of falsifiability and observability have proud pedigrees: falsifiability goes back to the mid-20th-century philosopher of science Karl Popper, and observability goes further back than that. Today they’re patrolled by self-appointed guardians, who relish dismissing some of the more fanciful notions in physics, cosmology and quantum mechanics as just so many castles in the sky. The cost of allowing such ideas into science, say the gatekeepers, would be to clear the path for all manner of manifestly unscientific nonsense.

But for a theoretical physicist, designing sky-castles is just part of the job. Spinning new ideas about how the world could be – or in some cases, how the world definitely isn’t – is central to their work. Some structures might be built up with great care over many years, and end up with peculiar names such as inflationary multiverse or superstring theory. Others are fabricated and dismissed casually over the course of a single afternoon, found and lost again by a lone adventurer in the troposphere of thought.

That doesn’t mean it’s just freestyle sky-castle architecture out there at the frontier. The goal of scientific theory-building is to understand the nature of the world with increasing accuracy over time. All that creative energy has to hook back onto reality at some point. But turning ingenuity into fact is much more nuanced than simply announcing that all ideas must meet the inflexible standards of falsifiability and observability. These are not measures of the quality of a scientific theory. They might be neat guidelines or heuristics, but as is usually the case with simple answers, they’re also wrong, or at least only half-right.
...

READ MORE HERE: Aeon

Conceitos causais em biologia: como que os caminhos diferem dos mecanismos e por que eles importam

terça-feira, abril 03, 2018

Causal concepts in biology: How pathways differ from mechanisms and why it matters

Ross, Lauren N. (2018) Causal concepts in biology: How pathways differ from mechanisms and why it matters. [Preprint]


Abstract

In the last two decades few topics in philosophy of science have received as much attention as mechanistic explanation. A significant motivation for these accounts is that scientists frequently use the term “mechanism” in their explanations of biological phenomena. While scientists appeal to a variety of causal concepts in their explanations, many philosophers argue or assume that all of these concepts are well understood with the single notion of mechanism (Robins and Craver 2009; Craver 2007). This reveals a significant problem with mainstream mechanistic accounts– although philosophers use the term “mechanism” interchangeably with other causal concepts, this is not something that scientists always do. This paper analyses two causal concepts in biology–the notions of “mechanism” and “pathway”–and how they figure in biological explanation. I argue that these concepts have unique features, that they are associated with distinct strategies of causal investigation, and that they figure in importantly different types of explanation.

Kewwords: causation, explanation, mechanism, mechanistic explanation, philosophy of biology, philosophy of neuroscience, philosophy of medicine.

FREE PREPRINT GRATIS: PhilSci

Charbel Niño El-Hani, os evolucionistas não sabem o que faz a seleção natural na teoria da evolução de Darwin

No dia 28 de março este blogger publicou EXTRA! EXTRA! EXTRA! Mudança paradigmática radical na teoria da evolução destacando o artigo Processes and patterns of interaction as units of selection: An introduction to ITSNTS thinking de W. Ford Doolittle and S. Andrew Inkpen, publicado no PNAS March 26, 2018. 201722232; https://doi.org/10.1073/pnas.1722232115.



Após leitura atenta do artigo de Doolittle e Inkpen, depreende-se que os cientistas evolucionistas não sabem o que faz a seleção natural como mecanismo evolucionário, e os autores deixaram isso bem claro no artigo. Consideremos seus questionamentos.
“O pensamento ITSNTS” questiona a teoria evolutiva padrão ESN (evolução por seleção natural):

1. A seleção natural não tem uma teoria de como ela age nas comunidades.

2. Os pontos de vista padrões da seleção natural não abordam a adaptação e a função de “multiespécies.”

3. A seleção natural não pode explicar as comunidades estáveis ou comunidades bacterianas redundantes.

4. A seleção natural não pode explicar os processos que beneficiam as comunidades de reprodutores dissimilares.

5. A seleção natural não pode explicar como os processos que beneficiam as múltiplas comunidades reestabelecerem a si mesmas.

6. Dupre argumenta que “muito da biologia contemporânea defende uma ontologia geralmente mecanicista e reducionista de ‘coisa’ (ou ‘substância’).”

7. O lugar comum do livro-texto focaliza no sucesso reprodutivo dos indivíduos é um hábito de pensamento que ignora a história contingente da síntese moderna e da genética de população.

8. Algumas formulações de seleção natural são vagas porque as unidades de seleção propostas têm “demais progenitores” (a reclamação de Godfrey-Smith). Isso desnorteia os conceitos de herança.

9. A seleção natural é ambígua sobre o que “benéfico” significa. “Não é claro que qualquer propriedade pode ser considerada ‘benéfica’ a comunidades não permanentes e não reprodutoras.”

10. Algumas formulações de seleção natural violam o Princípio de William” que afirma “a adaptação em um nível requer que tenha havido seleção naquele nível.”

11. Algumas funções “são mais estáveis ou ecologicamente resilientes do que são as composições taxonômicas das montagens executando-as.” Isso demanda uma explicação evolucionária.

12. A ESN não explica facilmente a redundância.

13. A ESN é vaga na questão do que é mais relevante para a evolução: a frequência de alelos na população ou o indivíduo portando-os?

14. Os biólogos estão indecisos sobre se os memes sofrem seleção natural. Sperber é um desses ‘cético de memes’ que Doolittle menciona.

15. Os biólogos também debatem se a linguagem ou a cultura são submetidas pela seleção natural.

16. É difícil determinar se a seleção natural se constitui em um mecanismo ou uma necessidade lógica (uma premissa aceita a priori).

17. Sober argumenta que a ENS é “uma verdade a priori no sentido de que nenhum experimento poderia refutá-la.”

18. A teoria da construção de nichos é outro ‘mecanismo’ da ENS que está sendo questionado entre os evolucionistas.

19. Os evolucionistas enfrentam as “transições embaraçosas em recontar a história da vida”, tal como a etapa da unicelularidade para a multicelularidade.
20. O que é mais importante: o diferencial de reprodução ou o diferencial de persistência? O que faz mais sentido e é mais ‘satisfatório’?

21. A dificuldade de se estabelecer linhagens relevantes para a ESN pode ser assim ilustrada: “Eu sou o filho de meu pai, mas o meu coração não é a descendência do coração de meu pai.”

22. Em quais variedades pode a ESN ser comparada? A evolução das funções da comunidade microbiana através dos intestinos análoga à evolução dos lagartos pelas ilhas?

23. Antes da proposta de Doolittle, estava faltando “um jeito sensível de se discutir as adaptações e funções relevantes às comunidades e ecossistemas em geral.”

24. Alguns evolucionistas têm dito que há uma “urgente necessidade de uma estrutura [teórica] geral” para decidir o que constitui a “saúde” de um sistema.

25. Um problema importante na teoria evolucionária é o papel dos componentes abióticos em ecossistemas. Eles podem desempenhar papéis importantes, mas não são reproduzidos biologicamente. Bouchard destacou, “a evolução como mudança em frequências alélicas parecem não se aplicar aos sistemas que têm um grupo heterogêneo de alelos e materia abiótico interagindo de modo sistemático.”

26. Há um século, os biólogos têm debatido em quais níveis o “princípio tipo lei” da seleção natural de Darwin opera. Ela opera em processos bem como em coisas?

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Charbel Niño El-Hani, lembra de uma conversa que tivemos após minha palestra sobre a teoria do Design Inteligente numa sessão da ABFHiB na Universidade Presbiteriana Mackenzie, São Paulo, SP, em 2007 (se não me falha a memória) na qual você me disse que eu tinha embarcado numa canoa furada. Lembra da minha resposta? Eu disse que apostava todas as minhas fichas no cavalo da TDI contra o pangaré da seleção natural de Darwin. Charbel, meu amigo, Doolittle e Inkpen estão me vindicando, e até aqui eu estou ganhando o derby.

Fui, nem sei por que rindo - mais uma vez este blogger é vindicado por evolucionistas, alguns de renome...

Convite para o abandono da significância estatística em pesquisas científicas

sábado, março 31, 2018

Abandon Statistical Significance

Blakeley B. McShane, David Gal, Andrew Gelman, Christian Robert, Jennifer L. Tackett

(Submitted on 22 Sep 2017)


In science publishing and many areas of research, the status quo is a lexicographic decision rule in which any result is first required to have a p-value that surpasses the 0.05 threshold and only then is consideration--often scant--given to such factors as prior and related evidence, plausibility of mechanism, study design and data quality, real world costs and benefits, novelty of finding, and other factors that vary by research domain. There have been recent proposals to change the p-value threshold, but instead we recommend abandoning the null hypothesis significance testing paradigm entirely, leaving p-values as just one of many pieces of information with no privileged role in scientific publication and decision making. We argue that this radical approach is both practical and sensible.

Subjects: Methodology (stat.ME)

MSC classes: 97K70

Cite as: arXiv:1709.07588 [stat.ME]

(or arXiv:1709.07588v1 [stat.ME] for this version)

Submission history

From: Andrew Gelman [view email] 

[v1] Fri, 22 Sep 2017 03:59:24 GMT (15kb)

FREE PDF GRATIS: arXiv

Falem mal, mas continuem falando da teoria do Design Inteligente

Revista Científica General José María Córdova

ISSN: 1900-6586
ISSN electrónico: 2500-7645 (En línea)

Escuela Militar de Cadetes General José María Córdova
Calle 80 N° 38-00
Bogotá-Colombia

Teléfono: 3770850 Ext. 1104

Correo electrónico: revistacientifica@esmic.edu.co


La evolución del diseño inteligente: entre religión y ciencia

Enrique Sandino Vargas, Marta Caccamo, Sumaya Hashim, Oskar Eng


Resumen

Este trabajo evalúa el diseño inteligente (DI) como una pseudociencia. La ciencia ha incorporado muchas definiciones; asimismo la pseudociencia. Ambas han sido discutidas en diversos ámbitos. En lo que atañe a la esfera política, están caracterizados por una pluralidad de conflictos de visiones en discusión. No existe una sola filosofía de la ciencia, y en consecuencia tampoco una sola metodología de la ciencia. Los criterios de demarcación no son una cuestión clara. Esto se torna problemático al evaluar el diseño inteligente. El diseño, en particular, tal como lo conciben los científicos que consideran que no hay razones para incluirlo en el campo científico en su pretensión de que carece de cientificidad. Lo que hacemos aquí es seleccionar un conjunto de definiciones de pseudociencia y ver si el DI satisface los criterios de demarcación. Dado que nuestra unidad de análisis es el DI, se plantea la pregunta si el diseño inteligente es una pseudociencia, o si se puede caracterizar el diseño inteligente como una o varias formas de pseudociencia.

Palabras clave

criterios de demarcación; diseño inteligente; naturalismo; pseudociencia; método científico

Texto completo: PDF

Referencias

Aquinas, T. (2010). Summa Theologica: Translated by Fathers of the English Dominican Province: MobileReference.

Baigrie, B.S., 1988. Siegel on the Rationality of Science, Philosophy of Science, 55: 435–441.

Beckwith, F. J. (2003). Science and religion twenty years after McLean v. Arkansas: Evolution, public education, and the new challenge of intelligent design. Harv. JL & Pub. Pol'y, 26, 455.

Behe, M. J. (1996). Darwin's black box: The biochemical challenge to evolution: Simon and Schuster.

Davis, P. W., Kenyon, D. H., & Thaxton, C. B. (1993). Of pandas and people: The central question of biological origins: Foundation for Thought & Ethics.

Dawkins, R. (1986). The blind watchmaker: why the evidence of evolution reveals a world without design: New York: WW Norton.

Dembski, W. (1998). Science and Design. First Things, 21-27.

Dembski, W., (1999). Intelligent Design: The Bridge Between Science & Theology.

Dembski, W. (2006). In defense of intelligent design. The Oxford Handbook of Religion and Science, Oxford Handbooks in Religion and Theology: Oxford University Press, Oxford.

Dembski, W., & McDowell, S. (2008). Understanding intelligent design: Harvest House Publishers.

Dunér, D. (2016). Swedenborg and the plurality of worlds: Astrotheology in the eighteenth century. Zygon®, 51(2), 450-479.

Gardner, Martin (1957), Fads and Fallacies in the Name of Science (2nd, revised & expanded ed.), Mineola, New York: Dover Publications, ISBN 0-486-20394-8,

George, M. (2013). What would Thomas Aquinas say about Intelligent Design? New Blackfriars, 94(1054), 676-700.

Fuller, Steve, (1985). The demarcation of science: a problem whose demise has been greatly exaggerated, Pacific Philosophical Quarterly, 66: 329–341.

Hansson, S., O. (2009). Cutting the Gordian Knot of demarcation. International Studies in the Philosophy of Science, 23, pp.237-243.

Hume, D. (2003). Dialogues Concerning Natural Religion.

Koperski, J. (2008). Two bad ways to attack intelligent design and two good ones. Zygon®, 43(2), 433-449.

Mc Pherson, T. (1972). What is the argument from design? The Argument from Design, 1-13: Springer.

Paley, W. (1833). Natural Theology: Or, Evidences of the Existence and Atttributes of the Deity: Collected from the Appearances of Nature: Lincoln Edmands & Company.

Peterson, G. R. (2002). The Intelligent‐Design Movement: Science or Ideology? Zygon®, 37(1), 7-23.

Pullen, S. (2005). Intelligent Design Or Evolution? : Why the Origin of Life and the Evolution of Molecular Knowledge Imply Design: Intelligent Design Books.

Sedley, D. (2008). Oxford studies in ancient philosophy (Vol. 33): Oxford Studies in Ancient Phil.

Wallis, C. (2005). The evolution wars. Time, 166(7), 26-35.

Wexler, J. D. (1997). Of Pandas, People, and the First Amendment: The Constitutionality of Teaching Intelligent Design in the Public Schools. Stanford Law Review, 439-470.

Woodruff, P. (2006). Socrates among the Sophists. A Companion to Socrates, 36.

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NOTA DESTE BLOGGER:

Um amigo destacou dois parágrafos deste artigo:
 

"The ID assumption is normative in that from its utterance; it requires the inference that anything, which is unexplainable by the naturalistic argument,
is designed. The scientific assumption is agnostic; it does not attribute all to evolution, it remains open-minded. In this sense, ID is pseudoscientific in that it fails to remain open-minded despite its lack of evidence and logical coherence."

Isso parece dizer que o DI é um argumento Designer das Lacunas, em vez de uma inferência a partir da complexidade especificada... e minimiza o modo que o Darwinismo atribui tudo à evolução.

Todavia, eles admitem:


"To the extent that both evolutionism and ID are based on unverifiable a priori metaphysical assumptions, on this level, ID remains comparably legitimate as the Darwinist argument. We cannot stake the assumptions of either paradigm against the other’s and claim that one is superior, as they are not comparable. In this sense, both ID and Darwinism remain sciences, legitimate under the axiom of their own a priori assumptions of the world and its creation."

Há anos salientamos que quaisquer críticas à TDI são, por tabela, críticas feitas à teoria da evolução de Darwin através da seleção natural e n mecanismos evolucionários (de A a Z, vai que um falhe...), pois sendo teorias de longo alcance histórico, a TDI e a Teoria da Evolução são metodologicamente idênticas!

Fui, nem sei por que pensando: Falem mal, mas falem da TDI...