Como as células "montam" seus esqueletos: mero acaso, fortuita necessidade ou design inteligente?

quinta-feira, janeiro 23, 2020

This is an unedited manuscript that has been accepted for publication. Nature Research are providing this early version of the manuscript as a service to our customers. The manuscript will undergo copyediting, typesetting and a proof review before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers apply.

Insights into the assembly and activation of the microtubule nucleator γ-TuRC

Peng Liu, Erik Zupa, Annett Neuner, Anna Böhler, Justus Loerke, Dirk Flemming, Thomas Ruppert, Till Rudack, Christoph Peter, Christian Spahn, Oliver J. Gruss, Stefan Pfeffer & Elmar Schiebel 

Nature (2019)


Abstract

Microtubules (MTs) are dynamic polymers of αβ-tubulin and play critical roles in cell signaling, cell migration, intracellular transport processes and chromosome segregation1. They assemble de novo from α/β-tubulin dimers in an essential process termed MT nucleation. Complexes containing the protein γ-tubulin serve as structural templates for the MT nucleation reaction2. In vertebrates, MTs are nucleated by the 2.2 MDa γ-tubulin ring complex (γ-TuRC) composed of γ-tubulin, five related γ-tubulin complex proteins (GCP2-6) and additional factors3. GCP6 is unique among the GCP proteins, because it carries an extended insertion domain of unknown function. High-resolution structural information on the γ-TuRC is not available, strongly limiting our understanding of MT formation in cells and tissue2. Here, we present the cryo-EM structure of γ-TuRC from Xenopus laevis at 4.8 Å global resolution, revealing a 14-spoked arrangement of GCPs and γ-tubulins in a partially flexible open left-handed spiral with a uniform sequence of GCP variants (Fig. 1a). Via specific interactions with other GCP proteins, the GCP6-specific insertion domain scaffolds the assembly of the γ-TuRC. Unexpectedly, we identified Actin as a bona fide structural component of γ-TuRC with functional relevance in MT nucleation. The γ-TuRC spiral geometry is suboptimal for MT nucleation and a controlled conformational rearrangement of the γ-TuRC is required for its activation. Collectively, our cryo-EM reconstruction provides unprecedented insights into the molecular organization, the assembly and the activation mechanism of vertebrate γ-TuRC and will serve as an important framework for the mechanistic understanding of fundamental biological processes associated with MT nucleation, e.g. meiotic and mitotic spindle formation and centriole biogensis 4.

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Jordan Peterson 'falou e disse': a teoria da evolução está cheia de falhas!

Os primeiros 'lagos de soda' podem ter fornecido a chave do ingrediente que faltava para a origem da vida 2 de 2

quarta-feira, janeiro 22, 2020

Geochimica et Cosmochimica Acta

Volume 260, 1 September 2019, Pages 124-132

Alkaline lake settings for concentrated prebiotic cyanide and the origin of life

J.D.Toner, D.C.Catling

University of Washington, Box 351310, Dept. Earth & Space Sciences, Seattle, WA 98195, USA

Received 4 April 2019, Accepted 18 June 2019, Available online 25 June 2019.

Associate editor: Nicholas Tosca

https://doi.org/10.1016/j.gca.2019.06.031 

Under a Creative Commons license

Lake Mono in California has so much salt, pillars are built over time.
Source/Fonte: (Image: © Matthew Dillon/Flickr/CC BY 2.0

Abstract

Cyanide plays a critical role in origin of life hypotheses that have received strong experimental support from cyanide-driven synthesis of amino acids, nucleotides, and lipid precursors. However, relatively high cyanide concentrations are needed. Such cyanide could have been supplied by reaction networks in which hydrogen cyanide in early Earth’s atmosphere reacted with iron to form ferrocyanide salts, followed by thermal decomposition of ferrocyanide salts to cyanide. Using an aqueous model supported by new experimental data, we show that sodium ferrocyanide salts precipitate in closed-basin, alkaline lakes over a wide range of plausible early Earth conditions. Such lakes were likely common on the early Earth because of chemical weathering of mafic or ultramafic rocks and evaporative concentration. Subsequent thermal decomposition of sedimentary sodium ferrocyanide yields sodium cyanide (NaCN), which dissolves in water to form NaCN-rich solutions. Thus, geochemical considerations newly identify a particular geological setting and NaCN feedstock nucleophile for prebiotic chemistry.





Keywords

Prebiotic chemistryearly EarthOrigin of lifeCyanideAlkaline lakes




FREE PDF GRATIS: Geochimica et Cosmochimica Acta

Os primeiros 'lagos de soda' podem ter fornecido a chave do ingrediente que faltava para a origem da vida 1 de 2

A carbonate-rich lake solution to the phosphate problem of the origin of life

Jonathan D. Toner and View ORCID ProfileDavid C. Catling

PNAS January 14, 2020 117 (2) 883-888; first published December 30, 2019 https://doi.org/10.1073/pnas.1916109117 

Edited by Jonathan I. Lunine, Cornell University, Ithaca, NY, and approved November 27, 2019 (received for review September 16, 2019)


Lake Mono in California has so much salt, pillars are built over time.
Source/Fonte: (Image: © Matthew Dillon/Flickr/CC BY 2.0

Significance

Phosphate is crucial for the origin of life because it is ubiquitous in key biomolecules. A major issue is that prebiotic syntheses use concentrated phosphate to incorporate phosphate into biomolecules, whereas natural waters are generally phosphate-poor because phosphate reacts with calcium to form low-solubility apatite minerals. Here we show that carbonate-rich lakes can concentrate phosphate to >1 molal levels by locking up calcium in carbonate minerals, which prevents phosphate removal by apatite precipitation. Phosphate-rich lakes may have preferentially formed on the prebiotic Earth because of carbonic acid weathering under CO2-rich atmospheres and the absence of microbial phosphate consumption. This specifically points to an origin of life in carbonate-rich lakes, and so defines aqueous conditions that prebiotic chemists should consider.

Abstract

Phosphate is central to the origin of life because it is a key component of nucleotides in genetic molecules, phospholipid cell membranes, and energy transfer molecules such as adenosine triphosphate. To incorporate phosphate into biomolecules, prebiotic experiments commonly use molar phosphate concentrations to overcome phosphate’s poor reactivity with organics in water. However, phosphate is generally limited to micromolar levels in the environment because it precipitates with calcium as low-solubility apatite minerals. This disparity between laboratory conditions and environmental constraints is an enigma known as “the phosphate problem.” Here we show that carbonate-rich lakes are a marked exception to phosphate-poor natural waters. In principle, modern carbonate-rich lakes could accumulate up to ∼0.1 molal phosphate under steady-state conditions of evaporation and stream inflow because calcium is sequestered into carbonate minerals. This prevents the loss of dissolved phosphate to apatite precipitation. Even higher phosphate concentrations (>1 molal) can form during evaporation in the absence of inflows. On the prebiotic Earth, carbonate-rich lakes were likely abundant and phosphate-rich relative to the present day because of the lack of microbial phosphate sinks and enhanced chemical weathering of phosphate minerals under relatively CO2-rich atmospheres. Furthermore, the prevailing CO2 conditions would have buffered phosphate-rich brines to moderate pH (pH 6.5 to 9). The accumulation of phosphate and other prebiotic reagents at concentration and pH levels relevant to experimental prebiotic syntheses of key biomolecules is a compelling reason to consider carbonate-rich lakes as plausible settings for the origin of life.


FREE PDF GRATIS: PNAS Sup. Info.

Três grupos diferentes de Design Inteligente

terça-feira, janeiro 21, 2020

TRÊS GRUPOS DIFERENTES DE DESIGN INTELIGENTE:

VISÃO ESTREITA - esta é a ciência do Design Inteligente tipificada por Michael Behe, William Dembski, outros teóricos, proponentes e defensores, tendo a Informação Complexa Especificada e a Complexidade Irredutível como SINAIS DE INTELIGÊNCIA empiricamente detectados na natureza.

VISÃO AMPLA – essa visão contempla o Design Inteligente aplicado a muitas coisas além da biologia. Ela procura reexaminar uma infinidade de assuntos e como a agência inteligente pode encontrar um lugar normativo.

MOVIMENTO DO DI - este é um grupo grande de ideias/movimentos anteriormente privados de direitos que buscam um retorno usando uma abordagem mais baseada na ciência. 

OBSERVAÇÃO: Como um dos precursores do Design Inteligente no Brasil em 1998, eu me considero membro dos três grupos. Todavia, às vezes nós precisamos ser mais claros sobre qual grupo estamos falando. Nas minhas palestras e postagens neste blog, eu me atenho estritamente à VISÃO ESTREITA do DI. 

De qualquer forma, o MOVIMENTO DO DI poderá sobreviver à morte das VISÕES ESTREITA e AMPLA do DI, pois não depende de nenhum ponto de vista específico. As duas visões têm um conteúdo científico muito mais específico e podem ser potencialmente falseadas.

Enézio E. de Almeida Filho

Mais uma hipótese sobre a origem da vida.

segunda-feira, janeiro 20, 2020

Isolation of an archaeon at the prokaryote–eukaryote interface

Hiroyuki Imachi, Masaru K. Nobu, Nozomi Nakahara, Yuki Morono, Miyuki Ogawara, Yoshihiro Takaki, Yoshinori Takano, Katsuyuki Uematsu, Tetsuro Ikuta, Motoo Ito, Yohei Matsui, Masayuki Miyazaki, Kazuyoshi Murata, Yumi Saito, Sanae Sakai, Chihong Song, Eiji Tasumi, Yuko Yamanaka, Takashi Yamaguchi, Yoichi Kamagata, Hideyuki Tamaki & Ken Takai 

Nature (2020)


Abstract

The origin of eukaryotes remains unclear1,2,3,4. Current data suggest that eukaryotes may have emerged from an archaeal lineage known as ‘Asgard’ archaea5,6. Despite the eukaryote-like genomic features that are found in these archaea, the evolutionary transition from archaea to eukaryotes remains unclear, owing to the lack of cultured representatives and corresponding physiological insights. Here we report the decade-long isolation of an Asgard archaeon related to Lokiarchaeota from deep marine sediment. The archaeon—‘Candidatus Prometheoarchaeum syntrophicum’ strain MK-D1—is an anaerobic, extremely slow-growing, small coccus (around 550 nm in diameter) that degrades amino acids through syntrophy. Although eukaryote-like intracellular complexes have been proposed for Asgard archaea6, the isolate has no visible organelle-like structure. Instead, Ca. P. syntrophicum is morphologically complex and has unique protrusions that are long and often branching. On the basis of the available data obtained from cultivation and genomics, and reasoned interpretations of the existing literature, we propose a hypothetical model for eukaryogenesis, termed the entangle–engulf–endogenize (also known as E3) model.

O caso difícil da origem da vida somente via RNA

sexta-feira, janeiro 17, 2020

The difficult case of an RNA-only origin of life
 
Kristian Le Vay; Hannes Mutschler

Emerg Top Life Sci (2019) 3 (5): 469–475.

https://doi.org/10.1042/ETLS20190024
 

Figure 1 

Abstract

The RNA world hypothesis is probably the most extensively studied model for the emergence of life on Earth. Despite a large body of evidence supporting the idea that RNA is capable of kick-starting autocatalytic self-replication and thus initiating the emergence of life, seemingly insurmountable weaknesses in the theory have also been highlighted. These problems could be overcome by novel experimental approaches, including out-of-equilibrium environments, and the exploration of an early co-evolution of RNA and other key biomolecules such as peptides and DNA, which might be necessary to mitigate the shortcomings of RNA-only systems.

Keywords: origins of life, prebiotic chemistry, RNA catalysis, RNA world, self-replication

Subjects: Chemical Biology, Evolutionary Biology, RNA, Synthetic Biology
 
FREE PDF GRATIS: Emerg Top Life Sci

O DNA pode ser usado para computação: mero acaso, fortuita necessidade ou design inteligente?

segunda-feira, janeiro 06, 2020

Programmable DNA Nanoindicator‐Based Platform for Large‐Scale Square Root Logic Biocomputing

Chunyang Zhou Hongmei Geng Pengfei Wang Chunlei Guo

First published: 29 October 2019 https://doi.org/10.1002/smll.201903489

Computer made from DNA can calculate the square root of 900
Abstract

The prospect of programming molecular computing systems to realize complex autonomous tasks has advanced the design of synthetic biochemical logic circuits. One way to implement digital and analog integrated circuits is to use noncovalent hybridization and strand displacement reactions in cell‐free and enzyme‐free nucleic acid systems. To date, DNA‐based circuits involving tens of logic gates capable of implementing basic and complex logic functions have been demonstrated experimentally. However, most of these circuits are still incapable of realizing complex mathematical operations, such as square root logic operations, which can only be carried out with 4 bit binary numbers. A high‐capacity DNA biocomputing system is demonstrated through the development of a 10 bit square root logic circuit. It can calculate the square root of a 10 bit binary number (within the decimal integer 900) by designing DNA sequences and programming DNA strand displacement reactions. The input signals are optimized through the output feedback to improve performance in more complex logical operations. This study provides a more universal approach for applications in biotechnology and bioengineering.

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Não publique muito, não pereça!

Fast Lane to Slow Science

Uta Frith

Published: November 16, 2019 DOI: https://doi.org/10.1016/j.tics.2019.10.007

Image result for fast lane

Fast Science is bad for scientists and bad for science. Slow Science may actually help us to make faster progress, but how can we slow down? Here, I offer preliminary suggestions for how we can transition to a healthier and more sustainable research culture.

Keywords collaboration diversity quality research culture

Como as bactérias controlam seu ciclo celular: mero acaso, fortuita necessidade ou design inteligente?

sábado, janeiro 04, 2020

Initiation of chromosome replication controls both division and replication cycles in E. coli through a double-adder mechanism

Guillaume Witz , Erik van Nimwegen, Thomas Julou
University of Basel, Switzerland; University of Bern, Switzerland

Research Article Nov 11, 2019 


https://iiif.elifesciences.org/lax:48063%2Felife-48063-fig4-v2.tif/full/full/0/default.jpg

Abstract

Living cells proliferate by completing and coordinating two cycles, a division cycle controlling cell size and a DNA replication cycle controlling the number of chromosomal copies. It remains unclear how bacteria such as Escherichia coli tightly coordinate those two cycles across a wide range of growth conditions. Here, we used time-lapse microscopy in combination with microfluidics to measure growth, division and replication in single E. coli cells in both slow and fast growth conditions. To compare different phenomenological cell cycle models, we introduce a statistical framework assessing their ability to capture the correlation structure observed in the data. In combination with stochastic simulations, our data indicate that the cell cycle is driven from one initiation event to the next rather than from birth to division and is controlled by two adder mechanisms: the added volume since the last initiation event determines the timing of both the next division and replication initiation events.
 
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A vida pode ter se originado em lagos com alto teor de fósforo

A carbonate-rich lake solution to the phosphate problem of the origin of life

Jonathan D. Toner and David C. Catling

PNAS first published December 30, 2019


Edited by Jonathan I. Lunine, Cornell University, Ithaca, NY, and approved November 27, 2019 (received for review September 16, 2019)


Significance

Phosphate is crucial for the origin of life because it is ubiquitous in key biomolecules. A major issue is that prebiotic syntheses use concentrated phosphate to incorporate phosphate into biomolecules, whereas natural waters are generally phosphate-poor because phosphate reacts with calcium to form low-solubility apatite minerals. Here we show that carbonate-rich lakes can concentrate phosphate to >1 molal levels by locking up calcium in carbonate minerals, which prevents phosphate removal by apatite precipitation. Phosphate-rich lakes may have preferentially formed on the prebiotic Earth because of carbonic acid weathering under CO2-rich atmospheres and the absence of microbial phosphate consumption. This specifically points to an origin of life in carbonate-rich lakes, and so defines aqueous conditions that prebiotic chemists should consider.

Abstract

Phosphate is central to the origin of life because it is a key component of nucleotides in genetic molecules, phospholipid cell membranes, and energy transfer molecules such as adenosine triphosphate. To incorporate phosphate into biomolecules, prebiotic experiments commonly use molar phosphate concentrations to overcome phosphate’s poor reactivity with organics in water. However, phosphate is generally limited to micromolar levels in the environment because it precipitates with calcium as low-solubility apatite minerals. This disparity between laboratory conditions and environmental constraints is an enigma known as “the phosphate problem.” Here we show that carbonate-rich lakes are a marked exception to phosphate-poor natural waters. In principle, modern carbonate-rich lakes could accumulate up to ∼0.1 molal phosphate under steady-state conditions of evaporation and stream inflow because calcium is sequestered into carbonate minerals. This prevents the loss of dissolved phosphate to apatite precipitation. Even higher phosphate concentrations (>1 molal) can form during evaporation in the absence of inflows. On the prebiotic Earth, carbonate-rich lakes were likely abundant and phosphate-rich relative to the present day because of the lack of microbial phosphate sinks and enhanced chemical weathering of phosphate minerals under relatively CO2-rich atmospheres. Furthermore, the prevailing CO2 conditions would have buffered phosphate-rich brines to moderate pH (pH 6.5 to 9). The accumulation of phosphate and other prebiotic reagents at concentration and pH levels relevant to experimental prebiotic syntheses of key biomolecules is a compelling reason to consider carbonate-rich lakes as plausible settings for the origin of life.


FREE PDF GRATIS: PNAS Sup. Info.

Design Inteligente 3.0

segunda-feira, dezembro 23, 2019


Dr. Stephen Meyer Talks about ID 3.0 from Discovery Institute CSC on Vimeo.

Áreas científicas organizadas pela pureza!

segunda-feira, dezembro 02, 2019


Purity
Source/Fonte: XKCD

Embriões de animais evoluíram antes dos animais

quinta-feira, novembro 28, 2019

The Early Ediacaran Caveasphaera Foreshadows the Evolutionary Origin of Animal-like Embryology

Zongjun Yin6, Kelly Vargas6, John Cunningham, Maoyan Zhu, Federica Marone, Philip Donoghue

Published:November 27, 2019 DOI: https://doi.org/10.1016/j.cub.2019.10.057


Figure thumbnail fx1
Highlights

• Caveasphaera is an enigmatic component of the 609-Ma Weng’an Biota of South China

• Yin et al. use X-ray tomography to characterize cellular structure and development


• Gastrulation-like cell division, ingression, detachment, and polar aggregation occur


• A holozoan affinity suggests the early evolution of metazoan-like development

Summary

The Ediacaran Weng’an Biota (Doushantuo Formation, 609 Ma old) is a rich microfossil assemblage that preserves biological structure to a subcellular level of fidelity and encompasses a range of developmental stages [1]. However, the animal embryo interpretation of the main components of the biota has been the subject of controversy [23]. Here, we describe the development of Caveasphaera, which varies in morphology from lensoid to a hollow spheroidal cage [4] to a solid spheroid [5] but has largely evaded description and interpretation. Caveasphaera is demonstrably cellular and develops within an envelope by cell division and migration, first defining the spheroidal perimeter via anastomosing cell masses that thicken and ingress as strands of cells that detach and subsequently aggregate in a polar region. Concomitantly, the overall diameter increases as does the volume of the cell mass, but after an initial phase of reductive palinotomy, the volume of individual cells remains the same through development. The process of cell ingression, detachment, and polar aggregation is analogous to gastrulation; together with evidence of functional cell adhesion and development within an envelope, this is suggestive of a holozoan affinity. Parental investment in the embryonic development of Caveasphaera and co-occurring Tianzhushania and Spiralicellula, as well as delayed onset of later development, may reflect an adaptation to the heterogeneous nature of the early Ediacaran nearshore marine environments in which early animals evolved.
 


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Estrutura do gancho flagelar nativo super enrolado como junta universal: mero acaso, fortuita necessidade ou design inteligente?

quarta-feira, novembro 27, 2019

Structure of the native supercoiled flagellar hook as a universal joint

Takayuki Kato, Fumiaki Makino, Tomoko Miyata, Péter Horváth & Keiichi Namba 

Nature Communications volume 10, Article number: 5295 (2019) 

Structure of native supercoiled hook.

Abstract

The Bacterial flagellar hook is a short supercoiled tubular structure made from a helical assembly of the hook protein FlgE. The hook acts as a universal joint that connects the flagellar basal body and filament, and smoothly transmits torque generated by the rotary motor to the helical filament propeller. In peritrichously flagellated bacteria, the hook allows the filaments to form a bundle behind the cell for swimming, and for the bundle to fall apart for tumbling. Here we report a native supercoiled hook structure at 3.6 Å resolution by cryoEM single particle image analysis of the polyhook. The atomic model built into the three-dimensional (3D) density map reveals the changes in subunit conformation and intersubunit interactions that occur upon compression and extension of the 11 protofilaments during their smoke ring-like rotation. These observations reveal how the hook functions as a dynamic molecular universal joint with high bending flexibility and twisting rigidity.

O pipeline de rastreamento de células revela como os circuitos de motores são construídos: mero acaso, fortuita necessidade ou design inteligente?

terça-feira, novembro 26, 2019

Cell Volume 179, ISSUE 2, P355-372.e23, October 03, 2019

Single-Cell Reconstruction of Emerging Population Activity in an Entire Developing Circuit

Yinan Wan, Ziqiang Wei, Loren L. Looger, Minoru Koyama, Shaul Druckmann, Philipp J. Keller


 
Source/Fonte: Nature

Highlights

• Neurons are tracked from birth to entire circuit at cell-type and functional levels

• Neurogenesis and emergence of coordinated activity is analyzed at a single-cell level

• Motoneurons, active first, form ensembles that synchronize globally, based on size

• Neuron maturation is stereotyped, based on birth time and anatomical origin

Summary

Animal survival requires a functioning nervous system to develop during embryogenesis. Newborn neurons must assemble into circuits producing activity patterns capable of instructing behaviors. Elucidating how this process is coordinated requires new methods that follow maturation and activity of all cells across a developing circuit. We present an imaging method for comprehensively tracking neuron lineages, movements, molecular identities, and activity in the entire developing zebrafish spinal cord, from neurogenesis until the emergence of patterned activity instructing the earliest spontaneous motor behavior. We found that motoneurons are active first and form local patterned ensembles with neighboring neurons. These ensembles merge, synchronize globally after reaching a threshold size, and finally recruit commissural interneurons to orchestrate the left-right alternating patterns important for locomotion in vertebrates. Individual neurons undergo functional maturation stereotypically based on their birth time and anatomical origin. Our study provides a general strategy for reconstructing how functioning circuits emerge during embryogenesis.
 
 
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Pare com o treinamento científico que exige "não pergunte"!

sexta-feira, novembro 22, 2019

WORLD VIEW 19 NOVEMBER 2019

Stop the science training that demands ‘don’t ask’

It’s time to trust students to handle doubt and diversity in science, says Jerry Ravetz.

Jerry Ravetz



As a child, I realized that my parents spoke in Yiddish when they didn’t want me to know what they were talking about, so I became aware that some knowledge was intended only for grown-ups — don’t ask. In college, I was taught an elegant theory of chemical combination based on excess electrons going into holes in the orbital shell of a neighbouring atom. But what about diatomic compounds like oxygen gas? Don’t ask; students aren’t ready to know. In physics, I learnt that Newton’s second law of motion is not an empirical, approximate relation such as Boyle’s and Hooke’s laws, and instead has a universal application; but what about the science of statics, in which forces are balanced and there is no acceleration? Don’t ask. Mere students are not worthy of an answer. Yet when I was moonlighting in the social sciences and humanities, I found my questions and opinions were respected, even if only as part of my learning experience.

Observant students will notice that social problems surrounding science are seldom mentioned in official curricula. And now, these pupils are starting to act. They have shamed their seniors into including more diverse contributors as faculty members and role models. Young scholars insolently ask their superiors why they fail to address the extinction crises elucidated by their research. Such subversions are reminiscent of the mass-produced heretical pamphlets circulated by Martin Luther’s supporters at the start of the Protestant Reformation in sixteenth-century Europe. The inherited authoritarian political structures of science education are becoming brittle — but still remain largely unchanged from my own school days.

The philosopher Thomas Kuhn once compared taught science to orthodox theology. A narrow, rigid education does not prepare anyone for the complexities of scientific research, applications and policy. If we discourage students from inquiring into the real nature of scientific truths, or exploring how society shapes the questions that researchers ask, how can we prepare them to maintain public trust in science in our ‘post-truth’ world? Diversity and doubt produce creativity; we must make room for them, and stop funnelling future scientists into narrow specialties that value technique over thought.

In the 1990s, Silvio Funtowicz, a philosopher of science, and I developed the concept of ‘post-normal science’, building on the Kuhnian terms ‘normal’ and ‘revolutionary’ science. It outlines how to use science in a society confronted with high-stakes decisions, where both facts and values are uncertain; it requires drawing on a broad community with broad inquiries. Suppressing questions from budding scientists is sure to suppress promising ideas and solutions.

...

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Sabe aquele DNA "Lixo"? É cheio de informação como os teóricos do Design Inteligente afirmaram!

quarta-feira, novembro 13, 2019

The Genomic Code: A Pervasive Encoding/Molding of Chromatin Structures and a Solution of the “Non‐Coding DNA” Mystery

Giorgio Bernardi

First published: 08 November 2019 https://doi.org/10.1002/bies.201900106

junk-dna
Source/Fonte: Mapping Ignorance

Abstract

Recent investigations have revealed 1) that the isochores of the human genome group into two super‐families characterized by two different long‐range 3D structures, and 2) that these structures, essentially based on the distribution and topology of short sequences, mold primary chromatin domains (and define nucleosome binding). More specifically, GC‐poor, gene‐poor isochores are low‐heterogeneity sequences with oligo‐A spikes that mold the lamina‐associated domains (LADs), whereas GC‐rich, gene‐rich isochores are characterized by single or multiple GC peaks that mold the topologically associating domains (TADs). The formation of these “primary TADs” may be followed by extrusion under the action of cohesin and CTCF. Finally, the genomic code, which is responsible for the pervasive encoding and molding of primary chromatin domains (LADs and primary TADs, namely the “gene spaces”/“spatial compartments”) resolves the longstanding problems of “non‐coding DNA,” “junk DNA,” and “selfish DNA” leading to a new vision of the genome as shaped by DNA sequences.

FREE PDF GRATIS: BioEssays

Fios elétricos vivos conectam-se a tubos sem-fim para maior estabilidade da grade microbiana eletrogênica: mero acaso, fortuita necessidade ou design inteligente?

sexta-feira, novembro 08, 2019

Worm tubes as conduits for the electrogenic microbial grid in marine sediments

Robert C. Aller*, Josephine Y. Aller, Qingzhi Zhu, Christina Heilbrun, Isaac Klingensmith and Aleya Kaushik†

School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794, USA.

↵*Corresponding author. Email: robert.aller@stonybrook.edu

↵† Present address: NOAA, Global Monitoring Division, Boulder, CO 80305, USA.

Science Advances 17 Jul 2019: Vol. 5, no. 7, eaaw3651



Abstract

Electrogenic cable bacteria can couple spatially separated redox reaction zones in marine sediments using multicellular filaments as electron conductors. Reported as generally absent from disturbed sediments, we have found subsurface cable aggregations associated with tubes of the parchment worm Chaetopterus variopedatus in otherwise intensely bioturbated deposits. Cable bacteria tap into tubes, which act as oxygenated conduits, creating a three-dimensional conducting network extending decimeters into sulfidic deposits. By elevating pH, promoting Mn, Fe-oxide precipitation in tube linings, and depleting S around tubes, they enhance tube preservation and favorable biogeochemical conditions within the tube. The presence of disseminated filaments a few cells in length away from oxygenated interfaces and the reported ability of cable bacteria to use a range of redox reaction couples suggest that these microbes are ubiquitous facultative opportunists and that long filaments are an end-member morphological adaptation to relatively stable redox domains.

FREE PDF GRATIS: Science Advances Sup. Info.

Biologia estrutural celular conforme revelada pela tomografia crioeletrônica: mero acaso, fortuita necessidade ou design inteligente?

quarta-feira, novembro 06, 2019

Cellular structural biology as revealed by cryo-electron tomography

Rossitza N. Irobalieva, Bruno Martins, Ohad Medalia

Journal of Cell Science 2016 129: 469-476; doi: 10.1242/jcs.171967


ABSTRACT

Understanding the function of cellular machines requires a thorough analysis of the structural elements that underline their function. Electron microscopy (EM) has been pivotal in providing information about cellular ultrastructure, as well as macromolecular organization. Biological materials can be physically fixed by vitrification and imaged with cryo-electron tomography (cryo-ET) in a close-to-native condition. Using this technique, one can acquire three-dimensional (3D) information about the macromolecular architecture of cells, depict unique cellular states and reconstruct molecular networks. Technical advances over the last few years, such as improved sample preparation and electron detection methods, have been instrumental in obtaining data with unprecedented structural details. This presents an exciting opportunity to explore the molecular architecture of both individual cells and multicellular organisms at nanometer to subnanometer resolution. In this Commentary, we focus on the recent developments and in situ applications of cryo-ET to cell and structural biology.

FREE PDF GRATIS: Journal of Cell Science

Faleceu Phillip E. Johnson, fundador do Movimento do Design Inteligente

sábado, novembro 02, 2019

Image result for Phillip E. Johnson
Phillip E. Johnson 1940-2019

O papel da ortogonalidade na expansão do código genético: mero acaso, fortuita necessidade ou design inteligente?

quinta-feira, outubro 31, 2019

The Role of Orthogonality in Genetic Code Expansion

by Pol Arranz-Gibert 1,2,†,Jaymin R. Patel 1,2,† andFarren J. Isaacs 1,2,*OrcID

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA

Systems Biology Institute, Yale University, West Haven, CT 06516, USA

Author to whom correspondence should be addressed.

† These authors contributed equally to this work.


Received: 20 June 2019 / Revised: 1 July 2019 / Accepted: 1 July 2019 / Published: 5 July 2019



Abstract

The genetic code defines how information in the genome is translated into protein. Aside from a handful of isolated exceptions, this code is universal. Researchers have developed techniques to artificially expand the genetic code, repurposing codons and translational machinery to incorporate nonstandard amino acids (nsAAs) into proteins. A key challenge for robust genetic code expansion is orthogonality; the engineered machinery used to introduce nsAAs into proteins must co-exist with native translation and gene expression without cross-reactivity or pleiotropy. The issue of orthogonality manifests at several levels, including those of codons, ribosomes, aminoacyl-tRNA synthetases, tRNAs, and elongation factors. In this concept paper, we describe advances in genome recoding, translational engineering and associated challenges rooted in establishing orthogonality needed to expand the genetic code. 

Keywords: genetic code expansion; translation; nonstandard amino acids; genome recoding; ribosome engineering; orthogonality; protein engineering

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Em busca da arqueologia galática

quarta-feira, outubro 30, 2019

In Pursuit of Galactic Archaeology: Astro2020 Science White Paper

Melissa Ness (Columbia/Flatiron), Jonathan Bird (Vanderbilt), Jennifer Johnson (Ohio State University), Gail Zasowski (University of Utah), Juna Kollmeier (Carnegie), Hans-Walter Rix (MPIA), Victor Silva Aguirre (Aarhus), Borja Anguiano (University of Virginia), Sarbani Basu (Yale), Anthony Brown (Leiden), Sven Buder (MPIA), Cristina Chiappini (AIP), Katia Cunha (NOAO), Elena Dongia (University of Wisconsin, Madison), Peter Frinchaboy (TCU), Saskia Hekker (MPI for Solar system research), Jason Hunt (Toronto), Kathryn Johnston (Columbia), Richard Lane (PUC), Sara Lucatello (INAF Osservatorio Astronomico di Padova), Szabolcs Meszaros (ELTE Gothard Astrophysical Observatory)Andres Meza (UDD), Ivan Minchev (AIP), David Nataf (JHU), Marc Pinsonneault (Ohio State University), Adrian M. Price-Whelan (Princeton), Robyn Sanderson (UPenn/Flatiron)Jennifer Sobeck (University of Washington), Keivan Stassun (Vanderbilt), Matthias Steinmetz (AIP), Yuan-Sen Ting (IAS/Princeton/OCIW), Kim Venn (Victoria), Xiangxiang Xue (NAOC)

(Submitted on 11 Jul 2019)


The next decade affords tremendous opportunity to achieve the goals of Galactic archaeology. That is, to reconstruct the evolutionary narrative of the Milky Way, based on the empirical data that describes its current morphological, dynamical, temporal and chemical structures. Here, we describe a path to achieving this goal. The critical observational objective is a Galaxy-scale, contiguous, comprehensive mapping of the disk's phase space, tracing where the majority of the stellar mass resides. An ensemble of recent, ongoing, and imminent surveys are working to deliver such a transformative stellar map. Once this empirical description of the dust-obscured disk is assembled, we will no longer be operationally limited by the observational data. The primary and significant challenge within stellar astronomy and Galactic archaeology will then be in fully utilizing these data. We outline the next-decade framework for obtaining and then realizing the potential of the data to chart the Galactic disk via its stars. One way to support the investment in the massive data assemblage will be to establish a Galactic Archaeology Consortium across the ensemble of stellar missions. This would reflect a long-term commitment to build and support a network of personnel in a dedicated effort to aggregate, engineer, and transform stellar measurements into a comprehensive perspective of our Galaxy.

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Colocando o "bang" no Big Bang!

terça-feira, outubro 29, 2019

Nonlinear Dynamics of Preheating after Multifield Inflation with Nonminimal Couplings

Rachel Nguyen, Jorinde van de Vis, Evangelos I. Sfakianakis, John T. Giblin, Jr., and David I. Kaiser

Phys. Rev. Lett. 123, 171301 – Published 25 October 2019

Source/Fonte: MIT News

ABSTRACT

We study the postinflation dynamics of multifield models involving nonminimal couplings using lattice simulations to capture significant nonlinear effects like backreaction and rescattering. We measure the effective equation of state and typical timescales for the onset of thermalization, which could affect the usual mapping between predictions for primordial perturbation spectra and measurements of anisotropies in the cosmic microwave background radiation. For large values of the nonminimal coupling constants, we find efficient particle production that gives rise to nearly instantaneous preheating. Moreover, the strong single-field attractor behavior that was previously identified persists until the end of preheating, thereby suppressing typical signatures of multifield models. We therefore find that predictions for primordial observables in this class of models retain a close match to the latest observations.

Revised 10 September 2019Received 10 June 2019


Published by the American Physical Society under the terms of the Creative Commons Attribution 4.0 International license. Further distribution of this work must maintain attribution to the author(s) and the published article’s title, journal citation, and DOI. Funded by SCOAP3.

Published by the American Physical Society

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Evolução: de uma "simples" bactéria até Beethoven

segunda-feira, outubro 28, 2019