Será que o cérebro humano se parece com o universo? Mero acaso, fortuita necessidade ou design inteligente?

terça-feira, novembro 17, 2020

Front. Phys., 16 November 2020 | https://doi.org/10.3389/fphy.2020.525731

The Quantitative Comparison Between the Neuronal Network and the Cosmic Web

www.frontiersin.orgF. Vazza1,2,3* and www.frontiersin.orgA. Feletti4,5

1Dipartimento di Fisica e Astronomia, Universitá di Bologna, , Bologna, Italy

2Hamburger Sternwarte, Hamburg, Germany

3Istituto di Radio Astronomia, INAF, Bologna, Italy

4Institute of Neurosurgery, Department of Neurosciences, Biomedicine, and Movement Sciences, University of Verona, Verona, Italy

5Azienda Ospedaliera‐Universitaria di Modena, Modena, Italy


1Left: section of cerebellum, with magnification factor 40x, obtained with electron microscopy (Dr. E. Zunarelli, University Hospital of Modena); right: section of a cosmological simulation, with an extension of 300 million light-years on each side (Vazza et al. 2019 A&A). Credit: University of Bologna

We investigate the similarities between two of the most challenging and complex systems in Nature: the network of neuronal cells in the human brain, and the cosmic network of galaxies. We explore the structural, morphological, network properties and the memory capacity of these two fascinating systems, with a quantitative approach. In order to have an homogeneous analysis of both systems, our procedure does not consider the true neural connectivity but an approximation of it, based on simple proximity. The tantalizing degree of similarity that our analysis exposes seems to suggest that the self-organization of both complex systems is likely being shaped by similar principles of network dynamics, despite the radically different scales and processes at play.

FREE PDF GRATIS: Frontiers in Physics

Mais uma hipótese sobre a origem da vida: modelos de precursores potenciais de células resistem às condições simuladas da Terra primitiva

quinta-feira, outubro 29, 2020

Impact of wet-dry cycling on the phase behavior and compartmentalization properties of complex coacervates

Hadi M. Fares, Alexander E. Marras, Jeffrey M. Ting, Matthew V. Tirrell & Christine D. Keating 

Nature Communications volume 11, Article number: 5423 (2020)



Abstract

Wet-dry cycling on the early Earth is thought to have facilitated production of molecular building blocks of life, but its impact on self-assembly and compartmentalization remains largely unexplored. Here, we investigate dehydration/rehydration of complex coacervates, which are membraneless compartments formed by phase separation of polyelectrolyte solutions. Solution compositions are identified for which tenfold water loss results in maintenance, disappearance, or appearance of coacervate droplets. Systems maintaining coacervates throughout the dehydration process are further evaluated to understand how their compartmentalization properties change with drying. Although added total RNA concentrations increase tenfold, RNA concentration within coacervates remains steady. Exterior RNA concentrations rise, and exchange rates for encapsulated versus free RNAs increase with dehydration. We explain these results in light of the phase diagram, with dehydration-driven ionic strength increase being particularly important in determining coacervate properties. This work shows that wet-dry cycling can alter the phase behavior and protocell-relevant functions of complex coacervates.

Editores de revistas científicas não devem contribuir para politizar a ciência!

segunda-feira, outubro 26, 2020

 Science journal editors shouldn’t contribute to politicizing science

By GENEVIEVE P. KANTER OCTOBER 23, 2020

Source/Fonte: Samuel Corum - Getty Images

When the editors of some of the world’s leading science journals agree on something, it is generally safe to assume that they are correct. So when prominent journals like ScienceNature, and the New England Journal of Medicine recently published editorials excoriating President Trump’s deadly bungling of the pandemic response and suppression of scientific activity, the editors accurately spotlighted the troubling deficiencies of the current administration.























































































But in advocating against or endorsing a presidential candidate, these editors made a grave error. In taking this extraordinary step, they made themselves vulnerable to charges of bias, overstepped their roles as science editors, and succumbed to the politicization of science that they and many other scientists find so alarming.

At first glance, these appear to be similar to run-of-the-mill newspaper endorsements. This analogy, however, is not quite right. At a newspaper, there is a wall between the news operation and the editorial office. It exists to prevent biases of the editorial staff from influencing news reporting. No such wall exists for science journals. The editors who write the editorials are the same ones who evaluate manuscripts and make the final decisions on whether to publish them.

There’s another problem: This political advocacy unnecessarily invites allusions to cronyism, echoing a less savory time when wealthy newspaper owners used their editorial pages to extol the merits of their political chums. Indeed, because of fears surrounding the appearance of undue influence and bias, many newspapers in recent years have abandoned political endorsements.

Read more here: STAT News

Transporte de membranas - elevadores condutores para o interior e exterior das células: mero acaso, fortuita necessidade ou design inteligente?

quinta-feira, outubro 15, 2020

Structural basis for the reaction cycle of DASS dicarboxylate transporters

David B Sauer, Noah Trebesch, Jennifer J Marden, Nicolette Cocco, Jinmei Song, Akiko Koide, Shohei Koide, Emad Tajkhorshid Is a corresponding author, Da-Neng Wang Is a corresponding author

Skirball Institute of Biomolecular Medicine, New York University School of Medicine, United States; Department of Cell Biology, New York University School of Medicine, United States; NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, United States; Perlmutter Cancer Center, New York University School of Medicine, United States; Department of Medicine, New York University School of Medicine, United States; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, United States

Research Article Sep 1, 2020



Abstract

Citrate, α-ketoglutarate and succinate are TCA cycle intermediates that also play essential roles in metabolic signaling and cellular regulation. These di- and tricarboxylates are imported into the cell by the divalent anion sodium symporter (DASS) family of plasma membrane transporters, which contains both cotransporters and exchangers. While DASS proteins transport substrates via an elevator mechanism, to date structures are only available for a single DASS cotransporter protein in a substrate-bound, inward-facing state. We report multiple cryo-EM and X-ray structures in four different states, including three hitherto unseen states, along with molecular dynamics simulations, of both a cotransporter and an exchanger. Comparison of these outward- and inward-facing structures reveal how the transport domain translates and rotates within the framework of the scaffold domain through the transport cycle. Additionally, we propose that DASS transporters ensure substrate coupling by a charge-compensation mechanism, and by structural changes upon substrate release.

FREE PDF GRATIS: eLIFE

Se o Big Bang não foi o começo, foi o que?

terça-feira, setembro 22, 2020

FORBES

Sep 17, 2020,02:00am EDT

If The Big Bang Wasn’t The Beginning, What Was It?

Ethan Siegel Senior Contributor

Starts With A Bang Contributor Group

Science

The Universe is out there, waiting for you to discover it


Our entire cosmic history is theoretically well-understood, but only because we understand the theory of gravitation that underlies it, and because we know the Universe's present expansion rate and energy composition. Light will always continue to propagate through this expanding Universe, and we will continue to receive that light arbitrarily far into the future, but it will be limited in time as far as what reaches us. We still have unanswered questions about our cosmic origins, but the age of the Universe is known. NICOLE RAGER FULLER / NATIONAL SCIENCE FOUNDATION

For more than 50 years, we’ve had definitive scientific evidence that our Universe, as we know it, began with the hot Big Bang. The Universe is expanding, cooling, and full of clumps (like planets, stars, and galaxies) today because it was smaller, hotter, denser, and more uniform in the past. If you extrapolate all the way back to the earliest moments possible, you can imagine that everything we see today was once concentrated into a single point: a singularity, which marks the birth of space and time itself.

At least, we thought that was the story: the Universe was born a finite amount of time ago, and started off with the Big Bang. Today, however, we know a whole lot more than we did back then, and the picture isn’t quite so clear. The Big Bang can no longer be described as the very beginning of the Universe that we know, and the hot Big Bang almost certainly doesn’t equate to the birth of space and time. So, if the Big Bang wasn’t truly the beginning, what was it? Here’s what the science tells us.

Our Universe, as we observe it today, almost certainly emerged from a hot, dense, almost-perfectly uniform state early on. In particular, there are four pieces of evidence that all point to this scenario:

- the Hubble expansion of the Universe, which shows that the amount that light from a distant object is redshifted is proportional to the distance to that object,

- the existence of a leftover glow — the Cosmic Microwave Background (CMB) — in all directions, with the same temperature everywhere just a few degrees above absolute zero,

- light elements — hydrogen, deuterium, helium-3, helium-4, and lithium-7 — that exist in a particular ratio of abundances back before any stars were formed,

- and a cosmic web of structure that gets denser and clumpier, with more space between larger and larger clumps, as time goes on.

FULL TEXT/TEXTO COMPLETO: FORBES

Megalodon, um antigo tubarão extinto de grande dimensão corporal.

segunda-feira, setembro 07, 2020

Body dimensions of the extinct giant shark Otodus megalodon: a 2D reconstruction

Jack A. Cooper, Catalina Pimiento, Humberto G. Ferrón & Michael J. Benton 

Scientific Reports volume 10, Article number: 14596 (2020) 




Abstract

Inferring the size of extinct animals is fraught with danger, especially when they were much larger than their modern relatives. Such extrapolations are particularly risky when allometry is present. The extinct giant shark †Otodus megalodon is known almost exclusively from fossilised teeth. Estimates of †O. megalodon body size have been made from its teeth, using the great white shark (Carcharodon carcharias) as the only modern analogue. This can be problematic as the two species likely belong to different families, and the position of the †Otodus lineage within Lamniformes is unclear. Here, we infer †O. megalodon body dimensions based on anatomical measurements of five ecologically and physiologically similar extant lamniforms: Carcharodon carcharias, Isurus oxyrinchus, Isurus paucus, Lamna ditropis and Lamna nasus. We first assessed for allometry in all analogues using linear regressions and geometric morphometric analyses. Finding no evidence of allometry, we made morphological extrapolations to infer body dimensions of †O. megalodon at different sizes. Our results suggest that a 16 m †O. megalodon likely had a head ~ 4.65 m long, a dorsal fin ~ 1.62 m tall and a tail ~ 3.85 m high. Morphometric analyses further suggest that its dorsal and caudal fins were adapted for swift predatory locomotion and long-swimming periods.

FREE PDF GRATIS: Scientific Reports

A estátua de Darwin vai ser demolida por causa do seu livro racista The Descent of Man???

Natural History Museum to review potentially 'offensive' Charles Darwin collection

An internal review in the wake of the Black Lives Matter protests has led to an audit into some rooms and items


By Craig Simpson

5 September 2020 • 7:00pm

Museum bosses are now desperately seeking to address what some staff believe are “legacies of colonies, slavery and empire” by potentially renaming, relabelling, or removing these traces in the institution.

The executive board told staff in documents seen by The Sunday Telegraph that “in light of Black Lives Matter and the recent anti-racist demonstrations around the world” the museum would undertake a review of existing room names and “whether any statues (or collections) or could potentially cause offence”.One of the institution’s directors said in internal documents that new action taken to address these issues would alter “the use and display of our collections and public spaces”.

Craig Simpson, “Natural History Museum to review potentially ‘offensive’ Charles Darwin collection” at Telegraph

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Nota deste blogger: Eu considero deplorável a derrubada/demolição de estátuas pelo seu valor histórico. Que Darwin era racista, e racista sutil, sempre expus aqui neste blog, apesar de seus outros escritos e defensores contemporâneos dizerem o contrário. A fúria da cultura do cancelamento vai demolir a estátua de Darwin no Museu de História Natural em Londres? É melhor proteger sua estátua ali.

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

sexta-feira, setembro 04, 2020

Journal of Theoretical Biology

Volume 501, 21 September 2020, 110352

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

Steinar Thorvaldsen a Ola Hössjer b

https://doi.org/10.1016/j.jtbi.2020.110352

Under a Creative Commons license Open Access



Highlights

• Statistical methods are appropriate for modelling fine-tuning.

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

• Constants and initial conditions of nature are deliberately tuned.

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

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

Abstract

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

Se não há ancestral comum e nem seleção natural, por que ainda chamamos de evolução?

quinta-feira, setembro 03, 2020

Annals of the New York Academy of Sciences


Patterns and impacts of nonvertical evolution in eukaryotes: a paradigm shift

Toni Gabaldón

First published: 28 August 2020 https://doi.org/10.1111/nyas.14471



Abstract

Evolution of eukaryotic species and their genomes has been traditionally understood as a vertical process in which genetic material is transmitted from parents to offspring along a lineage, and in which genetic exchange is restricted within species boundaries. However, mounting evidence from comparative genomics indicates that this paradigm is often violated. Horizontal gene transfer and mating between diverged lineages blur species boundaries and challenge the reconstruction of evolutionary histories of species and their genomes. Nonvertical evolution might be more restricted in eukaryotes than in prokaryotes, yet it is not negligible and can be common in certain groups. Recognition of such processes brings about the need to incorporate this complexity into our models, as well as to conceptually reframe eukaryotic diversity and evolution. Here, I review the recent work from genomics studies that supports the effects of nonvertical modes of evolution including introgression, hybridization, and horizontal gene transfer in different eukaryotic groups. I then discuss emerging patterns and effects, illustrated by specific examples, that support the conclusion that nonvertical processes are often at the root of important evolutionary transitions and adaptations. I will argue that a paradigm shift is needed to naturally accommodate nonvertical processes in eukaryotic evolution.

Site sobre bioluminescência

quarta-feira, setembro 02, 2020

 Pyrosomes, colonial salps, continue to be one of the most mysterious of bioluminescent organisms. Their glow can last 15 seconds or more, and it can be triggered by light, even cascading from one end of the colony to the other. The chemical origin remains unknown. It was thought to be bacterial, in part because of similar kinetics, but now appears to be intrinsic chemistry that lets this animal emit its impressive glow.

https://biolum.eemb.ucsb.edu 

A ontogenia da nadadeira sarcopterígea elucida a origem das mãos com dedos

quarta-feira, agosto 26, 2020

Sarcopterygian fin ontogeny elucidates the origin of hands with digits

Joost M. Woltering1,*, Iker Irisarri1,†, Rolf Ericsson2,‡, Jean M. P. Joss2, Paolo Sordino3 and Axel Meyer1

Science Advances 19 Aug 2020:

Vol. 6, no. 34, eabc3510



Abstract

How the hand and digits originated from fish fins during the Devonian fin-to-limb transition remains unsolved. Controversy in this conundrum stems from the scarcity of ontogenetic data from extant lobe-finned fishes. We report the patterning of an autopod-like domain by hoxa13 during fin development of the Australian lungfish, the most closely related extant fish relative of tetrapods. Differences from tetrapod limbs include the absence of digit-specific expansion of hoxd13 and hand2 and distal limitation of alx4 and pax9, which potentially evolved through an enhanced response to shh signaling in limbs. These developmental patterns indicate that the digit program originated in postaxial fin radials and later expanded anteriorly inside of a preexisting autopod-like domain during the evolution of limbs. Our findings provide a genetic framework for the transition of fins into limbs that supports the significance of classical models proposing a bending of the tetrapod metapterygial axis.

FREE PDF GRATIS: Science Advances

Introduction to Phylogenetic Networks - David A. Morrison

quinta-feira, agosto 20, 2020

 

Recent advances in rooted phylogenetic networks: the long road to ...

FREE DOWNLOAD GRATIS

Darwin, o problema da forma biológica permanece sem solução, mano!

segunda-feira, agosto 17, 2020

 On the problem of biological form

Marta Linde-Medina 

Theory in Biosciences volume 139, pages299–308(2020)

Ver a imagem de origem

Source/Fonte

Abstract

Embryonic development, which inspired the first theories of biological form, was eventually excluded from the conceptual framework of the Modern Synthesis as irrelevant. A major question during the last decades has centred on understanding whether new advances in developmental biology are compatible with the standard view or whether they compel a new theory. Here, I argue that the answer to this question depends on which concept of morphogenesis is held. Morphogenesis can be conceived as (1) a chemically driven or (2) a mechanically driven process. According to the first option, genetic regulatory networks drive morphogenesis. According to the second, morphogenesis results from an invariant tendency of embryonic tissues to restore changes in mechanical stress. While chemically driven morphogenesis allows an extension of the standard view, mechanically driven morphogenesis would deeply transform it. Which of these hypotheses has wider explanatory power is unknown. At present, the problem of biological form remains unsolved.

Subscription or payment needed/Requer assinatura ou pagamento: Theory in Biosciences

Darwin, modelar a biologia evolutiva na física não funciona, mano!

Historicity at the heart of biology

Maël Montévil 

Theory in Biosciences (2020)


Abstract

Most mathematical modeling in biology relies either implicitly or explicitly on the epistemology of physics. The underlying conception is that the historicity of biological objects would not matter to understand a situation here and now, or, at least, historicity would not impact the method of modeling. We analyze that it is not the case with concrete examples. Historicity forces a conceptual reconfiguration where equations no longer play a central role. We argue that all observations depend on objects defined by their historical origin instead of their relations as in physics. Therefore, we propose that biological variations and historicity come first, and regularities are constraints with limited validity in biology. Their proper theoretical and empirical use requires specific rationales.

Subscription or payment needed/Requer assinatura ou pagamento: Theory in Biosciences

Artigo de 2017 esperava sanar as fissuras/encobrir as rachaduras na biologia evolutiva

Evolutionary Biology volume 45, pages 127–139 (2018)

Hierarchy Theory of Evolution and the Extended Evolutionary Synthesis: Some Epistemic Bridges, Some Conceptual Rifts

Alejandro Fábregas-Tejeda & Francisco Vergara-Silva

Ver a imagem de origem

Abstract: 

Contemporary evolutionary biology comprises a plural landscape of multiple co-existent conceptual frameworks and strenuous voices that disagree on the nature and scope of evolutionary theory. Since the mid-eighties, some of these conceptual frameworks have denounced the ontologies of the Modern Synthesis and of the updated Standard Theory of Evolution as unfinished or even flawed. In this paper, we analyze and compare two of those conceptual frameworks, namely Niles Eldredge’s Hierarchy Theory of Evolution (with its extended ontology of evolutionary entities) and the Extended Evolutionary Synthesis (with its proposal of an extended ontology of evolutionary processes), in an attempt to map some epistemic bridges (e.g. compatible views of causation; niche construction) and some conceptual rifts (e.g. extra-genetic inheritance; different perspectives on macroevolution; contrasting standpoints held in the “externalism–internalism” debate) that exist between them. This paper seeks to encourage theoretical, philosophical and historiographical discussions about pluralism or the possible unification of contemporary evolutionary biology.

Subscription or payment needed/Requer assinatura ou pagamento: Evolutionary Biology

Microscopia revisitada

Revealing architectural order with quantitative label-free imaging and deep learning

Syuan-Ming Guo, Li-Hao Yeh, Jenny Folkesson, Ivan E Ivanov, Anitha P Krishnan, Matthew G Keefe, Ezzat Hashemi, David Shin, Bryant B Chhun, Nathan H Cho, Manuel D Leonetti, May H Han, Tomasz J Nowakowski, Shalin B Mehta 

Chan Zuckerberg Biohub, United States; Department of Anatomy, University of California, San Francisco, United States; Department of Neurology, Stanford University, United States



Abstract

We report quantitative label-free imaging with phase and polarization (QLIPP) for simultaneous measurement of density, anisotropy, and orientation of structures in unlabeled live cells and tissue slices. We combine QLIPP with deep neural networks to predict fluorescence images of diverse cell and tissue structures. QLIPP images reveal anatomical regions and axon tract orientation in prenatal human brain tissue sections that are not visible using brightfield imaging. We report a variant of U-Net architecture, multi-channel 2.5D U-Net, for computationally efficient prediction of fluorescence images in three dimensions and over large fields of view. Further, we develop data normalization methods for accurate prediction of myelin distribution over large brain regions. We show that experimental defects in labeling the human tissue can be rescued with quantitative label-free imaging and neural network model. We anticipate that the proposed method will enable new studies of architectural order at spatial scales ranging from organelles to tissue.

eLife digest

Microscopy is central to biological research and has enabled scientist to study the structure and dynamics of cells and their components within. Often, fluorescent dyes or trackers are used that can be detected under the microscope. However, this procedure can sometimes interfere with the biological processes being studied.

Now, Guo, Yeh, Folkesson et al. have developed a new approach to examine structures within tissues and cells without the need for a fluorescent label. The technique, called QLIPP, uses the phase and polarization of the light passing through the sample to get information about its makeup.

A computational model was used to decode the characteristics of the light and to provide information about the density and orientation of molecules in live cells and brain tissue samples of mice and human. This way, Guo et al. were able to reveal details that conventional microscopy would have missed. Then, a type of machine learning, known as ‘deep learning’, was used to translate the density and orientation images into fluorescence images, which enabled the researchers to predict specific structures in human brain tissue sections.

QLIPP can be added as a module to a microscope and its software is available open source. Guo et al. hope that this approach can be used across many fields of biology, for example, to map the connectivity of nerve cells in the human brain or to identify how cells respond to infection. However, further work in automating other aspects, such as sample preparation and analysis, will be needed to realize the full benefits.

FREE PDF GRATIS: eLife

Mais uma hipótese sobre a origem da vida: surgimento de atividade catalítica em um autorreplicador

terça-feira, agosto 04, 2020

Chance emergence of catalytic activity and promiscuity in a self-replicator

Jim Ottelé, Andreas S. Hussain, Clemens Mayer & Sijbren Otto

Nature Catalysis volume 3, pages547–553(2020)



Abstract

How life can emerge from inanimate matter is one of the grand questions in science. Self-replicating molecules are necessary for the transition from chemistry to biology, but they need to acquire additional functions for life to emerge. Catalysis is one of the most essential of such functionalities, but mechanisms through which self-replicators can acquire catalytic and, in extension, metabolic properties have remained elusive. Here we show how catalytic activity and promiscuity in a self-replicator emerges through co-option: features that are selected to benefit replication inadvertently result in an arrangement of chemical functionalities that is conducive to catalysis. Specifically, we report self-assembly driven self-replicators that promote both a model retro-aldol reaction and the cleavage of fluorenylmethoxycarbonyl groups, with the latter transformation exerting a positive feedback on replication (protometabolism). Such chance invention of new function at the molecular level marks a pivotal step toward the de novo synthesis of life.

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O impacto de Darwin na sociedade em menos de 3 minutos

sexta-feira, julho 31, 2020

<iframe width="560" height="315" src="https://www.youtube.com/embed/HzLkvoj5TTc" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe>

Origem da Vida: o dilema da mão de Deus???

quinta-feira, julho 30, 2020

Prebiotic chemistry and human intervention

Clemens Richert 

Nature Communications

Source/Fonte:

Abstract

Experimentalists in the field of prebiotic chemistry strive to re-enact what may have happened when life arose from inanimate material. How often human intervention was needed to obtain a specific result in their studies is worth reporting.

FREE PDF GRATIS: Nature Communications

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EXCERPT/EXCERTO

Plausibility is important. So, perhaps it is time to think about ways out of the “Hand of God” dilemma.
...
...one may want to state more explicitly what prebiotic scenario a specific experiment is believed to address. This will not solve the “Hand of God dilemma”, but it may allow the reader to gauge what geochemical conditions were assumed when the experiment was planned. 

The Paleobiology Database

sábado, julho 18, 2020

Image/Imagem: By Paleobiology Database - https://paleobiodb.org

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

terça-feira, junho 23, 2020

Journal of Theoretical Biology

Volume 501, 21 September 2020, 110352

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

Authors Steinar Thorvaldsen a Ola Hössjer b

Dep. of Education, University of Tromsø, Norway

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

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




Highlights

• Statistical methods are appropriate for modelling fine-tuning.

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

• Constants and initial conditions of nature are deliberately tuned.

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

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

Abstract

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

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

segunda-feira, junho 15, 2020

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

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



Abstract

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

FREE PDF GRATIS: Biology Letters

Evidência neurocientífica: mente irredutível (Parte 1)

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

sexta-feira, junho 12, 2020

Selective prebiotic formation of RNA pyrimidine and DNA purine nucleosides

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

Nature volume 582, pages60–66(2020)

Article

Published: 03 June 2020

Extended Data Fig. 1
Abstract

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

Subscription or payment needed/Requer assinatura ou pagamento: Nature

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Porque os dados nunca são brutos

sexta-feira, maio 22, 2020

Why Data Is Never Raw 

On the seductive myth of information free of human judgment

Source/Fonte: University of London

Nick Barrowman

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

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

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

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

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