Darwin acertou no varejo e errou por atacado: o que está errado com a biologia evolucionária?

quinta-feira, maio 24, 2018

Biology & Philosophy

March 2017, Volume 32, Issue 2, pp 263–279 | Cite as

What’s wrong with evolutionary biology?

Authors and affiliations

John J. Welch1

Email author

1.Department of GeneticsUniversity of CambridgeCambridgeUK

Open Access Article

First Online: 20 December 2016

Image result for theory of evolution darwin
Source/Fonte: skat

Abstract

There have been periodic claims that evolutionary biology needs urgent reform, and this article tries to account for the volume and persistence of this discontent. It is argued that a few inescapable properties of the field make it prone to criticisms of predictable kinds, whether or not the criticisms have any merit. For example, the variety of living things and the complexity of evolution make it easy to generate data that seem revolutionary (e.g. exceptions to well-established generalizations, or neglected factors in evolution), and lead to disappointment with existing explanatory frameworks (with their high levels of abstraction, and limited predictive power). It is then argued that special discontent stems from misunderstandings and dislike of one well-known but atypical research programme: the study of adaptive function, in the tradition of behavioural ecology. To achieve its goals, this research needs distinct tools, often including imaginary agency, and a partial description of the evolutionary process. This invites mistaken charges of narrowness and oversimplification (which come, not least, from researchers in other subfields), and these chime with anxieties about human agency and overall purpose. The article ends by discussing several ways in which calls to reform evolutionary biology actively hinder progress in the field.

Keywords

Adaptation Extended evolutionary synthesis Neo-Darwinism Inclusive fitness

FREE PDF GRATIS: Biology & Philosophy

Tchau, Darwin: o papel da epigenética na evolução humana

The role of epigenetics in human evolution 

Alexander Osborne

Bioscience Horizons: The International Journal of Student Research, Volume 10, 1 January 2017, hzx007, https://doi.org/10.1093/biohorizons/hzx007

Published: 28 July 2017 Article history

Received: 25 July 2016 Revision Received: 20 June 2017

Accepted: 10 July 2017


Source/Fonte: David Krantz

Abstract

This review aims to highlight the key areas in which changes to the epigenome have played an important role in the evolution and development of our species. Firstly, there will be a brief introduction into the topic of epigenetics to outline the current understanding of the subject and inform the reader of the basic mechanisms and functions of the epigenome. This will lead on to more focussed detail on the role played by epigenetic changes in the rapid evolution of our species and emergence from our ancestor species, as well as the Human Accelerated Regions that played a role in this. The discussion highlights how epigenetics has helped and hindered our species’ development via changes to the epigenome in more modern times, discussing case examples of documented instances where it is shown that epigenetics has played a role in the evolution of humanity.

epigenetics, evolution, human, methylation, HARs, modification

Issue Section: Review Article

FREE PDF GRATIS: Bioscience Horizons

A matemática lança luz sobre como as células vivas "pensam"

quarta-feira, maio 23, 2018

The topological requirements for robust perfect adaptation in networks of any size

Robyn P. Araujo & Lance A. Liotta

Nature Communications volume 9, Article number: 1757 (2018)


Download Citation

Biochemical networks Complexity Modularity Robustness

Received: 28 February 2017 Accepted: 03 April 2018

Published: 01 May 2018


Abstract

Robustness, and the ability to function and thrive amid changing and unfavorable environments, is a fundamental requirement for living systems. Until now it has been an open question how large and complex biological networks can exhibit robust behaviors, such as perfect adaptation to a variable stimulus, since complexity is generally associated with fragility. Here we report that all networks that exhibit robust perfect adaptation (RPA) to a persistent change in stimulus are decomposable into well-defined modules, of which there exist two distinct classes. These two modular classes represent a topological basis for all RPA-capable networks, and generate the full set of topological realizations of the internal model principle for RPA in complex, self-organizing, evolvable bionetworks. This unexpected result supports the notion that evolutionary processes are empowered by simple and scalable modular design principles that promote robust performance no matter how large or complex the underlying networks become.

Acknowledgements

This study was partially supported by NIH grants R33CA206937 and R01AR068436.

Author information

Affiliations

School of Mathematical Sciences, Queensland University of Technology, Brisbane, QLD, 4000, Australia

Robyn P. Araujo

Institute of Health and Biomedical Innovation (IHBI), 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, 4059, Australia

Robyn P. Araujo

Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle, Manassas, Virginia, 20110, USA

Lance A. Liotta

Contributions

R.P.A. conceived of the analytical methodology, and performed all derivations, proofs and computational simulations. R.P.A. and L.A.L. wrote the paper.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Robyn P. Araujo.

Nós devemos exigir evidência no processo de revisão por pares, especialmente nas pesquisas sobre a origem e evolução do universo e da vida!!!


Opinion: We Must Demand Evidence of Peer Review

Peer review varies in quality and thoroughness. Making it publicly available could improve it.

ISTOCK, TEMMUZCAN

By Nikolai Slavov | May 21, 2018

Have you read a paper and thought: “How could peer reviews support the publication of such a paper?” I have. More than once. Other times, I have read fascinating papers outside of my field and wondered what the concerns of the experts who peer reviewed the study were. What important caveats am I missing?




Sometimes, I am lucky and find the answers to such questions: A few publications, including those from EMBO Press and eLife, publish the peer reviews alongside the papers. Reading such peer reviews has provided an additional dimension of appreciating and understanding the experiments and the findings, especially when I am not very familiar with the topic. But for most other journals I cannot access the peer reviews that supported a paper’s publication because most journals hide them. 

How do we know that a journal conducts peer review? For most journals, the evidence is limited to our anecdotal experiences with the manuscripts that we review ourselves or that we and our friends have submitted. For me this evidence is mixed. I know of manuscripts that have been thoughtfully reviewed and manuscripts that have undergone very expedited peer review or no peer review at all before appearing in the most prestigious journals. This anecdotal evidence is rather weak. If you ask me to substantiate it, I have to refer you to a friend who may or may not be willing to tell you that his or her paper was barely peer reviewed. It is a huge problem that the evidence for such a centrally important process is hidden from public view.       
...

READ MORE HERE: The Scientist

A análise mais abrangente já feita dos primeiros fósseis de artrópodes do Período Cambriano: praticamente completo!

terça-feira, maio 22, 2018

Early fossil record of Euarthropoda and the Cambrian Explosion

Allison C. Daley, Jonathan B. Antcliffe, Harriet B. Drage, and Stephen Pates

PNAS May 22, 2018. 115 (21) 5323-5331; published ahead of print May 22, 2018. https://doi.org/10.1073/pnas.1719962115

Reconstruction of the Cambrian predator and stem-lineage euarthropod Anomalocaris canadensis, based on fossils from the Burgess Shale, Canada. Credit: Reconstruction by Natalia Patkiewicz
Source/Fonte: PhysOrg

Abstract

Euarthropoda is one of the best-preserved fossil animal groups and has been the most diverse animal phylum for over 500 million years. Fossil Konservat-Lagerstätten, such as Burgess Shale-type deposits (BSTs), show the evolution of the euarthropod stem lineage during the Cambrian from 518 million years ago (Ma). The stem lineage includes nonbiomineralized groups, such as Radiodonta (e.g., Anomalocaris) that provide insight into the step-by-step construction of euarthropod morphology, including the exoskeleton, biramous limbs, segmentation, and cephalic structures. Trilobites are crown group euarthropods that appear in the fossil record at 521 Ma, before the stem lineage fossils, implying a ghost lineage that needs to be constrained. These constraints come from the trace fossil record, which show the first evidence for total group Euarthropoda (e.g., Cruziana, Rusophycus) at around 537 Ma. A deep Precambrian root to the euarthropod evolutionary lineage is disproven by a comparison of Ediacaran and Cambrian lagerstätten. BSTs from the latest Ediacaran Period (e.g., Miaohe biota, 550 Ma) are abundantly fossiliferous with algae but completely lack animals, which are also missing from other Ediacaran windows, such as phosphate deposits (e.g., Doushantuo, 560 Ma). This constrains the appearance of the euarthropod stem lineage to no older than 550 Ma. While each of the major types of fossil evidence (BSTs, trace fossils, and biomineralized preservation) have their limitations and are incomplete in different ways, when taken together they allow a coherent picture to emerge of the origin and subsequent radiation of total group Euarthropoda during the Cambrian.

paleontology Paleozoic evolution Arthropoda Cambrian explosion

Source: PNAS

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Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao site Portal de Periódicos - CAPES/MEC podem ler gratuitamente este artigo do PNAS e mais 33.000 publicações científicas.

Causa da Explosão Cambriana: terrestre ou cósmica???

segunda-feira, maio 21, 2018

Progress in Biophysics and Molecular Biology

Available online 13 March 2018

In Press, Corrected Proof What are Corrected Proof articles?

Progress in Biophysics and Molecular Biology

Cause of Cambrian Explosion - Terrestrial or Cosmic?

Author Edward J. Steele a j Shirwan Al-Mufti b Kenneth A. Augustyn c Rohana Chandrajith d John P. Coghlan e S. G. Coulson b Sudipto Ghosh f Mark Gillman g Reginald M. Gorczynski h Brig Klyce b Godfrey Louis i Kithsiri Mahanama  j Keith R. Oliver k Julio Padron l Jiangwen Qu m John A. Schuster n W. E. Smith o Duane P. Snyder b…Yongsheng Liu v w


Under a Creative Commons license open access


Source/Fonte: Nature

Abstract

We review the salient evidence consistent with or predicted by the Hoyle-Wickramasinghe (H-W) thesis of Cometary (Cosmic) Biology. Much of this physical and biological evidence is multifactorial. One particular focus are the recent studies which date the emergence of the complex retroviruses of vertebrate lines at or just before the Cambrian Explosion of ∼500 Ma. Such viruses are known to be plausibly associated with major evolutionary genomic processes. We believe this coincidence is not fortuitous but is consistent with a key prediction of H-W theory whereby major extinction-diversification evolutionary boundaries coincide with virus-bearing cometary-bolide bombardment events. A second focus is the remarkable evolution of intelligent complexity (Cephalopods) culminating in the emergence of the Octopus. A third focus concerns the micro-organism fossil evidence contained within meteorites as well as the detection in the upper atmosphere of apparent incoming life-bearing particles from space. In our view the totality of the multifactorial data and critical analyses assembled by Fred Hoyle, Chandra Wickramasinghe and their many colleagues since the 1960s leads to a very plausible conclusion – life may have been seeded here on Earth by life-bearing comets as soon as conditions on Earth allowed it to flourish (about or just before 4.1 Billion years ago); and living organisms such as space-resistant and space-hardy bacteria, viruses, more complex eukaryotic cells, fertilised ova and seeds have been continuously delivered ever since to Earth so being one important driver of further terrestrial evolution which has resulted in considerable genetic diversity and which has led to the emergence of mankind.

Keywords

Cosmic biology Cambrian Explosion Retroviruses Panspermia Hypermutation & evolution Origin epidemics & pandemics

Último artigo de Stephen Hawking: uma saída simples da inflação eterna do universo???

domingo, maio 20, 2018

Journal of High Energy Physics

April 2018, 2018:147 | Cite as

A smooth exit from eternal inflation?

Authors and affiliations

S. W. Hawking 1

Thomas Hertog 2

Email author

1.DAMTP, CMS Cambridge U.K.

2.Institute for Theoretical Physics University of Leuven Leuven Belgium

Open AccessRegular Article - Theoretical Physics

First Online: 27 April 2018

Source/Fonte: Universe Review CA

Abstract

The usual theory of inflation breaks down in eternal inflation. We derive a dual description of eternal inflation in terms of a deformed Euclidean CFT located at the threshold of eternal inflation. The partition function gives the amplitude of different geometries of the threshold surface in the no-boundary state. Its local and global behavior in dual toy models shows that the amplitude is low for surfaces which are not nearly conformal to the round three-sphere and essentially zero for surfaces with negative curvature. Based on this we conjecture that the exit from eternal inflation does not produce an infinite fractal-like multiverse, but is finite and reasonably smooth.

Keywords

AdS-CFT Correspondence Gauge-gravity correspondence Models of Quantum Gravity Spacetime Singularities

Primeira pesquisa anatômica detalhada de bonobos revela e expõe as estórias da carochinha da evolução humana, bipedalismo e uso de ferramentas

REVIEW ARTICLE

Front. Ecol. Evol., 26 April 2018 | https://doi.org/10.3389/fevo.2018.00053

First Detailed Anatomical Study of Bonobos Reveals Intra-Specific Variations and Exposes Just-So Stories of Human Evolution, Bipedalism, and Tool Use

Rui Diogo*

Department of Anatomy, Howard University, Washington, DC, United States

Figure 1. Differences between head muscles of common chimps, bonobos, and humans, based and modified from Diogo et al. (2017b).

Just-so stories are prominent in human evolution literature because of our tendency to create simple progressionist narratives about our “special” place in nature, despite the fact that these stories are almost exclusively based on hard tissue data. How can we be so certain about the evolution of human facial communication, bipedalism, tool use, or speech without detailed knowledge of the internal anatomy of for instance, one of the two extant species more closely related to us, the bonobos? Here I show how many of these stories now become obsolete, after such a comprehensive knowledge on the anatomy of bonobos and other primates is finally put together. Each and every muscle that has been long accepted to be “uniquely human” and to provide “crucial singular functional adaptations” for our bipedalism, tool use and/or vocal/facial communication, is actually present as an intra-specific variant or even as normal phenotype in bonobos and/or other apes.

Just-so stories (Smith, 2016) are frequent in the literature about human evolution because of our tendency to build simple progressionist narratives about our “special” evolutionary history and place in nature (Gould, 1993, 2002). This is particularly striking because these stories are in reality almost exclusively based on hard tissue data. In fact, descriptions of the soft tissues of apes have been relatively scarce and mainly referred to just a few muscles of the head or limbs of a single taxon, in most cases (e.g., Tyson, 1699; Bischoff, 1880; Raven, 1950; Swindler and Wood, 1973; Diogo and Wood, 2011, 2012; Persaud and Loukas, 2014). For instance, the only study that specifically focused on the musculature of bonobos (Pan paniscus) was that of Miller (1952), which was based on dissections of a single adult and did not provide information for numerous head and limb muscles (Diogo and Wood, 2011, 2012). Strikingly, despite this scarcity of information, biologists and anthropologists have displayed a remarkable confidence in their stories about the origin and evolution of human soft tissues, including their phylogenetic distribution and “singular functional adaptations.”

To illustrate this fact, in this short paper I will refer here briefly to seven muscles that have long been generally seen as “unique human features” and linked with specific adaptations for our bipedalism, tool use, and vocal or facial communication. Firstly, the facial expression muscle risorius (Figure 1) has been generally accepted as a unique feature crucial for the evolution of our “gracile” smile and “specially sophisticated” facial communication abilities (Huber, 1931). In a very influential paper, Susman et al. argued—although (fortunately) not as confidently as the assertions done by some of the other authors cited here—that the hand muscle adductor pollicis accessorius (Figure 2; “Henle” or “interosseous volaris primus” muscle: Bello-Hellegouarch et al., 2013) is a unique feature likely related to our increased ability to manufacture and/or use tools (Susman et al., 1999). Similarly, the foot muscle adductor hallucis accessorius—which topologically corresponds to the adductor pollicis accessorius of the hand—is also often considered to be uniquely found in our bipedal species, being at least consistently present at early stages of our ontogenetic development (Cihak, 1972). The foot muscle fibularis tertius (Figure 3) is, according to Lewis' (1989) highly influential monograph on the evolution of our limbs, a unique feature most likely associated with our bipedal evolution (Lewis, 1989). The flexor pollicis longus and extensor pollicis brevis (Figure 2) are forearm muscles that insert onto the thumb and that are generally considered to be unique adaptations for human tool manufacture and use (Lewis, 1989). For instance, it has been experimentally shown that the recruitment to these two muscles allows human subjects to maintain the metacarpophalangeal joint in extension while flexing the distal phalanx of the thumb, i.e., two primary movements usually done when we grab/manipulate objects (Marzke et al., 1998; Williams et al., 2012). Lastly, the laryngeal muscle arytenoideus obliquus has long been considered to be a unique feature of humans—which also have an arytenoideus transversus, in contrast to the single arytenoideus muscle said to occur in all other primates—associated to our enhanced vocal communication (reviewed in Diogo and Wood, 2012).

Usando e navegando a árvore da vida das plantas

Using and navigating the plant tree of life

Douglas E. Soltis Michael J. Moore Emily B. Sessa Stephen A. Smith Pamela S. Soltis

First published: 27 April 2018 https://doi.org/10.1002/ajb2.1071


Image result for plants tree of life
Source/Fonte: One Zoom Tree of Life

Abstract

The “tree of life” has become a metaphor for the interconnectivity and breadth of all life on Earth. It also has come to symbolize the broad investigation of biodiversity, including both the reconstruction of phylogeny and the numerous downstream analyses that are possible with a firm phylogenetic underpinning. Only a few decades ago, the construction of large phylogenetic trees of hundreds of taxa (or more) was considered an impossible task due to the immense computational challenges posed by analyses of large data sets. And no wonder—the number of possible trees that can describe the relationships of just 200 species exceeds the number of atoms in the universe (Hillis, 1996). As a result, building the tree of all named life, including the green plant branch (Viridiplantae)—a major clade with perhaps 500,000 species—has long been considered a grand challenge in biology. However, a perfect storm of algorithm development, increases in computational power, and DNA sequencing improvements over the last decade has not only made the construction of large trees more feasible, but also allowed us to attain some far‐reaching goals—a noteworthy example being the recent publication of a first draft tree of all life (Hinchcliff et al., 2015).

In plant biology, the frequent reconstruction of large phylogenetic trees has had an immense impact on the field. Large trees have helped to resolve deep‐level relationships and resulted in the revision of classifications, including some of the most profound changes in our view of plant relationships over the past 200 years (e.g., reviewed in part by Gitzendanner et al., 2018, in this issue). Large trees have also ushered in a renaissance in the study of conservation, ecology, methods development, crop improvement, genome evolution, and much more. Building the plant tree of life has come to represent the biodiversity equivalent of the human genome project, with numerous and often unanticipated downstream outcomes.

Accompanying these exciting advances are equally significant challenges that remain for the construction of a better and more complete picture of the evolution of plant lineages. In addition to the computational challenges of larger data sets, these include conceptual and methodological barriers. For example, where it was once thought that simply increasing DNA sequence data would increase resolution of relationships, we now understand that increasing data leads to increasing analytical complexity. Furthermore, this complexity is not due solely to limitations in computational power and methodology, but in part reflects the underlying complexity of the evolutionary process and its impact on genomes. Nevertheless, current conceptual and computational limitations present fantastic opportunities for transformative developments in our understanding of plant evolution. In this special issue, we explore many of the uses and challenges of big trees and big data in plant biology. Diverse papers provide overviews of the current status of the green plant tree of life and describe some of the myriad applications of the knowledge of phylogenetic relationships as well as some of the challenges inherent in handling plant phylogenomic data.

FREE PDF GRATIS: American Journal of Botany

Movimento unidirecional em torno de ligações duplas em motores moleculares rotativos: buscando ideias no mero acaso, fortuita necessidade ou no design inteligente?

quinta-feira, maio 03, 2018

Molecular rotary motors: Unidirectional motion around double bonds

Diederik Roke, Sander J. Wezenberg, and Ben L. Feringa

PNAS April 30, 2018. 201712784; published ahead of print April 30, 2018. https://doi.org/10.1073/pnas.1712784115

Edited by J. Fraser Stoddart, Northwestern University, Evanston, IL, and approved April 6, 2018 (received for review January 17, 2018)


Abstract

The field of synthetic molecular machines has quickly evolved in recent years, growing from a fundamental curiosity to a highly active field of chemistry. Many different applications are being explored in areas such as catalysis, self-assembled and nanostructured materials, and molecular electronics. Rotary molecular motors hold great promise for achieving dynamic control of molecular functions as well as for powering nanoscale devices. However, for these motors to reach their full potential, many challenges still need to be addressed. In this paper we focus on the design principles of rotary motors featuring a double-bond axle and discuss the major challenges that are ahead of us. Although great progress has been made, further design improvements, for example in terms of efficiency, energy input, and environmental adaptability, will be crucial to fully exploit the opportunities that these rotary motors offer.

molecular motor alkene molecular machine

FREE PDF GRATIS: PNAS

Insight na remodelagem estrutural do anel FlhA responsável pela exportação de proteína do flagelo bacteriano tipo III

Insight into structural remodeling of the FlhA ring responsible for bacterial flagellar type III protein export

Naoya Terahara1,*, Yumi Inoue1,*, Noriyuki Kodera2, Yusuke V. Morimoto1,3,4, Takayuki Uchihashi2,5,6, Katsumi Imada7, Toshio Ando2,8, Keiichi Namba1,3,† and Tohru Minamino1,†

See all authors and affiliations

Science Advances 25 Apr 2018: Vol. 4, no. 4, eaao7054



Abstract

The bacterial flagellum is a supramolecular motility machine. Flagellar assembly begins with the basal body, followed by the hook and finally the filament. A carboxyl-terminal cytoplasmic domain of FlhA (FlhAC) forms a nonameric ring structure in the flagellar type III protein export apparatus and coordinates flagellar protein export with assembly. However, the mechanism of this process remains unknown. We report that a flexible linker of FlhAC (FlhAL) is required not only for FlhAC ring formation but also for substrate specificity switching of the protein export apparatus from the hook protein to the filament protein upon completion of the hook structure. FlhAL was required for cooperative ring formation of FlhAC. Alanine substitutions of residues involved in FlhAC ring formation interfered with the substrate specificity switching, thereby inhibiting filament assembly at the hook tip. These observations lead us to propose a mechanistic model for export switching involving structural remodeling of FlhAC.

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.

FREE PDF GRATIS: Science Advances

100% teleologia: usando a genômica de única célula para compreender processos de desenvolvimento e as decisões de destino celular

Using single‐cell genomics to understand developmental processes and cell fate decisions

Jonathan A Griffiths Antonio Scialdone John C Marioni

First published: 16 April 2018 https://doi.org/10.15252/msb.20178046


Abstract

High‐throughput ‐omics techniques have revolutionised biology, allowing for thorough and unbiased characterisation of the molecular states of biological systems. However, cellular decision‐making is inherently a unicellular process to which “bulk” ‐omics techniques are poorly suited, as they capture ensemble averages of cell states. Recently developed single‐cell methods bridge this gap, allowing high‐throughput molecular surveys of individual cells. In this review, we cover core concepts of analysis of single‐cell gene expression data and highlight areas of developmental biology where single‐cell techniques have made important contributions. These include understanding of cell‐to‐cell heterogeneity, the tracing of differentiation pathways, quantification of gene expression from specific alleles, and the future directions of cell lineage tracing and spatial gene expression analysis.

FREE PDF GRATIS: Molecular Systems Biology

Esteganografia: reações de multicomponentes fornecem moléculas chaves para comunicação secreta

Multicomponent reactions provide key molecules for secret communication

Andreas C. Boukis, Kevin Reiter, Maximiliane Frölich, Dennis Hofheinz & Michael A. R. Meier

Nature Communications volume 9, Article number: 1439 (2018)


Download Citation

Chemical libraries Information technology

Received: 27 September 2017 Accepted: 13 March 2018

Published online: 12 April 2018


Abstract

A convenient and inherently more secure communication channel for encoding messages via specifically designed molecular keys is introduced by combining advanced encryption standard cryptography with molecular steganography. The necessary molecular keys require large structural diversity, thus suggesting the application of multicomponent reactions. Herein, the Ugi four-component reaction of perfluorinated acids is utilized to establish an exemplary database consisting of 130 commercially available components. Considering all permutations, this combinatorial approach can unambiguously provide 500,000 molecular keys in only one synthetic procedure per key. The molecular keys are transferred nondigitally and concealed by either adsorption onto paper, coffee, tea or sugar as well as by dissolution in a perfume or in blood. Re-isolation and purification from these disguises is simplified by the perfluorinated sidechains of the molecular keys. High resolution tandem mass spectrometry can unequivocally determine the molecular structure and thus the identity of the key for a subsequent decryption of an encoded message.

Acknowledgements

We thank PD Dr. Weiss, T. Neck, and Dr. N. Boukis for the discussions and comments on early versions of this manuscript. A.B. is grateful for the Chemie Fonds fellowship from the VCI. This work was financially supported in part by SFB 1176 (Projects A3 and Q5). We thank Prof. Podlech for sharing lab space with us. We acknowledge support by Deutsche Forschungsgemeinschaft and Open Access Publishing Fund of Karlsruhe Institute of Technology.

Author information

Affiliations

Laboratory of Applied Chemistry, Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Straße am Forum 7, Karlsruhe, 76131, Germany

Andreas C. Boukis, Maximiliane Frölich & Michael A. R. Meier

Institute of Nano Technology (INT), Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen, 76344, Germany

Kevin Reiter

Institute for Theoretical Informatics (ITI), Karlsruhe Institute of Technology (KIT), Am Fasanengarten 5, Karlsruhe, 76131, Germany

Dennis Hofheinz

Contributions

A.B. and M.M. conceived and designed the project. A.B. designed the experiments with input from M.M. K.R. programed the analysis script. M.F. synthesized the molecular keys under the supervision of A.B. D.H. optimized the cryptography integration and programed the molecular encryption script. A.B. analyzed data, prepared the figures and wrote the paper, with feedback from all the authors.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Michael A. R. Meier.





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NOTA DESTE BLOGGER: A esteganografia (em grego significa “escrita oculta). É o estudo de técnicas que permitam esconder informações dentro de outros arquivos, sejam imagens, músicas, vídeos ou mesmo textos. A teoria do Design Inteligente tem na esteganografia um campo fértil de pesquisas.

Atenção guardas-cancelas epistêmicos da Nomenklatura científica: a importância científica da liberdade de expressão!

sexta-feira, abril 27, 2018

Published on April 13, 2018

The Scientific Importance of Free Speech

written by Adam Perkins


Editor’s note: this is a shortened version of a speech that the author was due to give last month at King’s College London which was canceled because the university deemed the event to be too ‘high risk’.

A quick Google search suggests that free speech is a regarded as an important virtue for a functional, enlightened society. For example, according to George Orwell: “If liberty means anything at all, it means the right to tell people what they do not want to hear.” Likewise, Ayaan Hirsi Ali remarked: “Free speech is the bedrock of liberty and a free society, and yes, it includes the right to blaspheme and offend.” In a similar vein, Bill Hicks declared: “Freedom of speech means you support the right of people to say exactly those ideas which you do not agree with”.

But why do we specifically need free speech in science? Surely we just take measurements and publish our data? No chit chat required. We need free speech in science because science is not really about microscopes, or pipettes, or test tubes, or even Large Hadron Colliders. These are merely tools that help us to accomplish a far greater mission, which is to choose between rival narratives, in the vicious, no-holds-barred battle of ideas that we call “science”.

For example, stomach problems such as gastritis and ulcers were historically viewed as the products of stress. This opinion was challenged in the late 1970s by the Australian doctors Robin Warren and Barry Marshall, who suspected that stomach problems were caused by infection with the bacteria Helicobacter pylori. Frustrated by skepticism from the medical establishment and by difficulties publishing his academic papers, in 1984, Barry Marshall appointed himself his own experimental subject and drank a Petri dish full of H. pylori culture. He promptly developed gastritis which was then cured with antibiotics, suggesting that H. pylori has a causal role in this type of illness. You would have thought that given this clear-cut evidence supporting Warren and Marshall’s opinion, their opponents would immediately concede defeat. But scientists are only human and opposition to Warren and Marshall persisted. In the end it was two decades before their crucial work on H. pylori gained the recognition it deserved, with the award of the 2005 Nobel Prize in Physiology or Medicine.

From this episode we can see that even in situations where laboratory experiments can provide clear evidence in favour of a particular scientific opinion, opponents will typically refuse to accept it. Instead scientists tend cling so stubbornly to their pet theories that no amount of evidence will change their minds and only death can bring an end to the argument, as famously observed by Max Planck:

A new scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die, and a new generation grows up that is familiar with it.

It is a salutary lesson that even in a society that permits free speech, Warren and Marshall had difficulty publishing their results. If their opponents had the legal power to silence them their breakthrough would have taken even longer to have become clinically accepted and even more people would have suffered unnecessarily with gastric illness that could have been cured quickly and easily with a course of antibiotics. But scientific domains in which a single experiment can provide a definitive answer are rare. For example, Charles Darwin’s principle of evolution by natural selection concerns slow, large-scale processes that are unsuited to testing in a laboratory. In these cases, we take a bird’s eye view of the facts of the matter and attempt to form an opinion about what they mean.

This allows a lot of room for argument, but as long as both sides are able to speak up, we can at least have a debate: when a researcher disagrees with the findings of an opponent’s study, they traditionally write an open letter to the journal editor critiquing the paper in question and setting out their counter-evidence. Their opponent then writes a rebuttal, with both letters being published in the journal with names attached so that the public can weigh up the opinions of the two parties and decide for themselves whose stance they favour. I recently took part in just such an exchange of letters in the elite journal Trends in Cognitive Sciences. The tone is fierce and neither side changed their opinions, but at least there is a debate that the public can observe and evaluate.

The existence of scientific debate is also crucial because as the Nobel Prize-winning physicist Richard Feynman remarked in 1963: “There is no authority who decides what is a good idea.” The absence of an authority who decides what is a good idea is a key point because it illustrates that science is a messy business and there is no absolute truth. This was articulated in Tom Schofield’s posthumously published essay in which he wrote:

[S]cience is not about finding the truth at all, but about finding better ways of being wrong. The best scientific theory is not the one that reveals the truth — that is impossible. It is the one that explains what we already know about the world in the simplest way possible, and that makes useful predictions about the future. When I accepted that I would always be wrong, and that my favourite theories are inevitably destined to be replaced by other, better, theories — that is when I really knew that I wanted to be a scientist.

When one side of a scientific debate is allowed to silence the other side, this is an impediment to scientific progress because it prevents bad theories being replaced by better theories. Or, even worse, it causes civilization to go backward, such as when a good theory is replaced by a bad theory that it previously displaced. The latter situation is what happened in the most famous illustration of the dire consequences that can occur when one side of a scientific debate is silenced. This occurred in connection with the theory that acquired characteristics are inherited. This idea had been out of fashion for decades, in part due to research in the 1880s by August Weismann. He conducted an experiment that entailed amputating the tails of 68 white mice, over 5 generations. He found that no mice were born without a tail or even with a shorter tail. He stated: “901 young were produced by five generations of artificially mutilated parents, and yet there was not a single example of a rudimentary tail or of any other abnormality in this organ.”

These findings and others like them led to the widespread acceptance of Mendelian genetics. Unfortunately for the people of the USSR, Mendelian genetics are incompatible with socialist ideology and so in the 1930s USSR were replaced with Trofim Lysenko’s socialism-friendly idea that acquired characteristics are inherited. Scientists who disagreed were imprisoned or executed. Soviet agriculture collapsed and millions starved.

Henceforth the tendency to silence scientists with inconvenient opinions has been labeled Lysenkoism since it provides the most famous example of the harm that can be done when competing scientific opinions cannot be expressed equally freely. Left-wingers tend to be the most prominent Lysenkoists but the suppression of scientific opinions can occur in other contexts too. The Space Shuttle Challenger disaster in 1986 is a famous example.
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Evolução molecular: como os blocos construtores da vida podem se formar no espaço

quinta-feira, abril 26, 2018

Glycine formation in CO2:CH4:NH3 ices induced by 0-70 eV electrons featured

The Journal of Chemical Physics 148, 164702 (2018); https://doi.org/10.1063/1.5021596

Sasan Esmaili, Andrew D. Bass, Pierre Cloutier, Léon Sanche, and Michael A. Huelsa)

Affiliations

Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, Quebec J1H5N4, Canada

a)Author to whom correspondence should be addressed: Michael.Huels@usherbrooke.ca and huels@kth.se. Tel.: 1-819-821-8000 (74776).

Source/Fonte: Science Daily

ABSTRACT

Glycine (Gly), the simplest amino-acid building-block of proteins, has been identified on icy dust grains in the interstellar medium, icy comets, and ice covered meteorites. These astrophysical ices contain simple molecules (e.g., CO2, H2O, CH4, HCN, and NH3) and are exposed to complex radiation fields, e.g., UV, γ, or X-rays, stellar/solar wind particles, or cosmic rays. While much current effort is focused on understanding the radiochemistry induced in these ices by high energy radiation, the effects of the abundant secondary low energy electrons (LEEs) it produces have been mostly assumed rather than studied. Here we present the results for the exposure of multilayer CO2:CH4:NH3 ice mixtures to 0-70 eV electrons under simulated astrophysical conditions. Mass selected temperature programmed desorption (TPD) of our electron irradiated films reveals multiple products, most notably intactglycine, which is supported by control measurements of both irradiated or un-irradiated binary mixture films, and un-irradiated CO2:CH4:NH3ices spiked with Gly. The threshold of Gly formation by LEEs is near 9 eV, while the TPD analysis of Gly film growth allows us to determine the “quantum” yield for 70 eV electrons to be about 0.004 Gly per incident electron. Our results show that simple amino acids can be formed directly from simple molecular ingredients, none of which possess preformed C—C or C—N bonds, by the copious secondary LEEs that are generated by ionizing radiation in astrophysical ices.

Inflação cosmológica reproduzida em laboratório?

A Rapidly Expanding Bose-Einstein Condensate: An Expanding Universe in the Lab

S. Eckel, A. Kumar, T. Jacobson, I. B. Spielman, and G. K. Campbell

Phys. Rev. X 8, 021021 – Published 19 April 2018


Source/Fonte: LeCosPa

ABSTRACT

We study the dynamics of a supersonically expanding, ring-shaped Bose-Einstein condensate both experimentally and theoretically. The expansion redshifts long-wavelength excitations, as in an expanding universe. After expansion, energy in the radial mode leads to the production of bulk topological excitations—solitons and vortices—driving the production of a large number of azimuthal phonons and, at late times, causing stochastic persistent currents. These complex nonlinear dynamics, fueled by the energy stored coherently in one mode, are reminiscent of a type of “preheating” that may have taken place at the end of inflation.

Revised 3 February 2018 Received 16 October 2017


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.

Published by the American Physical Society

Physics Subject Headings (PhySH)

Research Areas Acoustic phonons Physical Systems Bose-Einstein condensates Solitons Superfluids Vortices Properties Distances, redshifts, & velocities Gravitation, Cosmology & Astrophysics Atomic, Molecular & Optical 

FREE PDF GRATIS: Phys Rev X

Adaptação estocasticamente bombeada e movimento direcional de máquinas moleculares: mero acaso, fortuita necessidade ou design inteligente?

terça-feira, abril 24, 2018

Stochastically pumped adaptation and directional motion of molecular machines

R. Dean Astumian

PNAS March 9, 2018. 201714498; published ahead of print March 9, 2018. https://doi.org/10.1073/pnas.1714498115

Edited by J. Fraser Stoddart, Northwestern University, Evanston, IL, and approved February 5, 2018 (received for review November 7, 2017)


Abstract

Recent developments in synthetic molecular motors and pumps have sprung from a remarkable confluence of experiment and theory. Synthetic accomplishments have facilitated the ability to design and create molecules, many of them featuring mechanically bonded components, to carry out specific functions in their environment—walking along a polymeric track, unidirectional circling of one ring about another, synthesizing stereoisomers according to an external protocol, or pumping rings onto a long rod-like molecule to form and maintain high-energy, complex, nonequilibrium structures from simpler antecedents. Progress in the theory of nanoscale stochastic thermodynamics, specifically the generalization and extension of the principle of microscopic reversibility to the single-molecule regime, has enhanced the understanding of the design requirements for achieving strong unidirectional motion and high efficiency of these synthetic molecular machines for harnessing energy from external fluctuations to carry out mechanical and/or chemical functions in their environment. A key insight is that the interaction between the fluctuations and the transition state energies plays a central role in determining the steady-state concentrations. Kinetic asymmetry, a requirement for stochastic adaptation, occurs when there is an imbalance in the effect of the fluctuations on the forward and reverse rate constants. Because of strong viscosity, the motions of the machine can be viewed as mechanical equilibrium processes where mechanical resonances are simply impossible but where the probability distributions for the state occupancies and trajectories are very different from those that would be expected at thermodynamic equilibrium.

molecular machinestochastic pumpingkinetic asymmetry

FREE PDF GRATIS: PNAS