Resultados contraditórios: Origens dos principais clades de Archaea não correspondem com aquisição de genes de bactérias

Contradictory Results

Origins of major archaeal clades do not correspond to gene acquisitions from bacteria

Mathieu Groussin, Bastien Boussau, Gergely Szöllősi, Laura Eme, Manolo Gouy, Céline Brochier-Armanet, Vincent Daubin

doi: http://dx.doi.org/10.1101/019851

Abstract

In a recent article, Nelson-Sathi et al. [NS] report that the origins of Major Archaeal Lineages [MAL] correspond to massive group-specific gene acquisitions via horizontal gene transfer (HGT) from bacteria (Nelson-Sathi et al., 2015, Nature 517(7532):77-80). If correct, this would have fundamental implications for the process of diversification in microbes. However, a re-examination of these data and results shows that the methodology used by NS systematically inflates the number of genes acquired at the root of each MAL, and incorrectly assumes bacterial origins for these genes. A re-analysis of their data with appropriate phylogenetic models accounting for the dynamics of gene gain and loss between lineages supports the continuous acquisition of genes over long periods in the evolution of Archaea.

Copyright 

The copyright holder for this preprint is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.

FREE PDF GRATIS: bioRxiv

Sean Carroll fala sobre os níveis da realidade

Edge.org

May 27, 2015

http://www.edge.org

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THE THIRD CULTURE

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LAYERS OF REALITY

A Conversation with Sean Carroll

I've always studied the laws of physics. I've always been curious about how the universe works, where it comes from, what are the rules that govern the behavior of the universe at the deepest level, so I do physics for a living. I study cosmology and the Big Bang and what happened before the Big Bang, if anything. It's a system of things that hooks up in very complicated ways to our human scale lives. There's the natural world that scientists study, and we human beings are part of the natural world.

There's an old creationist myth that says there’s a problem with the fact that we live in a universe governed by the second law of thermodynamics: Disorder, or entropy, grows with time from early times to later times. If that were true, how in the world could it be the case that here on Earth something complicated and organized like human beings came to be? There's a simple response to this, which is that the second law of thermodynamics says that things grow disorderly in closed systems, and the earth is not a closed system. We get energy in a low entropy form from the sun. We radiate it out in a high entropy form to the universe. But okay, there's still a question: even if it's allowed for a structure to form here on Earth, why did it? Why does that happen? Is that something natural? Is that something that needs to be guided or does it just happen?

In some sense this is a physics problem. I've become increasingly interested in how the underlying laws of physics, which are very simple and mindless and just push particles around according to equations, take us from the very simple early universe near the Big Bang after 10 to the 100th years to the expanding, desolate, cold and empty space in our future, passing through the current stage of the history of the universe where things are rich and intricate and complex.

We know there's a law of nature, the second law of thermodynamics, that says that disorderliness grows with time. Is there another law of nature that governs how complexity evolves? One that talks about multiple layers of the structures and how they interact with each other? Embarrassingly enough, we don't even know how to define this problem yet. We don't know the right quantitative description for complexity. This is very early days. This is Copernicus, not even Kepler, much less Galileo or Newton. This is guessing at the ways to think about these problems. …[Continue]

SEAN CARROLL is a research professor at Caltech and the author of THE PARTICLE AT THE END OF THE UNIVERSE, which won the 2013 Royal Society Winton Prize, and FROM ETERNITY TO HERE: THE QUEST FOR THE ULTIMATE THEORY OF TIME. He has recently been awarded a Guggenheim Fellowship, the Gemant Award from the American Institute of Physics, and the Emperor Has No Clothes Award from the Freedom From Religion Foundation. Sean Carroll's EDGE Bio Page

Pesquisa sobre confiança cega em observação não cega em Ecologia, Evolução e Comportamento pede mais rigor científico nas pesquisas

PERSPECTIVE ARTICLE

Front. Ecol. Evol., 19 May 2015 | http://dx.doi.org/10.3389/fevo.2015.00051

Blind trust in unblinded observation in Ecology, Evolution, and Behavior

Melissa R. Kardish1,2*, Ulrich G. Mueller1, Sabrina Amador-Vargas1, Emma I. Dietrich1, Rong Ma1, Brian Barrett1 and Chi-Chun Fang1

1Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA

2Center for Population Biology, University of California, Davis, CA, USA

Mere illustration, not part of the article/Mera ilustração, não faz parte do artigo

ABSTRACT

We surveyed 492 recent studies in the fields of ecology, evolution, and behavior (EEB) to evaluate potential for observer bias and the need for blind experimentation in each study. While 248 articles included experiments that could have been influenced by observer bias, only 13.3% of these articles indicated that experiments were blinded. The use of blind observation therefore was either grossly underreported in the surveyed articles, or many EEB studies were not blinded. We hope that a concerted effort of the field of EEB—including researchers, peer-reviewers, and journal editors—will help promote and institute routine, blind observation as an essential standard that should be practiced by all sciences.

Training in the scientific method emphasizes accurate observation, unbiased experimentation, and objective thinking. Despite this training, much research remains infused with unconscious biases (Rosenthal and Rosnow, 2007; Fanelli, 2010), resulting in wasted effort (i.e., the need to rectify wrong conclusions) and even medical harm (Foster et al., 1975; Hróbjartsson et al., 2012; van Wilgenburg and Elgar, 2013; Kozlov et al., 2014; Tuyttens et al., 2014). It is unclear how much published science is affected by bias and might therefore be false (Ioannidis, 2005; Fanelli, 2012).

Unconscious confirmation bias is a common source of inaccurate observation where observers interpret what they see in a way that supports their expectations or preferred hypotheses. To eliminate confirmation bias, experimenters should blind themselves, for example by concealing any information that could bias observations (e.g., awareness of the hypothesis tested or of the treatment condition of a specific sample). While blinding is routine in medical and psychological research (Burghardt et al., 2012; Hróbjartsson et al., 2012; Begley, 2013), blinding is unfortunately not a universal practice in biology. For example, a survey of kin-recognition studies—a cornerstone of animal behavior—found that 71% of studies testing for kin recognition in ants did not report the use of blind observation, and, more disconcerting, studies that did not report blind observation reported significantly greater effect sizes than studies that reported blinding (van Wilgenburg and Elgar, 2013). Likewise, herbivory of woody plants was rated nearly 500% higher with unblinded methods compared to blinded methods (Kozlov et al., 2014). We here expand on such previous surveys by evaluating the methods of 492 research articles published recently in the general area of ecology, evolution, and behavior (EEB), specifically assessing the use of blind observation and the potential for observer bias to affect results.

For our survey, we selected nine prominent journals publishing in the area of EEB (e.g., Ecology, Evolution, American Naturalist, Animal Behavior) and EEB articles in four general-interest journals (Science, Nature, Proceedings of the National Academy of Sciences, Proceedings of the Royal Society B) (see Supplementary Materials, Appendix A). For each study, we first evaluated whether observations could potentially be influenced by observer bias, then asked whether blind observation was reported in the published methods. Because blinding is sometimes logistically difficult, for studies that did not report blind observation, we also evaluated whether blinding would be (i) easy, (ii) easy with a naïve experimenter, or (iii) difficult to implement. We attempted to evaluate relative importance of blind observation between studies, however, criteria for the importance of blind observation differ between experimental designs and between EEB research areas (see Table S1), and exact methodological details were sometimes difficult to evaluate for readers (a key reason why blinding should be routine to assure readers of unbiased observation). Two readers independently read and scored each article; if scores differed, the readers discussed the respective article in detail to reach a consensus (see Supplementary Materials for detailed protocols). Readers also identified experimental steps where blind observation would reduce any bias and evaluated possible methodologies that could have been used to reduce observer bias. Table S1 summarizes the rationale for scores of each article.

Across all 492 EEB articles surveyed, we judged 50.4% (n = 248) to have potential for observer bias, but only 13.3% (n = 33 of 248) of these articles stated use of blind observation. Some articles explicitly stated the use of blind observation in the methods (n = 24), while others indicated indirectly that experiments had been done blind (n = 9; e.g., use of a naïve experimenter; Figure 1). In the remaining articles (n = 244 of 492), it seemed unlikely that unblinded observation could bias observations, though many studies could easily have been blinded (Figure S1) (Balph and Balph, 1983). Therefore, either the use of blind observation was grossly underreported in the surveyed articles, or many studies were not conducted blind.

FREE PDF GRATIS: Frontiers in Ecology and Evolution

Um site dedicado ao fracasso das predições da teoria da evolução de Darwin

Darwin’s (failed) Predictions – Cornelius G. Hunter – 2015

Excerpt: 

This paper evaluates 23 fundamental (false) predictions of evolutionary theory from a wide range of different categories. The paper begins with a brief introduction to the nature of scientific predictions, and typical concerns evolutionists raise against investigating predictions of evolution. The paper next presents the individual predictions in seven categories: early evolution, evolutionary causes, molecular evolution, common descent, evolutionary phylogenies, evolutionary pathways, and behavior. Finally the conclusion summarizes these various predictions, their implications for evolution’s capacity to explain phenomena,

*Introduction

Why investigate evolution’s false predictions?

Responses to common objections

*Early evolution predictions

The DNA code is not unique

The cell’s fundamental molecules are universal

*Evolutionary causes predictions

Mutations are not adaptive

Embryology and common descent

Competition is greatest between neighbors

*Molecular evolution predictions

Protein evolution

Histone proteins cannot tolerate much change

The molecular clock keeps evolutionary time

*Common descent predictions

The pentadactyl pattern and common descent

Serological tests reveal evolutionary relationships

Biology is not lineage specific

Similar species share similar genes

MicroRNA

*Evolutionary phylogenies predictions

Genomic features are not sporadically distributed

Gene and host phylogenies are congruent

Gene phylogenies are congruent

The species should form an evolutionary tree

*Evolutionary pathways predictions

Complex structures evolved from simpler structures

Structures do not evolve before there is a need for them

Functionally unconstrained DNA is not conserved

Nature does not make leaps

*Behavior

Altruism

Cell death

*Conclusions

What false predictions tell us about evolution

https://sites.google.com/site/darwinspredictions/home

Placas de sinalização de divisão celular para cromossomos ao longo da "rodovia" de microtúbulos: mero acaso, fortuita necessidade ou design inteligente?

Published Online April 23 2015

Science 15 May 2015: 

Vol. 348 no. 6236 pp. 799-803 

DOI: 10.1126/science.aaa5175

REPORT

Microtubule detyrosination guides chromosomes during mitosis

Marin Barisic1,2, Ricardo Silva e Sousa3,*, Suvranta K. Tripathy3,*, Maria M. Magiera4,5,6,*, Anatoly V. Zaytsev3,7,8, Ana L. Pereira1,2, Carsten Janke4,5,6, Ekaterina L. Grishchuk3,†,‡, Helder Maiato1,2,9,†,‡

- Author Affiliations

1Chromosome Instability and Dynamics Laboratory, Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua do Campo Alegre 823, 4150-180 Porto, Portugal.

2Instituto de Investigação e Inovação em Saúde–i3S, Universidade do Porto, Portugal.

3Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

4Institut Curie, 91405 Orsay, France.

5Paris Sciences et Lettres (PSL) Research University, 75005 Paris, France.

6Centre National de la Recherche Scientifique UMR 3348, 91405 Orsay, France.

7Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences (RAS), Moscow, Russia.

8Federal Research and Clinical Centre of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.

9Cell Division Unit, Department of Experimental Biology, Faculdade de Medicina, Universidade do Porto, Alameda Professor Hernâni Monteiro, 4200-319 Porto, Portugal.

↵†Corresponding author. E-mail: maiato@ibmc.up.pt (H.M.); gekate@mail.med.upenn.edu (E.L.G.)

↵* These authors contributed equally to this work.

↵‡ These authors contributed equally to this work.

Source/Fonte: Ekaterina Grishchuk, PhD, Perelman School of Medicine, University of Pennsylvania  

ABSTRACT EDITOR'S SUMMARY

Before chromosomes segregate into daughter cells, they align at the mitotic spindle equator, a process known as chromosome congression. Centromere-associated protein E (CENP-E)/Kinesin-7 is a microtubule plus-end–directed kinetochore motor required for congression of pole-proximal chromosomes. Because the plus-ends of many astral microtubules in the spindle point to the cell cortex, it remains unknown how CENP-E guides pole-proximal chromosomes specifically toward the equator. We found that congression of pole-proximal chromosomes depended on specific posttranslational detyrosination of spindle microtubules that point to the equator. In vitro reconstitution experiments demonstrated that CENP-E–dependent transport was strongly enhanced on detyrosinated microtubules. Blocking tubulin tyrosination in cells caused ubiquitous detyrosination of spindle microtubules, and CENP-E transported chromosomes away from spindle poles in random directions. Thus, CENP-E–driven chromosome congression is guided by microtubule detyrosination.

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PERGUNTA INDISCRETA DESTE BLOGGER:

Mas Darwin não tinha eliminado de vez a teleologia da biologia em 1859??? Como a biologia do século 21, uma ciência de informação, ainda paga tributos e loas a uma hipótese de transmutação que não se corrobora no contexto de justificação teórica? 

Darwinismo: Ciência ou Ideologia???

Darwin e Wallace: associando humanos com ancestrais animais

Going the whole orang: Darwin, Wallace and the natural history of orangutans

John van Wyhe a, 1, , Peter C. Kjærgaard b, c, , 

a Department of Biological Sciences & Fellow of Tembusu College, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore

b Centre for Biocultural History, Aarhus University, Jens Chr. Skous Vej 7, 8000 Aarhus, Denmark

c The Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark

Available online 7 April 2015

Source/Fonte

Abstract

This article surveys the European discovery and early ideas about orangutans followed by the contrasting experiences with these animals of the co-founders of evolution by natural selection, Charles Darwin and Alfred Russel Wallace. The first non-human great ape that both of them interacted with was the orangutan. They were both profoundly influenced by what they saw, but the contexts of their observations could hardly be more different. Darwin met orangutans in the Zoological Gardens in London while Wallace saw them in the wild in Borneo. In different ways these observations helped shape their views of human evolution and humanity’s place in nature. Their findings played a major role in shaping some of the key questions that were pursued in human evolutionary studies during the rest of the nineteenth century.

Keywords

Orangutans; Great apes; Human evolution; Charles Darwin; Alfred Russel Wallace; Anthropology

FREE PDF GRATIS: 

Studies in History and Philosophy of Biological and Biomedical Sciences

Jerry Coyne ‘falou e disse’: a teoria da evolução não serve muito para coisas práticas ou comerciais

“Verdade seja dita, a [teoria da] evolução não tem produzido muitos benefícios práticos ou comerciais. Sim, a bactéria evolui resistência aos medicamentos, e sim, nós devemos tomar medidas defensivas, mas além disso não há muito o que dizer. A [teoria da] evolução não pode nos ajudar a predizer quais novas vacinas a fabricar porque os micróbios evoluem de modo imprevisível. Mas a [teoria da] evolução não ajudou a guiar o melhoramento do cruzamento animal e de plantas? Não muito. A maioria do melhoramento do cruzamento de plantas e animais ocorreu muito antes de nós sabermos qualquer coisa sobre a [teoria da] evolução, e isso veio pelas pessoas que seguiram o princípio genético de que ‘os semelhantes geram semelhantes’. Até hoje, como seus praticantes reconhecem, o campo da genética quantitativa tem sido de pouco valor em ajudar a melhorar as variedades. Os avanços futuros quase que certamente virão dos transgênicos, que não são de jeito nenhum baseados na [teoria da] evolução.” 

Jerry Coyne, "Selling Darwin: Does it matter whether evolution has any commercial applications?," resenhando The Evolving World: Evolution in Everyday Life by David P. Mindell, in Nature, Vol 442:983-984 (31 de agosto de 2006).

“Truth be told, evolution hasn’t yielded many practical or commercial benefits. Yes, bacteria evolve drug resistance, and yes, we must take countermeasures, but beyond that there is not much to say. Evolution cannot help us predict what new vaccines to manufacture because microbes evolve unpredictably. But hasn’t evolution helped guide animal and plant breeding? Not very much. Most improvement in crop plants and animals occurred long before we knew anything about evolution, and came about by people following the genetic principle of ‘like begets like’. Even now, as its practitioners admit, the field of quantitative genetics has been of little value in helping improve varieties. Future advances will almost certainly come from transgenics, which is not based on evolution at all.” 

Jerry Coyne, "Selling Darwin: Does it matter whether evolution has any commercial applications?," reviewing The Evolving World: Evolution in Everyday Life by David P. Mindell, in Nature, Vol 442:983-984 (August 31, 2006).

Subscription or payment needed/Requer assinatura ou pagamento: Nature

Picture source/Fonte da foto

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Calculando a carga mutacional em genomas humanos

Estimating the mutation load in human genomes

Brenna M. Henn, Laura R. Botigué, Carlos D. Bustamante, Andrew G. Clark & Simon Gravel

Affiliations Corresponding author

Nature Reviews Genetics 16, 333–343 (2015) doi:10.1038/nrg3931

Published online 12 May 2015

Abstract

Next-generation sequencing technology has facilitated the discovery of millions of genetic variants in human genomes. A sizeable fraction of these variants are predicted to be deleterious. Here, we review the pattern of deleterious alleles as ascertained in genome sequencing data sets and ask whether human populations differ in their predicted burden of deleterious alleles — a phenomenon known as mutation load. We discuss three demographic models that are predicted to affect mutation load and relate these models to the evidence (or the lack thereof) for variation in the efficacy of purifying selection in diverse human genomes. We also emphasize why accurate estimation of mutation load depends on assumptions regarding the distribution of dominance and selection coefficients — quantities that remain poorly characterized for current genomic data sets.

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Subscription or payment needed: Nature Reviews Genetics

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Os tímpanos de mamíferos, répteis e aves evoluíram independentemente

Developmental genetic bases behind the independent origin of the tympanic membrane in mammals and diapsids

Taro Kitazawa, Masaki Takechi, Tatsuya Hirasawa, Noritaka Adachi, Nicolas Narboux-Nême, Hideaki Kume, Kazuhiro Maeda, Tamami Hirai, Sachiko Miyagawa-Tomita, Yukiko Kurihara, Jiro Hitomi, Giovanni Levi, Shigeru Kuratani & Hiroki Kurihara

AffiliationsContributionsCorresponding author

Nature Communications 6, Article number: 6853 doi:10.1038/ncomms7853

Received 08 November 2014 Accepted 05 March 2015 Published 22 April 2015

Source/Fonte: Sciguru.org

Abstract

The amniote middle ear is a classical example of the evolutionary novelty. Although paleontological evidence supports the view that mammals and diapsids (modern reptiles and birds) independently acquired the middle ear after divergence from their common ancestor, the developmental bases of these transformations remain unknown. Here we show that lower-to-upper jaw transformation induced by inactivation of the Endothelin1-Dlx5/6 cascade involving Goosecoid results in loss of the tympanic membrane in mouse, but causes duplication of the tympanic membrane in chicken. Detailed anatomical analysis indicates that the relative positions of the primary jaw joint and first pharyngeal pouch led to the coupling of tympanic membrane formation with the lower jaw in mammals, but with the upper jaw in diapsids. We propose that differences in connection and release by various pharyngeal skeletal elements resulted in structural diversity, leading to the acquisition of the tympanic membrane in two distinct manners during amniote evolution.

Subject terms: Biological sciences Developmental biology Evolution

FREE PDF GRATIS: Nature Communications

Sup Info

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NOTA CAUSTICANTE DESTE BLOGGER:

E o que fazer daquela série de fósseis de ossos de mandíbulas de répteis que resultaram em ossos internos de ouvidos de mamíferos que argumentavam a favor de uma suposta evolução de mamíferos a partir de ancestrais reptilianos???

Mais uma hipótese de Darwin vai para a lata do lixo da História da Ciência: a hipótese da naturalização

Why Close Relatives Make Bad Neighbors: Phylogenetic Conservatism in Niche Preferences and Dispersal Disproves Darwin's Naturalization Hypothesis in the Thistle Tribe

Daniel S. Park1,* andDaniel Potter2

Author Information

1Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA

2Department of Plant Sciences, University of California, Davis, CA

* Correspondence should be addressed to:

Daniel S. Park

Department of Organismic and Evolutionary Biology, HUH 22 Divinity Ave. Harvard University, Cambridge, MA 02138.

E-mail: danielpark@fas.harvard.edu

Phone: 617-496-1566

This article has been accepted for publication and undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as doi: 10.1111/mec.13227

Keywords:

invasive species;phylogenetics;Cardueae; niche modeling;

dispersal;Darwin's Naturalization Hypothesis; biological invasions; thistles

Source/Fonte

Abstract

The number of exotic plant species that have been introduced into the United States far exceeds that of other groups of organisms, and many of these have become invasive. As in many regions of the globe, invasive members of the thistle tribe, Cardueae, are highly problematic in the California Floristic Province, an established biodiversity hotspot. While Darwin's Naturalization Hypothesis posits that plant invaders closely related to native species would be at a disadvantage, evidence has been found that introduced thistles more closely related to native species are more likely to become invasive. In order to elucidate the mechanisms behind this pattern, we modeled the ecological niches of thistle species present in the Province and compared niche similarity between taxa and their evolutionary relatedness, using fossil calibrated molecular phylogenies of the tribe. The predicted niches of invasive species were found to have higher degrees of overlap with native species than non-invasive introduced species do, and pairwise niche distance was significantly correlated with phylogenetic distance, suggesting phylogenetic niche conservatism. Invasive thistles also displayed superior dispersal capabilities compared to non-invasive introduced species, and these capabilities exhibited a phylogenetic signal. By analyzing the modeled ecological niches and dispersal capabilities of over a hundred thistle species, we demonstrate that exapted preferences to the invaded environment may explain why close exotic relatives may make bad neighbors in the thistle tribe.

This article is protected by copyright. All rights reserved.

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Payment or subscription needed/Requer assinatura ou pagamento: Molecular Ecology In Press

Problemas não resolvidos em biologia - o estado do pensamento atual

Unsolved problems in biology—The state of current thinking

Sukhendu B. Dev, 1, 

Wellcome Unit for the History of Medicine, Oxford University, 45-47 Banbury Rd, Oxford OX2 6PE, England, United Kingdom

Available online 14 February 2015

Abstract

Many outstanding problems have been solved in biology and medicine for which scientists have been awarded prestigious prizes including the Nobel Prize, Lasker Award and Breakthrough Prizes in life sciences. These have been the fruits of years of basic research. From time to time, publications have appeared listing “unsolved” problems in biology. In this article, I ask the question whether it is possible to have such a list, if not a unique one, at least one that is analogous to the Millennium Prize in mathematics. My approach to finding an answer to this question was to gather views of leading biologists. I have also included my own views. Analysis of all the responses received over several years has convinced me that it is difficult, but not impossible, to have such a prize. Biology is complex and very interdisciplinary these days at times involving large numbers of teams, unlike mathematics, where Andrew Wiles spent seven years in complete isolation and secrecy solving Fermat's last theorem. Such an approach is simply not possible in biology. Still I would like to suggest that a similar prize can be established by a panel of distinguished scientists. It would be awarded to those who solved one of the listed problems in biology that warrant a verifiable solution. Despite many different opinions, I found that there is some commonality in the responses I received – I go on to discuss what these are and how they may impact future thinking.

Keywords

Unsolved biological problems; Millennium Prize; Origin of life

FREE PDF GRATIS: Progress in Biophysics and Molecular Biology

Propriedades de assinatura da água: suas origens moleculares eletrônicas: mero acaso, fortuita necessidade ou design inteligente?

Signature properties of water: Their molecular electronic origins

Vlad P. Sokhana,1, Andrew P. Jonesb, Flaviu S. Cipciganb, Jason Craina,b, and Glenn J. Martynab,c
Author Affiliations

aNational Physical Laboratory, Teddington, Middlesex TW11 0LW, United Kingdom;

bSchool of Physics and Astronomy, The University of Edinburgh, Edinburgh EH9 3JZ, United Kingdom; and

cIBM Thomas J. Watson Research Center, Yorktown Heights, NY 10598

Edited by Paul Madden, University of Oxford, Oxford, United Kingdom, and accepted by the Editorial Board March 31, 2015 (received for review October 1, 2014)

Hexagonal-ring structure of proton-ordered ice II. Source/Fonte NPL / University of Edinburgh

Significance

Water is one of the most common substances yet it exhibits anomalous properties important for sustaining life. It has been an enduring challenge to understand how a molecule of such apparent simplicity can encode for complex and unusual behavior across a wide range of pressures and temperatures. We reveal that embedding a complete hierarchy of electronic responses within the molecule allows water’s phase behavior and signature properties to emerge naturally even within a simple model. The key result is a simple and accurate, prediction of liquid–gas phase equilibria from freezing to the critical point thus establishing a direct link between molecular and condensed phase properties and a sound physical basis for a conceptually simple but broadly transferable model for water.

Abstract

Water challenges our fundamental understanding of emergent materials properties from a molecular perspective. It exhibits a uniquely rich phenomenology including dramatic variations in behavior over the wide temperature range of the liquid into water’s crystalline phases and amorphous states. We show that many-body responses arising from water’s electronic structure are essential mechanisms harnessed by the molecule to encode for the distinguishing features of its condensed states. We treat the complete set of these many-body responses nonperturbatively within a coarse-grained electronic structure derived exclusively from single-molecule properties. Such a “strong coupling” approach generates interaction terms of all symmetries to all orders, thereby enabling unique transferability to diverse local environments such as those encountered along the coexistence curve. The symmetries of local motifs that can potentially emerge are not known a priori. Consequently, electronic responses unfiltered by artificial truncation are then required to embody the terms that tip the balance to the correct set of structures. Therefore, our fully responsive molecular model produces, a simple, accurate, and intuitive picture of water’s complexity and its molecular origin, predicting water’s signature physical properties from ice, through liquid–vapor coexistence, to the critical point.

subcritical water intermolecular interactions many-body dispersion coarse-grained model electronic responses

Footnotes

1To whom correspondence should be addressed. Email: vlad.sokhan@npl.co.uk.

Author contributions: V.P.S., J.C., and G.J.M. designed research; V.P.S. and F.S.C. performed research; V.P.S., A.P.J., F.S.C., J.C., and G.J.M. analyzed data; V.P.S., A.P.J., F.S.C., J.C., and G.J.M. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission. P.M. is a guest editor invited by the Editorial Board.

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Construindo o citoesqueleto do microtúbulo peça por peça através de princípios de design

Building the Microtubule Cytoskeleton Piece By Piece

Raymundo Alfaro-Aco and Sabine Petry*

- Author Affiliations

Princeton University, United States

↵* Corresponding author; email: spetry@princeton.edu

Abstract

The microtubule (MT) cytoskeleton gives cells their shape, organizes the cellular interior and segregates chromosomes. These functions rely on the precise arrangement of MTs, which is achieved by the coordinated action of MT associated proteins (MAPs). We highlight the first and most important examples of how different MAP activities are combined in vitro to create an ensemble function that exceeds the simple addition of their individual activities, and how the Xenopus leavis egg extract system has been utilized as a powerful intermediate between cellular and purified systems to uncover the design principles of self-organized MT networks in the cell.

cell division cytoskeleton microtubule microtubule-associated protein (MAP) mitotic spindle

Received January 14, 2015.

Accepted May 8, 2015.

Copyright © 2015, The American Society for Biochemistry and Molecular Biology

FREE PDF GRATIS: Journal of Biological Chemistry

Darwin feliz da vida: este site tem mais de 831.000 visitantes nos 5 continentes

Vide: ClustrMaps

Darwin feliz da vida com este blogger: 831.102 visitas 08/05/2015 às 19:05:00 e nos cinco continentes! O bom é que 11 entre 10 darwinistas visitam este blog para ficarem à par da falência fragorosa da teoria da evolução de Darwin através da seleção natural e n mecanismos evolucionários de A a Z (vai que um falhe...) no contexto de justificação teórica. Eles nem precisavam vir aqui, pois as publicações e pesquisas científicas que aqui menciono são encontradas no site CAPES/Periódicos.

Estrategicamente a Nomenklatura científica está em silêncio obsequioso, pois sabe que vem aí uma nova teoria geral da evolução, que não será selecionista e deve incorporar alguns aspectos teóricos neolamarckistas - a SÍNTESE EVOLUTIVA AMPLIADA/ESTENDIDA, mas deverá ser anunciada somente em 2020.

Aprendi na universidade que a ciência abomina o vazio epistemológico. Ora, se a SÍNTESE EVOLUTIVA MODERNA faliu fragorosamente no século 20 e começo do século 21, sob qual referencial teórico estão fazendo ciência evolucionária? Abracadabra? Leitura de mãos? Tarô? Entranhas de animais? Sonhos?

Fui, nem sei por que, rindo da cara de alguns cientistas da Nomenklatura científica de da maioria da Galera de meninos e meninas de Darwin que disseram que este blogger estava equivocado sobre a robustez epistêmica da maior ideia científica que toda a humanidade já teve, tão cientificamente comprovada como a lei da gravidade, assim como a Terra é redonda e gira em torno do Sol e não é o centro do universo. Retórica intimidante, mas vazia, pois o que vale em ciência são as evidências, e aqui neste quesito científico Darwin saí de mãos vazias desde 1859.

Que venga la nueva teoría de la evolución... 2020 está bem ali!!! 

O problema do cientificismo - Philip Kitcher

May 4, 2012

The Trouble with Scientism

Why history and the humanities are also a form of knowledge

By Philip Kitcher

There are two cathedrals in Coventry. The newer one, consecrated on May 25, 1962, stands beside the remains of the older one, which dates from the fourteenth century, a ruin testifying to the bombardment of the Blitz. Three years before the consecration, in one of the earliest ventures in the twinning of towns, Coventry had paired itself with Dresden. That gesture of reconciliation was recapitulated in 1962, when Benjamin Britten’s War Requiem received its first performance at the ceremony. The three soloists were an English tenor (Peter Pears), a German baritone (Dietrich Fischer-Dieskau), and a Russian soprano (Heather Harper).

Since the 1960s, historians have worked—and debated—to bring into focus the events of the night of February 13, 1945, in which an Allied bombing attack devastated the strategically irrelevant city of Dresden. An increased understanding of the decisions that led to the fire-bombing, and of the composition of the Dresden population that suffered the consequences, have altered subsequent judgments about the conduct of war. The critical light of history has been reflected in the contributions of novelists and critics, and of theorists of human rights. Social and political changes, in other words, followed the results of humanistic inquiry, and were intertwined with the reconciliatory efforts of the citizens of Coventry and Dresden. Even music and poetry played roles in this process: what history has taught us is reinforced by the lines from Wilfred Owen that Britten chose as the epigraph for his score—“My subject is war, and the pity of war. The poetry is in the pity. All a poet can do today is warn.” It is so easy to underrate the impact of the humanities and of the arts. Too many people, some of whom should know better, do it all the time. But understanding why the natural sciences are regarded as the gold standard for human knowledge is not hard. When molecular biologists are able to insert fragments of DNA into bacteria and turn the organisms into factories for churning out medically valuable substances, and when fundamental physics can predict the results of experiments with a precision comparable to measuring the distance across North America to within the thickness of a human hair, their achievements compel respect, and even awe. To derive one’s notion of human knowledge from the most striking accomplishments of the natural sciences easily generates a conviction that other forms of inquiry simply do not measure up. Their accomplishments can come to seem inferior, even worthless, at least until the day when these domains are absorbed within the scope of “real science.”

The conflict between the Naturwissenschaften and the Geisteswissenschaften goes back at least two centuries, and became intensified as ambitious, sometimes impatient researchers proposed to introduce natural scientific concepts and methods into the study of human psychology and human social behavior. Their efforts, and the attitudes of unconcealed disdain that often inspired them, prompted a reaction, from Vico to Dilthey and into our own time: the insistence that some questions are beyond the scope of natural scientific inquiry, too large, too complex, too imprecise, and too important to be addressed by blundering over-simplifications. From the nineteenth-century ventures in mechanistic psychology to contemporary attempts to introduce evolutionary concepts into the social sciences, “scientism” has been criticized for its “mutilation” (Verstümmelung, in Dilthey’s memorable term) of the phenomena to be explained.

The problem with scientism—which is of course not the same thing as science—is owed to a number of sources, and they deserve critical scrutiny. The enthusiasm for natural scientific imperialism rests on five observations. First, there is the sense that the humanities and social sciences are doomed to deliver a seemingly directionless sequence of theories and explanations, with no promise of additive progress. Second, there is the contrasting record of extraordinary success in some areas of natural science. Third, there is the explicit articulation of technique and method in the natural sciences, which fosters the conviction that natural scientists are able to acquire and combine evidence in particularly rigorous ways. Fourth, there is the perception that humanists and social scientists are only able to reason cogently when they confine themselves to conclusions of limited generality: insofar as they aim at significant—general—conclusions, their methods and their evidence are unrigorous. Finally, there is the commonplace perception that the humanities and social sciences have been dominated, for long periods of their histories, by spectacularly false theories, grand doctrines that enjoy enormous popularity until fashion changes, as their glaring shortcomings are disclosed.

These familiar observations have the unfortunate effect of transforming differences of degree into differences of kind, as enthusiasts for the alleged superiority of natural science readily succumb to stereotypes and over-generalizations, without regard for more subtle explanations. Let us consider the five foundations of this mistake in order.

The most obvious explanation for the difficulties of the Geisteswissenschaften, the humanities and the study of history and society, is that they deal with highly complex systems. Concrete results are often achieved in particular instances: historians and anthropologists are able to be precise and accurate by sacrificing generality, by clear-headedly disavowing the attempt to provide any grand overarching theory. No large vision of history emerges from our clearer understanding of the bombing of Dresden, but the details are no less powerful and significant. In this respect, moreover, matters are no different in the natural sciences. As we shall see, science often forgoes generality to achieve a precise and accurate answer to an important question.

In English we speak about science in the singular, but both French and German wisely retain the plural. The enterprises that we lump together are remarkably various in their methods, and also in the extent of their successes. The achievements of molecular engineering or of measurements derived from quantum theory do not hold across all of biology, or chemistry, or even physics. Geophysicists struggle to arrive at precise predictions of the risks of earthquakes in particular localities and regions. The difficulties of intervention and prediction are even more vivid in the case of contemporary climate science: although it should be uncontroversial that the Earth’s mean temperature is increasing, and that the warming trend is caused by human activities, and that a lower bound for the rise in temperature by 2200 (even if immediate action is taken) is two degrees Celsius, and that the frequency of extreme weather events will continue to rise, climatology can still issue no accurate predictions about the full range of effects on the various regions of the world. Numerous factors influence the interaction of the modifications of climate with patterns of wind and weather, and this complicates enormously the prediction of which regions will suffer drought, which agricultural sites will be disrupted, what new patterns of disease transmission will emerge, and a lot of other potential consequences about which we might want advance knowledge. (The most successful sciences are those lucky enough to study systems that are relatively simple and orderly. James Clerk Maxwell rightly commented that Galileo would not have redirected the physics of motion if he had begun with turbulence rather than with free fall in a vacuum.)

The emphasis on generality inspires scientific imperialism, conjuring a vision of a completely unified future science, encapsulated in a “theory of everything.” Organisms are aggregates of cells, cells are dynamic molecular systems, the molecules are composed of atoms, which in their turn decompose into fermions and bosons (or maybe into quarks or even strings). From these facts it is tempting to infer that all phenomena—including human actions and interaction—can “in principle” be understood ultimately in the language of physics, although for the moment we might settle for biology or neuroscience. This is a great temptation. We should resist it. Even if a process is constituted by the movements of a large number of constituent parts, this does not mean that it can be adequately explained by tracing those motions.

A tale from the history of human biology brings out the point. John Arbuthnot, an eighteenth-century British physician, noted a fact that greatly surprised him. Studying the registry of births in London between 1629 and 1710, he found that all of the years he reviewed showed a preponderance of male births: in his terms, each year was a “male year.” If you were a mad devotee of mechanistic analysis, you might think of explaining this—“in principle”—by tracing the motions of individual cells, first sperm and eggs, then parts of growing embryos, and showing how the maleness of each year was produced. But there is a better explanation, one that shows the record to be no accident. Evolutionary theory predicts that for many, but not all, species, the equilibrium sex-ratio will be 1:1 at sexual maturity. If it deviates, natural selection will favor the underrepresented sex: if boys are less common, invest in sons and you are likely to have more grandchildren. This means that if one sex is more likely to die before reaching reproductive age, more of that sex will have to be produced to start with. Since human males are the weaker sex—that is, they are more likely to die between birth and puberty—reproduction is biased in their favor.

The idea of a “theory of everything” is an absurd fantasy. Successful sciences are collections of models of different types of phenomena within their domains. The lucky ones can generate models that meet three desiderata: they are general, they are precise, they are accurate. Lots of sciences, natural sciences, are not so fortunate. As the ecologist Richard Levins pointed out decades ago, in many areas of biology—and, he might have added, in parts of physics, chemistry, and earth and atmospheric science as well—the good news is that you can satisfy any two of these desiderata, but at the cost of sacrificing the third. Contemporary climatology often settles for generality and accuracy without precision; ecologists focusing on particular species provide precise and accurate models that prove hard to generalize; and of course if you abandon accuracy, precision and generality are no problem at all.

...

Read more here/Leia mais aqui: New Republic

Uma nova teoria unificada de evolução: novo conceito neolamarckista pode facilitar a evolução neodarwinista

Environmental Epigenetics and a Unified Theory of the Molecular Aspects of Evolution: A Neo-Lamarckian Concept that Facilitates Neo-Darwinian Evolution

Michael K. Skinner

- Author Affiliations

Center for Reproductive Biology, School of Biological Sciences, Washington State University Pullman, WA, 99164-4236, USA

Correspondence: Michael K. Skinner, Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, Phone: 509-335-1524, Fax: 509-335-2176, Email: skinner@wsu.edu

Received December 29, 2014.

Revision received February 13, 2015.

Revision received March 10, 2015.

Accepted April 17, 2015.

Abstract

Environment has a critical role in the natural selection process for Darwinian evolution. The primary molecular component currently considered for neo-Darwinian evolution involves genetic alterations and random mutations that generate the phenotypic variation required for natural selection to act. The vast majority of environmental factors can not directly alter DNA sequence. Epigenetic mechanisms directly regulate genetic processes and can be dramatically altered by environmental factors. Therefore, environmental epigenetics provides a molecular mechanism to directly alter phenotypic variation generationally. Lamarck proposed in 1802 the concept that environment can directly alter phenotype in a heritable manner. Environmental epigenetics and epigenetic transgenerational inheritance provide molecular mechanisms for this process. Therefore, environment can on a molecular level influence the phenotypic variation directly. The ability of environmental epigenetics to alter phenotypic and genotypic variation directly can significantly impact natural selection. This neo-Lamarckian concept can facilitate neo-Darwinian evolution. A unified theory of evolution is presented to describe the integration of environmental epigenetic and genetic aspects of evolution.

Key words

Epigenetics Lamarck Darwin Natural Selection Environment Review

© The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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NOTA DESTE BLOGGER:

Quando afirmei em 1998 que a teoria da evolução de Darwin através da seleção e n mecanismos evolucionários (de A a Z, vai que um falhe...) e que estávamos diante de uma iminente mudança paradigmática em biologia evolucionária, alguns cientistas da Nomenklatura científica e a Galera dos meninos e meninas de Darwin não me levaram a sério, tentaram me demonizar e desqualificar no debate sobre a robustez epistêmica da Síntese Evolutiva Moderna no contexto de justificação teórica.

Não há nenhuma crise com a teoria da evolução, diziam esses sentinelas de Darwin. A teoria da evolução é a teoria científica mais comprovada assim como a lei da gravidade, assim como a Terra é redonda e gira em torno do Sol, e não está no centro do universo, y otras cositas mais.

Em ciência, nada como um dia atrás do outro. Eu estou radiante, pois mais uma vez um evolucionista honesto me reivindica ao propor soluções neolamarckistas para livrar a cara de Darwin - sua teoria não fecha as contas no contexto de justificação teórica desde 1859.

Lamarck redivivus vai ressuscitar Darwin???

Fui, nem sei por que, rindo da cara desses guardas-cancelas darwinistas!!!

Morcegos têm pelos sensoriais nas asas

Somatosensory Substrates of Flight Control in Bats

Kara L. Marshall1, Mohit Chadha2, 3, Laura A. deSouza4, Susanne J. Sterbing-D’Angelo5, 6, Cynthia F. Moss2, 3, 5, 6, , , Ellen A. Lumpkin1, 4, , 

1 Departments of Dermatology and Physiology and Cellular Biophysics, Columbia University, New York, NY 10032, USA

2 Program in Neuroscience and Cognitive Science, University of Maryland, College Park, MD 20742, USA

3 Department of Psychology, University of Maryland, College Park, MD 20742, USA

4 Program in Neurobiology and Behavior, Columbia University, New York, NY 10032, USA

5 Institute for Systems Research, University of Maryland, College Park, MD 20742, USA

Received 8 December 2014, Revised 11 March 2015, Accepted 29 March 2015, 

Available online 30 April 2015

Published: April 30, 2015

Highlights

• Segmental organization of wing innervation differs from known vertebrate forelimbs

• The bat wing has an atypical dermatome map that can be explained by its ontogeny

• Bat wings are equipped with an unusual repertoire of somatosensory receptors

• Sparse cortical coding represents inputs from biological airflow and touch sensors

Summary

Flight maneuvers require rapid sensory integration to generate adaptive motor output. Bats achieve remarkable agility with modified forelimbs that serve as airfoils while retaining capacity for object manipulation. Wing sensory inputs provide behaviorally relevant information to guide flight; however, components of wing sensory-motor circuits have not been analyzed. Here, we elucidate the organization of wing innervation in an insectivore, the big brown bat, Eptesicus fuscus. We demonstrate that wing sensory innervation differs from other vertebrate forelimbs, revealing a peripheral basis for the atypical topographic organization reported for bat somatosensory nuclei. Furthermore, the wing is innervated by an unusual complement of sensory neurons poised to report airflow and touch. Finally, we report that cortical neurons encode tactile and airflow inputs with sparse activity patterns. Together, our findings identify neural substrates of somatosensation in the bat wing and imply that evolutionary pressures giving rise to mammalian flight led to unusual sensorimotor projections.

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