Empacotando um genoma passo a passo: mero acaso, fortuita necessidade ou design inteligente?

domingo, janeiro 21, 2018

A pathway for mitotic chromosome formation
Johan H. Gibcus1,*, Kumiko Samejima2,*, Anton Goloborodko3,*, Itaru Samejima2, Natalia Naumova1, Johannes Nuebler3, Masato T. Kanemaki4, Linfeng Xie5, James R. Paulson5, William C. Earnshaw2,†, Leonid A. Mirny3,†, Job Dekker1,6,†
1Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
2Wellcome Centre for Cell Biology University of Edinburgh, King’s Buildings, Max Born Crescent Edinburgh EH9 3BF, Scotland, UK.
3Institute for Medical Engineering and Science, and Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
4Division of Molecular Cell Engineering, National Institute of Genetics, Research Organization of Information and Systems (ROIS), and Department of Genetics, SOKENDAI, Yata 1111, Mishima, Shizuoka 411-8540, Japan.
5Department of Chemistry, University of Wisconsin-Oshkosh, 800 Algoma Blvd, Oshkosh, WI 54901, USA.
6Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815-6789, USA.
Corresponding author. Email: bill.earnshaw@ed.ac.uk (W.C.E.); leonid@MIT.edu (L.A.M.); job.dekker@umassmed.edu (J.D.)
* These authors contributed equally to this work.
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Science  18 Jan 2018:
eaao6135
Source/Fonte: Anton Goloborodko

Abstract
Mitotic chromosomes fold as compact arrays of chromatin loops. To identify the pathway of mitotic chromosome formation, we combined imaging and Hi-C of synchronous DT40 cell cultures with polymer simulations. We show that in prophase, the interphase organization is rapidly lost in a condensin-dependent manner and arrays of consecutive 60 kb loops are formed. During prometaphase ~80 kb inner loops are nested within ~400 kb outer loops. The loop array acquires a helical arrangement with consecutive loops emanating from a central spiral-staircase condensin scaffold. The size of helical turns progressively increases during prometaphase to ~12 Mb. Acute depletion of condensin I or II shows that nested loops form by differential action of the two condensins while condensin II is required for helical winding.
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Origem da vida: a emergência espontânea de auto replicação em sistemas de reação química

Spontaneous emergence of self-replication in chemical reaction systems

Source/Fonte: Ruhr-Universität Bochum
Explaining the origin of life requires us to explain how self-replication arises. To be specific, how can a self-replicating entity develop spontaneously from a chemical reaction system in which no reaction is self-replicating? Previously proposed mathematical models either supply an explicit framework for a minimal living system or only consider catalyzed reactions, and thus fail to provide a comprehensive theory. We set up a general model for chemical reaction systems that properly accounts for energetics, kinetics and the conservation law. We find that (1) some systems are collectively-catalytic where reactants are transformed into end products with the assistance of intermediates (as in the citric acid cycle), while some others are self-replicating where different parts replicate each other and the system self-replicates as a whole (as in the formose reaction); (2) many alternative chemical universes often contain one or more such systems; (3) it is possible to construct a self-replicating system where the entropy of some parts spontaneously decreases, in a manner similar to that discussed by Schrodinger; (4) complex self-replicating molecules can emerge spontaneously and relatively easily from simple chemical reaction systems through a sequence of transitions. Together these results start to explain the origins of prebiotic evolution.
Comments: Supplementary Information (SI) attached. To view SI, please download and extract the zipped file listed under "Other formats"
Subjects: Adaptation and Self-Organizing Systems (nlin.AO); Molecular Networks (q-bio.MN)
Cite as: arXiv:1801.05872 [nlin.AO]
(or arXiv:1801.05872v1 [nlin.AO] for this version)

Submission history

From: Yu Liu [view email]
[v1] Wed, 17 Jan 2018 22:02:44 GMT (712kb,A)


FREE PDF GRATIS: ArXiv

Da genética forense à genômica forense - ampliando a inteligência investigativa do DNA - design inteligente em ação

quinta-feira, janeiro 18, 2018

From forensic epigenetics to forensic epigenomics: broadening DNA investigative intelligence

Athina Vidaki and Manfred Kayser

Genome Biology201718:238


Published: 21 December 2017


Abstract

Human genetic variation is a major resource in forensics, but does not allow all forensically relevant questions to be answered. Some questions may instead be addressable via epigenomics, as the epigenome acts as an interphase between the fixed genome and the dynamic environment. We envision future forensic applications of DNA methylation analysis that will broaden DNA-based forensic intelligence. Together with genetic prediction of appearance and biogeographic ancestry, epigenomic lifestyle prediction is expected to increase the ability of police to find unknown perpetrators of crime who are not identifiable using current forensic DNA profiling.

FREE PDF GRATIS: Genome Biology

Desligamento oficial da SBDI - Sociedade Brasileira do Design Inteligente

quarta-feira, janeiro 17, 2018

Embora meu nome ainda conste lá como membro da SBDI - Sociedade Brasileira do Design Inteligente, desde hoje 17 de janeiro de 2018, por razões estritamente pessoais, não faço mais parte dessa organização. Não pude acessar meus dados com a senha a mim conferida para fazer o devido desligamento. Espero que o responsável pela lista delete minha página. Foram 20 anos de labuta em prol da divulgação da Teoria do Design Inteligente, defendendo sua cientificidade e esclarecendo que ela não é criacionismo científico ou religioso. Continuarei defendendo e propondo a TDI qua ciência por aqui e em outras instâncias!

A estrutura líquida da elastina: mero acaso, fortuita necessidade ou design inteligente?

sábado, janeiro 13, 2018

The liquid structure of elastin

Sarah Rauscher, Régis Pomès

The Hospital for Sick Children, Canada University of Toronto, Canada

RESEARCH ARTICLE Nov 9, 2017

Peptide hydration in the liquid-like aggregate.

Abstract

The protein elastin imparts extensibility, elastic recoil, and resilience to tissues including arterial walls, skin, lung alveoli, and the uterus. Elastin and elastin-like peptides are hydrophobic, disordered, and undergo liquid-liquid phase separation upon self-assembly. Despite extensive study, the structure of elastin remains controversial. We use molecular dynamics simulations on a massive scale to elucidate the structural ensemble of aggregated elastin-like peptides. Consistent with the entropic nature of elastic recoil, the aggregated state is stabilized by the hydrophobic effect. However, self-assembly does not entail formation of a hydrophobic core. The polypeptide backbone forms transient, sparse hydrogen-bonded turns and remains significantly hydrated even as self-assembly triples the extent of non-polar side chain contacts. Individual chains in the assembly approach a maximally-disordered, melt-like state which may be called the liquid state of proteins. These findings resolve long-standing controversies regarding elastin structure and function and afford insight into the phase separation of disordered proteins.

https://doi.org/10.7554/eLife.26526.001

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A mobilidade da cinesina é conduzida por dinâmicas de sub regiões: mero acaso, fortuita necessidade ou design inteligente?

Kinesin motility is driven by subdomain dynamics

Wonmuk Hwang, Matthew J Lang, Martin Karplus

Texas A&M University, United States Korea Institute for Advanced Study, Korea Vanderbilt University, United States Vanderbilt University School of Medicine, United States Harvard University, United States ISIS, Université de Strasbourg, France

RESEARCH ARTICLE Nov 7, 2017

Motility of a Kin-1 dimer driven by subdomain dynamics.

Abstract

The microtubule (MT)-associated motor protein kinesin utilizes its conserved ATPase head to achieve diverse motility characteristics. Despite considerable knowledge about how its ATPase activity and MT binding are coupled to the motility cycle, the atomic mechanism of the core events remain to be found. To obtain insights into the mechanism, we performed 38.5 microseconds of all-atom molecular dynamics simulations of kinesin-MT complexes in different nucleotide states. Local subdomain dynamics were found to be essential for nucleotide processing. Catalytic water molecules are dynamically organized by the switch domains of the nucleotide binding pocket while ATP is torsionally strained. Hydrolysis products are 'pulled' by switch-I, and a new ATP is 'captured' by a concerted motion of the α0/L5/switch-I trio. The dynamic and wet kinesin-MT interface is tuned for rapid interactions while maintaining specificity. The proposed mechanism provides the flexibility necessary for walking in the crowded cellular environment.

https://doi.org/10.7554/eLife.28948.001

eLife digest

Motor proteins called kinesins perform a number of different roles inside cells, including transporting cargo and organizing filaments called microtubules to generate the force needed for a cell to divide. Kinesins move along the microtubules, with different kinesins moving in different ways: some ‘walk’, some jump, and some destroy the microtubule as they travel along it. All kinesins power their movements using the same molecule as fuel – adenosine triphosphate, known as ATP for short.

Energy stored in ATP is released by a chemical reaction known as hydrolysis, which uses water to break off specific parts of the ATP molecule. The site to which ATP binds in a kinesin has a similar structure to the ATP binding site of many other proteins that use ATP. However, little was known about the way in which kinesin uses ATP as a fuel, including how ATP binds to kinesin and is hydrolyzed, and how the products of hydrolysis are released. These events are used to power the motor protein.

Hwang et al. have used powerful computer simulation methods to examine in detail how ATP interacts with kinesin whilst moving across a microtubule. The simulations suggest that regions (or 'domains') of kinesin near the ATP binding site move around to help in processing ATP. These kinesin domains trap a nearby ATP molecule from the environment and help to deliver water molecules to ATP for hydrolysis. Hwang et al. also found that the domain motion subsequently helps in the release of the hydrolysis products by kinesin.

The domains around the ATP pocket vary among the kinesins and these differences may enable kinesins to fine-tune how they use ATP to move. Further investigations will help us understand why different kinesin families behave differently. They will also contribute to exploring how kinesin inhibitors might be used as anti-cancer drugs.

https://doi.org/10.7554/eLife.28948.002

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Redução de genoma, novidade fisiológica, e a dominância global das plantas com flores

sexta-feira, janeiro 12, 2018

Genome downsizing, physiological novelty, and the global dominance of flowering plants

Kevin A. Simonin , Adam B. Roddy 

Published: January 11, 2018https://doi.org/10.1371/journal.pbio.2003706

Source/Font: Casa de Sobra

Abstract

The abrupt origin and rapid diversification of the flowering plants during the Cretaceous has long been considered an “abominable mystery.” While the cause of their high diversity has been attributed largely to coevolution with pollinators and herbivores, their ability to outcompete the previously dominant ferns and gymnosperms has been the subject of many hypotheses. Common among these is that the angiosperms alone developed leaves with smaller, more numerous stomata and more highly branching venation networks that enable higher rates of transpiration, photosynthesis, and growth. Yet, how angiosperms pack their leaves with smaller, more abundant stomata and more veins is unknown but linked—we show—to simple biophysical constraints on cell size. Only angiosperm lineages underwent rapid genome downsizing during the early Cretaceous period, which facilitated the reductions in cell size necessary to pack more veins and stomata into their leaves, effectively bringing actual primary productivity closer to its maximum potential. Thus, the angiosperms' heightened competitive abilities are due in no small part to genome downsizing.

Author summary

The angiosperms, commonly referred to as the flowering plants, are the dominant plants in most terrestrial ecosystems, but how they came to be so successful is considered one of the most profound mysteries in evolutionary biology. Prevailing hypotheses have suggested that the angiosperms rose to dominance through an increase in their maximum potential photosynthesis and whole-plant carbon gain, allowing them to outcompete the ferns and gymnosperms that had previously dominated terrestrial ecosystems. Using a combination of anatomy, cytology, and modelling of liquid water transport and CO2 exchange between leaves and the atmosphere, we now provide strong evidence that the success and rapid spread of flowering plants around the world was the result of genome downsizing. Smaller genomes permit the construction of smaller cells that allow for greater CO2 uptake and photosynthetic carbon gain. Genome downsizing occurred only among the angiosperms, and we propose that it was a necessary prerequisite for rapid growth rates among land plants.

Citation: Simonin KA, Roddy AB (2018) Genome downsizing, physiological novelty, and the global dominance of flowering plants. PLoS Biol 16(1): e2003706. https://doi.org/10.1371/journal.pbio.2003706

Academic Editor: Andrew Tanentzap, University of Cambridge, United Kingdom of Great Britain and Northern Ireland

Received: July 13, 2017; Accepted: December 8, 2017; Published: January 11, 2018

Copyright: © 2018 Simonin, Roddy. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the paper and its Supporting Information files.

Funding: The authors received no specific funding for this work.

Competing interests: The authors have declared that no competing interests exist.

Abbreviations: AIC, Akaike Information Criterion; ci, leaf intercellular CO2 concentrations; Ds, stomatal density; Dv, leaf vein density; gs, max, maximum stomatal conductance; gs, op, operational stomatal conductance; lg, guard cell length; W, guard cell width

FREE PDF GRATIS: PLoS Biology

Quem disse que água e óleo não se misturam, seu hidrofóbico!

quinta-feira, janeiro 11, 2018

Creating nanoscale emulsions using condensation

Ingrid F. Guha, Sushant Anand & Kripa K. Varanasi

Nature Communications 8, Article number: 1371 (2017)


Download Citation

Chemical engineering Fluids Microfluidics

Received: 04 May 2017 Accepted: 12 September 2017

Published online: 08 November 2017


Abstract

Nanoscale emulsions are essential components in numerous products, ranging from processed foods to novel drug delivery systems. Existing emulsification methods rely either on the breakup of larger droplets or solvent exchange/inversion. Here we report a simple, scalable method of creating nanoscale water-in-oil emulsions by condensing water vapor onto a subcooled oil-surfactant solution. Our technique enables a bottom-up approach to forming small-scale emulsions. Nanoscale water droplets nucleate at the oil/air interface and spontaneously disperse within the oil, due to the spreading dynamics of oil on water. Oil-soluble surfactants stabilize the resulting emulsions. We find that the oil-surfactant concentration controls the spreading behavior of oil on water, as well as the peak size, polydispersity, and stability of the resulting emulsions. Using condensation, we form emulsions with peak radii around 100 nm and polydispersities around 10%. This emulsion formation technique may open different routes to creating emulsions, colloidal systems, and emulsion-based materials.

Acknowledgements

We thank the MIT Energy Initiative for financial support. I.F.G. is grateful for support from the NSF Graduate Research Fellowship Program. S.A. thanks the Society in Science—Branco Weiss Fellowship for financial support. The Biophysical Instrumentation Facility for the Study of Complex Macromolecular Systems (NSF-0070319) is gratefully acknowledged. We thank Dr. Arindam Das for his help with fabricating the sample container and Mr. Hassan Bararnia for assistance with DLS measurements (Supplementary Figs. 5, 6).

Author information

Author notes

Ingrid F. Guha and Sushant Anand contributed equally to this work.

Affiliations

Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA

Ingrid F. Guha

Department of Mechanical & Industrial Engineering, University of Illinois at Chicago, Chicago, IL, 60607, USA

Sushant Anand

Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA

Sushant Anand & Kripa K. Varanasi

Contributions

K.K.V and S.A. conceived the research; S.A., I.F.G., and K.K.V designed the research; I.F.G. and S.A. conducted the research; I.F.G., S.A., and K.K.V. prepared the manuscript.

Competing interests
The authors declare no competing financial interests.

Corresponding authors
Correspondence to Sushant Anand or Kripa K. Varanasi.

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Nature Communications Sup. Info. 1 Additional Sup. Info. Movie 1 Movie 2

A crença em Deus não está ligada à intuição ou pensamento racional?

Supernatural Belief Is Not Modulated by Intuitive Thinking Style or Cognitive Inhibition

Miguel Farias, Valerie van Mulukom, Guy Kahane, Ute Kreplin, Anna Joyce, Pedro Soares, Lluis Oviedo, Mathilde Hernu, Karolina Rokita, Julian Savulescu & Riikka Möttönen

Scientific Reports 7, Article number: 15100 (2017)


Download Citation

Cognitive controlHuman behaviour

Received: 24 April 2017 Accepted: 29 September 2017

Published online: 08 November 2017


Abstract

According to the Intuitive Belief Hypothesis, supernatural belief relies heavily on intuitive thinking—and decreases when analytic thinking is engaged. After pointing out various limitations in prior attempts to support this Intuitive Belief Hypothesis, we test it across three new studies using a variety of paradigms, ranging from a pilgrimage field study to a neurostimulation experiment. In all three studies, we found no relationship between intuitive or analytical thinking and supernatural belief. We conclude that it is premature to explain belief in gods as ‘intuitive’, and that other factors, such as socio-cultural upbringing, are likely to play a greater role in the emergence and maintenance of supernatural belief than cognitive style.

Acknowledgements

Supported by awards from the BIAL Foundation (62/06 and 380/14) to M.F., U.K., the John Templeton Foundation (57676) to M.F., R.M., G.K., J.S., and the Medical Research Council, UK (G1000566) to R.M. We thank Sangeetha Santhanam for her assistance with data collection for study 2.

Author information

Affiliations

Brain, Belief, & Behaviour Lab, Centre for Advances in Behavioural Science, Coventry University, Coventry, UK

Miguel Farias, Valerie van Mulukom & Anna Joyce
Philosophy Faculty, University of Oxford, Oxford, UK

Guy Kahane & Julian Savulescu
Department of Psychology, Massey University, Palmerston, New Zealand

Ute Kreplin
Faculty of Social and Human Sciences, Universidade Nova de Lisboa, Lisbon, Portugal

Pedro Soares
Pontificia Universita Antonianum, Rome, Italy

Lluis Oviedo
Institute of Cognitive and Culture, Queen’s University, Belfast, Ireland

Mathilde Hernu
National University of Ireland, Galway, Ireland

Karolina Rokita
Department of Experimental Psychology, University of Oxford, Oxford, UK

Riikka Möttönen
School of Psychology, The University of Nottingham, Nottingham, UK

Contributions

M.F., R.M., and G.K. designed overall research. M.F., V.M., R.M., G.K., and J.S. wrote the first draft. Study 1: M.F. designed research; M.F., P.S., and L.O. performed research; M.F. and V.M. analysed data and wrote it up. Study 2: M.F. and R.M. designed and performed research; M.F. and V.M. analysed data and wrote it up. Study 3: M.F., R.M., and G.K. designed research; U.K., A.J., K.R., and M.H. performed research. V.M., U.K., A.J., R.M. and M.F. analysed data and wrote it up.

Competing Interests

The authors declare that they have no competing interests.

Corresponding author

Correspondence to Miguel Farias.

FREE PDF GRATIS: Scientific Reports

Evolução do torque maior em motores flagelares bacterianos tipo Campylobacter: mero acaso, fortuita necessidade ou design inteligente?

quarta-feira, janeiro 10, 2018

Evolution of higher torque in Campylobacter-type bacterial flagellar motors

Bonnie Chaban, Izaak Coleman & Morgan Beeby

Scientific Reports 8, Article number: 97 (2018)


Download Citation

Bacterial evolution Cryoelectron tomography Molecular evolution

Received: 13 October 2017 Accepted: 05 December 2017

Published online: 08 January 2018

3-D model images of the eight studied bacterial motors. 
Source/Fonte: Morgan Beeby/Imperial College London

Abstract

Understanding the evolution of molecular machines underpins our understanding of the development of life on earth. A well-studied case are bacterial flagellar motors that spin helical propellers for bacterial motility. Diverse motors produce different torques, but how this diversity evolved remains unknown. To gain insights into evolution of the high-torque ε-proteobacterial motor exemplified by the Campylobacter jejuni motor, we inferred ancestral states by combining phylogenetics, electron cryotomography, and motility assays to characterize motors from Wolinella succinogenes, Arcobacter butzleri and Bdellovibrio bacteriovorus. Observation of ~12 stator complexes in many proteobacteria, yet ~17 in ε-proteobacteria suggest a “quantum leap” evolutionary event. Campylobacter-type motors have high stator occupancy in wider rings of additional stator complexes that are scaffolded by large proteinaceous periplasmic rings. We propose a model for motor evolution wherein independent inner- and outer-membrane structures fused to form a scaffold for additional stator complexes. Significantly, inner- and outer-membrane associated structures have evolved independently multiple times, suggesting that evolution of such structures is facile and poised the ε-proteobacteria to fuse them to form the high-torque Campylobacter-type motor.

Acknowledgements

The authors gratefully thank Tillmann Pape for electron microscopy assistance, Liz Sockett from the University of Nottingham for the gift of Bdellovibrio bacteriovorus, Erin Gaynor from the University of British Columbia for the gift of the straight Campylobacter mutant strain, and Bertus Beaumont, Josie Ferreira, and Florian Rossmann for critical reading of the manuscript. This work was supported by a Biotechnology and Biological Sciences Research Council Grant BB/L023091/1 (to M.B.).

Author information

Author notes

Bonnie Chaban

Present address: Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, 4556, QLD, Australia

Affiliations

Department of Life Sciences, Imperial College of London, London, SW7 2AZ, UK

Bonnie Chaban, Izaak Coleman & Morgan Beeby

Contributions

B.C. and I.C. performed phylogenetic analysis, B.C. collected tomographic and motility data, B.C., I.C. and M.B. analysed data. B.C. and M.B. wrote the main manuscript text and prepared figures. All authors reviewed the manuscript.

Competing Interests

The authors declare that they have no competing interests.

Corresponding author

Correspondence to Morgan Beeby.

Descoberta nova receita plausível para a origem da vida primeva na Terra

terça-feira, janeiro 09, 2018

Linked cycles of oxidative decarboxylation of glyoxylate as protometabolic analogs of the citric acid cycle

Greg Springsteen, Jayasudhan Reddy Yerabolu, Julia Nelson, Chandler Joel Rhea & Ramanarayanan Krishnamurthy

Nature Communications 9, Article number: 91 (2018)


Download Citation

Metabolic pathwaysOrganic chemistryChemical origin of lifeReaction mechanisms

Received: 23 August 2017 Accepted: 08 December 2017

Published online: 08 January 2018


Abstract

The development of metabolic approaches towards understanding the origins of life, which have focused mainly on the citric acid (TCA) cycle, have languished—primarily due to a lack of experimentally demonstrable and sustainable cycle(s) of reactions. We show here the existence of a protometabolic analog of the TCA involving two linked cycles, which convert glyoxylate into CO2 and produce aspartic acid in the presence of ammonia. The reactions proceed from either pyruvate, oxaloacetate or malonate in the presence of glyoxylate as the carbon source and hydrogen peroxide as the oxidant under neutral aqueous conditions and at mild temperatures. The reaction pathway demonstrates turnover under controlled conditions. These results indicate that simpler versions of metabolic cycles could have emerged under potential prebiotic conditions, laying the foundation for the appearance of more sophisticated metabolic pathways once control by (polymeric) catalysts became available.

Darwin, quem diria: a metafísica da evolução

segunda-feira, janeiro 08, 2018

Interface Focus. 2017 Oct 6; 7(5): 20160148.

Published online 2017 Aug 18. doi: 10.1098/rsfs.2016.0148 ReadCube 

PMCID: PMC5566809

The metaphysics of evolution

John Dupré

Egenis, University of Exeter, Exeter, UK

e-mail: ku.ca.retexe@erpud.a.j


Source/Fonte: New Scientist

ABSTRACT

This paper briefly describes process metaphysics, and argues that it is better suited for describing life than the more standard thing, or substance, metaphysics. It then explores the implications of process metaphysics for conceptualizing evolution. After explaining what it is for an organism to be a process, the paper takes up the Hull/Ghiselin thesis of species as individuals and explores the conditions under which a species or lineage could constitute an individual process. It is argued that only sexual species satisfy these conditions, and that within sexual species the degree of organization varies. This, in turn, has important implications for species' evolvability. One important moral is that evolution will work differently in different biological domains.

Keywords: process ontology, evolution, species, lineage, individual

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As redes de RNA nas origens da vida

sexta-feira, janeiro 05, 2018

RNA networks at the origins of life

Jessica A.M. Yeates and Niles Lehman (Portland State University, USA)


The origin of life has often been viewed as the advent of a single self-replicating molecular species, such as RNA. We propose a somewhat different approach in that a network of co-operating molecules could have kick-started life. This view has both theoretical and experimental support. The foundations for life, as we understand it on our planet, began some 4.5 billion years ago with the formation of the Earth 1 and by 4.0 billion years ago evidence for the presence of life existed. Within that timeframe, physical and chemical processes would have produced increasingly more complex interactions, moving from simple inorganic molecules to biopolymers capable of replication and variation. In order to answer the question of how life originated and to even understand what life is, empirical proof-ofconcept simple abiotic pathways demonstrating these transitions are needed. In this article, we discuss how networks of molecules, rather than single replicating molecular species, is an emerging view that may unlock some longstanding problems in the origins field. 

FREE PDF GRATIS: Biochemical Society

A vida sem água

Life without water

Kazuharu Arakawa and Mark Blaxter

(Keio University, Japan and University of Edinburgh, UK)

Tardigrade - Source/Fonte: Extreme Marine Org.

From space our planet is blue, and life here has evolved in the presence of abundant water. However, on land, water remains one of life’s major challenges. Fully two-fifths of the land surface is classified as arid: the hot and cold deserts, where water is largely unavailable. Even in biomes where water availability is generally good, seasonal, daily and sporadic conditions can mean that life has to be able to survive its absence. Surprisingly, some organisms are able to survive complete loss of all their body water, to undergo anhydrobiosis. This surprising ability has evolved many times, and is particularly prevalent in very small animals. The biochemistry of anhydrobiosis challenges ideas of what ‘being alive’ really means and promises exciting biotechnological applications.
....

FREE PDF GRATIS: Biochemical Society

O teorema fundamental da seleção natural de Fisher com mutações: outra história!

terça-feira, dezembro 26, 2017

Journal of Mathematical Biology

pp 1–34 | Cite as

The fundamental theorem of natural selection with mutations

Authors

Authors and affiliations

William F. Basener1 John C. Sanford2

1.Rochester Institute of TechnologyRochesterUSA

2.Horticulture SectionNYSAESGenevaUSA

Open AccessArticle

First Online: 07 November 2017

Source/Fonte:
Testing Natural Selection,H. Allen Orr
Scientific American 300, 44 - 51 (2009)

Abstract

The mutation–selection process is the most fundamental mechanism of evolution. In 1935, R. A. Fisher proved his fundamental theorem of natural selection, providing a model in which the rate of change of mean fitness is equal to the genetic variance of a species. Fisher did not include mutations in his model, but believed that mutations would provide a continual supply of variance resulting in perpetual increase in mean fitness, thus providing a foundation for neo-Darwinian theory. In this paper we re-examine Fisher’s Theorem, showing that because it disregards mutations, and because it is invalid beyond one instant in time, it has limited biological relevance. We build a differential equations model from Fisher’s first principles with mutations added, and prove a revised theorem showing the rate of change in mean fitness is equal to genetic variance plus a mutational effects term. We refer to our revised theorem as the fundamental theorem of natural selection with mutations. Our expanded theorem, and our associated analyses (analytic computation, numerical simulation, and visualization), provide a clearer understanding of the mutation–selection process, and allow application of biologically realistic parameters such as mutational effects. The expanded theorem has biological implications significantly different from what Fisher had envisioned.

Keywords

Population genetics Population dynamics Mutations Fitness Fisher Fundamental theorem of natural selection Natural selection Mutational meltdown 

As propriedades físico-químicas da água: mero acaso, fortuita necessidade ou design inteligente???

sexta-feira, dezembro 22, 2017

Chemical physics of water

Pablo G. Debenedetti a,1 and Michael L. Klein b,

Author Affiliations

a Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544;

b Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122

Source/Fonte: EcoSoft

There is hardly any aspect of our lives that is not profoundly influenced by water. From climate to commerce and agriculture to health, water shapes our physical environment, regulates the major energy exchanges that determine climate on Earth, and is the matrix that supports the physical and chemical processes of life as we know it (1). The chemistry and physics of water, which underlie all of its uses, its necessity for life, its effects on other molecules and on the environment, are very active areas of research at the present time. So, why is this? Surprisingly, there are major gaps in knowledge and understanding that persist despite this substance’s ubiquity and central importance. This Special Feature on the Chemical Physics of Water contains 10 articles and aims to be a representative cross-section of current frontier research in this field. Articles include both Perspectives and original research contributions. The pioneering paper by Bernal and Fowler dealing with the chemical physics of water appeared in 1933 (2). It focused on understanding the anomalous properties of water and its ionic solutions from a molecular perspective, inspired by the newly minted quantum mechanical theory of electronic structure. Since that time, theory and computer simulation have become established as essential complements to laboratory experiments in unraveling the crucial role of water in an array

↵1To whom correspondence may be addressed. Email: pdebene@princeton.edu or mike.klein@temple.edu.

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Introdução à informática evolucionária: autores são teóricos do Design Inteligente

Introduction to Evolutionary Informatics 1st Edition

by Robert J Marks II (Author),‎ William A Dembski (Author),‎ Winston Ewert (Author)

Science has made great strides in modeling space, time, mass and energy. Yet little attention has been paid to the precise representation of the information ubiquitous in nature.

Introduction to Evolutionary Informatics fuses results from complexity modeling and information theory that allow both meaning and design difficulty in nature to be measured in bits. Built on the foundation of a series of peer-reviewed papers published by the authors, the book is written at a level easily understandable to readers with knowledge of rudimentary high school math. Those seeking a quick first read or those not interested in mathematical detail can skip marked sections in the monograph and still experience the impact of this new and exciting model of nature's information.

This book is written for enthusiasts in science, engineering and mathematics interested in understanding the essential role of information in closely examined evolution theory. 

Readership: General/Popular; Enthusiasts in science, engineering and apologetics and to those interested in the information theoretic components of closely examined evolution.

Editorial Reviews

Review

An honest attempt to discuss what few people seem to realize is an important problem. Thought provoking! -- Gregory Chaitin "Professor, Federal University of Rio de Janeiro, Brazil"

With penetrating brilliance, and with a masterful exercise of pedagogy and wit, the authors take on Chaitin's challenge, that Darwin's theory should be subjectable to a mathematical assessment and either pass or fail. Surveying over seven decades of development in algorithmics and information theory, they make a compelling case that it fails. -- Bijan Nemati "Jet Propulsion Laboratory, California Institute of Technology, USA"

Introduction to Evolutionary Informatics is a lucid, entertaining, even witty discussion of important themes in evolutionary computation, relating them to information theory. It's far more than that, however. It is an assessment of how things might have come to be the way they are, applying an appropriate scientific skepticism to the hypothesis tha -- Donald Wunsch "Distinguished Professor and Director of the Applied Computational Intelligence Lab, Missouri University of Science & Technology, USA"

Darwinian pretensions notwithstanding, Marks, Dembski, and Ewert demonstrate rigorously and humorously that no unintelligent process can account for the wonders of life. -- Michael J Behe "Professor of Biological Sciences, Lehigh University, USA"

A very helpful book on this important issue of information. Information is the jewel of all science and engineering which is assumed but barely recognised in working systems. In this book Marks, Dembski and Ewert show the major principles in understanding what information is and show that it is always associated with design. -- Andy C McIntosh "Visiting Professor of Thermodynamics, School of Chemical and Process Engineering, University of Leeds, LEEDS, UK"

Though somewhat difficult, Marks, Dembski and Ewert have done a masterful job of making the book accessible to the engaged and thoughtful layperson. I could not endorse this book more highly. -- J P Moreland "Distinguished Professor of Philosophy, Biola University, USA"

This is an important and much needed step forward in making powerful concepts available at an accessible level. -- Ide Trotter "Trotter Capital Management Inc., Founder of the Trotter Prize & Endowed Lecture Series on Information, Complexity and Inference (Texas A&M, USA)"

This is a fine summary of an extremely interesting body of work. It is clear, well-organized, and mathematically sophisticated without being tedious (so many books of this sort have it the other way around). It should be read with profit by biologists, computer scientists, and philosophers. -- David Berlinski "David Berlinski"

Evolution requires the origin of new information. In this book, information experts Bob Marks, Bill Dembski, and Winston Ewert provide a comprehensive introduction to the models underlying evolution and the science of design. The authors demonstrate clearly that all evolutionary models rely implicitly on information that comes from intelligent desi -- Jonathan Wells "Senior Fellow, Discovery Institute"

Introduction to Evolutionary Informatics helps the non-expert reader grapple with a fundamental problem in science today: We cannot model information in the same way as we model matter and energy because there is no relationship between the metrics. As a result, much effort goes into attempting to explain information away. The authors show, using c -- Denyse O'Leary, Science Writer "Denyse O'Leary, Science Writer" --This text refers to the Hardcover edition.

About the Author

Robert J Marks II is Distinguished Professor of Engineering in the Department of Engineering at Baylor University, USA. Marks's professional awards include a NASA Tech Brief Award and a best paper award from the American Brachytherapy Society for prostate cancer research. He is Fellow of both IEEE and The Optical Society of America. His consulting activities include: Microsoft Corporation, DARPA, and Boeing Computer Services. He is listed as one of the "The 50 Most Influential Scientists in the World Today." By TheBestSchools.org. (2014). His contributions include: the Zhao-Atlas-Marks (ZAM) time-frequency distribution in the field of signal processing, and the Cheung Marks theorem in Shannon sampling theory.

Marks's research has been funded by organizations such as the National Science Foundation, General Electric, Southern California Edison, the Air Force Office of Scientific Research, the Office of Naval Research, the United States Naval Research Laboratory, the Whitaker Foundation, Boeing Defense, the National Institutes of Health, The Jet Propulsion Lab, Army Research Office, and NASA. His books include Handbook of Fourier Analysis and Its Applications (Oxford University Press), Introduction to Shannon Sampling and Interpolation Theory (Springer Verlag), and Neural Smithing: Supervised Learning in Feedforward Artificial Neural Networks (MIT Press) with Russ Reed. Marks has edited/co-edited five other volumes in fields such as power engineering, neural networks, and fuzzy logic. He was instrumental in defining the discipline of computational intelligence (CI) and is a co-editor of the first book using CI in the title: Computational Intelligence: Imitating Life (IEEE Press, 1994). His authored/coauthored book chapters include nine papers reprinted in collections of classic papers. Other book chapters include contributions to Michael Arbib's The Handbook of Brain Theory and Neural Networks (MIT Press, 1996), and Michael Licona et al.'s Evidence for God (Baker Books, 2010), Marks has also authored/co-authored hundreds of peer-reviewed conference and journal papers.

William A Dembski is Senior Research Scientist at the Evolutionary Informatics Lab in McGregor, Texas; and also Senior Fellow with Seattle's Discovery Institute, Washington, USA. He holds a BA in Psychology, MS in Statistics, PhD in Philosophy, and a PhD in Mathematics (awarded in 1988 by the University of Chicago, Chicago, Illinois, USA), and an MDiv degree from Princeton Theological Seminary (1996, New Jersey, USA). Dembski's work experience includes being an Associate Research Professor with the Conceptual Foundations of Science, Baylor University, Waco, Texas, USA. He has taught at Northwestern University, Evanston, Illinois, USA; the University of Notre Dame, Notre Dame, Indiana, USA; and the University of Dallas, Irving, Texas, USA. He has done postdoctoral work in mathematics with the Massachusetts Institute of Technology, Cambridge, USA; in physics with the University of Chicago, USA; and in computer science with Princeton University, Princeton, New Jersey, USA. He is a Mathematician and Philosopher. He has held National Science Foundation graduate and postdoctoral fellowships, and has published articles in mathematics, engineering, philosophy, and theology journals and is the author/editor of more than twenty books.

Winston Ewert is currently a Software Engineer in Vancouver, Canada. He is a Senior Research Scientist at the Evolutionary Informatics Lab. Ewert holds a PhD from Baylor University, Waco, Texas, USA. He has written a number of papers relating to search, information, and complexity including studies of computer models purporting to describe Darwinian evolution and developing information theoretic models to measure specified complexity.

Variação no relógio molecular dos primatas

Variation in the molecular clock of primates

Priya Moorjani a,b,1,2, Carlos Eduardo G. Amorim a,1, Peter F. Arndt c, and Molly Przeworski a,d,

Author Affiliations

a Department of Biological Sciences, Columbia University, New York, NY 10027;

b Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142;

c Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;

d Department of Systems Biology, Columbia University, New York, NY 10027

Edited by David C. Page, Whitehead Institute, Cambridge, MA, and approved July 19, 2016 (received for review January 8, 2016)


Significance

Much of our understanding of the chronology of human evolution relies on a fixed “molecular clock”; that is, a constant rate of substitutions per unit time. To evaluate the validity of this assumption, we analyze whole-genome sequences from 10 primate species. We find that there is substantial variation in the molecular clock between apes and monkeys and that rates even differ within hominines. Importantly, not all mutation types behave similarly; notably, transitions at CpG sites exhibit a more clocklike behavior than other substitutions, presumably because of their nonreplicative origin. Thus, the mutation spectra, and not just the overall substitution rates, are changing across primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions.

Abstract

Events in primate evolution are often dated by assuming a constant rate of substitution per unit time, but the validity of this assumption remains unclear. Among mammals, it is well known that there exists substantial variation in yearly substitution rates. Such variation is to be expected from differences in life history traits, suggesting it should also be found among primates. Motivated by these considerations, we analyze whole genomes from 10 primate species, including Old World Monkeys (OWMs), New World Monkeys (NWMs), and apes, focusing on putatively neutral autosomal sites and controlling for possible effects of biased gene conversion and methylation at CpG sites. We find that substitution rates are up to 64% higher in lineages leading from the hominoid–NWM ancestor to NWMs than to apes. Within apes, rates are ∼2% higher in chimpanzees and ∼7% higher in the gorilla than in humans. Substitution types subject to biased gene conversion show no more variation among species than those not subject to it. Not all mutation types behave similarly, however; in particular, transitions at CpG sites exhibit a more clocklike behavior than do other types, presumably because of their nonreplicative origin. Thus, not only the total rate, but also the mutational spectrum, varies among primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions. Taking this approach, we estimate the human and chimpanzee divergence time is 12.1 million years,​ and the human and gorilla divergence time is 15.1 million years​.

molecular clock mutation rate primate evolution CpG transition rate human–ape divergence time

Footnotes

1P.M. and C.E.G.A. contributed equally to this work.

2To whom correspondence may be addressed. Email: pm2730@columbia.edu or mp3284@columbia.edu.

Author contributions: P.M., C.E.G.A., and M.P. designed research; P.M., C.E.G.A., and M.P. performed research; P.M. and P.F.A. contributed new reagents/analytic tools; P.M., C.E.G.A., and M.P. analyzed data; and P.M., C.E.G.A., and M.P. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1600374113/-/DCSupplemental.

Freely available online through the PNAS open access option.

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