Doolittle 'falou e disse': nós simplesmente não podemos continuar sendo tão vagos sobre a 'função'

segunda-feira, janeiro 14, 2019

We simply cannot go on being so vague about ‘function’

W. Ford Doolittle Email author

Genome Biology201819:223


Published: 18 December 2018

The original article was published in Genome Biology 2018 19:208

Related image
Source/Fonte: Internet

Abstract

Function is an onerous concept, as the recent study by Steven Salzberg and colleagues demonstrates. We should be careful and always specific in using the ‘F-word’.

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A natureza da inferência do design e o status epistêmico do Design Inteligente

sábado, janeiro 12, 2019

International Philosophical Quarterly

ONLINE FIRST 

published on December 21, 2018

Dariusz Sagan


The Nature of Design Inference and the Epistemic Status of Intelligent Design

Abstract

This article considers the main methodological objections against the theory of intelligent design. In general, they claim that it lacks a scientific character and they emphasize that design cannot be detected using scientific tools. The critics focus on showing that intelligent design violates various methodological criteria. In response to these objections, this article examines the methodological claim made by its proponents that the characteristic effects of the designer’s activity do provide a sufficient basis for inferring design. This paper also argues that the procedure of inferring that a certain feature has been designed by a supernatural being does not differ in principle from design-detection procedures in other spheres of research.

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NOTA DESTE BLOGGER:

Dariusz Sagan, autor deste artigo, não faz parte do Movimento de Design Inteligente.

Quiralidade em "tempo real"

sexta-feira, janeiro 11, 2019

Ultrafast broadband circular dichroism in the deep ultraviolet

Malte Oppermann, Benjamin Bauer, Thomas Rossi, Francesco Zinna, Jan Helbing, Jérôme Lacour, and Majed Chergui

Ultrafast broadband circular dichroism in the deep ultraviolet

Malte Oppermann, Benjamin Bauer, Thomas Rossi, Francesco Zinna, Jan Helbing, Jérôme Lacour, and Majed Chergui

Author Affiliations

Malte Oppermann,1,* Benjamin Bauer,1 Thomas Rossi,1 Francesco Zinna,2 Jan Helbing,3 Jérôme Lacour,2 and Majed Chergui1

1Laboratoire de Spectroscopie Ultrarapide and Lausanne Centre for Ultrafast Science (LACUS), École Polytechnique Fédérale de Lausanne, ISIC-FSB, CH-1015 Lausanne, Switzerland

2Département de chimie organique, Université de Genève, Quai Ernest Ansermet 30, 1211 Genève 4, Switzerland

3Institut für Chemie, Universität Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland

*Corresponding author: malte.oppermann@epfl.ch

ORCID



Optica Vol. 6, Issue 1, pp. 56-60 (2019)



Abstract

The measurement of chirality and its temporal evolution are crucial for the understanding of a large range of biological functions and chemical reactions. Steady-state circular dichroism (CD) is a standard analytical tool for measuring chirality in chemistry and biology. Nevertheless, its push into the ultrafast time domain and in the deep-ultraviolet has remained a challenge, with only some isolated reports of subnanosecond CD. Here, we present a broadband time-resolved CD spectrometer in the deep ultraviolet (UV) spectral range with femtosecond time resolution. The setup employs a photoelastic modulator to achieve shot-to-shot polarization switching of a 20 kHz pulse train of broadband femtosecond deep-UV pulses (250–370 nm). The resulting sequence of alternating left- and right-circularly polarized probe pulses is employed in a pump-probe scheme with shot-to-shot dispersive detection and thus allows for the acquisition of broadband CD spectra of ground- and excited-state species. Through polarization scrambling of the probe pulses prior to detection, artifact-free static and transient CD spectra of enantiopure [Ru(bpy)3]2+ are successfully recorded with a sensitivity of <2 amino-acid="" and="" biological="" broadband="" changes="" chirality="" deep-uv="" detection="" dna="" due="" feasible.="" font="" in="" is="" its="" mdeg="" measurement="" now="" od="" of="" oligomers="" peptides="" residues="" sensitivity="" systems="" the="" to="" ultrafast="" unprecedented="" with="">

© 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

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Previsão de rotas mutacionais para novos fenótipos adaptativos

quarta-feira, janeiro 09, 2019

Predicting mutational routes to new adaptive phenotypes

Peter A Lind, Eric Libby, Jenny Herzog, Paul B Rainey
Massey University at Albany, New Zealand; Umeå University, Sweden; Santa Fe Institute, United States; Max Planck Institute for Evolutionary Biology, Germany; CNRS UMR 8231, PSL Research University, France


Abstract

Predicting evolutionary change poses numerous challenges. Here we take advantage of the model bacterium Pseudomonas fluorescens in which the genotype-to-phenotype map determining evolution of the adaptive ‘wrinkly spreader’ (WS) type is known. We present mathematical descriptions of three necessary regulatory pathways and use these to predict both the rate at which each mutational route is used and the expected mutational targets. To test predictions, mutation rates and targets were determined for each pathway. Unanticipated mutational hotspots caused experimental observations to depart from predictions but additional data led to refined models. A mismatch was observed between the spectra of WS-causing mutations obtained with and without selection due to low fitness of previously undetected WS-causing mutations. Our findings contribute toward the development of mechanistic models for forecasting evolution, highlight current limitations, and draw attention to challenges in predicting locus-specific mutational biases and fitness effects.


eLIFE Digest

Predicting evolution might sound like an impossible task. The immense complexity of biological systems and their interactions with the environment has meant that many biologists have abandoned the idea as a lost cause. But despite this, evolution often repeats itself. This repeatability offers hope for being able to spot in advance how evolution will happen. To make general predictions, it is necessary to understand the mechanisms underlying evolutionary pathways, and studying microbes in the laboratory allows for real-time experiments in evolution.

One of the best studied microbes for experimental evolution is Pseudomonas fluorescens, which repeatedly evolves flattened wrinkled colonies instead of round smooth ones when there is limited oxygen. The underlying molecular pathways that lead to this change have been studied in detail.

Lind et al. developed mathematical models to predict how often the three most common pathways would be used and which genes were most likely to be mutated. After controlling for the effects of natural selection and refining the models to take into account mutation hotspots, Lind et al. were able to accurately predict the genes that would be targeted by mutations.

The findings suggest that biologists need not lose hope when it comes to the goal of predicting evolution. A deep understanding of the molecular mechanisms of evolutionary changes are essential to predicting the mutations that lead to adaptive change. The results are an important first step towards forecasting organisms’ responses to changing conditions in the future. In the short term, this is important for medical issues, including antibiotic resistance, cancer and immune receptors. In the long term, predicting the course of evolution could be essential for survival of life on the planet.


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Algoritmos darwinistas funcionam teoricamente, mas não praticamente na evolução de software

terça-feira, janeiro 08, 2019

Why We Do Not Evolve Software? Analysis of Evolutionary Algorithms

Roman V Yampolskiy

First Published December 1, 2018


Article Information

Volume: 14

Article first published online: December 1, 2018; Issue published: January 1, 2018 

Received: October 15, 2018; Accepted: November 06, 2018

Roman V Yampolskiy

Department of Computer Engineering and Computer Science, J.B. Speed School of Engineering, University of Louisville, Louisville, KY, USA

Corresponding Author: Roman V Yampolskiy, Department of Computer Engineering and Computer Science, J.B. Speed School of Engineering, University of Louisville, Duthie Center for Engineering, 215, 222 Eastern Pkwy, Louisville, KY 40208, USA. Email: roman.yampolskiy@louisville.edu

This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (http://www.creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage).

Image result for darwinian algorithm

Abstract

In this article, we review the state-of-the-art results in evolutionary computation and observe that we do not evolve nontrivial software from scratch and with no human intervention. A number of possible explanations are considered, but we conclude that computational complexity of the problem prevents it from being solved as currently attempted. A detailed analysis of necessary and available computational resources is provided to support our findings.

Keywords Darwinian algorithm, genetic algorithm, genetic programming, optimization

FREE PDF GRATIS: Evolutionary Bioinformatics

Perda progressiva de função em um intensificador de membro durante a evolução de cobra

segunda-feira, janeiro 07, 2019

CELL VOLUME 167, ISSUE 3, P633-642.E11, OCTOBER 20, 2016

Progressive Loss of Function in a Limb Enhancer during Snake Evolution

Evgeny Z. Kvon Olga K. Kamneva Uirá S. Melo Diane E. Dickel Len A. Pennacchio Axel Visel

Open Archive Published: October 20, 2016




Highlights

• Activity of the critical ZRS limb enhancer is highly conserved across vertebrates

• ZRS enhancer has progressively lost its function during snake evolution

• Snake-specific nucleotide changes contributed to the loss of ZRS enhancer function

• Resurrection of snake enhancer function in vivo

Summary

The evolution of body shape is thought to be tightly coupled to changes in regulatory sequences, but specific molecular events associated with major morphological transitions in vertebrates have remained elusive. We identified snake-specific sequence changes within an otherwise highly conserved long-range limb enhancer of Sonic hedgehog (Shh). Transgenic mouse reporter assays revealed that the in vivo activity pattern of the enhancer is conserved across a wide range of vertebrates, including fish, but not in snakes. Genomic substitution of the mouse enhancer with its human or fish ortholog results in normal limb development. In contrast, replacement with snake orthologs caused severe limb reduction. Synthetic restoration of a single transcription factor binding site lost in the snake lineage reinstated full in vivo function to the snake enhancer. Our results demonstrate changes in a regulatory sequence associated with a major body plan transition and highlight the role of enhancers in morphological evolution.

Keywords cis-regulatory element enhancer limb development morphological evolution snakes CRISPR/Cas9 ZRS evo-devo Sonic hedgehog (Shh) genome editing

FREE PDF GRATIS: Cell

Pesquisa explica como as cobras perderam os membros?

Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution

Juliana G. Roscito, Katrin Sameith, Genis Parra, Bjoern E. Langer, Andreas Petzold, Claudia Moebius, Marc Bickle, Miguel Trefaut Rodrigues & Michael Hiller 

Nature Communications volume 9, Article number: 4737 (2018)

Source/Fonte: Science

Abstract

Detecting the genomic changes underlying phenotypic changes between species is a main goal of evolutionary biology and genomics. Evolutionary theory predicts that changes in cis-regulatory elements are important for morphological changes. We combined genome sequencing, functional genomics and genome-wide comparative analyses to investigate regulatory elements in lineages that lost morphological traits. We first show that limb loss in snakes is associated with widespread divergence of limb regulatory elements. We next show that eye degeneration in subterranean mammals is associated with widespread divergence of eye regulatory elements. In both cases, sequence divergence results in an extensive loss of transcription factor binding sites. Importantly, diverged regulatory elements are associated with genes required for normal limb patterning or normal eye development and function, suggesting that regulatory divergence contributed to the loss of these phenotypes. Together, our results show that genome-wide decay of the phenotype-specific cis-regulatory landscape is a hallmark of lost morphological traits.

Acknowledgements

We thank the genomics community for sequencing and assembling the genomes of the many vertebrates used here, and the UCSC genome browser group for providing software and genome annotations. We also thank Virag Sharma for running CESAR, Nadine Vastenhouw for experimental infrastructure, Tiago Ferreira for helping with dissection of mouse eyes, Terence Capellini for helpful comments on the manuscript and on the experimental assay, Aliona Bogdanova for cloning of plasmids, Jared Simpson for help with SGA, and Andreas Dahl and Sylke Winkler for DNA sequencing, the Computer Service Facilities of the MPI-CBG and MPI-PKS, and the DNA Sequencing, Microarray and Biomedical service facilities of the MPI-CBG for their support. This work was supported by the Max Planck Society, and by FAPESP stipends 2012/01319-8 and 2012/23360 to J.G.R.

Author information

Author notes

These authors contributed equally: Juliana G. Roscito, Katrin Sameith, Genis Parra.

Affiliations

Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany

Juliana G. Roscito, Katrin Sameith, Genis Parra, Bjoern E. Langer, Claudia Moebius, Marc Bickle & Michael Hiller

Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany

Juliana G. Roscito, Katrin Sameith, Genis Parra, Bjoern E. Langer & Michael Hiller

Center for Systems Biology Dresden, Dresden, 01307, Germany

Juliana G. Roscito, Katrin Sameith, Genis Parra, Bjoern E. Langer & Michael Hiller

Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brazil

Juliana G. Roscito & Miguel Trefaut Rodrigues

Center for Regenerative Therapies TU Dresden, Dresden, 01307, Germany

Andreas Petzold

Contributions

J.G.R. annotated the tegu genome, performed ATAC-seq, and analyzed the limb and eye loss trait. K.S. assembled and annotated the tegu genome and analyzed the limb and eye loss trait. G.P. performed the initial eye loss analysis. B.E.L. performed the TF-binding site analysis. A.P. helped with genome annotation. C.M., M.B. and J.G.R. performed luciferase assays. M.T.R. provided samples. M.H. conceived and supervised the study and performed data analysis. M.H., J.G.R. and K.S. wrote the manuscript. K.S. and J.G.R. made figures. All authors approved the final manuscript.

Competing interests

The authors declare no competing interests

Corresponding author

Correspondence to Michael Hiller.


Plus 23 Supplementary Data/Mais 23 Páginas de Dados Suplementares.

Um quarto das vítimas do Holocausto morreu em apenas três meses!!!

domingo, janeiro 06, 2019

Quantifying the Holocaust: Hyperintense kill rates during the Nazi genocide

Lewi Stone1,2

1Biomathematics Unit, School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.

2Mathematical Sciences, School of Science, RMIT University, Melbourne, Victoria, Australia. Email: lewistone100@gmail.com

Science Advances 02 Jan 2019:

Vol. 5, no. 1, eaau7292


Image result for quantificando o holocausto
Source/Fonte: AFP-Getty Images

Abstract

Operation Reinhard (1942–1943) was the largest single murder campaign of the Holocaust, during which some 1.7 million Jews from German-occupied Poland were murdered by the Nazis. Most perished in gas chambers at the death camps Belzec, Sobibor, and Treblinka. However, the tempo, kill rates, and spatial dynamics of these events were poorly documented. Using an unusual dataset originating from railway transportation records, this study identifies an extreme phase of hyperintense killing when >1.47 million Jews—more than 25% of the Jews killed in all 6 years of World War II—were murdered by the Nazis in an intense,100-day (~3-month) surge. Operation Reinhard is shown to be an extreme event, based on kill rate, number, and proportion (>99.9%) of the population murdered in camps, highlighting its singularly violent character, even compared to other more recent genocides. The Holocaust kill rate is some 10 times higher than estimates suggested by authorities on comparative genocide.

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Never again!/Nunca novamente! 

Never forget!/Nunca esquecer!

Never forgive!/Nunca perdoar!

Gregory Chaitin 'falou e disse': sem uma teoria matemática da evolução não há como demonstrar se Darwin estava errado ou certo!!!

quarta-feira, janeiro 02, 2019


"A honra da matemática exige que desenvolvamos uma teoria matemática da evolução e, provar ou não que Darwin estava errado ou certo."
 
"The honor of mathematics requires us to come up with a mathematical theory of evolution and either prove Darwin was wrong or right." 

Gregory Chaitin

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Até agora nenhuma teoria matemática da evolução.../Thus far no mathematical theory of evolution...

Darwin kaput!!!

Mais dois genes posteriores Hox e a dispersão de aglomerados Hox em equinodermos

terça-feira, janeiro 01, 2019

Two more Posterior Hox genes and Hox cluster dispersal in echinoderms

Réka Szabó and David E. K. FerrierEmail authorView ORCID ID profile

BMC Evolutionary Biology 201818:203


Received: 2 August 2018 Accepted: 23 November 2018 Published: 27 December 2018

Fig. 1 Schematic phylogenetic tree of Ambulacraria with chordates shown as the outgroup.

Abstract

Background

Hox genes are key elements in patterning animal development. They are renowned for their, often, clustered organisation in the genome, with supposed mechanistic links between the organisation of the genes and their expression. The widespread distribution and comparable functions of Hox genes across the animals has led to them being a major study system for comparing the molecular bases for construction and divergence of animal morphologies. Echinoderms (including sea urchins, sea stars, sea cucumbers, feather stars and brittle stars) possess one of the most unusual body plans in the animal kingdom with pronounced pentameral symmetry in the adults. Consequently, much interest has focused on their development, evolution and the role of the Hox genes in these processes. In this context, the organisation of echinoderm Hox gene clusters is distinctive. Within the classificatory system of Duboule, echinoderms constitute one of the clearest examples of Disorganized (D) clusters (i.e. intact clusters but with a gene order or orientation rearranged relative to the ancestral state).

Results

Here we describe two Hox genes (Hox11/13d and e) that have been overlooked in most previous work and have not been considered in reconstructions of echinoderm Hox complements and cluster organisation. The two genes are related to Posterior Hox genes and are present in all classes of echinoderm. Importantly, they do not reside in the Hox cluster of any species for which genomic linkage data is available.

Conclusion

Incorporating the two neglected Posterior Hox genes into assessments of echinoderm Hox gene complements and organisation shows that these animals in fact have Split (S) Hox clusters rather than simply Disorganized (D) clusters within the Duboule classification scheme. This then has implications for how these genes are likely regulated, with them no longer covered by any potential long-range Hox cluster-wide, or multigenic sub-cluster, regulatory mechanisms.

Keywords 

Hox11/13d Hox11/13e Posterior Hox genes Hox gene evolution

FREE PDF GRATIS: BMC Evolutionary Biology

Genes neandertais dão pistas para a evolução do cérebro humano

Neandertal Introgression Sheds Light on Modern Human Endocranial Globularity

Philipp Gunz 20 Amanda K. Tilot 20 Katharina Wittfeld Fabio Macciardi Hans J. Grabe Simon E. Fisher 21
Open Access Published: December 13, 2018 

DOI: https://doi.org/10.1016/j.cub.2018.10.065

Figure 1 Endocranial Shape Differences between Neandertals and Modern Humans

Highlights

• We use fossil skull data to derive an index of endocranial shape in human MRI scans

• In 4,468 Europeans, we screen introgressed Neandertal SNPs for association with the index

• Lead SNPs consistently associate with reduced globularity in five separate subsamples

• These SNPs affect neural expression of two genes linked to neurogenesis and myelination

Summary

One of the features that distinguishes modern humans from our extinct relatives and ancestors is a globular shape of the braincase [1, 2, 3, 4]. As the endocranium closely mirrors the outer shape of the brain, these differences might reflect altered neural architecture [4, 5]. However, in the absence of fossil brain tissue, the underlying neuroanatomical changes as well as their genetic bases remain elusive. To better understand the biological foundations of modern human endocranial shape, we turn to our closest extinct relatives: the Neandertals. Interbreeding between modern humans and Neandertals has resulted in introgressed fragments of Neandertal DNA in the genomes of present-day non-Africans [6, 7]. Based on shape analyses of fossil skull endocasts, we derive a measure of endocranial globularity from structural MRI scans of thousands of modern humans and study the effects of introgressed fragments of Neandertal DNA on this phenotype. We find that Neandertal alleles on chromosomes 1 and 18 are associated with reduced endocranial globularity. These alleles influence expression of two nearby genes, UBR4 and PHLPP1, which are involved in neurogenesis and myelination, respectively. Our findings show how integration of fossil skull data with archaic genomics and neuroimaging can suggest developmental mechanisms that may contribute to the unique modern human endocranial shape.

Keywords brain shape evolution homo sapiens gene expression genetic association Neandertal cerebellum myelination basal ganglia magnetic resonance imaging 

Results and Discussion

Neandertals (Figure 1A) and modern humans (Figure 1B) have similar endocranial volumes but distinct endocranial shapes. Modern humans have a globular-shaped braincase, with a round and expanded posterior cranial fossa housing the cerebellum, and more bulging parietal bones [2, 3, 4]. Contrasting the average endocranial shapes of modern humans and Neandertals, Kochiyama et al. [5] proposed that the biggest differences between these groups are found in the cerebellum. Comparative analyses suggest rapid evolutionary changes of this brain structure in great apes and humans [8, 9]. Our analysis of endocranial shape based on data from [4] demonstrates that other regions beyond the cerebellum are relatively larger in modern humans than in Neandertals, including parts of the prefrontal cortex and the occipital and temporal lobes (Figures 1C and 1D). In contrast, parietal bulging [2, 3, 4] is not linked to an increased surface area, suggesting that the parietal lobe is “displaced” by reorganization of other—presumably subcortical—parts of the brain.

FREE PDF GRATIS: Current Biology