Colin Patterson perguntou: Vocês podem me dizer algo sobre a evolução, qualquer coisa, que seja verdade?" 2/2

No dia 5 de novembro de 1981, Patterson deu uma palestra para o Grupo de Discussão de Sistemática no Museu Americano de História Natural, Nova York: 

"It's true that for the last eighteen months or so, I've been kicking around non-evolutionary or even anti-evolutionary ideas. I think always before in my life, when I've got up to speak on a subject, I've been confident of one thing – that I know more about it than anybody in the room, because I've worked on it.

Well, this time that isn't true. I'm speaking on two subjects, evolutionism and creationism, and I believe it's true to say that I know nothing whatever about either of them. One or the reasons I started taking this anti-evolutionary view, or let's call it non-evolutionary, was last year I had a sudden realization that for over twenty years I had thought that I was working on evolution in some way. Then one morning I woke up, and something had happened in the night, and it struck me that I had been working on this stuff for twenty years, and there was not one thing I knew about it. That's quite a shock, to learn that one can be so misled for so long.

So either there was something wrong with me, or there was something wrong with evolutionary theory. Naturally, I know there is nothing wrong with me, so for the last few weeks, I've tried putting a simple question to various people and groups of people.

The question is: Can you tell me anything you know about evolution, any one thing, any one thing that is true? I tried that question on the geology staff in the Field Museum of Natural History, and the only answer I got was silence. I tried it on the members of the Evolutionary Morphology Seminar at the University of Chicago, a very prestigious body of evolutionists, and all I got there was silence for a long time, and then eventually one person said, "Yes, I do know one thing. It ought not to be taught in high school.” [laughter]"

Colin Patterson perguntou: Vocês podem me dizer algo sobre a evolução, qualquer coisa, que seja verdade?" 1/2

No dia 5 de novembro de 1981, Patterson deu uma palestra para o Grupo de Discussão de Sistemática no Museu Americano de História Natural, Nova York: 

"It's true that for the last eighteen months or so, I've been kicking around non-evolutionary or even anti-evolutionary ideas. I think always before in my life, when I've got up to speak on a subject, I've been confident of one thing – that I know more about it than anybody in the room, because I've worked on it.

Well, this time that isn't true. I'm speaking on two subjects, evolutionism and creationism, and I believe it's true to say that I know nothing whatever about either of them. One or the reasons I started taking this anti-evolutionary view, or let's call it non-evolutionary, was last year I had a sudden realization that for over twenty years I had thought that I was working on evolution in some way. Then one morning I woke up, and something had happened in the night, and it struck me that I had been working on this stuff for twenty years, and there was not one thing I knew about it. That's quite a shock, to learn that one can be so misled for so long.

So either there was something wrong with me, or there was something wrong with evolutionary theory. Naturally, I know there is nothing wrong with me, so for the last few weeks, I've tried putting a simple question to various people and groups of people.

The question is: Can you tell me anything you know about evolution, any one thing, any one thing that is true? I tried that question on the geology staff in the Field Museum of Natural History, and the only answer I got was silence. I tried it on the members of the Evolutionary Morphology Seminar at the University of Chicago, a very prestigious body of evolutionists, and all I got there was silence for a long time, and then eventually one person said, "Yes, I do know one thing. It ought not to be taught in high school.” [laughter]"

Cresce o número de cientistas com Ph. D. céticos da teoria da evolução de Darwin

Darwin, mais complexidade: arquiteturas supramoleculares de camadas molecularmente finas independentes, mas robustas

Supramolecular architectures of molecularly thin yet robust free-standing layers

Mina Moradi1,2, Nadia L. Opara2,3, Ludovico G. Tulli1, Christian Wäckerlin4, Scott J. Dalgarno5, Simon J. Teat6, Milos Baljozovic2, Olha Popova7, Eric van Genderen2,*, Armin Kleibert8, Henning Stahlberg3, Jan Pieter Abrahams9,10, Celestino Padeste2, Philippe F.-X. Corvini1, Thomas A. Jung2,† and Patrick Shahgaldian1,†

1Institute of Chemistry and Bioanalytics, School of Life Sciences, University of Applied Sciences and Arts Northwestern Switzerland, Hofackerstrasse 35, CH-4132 Muttenz, Switzerland.

2Laboratory for Micro- and Nano-technology, Paul Scherrer Institute, Villigen CH-5232, Switzerland.

3Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.

4Empa–Swiss Federal Laboratories for Materials Science and Technology, CH-8600 Dübendorf, Switzerland.

5Institute of Chemical Sciences, Heriot-Watt University, Riccarton, Edinburgh, Scotland EH14 4AS, UK.

6Advanced Light Source, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS6R2100, Berkeley, CA 94720, USA.

7Department of Physics, University of Basel, Klingelbergstrasse 82, 4056 Basel, Switzerland.

8Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland.

9Biozentrum, University of Basel, Switzerland and Laboratory of Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland.

10Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, Netherlands.

↵†Corresponding author. Email: patrick.shahgaldian@fhnw.ch (P.S.); thomas.jung@psi.ch (T.A.J.)

↵* Present address: Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, CH-4058 Basel, Switzerland.

Science Advances 22 Feb 2019: Vol. 5, no. 2, eaav4489

DOI: 10.1126/sciadv.aav4489

Fig. 3

Molecular resolution AFM imaging of the monolayer of 1.

(A) AFM images of the monolayer of 1 transferred onto HOPG via the LS method. (B) The high-resolution image of the crystalline network of the monolayer shows a highly ordered network formed from the single molecules of 1. [C (top view) and D (side view)] Molecular model of the building blocks of 1 interacting via the proposed dipole-dipole interaction in the well-ordered monolayer.

Abstract

Stable, single-nanometer thin, and free-standing two-dimensional layers with controlled molecular architectures are desired for several applications ranging from (opto-)electronic devices to nanoparticle and single-biomolecule characterization. It is, however, challenging to construct these stable single molecular layers via self-assembly, as the cohesion of those systems is ensured only by in-plane bonds. We herein demonstrate that relatively weak noncovalent bonds of limited directionality such as dipole-dipole (–CN⋅⋅⋅NC–) interactions act in a synergistic fashion to stabilize crystalline monomolecular layers of tetrafunctional calixarenes. The monolayers produced, demonstrated to be free-standing, display a well-defined atomic structure on the single-nanometer scale and are robust under a wide range of conditions including photon and electron radiation. This work opens up new avenues for the fabrication of robust, single-component, and free-standing layers via bottom-up self-assembly.

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Darwin, mais complexidade, mano: descobrindo elementos químicos nas células

Chemical and Topographical Single‐Cell Imaging by Near‐Field Desorption Mass Spectrometry

Dr. Zhibin Yin Xiaoling Cheng Rong Liu Xiaoping Li Le Hang Prof. Wei Hang Jingyi Xu Prof. Xiaomei Yan Prof. Jianfeng Li Prof. Zhongqun Tian

First published: 02 January 2019

https://doi.org/10.1002/anie.201813744

 

Abstract

Simultaneously acquiring chemical and topographical information within a single cell at nanoscale resolutions is vital to cellular biology, yet it remains a great challenge due to limited lateral resolutions and detection sensitivities. Herein, the development of near‐field desorption mass spectrometry for correlated chemical and topographical imaging is reported, thereby bridging the gap between laser‐based mass spectrometry (MS) methods and multimodal single‐cell imaging. Using this integrated platform, an imaging resolution of 250 nm and 3D topographically reconstructed chemical single‐cell imaging were achieved. This technique offers more in‐depth cellular information than micrometer‐range laser‐based MS imaging methods. Considering the simplicity and compact size of the near‐field device, this technique can be introduced to MALDI‐MS, expanding the multimodal abilities of MS at nanoscale resolutions.

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Taxas evolutivas de trilobitas restringem a duração da explosão cambriana

Trilobite evolutionary rates constrain the duration of the Cambrian explosion

John R. Paterson, Gregory D. Edgecombe, and Michael S. Y. Lee

PNAS published ahead of print February 19, 2019 

https://doi.org/10.1073/pnas.1819366116

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Edited by Andrew H. Knoll, Harvard University, Cambridge, MA, and approved January 9, 2019 (received for review November 12, 2018)

Significance

The Cambrian explosion was arguably the most important biological event after the origin of life. Extensive research has been devoted to understanding when it began but far less on when this burst of evolution ended. We present a quantitative study that addresses these issues, using a large new dataset of Cambrian trilobites, the most abundant and diverse organisms during this time. Using probabilistic clock methods, we calculate rates of evolution in the earliest trilobites virtually identical to those throughout their Cambrian fossil history. We conclude that the Cambrian explosion was over by the time the typical Cambrian fossil record commences and reject an unfossilized Precambrian history for trilobites, solving a problem that had long troubled biologists since Darwin.

Abstract

Trilobites are often considered exemplary for understanding the Cambrian explosion of animal life, due to their unsurpassed diversity and abundance. These biomineralized arthropods appear abruptly in the fossil record with an established diversity, phylogenetic disparity, and provincialism at the beginning of Cambrian Series 2 (∼521 Ma), suggesting a protracted but cryptic earlier history that possibly extends into the Precambrian. However, recent analyses indicate elevated rates of phenotypic and genomic evolution for arthropods during the early Cambrian, thereby shortening the phylogenetic fuse. Furthermore, comparatively little research has been devoted to understanding the duration of the Cambrian explosion, after which normal Phanerozoic evolutionary rates were established. We test these hypotheses by applying Bayesian tip-dating methods to a comprehensive dataset of Cambrian trilobites. We show that trilobites have a Cambrian origin, as supported by the trace fossil record and molecular clocks. Surprisingly, they exhibit constant evolutionary rates across the entire Cambrian, for all aspects of the preserved phenotype: discrete, meristic, and continuous morphological traits. Our data therefore provide robust, quantitative evidence that by the time the typical Cambrian fossil record begins (∼521 Ma), the Cambrian explosion had already largely concluded. This suggests that a modern-style marine biosphere had rapidly emerged during the latest Ediacaran and earliest Cambrian (∼20 million years), followed by broad-scale evolutionary stasis throughout the remainder of the Cambrian.

Cambrian explosion evolutionary rates trilobites Bayesian tip-dating morphological clock

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Cálculo direto de mutações em grandes símios reconcilia a datação filogenética

Direct estimation of mutations in great apes reconciles phylogenetic dating

Søren Besenbacher, Christina Hvilsom, Tomas Marques-Bonet, Thomas Mailund & Mikkel Heide Schierup 

Nature Ecology & Evolution volume 3, pages 286–292 (2019) 

Source/Fonte: Nature Ecology & Evolution

Abstract

The human mutation rate per generation estimated from trio sequencing has revealed an almost linear relationship with the age of the father and the age of the mother, with fathers contributing about three times as many mutations per year as mothers. The yearly trio-based mutation rate estimate of around 0.43 × 10−9 is markedly lower than previous indirect estimates of about 1 × 10−9 per year from phylogenetic comparisons of the great apes calibrated by fossil evidence. This suggests either a slowdown in the accumulation of mutations per year in the human lineage over the past 10 million years or an inaccurate interpretation of the fossil record. Here we inferred de novo mutations in chimpanzee, gorilla, and orangutan parent-offspring trios. Extrapolating the relationship between the mutation rate and the age of parents from humans to these other great apes, we estimated that each species has higher mutation rates per year by factors of 1.50 ± 0.10, 1.51 ± 0.23, and 1.42 ± 0.22 for chimpanzee, gorilla, and orangutan, respectively, and by a factor of 1.48 ± 0.08 for the three species combined. These estimates suggest an appreciable slowdown in the yearly mutation rate in the human lineage that is likely to be recent as genome comparisons almost adhere to a molecular clock. If the nonhuman rates rather than the human rate are extrapolated over the phylogeny of the great apes, we estimate divergence and speciation times that are much more in line with the fossil record and the biogeography.

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Análise de leitura longa de DNA pode dar origem a erros

Correspondence | Published: 22 January 2019

Errors in long-read assemblies can critically affect protein prediction

Mick Watson & Amanda Warr

Nature Biotechnology volume 37, pages124–126 (2019)

Source/Fonte: QiagenScience

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Nature Biotechnology

Senciência e Consciência em Células Únicas: Como as Primeiras Mentes Surgiram nas Espécies Unicelulares

Sentience and Consciousness in Single Cells: How the First Minds Emerged in Unicellular Species

František Baluška Arthur Reber

First published: 04 February 2019

https://doi.org/10.1002/bies.201800229

Source/Fonte: Internet

Abstract

A reductionistic, bottom‐up, cellular‐based concept of the origins of sentience and consciousness has been put forward. Because all life is based on cells, any evolutionary theory of the emergence of sentience and consciousness must be grounded in mechanisms that take place in prokaryotes, the simplest unicellular species. It has been posited that subjective awareness is a fundamental property of cellular life. It emerges as an inherent feature of, and contemporaneously with, the very first life‐forms. All other varieties of mentation are the result of evolutionary mechanisms based on this singular event. Therefore, all forms of sentience and consciousness evolve from this original instantiation in prokaryotes. It has also been identified that three cellular structures and mechanisms that likely play critical roles here are excitable membranes, oscillating cytoskeletal polymers, and structurally flexible proteins. Finally, basic biophysical principles are proposed to guide those processes that underly the emergence of supracellular sentience from cellular sentience in multicellular organisms.

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Richard Dawkins, ateu militante: “Tomando a coragem de Darwin para combater a arrogância da fé”

Zoológicos humanos: A história esquecida do racismo científico dos Estados Unidos

Os dímeros da ATP sintase mitocondrial induzem a curvatura da membrana e se auto-montam em fileiras: mero acaso, fortuita necessidade ou design inteligente?

Dimers of mitochondrial ATP synthase induce membrane curvature and self-assemble into rows

Thorsten B. Blum, Alexander Hahn, Thomas Meier, Karen M. Davies, and Werner Kühlbrandt

PNAS published ahead of print February 13, 2019

https://doi.org/10.1073/pnas.1816556116

Edited by David J. DeRosier, Brandeis University, Waltham, MA, and approved January 3, 2019 (received for review September 25, 2018)

Proteoliposomes of reconstituted Y. lipolytica ATP synthase dimers. (A and C) ATP synthase dimers (yellow) form rows that bend the lipid bilayer (light blue). Insets shows cross-sections (white lines), indicating that dimer rows bend the lipid bilayer by ∼90° (dashed red lines). (B) Flat membrane regions are devoid of ATP synthase. (D) Parallel rows of bidirectionally inserted dimers bend the bilayer into a corrugated sheet. (Scale bars, 100 nm.)

Significance

The ATP synthase in the inner membrane of mitochondria generates most of the ATP that enables higher organisms to live. The inner membrane forms deep invaginations called cristae. Mitochondrial ATP synthases are dimeric complexes of two identical monomers. It is known that the ATP synthase dimers form rows along the tightly curved cristae ridges. Computer simulations suggest that the dimer rows bend the membrane locally, but this has not been shown experimentally. In this study, we use electron cryotomography to provide experimental proof that ATP synthase dimers assemble spontaneously into rows upon membrane reconstitution, and that these rows bend the membrane. The assembly of ATP synthase dimers into rows is most likely the first step in the formation of mitochondrial cristae.

Abstract

Mitochondrial ATP synthases form dimers, which assemble into long ribbons at the rims of the inner membrane cristae. We reconstituted detergent-purified mitochondrial ATP synthase dimers from the green algae Polytomella sp. and the yeast Yarrowia lipolytica into liposomes and examined them by electron cryotomography. Tomographic volumes revealed that ATP synthase dimers from both species self-assemble into rows and bend the lipid bilayer locally. The dimer rows and the induced degree of membrane curvature closely resemble those in the inner membrane cristae. Monomers of mitochondrial ATP synthase reconstituted into liposomes do not bend membrane visibly and do not form rows. No specific lipids or proteins other than ATP synthase dimers are required for row formation and membrane remodelling. Long rows of ATP synthase dimers are a conserved feature of mitochondrial inner membranes. They are required for cristae formation and a main factor in mitochondrial morphogenesis.

mitochondria ATP synthase membrane curvature electron cryotomography subtomogram averaging

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Como as proteínas se tornam incorporadas em uma membrana celular: mero acaso, fortuita necessidade ou design inteligente?

Insertion and folding pathways of single membrane proteins guided by translocases and insertases

Tetiana Serdiuk1, Anja Steudle2, Stefania A. Mari1, Selen Manioglu1, H. Ronald Kaback3,4,5, Andreas Kuhn2 and Daniel J. Müller1,*

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Science Advances 30 Jan 2019: Vol. 5, no. 1, eaau6824

DOI: 10.1126/sciadv.aau6824

Source/Fonte: Spark Notes

Abstract

Biogenesis in prokaryotes and eukaryotes requires the insertion of α-helical proteins into cellular membranes for which they use universally conserved cellular machineries. In bacterial inner membranes, insertion is facilitated by YidC insertase and SecYEG translocon working individually or cooperatively. How insertase and translocon fold a polypeptide into the native protein in the membrane is largely unknown. We apply single-molecule force spectroscopy assays to investigate the insertion and folding process of single lactose permease (LacY) precursors assisted by YidC and SecYEG. Both YidC and SecYEG initiate folding of the completely unfolded polypeptide by inserting a single structural segment. YidC then inserts the remaining segments in random order, whereas SecYEG inserts them sequentially. Each type of insertion process proceeds until LacY folding is complete. When YidC and SecYEG cooperate, the folding pathway of the membrane protein is dominated by the translocase. We propose that both of the fundamentally different pathways along which YidC and SecYEG insert and fold a polypeptide are essential components of membrane protein biogenesis.

Acknowledgments: 

We thank R. Newton for discussing the manuscript, R. E. Dalbey for providing plasmid pT7-7 encoding YidC with a His10-tag at the C terminus, D. Balasubramaniam and J. Sugihara for providing some of the LacY and YidC samples used, D. Fotiadis for providing plasmid encoding the PreScission protease, the BioEM Lab of the University of Basel for providing TEM access and assistance, and N. Beerenwinkel for encouraging and constructive comments. Funding: This work was supported by the ETH-Zürich (to D.J.M.), the Swiss National Science Foundation (grant 205320_160199 to D.J.M.), and the National Center of Competence in Research “NCCR Molecular Systems Engineering” (to D.J.M.). Author contributions: T.S., D.J.M., A.K., and H.R.K. designed the experiments. A.K. and A.S. designed the SecY-YidC fusion construct. A.S. cloned, expressed, purified, and reconstituted the SecYEG and SecYEG-YidC fusion construct. T.S. performed the SMFS experiments. S.A.M. recorded AFM and TEM images. S.M. recorded Western blots. All authors analyzed experimental data and wrote the paper. Competing interests: The authors declare that they have no competing interests. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the authors.

Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC).

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Proteínas análogas à linguagem natural: mero acaso, fortuita necessidade ou design inteligente?

Grammar of protein domain architectures

Lijia Yu, Deepak Kumar Tanwar, Emanuel Diego S. Penha, Yuri I. Wolf, Eugene V. Koonin, and Malay Kumar Basu

PNAS published ahead of print February 7, 2019

https://doi.org/10.1073/pnas.1814684116

Edited by Clyde A. Hutchison III, J. Craig Venter Institute, La Jolla, CA, and approved January 4, 2019 (received for review August 27, 2018).

Phylogenetic tree built from cross-entropy values. Domain bigram models were generated from 37 selected eukaryotic clades (Dataset S2) from the main branches of Eukaryota. The cross-entropies of bigram models were calculated in an all-vs.-all comparison. The entropy values were then normalized to create a distance matrix (see Methods for details), and the tree was constructed using the neighbor-joining method. The major groups are colored as shown in the legend.

Significance

Genomes appear similar to natural language texts, and protein domains can be treated as analogs of words. To investigate the linguistic properties of genomes further, we calculated the complexity of the “protein languages” in all major branches of life and identified a nearly universal value of information gain associated with the transition from a random domain arrangement to the current protein domain architecture. An exploration of the evolutionary relationship of the protein languages identified the domain combinations that discriminate between the major branches of cellular life. We conclude that there exists a “quasi-universal grammar” of protein domains and that the nearly constant information gain we identified corresponds to the minimal complexity required to maintain a functional cell.

Abstract

From an abstract, informational perspective, protein domains appear analogous to words in natural languages in which the rules of word association are dictated by linguistic rules, or grammar. Such rules exist for protein domains as well, because only a small fraction of all possible domain combinations is viable in evolution. We employ a popular linguistic technique, n-gram analysis, to probe the “proteome grammar”—that is, the rules of association of domains that generate various domain architectures of proteins. Comparison of the complexity measures of “protein languages” in major branches of life shows that the relative entropy difference (information gain) between the observed domain architectures and random domain combinations is highly conserved in evolution and is close to being a universal constant, at ∼1.2 bits. Substantial deviations from this constant are observed in only two major groups of organisms: a subset of Archaea that appears to be cells simplified to the limit, and animals that display extreme complexity. We also identify the n-grams that represent signatures of the major branches of cellular life. The results of this analysis bolster the analogy between genomes and natural language and show that a “quasi-universal grammar” underlies the evolution of domain architectures in all divisions of cellular life. The nearly universal value of information gain by the domain architectures could reflect the minimum complexity of signal processing that is required to maintain a functioning cell.

n-grambigramprotein domainlanguagedomain architecture

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Uma proposta para o futuro da publicação científica nas ciências da vida

A proposal for the future of scientific publishing in the life sciences

Bodo M. Stern , Erin K. O’Shea 

Published: February 12, 2019 https://doi.org/10.1371/journal.pbio.3000116

Source/Fonte: Internet

Abstract

Science advances through rich, scholarly discussion. More than ever before, digital tools allow us to take that dialogue online. To chart a new future for open publishing, we must consider alternatives to the core features of the legacy print publishing system, such as an access paywall and editorial selection before publication. Although journals have their strengths, the traditional approach of selecting articles before publication (“curate first, publish second”) forces a focus on “getting into the right journals,” which can delay dissemination of scientific work, create opportunity costs for pushing science forward, and promote undesirable behaviors among scientists and the institutions that evaluate them. We believe that a “publish first, curate second” approach with the following features would be a strong alternative: authors decide when and what to publish; peer review reports are published, either anonymously or with attribution; and curation occurs after publication, incorporating community feedback and expert judgment to select articles for target audiences and to evaluate whether scientific work has stood the test of time. These proposed changes could optimize publishing practices for the digital age, emphasizing transparency, peer-mediated improvement, and post-publication appraisal of scientific articles.

Citation: Stern BM, O’Shea EK (2019) A proposal for the future of scientific publishing in the life sciences. PLoS Biol 17(2): e3000116. https://doi.org/10.1371/journal.pbio.3000116

Published: February 12, 2019

Copyright: © 2019 Stern, O’Shea. 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.

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

Competing interests: We have read the journal's policy and the authors of this manuscript have the following competing interest: Both authors are employees of the Howard Hughes Medical Institute.

Abbreviations: CV, curriculum vitae; DOI, digital object identifier; HHMI, Howard Hughes Medical Institute; JIF, journal impact factor; ORCID, open researcher and contributor ID

Provenance: Not commissioned; externally peer-reviewed.

Darwin, olha só o presente: mais de 1.000 cientistas com Ph. D. são céticos da capacidade da seleção natural como mecanismo evolucionário!

Darwin, celebrando o seu dia, eis aqui uma lista de dissidentes científicos que, colocando em risco suas carreiras acadêmicas, questionam a capacidade da seleção natural como mecanismo responsável pelas novidades evolucionárias.  

Nova tradução de A Caixa Preta de Darwin: o desafio da bioquímica à teoria da evolução

A Caixa Preta de Darwin: o desafio da bioquímica à teoria da evolução

Ciências

Michael J. Behe

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Disponível a partir de 28/02/2019

Em 1996, A caixa preta de Darwin lançou ao mundo a Teoria do Design Inteligente: o argumento de que a natureza exibe evidências de design que vão muito além do acaso darwinista. O livro catalisou um debate bastante acalorado sobre a evolução, que continua cada vez mais a se intensificar nos Estados Unidos e no mundo, incluindo o Brasil. Em um amplo espectro científico, a obra se estabeleceu como o texto básico e fundamental do design inteligente (DI), o argumento que precisa ser considerado para determinar se a evolução, segundo propôs Darwin, é mesmo suficiente para explicar a vida da forma que hoje a conhecemos. No posfácio da edição comemorativa do 10º aniversário do livro, Behe explica como a complexidade descoberta por microbiologistas cresceu drasticamente desde a publicação de seu livro e como essa complexidade irredutível tem sido um desafio contínuo ao darwinismo, que, sistematicamente, tem falhado em explicá-la. No posfácio comemorativo desta edição de 2019, Behe reforça o poder crescente de seus argumentos – tão atuais e devastadores em 2019 quanto eram em 1996 – e comemora o crescimento do DI no Brasil e no mundo. A caixa preta de Darwin é histórico, indispensável e ainda mais importante hoje do que era em 1996!

Detalhes

ISBN: 978-85-8293-824-9

Ano: 2019

Nº Paginas: 432

Edição: 1

Dimensões: 16 x 23 cm

Peso: 0,600 g

Categoria: Ciências

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Dr. Vladimir Voeikov 'falou e disse': o neodarwinismo é ideologia e filosofia que impede o avanço da ciência

"A ideologia e filosofia do neodarwinismo que é vendida pelos seus adeptos como uma fundação teórico-científica da biologia impede seriamente o desenvolvimento da ciência e esconde dos seus estudantes os problemas reais da área."

"The ideology and philosophy of neo-Darwinism which is sold by its adepts as a scientific theoretical foundation of biology seriously hampers the development of science and hides from students the field’s real problems."

Dr. Vladimir L. Voeikov, Professor de Bioorgânica, Universidade Estadual de Moscou; membro da Academia Russa de Ciências Naturais/Professor of Bioorganic, Moscow State University; member of the Russian Academy of Natural Sciences.

Ele assinou a lista da Dissenção Científica do Darwinismo/He signed the Scientific Dissent from Darwinism list.

A “Máquina de Estabilização dos Oceanos” pode representar um fator primordial subjacente ao efeito do “aquecimento global na mudança climática”

ACS Vol.9 No.1, January 2019

The “Ocean Stabilization Machine” May Represent a Primary Factor Underlying the Effect of “Global Warming on Climate Change”

DOI: 10.4236/acs.2019.91009

Author(s) Yanjun Mao1, Jiqing Tan2*, Bomin Chen3, Huiyi Fan2 Affiliation(s)

1Climate Center, Zhejiang Meteorologic Bureau, Hangzhou, China.

2Earth Science School, Zhejiang University, Hangzhou, China.

3Shanghai Climate Center, Shanghai, China.

Source/Fonte: TreeHugger

ABSTRACT

Contemporary references to global warming pertain to the dramatic increase in monthly global land surface temperature (GLST) anomalies since 1976. In this paper, we argue that recent global warming is primarily a result of natural causes; we have established three steps that support this viewpoint. The first is to identify periodic functions that perfectly match all of the monthly anomaly data for GLST; the second is to identify monthly sea surface temperature (SST) anomalies that are located within different ocean basin domains and highly correlated with the monthly GLST anomalies; and the third is to determine whether the dramatically increasing (or dramatically decreasing) K-line diagram signals that coincide with GLST anomalies occurred in El Niño years (or La Niña years). We have identified 15,295 periodic functions that perfectly fit the monthly GLST anomalies from 1880 to 2013 and show that the monthly SST anomalies in six domains in different oceans are highly correlated with the monthly GLST anomalies. In addition, most of the annual dramatically increasing GLST anomalies occur in El Niño years; and most of the annual dramatically decreasing GLST anomalies occur in La Niña years. These findings indicate that the “ocean stabilization machine” might represent a primary factor underlying the effect of “global warming on climate change”.

KEYWORDS

Global Warming, Monthly Global Land Surface Temperature (GLST) Anomalies, Monthly SST Anomalies, Ocean Stabilization Machine, K-Line Diagram Signals

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Vida sem design intencional???

Life without design

Constructor theory is a new vision of physics, but it helps to answer a very old question: why is life possible at all?

Automotive Industry mural by Marvin Beerbohm, 1940. Detroit Public Library. Photo by Smithsonian Institution/Corbis

Chiara Marletto is a postdoctoral research associate and junior research fellow at Wolfson College at the University of Oxford.

2,400 words

Edited by Ed Lake

Living things have puzzled and challenged us since the dawn of our species. Even in the light of our modern scientific understanding, they seem remarkable. A merlin falcon hunting its prey, a hummingbird suspended in the air beside a flower, the self-reproduction of a bacterial cell: all are instances of stunning control and precision. How could anything so complex have originated from inert matter?

For millennia, some of the most brilliant thinkers have attempted to answer this question. Most of them concluded that living things must have been produced by an intentional design process. They were wrong, of course: the theory of evolution by variation and natural selection – Charles Darwin’s momentous leap – shows how those stupendously intricate mechanisms can come about without one. Yet the task of showing how life itself can arise without design is surprisingly vexed.

The very problem Darwin’s theory addresses is ultimately rooted in physics: living things have certain properties that seem to set them apart from other aggregations of inert matter. They have many different subparts – instantiating biological adaptations – all coordinating to some function. That’s the key property: they closely resemble objects that have literally been designed, such as factories and robots. For example, the ciliary muscles and the lens in the eye coordinate exquisitely to permit vision, just like the optical components of a sophisticated camera. In modern biology, this is called the appearance of design – a property described by Socrates and given canonical expression in 1802 by William Paley in his ‘watchmaker’ argument for the existence of God.

More generally, living things, again just like factories and robots, have the ability to perform physical transformations with a very high degree of precision, and to do so repeatedly and reliably. A goat’s jaws and heart just keep on chewing and beating for its whole lifetime. If you got the goat to graze your lawn, it would mow it to high accuracy and be just as capable of doing the same when presented with another lawn. It just keeps going: the goat is, among other things, a lawnmowing machine.

Unlike factories, all living things rely on a rather peculiar contrivance: the living cell. Cells can self-reproduce, manufacturing new instances of themselves in a process involving, at its heart, the faithful replication of the genetic information contained in the cell’s DNA. We find this capacity nowhere in the rest of nature. Even among human technologies, there are only dim foreshadowings of it, such as 3D printers that print some of their own spare parts.

Why should such features of living things constitute a problem for physics? Crucially, what can and cannot be made to happen in the physical world is determined by physical laws. For example, a perpetual motion machine cannot be constructed, no matter what resources are devoted to the task, as it is forbidden by those laws. Conversely, given the presence of life in our universe, physics must be such as to allow for it.

But our laws of physics provide only certain elementary objects, such as simple chemicals, in great numbers. These objects do not, in themselves, have the ability to repeatedly cause highly accurate transformations. Neither do they seem adapted to do anything in particular. If they do cause transformations, it is neither very accurately nor reliably: they wear out and make errors, their resources get depleted, and so on. In other words, the laws of physics contain no built-in facility for accurate transformations; nor, in particular, for biological adaptations that can bring such transformations about. They are no-design, in this special sense. Thus the problem with living things, expressed within physics, is that they are highly adapted to effect all sorts of transformations to high accuracy, whereas the laws of physics aren’t.

Given that life isn’t the output of an intentional design process, but evolved, how could living things have evolved given these design-free laws of physics? Darwin’s theory addresses this problem, explaining that variation and natural selection bring about the appearance of design. But this in itself doesn’t close the explanatory gap, as we can see especially clearly in the modern version of Darwin’s theory – neo-Darwinism. At its heart are the replicators, or genes – bits of DNA that are transmitted, by replication, to the next generation. Moreover, for replication to be as accurate as it is in living things, accurate self-reproduction of the cell is also required. In short, the theory presupposes the possibility of certain accurate physical transformations, and these are just what no-design laws of physics fail to provide in their starter kit.

Here’s where the puzzle arises. Biological replication and self‑reproduction are in fact such stupendously well‑orchestrated physical transformations that one must explain how they are possible under the simple, no‑design laws of physics such as ours. This additional explanation, which was not included in the theory of evolution, is essential for that theory to properly explain how living things arise without intentional design – to close the explanatory gap.

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Micróbios incomuns contêm pistas para o início da vida

Carboxydotrophy potential of uncultivated Hydrothermarchaeota from the subseafloor crustal biosphere

Stephanie A. Carr, Sean P. Jungbluth, Emiley A. Eloe-Fadrosh, Ramunas Stepanauskas, Tanja Woyke, Michael S. Rappé & Beth N. Orcutt

The ISME Journal (2019)

Abstract

The exploration of Earth’s terrestrial subsurface biosphere has led to the discovery of several new archaeal lineages of evolutionary significance. Similarly, the deep subseafloor crustal biosphere also harbors many unique, uncultured archaeal taxa, including those belonging to Candidatus Hydrothermarchaeota, formerly known as Marine Benthic Group-E. Recently, Hydrothermarchaeota was identified as an abundant lineage of Juan de Fuca Ridge flank crustal fluids, suggesting its adaptation to this extreme environment. Through the investigation of single-cell and metagenome-assembled genomes, we provide insight into the lineage’s evolutionary history and metabolic potential. Phylogenomic analysis reveals the Hydrothermarchaeota to be an early-branching archaeal phylum, branching between the superphylum DPANN, Euryarchaeota, and Asgard lineages. Hydrothermarchaeota genomes suggest a potential for dissimilative and assimilative carbon monoxide oxidation (carboxydotrophy), as well as sulfate and nitrate reduction. There is also a prevalence of chemotaxis and motility genes, indicating adaptive strategies for this nutrient-limited fluid-rock environment. These findings provide the first genomic interpretations of the Hydrothermarchaeota phylum and highlight the anoxic, hot, deep marine crustal biosphere as an important habitat for understanding the evolution of early life.

Acknowledgements

The authors thank the AT18-07 cruise party for their assistance including Andrew Fisher as chief scientist; Samuel Hulme, Geoff Wheat, and the late James Cowen for assistance with fluid sampling; Keir Becker for observatory expertise; and Tina Lin, Oliver Hseih, and the late Katrina Edwards for sample handling. We thank the staff of the Single Cell Genomics Center at Bigelow Laboratory for Ocean Sciences for expert handling, sorting, amplification, and sequencing of single cells, the Joint Genome Institute for metagenomic sequencing, Daniel Rogers for mcrA standards, and Bo Barker Jørgensen at Aarhus University for supporting Orcutt’s participation in the cruise. The 2011 cruise was supported by NSF grants MCB-0604014 (lead J. Cowen), OCE-0726887 (lead K. Becker), and OCE-1031808 (lead A. Fisher). SAC was supported by postdoctoral fellowships from the Center for Dark Energy Biosphere Investigations (C-DEBI; NSF award OCE-0939564) and the NSF (OCE-1521614). The efforts of SPJ and MSR were supported by NSF grants MCB-0604014 and OCE-1260723. BNO acknowledges support from C-DEBI, the NASA Astrobiology Institute (NNA13AA92A), and NSF (OCE-1233226). This work was also supported by the grants DEB-1441717 (NSF), OCE-1335810 (NSF) and CSP2013-987 (DOE JGI) to RS. The work conducted by the US Department of Energy Joint Genome Institute (JGI), a US Department of Energy Office of Science User Facility, is supported under contract no. DE-AC02-05CH11231. This is C-DEBI contribution number 451, HIMB contribution number 1747, and SOEST contribution number 10573.

Author information

Affiliations

Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA

Stephanie A. Carr, Ramunas Stepanauskas & Beth N. Orcutt

Hartwick College, Oneonta, NY, USA

Stephanie A. Carr

Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA

Sean P. Jungbluth

Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA

Sean P. Jungbluth, Emiley A. Eloe-Fadrosh & Tanja Woyke

Hawaii Institute of Marine Biology, University of Hawaii at Manoa, PO BOX 1346, Kaneohe, HI, 96744, USA

Sean P. Jungbluth & Michael S. Rappé

Conflict of interest

The authors declare that they have no conflict of interest.

Corresponding authors

Correspondence to Michael S. Rappé or Beth N. Orcutt.

FREE PDF GRATIS: The ISME Journal Sup. Info. 1 Sup.Info. 2

Pesquisa sugere que a vida era abundante na Terra 3,5 bilhões de anos atrás

Role of APS reductase in biogeochemical sulfur isotope fractionation

Min Sub Sim, Hideaki Ogata, Wolfgang Lubitz, Jess F. Adkins, Alex L. Sessions, Victoria J. Orphan & Shawn E. McGlynn 

Nature Communications volume 10, Article number: 44 (2019)

The pathway of dissimilatory sulfate reduction with the molecular structures of sulfur-containing metabolites and the enzymes catalyzing their transformation. Adenosine phosphosulfate reductase, the enzyme of interest in this study, breaks the first S–O bond in the sulfate group, which involves the transfer of two electrons

Abstract

Sulfur isotope fractionation resulting from microbial sulfate reduction (MSR) provides some of the earliest evidence of life, and secular variations in fractionation values reflect changes in biogeochemical cycles. Here we determine the sulfur isotope effect of the enzyme adenosine phosphosulfate reductase (Apr), which is present in all known organisms conducting MSR and catalyzes the first reductive step in the pathway and reinterpret the sedimentary sulfur isotope record over geological time. Small fractionations may be attributed to low sulfate concentrations and/or high respiration rates, whereas fractionations greater than that of Apr require a low chemical potential at that metabolic step. Since Archean sediments lack fractionation exceeding the Apr value of 20‰, they are indicative of sulfate reducers having had access to ample electron donors to drive their metabolisms. Large fractionations in post-Archean sediments are congruent with a decline of favorable electron donors as aerobic and other high potential metabolic competitors evolved.

Acknowledgments

This work was supported by the Research Resettlement Fund for the new faculty of Seoul National University to M.S.S., the NASA Research Opportunities in Space and Earth Sciences grant award number NNX14AO48G to S.E.M. and V.J.O., JSPS KAKENHI Grant Number 10751084 to S.E.M., and the Gordon and Betty Moore Foundation Grant GBMF 3306 to V.J.O. and A.L.S. This research was a part of the project titled ‘Understanding the deepsea biosphere on seafloor hydrothermal vents in the Indian Ridge (20170411)’, funded by the Ministry of Oceans and Fisheries, Korea. We are grateful for insightful and helpful conversations with Boswell A. Wing, David T. Johnston, David A. Fike, and Itay Halevy. We are especially grateful to Tatsuhiko Yagi and Yoshiki Higuchi for helping with initiating collaboration.

Author information

Affiliations

School of Earth and Environmental Sciences, Seoul National University, Seoul, 08826, South Korea

Min Sub Sim

Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, 91125, USA

Min Sub Sim, Jess F. Adkins, Alex L. Sessions, Victoria J. Orphan & Shawn E. McGlynn

Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, D-45470, Mülheim an der Ruhr, Germany

Hideaki Ogata & Wolfgang Lubitz

Institute of Low Temperature Science, Hokkaido University, Sapporo, 060-0819, Japan

Hideaki Ogata

Earth-Life Science Institute, Tokyo Institute of Technology, Ookayama, Tokyo, 152-8550, Japan

Shawn E. McGlynn

Contributions

M.S.S. and S.E.M. devised the study. H.O. and W.L. purified APS reductase, and M.S.S. executed enzymatic assay and sulfur isotope measurements. M.S.S. and S.E.M. wrote the first draft of the manuscript, and J.F.A., A.L.S., and V.J.O. contributed to interpretation and writing.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Min Sub Sim or Shawn E. McGlynn.

FREE PDF GRATIS: Nature Communications Sup. Info.

Cientistas estudam a organização da vida em uma escala planetária

Universal scaling across biochemical networks on Earth

Hyunju Kim1,2,*, Harrison B. Smith2,*, Cole Mathis1,3, Jason Raymond2 and Sara I. Walker1,2,4,5,†

1Beyond Center for Fundamental Concepts in Science, Arizona State University, Tempe, AZ, USA.

2School of Earth and Space Exploration, Arizona State University, Tempe, AZ, USA.

3Department of Physics, Arizona State University, Tempe, AZ, USA.

4ASU-SFI Center for Biosocial Complex Systems, Tempe, AZ, USA.

5Blue Marble Space Institute of Science, Seattle, WA, USA.

↵†Corresponding author. Email: sara.i.walker@asu.edu

↵* These authors contributed equally to this work.

Science Advances 16 Jan 2019:

Vol. 5, no. 1, eaau0149

DOI: 10.1126/sciadv.aau0149

Source/Fonte: Internet

Abstract

The application of network science to biology has advanced our understanding of the metabolism of individual organisms and the organization of ecosystems but has scarcely been applied to life at a planetary scale. To characterize planetary-scale biochemistry, we constructed biochemical networks using a global database of 28,146 annotated genomes and metagenomes and 8658 cataloged biochemical reactions. We uncover scaling laws governing biochemical diversity and network structure shared across levels of organization from individuals to ecosystems, to the biosphere as a whole. Comparing real biochemical reaction networks to random reaction networks reveals that the observed biological scaling is not a product of chemistry alone but instead emerges due to the particular structure of selected reactions commonly participating in living processes. We show that the topology of biochemical networks for the three domains of life is quantitatively distinguishable, with >80% accuracy in predicting evolutionary domain based on biochemical network size and average topology. Together, our results point to a deeper level of organization in biochemical networks than what has been understood so far.

FREE PDF GRATIS: Science Advances

Cromossomos Y masculinos não são 'terras genéticas desertas'

Heterochromatin-Enriched Assemblies Reveal the Sequence and Organization of the Drosophila melanogaster Y Chromosome

Ching-Ho Chang and Amanda M. Larracuente

GENETICS January 1, 2019 vol. 211 no. 1 333-348; https://doi.org/10.1534/genetics.118.301765

Source/Fonte

Abstract

Heterochromatic regions of the genome are repeat-rich and poor in protein coding genes, and are therefore underrepresented in even the best genome assemblies. One of the most difficult regions of the genome to assemble are sex-limited chromosomes. The Drosophila melanogaster Y chromosome is entirely heterochromatic, yet has wide-ranging effects on male fertility, fitness, and genome-wide gene expression. The genetic basis of this phenotypic variation is difficult to study, in part because we do not know the detailed organization of the Y chromosome. To study Y chromosome organization in D. melanogaster, we develop an assembly strategy involving the in silico enrichment of heterochromatic long single-molecule reads and use these reads to create targeted de novo assemblies of heterochromatic sequences. We assigned contigs to the Y chromosome using Illumina reads to identify male-specific sequences. Our pipeline extends the D. melanogaster reference genome by 11.9 Mb, closes 43.8% of the gaps, and improves overall contiguity. The addition of 10.6 MB of Y-linked sequence permitted us to study the organization of repeats and genes along the Y chromosome. We detected a high rate of duplication to the pericentric regions of the Y chromosome from other regions in the genome. Most of these duplicated genes exist in multiple copies. We detail the evolutionary history of one sex-linked gene family, crystal-Stellate. While the Y chromosome does not undergo crossing over, we observed high gene conversion rates within and between members of the crystal-Stellate gene family, Su(Ste), and PCKR, compared to genome-wide estimates. Our results suggest that gene conversion and gene duplication play an important role in the evolution of Y-linked genes.

DROSOPHILA MELANOGASTER GENOME Y CHROMOSOME LONG-READ ASSEMBLY GENE DUPLICATIONS GENE CONVERSION CRYSTAL-STELLATE GENETICS OF SEX

FREE PDF GRATIS: Genetics

Uma publicação científica darwinista convoca artigos sobre teleologia e educação da evolução

Call for Papers: Teleology and Evolution Education

Evolution: Education and Outreach invites original contributions exploring all aspects of teleological reasoning and teleological language pertinent to the teaching and learning of evolution. The scope of papers to be included in this special issue will range from theoretical reflections on the role that teleology should play in evolution education to empirical studies addressing teleology-related aspects of teaching and learning evolution. Submitted papers may, for example, address: the assessment of students’ teleological reasoning and teleological misconceptions about evolution; teaching strategies and learning environments focusing on teleology; or teachers’ teleology-related instructional practices and professional development. The literature on teleology is diverse; we welcome a range of positions from a variety of disciplines (e.g., cognitive psychology, learning sciences, biology education, philosophy of science).

Questions about contributions may be directed to Prof. Marcus Hammann, Guest Editor of the special issue, or to Editor-in-Chief Ross Nehm. Submissions are now open, with an anticipated publication date of December 2019.

Evolution: Education and Outreach is now celebrating its 10th anniversary, and has recently attained SCOPUS indexing.

Submitted papers will be reviewed in a timely manner and published directly after acceptance (i.e. without waiting for the accomplishment of all other contributions). Thanks to the Evolution: Education and Outreach open access policy, the articles published in this thematic series will have a wide, global audience.

Submission instructions

Before submitting your manuscript, please ensure you have carefully read the submission guidelines for Evolution: Education and Outreach. The complete manuscript should be submitted through the journal submission system. To ensure that you submit to the correct thematic series please select the appropriate section in the drop-down menu upon submission. In addition, indicate within your cover letter that you wish your manuscript to be considered as part of the thematic series on series title. All submissions will undergo rigorous peer review, and accepted articles will be published within the journal as a collection.

Submissions will also benefit from the usual advantages of open access publication:

Rapid publication: Online submission, electronic peer review and production make the process of publishing your article simple and efficient

High visibility and international readership in your field: Open access publication ensures high visibility and maximum exposure for your work - anyone with online access can read your article

No space constraints: Publishing online means unlimited space for figures, extensive data and video footage.

Authors retain copyright, licensing the article under a Creative Commons license: articles can be freely redistributed and reused as long as the article is correctly attributed.

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NOTA DESTE BLOGGER:

Mas Darwin não tinha eliminado de uma vez por todas a teleologia na biologia evolucionária???

Eu queria ver a cara de meus amigos professores universitários de Biologia e de História da Ciência que disseram que eu tinha embarcado numa canoa furada da teoria do Design Inteligente por propor a teleologia nas coisas biológicas. Eu queria ver a cara da Galera dos meninos e meninas de Darwin pelas suas provocações e deboches: a ciência está nos vindicando - a teleologia é real na natureza e pode ser detectada!!!