George Ellis: como reconhecer a causação de cima para baixo

Recognising Top-Down Causation

George Ellis, University of Cape Town

1: The Theme

A key assumption underlying most present day physical thought is the idea that causation is bottom up all the way: particle physics underlies nuclear physics, nuclear physics underlies atomic physics, atomic physics underlies chemistry, and so on. Thus all the higher level subjects are at least in principle reducible to particle physics, which is therefore the only fundamental science; as famously claimed by Dirac, chemistry is just an application of quantum physics [1].

However there are many topics that one cannot understand by assuming this one-way flow of causation. The flourishing subject of social neuroscience makes clear how social influences act down on individual brain structure [2]; studies in physiology demonstrate that downward causation is necessary in understanding the heart, where this form of causation can be represented as the influences of initial and boundary conditions on the solutions of the differential equations used to represent the lower level processes [3]; epigenetic studies demonstrate that biological development is crucially shaped by the environment [4].

What about physics? In this essay I will make the case that top-down causation is also prevalent in physics, even though this is not often recognised as such. This does not occur by violating physical laws; on the contrary, it occurs through the laws of physics, by setting constraints on lower level interactions. Thus my theme is that the foundational assumption that all causation is bottom up is wrong, even in the case of physics [5]. Some writers on this topic prefer to refer to “contextual effects” or “whole-part constraints”. These are perfectly acceptable terms, but I will make the case that the stronger term “top-down causation” is appropriate in many cases.

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BIOGRAPHY

George Francis Rayner Ellis is the Emeritus Distinguished Professor of Complex Systems in the Department of Mathematics and Applied Mathematics at the University of Cape Town in South Africa.

He co-authored The Large Scale Structure of Space-Time with University of Cambridge physicist Stephen Hawking, published in 1973, and is considered one of the world's leading theorists in cosmology. He is an active Quaker and in 2004 he won the Templeton Prize.

From 1989 to 1992 he served as President of the International Society on General Relativity and Gravitation. He is a past President of the International Society for Science and Religion. He is an A-rated researcher with the NRF.

Ellis attended the University of Cape Town, where he graduated with honors with a Bachelor of Science degree in physics with distinction. He received a PhD in applied mathematics and theoretical physics at Cambridge University.

Source/Fonte

Uma Web Verde ou um relógio molecular mega-enviesado???

Green Web or megabiased clock? Plant fossils from Gondwanan Patagonia speak on evolutionary radiations

Author for correspondence:

Peter Wilf

Tel: +1 814 865 6721

Email: pwilf@psu.edu

Received: 31 July 2014 Accepted: 12 September 2014

Peter Wilf1 and Ignacio H. Escapa2

1 Department of Geosciences, Pennsylvania State University, University Park, PA 16802, USA; 

2 CONICET, Museo Paleontol ogico

Egidio Feruglio, Avenida Fontana 140, 9100 Trelew, Chubut, Argentina

New Phytologist (2015) 207: 283–290

doi: 10.1111/nph.13114

Key words: divergence dating, evolutionary radiations, geochronology, Gondwana, molecular clocks, paleobotany, Patagonia.

Summary

Evolutionary divergence-age estimates derived from molecular ‘clocks’ are frequently correlated with paleogeographic, paleoclimatic and extinction events. One prominent hypothesis based on molecular data states that the dominant pattern of Southern Hemisphere biogeography is post-Gondwanan clade origins and subsequent dispersal across the oceans in a metaphoric ‘Green Web’. We tested this idea against well-dated Patagonian fossils of 19 plant lineages, representing organisms that actually lived on Gondwana. Most of these occurrences are substantially older than their respective, often post-Gondwanan molecular dates. The Green Web interpretation probably results from directional bias in molecular results. Gondwanan history remains fundamental to understanding Southern Hemisphere plant radiations, and we urge significantly greater caution when using molecular dating to interpret the biological impacts of geological events.

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EXCERPT:

We urge significantly greater caution when using molecular dates in the explicit context of geologic time and Earth history. The fossil record is always incomplete, but its exciting potential is only beginning to develop in many parts of the world. Future improvements in molecular dating seem very likely, but for now, fossils and geochronology provide the only rigorous, enduring temporal framework for evolutionary radiations.

Valores de apoio filogenético não são, necessariamente, informativos!!!

Phylogenetic support values are not necessarily informative: the case of the Serialia hypothesis (a mollusk phylogeny)

J Wolfgang WägeleEmail author, Harald Letsch, Annette Klussmann-Kolb, Christoph Mayer, Bernhard Misof and Heike Wägele

Frontiers in Zoology20096:12

DOI: 10.1186/1742-9994-6-12 © Wägele et al; licensee BioMed Central Ltd. 2009

Received: 02 April 2009 Accepted: 26 June 2009 Published: 26 June 2009

Abstract

Background

Molecular phylogenies are being published increasingly and many biologists rely on the most recent topologies. However, different phylogenetic trees often contain conflicting results and contradict significant background data. Not knowing how reliable traditional knowledge is, a crucial question concerns the quality of newly produced molecular data. The information content of DNA alignments is rarely discussed, as quality statements are mostly restricted to the statistical support of clades. Here we present a case study of a recently published mollusk phylogeny that contains surprising groupings, based on five genes and 108 species, and we apply new or rarely used tools for the analysis of the information content of alignments and for the filtering of noise (masking of random-like alignment regions, split decomposition, phylogenetic networks, quartet mapping).

Results

The data are very fragmentary and contain contaminations. We show that that signal-like patterns in the data set are conflicting and partly not distinct and that the reported strong support for a "rather surprising result" (monoplacophorans and chitons form a monophylum Serialia) does not exist at the level of primary homologies. Split-decomposition, quartet mapping and neighbornet analyses reveal conflicting nucleotide patterns and lack of distinct phylogenetic signal for the deeper phylogeny of mollusks.

Conclusion

Even though currently a majority of molecular phylogenies are being justified with reference to the 'statistical' support of clades in tree topologies, this confidence seems to be unfounded. Contradictions between phylogenies based on different analyses are already a strong indication of unnoticed pitfalls. The use of tree-independent tools for exploratory analyses of data quality is highly recommended. Concerning the new mollusk phylogeny more convincing evidence is needed.

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O mitogenoma de um Homo sapiens de 35.000 anos atrás apoia o retorno à África no Paleolítico

The mitogenome of a 35,000-year-old Homo sapiens from Europe supports a Palaeolithic back-migration to Africa

M. Hervella, E. M. Svensson, A. Alberdi, T. Günther, N. Izagirre, A. R. Munters, S. Alonso, M. Ioana, F. Ridiche, A. Soficaru, M. Jakobsson, M. G. Netea & C. de-la-Rua

Scientific Reports 6, Article number: 25501 (2016)

doi:10.1038/srep25501

Download Citation

Evolutionary biology Evolutionary genetics

Received: 15 February 2016 Accepted: 19 April 2016 Published online: 19 May 2016

Abstract

After the dispersal of modern humans (Homo sapiens) Out of Africa, hominins with a similar morphology to that of present-day humans initiated the gradual demographic expansion into Eurasia. The mitogenome (33-fold coverage) of the Peştera Muierii 1 individual (PM1) from Romania (35 ky cal BP) we present in this article corresponds fully to Homo sapiens, whilst exhibiting a mosaic of morphological features related to both modern humans and Neandertals. We have identified the PM1 mitogenome as a basal haplogroup U6*, not previously found in any ancient or present-day humans. The derived U6 haplotypes are predominantly found in present-day North-Western African populations. Concomitantly, those found in Europe have been attributed to recent gene-flow from North Africa. The presence of the basal haplogroup U6* in South East Europe (Romania) at 35 ky BP confirms a Eurasian origin of the U6 mitochondrial lineage. Consequently, we propose that the PM1 lineage is an offshoot to South East Europe that can be traced to the Early Upper Paleolithic back migration from Western Asia to North Africa, during which the U6 lineage diversified, until the emergence of the present-day U6 African lineages.

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Cometa 67P/Churyumov-Gerasimenko contém ingredientes necessários para a origem da vida

Prebiotic chemicals—amino acid and phosphorus—in the coma of comet 67P/Churyumov-Gerasimenko

Kathrin Altwegg1,2,*, Hans Balsiger1, Akiva Bar-Nun3, Jean-Jacques Berthelier4, Andre Bieler1,5, Peter Bochsler1, Christelle Briois6, Ursina Calmonte1, Michael R. Combi5, Hervé Cottin7, Johan De Keyser8, Frederik Dhooghe8, Bjorn Fiethe9, Stephen A. Fuselier10, Sébastien Gasc1, Tamas I. Gombosi5, Kenneth C. Hansen5, Myrtha Haessig1,10, Annette Jäckel1, Ernest Kopp1, Axel Korth11, Lena Le Roy2, Urs Mall11, Bernard Marty12, Olivier Mousis13, Tobias Owen14, Henri Rème15,16, Martin Rubin1, Thierry Sémon1, Chia-Yu Tzou1, James Hunter Waite10 and Peter Wurz1

+ Author Affiliations

↵*Corresponding author. Email: kathrin.altwegg@space.unibe.ch

Science Advances 27 May 2016:

Vol. 2, no. 5, e1600285

DOI: 10.1126/sciadv.1600285

Abstract

The importance of comets for the origin of life on Earth has been advocated for many decades. Amino acids are key ingredients in chemistry, leading to life as we know it. Many primitive meteorites contain amino acids, and it is generally believed that these are formed by aqueous alterations. In the collector aerogel and foil samples of the Stardust mission after the flyby at comet Wild 2, the simplest form of amino acids, glycine, has been found together with precursor molecules methylamine and ethylamine. Because of contamination issues of the samples, a cometary origin was deduced from the 13C isotopic signature. We report the presence of volatile glycine accompanied by methylamine and ethylamine in the coma of 67P/Churyumov-Gerasimenko measured by the ROSINA (Rosetta Orbiter Spectrometer for Ion and Neutral Analysis) mass spectrometer, confirming the Stardust results. Together with the detection of phosphorus and a multitude of organic molecules, this result demonstrates that comets could have played a crucial role in the emergence of life on Earth.

Keywords Origins of life chemistry astronomy comets prebiotic molecules amino acid 67P/Churyumov-Gerasimenko

Copyright © 2016, The Authors

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

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Sequência e fatores epigenéticos determinam a estrutura geral DNA

Direct evidence for sequence-dependent attraction between double-stranded DNA controlled by methylation

Jejoong Yoo, Hajin Kim, Aleksei Aksimentiev & Taekjip Ha

Affiliations Contributions Corresponding authors

Nature Communications 7, Article number: 11045 doi:10.1038/ncomms11045

Received 17 September 2015 Accepted 16 February 2016 Published 22 March 2016

Abstract

Although proteins mediate highly ordered DNA organization in vivo, theoretical studies suggest that homologous DNA duplexes can preferentially associate with one another even in the absence of proteins. Here we combine molecular dynamics simulations with single-molecule fluorescence resonance energy transfer experiments to examine the interactions between duplex DNA in the presence of spermine, a biological polycation. We find that AT-rich DNA duplexes associate more strongly than GC-rich duplexes, regardless of the sequence homology. Methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA–DNA attraction. Indeed, methylation of cytosines makes attraction between GC-rich DNA as strong as that between AT-rich DNA. Recent genome-wide chromosome organization studies showed that remote contact frequencies are higher for AT-rich and methylated DNA, suggesting that direct DNA–DNA interactions that we report here may play a role in the chromosome organization and gene regulation.

Subject terms: Biological sciences Biochemistry Biophysics Molecular biology

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Porque a ciência precisa quebrar o feitiço do materialismo reducionista

Why science needs to break the spell of reductive materialism

Stuart Kauffman is professor emeritus at the University of Pennsylvania. He was educated in philosophy, psychology and physiology at Dartmouth and Oxford, and obtained his medical degree from UCSF in 1968. He is an affiliate professor at the Institute for Systems Biology in Seattle. His latest book is Humanity in a Creative Universe (2016).

Published in association with Oxford University Press an Aeon Partner

Edited by Corey S Powell

We all sense something deeply deficient in our modern civilisation. Is it an absence of spirituality? Partly. A greedy materialism beyond what we really need? Yes, we are riding the tiger of late capitalism, where we make our living producing, selling and buying goods and services we often do not need on this finite planet. We cannot see ourselves, in part blinkered by unneeded scientism.

The central framework of current physics is that of entailing laws. The central image is the billiard table as boundary conditions and the set of all possible initial conditions of position and momenta of the balls on the table. Then, given Isaac Newton’s laws in differential form, we deduce the deterministic trajectories of the balls. Our model of how to do science is to deduce new consequences, test them, accept or reject the results by diverse criteria, then retain or modify our theories. Science proceeds as Aristotle might have wished, in part as deduction.

My aim is to begin to demolish this hegemony of reductive materialism and its grip on our scientific minds, and a far wider elicitation of a grossly misplaced scientism in modernity. Science is sciencia, knowledge. Being and becoming are more fundamental to all life and our humanity. We are, first of all, alive, and alive in a becoming biosphere. Despite bursts of extinction events and the fact that 99.9 per cent of all species that ever lived are gone, the biosphere flowers on. This flowering of the biosphere, more than a metaphor for human history, begins to suggest a mythic structure beyond that by which we currently live.

At the centre of my argument is a vexing question: since the Big Bang, why has the Universe become complex? I claim that at least part of the answer is that, as more complex things and linked processes are created, and can combine with one another to make yet more complex amalgams of things and processes, the space of possible things and linked processes becomes vastly larger, and the Universe has not had time to make all the possibilities.

Consider just carbon, hydrogen, nitrogen, oxygen, phosphorus and sulphur (CHNOPS), the atoms of organic chemistry. Now consider all possible molecules made of CHNOPS with, say, 100,000 atoms or fewer per molecule. (Coal is such a molecule, and the largest known coal molecule is about 1 × 2 × 1.5 miles somewhere in the United States, a single molecule made only of carbon, with far more than 100,000 carbon atoms.) We do not even know how to count the number of possible molecules containing CHNOPS with up to 100,000 atoms per molecule. But it is easy to see that the Universe cannot have had enough time to make them all.

...

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A seleção natural não sabe distinguir entre mutações benéficas e aleatórias em um ambiente flutuante!

Fate of a mutation in a fluctuating environment

Ivana Cvijovića,b,1, Benjamin H. Gooda,c,1, Elizabeth R. Jerisona,c, and 

Michael M. Desaia,c,2

Author Affiliations

Edited by Boris I. Shraiman, University of California, Santa Barbara, CA, and approved July 27, 2015 (received for review March 17, 2015)

Significance

Evolution in variable environments depends crucially on the fates of new mutations in the face of fluctuating selection pressures. In constant environments, the relationship between the selective effect of a mutation and the probability that it will eventually fix or go extinct is well understood. However, our understanding of fixation probabilities in fluctuating environmental conditions is limited. Here, we show that temporal fluctuations in environmental conditions can have dramatic effects on the fate of each new mutation, reducing the efficiency of natural selection and increasing the fixation probability of all mutations, including those that are strongly deleterious on average. This makes it difficult for a population to maintain specialist adaptations, even if their benefits outweigh their costs.

Abstract

Natural environments are never truly constant, but the evolutionary implications of temporally varying selection pressures remain poorly understood. Here we investigate how the fate of a new mutation in a fluctuating environment depends on the dynamics of environmental variation and on the selective pressures in each condition. We find that even when a mutation experiences many environmental epochs before fixing or going extinct, its fate is not necessarily determined by its time-averaged selective effect. Instead, environmental variability reduces the efficiency of selection across a broad parameter regime, rendering selection unable to distinguish between mutations that are substantially beneficial and substantially deleterious on average. Temporal fluctuations can also dramatically increase fixation probabilities, often making the details of these fluctuations more important than the average selection pressures acting on each new mutation. For example, mutations that result in a trade-off between conditions but are strongly deleterious on average can nevertheless be more likely to fix than mutations that are always neutral or beneficial. These effects can have important implications for patterns of molecular evolution in variable environments, and they suggest that it may often be difficult for populations to maintain specialist traits, even when their loss leads to a decline in time-averaged fitness.

population genetics fixation probability fluctuating environment effective diffusion

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Paul Davies 'falou e disse': afirmar que o universo está pululando de biologia é afirmar sem evidência

Maybe Life in the Cosmos Is Rare After All

The conclusion that the universe is teeming with biology is based on an unproved assumption

By Paul Davies on May 23, 2016

A planet like Kepler 22b could plausibly be habitable—but that doesn't mean it's inhabited Credit: Artists' rendering by NASA/Ames/JPL-Caltech. Public Domain

When I was a student in the 1960s almost all scientists believed we are alone in the universe. The search for intelligent life beyond Earth was ridiculed; one might as well have professed an interest in looking for fairies. The focus of skepticism concerned the origin of life, which was widely assumed to have been a chemical fluke of such incredibly low probability it would never have happened twice. “The origin of life appears at the moment to be almost a miracle,” was the way Francis Crick described it, “so many are the conditions which would have had to have been satisfied to get it going.” Jacques Monod concurred; in his 1976 book Chance and Necessity he wrote, “Man knows at last that he is alone in the indifferent immensity of the universe, whence which he has emerged by chance.”

Today the pendulum has swung decisively the other way. Many distinguished scientists proclaim that the universe is teeming with life, at least some of it intelligent. The biologist Christian de Duve went so far as to call life “a cosmic imperative.” Yet the science has hardly changed. We are almost as much in the dark today about the pathway from non-life to life as Darwin was when he wrote, “It is mere rubbish thinking at present of the origin of life; one might as well think of the origin of matter.”

There is no doubt that SETI – the search for extraterrestrial intelligence – has received a huge fillip from the recent discovery of hundreds of extra-solar planets. Astronomers think there could be billions of earthlike planets in our galaxy alone. Clearly there is no lack of habitable real estate out there. But habitable implies inhabited only if life actually arises.

I am often asked how likely it is that we will find intelligent life beyond Earth. The question is meaningless. Because we don’t know the process that transformed a mish-mash of chemicals into a living cell, with all its staggering complexity, it is impossible to calculate the probability that it will happen. You can’t estimate the odds of an unknown process. Astrobiologists, however, seem more preoccupied with the chances that microbial life will eventually evolve intelligence. Although biologists can’t do the math on that either, at least they understand the process; it is Darwinian evolution. But this is to put the cart before the horse. The biggest uncertainty surrounds the first step—getting the microbes in the first place.

...

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A exportação de RNA através do complexo de poros nucleares em eucariotos

Genes 2015, 6(1), 124-149; doi:10.3390/genes6010124

Review

RNA Export through the NPC in Eukaryotes

Masumi Okamura * , Haruko Inose and Seiji Masuda * 

Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan

* Authors to whom correspondence should be addressed.

Academic Editor: Roz Sandri-Goldin

Received: 28 November 2014 / Revised: 27 February 2015 / Accepted: 10 March 2015 / Published: 20 March 2015

(This article belongs to the Special Issue Mechanisms of mRNA Nuclear Export)

Abstract

In eukaryotic cells, RNAs are transcribed in the nucleus and exported to the cytoplasm through the nuclear pore complex. The RNA molecules that are exported from the nucleus into the cytoplasm include messenger RNAs (mRNAs), ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), micro RNAs (miRNAs), and viral mRNAs. Each RNA is transported by a specific nuclear export receptor. It is believed that most of the mRNAs are exported by Nxf1 (Mex67 in yeast), whereas rRNAs, snRNAs, and a certain subset of mRNAs are exported in a Crm1/Xpo1-dependent manner. tRNAs and miRNAs are exported by Xpot and Xpo5. However, multiple export receptors are involved in the export of some RNAs, such as 60S ribosomal subunit. In addition to these export receptors, some adapter proteins are required to export RNAs. The RNA export system of eukaryotic cells is also used by several types of RNA virus that depend on the machineries of the host cell in the nucleus for replication of their genome, therefore this review describes the RNA export system of two representative viruses. We also discuss the NPC anchoring-dependent mRNA export factors that directly recruit specific genes to the NPC.

Keywords: RNA export; mRNA; Nxf1; Crm1; Xpot; Xpo5

This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Novo livro: O debate do Design Inteligente e a tentação do cientificismo

The Intelligent Design Debate and the Temptation of Scientism

By Erkki Vesa Rope Kojonen

© 2016 – Routledge

226 pages

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Description Reviews Contents Author Series Subjects

About the Book

The controversy over Intelligent Design (ID) has now continued for over two decades, with no signs of ending. For its defenders, ID is revolutionary new science, and its opposition is merely ideological. For its critics, ID is both bad science and bad theology. But the polemical nature of the debate makes it difficult to understand the nature of the arguments on all sides. A balanced and deep analysis of a controversial debate, this volume argues that beliefs about the purposiveness or non-purposiveness of nature should not be based merely on science. Rather, the philosophical and theological nature of such questions should be openly acknowledged.

Hardback: 9781472472502 pub: 2016-05-11

Price: $149.95

ROUTLEDGE

Como íntrons podem ser transpostos para um organismo

Spliceosomal intronogenesis

Sujin Lee a and Scott W. Stevens  b,c,1

Author Affiliations

aGraduate Program in Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712;

bDepartment of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712;

cInstitute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712

Edited by Jef D. Boeke, New York University School of Medicine, New York, NY, and approved April 20, 2016 (received for review March 30, 2016)

Mere illustration/Mera ilustração

Significance

Eukaryotic transcripts contain spliceosomal introns that need to be removed by pre-mRNA splicing. Although several models have been proposed to identify the mechanism of intron gain over the evolution of eukaryotes, they remain models due to a lack of experimental validation. We developed a reporter system to detect selected intron gain and loss events and captured two intron gain events in which the intron derived from the reporter was transposed into the chromosomal loci of RPL8B and ADH2. This is, to our knowledge, the first demonstration of intron gain via intron transposition in any organism, and we suggest that these events are likely to have occurred by a reversal of the pre-mRNA splicing reaction followed by homologous recombination.

Abstract

The presence of intervening sequences, termed introns, is a defining characteristic of eukaryotic nuclear genomes. Once transcribed into pre-mRNA, these introns must be removed within the spliceosome before export of the processed mRNA to the cytoplasm, where it is translated into protein. Although intron loss has been demonstrated experimentally, several mysteries remain regarding the origin and propagation of introns. Indeed, documented evidence of gain of an intron has only been suggested by phylogenetic analyses. We report the use of a strategy that detects selected intron gain and loss events. We have experimentally verified, to our knowledge, the first demonstrations of intron transposition in any organism. From our screen, we detected two separate intron gain events characterized by the perfect transposition of a reporter intron into the yeast genes RPL8B and ADH2, respectively. We show that the newly acquired introns are able to be removed from their respective pre-mRNAs by the spliceosome. Additionally, the novel allele, RPL8Bint, is functional when overexpressed within the genome in a strain lacking the Rpl8 paralogue RPL8A, demonstrating that the gene targeted for intronogenesis is functional.

spliceosome intron evolution

Footnotes

1To whom correspondence should be addressed. Email: scott.stevens@austin.utexas.edu.

Author contributions: S.W.S. designed research; S.L. performed research; S.L. and S.W.S. analyzed data; and S.L. and S.W.S. 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.1605113113/-/DCSupplemental.

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A complexidade e diversidade das coisas vivas: 10 trilhões de espécies com os micróbios

Scaling laws predict global microbial diversity

Kenneth J. Locey a,1 and Jay T. Lennon a,1

Author Affiliations

aDepartment of Biology, Indiana University, Bloomington, IN 47405

Edited by David M. Karl, University of Hawaii, Honolulu, HI, and approved March 30, 2016 (received for review October 27, 2015)

Significance

Ecological scaling laws are intensively studied for their predictive power and universal nature but often fail to unify biodiversity across domains of life. Using a global-scale compilation of microbial and macrobial data, we uncover relationships of commonness and rarity that scale with abundance at similar rates for microorganisms and macroscopic plants and animals. We then show a unified scaling law that predicts the abundance of dominant species across 30 orders of magnitude to the scale of all microorganisms on Earth. Using this scaling law combined with the lognormal model of biodiversity, we predict that Earth is home to as many as 1 trillion (1012) microbial species.

Abstract

Scaling laws underpin unifying theories of biodiversity and are among the most predictively powerful relationships in biology. However, scaling laws developed for plants and animals often go untested or fail to hold for microorganisms. As a result, it is unclear whether scaling laws of biodiversity will span evolutionarily distant domains of life that encompass all modes of metabolism and scales of abundance. Using a global-scale compilation of ∼35,000 sites and ∼5.6⋅106 species, including the largest ever inventory of high-throughput molecular data and one of the largest compilations of plant and animal community data, we show similar rates of scaling in commonness and rarity across microorganisms and macroscopic plants and animals. We document a universal dominance scaling law that holds across 30 orders of magnitude, an unprecedented expanse that predicts the abundance of dominant ocean bacteria. In combining this scaling law with the lognormal model of biodiversity, we predict that Earth is home to upward of 1 trillion (1012) microbial species. Microbial biodiversity seems greater than ever anticipated yet predictable from the smallest to the largest microbiome.

biodiversity microbiology macroecology microbiome rare biosphere

Footnotes

1To whom correspondence may be addressed. Email: ken@weecology.org or lennonj@indiana.edu.

Author contributions: K.J.L. and J.T.L. designed research; K.J.L. performed research; K.J.L. and J.T.L. analyzed data; and K.J.L. and J.T.L. 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.1521291113/-/DCSupplemental.

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A Royal Society anunciará mudança paradigmática em biologia evolucionária!

Finalmente a Royal Society vai anunciar a lista de convidados para o encontro "repensar a evolução"

22 de maio de 2016 Postado por News 

De Suzan Mazur no Huffington Post:

O escritório de ciência da Royal Society diz que o suspense brevemente acabará. Dentro de duas semanas anunciará os nomes dos apresentadores/tópicos para a conferência — democraticamente, por e-mail, a todos que se registraram para assistir o encontro público. Além disso, eles adicionaram mais convidados na sua lista original. Os zoólogos talvez, finalmente, admitindo que os vírus fazem parte da tenda?

Alguém pode imaginar - mais política do que nas Nações Unidas.

Contudo, reclamações sobre a mudança paradigmática estão vindo não somente dos "inimigos", i.e., os suspeitos costumeiros (que provavelmente irão enviar seus "representantes" perturbadores para a reunião londrina) — mas de vozes mais comedidas e responsáveis como o biólogo Michael Lynch, da Universidade Indiana. Recentemente Lynch respondeu à minha história sobre a turma da Síntese Ampliada/Estendida, agora financiada pela Fundação Templeton com US$ 8 milhões, mas que ainda não consegue concordar numa definição para a Síntese Ampliada/Estendida, com esta nota:

“Superficial, boba, rasa, e auto-promocional. Eu e muitos outros consideramos isso como um completo embaraço para a área. Se alguém quer ampliar/estender algo em público, especialmente como um biólogo, alguém deve ter uma ideia muito boa do que está sendo ampliado/estendido”. Mais.

Não está parecendo como um lugar legal e quieto para dormir. Fiquem ligados.

De algum modo, eu venho percebendo uma mudança, em que eu percebo as pessoas abordando novos dados com muito menos acenos retóricos à autoridade do neodarwinismo.

Nota: Suzan Mazur é autora do livro Paradigm Shifters, acima destacado.

Vide também: O DNA "Lixo" de volta “com uma vingança”. Provavelmente não é um bom tempo de ser Dan Graur. Na verdade, um tempo melhor de ser Jonathan Wells.

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NOTA DESTE BLOGGER:

Desde 1998 eu venho destacando para a Nomenklatura científica, Galera de meninos e meninas de Darwin, e às editorias de ciência da Grande Mídia Tupiniquim que uma iminente e eminente mudança paradigmática se fazia necessária em biologia evolucionária. Não se importaram, fizeram pouco caso deste "simples professorzinho do Ensino Médio", e outros epítetos demonizando este que a Royal Society agora vindica - VEM AÍ UMA MUDANÇA PARADIGMÁTICA EM BIOLOGIA EVOLUCIONÁRIA!

Fui, nem sei por que, rindo da cara dos que apostaram todas as suas fichas epistemológicas no pangaré de Darwin. Eu dobro a aposta na Teoria do Design Inteligente (e seu aspecto de informação complexa especificada) que se não for incorporada na Síntese Evolutiva Ampliada/Estendida, já é uma teoria científica natimorta, pois a biologia do século 21 é uma ciência de informação!

Mapeamento global das interações RNA-RNA: o retorno vingativo do DNA "lixo"!

Global Mapping of Human RNA-RNA Interactions

Eesha Sharma3, Tim Sterne-Weiler3, Dave O’Hanlon, Benjamin J. Blencowe correspondence email

3Co-first author

DOI: http://dx.doi.org/10.1016/j.molcel.2016.04.030

Highlights

• LIGR-seq is a method for the global-scale mapping RNA-RNA interactions in vivo

• LIGR-seq data reveal a complex RNA-RNA interactome in human cells

• Hundreds of trans-interactions involving known and orphan ncRNAs are detected

• The orphan snoRNA SNORD83B regulates levels of its LIGR-seq-detected target mRNAs

Summary

The majority of the human genome is transcribed into non-coding (nc)RNAs that lack known biological functions or else are only partially characterized. Numerous characterized ncRNAs function via base pairing with target RNA sequences to direct their biological activities, which include critical roles in RNA processing, modification, turnover, and translation. To define roles for ncRNAs, we have developed a method enabling the global-scale mapping of RNA-RNA duplexes crosslinked in vivo, “LIGation of interacting RNA followed by high-throughput sequencing” (LIGR-seq). Applying this method in human cells reveals a remarkable landscape of RNA-RNA interactions involving all major classes of ncRNA and mRNA. LIGR-seq data reveal unexpected interactions between small nucleolar (sno)RNAs and mRNAs, including those involving the orphan C/D box snoRNA, SNORD83B, that control steady-state levels of its target mRNAs. LIGR-seq thus represents a powerful approach for illuminating the functions of the myriad of uncharacterized RNAs that act via base-pairing interactions.

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NOTA DESTE BLOGGER:

Veja como o EurekAlert (da AAAS - American Association for the Advancement of Science, a SBPC dos gringos) destacou o uso desta tecnologia:

Shedding light on the 'dark matter' of the genome

New tool allows scientists to understand the role of non-coding RNAs

UNIVERSITY OF TORONTO

What used to be dismissed by many as "junk DNA" is back with a vengeance as growing data points to the importance of non-coding RNAs (ncRNAs) -- genome's messages that do not code for proteins -- in development and disease. But our progress in understanding these molecules has been slow because of the lack of technologies that allow the systematic mapping of their functions.

...

ncRNAs come in multiple flavours: there's rRNA, tRNA, snRNA, snoRNA, piRNA, miRNA, and lncRNA, to name a few, where prefixes reflect the RNA's place in the cell or some aspect of its function. But the truth is that no one really knows the extent to which these ncRNAs control what goes on in the cell, nor how they do this. The new technology developed by Blencowe's group has been able to pick up new interactions involving all classes of RNAs and has already revealed some unexpected findings.

The team discovered new roles for small nucleolar RNAs (snoRNAs) that normally guide chemical modifications of other ncRNAs. It turns out that some snoRNAs can also regulate stability of a set of protein-coding mRNAs. In this way, snoRNAs can also directly influence which proteins are made, as well as their abundance, adding a new level of control in cell biology. And this is only the tip of the iceberg as the researchers plan to further develop and apply their technology to investigate the ncRNAs in different settings.

[NOTA BENE: Foram "eles" que disseram isso]

O que foi considerado pela Nomenklatura científica como DNA "lixo", está se mostrando cada vez mais um tesouro de informação genética. Pensar que em 1998, William Dembski, um dos principais teóricos da TDI afirmou:

William Dembski predicted function for non-coding "junk"-DNA based upon intelligent design:

But design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term "junk DNA." Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as "junk" merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how "non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development." Design encourages scientists to look for function where evolution discourages it.

in "Intelligent Science and Design", First Things, Vol. 86:21-27 (October 1998).

PERGUNTA CÁUSTICA DESTE BLOGGER:

Então, quem é que impede o avanço da ciência, cara-pálida? Os darwinistas ou a turma do Design Inteligente???

Práticas e perspectivas de professores de faculdade abordando crenças religiosas durante ensino da evolução

Practices and Perspectives of College Instructors on Addressing Religious Beliefs When Teaching Evolution

M. Elizabeth Barnes and Sara E. Brownell*

- Affiliations

Biology Education Research Lab, School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501

Jeff Schinske, Monitoring Editor

Submitted November 29, 2015. Revised February 17, 2016. Accepted February 17, 2016.

Abstract

Evolution is a core concept of biology, and yet many college biology students do not accept evolution because of their religious beliefs. However, we do not currently know how instructors perceive their role in helping students accept evolution or how they address the perceived conflict between religion and evolution when they teach evolution. This study explores instructor practices and beliefs related to mitigating students’ perceived conflict between religion and evolution. Interviews with 32 instructors revealed that many instructors do not believe it is their goal to help students accept evolution and that most instructors do not address the perceived conflict between religion and evolution. Instructors cited many barriers to discussing religion in the context of evolution in their classes, most notably the instructors’ own personal beliefs that religion and evolution may be incompatible. These data are exploratory and are intended to stimulate a series of questions about how we as college biology instructors teach evolution.

FREE PDF GRATIS: CBE Life Sci Educ

Footnotes

↵*Address correspondence to: Sara E. Brownell (Sara.brownell@asu.edu).

“ASCB®” and “The American Society for Cell Biology®” are registered trademarks of The American Society for Cell Biology.

Denis Noble e a evolução além do neodarwinismo: um novo quadro conceitual

EPIGENETICS: SCOPE AND MECHANISMS

Evolution beyond neo-Darwinism: a new conceptual framework

Denis Noble

Journal of Experimental Biology 2015 218: 7-13; doi: 10.1242/jeb.106310

Source/Fonte

Abstract

Experimental results in epigenetics and related fields of biological research show that the Modern Synthesis (neo-Darwinist) theory of evolution requires either extension or replacement. This article examines the conceptual framework of neo-Darwinism, including the concepts of ‘gene’, ‘selfish’, ‘code’, ‘program’, ‘blueprint’, ‘book of life’, ‘replicator’ and ‘vehicle’. This form of representation is a barrier to extending or replacing existing theory as it confuses conceptual and empirical matters. These need to be clearly distinguished. In the case of the central concept of ‘gene’, the definition has moved all the way from describing a necessary cause (defined in terms of the inheritable phenotype itself) to an empirically testable hypothesis (in terms of causation by DNA sequences). Neo-Darwinism also privileges ‘genes’ in causation, whereas in multi-way networks of interactions there can be no privileged cause. An alternative conceptual framework is proposed that avoids these problems, and which is more favourable to an integrated systems view of evolution.

Origin of this article

This paper represents the culmination of ideas previously developed in a book, The Music of Life (Noble, 2006), and four related articles (Noble, 2011b; Noble, 2012; Noble, 2013; Noble et al., 2014). Those publications raised many questions from readers in response to which the ‘Answers’ pages (http://musicoflife.co.uk/Answers-menu.html) of The Music of Life website were drafted. Those pages, in particular the page entitled The language of Neo-Darwinism, were written in preparation for the present article. The ideas have been extensively honed in response to further questions and comments.

FREE PDF GRATIS: The Journal of Experimental Biology

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NOTA DESTE BLOGGER:

O artigo de Denis Noble é de 2015, e a nova teoria geral da Evolução - a SÍNTESE EVOLUTIVA AMPLIADA/ESTENDIDA foi anunciada em agosto de 2015, mas a Nomenklatura científica pouco fala publicamente, e a Galera dos meninos e meninas de Darwin ouviram, mas nem saber o que dizer o que isso significa em termos de justificação teórica: Darwin não fechou a conta com a Síntese Evolutiva Moderna...

O diagrama de ligação de um sistema olfativo glomerular: mero acaso, fortuita necessidade ou design inteligente?

The wiring diagram of a glomerular olfactory system

Matthew E Berck Avinash Khandelwal Lindsey Claus Luis Hernandez-Nunez Guangwei Si Christopher J Tabone Feng Li James W Truman Richard D Fetter Matthieu Louis Aravinthan DT Samuel Albert Cardona 

Harvard University, United States; The Barcelona Institute of Science and Technology, Spain; Fly Base, United States; Janelia Research Campus, Howard Hughes Medical Institute, United States

DOI: http://dx.doi.org/10.7554/eLife.14859

Published May 13, 2016

Cite as eLife 2016;10.7554/eLife.14859

Source/Fonte: Nature Reviews Neuroscience

Abstract

The sense of smell enables animals to react to long-distance cues according to learned and innate valences. Here, we have mapped with electron microscopy the complete wiring diagram of the Drosophila larval antennal lobe, an olfactory neuropil similar to the vertebrate olfactory bulb. We found a canonical circuit with uniglomerular projection neurons (uPNs) relaying gain-controlled ORN activity to the mushroom body and the lateral horn. A second, parallel circuit with multiglomerular projection neurons (mPNs) and hierarchically connected local neurons (LNs) selectively integrates multiple ORN signals already at the first synapse. LN-LN synaptic connections putatively implement a bistable gain control mechanism that either computes odor saliency through panglomerular inhibition, or allows some glomeruli to respond to faint aversive odors in the presence of strong appetitive odors. This complete wiring diagram will support experimental and theoretical studies towards bridging the gap between circuits and behavior.

FREE PDF GRATIS: eLIFE