O surgimento da fisiologia e forma: seleção natural revisitada

segunda-feira, junho 06, 2016

Biology 2016, 5(2), 15; doi:10.3390/biology5020015

Commentary

The Emergence of Physiology and Form: Natural Selection Revisited

John S. Torday

Evolutionary Medicine Program, University of California, Los Angeles, CA 90502, USA

Academic Editor: Jukka Finne

Received: 17 February 2016 / Revised: 23 March 2016 / Accepted: 25 March 2016 / Published: 1 April 2016


Abstract

Natural Selection describes how species have evolved differentially, but it is descriptive, non-mechanistic. What mechanisms does Nature use to accomplish this feat? One known way in which ancient natural forces affect development, phylogeny and physiology is through gravitational effects that have evolved as mechanotransduction, seen in the lung, kidney and bone, linking as molecular homologies to skin and brain. Tracing the ontogenetic and phylogenetic changes that have facilitated mechanotransduction identifies specific homologous cell-types and functional molecular markers for lung homeostasis that reveal how and why complex physiologic traits have evolved from the unicellular to the multicellular state. Such data are reinforced by their reverse-evolutionary patterns in chronic degenerative diseases. The physiologic responses of model organisms like Dictyostelium and yeast to gravity provide deep comparative molecular phenotypic homologies, revealing mammalian Target of Rapamycin (mTOR) as the final common pathway for vertical integration of vertebrate physiologic evolution; mTOR integrates calcium/lipid epistatic balance as both the proximate and ultimate positive selection pressure for vertebrate physiologic evolution. The commonality of all vertebrate structure-function relationships can be reduced to calcium/lipid homeostatic regulation as the fractal unit of vertebrate physiology, demonstrating the primacy of the unicellular state as the fundament of physiologic evolution.

Keywords: Natural Selection; mechanotransduction; calcium; lipid; evolution; cell-cell interaction; fractal; ultimate; proximate

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.

FREE PDF GRATIS: Biology

Herança epigenética e seu papel em biologia evolucionária - reavaliação e novas perspectivas

Biology 2016, 5(2), 24; doi:10.3390/biology5020024

Essay

Epigenetic Inheritance and Its Role in Evolutionary Biology: Re-Evaluation and New Perspectives

Warren Burggren

Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203-5017, USA

Academic Editors: Chris O'Callaghan, Jukka Finne and John S. Torday

Received: 16 March 2016 / Revised: 26 April 2016 / Accepted: 11 May 2016 / Published: 25 May 2016


Abstract

Epigenetics increasingly occupies a pivotal position in our understanding of inheritance, natural selection and, perhaps, even evolution. A survey of the PubMed database, however, reveals that the great majority (>93%) of epigenetic papers have an intra-, rather than an inter-generational focus, primarily on mechanisms and disease. Approximately ~1% of epigenetic papers even mention the nexus of epigenetics, natural selection and evolution. Yet, when environments are dynamic (e.g., climate change effects), there may be an “epigenetic advantage” to phenotypic switching by epigenetic inheritance, rather than by gene mutation. An epigenetically-inherited trait can arise simultaneously in many individuals, as opposed to a single individual with a gene mutation. Moreover, a transient epigenetically-modified phenotype can be quickly “sunsetted”, with individuals reverting to the original phenotype. Thus, epigenetic phenotype switching is dynamic and temporary and can help bridge periods of environmental stress. Epigenetic inheritance likely contributes to evolution both directly and indirectly. While there is as yet incomplete evidence of direct permanent incorporation of a complex epigenetic phenotype into the genome, doubtlessly, the presence of epigenetic markers and the phenotypes they create (which may sort quite separately from the genotype within a population) will influence natural selection and, so, drive the collective genotype of a population.

Keywords: epigenetics; evolution; inheritance; natural selection; ecology; dynamics; climate change

FREE PDF GRATIS: Biology

Cientistas abrem os Arquivos X do mistério da duplicação e autocorreção do DNA

Direct observation of DNA threading in flap endonuclease complexes

Faizah A AlMalki, Claudia S Flemming, Jing Zhang, Min Feng, Svetlana E Sedelnikova, Tom Ceska, John B Rafferty, Jon R Sayers & Peter J Artymiuk

Affiliations Contributions Corresponding authors

Nature Structural & Molecular Biology (2016) doi:10.1038/nsmb.3241

Received 07 February 2016 Accepted 10 May 2016 Published online 06 June 2016


Abstract

Maintenance of genome integrity requires that branched nucleic acid molecules be accurately processed to produce double-helical DNA. Flap endonucleases are essential enzymes that trim such branched molecules generated by Okazaki-fragment synthesis during replication. Here, we report crystal structures of bacteriophage T5 flap endonuclease in complexes with intact DNA substrates and products, at resolutions of 1.9–2.2 Å. They reveal single-stranded DNA threading through a hole in the enzyme, which is enclosed by an inverted V-shaped helical arch straddling the active site. Residues lining the hole induce an unusual barb-like conformation in the DNA substrate, thereby juxtaposing the scissile phosphate and essential catalytic metal ions. A series of complexes and biochemical analyses show how the substrate's single-stranded branch approaches, threads through and finally emerges on the far side of the enzyme. Our studies suggest that substrate recognition involves an unusual 'fly-casting, thread, bend and barb' mechanism.

Subject terms: DNA synthesis Enzyme mechanisms X-ray crystallography

SUBSCRIPTION OR PAYMENT NEEDED/REQUER ASSINATURA OU PAGAMENTO:

Por um consenso sobre as idades dos genes

sábado, junho 04, 2016

Towards Consensus Gene Ages

Benjamin J. Liebeskind1,2,*, Claire D. McWhite1 and Edward M. Marcotte1

- Author Affiliations

1Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, & Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712

2Center for Computational Biology and Bioinformatics, University of Texas at Austin, TX 78712

↵*Author for Correspondence: Benjamin J. Liebeskind, Center for Systems and Synthetic Biology, University of Texas at Austin, Phone: 512-232-3919, Fax: 512-232-3472, Email: bliebeskind@austin.utexas.edu

Received March 6, 2016. Revision received April 18, 2016. Accepted May 1, 2016.


Abstract

Correctly estimating the age of a gene or gene family is important for a variety of fields, including molecular evolution, comparative genomics, and phylogenetics, and increasingly for systems biology and disease genetics. However, most studies use only a point estimate of a gene’s age, neglecting the substantial uncertainty involved in this estimation. Here, we characterize this uncertainty by investigating the effect of algorithm choice on gene-age inference and calculate consensus gene ages with attendant error distributions for a variety of model eukaryotes. We use thirteen orthology inference algorithms to create gene-age datasets and then characterize the error around each age-call on a per-gene and per-algorithm basis. Systematic error was found to be a large factor in estimating gene age, suggesting that simple consensus algorithms are not enough to give a reliable point estimate. We also found that different sources of error can affect downstream analyses, such as gene ontology enrichment. Our consensus gene-age datasets, with associated error terms, are made fully available at so that researchers can propagate this uncertainty through their analyses (geneages.org).

Key words

Ortholog Phylostratigraphy LECA LUCA

© The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

FREE PDF GRATIS: Genome Biol Evol

Organização celular única: o mais antigo meristema de raiz em um fóssil de 320 milhões de anos

Unique Cellular Organization in the Oldest Root Meristem

Alexander J. Hetherington, Joseph G. Dubrovsky, Liam Dolan correspondence email

Publication stage: In Press Corrected Proof

Open Access


Open access funded by European Research Council



Highlights

• The oldest fossilized root meristem is described from >300-million-year-old soil

• The discovery allows the first description of a fossilized root stem cell niche

• The cellular organization and therefore development of the meristem is unique

• The discovery reveals previously unknown diversity in plant meristem types

Summary

Roots and shoots of plant bodies develop from meristems—cell populations that self-renew and produce cells that undergo differentiation—located at the apices of axes [ 1 ].The oldest preserved root apices in which cellular anatomy can be imaged are found in nodules of permineralized fossil soils called coal balls [ 2 ], which formed in the Carboniferous coal swamp forests over 300 million years ago [ 3–9 ]. However, no fossil root apices described to date were actively growing at the time of preservation [ 3–10 ]. Because the cellular organization of meristems changes when root growth stops, it has been impossible to compare cellular dynamics as stem cells transition to differentiated cells in extinct and extant taxa [ 11 ]. We predicted that meristems of actively growing roots would be preserved in coal balls. Here we report the discovery of the first fossilized remains of an actively growing root meristem from permineralized Carboniferous soil with detail of the stem cells and differentiating cells preserved. The cellular organization of the meristem is unique. The position of the Körper-Kappe boundary, discrete root cap, and presence of many anticlinal cell divisions within a broad promeristem distinguish it from all other known root meristems. This discovery is important because it demonstrates that the same general cellular dynamics are conserved between the oldest extinct and extant root meristems. However, its unique cellular organization demonstrates that extant root meristem organization and development represents only a subset of the diversity that has existed since roots first evolved.

Received: March 18, 2016; Received in revised form: April 21, 2016; Accepted: April 25, 2016; Published: June 2, 2016

© 2016 The Authors. Published by Elsevier Inc.

FREE PDF GRATIS: Current Biology

Bolhas sonoras zunindo em torno do DNA são essenciais à vida: mero acaso, fortuita necessidade ou design inteligente?

Observation of coherent delocalized phonon-like modes in DNA under physiological conditions

Mario González-Jiménez, Gopakumar Ramakrishnan, Thomas Harwood, Adrian J. Lapthorn, Sharon M. Kelly, Elizabeth M. Ellis & Klaas Wynne

AffiliationsContributionsCorresponding author

Nature Communications 7, Article number: 11799 doi:10.1038/ncomms11799

Received 12 February 2016 Accepted 28 April 2016 Published 01 June 2016


Abstract

Underdamped terahertz-frequency delocalized phonon-like modes have long been suggested to play a role in the biological function of DNA. Such phonon modes involve the collective motion of many atoms and are prerequisite to understanding the molecular nature of macroscopic conformational changes and related biochemical phenomena. Initial predictions were based on simple theoretical models of DNA. However, such models do not take into account strong interactions with the surrounding water, which is likely to cause phonon modes to be heavily damped and localized. Here we apply state-of-the-art femtosecond optical Kerr effect spectroscopy, which is currently the only technique capable of taking low-frequency (GHz to THz) vibrational spectra in solution. We are able to demonstrate that phonon modes involving the hydrogen bond network between the strands exist in DNA at physiologically relevant conditions. In addition, the dynamics of the solvating water molecules is slowed down by about a factor of 20 compared with the bulk.

Subject terms: Physical sciences Biophysics Physical chemistry Molecular biology

FREE PDF GRATIS: Nature Communications

Físicos descobrem um número infinito de limites de velocidade quântica

sexta-feira, junho 03, 2016

Generalized Geometric Quantum Speed Limits

Diego Paiva Pires, Marco Cianciaruso, Lucas C. Céleri, Gerardo Adesso, and Diogo O. Soares-Pinto

Phys. Rev. X 6, 021031 – Published 2 June 2016

ABSTRACT

The attempt to gain a theoretical understanding of the concept of time in quantum mechanics has triggered significant progress towards the search for faster and more efficient quantum technologies. One of such advances consists in the interpretation of the time-energy uncertainty relations as lower bounds for the minimal evolution time between two distinguishable states of a quantum system, also known as quantum speed limits. We investigate how the nonuniqueness of a bona fide measure of distinguishability defined on the quantum-state space affects the quantum speed limits and can be exploited in order to derive improved bounds. Specifically, we establish an infinite family of quantum speed limits valid for unitary and nonunitary evolutions, based on an elegant information geometric formalism. Our work unifies and generalizes existing results on quantum speed limits and provides instances of novel bounds that are tighter than any established one based on the conventional quantum Fisher information. We illustrate our findings with relevant examples, demonstrating the importance of choosing different information metrics for open system dynamics, as well as clarifying the roles of classical populations versus quantum coherences, in the determination and saturation of the speed limits. Our results can find applications in the optimization and control of quantum technologies such as quantum computation and metrology, and might provide new insights in fundamental investigations of quantum thermodynamics.

Received 21 July 2015


This article is available under the terms of the Creative Commons Attribution 3.0 License. Further distribution of this work must maintain attribution to the author(s) and the published article’s title, journal citation, and DOI.

Published by the American Physical Society

AUTHORS & AFFILIATIONS

Diego Paiva Pires1,*, Marco Cianciaruso2,3,4,†, Lucas C. Céleri5,‡, Gerardo Adesso2,§, and Diogo O. Soares-Pinto1,∥

1Instituto de Física de São Carlos, Universidade de São Paulo, CP 369, 13560-970 São Carlos, São Paulo, Brazil
2School of Mathematical Sciences, The University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
3Dipartimento di Fisica “E. R. Caianiello,” Università degli Studi di Salerno, Via Giovanni Paolo II, I-84084 Fisciano (SA), Italy
4INFN, Sezione di Napoli, Gruppo Collegato di Salerno, I-84084 Fisciano (SA), Italy
5Instituto de Física, Universidade Federal de Goiás, 74.001-970 Goiânia, Goiás, Brazil

*diegopaivapires@gmail.com
†cianciaruso.marco@gmail.com
‡lucas@chibebe.org
§gerardo.adesso@nottingham.ac.uk
∥dosp@ifsc.usp.br

POPULAR SUMMARY

A fundamental question in physics pertains to how fast quantum states evolve. This so-called “quantum speed limit,” which corresponds to the minimum evolution time between two distinguishable states of a quantum system, is an important parameter for designing faster and more optimized information-processing machines. Here, we develop an elegant geometric formalism to provide general progress in the determination of quantum speed limits. This work unifies and improves previous findings and highlights, for the first time, the role of classical populations versus quantum coherences in the saturation of speed limits.

The new family of geometric quantum speed limits presented in this work is applicable to pure and mixed states and to all physical processes, both unitary and nonunitary (e.g., amplitude and phase damping). We express the quantum speed limits in terms of the shortest distance between two states in the quantum state space, according to different measures of distance. For any given dynamical process, the tightest speed limit can be determined by selecting the quantum metric that is most tailored to the initial state of a closed or open system.

Our results, which provide general prescriptions to optimize quantum protocols, pave the way for experimental demonstrations of controlled quantum dynamics operating at the ultimate speed limits using, for example, nuclear magnetic resonance technology. We expect that our findings will have an impact on the fields of quantum information, computation, simulation, and metrology.

FREE PDF GRATIS: Physical Review X

Etapas evolutivas no surgimento da vida deduzida da abordagem Bottom-Up e a hipótese GADV (abordagem Top-Down)

Life 2016, 6(1), 6; doi:10.3390/life6010006

Review

Evolutionary Steps in the Emergence of Life Deduced from the Bottom-Up Approach and GADV Hypothesis (Top-Down Approach)

Kenji Ikehara 1,2

1 G & L Kyosei Institute, Keihannna Labo-401, Hikaridai 1-7, Seika-cho, Sorakugun, Kyoto 619-0237, Japan; Tel./Fax: +81-774-73-4478

2 International Institute for Advanced Studies of Japan, Kizugawadai 9-3, Kizugawa, Kyoto 619-0225, Japan

Academic Editors: David Deamer, Bruce Damer and Niles Lehman

Received: 1 November 2015 / Accepted: 18 January 2016 / Published: 26 January 2016


Abstract

It is no doubt quite difficult to solve the riddle of the origin of life. So, firstly, I would like to point out the kinds of obstacles there are in solving this riddle and how we should tackle these difficult problems, reviewing the studies that have been conducted so far. After that, I will propose that the consecutive evolutionary steps in a timeline can be rationally deduced by using a common event as a juncture, which is obtained by two counter-directional approaches: one is the bottom-up approach through which many researchers have studied the origin of life, and the other is the top-down approach, through which I established the [GADV]-protein world hypothesis or GADV hypothesis on the origin of life starting from a study on the formation of entirely new genes in extant microorganisms. Last, I will describe the probable evolutionary process from the formation of Earth to the emergence of life, which was deduced by using a common event—the establishment of the first genetic code encoding [GADV]-amino acids—as a juncture for the results obtained from the two approaches.

Keywords: origin of life; [GADV]-protein world; GADV hypothesis; pseudo-replication; protein 0th-order structure

FREE PDF GRATIS: Life

Uma estrutura evolucionária para entender a origem dos eucariotos

Biology 2016, 5(2), 18; doi:10.3390/biology5020018

Review

An Evolutionary Framework for Understanding the Origin of Eukaryotes

Neil W. Blackstone

Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA; Tel.: +1-815-753-7899; Fax: +1-815-753-0461

Academic Editor: John S. Torday

Received: 28 February 2016 / Accepted: 25 April 2016 / Published: 27 April 2016


Abstract: 

Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

Keywords: comparative method; eukaryotes; evolutionary theory; levels of selection; mitochondria; modern synthesis; phylogenetic systematics

FREE PDF GRATIS: Biology

Evolução química e a origem da vida: uma análise

Chemical Evolution and Origin of Life: A Review

Avnish Kumar Arora*, Vivek Sheel Jaswal, Kuldeep Singh, Raman Singh

Chemistry Department, MMEC, M M University Mullana, Ambala (Haryana), India - 133207

Received on: 3-Mar-2016 Accepted and Published on: 21-Apr-2016


Abstract

Life has evolved approximately 3.7 billion years ago on Earth while the Earth itself was formed some 4.6 billion years ago. So it was the time of 0.9 billion years in which chemical reactions took place and formation of first living cell occurred. There are various views on origin of life. This review discusses and compares these theories with respect to chemical evolution and origin of life.

Keywords: Chemical evolution, Origin of life, metal oxides, clay, cyano complexes

FREE PDF GRATIS: Chemical Biology Letters

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NOTA DESTE BLOGGER:

Para o que foi proposto no artigo - a discussão e comparação das teorias de evolução química, os autores usaram pesquisas de 20-30 anos atrás, deixa muito a desejar em termos de atualização na literatura especializada!!!

Nanoestruturas inspiradas em borboletas podem classificar a luz: mas design na natureza é ilusão...

quinta-feira, junho 02, 2016

Biomimetic gyroid nanostructures exceeding their natural origins

Zongsong Gan1, Mark D. Turner1 and Min Gu1,2,3,*

+ Author Affiliations

↵*Corresponding author. Email: min.gu@rmit.edu.au

Science Advances 13 May 2016:

Vol. 2, no. 5, e1600084



Abstract

Using optical two-beam lithography with improved resolution and enhanced mechanical strength, we demonstrate the replication of gyroid photonic nanostructures found in the butterfly Callophrys rubi. These artificial structures are shown to have size, controllability, and uniformity that are superior to those of their biological counterparts. In particular, the elastic Young’s modulus of fabricated nanowires is enhanced by up to 20%. As such, the circular dichroism enabled by the gyroid nanostructures can operate in the near-ultraviolet wavelength region, shorter than that supported by the natural butterfly wings of C. rubi. This fabrication technique provides a unique tool for extracting three-dimensional photonic designs from nature and will aid the investigation of biomimetic nanostructures.

Keywords Gyroid nano-structures  optical two-beam lithography biomimetics mechanical strength circular dichroism

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.

FREE PDF GRATIS: Science Advances

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PERGUNTA DESTE BLOGGER:

Ué, procurando design, finalidade na natureza? Mas o Dawkins não disse que o design encontrado na natureza é ilusão? E não dizem também que Darwin eliminou a teleologia da Biologia de uma vez por todas??? Então por que procurar design numa ilusão? Por que buscar finalidade, se não existe isso na natureza???

Fui, nem sei por que, pensando que a rejeição de design na ciência se dá muito mais por razões subjetivas/ideológicas do que realmente uma rejeição científica. 

A teoria evolucionária darwinista pode ser levada a sério???

quarta-feira, junho 01, 2016

REDISCOVERING LIFE

Can Darwinian Evolutionary Theory Be Taken Seriously?

Stephen L. Talbott

This article is part of “RediscoveringLife.org”, a news portal for the Biology Worthy of LifeProject. Copyright 2016 The Nature Institute. All rights reserved.
By placing your cursor on scientific terms such as “development” (try it here), you may find them to be clickable links into a separate glossary window (or tab, if your browser is set that way). You can in any case open the glossary for browsing by clicking here.


Posted: May 17, 2016 (Article 30)

This article is the initial offering in a projected trilogy. The other two articles are tentatively entitled, “Evolution as a Story of Extended Development” and “The Intentional Organism”. The three pieces are intimately intertwined and mutually supportive. None of the three is fully intended to stand by itself, but, for the time being, this one must do just that.


Evolutionary biologists today find themselves in a troubled relationship with the American public. Their great source of discomfort and wonder lies in the fact that the theory of evolution is “still under siege”1 by a substantial and sometimes aggressively disbelieving population — this despite being “an established and accepted scientific theory for 150 years”.2 “What are we doing wrong?” asks Jason Wiles, a biologist and educator at Syracuse and McGill Universities. His answer: “We do not know”.3 And, in light of the vast institutional support undergirding evolutionary science, another educator wonders why “those exposed to evolution education do not generally demonstrate mastery of the concept”.4

The usual claim is that at least half of Americans doubt the prevailing theory, if not the very fact, of evolution. Or, at least, they recoil from the theory’s standard presentation, which tells them that the entire sweep of evolution, from microbes to man, has occurred through natural processes.5 “Natural”, in this context, means something like “purely material, purposeless, and inherently meaningless”.

Of course, rejecting the natural looks rather like bad karma. But then, embracing strictly material meaninglessness is not an obvious key to enlightenment. Do the meanings and values we derive through our experience in the world really belong to the world, or are biologists merely inventing things when they deem the truth desirable and their own work worthwhile? Are mentality and purpose alien to nature? — and if not, can they be alien to fundamental evolutionary processes?

Actually, no one doubts that human culture, with all its purposes and meanings, now plays a large role, both in our own evolutionary development and in the extinction, preservation, and modification of other species. Can we believe that our cultural ideas andintentions, which so effectively re-shape the material world, arrive on the scene only through ruptures in the natural fabric of the universe?

But the problem of meaning and purpose runs through all pre-human evolution as well. To see this, we need only observe the remarkable display of wisdom and carefully coordinated, apparently goal-directed activity so evident in dividing cells, developingembryos, mating animals, and organisms seeking food. We can hardly dismiss the evolutionary relevance of these adroit, adaptive, and seemingly intentional performances.

Perhaps we should pause and take a fresh look at things.

I would like to suggest that if half of all American citizens have become (as certain arch-defenders of biological orthodoxy like to put it) “science deniers”, then something important is afoot, and it does not look good for science. At the very least — if we assume the denial to be as unreservedly stupid as it is said to be — it would mean that science has massively and catastrophically failed our educational system. Or, if it’s not that stupid, perhaps half the population simply refuses, with more or less understanding, to tune into certain tendencies and philosophical commitments that have grossly distorted the interpretive framework governing most biological science today.6

The organism as a pretender

Some things are too obvious to deny, and not many biologists will flatly dispute the intelligently purposive, or teleological, character of organisms. “It would make no sense to talk of the purposiveness or adaptation of stars, mountains, or the laws of physics”, wrote Theodosius Dobzhansky, a geneticist and leading architect of twentieth-century evolutionary theory. But “adaptedness of living beings is too obvious to be overlooked ... Living beings have an internal, or natural, teleology”.7

Philosopher of biology Robert Arp puts it this way:

Thinkers cannot seem to get around [evolutionary biologist Robert] Trivers’ claim8 that “even the humblest creature, say, a virus, appears organized to do something; it acts as if it is trying to achieve some purpose” ... Darwin’s biology does not deny — rather, it reaffirms — the immanent teleology displayed in the striving of each living being to fulfill its specific ends ... Reproduction, growth, feeding, healing, courtship, parental care for the young — these and many other activities of organisms are goal-directed”.9

Here, however, is where a strange ambiguity begins. For even if what Arp points out seems obvious, he cannot quite bring himself to accept it at face value. So he hedges those remarks with a crucial qualification: “with respect to organisms, it is useful to think as ifthese entities have traits and processes that function in goal-directed ways” (his emphasis). In other words, the organism’s purposive behavior is not quite what it seems.

This “as if” has long been a cliché of evolutionary biology. In 1909, the prominent German evolutionary theorist, August Weismann, said that “the principle of [natural] selection solved the riddle, how it is possible to produce adaptedness without the intervention of a goal-determining force”.10

The idea was simple: there is always variation among organisms, and the ceaseless culling of the less fit among them by natural selection leaves the field to those organisms bearing the most useful variations. These are the organisms most fit for survival and reproduction — best adapted for functioning successfully in their prevailing environments. They therefore appear to be goal-directed beings, whether the goal is survival or any lesser goal serving the purpose of survival. But Weismann wants to assure us that there is noactual goal-seeking going on — or, as he puts it, no “goal-determining force” at work.

Julian Huxley, who coined the phrase “Modern Synthesis” to describe the now canonical, twentieth-century formulation of what is also called “neo-Darwinism”, wrote in 1942:

It was one of the great merits of Darwin himself to show that the purposiveness of organic structure and function was apparent only. The teleology of adaptationis a pseudo-teleology, capable of being accounted for on good mechanistic principles, without the intervention of purpose, conscious or subconscious, either on the part of the organism or of any outside power”.11

Here, again, we are said to be saved from the “intervention” of an alien force, as if real purpose and intelligence would be an offense against the natural world.

And, several decades later, the author who gave us the “selfish gene” warned us how hard it can be to escape illusion: “So overwhelming is the appearance of purposeful design that, even in this Darwinian era when we know ‘better’, we still find it difficult, indeed boringly pedantic, to refrain from teleological language when discussing adaptation”. And yet, Richard Dawkins is ever ready to remind us, “the theory of natural selection provides a mechanistic, causal account of how living things came to look as if they had been designed for a purpose”12 (emphasis added).

Dawkins’ formulation has the virtue of making explicit the fact that the organism of the long-running cliché is a designed artifact, or machine. The purposes posing the original problem — purposes that seemed to arise from a live sensing of the requirements of the present moment and a directional striving — have been quietly assumed away. They now become the functions of a machine-organism. So the question about the organism’s purposeful activity has disappeared in favor of this: “Was the design of the artifactual organism purposeful or not?”

Of course, Dawkins’ own strong predilection runs toward purposeless design by natural selection, a “blind watchmaker”13 who gives us an apparent purpose that — no need to worry! — isn’t quite the real thing. On the other hand, many of the opponents Dawkins commonly has in mind prefer an intelligent designer. What seems to have fallen out of the argument on both sides is the organism itself, which has vanished into the automatisms of engineered machinery. Its living powers have been transferred to a mysterious designer, blind or otherwise, who, having messed around with everyone’s ancestors, remains conveniently obscure for current scientific investigation.

Pursuing an illusion is hard to do

A rather odd urgency sounds through all this earnest insistence that, while organisms certainly look as if they possessed intelligent agency, we should not be so foolish as to be compelled by the evidence of our own eyes. And the claim is curiously vague. How, after all, might we distinguish between an organism capable of expressing wise intention, and an organism capable of conjuring an overwhelming illusion of wise intention? Is there, in fact, evidence that can properly override the judgment of our own eyes?

Suppose, having watched a powerful drama in which the players improvise on Shakespeare’s Hamlet, we were told that its meaningfulness — all the evident thought and intention of the players, all the unpredictable, yet coherent and directed storytelling activity — was somehow an illusion. What could we possibly make of this? Isn’t an appearance of meaningful dialogue already meaningful dialogue — and wouldn’t it remain so even if we subsequently found that it came to us, not as we thought, but in a ghostly vision? Pointing to a ghost that speaks meaningful words to us does nothing to banish the problem of meaning.

The same would be true if a cleverly programmed, artificially intelligent robot spoke those words. We would recognize a real — not a pseudo — intelligence somewhere behind the production of the meaningful speech. The question would not be whether we were seeing evidence of real intelligence, but where was its live origin.

It is easy to believe that the ubiquitous and casually spoken aphorisms about as ifteleology have never clearly been thought through. They may serve mainly as a convenient smokescreen for covering theoretical confusion — or, perhaps, a means of self-reassurance in the face of a powerful awareness of one’s own interior life, an awareness virtually impossible to shake off. “Yes, we are sometimes moved by profound meaning, and we pursue our own intentions; but that’s okay because none of this is quite what it seems to be”.

Or, which is much the same thing: “Darwin assumed only variation and natural selection, resulting in adaptation. The ‘results’ are the same as if they had been ‘intended’”.14 We might want to ask, “If the results really are the same as if they were intended, what makes them not really intended?” But perhaps it’s not worth the bother.

The thing to hold onto in all this is natural selection. If there seems to be real purpose in organisms, so we’re told, then natural selection explains it, or explains it away, in non-purposive terms. If there is only an illusion of purpose, natural selection is the responsible agent behind the illusion. Just as we trace the machine’s intelligence and intentions to a human designer, we must trace the organism’s intelligence and intentions, such as they may be, to natural selection, the blind, mindless, unintelligent, yet wondrously effective designer whose existence Darwin exposed.

But do we have any possible grounds for taking natural selection seriously as a designer of organisms and explainer of their intelligence? Before answering that question, we need to clarify some terminology by distinguishing between machines and organisms. The issues are fateful; they make or break the entire theoretical structure underlying modern biology.

Of machines, organisms, and agency

When we build a machine, we manipulate materials of the world so as to configure a set of causal physical relations adequate to our purposes. Following this configuration, the machine’s performance is shaped by those causal relations, yielding a result that is in some regards predictable so long as outside factors do not interfere. Everything “rolls along” within the preestablished physical constraints. Engineers and philosophers speak of the “initial conditions” of the system — its original, designed arrangement — which then constrains the subsequent performance.

Organisms are not machines.15 They are not endowed with a set of initial conditions, after which they carry forward the mechanistic implications of those conditions. The organism is, moment by moment, establishing new “initial” conditions. It is as if a machine were being redesigned at every moment — or would be like that if the organism were machine-like. In reality, the organism’s life is a continual “self-redesigning” — or, better, a self-expressing, or self-transforming. Its parts are not assembled once for all; they aregrown on the spot during development, so that the functional unity of the organism — the way its parts play together, and even what the parts are — obviously must be changing all along the way. If the organism were machine-like, it would be a different, newly constituted and redesigned machine each time you looked at it.

So the organism possesses, or is, a power of origination. It constantly brings about something new — something never wholly implied or determined by the physical relations of a moment ago.16 We could also think of it as a power of self-realization. The “design work” accounting for the organism is an activity inseparable from the organism’s own life. It is an expression of that life rather than a cause of it.

Machines and organisms have this in common: whatever is responsible for orchestrating causal arrangements — initially, in the case of machines, or continually, in the case of organisms — cannot itself be explained by those arrangements. This single fact calls into question the entire habit within biology of trying to explain the present purely as the consequence of material forces playing out of the past.

Biologists speak incessantly of mechanisms and of machine-like or programmed activity in organisms. But this is empty rhetoric. No one has ever pointed to a computer-like program in DNA, or in a cell, or in any larger structure. Nor has anyone shown us any physical machinery for executing such program instructions. Nor, for that matter, has anyone ever explained what constrains diffusible molecules in a watery medium to carry out intricate and elaborately sequenced operations, such as DNA replication or RNA splicing.

So, then, how do the organism’s self-designing, or self-expressing, intentions compare to our own purposive, engineering activity in designing machines? There is a crucial difference between the two. We do not cause the parts of a machine to grow together; we put them together. Our designing activity impinges on the machine “from the outside”. This is best understood by comparison with organisms.

As we have seen, the life of the organism is itself the designing power. Its agency is immanent in its own being, and is somehow expressed at the very roots of material causation. It brings forth this or that kind of growth with no need for the artifice of an alien hand arbitrarily intervening to arrange parts and causal relations this way or that. The choreographing is brought about, it would appear, from that same depth of reality where the causal forces themselves arise, not from “outside”. However we conceive this “inner” place, it is, at least for now, inaccessible to our own engineering prowess.

At the same time, we ourselves possess varieties of conscious activity that other organisms do not. When I refer to the organism’s intelligent agency, or its purposiveness, or its directed coordination of means to serve particular ends, I do not imply anything equivalent to our own conscious purposing or planning. But neither do I suggest somethinginferior to our particular sort of wisdom and power of action. If anything, we must consider organic life — for example, the life of our cells — to be an expression of a higher sort of intelligence and intention than we ourselves can yet imagine consciously achieving in the technological realm.

Rather than over-defining terms and transgressing the boundaries of my own understanding, I am inclined to leave the matter there. I will tend to use words such as “intelligence”, “purpose”, “intention”, and “agency” in the way we commonly use them, with the understanding that the reader will keep in mind the above considerations. Given the scientific culture’s reflexive recoil from the psychic and voluntary in all its manifestations, I prefer to err on the side of anthropomorphism rather than to encourage the usual dismissal of interior reality.

It needs adding, finally, that our recognition of intelligent and intentional expressions does not require us to understand everything about their source. We would have no difficulty distinguishing the significance of letters on a page from that of pebbles distributed on a sandy shore, even if we knew nothing about origins in either case. We can declare a functioning machine to be a designed object, whether or not we have any clue about who designed it. And if we find live, intelligent performances by organisms, we don’t have to know how, or from where, the intelligence gains its foothold before we accept the testimony of our eyes and understanding.


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Stephen L. Talbott
The Nature Institute; Ghent, New York

After many years working in the engineering organizations of computer manufacturers, Talbott joined The Nature Institute as Senior Researcher in 1998. He has long been concerned about distortions introduced in biology by technological thinking. He attempts to show how our understanding of the organism and its evolution is transformed once we recognize and take seriously the organism as an intelligent agent meaningfully (though not necessarily consciously) pursuing its own way of life.

A Ferrari dos motores celulares: mero acaso, fortuita necessidade ou design inteligente?

Architecture of a flagellar apparatus in the fast-swimming magnetotactic bacterium MO-1
Juanfang Ruan a,1, Takayuki Kato a,1, Claire-Lise Santini b, Tomoko Miyata a, Akihiro Kawamoto a, Wei-Jia Zhang b, Alain Bernadac c, Long-Fei Wu b, and Keiichi Namba a,d,2

Author Affiliations

aGraduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan;

bLaboratoire de Chimie Bactérienne, Unité Mixte de Recherche 7283, Aix-Marseille Université, Centre National de la Recherche Scientifique, F-13402, Marseille Cedex 20, France;

cService de Microscopie, Aix-Marseille Université, Institut de Microbiologie de la Méditerranée-Centre National de la Recherche Scientifique, F-13402, Marseille Cedex 20, France; and

dRiken Quantitative Biology Center, Suita, Osaka 565-0871, Japan

Edited by Howard C. Berg, Harvard University, Cambridge, MA, and approved November 2, 2012 (received for review September 2, 2012)




Abstract

The bacterial flagellum is a motility organelle that consists of a rotary motor and a helical propeller. The flagella usually work individually or by forming a loose bundle to produce thrust. However, the flagellar apparatus of marine bacterium MO-1 is a tight bundle of seven flagellar filaments enveloped in a sheath, and it has been a mystery as to how the flagella rotate smoothly in coordination. Here we have used electron cryotomography to visualize the 3D architecture of the sheathed flagella. The seven filaments are enveloped with 24 fibrils in the sheath, and their basal bodies are arranged in an intertwined hexagonal array similar to the thick and thin filaments of vertebrate skeletal muscles. This complex and exquisite architecture strongly suggests that the fibrils counter-rotate between flagella in direct contact to minimize the friction of high-speed rotation of individual flagella in the tight bundle within the sheath to enable MO-1 cells to swim at about 300 µm/s.

flagellar basal body magnetotactic motility

Footnotes

1J.R. and T.K. contributed equally to this work.

2To whom correspondence should be addressed. E-mail: keiichi@fbs.osaka-u.ac.jp.

Author contributions: L.-F.W. and K.N. designed research; J.R., T.K., T.M., and A.K. performed research; C.-L.S., T.M., A.K., W.-J.Z., and A.B. contributed new reagents/analytic tools; J.R., T.K., and K.N. analyzed data; and J.R., T.K., and K.N. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

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NOTA DESTE BLOGGER:

Como explicar, por etapas gradualistas darwinistas, a origem e evolução de uma bactéria que tem um pacote flagelar de sete motores magneticamente guiado e acionado por 24 engrenagens, e que vai de 0 a 300 micrômetros em um segundo, dez vezes mais rápido do que E. coli? Explica aí, Darwin!

Um sistema de corais extenso na foz do Rio Amazonas

An extensive reef system at the Amazon River mouth

Rodrigo L. Moura1,2, Gilberto M. Amado-Filho3, Fernando C. Moraes3,9, Poliana S. Brasileiro3, Paulo S. Salomon1,2, Michel M. Mahiques4, Alex C. Bastos5, Marcelo G. Almeida6, Jomar M. Silva Jr6, Beatriz F. Araujo6, Frederico P. Brito6, Thiago P. Rangel6, Braulio C. V. Oliveira6, Ricardo G. Bahia3, Rodolfo P. Paranhos1, Rodolfo J. S. Dias4, Eduardo Siegle4, Alberto G. Figueiredo Jr7, Renato C. Pereira8, Camille V. Leal1,9, Eduardo Hajdu9, Nils E. Asp10, Gustavo B. Gregoracci11, Sigrid Neumann-Leitão12, Patricia L. Yager13, Ronaldo B. Francini-Filho14, Adriana Fróes1, Mariana Campeão1, Bruno S. Silva1, Ana P. B. Moreira1, Louisi Oliveira1, Ana C. Soares1, Lais Araujo1, Nara L. Oliveira15, João B. Teixeira15, Rogerio A. B. Valle2, Cristiane C. Thompson1, Carlos E. Rezende6,* and Fabiano L. Thompson1,2,*

+ Author Affiliations

↵*Corresponding author: E-mail: fabianothompson1@gmail.com (F.L.T.); crezendeuenf@yahoo.com.br (C.E.R.)

Science Advances 22 Apr 2016:

Vol. 2, no. 4, e1501252


Source/Fonte: NASA

Abstract

Large rivers create major gaps in reef distribution along tropical shelves. The Amazon River represents 20% of the global riverine discharge to the ocean, generating up to a 1.3 × 106–km2 plume, and extensive muddy bottoms in the equatorial margin of South America. As a result, a wide area of the tropical North Atlantic is heavily affected in terms of salinity, pH, light penetration, and sedimentation. Such unfavorable conditions were thought to imprint a major gap in Western Atlantic reefs. We present an extensive carbonate system off the Amazon mouth, underneath the river plume. Significant carbonate sedimentation occurred during lowstand sea level, and still occurs in the outer shelf, resulting in complex hard-bottom topography. A permanent near-bottom wedge of ocean water, together with the seasonal nature of the plume’s eastward retroflection, conditions the existence of this extensive (~9500 km2) hard-bottom mosaic. The Amazon reefs transition from accretive to erosional structures and encompass extensive rhodolith beds. Carbonate structures function as a connectivity corridor for wide depth–ranging reef-associated species, being heavily colonized by large sponges and other structure-forming filter feeders that dwell under low light and high levels of particulates. The oxycline between the plume and subplume is associated with chemoautotrophic and anaerobic microbial metabolisms. The system described here provides several insights about the responses of tropical reefs to suboptimal and marginal reef-building conditions, which are accelerating worldwide due to global changes.

Keywords coral reefs mineralization phase shifts marine biogeography stepping stones

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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