Darwin, a evolução pré-darwinista é plausível? As evidências dizem NÃO!

sexta-feira, setembro 21, 2018

Is pre-Darwinian evolution plausible?

Marc TesseraEmail authorView ORCID ID profile
Biology Direct201813:18

https://doi.org/10.1186/s13062-018-0216-7

© The Author(s). 2018
Received: 29 December 2017 Accepted: 15 June 2018 Published: 21 September 2018 


 Abstract

Background

This essay highlights critical aspects of the plausibility of pre-Darwinian evolution. It is based on a critical review of some better-known open, far-from-equilibrium system-based scenarios supposed to explain processes that took place before Darwinian evolution had emerged and that resulted in the origin of the first systems capable of Darwinian evolution. The researchers’ responses to eight crucial questions are reviewed. The majority of the researchers claim that there would have been an evolutionary continuity between chemistry and “biology”. A key question is how did this evolution begin before Darwinian evolution had begun? In other words the question is whether pre-Darwinian evolution is plausible.

Results

Strengths and weaknesses of the reviewed scenarios are presented. They are distinguished between metabolism-first, replicator-first and combined metabolism-replicator models. The metabolism-first scenarios show major issues, the worst concerns heredity and chirality. Although the replicator-first scenarios answer the heredity question they have their own problems, notably chirality. Among the reviewed combined metabolism-replicator models, one shows the fewest issues. In particular, it seems to answer the chiral question, and eventually implies Darwinian evolution from the very beginning. Its main hypothesis needs to be validated with experimental data.

Conclusion

From this critical review it is that the concept of “pre-Darwinian evolution” appears questionable, in particular because it is unlikely if not impossible that any evolution in complexity over time may work without multiplication and heritability allowing the emergence of genetically and ecologically diverse lineages on which natural selection may operate. Only Darwinian evolution could have led to such an evolution. Thus, Pre-Darwinian evolution is not plausible according to the author. Surely, the answer to the question posed in the title is a prerequisite to the understanding of the origin of Darwinian evolution.

Reviewers

This article was reviewed by Purificacion Lopez-Garcia, Anthony Poole, Doron Lancet, and Thomas Dandekar. 

Keywords

Metabolism-first Replicator-first Combined metabolism-replicator scenarios
Pre-Darwinian evolution Prebiotic evolution Darwinian evolution Origin of life
Origin of Darwinian evolution
 
FREE PDF GRATIS: Biology Direct

Darwin, explica aí: moléculas de colesterol de 558 milhões de anos preservadas intactas?

Ancient steroids establish the Ediacaran fossil Dickinsonia as one of the earliest animals

Ilya Bobrovskiy1,*, Janet M. Hope1, Andrey Ivantsov2, Benjamin J. Nettersheim3, Christian Hallmann3,4, Jochen J. Brocks1,*
 
1Research School of Earth Sciences, Australian National University, Canberra ACT 2601, Australia.
 
2Borissiak Paleontological Institute, Russian Academy of Sciences, Moscow 117997, Russia.
 
3Max Planck Institute for Biogeochemistry, Jena 07745, Germany.
 
4MARUM–Center for Marine Environmental Sciences, University of Bremen, Bremen 28359, Germany.
 
*Corresponding author. Email: ilya.bobrovskiy@anu.edu.au (I.B.); jochen.brocks@anu.edu.au (J.J.B.)

 Science 21 Sep 2018: Vol. 361, Issue 6408, pp. 1246-1249
DOI: 10.1126/science.aat7228
 
Source/Fonte: The Australian National University (ANU)
 
Confirming the identity of early animals

The first complex organisms emerged during the Ediacaran period, around 600 million years ago. The taxonomic affiliation of many of these organisms has been difficult to discern. Fossils of Dickinsonia, bilaterally symmetrical oval organisms, have been particularly difficult to classify. Bobrovskiy et al. conducted an analysis using lipid biomarkers obtained from Dickinsonia fossils and found that the fossils contained almost exclusively cholesteroids, a marker found only in animals (see the Perspective by Summons and Erwin). Thus, Dickinsonia were basal animals. This supports the idea that the Ediacaran biota may have been a precursor to the explosion of animal forms later observed in the Cambrian, about 500 million years ago.

Science, this issue p. 1246; see also p. 1198

Abstract

The enigmatic Ediacara biota (571 million to 541 million years ago) represents the first macroscopic complex organisms in the geological record and may hold the key to our understanding of the origin of animals. Ediacaran macrofossils are as “strange as life on another planet” and have evaded taxonomic classification, with interpretations ranging from marine animals or giant single-celled protists to terrestrial lichens. Here, we show that lipid biomarkers extracted from organically preserved Ediacaran macrofossils unambiguously clarify their phylogeny. Dickinsonia and its relatives solely produced cholesteroids, a hallmark of animals. Our results make these iconic members of the Ediacara biota the oldest confirmed macroscopic animals in the rock record, indicating that the appearance of the Ediacara biota was indeed a prelude to the Cambrian explosion of animal life. 
 
Subscription or payment needed/Requer assinatura ou pagamento: Science
 
+++++
 
Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao Portal Periódicos CAPES/MEC podem ler gratuitamente este artigo da Science e de mais 33.000 publicações científicas. 

Novo livro de Michael Behe sobre o declínio de Darwin: a nova ciência do DNA desafia a teoria da evolução

quarta-feira, setembro 19, 2018

Darwin Devolves: The New Science About DNA that Challenges Evolution Hardcover – February 26, 2019
by Michael J. Behe (Author)

The scientist who has been dubbed the “Father of Intelligent Design” and author of the groundbreaking book Darwin’s Black Box contends that recent scientific discoveries further disprove Darwinism and strengthen the case for an intelligent creator.

In his controversial bestseller Darwin’s Black Box, biochemist Michael Behe challenged Darwin’s theory of evolution, arguing that science itself has proven that intelligent design is a better explanation for the origin of life. In Darwin Devolves, Behe advances his argument, presenting new research that offers a startling reconsideration of how Darwin’s mechanism works, weakening the theory’s validity even more.

A system of natural selection acting on random mutation, evolution can help make something look and act differently. But evolution never creates something organically. Behe contends that Darwinism actually works by a process of devolution—damaging cells in DNA in order to create something new at the lowest biological levels. This is important, he makes clear, because it shows the Darwinian process cannot explain the creation of life itself. “A process that so easily tears down sophisticated machinery is not one which will build complex, functional systems,” he writes.

In addition to disputing the methodology of Darwinism and how it conflicts with the concept of creation, Behe reveals that what makes Intelligent Design unique—and right—is that it acknowledges causation. Evolution proposes that organisms living today are descended with modification from organisms that lived in the distant past. But Intelligent Design goes a step further asking, what caused such astounding changes to take place? What is the reason or mechanism for evolution? For Behe, this is what makes Intelligent Design so important.
 
 
+++++
 

Darwin, as mutações genéticas frustram os esforços científicos de prever plenamente o nosso futuro

segunda-feira, setembro 17, 2018

The complex underpinnings of genetic background effects

Martin N. Mullis, Takeshi Matsui, Rachel Schell, Ryan Foree & Ian M. Ehrenreich 

Nature Communications volume 9, Article number: 3548 (2018) 

Article | OPEN | Published: 17 September 2018

Source/Fonte: Evolution Berkeley

Abstract

Genetic interactions between mutations and standing polymorphisms can cause mutations to show distinct phenotypic effects in different individuals. To characterize the genetic architecture of these so-called background effects, we genotype 1411 wild-type and mutant yeast cross progeny and measure their growth in 10 environments. Using these data, we map 1086 interactions between segregating loci and 7 different gene knockouts. Each knockout exhibits between 73 and 543 interactions, with 89% of all interactions involving higher-order epistasis between a knockout and multiple loci. Identified loci interact with as few as one knockout and as many as all seven knockouts. In mutants, loci interacting with fewer and more knockouts tend to show enhanced and reduced phenotypic effects, respectively. Cross–environment analysis reveals that most interactions between the knockouts and segregating loci also involve the environment. These results illustrate the complicated interactions between mutations, standing polymorphisms, and the environment that cause background effects.

Acknowledgements

We thank Norm Arnheim, Mark Chaisson, Matt Dean, Sasha Levy, David Pfennig, and Kevin Roy for comments on a draft of this manuscript. We also thank Alessandro Coradini, Jonathan Lee, and Fabian Seidl for input during the execution of this project and writing of this paper. The research described in this manuscript was supported by grant R01GM110255 from the National Institutes of Health, as well as a Computational and Evolutionary Molecular Biology fellowship from the Alfred P. Sloan Foundation to I.M.E. and a Research Enhancement Fellowship from the USC Graduate School to M.N.M. Many of the analyses described in this paper were performed on the USC High-Performance Computing cluster.

Author information

Author notes

These authors contributed equally: Martin N. Mullis, Takeshi Matsui, Rachel Schell.

Affiliations

Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA

Martin N. Mullis, Takeshi Matsui, Rachel Schell, Ryan Foree & Ian M. Ehrenreich

Contributions

M.N.M., T.M., R.S. and I.M.E. conceptualized this project. M.N.M., T.M., R.S. and R.F. performed experiments. M.N.M., T.M. and I.M.E. analyzed data. M.N.M., T.M., R.S. and I.M.E. wrote the paper.

Competing interests

The authors declare no competing interests.

Corresponding authors

Correspondence to Martin N. Mullis or Takeshi Matsui or Ian M. Ehrenreich.

Faleceu o geneticista Luigi Luca Cavalli-Sforza (1922-2018): um pássaro na gaiola dourada

quinta-feira, setembro 13, 2018

L.L. Cavalli-Sforza: A bird in a gilded cage

Open Behavioral Genetics, 2014, ISSN: 2446-3876

Peter Frost


Abstract 

Luigi Luca Cavalli-Sforza is a complex figure. On the one hand, he has publicly backed those who assert that human races do not exist. On the other hand, by aggregating large volumes of genetic data, he has proven the existence of large continental races, as well as smaller regional and micro ones. By developing the theory of gene-culture co-evolution, he has also shown that humans did not stop evolving genetically when they began to evolve culturally. In fact, the two processes have fed into each other, with humans having to adapt not only to the natural portion of their environment (climate, vegetation, wildlife, etc.) but also to the portion they themselves have created (mode of subsistence, behavioral norms, gender roles, class structure, belief system, etc.). This has led some to see a double game at work. While bowing to the mainstream taboos, Cavalli-Sforza has quietly amassed evidence that human races not only exist but also differ in ways that are more than skin deep. In time, his weighty tomes will speak louder than his official statements on race. This may indeed be how he sees himself, and it might explain certain contradictions between his public persona and his academic self. Oh, those naïve antiracists, if only they knew how they’re being outfoxed! Time will tell who is outfoxing whom. To date, the results speak for themselves. When in 1994 Cavalli-Sforza published The History and Geography of Human Genes, academics and nonacademics alike were talking more openly about race, as seen by the publication the same year of The Bell Curve and by the willingness of previously silent anthropologists, like Vincent Sarich, to step forward and speak out. That interval of glasnost soon ended, in no small part because of Cavalli-Sforza’s apparent conversion, as attested in his book, to the view that human races do not exist in any meaningful sense. Why did he convert? And did he really? I doubt there was any conversion. His change of heart was too rapid, and it happened while the zeitgeist was moving in the other direction. Perhaps he saw a chance to gain acceptance for his new tome. Or perhaps he received a letter one day, detailing his wartime record, the people he worked with, and the testing on human subjects … Cavalli-Sforza had to remake his life when the war ended. He never denied the nature of his wartime research (the time it takes for anthrax to kill its host) but tried to create the impression that he was doing pure research with no military implications. Yet this was Berlin, in 1943-1944. There was no money for pure research. Was he motivated by opportunism, the chance to gain experience in his field of study? Or did he feel loyalty to the Axis cause? It is difficult to say, and perhaps it doesn’t matter. It is enough to say that he later saw his wartime research as a stain on his record and tried to minimize it as much as possible. He was thus vulnerable to blackmail, or rather to his chronic fear of blackmail. We will probably never know the full story. One thing is sure. If Cavalli-Sforza is playing a double game, he has been playing it far too long. Such a strategy is excusable for an academic who is young, untenured, poorly known, and far from retirement, but these excuses hardly apply to a professor emeritus like Cavalli-Sforza. The time is overdue to speak frankly and, if need be, pay the price. Anyway, what else can he do now with his vast reserves of public esteem? Take it with him to the next world?

FREE PDF GRATIS: Open Behavioral Genetics

Darwin, não é mero acaso, nem fortuita necessidade, mas informação!

terça-feira, setembro 11, 2018

EMBO Reports

Will biologists become computer scientists?

A truly interdisciplinary effort by computer scientists and biologists to understand how cells process information may yield new insights for both fields

Anne Condon Hélène Kirchner Damien Larivière Wallace Marshall Vincent Noireaux Tsvi Tlusty Eric Fourmentin

First published: 30 July 2018 https://doi.org/10.15252/embr.201846628


Abstract

The idea that living systems could be understood and described as information‐processing systems has been around even before the first computers were built. From Alan Turing's considerable paper in 1936 to Erwin Schrödinger's work in 1944 and John von Neumann's work in 1948 [1], many scientists pondered about information storage and the possible existence of a logical processor within living cells. The discovery of the double‐helical structure of DNA in 1953 provided the material basis for these intuitions as it finally revealed how cells store inheritable information in a “digital” format. The recent success of genome transplantation experiments into recipient host cells [2]—akin to transferring software to another computer—further strengthened the hypothesis that living cells can be regarded as Turing Machines, as was suggested by Sydney Brenner [3] (see Sidebar 1 for a glossary and Sidebar 2 for further readings).

… many scientists pondered about information storage and the possible existence of a logical processor within living cells.

François Jacob and Jacques Monod were among the first biologists to understand gene expression as an algorithm.

In light of these and other experimental results that would support the hypothesis that some parts of living systems could be understood as information‐processing machines, the Fourmentin‐Guilbert Scientific Foundation invited international scholars from the life sciences, computer sciences and physical sciences (see Sidebar 3) to the I2CELL (from Information to Cells) seminar in February 2018 near Oxford, UK, to discuss and identify new research areas. Over 3 days, they debated on a broad range of subjects from computation, information handling, algorithms, robotics and viruses (of the digital and biological varieties) to explore analogies between cells and computers that could inspire new research, while keeping a critical approach to the benefits of similarities. …

+++++

Subscription or payment needed/Requer assinatura ou pagamento: EMBO Reports

+++++

NOTA DESTE BLOGGER: 

Qual teoria que tem a INFORMAÇÃO em seu arcabouço teórico? A atual teoria geral da evolução de Darwin - a Síntese Evolutiva Ampliada/Estendida lançada em agosto de 2015? Lidou apenas en passant. A única teoria que tem a INFORMAÇÃO no seu arcabouço teórico é a Teoria do Design Inteligente: informação complexa especificada.

Uma extraordinária diversificação de insetos no período Triássico Médio: Surgimento abrupto e estase!

sexta-feira, setembro 07, 2018

Middle-Late Triassic insect radiation revealed by diverse fossils and isotopic ages from China

Daran Zheng1,2, Su-Chin Chang2,*, He Wang1, Yan Fang1, Jun Wang2, Chongqing Feng2, Guwei Xie3,4, Edmund A. Jarzembowski1,5, Haichun Zhang1 and Bo Wang1,6,*


Science Advances 05 Sep 2018: Vol. 4, no. 9, eaat1380


Fig. 3 Representative fossils from Tongchuan and Karamay entomofaunas.

Tongchuan entomofauna (A to C, E to J, and L to O), and Karamay entomofauna (D and K). (A) Zygophlebia (Odonatoptera: Zygophlebiidae), NIGP163160; (B) Locustavidae (Orthoptera), NIGP162042; (C) Prochoristella (Mecoptera: Permochoristidae), NIGP162043; (D) Corixidae, NIGP162044; (E) Boreocixius (Hemiptera: Surijokocixiidae), NIGP162045; (F) Dunstaniidae (Hemiptera), NIGP162046; (G) Aphidoidea (Hemiptera), NIGP162047; (H) Chauliodites (Grylloblattida: Chaulioditidae), NIGP162048; (I) Cicadocorinae (Hemiptera: Progonocimicidae), NIGP162049; (J) Ichnogenus Folindusia (Trichoptera), NIGP162050; (K) Ichnogenus Terrindusia (Trichoptera), NIGP162051; (L) Myxophaga (Coleoptera), NIGP162052; (M) Elateriformia (Coleoptera), NIGP162053; (N) Dytiscoidea (Coleoptera), NIGP162054; (O) Cicadocorinae (Hemiptera: Progonocimicidae), NIGP162055. Scale bars, 5 mm (white), and 1 mm (black).

Abstract

The Triassic represented an important period that witnessed the diversification of marine and terrestrial ecosystems. The radiations of terrestrial plants and vertebrates during this period have been widely investigated; however, the Triassic history of insects, the most diverse group of organisms on Earth, remains enigmatic because of the rarity of Early-Middle Triassic fossils. We report new insect fossils from a Ladinian deposit (Tongchuan entomofauna) dated to approximately 238 to 237 million years ago and a Carnian deposit (Karamay entomofauna) in northwestern China, including the earliest definite caddisfly cases (Trichoptera), water boatmen (Hemiptera), diverse polyphagan beetles (Coleoptera), and scorpionflies (Mecoptera). The Tongchuan entomofauna is near the Ladinian-Carnian boundary in age, providing a calibration date for correlation to contemporaneous biotas. Our findings confirm that the clade Holometabola, comprising most of the modern-day insect species, experienced extraordinary diversification in the Middle-Late Triassic. Moreover, our results suggest that the diversification of aquatic insects (a key event of the “Mesozoic Lacustrine Revolution”) had already begun by the Middle Triassic, providing new insights into the early evolution of freshwater ecosystems.

FREE PDF GRATIS: Science Advances Sup. Info.

+++++

See Elizabeth Pennisi's article: 


+++++

Os autores escreveram:

“Our findings confirm that the clade Holometabola, comprising most of the modern-day insect species, experienced extraordinary diversification in the Middle-Late Triassic.” ... “In summary, our findings confirm that holometabolous and aquatic insects experienced a radiation event in the Middle Triassic.”  

Por que isso é importante: Porque é significativamente mais cedo do que o esperado - parcialmente baseado na evidência de fósseis, mas também em datas previamente propostas de pesquisas moleculares.  

No artigo da Pennisi:

“The sites underscore that this burst of evolution took place much earlier than researchers had thought, particularly for water-loving insects.” ... “This earlier date for the expansion of insect diversity aligns it with the explosion in plant diversity happening at that time.”  

Convém destacar que essas descobertas não são incomuns – é mais um padrão característico descoberto pelos paleontólogos - surgimento abrupto e estase.

Eita seleção natural preguiçosa - 237 milhões e tudo permanece como antes no quartel de Abrantes, oops de Darwin!

DNA, RNA e ferramentas de proteínas para editar informação genética em células humanas

terça-feira, setembro 04, 2018

iScience 
REVIEW| VOLUME 6, ISSUE , P247-263, AUGUST 31, 2018

DNA, RNA, and Protein Tools for Editing the Genetic Information in Human Cells

Xiaoyu Chen 2 Manuel A.F.V. Gonçalves

Published:August 03, 2018 DOI: https://doi.org/10.1016/j.isci.2018.08.001


Abstract

Solving the structure of DNA in 1953 has unleashed a tour de force in molecular biology that has illuminated how the genetic information stored in DNA is copied and flows downstream into RNA and proteins. Currently, increasingly powerful technologies permit not only reading and writing DNA in vitro but also editing the genetic instructions in cells from virtually any organism. Editing specific genomic sequences in living cells has been particularly accelerated with the introduction of programmable RNA-guided nucleases (RGNs) based on prokaryotic CRISPR adaptive immune systems. The repair of chromosomal breaks made by RGNs with donor DNA patches results in targeted genome editing involving the introduction of specific genetic changes at predefined genomic positions. Hence, donor DNAs, guide RNAs, and nuclease proteins, each representing the molecular entities underlying the storage, transmission, and expression of genetic information, are, once delivered into cells, put to work as agents of change of that very same genetic text. Here, after providing an outline of the programmable nuclease-assisted genome editing field, we review the increasingly diverse range of DNA, RNA, and protein components (e.g., nucleases and “nickases”) that, when brought together, underlie RGN-based genome editing in eukaryotic cells.

Subject Areas Techniques in Genetics Molecular Genetics Molecular Biology Experimental Approach

FREE PDF GRATIS: iScience

Homoquiralidade através da desnaturação induzida de fótons de RNA/DNA na origem da vida

segunda-feira, setembro 03, 2018


Homochirality through Photon-Induced Denaturing of RNA/DNA at the Origin of Life

Karo Michaelian ORCID

Department of Nuclear Physics and Application of Radiations, Instítuto de Física, Universidad Nacional Autónoma de México, A. P. 20-364, México, D.F. 01000, Mexico

Received: 27 April 2018 / Revised: 22 May 2018 / Accepted: 22 May 2018 / Published: 6 June 2018

(This article belongs to the Special Issue The Origin of Chirality in Life (Chiral Symmetry Breaking))


Abstract

Since a racemic mixture of chiral nucleotides frustrates the enzymeless extension of RNA and DNA, the origin of homochirality must be intimately connected with the origin of life. Homochirality theories have elected to presume abiotic mechanisms for prebiotic enantiomer enrichment and post amplification, but none, so far, has been generally accepted. Here I present a novel hypothesis for the procurement of homochirality from an asymmetry in right- over left-circularly polarized photon-induced denaturing of RNA and DNA at the Archean ocean surface as temperatures descended below that of RNA and DNA melting. This asymmetry is attributed to the small excess of right-handed circularly polarized submarine light during the afternoon, when surface water temperatures were highest and thus most conducive to photon-induced denaturing, and to a negative circular dichroism band extending from 230 to 270 nm for small oligos of RNA and DNA. Because D-nucleic acids have greater affinity for L-tryptophan due to stereochemistry, and because D-RNA/DNA+L-tryptophan complexes have an increased negative circular dichroism band between 230 and 270 nm, the homochirality of tryptophan can also be explained by this hypothesis. A numerical model is presented, demonstrating the efficacy of such a mechanism in procuring homochirality of RNA or DNA from an original racemic solution in as little as 270 Archean years. 

Keywords: homochirality; origin of life; non-equilibrium thermodynamics; photon dissipation; RNA; DNA; tryptophan

FREE PDF GRATIS: Life

Insights na geometria de centríolos revelada na criotomografia de centríolos duplos e triplos: mero acaso, fortuita necessidade ou design inteligente?

sexta-feira, agosto 31, 2018

Insights into centriole geometry revealed by cryotomography of doublet and triplet centrioles

Garrett A Greenan, Bettina Keszthelyi, Ronald D Vale, David A Agard Is a corresponding author

University of California, United States; Howard Hughes Medical Institute, United States

RESEARCH ARTICLE Aug 6, 2018

The proximal and distal centriole show several major structural differences.

Abstract

Centrioles are cylindrical assemblies comprised of 9 singlet, doublet, or triplet microtubules, essential for the formation of motile and sensory cilia. While the structure of the cilium is being defined at increasing resolution, centriolar structure remains poorly understood. Here, we used electron cryo-tomography to determine the structure of mammalian (triplet) and Drosophila (doublet) centrioles. Mammalian centrioles have two distinct domains: a 200 nm proximal core region connected by A-C linkers, and a distal domain where the C-tubule is incomplete and a pair of novel linkages stabilize the assembly producing a geometry more closely resembling the ciliary axoneme. Drosophila centrioles resemble the mammalian core, but with their doublet microtubules linked through the A tubules. The commonality of core-region length, and the abrupt transition in mammalian centrioles, suggests a conserved length-setting mechanism. The unexpected linker diversity suggests how unique centriolar architectures arise in different tissues and organisms.

FREE PDF GRATIS: eLife

Os fundamentos físicos da complexidade biológica: mero acaso, fortuita necessidade ou design inteligente?

Physical foundations of biological complexity

Yuri I. Wolf, Mikhail I. Katsnelson, and Eugene V. Koonin

PNAS published ahead of print August 27, 2018 


Contributed by Eugene V. Koonin, July 31, 2018 (sent for review May 21, 2018; reviewed by Sergei Maslov and Eörs Szathmáry)


Significance

Living organisms are characterized by a degree of hierarchical complexity that appears to be inaccessible to even the most complex inanimate objects. Routes and patterns of the evolution of complexity are poorly understood. We propose a general conceptual framework for emergence of complexity through competing interactions and frustrated states similar to those that yield patterns in striped glasses and cause self-organized criticality. We show that biological evolution is replete with competing interactions and frustration that, in particular, drive major transitions in evolution. The key distinction between biological and nonbiological systems seems to be the existence of long-term digital memory and phenotype-to-genotype feedback in living matter.

Abstract

Biological systems reach hierarchical complexity that has no counterpart outside the realm of biology. Undoubtedly, biological entities obey the fundamental physical laws. Can today’s physics provide an explanatory framework for understanding the evolution of biological complexity? We argue that the physical foundation for understanding the origin and evolution of complexity can be gleaned at the interface between the theory of frustrated states resulting in pattern formation in glass-like media and the theory of self-organized criticality (SOC). On the one hand, SOC has been shown to emerge in spin-glass systems of high dimensionality. On the other hand, SOC is often viewed as the most appropriate physical description of evolutionary transitions in biology. We unify these two faces of SOC by showing that emergence of complex features in biological evolution typically, if not always, is triggered by frustration that is caused by competing interactions at different organizational levels. Such competing interactions lead to SOC, which represents the optimal conditions for the emergence of complexity. Competing interactions and frustrated states permeate biology at all organizational levels and are tightly linked to the ubiquitous competition for limiting resources. This perspective extends from the comparatively simple phenomena occurring in glasses to large-scale events of biological evolution, such as major evolutionary transitions. Frustration caused by competing interactions in multidimensional systems could be the general driving force behind the emergence of complexity, within and beyond the domain of biology.

evolution of complexity competing interactions frustrated states spin glasses self-organized criticality

FREE PDF GRATIS: PNAS

Mais insights sobre a evolução dos motores de flagelos bacterianos

Acta Cryst. (2018). D74, 585-594


Insights into the evolution of bacterial flagellar motors from high-throughput in situ electron cryotomography and subtomogram averaging

F. M. Rossmann and M. Beeby

Source/Fonte: New Scientist


Abstract

In situ structural information on molecular machines can be invaluable in understanding their assembly, mechanism and evolution. Here, the use of electron cryotomography (ECT) to obtain significant insights into how an archetypal molecular machine, the bacterial flagellar motor, functions and how it has evolved is described. Over the last decade, studies using a high-throughput, medium-resolution ECT approach combined with genetics, phylogenetic reconstruction and phenotypic analysis have revealed surprising structural diversity in flagellar motors. Variations in the size and the number of torque-generating proteins in the motor visualized for the first time using ECT has shown that these variations have enabled bacteria to adapt their swimming torque to the environment. Much of the structural diversity can be explained in terms of scaffold structures that facilitate the incorporation of additional motor proteins, and more recent studies have begun to infer evolutionary pathways to higher torque-producing motors. This review seeks to highlight how the emerging power of ECT has enabled the inference of ancestral states from various bacterial species towards understanding how, and `why', flagellar motors have evolved from an ancestral motor to a diversity of variants with adapted or modified functions.

Keywords: low-abundance imaging; electron cryotomography; subtomogram averaging; bacterial flagellar motors; molecular evolution.


A escala de tempo da evolução da planta terrestre inicial

quinta-feira, agosto 30, 2018

The timescale of early land plant evolution

Jennifer L. Morris, Mark N. Puttick, James W. Clark, Dianne Edwards, Paul Kenrick, Silvia Pressel, Charles H. Wellman, Ziheng Yang, Harald Schneider, and Philip C. J. Donoghue

PNAS published ahead of print February 20, 2018 

Edited by Peter R. Crane, Oak Spring Garden Foundation, Upperville, VA, and approved January 17, 2018 (received for review November 10, 2017)


Significance

Establishing the timescale of early land plant evolution is essential to testing hypotheses on the coevolution of land plants and Earth’s System. Here, we establish a timescale for early land plant evolution that integrates over competing hypotheses on bryophyte−tracheophyte relationships. We estimate land plants to have emerged in a middle Cambrian–Early Ordovocian interval, and vascular plants to have emerged in the Late Ordovician−Silurian. This timescale implies an early establishment of terrestrial ecosystems by land plants that is in close accord with recent estimates for the origin of terrestrial animal lineages. Biogeochemical models that are constrained by the fossil record of early land plants, or attempt to explain their impact, must consider a much earlier, middle Cambrian–Early Ordovician, origin.

Abstract

Establishing the timescale of early land plant evolution is essential for testing hypotheses on the coevolution of land plants and Earth’s System. The sparseness of early land plant megafossils and stratigraphic controls on their distribution make the fossil record an unreliable guide, leaving only the molecular clock. However, the application of molecular clock methodology is challenged by the current impasse in attempts to resolve the evolutionary relationships among the living bryophytes and tracheophytes. Here, we establish a timescale for early land plant evolution that integrates over topological uncertainty by exploring the impact of competing hypotheses on bryophyte−tracheophyte relationships, among other variables, on divergence time estimation. We codify 37 fossil calibrations for Viridiplantae following best practice. We apply these calibrations in a Bayesian relaxed molecular clock analysis of a phylogenomic dataset encompassing the diversity of Embryophyta and their relatives within Viridiplantae. Topology and dataset sizes have little impact on age estimates, with greater differences among alternative clock models and calibration strategies. For all analyses, a Cambrian origin of Embryophyta is recovered with highest probability. The estimated ages for crown tracheophytes range from Late Ordovician to late Silurian. This timescale implies an early establishment of terrestrial ecosystems by land plants that is in close accord with recent estimates for the origin of terrestrial animal lineages. Biogeochemical models that are constrained by the fossil record of early land plants, or attempt to explain their impact, must consider the implications of a much earlier, middle Cambrian–Early Ordovician, origin.

plant evolution timescale phylogeny Embryophyta

FREE PDF GRATIS: PNAS Sup. Info.

Darwin, mais complexidade: canais de membrana mostram especificidade

Hydrophobic gating in BK channels

Zhiguang Jia, Mahdieh Yazdani, Guohui Zhang, Jianmin Cui & Jianhan Chen 

Nature Communications volume 9, Article number: 3408 (2018


Abstract

The gating mechanism of transmembrane ion channels is crucial for understanding how these proteins control ion flow across membranes in various physiological processes. Big potassium (BK) channels are particularly interesting with large single-channel conductance and dual regulation by membrane voltage and intracellular Ca2+. Recent atomistic structures of BK channels failed to identify structural features that could physically block the ion flow in the closed state. Here, we show that gating of BK channels does not seem to require a physical gate. Instead, changes in the pore shape and surface hydrophobicity in the Ca2+-free state allow the channel to readily undergo hydrophobic dewetting transitions, giving rise to a large free energy barrier for K+ permeation. Importantly, the dry pore remains physically open and is readily accessible to quaternary ammonium channel blockers. The hydrophobic gating mechanism is also consistent with scanning mutagenesis studies showing that modulation of pore hydrophobicity is correlated with activation properties.




Acknowledgments

All simulations were performed on the pikes GPU cluster housed in the Massachusetts Green High Performance Computing Cluster (MGHPCC). This work was supported by National Institutes of Health Grants R01 HL142301 (to J. Cui and J. Chen), R01 HL126774 (to J. Cui) and R01 GM114694 (to J. Cui).




Author information

Affiliations

Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA

Zhiguang Jia, Mahdieh Yazdani & Jianhan Chen

Department of Biomedical Engineering, Center for the Investigation of Membrane Excitability Disorders, Cardiac Bioelectricity and Arrhythmia Center, Washington University, St Louis, MO, 63130, USA

Guohui Zhang & Jianmin Cui

Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, 01003, USA

Jianhan Chen

Contributions

Conception and design of the study: Z.J., M.Y., G.Z., J. Cui, and J. Chen; Performing the simulation and analysis: Z.J. and M.Y.; Analysis and interpretation of data, drafting, and revising the manuscript: Z.J., M.Y., G.Z., J. Cui, and J. Chen.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Jianhan Chen.

Novo modelo sobre a origem da vida: redes de lipídios catalíticos

Systems protobiology: origin of life in lipid catalytic networks

Doron Lancet, Raphael Zidovetzki, Omer Markovitch

Published 25 July 2018. DOI: 10.1098/rsif.2018.0159

Source/Fonte: NASA

Abstract

Life is that which replicates and evolves, but there is no consensus on how life emerged. We advocate a systems protobiology view, whereby the first replicators were assemblies of spontaneously accreting, heterogeneous and mostly non-canonical amphiphiles. This view is substantiated by rigorous chemical kinetics simulations of the graded autocatalysis replication domain (GARD) model, based on the notion that the replication or reproduction of compositional information predated that of sequence information. GARD reveals the emergence of privileged non-equilibrium assemblies (composomes), which portray catalysis-based homeostatic (concentration-preserving) growth. Such a process, along with occasional assembly fission, embodies cell-like reproduction. GARD pre-RNA evolution is evidenced in the selection of different composomes within a sparse fitness landscape, in response to environmental chemical changes. These observations refute claims that GARD assemblies (or other mutually catalytic networks in the metabolism first scenario) cannot evolve. Composomes represent both a genotype and a selectable phenotype, anteceding present-day biology in which the two are mostly separated. Detailed GARD analyses show attractor-like transitions from random assemblies to self-organized composomes, with negative entropy change, thus establishing composomes as dissipative systems—hallmarks of life. We show a preliminary new version of our model, metabolic GARD (M-GARD), in which lipid covalent modifications are orchestrated by non-enzymatic lipid catalysts, themselves compositionally reproduced. M-GARD fills the gap of the lack of true metabolism in basic GARD, and is rewardingly supported by a published experimental instance of a lipid-based mutually catalytic network. Anticipating near-future far-reaching progress of molecular dynamics, M-GARD is slated to quantitatively depict elaborate protocells, with orchestrated reproduction of both lipid bilayer and lumenal content. Finally, a GARD analysis in a whole-planet context offers the potential for estimating the probability of life's emergence. The invigorated GARD scrutiny presented in this review enhances the validity of autocatalytic sets as a bona fide early evolution scenario and provides essential infrastructure for a paradigm shift towards a systems protobiology view of life's origin.

FREE PDF GRATIS: J R Soc Interface

Práticas de citação de alunos pós-graduados escrevendo revisões de literatura

quarta-feira, agosto 29, 2018

Citation practices of postgraduate students writing literature reviews

Author: Badenhorst, Cecile

Source: London Review of Education, Volume 16, Number 1, March 2018, pp. 121-135(15)

Publisher: UCL IOE Press




Abstract

Writing a literature review requires highly sophisticated academic literacies. Many postgraduate students find this genre a challenge. While there is a growing awareness of the need for explicit pedagogy to support students writing this genre, many pedagogical interventions fail to move beyond a focus on citations as a stylistic convention or as a way of avoiding plagiarism. What is missing is a pedagogy that relates citing to the more complex, fluid conceptual and ontological practices that are implicit in academic contexts. The purpose of this paper is to explore the citation patterns, complexity and discursive practices in master's students' literature reviews, and to inform pedagogy.

Keywords: ACADEMIC IDENTITY; ACADEMIC LITERACIES; ACADEMIC WRITING; LITERATURE REVIEWS; MASTER'S STUDENT WRITING; PEDAGOGY; POSTGRADUATE

Document Type: Research Article

Publication date: 27 de Março de 2018

FREE PDF GRATIS: London Review of Education

Periódico de Sociologia: por que os lobistas tão persistentemente chamam a evolução de um “Fato”

terça-feira, agosto 28, 2018

Periódico de Sociologia: por que os lobistas tão persistentemente chamam a evolução de um “Fato”

Evolution News | @DiscoveryCSC

27 de agosto de 2018, 1:03 PM


Quantas vezes você ouviu a frase “a evolução é um fato”? Até algumas pessoas muito inteligentes que você pode pensar poderiam saber melhor, foram enganados pela repetição constante das variações dessa declaração. Certamente você a ouviu em Friends. Você a ouviu em Cosmos. Você já a ouviu tantas vezes de muitos defensores da evolução que é quase sem sentido documentar a ubiquidade desse modo de falar.

Quando falam ao público, por que os defensores de Darwin são tão enfáticos que “a evolução é um fato científico”? Finalmente, um artigo em periódico importante de sociologia abordou esta questão. No artigo “Evolution as a fact? A discourse analysis”, os autores Jason Jean e Yixi Lu confirmam o que nós sabíamos o tempo todo: os defensores da evolução chamam a evolução de um “fato” a fim de fazer a evolução aparecer mais certa para o público.

O que nós sabíamos o tempo todo

Você não precisa acreditar no que dissemos. Eis o que diz o artigo:

The primary goal of those who advocate for this discourse has always been to counter antievolutionism by associating the term ‘fact’ with evolution, thereby making evolution appear more certain to the public. … [A]dvocates clearly show how the discourse is driven by concerns external to the scientific vernacular and the practice of science, namely a perceived need to make evolution appear more certain to the public.

[O principal objetivo daqueles que defendem esse discurso tem sido sempre de contra-atacar o antievolucionismo associando o termo ‘fato’ com a evolução, desse modo fazendo a evolução parecer mais certa para o público. … [D]efensores claramente mostram como o discurso é conduzido por preocupações externas para o vernáculo científico e a prática da ciência, isto é, uma necessidade percebida de fazer a evolução parecer mais certa para o público.]

Jason Jean and Yixi Lu, “Evolution as a fact? A discourse analysis,” Social Studies of Science, Vol. 48(4) 615-632 (2018).

Ao empregar esta retórica, os ativistas darwinistas também têm um objetivo secundário — é reivindicar sua “autoridade intelectual” e alcançar “negação de… recursos”, especificamente “autoridade intelectual e oportunidades de carreira” para os céticos de Darwin. O que, você também não está surpreso em saber disso? Eis como foi colocado no artigo:

The discourse encompasses all instances where public scientists (Turner, 1980) describe evolution as a fact. Public scientists are those who engage in the practice of public science, where scientists or anyone claiming to speak for science address an audience in order to achieve their professional goals. These goals, according to Gieryn (1983), are the ‘acquisition of intellectual authority and career opportunities; denial of these resources to “pseudoscientists”; and protection of the autonomy of scientific research from political interference.’ (p. 781)

[O discurso abrange todas as ocorrências onde os cientistas públicos (Turner, 1980) descrevem a evolução como um fato. Cientistas públicos são aqueles que se envolvem na prática de ciência pública, onde os cientistas ou quem afirmar falar pela ciência se dirige a uma audiência a fim alcançar seus objetivos profissionais. Esses objetivos, segundo Gieryn (1983), são a ‘aquisição de autoridade intelectual e de oportunidades de carreira; negar esses recursos para os “pseudocientistas”; e proteção da autonomia da pesquisa científica de interferência política.’ (p. 781)]

Mas há um problema: a maioria dos cientistas não concorda sobre o que exatamente palavras tais como “fato”, “teoria”, ou “hipótese” significam. A menos que esses termos sejam cuidadosamente definidos, quando os defensores da evolução afirmam que a evolução é um “fato”, eles não estão promovendo um entendimento claro e cuidadoso de qualquer ideia científica. Antes, eles perpetuam o que o artigo chama de “um pântano discursivo”. 

“Uma ideia extremamente provável”

Os autores explicam que “a incapacidade dos defensores em concordar sobre como os fatos são definidos, descritos e relacionados às hipóteses e teorias tem resultado na criação de um pântano cada vez mais crescente”. Em uma passagem bem pesquisada, eles relacionam muitos dos rótulos “contraditórios”, mas retoricamente fortes que são aplicados à evolução quando ela é “empurrada” para o público. Esses rótulos incluem chamara a evolução:

• “a verdade”

• “realidade”

• “um fato histórico”

• “uma ideia extremamente provável”

• “uma hipótese bem substanciada”

• “uma teoria bem substanciada”

• “uma teoria matriz”

• “um fato de senso comum”

• “um fato, não uma teoria”

• “um fato e uma teoria”

• “um fato, uma teoria e um caminho”

O artigo argumenta que os ativistas evolucionistas dessa maneira “tomam termos científicos tradicionalmente ambíguos, e os definem e suas relações uns com os outros de modos controversos, contraditórios e confusos”. Este discurso “contraditório” cria problemas sérios para o entendimento da ciência pelo público — wque o artigo dhama de “confusão vernacular”. Na verdade, este modo confuse de falar mostra que os defensores da evolução realmente não estão lá interessados em explicar cuidadosamente para o público o que significam termos como “hipótese”, “teoria” e “fato” — eles estão mais interessados em que você descreia os céticos de Darwin e aceite a evolução:

Considerando-se essas questões, é possível concluir que o discurso nunca foi tencionado explicar apropriadamente a terminologia científica para o público. Associando o termo ‘fato’ com a evolução é, na verdade, um meio de atacar as afirmações e argumentos dos antievolucionistas, apesar das consequências negativas de uma terminologia científica minoritária, ignorando os consensos científicos estabelecidos, e criando um pântano de explicações contraditórias e confusas de como a evolução é um fato. Na sua detalhada análise das questões envolvidas, o biólogo Kirk Fitzhugh (2008: 112) desconsidera o discurso, referindo-se a ele como uma série de ‘slogans que promovem equívocos’.

Em última análise, o artigo objetiva racionalizar o discurso público e encorajar os cientistas que são defensores de Darwin a pararem de abusar de termos como “fato” ou “teoria” simplesmente com o propósito de defender a evolução. Isso é um bom objetivo, e boa sorte com isso. Controlar uma turba deve ser muito mais fácil.

Uma “Zona Livre de Crítica”

Melhorar a retórica dos lobistas de Darwin parece ser um resultado especialmente improvável desde que, como os autores observaram astutamente, esses defensores públicos da evolução adotaram um “acordo implícito” no qual eles se recusam a criticar uns aos outros publicamente. O artigo chama isso de uma “zona livre de crítica” entre os defensores de Darwin. Considere esta passagem impressionante:

The second implicit agreement is that no discourse advocate is allowed to subject another advocate’s cultural cartography to criticism. Among all the discourse advocates and users discussed here, none have made a single criticism of the cultural cartographies used by other advocates, and they routinely cite one another in support of their discourse advocacy (Gregory, 2008; Hughes, 1982; McComas, 1997; Moran, 2002). This agreement has assisted in the establishment of a ‘criticism-free zone’ in public science, in which discourse advocates can make seemingly any claim regarding key scientific terms.

… This criticism-free zone has thus far gone unnoticed, as discourse advocates and users reserve their attacks for antievolutionists.

[O segundo acordo implícito é que nenhum defensor do discurso é permitido sujeitar a cartografia cultural de outro defensor à crítica. Entre todos os defensores e usuários do discurso discutido aqui, nenhum deles fez uma só crítica das cartografias culturais usadas por outros defensores, e eles rotineiramente citam uns aos outros no apoio de seu discurso de defesa (Gregory, 2008; Hughes, 1982; McComas, 1997; Moran, 2002). Este acordo tem ajudado no estabelecimento de uma ‘zona livre de crítica’ na ciência pública, na qual os defensores do discurso podem, aparentemente, fazer qualquer afirmação concernente termos científicos fundamentais.

… Esta zona livre de crítica tem passado desapercebida, pois os defensores e usuários do discurso reservam seus ataques para os antievolucionistas.]

“A evolução é um fato, Fato, FATO!”

Isto é muito perceptivo. Os defensores públicos da evolução certamente tendem a ser suave suns com os outros a fim de concentrar seu fogo sobre os céticos de Darwin. O artigo poderia causar um furor, pois tem violado este “acordo implícito” de que os acadêmicos convencionais nunca devem criticar os defensores públicos da evolução. Porque esses autores ousaram dizer a verdade e criticar aquilo que, de outro modo, está além da crítica, eles podem se preparar para respostas duras dos lobistas de Darwin.

Qual é o ponto essencial deste artigo? Bem, um é que na próxima vez que alguém lhe disser “A evolução é um fato, Fato, FATO!”, como faz Michael Ruse no seu livro Darwinism Defended [Darwinismo defendido] (p. 58), pergunte o que ele quis dizer com “evolução” e com “fato”. Você também pode relembrar-lhe que pessoas que usam esse tipo de retórica estão simplesmente cometendo bullying de sua audiência enquanto, no processo, prejudicando o entendimento da ciência pelo público.

Source/Fonte: Evolution News