Darwinismo universal: checando a saúde aos 40 anos - Tim Lewens

Watch our latest lecture from Professor Tim Lewens; Universal Darwinism: A Health check at Forty, as part of our annual lecture programme.

Professor Lewens reflects Richard Dawkins 1983 paper ‘Universal Darwinism’ and argues that adaptation always requires some interplay between variation and selection, at some point in the history of the adapted system.

Watch now on Youtube: https://youtu.be/spbC2WxMsMk 54:25

O que há de errado em chamar o design inteligente de "antievolução"?

O que há de errado em chamar o design inteligente de "antievolução"?

Casey Luskin

26 de março de 2021, 8:18 AM

O termo “antievolução” tem sido usado por décadas, repetidamente, por um número incontável de defensores de Darwin e críticos da teoria do design inteligente. Eugenie Scott intitulou um ensaio de 1997 na Annual Review of Anthropology de “Antievolution and creationism in the United States” (Antievolução e criacionismo nos Estados Unidos), usando o termo cerca de 50 vezes. Ela dificilmente foi a primeira. Em 1985, um artigo na Perspectives in Biology and Medicine citou o "movimento antievolução" e uma carta de 1977 no The American Biology Teacher, do fundador do National Center for Science Education, Stanley Weinberg, e mencionou o “Arkansas anti-evolution statute” (Estatuto antievolução de Arkansas). Isso se seguiu a uma carta de 1971 no mesmo jornal que lamentava "polêmicas antievolucionistas".

Portanto, esse tipo de retórica vem de muito tempo. E é usado com frequência entre os estudiosos como se fosse um termo acadêmico exato.

O que há de errado com o termo, pelo menos no que se refere ao design inteligente (DI)? Bem, é uma caracterização vaga e ambígua que busca manchar o DI como se o DI fosse contra todas as formas de evolução. No entanto, o design inteligente não é contra todas as formas de evolução.

Três Definições de “Evolução”

Existem três definições gerais de evolução usadas na literatura científica:

Evolução # 1: Mudança ao longo do tempo: mudanças em pequena escala em uma população de organismos.

Evolução # 2: descendência comum universal: a visão de que todos os organismos são relacionados e descendem de um único ancestral comum.

Evolução # 3: Seleção natural: a visão de que um processo não guiado de seleção natural agindo sobre a mutação aleatória tem sido o mecanismo primário que conduz a evolução da vida.

Todos concordam que o DI é compatível com Evolução # 1 e Evolução # 2. Todos também concordam que a Evolução # 1 é verdadeira. Há uma diversidade de pontos de vista dentro do campo do DI sobre a Evolução # 2. Mas todos os proponentes do design concordam que, como teoria científica, o DI é pelo menos potencialmente compatível com alguma forma de descendência comum. Se a evidência suporta descendência comum é uma questão separada.

Todos os proponentes do DI também concordam que a Evolução # 3 tem algum mérito e explica pelo menos algumas características da natureza. A grande maioria dos proponentes do DI sustentaria que a Evolução # 3 tem limites explicativos, o que significa que há muitas características complexas da biologia não passíveis de explicações neodarwinianas, nem explicação por outros mecanismos cegos relacionados (por exemplo, mutações neutras, deriva genética, etc. ) Mas todos concordam que a seleção natural e a mutação aleatória são forças reais na natureza com pelo menos algum poder explicativo. Todos nós concordaríamos que a evolução neutra também ocorre.

Porque os proponentes do DI (a) concordam com certas definições de evolução e/ou (b) concordam que certas definições de evolução são verdadeiras, usar o termo “antievolução” contra o DI representa-nos erroneamente. O DI não é “antievolução” e, de fato, dependendo de como você define evolução, o DI pode se sentir bastante confortável com a evolução. Dependendo de como você vê o DI, ele pode até formar um tipo de teoria da evolução.

“Antievolução” e “Anticiência”

Há uma última razão pela qual devemos rejeitar a pecha de "antievolução": como Paul Nelson sugeriu, isso tenta pintar o DI sob uma luz negativa, como puramente "anti" algo, uma oposição automática, como, de fato, “Anticiência”. Se o DI é anti qualquer coisa, ele é anti respostas pressupostas. O que explica a complexidade e a diversificação da vida? Se a resposta for evolução (em uma ou mais de suas várias definições), ótimo - a comunidade DI quer saber disso. De minha parte, fiz ou fui Professor Assistente em mais de uma dúzia de cursos que cobrem a evolução tanto na graduação quanto na pós-graduação. Fiz isso porque queria aprender e estudar a evolução. Não sou antievolução - quero saber mais sobre o que a evolução pode e não pode explicar!

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NOTA DESTE BLOGGER:

ESTA É A POSIÇÃO OFICIAL DA TEORIA DO DESIGN INTELIGENTE: 

NÃO É CRIACIONISMO TEÍSTA OU CIENTÍFICO!

Evidências de Dawkins a favor da evolução são obsoletas e devem ser aposentadas

Obsolete Dawkinsian evidence for evolution

For the public understanding of phylogenomics, an argument used by Richard Dawkins should be retired

Richard Buggs

Professor, Queen Mary University of London

Published Mar 23, 2021

It is with hesitation that I pen a blog post that could be construed as critical of Richard Dawkins FRS. Many members of this Nature Ecology & Evolution Community may have first come to understand the Darwinian mechanism through his lucid prose. His books have sold by their millions and feature on many an undergraduate reading list. School science teachers around the globe teach what they have learned from him. In the public imagination he is our greatest living evolutionary biologist.

But for these reasons it is important to point out where he has erred. Or at least, where scientific progress has discredited his claims. Because of his wide influence, it is in the interests of the public understanding of science that any mistakes he has made should be explicitly corrected.

In seeking to do so, I am encouraged by statements that Dawkins has often made about willingness of scientists to have their ideas disproven. With that in mind, I can have no doubt that he himself will welcome and seriously consider this post, should he happen upon it.

My concern is that Richard Dawkins has made very public statements that, if taken to be true today, seriously misrepresent the field of phylogenetics in the era of whole genome sequencing.

Take a look at this video hosted by the Richard Dawkins Foundation for Reason & Science YouTube Channel. In the video (8:40 minutes in), Dawkins is asked to name the single best piece of evidence for evolution. His response is to claim that phylogenetic analyses of different genes and pseudogenes each independently give us "the same family tree" for the species that carry them. This congruence between gene trees is "overwhelmingly strong evidence" for evolution - the only alternative being a deceptive creator.

...

Read more here/Leia mais aqui: Nature Portfolio Ecology & Evolution

Modelagem científica com diagramas

Scientific modelling with diagrams

Ulrich E. Stegmann

Synthese volume 198, pages2675–2694(2021)

Diamond-shaped cavities on the surface of a DNA double helix (Gamow 1954 [his Fig. 1]). Circles—bases; shapes with concave sides—cavities. Reprinted with permission from Nature

Abstract

Diagrams can serve as representational models in scientific research, yet important questions remain about how they do so. I address some of these questions with a historical case study, in which diagrams were modified extensively in order to elaborate an early hypothesis of protein synthesis. The diagrams’ modelling role relied mainly on two features: diagrams were modified according to syntactic rules, which temporarily replaced physico-chemical reasoning, and diagram-to-target inferences were based on semantic interpretations. I then explore the lessons for the relative roles of syntax, semantics, external marks, and mental images, for justifying diagram-to-target inferences, and for the “artefactual approach” to scientific models.

FREE PDF GRATIS: Synthese

Representações visuais de nosso passado evolutivo: atualmente são mais arte do que ciência.

Front. Ecol. Evol., 26 February 2021 | https://doi.org/10.3389/fevo.2021.639048

Visual Depictions of Our Evolutionary Past: A Broad Case Study Concerning the Need for Quantitative Methods of Soft Tissue Reconstruction and Art-Science Collaborations

Ryan M. Campbell1*†, Gabriel Vinas2†, Maciej Henneberg1,3† and Rui Diogo4†

1Department of Anatomy & Pathology, University of Adelaide, Adelaide, SA, Australia

2Department of Sculpture, Arizona State University, Tempe, AZ, United States

3Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland

4Department of Anatomy, Howard University, Washington, DC, United States

Two facial reconstructions of the Taung child (without hair and pigment) that were produced 1 year apart. Please note how variability between these reconstructions is exemplified by the subjective decision to depict the subject as more apelike (A) or more humanlike (B).

Flip through scientific textbooks illustrating ideas about human evolution or visit any number of museums of natural history and you will notice an abundance of reconstructions attempting to depict the appearance of ancient hominins. Spend some time comparing reconstructions of the same specimen and notice an obvious fact: hominin reconstructions vary in appearance considerably. In this review, we summarize existing methods of reconstruction to analyze this variability. It is argued that variability between hominin reconstructions is likely the result of unreliable reconstruction methods and misinterpretation of available evidence. We also discuss the risk of disseminating erroneous ideas about human evolution through the use of unscientific reconstructions in museums and publications. The role an artist plays is also analyzed and criticized given how the aforementioned reconstructions have become readily accepted to line the halls of even the most trusted institutions. In conclusion, improved reconstruction methods hold promise for the prediction of hominin soft tissues, as well as for disseminating current scientific understandings of human evolution in the future.

FREE PDF GRATIS: Front. Ecol. Evol.

Medindo a complexidade em organismos e organizações

Measuring complexity in organisms and organizations

Nancy Rebout, Jean-Christophe Lone, Arianna De Marco, Roberto Cozzolino, Alban Lemasson and Bernard Thierry

Published:17 March 2021 https://doi.org/10.1098/rsos.200895

Source/Fonte: Métode

 Range of genome size in organisms of the three domains of life.

Abstract

While there is no consensus about the definition of complexity, it is widely accepted that the ability to produce uncertainty is the most prominent characteristic of complex systems. We introduce new metrics that purport to quantify the complexity of living organisms and social organizations based on their levels of uncertainty. We consider three major dimensions regarding complexity: diversity based on the number of system elements and the number of categories of these elements; flexibility which bears upon variations in the elements; and combinability which refers to the patterns of connection between elements. These three dimensions are quantified using Shannon's uncertainty formula, and they can be integrated to provide a tripartite complexity index. We provide a calculation example that illustrates the use of these indices for comparing the complexity of different social systems. These indices distinguish themselves by a theoretical basis grounded on the amount of uncertainty, and the requirement that several aspects of the systems be accounted for to compare their degree of complexity. We expect that these new complexity indices will encourage research programmes aiming to compare the complexity levels of systems belonging to different realms.

FREE PDF GRATIS: Open Science

A fotossíntese pode ser tão antiga quanto a própria vida

Biochimica et Biophysica Acta (BBA) - Bioenergetics

Volume 1862, Issue 6, 1 June 2021, 148400

Time-resolved comparative molecular evolution of oxygenic photosynthesis

Thomas Oliver a, PatriciaSánchez-Baracaldo b, Anthony W.Larkum c, A. WilliamRutherford a, Tanai Cardona a

a Department of Life Sciences, Imperial College London, London, UK

b School of Geographical Sciences, University of Bristol, Bristol, UK

c University of Technology Sydney, Ultimo, NSW, Australia

Received 8 July 2020, Revised 1 February 2021, Accepted 12 February 2021, Available online 19 February 2021.

https://doi.org/10.1016/j.bbabio.2021.148400

Colonies of cyanobacteria under the microscope. Credit: Ye.Maltsev/Shutterstock

Highlights

• The origin of oxygenic photosynthesis cannot be located on a species tree.

• Vampirovibrionia, Sericytochromatia and Margulisbacteria lost photosynthesis.

• Photosystem II can be as old as the oldest enzymes.

• Earliest type II reaction centres were structurally like water-splitting Photosystem II.

• Anoxygenic photosynthesis is not more primitive than oxygenic photosynthesis.

Abstract

Oxygenic photosynthesis starts with the oxidation of water to O2, a light-driven reaction catalysed by photosystem II. Cyanobacteria are the only prokaryotes capable of water oxidation and therefore, it is assumed that the origin of oxygenic photosynthesis is a late innovation relative to the origin of life and bioenergetics. However, when exactly water oxidation originated remains an unanswered question. Here we use phylogenetic analysis to study a gene duplication event that is unique to photosystem II: the duplication that led to the evolution of the core antenna subunits CP43 and CP47. We compare the changes in the rates of evolution of this duplication with those of some of the oldest well-described events in the history of life: namely, the duplication leading to the Alpha and Beta subunits of the catalytic head of ATP synthase, and the divergence of archaeal and bacterial RNA polymerases and ribosomes. We also compare it with more recent events such as the duplication of Cyanobacteria-specific FtsH metalloprotease subunits and the radiation leading to Margulisbacteria, Sericytochromatia, Vampirovibrionia, and other clades containing anoxygenic phototrophs. We demonstrate that the ancestral core duplication of photosystem II exhibits patterns in the rates of protein evolution through geological time that are nearly identical to those of the ATP synthase, RNA polymerase, or the ribosome. Furthermore, we use ancestral sequence reconstruction in combination with comparative structural biology of photosystem subunits, to provide additional evidence supporting the premise that water oxidation had originated before the ancestral core duplications. Our work suggests that photosynthetic water oxidation originated closer to the origin of life and bioenergetics than can be documented based on phylogenetic or phylogenomic species trees alone.

Abbreviations

MRCA most recent common ancestor LUCA the last universal common ancestor or the most recent common ancestor of life MSV Margulis bacteria, Sericytochromatia and Vampirovibrionia PSII photosystem IIPSI photosystem ICBP chlorophyll-binding protein RC reaction centre ROS reactive oxygen species GOE Great Oxidation Eventd D0 duplication leading to the origin of D1 and D2 subunits of photosystem IIdCP duplication leading to the origin of CP43 and CP47 subunits of photosystem IIdAB duplication leading to the origin of Alpha and Beta subunits of ATP synthaseΔT the span of time between dD0, dCP, dAB, or the LUCA, and the MRCA of Cyanobacteria MaMega-annum, million years GaGiga-annum, billion yearsν Rate of amino acid substitutions per siteδ Ga−1 Amino acid substitutions per site per billion years

Keywords

Origin of photosynthesis Origin of life Cyanobacteria Photosystem Reaction centre Water oxidation

FREE PDF GRATIS: Biochimica et Biophysica Acta

Mais uma hipótese sobre a origem da vida: a morte permitiu a complexidade na evolução química

Chemical Fueling Enables Molecular Complexification of Self‐Replicators

Shuo Yang Gael Schaeffer Elio Mattia Omer Markovitch Kai Liu Andreas S. Hussain Jim Ottelé Ankush Sood Sijbren Otto

First published: 10 March 2021 https://doi.org/10.1002/anie.202016196

Abstract

Unravelling how the complexity of living systems can (have) emerge(d) from simple chemical reactions is one of the grand challenges in contemporary science. Evolving systems of self‐replicating molecules may hold the key to this question. Here we show that, when a system of replicators is subjected to a regime where replication competes with replicator destruction, simple and fast replicators can give way to more complex and slower ones. The structurally more complex replicator was found to be functionally more proficient in the catalysis of a model reaction. These results show that chemical fueling can maintain systems of replicators out of equilibrium, populating more complex replicators that are otherwise not readily accessible. Such complexification represents an important requirement for achieving open‐ended evolution as it should allow improved and ultimately also new functions to emerge.

FREE PDF GRATIS: Angewandte Chemie International Edition Sup. Info.

Quantas mudanças genéticas criam novas espécies?

How many genetic changes create new species?

Patrik Nosil 1,2, Jeffrey L. Feder 3, Zachariah Gompert 2

See all authors and affiliations

Science 19 Feb 2021: Vol. 371, Issue 6531, pp. 777-779

DOI: 10.1126/science.abf6671

A genetic region that controls coloration generates morphs of Midas cichlid fish, but speciation involves traits controlled by a number of different genes.

PHOTO: AD KONINGS

The formation of new species generates biodiversity and is often driven by evolution through natural selection. However, the number of genetic changes involved in speciation is largely unknown. Many theoretical models predict that if speciation occurs without geographic isolation, it will be driven by a small number of genes. The logic is that only the few genes that experience the strongest natural selection can overcome the homogenizing effect of genetic mixing (i.e., gene flow) to diverge between populations. However, empirical studies in plants and animals now suggest that speciation—even with gene flow—involves differentiation in surprisingly many genetic regions. This is thought possible because the effects of selection can become coupled across correlated genes such that the selection each gene experiences is much stronger than it would receive in isolation. Thus, the potential for genes to evolve collectively because of coupling may be a key to understanding speciation.

FREE PDF GRATIS: Science

Evidência de proteínas, cromossomos e marcadores químicos de DNA em cartilagem de dinossauro excepcionalmente preservada!

Evidence of proteins, chromosomes and chemical markers of DNA in exceptionally preserved dinosaur cartilage

Alida M Bailleul, Wenxia Zheng, John R Horner, Brian K Hall, Casey M Holliday, Mary H Schweitzer

National Science Review, Volume 7, Issue 4, April 2020, Pages 815–822, https://doi.org/10.1093/nsr/nwz206

Published: 12 January 2020

Ground section of Hypacrosaurus (MOR 548) supraoccipital shows exceptional histological preservation of calcified cartilage. 

Abstract

A histological ground-section from a duck-billed dinosaur nestling (Hypacrosaurus stebingeri) revealed microstructures morphologically consistent with nuclei and chromosomes in cells within calcified cartilage. We hypothesized that this exceptional cellular preservation extended to the molecular level and had molecular features in common with extant avian cartilage. Histochemical and immunological evidence supports in situ preservation of extracellular matrix components found in extant cartilage, including glycosaminoglycans and collagen type II. Furthermore, isolated Hypacrosaurus chondrocytes react positively with two DNA intercalating stains. Specific DNA staining is only observed inside the isolated cells, suggesting endogenous nuclear material survived fossilization. Our data support the hypothesis that calcified cartilage is preserved at the molecular level in this Mesozoic material, and suggest that remnants of once-living chondrocytes, including their DNA, may preserve for millions of years.

cartilage, dinosaur, nuclei, chromosomes, collagen II, DNA markers

Issue Section: MOLECULAR BIOLOGY & GENETICS

Free PDF Gratis: National Science Review

Genes e genomas e complexidade desnecessária em medicina de precisão

Genes and genomes and unnecessary complexity in precision medicine

Rama S. Singh & Bhagwati P. Gupta

npj Genomic Medicine volume 5, Article number: 21 (2020)

Source/Fonte: GEN

Abstract

The sequencing of the human genome heralded the new age of ‘genetic medicine’ and raised the hope of precision medicine facilitating prolonged and healthy lives. Recent studies have dampened this expectation, as the relationships among mutations (termed ‘risk factors’), biological processes, and diseases have emerged to be more complex than initially anticipated. In this review, we elaborate upon the nature of the relationship between genotype and phenotype, between chance-laden molecular complexity and the evolution of complex traits, and the relevance of this relationship to precision medicine. Molecular contingency, i.e., chance-driven molecular changes, in conjunction with the blind nature of evolutionary processes, creates genetic redundancy or multiple molecular pathways to the same phenotype; as time goes on, these pathways become more complex, interconnected, and hierarchically integrated. Based on the proposition that gene-gene interactions provide the major source of variation for evolutionary change, we present a theory of molecular complexity and posit that it consists of two parts, necessary and unnecessary complexity, both of which are inseparable and increase over time. We argue that, unlike necessary complexity, comprising all aspects of the organism’s genetic program, unnecessary complexity is evolutionary baggage: the result of molecular constraints, historical circumstances, and the blind nature of evolutionary forces. In the short term, unnecessary complexity can give rise to similar risk factors with different genetic backgrounds; in the long term, genes become functionally interconnected and integrated, directly or indirectly, affecting multiple traits simultaneously. We reason that in addition to personal genomics and precision medicine, unnecessary complexity has consequences in evolutionary biology.

FREE PDF GRATIS: npj genomic medicine

Cientistas surpresos: descobriram plantas sob o gelo a quase mil e quatrocentos metros de profundidade na Groenlândia

A multimillion-year-old record of Greenland vegetation and glacial history preserved in sediment beneath 1.4 km of ice at Camp Century

Andrew J. Christ, Paul R. Bierman, Joerg M. Schaefer, Dorthe Dahl-Jensen, Jørgen P. Steffensen, Lee B. Corbett, Dorothy M. Peteet, Elizabeth K. Thomas, Eric J. Steig, Tammy M. Rittenour, Jean-Louis Tison, Pierre-Henri Blard, Nicolas Perdrial, David P. Dethier, Andrea Lini, Alan J. Hidy, Marc W. Caffee, and John Southon

PNAS March 30, 2021 118 (13) e2021442118; https://doi.org/10.1073/pnas.2021442118 

Edited by Mark Thiemens, University of California San Diego, La Jolla, CA, and approved January 27, 2021 (received for review October 23, 2020)

Source/Fonte: NASA

Significance

Understanding Greenland Ice Sheet history is critical for predicting its response to future climate warming and contribution to sea-level rise. We analyzed sediment at the bottom of the Camp Century ice core, collected 120 km from the coast in northwestern Greenland. The sediment, frozen under nearly 1.4 km of ice, contains well-preserved fossil plants and biomolecules sourced from at least two ice-free warm periods in the past few million years. Enriched stable isotopes in pore ice indicate precipitation at lower elevations than present, implying ice-sheet absence. The similarity of cosmogenic isotope ratios in the upper-most sediment to those measured in bedrock near the center of Greenland suggests that the ice sheet melted and re-formed at least once during the past million years.

Abstract

Understanding the history of the Greenland Ice Sheet (GrIS) is critical for determining its sensitivity to warming and contribution to sea level; however, that history is poorly known before the last interglacial. Most knowledge comes from interpretation of marine sediment, an indirect record of past ice-sheet extent and behavior. Subglacial sediment and rock, retrieved at the base of ice cores, provide terrestrial evidence for GrIS behavior during the Pleistocene. Here, we use multiple methods to determine GrIS history from subglacial sediment at the base of the Camp Century ice core collected in 1966. This material contains a stratigraphic record of glaciation and vegetation in northwestern Greenland spanning the Pleistocene. Enriched stable isotopes of pore-ice suggest precipitation at lower elevations implying ice-sheet absence. Plant macrofossils and biomarkers in the sediment indicate that paleo-ecosystems from previous interglacial periods are preserved beneath the GrIS. Cosmogenic 26Al/10Be and luminescence data bracket the burial of the lower-most sediment between <3.2 ± 0.4 Ma and >0.7 to 1.4 Ma. In the upper-most sediment, cosmogenic 26Al/10Be data require exposure within the last 1.0 ± 0.1 My. The unique subglacial sedimentary record from Camp Century documents at least two episodes of ice-free, vegetated conditions, each followed by glaciation. The lower sediment derives from an Early Pleistocene GrIS advance. 26Al/10Be ratios in the upper-most sediment match those in subglacial bedrock from central Greenland, suggesting similar ice-cover histories across the GrIS. We conclude that the GrIS persisted through much of the Pleistocene but melted and reformed at least once since 1.1 Ma.

Pleistocene ice core Arctic climate ice sheet

Subscription or payment needed/Requer assinatura ou pagamento: PNAS

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Mais uma hipótese sobre a origem da vida: Um raio antigo pode ter gerado vida na Terra!

Lightning strikes as a major facilitator of prebiotic phosphorus reduction on early Earth

Benjamin L. Hess, Sandra Piazolo & Jason Harvey

Nature Communications volume 12, Article number: 1535 (2021)

Source/Fonte

Abstract

When hydrated, phosphides such as the mineral schreibersite, (Fe,Ni)3P, allow for the synthesis of important phosphorus-bearing organic compounds. Such phosphides are common accessory minerals in meteorites; consequently, meteorites are proposed to be a main source of prebiotic reactive phosphorus on early Earth. Here, we propose an alternative source for widespread phosphorus reduction, arguing that lightning strikes on early Earth potentially formed 10–1000 kg of phosphide and 100–10,000 kg of phosphite and hypophosphite annually. Therefore, lightning could have been a significant source of prebiotic, reactive phosphorus which would have been concentrated on landmasses in tropical regions. Lightning strikes could likewise provide a continual source of prebiotic reactive phosphorus independent of meteorite flux on other Earth-like planets, potentially facilitating the emergence of terrestrial life indefinitely.

FREE PDF GRATIS: Nature Communications Sup. Info.

Testes moleculares apoiam a viabilidade de elementos terrestres raros como agentes preservadores de biomoléculas fósseis

Molecular tests support the viability of rare earth elements as proxies for fossil biomolecule preservation

Paul V. Ullmann, Kristyn K. Voegele, David E. Grandstaff, Richard D. Ash, Wenxia Zheng, Elena R. Schroeter, Mary H. Schweitzer & Kenneth J. Lacovara

Scientific Reports volume 10, Article number: 15566 (2020)

Reproduced, with permission from Geochimica et Cosmochimica Acta, from Ullmann et al.

Abstract

The rare earth element (REE) composition of a fossil bone reflects its chemical alteration during diagenesis. Consequently, fossils presenting low REE concentrations and/or REE profiles indicative of simple diffusion, signifying minimal alteration, have been proposed as ideal candidates for paleomolecular investigation. We directly tested this prediction by conducting multiple biomolecular assays on a well-preserved fibula of the dinosaur Edmontosaurus from the Cretaceous Hell Creek Formation previously found to exhibit low REE concentrations and steeply-declining REE profiles. Gel electrophoresis identified the presence of organic material in this specimen, and subsequent immunofluorescence and enzyme-linked immunosorbant assays identified preservation of epitopes of the structural protein collagen I. Our results thereby support the utility of REE profiles as proxies for soft tissue and biomolecular preservation in fossil bones. Based on considerations of trace element taphonomy, we also draw predictions as to the biomolecular recovery potential of additional REE profile types exhibited by fossil bones.

FREE PDF GRATIS: Scientific Reports Sup. Info.

Um modelo do Cosmos no antigo mecanismo grego de Anticítera

A Model of the Cosmos in the ancient Greek Antikythera Mechanism

Tony Freeth, David Higgon, Aris Dacanalis, Lindsay MacDonald, Myrto Georgakopoulou & Adam Wojcik

Scientific Reports volume 11, Article number: 5821 (2021)

Source/Fonte: The New York Times

Abstract

The Antikythera Mechanism, an ancient Greek astronomical calculator, has challenged researchers since its discovery in 1901. Now split into 82 fragments, only a third of the original survives, including 30 corroded bronze gearwheels. Microfocus X-ray Computed Tomography (X-ray CT) in 2005 decoded the structure of the rear of the machine but the front remained largely unresolved. X-ray CT also revealed inscriptions describing the motions of the Sun, Moon and all five planets known in antiquity and how they were displayed at the front as an ancient Greek Cosmos. Inscriptions specifying complex planetary periods forced new thinking on the mechanization of this Cosmos, but no previous reconstruction has come close to matching the data. Our discoveries lead to a new model, satisfying and explaining the evidence. Solving this complex 3D puzzle reveals a creation of genius—combining cycles from Babylonian astronomy, mathematics from Plato’s Academy and ancient Greek astronomical theories.

FREE PDF GRATIS: Nature Communications Sup. Info. 4

Tubos de fibra óptica na retina fazem muito mais do que simples transferência de imagem: mero acaso, fortuita necessidade ou design inteligente?

Müller cells separate between wavelengths to improve day vision with minimal effect upon night vision

Amichai M. Labin, Shadi K. Safuri, Erez N. Ribak & Ido Perlman

Nature Communications volume 5, Article number: 4319 (2014)

Source/Fonte: vision-research.eu

Abstract

Vision starts with the absorption of light by the retinal photoreceptors—cones and rods. However, due to the ‘inverted’ structure of the retina, the incident light must propagate through reflecting and scattering cellular layers before reaching the photoreceptors. It has been recently suggested that Müller cells function as optical fibres in the retina, transferring light illuminating the retinal surface onto the cone photoreceptors. Here we show that Müller cells are wavelength-dependent wave-guides, concentrating the green-red part of the visible spectrum onto cones and allowing the blue-purple part to leak onto nearby rods. This phenomenon is observed in the isolated retina and explained by a computational model, for the guinea pig and the human parafoveal retina. Therefore, light propagation by Müller cells through the retina can be considered as an integral part of the first step in the visual process, increasing photon absorption by cones while minimally affecting rod-mediated vision.

FREE PDF GRATIS: Nature Communications Sup. Info.

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Having the photoreceptors at the back of the retina is not a design constraint, it is a design feature. The idea that the vertebrate eye, like a traditional front-illuminated camera, might have been improved somehow if it had only been able to orient its wiring behind the photoreceptor layer, like a cephalopod, is folly. 

Ter os fotorreceptores na parte posterior da retina não é uma limitação de design, é uma característica de design. A ideia de que o olho dos vertebrados, como uma câmera tradicional com iluminação frontal, poderia ter sido melhorada de alguma forma se tivesse sido capaz de orientar sua fiação atrás da camada fotorreceptora, como um cefalópode, é bobagem.

PhysOrg

A paleontologia molecular como uma área emocionante, desafiadora e controversa.

Molecular paleontology as an exciting, challenging and controversial field

Yanhong Pan

National Science Review, Volume 7, Issue 4, April 2020, Page 823, 

https://doi.org/10.1093/nsr/nwaa001  

Published: 07 January 2020

Source/Fonte

Abstract

Molecular paleontology is the study of ancient complex biomolecules associated within deep-time fossils, which may provide important information for understanding the organisms’ evolution and fossilization process at the molecular level, as well as facilitating the recognition of preserved biomarkers in order to identify life on other planets [1,2]. In the paper by Bailleul et al. [3], the authors report the discovery of well-preserved subcellular structures morphologically consistent with nuclei and chromosomes in histological ground sections from skull bones of an Upper Cretaceous baby dinosaur. However, as the authors have stated that morphology alone is insufficient to diagnose any cellular or subcellular structures, they conducted further histochemical (Alcian blue stain for extracellular matrix of cartilage; PI and DAPI stains for chemical markers consistent with DNA) and immunological (antibodies against avian collagen II) tests. All tests were positive, providing strong evidence suggesting in situ preservation of extracellular matrix components, and even endogenous nuclear materials. This case study reveals interesting evidence of exceptional preservation in fossils at both molecular and morphological levels, and opens the door for extensive further research, making the argument that DNA sequencing is worth exploring. The present study is significant for at least two reasons. First, it demonstrates that fossils displaying well-preserved cellular and subcellular structures may also preserve molecular information. Second, this study clearly shows that the search for ancient biomolecules should not be constrained by the so-called temporal limit, e.g. the assumption that proteins cannot survive in the fossil record beyond ∼1 Ma and ∼100 000 years for DNA. The preservation mechanism of soft tissues in fossils is far more complex than we have observed in modern environments through taphonomy experiments.

The last decade has borne witness to numerous discoveries that have provided mounting evidence of molecular preservation in deep-time fossils, e.g. proteins, certain carbohydrates such as chitin and cellulose, sterol lipids and pigments [4–8]. As this is a relatively new field, searching for ancient molecules in fossils is full of challenges, e.g. inevitable contaminations, immature techniques and unknown modifications of molecules over geological time. Thus, new discoveries in molecular paleontology are often accompanied by controversy. However, controversy is a crucial part of scientific progress and incorrect ideas do less harm to science than false evidence. To promote the discipline of molecular paleontology, we need to overcome bias and prejudice from colleagues in and outside the field, particularly with regard to the presumed ‘preservational limit’. Another common critic plaguing discoveries of ancient biomolecules concerns the repeatability of the results; however, it is an obvious bias to declare that the result cannot be replicated if different techniques or methods are used.

Finally, it is recognized that ‘exceptional claims require exceptional evidence’ and multiple independent lines of evidence should be provided in support of any new discovery of ancient biomolecules in deep-time fossils as done by Bailleul et al. [3]. With the recent and rapid technological developments, we are optimistic that the field of molecular paleontology will grow rapidly and provide additional evidence of unexpected fossil biomolecules from geological ages previously held to be too old for such biomolecules to survive.

FREE PDF GRATIS: National Science Review

Informação - a simplicidade escondida da biologia: mero acaso, fortuita necessidade ou design inteligente?

The hidden simplicity of biology

Paul Davies, Sara Walker

Biodesign Institute CLAS-NS: Physics CLAS-NS: Beyond Center CLAS: Administration CLAS-NS: Earth and Space Exploration, School of (SESE)

Research output: Contribution to journal › Review article › peer-review

Source/Fonte

Abstract

Life is so remarkable, and so unlike any other physical system, that it is tempting to attribute special factors to it. Physics is founded on the assumption that universal laws and principles underlie all natural phenomena, but is it far from clear that there are 'laws of life' with serious descriptive or predictive power analogous to the laws of physics. Nor is there (yet) a 'theoretical biology' in the same sense as theoretical physics. Part of the obstacle in developing a universal theory of biological organization concerns the daunting complexity of living organisms. However, many attempts have been made to glimpse simplicity lurking within this complexity, and to capture this simplicity mathematically. In this paper we review a promising new line of inquiry to bring coherence and order to the realm of biology by focusing on 'information' as a unifying concept.

Original languageEnglish (US)

Article number102601

JournalReports on Progress in Physics

Volume79

Issue number10

StatePublished - Sep 9 2016

Access to Document

DOI: 10.1088/0034-4885/79/10/102601

Keywords

biological laws complexity emergence

Origem da vida: o problema do ovo e da galinha - mero acaso, fortuita necessidade ou design inteligente?

tRNA sequences can assemble into a replicator

Alexandra Kühnlein, Simon A Lanzmich, Dieter Braun Is a corresponding author

Systems Biophysics, Physics Department, Center for NanoScience, Ludwig-Maximilians-Universität München, Germany

Research Article Mar 2, 2021

Heat-driven replication by hybridization using hairpin structures inspired from transfer RNA.

Abstract

Can replication and translation emerge in a single mechanism via self-assembly? The key molecule, transfer RNA (tRNA), is one of the most ancient molecules and contains the genetic code. Our experiments show how a pool of oligonucleotides, adapted with minor mutations from tRNA, spontaneously formed molecular assemblies and replicated information autonomously using only reversible hybridization under thermal oscillations. The pool of cross-complementary hairpins self-selected by agglomeration and sedimentation. The metastable DNA hairpins bound to a template and then interconnected by hybridization. Thermal oscillations separated replicates from their templates and drove an exponential, cross-catalytic replication. The molecular assembly could encode and replicate binary sequences with a replication fidelity corresponding to 85–90 % per nucleotide. The replication by a self-assembly of tRNA-like sequences suggests that early forms of tRNA could have been involved in molecular replication. This would link the evolution of translation to a mechanism of molecular replication.

eLife digest

The genetic code stored within DNA contains the instructions for manufacturing all the proteins organisms need to develop, grow and survive. This requires molecular machines that ‘transcribe’ regions of the genetic code into RNA molecules which are then ‘translated’ into the string of amino acids that form the final protein. However, these molecular machines and other proteins are also needed to replicate and synthesize the sequences stored in DNA. This presents evolutionary biologists with a ‘chicken-and-egg’ situation: which came first, the DNA sequences needed to manufacture proteins or the proteins needed to transcribe and translate DNA?

Understanding the order in which DNA replication and protein translation evolved is challenging as these processes are tightly intertwined in modern-day species. One theory, known as the ‘RNA world hypothesis’, suggests that all life on Earth began with a single RNA molecule that was able to make copies of itself, as DNA does today. To investigate this hypothesis, Kühnlein, Lanzmich and Braun studied a molecule called transfer RNA (or tRNA for short) which is responsible for translating RNA into proteins. tRNA is assumed to be one of the earliest evolved molecules in biology. Yet, why it was present in early life forms before it was needed for translation still remained somewhat of a mystery.

To gain a better understanding of tRNA’s role early in evolution, Kühnlein, Lanzmich and Braun made small changes to its genetic code and then carried out tests on these tRNA-like sequences. The experiments showed these ‘early’ forms of tRNA can actually self-assemble into a molecule which is capable of replicating the information stored in its sequence. It suggests early forms of tRNA could have been involved in replication before modern tRNA developed its role in protein translation.

With these experiments, Kühnlein, Lanzmich and Braun have identified a possible evolutionary link between DNA replication and protein translation, suggesting the two processes emerged through one shared pathway: tRNA. This deepens our understanding about the origins of early life, while taking biochemists one step closer to their distant goal of recreating self-replicating molecular machines in the laboratory.

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Implicações para a evolução do DNA e darwinismo molecular

Energy mapping of the genetic code and genomic domains: implications for code evolution and molecular Darwinism

Published online by Cambridge University Press: 04 November 2020

Horst H. Klump, Jens Völker and Kenneth J. Breslauer

Abstract

When the iconic DNA genetic code is expressed in terms of energy differentials, one observes that information embedded in chemical sequences, including some biological outcomes, correlate with distinctive free energy profiles. Specifically, we find correlations between codon usage and codon free energy, suggestive of a thermodynamic selection for codon usage. We also find correlations between what are considered ancient amino acids and high codon free energy values. Such correlations may be reflective of the sequence-based genetic code fundamentally mapping as an energy code. In such a perspective, one can envision the genetic code as composed of interlocking thermodynamic cycles that allow codons to ‘evolve’ from each other through a series of sequential transitions and transversions, which are influenced by an energy landscape modulated by both thermodynamic and kinetic factors. As such, early evolution of the genetic code may have been driven, in part, by differential energetics, as opposed exclusively by the functionality of any gene product. In such a scenario, evolutionary pressures can, in part, derive from the optimization of biophysical properties (e.g. relative stabilities and relative rates), in addition to the classic perspective of being driven by a phenotypical adaptive advantage (natural selection). Such differential energy mapping of the genetic code, as well as larger genomic domains, may reflect an energetically resolved and evolved genomic landscape, consistent with a type of differential, energy-driven ‘molecular Darwinism’. It should not be surprising that evolution of the code was influenced by differential energetics, as thermodynamics is the most general and universal branch of science that operates over all time and length scales.

Keywords Codon energy distribution spectrum, codon free energies, codon usage frequency, energy code, interlocking thermodynamic cycles, molecular evolution

FREE PDF GRATIS: Quarterly Reviews of Biophysics