Se o design na natureza é mera ilusão, por que procurar design na natureza?

A DNA origami rotary ratchet motor

Anna-Katharina Pumm, Wouter Engelen, Enzo Kopperger, Jonas Isensee, Matthias Vogt, Viktorija Kozina, Massimo Kube, Maximilian N. Honemann, Eva Bertosin, Martin Langecker, Ramin Golestanian, Friedrich C. Simmel & Hendrik Dietz 

Nature volume 607, pages492–498 (2022)

Fig. 1: Motor design and experimental setup.

Abstract

To impart directionality to the motions of a molecular mechanism, one must overcome the random thermal forces that are ubiquitous on such small scales and in liquid solution at ambient temperature. In equilibrium without energy supply, directional motion cannot be sustained without violating the laws of thermodynamics. Under conditions away from thermodynamic equilibrium, directional motion may be achieved within the framework of Brownian ratchets, which are diffusive mechanisms that have broken inversion symmetry1,2,3,4,5. Ratcheting is thought to underpin the function of many natural biological motors, such as the F1F0-ATPase6,7,8, and it has been demonstrated experimentally in synthetic microscale systems (for example, to our knowledge, first in ref. 3) and also in artificial molecular motors created by organic chemical synthesis9,10,11,12. DNA nanotechnology13 has yielded a variety of nanoscale mechanisms, including pivots, hinges, crank sliders and rotary systems14,15,16,17, which can adopt different configurations, for example, triggered by strand-displacement reactions18,19 or by changing environmental parameters such as pH, ionic strength, temperature, external fields and by coupling their motions to those of natural motor proteins20,21,22,23,24,25,26. This previous work and considering low-Reynolds-number dynamics and inherent stochasticity27,28 led us to develop a nanoscale rotary motor built from DNA origami that is driven by ratcheting and whose mechanical capabilities approach those of biological motors such as F1F0-ATPase.

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O desenvolvimento embrionário inicial diverso de vertebrados e implicações sobre sua ancestralidade

The diverse early embryonic development of vertebrates and implications regarding their ancestry

David Swift

Image/Imagem: Nature Reviews Molecular Cell Biology 

Abstract

It is well known that the embryonic development of vertebrates from different classes (e.g., fish, reptiles, mammals) pass through a “phylotypic stage” when they look similar, and this apparent homology is widely seen as evidence of their common ancestry. However, despite their morphological similarities, and contrary to evolutionary expectations, the phylotypic stages of different vertebrate classes arise in radically diverse ways. This diversity clearly counters the superficial appearance of homology of the phylotypic stage, and the plain inference is that vertebrates have not evolved from a common vertebrate ancestor. The diversity extends through all stages of early development—including cleavage and formation of the blastula, gastrulation, neurulation, and formation of the gut and extraembryonic membranes. This paper focuses on gastrulation, during which the germ layers originate and the vertebrate body-plan begins to form. Despite its key role in embryonic development, gastrulation occurs in fundamentally different ways in different classes of vertebrates. The inference against common ancestry becomes progressively stronger as more is discovered about the genetic and molecular mechanisms that implement development. It is increasingly evident that these are of such complexity that it is unrealistic to think that undirected variations (random mutations) could produce constructive changes to development, such as those required to account for a diversification of development from that of a common ancestor, especially while retaining a similar phylotypic stage.

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Edição especial do PNAS sobre os 200 anos do nascimento de Gregor Mendel e suas descobertas científicas

Image/Imagem: Mendel Museum - Brno, Czech Republic

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Cronometragem e tomada de decisão em células vivas: mero acaso, fortuita necessidade ou design inteligente?

Time-keeping and decision-making in living cells: Part I

John J. Tyson, Attila Csikasz-Nagy, Didier Gonze, Jae Kyoung Kim, Silvia Santos and Jana Wolf

Published:15 April 2022 https://doi.org/10.1098/rsfs.2022.0011

Figure 1. Some components of the information-processing system (IPS) in a mammalian cell. 

Abstract

To survive and reproduce, a cell must process information from its environment and its own internal state and respond accordingly, in terms of metabolic activity, gene expression, movement, growth, division and differentiation. These signal–response decisions are made by complex networks of interacting genes and proteins, which function as biochemical switches and clocks, and other recognizable information-processing circuitry. This theme issue of Interface Focus (in two parts) brings together articles on time-keeping and decision-making in living cells—work that uses precise mathematical modelling of underlying molecular regulatory networks to understand important features of cell physiology. Part I focuses on time-keeping: mechanisms and dynamics of biological oscillators and modes of synchronization and entrainment of oscillators, with special attention to circadian clocks.

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Darwin, nós temos um problema: o DNA lixo é funcional e faz uma grande diferença.

Not functional yet a difference maker: junk DNA as a case study

Joyce C. Havstad & Alexander F. Palazzo 

Biology & Philosophy volume 37, Article number: 29 (2022) 

Abstract

It is often thought that non-junk or coding DNA is more significant than other cellular elements, including so-called junk DNA. This is for two main reasons: (1) because coding DNA is often targeted by historical or current selection, it is considered functionally special and (2) because its mode of action is uniquely specific amongst the other actual difference makers in the cell, it is considered causally special. Here, we challenge both these presumptions. With respect to function, we argue that there is previously unappreciated reason to think that junk DNA is significant, since it can alter the cellular environment, and those alterations can influence how organism-level selection operates. With respect to causality, we argue that there is again reason to think that junk DNA is significant, since it too (like coding DNA) is remarkably causally specific (in Waters’, in J Philos 104:551–579, 2007 sense). As a result, something is missing from the received view of significance in molecular biology—a view which emphasizes specificity and neglects something we term ‘reach’. With the special case of junk DNA in mind, we explore how to model and understand the causal specificity, reach, and corresponding efficacy of difference makers in biology. The account contains implications for how evolution shapes the genome, as well as advances our understanding of multi-level selection.

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Darwin, nós temos um problema: a conectividade de áreas de linguagem são únicas no cérebro humano

Comparing human and chimpanzee temporal lobe neuroanatomy reveals modifications to human language hubs beyond the frontotemporal arcuate fasciculus

Joanna Sierpowska, Katherine L. Bryant, Nikki Janssen, +4 , Guilherme Blazquez Freches, Manon Römkens, Margot Mangnus, Rogier B. Mars, and Vitoria Piai

Edited by Marcus Raichle, Washington University in St. Louis, St. Louis, MO; received October 7, 2021; accepted May 11, 2022

July 5, 2022

119 (28) e2118295119

https://doi.org/10.1073/pnas.2118295119

Image/Imagem: Time Magazine - Tim O'Brien

Significance

Communication through language is a great achievement of evolution. In humans, the arcuate fasciculus, white matter that extended dramatically during evolution, is known to subserve language. We investigated whether connections through critical language centers in the temporal lobe are uniquely human. We show that connectivity in the posterior temporal lobe via the arcuate fasciculus expanded bilaterally to frontal and parietal cortices in humans compared with chimpanzees. Concomitantly, the ventral tracts connect more strongly to posterior temporal regions in the chimpanzees than in humans. In the anterior temporal lobe, connections shared between both species and uniquely human expansions are present. Changes to human language streams extend beyond the arcuate fasciculus, including a suite of expansions to connectivity within the temporal lobes.

Abstract

The biological foundation for the language-ready brain in the human lineage remains a debated subject. In humans, the arcuate fasciculus (AF) white matter and the posterior portions of the middle temporal gyrus are crucial for language. Compared with other primates, the human AF has been shown to dramatically extend into the posterior temporal lobe, which forms the basis of a number of models of the structural connectivity basis of language. Recent advances in both language research and comparative neuroimaging invite a reassessment of the anatomical differences in language streams between humans and our closest relatives. Here, we show that posterior temporal connectivity via the AF in humans compared with chimpanzees is expanded in terms of its connectivity not just to the ventral frontal cortex but also to the parietal cortex. At the same time, posterior temporal regions connect more strongly to the ventral white matter in chimpanzees as opposed to humans. This pattern is present in both brain hemispheres. Additionally, we show that the anterior temporal lobe harbors a combination of connections present in both species through the inferior fronto-occipital fascicle and human-unique expansions through the uncinate and middle and inferior longitudinal fascicles. These findings elucidate structural changes that are unique to humans and may underlie the anatomical foundations for full-fledged language capacity.

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Darwin, nós temos um problema: novo método de datação destrói nossa compreensão da evolução humana!

THE PAST — JULY 7, 2022 

Jasna Hodzic

New dating method shatters our understanding of human evolution

Fossils of Australopithecus in a South African cave are one million years older than previously thought. This challenges the consensus that humans first evolved in East Africa.

KEY TAKEAWAYS

- The Sterkfontein caves in South Africa are home to hundreds of fossils of early hominins in the genus Australopithecus. Original age estimates of these fossils suggested that they were no more than 2.4 million years old — younger than our genus, Homo. 

- Researchers used a new, more accurate technique to redate the fossils and made an important discovery: The fossils were much older than previously thought. They were deposited between 3.4 million and 3.7 million years ago. 

- The finding challenges our understanding of human evolution, including the consensus that we evolved in East Africa. 

Hominins link the great apes with modern humans on the evolutionary tree. Ancestral hominins mark a crucial transition in the story of human evolution, and they have fascinated paleoanthropologists for decades. 

In 1936, South African doctor and paleontologist Robert Broom made a historic discovery in the Sterkfontein caves in South Africa. Broom discovered the first adult specimen of the genus Australopithecus, a group of early hominins from which our own genus, Homo, emerged. 

Since 1936, the Sterkfontein caves have become ground zero for Australopithecus research and fossil finds. The complex cave system runs 60 meters deep, and it has revealed hundreds of Australopithecus fossils within its sediment. From these rocks emerged notable discoveries, such as the nearly complete skeletons of specimens dubbed “Little Foot” and “Mrs. Ples.”

Age is just a method

The cave features six areas, or members: Members 1 to 3 lie underground, while Members 4 to 6 are exposed to the air because of erosion in the cave roof. Most Australopithecus fossils are in Member 4. The Sterkfontein caves are one part of a World Heritage Site with a telling name — the Cradle of Humankind. 

The complex cave system still houses many secrets, but the discoveries already made retain mysteries of their own. Among the most debated issues is the age of the fossils found in Member 4. Researchers have estimated the age of Australopithecus in the lower Member 2 section at 3.7 million years, which jars with the estimated age of the fossils found higher in the cave. Researchers originally estimated the fossils in Member 4 to be between 2 million and 2.4 million years old. The geological peculiarities of the cave challenge traditional methods of aging fossils, casting further doubt on the accuracy of these estimations.

Purdue University’s Darryl Granger is among the researchers who questioned the age of the Member 4 Australopithecus. Recently, Granger and a team of scientists from France and South Africa endeavored to redate the famous fossils using a new method. They published their results in the Proceedings of the National Academy of Sciences. 

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Read more here/Leia mais aqui: The Big Think.

A crise de irreprodutibilidade da ciência moderna - Causas, consequências e caminho para reforma

A crise de irreprodutibilidade da ciência moderna - Causas, consequências e caminho para reforma - Relatório (em inglês) da National Association of Scholars.

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Perspectiva evolutiva sobre a origem e diversificação da vida celular e a virosfera

 Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere 

Anja Spang, Tara A Mahendrarajah, Pierre Offre, Courtney W Stairs Author Notes

Genome Biology and Evolution, Volume 14, Issue 6, June 2022, evac034, 

https://doi.org/10.1093/gbe/evac034

Published: 26 February 2022 Article history Accepted: 18 February 2022 Published: 26 February 2022 Corrected and typeset: 06 June 2022

The tree is a schematic representation of the relationship of the major domains of life, comprised of the primary domains of Archaea and Bacteria and the secondary domain of Eukaryotes. (Credit: Anja Spang)

Abstract

The tree of life (TOL) is a powerful framework to depict the evolutionary history of cellular organisms through time, from our microbial origins to the diversification of multicellular eukaryotes that shape the visible biosphere today. During the past decades, our perception of the TOL has fundamentally changed, in part, due to profound methodological advances, which allowed a more objective approach to studying organismal and viral diversity and led to the discovery of major new branches in the TOL as well as viral lineages. Phylogenetic and comparative genomics analyses of these data have, among others, revolutionized our understanding of the deep roots and diversity of microbial life, the origin of the eukaryotic cell, eukaryotic diversity, as well as the origin, and diversification of viruses. In this review, we provide an overview of some of the recent discoveries on the evolutionary history of cellular organisms and their viruses and discuss a variety of complementary techniques that we consider crucial for making further progress in our understanding of the TOL and its interconnection with the virosphere.

Key words tree of life, viruses, archaea, bacteria and eukaryotes, eukaryogenesis, diversity and evolution, methodological progress

Significance

Our review provides a timely overview of how recent methodological progress has allowed an updated view on the tree of life and its connection to the virosphere. It covers topics ranging from last universal common ancestor to last eukaryotic common ancestor and the extant diversity of prokaryotic and eukaryotic life as well as viruses. Furthermore, we summarize current developments in the field that can help to make further progress in our understanding of deep evolution in the coming years.

FREE PDF GRATIS: Genome Biology Evolution

Desvendando as origens de LUCA e LECA na Árvore da Vida

Highlight: Unraveling the Origins of LUCA and LECA on the Tree of Life 

Casey McGrath

Genome Biology and Evolution, Volume 14, Issue 6, June 2022, evac072,

https://doi.org/10.1093/gbe/evac072

Published: 06 June 2022 Article history Accepted: 10 May 2022 Published: 06 June 2022

Tree of life. The tree of life contains three major branches—bacteria, archaea, and eukaryotes. Proposed locations for LUCA and LECA are shown. LUCA, last universal common ancestor; LECA, last eukaryotic common ancestor. Adapted from Spang et al. (2022).

The latest Virtual Issue from Genome Biology and Evolution highlights articles that provide new insight into the deep evolutionary relationships among extant organisms and the origin of eukaryotes from among archaeal lineages. All cellular organisms are descended from a shared ancestor, often referred to as LUCA—the last universal common ancestor. Relationships among these organisms can be depicted by an evolutionary network known as the “tree of life”, which for the past few decades has included three major forms of life—bacteria, archaea, and eukaryotes (fig. 1). Evolutionary biologists have long sought to understand the placement of LUCA within this framework, as well as the origin of LECA—the last eukaryotic common ancestor. Unfortunately, accurately inferring relationships among microbial lineages presents a major challenge due to the vast evolutionary distances involved, as well as the frequent lateral transfer of genetic material between lineages. Recently, however, new data and methods have resulted in profound changes to our understanding of the tree of life.

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Darwin, nós temos um grande problema: as pesquisas do genoma e proteoma do LUCA não concordam entre si!

The evolution of proteome: From the primeval to the very dawn of LUCA

MiryamPalacios-Pérez, Marco V.José

Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México CDMX, C.P. 04510, Mexico

First published: 03 June 2022

https://doi.org/10.1002/ece3.8930

Image/Imagem: BioSystems

Abstract

The availability of genomic and proteomic data from across the tree of life has made it possible to infer features of the genome and proteome of the last universal common ancestor (LUCA). A number of studies have done so, all using a unique set of methods and bioinformatics databases. Here, we compare predictions across eight such studies and measure both their agreement with one another and with the consensus predictions among them. We find that some LUCA genome studies show a strong agreement with the consensus predictions of the others, but that no individual study shares a high or even moderate degree of similarity with any other individual study. From these observations, we conclude that the consensus among studies provides a more accurate depiction of the core proteome of the LUCA and its functional repertoire. The set of consensus LUCA protein family predictions between all of these studies portrays a LUCA genome that, at minimum, encoded functions related to protein synthesis, amino acid metabolism, nucleotide metabolism, and the use of common, nucleotide-derived organic cofactors.

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EXCERPT:

"We undertook this study with the hypothesis that the specific predictions of the various studies on the LUCA genome or proteome performed over the last two decades would largely agree with one another. We expected that each study should have some unknowable level of error because it is inherently difficult to infer specific details about life forms that existed at least 3.5 billion years ago. However, if the previously published LUCA genome or proteome studies are at all accurate, they should agree with one another and, because these studies have used largely independent approaches to infer features of the LUCA genome and proteome, agreement between them could be taken as support for this sort of approach."

Surprisingly, we found that studies of the genome or proteome of the LUCA do not uniformly agree with one another.”

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Darwin, we got a huge problem!!! Over!!!

Uma relíquia de design: contra as funções próprias da biologia. Será?

A relic of design: against proper functions in biology

Emanuele Ratti & Pierre-Luc Germain 

Biology & Philosophy volume 37, Article number: 27 (2022)

 

Abstract

The notion of biological function is fraught with difficulties—intrinsically and irremediably so, we argue. The physiological practice of functional ascription originates from a time when organisms were thought to be designed and remained largely unchanged since. In a secularized worldview, this creates a paradox which accounts of functions as selected effect attempt to resolve. This attempt, we argue, misses its target in physiology and it brings problems of its own. Instead, we propose that a better solution to the conundrum of biological functions is to abandon the notion altogether, a prospect not only less daunting than it appears, but arguably the natural continuation of the naturalisation of biology.

FREE PDF: Biology & Philosophy

Alguns problemas abertos em Biologia Matemática

Open Problems in Mathematical Biology

Sean T. Vittadello, Michael P.H. Stumpf

Image/Imagem

Biology is data-rich, and it is equally rich in concepts and hypotheses. Part of trying to understand biological processes and systems is therefore to confront our ideas and hypotheses with data using statistical methods to determine the extent to which our hypotheses agree with reality. But doing so in a systematic way is becoming increasingly challenging as our hypotheses become more detailed, and our data becomes more complex. Mathematical methods are therefore gaining in importance across the life- and biomedical sciences. Mathematical models allow us to test our understanding, make testable predictions about future behaviour, and gain insights into how we can control the behaviour of biological systems. It has been argued that mathematical methods can be of great benefit to biologists to make sense of data. But mathematics and mathematicians are set to benefit equally from considering the often bewildering complexity inherent to living systems. Here we present a small selection of open problems and challenges in mathematical biology. We have chosen these open problems because they are of both biological and mathematical interest.

Comments: 31 pages, 2 figures, 115 references

Subjects: Quantitative Methods (q-bio.QM); Biological Physics (physics.bio-ph)

Cite as: arXiv:2206.09516 [q-bio.QM]

  (or arXiv:2206.09516v1 [q-bio.QM] for this version)

https://doi.org/10.48550/arXiv.2206.09516

Focus to learn more

Submission history

From: Michael Stumpf [view email]

[v1] Mon, 20 Jun 2022 00:31:27 UTC (1,210 KB)

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Asa de mariposa: isolante acústico natural de eficiência imbatível: mero acaso, fortuita necessidade ou design inteligente?

 Moth wings as sound absorber metasurface

Thomas R. Neil, Zhiyuan Shen, Daniel Robert, Bruce W. Drinkwater and Marc W. Holderied

Published:15 June 2022 https://doi.org/10.1098/rspa.2022.0046

Image/Imagem: University of Bristol

Abstract

In noise control applications, a perfect metasurface absorber would have the desirable traits of not only mitigating unwanted sound, but also being much thinner than the wavelengths of interest. Such deep-subwavelength performance is difficult to achieve technologically, yet moth wings, as natural metamaterials, offer functionality as efficient sound absorbers through the action of the numerous resonant scales that decorate their wing membrane. Here, we quantify the potential for moth wings to act as a sound-absorbing metasurface coating for acoustically reflective substrates. Moth wings were found to be efficient sound absorbers, reducing reflection from an acoustically hard surface by up to 87% at the lowest frequency tested (20 kHz), despite a thickness to wavelength ratio of up to 1/50. Remarkably, after the removal of the scales from the dorsal surface the wing's orientation on the surface changed its absorptive performance: absorption remains high when the bald wing membrane faces the sound but breaks down almost completely in the reverse orientation. Numerical simulations confirm the strong influence of the air gap below the wing membrane but only when it is adorned with scales. The finding that moth wings act as deep-subwavelength sound-absorbing metasurfaces opens the door to bioinspired, high-performance sound mitigation solutions.

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Origem e evolução inicial da célula eucariótica

Origin and Early Evolution of the Eukaryotic Cell

Annual Review of Microbiology

Vol. 75:631-647 (Volume publication date October 2021)

First published as a Review in Advance on August 3, 2021

https://doi.org/10.1146/annurev-micro-090817-062213 

Image/Imagem

Toni Gabaldón1,2,3

1Barcelona Supercomputing Centre (BCS-CNS), 08034 Barcelona, Spain; email: toni.gabaldon.bcn@gmail.com

2Institute for Research in Biomedicine (IRB), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain

3Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain

Abstract

The origin of eukaryotes has been defined as the major evolutionary transition since the origin of life itself. Most hallmark traits of eukaryotes, such as their intricate intracellular organization, can be traced back to a putative common ancestor that predated the broad diversity of extant eukaryotes. However, little is known about the nature and relative order of events that occurred in the path from preexisting prokaryotes to this already sophisticated ancestor. The origin of mitochondria from the endosymbiosis of an alphaproteobacterium is one of the few robustly established events to which most hypotheses on the origin of eukaryotes are anchored, but the debate is still open regarding the time of this acquisition, the nature of the host, and the ecological and metabolic interactions between the symbiotic partners. After the acquisition of mitochondria, eukaryotes underwent a fast radiation into several major clades whose phylogenetic relationships have been largely elusive. Recent progress in the comparative analyses of a growing number of genomes is shedding light on the early events of eukaryotic evolution as well as on the root and branching patterns of the tree of eukaryotes. Here I discuss current knowledge and debates on the origin and early evolution of eukaryotes. I focus particularly on how phylogenomic analyses have challenged some of the early assumptions about eukaryotic evolution, including the widespread idea that mitochondrial symbiosis in an archaeal host was the earliest event in eukaryogenesis.

Keywords eukaryogenesis, mitochondria, endosymbiosis, eukaryotic evolution, LECA

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As mitocôndrias e a origem dos eucariontes

 

Mitochondria and the origin of eukaryotes

Were the powerhouse organelles a driving force or a late addition in the evolution of more complex cells like ours?

By Viviane Callier 06.08.2022

For billions of years after the origin of life, the only living things on Earth were tiny, primitive cells resembling today’s bacteria. But then, more than 1.5 billion years ago, something remarkable happened: One of those primitive cells, belonging to a group known as the archaea, swallowed a different one — a bacterium.

Instead of being digested, the bacterium took up permanent residence within the other organism as what biologists call an endosymbiont. Eventually, it integrated fully into its archaeal host cell, becoming what we know today as the mitochondrion, the crucial energy-producing component of the cell.

Its acquisition has long been viewed as the key step in what is arguably the most important evolutionary leap since the origin of life itself: the transition from early primitive cells, or prokaryotes, to the more sophisticated cells of higher organisms, or eukaryotes, including ourselves.

It’s a neat story you’ll find in most biology textbooks — but is it quite that simple? In the last few years, new evidence has challenged the notion that mitochondria played a seminal role in this transition. Researchers sequencing the genomes of modern-day relatives of the first eukaryotes have found many unexpected genes that don’t seem to come from either the host or the endosymbiont. And that, some scientists suggest, might mean that the evolution of the first eukaryotes involved more than two partners and happened more gradually than suspected.

Others don’t see a reason yet to abandon the theory that the acquisition of the mitochondrion was the spark that ignited the rapid evolution of eukaryotes — giving rise, eons later, to plants, animals, vertebrates, people. Fresh evidence from genomics and cell biology may help resolve the debate, while also pointing to knowledge gaps that still need to be filled to understand one of the foundational events in our own ancestry, the origin of complex cells.

Read more here/Leia mais aqui: Knowable Magazine

Darwin, nós temos um problema: a fisiologia restaura o propósito na biologia evolutiva

Physiology restores purpose to evolutionary biology

Raymond Noble, Denis Noble

Biological Journal of the Linnean Society, blac049, 

Published: 08 June 2022 

Article history Received: 26 November 2021 Revision received: 02 April 2022 Accepted: 08 April 2022

Published: 08 June 2022

Image/Imagem

Abstract

Life is purposefully creative in a continuous process of maintaining integrity; it adapts to counteract change. This is an ongoing, iterative process. Its actions are essentially directed to this purpose. Life exists to exist. Physiology is the study of purposeful living function. Function necessarily implies purpose. This was accepted all the way from William Harvey in the 17th century, who identified the purpose of the heart to pump blood and so feed the organs and tissues of the body, through many 19th and early 20th century examples. But late 20th century physiology was obliged to hide these ideas in shame. Teleology became the ‘lady who no physiologist could do without, but who could not be acknowledged in public.’ This emasculation of the discipline accelerated once the Central Dogma of molecular biology was formulated, and once physiology had become sidelined as concerned only with the disposable vehicle of evolution. This development has to be reversed. Even on the practical criterion of relevance to health care, gene-centrism has been a disaster, since prediction from elements to the whole system only rarely succeeds, whereas identifying whole system functions invariably makes testable predictions at an elemental level.

Key words biological function, Central Dogma, purpose in biology, teleology

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Biological Journal of the Linnean Society

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Físicos reescrevem a lei fundamental que leva à desordem

Physicists Rewrite the Fundamental Law That Leads to Disorder

The second law of thermodynamics is among the most sacred in all of science, but it has always rested on 19th century arguments about probability. New arguments trace its true source to the flows of quantum information.

Is the rise of entropy merely probabilistic, or can it be straightened out by use of clear quantum axioms?

Maggie Chiang for Quanta Magazine

In all of physical law, there’s arguably no principle more sacrosanct than the second law of thermodynamics — the notion that entropy, a measure of disorder, will always stay the same or increase. “If someone points out to you that your pet theory of the universe is in disagreement with Maxwell’s equations — then so much the worse for Maxwell’s equations,” wrote the British astrophysicist Arthur Eddington in his 1928 book The Nature of the Physical World. “If it is found to be contradicted by observation — well, these experimentalists do bungle things sometimes. But if your theory is found to be against the second law of thermodynamics I can give you no hope; there is nothing for it but to collapse in deepest humiliation.” No violation of this law has ever been observed, nor is any expected.

But something about the second law troubles physicists. Some are not convinced that we understand it properly or that its foundations are firm. Although it’s called a law, it’s usually regarded as merely probabilistic: It stipulates that the outcome of any process will be the most probable one (which effectively means the outcome is inevitable given the numbers involved).

Yet physicists don’t just want descriptions of what will probably happen. “We like laws of physics to be exact,” said the physicist Chiara Marletto of the University of Oxford. Can the second law be tightened up into more than just a statement of likelihoods?

A number of independent groups appear to have done just that. They may have woven the second law out of the fundamental principles of quantum mechanics — which, some suspect, have directionality and irreversibility built into them at the deepest level. According to this view, the second law comes about not because of classical probabilities but because of quantum effects such as entanglement. It arises from the ways in which quantum systems share information, and from cornerstone quantum principles that decree what is allowed to happen and what is not. In this telling, an increase in entropy is not just the most likely outcome of change. It is a logical consequence of the most fundamental resource that we know of — the quantum resource of information.

Quantum Inevitability

Thermodynamics was conceived in the early 19th century to describe the flow of heat and the production of work. The need for such a theory was urgently felt as steam power drove the Industrial Revolution, and engineers wanted to make their devices as efficient as possible.

In the end, thermodynamics wasn’t much help in making better engines and machinery. Instead, it became one of the central pillars of modern physics, providing criteria that govern all processes of change.

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Read more here/Leia mais aqui: Quanta Magazine

Darwin, estudo sugere que a maioria das árvores evolutivas pode estar errada...

Molecular phylogenies map to biogeography better than morphological ones

Jack W. Oyston, Mark Wilkinson, Marcello Ruta & Matthew A. Wills 

Communications Biology volume 5, Article number: 521 (2022)

Schematic universal tree updated from (Woese et al., 1990)

Abstract

Phylogenetic relationships are inferred principally from two classes of data: morphological and molecular. Currently, most phylogenies of extant taxa are inferred from molecules and when morphological and molecular trees conflict the latter are often preferred. Although supported by simulations, the superiority of molecular trees has rarely been assessed empirically. Here we test phylogenetic accuracy using two independent data sources: biogeographic distributions and fossil first occurrences. For 48 pairs of morphological and molecular trees we show that, on average, molecular trees provide a better fit to biogeographic data than their morphological counterparts and that biogeographic congruence increases over research time. We find no significant differences in stratigraphic congruence between morphological and molecular trees. These results have implications for understanding the distribution of homoplasy in morphological data sets, the utility of morphology as a test of molecular hypotheses and the implications of analysing fossil groups for which molecular data are unavailable.

FREE PDF GRATIS: Communications Biology 

O neodarwinismo deve mudar se quiser sobreviver

Neo-Darwinism must Mutate to survive

Olen R.Brown a David A.Hullender b

a Dalton Cardiovascular Research Center, University of Missouri- Columbia, USA

b Professor of Mechanical and Aerospace Engineering at the University of Texas at Arlington, USA

Received 15 November 2021, Revised 6 April 2022, Accepted 12 April 2022, Available online 16 April 2022.

https://doi.org/10.1016/j.pbiomolbio.2022.04.005 

Image/Imagem: BioScience

Abstract

Darwinian evolution is a nineteenth century descriptive concept that itself has evolved. Selection by survival of the fittest was a captivating idea. Microevolution was biologically and empirically verified by discovery of mutations. There has been limited progress to the modern synthesis. The central focus of this perspective is to provide evidence to document that selection based on survival of the fittest is insufficient for other than microevolution. Realistic probability calculations based on probabilities associated with microevolution are presented. However, macroevolution (required for all speciation events and the complexifications appearing in the Cambrian explosion) are shown to be probabilistically highly implausible (on the order of 10−50) when based on selection by survival of the fittest. We conclude that macroevolution via survival of the fittest is not salvageable by arguments for random genetic drift and other proposed mechanisms. Evolutionary biology is relevant to cancer mechanisms with significance beyond academics. We challenge evolutionary biology to advance boldly beyond the inadequacies of the modern synthesis toward a unifying theory modeled after the Grand Unified Theory in physics. This should include the possibility of a fifth force in nature. Mathematics should be rigorously applied to current and future evolutionary empirical discoveries. We present justification that molecular biology and biochemistry must evolve to aeon (life) chemistry that acknowledges the uniqueness of enzymes for life. To evolve, biological evolution must face the known deficiencies, especially the limitations of the concept survival of the fittest, and seek solutions in Eigen's concept of self-organization, Schrödinger's negentropy, and novel approaches.

Keywords Evolution Modern synthesis Negentropy Probability Selection Selforganization Survival of fittest

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Progress in Biophysics and Molecular Biology

Darwin, mais turbulência na base da Árvore da Vida - eucariogênese, o surgimento de um superorganismo emergente

Eukaryogenesis: The Rise of an Emergent Superorganism

Philip J. L. Bell*

Microbiogen Pty Ltd., Sydney, NSW, Australia

Image/Imagem: Wiley Online Library

Although it is widely taught that all modern life descended via modification from a last universal common ancestor (LUCA), this dominant paradigm is yet to provide a generally accepted explanation for the chasm in design between prokaryotic and eukaryotic cells. Counter to this dominant paradigm, the viral eukaryogenesis (VE) hypothesis proposes that the eukaryotes originated as an emergent superorganism and thus did not evolve from LUCA via descent with incremental modification. According to the VE hypothesis, the eukaryotic nucleus descends from a viral factory, the mitochondrion descends from an enslaved alpha-proteobacteria and the cytoplasm and plasma membrane descend from an archaeal host. A virus initiated the eukaryogenesis process by colonising an archaeal host to create a virocell that had its metabolism reprogrammed to support the viral factory. Subsequently, viral processes facilitated the entry of a bacterium into the archaeal cytoplasm which was also eventually reprogrammed to support the viral factory. As the viral factory increased control of the consortium, the archaeal genome was lost, the bacterial genome was greatly reduced and the viral factory eventually evolved into the nucleus. It is proposed that the interaction between these three simple components generated a superorganism whose emergent properties allowed the evolution of eukaryotic complexity. If the radical tenets of the VE hypothesis are ultimately accepted, current biological paradigms regarding viruses, cell theory, LUCA and the universal Tree of Life (ToL) should be fundamentally altered or completely abandoned.

FREE PDF GRATIS: Frontiers in Microbiology