Cientistas apoiam a desobediência civil em massa para forçar ação climática!

segunda-feira, outubro 14, 2019

Scientists endorse mass civil disobedience to force climate action
Matthew Green

LONDON (Reuters) - Almost 400 scientists have endorsed a civil disobedience campaign aimed at forcing governments to take rapid action to tackle climate change, warning that failure could inflict “incalculable human suffering.”

Julia Steinberger, an ecological economist at Britain's University of Leeds, endorses mass civil disobedience to pressure governments to tackle climate change at a protest at London's Science Museum
Julia Steinberger, an ecological economist at Britain's University of Leeds, endorses mass civil disobedience to pressure governments to tackle climate change at a protest at London's Science Museum, Britain October 12, 2019. Louise Jasper/Handout via REUTERS

In a joint declaration, climate scientists, physicists, biologists, engineers and others from at least 20 countries broke with the caution traditionally associated with academia to side with peaceful protesters courting arrest from Amsterdam to Melbourne.

Wearing white laboratory coats to symbolize their research credentials, a group of about 20 of the signatories gathered on Saturday to read out the text outside London’s century-old Science Museum in the city’s upmarket Kensington district.

“We believe that the continued governmental inaction over the climate and ecological crisis now justifies peaceful and non-violent protest and direct action, even if this goes beyond the bounds of the current law,” said Emily Grossman, a science broadcaster with a PhD in molecular biology. She read the declaration on behalf of the group.

“We therefore support those who are rising up peacefully against governments around the world that are failing to act proportionately to the scale of the crisis,” she said.

The declaration was coordinated by a group of scientists who support Extinction Rebellion, a civil disobedience campaign that formed in Britain a year ago and has since sparked offshoots in dozens of countries.
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READ MORE HERE: Reuters

!FUIMOS DISEÑADOS! Información genética. Marcos Eberlin

sexta-feira, outubro 11, 2019

Construindo um modelo melhor da retina

quinta-feira, outubro 10, 2019

Tissue Engineering: Building a better model of the retina

Milica Radisic 

University of Toronto, Canada

INSIGHT Oct 4, 2019

DOI: 10.7554/eLife.51183

Retina-on-a-chip combines the benefits of organoids and organ-on-a-chip engineering.
Each chip has a vascular-like compartment (red) which is separated from the four organoid compartments above by a porous membrane. Schematic diagram (right) showing the various layers of cells in the retinal organoid (top) and the retinal pigment epithelium cells (RPE; yellow).

Image credit: Achberger et al. (CC BY 4.0)

Abstract

Researchers have combined organ-on-a-chip engineering with the benefits of organoids to make improved models of the human retina.

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Michael Behe na Universidade Presbiteriana Mackenzie em Campinas, SP

sexta-feira, setembro 27, 2019


Mackenzie Discovery recebe o maior defensor do Design Inteligente

quinta-feira, setembro 26, 2019

 
 Michael Behe estará pela terceira vez no país e relançará livro

25.09.2019 19h00 Comunicação - Marketing Mackenzie
 
Compartilhe nas Redes Sociais
 
Considerado um dos maiores expoentes e defensores da Teoria do Design Inteligente (TDI), o físico estado-unidense, Michael Behe, estará na Universidade Presbiteriana Mackenzie (UPM), para participar do II TDI São Paulo, em 15 de Outubro. No evento, o cientista falará sobre as novidades nas discussões sobre o surgimento da vida no Planeta Terra, além de relançar uma de suas obras mais importantes. 

Em sua terceira vinda ao Brasil, Behe apresentará o que há de mais recente no debate entre as Teoria da Evolução a TDI, com evidências científicas sobre a (bio)química da vida e a física do Universo. O simpósio é organizado pelo Discovery Mackenzie e pela Editora Mackenzie.

De acordo com o coordenador do centro de pesquisas, Marcos Eberlin, a vinda do renomado cientista será de grande importância para a formação dos alunos da UPM, como formadores de opinião. “Behe é o maior expoente mundial de uma teoria de vanguarda. A aceitação da TDI, que se mostra cada dia mais eminente, certamente influenciará a nossa sociedade, e os alunos do Mackenzie precisam participar desse momento histórico”, afirmou.

Teoria do Design Inteligente afirma que os seres humanos foram criados prontos e por uma mente inteligente, ao contrário das proposições feitas pelo Darwinismo. A TDI é baseada em conhecimentos científicos, principalmente no campo da química e da bioquímica.

Michael Behe é membro do Discovery Institute, nos EUA, uma dos centros mais atuantes no debate sobre a TDI no Mundo. Já o Discovery Mackenzie é o primeiro Núcleo de Pesquisas no mundo instalado em uma Universidade, e promove o debate científico sobre as nossas origens à luz da disputa entre evolução e Design Inteligente. 

Eberlin acredita que a vinda do cientista aprofundará ainda mais as relações entre os centros de pesquisas. A visita do físico significará, “o fortalecimento do Mackenzie como uma instituição de vanguarda, que dá no Brasil o primeiro passo em uma revolução que tudo indica levará a ciência a um novo paradigma sobre nossas origens”, afirmou o coordenador. 

Lançamento

Além de participar do evento na UPM, Michael Behe promoverá o relançamento do livro A Caixa Preta de Darwin, considerado um livro histórico para a TDI. A publicação será relançada pela Editora Mackenzie. 

O cientista também é autor do livro Darwin Devolves (A Involução de Darwin, em português) que será lançado em breve lançado pela mesma editora.

Fonte: Universidade Presbiteriana Mackenzie

Terra Plana: Douglas Aleodin não reflete a posição do Design Inteligente sobre essa questão absurda!!!

domingo, setembro 22, 2019



Fonte: O Estado de São Paulo

Enquanto Caio Fábio diz entender de Física Quântica, Sean Carroll diz que os físicos não entendem!!!

quarta-feira, setembro 18, 2019

The New York Times

Opinion

Even Physicists Don’t Understand Quantum Mechanics
Worse, they don’t seem to want to understand it.

By Sean Carroll

Dr. Carroll is a physicist.

Sept. 7, 2019

Alejandro Guijarro, Tristan Hoare Gallery, London


“I think I can safely say that nobody really understands quantum mechanics,” observed the physicist and Nobel laureate Richard Feynman. That’s not surprising, as far as it goes. Science makes progress by confronting our lack of understanding, and quantum mechanics has a reputation for being especially mysterious.

What’s surprising is that physicists seem to be O.K. with not understanding the most important theory they have.

Quantum mechanics, assembled gradually by a group of brilliant minds over the first decades of the 20th century, is an incredibly successful theory. We need it to account for how atoms decay, why stars shine, how transistors and lasers work and, for that matter, why tables and chairs are solid rather than immediately collapsing onto the floor.

Scientists can use quantum mechanics with perfect confidence. But it’s a black box. We can set up a physical situation, and make predictions about what will happen next that are verified to spectacular accuracy. What we don’t do is claim to understand quantum mechanics. Physicists don’t understand their own theory any better than a typical smartphone user understands what’s going on inside the device.

There are two problems. One is that quantum mechanics, as it is enshrined in textbooks, seems to require separate rules for how quantum objects behave when we’re not looking at them, and how they behave when they are being observed. When we’re not looking, they exist in “superpositions” of different possibilities, such as being at any one of various locations in space. But when we look, they suddenly snap into just a single location, and that’s where we see them. We can’t predict exactly what that location will be; the best we can do is calculate the probability of different outcomes.

The whole thing is preposterous. Why are observations special? What counts as an “observation,” anyway? When exactly does it happen? Does it need to be performed by a person? Is consciousness somehow involved in the basic rules of reality? Together these questions are known as the “measurement problem” of quantum theory.
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READ MORE HERE: The New York Times

+++++

NOTA BENE: 

Na entrevista concedida a Luiz Felipe Pondé sobre espiritualidade cristã, em 15/09/2019, Caio Fábio, teólogo, diz entender de Física Quântica sub specie aeternitatis. É este o pano de fundo desta postagem. 

Tabela periódica de moléculas???

terça-feira, setembro 17, 2019

Periodicity of molecular clusters based on symmetry-adapted orbital model

Takamasa Tsukamoto, Naoki Haruta, Tetsuya Kambe, Akiyoshi Kuzume & Kimihisa Yamamoto 

Nature Communications volume 10, Article number: 3727 (2019)

Source/Fonte: Biotecnika

Abstract

The periodic table has always contributed to the discovery of a number of elements. Is there no such principle for larger-scale substances than atoms? Many stable substances such as clusters have been predicted based on the jellium model, which usually assumes that their structures are approximately spherical. The jellium model is effective to explain subglobular clusters such as icosahedral clusters. To broaden the scope of this model, we propose the symmetry-adapted orbital model, which explicitly takes into account the level splittings of the electronic orbitals due to lower structural symmetries. This refinement indicates the possibility of an abundance of stable clusters with various shapes that obey a certain periodicity. Many existing substances are also governed by the same rule. Consequently, all substances with the same symmetry can be unified into a periodic framework in analogy to the periodic table of elements, which will act as a useful compass to find missing substances.

Energética e potências nas células vivas: mero acaso, fortuita necessidade ou design inteligente?

sábado, setembro 14, 2019

Energetics and forces in living cells

Proteins can act as exquisite nanomachines to produce or sense the motion associated with cell division, intercellular trafficking, muscle contraction, and countless other activities.

Physics Today 68, 2, 27 (2015); https://doi.org/10.1063/PT.3.2686

Alex Dunn is an assistant professor of chemical engineering and Andrew Price is a doctoral student in biophysics, both at Stanford University in Stanford, California.



Life is intrinsically mechanical. Animals run, fly, and swim. Plants move daily to track the Sun. Even microscopic organisms, first observed more than three centuries ago when Antoni van Leeuwenhoek trained his microscope on pond water, swarm and tumble. A look at our own cells reveals that subcellular components are in constant motion, which allows living cells to grow, divide, change shape, and move.

In addition to producing motion, our bodies must also sense it. Living cells respond to a wide variety of mechanical stimuli, including stretch, fluid flow, osmotic potential, and the stiffness of their surroundings. Our senses of hearing and touch require nerve cells to detect minuscule mechanical forces. And our ability to regulate blood pressure across meters of height depends on mechanosensitive arteries and arterioles distributed throughout the body.

More subtly, living tissues are remarkably sensitive to the mechanical cues provided by their surroundings. Stem cells grown on soft surfaces are primed to differentiate and form correspondingly soft tissues such as fat or nervous tissue, whereas cells grown on harder surfaces differentiate to form bone cells.1 On longer length scales, the growth and development of our organs require precise changes in shape, with tightly controlled tissue-level mechanical stresses and strains. The mechanosensory response is also apparent in everyday life: Consistent exercise, for instance, leads to increases in bone and muscle mass, and slacking off reverses the gains.

To make complex morphogenetic decisions, our cells must constantly communicate with each other. Much of the intercellular communication is through chemical signals, but growing evidence suggests that physical mechanisms provide significant control as well.2 The image above, a still from a video of the development of a fruit-fly embryo, exemplifies the complex orchestration among hundreds of cells. Individual cells are squeezed, pushed, and pulled across significant distances to form different parts of the developing body.

Although motion is a pervasive aspect of life, until recently biologists had little understanding of how living things produce, detect, and respond to mechanical cues at the cellular level. Only in the past decade have researchers learned key aspects of how living cells pull that off and how those different functions are integrated among groups of cells within tissues. Although the molecular details of how a cell works are complex, some relatively simple physical models provide powerful hints.
...

FREE PDF GRATIS: Physics Today

Frotas de máquinas microscópicas trabalham em nossas células, realizando tarefas biológicas essenciais e nos mantendo vivos: mero acaso, fortuita necessidade ou design inteligente?

Self-straining of actively crosslinked microtubule networks

Sebastian Fürthauer, Bezia Lemma, Peter J. Foster, Stephanie C. Ems-McClung, Che-Hang Yu, Claire E. Walczak, Zvonimir Dogic, Daniel J. Needleman & Michael J. Shelley 

Nature Physics (2019) 


Source/Fonte: Emmanuel Dumont
Abstract

Cytoskeletal networks are foundational examples of active matter and central to self-organized structures in the cell. In vivo, these networks are active and densely crosslinked. Relating their large-scale dynamics to the properties of their constituents remains an unsolved problem. Here, we study an in vitro active gel made from aligned microtubules and XCTK2 kinesin motors. Using photobleaching, we demonstrate that the gel’s aligned microtubules, driven by motors, continually slide past each other at a speed independent of the local microtubule polarity and motor concentration. This phenomenon is also observed, and remains unexplained, in spindles. We derive a general framework for coarse graining microtubule gels crosslinked by molecular motors from microscopic considerations. Using microtubule–microtubule coupling through a force–velocity relationship for kinesin, this theory naturally explains the experimental results: motors generate an active strain rate in regions of changing polarity, which allows microtubules of opposite polarities to slide past each other without stressing the material.

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Otimização no código genético robusto em relação aos conjuntos de códigos de comparação: mero acaso, fortuita necessidade ou design inteligente?

quarta-feira, setembro 11, 2019

Biosystems

Volume 185, November 2019, 104023
  
Optimality in the standard genetic code is robust with respect to comparison code sets
Received 15 May 2019, Revised 22 August 2019, Accepted 24 August 2019, Available online 11 September 2019.



Abstract

The genetic code and its evolution have been studied by many different approaches. One approach is to compare the properties of the standard genetic code (SGC) to theoretical alternative codes in order to determine how optimal it is and from this infer whether or not it is likely that it has undergone a selective evolutionary process. Many different properties have been studied in this way in the literature. Less focus has been put on the alternative code sets which are used as a comparison to the standard code. Each implicitly represents an evolutionary hypothesis and the sets used differ greatly across the literature. Here we determine the influence of the comparison set on the results of the optimality calculation by using codes based upon different sub-structures of the SGC. With these results we can generalize the results to different evolutionary hypotheses. We find that the SGC's optimality is very robust, as no code set with no optimised properties is found. We therefore conclude that the optimality of the SGC is a robust feature across all evolutionary hypotheses. Our results provide important information for any future studies on the evolution of the standard genetic code. We also studied properties of the SGC concerning overlapping genes, which have recently been found to be more widespread than often believed. Although our results are not conclusive yet we find additional intriguing structures in the SGC that need explanation.

Keywords Genetics Genetic code Evolutionary genetics

FREE PDF GRATIS: Biosystems

Darwin, mais complexidade: como que nós temos muitos tipos diferentes de neurônios em nossos cérebros?

sábado, setembro 07, 2019

Splicing in a single neuron is coordinately controlled by RNA binding proteins and transcription factors

Morgan Thompson, Ryan Bixby, Robert Dalton, Alexa Vandenburg, John A Calarco, Adam D Norris Is a corresponding author

Southern Methodist University, United States; University of Toronto, Canada

RESEARCH ARTICLE Jul 19, 2019 




Abstract

Single-cell transcriptomes are established by transcription factors (TFs), which determine a cell's gene-expression complement. Post-transcriptional regulation of single-cell transcriptomes, and the RNA binding proteins (RBPs) responsible, are more technically challenging to determine, and combinatorial TF-RBP coordination of single-cell transcriptomes remains unexplored. We used fluorescent reporters to visualize alternative splicing in single Caenorhabditis elegans neurons, identifying complex splicing patterns in the neuronal kinase sad-1. Most neurons express both isoforms, but the ALM mechanosensory neuron expresses only the exon-included isoform, while its developmental sister cell the BDU neuron expresses only the exon-skipped isoform. A cascade of three cell-specific TFs and two RBPs are combinatorially required for sad-1 exon inclusion. Mechanistically, TFs combinatorially ensure expression of RBPs, which interact with sad-1 pre-mRNA. Thus a combinatorial TF-RBP code controls single-neuron sad-1 splicing. Additionally, we find ‘phenotypic convergence,’ previously observed for TFs, also applies to RBPs: different RBP combinations generate similar splicing outcomes in different neurons.




eLife digest
All the cells in the human nervous system contain the same genetic information, and yet there are many kinds of neurons, each with different features and roles in the body. Proteins known as transcription factors help to establish this diversity by switching on different genes in different types of cells.


A mechanism known as RNA splicing, which is regulated by RNA binding proteins, can also provide another layer of regulation. When a gene is switched on, a faithful copy of its sequence is produced in the form of an RNA molecule, which will then be ‘read’ to create a protein. However, the RNA molecules may first be processed to create templates that can differ between cell types: this means that a single gene can code for slightly different proteins, some of them specific to a given cell type. Yet, very little is known about how RNA splicing can generate more diversity in the nervous system.


To investigate, Thompson et al. developed a fluorescent reporter system that helped them track how the RNA of a gene called sad-1 is spliced in individual neurons of the worm Caenorhabditis elegans. This showed that sad-1 was turned on in all neurons, but the particular spliced versions varied widely between different types of nerve cells.


Additional experiments combined old school and cutting-edge genetics technics such as CRISPR/Cas9 to identify the proteins that control the splicing of sad-1 in different kinds of neurons. Despite not directly participating in RNA splicing, a number of transcription factors were shown to be involved. These molecular switches were turning on genes that code for RNA binding proteins differently between types of neurons, which in turn led sad-1 to be spliced according to neuron-specific patterns.


The findings by Thompson et al. could provide some insight into how mammals can establish many types of neurons; however, a technical hurdle stands in the way of this line of research, as it is still difficult to detect splicing in single neurons in these species.



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A Inquisição Secular: Darwin locuta, causa finita!

sexta-feira, setembro 06, 2019

The secular inquisition 
 

 
 
A few days ago, the philosopher John Gray wrote on the Unherd website a bleak but precisely directed analysis of why the humanities can’t be saved. It used to be said, he wrote, that the humanities taught people how to think. No longer.

“Students learn an intra-academic argot – intersectionality, hetero-normativity and the like — that has zero utility in the world in which they will go on to live.They also learn that disagreement in ethics and politics is illegitimate. Anyone who departs from the prevailing progressive consensus is not just mistaken but malevolent. When enforced in universities, this is a prescription for censorship and conformism. What is being inculcated is not freedom of mind, but freedom from thought”.

Gray was echoing the despair of Sir Roger Scruton, himself a victim of vicious bullying by closed minds. Sir Roger recently observed that the intellectual corruption of the humanities had led him to conclude that those departments should be shut down altogether and the universities be reduced to institutions of scientific inquiry alone.

For many years, I have been writing about these trends and attempting to explain why western society seems to be tearing itself up by the roots. Much of the current discussion about the malign development of hate-fuelled divisions, identity politics and other aspects of our culture wars echoes the analysis in my own books: All Must Have Prizes (1996), The Sex-Change Society: Feminised Britain and the Neutered Male ( 1999) and The World Turned Upside-Down: the Global Battle over God, Truth and Power (2010).

As a result, I will be publishing on this blog a series of excerpts from these three books (the first two of which are now sadly out of print) in the hope they may further help illuminate today’s great cultural battleground.

Today I start with an excerpt from a chapter entitled “The Secular Inquisition” from The World Turned Upside-Down.

What have the issues of anthropogenic global warming, the war in Iraq, Israel and scientism got in common? Not a lot, you might think. But in fact a number of threads link them all. Most fundamentally, they all involve the promotion of beliefs that purport to be unchallengeable truths but are in fact ideologies in which evidence is manipulated, twisted and distorted to support and “prove” their governing idea. All are therefore based on false or unsupported beliefs that are presented as axiomatically true. Moreover, because each assumes itself to be proclaiming the sole and exclusive truth, it cannot permit any challenge to itself. It has to maintain at all costs the integrity of the falsehood. So all challenges have to be resisted through coercive means. Knowledge is thus forced to give way to power. Reason is replaced by bullying, intimidation and the suppression of debate.

This makes them all deeply regressive movements of thought, which corrode the most fundamental concept of the Western world. The principal characteristic of Western modernity is freedom of thought and expression and the ability to express dissent. The eighteenth-century Enlightenment ushered in the modern age by breaking the power of the church to control the terms of debate and punish heresy. Church and state were separated, and a space was created for individual freedom and the toleration of differences—the essence of a liberal society.

Cultural Totalitarianism

While it would be a mistake to idealize the eighteenth and nineteenth centuries, this era in Britain and America did provide a breathing space between the religious tyranny of the age that preceded it and the horrors that were to follow. Yet the French Revolution and the Terror unleashed by it presented the inescapable evidence that the Enlightenment, far from consigning murderous obscurantism to the dustbin of history, contained powerful strands from the start that would merely secularize tyranny. In the twentieth century, the political totalitarianism of communism and fascism, although overtly antireligious, echoed the premodern despotism of the church by declaring themselves the arbiters of a totalizing worldview in which all dissent would be crushed. Now, with both communism and fascism defeated, the West has fallen victim to a third variation on the theme of totalitarianism: not religious or political this time, but cultural. It is what J. L. Talmon identified back in 1952 as “totalitarian democracy,” which he characterized as “a dictatorship based on ideology and the enthusiasm of the masses.”

If religious totalitarianism was rule by the church and political totalitarianism was rule by the “general will,” cultural totalitarianism is rule by the subjective individual, freed from all external authority and constraints. Morality is privatized so that everyone becomes his or her own moral authority, while the laws and traditions rooted in Christianity and the Hebrew Bible have come under explicit attack. The old order of Western civilization, resting on the external authorities of religion and culture, has to be destroyed. With no order or purpose in the world, moral and cultural relativism are the rule; any attempt to prioritize any culture or lifestyle over any other is illegitimate.

The paradox—and it is acute—is that this relativist doctrine itself assumes the form of a dogmatic moralizing agenda that takes an absolutist position against all who challenge it and seeks to stamp out all deviations. Medieval Christianity—like contemporary Islamism—stamped out dissent by killing or conversion; Western liberals do it by social and professional ostracism and legal discrimination. It is a kind of secular Inquisition. And the grand inquisitors are to be found within the intelligentsia—in the universities, the media, the law, the political and professional classes—who not only have systematically undermined the foundations of Western society but are heavily engaged in attempting to suppress any challenge or protest.

It is paradoxical but not surprising that the assault on intellectual liberty is taking place within the institutions of reason. For decades, these have been dominated by a variety of wrecking ideologies such as anti-capitalism, anti-imperialism, utilitarianism, feminism, multiculturalism and environmentalism. What they all have in common is the aim of overturning the established order in the West. What was previously marginalized or forbidden has become permitted and even mandatory; what was previously the norm has become forbidden and marginalized. As the philosopher Roger Scruton has written, the curriculum in the humanities is “relativist in favour of transgression and absolutist against authority.” Because these are ideologies, they wrench facts and evidence to fit their governing idea. They are inimical to reason and independent thought—and thus to freedom, because reason and liberty are inseparable bedfellows.

As Sir Karl Popper has observed, reason grows by way of mutual criticism and through the development of institutions that safeguard the liberty to criticize and thus preserve freedom of thought. Because it treats people impartially, reason is therefore closely linked to equality. Pseudo-rationalism, by contrast, is “the immodest belief in one’s superior intellectual gifts—the claim to be initiated, to know with certainty, to possess an infallible instrument of discovery.” This pseudo-rationalism, the enemy of reason, is precisely what has the Western intelligentsia in its grip.

It is hard to overstate the influence on our culture that is wielded by the doctrines of anti-imperialism, multiculturalism, feminism, environmentalism and the like. They form the unchallengeable orthodoxy within academia, the base camp for their “long march through the institutions,” which they have colonized with stunning success. The center of political gravity has been shifted so that anyone who does not share these values is defined as extreme.

“Progressives” on the left believe that their secular, materialistic, individualistic and utilitarian values represent not a point of view but virtue itself. No decent person can therefore oppose them. In Manichean fashion, the left divides the world into two rival camps of good and evil, creating as the sole alternative to itself a demonic political camp called “the right,” to which everyone who challenges it is automatically consigned. Since “the right” is by definition evil, to dispute any left-wing shibboleth is to put oneself beyond the moral pale. There can be no dissent or argument at all. Only one worldview is to be permitted. Anyone who supports Israel or the Americans in Iraq, or is skeptical of anthropogenic global warming, or opposes multiculturalism or utilitarianism, or supports capitalism or is a believing Christian is “right-wing” and therefore evil.

A central doctrine in the progressive orthodoxy is that “discrimination” is the supreme crime. The very idea of a hierarchy of cultures, beliefs or lifestyles is deemed to be discriminatory. According to the ideology of nondiscrimination, all self-designated “victim” groups can do no wrong, while the majority culture can do no right. Morality is redefined around subjective feelings. Any objective evidence of harm that may be done by “victim” groups is swept away; all that matters is that they must not be made to feel bad about themselves, nor be put at any disadvantage even if it results from their own actions.

Activities previously marginalized or considered transgressive are now privileged, while those considered to embody normative values are actively discriminated against. In the cause of nonjudgmentalism, only those who are in favor of moral judgments based on the ethical codes of the Bible are to be judged and condemned. In the cause of antidiscrimination, only those who believe in a level playing field are to be discriminated against. In the cause of freedom, those who seek to limit anarchic behavior in order to prevent harm are to be denied the freedom to do so.

...

READ MORE HERE: MelanniePhillips

Comparando as vocalizações dos primatas: profundo abismo na capacidade cognitiva dos humanos

quarta-feira, setembro 04, 2019

CONCEPTUAL ANALYSIS ARTICLE

Front. Psychol., 03 September 2019  

Systems Underlying Human and Old World Monkey Communication: One, Two, or Infinite

Shigeru Miyagawa1,2* and Esther Clarke1,3

1Linguistics and Philosophy, Massachusetts Institute of Technology, Cambridge, MA, United States

2Office of Open Learning, Massachusetts Institute of Technology, Cambridge, MA, United States

3Behavioral Ecology and Evolution Research (BEER) Group, Durham University, Durham, United Kingdom

Source/Fonte: MIT News


Abstract

Using artificially synthesized stimuli, previous research has shown that cotton-top tamarin monkeys easily learn simple AB grammar sequences, but not the more complex AnBn sequences that require hierarchical structure. Humans have no trouble learning AnBn combinations. A more recent study, using similar artificially created stimuli, showed that there is a neuroanatomical difference in the brain between these two kinds of arrays. While the simpler AB sequences recruit the frontal operculum, the AnBn array recruits the phylogenetically newer Broca’s area. We propose that on close inspection, reported vocal repertoires of Old World Monkeys show that these nonhuman primates are capable of calls that have two items in them, but never more than two. These are simple AB sequences, as predicted by previous research. In addition, we suggest the two-item call cannot be the result of a combinatorial operation that we see in human language, where the recursive operation of Merge allows for a potentially infinite array of structures. In our view, the two-item calls of nonhuman primates result from a dual-compartment frame into which each of the calls can fit without having to be combined by an operation such as Merge.

FREE PDF GRATIS: Frontiers in Psychology

Rastreando a evolução da visão

sexta-feira, agosto 23, 2019

Chromophore-Independent Roles of Opsin Apoproteins in Drosophila Mechanoreceptors

Radoslaw Katana, Chonglin Guan, Damiano Zanini, Christoph F. Schmidt, Steven G. Britt, Martin C. Göpfert

Published:August 22, 2019 DOI: https://doi.org/10.1016/j.cub.2019.07.036


Highlights

• Drosophila mechanosensation requires opsins but no retinal chromophore

• Mechanosensory opsin function is independent of the retinal attachment site

• Mechanosensation involves visual chromophore pathway components

• Mechanosensory organs express chromophore pathway genes

Summary

Rhodopsins, the major light-detecting molecules of animal visual systems [1], consist of opsin apoproteins that covalently bind a retinal chromophore with a conserved lysine residue [1, 2]. In addition to capturing photons, this chromophore contributes to rhodopsin maturation [3, 4], trafficking [3, 4], and stabilization [5], and defects in chromophore synthesis and recycling can cause dysfunction of the retina and dystrophy [6, 7, 8, 9]. Indications that opsin apoproteins alone might have biological roles have come from archaebacteria and platyhelminths, which present opsin-like proteins that lack the chromophore binding site and are deemed to function independently of light [10, 11]. Light-independent sensory roles have been documented for Drosophila opsins [12, 13, 14, 15], yet also these unconventional opsin functions are thought to require chromophore binding [12, 13, 15]. Unconjugated opsin apoproteins act as phospholipid scramblases in mammalian photoreceptor disks [16], yet chromophore-independent roles of opsin apoproteins outside of eyes have, to the best of our knowledge, hitherto not been described. Drosophila chordotonal mechanoreceptors require opsins [13, 15], and we find that their function remains uncompromised by nutrient carotenoid depletion. Disrupting carotenoid uptake and cleavage also left the mechanoreceptors unaffected, and manipulating the chromophore attachment site of the fly’s major visual opsin Rh1 impaired photoreceptor, but not mechanoreceptor, function. Notwithstanding this chromophore independence, some proteins that process and recycle the chromophore in the retina are also required in mechanoreceptors, including visual cycle components that recycle the chromophore upon its photoisomerization. Our results thus establish biological function for unconjugated opsin apoproteins outside of eyes and, in addition, document chromophore-independent roles for chromophore pathway components.

Keywords chordotonal organ mechanosensation opsin apoprotein phototransduction retinal chromophore sensory cell-type evolution 

FREE PDF GRATIS: Cell

A plasticidade fenotípica inicia o viés de desenvolvimento?

quinta-feira, agosto 22, 2019

Does phenotypic plasticity initiate developmental bias?

Kevin J. Parsons Kirsty McWhinnie Natalie Pilakouta Lynsey Walker

First published: 26 July 2019




Abstract

The generation of variation is paramount for the action of natural selection. Although biologists are now moving beyond the idea that random mutation provides the sole source of variation for adaptive evolution, we still assume that variation occurs randomly. In this review, we discuss an alternative view for how phenotypic plasticity, which has become well accepted as a source of phenotypic variation within evolutionary biology, can generate nonrandom variation. Although phenotypic plasticity is often defined as a property of a genotype, we argue that it needs to be considered more explicitly as a property of developmental systems involving more than the genotype. We provide examples of where plasticity could be initiating developmental bias, either through direct active responses to similar stimuli across populations or as the result of programmed variation within developmental systems. Such biased variation can echo past adaptations that reflect the evolutionary history of a lineage but can also serve to initiate evolution when environments change. Such adaptive programs can remain latent for millions of years and allow development to harbor an array of complex adaptations that can initiate new bouts of evolution. Specifically, we address how ideas such as the flexible stem hypothesis and cryptic genetic variation overlap, how modularity among traits can direct the outcomes of plasticity, and how the structure of developmental signaling pathways is limited to a few outcomes. We highlight key questions throughout and conclude by providing suggestions for future research that can address how plasticity initiates and harbors developmental bias.

FREE PDF GRATIS: Evolution and Development

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EXCERPT:

“Although biologists are now moving beyond the idea that random mutation provides the sole source of variation for adaptive evolution, we still assume that variation occurs randomly...Darwin's idea that variation is generated randomly has largely been taken for granted rather than tested, representing a fundamental gap in our understanding of evolution.”

Desafios matemáticos à teoria da evolução - Berlinski, Meyer, e Gelernter

segunda-feira, julho 22, 2019

Origem da vida: tempo esgotado!

sexta-feira, julho 19, 2019

Time Out

Image result for james tour 

This essay comprises an argument, but it also contains an appeal to the OOL community. The history of science suggests that on occasion what is required for research to flourish is not further research—at least to the extent that further research involves doing the same thing. This is one of those times.

Needed for Life

Four molecules are needed for life: nucleotides, carbohydrates, proteins, and lipids. Nucleotides are composed of a trimeric nucleobase-carbohydrate-phosphate combination, and once polymerized, constitute DNA and RNA. Five different nucleobases comprise the entire alphabet for DNA and RNA. The nucleotides and their subsequent DNA and RNA structures are homochiral, yielding one of two possible enantiomers. Amino acids are most often homochiral. When amino acids are polymerized, they form proteins and enzymes. Proteins and enzymes also display a tertiary homochirality. Lipids are dipolar molecules with a polar water-soluble head and a non-polar water-insoluble tail. They, too, are most often homochiral. Cells use carbohydrates for energy, and carbohydrates, along with proteins, are identification-receptors. Carbohydrates are also homochiral, and their polymeric forms take on tertiary homochiral shapes. OOL researchers have spent a great deal of time trying to make these four classes of molecules, but with scant success.

Constructing the molecules necessary for life from their prebiotic precursors represents one goal of OOL research; putting them together, another. Some of synthetic chemistry is pedestrian, and some ingenious. Fundamental questions remain unaddressed. Claims that these structures could be prepared under prebiotic conditions in high enantiomeric purity using inorganic templates, or any presumed templates, have never been realized. The carbohydrates, amino acids, lipids, and other compounds within each of these classes require specific methods in order to control their regiochemistry and stereochemistry. The differences in reaction rates often require chiral systems acting upon chiral molecules. If this were possible under prebiotic conditions, it is odd that it cannot be replicated by synthetic chemists.

They have, after all, had 67 years to try.

Synthetic Hyperbole

Consider the class of experiments that deal with the assembly of chemicals into what are referred to as protocells—“a self-organized, endogenously ordered, spherical collection of lipids proposed as a stepping-stone to the origin of life.”2 In 2017, a team from the Origins of Life Initiative at Harvard University performed a type of polymerization reaction in water known as the reversible addition–fragmentation chain transfer.3 This reaction type is not seen in nature, and neither are the monomers that figure in the experiment. Still, this is standard chemistry. Polymers are made by a controlled radical polymerization reaction, where two different monomer types are added sequentially to a chain bearing both a hydrophobic and a hydrophilic block. Researchers observed polymeric vesicles forming during polymerization—interesting, but not extraordinary. The vesicles grew to bursting as researchers kept the radical chain growing through ultraviolet light activation. There is, in this, nothing surprising: the forces between the growing vesicle and the surrounding water dictate a critical growth volume before the vesicle ruptures.

The claims should have ended there.

Here is how the work was portrayed in the published article:
The observed net oscillatory vesicle population grows in a manner that reminds one of some elementary modes of sustainable (while there is available “food”!) population growth seen among living systems. The data supports an interpretation in terms of a micron scale self-assembled molecular system capable of embodying and mimicking some aspects of “simple” extant life, including self-assembly from a homogenous but active chemical medium, membrane formation, metabolism, a primitive form of self-replication, and hints of elementary system selection due to a spontaneous light triggered Marangoni instability [provoked by surface tension gradients].4
These claims were then rephrased and presented to the public by the Harvard Gazette:
A Harvard researcher seeking a model for the earliest cells has created a system that self-assembles from a chemical soup into cell-like structures that grow, move in response to light, replicate, and exhibit signs of rudimentary evolutionary selection [emphasis added].5
This degree of hyperbole is excessive.6 Nothing in this experiment had growing cell-like structures with replication, or that exhibited aspects of evolutionary selection.

Teams from the University of California and the University of New South Wales recently conducted lipid bilayer assembly experiments, publishing a summary of their work in 2017.7 They combined nucleotides and lipids in water to form lamellae, with the nucleotides sandwiched between the layers. Nucleotides are trimers of nucleobase-carbohydrate-phosphate, and, in this case, both nucleotides and lipids were purchased in pure homochiral form. Both teams then demonstrated that a condensation polymerization of the nucleotides can take place within the lamella upon dehydration. Polymerization takes place by means of a reaction between pre-loaded phosphate and the purchased stereo-defined alcohol moiety found on a neighboring nucleotide. Similar reactions, they conjectured, may have occurred at the edge of hydrothermal fields, volcanic landmasses providing the necessary heat for reactions.

The chemistry that figures in these experiments is unremarkable. Bear in mind that derivatives were all pre-loaded. To provide the essential concentrations for the reactions, researchers removed the water, thus driving the intermolecular reactions to form oligomers that resembled nucleic acids. The problem with condensation polymerization is obvious: any alcohol can compete for the reactive electrophilic site. In the case under consideration, researchers added no other alcohols. They were scrupulous, but the system was stacked. Condensation polymerization reactions need to be very pure, free of competing nucleophilic and electrophilic components. Witness the Carothers equation, which defines degrees of polymerization based upon monomer purity.8 If there happened to be amino acids or carbohydrates mixed with the nucleotides, they would terminate or interrupt the growth of the oligonucleotides. What is more, the researchers did not confirm the integrity of the structures they claimed to have derived. If carefully analyzed, these structures would likely have shown attacks from unintended hydroxyl sites. Since their sequences are essentially random, short oligonucleotides are not realistic precursors to RNA. An alphabet soup is not a precursor to a poem. The authors go on to suggest that the lamella sandwiching oligonucleotides eventually break off to form lipid bilayer vesicles. These contain the oligonucleotide-within-vesicle constructs, which they call protocells. The conversion of planar lamella into multilamellar vesicles as they hydrate is well established, but shearing forces are generally required to form the requisite lipid bilayer vesicle. For this reason, yields were likely to be low.9 It is hard to imagine finding highly purified homochiral nucleotides trapped in a pure lipid lamella on the prebiotic earth.

But set all that aside. These vesicles bear almost no resemblance to cellular lipid bilayers. Lipid bilayer balls are not cellular lipid bilayers. One would never know this from reading the authors’ account. “Then, in the gel phase,” they write, “protocells pack together in a system called a progenote and exchange sets of polymers, selecting those that enhance survival during many cycles.”10 Chemicals, of course, are indifferent to their survival. No mechanism is described to demonstrate how protocells would bear different sets of polymers or exchange polymers among them. Terms from biology have generally been misappropriated in a way that makes no chemical sense. This is not an isolated or incidental defect. It reappears when the authors write that “[t]he best-adapted protocells spread to other pools or streams, moving by wind and water…”11 Best-adapted? Microbial communities apparently “evolve into a primitive metabolism required by the earliest forms of life.” Molecules do not evolve, and nothing is being metabolized. Condensation polymerization is a simple chemical reaction based upon the addition of nucleophiles to electrophiles with loss of water. Such a reaction is never referred to as a form of metabolism within synthetic chemistry.

Terminology is one thing, non-sequiturs quite another. “After much trial and error,” the authors write, “one protocell assembles the complicated molecular machinery that enables it to divide into daughter cells. This paves the way for the first living microbial community.” How is the molecular machinery made? They do not say. The mechanisms needed for cellular division are complex, requiring cascades of precisely functioning enzymes. There is nothing between what the authors demonstrate and what they claim to have established, and nothing they propose “paves the way for the first living microbial community.”
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READ MORE HERE: Inference

Você não deve confiar em experimentos que afirmam a existência de universos paralelos

quarta-feira, julho 17, 2019

You Must Not Trust Experiments That Claim The Existence Of Parallel Universes

Ethan Siegel Contributor
Starts With A Bang Contributor Group Science 

The Universe is out there, waiting for you to discover it.
 

A representation of the different parallel "worlds" that might exist in other pockets of the multiverse, or anyplace else that theoretical physicists can concoct. Public domain

Is there another Universe out there? The Universe we know and inhabit, the one that began at the start of the hot Big Bang, might not be the only one out there. Perhaps one was created at the same time as ours was, but where time runs backwards instead of forwards. Perhaps there are an infinite number of parallel Universes out there, spawned by an eternally inflating Universe. Or, as has been in the media lately, perhaps there's literally a mirror Universe out there, where the particles we know of are replaced with an exotic version of themselves: mirror matter. 

Most scenarios involving parallel Universes like this are untestable, as we're restricted to living in our own Universe, disconnected from any others. Yet if one particular idea is right, there might be an experimental signature awaiting our investigations. But even if it yields positive results, you shouldn't trust it. Here's why. 

Whenever you have an experimental or observational result you cannot explain with your current theories, you have to take note of it. Robust measurements that defy the expectations of our predictions might turn out to be nothing — they might go away with more, improved data — or they might simply be errors. This has famously been the case many times, even recently, such as with
 
In all these cases, there was either an error with the way the team did the analysis or attributed the signal's components, an error in the experimental setup, or the observed effect was simply a random statistical fluctuation.
 
This happens. However, sometimes there are results that really do appear to be puzzles: the experiments shouldn't turn out the way they did if the Universe works the way we think it does. These results often turn out to be omens that we're about to discover new physics, but they also frequently turn out to be red herrings that lead nowhere. Even worse, they can turn out to be duds, where they only appear to be interesting because someone, somewhere, made an error.
...
 
READ MORE HERE: Forbes

Maquinaria de replicação de DNA capturada em detalhes a nível atômico: mero acaso, fortuita necessidade ou design inteligente?

segunda-feira, julho 15, 2019

DNA translocation mechanism of the MCM complex and implications for replication initiation

Martin Meagher, Leslie B. Epling & Eric J. Enemark 

Nature Communications volume 10, Article number: 3117 (2019) 

Fig. 8
Proposed MCM:DNA aspects of replication initiation. 

Abstract

The DNA translocation activity of the minichromosome maintenance (MCM) complex powers DNA strand separation of the replication forks of eukaryotes and archaea. Here we illustrate an atomic level mechanism for this activity with a crystal structure of an archaeal MCM hexamer bound to single-stranded DNA and nucleotide cofactors. Sequence conservation indicates this rotary mechanism is fully possible for all eukaryotes and archaea. The structure definitively demonstrates the ring orients during translocation with the N-terminal domain leading, indicating that the translocation activity could also provide the physical basis of replication initiation where a double-hexamer idly encircling double-stranded DNA transforms to single-hexamers that encircle only one strand. In this mechanism, each strand binds to the N-terminal tier of one hexamer and the AAA+ tier of the other hexamer such that one ring pulls on the other, aligning equivalent interfaces to enable each hexamer to pull its translocation strand outside of the opposing hexamer.

Principais etapas iniciais para a origem da vida ocorrem sob variedade de condições

terça-feira, julho 09, 2019

Nitrogen heterocycles form peptide nucleic acid precursors in complex prebiotic mixtures

Laura E. Rodriguez, Christopher H. House, Karen E. Smith, Melissa R. Roberts & Michael P. Callahan 

Scientific Reports volume 9, Article number: 9281 (2019)

Fig. 5: Nitrogen heterocycles form peptide nucleic acid precursors in complex prebiotic mixtures

Abstract

The ability to store information is believed to have been crucial for the origin and evolution of life; however, little is known about the genetic polymers relevant to abiogenesis. Nitrogen heterocycles (N-heterocycles) are plausible components of such polymers as they may have been readily available on early Earth and are the means by which the extant genetic macromolecules RNA and DNA store information. Here, we report the reactivity of numerous N-heterocycles in highly complex mixtures, which were generated using a Miller-Urey spark discharge apparatus with either a reducing or neutral atmosphere, to investigate how N-heterocycles are modified under plausible prebiotic conditions. High throughput mass spectrometry was used to identify N-heterocycle adducts. Additionally, tandem mass spectrometry and nuclear magnetic resonance spectroscopy were used to elucidate reaction pathways for select reactions. Remarkably, we found that the majority of N-heterocycles, including the canonical nucleobases, gain short carbonyl side chains in our complex mixtures via a Strecker-like synthesis or Michael addition. These types of N-heterocycle adducts are subunits of the proposed RNA precursor, peptide nucleic acids (PNAs). The ease with which these carbonylated heterocycles form under both reducing and neutral atmospheres is suggestive that PNAs could be prebiotically feasible on early Earth.

FREE PDF GRATIS: Scientific Reports Sup. Info.