Os limites da informação

sábado, abril 22, 2017

The Limits of Information 

Source/Fonte: HABBENINK (habbenink.com)
There is a long, winding, and vexing wrangle among philosophers on the nature and validity of our knowledge of the physical world. Take the example of color. A stroll through the garden reveals a busy bee extracting nectar from a yellow rose. I see the yellow rose owing to certain pigments in the cone receptors of my retina. In a normally sighted person, the neurochemistry of vision operates over a range of wavelengths from about 360 to 760 nanometers (nm) — roughly violet to a deep red. What English-speaking percipients describe as “yellow” is in the near vicinity of 580 nm, a little above the eye’s peak sensitivity. For the honey bee, matters are quite different. Its compound eyes are equipped with three types of retinal receptors — one for very short wavelengths (peaking at 344 nm, or ultraviolet), a medium-type (peaking at 436, or blue), and one for long wavelengths (peaking at 544, or green). Though we and the bee may share floral preferences — revealed in the bee’s foraging and in our table settings — the bee’s representation of the external world clearly includes features to which we are blind.

Were all sources of electromagnetic radiation to fall at wavelengths shorter than 340 nm, the affairs of the world would pass us unseen. (And eyes like ours wouldn’t work very well anyway, since excessive exposure to ultraviolent radiation renders the human lens increasingly opaque as a result of cataracts.) Our inability to see (or to endure) much ultraviolet radiation is a heavy price to pay for our eyesight, but it does protect the human retina from destruction by this same radiation. The moral of the tale so far is that creatures are fitted out for the world as given, and modes of adaptation come at a price.
Is this explanation of human perception no more than a poor glimpse into evolutionary forces? Here we face yet another of philosophy’s enduring engagements, to wit: What counts as an explanation, and what standard is to be applied in evaluating competing explanations?
Explaining the World

In 1814, Pierre-Simon Laplace presented his famous “demon,” as it has come to be known. Imagine a superior intelligence who, knowing the precise location and momentum of every atom in the universe, can account for the past and predict the future from the laws of classical mechanics. For this intelligence, Laplace wrote, “nothing would be uncertain and the future, as the past, would be present to its eyes.” To explain the nature of a thing or occurrence, by this way of thinking, would require that we know with certainty the physical processes at the smallest level, because they determine the events at any larger level.
But then, some two centuries after Laplace, comes Werner Heisenberg and quantum mechanics rendering uncertain any attempt to specify a particle’s position and momentum simultaneously. Of course, uncertainty at the quantum level may impose no barrier to determinism at the macro-level, but even this proposition raises questions regarding the nature of explanation and the level at which scientific explanations are of the right sort.
But why assume there is a fixed and right sort of explanation? Sometimes taken to be the “realist” position in the philosophical debate between realists and anti-realists, the idea that there is a right sort of explanation is predicated on a core of metaphysical precepts. Dominant these days among such ideas is physicalism, which takes physical events and objects to be the sole and ultimate furniture of reality. Explaining such events and objects then calls for what is finally a causal account. In principle, all that is really real, even all that we cannot yet observe, is subject to explanations located within a causally closed system — that is, one admitting only of physical causes.
In 1980, Bas van Fraassen published The Scientific Image in opposition to the prevailing belief that scientific theories offer a true and closed account of how things “really” are. His “constructive empiricism” limits the reach of science to what is observable. Accordingly, to endorse a scientific theory entails no more than the belief that the theory is empirically adequate, which does not require that we make any grand claims about the nature of reality. This is a more modest position, requiring only agnosticism in the matter of hidden variables and unseen processes. Allegedly complete systems are simply too grandiose for serious consideration.
In his later book The Empirical Stance (2002), van Fraassen argues for the rejection of metaphysics as foundational for science and, indeed, the rejection of “foundationalism” itself — “the project to construct all knowledge on a foundation that cannot be false, by a method that cannot introduce falsity.” A commitment to empirical adequacy can never satisfy the lust for indubitable certainties regarding reality. Whereas the scientific realist begins with metaphysical presuppositions that would have authority in the matter of relevant and irrelevant observations, the empirical stance puts one in a different position: that of an observer whose choice of observables is aimed at adequacy in accounts of how things are. This stance, on van Fraassen’s understanding, liberates one from the burden of futile gestures.

Formação de nucleobases em uma atmosfera redutora Miller-Urey - será???

quinta-feira, abril 20, 2017

Formation of nucleobases in a Miller–Urey reducing atmosphere

Martin Ferusa, Fabio Pietruccib, Antonino Marco Saittab, Antonín Knížeka,c, Petr Kubelíka, Ondřej Ivaneka, Violetta Shestivskaa, and Svatopluk Civiša,1

Author Affiliations

a J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, CZ18223 Prague 8, Czech Republic;

b Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, Université Pierre et Marie Curie, Sorbonne Universités, CNRS, Muséum National d’Histoire Naturelle, Institut de Recherche pour le Développement, UMR 7590, F-75005 Paris, France;

c Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, CZ12840 Prague 2, Czech Republic

Edited by Jerrold Meinwald, Cornell University, Ithaca, NY, and approved March 13, 2017 (received for review January 6, 2017)

Source/Fonte: https://media.giphy.com/media/APKV6mdZxThIs/giphy.gif



The study shows that Miller–Urey experiments produce RNA nucleobases in discharges and laser-driven plasma impact simulations carried out in a simple prototype of reducing atmosphere containing ammonia and carbon monoxide. We carried out a self-standing description of chemistry relevant to hypothesis of abiotic synthesis of RNA nucleobases related to early-Earth chemical evolution under reducing conditions. The research addresses the chemistry of simple-model reducing atmosphere (NH3 + CO + H2O) and the role of formamide as an intermediate of nucleobase formation in Miller–Urey experiment. The explorations combine experiments performed using modern techniques of large, high-power shock wave plasma generation by hall terawatt lasers, electric discharges, and state-of-the-art ab initio free-energy calculations.


The Miller–Urey experiments pioneered modern research on the molecular origins of life, but their actual relevance in this field was later questioned because the gas mixture used in their research is considered too reducing with respect to the most accepted hypotheses for the conditions on primordial Earth. In particular, the production of only amino acids has been taken as evidence of the limited relevance of the results. Here, we report an experimental work, combined with state-of-the-art computational methods, in which both electric discharge and laser-driven plasma impact simulations were carried out in a reducing atmosphere containing NH3 + CO. We show that RNA nucleobases are synthesized in these experiments, strongly supporting the possibility of the emergence of biologically relevant molecules in a reducing atmosphere. The reconstructed synthetic pathways indicate that small radicals and formamide play a crucial role, in agreement with a number of recent experimental and theoretical results.

life origins asteroid impact reducing atmosphere


1To whom correspondence should be addressed. Email: svatopluk.civis@jh-inst.cas.cz.

Author contributions: M.F., F.P., A.M.S., and S.C. designed research; M.F., A.K., O.I., and S.C. performed experimental research; F.P. and A.M.S. performed computer simulations; M.F., F.P., A.M.S., P.K., O.I., V.S., and S.C. analyzed data; and M.F., F.P., A.M.S., and S.C. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1700010114/-/DCSupplemental.


Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao site Portal de Periódicos CAPES/MEC podem ler gratuitamente este artigo do PNAS e de mais 33.000 publicações científicas.



Repare que eles transformaram a frase "laser-driven plasma impact simulations" em "we show that RNA nucleobases are synthesized in these experiments..." Uau! Simulações virtuais!
Será? Onde? Dentro do computador? Ou dentro do programa? Ou simplesmente dentro das bases de dados? As perguntas que devem ser feitas: Vocês podem nos dizer o estado racêmico dessas nucleobases simuladas? E quantos isômeros inativos se formaram comparados com as versões dos isômeros biologicamente ativos? Dá para ficar rico vendendo esse material para outros químicos?
Se um computador esteve envolvido, então tudo é VIRTUAL. Pelas barbas de Darwin, não poluam a literatura científica com dados vituais.

Explorando a química da armazenagem e propagação da informação genética através da engenharia da polimerase: design inteligente!

Exploring the Chemistry of Genetic Information Storage and Propagation through Polymerase Engineering

Gillian Houlihan, Sebastian Arangundy-Franklin, and Philipp Holliger* 

MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K.

Acc. Chem. Res., 2017, 50 (4), pp 1079–1087

Publication Date (Web): April 6, 2017

Copyright © 2017 American Chemical Society

*Philipp Holliger. E-mail: ph1@mrc-lmb.cam.ac.uk.



Nucleic acids are a distinct form of sequence-defined biopolymer. What sets them apart from other biopolymers such as polypeptides or polysaccharides is their unique capacity to encode, store, and propagate genetic information (molecular heredity). In nature, just two closely related nucleic acids, DNA and RNA, function as repositories and carriers of genetic information. They therefore are the molecular embodiment of biological information. This naturally leads to questions regarding the degree of variation from this seemingly ideal “Goldilocks” chemistry that would still be compatible with the fundamental property of molecular heredity.

To address this question, chemists have created a panoply of synthetic nucleic acids comprising unnatural sugar ring congeners, backbone linkages, and nucleobases in order to establish the molecular parameters for encoding genetic information and its emergence at the origin of life. A deeper analysis of the potential of these synthetic genetic polymers for molecular heredity requires a means of replication and a determination of the fidelity of information transfer. While non-enzymatic synthesis is an increasingly powerful method, it currently remains restricted to short polymers. Here we discuss efforts toward establishing enzymatic synthesis, replication, and evolution of synthetic genetic polymers through the engineering of polymerase enzymes found in nature.

To endow natural polymerases with the ability to efficiently utilize non-cognate nucleotide substrates, novel strategies for the screening and directed evolution of polymerase function have been realized. High throughput plate-based screens, phage display, and water-in-oil emulsion technology based methods have yielded a number of engineered polymerases, some of which can synthesize and reverse transcribe synthetic genetic polymers with good efficiency and fidelity.

The inception of such polymerases demonstrates that, at a basic level at least, molecular heredity is not restricted to the natural nucleic acids DNA and RNA, but may be found in a large (if finite) number of synthetic genetic polymers. And it has opened up these novel sequence spaces for investigation. Although largely unexplored, first tentative forays have yielded ligands (aptamers) against a range of targets and several catalysts elaborated in a range of different chemistries. Finally, taking the lead from established DNA designs, simple polyhedron nanostructures have been described.

We anticipate that further progress in this area will expand the range of synthetic genetic polymers that can be synthesized, replicated, and evolved providing access to a rich sequence, structure, and phenotypic space. “Synthetic genetics”, that is, the exploration of these spaces, will illuminate the chemical parameter range for en- and decoding information, 3D folding, and catalysis and yield novel ligands, catalysts, and nanostructures and devices for applications in biotechnology and medicine.

A arma secreta do DNA contra nós e emaranhados: mero acaso, fortuita necessidade ou design inteligente?

DNA's secret weapon against knots and tangles

A simple process seems to explain how massive genomes stay organized. But no one can agree on what powers it.

Elie Dolgin
19 April 2017

Leonid Mirny swivels in his office chair and grabs the power cord for his laptop. He practically bounces in his seat as he threads the cable through his fingers, creating a doughnut-sized loop. “It's a dynamic process of motors constantly extruding loops!” says Mirny, a biophysicist here at the Massachusetts Institute of Technology in Cambridge.
Mirny's excitement isn't about keeping computer accessories orderly. Rather, he's talking about a central organizing principle of the genome — how roughly 2 metres of DNA can be squeezed into nearly every cell of the human body without getting tangled up like last year's Christmas lights.
He argues that DNA is constantly being slipped through ring-like motor proteins to make loops. This process, called loop extrusion, helps to keep local regions of DNA together, disentangling them from other parts of the genome and even giving shape and structure to the chromosomes.
Scientists have bandied about similar hypotheses for decades, but Mirny's model, and a similar one championed by Erez Lieberman Aiden, a geneticist at Baylor College of Medicine in Houston, Texas, add a new level of molecular detail at a time of explosive growth for research into the 3D structure of the genome. The models neatly explain the data flowing from high-profile projects on how different parts of the genome interact physically — which is why they've garnered so much attention.
But these simple explanations are not without controversy. Although it has become increasingly clear that genome looping regulates gene expression, possibly contributing to cell development and diseases such as cancer, the predictions of the models go beyond what anyone has ever seen experimentally.
For one thing, the identity of the molecular machine that forms the loops remains a mystery. If the leading protein candidate acted like a motor, as Mirny proposes, it would guzzle energy faster than it has ever been seen to do. “As a physicist friend of mine tells me, 'This is kind of the Higgs boson of your field',” says Mirny; it explains one of the deepest mysteries of genome biology, but could take years to prove.
And although Mirny's model is extremely similar to Lieberman Aiden's — and the differences esoteric — sorting out which is right is more than a matter of tying up loose ends. If Mirny is correct, “it's a complete revolution in DNA enzymology”, says Kim Nasmyth, a leading chromosome researcher at the University of Oxford, UK. What's actually powering the loop formation, he adds, “has got to be the biggest problem in genome biology right now”.

A SBPC apoia a Marcha da Ciência: um apoio à conformidade de pensamento - pobre Ciência!!!

quarta-feira, abril 19, 2017

The March for Science is Really a March for Conformity

By JONATHAN WELLS Published on April 18, 2017 • 34 Comments

I am a scientist, but I won’t be joining the worldwide March for Science April 22. That’s because it’s really a march for something that undermines good science.

March organizers say “our diversity is our greatest strength.” They say “a wealth of opinions, perspectives, and ideas is critical for the scientific process.” But they don’t really mean it. Their passion for diversity extends to race, religion, nationality, gender and sexual orientation, but not to opinions, perspectives and ideas.

In particular, it doesn’t extend to diversity of opinion about two controversial ideas. The first idea is that you evolved from ape-like ancestors by unguided processes such as accidental mutation and natural selection. The second idea is that manmade global warming threatens civilization, and our government must take drastic action to stop it, even if that means wrecking the economy.

Skeptics of the first idea are labeled “creationists.” Often, they are expelled from science altogether. And if global warming alarmists have their way, skeptics of the second idea may soon be criminally prosecuted.

Note the hypocrisy. Organizers describe the march as “a call to support and safeguard the scientific community.” But then they silence and expel those who won’t bow to the community’s majority opinion — the “scientific consensus.”

History should teach us to be wary of consensus. In 1750, the scientific consensus held that maggots are generated spontaneously in rotting garbage. In 1900, it held that atoms consist of electrons orbiting a nucleus like planets around the sun. In 1910, it held that the continents had never moved. In 1940, it held that protein, not DNA, is the stuff of heredity.

All of these views turned out to be wrong. And the history of science is full of other such cases.

The Message of the March: Ignore the Evidence and Trust Us

Some of our newly elected politicians refuse to bow to the scientific consensus on evolution and global warming. So defenders of the consensus are marching to pressure them to submit.

The American Association for the Advancement of Science (AAAS) is a big supporter of the march. So is the National Center for Science Education (NCSE).

The AAAS vigorously defends evolution. The NCSE insists “there is no scientific debate” over evolution. And they strongly oppose criticisms of it. They were in classic form last month in Indiana. The Indiana Senate had resolved that students should be “informed” about “scientific evidence” regarding evolution and develop “critical thinking skills.” The NCSE called this language “antiscience.” Why? It might lead students to raise uncomfortable questions about the evidence for evolution.

As a biologist I know there is a scientific debate over the evidence for evolution. There are dissenters. And some are willing to speak out publicly even though doing so may threaten their careers.

The reason for the dissent is simple. The evidence does not support Darwinian evolution. Mutation and natural selection have never been observed to produce anything more than minor changes within existing species.

In place of evidence-based science, Darwin and his followers have relied on materialistic philosophy. That philosophy says only matter and physical forces are real. It says mind, spirit, free will, God and intelligent design are illusions.

In 1859, Darwin wrote that he “would give absolutely nothing” for his theory if it required “miraculous additions at any one stage of descent.” He allowed only unguided natural processes. In other words, Darwinism is materialistic.

For many in the nineteenth century, this was its most attractive feature. As Historian Neal Gillespie explained, “It was more Darwin’s insistence on totally natural explanations than on natural selection that won their adherence.”

As a scientist, I am bothered by this. Science is supposed to seek truth by testing hypotheses against the evidence. But evolution is materialistic story-telling. And the story persists even when the evidence contradicts it. I call this “zombie science,” and I describe many examples of it in my book of the same name. I’ll mention just one here. Students are shown drawings of some embryos of animals with backbones. In the drawings, all the embryos look similar in their earliest stages. Darwin believed this showed that we evolved from fish. But the story is false. Worse, mainstream biologists have long known that the drawings are false. They know that human and fish embryos look very different in their early stages. But many textbooks recycle the lie year after year anyway. Why? Because the materialistic story must be true.

The Sky is Falling

The Union of Concerned Scientists (UCS) is a big supporter of the March for Science. The UCS started as a leftist political movement in the 1960s, and it still champions various progressive causes. One of these is environmental activism. According to the UCS, “an overwhelming majority of climate scientists” believe in manmade global warming. More than that, “there is no debate” among scientists over global warming. None. Nada.

The AAAS and NCSE are also determined to enforce the consensus on global warming.

But there is a scientific debate over manmade global warming. Some climate scientists think the evidence does not support the consensus. The way to address the question is to debate the issue. It’s to weigh the evidence pro and con. Yet the UCS would silence dissenting scientists.

What really matters in science is not an opinion poll. It is the evidence. And some scientists argue persuasively that the evidence does not support Darwinian evolution or manmade global warming.

So the March for Science is not really about “evidence-based policies.” It is about enforcing the scientific consensus. It is about materialistic philosophy and progressive politics. And you’d better believe it!

Jonathan Wells, Ph.D. is a senior fellow of Discover Institute’s Center for Science and Culture. He’s the author of Icons of Evolution, The Politically Incorrect Guide to Evolution and Intelligent Design, and the new book Zombie Science: More Icons of Evolution.

Source/Fonte: The Stream


A SBPC apoia essa marcha de conformidade de pensamento - Síndrome de Soldadinhos de Chumbo, onde todo o mundo pensa a mesma coisa e ninguém pensa em mais nada. Pobre ciência tupiniquim!!!

Unpaywall: leia gratuitamente alguns artigos científicos

quinta-feira, abril 13, 2017

Instale a extensão do Unpaywall nos browsers Chrome e Firefox, e leia gratuitamente alguns artigos científicos.

Nature dando espaço para o estruturalismo? Edição especial sobre o livro On Growth and Form, de D'Arcy Thompson.

The 100-year-old challenge to Darwin that is still making waves in research

On Growth and Form showed how physical and mathematical forces affect natural selection.

12 April 2017

Source/Fonte: Wild Horizons/UIG via Getty

The shape of this chambered nautilus is one of many biological features that D’Arcy Thompson used maths to explain.

This year marks the centenary of what seems now to be an extraordinary event in publishing: the time when a UK local newspaper reviewed a dense, nearly 800-page treatise on mathematical biology that sought to place physical constraints on the processes of Darwinism.

And what’s more, the Dundee Advertiser loved the book and recommended it to readers. When the author, it noted, wrote of maths, “he never fails to translate his mathematics into English; and he is one of the relatively few men of science who can write in flawless English and who never grudge the effort to make every sentence balanced and good.”

The Dundee Advertiser is still going, although it has changed identity: a decade after the review was published, it merged with The Courier, and that is how most people refer to it today. The book is still going, too. If anything, its title — alongside its balanced and good sentences — has become more iconic and recognized as the years have ticked by.

The book is On Growth and Form by D’Arcy Thompson. This week, Nature offers its own appreciation, with a series of articles in print and online that celebrate the book’s impact, ideas and lasting legacy.


"Testando" a teoria do multiverso: Bayes, ajuste fino e tipicidade.

Testing the Multiverse: Bayes, Fine-Tuning and Typicality

(Submitted on 6 Apr 2017)

Theory testing in the physical sciences has been revolutionized in recent decades by Bayesian approaches to probability theory. Here, I will consider Bayesian approaches to theory extensions, that is, theories like inflation which aim to provide a deeper explanation for some aspect of our models (in this case, the standard model of cosmology) that seem unnatural or fine-tuned. In particular, I will consider how cosmologists can test the multiverse using observations of this universe.

Comments: 19 pages, 3 figures. Conference proceedings: to appear in "The Philosophy of Cosmology", edited by Khalil Chamcham, Joseph Silk, John D. Barrow, and Simon Saunders. Cambridge University Press, 2017

Subjects: Cosmology and Nongalactic Astrophysics (astro-ph.CO); History and Philosophy of Physics (physics.hist-ph)

Cite as: arXiv:1704.01680 [astro-ph.CO]

(or arXiv:1704.01680v1 [astro-ph.CO] for this version)

Submission history

From: Luke Barnes [view email

[v1] Thu, 6 Apr 2017 01:35:35 GMT (283kb,D)


Descoberta a sexta base do DNA? Será? Nada mais a respeito?

quarta-feira, abril 12, 2017

An Adenine Code for DNA: A Second Life for N6-Methyladenine

Holger Heyn, Manel Esteller 

Published Online: April 30, 2015

Open Archive

Article Info

Publication History

Published online: April 30, 2015


DNA N6-methyladenine (6mA) protects against restriction enzymes in bacteria. However, isolated reports have suggested additional activities and its presence in other organisms, such as unicellular eukaryotes. New data now find that 6mA may have a gene regulatory function in green alga, worm, and fly, suggesting m6A as a potential “epigenetic” mark.


Sistematizando as doze virtudes teóricas

terça-feira, abril 11, 2017


pp 1–33

Systematizing the theoretical virtues


Authors and affiliations

Michael N. Keas1

Email author

View author's OrcID profile

1.History and Philosophy of Science, Faculty of HumanitiesThe College at SouthwesternFort WorthUSA

Open Access Article

First Online: 10 March 2017

Cite this article as:

Keas, M.N. Synthese (2017). doi:10.1007/s11229-017-1355-6

Source/Fonte: Adaptive Landscapes, via http://adaptive-landscapes.org/


There are at least twelve major virtues of good theories: evidential accuracy, causal adequacy, explanatory depth, internal consistency, internal coherence, universal coherence, beauty, simplicity, unification, durability, fruitfulness, and applicability. These virtues are best classified into four classes: evidential, coherential, aesthetic, and diachronic. Each virtue class contains at least three virtues that sequentially follow a repeating pattern of progressive disclosure and expansion. Systematizing the theoretical virtues in this manner clarifies each virtue and suggests how they might have a coordinated and cumulative role in theory formation and evaluation across the disciplines—with allowance for discipline specific modification. An informal and flexible logic of theory choice is in the making here. Evidential accuracy (empirical fit), according to my systematization, is not a largely isolated trait of good theories, as some (realists and antirealists) have made it out to be. Rather, it bears multifaceted relationships, constituting significant epistemic entanglements, with other theoretical virtues.


Theoretical virtues Inference to the best explanation Epistemic value Aesthetics Prediction Science–technology relations


Máquinas moleculares construídas pelo homem: se o design na natureza é ilusão, por que correr atrás do vento???

DOI: 10.1039/C5CS00874C (Tutorial Review) Chem. Soc. Rev., 2016, 45, 6118-6129

Man-made molecular machines: membrane bound

Matthew A. Watson and Scott L. Cockroft * 

EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh, EH9 3FJ, UK. E-mail: scott.cockroft@ed.ac.uk

Received 25th November 2015

First published on the web 2nd March 2016


Nature's molecular machines are a constant source of inspiration to the chemist. Many of these molecular machines function within lipid membranes, allowing them to exploit potential gradients between spatially close, but chemically distinct environments to fuel their work cycle. Indeed, the realisation of such principles in synthetic transmembrane systems remains a tantalising goal. This tutorial review opens by highlighting seminal examples of synthetic molecular machines. We illustrate the importance of surfaces for facilitating the extraction of work from molecular switches and motors. We chart the development of man-made transmembrane systems; from passive to machine-like stimuli-responsive channels, to fully autonomous transmembrane molecular machines. Finally, we highlight higher-order compartmentalised systems that exhibit emergent properties. We suggest that such higher-order architectures could serve as platforms for sophisticated devices that co-ordinate the activity of numerous transmembrane molecular machines.

Key learning points

(1) Illustrative examples of natural transmembrane molecular machines.

(2) The conceptual basis of molecular machines, categorisation of machine behaviour.

(3) The state of the art of synthetic molecular machines operating in solution and at interfaces.

(4) The progress towards and the future of man-made transmembrane molecular machines.


Cada vez mais complexidade em máquinas moleculares: mero acaso, fortuita necessidade ou design inteligente?

Controlling Motion at the Nanoscale: Rise of the Molecular Machines

John M. Abendroth†, Oleksandr S. Bushuyev‡, Paul S. Weiss*†§, and Christopher J. Barrett*†‡

† California NanoSystems Institute and Department of Chemistry & Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, United States

‡ Department of Chemistry, McGill University, Montreal, QC, Canada

§ Department of Materials Science & Engineering, University of California, Los Angeles, Los Angeles, California 90095, United States

ACS Nano, 2015, 9 (8), pp 7746–7768

Publication Date (Web): July 14, 2015

Copyright © 2015 American Chemical Society

*Address correspondence to psw@cnsi.ucla.edu, christopher.barrett@mcgill.ca.

ACS Editors' Choice - This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes.


As our understanding and control of intra- and intermolecular interactions evolve, ever more complex molecular systems are synthesized and assembled that are capable of performing work or completing sophisticated tasks at the molecular scale. Commonly referred to as molecular machines, these dynamic systems comprise an astonishingly diverse class of motifs and are designed to respond to a plethora of actuation stimuli. In this Review, we outline the conditions that distinguish simple switches and rotors from machines and draw from a variety of fields to highlight some of the most exciting recent examples of opportunities for driven molecular mechanics. Emphasis is placed on the need for controllable and hierarchical assembly of these molecular components to display measurable effects at the micro-, meso-, and macroscales. As in Nature, this strategy will lead to dramatic amplification of the work performed via the collective action of many machines organized in linear chains, on functionalized surfaces, or in three-dimensional assemblies.


amphidynamic crystals; azobenzene; DNA nanotechnology; hierarchical assembly; mechanically interlocked molecules; molecular machines; molecular switches; photomechanical crystals; rotors and motors; thermo/photosalient crystals


Contrariando a teoria da evolução de Darwin, os polvos, as lulas e os chocos desafiam o "dogma central" da genética editando seus proteomas!

segunda-feira, abril 10, 2017

Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods

Noa Liscovitch-Brauer, Shahar Alon, Hagit T. Porath, Boaz Elstein, Ron Unger, Tamar Ziv, Arie Admon, Erez Y. Levanon, Joshua J.C. Rosenthal 8, Eli Eisenberg.

8Lead Contact

Publication History

Published: April 6, 2017 Accepted: March 16, 2017

Received in revised form: February 2, 2017 Received: December 5, 2016

Source/Fonte: Tom Kleindinst


• Unlike other taxa, cephalopods diversify their proteomes extensively by RNA editing

• Extensive recoding is specific to the behaviorally complex coleiods

• Unlike mammals, cephalopod recoding is evolutionarily conserved and often adaptive

• Transcriptome diversification comes at the expense of slowed-down genome evolution


RNA editing, a post-transcriptional process, allows the diversification of proteomes beyond the genomic blueprint; however it is infrequently used among animals for this purpose. Recent reports suggesting increased levels of RNA editing in squids thus raise the question of the nature and effects of these events. We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites. Editing is enriched in the nervous system, affecting molecules pertinent for excitability and neuronal morphology. The genomic sequence flanking editing sites is highly conserved, suggesting that the process confers a selective advantage. Due to the large number of sites, the surrounding conservation greatly reduces the number of mutations and genomic polymorphisms in protein-coding regions. This trade-off between genome evolution and transcriptome plasticity highlights the importance of RNA recoding as a strategy for diversifying proteins, particularly those associated with neural function.


O Ovatiovermis cribratus, um lobopodiano do período Cambriano, não tinha uma carapaça protetora dura

Cambrian suspension-feeding lobopodians and the early radiation of panarthropods

Jean-Bernard CaronEmail authorView ORCID ID profile and Cédric Aria

BMC Evolutionary Biology BMC series – open, inclusive and trusted 201717:29

DOI: 10.1186/s12862-016-0858-y © The Author(s). 2017 

Received: 26 May 2016 Accepted: 17 December 2016Published: 31 January 2017

Source/Fonte: Lars Fields, Phlesch Bubble Productions © Royal Ontario Museum



Arthropoda, Tardigrada and Onychophora evolved from lobopodians, a paraphyletic group of disparate Palaeozoic vermiform animals with soft legs. Although the morphological diversity that this group encompasses likely illustrates the importance of niche diversification in the early radiation of panarthropods, the ecology of lobopodians remains poorly characterized.


Here we describe a new luolishaniid taxon from the middle Cambrian Burgess Shale (Walcott Quarry) in British Columbia, Canada, whose specialized morphology epitomizes the suspension-feeding ecology of this clade, and is convergent with some modern marine animals, such as caprellid crustaceans. This species possesses two long pairs and four shorter pairs of elongate spinose lobopods at the front, each bearing two slender claws, and three pairs of stout lobopods bearing single, strong, hook-like anterior-facing claws at the back. The trunk is remarkably bare, widening rearwards, and, at the front, extends beyond the first pair of lobopods into a small “head” bearing a pair of visual organs and a short proboscis with numerous teeth. Based on a critical reappraisal of character coding in lobopodians and using Bayesian and parsimony-based tree searches, two alternative scenarios for early panarthropod evolution are retrieved. In both cases, hallucigeniids and luolishaniids are found to be extinct radiative stem group panarthropods, in contrast to previous analyses supporting a position of hallucigeniids as part of total-group Onychophora. Our Bayesian topology finds luolishaniids and hallucigeniids to form two successive clades at the base of Panarthropoda. Disparity analyses suggest that luolishaniids, hallucigeniids and total-group Onychophora each occupy a distinct region of morphospace.


Hallucigeniids and luolishaniids were comparably diverse and successful, representing two major lobopodian clades in the early Palaeozoic, and both evolved body plans adapted to different forms of suspension feeding. A Bayesian approach to cladistics supports the view that a semi-sessile, suspension-feeding lifestyle characterized the origin and rise of Panarthropoda from cycloneuralian body plans.


Onychophora Velvet worm Cambrian evolutionary radiation Stem-group Disparity

FREE PDF GRATIS: BMC Evolutionary Biology

StudySwap: plataforma online objetiva facilitar a replicação de pesquisas

StudySwap: A platform for interlab replication, collaboration, and research resource exchange.

Nós topológicos e links em proteínas: mero acaso, fortuita necessidade ou design inteligente?

sábado, abril 08, 2017

Topological knots and links in proteins

Pawel Dabrowski-Tumanski a,b and Joanna I. Sulkowska a,b,1  

Author Affiliations

aFaculty of Chemistry, University of Warsaw, 02-093, Warsaw, Poland;

bCentre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland

Edited by George H. Lorimer, University of Maryland, College Park, MD, and approved February 1, 2017 (received for review September 23, 2016)


Twenty years after a discovery of knotted proteins, we found that some single-protein chains can form links, which have even more complex structures than knots. We derive conditions that proteins need to meet to form links. We search through the entire Protein Data Bank and identify several chains that form a Hopf link and a Solomon link. The link motif has not been recognized before; however, it is clearly of important functional significance in proteins. In this article, we relate topological properties of proteins with links to their function and stability and show that the link topology is characteristic of eukaryotes only.


Twenty years after their discovery, knots in proteins are now quite well understood. They are believed to be functionally advantageous and provide extra stability to protein chains. In this work, we go one step further and search for links—entangled structures, more complex than knots, which consist of several components. We derive conditions that proteins need to meet to be able to form links. We search through the entire Protein Data Bank and identify several sequentially nonhomologous chains that form a Hopf link and a Solomon link. We relate topological properties of these proteins to their function and stability and show that the link topology is characteristic of eukaryotes only. We also explain how the presence of links affects the folding pathways of proteins. Finally, we define necessary conditions to form Borromean rings in proteins and show that no structure in the Protein Data Bank forms a link of this type.

folding catenanes slipknot lasso disulphide bridge


1To whom correspondence should be addressed. Email: jsulkowska@chem.uw.edu.pl.

Author contributions: P.D.-T. and J.I.S. designed research; P.D.-T. performed research; P.D.-T. and J.I.S. analyzed data; and P.D.-T. and J.I.S. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1615862114/-/DCSupplemental.

Freely available online through the PNAS open access option.


Usando a biologia sintética para explorar princípios de desenvolvimento

sexta-feira, abril 07, 2017

Using synthetic biology to explore principles of development

Jamie Davies

Development 2017 144: 1146-1158; doi: 10.1242/dev.144196


Developmental biology is mainly analytical: researchers study embryos, suggest hypotheses and test them through experimental perturbation. From the results of many experiments, the community distils the principles thought to underlie embryogenesis. Verifying these principles, however, is a challenge. One promising approach is to use synthetic biology techniques to engineer simple genetic or cellular systems that follow these principles and to see whether they perform as expected. As I review here, this approach has already been used to test ideas of patterning, differentiation and morphogenesis. It is also being applied to evo-devo studies to explore alternative mechanisms of development and ‘roads not taken’ by natural evolution.

FREE PDF GRATIS: Development