The Virtual Human Embryo Project: morfologia embrionária digitalmente reproduzida

quarta-feira, setembro 20, 2017

The Virtual Human Embryo

Welcome to The Virtual Human Embryo (VHE), a 14,250-page, illustrated atlas of human embryology, which presents all 23 Carnegie Stages of development during the 8-week embryonic period.

This $3.2 million, 11-year initiative engaged a team led by Dr. Raymond F. Gasser—one of the leading embryologists of the last half century. His team created thousands of restored, digitized, and labeled serial sections from the world's largest collection of preserved human embryos. They used these serial sections to create animations, fly-throughs, and 3-D reconstructions.

The VHE is now available to researchers, educators, and students everywhere. Read More...

Abordando as questões éticas levantadas pelas entidades sintéticas humanas com características tipo embrião

Addressing the ethical issues raised by synthetic human entities with embryo-like features

John Aach, Jeantine Lunshof Eswar Iyer George M Church

Harvard Medical School, United States University of Groningen, The Netherlands



The "14-day rule" for embryo research stipulates that experiments with intact human embryos must not allow them to develop beyond 14 days or the appearance of the primitive streak. However, recent experiments showing that suitably cultured human pluripotent stem cells can self-organize and recapitulate embryonic features have highlighted difficulties with the 14-day rule and led to calls for its reassessment. Here we argue that these and related experiments raise more foundational issues that cannot be fixed by adjusting the 14-day rule, because the framework underlying the rule cannot adequately describe the ways by which synthetic human entities with embryo-like features (SHEEFs) might develop morally concerning features through altered forms of development. We propose that limits on research with SHEEFs be based as directly as possible on the generation of such features, and recommend that the research and bioethics communities lead a wide-ranging inquiry aimed at mapping out solutions to the ethical problems raised by them.

FREE PDF GRATIS: eLIFE Correction/Correção

A história inicial dos Neandertais e Denisovans

Early history of Neanderthals and Denisovans

Alan R. Rogers a,1, Ryan J. Bohlender b, and Chad D. Huff b ReadCube 

Author Affiliations

a Department of Anthropology, University of Utah, Salt Lake City, UT 84112;

b Department of Epidemiology, MD Anderson Cancer Center, Houston, TX 77030

Edited by Richard G. Klein, Stanford University, Stanford, CA, and approved July 7, 2017 (received for review April 18, 2017)

Source/Fonte: New Scientist


Neanderthals and Denisovans were human populations that separated from the modern lineage early in the Middle Pleistocene. Many modern humans carry DNA derived from these archaic populations by interbreeding during the Late Pleistocene. We develop a statistical method to study the early history of these archaic populations. We show that the archaic lineage was very small during the 10,000 y that followed its separation from the modern lineage. It then split into two regional populations, the Neanderthals and the Denisovans. The Neanderthal population grew large and separated into largely isolated local groups.


Extensive DNA sequence data have made it possible to reconstruct human evolutionary history in unprecedented detail. We introduce a method to study the past several hundred thousand years. Our results show that (i) the Neanderthal–Denisovan lineage declined to a small size just after separating from the modern lineage, (ii) Neanderthals and Denisovans separated soon thereafter, and (iii) the subsequent Neanderthal population was large and deeply subdivided. They also (iv) support previous estimates of gene flow from Neanderthals into modern Eurasians. These results suggest an archaic human diaspora early in the Middle Pleistocene.

human evolution archaic admixture introgression Neanderthals Denisovans


1To whom correspondence should be addressed. Email:

Author contributions: A.R.R. and C.D.H. designed research; A.R.R. and R.J.B. performed research; A.R.R. and R.J.B. analyzed data; and A.R.R. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

See Commentary on page 9761.

This article contains supporting information online at

Freely available online through the PNAS open access option.


60 anos do dogma central da biologia

terça-feira, setembro 19, 2017

60 years ago, Francis Crick changed the logic of biology

Matthew Cobb 

Published: September 18, 2017


In September 1957, Francis Crick gave a lecture in which he outlined key ideas about gene function, in particular what he called the central dogma. These ideas still frame how we understand life. This essay explores the concepts he developed in this influential lecture, including his prediction that we would study evolution by comparing sequences.

Citation: Cobb M (2017) 60 years ago, Francis Crick changed the logic of biology. PLoS Biol 15(9): e2003243.

Published: September 18, 2017

Copyright: © 2017 Matthew Cobb. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding: Cold Spring Harbor Laboratory Sydney Brenner Research Scholarship. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Provenance: Not commissioned; externally peer reviewed.


O status epistêmico da teoria evolucionária

The Epistemic Status of Evolutionary Theory

Gijsbert van den Brink, Jeroen de Ridder & René van Woudenberg

Pages 1-19 | Published online: 18 Sep 2017

Source/Fonte: Internet image


The theory of evolution continues to be a bone of contention among certain groups of theistic believers. This paper aims to bring some light to the debate about it, by introducing a framework for epistemic appraisal which can provide a realistic and sober assessment of the epistemic credentials of the various parts of evolutionary theory. The upshot is a more nuanced epistemic appraisal of the theory of evolution, which shows that there are significant differences in epistemic standing between its various parts. Any serious conversation about the theory of evolution ought to reflect these facts.

KEYWORDS: Evolution, epistemic status, creationism, scientific theory, ancient earth, common ancestry

FREE PDF GRATIS: Theology and Science

John Stuart Mill 'falou e disse': conhecer todo o assunto requer ouvir o que outros têm a dizer

segunda-feira, setembro 18, 2017

“A única maneira pela qual um ser humano pode fazer alguma abordagem em conhecer todo o assunto, é ouvir o que pode ser dito por pessoas de toda a variedade de opinião e estudar todos os modos nos quais pode ser observado por cada caráter de mente. Nenhum homem sábio jamais adquiriu sua sabedoria de qualquer modo, a não ser isso; nem está na natureza do intelecto humano se tornar sábio de qualquer outra maneira.”

the only way in which a human being can make some approach to knowing the whole of a subject, is by hearing what can be said about it by persons of every variety of opinion, and studying all modes in which it can be looked at by every character of mind. No wise man ever acquired his wisdom in any mode but this; nor is it in the nature of human intellect to become wise in any other manner.”

― John Stuart Mill, On Liberty Source/Fonte 

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De onde vêm as células do coração?

sábado, setembro 16, 2017

Id genes are essential for early heart formation

Thomas J. Cunningham1,10, Michael S. Yu1,2,10, Wesley L. McKeithan1,3,4,10, Sean Spiering1, Florent Carrette1, Chun-Teng Huang1, Paul J. Bushway2, Matthew Tierney1, Sonia Albini1, Mauro Giacca5, Miguel Mano6, Pier Lorenzo Puri1,7, Alessandra Sacco1, Pilar Ruiz-Lozano1,8, Jean-Francois Riou9, Muriel Umbhauer9, Gregg Duester1, Mark Mercola1,4,11 and Alexandre R. Colas1,11

- Author Affiliations

1Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, 92037, USA;

2Department of Bioengineering, University of California at San Diego, La Jolla, California 92037, USA;

3Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, USA;

4Department of Medicine and Cardiovascular Institute, Stanford University, Palo Alto, California 94305, USA;

5International Centre for Genetic Engineering and Biotechnology, 34149 Trieste, Italy;

6Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal;

7Istituti di Ricovero e Cura a Carattere Scientifico, Fondazione Santa Lucia, 00179 Rome, Italy;

8Regencor, Inc., Los Altos, California 94022, USA;

9UMR 7622 Developmental Biology, Sorbonne Universités, University Pierre and Marie Curie, F- 75005 Paris, France

Corresponding author:

↵10 These authors contributed equally to this work.

↵11 These authors contributed equally to this work.


Deciphering the fundamental mechanisms controlling cardiac specification is critical for our understanding of how heart formation is initiated during embryonic development and for applying stem cell biology to regenerative medicine and disease modeling. Using systematic and unbiased functional screening approaches, we discovered that the Id family of helix–loop–helix proteins is both necessary and sufficient to direct cardiac mesoderm formation in frog embryos and human embryonic stem cells. Mechanistically, Id proteins specify cardiac cell fate by repressing two inhibitors of cardiogenic mesoderm formation—Tcf3 and Foxa2—and activating inducers Evx1, Grrp1, and Mesp1. Most importantly, CRISPR/Cas9-mediated ablation of the entire Id (Id1–4) family in mouse embryos leads to failure of anterior cardiac progenitor specification and the development of heartless embryos. Thus, Id proteins play a central and evolutionarily conserved role during heart formation and provide a novel means to efficiently produce cardiovascular progenitors for regenerative medicine and drug discovery applications.


cardiac progenitors cardiac mesoderm specification heartless Id proteins CRISPR/Cas9-mediated quadruple knockout platform for cardiac disease modeling and drug discovery


Supplemental material is available for this article.

Article published online ahead of print. Article and publication date are online at

Freely available online through the Genes & Development Open Access option.

Received April 12, 2017. Accepted July 17, 2017.

© 2017 Cunningham et al.; Published by Cold Spring Harbor Laboratory Press

This article, published in Genes & Development, is available under a Creative Commons License (Attribution 4.0 International), as described at

FREE PDF GRATIS: Genes & Development [7.8 MBs] 

Modelo do sistema imunológico humano de cobaia humanizada inadequado para pesquisas de células-tronco

Alloimmune Responses of Humanized Mice to Human Pluripotent Stem Cell Therapeutics

Nigel G. Kooreman9, Patricia E. de Almeida9, Jonathan P. Stack9, Raman V. Nelakanti, Sebastian Diecke, Ning-Yi Shao, Rutger-Jan Swijnenburg, Veronica Sanchez-Freire, Elena Matsa, Chun Liu, Andrew J. Connolly, Jaap F. Hamming, Paul H.A. Quax, Michael A. Brehm, Dale L. Greiner, Dale L. Greiner, Leonard D. Shultz, Joseph C. Wu10. 

9These authors contributed equally

10Lead Contact

Open access funded by Bloodwise

Article Info

Publication History

Published: August 22, 2017 Accepted: July 26, 2017

Received in revised form: April 23, 2017 Received: July 9, 2015

User License

Creative Commons Attribution (CC BY 4.0)


• Innate immunity is crucial in rejection of minor HA mismatched grafts

• Stem cell alloimmune responses modeled with an “allogenized mouse”

• Humanized mice are unable to fully model immune responses to stem cell allografts

Splenocytes and graft-infiltrating lymphocytes display an exhausted phenotype


There is growing interest in using embryonic stem cell (ESC) and induced pluripotent stem cell (iPSC) derivatives for tissue regeneration. However, an increased understanding of human immune responses to stem cell-derived allografts is necessary for maintaining long-term graft persistence. To model this alloimmunity, humanized mice engrafted with human hematopoietic and immune cells could prove to be useful. In this study, an in-depth analysis of graft-infiltrating human lymphocytes and splenocytes revealed that humanized mice incompletely model human immune responses toward allogeneic stem cells and their derivatives. Furthermore, using an “allogenized” mouse model, we show the feasibility of reconstituting immunodeficient mice with a functional mouse immune system and describe a key role of innate immune cells in the rejection of mouse stem cell allografts.


Diretrizes éticas COPE para revisores paritários

COPE Ethical Guidelines for Peer Reviewers

Peer review in all its forms plays an important role in ensuring the integrity of the scholarly record. The process depends to a large extent on trust, and requires that everyone involved behaves responsibly and ethically. Peer reviewers play a central and critical part in the peer-review process, but too often come to the role without any guidance and unaware of their ethical obligations. COPE has produced some guidelines which set out the basic principles and standards to which all peer reviewers should adhere during the peer-review process in research publication. The aim has been to make them generic so that they can be applied across disciplines.

Origem dos animais: o relógio molecular e o registro fóssil podem ser reconciliados?

quinta-feira, setembro 14, 2017

The origin of animals: Can molecular clocks and the fossil record be reconciled?

John A. Cunningham, Alexander G. Liu, Stefan Bengtson, Philip C. J. Donoghue

First published: 5 December 2016 Full publication history


The evolutionary emergence of animals is one of the most significant episodes in the history of life, but its timing remains poorly constrained. Molecular clocks estimate that animals originated and began diversifying over 100 million years before the first definitive metazoan fossil evidence in the Cambrian. However, closer inspection reveals that clock estimates and the fossil record are less divergent than is often claimed. Modern clock analyses do not predict the presence of the crown-representatives of most animal phyla in the Neoproterozoic. Furthermore, despite challenges provided by incomplete preservation, a paucity of phylogenetically informative characters, and uncertain expectations of the anatomy of early animals, a number of Neoproterozoic fossils can reasonably be interpreted as metazoans. A considerable discrepancy remains, but much of this can be explained by the limited preservation potential of early metazoans and the difficulties associated with their identification in the fossil record. Critical assessment of both records may permit better resolution of the tempo and mode of early animal evolution.


Contra a maré - livro crítico sobre como a Física e a Astronomia são feitas

Against the tide - A Critical Review by Scientists of How Physics and Astronomy Get Done

Martín López Corredoira & Carlos Castro Perelman (Eds.) 


Nobody should have a monopoly of the truth in this universe. The censorship and suppression of challenging ideas against the tide of mainstream research, the blacklisting of scientists, for instance, is neither the best way to do and filter science, nor to promote progress in the human knowledge. The removal of good and novel ideas from the scientific stage is very detrimental to the pursuit of the truth. There are instances in which a mere unqualified belief can occasionally be converted into a generally accepted scientific theory through the screening action of refereed literature and meetings planned by the scientific organizing committees and through the distribution of funds controlled by "club opinions". It leads to unitary paradigms and unitary thinking not necessarily associated to the unique truth. This is the topic of this book: to critically analyze the problems of the official (and sometimes illicit) mechanisms under which current science (physics and astronomy in particular) is being administered and filtered today, along with the onerous consequences these mechanisms have on all of us.

Apart from the editors, Juan Miguel Campanario, Brian Martin, Wolfgang Kundt, J. Marvin Herndon, Marian Apostol, Halton C. Arp, Tom Van Flandern, Andrei P. Kirilyuk, Dmitri Rabounski and Henry H. Bauer, all of them professional researchers, reveal a pessimistic view of the miseries of the actual system, while a glimmer of hope remains in the "leitmotiv" claim towards the freedom in doing research and attaining an acceptable level of ethics in science.

About The Author


Martín López Corredoira is a researcher at the Instituto de Astrofísica de Canarias (Tenerife, Spain). He holds a Ph.D. in Physics from the University of La Laguna at Tenerife and a Ph.D. in Philosophy from the University of Seville (Spain). He has authored articles in peer reviewed journals of astrophysics, and two books on philosophy in Spanish: Diálogos entre Razón y Sentimiento and Somos Fragmentos de Naturaleza Arrastrados por Sus Leyes.

Carlos Castro Perelman is a researcher affiliated with the Center for Theoretical Studies of Physical Systems at Clark Atlanta University (USA). He has a Ph.D. in Physics from the University of Texas at Austin and a B.S. from the Massachusetts Institute of Technology. He is the author of over 115 articles on such topics as: the extended relativity theory in Clifford spaces, gravity, supersymmetry, strings, p-branes, fractals, quantum field theory, mathematical physics, number theory


by Martín López Corredoira and Carlos Castro Perelman

It is always necessary to take a critical look at the way in which scientific research actually gets done. While Philosophy and Sociology have long established themselves as full-blown academic disciplines with an ever-increasing literature, there is a dearth of such literature written by practising scientists. The aim of this book is to gather the views of some working physicists and astronomers on the influence of the social structures of science within which scientists are obliged to carry out their research, and examine the ways in which they are sometimes used in negative ways to destroy careers and hinder innovative research. At the present time there are no widely known academic outlets where scientists can express their opinions about the scientific establishment. Not so long ago there were astronomical journals where one could raise these issues but these journals have either ceased to exist or have been revamped into pure research journals. Physicists have no outlet for expressing their views—especially unorthodox views—on the nature of the scientific method and/or social structures affecting their research because journals for physicists are solely dedicated to research. This book aims to fill this current gap in the literature with a sample of critical papers.

The essay “Challenging dominant physics paradigms” by Campanario and Martin is a general analysis of the difficulties found by well-qualified scientists to challenge scientific orthodoxy. Particular cases of dissidence are reflected in the autobiographical odysseys narrated by Kundt, Arp or Castro Perelman. Castro Perelman tells us about the illicit, shameful censorship and blacklisting of scientists taking place in the electronic e-archives web-site <> and which is the most important internet site for preprints in Physics, Astronomy and Mathematics. Scientific and political elites in Western democracies control the system, according to Arp. Anonymity in the peer-review system is susceptible of corruption—says Marvin Herndon—and interferes with the objective examination of extraordinary ideas on their merits—says Van Flandern. These problems of science are worldwide and present in rich countries like the United States, as pointed out by Marvin Herndon, as well as in developing countries. Apostol talks about the corruption, decadence and mafias in Romania hidden behind the use of politically correct terms: “technological transfer”, “international cooperation”, “scientometrics”, etc. Like the example of Romania, many other countries have similar problems. The same problems in Physics and Astronomy are widespread in all fields of science and in all areas of research performed by humans. One representative of the text outside the fields of Physics and Astronomy is the essay by Bauer, where a critical study of analytical chemistry and the conflict of interests in science is presented. We considered it interesting because the context of his essay is applicable to all the sciences in general. The situation in Astrophysics is widely described in López Corredoira’s essay on the oldest profession. Kundt tackles some aspects of astrophysics too, Arp focuses in the research of cosmology, and Van Flandern’s article focuses on the solar system. 

FREE PDF GRATIS: University of Wollongong

A aptidão darwinista desmoronando diante das evidências - não é mensurável

segunda-feira, setembro 11, 2017

Variability in Fitness Effects Can Preclude Selection of the Fittest

Annual Review of Ecology, Evolution, and Systematics

Vol. 48:- (Volume publication date December 2017) 

Review in Advance first posted online on August 28, 2017. (Changes may still occur before final publication.) 

Christopher J. Graves1,2 and Daniel M. Weinreich1,2

1Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, 02912; email:,

2Center for Computational and Molecular Biology, Brown University, Providence, Rhode Island, 02912

The fitness of a genetic trait (an allele) may vary over time, rather than remain constant. In this simple model, populations with two different alleles (black or yellow) see-saw between advantage and disadvantage as their relative fitness changes over time (blue line below). Credit: Weinreich et. al. - PhysOrg


Evolutionary biologists often predict the outcome of natural selection on an allele by measuring its effects on lifetime survival and reproduction of individual carriers. However, alleles affecting traits like sex, evolvability, and cooperation can cause fitness effects that depend heavily on differences in the environmental, social, and genetic context of individuals carrying the allele. This variability makes it difficult to summarize the evolutionary fate of an allele solely on the basis of its effects on any one individual. Attempts to average over this variability can sometimes salvage the concept of fitness. In other cases, evolutionary outcomes can be predicted only by considering the entire genealogy of an allele, thus limiting the utility of individual fitness altogether. We describe a number of intriguing new evolutionary phenomena that have emerged in studies that explicitly model long-term lineage dynamics and discuss implications for the evolution of infectious diseases.

Expected final online publication date for the Annual Review of Ecology, Evolution, and Systematics Volume 48 is November 2, 2017. Please see for revised estimates.





The phrase "survival of the fittest" makes the principle of evolution by natural selection easy to understand—individuals with a trait that adapts them well to their circumstances are more likely to pass that trait along. But as a new study explains, multiple factors make predicting the fate of a trait fiendishly difficult.

Fundamentally, the problem is that a trait conveyed by a gene variant, or allele, may be advantageous for one or a few generations, but provide no advantage or become a liability when circumstances change, said senior author Daniel Weinreich, a professor of ecology and evolutionary biology at Brown University. But most theoretical models of population genetics assume that fitness remains constant.

Perhaps the most obvious way that the fitness of a trait can vary is that the environment can change, not only over time but also over space.

Another dimension that can vary is the "social" life of alleles. Alleles that result in "cheating" are abundant in nature, but they are most effective when they are rare. Once everyone is cheating, it might no longer be an advantage, so the trait over time can become a victim of its own success.

That any of these circumstances can change over time adds yet another layer of complexity, Weinreich said, because the rate at which circumstances change matters.

Indeed, Weinreich said, many models for predicting the fate of alleles have overlooked the possibility that traits can go completely extinct.

Meanwhile, the rate of environmental change is very similar to the rate at which natural selection acts, the math becomes especially tricky.

Weinreich said he plans to delve deeper into the complexities of changes in fitness deriving from varying rates of change in social (e.g. cheaters), genetic (e.g. competing alleles) or environmental (e.g., weather) parameters.

“The overlap between ecological and evolutionary processes—that those two things speak to each other very intimately in a way that’s been overlooked in many models—is the way forward,” Weinreich said. “That’s what’s needed to make critical improvements to models.“

Três modos de evolução por seleção natural e deriva: uma nova ou uma síntese evolutiva ampliada/estendida???

sexta-feira, setembro 08, 2017

Biological Theory

June 2017, Volume 12, Issue 2, pp 67–71

Three Modes of Evolution by Natural Selection and Drift: A New or an Extended Evolutionary Synthesis?

Authors Authors and affiliations

Marion Blute1

1.Department of Sociology University of Toronto Toronto Canada


According to sources both in print and at a recent meeting, evolutionary theory is currently undergoing change which some would characterize as a New Synthesis, and others as an Extended Synthesis. This article argues that the important changes involve recognizing that there are three means by which evolutionary change can be initiated (genetically, ecologically, and developmentally) and three corresponding modes of evolutionary drift. It compares the three and goes on to discuss the scale of innovation and extended or inclusive and Lamarckian inheritance. It concludes from these that “new trends in evolutionary biology” are in part a new, and in part an extended evolutionary synthesis.

Keywords Evolutionary drift Extended evolutionary synthesis Extended inheritance Lamarckian inheritance Lamarckian evolution New evolutionary synthesis



"According to sources both in print and at a recent meeting, evolutionary theory is currently undergoing change which some would characterize as a New Synthesis, and others as an Extended Synthesis." 

O Darwinismo está sendo sistematicamente rebaixado como maneira de entender e explicar a evolução.

E este blogger, entre outros críticos e oponentes do Darwinismo, apontou já em 1998, a necessidade de uma profunda revisão no corpus teórico evolucionário ou o simples descarte da Síntese Evolutiva Moderna. Alguns da Nomenklatura científica, muitos da Galera dos meninos e meninas de Darwin disseram que o entào "simples professorzinho do ensino médio" (com muito orgulho) não sabia e nem sabe o que é ciência.

A nova teoria geral da evolução - a Síntese Evolutiva Ampliada/Estendida foi anunciada em agosto de 2015, mas pouco debatida publicamente no que isso significa para a Síntese Evolutiva Moderna, considerada como teoria científica morta por Stephen Jay Gould em 1980, mas que posava como ortodoxa somente nos livros didáticos. 37 anos decorridos para anunciar sua falência epistêmica.

Pergunta caústica deste blogger: se a ciência abomina o vazio teórico, como fizeram biologia evolucionária ao longo de quase quatro décadas? Abracadabra? Abre-te, Sésamo! Cartas de tarô? Horóscopo? Vísceras de animais? E a desonestidade acadêmica fica visível, pois sabiam da falência epistêmica da Síntese Evolutiva Moderna, mas faziam biologia evolucionária com um paradigma morto!

Fui, nem sei porque rindo da cara desses em descompasso com a literatura especializada e dissonantes cognitivos do status epistêmico da teoria da evolução de Darwin através da seleção natural e n mecanismos evolucionários (de A a Z, vai que um falhe...) no contexto de justificação teórica.

Darwin kaput! Viva Darwin!


Subscription or payment needed/Requer assinatura ou pagamentoBiological Theory

ALERTA: Cresce o número de publicações "científicas" predatórias no mundo inteiro!!!

quinta-feira, setembro 07, 2017

Stop this waste of people, animals and money

David Moher, Larissa Shamseer, Kelly D. Cobey, Manoj M. Lalu, James Galipeau, Marc T. Avey, Nadera Ahmadzai, Mostafa Alabousi, Pauline Barbeau, Andrew Beck, Raymond Daniel, Robert Frank, Mona Ghannad, Candyce Hamel, Mona Hersi, Brian Hutton, Inga Isupov, Trevor A. McGrath, Matthew D. F. McInnes, Matthew J. Page, Misty Pratt, Kusala Pussegoda, Beverley Shea, Anubhav Srivastava, Adrienne Stevenset al.

06 September 2017

Predatory journals have shoddy reporting and include papers from wealthy nations, find David Moher, Larissa Shamseer, Kelly Cobey and colleagues.

Subject terms: Publishing Ethics Research management Lab life

Predatory journals are easy to please. They seem to accept papers with little regard for quality, at a fraction of the cost charged by mainstream open-access journals. These supposedly scholarly publishing entities are murky operations, making money by collecting fees while failing to deliver on their claims of being open access and failing to provide services such as peer review and archiving.

Despite abundant evidence that the bar is low, not much is known about who publishes in this shady realm, and what the papers are like. Common wisdom assumes that the hazard of predatory publishing is restricted mainly to the developing world. In one famous sting, a journalist for Science sent a purposely flawed paper to 140 presumed predatory titles (and to a roughly equal number of other open-access titles), pretending to be a biologist based in African capital cities1. At least two earlier, smaller surveys found that most authors were in India or elsewhere in Asia23. A campaign to warn scholars about predatory journals has concentrated its efforts in Africa, China, India, the Middle East and Russia. Frequent, aggressive solicitations from predatory publishers are generally considered merely a nuisance for scientists from rich countries, not a threat to scholarly integrity.
Our evidence disputes this view. We spent 12 months rigorously characterizing nearly 2,000 biomedical articles from more than 200 journals thought likely to be predatory. More than half of the corresponding authors hailed from high- and upper-middle-income countries as defined by the World Bank.
Of the 17% of sampled articles that reported a funding source, the most frequently named funder was the US National Institutes of Health (NIH). The United States produced more articles in our sample than all other countries save India. Harvard University (with 9 articles) in Cambridge, Massachusetts, and the University of Texas (with 11 articles across all campuses) were among the eight institutions with the most articles. It is easy to imagine other, similar institutions coming up in a different sample. The point is, the problem of predatory journals is more urgent than many realize.
Articles in our sample consistently failed to report key information necessary for readers to assess, reproduce and build on the findings. Fewer than 10% of studies claiming to be randomized controlled trials described how patients were allocated to treatment groups; where blinding was possible, fewer than one-quarter noted whether patients and outcome assessors were blinded to group assignment.
Whether authors are being duped or are overzealously seeking to lengthen their publication lists, this represents enormous waste. Just the subset of articles that we examined contained data from more than 2 million individuals and over 8,000 animals. By extrapolation, we estimate that at least 18,000 funded biomedical-research studies are tucked away in poorly indexed, scientifically questionable journals. Little of this work will advance science. It is too dodgily reported (and possibly badly conducted) and too hard to find.
In our view, publishing in predatory journals is unethical. Individuals who agree to be studied expect that their participation could benefit future patients. Use of animals in biomedical research is rationalized on the assumption that experiments will contribute valuable information. Even assuming authors are publishing more than one paper from their study (and some are), they should be held to a higher standard of disclosure. Publishers, funders and research institutions must join together to prevent research from ending up in predatory journals.

O embrião de Drosophila em resolução de transcriptoma de célula única: mero acaso, fortuita necessidade ou design inteligente?

quarta-feira, setembro 06, 2017

The Drosophila embryo at single-cell transcriptome resolution

Nikos Karaiskos1,*, Philipp Wahle2,*, Jonathan Alles1, Anastasiya Boltengagen1, Salah Ayoub1, Claudia Kipar2, Christine Kocks1, Nikolaus Rajewsky1,†, Robert P. Zinzen2,†

1Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.

2Systems Biology of Neural Tissue Differentiation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.

↵†Corresponding author. Email: (N.R.); (R.P.Z.)

↵* These authors contributed equally to this work.

Science 31 Aug 2017:eaan3235


By the onset of morphogenesis, Drosophila embryos consist of about 6000 cells that express distinct gene combinations. Here, we used single-cell sequencing of precisely staged embryos and devised DistMap, a computational mapping strategy to reconstruct the embryo and to predict spatial gene expression approaching single-cell resolution. We produce a virtual embryo with about 8000 expressed genes per cell. Our interactive “Drosophila-Virtual-Expression-eXplorer” (DVEX) database generates three-dimensional virtual in situ hybridizations and computes gene expression gradients. We used DVEX to uncover patterned expression of transcription factors and long noncoding RNAs, as well as signaling pathway components. Spatial regulation of Hippo signaling during early embryogenesis suggests a mechanism for establishing asynchronous cell proliferation. Our approach is suitable to generate transcriptomic blueprints for other complex tissues.


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A glia é vital para o desenvolvimento neuronal no cérebro: mero acaso, fortuita necessidade ou design inteligente?

Glia relay differentiation cues to coordinate neuronal development in Drosophila

Vilaiwan M. Fernandes*,†, Zhenqing Chen†,‡, Anthony M. Rossi, Jaqueline Zipfel§, Claude Desplan

Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA.

↵*Corresponding author. Email:

↵† These authors contributed equally to this work.

↵‡ Present address: Carl R. Woese Institute for Genomic Biology, Department of Cell and Developmental Biology, University of Illinois, Urbana, IL 61801, USA.

↵§ Present address: Institut für Neuro- und Verhaltensbiologie, Badestraße 9, 48149 Münster, Germany.

Science 01 Sep 2017:Vol. 357, Issue 6354, pp. 886-891


Neuronal birth and specification must be coordinated across the developing brain to generate the neurons that constitute neural circuits. We used the Drosophila visual system to investigate how development is coordinated to establish retinotopy, a feature of all visual systems. Photoreceptors achieve retinotopy by inducing their target field in the optic lobe, the lamina neurons, with a secreted differentiation cue, epidermal growth factor (EGF). We find that communication between photoreceptors and lamina cells requires a signaling relay through glia. In response to photoreceptor-EGF, glia produce insulin-like peptides, which induce lamina neuronal differentiation. Our study identifies a role for glia in coordinating neuronal development across distinct brain regions, thus reconciling the timing of column assembly with that of delayed differentiation, as well as the spatiotemporal pattern of lamina neuron differentiation.


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Dois códigos genéticos - sintaxe repetitiva para RNAs ativos não codificantes; sintaxe não repetitiva para os arquivos de DNA

segunda-feira, setembro 04, 2017

Two genetic codes: Repetitive syntax for active non-coding RNAs; non-repetitive syntax for the DNA archives

Guenther Witzany

Article: e1297352 | Received 14 Feb 2017, Accepted 16 Feb 2017, Published online: 15 Mar 2017


Current knowledge of the RNA world indicates 2 different genetic codes being present throughout the living world. In contrast to non-coding RNAs that are built of repetitive nucleotide syntax, the sequences that serve as templates for proteins share—as main characteristics—a non-repetitive syntax. Whereas non-coding RNAs build groups that serve as regulatory tools in nearly all genetic processes, the coding sections represent the evolutionarily successful function of the genetic information storage medium. This indicates that the differences in their syntax structure are coherent with the differences of the functions they represent. Interestingly, these 2 genetic codes resemble the function of all natural languages, i.e., the repetitive non-coding sequences serve as appropriate tool for organization, coordination and regulation of group behavior, and the non-repetitive coding sequences are for conservation of instrumental constructions, plans, blueprints for complex protein-body architecture. This differentiation may help to better understand RNA group behavioral motifs.

EYWORDS: DNA, repetitive sequences, RNA, RNA stem loops, RNA group identities