Epigenética e a evolução dos tentilhões de Darwin

sexta-feira, agosto 29, 2014

Epigenetics and the Evolution of Darwin’s Finches

Michael K. Skinner1,*, Carlos Gurerrero-Bosagna1,3, M. Muksitul Haque1, Eric E. Nilsson1, Jennifer A.H. Koop2,4, Sarah A. Knutie2 and Dale H. Clayton2

- Author Affiliations

1Center for Reproductive Biology, School of Biological Sciences, Washington State University
2Department of Biology, University of Utah
3Present address: Department of Physics, Biology and Chemistry (IFM), Linköping University, Sweden
4Present address: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ

↵*Corresponding author: E-mail: skinner@wsu.edu.

Accepted July 18, 2014.


The prevailing theory for the molecular basis of evolution involves genetic mutations that ultimately generate the heritable phenotypic variation on which natural selection acts. However, epigenetic transgenerational inheritance of phenotypic variation may also play an important role in evolutionary change. A growing number of studies have demonstrated the presence of epigenetic inheritance in a variety of different organisms that can persist for hundreds of generations. The possibility that epigenetic changes can accumulate over longer periods of evolutionary time has seldom been tested empirically. This study was designed to compare epigenetic changes among several closely related species of Darwin’s finches, a well-known example of adaptive radiation. Erythrocyte DNA was obtained from five species of sympatric Darwin’s finches that vary in phylogenetic relatedness. Genome-wide alterations in genetic mutations using copy number variation (CNV) were compared with epigenetic alterations associated with differential DNA methylation regions (epimutations). Epimutations were more common than genetic CNV mutations among the five species; furthermore, the number of epimutations increased monotonically with phylogenetic distance. Interestingly, the number of genetic CNV mutations did not consistently increase with phylogenetic distance. The number, chromosomal locations, regional clustering, and lack of overlap of epimutations and genetic mutations suggest that epigenetic changes are distinct and that they correlate with the evolutionary history of Darwin’s finches. The potential functional significance of the epimutations was explored by comparing their locations on the genome to the location of evolutionarily important genes and cellular pathways in birds. Specific epimutations were associated with genes related to the bone morphogenic protein, toll receptor, and melanogenesis signaling pathways. Species-specific epimutations were significantly overrepresented in these pathways. As environmental factors are known to result in heritable changes in the epigenome, it is possible that epigenetic changes contribute to the molecular basis of the evolution of Darwin’s finches.

Key words

epimutations DNA methylation copy number variation phylogeny adaptive radiation BMP toll melanogenesis

© The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

As palestras de Feynman sobre Física disponíveis para assistir online gratuitamente

ENCODE, a enciclopédia de como funcionam os genomas ficando cada vez maior.

quarta-feira, agosto 27, 2014

Comparative analysis of the transcriptome across distant species

Mark B. Gerstein, Joel Rozowsky, Koon-Kiu Yan, Daifeng Wang, Chao Cheng, James B. Brown, Carrie A. Davis, LaDeana Hillier, Cristina Sisu, Jingyi Jessica Li, Baikang Pei, Arif O. Harmanci, Michael O. Duff, Sarah Djebali, Roger P. Alexander, Burak H. Alver, Raymond Auerbach, Kimberly Bell, Peter J. Bickel, Max E. Boeck, Nathan P. Boley, Benjamin W. Booth, Lucy Cherbas, Peter Cherbas, Chao Di et al.

AffiliationsContributionsCorresponding authors

Nature 512, 445–448 (28 August 2014) doi:10.1038/nature13424

Received 10 April 2013 Accepted 30 April 2014 Published online 27 August 2014

Source/Fonte: Nature

The transcriptome is the readout of the genome. Identifying common features in it across distant species can reveal fundamental principles. To this end, the ENCODE and modENCODE consortia have generated large amounts of matched RNA-sequencing data for human, worm and fly. Uniform processing and comprehensive annotation of these data allow comparison across metazoan phyla, extending beyond earlier within-phylum transcriptome comparisons and revealing ancient, conserved features1, 2, 3, 4, 5, 6. Specifically, we discover co-expression modules shared across animals, many of which are enriched in developmental genes. Moreover, we use expression patterns to align the stages in worm and fly development and find a novel pairing between worm embryo and fly pupae, in addition to the embryo-to-embryo and larvae-to-larvae pairings. Furthermore, we find that the extent of non-canonical, non-coding transcription is similar in each organism, per base pair. Finally, we find in all three organisms that the gene-expression levels, both coding and non-coding, can be quantitatively predicted from chromatin features at the promoter using a ‘universal model’ based on a single set of organism-independent parameters.

Subject terms: Comparative genomics Transcriptomics


Traços linguísticos de uma fraude científica: o caso de Diederik Stapel

Linguistic Traces of a Scientific Fraud: The Case of Diederik Stapel

David M. Markowitz mail, Jeffrey T. Hancock

Published: August 25, 2014DOI: 10.1371/journal.pone.0105937


When scientists report false data, does their writing style reflect their deception? In this study, we investigated the linguistic patterns of fraudulent (N = 24; 170,008 words) and genuine publications (N = 25; 189,705 words) first-authored by social psychologist Diederik Stapel. The analysis revealed that Stapel's fraudulent papers contained linguistic changes in science-related discourse dimensions, including more terms pertaining to methods, investigation, and certainty than his genuine papers. His writing style also matched patterns in other deceptive language, including fewer adjectives in fraudulent publications relative to genuine publications. Using differences in language dimensions we were able to classify Stapel's publications with above chance accuracy. Beyond these discourse dimensions, Stapel included fewer co-authors when reporting fake data than genuine data, although other evidentiary claims (e.g., number of references and experiments) did not differ across the two article types. This research supports recent findings that language cues vary systematically with deception, and that deception can be revealed in fraudulent scientific discourse.

Citation: Markowitz DM, Hancock JT (2014) Linguistic Traces of a Scientific Fraud: The Case of Diederik Stapel. PLoS ONE 9(8): e105937. doi:10.1371/journal.pone.0105937

Editor: Daniele Fanelli, Université de Montréal, Canada

Received: October 4, 2013; Accepted: July 29, 2014; Published: August 25, 2014

Copyright: © 2014 Markowitz and Hancock. 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: The authors have no support or funding to report.

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


A redundância do código genético permite a pausa de tradução - Mero acaso, fortuita necessidade ou design inteligente?

segunda-feira, agosto 25, 2014

REVIEW ARTICLE Front. Genet., 20 May 2014 | doi: 10.3389/fgene.2014.00140
Redundancy of the genetic code enables translational pausing

David J. D'Onofrio 1,2 and David L. Abel 3 

1Control Systems Modeling and Simulation, General Dynamics, Sterling Heights, MI, USA

2Department of Humanities and Science, Math Department, College of Humanities and Science, University of Phoenix, Detroit, MI, USA

3Department of ProtoBioCybernetics/ProtoBioSemiotics, The Gene Emergence Project of The Origin of Life Science Foundation, Inc., Greenbelt, MD, USA

The codon redundancy (“degeneracy”) found in protein-coding regions of mRNA also prescribes Translational Pausing (TP). When coupled with the appropriate interpreters, multiple meanings and functions are programmed into the same sequence of configurable switch-settings. This additional layer of Ontological Prescriptive Information (PIo) purposely slows or speeds up the translation-decoding process within the ribosome. Variable translation rates help prescribe functional folding of the nascent protein. Redundancy of the codon to amino acid mapping, therefore, is anything but superfluous or degenerate. Redundancy programming allows for simultaneous dual prescriptions of TP and amino acid assignments without cross-talk. This allows both functions to be coincident and realizable. We will demonstrate that the TP schema is a bona fide rule-based code, conforming to logical code-like properties. Second, we will demonstrate that this TP code is programmed into the supposedly degenerate redundancy of the codon table. We will show that algorithmic processes play a dominant role in the realization of this multi-dimensional code.

Keywords: algorithm, translational pausing, ribosome, regulation, co-translational folding, Shine Dalgarno sequences, degeneracy, multi-dimensional code

Citation: D'Onofrio DJ and Abel DL (2014) Redundancy of the genetic code enables translational pausing. Front. Genet. 5:140. doi: 10.3389/fgene.2014.00140
Received: 02 March 2014; Paper pending published: 27 March 2014;
Accepted: 28 April 2014; Published online: 20 May 2014.
Edited by:Firas H. Kobeissy, University of Florida, USA
Reviewed by:Firas H. Kobeissy, University of Florida, USA
Georges Nemer, American University of Beirut, Lebanon

Copyright © 2014 D'Onofrio and Abel. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

*Correspondence: David J. D'Onofrio, Department of Humanities and Science, University of Phoenix, 4400 Town Center, Southfield, MI 48127, USA e-mail: davidj@email.phoenix.edu

Nós somos uma colcha de retalhos genéticos: mudança paradigmática em genômica?

sexta-feira, agosto 22, 2014

I Contain Multitudes

Our bodies are a genetic patchwork, possessing variation from cell to cell. Is that a good thing?

Olena Shmahalo for Quanta Magazine

Even healthy brains harbor genetic diversity, though scientists disagree over the extent.

August 21, 2014

Your DNA is supposed to be your blueprint, your unique master code, identical in every one of your tens of trillions of cells. It is why you are you, indivisible and whole, consistent from tip to toe.

But that’s really just a biological fairy tale. In reality, you are an assemblage of genetically distinctive cells, some of which have radically different operating instructions. This fact has only become clear in the last decade. Even though each of your cells supposedly contains a replica of the DNA in the fertilized egg that began your life, mutations, copying errors and editing mistakes began modifying that code as soon as your zygote self began to divide. In your adult body, your DNA is peppered by pinpoint mutations, riddled with repeated or rearranged or missing information, even lacking huge chromosome-sized chunks. Your data is hopelessly corrupt.

Most genome scientists assume that this DNA diversity, called “somatic mutation” or “structural variation,” is bad. Mutations and other genetic changes can alter the function of the cell, usually for the worse. Disorderly DNA is a hallmark of cancers, and genomic variation can cause a suite of brain disorders and malformations. It makes sense: Cells working off garbled information probably don’t function very well.

Most research to date has focused on how aberrant DNA drives disease, but even healthy bodies harbor genetic disorder. In the last few years, some researchers report that anywhere from 10 to 40 percent of brain cells and between 30 and 90 percent of human liver cells are aneuploid, meaning that one entire chromosome is either missing or duplicated. Copy number variations, in which chunks of DNA between 100 and a few million letters in length are multiplied or eliminated, also seem to be widespread in healthy people.

The exact extent of cell-to-cell diversity is still unclear and a matter of some debate. It’s only in the last two years that scientists have been able to look carefully at just one genome at a time, with the advent of new methods of single-cell DNA sequencing. (Earlier methods averaged the results of thousands or millions of cells and could only detect huge aberrations or relatively common ones.) Because this work is so new, each study includes surprises: A single-cell genome sequencing study of 97 neurons from healthy brains, published today by Christopher Walsh, a neurologist at Boston Children’s Hospital and Howard Hughes Medical Institute, and the postdoctoral researcher Xuyu Cai found few that were aneuploid — less than 5 percent. But most had at least one good-sized copy number variation.

Walsh’s findings and others mark a third phase in human genomics. When the complete DNA of one human being was first sequenced in 2000, it was considered to be “the” human genome. Soon after, researchers began to explore the differences between individuals, launching the era of the “personal genome.” Now science is entering the age of the microgenome, in which research begins to explore the worlds within us, examining our inherent imperfections and contradictions, the multitudes we contain.

With that third phase comes a deeper question. What do our genetic contradictions mean? Do they play an important role in our biology? At this point, just about every genome scientist has a slightly different take. One surprising theory suggests that DNA diversity might be good for you. It’s a feature, not a bug.

According to this idea, genetic heterogeneity allows bodies to be more adaptive and resilient. The logic comes from evolutionary biology. Genetic diversity is clearly beneficial for a population or species, because a few individuals will likely be randomly equipped to survive unpredictable environmental changes, such as a drought or an epidemic. Along similar lines, some biologists have proposed that genetic diversity might also be beneficial within the individual. If new conditions demand new abilities or functions, such as surviving an environmental toxin or learning a new skill, genetic heterogeneity increases the odds that at least some cells will be able to thrive in this new situation. “I think of the body as a population of cells, similar to the population of human organisms walking this earth,” said James Lupski, a geneticist at Baylor College of Medicine, who studies how DNA alterations shape human traits. In any such population, “there’s a lot to be said for generating variation, and allowing the most fit variation to be selected out.”

Courtesy of Fred Gage
Our genetically diverse brains might be one reason we are all so different, suspects Salk Institute neurobiologist Fred Gage.

The most radical version of this argument comes from Fred Gage, a Salk Institute neurobiologist best known for pioneering studies in neuroplasticity, the adult brain’s ability to adapt. His team has found several types of genetic variation to be common in normal adult human brains, and he thinks this diversity could help explain the organ’s amazingly complex structure and remarkable flexibility. “We can’t predict what will happen to us in our 80 years of life,” he said. “We have to build in mechanisms of diversity that will help us adapt to the things that happen to us.” Experts in liver biology propose a similar idea. They even have preliminary evidence that genetic diversity actually can make the organ more resilient.


Possivelmente a teoria fundamental da natureza não tenha nenhuma escala

quinta-feira, agosto 21, 2014


We explore the possibility that the fundamental theory of nature does not contain any scale. This implies a renormalizable quantum gravity theory where the graviton kinetic term has 4 derivatives, and can be reinterpreted as gravity minus an anti-graviton. We compute the super-Planckian RGE of adimensional gravity coupled to a generic matter sector. The Planck scale and a flat space can arise dynamically at quantum level provided that a quartic scalar coupling and its β function vanish at the Planck scale. This is how the Higgs boson behaves for Mh125 GeV at Mt171 GeV. Within agravity, inflation is a generic phenomenon: the slow-roll parameters are given by the β-functions of the theory, and are small if couplings are perturbative. The predictions ns0.967 and r0.13 arise if the inflaton is identified with the Higgs of gravity. Furthermore, quadratically divergent corrections to the Higgs mass vanish: a small weak scale is natural and can be generated by agravity quantum corrections.
Comments:24 pages. References added, final version to appear on JHEP
Subjects:High Energy Physics - Phenomenology (hep-ph); Cosmology and Nongalactic Astrophysics (astro-ph.CO); General Relativity and Quantum Cosmology (gr-qc); High Energy Physics - Theory (hep-th)
Report number:FTUAM-14-9, IFT-UAM/CSIC-14-021
Cite as:arXiv:1403.4226 [hep-ph]
(or arXiv:1403.4226v2 [hep-ph] for this version)

Submission history

From: Alessandro Strumia [view email]
[v1] Mon, 17 Mar 2014 19:38:37 GMT (229kb,D)
[v2] Wed, 4 Jun 2014 13:00:59 GMT (329kb,D)

Workshop sobre cientificismo na City University de Nova York - 16-17 de maio de 2014


Welcome to the site of a workshop on the concept of "scientism" organized at the Graduate Center of the City University of New York by Massimo Pigliucci (CUNY-Lehman College), with Maarten Boudry (Ghent University) as a co-organizer. The workshop will take place on May 16 & 17, 2014, and is sponsored by the Committee for Interdisciplinary Science Studies at the Graduate Center (many thanks to Jesse Prinz for this!).

Rationale: Science is one of the marvels of the human intellect, but nowadays one often hears about a sin called “scientism.” There is no agreed upon definition of the term, but as a first approximation, it describes an exaggerated deference towards science, or unwarranted belief in the superiority and universal applicability of scientific methods. Such worries about the limits of science are not new. With every advance of science into new territory, there have been concerns about its overblown ambitions. Is science endangering other forms of inquiry? Those who stand accused of “scientism” often dismiss the charge as a form of resistance against scientific progress. This symposium aims at exploring the concept of scientism, asking whether the term captures an interesting intellectual position, and whether it is something to worry about. Is it a well-developed position about the (epistemic) superiority of science over other modes of inquiry, or more like an attitude of glowing admiration for science? What, if any, are the potential dangers of scientism? Given the ubiquitous usage of the term “scientism,” in a wide variety of contrasting contexts, we think a philosophical discussions of the concept is long overdue.

Some useful references:

Haack, S. (2008). Putting Philosophy to Work: Inquiry and Its Place in Culture--Essays on Science, Religion, Law, Literature, and Life: Prometheus Books.
Ladyman, J. and D. Ross (2007). Every thing must go: Metaphysics naturalized. Oxford: Oxford University Press 

Pigliucci, M. and M. Boudry (Eds.). (2013). Philosophy of Pseudoscience: Reconsidering the Demarcation Project. Chicago: University of Chicago Press. 


Apresentando um novo site: From Darwin to Hitler [De Darwin a Hitler]

terça-feira, agosto 19, 2014

Evolution News & Views 18 de agosto de 2014 11:05 AM | Permalink

Reserve um tempo para investigar um recurso online que está disponível agora: um novo website, From Darwin to Hitler, destacando a pesquisa de nosso colega do Discovery Institute e historiador da Universidade Estadual da Califórnia, Richard Weikart, autor dos livros From Darwin to Hitler: Evolutionary Ethics, Eugenics, and Racism in Germany e Hitler's Ethic: The Nazi Pursuit of Evolutionary Progress.
Você encontrará links para os livros e artigos do Dr. Weikart, bem como o novo documentário do Discovery Institute, The Biology of the Second Reich [A biologia do Terceiro Reich], e uma palestra do Dr. Weikart, "From Darwin to Hitler," [De Darwin a Hitler] apresentada pela University of California Television.
Essas são questões importantes no estudo de História, Cultura, e Ciência, com a relevância para o nosso tempo. Favor compartilhar o novo site From Darwin to Hitler com seus amigos.

Um multiverso medieval: modelo matemático do universo de Robert Grosseteste do século 13

segunda-feira, agosto 18, 2014

A Medieval Multiverse: Mathematical Modelling of the 13th Century Universe of Robert Grosseteste

Richard G. Bower (Durham), Tom C. B. McLeish F.R.S. (Durham), Brian K. Tanner (Durham), Hannah E. Smithson (Oxford), Cecilia Panti (Rome), Neil Lewis (Georgetown), Giles E. M. Gasper (Durham)

(Submitted on 4 Mar 2014 (v1), last revised 10 Mar 2014 (this version, v2))

In his treatise on light, written in about 1225, Robert Grosseteste describes a cosmological model in which the Universe is created in a big-bang like explosion and subsequent condensation. He postulates that the fundamental coupling of light and matter gives rises to the material body of the entire cosmos. Expansion is arrested when matter reaches a minimum density and subsequent emission of light from the outer region leads to compression and rarefaction of the inner bodily mass so as to create nine celestial spheres, with an imperfect residual core. In this paper we reformulate the Latin description in terms of a modern mathematical model. The equations which describe the coupling of light and matter are solved numerically, subject to initial conditions and critical criteria consistent with the text. Formation of a universe with a non-infinite number of perfected spheres is extremely sensitive to the initial conditions, the intensity of the light and the transparency of these spheres. In this "medieval multiverse", only a small range of opacity and initial density profiles lead to a stable universe with nine perfected spheres. As in current cosmological thinking, the existence of Grosseteste's universe relies on a very special combination of fundamental parameters.

Comments: 16 pages, 8 figures. Accepted for Proceedings of the Royal Society (A) subject to minor revisions. Animated versions of the figures are available at this http URL

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

Cite as: arXiv:1403.0769 [physics.hist-ph]

(or arXiv:1403.0769v2 [physics.hist-ph] for this version)

Submission history

From: Richard Bower [view email] 

[v1] Tue, 4 Mar 2014 12:54:50 GMT (1405kb)

[v2] Mon, 10 Mar 2014 22:54:45 GMT (1405kb)





Não pense que o modelo de multiverso de Robert Grosseteste, por ser do século 13, seja estapafúrdio - tem muito mais matemática que falta em muitos estudos e pesquisas cosmológicas atuais.

Sobre a existência e a exclusividade do método científico

sábado, agosto 16, 2014

Biological Theory

September 2014, Volume 9, Issue 3, pp 331-346,

Open Access

Date: 02 Apr 2014

On the Existence and Uniqueness of the Scientific Method

Jorge Wagensberg


The ultimate utility of science is widely agreed upon: the comprehension of reality. But there is much controversy about what scientific understanding actually means, and how we should proceed in order to gain new scientific understanding. Is there a method for acquiring new scientific knowledge? Is this method unique and universal? There has been no shortage of proposals, but neither has there been a shortage of skeptics about these proposals. This article proffers for discussion a potential scientific method that aspires to be unique and universal and is rooted in the recent and ancient history of scientific thinking. Curiously, conclusions can be inferred from this scientific method that also concern education and the transmission of science to others.

FREE PDF GRATIS: Biological Theory

Leo Kadanoff, da Universidade de Chicago, 'falou e disse': os darwinistas devem ir para casa pensar sobre a evolução

sexta-feira, agosto 15, 2014

"Eu penso que a bola está no lado das pessoas que creem na evolução. Elas têm que lidar com essas questões. …Bill (Dembski) ele apresentou o seu caso e nós todos devemos ir para casa e pensar."

"I think the ball is in the court of people who believe in evolution. They have to deal with these questions. …Bill (Dembski) has made his case and we should all go home and think."

Leo P. Kadanoff, matemático e físico teórico da Universidade de Chicago.


William Dembski tinha sido convidado pelo Prof. Leo P. Kadanoff para falar na Universidade de Chicago, nos Seminários em Computação na Ciência, "Conservation of Information in Evolutionary Search".

Como sempre, houve comoção entre os darwinistas fundamentalistas xiitas como Jerry Coyne, pela presença de um teórico do Design Inteligente a fim de falar sobre a conservação da informação ser um problema que a teoria da evolução sai de mãos vazias no contexto de justificação teórica.

Quem convidou Bill Dembski - Leo P. Kadanoff, não é um professor qualquer como muitos aqui no Brasil que escrevem manifestos, e tudo fazem para cancelar eventos assim em universidades brasileiras - vide o caso do Prof. Leandro Russovski Tessler, da Unicamp. Quem é Tessler diante de Kadoff? Nem dá para comparar as carreiras científico-acadêmicas... O mais cientificamente respeitado e reconhecido acolhe o discurso considerado "herege". Já o outro... O outro é o outro, fazer o quê!

O modelo do universo de Einstein de 1931 revisitado: uma análise e tradução de um modelo do universo esquecido

Einstein's cosmic model of 1931 revisited: an analysis and translation of a forgotten model of the universe

C.O Raifeartaigh, B.McCann

(Submitted on 8 Dec 2013 (v1), last revised 17 Jan 2014 (this version, v2))

We present a translation and analysis of a cosmic model published by Einstein in 1931. The paper, which is not widely known, features a model of a universe that undergoes an expansion followed by a contraction, quite different to his static model of 1917 or the monotonic Einstein-de Sitter model of 1932. The paper offers many insights into the cosmology of Albert Einstein in the light of the first evidence for an expanding universe, and we discuss his views of issues such as the curvature of space, the cosmological constant, the singularity and the timespan of the expansion. We argue that retrospective descriptions of this model as cyclic or periodic are not historically or mathematically accurate. We find that calculations in the paper of the matter density and radius of the universe contain a numerical error, a finding that is supported by writing on a blackboard used by Einstein during a lecture at Oxford University in May 1931. Our article concludes with a general discussion of his philosophy of cosmology.

Comments: Accepted for publication in the European Physical Journal (H). The article includes a first English translation of Einstein's 1931 SAW paper and the discovery of an error in Einstein's calculation of the matter density of the universe. 30 pages, 2 figures

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

Cite as: arXiv:1312.2192 [physics.hist-ph]

(or arXiv:1312.2192v2 [physics.hist-ph] for this version)

Submission history

From: Cormac O Raifeartaigh [view email] 

[v1] Sun, 8 Dec 2013 11:11:55 GMT (651kb)

[v2] Fri, 17 Jan 2014 17:09:30 GMT (644kb)

Desvendando o código bioelétrico na embriogênese

Commun Integr Biol. 2013 Jan 1;6(1):e22595. doi: 10.4161/cib.22595.

Cracking the bioelectric code: Probing endogenous ionic controls of pattern formation.

Tseng A1, Levin M.

Author information

1Department of Biology and Tufts Center for Regenerative and Developmental Biology; Medford, MA USA.


Patterns of resting potential in non-excitable cells of living tissue are now known to be instructive signals for pattern formation during embryogenesis, regeneration and cancer suppression. The development of molecular-level techniques for tracking ion flows and functionally manipulating the activity of ion channels and pumps has begun to reveal the mechanisms by which voltage gradients regulate cell behaviors and the assembly of complex large-scale structures. A recent paper demonstrated that a specific voltage range is necessary for demarcation of eye fields in the frog embryo. Remarkably, artificially setting other somatic cells to the eye-specific voltage range resulted in formation of eyes in aberrant locations, including tissues that are not in the normal anterior ectoderm lineage: eyes could be formed in the gut, on the tail, or in the lateral plate mesoderm. These data challenge the existing models of eye fate restriction and tissue competence maps, and suggest the presence of a bioelectric code-a mapping of physiological properties to anatomical outcomes. This Addendum summarizes the current state of knowledge in developmental bioelectricity, proposes three possible interpretations of the bioelectric code that functionally maps physiological states to anatomical outcomes, and highlights the biggest open questions in this field. We also suggest a speculative hypothesis at the intersection of cognitive science and developmental biology: that bioelectrical signaling among non-excitable cells coupled by gap junctions simulates neural network-like dynamics, and underlies the information processing functions required by complex pattern formation in vivo. Understanding and learning to control the information stored in physiological networks will have transformative implications for developmental biology, regenerative medicine and synthetic bioengineering.


bioelectricity; ion channels; pattern formation; regeneration

Quais formas de limitação da autonomia da ciência são epistemologicamente aceitáveis (e politicamente desejáveis)?

Which forms of limitation of the autonomy of science are epistemologically acceptable (and politically desirable)?

Ruphy, Stephanie (2014) Which forms of limitation of the autonomy of science are epistemologically acceptable (and politically desirable)?

In: [2014] Philosophy of Science Assoc. 24th Biennial Mtg (Chicago, IL).


This paper will investigate whether constraints on possible forms of limitation of the autonomy of science can be derived from epistemological considerations. Proponents of the autonomy of science often link autonomy with virtues such as epistemic fecundity, capacity to generate technological innovations and capacity to produce neutral expertise. I will critically discuss several important epistemological assumptions underlying these links, in particular the “unpredictability argument”. This will allow me to spell out conditions to be met by any form of limitation of the autonomy of science to be epistemologically acceptable. These conditions can then be used as a framework to evaluate possible or existing forms of limitations of the autonomy of science. And it will turn out that the option of direct public participation (a lively option in philosophy of science today) might not be the best way to go to democratize the setting of research agenda.

FREE PDF GRATIS: Philsci-Archive

Primeiro Congresso de Design Inteligente no Brasil - The Royal Palm Plaza, Campinas, SP, 14-16 Nov. 2014

quarta-feira, agosto 13, 2014

Ficaram prontos os cartazes (A5) do 1o. TDI Brasil para você usar na divulgação do congresso.

Envie um email para a secretária do 1o. TDI Brasil - Luciana Vialta (lucianavialta@gmail.com) pedindo alguns folders, com seu endereço completo, que lhe enviaremos por correio. Divulgue! Contamos com você!

Calibração melhorada do relógio mitocondrial humano usando genomas antigos

Improved Calibration of the Human Mitochondrial Clock Using Ancient Genomes

Adrien Rieux*,1, Anders Eriksson2, Mingkun Li3, Benjamin Sobkowiak1, Lucy A. Weinert1,4, Vera Warmuth1,2, Andres Ruiz-Linares1, Andrea Manica2 and François Balloux*,1

- Author Affiliations

1UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom

2Department of Zoology, University of Cambridge, Cambridge, United Kingdom

3Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany

4Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom

↵*Corresponding author: E-mail: a.rieux@ucl.ac.uk, f.balloux@ucl.ac.uk.


Reliable estimates of the rate at which DNA accumulates mutations (the substitution rate) are crucial for our understanding of the evolution and past demography of virtually any species. In humans, there are considerable uncertainties around these rates, with substantial variation among recent published estimates. Substitution rates have traditionally been estimated by associating dated events to the root (e.g., the divergence between humans and chimpanzees) or to internal nodes in a phylogenetic tree (e.g., first entry into the Americas). The recent availability of ancient mitochondrial DNA sequences allows for a more direct calibration by assigning the age of the sequenced samples to the tips within the human phylogenetic tree. But studies also vary greatly in the methodology employed and in the sequence panels analyzed, making it difficult to tease apart the causes for the differences between previous estimates. To clarify this issue, we compiled a comprehensive data set of 350 ancient and modern human complete mitochondrial DNA genomes, among which 146 were generated for the purpose of this study and estimated substitution rates using calibrations based both on dated nodes and tips. Our results demonstrate that, for the same data set, estimates based on individual dated tips are far more consistent with each other than those based on nodes and should thus be considered as more reliable.

Key words

Bayesian phylogenetic inference mitochondrial substitution rates divergence times human calibration strategy ancient genomes molecular clock

© The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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LUCA, seus problemas acabaram - uma base bioenergética da divergência de membrana em Arquea e Bactéria.

A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria

Víctor Sojo, Andrew Pomiankowski, Nick Lane mail

Published: August 12, 2014DOI: 10.1371/journal.pbio.1001926

Source/Fonte: Nature


Membrane bioenergetics are universal, yet the phospholipid membranes of archaea and bacteria—the deepest branches in the tree of life—are fundamentally different. This deep divergence in membrane chemistry is reflected in other stark differences between the two domains, including ion pumping and DNA replication. We resolve this paradox by considering the energy requirements of the last universal common ancestor (LUCA). We develop a mathematical model based on the premise that LUCA depended on natural proton gradients. Our analysis shows that such gradients can power carbon and energy metabolism, but only in leaky cells with a proton permeability equivalent to fatty acid vesicles. Membranes with lower permeability (equivalent to modern phospholipids) collapse free-energy availability, precluding exploitation of natural gradients. Pumping protons across leaky membranes offers no advantage, even when permeability is decreased 1,000-fold. We hypothesize that a sodium-proton antiporter (SPAP) provided the first step towards modern membranes. SPAP increases the free energy available from natural proton gradients by ~60%, enabling survival in 50-fold lower gradients, thereby facilitating ecological spread and divergence. Critically, SPAP also provides a steadily amplifying advantage to proton pumping as membrane permeability falls, for the first time favoring the evolution of ion-tight phospholipid membranes. The phospholipids of archaea and bacteria incorporate different stereoisomers of glycerol phosphate. We conclude that the enzymes involved took these alternatives by chance in independent populations that had already evolved distinct ion pumps. Our model offers a quantitatively robust explanation for why membrane bioenergetics are universal, yet ion pumps and phospholipid membranes arose later and independently in separate populations. Our findings elucidate the paradox that archaea and bacteria share DNA transcription, ribosomal translation, and ATP synthase, yet differ in equally fundamental traits that depend on the membrane, including DNA replication.

Author Summary

The archaea and bacteria are the deepest branches of the tree of life. The two groups are similar in morphology and share some fundamental biochemistry, including the genetic code, but the differences between them are stark, and rank among the great unsolved problems in biology. The composition of cell membranes and walls is utterly different in the two groups, while the mechanism of DNA replication seems unrelated. We address a specific paradox, giving new insight into this deep evolutionary split: membrane bioenergetics are universal, yet the membranes themselves are not. We resolve this paradox by considering the energetics of a hypothetical last universal common ancestor (LUCA) in geochemically sustained proton gradients. Using a quantitative model, we show that LUCA could have used proton gradients to drive carbon and energy metabolism, but only if the membranes were leaky. This requirement precluded ion pumping and the early evolution of phospholipid membranes. We constrain a pathway leading from LUCA to the deep divergence of archaea and bacteria on the basis of incremental increases in free-energy availability. We support our inferences with comparative biochemistry and phylogenetics, and show why the late evolution of modern membranes forced divergence in other traits such as DNA replication.

Citation: Sojo V, Pomiankowski A, Lane N (2014) A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria. PLoS Biol 12(8): e1001926. doi:10.1371/journal.pbio.1001926

Academic Editor: David Penny, Massey University, New Zealand

Received: February 26, 2014; Accepted: July 2, 2014; Published: August 12, 2014

Copyright: © 2014 Sojo et al. 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: EPSRC PhD studentship (Victor Sojo), Research grants EPSRC (EP/F500351/1, EP/I017909/1) (Andrew Pomiankowski), Leverhulme Trust (RPG-425) Research grant (Nick Lane). The funders 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.

Abbreviations: Ech, energy-converting hydrogenase; LUCA, last universal common ancestor; SPAP, sodium-proton antiporter; ATPase, ATP synthase