Sarewitz ‘falou e disse’: consenso em ciência está em desacordo com o empreendimento científico vibrante

sábado, dezembro 31, 2011

“Só a ideia de que a ciência expressa melhor a sua autoridade através de declarações consensuais está em desacordo com o empreendimento científico vibrante. Consenso é para livros didáticos [*]; para o seu progresso a ciência real depende de contínuos desafios ao estado atual do sempre imperfeito conhecimento. A ciência forneceria melhor valor para política se articulasse o mais amplo conjunto de interpretações, opções e perspectivas plausíveis, imaginadas pelos melhores especialistas, em vez de forçar a convergência a uma voz supostamente unificada”.— Daniel Sarewitz, Nature 10/6/2011 


“The very idea that science best expresses its authority through consensus statements is at odds with a vibrant scientific enterprise. Consensus is for textbooks; real science depends for its progress on continual challenges to the current state of always-imperfect knowledge. Science would provide better value to politics if it articulated the broadest set of plausible interpretations, options and perspectives, imagined by the best experts, rather than forcing convergence to an allegedly unified voice”.— Daniel Sarewitz, Nature 10/6/2011 



Nem em livros didáticos deve existir consenso. Afinal de contas, consenso é coisa de político, e político é uma classe no Brasil conhecida pela sua ávida corrupção e desmandos.

Livros didáticos sobre ciências devem ensinar ciências objetivamente e questionando as teorias através do contexto de justificação teórica! Não querer isso, como não quer a Nomenklatura científica, é ser igual ou pior do que os políticos corruptos! 

Em 2003 e 2005 apresentamos ao MEC/SEMTEC uma análise crítica de nossos melhores livros didáticos de Biologia do ensino médio, destacando duas fraudes e várias distorções de evidências científicas a favor do fato, Fato, FATO da evolução.

Nada foi feito publicamente pelo MEC/SEMTEC/PNLEM. Sei de dois autores, Amabis e Martho, que deixaram de usar as duas fraudes, mas não explicaram no seu livro novo as razões por que deixaram de utilizá-las. O nome disso é 171 Epistêmico, desonestidade acadêmica!

O que é vida? Parte II: A pobreza do darwinismo

30 December 2011

What Is Life? Part II: The Poverty of Darwinism


In “Part I: The Problem of Agency,” I showed that our normative concepts (roughly, noncausal requirement, purpose, value, and meaning) are intimately related conceptually to one another and to the notion of agency.

Next, I showed that the concept of normative agency, thus defined, is properly applicable to even the most primitive forms of life—even single cells may be properly viewed as normative agents. Thus, conceptually speaking, agency appears to be an essential feature—probably theessential feature—of life itself.

And finally, I ended by asserting that the most reasonable explanation for these facts is that our concept of agency refers to a real phenomenon—agency is an objectively existing property of all organisms.

These claims may appear fantastic to most defenders—and even many critics—of the mainstream Darwinian view of life. Therefore, two more discussions will be required before my via media position between reductionism and theism may begin (I hope) to take on an air of plausibility.

First, I must show why the problem I am addressing—roughly, the place of normativity in the universe—has not already been solved by mainstream science. That is the topic of this column.

Second, I must offer at least some hint of a new direction for future research. Logically, it ought to be enough to point out the inadequacy of our current scientific worldview. But rhetorically, in order for my view to appear plausible, I need to give at least some positive indication of what a post-Darwinian scientific worldview might look like. So, that will be the topic of Part III.

Before proceeding, I would like to acknowledge that not everyone who broadly accepts the mainstream scientific story is a normative nihilist. In the first place, most biologists are probably content to pay lip service to the Darwinian metaphysics without giving too much thought to what it actually entails. They just go about their business—in the laboratory and around the dinner table—with the vague idea that somehow the theory of natural selection makes sense of it all. My remarks are not really addressed to such folks, who are simply unconcerned, professionally or personally, with philosophy or consistency between the different aspects of their lives and experience.

Rather, my remarks here are addressed to those—be they naturalistic philosophers or scientists who make grandiose metaphysical claims for Darwinism—who do concern themselves with the big picture. They do philosophy the honor of taking the problem of normativity seriously, but they do so by viewing our normative concepts as illusory—as referring to nothing real. They claim that the theory of natural selection—supplemented by physics, chemistry, and molecular biology—provides an empirically complete and logically coherent explanation for all the data of biology, and that our normative concepts simply fail to refer to anything objectively existing. These are the folks to whom this column is mainly addressed.

But there is another group, as well, who more or less accept the mainstream scientific worldview at face value, but who balk at its materialistic and reductionist implications. I am thinking of those philosophers who take a basically dualistic approach to the problem, arguing that the domain of normativity—and the realm of human subjective experience, more generally—has its own separate reality, which natural science is simply incompetent to address. There are both theistic and naturalistic versions of this position.

I admit that the naturalistic forms of dualism (broadly, Kantian and phenomenological approaches) are in many ways attractive.(1) But ultimately I reject them, for two reasons. First, the metaphysical division they postulate seems an arbitrary limitation on our search for understanding. Unification—showing how the various parts of our experience cohere—is the very essence of understanding, and there seems no a priori reason why the problems of normativity and agency should be sealed off from empirical inquiry. Of course, it remains for me to show how “unification” can be pursued in a nonreductionist spirit (see Part III).

The other reason why I feel the dualistic approach ought to be rejected is pragmatic. Some philosophers may see in dualism an irenic solution to our problem, but scientists are not likely to go along with them. And, unfortunately, wherever the scientists lead, they tend to drag the rest of us by the nose along with them. The materialist and reductionist vision of the world favored by consistent Darwinists—what I have been calling “value” or “normative” nihilism—is gaining ground with the public at an alarming rate. If it isn’t effectively challenged, our very humanity may be at risk. The most effective way to mount such a challenge is to demonstrate the conceptual and empirical bankruptcy of the Darwinian reductionist worldview.

Let us now turn, then, to this pressing task.

* * *

By “Darwinism,” I mean the claim that the theory of natural selection provides a logically coherent and empirically adequate explanatory framework that is capable of accounting for all biological phenomena in purely mechanistic terms.

Note that challenging this reductionist explanatory framework in no way calls evolution (common descent) into question. It simply raises the question whether our current understanding of life—and so of evolution—makes sense.(2)

It is sometimes hard for those who have not thought very much about these matters to realize what a radical claim Darwinism, so defined, makes. The claim is that our concepts of purpose, value, and meaning—and many other related concepts—literally refer to nothing. Nothing exists in reality corresponding to these ideas. All that really exists is just matter, energy, physical forces, and the principle of natural selection. And with these scientific concepts, we are supposed to be able to give a complete account of everything there is to know about living systems, including ourselves.

So, let’s see if this is true—if it is really the case that the theory of natural selection, together with molecular biology and the rest, provides us with a conceptually and empirically adequate account of biological reality.

The first thing to observe is that the Darwinian explanatory framework cannot do everything it claims to do unless it strictly avoids invoking any normative concepts. That means it may neither appeal to any normative concepts explicity, nor tacitly presuppose any such concepts. If it does explicitly invoke or tacitly assume such concepts, then—at best—it is begging the question of normativity, or—at worst—it is simply incoherent.

Now, it is a striking fact that actual biological practice is replete with normative terminology. You can hardly listen to a lecture in a biology class—you can scarcely find a single page in a biology paper or textbook—that does not violate this prohibition on normative language.

At every step of the way, biology demands consideration of functions (a variety of purpose), requirements, needs, and the reasons why things happen. Everything that happens in organisms seems to have an evaluative dimension as well: We speak constantly of success and failure, good and bad, better and worse, correct and incorrect, etc.

Then, there is the whole range of intentional discourse that has entered biology over the past couple of generations. Biologists cannot get along nowadays without using intentional terms like sign, signal, message, messenger, code, representation, transcription, translation, proofreading, editing, and many others, all borrowed from the ordinary vocabulary for discussing various aspects of human language use.(3)

In short, it appears impossible to discuss biological systems intelligibly for any length of time using only the vocabulary of the natural sciences. Normative vocabulary is simply essential to biological discourse—whether in technical language or in everyday speech. It seems that we have no choice but to employ normative concepts in order to describe living things adequately, and yet we have no need of them to describe the nonliving world.

Presumably, this is no mere coincidence, but rather is due to the fact that living systems are physically quite different from nonliving systems. The fact that we must make use of normative concepts in the one case, but not in the other, provides us with an important clue about the real nature of living systems, if only we choose to pursue it.

Now, the Darwinist will be unimpressed by all of this. He will say that the difference in our way of thinking and speaking about living things is simply an artifact of our cognitive limitations. He cannot very well deny that biological discourse is shot-through with normative terminology, but he can and will deny that we ought to draw any deep metaphysical conclusions from this fact. Rather, he will blithely brush the problem away, saying that the normative language of biology is merely a convenient way of speaking—a façon de parler—and that no particular importance should be attached to it. It is useful in practice, as a heuristic device, but in principle it is not necessary.

Why is it not necessary? Because according to the Darwinist, in principle we know how to substitute the language of the physical sciences for the normative terminology. That is, the Darwinist claims we can take any particular normative term and translate it into terms of physics and chemistry—with the help of the theory of natural selection—without loss of explanatory power.

This, then, is the crucial claim that we must evaluate. Can the Darwinist really use natural selection to rid his theoretical framework of explicit and implicit reliance upon normative concepts? If he can, then he wins, and we must admit that our entire human spiritual world of purpose, value, and meaning is just a tissue of illusion. If he cannot, then he loses, and natural selection goes out the window as the foundation for the modern scientific worldview.

Normative nihilism, yes or no? The intellectual stakes could hardly be higher.

To save space, I am going to assume the reader is familiar with the basics of the theory of natural selection, and go straight to the heart of the Darwinist’s reductionist strategy. The fundamental idea—the essence of Darwinism as a metaphysical system—is that all the appearance of normativity and agency in living things can be explained away in two steps:

(1) We assume that the cell is a machine—all its operations may explained through local physical interactions, and there is no global constraint on the local interactions. Let’s call this the mechanical principle.

(2) The functional coordination of the parts comes about purely through the process of natural selection—random variation and selective retention. Let’s call this theselection principle.


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O que é vida? Parte !: O problema de agência

28 December 2011

What Is Life? Part I: The Problem of Agency


Is there a third way between Darwinian normative nihilism and theism? In other words, is there a different way to deal with the fact that purpose, value, and meaning seem to have a very real grip on our hearts and minds, besides dismissing them as an illusion, with the Darwinist, or appealing to God as their guarantor, with the theist?

Most debates over evolution and human nature simply assume that the answer to these questions is “No.” They oscillate between the two poles of scientific reductionism and theism.

In this post, and two follow-ups, I will make the case for answering these questions with a tentative “Yes.” More specifically, I will show (i) why we have good reason to believe that agency in a strong normative sense is an objective feature of reality (Part I), (ii) why the mainstream Darwinian account of life is radically inadequate (Part II), and (iii) which areas of current scientific investigation might conceivably point the way towards a deeper understanding of living things, and thus of ourselves (Part III).

A blog is obviously no place to try to do serious philosophy. Yet, the exploration of any potential middle ground between reductionism and theism may be of considerable interest to the general public. Also, I have been criticizing Darwinian reductionism in this space from a non-theistic perspective, and I owe interested readers a more detailed account of how this amounts to a coherent position. For these reasons, in this series I will treat these rather involved matters as simply and succinctly as I can.(1)

* * *

I will try to keep jargon to a minimum in this column, but there is one philosophers’ term of art that I need to introduce because there is no ordinary English equivalent for it. That word is “norm,” along with its corresponding adjectival form, “normative,” and abstract noun, “normativity,” which refers to the existence of norms as a feature of the world. So, the first thing I must do is explain what I mean by “norms.”

In ordinary speech, a “norm” is a criterion or a standard. The English word derives from the Latin term for a carpenter’s square—something which sets the standard to which an edge on a table, say, is expected to conform. A shopping list is another sort of norm—when I get home, the contents of my shopping bags should match my shopping list.

Thus, the square plays a role in determining the shape of the table by influencing the carpenter’s actions and the list plays a role in determining the contents of my bags by determining my actions at the grocery store. In general, norms are things that direct or govern our actions and the results of our actions on the world around us. They exert influence over us by getting us to act in such a way as to produce results in accordance with them.

A more succinct way of putting all this is to say that norms are requirements upon our action.

However, the sort of influence that normative requirements have over us is very different from the sort of influence that the laws of nature have over us. This might not be immediately obvious, because we sometimes use the same words to describe results required by norms and results required by natural causes or laws.

For example, I might say I was “required” to stop “because” the light was red and I might also say that the apple was “required” to fall “because” of gravity. But clearly the sense of “requirement” and the sense of “because” are entirely different in the two cases.

I had a choice about whether or not to stop the car, whereas the apple had no choice about whether to fall. The red light was acting upon me as a normative requirement, not as a law of nature. No law of nature prevented me from running the red light. So, a normative requirement is a very different sort of thing from a causal requirement.

Another aspect of norms is that they form a basis for evaluation. Both the carpenter and I may be evaluated on the closeness of the match between our respective norms and our respective results. If the first table the carpenter cuts is too far out of square, he may need to cut another piece of wood. Similarly, if the contents of my shopping bags are too far out of agreement with my shopping list, I may have to return to the grocery store. In other words, one may succeed or fail to apply a norm correctly.

So, the concept of value is logically connected to the concept of normative requirement. The logical implication works in the other direction, as well. To say that something is absolutely good or bad is to say that it satisfies or fails to satisfy some requirement. To say that the thing is comparatively better or worse than something else is to say that the first thing satisfies a requirement more or less nearly than the second thing.

Purpose enters this picture when we think about the relation between normative requirements and results. A normative requirement is like a target an agent is trying to hit. We also say that agents try to attain their goals, fulfill their purposes, and reach their ends. I use all these terms more or less interchangeably. Whatever term we use, practically all action—indeed all biological activity whatever—involves aiming at something, where the target aimed at has the character of a normative requirement.

Another way of looking at biological purpose is this. Purposes consist in virtual (not-yet-realized) states that represent future possible states of the world. These virtual states exert a normative requirement on an agent such that the agent strives to bring the world into conformity with them—to realize the virtual states in the actual world, as one might put it. For example, a hungry animal has the purpose of finding and consuming food. Before it does so, its actions are guided by the normative requirement of eating. After it has eaten, the actual state of the world conforms more closely to the earlier virtual state that was exerting the requirement and directing the action, and we say it has achieved its purpose.

Needless to say, these virtual states must be embodied in the agent (organism) in the present, somehow. I am not saying the future as such can influence the past (so-called “backwards causation”). I must set aside this worry for now, but I will return to it in Part III.

So far, I have shown that the ideas of normative requirement, value, and purpose are intimately linked, conceptually. This most likely means that the phenomena in nature to which they refer are aspects of a single, complex phenomenon. That phenomenon is clearly agency—the power that agents (organisms) have of acting on the world. Therefore, normative requirement, value, and purpose are aspects of agency, and agency is the real heart of the problem we are investigating.

The last step is to see that the problem of agency is quite general. In other words, agency is an essential—I would say the essential—feature, not just of human beings, and not just of the higher animals, but of all living things. It is what distinguishes living systems from nonliving things.

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Liberdade, igualdade e fraternidade deram erradas por que???

Disquem 0800-666

Afinal de contas, somos primos de chimpanzés ou de orangotangos???

sexta-feira, dezembro 30, 2011

Sobre a semelhança genética de 99% entre chimpanzés e humanos 

Os genomas de chimpanzés e humanos são 99% semelhantes! Este é o meme darwiniano repetido ad nauseam na Grande Mídia, sem considerar outras pesquisas que contrariam este mantra dogmático. Considere-se as seguintes publicações científicas: 

1. Esta semelhança já foi chamada de mito na Science 29 June 2007 

2. As evidências contrárias a esta semelhança de 99% está cada vez mais aparecendo na publicações científicas como a Nature 463 536-539, 28 January 2010 

3. O geneticista Richard Buggs tem refletido sobre esta questão científica, e predisse que “quando nós tivermos um genoma de chimpanzé completo e confiável, a semelhança geral com o genoma humano vai se provar próxima dos 70% (muito distante dos 99%). 

“To compare the two [human and chimpanzee] genomes, the first thing we must do is to line up the parts of each genome that are similar. When we do this alignment, we discover that only 2400 million of the human genome's 3164.7 million 'letters' align with the chimpanzee genome - that is, 76% of the human genome. Some scientists have argued that the 24% of the human genome that does not line up with the chimpanzee genome is useless "junk DNA". However, it now seems that this DNA could contain over 600 protein-coding genes, and also code for functional RNA molecules. 

Looking closely at the chimpanzee-like 76% of the human genome, we find that to make an exact alignment, we often have to introduce artificial gaps in either the human or the chimp genome. These gaps give another 3% difference. So now we have a 73% similarity between the two genomes. 

In the neatly aligned sequences we now find another form of difference, where a single 'letter' is different between the human and chimp genomes. These provide another 1.23% difference between the two genomes. Thus, the percentage difference is now at around 72%. 

We also find places where two pieces of human genome align with only one piece of chimp genome, or two pieces of chimp genome align with one piece of human genome. This "copy number variation" causes another 2.7% difference between the two species. Therefore the total similarity of the genomes could be below 70%.”

4. A construção de árvores filogenéticas baseadas em diversos genes existe a possibilidade de sub-árvores filogenéticas entrarem em conflito. 

5. A arqueologia genética demonstra que nós somos mais assemelhados com os orangotangos do que com chimpanzés (uma espécie mais distante dos humanos). Publicado na Genome Research:

6. As árvores filogenéticas são baseadas na pressuposição simples de que o grau de semelhança genética reflete o grau de relação evolucionária. Um artigo destaca isso: 

“molecular systematics is (largely) based on the assumption, first clearly articulated by Zuckerkandl and Pauling (1962), that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity (or dissimilarity) between taxa in the context of a Darwinian model of continual and gradual change. Review of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the 'molecular assumption.' ... For historians and philosophers of science the questions that arise are how belief in the infallibility of molecular data for reconstructing evolutionary relationships emerged, and how this belief became so central ... 

7. Mais dados genéticos estão contradizendo a filogenia evolucionária padrão de humanos e macacos. Um artigo publicado no Molecular Biology and Evolution, em 2007, afirma: 

“For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place”. 

O status epistêmico da semelhança entre os genomas de chimpanzés e humanos demanda mais pesquisas, pois a questão ainda não está definida como alardeiam os darwinistas. 

Afinal de contas, somos primos de chimpanzés ou de orangotangos??? Darwin, lança uma luz aí, mano!!! 

Feliz Ano Novo 2012 ou 5773?

Authorized use/Uso autorizado: Yaakov Kirschen The Dry Bones Blog

1. Olá! Eu sou o Pai Tempo, e este é o ano 2012!

2. Desculpe. Nós somos judeus, e estamos esperando pelo ano 5773.

3. Ele vai chegar em setembro.

4. De qualquer maneira, muito obrigado.


Para, por e com Israel, sempre! Apesar de [preencher as lacunas]

A evolução das famílias de genes de mamíferos

quinta-feira, dezembro 29, 2011

The Evolution of Mammalian Gene Families

Jeffery P. Demuth1, Tijl De Bie2, Jason E. Stajich3, Nello Cristianini4, Matthew W. Hahn1*

1 Department of Biology and School of Informatics, Indiana University, Bloomington, Indiana, United States of America, 2School of Electronics and Computer Science, ISIS Group, University of Southampton, Southampton, United Kingdom, 3Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina, United States of America, 4Department of Statistics, University of California Davis, Davis, California, United States of America


1 Gene families are groups of homologous genes that are likely to have highly similar functions. Differences in family size due to lineage-specific gene duplication and gene loss may provide clues to the evolutionary forces that have shaped mammalian genomes. Here we analyze the gene families contained within the whole genomes of human, chimpanzee, mouse, rat, and dog. In total we find that more than half of the 9,990 families present in the mammalian common ancestor have either expanded or contracted along at least one lineage. Additionally, we find that a large number of families are completely lost from one or more mammalian genomes, and a similar number of gene families have arisen subsequent to the mammalian common ancestor. Along the lineage leading to modern humans we infer the gain of 689 genes and the loss of 86 genes since the split from chimpanzees, including changes likely driven by adaptive natural selection. Our results imply that humans and chimpanzees differ by at least 6% (1,418 of 22,000 genes) in their complement of genes, which stands in stark contrast to the oft-cited 1.5% difference between orthologous nucleotide sequences. This genomic “revolving door” of gene gain and loss represents a large number of genetic differences separating humans from our closest relatives.

Citation: Demuth JP, Bie TD, Stajich JE, Cristianini N, Hahn MW (2006) The Evolution of Mammalian Gene Families. PLoS ONE 1(1): e85. doi:10.1371/journal.pone.0000085

Academic Editor: Justin Borevitz, University of Chicago, United States of America

Received: October 26, 2006; Accepted: November 14, 2006; Published: December 20, 2006

Copyright: © 2006 Demuth 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: This work was supported by grants from the National Science Foundation (MCB-0528465 and DBI-0543586) to MWH and the National Institutes of Health (R33HG003070-01) to NC. TDB acknowledges support from the CoE EF/05/007 SymBioSys, and from GOA/2005/04, both from the Research Council K.U. Leuven. MWH and JPD are also supported by the METACyt Initiative of Indiana University, funded in part through a major grant from the Lilly Endowment, Inc. None of the sponsors played any role in any part of the study.

* To whom correspondence should be addressed. E-mail:

a Katholieke Universiteit Leuven, OKP Research Group, Leuven, Belgium

b Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America

c Department of Engineering Mathematics, University Of Bristol, Bristol, United Kingdom


As mandíbulas de Leviatã


The giant bite of a new raptorial sperm whale from the Miocene epoch of Peru

Olivier Lambert, Giovanni Bianucci, Klaas Post, Christian de Muizon, Rodolfo Salas-Gismondi, Mario Urbina & Jelle Reumer



Corresponding authors

Nature 466, 105–108 (01 July 2010) doi:10.1038/nature09067

Received 08 February 2010 Accepted 25 March 2010


The modern giant sperm whale Physeter macrocephalus, one of the largest known predators, preys upon cephalopods at great depths1, 2. Lacking a functional upper dentition, it relies on suction for catching its prey3; in contrast, several smaller Miocene sperm whales (Physeteroidea) have been interpreted as raptorial (versus suction) feeders4, 5, analogous to the modern killer whale Orcinus orca. Whereas very large physeteroid teeth have been discovered in various Miocene localities, associated diagnostic cranial remains have not been found so far6, 7, 8. Here we report the discovery of a new giant sperm whale from the Middle Miocene of Peru (approximately 12–13 million years ago), Leviathan melvillei, described on the basis of a skull with teeth and mandible. With a 3-m-long head, very large upper and lower teeth (maximum diameter and length of 12 cm and greater than 36 cm, respectively), robust jaws and a temporal fossa considerably larger than in Physeter, this stem physeteroid represents one of the largest raptorial predators and, to our knowledge, the biggest tetrapod bite ever found. The appearance of gigantic raptorial sperm whales in the fossil record coincides with a phase of diversification and size-range increase of the baleen-bearing mysticetes in the Miocene. We propose that Leviathan fed mostly on high-energy content medium-size baleen whales. As a top predator, together with the contemporaneous giant shark Carcharocles megalodon, it probably had a profound impact on the structuring of Miocene marine communities. The development of a vast supracranial basin in Leviathan, extending on the rostrum as in Physeter, might indicate the presence of an enlarged spermaceti organ in the former that is not associated with deep diving or obligatory suction feeding.

Subject terms: Palaeontology, Evolution, Earth sciences



Tradução do código genético apresenta uma compensação linear entre eficiência e precisão da seleção tRNA

Genetic code translation displays a linear trade-off between efficiency and accuracy of tRNA selection

Magnus Johansson, Jingji Zhang, and Måns Ehrenberg1

Author Affiliations
Department of Cell and Molecular Biology, Biomedical Center, Uppsala University, Box 596, 751 24 Uppsala, Sweden

Edited by Peter B. Moore, Yale University, New Haven, CT, and approved November 11, 2011 (received for review October 6, 2011)


Rapid and accurate translation of the genetic code into protein is fundamental to life. Yet due to lack of a suitable assay, little is known about the accuracy-determining parameters and their correlation with translational speed. Here, we develop such an assay, based on Mg2+ concentration changes, to determine maximal accuracy limits for a complete set of single-mismatch codon–anticodon interactions. We found a simple, linear trade-off between efficiency of cognate codon reading and accuracy of tRNA selection. The maximal accuracy was highest for the second codon position and lowest for the third. The results rationalize the existence of proofreading in code reading and have implications for the understanding of tRNA modifications, as well as of translation error-modulating ribosomal mutations and antibiotics. Finally, the results bridge the gap between in vivo and in vitro translation and allow us to calibrate our test tube conditions to represent the environment inside the living cell.

fidelity, rate-accuracy trade-off, ribosome. protein synthesis, elongation


1To whom correspondence should be addressed.

Author contributions: M.J. and M.E. designed research; M.J. and J.Z. performed research; M.J., J.Z., and M.E. analyzed data; and M.J. and M.E. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information on-line at

Freely available online through the PNAS open access option. 



Contribuição das especulações transformistas de Darwin na origem e evolução desta extrema complexidade de sistema biológico: ZERO, NADA, NIL!!!

Regeneração tipo vertebrado no cordado invertebrado Anfioxo

quarta-feira, dezembro 28, 2011

Vertebrate-like regeneration in the invertebrate chordate amphioxus

Ildikó M. L. Somorjai a,b,1,2, Rajmund L. Somorjai c, Jordi Garcia-Fernàndez b,1, and Hector Escrivà a,1

Author Affiliations

aObservatoire Océanologique de Banyuls-sur-Mer, Centre National de la Recherche Scientifique and Université Pierre et Marie Curie Paris VI, F-66650 Banyus-sur-Mer, France;
bDepartament de Genètica, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain; and
cNational Research Council of Canada, Institute for Biodiagnostics, Winnipeg, MB, R3B 1Y6, Canada

Edited by Sean B. Carroll, University of Wisconsin, Madison, WI, and approved November 23, 2011 (received for review January 5, 2011)


An important question in biology is why some animals are able to regenerate, whereas others are not. The basal chordate amphioxus is uniquely positioned to address the evolution of regeneration. We report here the high regeneration potential of the European amphioxus Branchiostoma lanceolatum. Adults regenerate both anterior and posterior structures, including neural tube, notochord, fin, and muscle. Development of a classifier based on tail regeneration profiles predicts the assignment of young and old adults to their own class with >94% accuracy. The process involves loss of differentiated characteristics, formation of an msx-expressing blastema, and neurogenesis. Moreover, regeneration is linked to the activation of satellite-like Pax3/7 progenitor cells, the extent of which declines with size and age. Our results provide a framework for understanding the evolution and diversity of regeneration mechanisms in vertebrates.

invertebrate chordate-vertebrate transition, stem cells, cephalochordate


1To whom correspondence may be addressed. 

2Present address: Centre for Organismal Studies (COS), University of Heidelberg, 69120 Heidelberg, Germany.

Author contributions: I.M.L.S. and R.L.S. designed research; I.M.L.S. and R.L.S. performed research; I.M.L.S., R.L.S., J.G.-F., and H.E. contributed new reagents/analytic tools; I.M.L.S. and R.L.S. analyzed data; and I.M.L.S., R.L.S., J.G.-F., and H.E. wrote the paper.

The authors declare no conflict of interest.

*This Direct Submission article had a prearranged editor.

This article contains supporting information online at

Freely available online through the PNAS open access option.


Uma newsletter de biociência que não está jorrando Darwin?

terça-feira, dezembro 27, 2011

Uma newsletter de biociência que não está jorrando Darwin?

26 de dezembro de 2011 Postado por News sob Epigenetics, Genetics, News

Um amigo escreve, sobre a newsletter de biociência, Primavera de 2012, da Universidade do Texas Bioscience, destacando a refrescante ausência da louvação a Darwin:

"Vocês repararam a falta significante de darwinismo dogmático nesta newsletter? Lendo o artigo “The Epigenetic Landscape” [O cenário epigenético], palavras como “Darwin”  e “evolução” não ocorreram nenhuma vez. Mas eles disseram coisas como “A epigenética tende a ser multidimensional na natureza”, “A epigenética, por definição, é quando não há nenhuma mudança no DNA, mas o fenótipo é diferente”, “Nossa pesquisa tem a ver com o que nós chamamos de mutações não-codificantes. As pessoas costumavam chamar isso de DNA lixo”, e “Isso é algum tipo de herança de um caractere adquirido no sentido lamarckiano?”

Nas p. 4 e 5, eles discutem o Course Transformation Project (CTP) [Projeto de Transformação do Curso] para introdução de  cursos de biologia. O novo curso BIO 311C tem "3 Grandes Ideias”. Surpreendentemente, a evolução não foi nenhuma das três grandes ideias. A Grande Ideia # 1 é “A estrutura se relaciona com a função”, que depois é dividida em 5 sub-tópicos, e a Grande Ideia # 3 afirma “A estrutura das células evoluiu para desempenha uma variedade de funções essenciais”. Se eles tivessem simplesmente substituído "evoluiu" por “foi intencionalmente planejado", isso seria um grande curso!

Talvez o pessoal da newsletter será importunado em seguida para fazer penitências a Darwin a fim de provar sua submissão, e será interessante ver como isso vai ser.

Nós não estamos preocupados com isso, porque alguns - a esta altura – aqueles que recusam jorrar as penitências se juntam a um grupo crescente de refuseniks. Os que se submeterem, conhecendo a verdade, podem calcular melhor o seu valor.

Siga o UD News no Twitter!




Barítonos podem até ser machos atraentes, mas não são garantia de boa qualidade de sêmen

Low Pitched Voices Are Perceived as Masculine and Attractive but Do They Predict Semen Quality in Men?

Leigh W. Simmons1,2*, Marianne Peters1,2,Gillian Rhodes2

1 Centre for Evolutionary Biology, School of Animal Biology (M092), University of Western Australia, Crawley, Western Australia, Australia, 2 ARC Centre of Excellence in Cognition and its Disorders, School of Psychology, University of Western Australia, Crawley, Western Australia, Australia


Women find masculinity in men's faces, bodies, and voices attractive, and women's preferences for men's masculine features are thought to be biological adaptations for finding a high quality mate. Fertility is an important aspect of mate quality. Here we test the phenotype-linked fertility hypothesis, which proposes that male secondary sexual characters are positively related to semen quality, allowing females to obtain direct benefits from mate choice. Specifically, we examined women's preferences for men's voice pitch, and its relationship with men's semen quality. Consistent with previous voice research, women judged lower pitched voices as more masculine and more attractive. However men with lower pitched voices did not have better semen quality. On the contrary, men whose voices were rated as more attractive tended to have lower concentrations of sperm in their ejaculate. These data are more consistent with a trade off between sperm production and male investment in competing for and attracting females, than with the phenotype-linked fertility hypothesis.

Citation: Simmons LW, Peters M, Rhodes G (2011) Low Pitched Voices Are Perceived as Masculine and Attractive but Do They Predict Semen Quality in Men? PLoS ONE 6(12): e29271. doi:10.1371/journal.pone.0029271

Editor: Jerson Laks, Federal University of Rio de Janeiro, Brazil

Received: October 5, 2011; Accepted: November 23, 2011; Published: December 21, 2011

Copyright: © 2011 Simmons 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: This work was supported by Australian Research Council Professorial Fellowships to Gillian Rhodes and Leigh Simmons. It was also supported by the Australian Research Council Centre of Excellence for Cognition and its Disorders (project number CE110001021). 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.



Sugiro um nome para esta teoria evolucionária musical bizarra: Teoria do Caos na escolha de parceiros!!!

A explosão Cambriana cada vez mais detonando as especulações transformistas de Darwin

segunda-feira, dezembro 26, 2011

Darwin já sabia em 1859 que a 'explosão Cambriana' (não era este o termo, mas os fósseis daquele período já eram conhecidos) detonava as suas especulações transformistas: todos os filos animais mais antigos já apareciam ali completamente funcionais e sem elos transicionais. 

NOTA BENE: Os autores dos livros didáticos de Biologia do ensino médio OMITEM INTENCIONALMENTE as implicações da Explosão Cambriana para a corroboração da teoria da evolução de Darwin através da seleção natural e n mecanismos evolucionários de A a Z no contexto de justificação teórica. 

Por que OMITEM INTENCIONALMENTE? Porque para ocorrer novidades evolucionárias - novas formas biológicas, é preciso muita informação genética. E a janela geológica é muito pequena para a evolução ocorrer: uns 10 milhões de anos!!!

O nome disso é DESONESTIDADE ACADÊMICA, 171 EPISTÊMICO, mas o MEC/SEMTEC/PNLEM é que aprova esses livros didáticos.

Bem, enquanto esta DESONESTIDADE ACADÊMICA permanece entre nós, vamos à literatura especializada e verificar o que os cientistas evolucionistas honestos estão dizendo sobre as descobertas feitas de fósseis no pré-Cambriano.

Novas técnicas estão permitindo uma inspeção mais nítida e próxima dos alegados embriões. Uma equipe internacional de pesquisadores utilizaram um microscópio não-invasivo de síncrotron, e apresentaram suas descobertas na revista  Science. E qual foi o resultado: não são embriões, mas cistos de protistas.

N. J. Butterfield, explicou na mesma edição da
Science, a miséria do desapontamento dos darwinistas: 

"Ever since Darwin there has been a disturbing void, bothpaleontological and psychological, at the base of the Phanerozoic eon. If his theory of gradualistic evolution be true, then surely the pre-Phanerozoic oceans must have swarmed with living animals—despite their conspicuous absence from the early fossil record. Thus, the 1998 report of fossilized animal embryos in the early Ediacaran Doushantuo Formation of South China was met with almost palpable relief. It was indeed the fossil record that had let us down, not the textbooks, and certainly not the exciting new insights from molecular clocks. All was not as it seemed, however, and new data from Huldtgren et al. on page 1696 of this issue, look set to revoke the status of these most celebrated Ediacaran fossils. 

O ponto principal é que esses esporos não estão a caminho de se tornar planos corporais de animais. “Although unquestionably eukaryotic, the fossils are not metazoan, or even properly multicellular by all appearances,” disse Butterfield. 

The researchers tried to put a semi-happy face on their conclusion by claiming it might still represent a transition “that evolved after the last common ancestor of animals and fungi, but before the last common ancestor of living (that is, crown-group) animals”.

Here’s what Butterfield had to say about that: “In terms of progressivist storytelling, this all seems a little too good to be true,” since other microbes have a similar growth habit. The authors even acknowledge that “the much broader distribution of this habit undermines its utility as a phylogenetic marker,” Butterfield added.

Butterfield relutou em manter sua equanimidade apesar do seu desapontamento: 

“Interpretation at this level is inevitably impressionistic, but to my eye there is still a case for identifying the Doushantuo fossils as embryos, albeit algal rather than animal.”

Eu nem preciso dizer, mas uma alga não é nada como um animal (Ex.: um trilobita com membros articulados e olhos complexos).


Science 23 December 2011: 
Vol. 334 no. 6063 pp. 1696-1699 
DOI: 10.1126/science.1209537

Fossilized Nuclei and Germination Structures Identify Ediacaran “Animal Embryos” as Encysting Protists

Therese Huldtgren1,2, John A. Cunningham3Chongyu Yin4Marco Stampanoni5,6Federica Marone5Philip C. J. Donoghue3,*Stefan Bengtson1,7,*

Author Affiliations

1Department of Palaeozoology, Swedish Museum of Natural History, 10405 Stockholm, Sweden.
2Department of Geological Sciences, Stockholm University, 10691 Stockholm, Sweden.
3Department of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK.
4Institute of Geology, Chinese Academy of Geological Sciences, Beijing 100037, China.
5Swiss Light Source, Paul Scherrer Institute, CH-5232 Villigen, Switzerland.
6Institute for Biomedical Engineering, University and Eidgenössische Technische Hochschule Zürich, CH-8092 Zürich, Switzerland.
7Nordic Center for Earth Evolution, Swedish Museum of Natural History, 10405 Stockholm, Sweden.

*To whom correspondence should be addressed. E-mail: (S.B.); (P.C.J.D.)


Globular fossils showing palintomic cell cleavage in the Ediacaran Doushantuo Formation, China, are widely regarded as embryos of early metazoans, although metazoan synapomorphies, tissue differentiation, and associated juveniles or adults are lacking. We demonstrate using synchrotron-based x-ray tomographic microscopy that the fossils have features incompatible with multicellular metazoan embryos. The developmental pattern is comparable with nonmetazoan holozoans, including germination stages that preclude postcleavage embryology characteristic of metazoans. We conclude that these fossils are neither animals nor embryos. They belong outside crown-group Metazoa, within total-group Holozoa (the sister clade to Fungi that includes Metazoa, Choanoflagellata, and Mesomycetozoea) or perhaps on even more distant branches in the eukaryote tree. They represent an evolutionary grade in which palintomic cleavage served the function of producing propagules for dispersion.

Received for publication 8 June 2011.
Accepted for publication 16 November 2011.


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