Ministério Público quer proteção de fósseis de dinossauros em SP

JC e-mail 4591, de 26 de Setembro de 2012.

 

14. Ministério Público quer proteção de fósseis de dinossauros em SP

Sítios arqueológicos em áreas particulares de três cidades do noroeste paulista estariam ameaçados, diz o MPF.

O Ministério Público Federal de Jales, a 601 quilômetros de São Paulo, entrou com ação civil pública na Justiça Federal visando à preservação de sete depósitos com fósseis de dinossauros do Período Cretáceo, há pelo menos 65 milhões de anos.

De acordo com o MPF, eles formam um dos maiores complexos fossilíferos do País, mas correm o risco de se perderem. A ameaça vem principalmente das plantações de cana-de-açúcar e da criação de animais que invadem os sítios paleontológicos, localizados em áreas particulares.

O MPF pediu uma liminar para que as prefeituras de General Salgado, Auriflama e São João de Iracema, além de órgãos da União e do Estado, apresentem em 60 dias o mapeamento dos sítios e um plano para preservá-los.

Na região, os cientistas identificaram 17 espécimes de répteis do Cretáceo, pertencentes a três diferentes espécies de crocodiliformes de médio a grande porte. Duas delas foram descritas a partir desses achados, a Baurussuchus e Armadillosuchus arrudae.

Em General Salgado, onde está a maioria dos sítios, os fósseis foram encontrados na década de 1990. "Além dos esqueletos fossilizados, foram encontrados outros vestígios de vida daquele período (icnofósseis), como cascas de ovos, gastrólitos (pedras presentes no sistema digestivo de animais), coprólitos (fezes conservadas por processo de mineralização), rastros de vertebrados e invertebrados conservados na rocha", descreve na ação o procurador Thiago Lacerda Nobre.

As descobertas foram consideradas "de notável importância científica" pela Comissão Brasileira de Sítios Geológicos e Paleobiológicos, que encaminhou à Global Indicative List of Geological Sites, órgão de referência internacional dos sítios geológicos, recomendação para que o sítio fossilífero de General Salgado fosse considerado Patrimônio Mundial da Humanidade. Segundo Nobre, o laudo do Departamento Nacional de Produção Mineral (DNPM) concluiu ser grande o potencial de novos achados.

Além das prefeituras, o MPF atribui a órgãos federais, como o DNPM e o Ibama, e ao governo estadual a responsabilidade pela preservação. A ação pede a apresentação, em 120 dias, de projeto de criação de unidades de conservação do patrimônio natural, a serem criadas até três meses depois. A prefeitura de General Salgado informou que há um plano para preservar o sítio, mas o projeto depende do próximo prefeito. Auriflama e São João de Iracema aguardarão notificação da Justiça. O Ibama também não tinha conhecimento da ação e o DNPM colabora com o MPF para preservar os sítios.

(O Estado de São Paulo)

A pior de todas as hipóteses científicas sobre a origem da vida

The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)

Harold S Bernhardt 1

Email: harold.bernhardt@otago.ac.nz

1 Department of Biochemistry, University of Otago, P.O. Box 56, Dunedin, New Zealand

Abstract

The problems associated with the RNA world hypothesis are well known. In the following I discuss some of these difficulties, some of the alternative hypotheses that have been proposed, and some of the problems with these alternative models. From a biosynthetic – as well as, arguably, evolutionary – perspective, DNA is a modified RNA, and so the chicken and-egg dilemma of “which came first?” boils down to a choice between RNA and protein. This is not just a question of cause and effect, but also one of statistical likelihood, as the chance of two such different types of macromolecule arising simultaneously would appear unlikely. The RNA world hypothesis is an example of a ‘top down’ (or should it be ‘present back’?) approach to early evolution: how can we simplify modern biological systems to give a plausible evolutionary pathway that preserves continuity of function? The discovery that RNA possesses catalytic ability provides a potential solution: a single macromolecule could have originally carried out both replication and catalysis. RNA – which constitutes the genome of RNA viruses, and catalyzes peptide synthesis on the ribosome – could have been both the chicken and the egg! However, the following objections have been raised to the RNA world hypothesis: (i) RNA is too complex a molecule to have arisen prebiotically; (ii) RNA is inherently unstable; (iii) catalysis is a relatively rare property of long RNA sequences only; and (iv) the catalytic repertoire of RNA is too limited. I will offer some possible responses to these objections in the light of work by our and other labs. Finally, I will critically discuss an alternative theory to the RNA world hypothesis known as ‘proteins first’, which holds that proteins either preceded RNA in evolution, or – at the very least – that proteins and RNA coevolved. I will argue that, while theoretically possible, such a hypothesis is probably unprovable, and that the RNA world hypothesis, although far from perfect or complete, is the best we currently have to help understand the backstory to contemporary biology.

Reviewers

This article was reviewed by Eugene Koonin, Anthony Poole and Michael Yarus (nominated by Laura Landweber).

Keywords RNA world hypothesis, Proteins first, Acidic pH, tRNA introns, Small ribozymes

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NOTA DESTE BLOGGER:

O Mundo RNA, segundo Harold S Bernhardt, é a pior de todas as hipóteses científicas, porque não é corroborada no contexto de justificação teórica, mas é a única que temos!!!

Macacos me mordam, durma-se com um barulho desses - a ciência, uma busca pela verdade, repousa agora nas piores teorias e hipóteses, mas se são as únicas que temos, é com essas que se faz ciência normal hoje em dia!

E as evidências? Ora, as evidências que se danem, o que vale é a teoria (Atribuída a Dobzhansky no Brasil, mas seus alunos sobreviventes se recusam a comentar). E nossos alunos do ensino médio ainda aprendem o Mundo RNA como verdade científica...

Pobre ciência!!!

Repensando o (im)possível em evolução

Progress in Biophysics and Molecular Biology (2013)

March 18-21, 2012, Oxford Workshop on “Conceptual Foundations of Systems Biology”

Rethinking the (Im)Possible in Evolution

James A. Shapiro

Gordon Center for Integrative Science W123B

University of Chicago, jsha@uchicago.edu

Introduction: The philosophical background

Science inevitably operates in ignorance of future developments. Results and concepts that seem inconceivable in one period become conventional wisdom in later decades and centuries. The history of science is replete with examples (Kuhn 1962). Moreover, it is often the case that we cannot perceive the blinders we impose on ourselves out of philosophical commitments rather than empirical necessities.

Evolutionary thinking began in the 18th Century, at the same time as other fields in biology were transforming into more professional and rigorous disciplines (Stott 2012). In the second half of the 19th Century, the Darwinian ideas of gradual change and natural selection as a creative force engaged in a fierce battle with religious ideas of divine creation over the explanation of biological diversity. In order to combat the teleological arguments of William Paley for a divine watchmaker (Paley 1802 (republished 2006)), the evolutionists rigorously excluded all notions of goal-oriented activity from their theories. In keeping with 19th Century mathematical thermodynamics, they insisted upon randomness at the microscopic level as the basis for macroscopic effects.

As evolutionary thinking integrated Mendelian genetics into the neo-Darwinian Modern Synthesis (Huxley 1942), it adopted the mechanistic thinking that prevailed following the intense Mechanism-Vitalism debate of the early 20th Century. The vitalists, like Hans Driesch, argued that there must be something special about living organisms that informed their activities (Driesch 1908). The mechanicists, led by Driesch’s fellow student, Wilhelm Roux, insisted that only demonstrable physical or chemical entities could be invoked to account for biological phenomena (Roux 1895). Since the vitalists could not explain the nature of their hypothetical special life force, the mechanists prevailed for the rest of the 20th Century.

The issues in the Mechanism-Vitalism debate survive to the present day. In the 1950s, molecular biology and the identification of DNA as “the secret of life” were seen as the final triumph of the mechanists’ physico-chemical view of living organisms. It became possible to describe the cell and multicellular organisms in precise molecular terms. However, the rest of the 20th Century and the beginning of the 21st Century provided a finely ironic turn to the philosophical debate.

As molecular biology advanced, it began to uncover ever more complex and sophisticated multi-molecular networks that carry out sensory, communication, regulatory and decision-making activities within and between cells (Gerhart and Kirschner 1997; Alberts, Johnson et al. 2002). At the same time, the 20th Century development of cybernetics, computers and electronic information-processing systems began to provide real-world examples for capacities the vitalists saw at work in living organisms. The information revolution had come to biology.

This contribution to the workshop attempts to outline how the biological information revolution and its underlying molecular observations impact our thinking about evolution. The intentionally ambivalent title is there for the following reason. Showing how previously excluded (i.e., impossible) notions have been supported by empirical observations inevitably allows us to consider previously excluded concepts as feasible (i.e., possible) hypotheses.

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NOTA DESTE BLOGGER:

Já cansei de mencionar aqui neste blog que a Biologia do final do século 20 e começo do século 21 é uma ciência de informação. A tarefa, nada fácil para a Nomenklatura científica, é explicar a origem da informação biológica. Até onde sabemos, os cientistas são profundamente ignorantes sobre esta questão!

Algum cientista tupiniquim se habilita??? Francisco Salzano, Sergio Danilo Junho Pena et al (a turma que escreveu a carta ao presidente da Academia Brasileira de Ciências), ou a estudantada da Sociedade Brasileira de Genética deixa de lado os Manifestos e faz ciência normal em busca de uma explicação estritamente naturalista em termos físico-químicos??? Ou a físico-química não explica a origem da informação genética???

Deslocação do quadro de leitura programada (do código genético) ribossômica vai além dos vírus

Volume 1, Number 11, 2006 / Microbe

Programmed Ribosomal Frameshifting Goes beyond Viruses

Jonathan D. Dinman

Organisms from all three kingdoms use frameshifting to regulate gene expression, perhaps signaling a paradigm shift.

Summary

• Programmed ribosomal frameshifting (PRF) enables mainly viruses but also other organisms to adjust the reading frame of messenger RNA and thus to pack more information into their genomes.

• Organisms from all three kingdoms use PRF as a posttranscriptional mechanism to regulate gene expression, perhaps signaling a paradigm shift as to what constitutes the “correct” reading frame for mRNA molecules.

• Despite the use of several bioinformatic strategies, identifying -1 PRF signals remains daunting, even as computational power continues to increase.

• PRF might be an extremely old remnant of a prebiotic RNA world.

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NOTA DESTE BLOGGER:

Em 2006 eu escrevi no meu perfil neste blog:

"Por que sou ‘pós-darwinista’? Porque já fui evolucionista de carteirinha. Hoje, sou cético da teoria macroevolutiva como verdade científica. Contudo, meu ceticismo ao ‘dogma central’ darwinista não é baseado em relatos da criação de textos sagrados. Foi a séria e conflituosa consideração do debate que ocorre intramuros e nas publicações científicas há muitos anos sobre a insuficiência epistêmica da teoria geral da evolução.

Eu fui ateu marxista-leninista. Hoje, não tenho mais fé cega no ateísmo. Não creio mais na interpretação literal dos dogmas de Darwin aceitos ‘a priori’ e defendidos ideologicamente com unhas e dentes pela Nomenklatura científica. A Ciência me deu esta convicção. Aprendi na universidade: quando uma teoria científica não é apoiada pelas evidências, ela deve ser revista ou simplesmente descartada. Sou pós-darwinista me antecipando à iminente e eminente ruptura paradigmática em biologia evolutiva. Chegou a hora de dizer adeus a Darwin."

Bem, aí está um desses artigos de 2006 (quando meu blog foi lançado) em que se afirma a necessidade de uma mudança paradigmática em biologia evolucionária. Muito mais agora com o ENCODE mandando para a lata de lixo da História da Ciência a hipótese de DNA "lixo" defendida com unhas e dentes pelos darwinistas ortodoxos fundamentalistas xiitas como sendo uma evidência contra a teoria do Design Inteligente.

Fui, nem sei por que, rachando de rir da cara de alguns na Nomenklatura científica (os que escrevem cartas chorando as pitangas e os que escrevem manifestos tipo estudantes) [Vocês não sabem de quem estou falando???] e da Galera de meninos e meninas de Darwin que ficou sem pai e sem mãe com o avanço da ciência e a divulgação de pesquisas revelando níveis de complexidade que cada vez mais enfraquecem Darwin (o homem que teve a maior ideia que toda a humanidade já teve) e fortalecem a posição dos teóricos do Design Inteligente.

Frans de Waal laureado com o prêmio igNobel de 2012

ANATOMY PRIZE: Frans de Waal [The Netherlands and USA] and Jennifer Pokorny [USA] for discovering that chimpanzees can identify other chimpanzees individually from seeing photographs of their rear ends.

REFERENCE: "Faces and Behinds: Chimpanzee Sex Perception" Frans B.M. de Waal and Jennifer J. Pokorny, Advanced Science Letters, vol. 1, 99–103, 2008.

ATTENDING THE CEREMONY: Frans de Waal and Jennifer Pokorny

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FREE PDF GRATIS: Emory University

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Frans B. M. de Waal

C. H. Candler Professor of Primate Behavior

399 Psychology Building

36 Eagle Row 

Emory University

Atlanta, GA 30322

Phone:  404-727-7898; Fax: 404-727-0372 

Email: dewaal@emory.edu

Dr. de Waal received his Ph.D. in Biology and Zoology from Utrecht University, the Netherlands, in 1977. He completed his postdoctoral study of chimpanzees while associated with Utrecht University, in 1981, and moved the same year to the USA. He has been a National Academy of Sciences member since 2004, and a Royal Dutch Academy of Sciences member since 1993. Time featured him in 2007 as one of the World's One Hundred Most Influential People. He is also the Director of Living Links at the Yerkes National Primate Research Center.

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NOTA DESTE BLOGGER:

Também pudera, com uma pesquisa sobre chimpanzés reconhecerem sexualmente outros chimpanzés através de fotografias de seus traseiros...

O gene (egoísta) já era!!!

Evolution News & Views 19 de setembro de 2012 5:34 AM | Permalink

Como muita gente do resto do mundo que segue as notícias da ciência, nós ficamos impressionados pelas implicações do ENCODE 2.0. Lendo os artigos e considerando os dados, está bem claro que a unidade chamada "gene" já era. Isto significa dizer que, o "gene" está para a morfogênese assim como o "flogisto" está para a química e física... um conceito obsoleto. E com o primeiro desprovido de conteúdo, o referencial teórico da genética evolucionária/populacional, bem, já era. Isso mesmo: Já era. E então o que nós herdamos? Um fenótipo (= sequências de RNA; transcrições).

Repare bem:

“...três quartos do genoma humano são capazes de ser transcrito, bem como as observações sobre o alcance e os níveis de expressão, a localização, os destinos de processamento, as regiões reguladoras e as modificações de quase todos os milhares de RNAs atualmente anotados e previamente não anotados. Essas observações, consideradas em conjunto, impele à redefinição do conceito de um gene.

Isso apoia e é consistente com observações anteriores de um genoma altamente transcrito intercalado, mas mais importante, impele à reconsideração da definição de um gene. Como isso é uma característica consistente de genomas anotados, nós iríamos propor que o TRANSCRITO seja considerado como A UNIDADE ATÔMICA BÁSICA DA HEREDITARIEDADE. Concomitantemente, o termo gene denotaria então um conceito de ordem superior projetado (SIC) em capturar todos esses transcritos (eventualmente divorciados de suas localidades genômicas) que contribuem para um dado traço fenotípico.” (Landscape of transcription in human cells. Sarah Djebali et al. Nature 2012 489: 101-108.)

“...three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.

This supports and is consistent with earlier observations of a highly interleaved transcribed genome, but more importantly, prompts the reconsideration of the definition of a gene. As this is a consistent characteristic of annotated genomes, we would propose that the TRANSCRIPT be considered as THE BASIC ATOMIC UNIT OF INHERITANCE. Concomitantly, the term gene would then denote a higher-order concept intended to capture all those transcripts (eventually divorced from their genomic locations) that contribute to a given phenotypic trait.”(Landscape of transcription in human cells. Sarah Djebali et al. Nature 2012 489: 101-108.)

E:

“Embora o gene tenha sido convencionalmente considerado como a unidade fundamental de organização genômica, agora, com base nos dados do ENCODE é convincentemente argumentado que esta unidade não é o gene, mas antes o transcrito (Washietl et al. 2007; Djebali et al. 2012a). Nesta visão, os genes representam uma estrutura de ordem superior em torno dos quais os transcritos individuais se amalgamam, criando uma entidade polifuncional que assume formas diferentes sob diferentes estados celulares, guiados pela utilização diferencial do DNA regulador.” (What does our genome encode? John A. Stamatoyannopoulos Genome Res. 2012 22: 1602-1611.)

“Although the gene has conventionally been viewed as the fundamental unit of genomic organization, on the basis of ENCODE data it is now compellingly argued that this unit is not the gene but rather the transcript (Washietl et al. 2007; Djebali et al. 2012a). On this view, genes represent a higher-order framework around which individual transcripts coalesce, creating a poly-functional entity that assumes different forms under different cellular states, guided by differential utilization of regulatory DNA.” (What does our genome encode? John A. Stamatoyannopoulos Genome Res. 2012 22: 1602-1611.)

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NOTA DESTE BLOGGER:

Traduzindo em miúdos epistemológicos - a hipótese do gene egoísta de Dawkins é um DELIRIUM TREMENS. E já foi tarde para a lata do lixo da História da Ciência!!!

Por este critério, o Darwinismo seria pseudociência!!!

September 17, 2012

Separating the Pseudo From Science

By Michael D. Gordin

Jonathan Twingley for The Chronicle Review

The term "pseudoscience" gets thrown around quite a bit these days, most notably in debates about the dominant consensus on anthropogenic climate change. Say "pseudoscience," and immediately a bunch of doctrines leap to mind: astrology, phrenology, eugenics, ufology, and so on. Do they have anything in common? Some posit unknown forces of nature, others don't. Some are advocated by outsiders to the scientific community, while others have been backed by the elite. And the status of each can fluctuate over time. (Astrology, for example, was considered an exemplary field of natural knowledge from antiquity through the Renaissance.)

For millennia, philosophers have attempted to erect a boundary between those domains of knowledge that are legitimate and those that are anything but­—from Hippocrates' essay on "the sacred disease" (epilepsy) to editorials decrying creationism. The renowned philosopher Karl Popper coined the term "demarcation problem" to describe the quest to distinguish science from pseudoscience. He also proposed a solution. As Popper argued in a 1953 lecture, "The criterion of the scientific status of a theory is its falsifiability." In other words, if a theory articulates which empirical conditions would invalidate it, then the theory is scientific; if it doesn't, it's pseudoscience.

That seems clear enough. Unfortunately, it doesn't work. Epistemologists present several challenges to Popper's argument. First, how would you know when a theory has been falsified? Suppose you are testing a particular claim using a mass spectrometer, and you get a disagreeing result. The theory might be falsified, or your mass spectrometer could be on the fritz. Scientists do not actually troll the literature with a falsifiability detector, knocking out erroneous claims right and left. Rather, they consider their instruments, other possible explanations, alternative data sets, and so on. Rendering a theory false is a lot more complicated than Popper imagined—and thus determining what is, in principle, falsifiable is fairly muddled.

The second problem is that Popper fails to demarcate in the right place. Creationism, for example, makes a series of falsifiable claims about radioactive dating, rates of erosion, and so on, while the more "historical" sciences, like geology and astronomy, pose theories that are more explanatory narratives than up-or-down (and therefore falsifiable) protocol statements of empirical bullet points. Any criterion had better at least replicate our common-sense notion of "science," and so far no clear criterion has been able to do so. No wonder most philosophers have given up on the task. As the prominent philosopher of science Larry Laudan put it 30 years ago: "If we would stand up and be counted on the side of reason, we ought to drop terms like 'pseudoscience' and 'unscientific' from our vocabulary; they are just hollow phrases that do only emotive work for us." Demarcation is distinctly out of fashion among philosophers today.

On the other hand, "emotive work" is pretty interesting from a historical perspective. Scientists consider a great many doctrines to be wrong, even wrongheaded, but not all of them get labeled "pseudoscience." No one in the history of the world has ever considered himself a pseudoscientist. It is a term of abuse that is deployed by some members of a scientific community against individuals they consider threatening. By tracking under which conditions scientists denigrate others as "pseudoscientists," we can actually learn how scientists define healthy science at a particular moment. Instead of attempting to find a one-size-fits-all demarcation criterion, we should think about pseudoscience historically. This helps us understand how science functioned in the past as well as in the present.

Over the past several years, I've undertaken to do just that, in studying Immanuel Velikovsky. Velikovsky (1895-1979) is no longer a household name—very few people under 50 have heard of him—but from 1950 to 1980 he dominated debates about demarcation. At issue were his catastrophist theories, first promulgated in his 1950 blockbuster Worlds in Collision (published by Macmillan, then the most respected publisher of scientific books in the United States), and later extended and elaborated in a half-dozen further volumes.

Velikovsky had a big idea. When he read ancient myths and legends from around the world—especially the Hebrew Bible and other texts from the ancient Near East—he came across similar images: fire raining from the heavens, enormous earthquakes, epic flooding, and so on. What if these were not just metaphors or hallucinations, but actual eyewitness observations? What if they described not different disasters, but one single global catastrophe? Velikovsky claimed that by properly correlating and interpreting these texts, one could deduce the outlines of a series of celestial catastrophes, beginning around 1500 BC.

In brief, according to Velikovsky, a comet was ejected from Jupiter and became gravitationally and electromagnetically trapped by Earth, wreaking enormous trauma on our planet. After breaking free and struggling with a displaced Mars, the comet settled into an orbit around our Sun. We now call this destructive comet Venus. Velikovsky's theory unified an idiosyncratic version of ancient history with a new account of the solar system; it also contravened every accepted premise of geology, paleontology, and celestial mechanics.

The fate of Velikovsky's theory is instructive for two principal reasons. First, Worlds in Collision was, so to speak, "born pseudoscientific." Before it, fringe doctrines (say, parapsychology or phrenology) had been introduced by a given scientist, a lively debate ensued, and those doctrines were then excised (and their proponents exiled) from the scientific community. Not so with Velikovsky. Although he was trained as a medical doctor and psychoanalyst, he was not a member of any of the communities with which his book engaged. His theories were not discussed dispassionately and then set aside; they were vehemently attacked even before the book appeared (the advance publicity set certain people off), the publisher was threatened with a boycott, and for decades he remained a prime target for self-appointed demarcators, including the distinguished astronomers Harlow Shapley and Carl Sagan.

The emergence of this new method of policing pseudoscience says a lot about the organization of science during the cold war. In the geopolitical clash between the United States and the Soviet Union, science and technology assumed a central place (think of nuclear weapons, or Sputnik). As a result, science was better financed, more visible, and more prestigious than ever, but also laden with newfound anxieties about oversight and integrity.

A second reason to focus on Velikovsky is the nature of the evidence. Most fringe doctrines do not survive their creators; with their deaths comes a cleaning of the attic and a trip to the dump. But in 2005, Firestone Library at Princeton University announced the opening of the Immanuel Velikovsky Papers to researchers. (Velikovsky had lived in Princeton, N.J., from 1952 until his death, and he was a frequent presence in the library and around town, although he never had any affiliation with the university.) I went to take a look, the name striking a chord from my youthful reading of UFO lore and other nerdy arcana.

His papers are among the most comprehensive personal archives I have ever seen, spanning 65 linear feet of material: drafts of manuscripts, fan mail, hate mail, assorted correspondence, and much more. Here we can trace the microdynamics of a demonized theory from birth, charting its rise in popularity and eventually its fairly sudden senescence after Velikovsky's death.

One could do a lot with this material: elucidate how both mainstream and marginal publishing worked, for example, or track how social movements on the fringe coalesce and develop. I chose to sift through Velikovsky's manuscripts and explore the issue of pseudoscience. A few hours poring over the vitriolic correspondence by scientists excoriating Macmillan for publishing Worlds in Collision and threatening a boycott of the press were so fascinating that I felt I needed to keep reading about how boundaries of science were being defended. I was most struck by one dominant theme running through all the pro- and anti-Velikovsky documents: Everyone demarcates.

...

Read more here/Leia mais aqui: The Chronicle of Higher Education

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NOTA DESTE BLOGGER:

Se o Darwinismo for submetido aos critérios expostos pelo Autor, vai ser identificado como pseudociência!!! Repare que ele critica o criacionismo, mas não critica a teoria do Design Inteligente. Ele sabe que tanto o Darwinismo quanto o DI são teorias científicas de longo alcance histórico, e criticar o DI é criticar também o Darwinismo.

Tem darwinista que nem sabe disso - a teoria da evolução é uma teoria de longo alcance histórico, e aprende aqui no blog de um defensor do Design Inteligente.

O DNA embaralha tudo e não confirma a Árvore da Vida de Darwin

Breakdown of Phylogenetic Signal: A Survey of Microsatellite Densities in 454 Shotgun Sequences from 154 Non Model Eukaryote Species

Emese Meglécz1,2*, Gabriel Nève1,2, Ed Biffin3, Michael G. Gardner2,3,4

1 IMBE UMR 7263 CNRS IRD, Aix-Marseille University, Marseille, France, 2 School of Biological Sciences, Flinders University, Adelaide, Australia, 3 Australian Centre for Evolutionary Biology and Biodiversity, School of Earth and Environmental Science, University of Adelaide, Adelaide, Australia, 4 Evolutionary Biology Unit, South Australian Museum, Adelaide, Australia

Abstract 

Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be gained from a comparison of their distribution within a phylogenetic context. Although information for model species is accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of the variation that exists within groups has been conducted. In this study, we examined microsatellite coverage and motif patterns from 454 shotgun sequences of 154 Eukaryote species from eight distantly related phyla (Cnidaria, Arthropoda, Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and Streptophyta) to test if a consistent phylogenetic pattern emerges from the microsatellite composition of these species. It is clear from our results that data from model species provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.

Citation: Meglécz E, Nève G, Biffin E, Gardner MG (2012) Breakdown of Phylogenetic Signal: A Survey of Microsatellite Densities in 454 Shotgun Sequences from 154 Non Model Eukaryote Species. PLoS ONE 7(7): e40861. doi:10.1371/journal.pone.0040861

Editor: Richard Cordaux, University of Poitiers, France

Received: March 19, 2012; Accepted: June 14, 2012; Published: July 16, 2012

Copyright: © 2012 Meglécz 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: Development of this work was funded by institutional support from the Flinders University and the Department of Environment and Natural Resources South Australia. 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.

* E-mail: emese.meglecz@imbe.fr

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NOTA DESTE BLOGGER:

A Árvore da Vida de Darwin deveria ser mostrada pelo DNA, mas não mostra. Por que??? Os autores não tiveram a coragem de dizer que a teoria da evolução de Darwin está errada, mas é o que a pesquisa deles revela! Os dados não revelam um padrão filogenético, mas design comum com alguma variação!!!  

As estórias da carochinha evolucionárias podem explicar a mente humana???

BOOKS

IT AIN’T NECESSARILY SO

How much do evolutionary stories reveal about the mind?

BY ANTHONY GOTTLIEB

SEPTEMBER 17, 2012

When Rudyard Kipling first published his fables about how the camel got his hump and the rhinoceros his wrinkly folds of skin, he explained that they would lull his daughter to sleep only if they were always told “just so,” with no new variations. The “Just So Stories” have become a byword for seductively simple myths, though one of Kipling’s turns out to be half true.

Exactly how our mental traits became established makes no practical difference.

The Leopard and the Ethiopian were hungry, the story goes, because the Giraffe and the Zebra had moved to a dense forest and were impossible to catch. So the Ethiopian changed his skin to a blackish brown, which allowed him to creep up on them. He also used his inky fingers to make spots on the Leopard’s coat, so that his friend could hunt stealthily, too—which now seems to be about right, minus the Ethiopian. A recent article in a biology journal approvingly quotes Kipling on the places “full of trees and bushes and stripy, speckly, patchy-blatchy shadows” where cats have patterned coats. The study matched the coloring of thirty-five species to their habitats and habits, which, together with other clues, is hard evidence that cats’ flank patterns mostly evolved through natural selection as camouflage. There are some puzzles—cheetahs have spots, though they prefer open hunting grounds—but that’s to be expected, since the footsteps of evolution can be as hard to retrace as those of a speckly leopard in the forest.

The idea of natural selection itself began as a just-so story, more than two millennia before Darwin. Darwin belatedly learned this when, a few years after the publication of “On the Origin of Species,” in 1859, a town clerk in Surrey sent him some lines of Aristotle, reporting an apparently crazy tale from Empedocles. According to Empedocles, most of the parts of animals had originally been thrown together at random: “Here sprang up many faces without necks, arms wandered without shoulders . . . and eyes strayed alone, in need of foreheads.” Yet whenever a set of parts turned out to be useful the creatures that were lucky enough to have them “survived, being organised spontaneously in a fitting way, whereas those which grew otherwise perished.” In later editions of “Origin,” Darwin added a footnote about the tale, remarking, “We here see the principle of natural selection shadowed forth.”

Today’s biologists tend to be cautious about labelling any trait an evolutionary adaptation—that is, one that spread through a population because it provided a reproductive advantage. It’s a concept that is easily abused, and often “invoked to resolve problems that do not exist,” the late George Williams, an influential evolutionary biologist, warned. When it comes to studying ourselves, though, such admonitions are hard to heed. So strong is the temptation to explain our minds by evolutionary “Just So Stories,” Stephen Jay Gould argued in 1978, that a lack of hard evidence for them is frequently overlooked (his may well have been the first pejorative use of Kipling’s term). Gould, a Harvard paleontologist and a popular-science writer, who died in 2002, was taking aim mainly at the rising ambitions of sociobiology. He had no argument with its work on bees, wasps, and ants, he said. But linking the behavior of humans to their evolutionary past was fraught with perils, not least because of the difficulty of disentangling culture and biology. Gould saw no prospect that sociobiology would achieve its grandest aim: a “reduction” of the human sciences to Darwinian theory. This was no straw man. The previous year, Robert Trivers, a founder of the discipline, told Time that, “sooner or later, political science, law, economics, psychology, psychiatry, and anthropology will all be branches of sociobiology.” The sociobiologists believed that the concept of natural selection was a key that would unlock all the sciences of man, by revealing the evolutionary origins of behavior.

The dream has not died. “Homo Mysterious: Evolutionary Puzzles of Human Nature” (Oxford), a new book by David Barash, a professor of psychology and biology at the University of Washington, Seattle, inadvertently illustrates how just-so stories about humanity remain strikingly oversold. As Barash works through the common evolutionary speculations about our sexual behavior, mental abilities, religion, and art, he shows how far we still are from knowing how to talk about the evolution of the mind.

Evolutionary psychologists are not as imperialist in their ambitions as their sociobiologist forebears of the nineteen-seventies, but they tend to be no less hubristic in their claims. An evolutionary perspective “has profound implications for applied disciplines such as law, medicine, business and education,” Douglas Kenrick, of Arizona State University, writes in his recent book “Sex, Murder and the Meaning of Life.” The latest edition of a leading textbook, “Evolutionary Psychology: The New Science of the Mind,” by David Buss, of the University of Texas at Austin, announces that an evolutionary approach can integrate the disparate branches of psychology, and is “beginning to transform” the study of the arts, religion, economics, and sociology.

There are plenty of factions in this newish science of the mind. The most influential sprang up in the nineteen-eighties at the University of California, Santa Barbara, was popularized in books by Steven Pinker and others in the nineteen-nineties, and has largely won over science reporters. It focusses on the challenges our ancestors faced when they were hunter-gatherers on the African savanna in the Pleistocene era (between approximately 1.7 million and ten thousand years ago), and it has a snappy slogan: “Our modern skulls house a Stone Age mind.” This mind is regarded as a set of software modules that were written by natural selection and now constitute a universal human nature. We are, in short, all running apps from Fred Flintstone’s not-very-smartphone. Work out what those apps are—so the theory goes—and you will see what the mind was designed to do.

Designed? The coup of natural selection was to explain how nature appears to be designed when in fact it is not, so that a leopard does not need an Ethiopian (or a God) to get his spots. Mostly, it doesn’t matter when biologists speak figuratively of design in nature, or the “purpose” for which something evolved. This is useful shorthand, as long as it’s understood that no forward planning or blueprints are involved. But that caveat is often forgotten when we’re talking about the “design” of our minds or our behavior.

Barash writes that “the brain’s purpose is to direct our internal organs and our external behavior in a way that maximizes our evolutionary success.” That sounds straightforward enough. The trouble is that evolution has to make compromises, since it must work with the materials at hand, often while trying to solve several challenges at once. Any trait or organ may therefore be something of a botch, from the perspective of natural selection, even if the creature as a whole was the best job that could be done in the circumstances. If nature always stuck to simple plans, it would be easier to track the paths of evolution, but nature does not have that luxury.

In theory, if you did manage to trace how the brain was shaped by natural selection, you might shed some light on how the mind works. But you don’t have to know about the evolution of an organ in order to understand it. The heart is just as much a product of evolution as the brain, yet William Harvey figured out how it works two centuries before natural selection was discovered. Neither of the most solid post-Darwinian accounts of mental mechanisms—Noam Chomsky’s work on language and David Marr’s on vision—drew on evolutionary stories.

...

Read more here/Leia mais aqui: The New Yorker

Máximo Sandín, biólogo evolucionista fala sobre a evolução que os evolucionistas brasileiros não ousam falar

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Máximo Sandín

EVOLUCIÓN: UNA BELLA HISTORIA

26 Noviembre 2010.

Instituto de Bioingeniería. Universidad Miguel Hernández de Elche

SEMANA DE LA CIENCIA 2010

¿Está bien fundamentada la biología del siglo XXI a la luz de los nuevos hallazgos científicos? ¿Desde que año se empezó a postular los términos de micro-evolución y macro-evolución?¿Es cuestionable o no la teoria de la Selección Natural concebida por Darwin? ¿Que repercusión tuvo Lamarck sobre Darwin y en su posterior teoría? ¿Es plausible cuestionar la teoría de la evolución, o es mejor aceptarla sin cuestionar ni revisar los orígenes y argumentos? ¿Que papel tiene el periodo Cámbrico en la historia del mundo? ¿Se puede afirmar con total certeza que hemos descubierto el origen de la vida, y cómo hemos llegado hasta aquí? 

Tal vez sería más humilde y honesto reconocer que, desde el punto de vista científico apenas conocemos sobre la enorme complejidad de la naturaleza y vida.

Máximo Sandín es Doctor en Ciencias Biólogicas por la Universidad Complutense de Madrid y Doctor en Bioantropología por la Universidad Autónoma de Madrid, y ejerce como profesor de Evolución Humana y Ecología en el Departamento de Biología de la Universidad Autónoma de Madrid y miembro del Consejo Científico de ATTAC.

O mito evolucionista do DNA lixo foi para lata do lixo da História da Ciência

'Junk DNA' Debunked

Studies Find Human Genomic Makeup Is Vastly Messier; New Disease Links Seen

Press Association - Associated Press

Researchers describe DNA studies Wednesday that could point the way to new methods to detect and treat disease. From left, Tim Hubbard of Wellcome Trust Sanger Institute, Roderic Guigo of the Centre for Genomic Regulation and Ewan Birney of the European Bioinformatics Institute.

The deepest look into the human genome so far shows it to be a richer, messier and more intriguing place than was believed just a decade ago, scientists said Wednesday.

While the findings underscore the challenges of tackling complex diseases, they also offer scientists new terrain to unearth better treatments.

The new insight is the product of Encode, or Encyclopedia of DNA Elements, a vast, multiyear project that aims to pin down the workings of the human genome in unprecedented detail.

Encode succeeded the Human Genome Project, which identified the 20,000 genes that underpin the blueprint of human biology. But scientists discovered that those 20,000 genes constituted less than 2% of the human genome. The task of Encode was to explore the remaining 98%—the so-called junk DNA—that lies between those genes and was thought to be a biological desert.

That desert, it turns out, is teeming with action. Almost 80% of the genome is biochemically active, a finding that surprised scientists.

In addition, large stretches of DNA that appeared to serve no functional purpose in fact contain about 400,000 regulators, known as enhancers, that help activate or silence genes, even though they sit far from the genes themselves.

The discovery "is like a huge set of floodlights being switched on" to illuminate the darkest reaches of the genetic code, said Ewan Birney of the European Bioinformtics Institute in the U.K., lead analysis coordinator for the Encode results.

For example, the new research helped scientists to discover that a particular type of regulatory switch, known as the GATA family of transcription factors, was associated with the risk of Crohn's disease, an inflammatory bowel condition. The data helped narrow down this link from a possible 2,000 options, said Dr. Birney.

"That's a new association, and we're saying we have about 400 of those" showing other such biological links, he added.

...

Read more here/Leia mais aqui: The Wall Street Journal

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NOTA DESTE BLOGGER:

Desde 1998 os teóricos do Design Inteligente afirmavam que o DNA "lixo" iria se revelar uma riqueza de informação genética. O argumento era usado pelos evolucionistas ortodoxos fundamentalistas xiitas como um argumento contra a teoria do Design Inteligente e a favor da teoria da evolução de Darwin. Não podem mais usar este argumento, e levaram uma bordoada epistêmica no contexto de justificação teórica que vindica mais a posição do Design Inteligente do que Darwin. Em ciência, o que vale são as evidências e não a teoria!

Pobre Galera dos meninos e meninas de Darwin: vocês não vão poder mais usar este argumento contra o DI.

Fui, nem sei por que, rindo da cara de alguns amigos meus na Nomenklatura científica que eram (ainda são???) ardentes defensores do dogma evolucionista do DNA "lixo". Minhas condolências para vocês do fundo do meu coração!!!  

Shapiro (não DI) e Sternberg (DI) anteciparam a queda do DNA "lixo"

Shapiro and Sternberg Anticipated the Fall of Junk DNA

Mere illustration/Mera ilustração - Source/Fonte 

By Doug Axe

See this recent Huffington Post blog piece by Jim Shapiro, describing how he and Rick Sternberg (now at Biologic Institute) foresaw meaning in “junk DNA.”

Here’s an excerpt:

In 2005, I published two articles on the functional importance of repetitive DNA with Rick von Sternberg. The major article was entitled “Why repetitive DNA is essential to genome function.”

These articles with Rick are important to me (and to this blog) for two reasons. The first is that shortly after we submitted them, Rick became a momentary celebrity of the Intelligent Design movement. Critics have taken my co-authorship with Rick as an excuse for “guilt-by-association” claims that I have some ID or Creationist agenda, an allegation with no basis in anything I have written.

The second reason the two articles with Rick are important is because they were, frankly, prescient, anticipating the recent ENCODE results. Our basic idea was that the genome is a highly sophisticated information storage organelle. Just like electronic data storage devices, the genome must be highly formatted by generic (i.e. repeated) signals that make it possible to access the stored information when and where it will be useful.

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NOTA DESTE BLOGGER:

Embora não tendo predito a queda do DNA "lixo", William Dembski, um dos teóricos do Design Inteligente predisse em 1998 que aquelas regiões do DNA se mostrariam funcionais. "Intelligent Science and Design," First Things, Vol. 86:21-27 (October 1998).

E ainda dizem que a turma do Design Inteligente não sabe o que é e nem fazer ciência, e que nossa teoria impede o avanço da ciência. Quem impediu o avanço da ciência, cara-pálida? Pelo menos uma década em ciência (saúde especialmente) foi perdida pela manutenção ferrenha de um paradigma que colapsou fragrosamente agora com a publicação dos artigos do ENCODE.

Os darwinistas ortodoxos xiitas fundamentalistas, como era de se esperar, estão esperneando! E sem razão... pois é assim que a ciência avança: abandonando-se as posições tidas como verdades, mas que são suplantadas pelas novas evidências encontradas na natureza.

Chupa essa manga epistêmica Nomenklatura científica e Galera de meninos e meninas de Darwin!!!

Revista Proteomics dedica edição especial ao Brasil - tem gente do Design Inteligente no meio!

Revista Proteomics dedica edição especial ao Brasil

12/09/2012

Por Karina Toledo

Agência FAPESP – Nem futebol, nem carnaval. O Brasil pode ser considerado em breve “o país da proteômica”, destaca o editorial de outubro da revista Proteomics, uma das publicações com maior fator de impacto na área.

Além da bandeira verde e amarela na capa, a edição especial, intitulada “Proteomics in Brazil”, traz 16 artigos de pesquisadores brasileiros. A organização é de Daniel Martins de Souza, ex-bolsista de doutorado e pós-doutorado da FAPESP que atualmente trabalha como pesquisador associado no Max-Planck-Institut für Psychiatrie e na Ludwig Maximilians Universität – ambos na Alemanha.

“É a primeira vez que a revista dedica uma edição inteira a um país”, contou Souza à Agência FAPESP. A ideia de fazer uma publicação temática partiu do próprio pesquisador e foi bem recebida pelo editor-chefe, Michael Dunn.

“Dunn me disse que o número de artigos enviados por brasileiros tem crescido, então sugeri fazer um especial só com pesquisas do país. Ele concordou e me convidou para coordenar a edição”, contou Souza.

A serviço dos genes

A proteômica é um campo de estudo relativamente novo, que surgiu nos anos 1990 a partir do conceito de genoma. “Ela se dedica a investigar o proteoma, ou seja, o conjunto de proteínas expressas por uma célula, tecido ou ser, em um dado momento, em uma dada condição, sob o comando do genoma”, explicou Souza.

Mas ao contrário do genoma, que é estático, o proteoma é extremamente dinâmico. Ele se modifica de acordo com as condições e estímulos a que o organismo é exposto. “Entender como a expressão das proteínas se altera por causa de uma doença, por exemplo, permite compreender melhor as vias bioquímicas envolvidas, encontrar potenciais biomarcadores e tratamentos mais direcionados”, afirmou o pesquisador.

O Brasil tem acompanhado o crescimento mundial das pesquisas na área, com uma produção científica bastante diversificada, segundo a avaliação de Souza. No editorial, o pesquisador lembra que os primeiros passos foram dados ainda nos anos 1980, por profissionais que trabalhavam com química de proteínas e espectrometria de massas.

“Os centros pioneiros foram a Universidade de Brasília (UnB) e a Universidade Estadual de Campinas (Unicamp). Hoje se destaca a Rede Proteômica do Rio de Janeiro, composta por cientistas da Universidade Federal do Rio de Janeiro (UFRJ) e da Fiocruz. Faz-se também proteômica no Instituto Butantã, na Universidade de São Paulo (USP) e no Laboratório Nacional de Luz Síncrotron (LNLS)”, comentou.

Edição temática inédita traz 16 artigos de pesquisadores brasileiros e aborda temas variados, como câncer, pragas agrícolas, qualidade do leite e biodiversidade

Graças ao trabalho desses grupos, afirmou Souza no editorial, o país ganhou massa crítica suficiente para criar a Sociedade Proteômica Brasileira. A inauguração da entidade deve ocorrer ainda em 2012 sob liderança de Gilberto Domont da UFRJ.

Os artigos selecionados para a edição temática da Proteomics são, de acordo com Souza, tão variados quanto as pesquisas realizadas no Brasil. “Há trabalhos relacionados a câncer, esclerose múltipla, resistência à insulina, células-tronco de cordão umbilical, pragas agrícolas e até estudos mais funcionais, sobre interação e estrutura de proteínas”, contou.

O texto de abertura é um artigo opinativo, no qual os pesquisadores Magno Junqueira, da UnB, e Paulo Costa Carvalho, da Fiocruz, falam sobre os desafios de explorar a rica biodiversidade brasileira por meio de técnicas proteômicas.

Em outro trabalho assinado por cientistas da Unicamp e da Fiocruz, um modelo animal é usado para estudar as proteínas expressas em uma situação de exaustão física. “A ideia é descobrir marcadores proteicos que indiquem quando um atleta está prestes a desenvolver uma lesão por esforço excessivo”, explicou Souza.

Já a imagem do copo de leite em destaque na capa da revista faz referência à uma pesquisa realizada na Faculdade de Medicina Veterinária e Zootecnia da USP, em parceria com a Unicamp e com a empresa alemã Bruker Daltonics.

NOTA DESTE BLOGGER: O Prof. Dr. Marcos Nogueira Eberlin, Departamento de Química Orgânica, Instituto de Química, Universidade Estadual de Campinas,  é o autor para correspondência. SPCNCT (Só pra contrariar a Nomenklatura científica tupiniquim), além de ser membro da Academia Brasileira de Ciências, o Dr. Eberlin é membro do NBDI - Núcleo Brasileiro de Design Inteligente.

“Os autores desenvolveram um método que identifica bactérias presentes no leite por meio de proteínas ribossomais, ou seja, sem a necessidade de cultivo”, contou Souza.

E como a questão das doenças negligenciadas não podia faltar, pesquisadores da Fiocruz do Paraná publicaram um estudo proteômico do Trypanosoma cruzi, protozoário causador da doença de Chagas. No trabalho, foram identificadas proteínas importantes para o processo de diferenciação do parasita e para a infecção do hospedeiro.

Todos os artigos já estão disponíveis para consulta no site da revista. A versão impressa será publicada em outubro.

Biogenesis: Theories of Life's Origin - um livro de Noam Lahav, antigo mas devastador às teorias da evolução química

Biogenesis: Theories of Life's Origin 

Noam Lahav

ISBN13: 9780195117554

ISBN10: 0195117557

Paperback, 368 pages

Jan 1999, In Stock

Price: $80.00

Description

Biogenesis provides a detailed, critical discussion of the modern scientific study of the origin of life. It covers the entire history, including the biological, geological, and cosmological background. The author explains the rationale behind the main assumptions and experimental strategies of the study of the origin of life, and reviews its plethora of theories, models, scenarios, and controversies. 

The book begins with the history of the search for life's origin from the Greek philosophers to contemporary scientists. The author introduces the reader to important aspects of scientific thinking, and covers the biases, successes, and failures of these thinkers. Part II succinctly describes selected attributes of life, which are connected to theories and controversies of the studies of the origin of life. The main features of the solar system and Earth, where life is assumed to have originated, are briefly reviewed in Part III. This section covers the formation of the planet, its primordial atmosphere and seas, and the Gaia theory. Part IV investigates the rationale of the scientific theories of the origin of life. It begins with the fundamental assumptions and guidelines, as well as the main experimental strategies used by origin-of-life researchers. The book proceeds with a search for clues in both the geological and biological records. It concludes with a critical, but objective discussion of the main reactions, processes, models, and scenarios suggested for the emergence of various attributes of life in prebiotic environment and the transition from inanimate to animate.

Reviews

"Before we can even address the origin of life, there looms the question of what life is anyway. In Biogenesis, Lahav quotes definitions of life culled from the scientific literature from 1855 to 1997. We see the special concerns of each, from Spenser's emphasis on evolution, to Schrodinger's on the law of physics, to Kauffman's on complexity theory. In pursuit of answers, scientists are using every technique from laboratory experiments to deep sea exploration to computer simulations. The most complete account of every approach and each important concept, theory, and experiment is found in this book. It is an invaluable resource for all serious students of origin-of-life research. Although much of this book is very technical, it is written in a highly accessible style. It is an outstanding contribution to the field." - Lucy Horwitz, Boston Book Review, March 2000

Product Details

368 pages; 6 halftones, & 53 line illus; 6-1/8 x 9-1/4;

ISBN13: 978-0-19-511755-4

ISBN10: 0-19-511755-7

About the Author(s)

Noam Lahav, Emeritus Professor of Origin of life and Soil Science, Hebrew University of Jerusalem, Israel