Celebrando Darwin sob sua ótica do valor da falsidade na ciência

**Eduardo** Mensagens : 5997 Idade : 54 Inscrição : 08/05/2010

Dia 12 de fevereiro é celebrado nauseabundamente o Dia de Darwin pelo mundo inteiro. Este blogger não vai deixar esta data passar em branco, e vai fazer a sua parte para celebrar a ocasião. Afinal de contas, Darwin é o homem que teve a maior ideia que toda a humanidade já teve, e vale a pena celebrar este dia sob a ótica do próprio Darwin:

“Falsos fatos são altamente prejudiciais para o progresso da ciência, pois frequentemente eles duram muito tempo; mas as falsas opiniões, se apoiadas por alguma evidência, causam pouco dano, pois todo mundo toma um prazer salutar em provar a sua falsidade; e quando isso é feito, um caminho para o erro é fechado e a estrada para a verdade, frequentemente, é aberta ao mesmo tempo.”

“False facts are highly injurious to the progress of science, for they often endure long; but false views, if supported by some evidence, do little harm, for everyone takes a salutary pleasure in proving their falseness; and when this is done, one path towards error is closed and the road to truth is often at the same time opened.” Darwin in Descent of Man (1871, p. 385)

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FATO FALSO DE DARWIN 1:
Conflicting phylogenetic signals at the base of the metazoan tree

Antonis Rokas, a,1 Nicole King, a,1 John Finnerty, b and Sean B. Carroll a, *
a Howard Hughes Medical Institute and Laboratory of Molecular Biology, University of Wisconsin-Madison, 1525 Linden Drive,
Madison, WI 53706-1596, USA
b Department of Biology, Boston University, 5 Cummington St., Boston, MA 02215, USA
*Author for correspondence (e-mail: sbcarrol@facstaff.wisc.edu)

SUMMARY
A phylogenetic framework is essential for understanding the origin and evolution of metazoan development. Despite a number of recent molecular studies and a rich fossil record of sponges and cnidarians, the evolutionary relationships of the early branching metazoan groups to each other and to a putative outgroup, the choanoflagellates, remain uncertain. This situation may be the result of the limited amount of phylogenetic information found in single genes and the small number of relevant taxa surveyed. To alleviate the effect of these analytical factors in the phylogenetic reconstruction of early branching metazoan lineages, we cloned multiple protein-coding genes from two choanoflagellates and diverse sponges, cnidarians, and a ctenophore. Comparisons of sequences for a-tubulin, b-tubulin, elongation factor 2, HSP90, and HSP70 robustly support the hypothesis that choanoflagellates are closely affiliated with animals. However, analyses of single and concatenated amino acid sequences fail to resolve the relationships either between early branching metazoan groups or between Metazoa and choanoflagellates. We demonstrate that variable rates of evolution among lineages, sensitivity of the analyses to taxon selection, and conflicts in the phylogenetic signal contained in different amino acid sequences obscure the phylogenetic associations among the early branching Metazoa. These factors raise concerns about the ability to resolve the phylogenetic history of animals with molecular sequences. A consensus view of animal evolution may require investigations of genome-scale characters.
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Vale a pena celebrar o Dia de Darwin sob a ótica do próprio Darwin:

“Falsos fatos são altamente prejudiciais para o progresso da ciência, pois frequentemente eles duram muito tempo; mas as falsas opiniões, se apoiadas por alguma evidência, causam pouco dano, pois todo mundo toma um prazer salutar em provar a sua falsidade; e quando isso feito, um caminho para o erro é fechado e a estrada para a verdade, frequentemente, é aberta ao mesmo tempo.”

“False facts are highly injurious to the progress of science, for they often endure long; but false views, if supported by some evidence, do little harm, for everyone takes a salutary pleasure in proving their falseness; and when this is done, one path towards error is closed and the road to truth is often at the same time opened.” Darwin in Descent of Man (1871, p. 385)
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FATO FALSO 2:

Gene tree discordance, phylogenetic inference and the multispecies coalescent
James H. Degnan 1,2 and Noah A. Rosenberg 1,3,4
1 Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
2 Current address: Department of Mathematics and Statistics, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
3 Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA
4 Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA

Abstract

The ﬁeld of phylogenetics is entering a new era in which trees of historical relationships between species are increasingly inferred from multilocus and genomic data. A major challenge for incorporating such large amounts of data into inference of species trees is that conﬂicting genealogical histories often exist in different genes throughout the genome. Recent advances in genealogical modeling suggest that resolving close species relationships is not quite as simple as applying more data to the problem. Here we discuss the complexities of genealogical discordance and review the issues that new methods for multilocus species tree inference will need to address to account successfully for naturally occurring genomic variability in evolutionary histories.
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Darwin, o homem que teve a maior ideia que toda a humanidade já teve assim escreveu sobre o valor dos falsos fatos na ciência, e sua sugestão deve ser mais seguida pelos cientistas evolucionistas:

“Falsos fatos são altamente prejudiciais para o progresso da ciência, pois frequentemente eles duram muito tempo; mas as falsas opiniões, se apoiadas por alguma evidência, causam pouco dano, pois todo mundo toma um prazer salutar em provar a sua falsidade; e quando isso feito, um caminho para o erro é fechado e a estrada para a verdade, frequentemente, é aberta ao mesmo tempo.”

“False facts are highly injurious to the progress of science, for they often endure long; but false views, if supported by some evidence, do little harm, for everyone takes a salutary pleasure in proving their falseness; and when this is done, one path towards error is closed and the road to truth is often at the same time opened.” Darwin in Descent of Man (1871, p. 385)
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FALSO FATO 3:

Large-Scale Taxonomic Profiling of Eukaryotic Model Organisms: A Comparison of Orthologous Proteins Encoded by the Human, Fly, Nematode, and Yeast Genomes

Arcady R. Mushegian1,5, James R. Garey2, Jason Martin1,4, and Leo X. Liu3

-Author Affiliations

1AxyS Pharmaceuticals, Inc., La Jolla, California 92037 USA; 2Department of Biological Sciences, University of South Florida, Tampa, Florida 33620 USA; 3NemaPharm, Inc., Cambridge, Massachusetts 02139 USA

Abstract

Comparisons of DNA and protein sequences between humans and model organisms, including the yeast Saccharomyces cerevisiae, the nematode Caenorhabditis elegans, and the fruit fly Drosophila melanogaster, are a significant source of information about the function of human genes and proteins in both normal and disease states. Important questions regarding cross-species sequence comparison remain unanswered, including (1) the fraction of the metabolic, signaling, and regulatory pathways that is shared by humans and the various model organisms; and (2) the validity of functional inferences based on sequence homology. We addressed these questions by analyzing the available fractions of human, fly, nematode, and yeast genomes for orthologous protein-coding genes, applying strict criteria to distinguish between candidate orthologous and paralogous proteins. Forty-two quartets of proteins could be identified as candidate orthologs. Twenty-four Drosophila protein sequences were more similar to their human orthologs than the corresponding nematode proteins. Analysis of sequence substitutions and evolutionary distances in this data set revealed that most C. elegans genes are evolving more rapidly than Drosophila genes, suggesting that unequal evolutionary rates may contribute to the differences in similarity to human protein sequences. The available fraction of Drosophila proteins appears to lack representatives of many protein families and domains, reflecting the relative paucity of genomic data from this species.

Footnotes

↵4 Present address: Genos Biosciences, Inc., La Jolla, California 92037 USA.

↵5 Corresponding author.

E-MAIL arcady@axyspharm.com; FAX (619) 452-6653.

Received December 15, 1997.
Accepted April 21, 1998.
Cold Spring Harbor Laboratory Press

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Neste dia 12 de fevereiro, este blogger não deixou de celebrar o Dia de Darwin, e sendo muito mais darwinista do que muitos darwinistas, celebrei este dia sob a ótica do próprio Darwin:

“Falsos fatos são altamente prejudiciais para o progresso da ciência, pois frequentemente eles duram muito tempo; mas as falsas opiniões, se apoiadas por alguma evidência, causam pouco dano, pois todo mundo toma um prazer salutar em provar a sua falsidade; e quando isso feito, um caminho para o erro é fechado e a estrada para a verdade, frequentemente, é aberta ao mesmo tempo.”

“False facts are highly injurious to the progress of science, for they often endure long; but false views, if supported by some evidence, do little harm, for everyone takes a salutary pleasure in proving their falseness; and when this is done, one path towards error is closed and the road to truth is often at the same time opened.” Darwin in Descent of Man (1871, p. 385)

Não teria sido esta realmente a maior ideia que toda a humanidade já teve???

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FALSO FATO 4:

Mosaic retroposon insertion patterns in placental mammals

Gennady Churakov1,3,5, Jan Ole Kriegs1,3,4, Robert Baertsch2, Anja Zemann1,
Jürgen Brosius1 and Jürgen Schmitz1,5

-Author Affiliations

1 Institute of Experimental Pathology, Center for Molecular Biology of Inflammation, University of Münster, 48149 Münster, Germany;
2 Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA

↵3 These authors contributed equally to this work.

Abstract

One and a half centuries after Charles Darwin and Alfred Russel Wallace outlined our current understanding of evolution, a new scientific era is dawning that enables direct observations of genetic variation. However, pure sequence-based molecular attempts to resolve the basal origin of placental mammals have so far resulted only in apparently conflicting hypotheses. By contrast, in the mammalian genomes where they were highly active, the insertion of retroelements and their comparative insertion patterns constitute a neutral, virtually homoplasy-free archive of evolutionary histories. The “presence” of a retroelement at an orthologous genomic position in two species indicates their common ancestry in contrast to its “absence” in more distant species. To resolve the placental origin controversy we extracted ∼2 million potentially phylogenetically informative, retroposon-containing loci from representatives of the major placental mammalian lineages and found highly significant evidence challenging all current single hypotheses of their basal origin. The Exafroplacentalia hypothesis (Afrotheria as the sister group to all remaining placentals) is significantly supported by five retroposon insertions, the Epitheria hypothesis (Xenarthra as the sister group to all remaining placentals) by nine insertion patterns, and the Atlantogenata hypothesis (a monophyletic clade comprising Xenarthra and Afrotheria as the sister group to Boreotheria comprising all remaining placentals) by eight insertion patterns. These findings provide significant support for a “soft” polytomy of the major mammalian clades. Ancestral successive hybridization events and/or incomplete lineage sorting associated with short speciation intervals are viable explanations for the mosaic retroposon insertion patterns of recent placental mammals and for the futile search for a clear root dichotomy.

Footnotes

↵4 Present address: LWL-Museum für Naturkunde, 48161 Münster, Germany.

↵5 Corresponding authors.

E-mail jueschm@uni-muenster.de; fax 49-251-8352134.

E-mail churakov@uni-muenster.de; fax 49-251-8352134.

[Supplemental material is available online at www.genome.org.]

Article is online at http://www.genome.org/cgi/doi/10.1101/gr.090647.108.

Received December 19, 2008.
Accepted March 3, 2009.
Copyright © 2009 by Cold Spring Harbor Laboratory Press

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NOTA CAUSTICANTE DESTE BLOGGER:

A literatura científica tem uma montanha de pesquisas e artigos em que os falsos fatos darwinianos são expostos questionando aspectos fundamentais da teoria geral da evolução através da seleção natural. Nesses quatro exemplos de falsos fatos, a hipótese da Árvore da Vida de Darwin é desafiada e mostrada falsa pelas evidências.

Fui, nem sei por que, pensando, qual foi mesmo a maior ideia que toda a humanidade já teve???

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