Plenty of Time

There's Plenty of Time for Evolution, PNAS

Abstract: Objections to Darwinian evolution are often based on the time required to carry out the necessary mutations. Seemingly, exponential numbers of mutations are needed. We show that such estimates ignore the effects of natural selection, and that the numbers of necessary mutations are thereby reduced to about K log L, rather than KL, where L is the length of the genomic “word,” and K is the number of possible “letters” that can occupy any position in the word. The required theory makes contact with the theory of radix-exchange sorting in theoretical computer science, and the asymptotic analysis of certain sums that occur there.

• Source: There's Plenty of Time for Evolution, Herbert S. Wilf, Warren J. Ewens, DOI: 10.1073/pnas.1016207107, PNAS, Published online before print, 2010/12/13

Wolfram Alpha o las posibilidades de maneras alternativas de acceso al conocimiento científico

Me referiré al sitio Wolfram Alpha http://www.wolframalpha.com/

Hace unos días me topé con este sitio. Me sentí gratamente impresionado porque en cierta medida estaba viendo un ejemplo cristalizado de una vaga idea que rondaba hace un rato mi cabeza. Esa idea respecto a cómo probablemente estaremos haciendo ciencia en unas décadas.
Hoy por hoy, en pleno refinamiento, creo que ya se nos ofrece una fuente muy interesante de información. Mucho mas refinada que simplemente "googlear". La explicitación de los supuestos de búsquedas y la contextualización de la información es, para la parte de mi cerebro que se regodea en lo analítico, mas que estimulante.

Por lo que pude probar es muy bueno para datos astronómicos, de "stock markets" o datos macroeconómicos. Obviamente que su núcleo duro mas desarrollado es la matemática y en ese aspecto descolla. Respecto a la Biología deja todavía mucho que desear pero no sorprende que se necesite mas tiempo para formalizar en los términos propuestos una disciplina tan empírica.
Aquí abajo les dejo la charla TED de su creador y podrán apreciar las posibilidades a futuro de este emprendimiento. A mi realmente me entusiasmó en su potencialidad.

Dejo un par de cuestiones planteadas:

¿Cómo repercutirá este tipo de desarrollos en el manejo actual de información científica via editoriales y publicaciones?

¿Estamos frente al amanecer de un nuevo perfil de investigador? ¿Buceadores de datos y creativos buscadores de patrones?

¿Ciencia con poca (o nula) infraestructura? ? ¿Se propone un tipo de trabajo científico donde países centrales y periféricos están en mejores condiciones de igualdad o todavía habrá brechas por las diferencias en la capacidad de formar capital humano?

Y por último (Para aquellos familiarizados con la obra del gran Asimov). Multivac, esa grandiosa red de información tan central en muchos de sus cuentos, fue interpretada por muchos como un adelanto visionario de lo que sería Internet. Pero ahora cuando escucho a Stephen Wolfram y las potencialidades de Wofram Alpha...bueno... tranquilamente Don Isaac prefirió saltearse uno de los mayores inventos del siglo XX para directamente escribir sobre su evolución en el siglo XXI. Por suerte, todo está por verse.


http://www.ted.com/talks/stephen_wolfram_computing_a_theory_of_everything.html

Noticias sobre Complejidad

A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus, Science

Abstract: Life is mostly composed of the elements carbon, hydrogen, nitrogen, oxygen, sulfur, and phosphorus. Although these six elements make up nucleic acids, proteins, and lipids and thus the bulk of living matter, it is theoretically possible that some other elements in the periodic table could serve the same functions. Here, we describe a bacterium, strain GFAJ-1 of the Halomonadaceae, isolated from Mono Lake, California, which substitutes arsenic for phosphorus to sustain its growth. Our data show evidence for arsenate in macromolecules that normally contain phosphate, most notably nucleic acids and proteins. Exchange of one of the major bioelements may have profound evolutionary and geochemical significance.

o Source: A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus, Felisa Wolfe-Simon, et al., DOI: 10.1126/science.1197258, Science Published Online, 2010/12/02

Swarm Intelligence in Animal Groups: When Can a Collective Out-Perform an Expert?, PLoS ONE

Excerpt: Using a set of simple models, we present theoretical conditions (involving group size, and diversity of individual information) under which groups should aggregate information, or follow an expert, when faced with a binary choice. We found that, in single-shot decisions, experts are almost always more accurate than the collective across a range of conditions. However, for repeated decisions - where individuals are able to consider the success of previous decision outcomes - the collective's aggregated information is almost always superior.

o Source: Swarm Intelligence in Animal Groups: When Can a Collective Out-Perform an Expert?, Katsikopoulos KV, King AJ, DOI: 10.1371/journal.pone.0015505, PLoS ONE 5(11): e15505, October 2010

Infectious Disease Modeling of Social Contagion in Networks, PLoS Comput Biol

Excerpt: Information, trends, behaviors and even health states may spread between contacts in a social network, similar to disease transmission. However, a major difference is that as well as being spread infectiously, it is possible to acquire this state spontaneously. For example, you can gain knowledge of a particular piece of information either by being told about it, or by discovering it yourself. In this paper we introduce a mathematical modeling framework that allows us to compare the dynamics of these social contagions to traditional infectious diseases. (...) As an example, we study the spread of obesity (...)

§ Source: Infectious Disease Modeling of Social Contagion in Networks, Alison L. Hill, David G. Rand, Martin A. Nowak, Nicholas A. Christakis, DOI: 10.1371/journal.pcbi.1000968, PLoS Comput Biol 6(11): e1000968, 2010/11/04

Cycling in the Complexity of Early Societies, Cliodynamics

Abstract Excerpt: Warfare is commonly viewed as a driving force of the process of aggregation of initially independent villages into larger and more complex political units that started several thousand years ago and quickly lead to the appearance of chiefdoms, states, and empires. Here we build on extensions and generalizations of Carneiro’s (1970) argument to develop a spatially explicit agent-based model of the emergence of early complex societies via warfare. (...) A general prediction of our model is continuous stochastic cycling in which the growth of individual polities in size, wealth/power, and complexity is interrupted by their quick collapse. (...)

o Source: Cycling in the Complexity of Early Societies, Gavrilets, Sergey, Anderson, David G, Turchin, Peter, Cliodynamics: The Journal of Theoretical and Mathematical History 1(1), 2010

New Clues About What Makes the Human Brain Special, Science

Excerpt: (...) researchers who've examined preserved samples of cerebral cortex from humans and several species of ape say they've found some intriguing clues about what makes the human brain unique. They report that in a particular region of the prefrontal cortex, an area that contributes to abstract thinking and other sophisticated cognition, neurons have more space between them in the human brain than in the brains of apes. This extra space allows more room for connections between neurons (...)

o Source: New Clues About What Makes the Human Brain Special, Greg Miller, DOI: 10.1126/science.330.6008.1167, Science Vol. 330 no. 6008 p. 1167, 2010/11/26

Sixteen common misconceptions about the evolution of cooperation in humans, Evolution and Human Behavior

Abstract: The occurrence of cooperation poses a problem for the biological and social sciences. However, many aspects of the biological and social science literatures on this subject have developed relatively independently, with a lack of interaction. This has led to a number of misunderstandings with regard to how natural selection operates and the conditions under which cooperation can be favoured. Our aim here is to provide an accessible overview of social evolution theory and the evolutionary work on cooperation, emphasising common misconceptions.

o Source: Sixteen common misconceptions about the evolution of cooperation in humans, West SA, Mouden CE, Gardner A, DOI: 10.1016/j.evolhumbehav.2010.08.001, Evolution and Human Behavior, in Press, November 2010

Selección del "Complexity Digest"

Irremediable Complexity?, Science

Excerpt: Many of the cell's macromolecular machines appear gratuitously complex, comprising more components than their basic functions seem to demand. How can we make sense of this complexity in the light of evolution? One possibility is a neutral ratchet-like process described more than a decade ago, subsequently called constructive neutral evolution. This model provides an explanatory counterpoint to the selectionist or adaptationist views that pervade molecular biology.

• Source: Irremediable Complexity?, Michael W. Gray, Julius Lukeš, John M. Archibald, Patrick J. Keeling, and W. Ford Doolittle, DOI: 10.1126/science.1198594, Science Vol. 330 no. 6006 pp. 920-921, 2010/11/12

Denis Dutton: A Darwinian theory of beauty, TED.com

About this talk: TED collaborates with animator Andrew Park to illustrate Denis Dutton's provocative theory on beauty -- that art, music and other beautiful things, far from being simply "in the eye of the beholder," are a core part of human nature with deep evolutionary origins.

• Source: Denis Dutton: A Darwinian theory of beauty, TED.com, 2010/11
• VIDEO - Watch this talk

Life is physics: evolution as a collective phenomenon far from equilibrium, arXiv

Excerpt: Evolution is the fundamental physical process that gives rise to biological phenomena. Yet it is widely treated as a subset of population genetics, and thus its scope is artificially limited. As a result, the key issues of how rapidly evolution occurs, and its coupling to ecology have not been satisfactorily addressed and formulated. The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology and the global environment. This review focuses on evolution as a problem in non-equilibrium statistical mechanics (...)

• Source: Life is physics: evolution as a collective phenomenon far from equilibrium, Nigel Goldenfeld and Carl Woese, arXiv:1011.4125, 2010/11/18

Selección de "Noticias Complejas"

What Is Epigenetics?, Science

Excerpt: The cells in a multicellular organism have nominally identical DNA sequences (and therefore the same genetic instruction sets), yet maintain different terminal phenotypes. This nongenetic cellular memory, which records developmental and environmental cues (and alternative cell states in unicellular organisms), is the basis of epi-(above)"genetics.

• Source: What Is Epigenetics?, Guy Riddihough and Laura M. Zahn, DOI: 10.1126/science.330.6004.611, Science Vol. 330. no. 6004, p. 611, 2010/10/29
• VIDEO - What Is Epigenetics?

Is Life Impossible? Information, Sex, and the Origin of Complex Organisms, Evolution

Excerpt: The earliest organisms are thought to have had high mutation rates. It has been asserted that these high mutation rates would have severely limited the information content of early genomes. This has led to a well-known “paradox” because, in contemporary organisms, the mechanisms that suppress mutations are quite complex and a substantial amount of information is required to construct these mechanisms. The paradox arises because it is not clear how efficient error-suppressing mechanisms could have evolved, and thus allowed the evolution of complex organisms, at a time when mutation rates were too high to permit the maintenance of very substantial amounts of information within genomes. Here, we use concepts from the formal theory of information to calculate the amount of genomic information that can be maintained. (...)

• Source: Is Life Impossible? Information, Sex, and the Origin of Complex Organisms, Joel R. Peck, David Waxman, DOI: 10.1111/j.1558-5646.2010.01074.x, Evolution Volume 64, Issue 11, pages 3300�"3309, 2010/11

A map of human genome variation from population-scale sequencing, Nature

Excerpt: The 1000 Genomes Project aims to provide a deep characterization of human genome sequence variation as a foundation for investigating the relationship between genotype and phenotype. Here we present results of the pilot phase of the project, designed to develop and compare different strategies for genome-wide sequencing with high-throughput platforms.

• Source: A map of human genome variation from population-scale sequencing, The 1000 Genomes Project Consortium, DOI: 10.1038/nature09534, Nature 467 , 1061"1073, 2010/10/27

Diversity of Human Copy Number Variation and Multicopy Genes, Science

Excerpt: Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. (...) These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ~1000 genes accessible to genetic studies of disease association.

• Source: Diversity of Human Copy Number Variation and Multicopy Genes, Peter H. Sudmant, et al., DOI: 10.1126/science.1197005, Science Vol. 330. no. 6004, pp. 641 - 646, 2010/10/29

Genome size, self-organization and DNA's dark matter, Complexity

Abstract: Chromosomes exhibit several features indicating that its spatiotemporal dynamics is self-organized. It has been recently suggested that a negative correlation between genome size and mean chromosome number would also be a fingerprint of selforganization, related to how human language is organized at the level of words and syllables. However, the vast dominance of non-coding DNA in eukaryotic genomes should prevent an interpretation of genome/chromosome size based on functional trade-offs related to information storage and transmission. Moreover, the reported negative correlation is shown to be an inevitable consequence of the definitions of chromosome and genome length and it is thus unrelated to any type of special generative process.

• Source: Genome size, self-organization and DNA's dark matter, Ricard V. Solé, DOI: 10.1002/cplx.20326, Complexity Volume 16, Issue 1, pages 20"23, 2010/09-10

The Origins Of Modern Biodiversity On Land, Phil. Trans. B

Excerpt: Comparative studies of large phylogenies of living and extinct groups have shown that most biodiversity arises from a small number of highly species-rich clades. To understand biodiversity, it is important to examine the history of these clades on geological time scales. This is part of a distinct phylogenetic expansion view of macroevolution, and contrasts with the alternative, non-phylogenetic equilibrium approach to the history of biodiversity. The latter viewpoint focuses on density-dependent models in which all life is described by a single global-scale model, and a case is made here that this approach may be less successful at representing the shape of the evolution of life.

• Source: The Origins Of Modern Biodiversity On Land, M. J. Benton - mike.bentonbristol.ac.uk, DOI: 10.1098/rstb.2010.0269, Phil. Trans. R. Soc. B, 2010/11/27:558, 3667-3679