Phylogeology – A New Revolution in Phylogenetics

Para quitar el mal sabor de boca del sarcasmo verosímil de la semana pasada aquí les dejo algo que es realmente para dar risa: olvidemos las biomoléculas como el ADN; lo nuevo son los DATOS ATOMICOS! Asi es, filogenetica mas alla de lo molecular.

Systematics and Biogeography: Phylogeology – A New Revolution in Phylogenetics

Evolutionary biologists were stunned this week by the news of Geological Phylogenetics. "Genetics is dead" says geologist Prof. Trevor Bruce of the University of Ulladulla, Australia. For 20 years molecular DNA has changed the way biologists do phylogenetics. Geological Phylogenetics, or Phylogeology, proposes to dispense with biological data all together. Prof. Bruce explains, "Molecular systematics has removed any notion of morphology, anatomy and taxonomy. We intend to get rid of molecules, making phylogenetics essentially free of any biological data".

The benefits of phylogeology are that only atoms will be analyzed. "All you need is a very large industrial-strength food processor and a mass spectrometer". Prof Bruce's team has successfully pureed an array of organisms including two pot plants, a goldfish and Dr. Hall's cat. "She wasn't too happy about it, so we made her first author" says Prof. Bruce. "So far we have analyzed percentages of 30 common elements including carbon, calcium iron and copper". And success! Already Prof. Bruce's team has the data for most common household pets and their relationships. "It's simple" explains Dr. Hall, "a dog and a cat will have a similar atomic make-up, just like two similar rocks. As genetics has brought its methods and theory into phylogenetics, we bring geological techniques. Pureeing and 'mass-specing' critters are one of them".

LEA LA NOTA COMPLETA AQUI:
http://urhomology.blogspot.com/2009/04/phylogeology-new-revolution-in.html

Cladistics wars 2.0 | Archetype

Cladistics wars 2.0 | Archetype

Wednesday, April 22nd, 2009 | Cladistics, Education, Metablogging, Science
Autor: Roberto Keller

There is a skirmish going on at Dechronization blog right now. This is a coauthored blog about phylogenetics. I like this blog (its right there on my blogroll —->). There are surprisingly very few blogs about phylogenetic methods these days, despite the wide use that phylogenies currently have in evolutionary biology and beyond (e.g., linguistics). I will complain that, for nine authors, they post little, sometimes not a single post during a month.

The hot post in question is a mocking of an announcement about a (to be honest, very successful) workshop in phylogenetic methods cosponsored by the Willi Hennig Society and so far held in different continents.

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Lea el comentario completo en:

"Archetype, Ant reconstruction one homology at a time"

blog por Roberto Keller

Cladogramas "a flor de piel"

Algunos cladistas lo traen en la sangre, otros en el corazón.
Estos en la piel!
Así o mas fanáticos!
Diviértanse!



Las fotos vienen de la colección Science Tattoo Emporium, por Carl Zimmer.

http://blogs.discovermagazine.com/loom/science-tattoo-emporium/?nggpage=13&pid=79

http://blogs.discovermagazine.com/loom/science-tattoo-emporium/?nggpage=9&pid=37

http://blogs.discovermagazine.com/loom/science-tattoo-emporium/?nggpage=16&pid=113

Sarcasmo verosimil

Hay muchos ejemplos de argumentos epistemologicos y metodologicos publicados sobre la competencia de alternativas sobre como enfocar el problema de la reconstrucción de la filogenia si con métodos basados en parsimonia o en métodos probabilistas basados en verosimilitudes y probabilidades posteriores Bayesianas.

Por encima de los intercambios en los espacios académicos entre los cladistas de parsimonia y entre los filogenéticos de verosimilitud hay una guerra de "infomerciales" en la arena social de los congresos, los cursos y por supuesto los blogs. Un ejemplo reciente es la versión mordaz publicada por S. Magruder en el blog "Dechronization" sobre el anuncio del taller de Cladística de la OSU+Hennig Society y los comentarios que ha sucitado.

Cladistics Workshop Announced

The Ohio State University and the Willi Hennig Society have just announced this summer's Workshop in Phylogenetics Indoctrination in Cladistics Workshop. Some twenty students will receive fellowships to attend this workshop from the Willi Hennig Society. With these fellowships, students will be able to receive four days of instruction on the proper use of outdated methodologies for only $600. On the fifth day, the workshop will make a foray into the 21st century with a lecture on model based phylogenetics and a laboratory on the use of RAxML, Garli and MrBayes. Instruction on model-based methods will be provided by Dr. Christopher Randle, whose only publications on Bayesian methods are critiques (1, 2) and whose recent publications rely either exclusively on parsimony (3) or give preference to parsimony over maximum likelihood when the two methods are largely congruent (4). I'm sure Dr. Randle is an excellent scientist, but his presence as the sole instructor of model-based methods suggests that this workshop is going to be about as balanced as Fox News.

Creo que nuestros lectores encontraran no solo divertido sino educativo darse cuenta de este tipo de "infomerciales", puestos al aire para cuestionar ideas y personalidad de los miembros de ambos grupos de cientificos como tecnica de mercadeo. Desde luego, tambien hay presentaciones de iguales caracteristicas protagonizados por los cladistas de parsimonia con las mismas intenciones de mercadeo.
Mi granito de arena: La decisión de proceder con epistemología A o B y consecuentemente aplicar método A o B, obviamente no deberia depender de lo persuasivo de los "infomerciales". Uds que creen?

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Actualización (22 Abril): La "entrada" original en "Dechronization" ha sido borrada con una nota y un comentario de M. Brandley, pidiendo disculpas "I also apologize to the Dechron blog organizers and its readers for not treating this as a public scientific forum with a high standard of ethics."

Dechronization Interviews Jack Sullivan, Editor-in-Chief of Systematic Biology

En el blog "Dechronization" se ha publicado una entrevista muy interesante a Jack Sullivan, Editor-in-Chief de Systematic Biology.

Esta es la primera pregunta (y la respuesta):

Question: What are the most exciting recent developments in systematics?

I think there are three. First, there are second-order statistical analyses that can now be applied across a sample of trees from a Bayesian posterior distribution. These include biogeography, comparative methods, and macroevolutionary tests. We used to have to rely on a single tree for our analyses; now we can do the same analyses accounting for phylogenetic uncertainty by sampling from the posterior distribution of trees.

Second, the explicit accommodation of incongruence in analyses of multilocus data through the use of the coalescent. I think it will be really cool when we can use these approaches to differentiate between incongruence caused by coalescent stochasticity from that caused by nonvertical transmission such as horizontal gene transfer or hybridization.

Third, the development of phylogenomics. I remember a symposium debate at the Evolution meetings when I was a graduate student in the early 1990s. The debate was about total evidence approaches versus other methods. During the debate, someone raised the question of, “If we could sequence every single nucleotide in the genome, would we then get the best possible estimate of the phylogeny?” I think that emerging datasets demonstrate that the answer to this question might be, “not necessarily.”

Les recomiendo leer la entrevista completa en:
http://treethinkers.blogspot.com/2009/04/dechronization-interviews-jack-sullivan.html

Filogenetica.org temporalmente abajo

El sitio web Filogenetica.org ha estado inaccesible desde el Domingo.
Hoy recibi este mensaje explicativo: "contingencia tecnica" de los servidores del proovedor del servicio de hospedaje, SuEmpresa.com.

A los visitantes de Filogenetica.org les pido disculpas por esta interrupcion.
El sitio web debera estar en linea pronto segun la promesa de SuEmpresa.com.

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Actualización Abril 16: Poco a poco han estado disponibles en linea algunas paginas del sitio. El fin de semana tratare de restablecer el sitio completo.