Finalmente, el tren ES la onda (mas que la Taq! aunque igual de caro), asi que unas mentadas de madre a Ernesto Zedillo por vender los Trenes Mexicanos. Nos quito el romanticismo de viajar en bola, viendo paisajes bonitos y con la oportunidad de ligar chicas guapas. Yo, encontre mi francesa.
Sunday, December 23, 2007
Posted by Daemios at 12:52 PM
Wednesday, November 21, 2007
A masterpiece of science blogging was posted here (http://suicyte.wordpress.com/2007/11/20/smallest-primate-ever-discovered/), addressing the finding of primate sequences in the GOS dataset, just one of the unassesed ambiguities in metagenomics.
The post is beautifully written and made me laugh really loud. The point is that metagenomics is sometimes being overselled just in the very same way as genomics has been (see Eisen's blog for just some examples) and this leads to an skeptic counterwave.
My brief cons and pros:
a) metagenomics offers indeed the unprecedented opportunity to explore unculturable microbial diversity, which no other tool can do.
b) metagenomics is not only a technological advance like genomics was, it fits perfectly in an ecological (community/ecosystemic) theoretical background
c) no matter what everybody says, the GOS sampling has provided an incredible amount of data on previously unknown (and often unimagined) microbial diversity
d) criticisms on the amount of money spent on metagenomics seem to me like questioning the financial support on Humboldt's (or any other naturalist) voyages, which were explorative and not precisely focused on any hypothesis.
e) metagenomics is obviously error-prone, and it's biases have been poorly evaluated
f) metagenomics is much more useful in small, simple communities where a reasonable coverage can be achieved
g) metagenomics is much more useful in well known, deeply studied natural communities where it is employed to answer specific biological questions
h) metagenomics is expensive!
i) a great deal of work is still to be done on: defining parameters for comparing different samples, assessing taxonomical and functional biases, increasing assembly effectiveness and contig construction, improving functional prediction, developing tools for the analysis of such huge datasets, etc.
j) metagenomics is best when interdisciplinary, that is when it's used along with techniques and analyses from other disciplines that might provide physiological, evolutionary or ecological information
That being said, metagenomics rocks!
Rusch DB, Halpern AL, Sutton G, Heidelberg KB, Williamson S, Yooseph S, Wu D, Eisen JA, Hoffman JM, Remington K, Beeson K, Tran B, Smith H, Baden-Tillson H, Stewart C, Thorpe J, Freeman J, Andrews-Pfannkoch C, Venter JE, Li K, Kravitz S, Heidelberg JF, Utterback T, Rogers YH, Falcón LI, Souza V, Bonilla-Rosso G, Eguiarte LE, Karl DM, Sathyendranath S, Platt T, Bermingham E, Gallardo V, Tamayo-Castillo G, Ferrari MR, Strausberg RL, Nealson K, Friedman R, Frazier M, & Venter JC (2007). The Sorcerer II Global Ocean Sampling expedition: northwest Atlantic through eastern tropical Pacific. PLoS biology, 5 (3) PMID: 17355176
Thursday, November 08, 2007
More Day of The Dead Photos Here!
Encore, and late again, I'm posting on the Day of the Dead: an ancient mexican tradition from precolombine ages that was eventually merged by the spaniard priests with All Saints festivity. It is a very eclectic tradition with mexica and catholic elements. The original idea was to host all your deceased relatives at home on a specific day (originally in march, nowadays in November 1st and 2nd). They come back from Mictlán (the land of the dead) to visit and regain energies to continue their long journey towards their final home.
It is a festivity, a respectful party where you share and enjoy with your deceased relatives while mourning and remembering them. An altar is usually set up containing several elments: cempasúchitl flowers whose scent shall guide the dead towards home; copal (copalli is the nahuatl word for incense, product of the resins of the tree Bursera bipinata lay to burn) to cleanse the room; yolk bread of dead to feed your host; water to ease their thirst; salt for purification; chairs and a petate (knit mat of palm leaves) where they can lay to rest overnight; and candles.
A set of little skulls made of sugar simbolizing a tzompantli (skull altar of glory) with the names of the deceased written of the forefront, mixed up with skulls with skulls with the name of the living relatives on their forefront are an amusing and humble reminder of the thin distinction between life and death. All the altar is adorned with thin purple (catholic color for mourning) and orange (mexica color for mouring) papers cut with death alusions.
Finally, you can't forget to include the personal belongings of your deads, which function as evidence that you stil remember your dead and also to let them use them again and remember how their life was. You also cook mole (a complex dish used in important festivities) and whatever your deceased might have liked the most, along with cigarrettes and mezcal (distilled alcoholic beverage from Agave) to party, fruits as the product of the Earth (mandarin/clementine and sugarcane) and guava, tejocote and pumpkin candy.
These are some pictures from the megaaltars set up at Zocalo (Mexico City's central plaza) and at UNAM (our OpenAccess National University hehe) and... click here for last year's entry (nothing new, just different pictures), and more photos here and here inside my picasa web albums...
Posted by Daemios at 4:10 PM
Monday, October 15, 2007
El pasado 11 de octubre la comunidad científica sufrió una dolorosa pérdida al fallecer la Dra. Anita Hoffman, una de las más grandes figuras pioneras de la biología en México. La Dra. Hoffman dedicó su vida al estudio de arácnidos, posicionando el Laboratorio de Acarología de la Facultad de Ciencias de la UNAM (que lleva su nombre) como punta en el estudio de arácnidos. Por si fuera poco, la Dra. Hoffman formó a una gran parte de acarólogos y entomólogos de hoy, y produjo al menos dos libros de difusión en la Colección La Ciencia Desde México: "El Maravilloso Mundo de los Arácnidos" y "Animales Desconocidos: Relatos Acarológicos".
Tuve la oportunidad de conocer a la Dra. Hoffman durante una breve estancia que realicé hace ya una eternidad trabajando con ácaros acuáticos con mi maestro y amigo el Dr. Gerardo Rivas. Era admirable verla llegar con sus ochentaytantos al tercer piso de la facultad todavía con energía suficiente para regañar a varios. Y tras no se cuantos años de ser acaróloga, me tocó verla un día frente a una pecerita convertida en terrario mirando unos trombídidos medio fascinada. Digo, no me quedé en acarología pero sí le agarré gusto a los acaritos... que para saber un poquito más de ellos se puede consultar la página del Lab. Acarología Anita Hoffman y sus fotos ó la Colección Nacional de Ácaros en el Instituto de Biología de la UNAM.
La pérdida de la Dra. Hoffman representa icónicamente el fin de una etapa, tanto para la ciencia mexicana como para mí. Que esta breve entrada sirva como muestra de respeto a Anita Hoffman como aracnóloga pionera en México.
Posted by Daemios at 10:23 AM
Sunday, September 30, 2007
For all scientific-embedded procrastinators, two major links you should definitively check [mmmhh.. sounds like an infomercial] Thanks to LD Maldonado for these!
It's Doug Zongker's presentation of one of his most famous works in the AAAS sessions... It's only 4 min long and worth it!
Should you feel like reviewing his paper for further comprehension, you can find it linked here.
(I would need the hands of all my 35-members lab to count the number of presentations I've seen with less content)
An excellent piece of work on one of the most fascinating and often overlooked animals. Click to open[And makes me wonder how much of a prefabricated production pipeline nowadays science really is]
Posted by Daemios at 1:08 AM
Wednesday, September 26, 2007
Hehe... Well, I finally found the only hardware where windows can be acknowledged as useful... y'don't believe me? belive the Lee, or this documentary, or that Gates guy at Windows 98 presentation... or those scuba divers from Sun... eh? oh yea, Windows is for graphics... suuuure! and besides bluescreens are in the past! check new WindowsVista!!!
nah... windows sucks, just go Linux!
Original idea and actual performance courtesy of The Dude, but I took the picture!
Tomorrow I'll try to come up with something against Mac... now jus lessgo bowlin'....
Posted by Daemios at 10:14 PM
Monday, September 24, 2007
...or the neverending story...
courtesy of exquisite Mr. Tona (damn!)...
I'm brave enough to post it because I've broken the loop!!!!
Posted by Daemios at 11:58 PM
Saturday, September 22, 2007
Pues en la nostalgia irapuatense situada apenitas entre la soledad del lab molecular y la nada (o la milpa para ser específicos) le entran ganas de agradecer a uno... se les extraña pero no tanto!
aún así, gracias por los paros de docencia. Que quieren, me enternece ver a edgardo a medianoche de sábado preparando la clase de recombinación para mis pupilos, así que gracias a:
Ana, Esme, Reni, Edgardo, Jules, More, Eria, Valeria y Andrea
y muchas también a Fred...
!gracias por aportar a la esquizofrenia del grupo 5081!
Posted by Daemios at 1:31 AM
Sunday, September 09, 2007
Tuesday, September 04, 2007
Well, after a mail from Jeff about Cuatrocienegas, I thought of finally writing about it here...
So, briefly Cuatrocienegas de Carranza is a small town at the middle of Cuatrocienegas Basin in the northernmost part of Mexico, inside Coahuila state. It was the homeland of Don Venustiano Carranza, a figure from the revolution famous for being president, almost achieving Veracruz independence and the killing of Emiliano Zapata.
Cuatrocienegas' Basin host one of the most hostile and attractive environment I've ever encountered. Its summer temperature can be as high as 52 C, and as low as -5 C in the winter. It is dominated by an haloxerophytic environment. Annual precipitation is less than 120 cc. Half of it is gypsum rock rich while the other half is calcite rich. It hosts many endemic species, including a cilindropuntia cactus and a desert turtle. Arguably, its main atraction is the system of surface water bodies called Pozas, that seem to date back to when pangaea opened and gave place to Tethys Sea. Hence, a strange diversity can be found: they're the home of desert fishes
which are more similar to marine fishes than to freshwater ones. They also present one of the most ancient and fascinating organisms in the world: microbialites or microbial mats and stromatolites, complex and fully functional ecosystems dominated by bacteria and archaea that deposit calcium carbonate and gypsum, giving rise to hard bodies.
Here some photos of the last field trip:
the not-so-portable molecular lab at the kitchen...
The Eguiarte-Souza Lab sunsetting at the dunes
Twin Ponds' contrasting colours, nearby Pozas Azules...
Dune, sky and cloud from Gypsum Dunes...
Such a strange bunch of people woould only meet at a strange place... Jeiry from Biotechnology Institute, Rafael from UNAM's filmothequem Eugenia and Fernando from Argentina, Me from nowherespecial and Vero from Chile... all at the Gypsum Quarry..
Filming sampling at Rio Mezquites' lunar red ponds...
Posted by Daemios at 1:20 AM
Tuesday, July 31, 2007
Well, continuing our trip, we stayed in Chetumal, a city whit a beautiful seashore and nothing else. I expected to see a friend there but couldn't reach her. (Bety? tuve allá y no te localicé)
We sampled in Laguna Bacalar, one of the very few permanent surface water systems in the Peninsula. With shallow waters and muddy bottoms, it is supposed to have seven diferent colours, each from a different cenote whose waters fed the lagoon. Place is just great. Period.We also sampled the (one and only) Cenote Azul, whose mouth is communicated with Bacalar. The colour is fantastic and it's more than 40 mts deep.
Some samples of what the team found: aquatic mites (I shall post on them somewhen), this is something like a huge Eylais,
we also found an amplypygii, an order of arachnids also known as "tailless whip scorpions" by anglophonics, and as "heart-spiders" or "tendarapos" by us.
and finally... an onychophor!!! from phylum Onychophora (bearing nails), also knwon as "velvet worms" or "spitting worms" because they secrete a glue from a specialized gland close to their heads. They're very rare to find and extremely poorly studied (nobody would accept a thesis on them here) this is my second most favorite animal in the world... from a time between annelids and arthropods. I'm so excited about this! I'll post a video soon. In the meantime, a link to wikipedia
Posted by Daemios at 1:55 PM
Wednesday, July 04, 2007
Posted by Daemios at 5:48 PM
Monday, June 25, 2007
Pues el viernes visité un hospital por probable apendicitis... pero "felizmente", "sólo" tengo gastroenteritis grave... estrenando antibióticos y tragando atole de arroz sin leche ni azúcar...
resulté más visceral de lo que creía...
Posted by Daemios at 3:26 PM
Thursday, June 21, 2007
Phew! evaluations are finally over and... I survived!
So to all: PLoS ONE is a new peer-reviewed OpenAccess online publication innovating in the post-review process... meaning that:
1) y' get it for FREE
2) information and data is public
3) y' can actually participate in reviewing the paper!!!
more information 'bout PLoS ONE in its website PLoS ONE (obviously), 'bout open access here defined and in PLoS' OpenAccess website and which I can republish here under Creative Commons License, and in Jonathan Eisen's (the OpenAccess Cruzader) blog:
Hence, PLoS ONE is like a Peer-Reviewed Journal with all the benefits of OpenAccess PLUS a Blog-Like post-publication Interactive Review Process. So, everyone with a background on whatever-each-paper-is-about should check in and contribute to the post-publication review. All y'need is to visit PLoS ONE homepage, register (y'only need to identify yourself nonambiguously and your email account) and write!
An Open Access Publication is one that meets the following two conditions:
- The author(s) and copyright holder(s) grant(s) to all users a free, irrevocable, worldwide, perpetual right of access to, and a license to copy, use, distribute, transmit and display the work publicly and to make and distribute derivative works, in any digital medium for any responsible purpose, subject to proper attribution of authorship, as well as the right to make small numbers of printed copies for their personal use.
- A complete version of the work and all supplemental materials, including a copy of the permission as stated above, in a suitable standard electronic format is deposited immediately upon initial publication in at least one online repository that is supported by an academic institution, scholarly society, government agency, or other well-established organization that seeks to enable open access, unrestricted distribution, interoperability, and long-term archiving (for the biomedical sciences, PubMed Central is such a repository).
 Open access is a property of individual works, not necessarily journals or publishers.
 Community standards, rather than copyright law, will continue to provide the mechanism for enforcement of proper attribution and responsible use of the published work, as they do now.
Here, just to tease you, I leave this just-published paper published by John R. Talbott from Africans Against Aids which might generate the need of opinion in many of you:
John R. Talbott*
HIV/AIDS prevalence rates across countries of the world vary more than 500-fold from .06% in Hungary to 33.4% in Swaziland. One of the most cited research papers in the field, utilizing cross country regression analysis to analyze other correlates with this HIV prevalence data, is flawed in that it weights each country's results by the country's population.
Based on cross-country linear and multiple regressions using newly gathered data from UNAIDS, the number of female commercial sex workers as a percentage of the female adult population is robustly positively correlated with countrywide HIV/AIDS prevalence levels. Confirming earlier studies, female illiteracy levels, gender illiteracy differences and income inequality within countries are also significantly positively correlated with HIV/AIDS levels. Muslims as a percentage of the population, itself highly correlated with country circumcision rates and previously found to be negatively correlated with HIV/AIDS prevalence, is insignificant when the percentage of commercial sex workers in a population is included in the analysis.
This paper provides strong evidence that when conducted properly, cross country regression data does not support the theory that male circumcision is the key to slowing the AIDS epidemic. Rather, it is the number of infected prostitutes in a country that is highly significant and robust in explaining HIV prevalence levels across countries. An explanation is offered for why Africa has been hit the hardest by the AIDS pandemic and why there appears to be very little correlation between HIV/AIDS infection rates and country wealth.
Posted by Daemios at 9:59 AM
Wednesday, June 20, 2007
Pues nada más haciéndole propaganda a Edgardo otra vez: su explicación del superenrrollamiento del DNA en su blog labjournal es simplemente estupenda. Quién lo iba a saber, antes cuando estudiábamos juntos no explicaba tan bien las cosas, me cae!
Posted by Daemios at 11:11 AM
Tuesday, June 05, 2007
Un símbolo muy claro de lo que siento que le está sucediendo a este país... naturalito, así en una pared linda pero inútil de Pátzcuaro
Y en contra de mi propia incredulidad... resulta que sí hay campo de trabajo para los que estudian en la renombrada escuela guayaba que posteé más abajo... el único inconveniente es que hay que mudarse a Pátzcuaro...
tengo un buen de fotos más en el picasa... si les interesa
Posted by Daemios at 2:04 PM
Thursday, May 17, 2007
No mas amarillismo, ora sí, aquí y ahora:
Se saturó el Océano Sur, el que era el principal capturador de CO2 en el planeta.
El reporte completo salió en Science (ni modo)...
es el primer anuncio de un nuevo mundo (mñaaaa!)
sure, there's no fucking global warming, assholes...
Posted by Daemios at 6:35 PM
Wednesday, May 16, 2007
Ok. Me tranquiliza que en Cuernavaca Morelos, capital guayaba por excelencia, se tenga éste tipo de propuestas educativas: educar uñas. Justito enfrente del jardín Bordá.
"... me miraban falto de color, tieso y como embobado mirando al suelo, pálido casi transparentoso, vacío.
-Mal de amores - decían- mal de amores es lo que tiene ese muchacho.-
nosotros lo sabemos bien, el cascarón lastimero que miraban era tan sólo mi muda."
Posted by Daemios at 10:22 AM
Tuesday, April 24, 2007
Ok. Como es la entrada 50, publico doble. Otra propaganda: PhD comics... francamente no se de que me río. Cliquen en la imagen pa ver otros. Y sí, nada es nuevo bajo el sol... se lo pirateé (¿o piratié?) a The Dude,
Posted by Daemios at 3:59 PM
Posted by Daemios at 11:49 AM
Friday, March 30, 2007
sobra decir más... ora le tocó a los germanos
Posted by Daemios at 6:46 PM
Sunday, March 25, 2007
Grafitis... "lo que es el ingenio popular", visiten este flog de callespintadas (http://ubbiar.fotolog.com/callespintadas/) que es una maravilla! (... uno debe traer siempre una camarita digital por ahí pa cuando se necesite), las fotos son de allí pa hacerle propaganda. la petición de no tirar gatos no se la tomen personal, acá sí vengan a echarlos. el comentario de la de enmedio se sugiere que es de algún exfan de santaclós.... y lo que es la intolerancia con los pobres satanistas no?
hubiera tomado la foto del clásico puma del circuito bicicletero que en varios basureros rezaba:
Posted by Daemios at 1:51 PM