Wednesday, November 21, 2007

To Metagenome or not to Metagenome

A masterpiece of science blogging was posted here (, 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!

ResearchBlogging.orgRusch 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

Dia de Muertos / Day of the Dead

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...