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
Paris nos recibio frio y obscuro. El periferico parisino resulta menos feo pero igual de tedioso para perderse. Aunque se recorre en menos tiempo. 
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