Thursday, September 01, 2011

Guardians of microbial diversity: some follow up links re species counting

Just some follow up links regarding counting species which I wrote about recently:
Oh and I am working on some T-shirts if you want to advertise your microbial loyalty
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4 comments:

  1. -DG9/01/2011 11:53 AM

    Maybe I'm biased, since I knw several of the PLoS paper's authors quite well, but at least two of the senior authors on that paper are Protistologists, heavily involved in microbial diversity studies.

    Perhaps the shortcomings of the method as applied to prokaryotes could have been more explicit given the targeted general audience but the results are a function of the data (and restrictive conventions required for species descriptions) in the taxonomic databases used.

    Not to mention of course the problems associated with defining species concepts for prokaryotes in the first place of course.

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  2. Jonathan Eisen9/01/2011 12:09 PM

    As I have repeatedly said, I like the paper overall. But they really should have made much more explicit statements about the limitations of the analysis of bacteria and archaea. When one's numbers are so far off of what is reasonable, you simply cannot fall back on "this is a function of the data". This is an indication that either one's method is fundamentally flawed or the data as used are essentially completely inappropriate. Either way, they did a very bad job of placing their results on bacteria and archaea in context, which is why I created the Mendeley group on counting bacterial and archaeal species that I refer to in my original post.

    As for problems defining species, I don't think those are really a big deal and are not really relevant here. The fact is, the described species of bacteria and archaea are known to simply not even remotely represent anything close to the true diversity, whatever definition one uses.

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  3. -DG9/01/2011 12:29 PM


    "this is a function of the data". This is an indication that either one's method is fundamentally flawed or the data as used are essentially completely inappropriate

    I think it is definitely the latter, which was what I meant by the results being a function of the data.


    As for problems defining species, I don't think those are really a big deal and are not really relevant here. The fact is, the described species of bacteria and archaea are known to simply not even remotely represent anything close to the true diversity, whatever definition one uses.

    I agree and disagree. I agree that the number of described bacteria and archaea don't represent anything close to true diversity but I disagree that what we call a species isn't pertinent. But I have definitely soaked up a lot of what Ford Doolittle and others have to say about what a species even means in the context of bacteria and archaea.

    I think counting diversity among prokaryotes is good, I'm just not convinced that trying to enumerate them as well defined species is appropriate or even possible.

    Anyway, I also agree that the limitations with regards to the applicability of the method to prokaryotes should have been spelled out more explicitly. I just wanted to point out that two of the authors are definitely not "meta-centric." In fact they are very concerned about things like microbial diversity, evolution, and ecosystems. They just focus primarily on microbial eukaryotes.

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  4. Jonathan Eisen9/01/2011 2:49 PM

    Well, I try very very hard to separate criticisms of scientists and authors from criticism of the science and the papers. I myself have many times done things like sign on to bad press releases, ignore microbial diversity, mistate my findings, etc. So what I aim for in my blogging is to discuss the work of others, not the people per se (though I screw this up from time to time ...). So I am happy to know some of the authors are microbiocentric ... and again .. I think what they did was very interesting.

    As for the species question, I was thinking about bigger picture items - like phylogenetic diversity as opposed to species richness. I care more about phylogenetic diversity and genomic diversity than species richness so perhaps I gloss over issues in species definition. But I am more in the Peg Riley camp in that I think bacterial and archaeal species are actually not so hard to define in most cases ....

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