Friday, May 09, 2014

Bad microbiology reporting of the month award: C-Net on IBM "Sequencing the City" meeting

Well, I am still really annoyed by this unbearable article on C-Net yesterday: IBM sees big opportunity in sequencing microbes by Daniel Terdiman.  The article is about this "Sequencing the City" meeting organized by IBM that was on Tuesday and Wednesday.  I talked at the meeting on Tuesday (I could not go on Wednesday).  For more about my talk see: What to do when you realize the meeting you are speaking at is a YAMMM (yet another mostly male meeting)?.  But I am not criticizing the meeting here.  I am criticizing the article in C-Net which has many many flaws. For example consider:
According to James Kaufman, a research manager at the Almaden Research Center, the move to study metagenomics -- the study of systems of micro-organisms -- came from what he called a tipping point in big data. As more and more government-funded institutions study organisms and bacteria, they've collected more information about them, and submitted much of their work to centralized databases. "So there's a growing library of genomes across the field of life," Kaufman said. "That made possible metagenomics."
What?  Metagenomics has been around for a long time.  Sure, many people in the field are taking advantage of so called big data, but there was no "tipping point" needed to launch the field.  This is just completely misguided.
And then even worse
The result: We can now look at and understand whole ecosystems at the bacterial level. One example of how that manifests is what IBM refers to as the Human Microbiome Project. According to an IBM document, that's about characterizing "microbial communities found at multiple human body sites to discover correlations between changes in the microbiome with changes in human health."
So - there have been dozens of high profile papers from the Human Microbiome Project.  There are hundreds of web pages with information about the project.  It was started years and years ago.  And the reporter quotes an "IBM document" to tell us what the Human Microbiome Project is?   And even worse the reporter says "what IBM refers to as the Human Microbiome Project" like they ran it / designed it.  Good that they refer to it as the Human Microbiome Project.  You know why?  Because that is what it is known as to all the other $(&@)(* people in the whole (%&# world.

The reporter goes on to write
This kind of work is not entirely new, but the scientists who will be gathering at IBM Research this week are grappling with one conundrum: they don't know what they don't know. So a big topic of conversation, and a big part of what IBM would like to see advanced, is "the ability to do metagenomics on the scale of a city or the world....That will depend on software services available in the cloud," Kaufman said. "It has to be cheap, easy, and accessible from anywhere. That's what we're really good at."
Once again making it seem like IBM is somehow leading this field.  Not to pick on IBM here.  I am glad they organized the meeting.  But either the reporter just got handed a press release from IBM and wrote it up, or did not do any type of background research, or both.  Sure IBM would like to see this.  But so would lots of other people.  Why make this all about IBM?  There are so many people who have done interesting work in the area of "microbiology of the built environment" - why are none of them even discussed?  What exactly is the point of this article if not to simply be a PR piece for IBM?  Aaaaaarg.

UPDATE 5/9 Storify of some of the Tweets about the meeting


  1. Hi Jonathan,

    I'm looking forward to listening to your talk over the weekend.

    In addition to IBM, I notice recently that Google and Intel, companies that traditionally do not have a positions in biology, suddenly are expressing interest in "big data" and genetics/genomics, and in this case, the microbiome.

    Anyway, your slides look great.

    Thanks for posting the talk and the slides.

  2. I enjoy looking at the slides to the talk and also think the use of impactstory as a platform for a public domain project is cool.

    I had fun looking as some of your slides. Great that these are on the web.

    Again, so sorry about your beautiful cat, Annapurna.

  3. Oh.. but "tipping point" is -such- a great hype-filled buzz phrase! Everyone in the media should just bundle it all up together with a nice front page story in Newsweek. Something like: "The Tipping Point of the Microbiome's Dark Matter". or "The Next Gen Cloud of Metagenomics Big Data". Makes no sense to me - but I guarantee someone in the media will somehow "understand it" :|


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