Friday, January 01, 2010

Barcoding, taxonomy and citizen CSI

I just love the continued coverage of the story of the students from Trinity School in New York (a high school) who do investigative DNA barcoding projects. (There is a good new story about this on the LA Times blogs at:Think that sheep's mik cheese comes from a sheep? DNA doesn't lie | Booster Shots | Los Angeles Times)

In the most recent example, two students, Brenda Tan and Matt Cost, did some home barcoding in collaboration with people from the AMNH and Rockefeller University.

Among their findings:

  • "an invasive species of insect in a box of grapefruit from Texas"
  • "what could be a new species or subspecies of New York cockroach"
  • multiple mislabelled food products including (quoted from the press release, I note)
    • An expensive specialty “sheep’s milk” cheese made in fact from cow’s milk;
    • “Venison” dog treats made of beef;
    • “Sturgeon caviar” that was really Mississippi paddlefish;
    • A delicacy called “dried shark,” which proved to be freshwater Nile perch from Africa;
    • A label of “frozen yellow catfish” on walking catfish, an invasive species;
    • “Dried olidus” (smelt) that proved to be Japanese anchovy, an unrelated fish;
    • “Caribbean red snapper” that turned out to be Malabar blood snapper, a fish from Southeast Asia.
And what I find most interesting, is this built upon work of other students from Trinity Kate Stoeckle and Louisa Strauss who had done a restaurant based barcoding study last year. 

This type of work is cool in so many ways.  It gets students into science.  It is an applied us of taxonomy (though I note, barcoding is not without controversy in the taxonomy community). It is a useful form of citizen science -- and may eventually provide a way to keep dishonest sellers on their toes ... Kudos to all involved in this 

More on this story can be found at


  1. I was listening to an NPR report about diy science project and I thought it was cool--sequencing traffic light buttons metagenomes and stuff like that.
    Where does similar stuff get published in your opinion?

  2. Thanks for blogging about this, Jonathan (I oversaw the project at AMNH). Simple genetic identification methods, like barcoding, are great educational tools. We actually use barcoding a lot at the AMNH, especially as part of our high school science classes. It's very interesting to see how discussions with high school students can range from alignment methods, BLAST, tree-building and long-branch attraction to conservation biology and invasive species.

  3. Ramy

    Such stuff can end up being published anywhere. Depends on the scientific question(s) being asked. If it is about just microbial diversity (which is usually hte case for metagenomics) it might end up in microbiology focused journals but if it is about animals (such as with many of the barcoding studies) it might end up somewhere else.

  4. I agree that theoretically they can publish anywhere, but practically, they will fail the QC steps in almost half of the journals unless they belong to a research institution. For example, if the work involves any animals, even invertebrates, they might need to declare the "approval of the institutional ethical committees." There are also complications with the raw data and their handling. Usually editors trust known scientists from known institutions but would be more suspicious of raw data/primary data pieces from unknown (or nonexistent) institutions.

  5. Ugh - Ramy you are probably right but that bothers me. The more we can judge scientific research by its content and not who it is from or where it is published, the better off we are.

  6. Are these kind of experiments doable by amateurs at this point? Specifically, I'm talking about the extraction/PCR/sequencing steps.

    In this case, sounds like the high school kids did the sample acquisitions and then AMNH did the latter steps.

    Is it possible for amateurs to "DIY" it on these latter steps?

    I've been told extraction and PCR actually could be taken up as a home hobby. Might be better to "outsource" the sequencing.


  7. Extraction and PCR are definitely doable at home --- sequencing not so much right now.


Most recent post

My Ode to Yolo Bypass

Gave my 1st ever talk about Yolo Bypass and my 1st ever talk about Nature Photography. Here it is ...