DNA Barcoding, a reply from Alex Smith

It seems my barcoding rant from last week has caught the eye of Alex Smith of the University of Guelph.  Alex is the force behind numerous DNA barcoding projects, including the pioneering study on Malagasy trap-jaw ants, and I have elevated his reply from the comments:

Hi Alex – happened by myrmecos this morning, saw your essay and the comments that have piled up over the past several days and couldn’t help add my two cents.

1) A barcode is a epistemological tool, an ‘evaluation criteria’ for identification and can act as a catalyst for discovery. It is not an ontological truth that defines a species. Anyone who has proposed barcoding as a concept is clearly incorrect – but has anyone? “We test the epistemological hypothesis that the barcode MOTU can be used as a surrogate for the identification of diversity within and between collection localities.” (Smith et al 2005). To paraphrase Fitzhugh (2008) barcodes can be used as an “epistemological bases for indicating phylogenetic hypotheses”.

2) Identifying the species and ignoring the biology? Much of what the people that I work with have tried to do have been far more integrative than such a statement suggests (Fisher and Smith 2008, Smith et al 2008, 2007, 2006). Again – I know of no one that would support the idea to ‘ignore biology’.

3) Many of the pros for integrating DNA into existing taxonomy, ecology, and evolutionary biology programs are accentuated if one of the genes is a standardised marker that permits comparison between localities, researchers and taxa. This is a clear plus to inclusion of a standardized gene – and but clearly stops short of being an argument for stopping all questions after this first pass evalulation.

4) ‘the barcoders’ – This is a straw man. There is no mob of phylogenetically illiterate cabal of taxonomy-hating gel jockeys. I hope that the moment in time when ‘us, them’ language can be used to characterise, or be made caricatures of, is passing. This is a tool – I know of no contractors who call themselves ‘#2 Robertson’s” because that is their standard first pass screw when constructing a home. There is no them.

Will a standardized single gene identifier solve all problems in biology? Un-equivically no. Could it make future hypotheses regarding species membership and terminology more transparent and reproducible – yes. Many people’s distaste for the metaphor is abundantly clear, but I’ve got to tell you that what I’ve experienced for the past five years is that when talking to many people on the planet (the non-biologists, the teachers, the government bureaucrat,, the administrators, the… generally majority of humanity) – the edges of the metaphor where it is biologically meaningless become less relevant. What is more immediately relevant is that ‘they ‘understand an IUPAC identifier; this code gives me information about something (most often the price). Is co-opting this societal understanding to add to some degree of biological literacy “marketeering” or is it communicating science?

7 thoughts on “DNA Barcoding, a reply from Alex Smith”

  1. I agree with most of Alex’s comments.

    But I still find it difficult to think of the term ‘barcode’ primarily as a metaphor for communicating science to the public when most of the talks from the barcoding community feel like ShamWow commercials.

  2. RachelinBoston

    “There is no mob of phylogenetically illiterate cabal of taxonomy-hating gel jockeys.”

    What a fantastic sentence.

    I appreciate Alex’s balanced response. I work in the field of genetics and have long believed (as the original barcoding blog post stated) that genetic sequence should become a more important taxonomical classifier than phenotypic traits. If the terminology causes people to balk, then by all means, let’s change the terminology. But the science behind it is sound.

  3. I dissagree with you RachlinBoston. At some point I would like to see genotypes, phenotypes, and ecology all used as taxonomic qualifiers equally, but I can see no reason to elevate genetic sequence above those other two in designating species. I think the difference comes from differences in the very definition of the term ‘species’. Whereas one person thinks of a species as a reproducing metapopulation, another thinks of a species as a genetic sequence. Others are more abstract, seeing a species as simply a phylogenetic hypothesis, or as a placeholder for an n-dimentional hyperset of information. Clearly, if we do not even agree upon what a species is, or even if a species exists in reality or only in concept, we can’t possibly agree upon the methods to detect, classify, and diagnose species.

    ~Kai

  4. James C. Trager

    I appreciate the underpinnings of your argument, Rachel, but until your genetics colleagues come up with that inexpensive, whole-genome-analyzing tricorder thingy, I’m going to keep measuring and carefully recording the morphological, ecological and behavioral characteristics of ants for use in classifying and identifying them.

    Indeed, even after the advent of the “GenomiCorder” (Can I call dibs on this catchy name for the device?), this will continue to be necessary for observers of whole, live organisms to be satisified that we know what we are studying. I know, we’re a dwindling lot, but I hope that like the economic depression, this is only a temporary condition, and that as long as there are beautiful, living organisms to be had, there will be my ilk around to understand and communicate about them to people.

    So, we come round to the idea, that as biodiversity is threatened, those of us who strive to appreciate and comprehend and intepret the richness of life perhaps feel a bit threatened, too — though certainly not only by barcoding, etc. We don’t wish to have our genuine talents supplanted by what is only one of many useful tools in species recognition, not the least of the others being the years of formal and self-training, and field experience that we gain through the course of a life devoted to coming to know our organisms.

  5. Alex Smith writes:

    …the edges of the metaphor where it is biologically meaningless become less relevant. What is more immediately relevant is that ‘they ‘understand an IUPAC identifier; this code gives me information about something (most often the price). Is co-opting this societal understanding to add to some degree of biological literacy “marketeering” or is it communicating science?

    The trouble isn’t that the metaphor degrades at the edges, as all metaphors do. It’s that barcoding is a bad metaphor to begin with. Species simply do not have barcodes, even if species identity can often be predicted with genetic data from a standard locus.

    The human mind has a number of useful quirks, and one of them is the tendency to sort everything into neat little categories. Black vs. White is something we humans do remarkably well. We also like our species neat, tidy, and typological. That’s why creationism has intuitive appeal for many people. It’s also why barcoding is so easy for the non-specialist to understand.

    In effect, I fear the terminology of “barcoding” does the opposite of communication. Instead of enlightening with new knowledge, it reinforces our preexisting notions about the nature of species. The terminology resonates with our prejudices. So what if it is easy to understand? It’s also wrong.

    So the public latches on to “barcoding”. Perhaps that makes it easier to explain some concepts of biodiversity. But the more that the public “understands” DNA barcoding, at least in the simplistic sense as it is portrayed in the media, the less they’re going to understand population genetics, evolution, speciation, and any number of other processes that are at work in the real world.

    (added in edit: I put “barcoding” in quotes here because I am concerned with the terminology of the method, rather than the method itself)

  6. I am not a huge fan of the term “DNA barcoding” either, but the analogy does hold up in most cases. Surely there are canned goods sitting at Schnuck’s whose real barcode labels have been damaged, ripped, or otherwise damaged, and these products need to be “identified” via other means (morphology?) – “looks like a can of peas; can you give me a price check on Schnuck’s brand peas?” Plus, I’d rather communicate the power and excitement of science using black & white analogies than muddy the waters with complexities and rare exceptions (“it’s mostly like that, except in cases where it’s like this, this, and this” – I’ve probably just lost their attention).

    Also, the notion that taxonomy is dead or dying is beyond absurd. Just look at the discussion buzzing over Darwinius masillae or any of the many ATBI, PBI, AToL, PEET, EoL, tolweb, and other projects going right now. We taxonomists are now more sophisticated and active than ever, though we aren’t very good, perhaps, at communicating this fact to Joe Citizen or even Jane Scientist.

  7. p.s. I am VERY much in favor of using DNA barcodes to test species concepts and enable diagnosis. Sequencing one or more “appropriate” (more exploration is warranted here) gene fragments should *always* be part of the process when possible, BUT we should never lose sight of their limitations. DNA barcoding is not a panacea but rather an incredibly useful tool – at least in my experience, but I don’t study Orthoptera!

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