Barcoding and the Pornographic Species Definition

Every time there’s an article about species barcoding–using a short DNA sequence to identify species–there always seems to be people who get all het up:

Barcoding, which is something I have criticised and discussed before here, and here, treats species as things that have some invariant property (in this case, a segment of the COI gene) that maps directly onto the entities one-to-one. As Brent Mishler, head of the Berkeley herbarium, says

We’re not accusing Hebert of being a creationist, just of acting like one.

Why? Because creationists treat species as having invariant properties. Biology, especially evolutionary genetics, suggests that while it may be true that most members of a species will tend to share most genes, if a gene can vary and still work, it will in a large enough population, and it may also have nonfunctional duplicates that will skew the results. In short, it may work for many species, but it won’t work for them all.

What the result will be, given the delay in describing and naming species (there are some ten million animal species known, which may be as little as a quarter of all animal species alive), and checking whether the barcodes actually do map onto actual species, is that the barcodes will become the species for large numbers of animals. That is, if we diagnose them by the barcodes, then that is what is a species – something that has an assayable barcode.

This puts the diagnostic cart before the taxonomic horse, so to speak. It makes the results of the epistemology the matter of the ontology. It’s a common slide in systematics, but it remains a problem nonetheless.

I’ve always thought that there are two types of species definitions: mechanistic or process definitions, and taxonomic definitions. These have completely different goals, and so, are often incompatible with each other. Species definitions that are based on the process of speciation, such as Templeton’s Cohesion Species Concept or the Biological Species Concept, are very useful for our understanding of how populations diverge to such a degree that they become separate species.
However, these definitions are not very useful when you’re actually trying to place things in classes. It simply isn’t feasible to conduct interbreeding experiments to determine if individuals are part of the same species as defined by the Biological Species Concept. That’s where taxonomic or what I like to call pornographic species concepts are useful (I call them pornographic after the U.S. Supreme Court justice who proclaimed regarding pornography, “I know it when I see it.”).
With E. coli, for instance, there are many conceptually sound ways to determine what is and is not E. coli, but when I’m isolating colonies off of an agar plate, I choose those colonies, that on certain growth media, turn bright pink, turn an indole-containing solution red, and don’t grow with citrate as a carbon source. Are there bacteria that genetically could be considered E. coli that don’t meet these criteria? Absolutely. But at some point, I need to be able to classify things. There’s no theory here, but if an ecologist wants to count things, or delimit the set of organisms with which she works, then taxonomic species definitions are very useful.
Maybe we need to adopt the term operational taxonomic unit for classification schemes, and reserve species for evolutionary discussions.

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2 Responses to Barcoding and the Pornographic Species Definition

  1. Edward says:

    Classification is a mathematical concept, not a scientific one. What do I mean by that? In order to classify things with 100% accuracy, you need precise clear axiomatic definitions. Real biology does not, as Mike implicitly acknowledges, does not admit such clear-cut definitions. Science is about quantifying uncertainty, and in that context, I do see some utility in using genetic markers to help assign organisms to species, but ANY assignment will have some false-positive and false-negative rate. So, saying “99.999% of organisms with these genetic sequences have been found to belong to this species and 0.2% of the members of this species have been observed not to have all these sequences” strikes me as a useful scientific statement. Saying “We define a species to be an organism with these genetic sequences” ignores too much of what we understand of biology.
    As an aside: If anyone saw “The Last Enemy” recently on PBS Masterpiece (or previously on BBC), there was one element of the plot that is related to this topic and I think this fictional show got completely wrong: A virus is developed that kills one human ethnic group, but only makes members of other ethnic groups sick. While it is possible to make a very good guess of an individual’s ethnic group based on their genetic make-up, I am not aware of any markers that do so with 100% certainty. In particular, I am not aware of any genetic variation or combination of genetic variations that are unique to a particular ethnic population, so I suspect that such a virus that targets an ethnic group is impossible.

  2. C E Harrington says:

    I am trying to find a site that will be able to answer a question about genetic compatibility. If anyone knows about one, please let me know. My email is:
    Thank you.

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