Deep Ocean Trawls, Flat Land Crawls

The Census of Marine Zooplankton, a part of the Census of Marine Life has quite literally netted some results that were reported in the media today. The key messages of the study, as with almost every biodiversity study ever done, are that there are many new species out there awaiting discovery, that more collection will surely throw up more new discoveries, and what we have already found is only incompletely understood.

One bugbear I have, though, and it's a really big tardigrade, is how DNA sequencing is being touted as a "quick and easy [way] to identify species". Call me a stick in the mud, but I believe that there is more to species uniqueness than DNA sequence uniqueness. The relationship between the numerical difference in DNA sequence and the taxonomic level of difference (be it individual variation within a population, variation between two divergent populations, the difference between two species, genera, etc.) is incompletely known. The difference between two species might not even show up as a different sequence, specifically where polyploidy is the mode of speciation, for instance in plants. Simply put, for a biologist to make a judgement call and call an entity a 'species' is for him or her to propose a hypothesis about the reason for that taxon's uniqueness. There is no simple formula to calculate whether two taxa are different species, simply by counting the number of nucleotide-pairs which are different between the two genome sequences. DNA 'barcodes' are a very attractive idea, partly because of the convenience that the name calls up: one imagines that one can simply scan the DNA like one would scan the barcode a supermarket counter, and in an instant determine the species name.

I am not against the practice of gathering genetical data on the organisms that are being trawled up by these research hauls. They represent a valuable resource for all biologists to make use of: for comparative studies, for tracking down homologous genes, for studying genetical variation in large populations. I am, however, opposed to the misleading concept of DNA 'barcoding' that is often advertised. Personally, I feel that if we only use this DNA data for crunching numbers and generating barcodes, then we are underutilising their potential. There is much biology behind the genetic consequences of speciation and variation that we can learn by putting DNA and morphological data together. For instance, two individuals might be morphologically indistinguishable but hugely divergent in their DNA. This might represent either a cryptic (hidden) species difference, or a single species with a large degree of hidden variation. In the first case, many questions can be asked, for instance how speciation can occur between two populations that look the same: is there a behavioral or physiological basis, is the morphological analysis insufficiently fine, and so on? In the second case, one can ask what is the nature of the sequence difference that we are looking at: different alleles, chromosomal rearrangements, how interbreeding can still result in a cohesive individual genome if the parental sequences are so different. On the other hand, it is also possible for speciation to occur simply by changes in a few genes, barely detectable above the 'noise' of individual variation within a species, for instance if those genes control key aspects of mating behavior, of foraging (because that determines the ecological niche that a species occupies), even of coloration, and (in the case of strongly pleiotropic and developmental genes), the overall form of the organism. In that case one might be justified to ask whether the large morphological differences should be interpreted as difference in species, given that the genetic difference is so small: might it not be possible that they still interbreed? And interbreeding, is in itself another host of questions to be answered. Summing up, all these possible questions, I feel, is more valuable than Procrustean barcoding. I'm certainly not accusing the biologists involved in this study of not thinking of all these things: I'm sure they've got way more ideas and interpretation than I can ever muster, but promising a 'barcode' of life is something that seriously rankles me.

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In other news I have felt the awful feeling of running out of steam. During today's twice-weekly run in camp I started off fairly fast but got overtaken by a few folks and at the end lagged quite far behind. The strangest thing was, when I was trying to run faster to catch up, my legs couldn't respond by increasing their stride or rate of movement even though I wanted them to. I'm not used to that sort of feeling, and I think the food and inactivity during the long break has gotten to me. I had a bad dream some time ago, that might have recurred because it gave me the strongest sense of deja vu, where I was walking, but when I had to run I simply forgot what running was. I couldn't move and tripped over my legs, and I didn't understand why.

I hope it's not a premonition of things to come.