Berlin and barcodes

Aristotle has been on my mind this week. I was at a workshop at the Botanischer Garten und Botanischen Museum in Berlin talking about topics far removed from Ancient Greek philosophers but, somehow, Aristotle kept intruding. The chain of thought went something like this: we were discussing a relatively new technique for identifying organisms called DNA barcoding. This is a technique similar to the genetic fingerprinting that is used to catch criminals (or, to use a topical example, to find horse meat in lasagne).  Instead of differentiating between humans, this variant allows us to distinguish different species of plant, animal or micro-organism. For those of us who deal with the microscopic world, putting a name on an organism is a time-consuming task for a highly-experienced individual and the possibility of doing this faster, and with a lower risk of mistakes, has huge potential.

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The tropical greenhouse at the Botanischen Garten in Berlin on a chilly April morning.

But why Aristotle? I wrote about beavers in a post a couple of weeks ago and, I’m guessing, the word ‘beaver’ conjured up an image of a medium-sized aquatic rodent with big teeth and a large flat tail. We tend to use the shape and physical properties of plants and animals as a mental shorthand to summarise the species. Strictly speaking, beavers are defined by a much wider set of properties, key amongst which is the ability of Mr and Mrs Beaver to produce healthy, fertile offspring. We can reduce “beaver” to a set of descriptive phrases but, in reality, a beaver is, well, beaverish. And this is where Aristotle comes in to the story. He looked at common objects such as tables and realised that these had properties that were more than just five pieces of wood. There was, in other words, a quintessence to a table that was irreducible.

The problem that those of us who study algae face is that their size means that there are relatively few features visible under the light microscope with which we can elucidate this quintessence (as the images in some previous posts will testify).  Until recently, the response was to wait for improvements in optical technology and the arrival of electron microscopy to give greater resolution and, therefore, more characteristics on which to base descriptions.  However, this still means that, unless you have a very expensive microscope and a highly-trained analyst, you can’t name many algae accurately.

What if we had access to a completely different set of characteristics?  There have been several attempts over the years to use biochemical characteristics to differentiate algae but none have the precision to compete with identification based on size and shape.   But the recent advances in molecular biology do seem to offer real possibilities.  More so now because the latest equipment can process samples at such a rate that the cost per sample is likely to be considerably lower than that for a conventional analysis.  You can forget the brilliance of the science, it is this that is making hard-nosed managers in the commercial and government sectors look hard at DNA barcoding.

All the characteristics of any living organism are controlled by its genes so DNA barcoding is not so very different to identification based on size and shape except that size and shape are, themselves, variable.   Grow a houseplant in a shaded corner of a room and it may look quite different to the same plant grown in full sunlight even though their genes are more-or-less identical.  On the other hand, identification based on size and shape gives you information from many genes simultaneously whereas a DNA barcode is one tiny fragment of one gene.

All is shaping up nicely for a vigorous debate.  In one camp, there is a large group of individuals who have spent years acquiring skills they are not going to relinquish to a technician with an expensive machine without a fuss.  In the other camp, a group who see potentials for overcoming the limitations of our traditional approaches, albeit recognising that some sacred cows may get damaged in the process.

This brings me back to the meeting in the Botanischen Museum.  The medium-term plan is to make sure that all the groups around Europe who work on these methods have broad agreement on the methods that are being used.   Because the EU frames our environmental legislation, there are many benefits if countries are using similar methods to assess the state of their environments.  Within this broad objective, however, there is also a hope that we can strengthen the links between the traditional and modern approaches to identifying organisms.  Ensuring that every barcode is linked to a photograph of the organism from which it was extracted would seem to be an obvious  check yet this is not a requirement of Genbank, the world’s major DNA depositary. As I have worked with CEN, the European Standards Organisation in the past, I gave a short Powerpoint presentation.  The irony struck me as I talked: I had to bring a special adaptor so that my iPad could plug into the data projector along with a second adaptor so that my three-pin plug could fit the European two-pin power sockets.  Yet I was the one extolling the benefits of standardisation…

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One thought on “Berlin and barcodes

  1. Pingback: When a picture is worth a thousand base pairs … – microscopesandmonsters

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