Friday 23 May 2014

The Type Specimen

When the human genome was delivered into the public domain by Tony "Biotech" Blair and Bill "Compute-guy" Clinton in 2000 we binfoes were all justifiably stoked and/or proud to have contributed in a small-small way or to have known people who had helped make sense of the 3 billion base-pairs that is our genome. It is not wholly clear whose genome was chosen to represent us all.  The Human Genome Project took DNA from five individuals of different ethnicities and created a composite human genome. They were spooked into getting the material into publishable form by J Craig Venter's threat to sequence the whole thing licketty-spit as a commercial venture while the HGP was still plodding towards Bethlehem.  It is a racing certainty that JCV is the main contributor of DNA as well as oomph and leadership to this commercially funded Celera genome.  Celera ("The Swift") being the name of JCV's company.  It is rather more certain that the dog (Canis familiaris) genome was clagged together from DNA contributed (without informed consent) by Venter's poodle "Shadow" (seen here).  Of course we realise with 20/20 hindsight that the completion of The human genome was not the end but rather the beginning a huge series of projects to document the extent genetic variation among us.

The idea that there should be a single genome to represent a species and against which the rest of us are compared goes back a long way: ante-dating the discovery of the structure of DNA let alone our ability to unravel its weave. The idea of a type specimen is at least 250 years old.  Before we had computers to store DNA information or -80C freezers to store the actual DNA, there was a physical specimen in a museum - for small mammals often a preserved skin and skull with a hand-written luggage label tied securely to a hind-leg.  If you turn over a rock in a tropical paradise and catch whatever scuttles away from you, it is not unlikely that you have in your hand a species unknown to science. You verify this by comparing your skull-and-skin to a lot of type specimens in a lot of museums, which is time-consuming but involves travel and schmoozing with fellow enthusiasts in Cambridge MA, and Cambridge UK, Utica NY and Uppsala SE.  If it's different, you get to name it which allows you to exercise hubris, flattery, or a sense of humour. According to the International Code of Zoological Nomenclature (ICZN) and the International Code of Nomenclature for algae, fungi, and plants (ICN), the name has to be a Linnaean 'binomer' using Latin or Greek roots or making a proper name look Latin or Greek. Megascops koepckeae (the big owl of  Maria Köpcke) which I mentioned a few days ago is a good example. Because these names are foreign it is conventional to italicise them. The first name represents the Genus - a group of related species - and is always Capitalised.  The second part identifies the species and is always lower case even if, as here, it is derived from a proper name.  Getting to know these conventions is part of what we teach at The Institute.  You know you have arrived as a scientist when you tsk tsk or snicker at some poor mutt of a journo who writes Caerostris Darwini rather than Caerostris darwini.  The poor journo, having an Arts Block education, at least knows where to put his apostrophes, which is more than we can say of most scientists.
The person we have most to thank for sorting the business of naming and classifying the denizens of the living world is Carl von Linné as his mum knew him or Carolus Linnæus as he's known to science from the days when all of us were fluent in dog-Latin. He was born on 23rd May (!today!) in 1707, more than 300 years ago, and has been claimed as the father of modern biological science or even Princeps botanicorum. Before Linnaeus the distinctive characteristics of each species written in Latin were the definition: "Physalis annua ramosissima, ramis angulosis glabris, foliis dentato-serratis".  Everyone knew what group of mutually-interfertile organisms that referred to.  Everyone who read Latin, that is, and had sufficient expertise to recognise a bit of  foliis dentato-serratis if it jumped up to bite them. Linnaeus added a binomer, here Physalis angulata or P. angulata to its pals. The ICZN and the ICN have appointed themselves to keep this system on the rails, make sure the same thing doesn't have two names and the same name doesn't include two species. It gets complicated because the data is biological - noisy, inconsistent, ever-changing and biodegradable.

Linnaeus wrote his ideas down and made a start on classifying the whole living world in a modest pamphlet called Systema Naturæ which was published in the Netherlands when he was 28.  He wasn't the first to use binomers (that honour might go to Gaspard and Johann Bauhin) but he was the first to use them consistently.  By the time Systema Naturæ reached its 10th edition in 1758 it included 4400 animals and 7700 plants, all named and ordered into a hierarchy of inclusive groups: species - genus - family - order - class - kingdom - domain. Along with Sus scrofaTroglodytes troglodytes, Equus caballusMeles meles, Panthera pardus and Loxodonta africana (pig, wren, horse, badger, leopard, elephant) Linnaeus recognised that we also fit into his classification of nature.  Because he used himself to describe this species, he has become the type specimen!  I have just discovered that fact and it has made me quite absurdly buoyant.  He named this our own species Homo sapiens which, because he was describing himself, is entirely appropriate.  If he looked out of the window of his home in Uppsala or into the wider world at the hubris, folly, cruelty and greed of his conspecifics, he'd have been forced to name us Homo dingbatius.

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