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Month: January 2010

Are author names really necessary?

Although there are standards for abbreviation of author names (notably Brummitt in botany) these are not always followed and often embellished. Furthermore it is believed that the added nomenclatural precision author names add is not worth the cost of their inclusion. If author names were included then every variation of authority string would result in a new URI implying the existence of a new taxon. This would defeat the principle goal of speciesindex.org – to get people using the same URIs for the same things. Homonyms are rare it is even rarer that they cause problems outside of taxonomy and nomenclature.
Consider the following classification of confidence limits from International Panel on Climate Change (taken from here)
virtually certain – more than 99%
extremely likely – more than 95%
very likely – more than 90%
likely – more than 60%
more likely than not – more than 50%
unlikely – less than 33%
very unlikely – less than 10%
extremely unlikely – less than 5%
Now consider the estimate in Paton et al (2008) Taxon 57:602-611 that 4.1% of plant names have homonyms i.e. it is “extremely unlikely” that any one name is a homonym. Also consider the following list of kinds of homonyms:
Nomenclatural Artefacts These occur where the same taxon is published multiple times. Perhaps the same publication comes out in two languages or is published a second time with a slightly different title and set of authors. For all intent and purposes these do not matter as the names are intended to refer to the same taxon.
Competitive Publication New material is found. Two authors publish accounts based on it using the same names. The taxa are substantively the same.
Quickly Synonymised. An author publishes new species only for someone to quickly realise that this is a homonym and publish the fact. Subsequent publications place it in synonymy and it is never widely used. The name in circulation will almost always refer to the correct taxon but the homonym will be kept in circulation due to always being mentioned as being a homonym in monographs, floras and faunas. Modern indexing will exasperate this situation.
Back From The Dead Everyone is happy using a junior (or later) homonym without knowing it when a taxonomist finds a publication containing the senior (earlier) homonym and overturns the nomenclatural apple cart. The rules of nomenclature say that the taxon now needs a new name even if the senior homonym is not currently the name of an accepted taxon. There is a case for nomenclatural conservation of the junior homonym or rejecting the senior homonym. Either way the original usage of the name is the most common.
Problematic Homonyms The same name string is widely used for multiple taxon concepts. This is rarer in terms of nomenclatural homonyms (where different names have actually been published) than it is where authors have simply used the same name in different senses (taxon concepts and/or misapplied names). This is particularly common with European names being used for the “wrong” taxa in the New World. Author strings are of no help here as the nomenclature is correct only the usage incorrect. A full-blown taxon concept based approach is needed to handle these situations.
Speciesindex.org takes the premise that names specified to nomenclatural code, rank, spelling and, in the case of zoological names, year are “virtually certain” to be referring to the same general taxon.

It is customary for scientists to cite the author of a scientific name whenever that name is used. Indeed it is considered grossly amateurish in some circles to omit such details. This causes problems because, although there are standards for abbreviation of author names (notably Brummitt in botany), these are not always followed and often embellished. This means that the entire string of name characters is never guaranteed to be unique. To a machine every variation of authority string would results in a new combination of characters and implies the existence of a new taxon

What if we just stopped using author strings (other than in monographs) and ignore them when other people use them?

DIY Book Scanner: Learn By Doing

Simple Scanner
Almost Free Scanner

In the last weekend of the Christmas break I was sat in Starbucks in Waterstones in Edinburgh considering which of a stack of potential books I was going to spend my Christmas book tokens on. I had just been playing with a Sony eBook reader and so was thinking maybe I should take the plunge and go digital with books as well as the rest of my life.

I wondered what I would do with my existing books. It would be nice to be able search through these and have them all with me when I travel. There would be issues with copyright if I were to copy them but there would also be technical problems. How would I get them in EPUB or PDF format? I did some Googling and came across a great site diybookscanner.org. There are some really innovative designs on this site and it got my obsessive thoughts going. There were two problems.

  • I only had 48 hours to play before going back to work and my wife and kids wanted some of that time.
  • I didn’t have a workshop. Just a desk and some simple tools.

Could I produce a scanner in that time? Would it work?

When will eBooks stop being a rip off?

3374-originalAmazon are selling an ebook of Siddhartha by Herman Hess for the Kindle for $3.51 and it appears in different versions for even more. Siddhartha is out of copyright so it costs them nothing for the rights on this book. The $3.51 is all for them.

Does this mean that $3.51 is the cost of distributing an eBook through the Amazon system? That would imply that the publisher (nee the author) would get the value of any ebook that retailed for over this sum. With Zen and the Art of Motorcycle Maintenance by Robert M. Pirsig (which retails for $9.58 on Kindle) for example the authors would get $6.07? Somehow I doubt it!

That price tag of $9.58 doesn’t compare very well with $10.19 for the paperback version of Pirsig’s book.  The Kindle version can be yours in 60 seconds or less but it is controlled by Digital Rights Management (DRM) so really all you are buying is the right to have a permanent relationship with Amazon who will supply you with a copy to read on an authorised device. For 61c more you could have one made out of real paper that you could hand on to a friend or loved one, sell, donate to charity or even burn to keep warm. Sure it won’t last forever but it still has a residual value. My paper copy is yellowing but perfectly readable. It was printed in 1978 (that is 32 years ago!). It has a price tag of £1 and I bought it from a second hand shop for £1.50 ($2 ish) about 10 years ago.

The Present Moment Does Not Exist

It is just past Christmas and the turning of the decade so I thought it would be worth capturing a train of thought on time and space.

  • The future doesn’t exist yet.
  • The past no longer exists.
  • The present moment is vanishingly small.

Consider the sounds you hear in a piece of music. Sound is the changing in air pressure that moves our ear drums backwards and forwards. To hear Middle C we need to listen to a sound for a long enough period to judge that the air pressure is changing around 261 times per second. At any one moment our ear drums are stationary. There is no sound in the now.