Now what would a physicist know about taxonomy?

February 19th, 2010

You can know the name of a bird in all the languages of the world, but when you’re finished, you’ll know absolutely nothing whatever about the bird… So let’s look at the bird and see what it’s doing — that’s what counts. I learned very early the difference between knowing the name of something and knowing something.

Richard Feynman: ”What is Science?”, presented at the fifteenth annual meeting of the National Science Teachers Association, in New York City (1966) published in The Physics Teacher Vol. 7, issue 6 (1969)

Author: Roger Hyam Categories: Biodiversity Informatics Tags:

On reaching 1,000 Comments.

February 2nd, 2010

My blog post “Bitter taste after eating for days – caused by pine nuts?” has just past the 1,000 comments mark. Today’s count is 1,013.

I have been thinking of trying to get funding to research a DNA barcoding system for pine nuts. I am sitting here surrounded by people working on DNA barcoding of plants and it seems a feasible thing to do but I keep putting it off. Having this constant stream of comments coming in makes me think I should do something about it.

Now if everyone sends me $100 on PayPal – just kidding :)

Author: Roger Hyam Categories: Misc Tags:

Fish Oils Contradictions

January 26th, 2010

This page on the NHS England website claims that eating fish oils (long chain Omega-3 I assume rather than any Omega-3) help prevent depression. It says:

Omega-3 fatty acid

Research has shown a link between the amount of a fish people in different countries eat and the level of depression. In Japan, where people eat on average 70kg (150lbs) of fish a year, the rate of depression is 0.12%. Whereas in New Zealand, where people eat only 18kg (40lbs) of fish a year, the rate of depression is almost 50 times higher.

It is though that a chemical found in fish – omega-3 fatty acid – may help your brain work more efficiently, so serotonin (which can boost your mood) has more of an effect on you.

Fish that contains a lot of omega-3 fatty acid includes salmon, sardines and mackerel. Vegetarian alternatives include walnuts and tofu, and omega-3 food supplements are also available over the counter (OTC) from health shops.

I don’t think this would get through on Wikipedia. “Research has shown” are weasel words if you don’t say who’s research and where. This is a shame because on the same site is a well balanced report on a reasonable study of whether a mediterranean diet prevents depression. The contradiction between these articles is interesting.

To show how ridiculous the fish oil claim – that people in Japan are less depressed because they eat more fish –  real is consider the graph below (taken from the EqualityTrust.org.uk site – a great site go and donate now).

Income Inequality vs Mental Health from Equality Trust

Income Inequality vs Mental Health from Equality Trust

It shows that there is a correlation between mental health and inequality and that New Zealand is a ‘worse’ place than Japan for mental health ‘because’ NZ is a more unequal society. Is there are causal link between fish consumption and income inequality I wonder?

Given the choice between depression being caused by a chemical imbalance and  depression being caused by a more complex set of social (even ethical or religious) conditions it is easy to see which the market would prefer to respond to. Eat more fish! Take these supplements!

I have a load of material on the fish oil ‘conspiracy’ that I’ll have to find time to post. In the mean time if anyone has actual scientific research showing that eating fish makes people happy (other than just because they like the taste) I’d love to see it.

Author: Roger Hyam Categories: Misc Tags:

Are author names really necessary?

January 21st, 2010
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? Read more…

Author: Roger Hyam Categories: Biodiversity Informatics Tags:

DIY Book Scanner: Learn By Doing

January 13th, 2010
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? Read more…

Author: Roger Hyam Categories: Photography, Technolust Tags: