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)

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

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

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.

]]> http://www.hyam.net/blog/archives/806/feed 3 http://www.hyam.net/blog/archives/796 http://www.hyam.net/blog/archives/796#comments Thu, 21 Jan 2010 15:43:18 +0000 Roger Hyam http://www.hyam.net/blog/?p=796 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.

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?

The added nomenclatural precision author names bring is not worth the cost of their inclusion. Homonyms, where two taxa have the same name string excluding the author string are rare especially if, in zoology, we still include the year of publication of the name.  It is even rarer that homonyms 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 I just made up:

• 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.

Why not take 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 taxon. It might make our lives a little simpler.

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?

Most of the plans on diybookscanner.org are pretty complex involving placing the book on a stand on a table and having multiple lights and cameras pointing down at it. I don’t have a table. At least I don’t have a table that isn’t already filled with stuff. So the design I came up with (pictured) turns the system upside down and puts the camera on a tripod near the floor. A frame made from some scrap wood holds a piece of glass from a clip picture frame. The camera is on a tripod on the floor. This is like some photocopiers for books. Lighting is provided by a desk lamp (fluorescent tube) under the desk at approx 45 degrees to the glass.

Setting up involves lying on the floor on your back to focus the camera and line it up with the page. This may be the usability issue that will prevent me commercialising it!

Example Page Image

In operation I have an electronic cable release on the floor that I press with my big toe keeping both hands free to manipulate the book. I take the right page, turn the book round and take the left page (the other way up), pick the book up and turn the page, repeat right and left. I did a 228 page book in under 30 minutes like this. The book was Gotama The Buddha by Ananda Coomaraswamy which I believe is out of copyright.

The resulting images are sideways on and need to be rotated 90 degrees alternately left or right. I wrote a PHP5 command line script (process_src.php) to do this. It will also do simple cropping. There is an example page image shown.

This combination means I can get from physical book to page images pretty quickly for a small book. I can flick through the pages on my laptop but they are nothing without OCR and I have run out of time! The brief attempts I have had at OCRing some of the page images have been pretty disappointing.

Is the OCR the achilles heal of the process? If I did get good OCR how easy would it be to get the text into re-flowing EPUB or similar format. These will have to be the subjects of more thought and perhaps more experimenting if I find the time.

One thing is for sure – I have more of an appreciation for the imaging process and eBook world.

Note: I do not condone the breach of copyright. Authors deserve paying for their work

Important Note: Be very careful if you try and make one of these as you end up with a piece of glass strapped to the edge of a table which is dangerous – particularly with kids around. Put a guard on it when you aren’t using it.

I wondered what the mean/median genus size is but got distracted into wondering “Given any one species what does knowing the genus tell me about that species?”. I figured that we (being human) have rough classes of sizes of groups of thing. Firstly there are the unique things – monotypic genera. Then there are the small groups of things that fit in our working memory (7+/- 2). Then there are groups of things that are large but memorable like the size of a class of school children (in the UK) up to about 30. A typical teacher can probably list them and a taxonomist who was monographing such a group could probably list the species. Over 30 I figure we have the kind-of-things category where we just give up and may know set individuals but are more likely to think of set characteristics. This size includes anything over 30 right up to the super genera with thousands of species.

What does this mean in practice? I don’t know. Maybe something will come to you.

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.

Because, unlike Zen and the Art of Motorcycle Maintenance, Siddhartha is out of copyright you can get a legal non-DRM ebook copy from FeedBooks and other places for free. You are free to do as you please with this. If you have an iPhone or iPod Touch you can use Stanza to download a copy for free to your device in less than 60 seconds just like you can with a Kindle. Fortunately Amazon have released a Kindle reader for the iPhone/iPod Touch so you can have two applications on the same device that you can download the same book with. With the Amazon one you have to pay $3.51 for the privilege with the Stanza one you can do it for free. “Ah but the free one probably isn’t formatted as well or something.” I hear you say. Well you are wrong. It is the other way round. The text doesn’t wrap correctly in the Kindle application. So Amazon are attempting to charge for something that is free (as in speech) and adding minus value to it. If you don’t believe me and you have a iPhone or iPod Touch you can try this for free yourself as the first chapter of the Kindle version is free (as in beer).

Don’t get me wrong. I am the kind of guy who gets excited about gadgets and I think ebooks are really important and going to be a major medium in the next few years. I like real books but would willingly do most of my reading off a gadget and reduce the clutter in my flat. Don’t go assuming that I don’t want to pay for anything either. I do that all the time. In fact I get an urge at least once a year to give Steve Jobs lots of my money.

What I object to is people being ripped off. The thought that someone might pay $3.51 for a faulty version of something they could have for free bothers me. The thought that this process will encourage people to break copyright on works by living authors and so rip them off also bothers me. If Zen and the Art of Motorcycle Maintenance was available as an ebook for half the paper back cost and Robert Pirsig got most of the money then it would seem like a good deal. As it is Amazon (and probably other publishers) are setting the precedent that it is OK to rip people off. It is hard for them morally to turn around and condemn someone who scans and distributes copyright works for free. Sure they can do it legally but they have lost the battle for ‘hearts and minds’.

My hope is that the publishing industry (the bit between authors and readers) will see sense and rapidly move to a position where ebooks are available at reasonable cost – perhaps DRM free. Their role is to add value that can be charged for. If they charge more for the value they add than it is worth then the market will find a way around them. Exciting times!

Amazon have

• 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. To have sound we need to store in our minds all the changes in pressure we have encountered recently. What is now is a static record of what has happened (or appears to have happened) in the past – the log of all the backward and forward movements of our ear drum. The log exists now but the movements don’t. They are in the past and so non-existent.

As with sound all our senses require change. Photons (as waves or particles) must hit the retinas of our eyes for light to occur. Pressure must change on our skin for touch to be sensed. Chemicals must combine in our nose for smell to occur. All the senses rely on the electrical and chemical actions of nerve cells to occur in sequence over time. At any one moment all is still. Nothing is sensed. Nothing is perceived.

Although this all follows logically from high school science it appears to have absolutely no relation to what we experience as now. We feel like we have an intermate relationship with the world in realtime. Perhaps there are two types of now. The logical now (I’ll use now with a small n) and the experienced now (Now with a big N as it is the one we care about here).

When listening to a piece of music we have a sense of Now that includes not only our memories of what occurred before now (necessary for sound to occur at all) but also our anticipation of what is to come. Music, like life, would be nothing without rhythm and suspense. We therefore project forward in time to imagine what sound should happen next. The musician can induce pleasure by either creating sound as expected or sometimes deviating from what we expect. In this way our experience of Now, unlike now, expands both forward and backwards within this notional linear time.

You may think this madness but time is often thought of as illusory: “The distinction between past, present and future is only an illusion, however persistent” (Einstein 1955)

If this objective sense of Now is true of time is it also true of space? Taking the schoolboy approach to Euclidean geometry it would seem so. ‘here’ could be taken as a point without any dimensions (vanishingly small like ‘now’) but then it would be difficult to for me to say something like “See you back here in 15 minutes?” Neither of us would fit into here. Indeed nothing fits into here by definition. Nothing can be here – yet things blatantly are. We therefore have our own experiential ‘Here’ that we adapt to the context. “There are no lions Here.” means there are no lions in a reasonable distance. On the other hand “The aliens are Here!” could mean anywhere on earth rather than just this room. When I talk to a friend on the phone it is as if he is Here but it must seem to him that I am There also. Where exactly the conversation takes place is complex.

Suppose you are saddened by the loss of a loved one. They are no longer with us in the here and now. But how can this be? They were never with us in the rational here and now as these things are vanishingly small. They can only have ever occupied the experiential Here and Now that we make up as we go along. Why then are we sad? We are sad because we choose (in some way) to consider them no longer part of our experience.  We shrink our Now to a point that does not include them. Our grief wells up to fill our entire experience but only because we have a narrow definition of what our Now is. We can choose to have a broader experience that includes before and after our current grief – making it a richer bitter-sweet experience. Indeed this richer experience is present before they die as we can experience that they are not with us in the future as they weren’t with us in the past – all in the Now.

I believe this is an aspect of the contemplative religions and one of the ways in which mindfulness based practices basically make us happier and more compassionate. Through practice we can become more adept at expanding and manipulating our Here and Now. Concerns of time and space can be optional – at least from an emotional point of view.

Tremendous energy is required to re-animate the dead.

At last month’s TDWG2009 conference I was on a panel for a brief discussion at the end of a session. There were around 200 people in the audience and handful of us up front as lambs for the slaughter.

One of the questions from the floor concerned the automation of the taxonomic process. I don’t recall the precise question but it triggered one of my (probably boring) canned responses.

I pointed out that the usual practice in software engineering, when asked to automate a system, is to produce a Domain Model based on an analysis of some Use Cases that then leads on to some Object Model or implementation model that is actually created in software. The assumption behind this is that whatever was being done was good but needs to be done faster – with computers!

In biodiversity informatics, and particularly in biological taxonomy, this is not such a good idea. Current working practice was developed in the light of the prevailing technology of the time. If computers and the internet had been available from the start things would probably have been done differently. The worst thing we can do now is automate a paper based system. We should take the opportunity to re-engineer our working practices. To ask the dangerous questions (that are usually only asked by those students who drop out and become multi-millionaires) like “Why do we bother doing this bit?”

Imagine my delight when I got this email from David King at the Open University agreeing with me!

You struck a chord with me in your wrap up session. Several decades ago my first job was with British Steel (remember them?). Anyway, I was in the Computer Department looking after a production service  mainframe with 8Mb of memory and leading edge technology like that. When we recruited applications programmers they were told in no uncertain terms that to simply take an existing paper based workflow and replace it with one that just mapped one piece of a paper to one screen was tantamount to a sackable offence. If we were going to the expense, bother and risk of changing an existing workflow then we should take the opportunity to review it in the light of what is now possible with a computer… [my emphasis added]

Clearly great minds think alike (as fools seldom differ).

It is a good job nobody in the biodiversity informatics community is working to reproduce paper publications like this  Ranunculaceae page on eFloras! I am not picking on eFloras here. There are many similar projects and I am tacitly involved in some of them. Perhaps we are all committing sackable offences. My point is this. If (and it is a big IF), it is necessary to present data like an “old fashioned” printed flora or fauna then it should only be seen as a byproduct of the taxonomic process. The specimen, character and observational data should be primary as it can be re-purposed. Data in document form (even if it is hyperlinked) is effectively dead and requires an enormous effort to re-animate – just like Frankinstien’s monster. Perhaps we should stop producing documents like this completely.

• Report on authoritative taxonomic standards from multiple sources suitable for deployment within European Research Area – resubmission with some clarifications. (PDF = PESI_D4.1_Standards_Report_v2.1.pdf )
• Report on Procedures and Mechanisms for the Functioning of Nomenclators within the e-Infrastructure. (PDF = PESI_D4.2_Nomenclators_Role_Report_v1.1 )

Read and enjoy!