Roger Hyam

November 17, 2008

UUIDs may be Dangerous

Filed under: Biodiversity Informatics — Tags: — admin @ 11:18 am

There is no doubt that Globally Unique Identifiers (GUIDs) are important and not just because I have been hammering on about them for the last few years. It is hard to imagine a world where biodiversity data can flow from one application to another without some kind of tagging of that data to show its provenance. The question we can’t get beyond is how to tag the data.

TDWG recommends the use of LSIDs -which are pretty restricted to the life science community (the clue is in the name). Publishers see books, journals and papers as “assets” and therefore legitimately use DOIs. Neither of these technologies play nicely with Semantic Web technologies al la W3C and so some people prefer PURLs or even Plain Old URL.

All these types of GUID are resolvable. Each can act as a form of address (by a variety of mechanisms). An implication of this is that each must be associated with some form of issuing/resolving authority. If you or your PC comes across one of these things it can look it up and get an authoritative answer as to what data it represents and who “owns” or curates that data.

Running some form of authority implies having access to some technical resources such as a web server and possibly DNS server. In the case of DOIs it implies paying some one else to run the infrastructure for you. This is not easy for many data suppliers.

UUIDs to the rescue! UUIDs are great. Just get the computer to make up a string of random digits that is complex enough to be guaranteed globally unique. Anyone should be able to tag anything with a GUID. This solves the multiple routes problem. If a consumer receives two pieces of data that bear the same UUID then they can assume that the two pieces of data are actually the same thing and one can be ignored.

But what happens if the two pieces of data tagged with the same UUID differ? Perhaps one has an extra field or two. How do we know which is correct? Perhaps one was originally created as the result of a search and the other was harvested as an RSS feed and the two mechanisms give different versions or views of the object identified by the UUID. Or perhaps one has been changed by some intermediary. How does the consumer of the information resolve the situation?

One way would be to approach an indexing service that has recorded the occurrence of all the UUIDs. Google’s pretty good at this kind of thing but it would not be possible to differentiate on Google between pages that mention the UUID and those that contain the authoritative data associated with the UUID. To do this we would need a real register that maps UUID to data source. At this point we are close to recreating the Handle system that drives DOIs and the advantages of UUIDs are slipping away. You can’t just use UUIDs you must use registered UUIDs!

It gets worse. Suppose I have created the preferred description of a taxon. I tag it with a UUID to uniquely identify it. Other people refer to it using the UUID. All is well in the world until an awkward person disagrees with me. Perhaps I haven’t added new data to my description or corrected errors. So the awkward person puts up their own description of the taxon and tags it with the same UUID - they redefine the meaning of that UUID by cutting and pasting it to a new authoritative description. They want to say “this is the correct description”. Nobody owns the UUID so there is no arbiter. If their is a register of UUIDs then they could perhaps sort it out but they couldn’t stop other people from setting up their own registers that favour different interpretations of particular UUIDs. This situation is very similar to the taxon name problem we have. No one owns a name so who has the definitive description of the taxon that name should be used for - nobody!

So UUIDs are dangerous. They appear to give a simple way to uniquely tag things but it is likely humans will mess this up. The fact that machines will not generate the same UUID twice is irrelivant if humans can cut and paste them with impunity.

October 15, 2008

Eco PC Nuts?

Filed under: Technolust — admin @ 9:20 am

Here is a story on the BBC about a USB device that you plug into your PC to enable it to be put to sleep at the touch of a single button. It is incredible that some one is selling a product to do that. For starters my Macs do it by default. Just close the lid of a laptop or touch the power button on a iMac and they go to sleep. They come back pretty instantly as well. The other point is that I am sure my old Dell desktop used to have the option to set the power button to do precisely this behaviour with Windows XP though of course it used to take hours to come back and used to crash on me etc. One could always set the PC to power down gracefully as you stop using it i.e slow the disc then the screen then the processor and full sleep after a few minutes of non-use but that would take more thought.

There is nothing like a gaget to fix bad design and sloppy thinking. They’ll make a fortune with it.

October 11, 2008

Nuts sent off

Filed under: Misc — admin @ 1:40 pm

The nice people at Julian Graves wrote straight back to my email and sent me a post paid envelope so that I could send the nuts back to them for analysis. Lets wait and see what they say.

BTW Julian Graves has be bought by Holland and Barrett.

The bitter taste remains especially after eating carbohydrate rich things like white bread. Perhaps a link to saliva amylase? Does not appear to be getting any worse. If anything it is clearing. I don’t have a noticable cold or anything though the glands in my throat are up a little an infection of some kind would be a good candidate.

It is amazing how trivial a thing this to write about but I am fascinated and imagine some one else with the same taste sensation would find it fascinating. To anyone else this must be horrendous!

October 9, 2008

More Nuts

Filed under: Misc — admin @ 9:57 am

The bitter taste in my mouth continues so my investigation goes on. The suspect ‘baby pine nuts’ came from Julian Graves store in Livingston a couple of weeks ago. I remember they had both regular and small pine nuts and we bought the small but as I quickly discarded the packaging I don’t have any information about them beyond my memory.

So off to the Edinburgh Julian Graves to see if I could find some more but this is a small store and only had the regular pine nuts. I bought them for comparative purposes. Here are the pictures of the two types of nuts.

Baby Pine Nuts from Julian Graves Edinburgh

Baby Pine Nuts from Julian Graves Livingston

Regular pine nuts from Julian Graves Edinburgh

Regular pine nuts from Julian Graves Edinburgh

The smaller ones appear to be more oily - they stuck to the scanner lid when the others didn’t. Perhaps they are just lower grade and off?

The new packet I have does not state the country of origin which we need if we are going to track down the species. I did think this had to be listed for legal reasons in the UK.

Next step write to Julian Graves and ask them.

October 8, 2008

Bitter taste after eating for days - caused by pine nuts?

Filed under: Misc — admin @ 12:02 pm

I started to get a bitter taste in my mouth after eating. At first I thought I was going to die so I Googled on it - how many people a minute go through that process! My scatter gun approach to diagnosis came up with a series of suggestions. I either had jaundice or I was diabetic or I had eaten pine nuts (possibly from China) in the last few days. My skin isn’t yellow and my pee isn’t orange and I am not thirsty all the time but I had eaten a new kind of pine nut in the last few days so the third option looks like it warrants attention. After Googling start blogging.

There is a very short scientific-like paper out there Taste disturbances after pine nut ingestion. In the initial case the pine nuts were oxidized and not fit for consumption but six other cases are mentioned and it is not clear if these were oxidized. A test subject also consumed two portions of nuts which I guess they wouldn’t do if they were oxidized. Importantly there was no fungal contamination, no pesticide contamination and they didn’t know what species of tree the nuts were from but they had come from China.

The wikipedia pine nut page currently summarises and has a few links to discussion groups where the effect is mentioned.

Now I eat pine nuts a lot (I am a veggie) and this is the first time this has happened. It is also the first time I have had ‘Baby’ pine nuts which were sold as being small. My theory is that these are actually a different species of pine nut. This would be fun to investigate.

What candidates do we have among commonly eaten pine nut species ( according to Wikipedia)

Pinus gerardiana, known as the Chilgoza Pine, ‘noosa’, or ‘neoza’, is a pine native to the northwestern Himalaya in eastern Afghanistan, Pakistan, and northwest India, growing at elevations between 1800-3350 m. It often occurs in association with Blue Pine (Pinus wallichiana) and Deodar Cedar (Cedrus deodara).(Wikipedia) - This is a possible one. Are its seeds smaller than P. koraiensis I wonder?

Pinus koraiensis is Korean Pine. It is native to eastern Asia, Manchuria, far eastern Russia, Korea and central Japan. Korean Pine differs from the closely related Siberian Pine in having larger cones with reflexed scale tips, and longer needles. The seeds are extensively harvested and sold as pine nuts, particularly in northeastern China; it is the most widely traded pine nut in international commerce. - Very likely. (Wikipedia)

Pinus pinea Stone Pine (or Umbrella Pine) Native of Southern Europe in the Mediterranean region (Wikipedia) - not likely contender.

Pinus edulis Colorado Pinyon or Two-needle Pinyo is native to the United States and so not likely contender.

Pinus cembroides Mexican Pinyon - mexican so not likely to bother us.

Pinus monophylla Single-leaf Pinyon - USA native so not likely to bother us.

Looks like there are two contenders. Common things happen commonly so I have probably been eating P. koraiensis for years as it is the most commonly traded. Perhaps these new seeds are P. gerardiana?

I will investigate further.

September 21, 2008

Another bleeding lefty

Filed under: Misc — admin @ 7:27 pm

Well I got a link to a US political on line test and I am just another bleeding lefty - ah well no great surprise there then though I would describe myself as a liberal… Take the test if you like. Link at the bottom.

You are a

Social Liberal
(66% permissive)

and an…

Economic Liberal
(15% permissive)

You are best described as a:

Socialist



Link: The Politics Test on OkCupid.com: Free Online Dating
Also : The OkCupid Dating Persona Test

September 19, 2008

Jill Bolte Taylor

Filed under: Misc — admin @ 9:53 pm

This is just an amazing 20 minutes.

September 1, 2008

Starling - a ghost story

Filed under: Misc — admin @ 1:04 pm

On a recent BBC documentary about bird mimics wildlife sound recordist Chris Watson told a wonderful ghost story that has that great quality of raising questions in the heart about our place in the world and the nature of causality. Have a listen:

Starling Ghost Story (5 min MP3 3.6mb)

The original documentary is available from the BBC here but this link will no doubt stop working after a while.

Wonderful radio - sent a chill down my spine.

August 28, 2008

Edinburgh goes down hill?

Filed under: Misc — admin @ 1:29 pm

Last year Channel 4 declared Edinburgh the best place to live in the UK according to a comparison of facilities, house prices and jobs etc.

But today the BBC news website reports a study that says it is the least cheerful place in the UK.

Does this mean living in the best place makes people sad - probably.

August 9, 2008

Where am I?

Filed under: Misc — admin @ 6:36 pm

Just stopped at a motorway services on the way ‘down south’. I had to ask the lady who sold me coffee where I was because from the inside it could be any service station. This isn’t globalization this is regular human homogenization.

It is Keel apparently.

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