Dawn has epilepsy which means that 20-40 times each day she misses a few seconds of what is going on – yet nobody notices.  She finds it disturbing especially when compared to the experiences she has had with her grandmother suffering from Alzheimer’s. The thing that struck me was the phrase “I worry constantly about how much we remember.” This made me think of the suffering that even the thought that one might not remember something can create.

My mother had a ‘perfect’ memory right up until the end of her life. I take this as a great blessing because for much of my life I had someone who was certain they could remember almost everything whilst my memory was incredibly fickle and would constantly play tricks on me. The blessing was bestowed when, at some forgotten point in time, I realised that both of us had very similar powers of memory. Mum was just more confident in asserting that she was right. She would declare something to have happened and, because there was often no way of knowing otherwise, it may as well have been that way – someone had moved the car keys and if she was alone in the house she quickly dismissed the incident.

What this part of my relationship with my mother taught me was that your attitude to your memory is more important than what you remember. As I got into bed after another long day and yielded to the wonderful sensation of pillow, sheets and duvet it occurred to me that I have got into this same bed over 6,000 times. How many of those can I recall? I could say none or all. They merge into a feeling of getting into my own bed. Does it bother me that I can’t remember probably 5,900+ times I have done something significant to my life – no. Yet some memories do bother me. What year did my father die? What is the anniversary of my mother’s death? What was my grandfather’s name? How callous that I get them wrong when they are so fundamental to my life – to my identity.

This is the crux of it – identity. To forget ourselves is synonymous with death.

I believe most people work on the basis that they are their personal histories. When we find contradictions between memory and our present reality we are literally wounded and we feel pain. Fortunately we fudge over inconsistencies to avoid the pain. Dawn’s missing moments are an example of this happening within a clinical condition but it is common for all of us.

I just read a wonderful book “Thinking, Fast and Slow” by Daniel Kahneman where the author summarises our internal mental processes in terms of two systems. System 1 is unconscious, fast and simply serves up options to System 2 which is our reasoning mind. The cocktail party effect, where you pick out your name being mentioned across a crowded room, is an example of how System 1 monitors everything and only tells you (System 2) about what is relevant. (There is much more to this and I recommend the book.) Memory is a System 1 process. You think “Where are the car keys” and you just know. The “just know” is System 1 going off and fetching that information for you.

System 1 maintains this flow of ideas and thoughts to your conscious mind to maintain the sense of a coherent self and it will create ‘false’ memories and make up excuses if necessary. It basically tells you what you what is needed to support the view of yourself you have.

In Buddhism there is the notion of the Seed Consciousness (ālayavijñāna) which is very similar. Stimuli (which may include our own thoughts as well as external prods) trigger seeds in our subconscious store house to germinate and bear fruit in our conscious mind. The contents of the store govern how we see the world. The task of meditative practice is to purify the store house so that it contains more flower seeds than weed seeds. Everything starts coming up roses!

Now for the scary stuff. You don’t remember most stuff – like the umpteen thousand times you have cleaned your teeth – and your System 1 will seamlessly imagine things to fill the cracks should you need to remember something that is no longer available or perhaps never happened – just like with my mother. The danger is that consider yourself a forgetful person and System 1 starts pointing out all the cracks just to prove you right – like it did with me.

Now for the cool stuff. Because your attitude governs how you remember and what you remember governs how you interpret the world by changing your attitude now you can actually change everything: past, present and future. It sounds crazy but think it through. If you work to change how  you habitually react in the present moment then you change the past. Not physically. You won’t suddenly find that you won the lottery five years ago but you will remember more positive things and see the positive side of things you had thought negative.

One of the experiments that Daniel Kahneman mentions in his book really strikes me. They got people to fill in a questionnaire that assessed two things: their current mental state and an assessment of their lives so far. The trick came in that they asked each participant to photocopy a sheet of paper before filling in the questionnaire. For half the people there was a small value coin left on the photocopier and for the other half their wasn’t. Not surprisingly the half that found the coin were recorded as being in a better mood but they also gave a better assessment of their past lives. Placing a coin on a photocopier had changed how these people felt about their past. I would say it had actually changed their pasts because so much of the emotional content of the past can only exist in memory.

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The pamphlet is released under a Creative Commons license and you can download it as a PDF, a PDF designed for booklet printing and as an eBook in ePub format from the downloads page.

Download a digital copy to read and freely distribute from the
downloads page.

Near the end of 2010 I became frustrated with what I thought of as the “barriers to entry” for people who were interested in developing a meditation practice. It was as if the very bottom rung of an otherwise excellent learning ladder was missing.

I had just embarked on the MSc course in mindfulness at Bangor University. Friends and relations would ask what it was all about. You can’t explain this kind of thing in a social setting so I’d come away feeling frustrated having probably just confused them. Some of these people were genuinely interested but they weren’t going to invest the time in reading a whole book or attending a course. They needed a lower bar. Something they could read over a cup of coffee or on a short train journey that might lead to something more.

New people would come to our sangha evenings with little or no experience of meditation and we had nothing to give them in their hand. We might spend a few minutes explaining our practice but this was largely taken up with the order of service for the evening rather than the fundamentals of meditation. I felt they may be leaving a little bemused by the whole thing.

In response to these stimuli I started writing a pamphlet. Although I love digital media and think it is the way everything is headed I believe what is needed here is a physical object that can be given as a gift. I was also inspired by the notion of becoming an old style Pamphleteer!

It has taken me over a year to complete the first version of a sixteen page A5 publication and I could carry on refining it forever. It has been a good practice to work up the text and then pass it around a few friends for their comments before reworking it. Accepting criticisms of the written word and filtering out what to include and what not is wonderful for exposing ones ego tendencies! Writing this has been quite a struggle but I hope it doesn’t show in the text.

Please make use of the pamphlet and let me know what you think. If you would like a hard copy (with a coloured cover!) then drop me an email at the address in the pamphlet and I’ll see what I can do.

This post is a follow on from a previous one where I discuss mapping the Rhododendron monographs to EoL. It is an opinionated rant but I offer it in the hope that it will be of some use.

When monographs/floras/faunas are mentioned in the context of digitization people usually chirp up with PDF or, if they are more clued up on biodiversity informatics,  TaXMLit and INOTAXA (Hi to Anna if you are reading) or TaxonX and Plazi.org (Hi to Donat).  The point I am going to make in this blog post is not against these ways of marking up taxonomic literature but more the nature of the monographic/floristic/faunistic taxonomic product itself. I am far more familiar with the botanical side of things so apologies to zoologists in advance.

The problem is what I call the “narrative form” of monographic data not whether it is available in print, pdf, ebook or lovingly marked up XML. These publications are arranged hierarchically. There is introductory material, family descriptions, generic descriptions, species descriptions, subspecies descriptions. These descriptions are nested within each other and it isn’t always clear what information in one level of the hierarchy is repeated at lower levels. Descriptions are diagnostic within the frame of reference of that treatment i.e. they provided enough detail to separate that taxon from the others at that level in that particular hierarchy. Differentiating the taxon from other taxa in other treatments of the same or overlapping groups is usually relegated to notes.

Today we talk of monographs having this form because they reflect phylogeny. Previously they reflected a more ill-defined ‘affinity’ or natural ordering. Originally hierarchies were used as an aide-mémoire. This results in a mishmash of  concepts that it is difficult to decode. Phylogenies do not have ranks or a linear order yet monographs do. So what does the order and rank in a phylogenetically based monograph represent? If these things exist as aide-mémoire then why aren’t they totally arbitrary – merely picking out the most easy to remember characteristics of different groups and making no attempt to represent evolutionary history.

Imagine approaching a monograph/flora/fauna with a species name. You look it up in the index. Turn to the right page and then have to assemble a description of the taxon by reading back up the taxonomic hierarchy – unless of course the author has redundantly repeated all the descriptive data in the species level account which begs the question of what the higher level accounts are for.

Now suppose you have in your hand an unknown specimen. First thing you need to do is to know the family and possibly the genus so you can find the right work to look it up in. There is rarely a multi access approach to getting you near to a taxon such as “deciduous trees with palmate leaves”. You have to be a taxonomist, have fertile material and more or less know what the thing is before you even start. By definition the monographs are not optimized for identification of specimens.

This means that these works are mainly of use to taxonomists who are familiar with the groups concerned. But what do they use them for?

If a taxonomist is working on a new revision they won’t be consulting current, extant monographs very much. That work has been done and shouldn’t need revising for decades. They will be working on material that hasn’t been monographed for decades if ever and needs to be classified. If they are finding new species within a recently monographed group then they will be turning over the apple cart because the descriptions in that monograph are now out of date because the monographic form is designed to be comprehensive.

What is more likely is that a taxonomist will use existing monographs to produce secondary taxonomic products such as field guides – and this is where my key point comes in.

Remixing

Suppose you want to produce a secondary taxonomic product. Say a guide to the lowland trees of a country. Even if you had a checklist of all the species of the country how would you know which were lowland trees? That kind of habit character is likely to be buried in descriptions. Even if you had your list of the species how would you build your guide? How would you pull together free standing descriptions of each taxon? The only way at the moment is to roll your sleeves up an become a taxonomist. Start writing new descriptions based on the contents of monographs (in which the descriptions are designed to differentiate your target taxa from taxa that will not be included in your guide). This kind of thing should really be done automatically. We should be able to do a search for all the species that are considered trees and occur below a certain altitude and find free standing descriptions of these species that we can load on our phone or tablet or print in a booklet and take into the field. The stuff that taxonomists currently produce does not support this kind of behaviour.

What about putting the monograph on the web? If someone links to a species what do we show on the page that is displayed? Do we include the genus description as well? What if the species description doesn’t mention the generic characteristics? Do we include the subspecific taxa? What if the subspecific taxon is only defined in terms of its minor differences to the main species – “var. alba”

Two years ago I discussed how difficult it is was to handle hierarchies in Synonyms Are SubClasses And Higher Taxa Are Just Tags which is a little more technical than this piece but makes similar points.

Tough Love

Producing electronic versions of narrative monographic works is OK  from a political point of view and, if you are doing a print copy you may as well do an ebook and pdf but from the point of view of a non-taxonomist it is of little value and we shouldn’t kid ourselves that we are increasing accessibility very much. It may even be counter productive because people think they have produced an electronic resource when all they have produced is a facsimile of the paper one that is probably slower to use.

My Suggestion

Taxonomy needs to move to a One Species Per Publication model – I call this a fact sheet based approach. Instead of producing monographs of groups taxonomists should produce single free standing publications, one per single species with a global scope. If their primary interest is in phylogeny then they produce separate papers that only discuss the relationships between species that are already described in the free standing publications. This approach is far more appropriate for this digital age for the following reasons:

• Referable - Single species can be used and referenced like other scientific or web resources. It is possible to refer to the use of a species in a study or in legislation and reference a single source that just describes that species. A lawyer can right a document that says we want to conserve species X as described in publication Y and that statement is not entailed with all the other taxa and data that is presented in publication Y.
• Remixable - It is possible to pull together a set of species descriptions to form a new resource. This may be done either automatically, say from a list of occurrence records for a region or habitat, or on a pick’n'mix basis (see taggable below).
• Granular Versionability (= Stability) - It is possible to replace individual species definitions in a set of definitions without having to reversion the whole lot. A new phylogeny or new species in a genus need not change other species in the genus that may be subjects of legal protection etc.
• Data transparent - In a typical monograph the data is of varying quality. One species may be based on five hundred specimens and another on only five. This isn’t always clear from casual use of the monograph where specimens examined and data analysis are typically presented separately from the main treatment. If all the data used to define a species is presented in a single publication then things become a great deal clearer.
• Granular Peer Review - Not all monographs are peer reviewed. Those that are are taken all or nothing. Suppose a monograph of twenty species is presented. It may be very good and have a good phylogenetic analysis etc. Perhaps two of the species are not particularly well defined but it is of high enough merit as a whole to be published. The result is that 10% of species are not particularly well defined! It would have been better to pass eighteen species and reject two. Taxonomy is riddled with such species. You only need to read a monograph that is sinking ill-defined species from the previous monograph that probably shouldn’t have been published in the first place – whilst creating new ill-defined species of its own.
• Taggable - Anything that can be reliably referenced can be tagged. This means that it becomes possible to build meaningful lists of species that can be pulled together into useable products. The tagging does not have to be done by the authors. For example IUCN tags species with conservation status and a group working on functional ecology may tag them with their functions in the environment. It is then possible to pull together a list (with descriptions) of endangered species that perform a certain role in the environment. Currently this process only leads to a list of names that can be handed off for someone to work on trying to establish what the different sources meant by those names.
• Faster More Agile Development - We can’t describe all the species on earth in the way we have been doing with the resource available in a reasonable time. This is not an unusual problem. All domains are faced with challenges that can’t be addressed by the resources available. In software engineering the ‘agile’ approach to this problem is to prioritize development of important, doable things to build an initial working system and then revisit and re-prioritize what needs doing next. Publish results quickly and often. In taxonomy the opposite approach is often taken. A group is selected for monograph and worked on until resources are exhausted and the monograph is then published. By adopting a One Species Per Publication approach the ‘easy’ species would be published as soon as the researcher was sure they were ‘good’ taxa making their work available for others to use and give feed back on years sooner than is traditionally the case and whilst resources are still available to respond. Should the project stall or fail to complete then possibly the most valuable results will already be in circulation and not lost to science. Those enormous genera that are a life times work for someone could be chipped away at by the army of short term employees who are replacing career scientists!
• It would make the job of aggregators like EoL much, much easier! If we accept the fact that we need projects like EoL (which I think we all do) then we must also accept that we need to produce data in a form that they can use.

Summary

This is a long post so to summarize my proposal

1. Stop writing monographs or  floristic or faunistic regional accounts of taxonomic groups.
2. Produce individual, self contained fact sheets of single species that are global in scope.
3. Use ‘Agile’ development techniques to produce and update these rapidly.
4. Treat phylogenies as separate products that handle the arrangement of the entities described in fact sheets.

I am sure this will put a lot of peoples backs up. Please leave a comment if you agree and well as if you want to see my lynched.

1. Text is obtained from the source monograph either via OCR or access to the original word processor documents.
2. The text is topped-and-tailed to remove the introduction and any appendices and indexes.
3. Text is converted to UTF-8 if it isn’t already.
4. An XML header and foot are put in place and any non-XML characters are escaped  – this actually came down to just replacing & with &
5. The text is now in a well formed XML document.
6. A series of custom regular expression based replacements are carried out to put XML tags at the start of each of the recognizable ‘fields’ in the species accounts. These have to be find tuned to the document as the styles of the monographs are subtly different. Even the monographs published in the same journal had some differences. It is not possible to identify the start and end of each document element automatically. This is for three reasons:
   1. OCR errors mean the punctuation, some letters and line breaks are inconsistent.
   2. Original documents have typos in them. A classic is a period appearing inside or outside or inside and outside a closing parenthesis.
   3. There are no consistent markers in the source documents structure for some fields. For example the final sentence of the description may  contain a description of the habitat, frequency and altitude but the order and style may vary presumably to make the text more pleasant to read. The only way to resolve this is by human intervention.
7. The text is no longer in a well formed XML document!
8. The text is manually edited whilst consulting the published hard copy to insert missing XML tags and correct really obvious OCR errors. In some places actual editing of the text is needed to get it to fit a uniform document structure as in the habitat example above.
9. The text is now back to being a well formed XML document.
10. An XSL transformation is carried out on the XML to turn it into ‘clean’ species accounts and alter the structure slightly.
11. An XSL transformation is carried out to convert the clean species accounts into SQL insert statements for a simple MySQL database. The structure of this database is very like an RDF triple store (actually a quad store as there is a column for source). A canonical, simplified taxon name (without authority or rank) is used as the equivalent of the URI to identify each ‘object’ in the database. Putting the data in a database makes it much easier to clean up and to extract some additional data. An alternative would be to have a single large XML document and write XPath queries.

By writing queries that join the Rhododendron database to institutional databases I can create lists of living and dead specimens at Royal Botanic Garden Edinburgh and extract images from the herbarium digitisation project. Previously I extracted images from BHL that I can also join in. I can do things like ‘tag’  species with the ISO country codes, whether they are epiphytes, their altitude range – all interesting facts. I can imagine someone asking a real question such as “Give me accounts for all the rhododendrons that occur above X meters in Thailand”.

I could write a bespoke front end to the database that enables this functionality but this wouldn’t help someone answer the question “Give me accounts for all the XYZs that occur above X meters in Thailand”. Let’s face it only a small bunch of taxonomists and enthusiasts are interested in data that only includes rhododendrons. For most people this data will  never be the whole answer. I am being funded to do this work so that we can get the information from the Edinburgh Rhododendron monographs into the Encyclopedia of Life. There it can be mixed in with data from many other sources and so move towards answering the questions “most people” are likely to ask.

‘Properties’ I Have Captured

From the workflow described above you can see that the  properties I have in my database have to represent the document structure of the monographs – plus some tags extracted by very simple data mining.  The properties are:

• altitude (around, max, min, range) – Many accounts include a range of numbers or maybe a single ‘circa’ number.
• description – Diagnostic description. Importantly this may or may not include characters that have been mentioned higher up the taxonomy in a group, subsection, section or subgenus description.
• distribution – Usually the country and province. Sometimes individual mountains or parks.
• habitat – a sentence describing the habitat but often including whether it is epiphytic or terrestrial (shouldn’t this be habit?) and also whether it is common or not.
• icon-ref – a citation of where an image can be found in the literature.
• image – a link to a Curtis image.
• name (author, cite, formatted) – Three properties breaking down the name
• type - The type citation string for the accepted name of the taxon.
• note – All sorts of things in here! Almost all accounts have some comment varying from “Known only from type collection” to several paragraphs of text. May include derivation of name. May occur multiple times  for a species.
• occursInCountryIso – this was extracted by simply looking for country names in the distribution field
• rank - the database contains facts about the subspecies, varieties and even forma that occur in the monographs (see below)
• subgenus – a single word indicating which subgenus the species is in. Subgenera in Rhododendron could be thought of as genera …
• synonyms – this is a block of text representing all the names, types and citations that came in the synonyms paragraph.

To get these properties into EoL I need to squeeze them into the EoL Transfer Schema . (Here I need to have a declaration of interest in that I think I was in on the original design of this at a workshop at GBIF as few years ago.) The basic structure is like this:

• Document
  • Taxon
    • Name
    • Source
    • Other Metadata…
    • DataObject
      • Type
      • Source
      • Other metadata…
      • Value
    • DataObject
      • ..
  • Taxon
    • …

So a document contains a number of taxa and each taxon contains some metadata plus a number of DataObjects. Each DataObject is of a ‘type’ and has its own metadata plus a value of some kind – such as text or a link to an object. This is a very generic data structure that allows for expansion by adding new types of DataObject.

All I need to do is hack together a PHP script to map my properties to the DataObject types and I can go back to trying to clean up the data. This is what the types look like:

Associations, Behaviour, Biology, Conservation, ConservationStatus, Cyclicity, Cytology, Description, DiagnosticDescription, Diseases, Dispersal, Distribution, Ecology, Evolution, GeneralDescription, Genetics, Growth, Habitat, Key, Legislation, LifeCycle, LifeExpectancy, LookAlikes, Management, Migration, MolecularBiology, Morphology, Physiology, PopulationBiology, Procedures, Reproduction, RiskStatement, Size, TaxonBiology, Threats, Trends, TrophicStrategy, Uses

These map to subject types on taxon pages within EoL. There is a description of these on the EoL help pages.

This is where I run into a problem. My properties don’t map to these subject types. The only matches I really have are Distribution, Description and Habitat. The advice is to put “note” type data under “Description” so probably 90% of what I have goes into “Description” DataObjects. Why have I just spent the last umpteen weeks marking all this stuff up?

There are interesting and important questions here:

• How important is semantic mark up of this kind of data? What advantages are gained over just treating each species treatment as a single block of text? I could still pull out all the ones that occur in China etc.
• If the EoL Subject Types are a list of the kinds of information people want to see on species pages and they don’t match the data that is captured in a monograph should we continue to produce monographs in their current form? Who is driving the production of data, the users or tradition?

See the chosen photo on blipfoto.com

I spent several evenings last week trying to make an interval timer for shooting time lapse movies out of a Lego Mindstorms robotics kit. This involved several trips to Maplin and some soldering as well as learning to program in the weird drag and drop enviroment. I’d nearly finished when I came across a cheap interval timer on ebay. Didn’t cost much more than the parts I had bought at Maplin and is loads better. Ho hum… I had fun tinkering.

This is my first attempt with the ebay time. There is a great deal wrong with it but I think I know what to do next.

I have just been introduced to blipfoto.com. A photo journal where you upload an image a day. It has re-kindled my desire to take photos. It will be interesting to see how long it keeps my interest. There appear to be quite a few people who are addicted! I have added a plug-in to the sidebar of this blog. As you can only add an image a day to blipfoto.com there are likely to be some near-misses. Here is one for 27th November.

Eric was my father’s older brother. Here is a picture of them together. It must have been taken about seven or eight years before Eric’s death. He was killed in operation Goodwood to the East of Caen in Normandy in 1944. He was in a tank. He was 20 years old. I took a picture of his grave and of the graveyard in Normandy.

I have no recollection of my father ever mentioning Eric which says a great deal. My mother would talk about him. She didn’t know him personally but said that his death had devastated my father’s family.

My overriding thought on visiting his grave was that this is the only grave in the family. My grandparents and parents are all dead, cremated and gone with no monuments. They all lived vastly longer lives than Eric. It was an odd thought. In some way this one short life and lump of stone was anchoring all these other people.

I have tried to talk about this in the intervening six months but on several occasions received a somewhat disparaging “Oh that is very popular at the moment” kind of response. I believe that they are right. There is a great deal of interest in remembrance of the war dead at the moment. Perhaps this is the product of the long running conflicts in Iraq and Afghanistan – a Royal Wootton Basset effect. Maybe people are feeling that we are losing touch with the great European wars of the 20th century as that generation passes on. It may be just that the countless war documentaries produced to fill the endless hours of multichannel television have finally sunken home.

I find it all vaguely annoying because I want to talk about Remembrance as opposed to Remembering and Eric’s story is a key into that for me. I can’t remember someone I never met but his life and death still have great significance for me.

When Jesus beseeched his followers to “Do this in remembrance of me” at the last supper he didn’t mean make a documentary about his life and make sure you remember all the facts. He meant something else. When people carved “Lest we forget” onto war memorials they weren’t instructing future generations to literally remember all the names and dates of the people on the memorial. They meant something else. What they meant, of course, was that we should bring these things to mind. Think of them not just about them. This is why only silence will do. Words are about remembering. Silence is about remembrance.

For me this is integrally linked with my mindfulness meditation practice. Mindfulness comes from the ancient Indian word sati which has strong connotations of remembrance. It is bringing the present to mind as one might bring the past to mind. Remembrance of those who have gone before is pausing to be present now. Being here for them and for us.

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Taken with 110mm modified cassegrain and Nikon D80.