An Exercise in Irrelevance

It’s been relatively quiet from me for the last few weeks. One of the reasons for this is that I have been submitting a JISC bid. I’ve not submitted a JISC bid before, so it was quite a lot of work; it’s exactly the same as a research council proposal, except for all the bits that differ.

The bid, in this case, was for extensions to the Knowledgeblog environment; we want to make sure that it supports research better than at the current time. Our initial experiences were generally good, with a few naysayers. Additionally, we wanted much better linking to external forms of data; array express, Swissprot and the like. And, finally, we wanted to trial this out against a set of specific use cases. Critically, I also got tired of writing “knowledgeblog” the entire time, so they will now be “k-blogs”.

If it gets accepted, we proposing to develop some additional functionality, often reusing existing software. We really are trying to avoid developing any software that we don’t have to. The plans include:

1. A documented k-blog process, including information on who does want, and how to use various existing tools (word and latex in particular).
2. Proper support for referencing — authors should be able to drop in a PMID, or DOI and get a reference list and in-text citation automatically.
3. Various metadata support, so that the in-text citations have semantics from the readers side.
4. Trackback proxying for those resources which don’t support trackbacks.
5. Integration and additional tooling for adding references and cross-links.

I’m hoping that we get the money; if we do, the work will give us a platform on which to build a publishing environment, a place for an educational resource, and finally, and excellent extension point for playing with semantic forms of publishing. I am not sure what the odds are; I know quite a few other proposals are going in, and there’s a reasonable chance that George Osbourne will cut the money back before its awarded. All I can do now is wait.

I’ll probably blog the whole proposal in a few days; this gives me a chance to try out the “blogging from Word” experience. How exciting.

I have a new PhD position available; I am looking to extend some work that I was involved with a while ago now, but into a new area of biology. The idea is that we build an ontological model of the mitochondria, and the knowledge that exists about it. We should be able to build a light-weight model that covers many areas of the biology as an entire system. This will be useful both as an integration point (a traditional use for ontologies), but also so that we can make predictions and search for inconsistencies in the model. In other words, the ontology should be an integral part of the scientific process; we represent a hypothesis ontological and then let the reasoner search for the data for contradictions.

This is quite exciting, as we did the original work quite a few years ago, and it looked very promising; despite the gap, I still think this could work really well. Since that time, system biology has gained currency; this work fits, as we aim to look at the mitochondria as a whole. Instead of an in depth mathematical model of part of the mitochondria, as is common in systems biology, we will have a light-weight logical model of both what we know about the mitochondria and how we know it.

Please feel free to distribute this!

PhD Studentship, 2010

EPSRC PhD Studentship Building a logical model of biology: the Ontology of Mitochondria

For this project, you will use cutting edge technology designed for the Semantic Web, and apply it to the new field of systems biology. Specifically, you will develop an OWL ontology, a formal, logically specified model, to describe the mitochondria, a subsystem of the cell. You will use this to integrate large amounts of real-world data, to search for inconsistencies and produce a predictions about the underlying biology. From a computing perspective, this will result in insights both about the technology, and its scalablity; from a systems biology perspective, you gain understanding of the value of models which are wider than traditional mathematical models; from a biomedical perspective, you may gain insight in the functioning and behaviour of a medically important system of the cell.

This is a challenging multi-disciplinary project; applicants are not expected to understand all its aspects at the outset; as a result, it is of interest to those from either a computing science, computational biology or bioinformatics background. Any experience of ontologies, modelling or mitochondrial biology will be an advantage, but is not required. A willingness to learn is critical; students will spend significant time in both a computing science and biology environment, and will become familiar with both.

You should have either a First or 2.1 in Computing Science, a Biological Science or Mathematics, and a distinction level Masters degree in a related subject. Equivalent experience will also be considered.

Depending on how you meet the EPSRC’s eligibility criteria, you may be entitled to a full or a partial award. A full award covers tuition fees at the UK/EU rate and an annual stipend of £13,290 (2009/10). A partial award covers fees at the UK/EU rate only.

For further details, please contact Phillip Lord <phillip.lord@newcastle.ac.uk>.

I’m on my way to the second Knowledge Blog meeting. Well, sort of. The first meeting was badged the “Ontogenesis Tutorial” meeting; the focus was on developing a tutorial resource for ontologies. Actually, much the same will be true of this meeting, but I’ve decided that, for this meeting, as well as addressing the reviews for my own article on Ontogenesis, I am going to want to spend some time supporting the process itself. In the first place, this means writing a couple of articles for Process: a new knowledge blog that I am starting for discussion of the process itself.

Since the first meeting, I’ve had plenty of time to reflect on the general idea of knowledgeblogging. As far as I can see, there is one overwhelming truth about the situation; we got 15 articles in 2 days and, since then, we have been averaging between 500 and 1000 page hits a month. Now, of course, it’s an open question whether this is at all sustainable; we have no advertising and no financial support. But, still, our most read article (“What is an Ontology”) has had several hundred reads and, bottom line, that is pretty good going for an academic article. We might like to think that the work that we do is important (well, it is!), but in publishing terms we are pretty much of a niche market.

On the negative side, we have had articles flooding in and none of those from the last meeting have got any further. Thinking back to Nupedia, many moons ago, it’s obvious that getting an authorship is always going to be a problem.

I’m also going to have to think of a snappier and short name for than “knowledgeblog” which is taking far too long to type. So far:

k-log

Simple, straightforward, but already used

knowblog

Good, but a homonym for “noblog” which is confusing.

knoblog

Pronounced “noh-blog” would be great, but English is not a phoentic language

knob

“KNOweledge Blog” — excellent in many ways, but I realise that the entire world does not share my slightly puerile sense of humour.

Hmmm. Comments welcome. So long as they are not about my puerile sense of humour.

Introduction

A few weeks ago I unsubscribed from the BFO discuss mailing list. I’ve been reading and posting there since March 2007; in that time I’ve managed to send 492 mail messages which surprises even me. As a mailing list, BFO discuss is a slightly bruising experience: it’s a bit like a bar fight; one person swings a punch and everyone just piles in. I joined the mailing list because BFO has become somewhat of a force within the bio-ontology community and I wanted to help make sure it was fit for purpose; however, I have to admit that I have been as guilty of reaching for nearest available pool cue as the next ontologist. Not the best side of me, but there you have it.

During my time on the mailing list, I have learnt a lot about BFO and the realist philosophy that, in theory, underpins it. Actually, BFO is not at all bad; for me, though, realism is largely without merit. One of the main difficulties with realism is that is carries with it the idea that, by thinking very hard, you can come up with a “representation of reality”. I think that this is mistaken. As scientists, we should be wary of thinking too much; our role, whenever possible, is to think just enough to get us to the start of the next experiment. This doesn’t seem to happen with BFO; in the time that I have been on the mailing list, BFO itself has changed very little; the constant feedback and iteration to accommodate new knowledge and experience is largely not happening. I have qualms with many parts of BFO (for example, I have discussed the issues with the Realizable Entity hierarchy). However, for me, the worse outcome of the philosophical approach have happened as a result of not considering the advanced models that physics has produced to explain the experimental data that we see. I give four examples.

Length in Space

BFO makes a very high-level split between Independent and Dependent Continuants. A continuant is something that persists over time, but which exists in full for this entire time: my computer or me, for instance, as opposed to a process, not all of which exists at any point in time. The distinction between an independent and dependent continuant depends on whether this entity exists on its own; for my height, a dependent continuant, to exist, I also have to exist. Once I cease to exist, so does my height. This seems okay, but in tying physical dimensions to an independent continuant, BFO has made a fundamental error: how do we express the length of a Spatial Region? Length is a dependent continuant and, so, there must be independent continuant in which is inheres. Unfortunately, Spatial Region is not an independent continuant itself.

There are solutions, of course; we can think of another relation, other than inheres to link Spatial Region and Length. But, we still need a Independent Continuant to exist that this length inheres in. Another possibility is to describe the length of a spatial region as the length of a Independent Continuant that could exists in it. But, it is easy to think of Spatial Regions in which no Independent Continuant can exist (for example, the Spatial Region 1m longer than the longest object in the universe). BFO would be modelling the world backward; physics uses a coordinate system and places objects within that; this approach would use objects to define the coordinate system.

Currently, this problem seems to have been accepted by some of the authors of BFO; however, there is no solution. If BFO had started from the mathematical models of physics, to me it seems likely that we would not be in this position.

Change in Process

BFO suggests that Occurrents (such as a process) can have properties in a similar way that independent continuants can have qualities. I have a length, a process may have a duration. However, BFO suggests that the properties of a an Occurrent cannot change; rather, there must be a new Occurrent.

Again, this makes little sense, and ignores very simple physical examples. Consider, for example, a car first travelling at 10ms^-1, then 20ms^-1. Consider the process of motion. BFO would have us model this as 3 processes; car moving at 10ms^-1, car moving at 20ms^-1 and a single motion process of which the other two are part.

For a simple example, this style of modelling may work. However, consider the earth travelling around the sun. The problem is that the motion is continually changing; the earth’s velocity changes infinitesimally toward the sun, so it’s always accelerating. Worse, the acceleration also changes infinitesimally, as the earth’s relative location to sun changes. So, to model this in BFO, we need an infinite number of processes (for both the motion and acceleration). We could argue that while the velocity and acceleration change constantly, the angular velocity and speed of the earth is constant, so why not model the process in these terms? Unfortunately, even this is not true; the earth moves in an ellipse, not a circle, even if its very close to a circle. So, the angular velocity and speed change continually also.

The physics of this is, as I have said, straightforward. The earth’s motion has a velocity and acceleration expressed as (nearly) two sine waves along the two axes.

Rate of Change

In order to get to the subtleties in a clearer fashion, we remind you of a joke which you surely must have heard. At the point where a lady in a car is caught by a cop, the cop comes up to her and says, “Lady, you were going 60 miles an hour!” She says, “That’s impossible, sir, I was travelling only seven minutes. It is ridiculous – how can I go 60 miles an hour when I wasn’t going an hour?”

— Richard Feynman

In a short, recent thread, it appears that there has been discussion on those qualities that need a period of time to have meaning. The examples given include velocity and acceleration. But does this make any sense? It is certainly the case, as the Feynman quote shows, that the definition of velocity is not obvious. But it’s also a known issue. Feynman’s story shows that it can be very hard to describe exactly what you mean when talking about velocity; it’s for this reason that physics uses mathematical notation, where we can be precise. Velocity is \(dr/dt\), acceleration is \(d^{2}r/dt^{2}\). As I have said, these examples do not stand alone — the same applies to many other qualities, including those where change is not over time.

In short, it makes little sense to create distinctions in our physical model of the world that physics does not make. We are creating work for ourselves and confusion for everyone else.

Absolute Space

BFO distinguishes between Sites and SpatialRegions; the idea is to distinguish between bits of space in general, and holes — the lumen of the gut, for instance. This seems reasonable at first sight. However, this is being done by suggesting that a Site is relative to an IndependentContinuant while SpatialRegions are absolute.

In short, over 100 years after Michelson-Morley, BFO has reinvented absolute space. The justification for this is that, according to one of the authors, without absolute space, problems arise. The problems haven’t been described in detail, but apparently, involve things moving through space or changing shape.

BFO is put forward as a “realist” ontology — that is it models the key entities as they exist in reality. And, the reality is this; there is no evidence that absolute space exists and, indeed, very strong evidence that it does not. It is also hard to see how this could cause problems; Einstein removed absolute space from the model that physics uses a century ago. Now, admittedly, this produces some really weird and counter-intuitive results, but only when two objects are moving rapidly with respect to each other. Relativity does not cause any problems that are not necessary to describe the world. In practice for “everyday” physics, the upshot is that you just define (or assume) a frame of reference; there is normally an obvious one, but any frame will do, and the results will come out the same.

My post on this produced some interesting replies. Bjoern Peters straightforwardly agreed. Alan Ruttenberg suggested that I was arguing space doesn’t exist; while Barry Smith argued that having this (false!) distinction in BFO is necessary for practical reasons.

At which point, I unsubscribed.

Conclusions

I am not arguing here that BFO is totally broken or has no purpose. To some extent, I am yet to be convinced that having any upper ontology helps with ontology building: arguing against, they are hard to understand and often result in a top-down design which ends in philosophical arguments and analysis paralysis; arguing for, they provide some basic structure or a design pattern, which can ease the task of starting to build an ontology, or to understand someone else’s. I am unsure yet whether they help with (computational) interoperability; by analogy to software, design patterns are good for the developer but do not provide any more guarantees. In general, though, I work on the basis that the use of a common framework seems a sensible idea; it is something we should try until we have enough data to make a more coherent decision. BFO provides one such basic framework; and, in general, it’s okay so long as we do not take it too seriously. We should be willing to ignore it when it fails.

However, realism has much less going for it. It is based on the conceit that we should look at reality; now, within a scientific context, this means experimental data. The statement that science should use experimental data, though, is obvious and is a truism; it cannot, therefore, itself define a methodology.

In practice, however, BFO has been built leaning on 2000 years of philosophy; and here lies the mistake. We should acknowledge our limitations as ontologists; we have nothing at all to add to a physical model of the universe as the physicists have already done it. All we need is to represent their model; we should not be looking at experimental data, because someone else has already done it for us. The problems described here are all avoided by the simple mathematical model that physics uses — 4 dimensions, or real number lines, at 90 degrees to each other, and by the use of calculus to describe change.

In BFO, we see an attempt to consider the key entities as they exist in reality; and, the bottom line here, is that at least for these few classes, BFO has done a bad job of it. It has misunderstood lengths and space, developed a process model that is unmanageable and made distinctions that are known to be wrong. Biology is built on top of the other sciences, and it will not benefit the cause of bio-ontologies if we ignore them. Worse biologists attempting to use BFO will find it hard to apply models which are demonstrably wrong; what criteria can we apply to distinguish SpatialRegions and Sites, when physics tells us that these criteria do not and cannot exist? Finally, as ontologists, we should accept our limitations and the limitations of the technology; we should not attempt to re-represent knowledge which has already been modelled in more appropriate ways.

We should be experimenting and testing more than we are thinking; we should be embracing change when we are wrong. We should be leaning on 200 years of physics and biology, not 2000 years of philosophy.

Managed to see “On What a Lovely War” on Friday, at the northern stage. I’ve not see it before although I’ve been aware of the play since they did it while I was at school. I guess that being based on World War I, the show starts from an emotional strong point, but the mix of light-hearted and optimistic songs, set against the deaths of millions works as well as it ever did; this version of it was magnificent, with the instrumentation on stage, as props, actors moving backward and forward between playing, singing and acting. Perhaps the most moving section was the 1914 football match in no mans’ land, ironic as it has no music over it.

The whole play is encapsulated, though, by its version of “Keep the Home Fires Burning” — the original is a light and jaunty number, although with a melancholy for home. Here, it is performed by a lone nurse, lending it a poignancy that is in the song, but which is hidden in most versions; the combination of the simple lyric and delicate melody is heart-breaking.

I knew that it was an Ivor Novello song; I didn’t know that it was his first big hit and defined his career to the extent that his grave reads “Ivor Novello 6th March 1951 Till you are home once more“. Nor did I know that this epitaph are the words of another — Lena Guilbert Ford, an American poet who wrote the lyrics, but has otherwise moved through history leaving only this song and a forlorn edit page to show her passing. A little more digging got me to an archive from New York Times:

London, March 12 — Two bombs were dropped together on the house of Mrs. Lena Guilbert Ford, the American poet who was killed in the air raid last week, and on the adjoining dwelling, an army expert testified at the inquest today. The bombs exploded simultaneously.

The Coroner’s jury found the death of Mrs. Ford, best known as author of the war song, “Keep the Home Fires Burning,” and that of her son, Walter was due to “suffocation from the collapse of a house caused by the explosion of bombs from a hostile aircraft”.

— New York Times (1918)

The rest of the article is a distressing account of the inquest, which tried to determine whether the mother outlived the son which had implications for inheritance.

She made little more impact on history because she was in it for only a short time more, dying in the declining years of World War I, a civilian casualty of a new form of warfare. One more tragedy among 20 million.

As one person said of my blog, it’s a bit weird, what with you thinking you’re still in India. It’s been a long time now, that we’ve been back, and I’ve had a lot of time to reflect on the experience. Writing the blog has served it’s purpose though; since I’ve been back, I’ve marked exams, taught two modules, run a meeting and submitted a paper. The holiday seems a long time ago, but the notes I took for the blog has helped me to remember the experience; for this reason, even though I wrote most of these reflections while travelling, I’ve decided to write these from the present, as opposed to the past present tense all the other posts have used.

I’ve also noticed that my page view stats have plummeted to the point that they are flat-lining around 1 a day (which is probably google). Perhaps I should get back to wittering about ontologies.

One of the most pervasive parts of the experience was the architecture; we saw many different styles and many different buildings. It was magnificent, finely wrought and cleverly details. This seems to reflect a wider delight in design and ornamentation, which you seem everywhere. The women’s clothes are brightly coloured, even when they are digging holes in the road. The tuk-tuks are covered in flowers. Even the mud huts in the agricultural areas have intricate and sweeping patterns inscribed in the cow dung. It’s all in stark contrast to both the garishness of the Bollywood experience and the surrounding environment.

The food mostly lived up to my expectations. From the home cooked food in Agra, the Shanti Restaurant in Jaislmer to the thali in Mehrangarh fort, we had some really good meals. On the whole, it wasn’t a new experience. The food is not that far removed from the UK curry, although with a few unique ingredients — the Rajastani desert beans — and the careful use of coconut. Like my experiences with Italy the best thing about the food is that it’s easy to get. Everywhere you go, good food surrounds, you don’t have to hunt for it and it’s not expensive. It’s just expected, as a matter of course. Compared to the 3 quid, ready-packed, pub food that we get here, it’s magnificent. I think we have a lot to learn from India.

The poverty and degradation has been grinding — much less so in India than in Dhaka, and it’s not the first time that I have seen it, but it’s always depressing. I suspect that we only see the edges of it, and the worst of the Shantis were away from the road, but this was enough for me.

I heard less music while I was there than I would have liked—the percussion was limited to tourist and ceremonial occasions, the rest was garish Hindi pop which totally lacks in appeal to me. So, much like home then.

The pollution I expected, but India, or at least the part of it that I say, was a very dirty place. — no where is clean, with animals on the street, rubbish everywhere, and the in-town midden being the most common disposal path. I guess the cows makes some sense, as they at least dispose of the organic material and produce something useful, if smelly. Even in Delhi, just outside of our, relatively posh, hotel the place was a mess, with sand heaps everywhere, an unusable pavement, and around the corner raw sewage was spilling onto the streets from a broken pipe. I have a relatively high tolerance for this sort of thing, but really this was too much. It will remain, I suspect, till they treat their public space like their private space.

A more pleasant aspect of India was the diversity of smell. Herbs and spices fill the air, both as a byproduct of the cooking and from incense. Back home, we everything that we use is chemical, even for strong smells such as lemon. Coming back to the UK, my senses where heightened to nasal assault that my own society has turned into; it’s pointless and we should stop it.

India is becoming a world power; I thilannk it’s clear that this century will be defined by it and China; I’m glad to have visited it, particularly at the time that I have. I’ve seen many good things here; but, then, many less good. I hope that India finds solutions for its problems and builds on its strengths; ultimately, it is going to have a larger and larger impact on this society as I get older.

My favourite memories of the journey; chilling out in the Shanti resturant looking over the desert from Jaislmer, the bus journey, hideous, crazy and dangerous though it was, and finally in Jaipur the observatory and the kites from the Wind Palace.

Outside the Hotel le Roi is a messy street, but inside it’s nice. The drive here was hectic and smelly, with many miles of crawling through traffic. Not nice at all. We had another near accident when a lorry in the lane next to us lost a tyre and the car was hit with large chunks of Rubber.

We came from the Taj Mahal. It’s been described in detail by many others; the sunlight scintillates of the marble facade, leaving you speechless; but, not if it’s foggy. Despite this, it is a magnificent building and visiting it is well worth while. I guess nothing can quite live up to is reputation once it becomes a world icon.

Just had to phone reception. The room heating controls don’t work, with the room getting colder and colder, so they have bought up a fan heater.

And that’s it; tomorrow, we go to the airport and fly home.

We started off today at the Amber fort in Jaipur. For some reason, the hawking here seems particularly heavy, a theme that was to continue. The Amber fort, though, is magnificent — it’s a labyrinth of connecting rooms, built through the walls of several connecting courtyards. Strange for me, the most interesting bit was the latrines (historical, not modern day, I hasten to add) and the water system. They had underground storage facilities, a system for elevating the water. In general, though I had a great time wandering through the rooms, finding new places.

After that we drove to a Agra Fort; we were short of time, but we managed to see much of it — the rooms were strange, over built over several levels. Finally, we saw the mosque at the back with relentless hawking, including demands for money in exchange for shoe guarding.

Finally a hellish journey into Agra — it was foggy and polluted, worse in the cold snap I suspect than normal. The driver didn’t know his way, and his relentless stopping resulted in a bike crashing into this rear end; minor injuries, fortunately, no worse. We finally got to the Garden Villas guest house, where we were staying. This was inside a drab, gated community, but inside the rooms were good with a warm welcome and an excellent, home-cooked curry. No complaints there.

As a city Jaipur is like many that we have been too — busy, polluted and unattractive, and also very in-your-face; yes, thank you, I am sure that are many elephants, but I still don’t want your tuk-tuk. We did see the Jantar Mantar observatory. This is a magnificent place, full of angles and careful measurements — Jai Singh thought that bigger was better. Each instrument had a careful description, telling you what it measured and what this measurement was for; although the signs kept of mixing up “accuracy” and “resolution” which bugged me a bit. The thing that confused me was that most of the instruments fall into two categories; those for measuring angles and sundials for measuring time. Time and space all sorted, it seems, but time only measurable during the day and space only measurable at night.

The city palace is okay; there are some good things inside, but it’s not as well done as Jodphur. The Wind Palace on the other hand is just a big building, but it’s fun to climb and the view from the top is great. Today is a saturday, and the place is full of tourists — many want to talk and I’ve been asked my name and photographed with many people. But the image that is going to stick in my mind are the kites circling overhead — hundreds of them fluttering in the wind, steered by intensely concentrating kids, perched on the sprawling rooftops. I have a grainy photograph which was the best I could do.

Finished off with dinner in the hotel cafe; the last time I had a curry with no spices at all was in Canada. That time, at least, it was served hot. If you stay in the Hotel Arya Niwas, well, avoid the food. Otherwise, it’s pretty nice.

The bus journey wasn’t that bad as it happened. The environmental conditions inside were okay; the heat disappeared pretty quickly; the temperature was nice till sundown, then I put more and more clothes on until I ran out. My feet got cold, but the rest of me was okay. The motion was a bit wierd and rolling, but in general I like travelling overnight and with horizontal. If there was some kind of night bus in the UK, I think that I’d take it pretty often; obviously I’d prefer something that wasn’t packed to the rafters and has some basic safety standards.

Oh, and a toilet.