An Exercise in Irrelevance

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.