Global Philosophy: What Philosophy Ought to Be

Philosophy

These essays are about education, learning, rational inquiry, philosophy, science studies, problem solving, academic inquiry, global problems, wisdom and, above all, the urgent need for an academic revolution.
             Despite this range and diversity of topics, there is a common underlying theme.  Education ought to be devoted, much more than it is, to the exploration real-life, open problems; it ought not to be restricted to learning up solutions to already solved problems - especially if nothing is said about the problems that provoked the solutions in the first place.  There should be much more emphasis on learning how to engage in cooperatively rational exploration of problems: even five year olds could begin to learn how to do this.  A central task of philosophy ought to be to keep alive awareness of our unsolved fundamental problems - especially our most fundamental problem of all, encompassing all others: How can our human world - and the world of sentient life more generally - imbued with the experiential, consciousness, free will, meaning and value, exist and best flourish embedded as it is in the physical universe?  This is both our fundamental intellectual problem and our fundamental problem of living.
             As far as the latter is concerned, we are at present heading towards disaster - as our immense, unsolved global problems tell us: population growth, destruction of natural habitats and rapid extinction of species, vast inequalities of wealth and power around the world, pollution of earth, sea and air, our proclivity for war, and above all global warming. If we are to resolve our conflicts and global problems more intelligently, effectively and humanely than we have managed to do so far, then we have to learn how to do it.  That, in turn, requires that our institutions of learning, our universities and schools, are rationally designed and devoted to the task.  At present they are not.  That is the crisis behind all the others.  From the past we have inherited the idea that the basic intellectual aim of inquiry ought to be to acquire knowledge.  First, knowledge is to be acquired; then, secondarily, it can be applied to help solve social problems.  But this is dangerously and damagingly irrational, and it is this irrationality that is, in part, responsible for the genesis of our current global problems, and our current incapacity to solve them.  As a matter of supreme urgency, we need to transform academia so that it becomes rationally devoted to helping humanity learn how to make progress towards as good and wise a world as possible.  This would involve putting problems of living - including global problems - at the heart of academia, problems of knowledge and technological know-how emerging out of, and feeding back into, the central task to help people tackle problems of living in increasingly cooperatively rational ways.  Almost every department and aspect of academia needs to change.  We need a new kind of academic inquiry devoted, not just to knowledge, but rather to wisdom - wisdom being the capacity to realize what is of value in life for oneself and others, wisdom including knowledge and technological know-how, but much else besides.
             So, this is what these essays seek to provoke: a concerted effort to transform our institutions of learning so that they become rationally and effectively devoted to helping us learn how to create a wiser world.
             With these essays before me, I can see that there is one crucial element of learning about which they say nothing - or nothing explicit.  The vital role of play in learning.  All mammals - or at any rate almost all mammals - learn by means of play.  Cats, tigers, foxes and other predators learn to hunt by means of endless mock fights when kittens and cubs.  Deer, sheep and antelope learn to escape by means of playful leaps and bounds when young.  We are mammals too.  Almost certainly, we learnt how to be adult human beings by means of play during the millions of years we evolved into homo sapiens living in hunting and gathering tribes.  Children today, out of school, learn by means of play.  Learning by means of play is almost certainly fundamental to our makeup.  Education needs to exploit it.  Schools and universities need to become places of play.  Successful problem solving is often likely to be playful in character.  The youthful Einstein called doing physics "getting up to mischief".
             But our most serious problems of living are so grim, so imbued with suffering, wasted lives and unnecessary death that the idea of approaching them in a playful spirit seems sacrilegious.  We need to keep alive tackling of intellectual problems so that playful capacities can be exercised - if for no other reason (and other reasons there are, of course, aplenty).  There are two really worthy impulses behind all rational inquiry: delight and compassion.

Global Philosophy: Preface Learning, Global Problems and Play These essays are about education, learning, rational inquiry, philosophy, science studies, problem solving, academic inquiry, global problems, wisdom and, above all, the urgent need for an academic revolution. Despite this range and diversity of topics, there is a common underlying theme. Education ought to be devoted, much more than it is, to the exploration of real-life, open problems; it ought not to be restricted to learning up solutions to already solved problems especially if nothing is said about the problems that provoked the solutions in the first place. There should be much more emphasis on learning how to engage in cooperatively rational exploration of problems: even five year olds could begin to learn how to do this. A central task of philosophy ought to be to keep alive awareness of our unsolved fundamental problems especially our most fundamental problem of all, encompassing all others: How can our human world and the world of sentient life more generally imbued with the experiential, consciousness, free will, meaning and value, exist and best flourish embedded as it is in the physical universe? This is both our fundamental intellectual problem and our fundamental problem of living. As far as the latter is concerned, we are at present heading towards disaster as our immense, unsolved global problems tell us: population growth, destruction of natural habitats and rapid extinction of species, vast inequalities of wealth and power around the world, pollution of earth, sea and air, our proclivity for war, and above all global warming. If we are to resolve our conflicts and global problems more intelligently, effectively and humanely than we have managed to do so far, then we have to learn how to do it. That, in turn, requires that our institutions of learning, our universities and schools, are rationally designed and devoted to the task. At present they are not. That is the crisis behind all the others. From the past we have inherited the idea that the basic intellectual aim of inquiry ought to be to acquire knowledge. First, knowledge is to be acquired; then, secondarily, it can be applied to help solve social problems. But this is dangerously and damagingly irrational, and it is this irrationality that is, in part, responsible for the genesis of our current global problems, and our current incapacity to solve them. As a matter of supreme urgency, we need to transform academia so that it becomes rationally devoted to helping humanity learn how to make progress towards as good and wise a world as possible. This would involve putting problems of living including global problems at the heart of academia, problems of knowledge and technological know-how emerging out of, and feeding back into, the central task to help people tackle problems of living in increasingly cooperatively rational ways. Almost every department and aspect of academia needs to change. We need a new kind of academic inquiry devoted, not just to knowledge, but rather to wisdom wisdom being the capacity to realize what is of value in life for oneself and others, wisdom including knowledge and technological know-how, but much else besides. So, this is what these essays seek to provoke: a concerted effort to transform our institutions of learning so that they become rationally and effectively devoted to helping us learn how to create a wiser world. With these essays before me, I can see that there is one crucial element of learning about which they say nothing or nothing explicit. The vital role of play in learning. All mammals or at any rate almost all mammals learn by means of play. Cats, tigers, foxes and other predators learn to hunt by means of endless mock fights when kittens and cubs. Deer, sheep and antelope learn to escape by means of playful leaps and bounds when young. We are mammals too. Almost certainly, we learnt how to be adult human beings by means of play during the millions of years we evolved into homo sapiens living in hunting and gathering tribes. Children today, out of school, learn by means of play. Learning by means of play is almost certainly fundamental to our makeup. Education needs to exploit it. Schools and universities need to become places of play. Successful problem solving is often likely to be playful in character. The youthful Einstein called doing physics "getting up to mischief". But our most serious problems of living are so grim, so imbued with suffering, wasted lives and unnecessary death that the idea of approaching them in a playful spirit seems sacrilegious. We need to keep alive tackling of intellectual problems so that playful capacities can be exercised if for no other reason (and other reasons there are, of course, aplenty). There are two really worthy impulses behind all rational inquiry: delight and compassion.


Philosophy

This article explores the issue of homelessness from the perspective of someone who has experienced homelessness, as someone who has worked with the homeless and heard the stories of âour friends on the streetâ, as a mother distressed to see other mothersâ children, no matter their age, in such dire circumstances, and as a philosopher driven to interrogate the hidden assumptions and beliefs motivating our choices, judgments, and behavior. I wish to stress that homelessness must be addressed from the philosophical perspective not only with regard to the individual, but also with regard to the individual as belonging to the âweâ. This âweâ must include all the people involved, from the homeless person laying out her swag under the bridge, to the policy-makers earning fabulous salaries. Iâll propose that a deeper understanding of whatâs called âdouble incorporationâ is a crucial step towards galvanizing political will to implement solutions that have already been identified.

Homelessness	and	the	Limits	of	Hospitality Philosophy	Now Homelessness	and	the	limits	of	hospitality https://philosophynow.org/issues/123/Homelessness_and_the_Limits_of_Hospitality Philosophy Now – Issue 123 https://philosophynow.org/issues/123/Homelessness_and_the_Limits_of_Hospitality Homelessness & the Limits of Hospitality Anya Daly says we'll solve homelessness only when we see it as our problem. "No face can be approached with empty hands and closed home." "The need of the other is my spiritual need." Emmanuel Levinas Coming home on the tram my gaze met that of a young man shouldering a carry-all – heavy, and torn in parts. I looked away quickly. Clearly that carry-all carried all his belongings, and, I hoped, food for the wet, icy night ahead under the bridge. I knew I was going home to company and a hearty soup. Part of me wanted to suggest he come back and share soup with us; but the greater part was fearful: he could be dangerous, perhaps a drug user, and even if neither of these, how could we then turn him out into the cold again? The limits of my hospitality – my fear. This article explores the issue of homelessness from the perspective of someone who has experienced homelessness, as someone who has worked with the homeless and heard the stories of 'our friends on the street', as a mother distressed to see other mothers' children, no matter their age, in such dire circumstances, and as a philosopher driven to interrogate the hidden assumptions and beliefs motivating our choices, judgments, and behavior. I wish to stress that homelessness must be addressed from the philosophical perspective not only with regard to the individual, but also with regard to the individual as belonging to the 'we'. This 'we' must include all the people involved, from the homeless person laying out her swag under the bridge, to the policy-makers earning fabulous salaries. I'll propose that a deeper understanding of what's called 'double incorporation' is a crucial step towards galvanizing political will to implement solutions that have already been identified. The first part of this article will relate my experience with regard to homelessness to provide context. The second part will examine some philosophical considerations around the notion of 'home'. I am taking a phenomenological approach to this discussion, not an analytic approach which depends predominantly on arguments. For phenomenology, the world is not reducible to propositions, and so it depends on a wide repertoire of philosophical methods – detailed descriptive analysis and evocations as well as arguments. Philosophical understanding, for phenomenology, is as much a 'showing' as a 'telling'. The Lived Experience of Homelessness The problem of homelessness first hit me when I was living in Paris when there was a huge housing crisis. At one point there were tents all along the Canal Saint Martin and filling the Place de la République. There were many, many beggars on the streets. I remember for the last months of one winter I would cross the canal at a small bridge under which lived an old man and a young woman. In the morning I would regularly see her preparing herself for her work day – doing her hair, putting on her make-up, and tidying away her bedding. Clearly, she had a job but the salary could not cover rent. That was shocking for me, especially when I learnt of the rich people who had many vacant apartments they did not want to rent, either because they were waiting for the rental market to give higher returns or because it was more advantageous for them to just keep the apartments empty, solely as investments. In my fifth year in France I moved to Toulouse and there suffered a life-threatening accident. On my return to Australia I was homeless because I was unable to work. Fortunately for me, I had family and friends who ensured I always had a roof over my head. That year I lived in six different situations before gaining affordable housing. Even in the comparatively favorable situation of being cared for, I was deeply shaken in my sense of self because of the loss of independence, because I had no base that was mine. So once I had regained my health I volunteered with the Salvation Army, raising funds, and also with the Orange Sky Laundry, a mobile laundry service for the homeless established by two young Brisbane men and run entirely with volunteers. It now operates in fourteen cities in Australia. The service is as much about the conversations as getting the laundry done. The site I worked at in Melbourne was in the posh part of the central city, in what is known as the Paris end of Collins Street. In fact we parked the van and set up our chairs directly outside Dior, adjacent to a small terrace area that the homeless people had taken over. They called it 'the community kitchen', since from there they organised collections of food donations from the various cafés around the inner city. Of course the businesses were not happy about this – these destitute people were occupying prime real estate – and eventually the city council cleared out all their belongings, removed the seats, and installed plant boxes. So what had been effectively the equivalent of a home-base for them was destroyed. Some were given emergency accommodation, but most had to find another place to doss. It felt good to be doing something. The practical aid, the solidarity, and the sympathy were clearly appreciated; and, I must confess, it did help to somewhat relieve my own distress and guilt about their desperate and, more often than not, deteriorating lives. To an extent, we are all complicit in this terrible injustice. We have allowed the neoliberal agenda to override our consciences, to override our fellow-feeling, and to allow us to conveniently ignore the core value of 'fair play'. Most certainly we can say that some of these people have contributed, sometimes significantly, to their own wretched situations; but nonetheless, the systemic injustices are pervasive and pernicious. The paths to sleeping rough are numerous: domestic violence; sexual abuse; debt; psychiatric problems; unemployment; underemployment; the bank foreclosing on the home or farm; PTSD following military service; incapacitating accidents; drug and alcohol addiction; not having the means to get back to a home country; having relied on the support of friends and family one time too many; family break-up; housing which is dangerous because of drugs and violence, etc. This is clearly not a 'one size fits all' problem; it is various and multifaceted. In August 2016 I participated in a one-day workshop titled 'Homelessness and Housing Insecurity'. One observation from the only participating anthropologist was the need to consider factors upstream from the outcome of homelessness: nothing less than critiquing the economic system which has without question set the stage for it, and for many other social injustices which in turn feed into the injustice of homelessness. But in my view we need to go even further upstream to look for causes in our conceptions of ourselves; specifically, in the persisting delusion of our radical separateness from others. This individualistic view of self underpins the sense of entitlement of many (not all) of the wealthy, who refuse to help. While the opposing view of interdependency is slowly gaining currency, it has yet to filter through to tangible outcomes with policy-makers, politicians, the big end of town, and the general public. Homelessness is not just a problem for the individual enduring it. It has direct consequences for the wider society, including for you and me. And simply, we must ask ourselves, what kind of society do we want to live in? So with this in mind, in the next part of this article I wish to venture into the philosophical questions concerning the nature of the self with regard to this issue of homelessness. I will do so by drawing on the work of key figures in the phenomenological tradition – notably Levinas, Merleau-Ponty, and Scheler. Self, Place, Belonging & Hospitality In his book Totality and Infinity (1961, trans 1969), in the chapter titled 'Dwelling', Emmanuel Levinas offers an extended meditation on the notions of 'dwelling, habitation, home and hospitality'. For Levinas, hospitality operates in two domains – the ethical and the political. Within the ethical domain, the individual has a moral obligation to give shelter under their own roof. In the political domain, as citizens of a country, to be hospitable we must welcome all those who truly seek refuge into our homeland. Levinas sets out various conceptions of 'home'. Home is an implement which offers protection from the elements and enemies; as an implement it may also be a source of pleasure, such as when using a good tool can provide immense satisfaction. Home may also be considered a possession which is convertible into money. Levinas also describes home as the place of recollection – a place of gathering the self, thus providing our launching place for our activity in the world. Finally, home is a place of interiority – of safety, intimacy, and welcome. It is home in these last two senses that I wish to explore: home as the shelter from external threats, and as a place to recollect the self – to revive and to gather resources needed to venture into the world and contribute to society. As Levinas writes: "To dwell, is not the simple fact of the anonymous reality of a being cast into existence, as a stone one casts behind oneself; it is recollection, a coming to oneself, a retreat home with oneself as in a land of refuge, which answers to a hospitality, an expectancy, a human welcome" (p.156). Here we can see Levinas expressing a view common to many philosophical and psychological traditions, of home as being a symbol for the self. And there is an inside and an outside to this self. He says: "Man abides in the world as having come to it from a private domain, from being at home with himself, to which at each moment he can retire... he goes forth outside from an inwardness. Yet this inwardness opens up in a home which is situated in the outside – for the home, as a building, belongs to a world of objects" (p.152). Like the embodied self, the home has both an interior and an exterior; and as there are doors and windows for the home, so too there are also the self's expressive doors of face, gesture and language. Neither the home nor the self are impenetrable interiorities, entirely separate from others and the outside world. These challenges to the interiority and exteriority divide are also key to the thought of another French phenomenologist, Maurice Merleau-Ponty, who argues for an intrinsic interdependence between self and other.in his book The Phenomenology of Perception (1962). For MerleauPonty, subjectivity is an intersubjectivity, and otherness is a category both internal to and constitutive of the self. It is due to this self-alienation internal to the subject that other selves, alter egos, and all interactions with other people, become possible. This way of thinking about our intersubjectivity can provide a useful means of inquiring into homelessness. It is clear that something philosophically interesting is going on in our profound distress with regard to the plight of the homeless. I propose it is because the sight of homeless people challenges our sense of entitlement and also our sense of self and belonging. It makes us recognise how fragile these things in fact are; that we too could potentially become victim to any number of the misfortunes, such as have been visited on those living under bridges and on streets. There is also the fear of those living an unrooted life, without community and therefore without the demands and constraints of social belonging. The homeless person becomes truly alien. As philosopher Anthony Steinbock has proposed in his article 'Homelessness and the Homeless Movement' (Human Studies, 17 (2), 1994), drawing on the phenomenologist Edmund Husserl, our own 'homeworlds' are co-constituted by the 'alienworld' of the homeless. The homeless do not belong to our community; they do not share our culture, our values, our social etiquette, our ways of eating and urinating. This is why our efforts are usually inadequate to addressing the problems of homelessness: one of the dangers for any intervention is that the homeless person becomes a project of the helper intervening; and then what inevitably comes into play is an almost coercive normalizing of the homeless person. The challenge is to offer support in a way that does not violate their autonomy, nor render them predictable, controllable, and acceptable according to our own standards. The Double Incorporation Here I want to engage with the key phenomenological idea that, just as Merleau-Ponty asserted, subjectivity is an intersubjectivity; or as the German phenomenologist Max Scheler describes the double incorporation of the 'I' within the 'we' and the 'we' within the 'I' in The Nature of Sympathy (1913, trans 2009): "community is in some sense implicit in every individual, and that man is not only part of society, but that society and the social bond are an essential part of himself: that not only is the 'I' a member of the 'we', but also that the 'we' is a necessary member of the 'I'" (pps.229, 230). This view rejects the idea of the isolated, atomistic subject, and instead says that in the core of our subjectivity is both the 'I' perspective and the 'we' perspective. When identification centers solely on the 'I', the person is dominated by individualism and competition. However, when the sense of self embraces the 'we', the values become collective ones and the orientation is characterized by cooperation. The more the circle of 'we' is widened, the more the subject is available to others. The subject with the 'we' orientation identifies as being one among others, as belonging – whether at the level of family, community, species, or at its most expanded, as one sentient being among others. Empathic responsiveness is not guaranteed, however, because if the 'we' is defined narrowly and constrained only to certain others – to family, race, the religious community, etc – the excluded do not arouse any sense of fellow-feeling, and in fact they may rather incite fear, aversion, hatred and aggression. We see this also with the stigmatization of the homeless. Despite their tragic circumstances, they are not recognized as deserving of a place, of belonging: they are excluded. And it is this alienation even more than the physical discomforts of sleeping rough and the challenges of survival that leads to the psychological deterioration of the homeless. They are living within a society to which they do not belong, and from which there is no welcome. This, I propose, because of the double incorporation, is a violence towards them at the most basic level of their sense of self. And this is why so many homeless people display symptoms of compounded trauma, combining the impacts of whatever led them to the streets in the first place with their rejection and exclusion from the wider society. So the question is, how can we get especially the politicians and the big end of town to expand their sense of 'we'? Albert Einstein captures exactly the core of the issue when he writes: "A human being is part of a whole, called by us 'universe' – a part limited in time and space. He experiences himself, his thoughts and feelings, as something separated from the rest... a kind of optical delusion of his consciousness. This delusion is a kind of prison for us, restricting us to our personal desires and to affection for a few persons nearest to us. Our task must be to free ourselves from this prison by widening our circle of compassion to embrace all living creatures and the whole of nature in its beauty." (Letter from Einstein to a father on the death of his son, 12/02/1950.) Homeless people are citizens with rights to vote; but their other basic human rights are not being respected: the right to a home, a shelter from the elements and from external threat, a base from which to carve out a place in the working world and the social world. Homelessness is my problem and your problem. Solutions to homelessness lie not just in social action, policy, or economics, but most fundamentally in our conceptions of ourselves and our society. When we can break out of the prison of the delusion of our separateness, and meet these others in solidarity, then the political will to address homelessness, and many other social injustices, will be found. © Dr Anya Daly 2017 Anya Daly has recently published Merleau-Ponty and the Ethics of Intersubjectivity (Palgrave Macmillan, 2016). She currently holds an Irish Council Postdoctoral Research Fellowship at University College Dublin, and is working on a project concerning the subjective bases of violence, destructiveness and ethical failure.


Metaphysics and Contemporary Science: Why the question of the synthetic a priori shouldnât not be abandoned prematurely

Philosophy

The problem of synthetic judgements touches on the question of whether philosophy can draw independent statements about reality in the first place. For Kant, the synthetic judgements a priori formulate the conditions of the possibility for objectively valid knowledge. Despite the principle fallibility of its statements, modern science aims for objective knowledge. This gives the topic of synthetic a priori unbroken currency.
          This paper aims to show that a modernized version of transcendental philosophy, if it is to be feasible at all, must âbid farewellâ to the concept of being âfree of empiricismâ or the âpurityâ of the a priori. Approaches to this end can already been found in Kantâs reflections on non-pure synthetic knowledge. Moreover, the a priori validity of knowledge does not exclude the possibility that it can be discovered empirically. In keeping with Kant, Fries and Nelson anticipated this separation (usually first attributed to Reichenbach) between the validity and discovery context of knowledge and pointed out that the a priori could be discovered empirically, but never proven.
          There are currently still good reasons why transcendental philosophical concepts are of fundamental importance for modern science, although it must not be overlooked that even within the framework of a modernized transcendental philosophy, several unsolved problems remain or are raised. For example, the irredeemability of the universal validity and necessary claims of the a priori, the problem of a clear demarcation between the phenomenal and noumenal world. Moreover, the âbeautiful structureâ or the Kantian system, which constituted its persuasive power, is lost.

Kay Herrmann Metaphysics and Contemporary Science: Why the question of the synthetic a priori shouldn't not be abandoned prematurely (2019, unpublished) Content 1 On the question of the objective validity of scientific knowledge 2 Synthetic judgements a priori 3 Reinterpretations of the a priori 4 The Fries-Nelson thesis 5 Perspectives of a modern apriorism Keywords synthetic judgments a priori, transcendental philosophy, non-pure synthetic a priori knowledge, noumenal, phenomenal, objective knowledge, Immanuel Kant, Jakob Friedrich Fries, Leonard Nelson Abstract The problem of synthetic judgements touches on the question of whether philosophy can draw independent statements about reality in the first place. For Kant, the synthetic judgements a priori formulate the conditions of the possibility for objectively valid knowledge. Despite the principle fallibility of its statements, modern science aims for objective knowledge. This gives the topic of synthetic a priori unbroken currency. This paper aims to show that a modernized version of transcendental philosophy, if it is to be feasible at all, must "bid farewell" to the concept of being "free of empiricism" or the "purity" of the a priori. Approaches to this end can already been found in Kant's reflections on nonpure synthetic knowledge. Moreover, the a priori validity of knowledge does not exclude the possibility that it can be discovered empirically. In keeping with Kant, Fries and Nelson anticipated this separation (usually first attributed to Reichenbach) between the validity and discovery context of knowledge and pointed out that the a priori could be discovered empirically, but never proven. There are currently still good reasons why transcendental philosophical concepts are of fundamental importance for modern science, although it must not be overlooked that even within the framework of a modernized transcendental philosophy, several unsolved problems remain or are raised. For example, the irredeemability of the universal validity and necessary 2 claims of the a priori, the problem of a clear demarcation between the phenomenal and noumenal world. Moreover, the "beautiful structure" or the Kantian system, which constituted its persuasive power, is lost. 1 On the question of the objective validity of scientific knowledge Certainly the question that must be posed today is whether it is at all still appropriate to ask about a priori concepts in the sciences. Today the classical ideal of science, at the center of which is the search for an unshakeable foundation, has long been replaced by an essentially hypothetical-deductive concept of science, which no longer regards science as a system of secured propositions. Instead, it assumes that all knowledge is provisional. Of course, anyone who attempts to describe reality in an objectifying manner can be mistaken. However, to assume the fallibility of knowledge is not tantamount to renouncing an objectifying description of reality (i.e. a description that is at least principally unambiguously verifiable and comprehensible by anyone and at any time). Though admitting the fallibility of any empirical knowledge, Popper, for example, does not deny that science is based on objective knowledge, "Wir werden also sagen: Die Objektivität der wissenschaftlichen Sätze liegt darin, dass sie intersubjektiv nachprüfbar sein müssen." (Popper, Logik der Forschung p. 51)1 Those who acknowledge the possibility of objectivity of scientific knowledge are confronted with the question of the conditions of the possibility of objective knowledge and thus also with the question of synthetic knowledge a priori, whereas synthetic a priori concerns precisely the conditions that make objective knowledge possible in the first place. Wolfgang Stegmüller addresses another topic that is brought up in conjunction with the question of synthetic knowledge a priori: ultimately it is a question of whether philosophy can make independent statements about reality at all or whether all statements about reality are a matter of empirical sciences (cf. Stegmüller, 1989 p. XXVII). Therefore the identity of philosophy as an independent discipline is up for debate. 2 Synthetic judgements a priori Philosophy has a long tradition of distinguishing between "a priori" and "a posteriori." This tradition can be traced back to Aristoteles, who divided things into "earlier" and "later." (Cf. Aristoteles, Metaphysics, V. 11, 1018b. in: Schwarz, 1970 p. 131). In the 14th century, Albert von Sachsen differentiated between evidence that deduces (demonstratio a priori) from causes 1 "I shall therefore say that the objectivity of scientific statements lies in the fact that they can be intersubjectively tested." 3 (reasons) effects (consequences), and justifications (demonstatio a posteriori) that move from effects (consequences) to the causes (reasons). In his Critique of Pure Reason (B), Kant initially defines the concept of "a priori" as "negative": " Wir werden also im Verfolg unter Erkenntnissen a priori nicht solche verstehen, die von dieser oder jener, sondern die schlechterdings von aller Erfahrung unabhängig stattfinden." (KrV 2 f.)2 Kant later states a criterion for distinguishing between "a priori" and "a posteriori": for him, "necessity" and (strict or limited) "generality" are the two (only) "positive" determinants of the a priori. One specific characteristic of the second edition of the Critique of Pure Reason (B) is Kant's distinguishing between pure and non-pure knowledge a priori: "Von den Erkenntnissen a priori heissen aber diejenigen rein, denen gar nichts Empirisches beigemischt ist." (KrV 3)3 Accordingly, knowledge is pure if "nothing empirical is intermixed," otherwise it is non-pure. In other words, a judgement is not pure if it contains terms that are "drawn from experience." If, on the other hand, it only contains terms that are not "drawn from experience," one can speak of a pure judgement. Kant emphasizes that a priori knowledge does not always have to be "pure." Since this comment happens to be an addition to the second edition to the Critique of Pure Reason (B), and no identical passage can be found in the first edition of the Critique of Pure Reason (A), it can be assumed that such a distinction was not insignificant for Kant (cf. Cramer, 1985, p. 27). Kant regards the principle of causality as an example of "non-pure judgement a priori" (KrV 3). 3 Reinterpretations of the a priori In the context of modern reinterpretations, a priori is used in definitions such as the following: what is presupposed in the formation of theory; presuppositions that enable certain explanations, derivations, knowledge and experiences in the first place, what is not based upon experience, what cannot be refuted by experience. 2 "In the sequel therefore we will understand by a priori cognitions not those that occur independently of this or that experience, but rather those that occur absolutely independently of all experience." (Kant 137) All English language quotes from Immanuel Kant are taken from the 1998 edition published by Cambridge University press. 3 "Among a priori cognitions, however, those are called pure with which nothing empirical is intermixed." (Kant 137) 4 Sometimes the a priori is also understood in the sense of the following reinterpretations. a) Genetic a priori Konrad Lorenz interprets a priori realistically in the sense of a phylogenetically originated organ function, which (seen from a Darwinist perspective) developed in adaptation to environmental factors. Today, this approach is continued in evolutionary epistemology. b) Relative a priori This can be understood to mean older theories, principles from theories (frequently older, e.g. Galileo's principle of relativity) – which are of methodological value for establishing the theory that follows – or relatively stable components of a theory (e.g. in the sense of the theoretical center within the framework of the structuralist theoretical concept of J. D. Sneed and Wolfgang Stegmüller). (cf. Herrmann, 2012) c) Pre-scientific a priori This includes everyday experiences, the linguistic context, social and cultural framework conditions of a theory, but also instrumental (e.g. the bodies considered should be regarded as firm), (cf. Hübner, 1973 p. 120) judicial (e.g. criteria for the acceptance or the rejection of theories) (cf. Hübner, 1973 p. 120) or normative (e.g. simplicity, high degree of falsification) (cf. Hübner, 1973 p. 120) determinations. Such empirical reinterpretations of the a priori (e.g. in the sense of evolutionary epistemology), however, leave open the Kantian problem of where scientific knowledge might receive its objective validity from if all rules were only empirically proven. The criticism of any empirical theory of knowledge can hardly be formulated better and more succinctly than by Kant himself: " Denn wo wollte selbst Erfahrung ihre Gewissheit hernehmen, wenn alle Regeln, nach denen sie fortgeht, immer wieder empirisch, mithin zufällig wären; daher man diese schwerlich für erste Grundsätze gelten lassen kann." (KrV 5)4 This also applies to attempts to interpret the a priori in the sense of norms of actions. Such attempts are confronted with the problem from which I take the certainty that corresponding 4 "For where would experience itself get its certainty if all rules in accordance with which it proceeds were themselves in turn always empirical, thus contingent?; a hence one could hardly allow these to count as first principles." (Kant 138) 5 prescriptions (i.e. norms or instructions for actions) are suitable for producing functional measuring instruments with the desired properties, if I do not presuppose the principle of causality (e.g. in the form of "Whenever A is fulfilled, then I can also cause B). 4. The Fries-Nelson thesis Jakob Friedrich Fries and the associated schools closely followed Kant's apriorism. Leonard Nelson, the founder of the New Friesian School, stresses that a natural science free of metaphysics is a relapse into an lawless natural science (cf. Nelson, Ist metaphysikfreie Naturwissenschaft möglich? p. 273f.). However, Nelson criticized Kant for having tried to prove the synthetic a priori principles for knowledge (cf. Nelson, Über das sogenannte Erkenntnisproblem p. 229). Such proof must have first premises whose certainty cannot again be based on a proof (cf. Nelson, Über das sogenannte Erkenntnisproblem p. 230). Jakob Friedrich Fries had been able to show that reason was not empty, but contained a general and necessary regularity which was only repeated in the reflection (cf. Nelson, Die philosophischen Grundlagen des Liberalismus p. 34) Thus there could definitely be a knowledge a posteriori through which the knowledge would a priori only be discovered (cf. Nelson, Typische Denkfehler p. 214). This discovery procedure is the "dissecting method of critique" from Fries (cf. Nelson, Über das sogenannte Erkenntnisproblem, p. 329), in which the metaphysical principles (cf. Nelson, Über das sogenannte Erkenntnisproblem, p. 327) are to be made conscious. Fries was accused of psychologism because of the assertion that the a priori can be recognized via a posteriori. Influence by Hegel, the philosopher Kuno Fischer compresses this accusation in his address as Prorector in Jena on The Two Kantian Schools in Jena (1862) with his wellknown verdict: "What is a priori, can never be known a posteriori." Leonard Nelson countered Fischer by claiming that the empirical character of the critique of reason does not contradict the "Apriorität der durch sie zu begründenden metaphysischen Erkenntnis" (Nelson, Typische Denkfehler p. 214).5 He reformulates Fischer's dictum as follows: " Eine Erkenntnis a priori – denn nur Erkenntnisse können dieses Merkmal haben – kann nicht a posteriori erkannt werden" (Nelson, Typische Denkfehler p. 214).6 (Nelson, Typische Denkfehler p. 215) He emphasizes that the appearance of evidence is produced when "a 5 " a priority of the metaphysical knowledge to be justified by it" 6 "An insight a priori – because only insights can have this characteristic – cannot be recognized a posteriori." 6 priori" and "a posteriori" are thought of as exclusive characteristics. Admittedly, "knowledge a priori" could not be "knowledge a posteriori," from which, however, it did not follow that knowledge a priori could not be recognized a posteriori – there could certainly be knowledge a posteriori, through which knowledge a priori was only discovered (cf. Nelson, Typische Denkfehler p. 215) Fries and Nelson divide two different aspects of knowledge: the question of validity and the question of discovery. Later Hans Reichenbach drew the distinction between a context of discovery and a context of justification of scientific knowledge. The context of discovery is about empirical conditions under which scientific knowledge or scientific theories emerge or are found, whereas the context of justification focuses on questions of validity (presumably true, empirically proven, etc.). If we translate the talk of a synthetic a priori into the language of today's theory of science, one could say that it is about minimal conditions of (not just inevitably human) knowledge par excellence, i.e. a minimal set of conditions in order to be able to speak of knowledge at all. With regard to such minimal conditions for knowledge, the summary of the considerations of Fries and Nelson can be formulated in this way: For the possibility of objective knowledge, a minimum set of general conditions (independent of the nature of the subject of knowledge) is necessary, which can be found by the analysis of the real processes of knowledge. (Fries-Nelson Thesis) What belongs to these conditions? For example, this includes: the ability to distinguish a world-for-myself (phaenomena) from an independent world-for-itself (noumena), the ability to form invariants, the ability to establish causal connections and anticipate the future, the notion of space and temporality, the ego-consciousness, etc. 5 Perspectives of a modern apriorism Kant named essential minimal conditions for objective knowledge. However, the claim, of wanting to generate these with evidence can no longer be maintained today. This is the important significance of the Fries and Nelson Kant critique. The following considerations should illustrate that such conditions can be found in experience. 7 Kant's differentiation of all objects into pheanomena and noumena remains fundamentally significant. This distinction can already be found in everyday thought in the separation between an "inner" and an "outer" world, a distinction that is problematic to the extent that the spatial itself is a subjective constructive principle belonging to the "inner" world (cf. Roth, Das realen Gehirn und seine Wirklichkeit p. 239). Kant's central insight that, for example, a sensation called "red" can never be compared with noumenal objects in order to see that they have the same property, had a decisive influence on the development of internal realism (cf. Putnam, 1981 p. 63). Another approach can be found with the Kantian concept of object. Kant's discussion of the concept of object is so general that it still applies to quantum theory itself (cf. Strohmeyer, 2014 p. 81). Correspondingly, Kant defines the concept of object as follows: "Object aber ist das, in dessen Begriff das Mannigfaltige einer gegebenen Anschauung vereinigt ist. Nun erfordert aber alle Vereinigung der Vorstellungen Einheit des Bewusstseins in der Synthesis derselben. Folglich ist die Einheit des Bewusstseins dasjenige, was allein die Beziehung der Vorstellungen auf einen Gegenstand, mithin ihre objective Gültigkeit, folglich dass sie Erkenntnisse werden, ausmacht, und worauf folglich selbst die Möglichkeit des Verstandes beruht." (KrV 137)7 If one wants to follow this determination of an object as a valid union of the multiplicity of given ideas for all subjects by a uniform rule, then this interpretation even applies to a quantum-mechanical object (electron, atom, crystal, photon), which can be understood analogously as a uniform and objective rule for uniting different data observed. One can argue in the same way in regard to Kant's concept of substance. According to the first analogy of experience, the persistence of substance means the numerical preservation over time (or temporal invariance). Apparently not even the simple forms of perception can manage without the formation of invariants: no animal could survive without recognizing certain objects or animals of the same species. In the formation of physical theory, the transcendental concept of substance returns in the form of conservation quantities (energy, momentum, angular momentum, etc.). 7 "An object, however, is that in the concept of which the manifold of a given intuition is united. Now, however, all unification of representations requires unity of consciousness in the synthesis of them. Consequently the unity of consciousness is that which alone constitutes the relation of representations to an object, thus their objective validity, and consequently is that which makes them into cognitions and on which even the possibility of the understanding rests." (Kant 249) 8 In chemistry, for example, the number of atoms in a chemical element that do not change during a chemical reaction can be thought of as the substantial, since the numerical value of this number remains unchanged. As with the concepts of substance and objects, the principle of causality already plays an important in everyday experience. If I burn myself with a flame, I causally connect the experience of pain with the flame. Moreover, when a flame is perceived, this provokes the expectation of a new experience of pain occurs. However, this does not yet fully explain the expectation of a renewed pain experience, since only the moment of the identical and persistent makes it possible for memory to produce the expectation of the same (the pain experience). (cf. Nelson, Critical Philosophy of Nature, p. 137.) Without the concept of causality, it could be quite difficult to speak of a difference between stable regularities and an arbitrary (albeit expedient and economic) summary of facts of experience. Causal connections are ultimately descriptions of stable regularities in the behavior of real systems. Even empiricists such as Carnap, Popper and Quine simply cannot avoid assuming the existence of "regularities of nature." (cf. Drieschner, 2000 p. 401) But precisely the prerequisite that "there must be regularities in nature" is a general and necessary condition for the possibility of knowledge; that is, what is rejected by modern empiricists, namely a synthetic judgment a priori (cf. Herrmann, 2012 p. 162). According to Kant's definition of causality, everything that happens presupposes something that is followed by a rule. For instance, (to take an example from classical physics), one can think of the movement of a billiard ball as the result of a ball striking it. But also in quantum mechanics a process, which is determined by the Schrödinger equation, is causal in the sense that a state Φ(r, t2) always presupposes an earlier state Φ(r, t1), which it follows according to a rule. The reaction processes in chemistry, in which chemical compounds are converted into others according to fixed rules, also correspond to this causal understanding. However, Kant's principle of causality is regarded as a prime example of a so-called non-pure synthetic judgement a priori, since the concept of "change" contained in it is empirical, i.e. stemming from experience. This opens up the possibility of regarding natural laws, which ultimately formulate correlations between earlier and later states, as knowledge that belong a priori to the class of non-pure synthetic judgements. For laws of nature formulate precisely general and necessary conditions of the possibility of knowledge, and in doing so they fall back on empirical 9 concepts or have been abstracted from experience. Naturally, the claim to general and necessary validity of a natural law is empirically not redeemable, but this would not have to speak against it. The quintessence of all these considerations can be formulated as follows: In order to be able to lay claim to the objective validity of knowledge, certain general and necessary premises have to be taken into account. Only in this way can knowledge be comprehensible for everyone, everywhere, and at all times. Such conditions are precisely the synthetic judgements a priori. According to the perspective represented here, they cannot be located in the realm of Platonic entities (for instance, in the context of Frege's logicism) nor are they relative truths (as for instance in the sense of Reichenbach, Heisenberg or Stegmüller), nor can they be equated with certain organ functions (as for instance in evolutionary epistemology); they must certainly be regarded as absolute, but they are closely connected with empiricism, cause it without being conditioned by it, are contained in it "all along" and can be discovered empirically. With its modernization, however, Kant's transcendental philosophy undergoes a far-reaching change with which the beautiful "architectonics" of the Kantian system, which constituted its persuasiveness, are also lost. Moreover, the claim to unlimited generality and the necessity of synthetic judgements a priori remains an irredeemable postulate. Moreover, even a modern a priori has not yet found a sufficient answer to the question of where at all the border between phenomenal and noumenal world can be drawn. However, even for today's philosophy there still remains the Kantian task, which Putnam suggests in the following words: "giving a sane and human description of the scope of reason." (cf. Putnam, 1981 p. 126) 10 Abbreviations KrV In this paper this refers to the 2nd edition of Critique of Pure Reason GS Leonard Nelson. Gesammelte Schriften. Ed. Paul Bernays et al. (Hamburg 1970–1977), Vols. I– IX. Literatur Aristoteles: Metaphysik. Schriften zur Ersten Philosophie. F. F. Schwarz, ed. and trans., Stuttgart 1970. Cramer, K.: Nicht-reine synthetische Urteile a priori. Ein Problem der Transzendentalphilosophie Immanuel Kants, Heidelberg 1985. Drieschner, M.: Naturwissenschaft a priori: Die Strenge des kantischen Anspruchs oder Karl Popper ein Idealist? In: Mittelstaedt, P./Vollmer, G. (eds.): Was sind und warum gelten Naturgesetze? Philosophia naturalis (2000), Vol. 37, No. 2, pp. 395–407. Herrmann, K.: Apriori im Wandel – Für und wider eine kritische Metaphysik der Natur, Heidelberg 2012. Hübner, K.: "A priori – A posteriori". In: Krings, H./Baumgartner, H. M./Wild, Ch. (eds.): Handbuch philosophischer Grundbegriffe, Vol. 1, 1973, pp. 119–125. Kant, I.: Kritik der reinen Vernunft (2nd Ed. 1787). In: Kants Werke. Akademie-Textausgabe. Unveränderter photomechanischer Abdruck des Textes der von der Preussischen Akademie der Wissenschaften 1902 begonnenen Ausgabe von Kants gesammelten Schriften. Vol. III, Berlin 1968. Kant, I.: Critique of pure reason, Paul Guyer, Allen W. Wood ed. and trans., Cambridge 1998. Nelson, L.: Kritische Naturphilosophie. Mitschriften aus dem Nachlass. Kay Herrmann and Jörg Schroth eds., Heidelberg 2004. Nelson, L.: Typische Denkfehler in der Philosophie: Nachschrift der Vorlesung vom Sommersemester 1921, Hamburg 2011. 11 Nelson, Leonard: Ist metaphysikfreie Naturwissenschaft möglich?, in: GS III, 231–281. Nelson, Leonard: Über das sogenannte Erkenntnisproblem, in: GS II, 59–393. Nelson, Leonard: Die philosophischen Grundlagen des Liberalismus, in: GS IX, 27–42. Popper, K. R.: Logik der Forschung. 9th Ed., Tübingen 1989. Putnam, H.: Reason, Truth and History, Cambridge University Press 1981. Roth, G.: Erkenntnis und Realität: Das reale Gehirn und seine Wirklichkeit. In: Schmidt, S. J. (ed.): Der Diskurs des Radikalen Konstruktivismus, Frankfurt a. M. 1987, pp. 229–255. Schepers, H.: Article: "A priori/a posteriori". In: Ritter, J. (Ed.): Historisches Wörterbuch der Philosophie, Bd. 1, Basel/Stuttgart 1971, Cols. 462–467. Schroth, Jörg, Regressive Methode der Abstraktion und unmittelbare Erkenntnis bei Leonard Nelson, in: Kleinknecht, Reinhard/Neisser, Barbara (Eds.) (1994): Leonard Nelson in der Diskussion, Frankfurt a. M. (184 p.) (= "Sokratisches Philosophieren" – Schriftenreihe der Philosophisch-Politischen Akademie, Silvia Knappe, Dieter Krohn, Nora Walter, eds. Vol 1)., pp. 114–50. Stegmüller, W.: Hauptströmungen der Gegenwartsphilosophie. Eine kritische Einführung. Vol. 1, 7th Ed., Stuttgart 1989. Strohmeyer, I.: Kantischer und moderner Apriorismus, Würzburg 2014.


Philosophy

The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus-based controlled vocabulary of terms and relations dedicated to the salivaomics domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry. The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB.
          Background
          Saliva (oral fluid) is an emerging biofluid for non-invasive
          diagnostics used in the detection of human diseases. The
          need to advance saliva research is strongly emphasized by
          the National Institute of Dental and Craniofacial
          Research (NIDCR), and is included in the NIDCR's 2004-
          2009 expert panel long-term research agenda [1]. The
          ability to monitor health status, disease onset, progression,
          recurrence and treatment outcome through noninvasive
          means is highly important to advancing health
          care management. Saliva is a perfect medium to be
          explored for personalized individual medicine including
          diagnostics, offering a non-invasive, easy to obtain means
          for detecting and monitoring diseases. Saliva testing
          potentially allows the patient to collect their own saliva
          samples at home, yielding convenience for the patient and
          savings in health costs, and facilitating multiple sampling.
          Specimen collection is less objectionable to patients and
          easier in children and elderly individuals.
          Due to these advantages

Ai et al. BMC Bioinformatics 2010, 11:302 http://www.biomedcentral.com/1471-2105/11/302 Open AccessR E S E A R C H A R T I C L EResearch articleSaliva Ontology: An ontology-based framework for a Salivaomics Knowledge Base Jiye Ai†1, Barry Smith†2 and David T Wong*†1 Abstract Background: The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). Results: We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus-based controlled vocabulary of terms and relations dedicated to the salivaomics domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry. Conclusions: The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB. Background Saliva (oral fluid) is an emerging biofluid for non-invasive diagnostics used in the detection of human diseases. The need to advance saliva research is strongly emphasized by the National Institute of Dental and Craniofacial Research (NIDCR), and is included in the NIDCR's 20042009 expert panel long-term research agenda [1]. The ability to monitor health status, disease onset, progression, recurrence and treatment outcome through noninvasive means is highly important to advancing health care management. Saliva is a perfect medium to be explored for personalized individual medicine including diagnostics, offering a non-invasive, easy to obtain means for detecting and monitoring diseases. Saliva testing potentially allows the patient to collect their own saliva samples at home, yielding convenience for the patient and savings in health costs, and facilitating multiple sampling. Specimen collection is less objectionable to patients and easier in children and elderly individuals. Due to these advantages, finding biomarkers in saliva for the detection of serious illnesses such as cancers has been on the national healthcare agenda for several years, and the National Cancer Institute has accordingly recognized saliva as a promising source for cancer biomarkers [2]. A mandate in the Government Performance Report Act (GPRA) report is that by year 2013 proof of principle will be obtained for the ability of saliva to monitor health and diagnose one systemic disease [3]. For the past six years the UCLA salivaomics research group has developed proteome, transcriptome, microRNA, metabolome, genome, microbiome, and point-of-care salivary diagnostic technologies. These research resources have proved highly valuable to basic and translational research groups around the world. Sjögren's syndrome (SS) is an autoimmune disease that affects exocrine tissues, especially salivary glands and lacrimal glands. The autoimmune-mediated damage of the salivary and lacrimal glands leads to a decrease in the production of saliva and tears and to the development of dry mouth and dry eyes. Without the lubricating and protective functions of saliva and tears, the oral and ocular surfaces are subject to infections and discomfort leading to significantly reduced quality of life. The disease can present either as primary Sjögren's syndrome (pSS), when * Correspondence: firstname.lastname@example.com 1 University of California at Los Angeles School of Dentistry and Dental Research Institute, 73-017 Center for Health Sciences, 10833 Le Conte Avenue, University of California, Los Angeles, CA 90095-1668 USA † Contributed equally Full list of author information is available at the end of the article© 2010 Ai et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Ai et al. BMC Bioinformatics 2010, 11:302 http://www.biomedcentral.com/1471-2105/11/302 Page 2 of 8no other autoimmune diseases are present, or as secondary Sjögren's syndrome (sSS), which involves co-presence of some other autoimmune diseases. Sjögren's syndrome is one of the most common autoimmune disorders in the US, with an estimated prevalence of ~4 million people, affecting primarily women (in a ratio of 9 to 1). In addition, pSS patients have a 40-fold higher risk of developing malignant lymphoma than the general population. The rapid development and maturity of the genomics field has led to the emergence of other omics studies, such as proteomics and transcriptomics, which are now being implemented widely in studies of human disease. Clearly, mining the data from multiple omics studies can provide deeper insight into the workings of biological systems than can be obtained from any single omics study. Omics databases such as PharmGKB (the Pharmacogenomics Knowledge Base [4]) and EPO-KB (the Empirical Proteomic Ontology Knowledge Base [5]) serve as important resources for the emerging discipline of systems biology as applied to the understanding of pathogenesis in humans and in model organisms. However, systematic management and analysis, and above all the integration, of omics datasets remains challenging, and the problems are compounded when these datasets need to be integrated with data of other sorts, including diagnostic data obtained by clinicians. As a computational and informatics infrastructure that can permit global exploration and utilization, the Salivaomics Knowledge Base (SKB) is being created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry [6], including the new Saliva Ontology (SALO) that is described in this communication. The Salivaomics Knowledge Base (SKB; http:// www.skb.ucla.edu/) is a data repository, management system and web resource constructed to support human salivary proteomics, transcriptomics, miRNA, metabolomics and microbiome research. The SKB will provide the first web resource dedicated to salivary omics studies and will contain the data and information needed to explore the biology, diagnostic potentials, pharmacoproteomics and pharmacogenomics of human saliva. At the same time it will allow a systems approach to the utilization of salivary diagnostic technology for personalized medicine applications. It has an effective information retrieval system and carefully designed data format and employs an open data model. Figure 1 shows the SKB's three-tier service oriented architecture with a Data Layer, Ontology Layer and Interface Layer. Results and Discussion We are creating the Saliva Ontology (SALO; http:// www.skb.ucla.edu/SALO/) as a consensus-based controlled vocabulary of terms and relations dedicated to salivaomics and to saliva-related diagnostics. Figure 2 displays a fragment of SALO in its current form. SALO The Saliva Ontology (SALO) is being created through cross-disciplinary interaction between saliva experts, protein experts, diagnosticians, and ontologists. To aid development and testing of SALO, we are incrementally developing a corpus of saliva-relevant literature in SKB to assist in identifying core terms, synonyms and definitions for inclusion within the ontology, and to provide examples of usage and links between SALO content and the corresponding items through their PubMed identifiers. In this way a growing body of semantically enhanced web-enabled literature will be created within the SKB to support future research. Additional resources upon which we will draw in populating and validating SALO will include the results of experiments in dataand textmining using the ontology, and cross-linking to existing ontologies and terminology resources involving treatment of saliva-relevant phenomena. We will also identify and represent within SALO relationships to saliva-relevant types represented in ontologies such as Gene Ontology (GO) [7], the Protein Ontology (PRO) [8], Ontology for Biomedical Investigations (OBI) and Chemical Entities of Biological Interest (CHEBI) [9] and also provide links to corresponding SNOMED CT terms where availFigure 1 The SKB architecture. The SKB is based on a three-layer architecture. Data sources are stored in the data layer. In the ontology layer data elements from these data sources are mapped to nodes in controlled vocabularies. The interface layer allows query, browsing and submission. For instance, the interface layer receives user requests, submits queries to the data layer through the ontology layer and obtains corresponding results. The three layers connect data from consumers (users submitting query) with data providers (data sources) via ontologies. Ai et al. BMC Bioinformatics 2010, 11:302 http://www.biomedcentral.com/1471-2105/11/302 Page 3 of 8able. To facilitate the maintenance of SALO and its use in literature curation, text-mining tools such as GATE http:/ /gate.ac.uk/ and the Python Natural Language Toolkit are being used. SALO will be a public domain resource and entirely web-based. Each term in the ontology will have its own URL which will point to a webpage providing definitions, PubMed sources, references to annotations in SKB and to external databases. The goal of the SKB is then to integrate, store, organize and manage all saliva-relevant experimental data annotated and connected through SALO and its associated ontologies. SKB will include also data about saliva-related experiments, which will be captured using the Ontology for Biomedical Investigations (OBI) in tandem with the SALO ontology. SALO Development In order to build on the solid foundations of prior work on biomedical ontologies and on the associated software tools and ontology application techniques, we will work with the Open Biomedical Ontologies (OBO) Foundry, and with the developers of OBO ontologies such as GO, PRO, CHEBI, and OBI in order to ensure conformity with current best practices and to guarantee non-redundant development. We follow the principles of the OBO Foundry in constructing SALO in order to ensure that SALO is semantically interoperable with the other OBO ontologies[6]. Salivaomics Standard Literature Corpus We have access to full-text articles of the biomedical journals from PubMed until 2009 and are using these as our primary resource in creating the Salivaomics Standard Literature Corpus (draft version here: http:// www.skb.ucla.edu/SSLC/). First we created a list of representative saliva literature items in collaboration with the following scientific leaders (in alphabetical order by last name) in saliva research: Arie V. Nieuw Amerongen (Free University and University of Amsterdam, The Netherlands) Bruce Baum (National Institutes of Health/NIDCR) William Giannobile (University of Michigan) James Melvin (University of Rochester) Nelson Rhodus (University of Minnesota) Charles Streckfus (The University of Texas Health Science Center at Houston) Arjan Vissink (University Medical Center Groningen, The Netherlands) Stephen Wotman (Case Western Reserve University) Chih-Ko Yeh (University of Texas Health Science Center at San Antonio). 31 literature items for inclusion were then selected on the basis of numbers of citations. Some of the articles in the corpus are specifically related to the Sjögren's syndrome test-case. This corpus now forms a constituent part of the SKB, where the SALO ontology, in tandem with GO, PRO and other ontologies, is being applied to create semantically enhanced versions of the initially selected representative articles through a process of manual curation. In an interesting positive feedback effect, the process of annotating the corpus will in addition bring benefits to the process of development of the SALO ontology itself, Figure 2 A fragment of SALO in its current form. Ai et al. BMC Bioinformatics 2010, 11:302 http://www.biomedcentral.com/1471-2105/11/302 Page 4 of 8since it will help us to identify gaps in the ontology discovered in the process of curation. Where an expression that is relevant to saliva research is used in the corpus but is not already present in SALO, a new ontology term will be proposed and then either added to SALO or submitted to one of the other relevant ontologies for inclusion. In this way, the comprehensiveness of SALO can be incrementally achieved relative to the state of the art in salivaomics research at any given stage, and in a way which ensures the alignment of SALO with other major ontologies. In addition to the manual curation of the saliva corpus, we are also using text-mining algorithms to the 23,467 PubMed articles identified as containing occurrences of the term "saliva" in their title or abstract. Specifically we are applying information extraction algorithms for segmentation, part-of-speech tagging, semantic labelling, and entity and relation chunking recognition to these articles. Figure 3 displays the result of entity chunking recognition applied to the text of one sample article. This strategy, too, will identify additional terms needed in the Saliva Ontology or in the related ontologies with which SALO must interoperate. We will thus pursue both manual and automatic processes for annotating the literature in our corpus, amending SALO incrementally, and also submitting necessary amendment requests to related ontologies as we proceed. SALO Resources The Saliva Ontology consists of both hierarchical (is_a) structures supporting saliva-domain taxonomies and additional relationships (such as part_of, derives_from, has_function) taken from the OBO Relation Ontology [10]. Figure 4 illustrates some illustrative examples of links between SALO and other ontologies. SALO is a formal ontology created using the W3C standard Ontology Web Language (OWL 2.0). The public release OWL versions of the ontology will be published in the NCBO BioPortal. For quality assurance and dissemination purposes, parallel versions will be created (using standard conversion software) in the OBO format that is used by the GO Consortium and still favored by many biologists. These OBO versions will be submitted for inclusion in the OBO ontology library. SALO will employ the OBO Foundry principles http:// www.obofoundry.org/crit.shtml in its development. This will help to ensure that the ontology is open, well-documented, specific to the domain (saliva, including salivaomics), and that it works well with other biomedical ontologies. The principles require that both logical and natural language definitions are provided for each term in the ontology, and also that links between terms are asserted using relational expressions which have been logically defined in a way to the OBO Relation Ontology [10]. Cross-ontology reasoning is thereby supported by the definitional structure of the ontologies involved. Ontology of the Salivary Markers for Sjögren's Syndrome (SS) SALO will be tested specifically in light of its capacity to meet the ontology needs for managing data derived from research on the use of a salivary genetic marker for Sjögren's syndrome (SS). In results of a complete screening for the TRIM21 gene in patients with primary SS are presented [11], together with results of a gene association study. A single-nucleFigure 3 A result of entity chunking recognition for the text of one sample article. Figure 4 Links between SALO and other ontologies. Ai et al. BMC Bioinformatics 2010, 11:302 http://www.biomedcentral.com/1471-2105/11/302 Page 5 of 8otide polymorphism (SNP) in intron 3 was found to be strongly associated with the presence of anti-Ro 52 kd autoantibodies in primary SS. SS-relevant portions of our ontology will be validated through our work on annotation of representative research literature on Sjögren's syndrome (including Sjögren's Syndrome Knowledge Base http:// sskb.umn.edu/), through our research on the SS-A protein and on the TRIM21 gene. Figure 5, illustrates some of the relations involved in a saliva-specific genetic marker for Sjögren's syndrome. The end-result of this work is two-fold: (1) A better understanding of relationships between diseases and multiple biomarkers because more useful information can be obtained based on the ontology annotation and classification. (2) A better aid for data interpretation, analysis and mining through the ontology annotation. Conclusions Saliva Ontology is an ongoing exploratory initiative. The ontology is being constructed to interoperate with the Gene Ontology (GO), the Protein Ontology (PRO), the CHEBI Small Molecule Ontology and other standard ontology and terminology resources, including SNOMED CT. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the semantic enhancement of a representative corpus of salivaomics research literature that is to be included in the SKB. Methods Ontology is the science of what is, of the kinds and structures of objects, properties, events, processes and relations in every area of reality [12]. As applied in the biomedical domain, ontology plays a key role in providing consensus-based controlled vocabularies serving the consistent annotation of biological and medical data and information, most conspicuously within the framework of the Gene Ontology (GO) [7] and now of its sister ontologies within the Open Biomedical Ontologies Foundry http://obofoundry.org. We believe that an approach to the analysis of saliva in terms of a controlled structured vocabulary and a common set of measurement data elements developed along OBO Foundry lines can provide a cost-effective approach to support the coordinated screening of large populations in such a way as to yield data that is capable of being aggregated for statistical purposes and for example in the context of metaanalysis. Currently, ontologies support data integration primarily through data annotation (or 'tagging'), including the annotation of data reported in the peer-reviewed scientific literature [13]. While the value of such data annotation has been demonstrated in molecular and model organism biology and in the analysis of gene expression data [14-16], the potential of ontology-based annotation in the clinical domain has been largely unrealized due to limitations in current ontology development practices, including: 1. Most ontologies consist of only a few well-defined relations, primarily the is_a (e.g. heart is_a organ) and part_of (e.g. aortic valve part_of heart) relations, and they only relate terms within a single taxonomy [17,18]. This results in an inability to capture higher levels of biological complexity. 2. Most ontologies and terminology artifacts lack a sound logical underpinning, rest on mixed modes of classification and inadequate formal definitions, resulting in an inability to support sophisticated computation [19-24]. To address these and related shortfalls, the OBO Foundry was created in 2006 by a group of developers of OBO ontologies on the basis of an evolving set of principles designed to foster the creation of an evolving set of best practice in ontology development. The first list of ontologies satisfying OBO Foundry peer review was released in April 2010. OBO ontologies are designed to represent in an interoperable fashion the biomedical reality from which data are sampled. Their development within the framework of a common top-level ontology (Basic Formal Ontology [25]) and consistent employment of a common set of relations [10] allows Foundry ontologies to be used together as interoperable modules within an evolving larger network. The relations themselves are Figure 5 Relations involved in a saliva-specific genetic marker for Sjögren's syndrome. Ai et al. BMC Bioinformatics 2010, 11:302 http://www.biomedcentral.com/1471-2105/11/302 Page 6 of 8formalized in such a way as to ensure support for sophisticated computation both within and across ontologies [10]. We capitalize on and contribute to the OBO Foundry initiative in this work. One important element therein is the distinction between reference and application ontologies. [26]. The former correspond in medicine to the basic biomedical sciences such as anatomy and physiology. The latter correspond to the clinical specialisms and sub-specialisms, for example pediatric surgery or radiation oncology. Just as the clinical specialisms draw on the methods, theories and terminologies of the basic biomedical sciences for a variety of purposes, including the education of clinicians and the formulation of clinical research hypotheses, so, within the OBO Foundry framework, application ontologies draw on reference ontologies to serve as feeders of lexically more simple terms (such as 'protein' or 'disease') to be used in the construction of the more specialized compound terms by which the application ontologies are composed. SALO is in this sense an application ontology. It draws primarily on four reference ontologies Protein Ontology (PRO), Gene Ontology (GO), Chemical Entities of Biological Interest (CHEBI) and Ontology for Biomedical Investigations (OBI) which are described in more detail below. All terms in SALO, other than those created anew because they relate specifically to the SALO domain, will as far as possible be derived from the mentioned sources. Thus for example all protein terms in SALO will be taken from the Protein Ontology. Where PRO does not have the needed terms, then requests for inclusion of these terms in PRO will be submitted to the PRO tracker [8]. The Protein Ontology (PRO) The Protein Ontology Consortium, led by researchers affiliated with the Universal Protein Knowledgebase (UniProt, http://www.pir.uniprot.org/), developed the PRO framework [8] with two axes of classification, based, respectively, on the protein structural units of domains, and on full-length protein sequences and their modifications. This second axis represents the various protein entities (such as splice variants, cleavage products) that can derive from a single gene. Because proteins themselves are combinations of domains with additional sequence, the two axes of classification are related via the has_part relation. We are collaborating with PRO's developers in the curation of those sections of PRO relating to those proteins which are of primary interest to the saliva domain. We will also participate in PRO dissemination activities in order to expand the community of users of both SALO and SKB. The Gene Ontology (GO) The Gene Ontology (GO) project is a collaborative effort to develop and use ontologies to support biologically meaningful annotation of genes and their products in a wide variety of organisms. Major model organism databases and other bioinformatics resource centers contribute to the project [27]. The GO provides a systematic language for the consistent description of attributes of genes and gene products in three key biological domains that are shared by all organisms: molecular function, biological process and cellular component. GO's value derives in large part from the fact that it has been utilized for the systematic annotation by trained biologist-curators of experimental results pertaining to multiple species of organisms and communicated in the peer-reviewed scientific literature. Some 50,000 journal articles have been annotated in this way, and their content has thereby been made accessible to computer-aided discovery. We will collaborate with GO's developers in the curation of those sections of GO relating to gene products of primary interest to the saliva domain. Chemical Entities of Biological Interest (CHEBI) Chemical Entities of Biological Interest (CHEBI) is a freely available ontology of molecular entities focused on 'small' chemical compounds. The molecular entities in question are either natural products or synthetic products used to intervene in the processes of living organisms. Genome-encoded macromolecules (nucleic acids, proteins and peptides derived from proteins by cleavage) are not as a rule included. In addition to molecular entities, CHEBI contains what are called 'groups' (parts of molecular entities) and classes of entities. CHEBI includes an ontological classification whereby the relationships between molecular entities or classes of entities and there is_a parents and children are specified. CHEBI is available online at http://www.ebi.ac.uk/chebi/[9]. We will collaborate with CHEBI's developers in the curation of those sections of CHEBI relating to the chemical compounds of primary interest in the saliva domain. Ontology for Biomedical Investigations (OBI) The Ontology for Biomedical Investigations (OBI) addresses the need for controlled vocabularies to support integration of experimental data, a need originally identified in the transcriptomics domain by the Microarray Gene Expression Data Society (MGED), which developed the MGED Ontology as an annotation resource for microarray data. In response to the recognition of convergent needs in areas such as protein and metabolite characterization, this effort was broadened to become what was initially known as FuGO (Functional Genomics Investigation Ontology) the ontology associated with the FUGE (Functional Genomics Experiment) data model [28]. The coverage of FuGO was then further expanded in 2006 to include clinical trials and epidemiological studies, biomedical imaging and a variety of further experimentation domains, to become what is today OBI, an ontology Ai et al. BMC Bioinformatics 2010, 11:302 http://www.biomedcentral.com/1471-2105/11/302 Page 7 of 8designed to serve the coordinated representation of designs, protocols, instrumentation, materials, processes, data and types of analysis in all areas of biological and biomedical investigation. Twenty five groups are now involved in building OBI, deriving from all areas of omics research, and the Foundry discipline, including the BFO (Basic Formal Ontology) top-level framework, has proven essential to its distributed development [6]. OBI is used in our work as a source for ontological representation of biomarkers and related terms pertaining to sample collection and to diagnostic and experimental uses of saliva, as well as to associated protocols, instrumentation, statistical methods, and so forth. SNOMED CT Since SALO is designed for use in support of clinical research and treatment, it is important that it be aligned as closely as possible with the SNOMED® Systematized Nomenclature of Medicine, which is designed to provide the terminology needed to code the entire medical record. The current version of SNOMED is SNOMED CT (for 'Clinical Terms'), which is maintained by the International Health Terminology Standards Development Organization (IHTSDO) in Copenhagen. At its simplest, SNOMED CT is a controlled vocabulary of expressions used in healthcare reporting, as for example in an electronic health record. 'Controlled' means that the content of the terminology is designed to provide a wellmanaged non-redundant set of codes and associated expressions to ensure consistency of clinical coding. Quality assurance procedures are in place, which are designed to ensure that the terminology is structurally sound, biomedically accurate and consistent with current practice. Unfortunately, while SNOMED is built around an evolving core vocabulary that is largely the work of the College of American Pathologists (CAP), it has been subjected at different times to various different sorts of combinations with other terminological resources, deriving mainly from the UK. The result is that, even after considerable efforts on the part of the new IHTSDO organization, SNOMED remains a terminology resource that is marked by multiple redundancies and associated inconsistencies of coding [29]. It is for this reason that we did not utilize SNOMED content in constructing SALO, but rather are working to ensure alignment between SNOMED CT and the results of our work on the Saliva Ontology by incorporating SNOMED CT terms where needed. At the same time, we will submit all clinically relevant new saliva-related terminology content created within the SALO framework to the IHTSDO Content Committee with a recommendation for inclusion for inclusion in future versions of SNOMED CT. Saliva and Ontology No dedicated ontology has thus far been defined in direct relation to oral biological fluids [30], and the treatment of saliva in ontology and terminology resources has thus been insufficient for purposes of saliva research. SNOMED CT returns 39 records for the search term 'saliva', including 'saliva (substance)', 'normal saliva (finding), and 'saliva-induced contact dermatitis (disorder)'. Saliva (substance) is asserted in the SNOMED CT concept hierarchy to be a digestive system fluid, which is in turn a body fluid. In The Foundational Model of Anatomy ontology (FMA), saliva is a subordinate of portion of secreted substance; no definition is provided [17]. Given the intention of the IHTSDO to align the SNOMED treatment of anatomy (including bodily substances) with that of the FMA, and given our existing collaboration with both the IHTSDO editorial community and the FMA's developers, we will work with both communities to create, through SALO, a more detailed representation of the ontology of this bodily fluid that is optimized to meet the needs of both the clinical diagnostic community and the cross-disciplinary community of omics researchers. Results similar to those obtained from the analysis of SNOMED apply also to other terminology resources. The Cyc ontology (which contains hundreds of thousands of terms in all domains) [31], defines Saliva is: A Type of: bodily secretion and liquid, whereby it is asserted merely that it is: An Instance of tangible stuff type. In WordNet, saliva is defined as a clear liquid secreted into the mouth by the salivary glands and mucous glands of the mouth; it is asserted that saliva moistens the mouth and starts the digestion of starches [32]. Authors' contributions JA, BS and DTW conceived of the study; JA and BS designed the ontology; JA, BS and DTW drafted the manuscript. All authors made equal contributions to and read and approved the final manuscript. Acknowledgements This work was supported by the US National Institutes of Health under grant number U01DE016275, U01DE017790 and U54HG004028. We are grateful to Alan Ruttenberg (coordinating editor of the OBO Foundry) for his help in the review of the SALO. Author Details 1University of California at Los Angeles School of Dentistry and Dental Research Institute, 73-017 Center for Health Sciences, 10833 Le Conte Avenue, University of California, Los Angeles, CA 90095-1668 USA and 2Department of Philosophy, 135 Park Hall, University at Buffalo, Buffalo, NY 14260 USA References 1. 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