Linking the Gene Ontology with Social
Ontology: A Prolegomena to the Ontology
of Personhood
David R. KOEPSELL1
SUNY Buffalo/Yale Center for Bioethics
Abstract. The Gene Ontology captures information at a very small scale, namely:
molecular function, biological process, and cellular components. At this level, the
Gene Ontology project should be capable of developing a semantics for every
relation of genomic data to protein synthesis to the biological processes that result.
In essence, the Gene Ontology should be able to describe the complete
biomechanical functioning of an organism. But what of the social ontological
statuses of organisms, and the relations of individuals to their higher level
functions? Can the Gene Ontology account for higher level activities of an
organism (such as intentionality, rights, property relations, etc)? Without leaping
to conclusions about whether higher level functions are in fact naturalistically
based, we should develop a semantics to serve as a hypothetical bridge should
genomics lead us in that direction.
Keywords: genome, Gene Ontology, social ontology, bridge ontology, organism,
legal ontology
1. Introduction
Genomes carry the instructions for the complete functioning of
organisms. The human genome, for instance, contains about 3 billion base
pairs, which coordinate, through a variety of molecular, cellular and biological
processes, the development, functioning and reproduction of individual
humans. Describing the relations between the genome and its expression is
1
drkoepsell@gmail.com ; home page: http://www.davidkoepsell.com. Presently Research Assistant
Professor at SUNY Buffalo Dept. of Philosophy -- coordinator of Graduate Research Ethics; Donaghue
Visiting Scholar in Research Ethics at the Yale Center for Bioethics, 2006-2007.
clearly a challenging ontological puzzle. The data architecture for the genome
evolved, and is not necessarily plainly visible nor elegant. The genome itself
carries apparently large chunks of junk that does not seem to play any practical
role – at least not any more. Moreover, the useful data is not always coded in
generally transparent ways, and useful units of information come in various
sizes, places on the chromosomes, and not always contiguously. Thus, while
the working definition of a gene (the largest of which is nearly 2.3 million base
pairs long) is still the unit of information involved in making a particular
protein, units of useful, or at least “effective,” information come in packets as
small as a single base pair. Moreover, the old notion of “one gene, one
polypeptide” has been challenged with the completion of the human genome
project, which helped scientists conclude that individual genes may in fact code
for as many as three proteins.
To decipher the relation of the information contained in an individual’s
genome, and the individual himself, clearly requires ontology. The Gene
Ontology (GO) is aimed at attempting to gather data from gene discovery and
correlate it in a useful ontology in order to fully describe an organism’s
phenotype based on its genotype. Yet, lacking from this is any form of bridge
to describe the individual beyond its phenotype. Because human persons
appear to be more complex than the biomechanical processes that compose
them, a complete Gene Ontology will only describe individuals at one level.
Ontologies developed in fields such as law, sociology, psychology, and at the
level of social institutions, all consider persons as complex, intentional,
thinking beings imbued with features such as rights, duties, and relations to
subjects and objects above the biomechanical level. Can a bridge ontology be
developed that will tie the Gene Ontology together with ontologies of persons,
and allow for semantic links among future ontologies in the biological, social,
and especially legal domains?
2. The Gene Ontology: Overbroad and Insufficient
The Gene Ontology does not describe persons, nor is it limited even to
human beings. Rather, because genes often direct the same biochemical
processes from one species to another, their ontologies capture relations among
genes, proteins and biological processes across domains. As it turns out, for
instance, the gene responsible for color vision exists in species as diverse as
humans and drosophila melanogaster (the fruit fly). This information is
tremendously helpful in identifying the evolutionary basis of inherited genetic
traits among and within species, as well as diseases. The culmination of the
Gene Ontology project, if there ever is one, will be a generic description of all
genes and resulting proteins as well as biological processes, not restricted to
any one species. Onto this, one could superimpose just the human genome,
and acquire a general understanding of the functioning of a generic human
organism, or a particular human’s genome, and understand fully the
functioning of that individual at least on a biomechanical level. However, such
an understanding, while perhaps biomechanically describing the functional
basis of a person, fails to account for essential, higher order features of
personhood. The Gene Ontology is thus both overbroad and insufficient on its
own to incorporate or account for social ontologies that describe or involve
persons as objects.
At one level, then, the Gene Ontology describes a common set of
phenotypes expressed by genes among all species, but also describes (ideally)
some generic member of a species. Imagine then that we can sequence an
individual’s genome, and have the complete Gene Ontology before us. That
complete ontology will give us a snapshot of the biomechanical processes
involved in that person, but will it describe the person per se? There are some
heady philosophical issues tied up with a complete description of a person
which we need not delve into for the moment, but a couple of criteria not
already described by the GO are worth mentioning. Persons are complex
continuants, whereas the most complex objects described by the Gene
Ontology are simple chemical processes (occurrents). Even assuming a
completely naturalistic basis for complex person-processes (like intending,
bearing rights, reasoning, etc.) the sum of all the pysio-chemical processes
described in the Gene Ontology still does not amount to a description of the
continuant “person.” Intentionality is at most an emergent phenomenon,
dependant on biomechanical processes, but in itself much more. It is at least a
computationally highly complex neurochemical process, as yet uncontemplated
by any of the categories or relations exiting in the current Gene Ontology.
Another way to consider this is to ask: to what degree is an individual
the sum of the entities expressed by his genomic data? Certainly, genomic data
encodes something very important in describing a particular human, but it
seems unlikely that it can fully describe an individual adult person. One reason
is that the genomic data, while it codes for many, if not every, trait of an
individual (including hair color, eye color, intelligence, and perhaps even
preferences and tastes), fails to capture other historical factors that go into
forming an adult person. On the other hand, infant persons are legally and
socially relevant, and for a time, at least, little more than the sum of the entities
expressed phenotypically by their genomic data.
A complete ontology of personhood will necessarily include the human
Gene Ontology and the other necessary and sufficient conditions of
personhood. A complete ontology of personhood is necessary for other social
ontologies. Since the Gene Ontology seeks to capture useful descriptions of
much of what composes a human, and science shows that a good many features
of personhood (e.g. behaviors, predilections, intelligence) are hereditable and
many of them are genetically based. There is a dilemma: extend the Gene
Ontology to capture relations and features of personhood, or develop a bridge
ontology? As discussed below, one or the other is necessary for existing and
future social ontologies.
3. The Necessity and Use of an Ontology of Personhood
The necessity for linking the Gene Ontology with social ontologies is
most apparent considering legal ontologies, in which nearly every legal
category contemplates some right or duty owed among persons, rather than
simply humans. Increasingly, new ethical and legal issues regarding the
relations between persons and either a generic human genome or an
individual’s particular genome (or some portion thereof) require ontological
clarity regarding the statuses of those relations. The Gene Ontology describes
the expression of the genome in the phenotype, and ultimately seeks to do so
completely and comprehensively. Legal ontologies describe the relationships
of persons to property and other persons. One glaring gap common to medical,
biological, and social ontologies is a coherent description of the relations
among individuals, their particular genomes, and the generic “map” of the
human genome. The Gene Ontology does not presently have sufficient
categories to deal with those sorts of relations, though it could conceivably at
some level of complexity. Thus, while the Gene Ontology describes cellular
components and biological functions, it does not yet encompass things like
“mental states or processes” composed of the former, or the potentiality
thereof, either of which is generally considered necessary for personhood in
legal ontologies.
Genes account for a number of persistent and legally relevant mental
states that are considered to negate legal intentionality. A genetic link has been
found between Aph-1b and mental illnesses such as schizophrenia. Genetic
links seem likely with other mental illnesses and certain forms of mental
retardation (such as defects on the FMR-1 gene), any of which may create the
legally and socially relevant state of lacking capacity for sufficient
intentionality for legal or social accountability. Genes seem also to be
responsible for severe conditions such as microencephalia and Lissencephaly
both of which may also diminish or negate the legal status of personhood.
While cognitive defects may have a number of other possible causes, the
potential for firm genetic links to persistent states that interfere with
personhood suggests that other necessary “healthy” genetic bases exist for the
presence in a human of the mental states considered to be relevant to
personhood, or upon which personhood may necessarily depend.
As a further example, the legal class “disabled” person” encompasses
those who are congenitally disabled, as well as those who may acquire a
disability. Defining a class of genomic disabilities, in other words -- finding
genetic causes for a range of known disabilities, could have significant legal
implications for those covered by such acts as the Americans with Disabilities
Act (ADA). The benefits, and potential complications, of being able to
determine with certainty the genomic existence of a particular individual’s
disability are obvious. Linking legal and biomedical ontologies, and having
access at some point to an individual’s genomic data, will clarify issues
regarding the status of a particular “disabled person,” and potentially
streamline processes under the ADA as well as insurance and medical schemes.
Distinctions among racial “classes” or “races” have been used both
legally and socially to broadly define ethnic classes, generally based on
phenotype, and to legitimize and then later remunerate for disparate treatment
of individuals and groups. Genomic research has cast doubt on the entire
notion of “race” but has also shown some use for ethnic/geographic
distinctions among groups in drug development. The nascent field of
pharmacogenomics is aimed at targeting populations (which seem in some
instances to fall along classical racial lines) with more appropriate drugs. It
seems that certain ethnic groups respond in empirically different ways due to
minor differences in genotype. [1] Genomic data, which can map these relevant
genomic differences, will have significant legal and ethical repercussions.
Remuneration or affirmative action schemes meant to provide relief to a
historically oppressed class may be bolstered or hindered, depending upon how
we treat discoveries regarding classical notions of race, and how we class
individuals among various ethnic groups.
What is clear is that as we refine the GO and other biomedical ontologies,
some accommodation, either by new categories in those ontologies, or in
bridge ontologies of persons and subclasses of persons, will add significant
value to both legal and biomedical ontologies.
Indeed, Barry Smith and others have done much to fix the errors and
gaps in the GO and other biomedical ontologies through refinements in the GO
and Open Biomedical Ontology (OBO) semantics and logic. [2], [3], and [4].
However, little has been done to link legal and biomedical ontologies, despite
the obvious necessity and potential benefits. For instance, criminal liability
attaches only to sane, adult persons. Only persons may be held criminally
liable for wrongdoing. If biological and genetic conditions are responsible for
certain forms of legal insanity or other incapacity, then it will be considerably
helpful for those accessing legal ontologies to have all relevant evidence of
biomedical or genetic determinants of various incapacities. As well, larger
“philosophical” issues such as the ethics and legality of abortion or euthanasia
depend on definitions of personhood that could be further clarified by access to
a GO that accounts for all the necessary features of personhood and not mere
human-ness.
A rights-bearing person and a fresh human corpse are socially and
legally distinct, although, at least momentarily, biologically and
biomechanically (on the cellular level) indistinguishable. The law and culture,
however, distinguish between the two by punishing, for instance, the fatal
stabbing of one differently than the impalement of the other. The distinction is
the same as the ontological distinction between mere humans and persons. The
complete ontology of a person will include all relevant genomic features (i.e.
those responsible for the requisite mental and physical states) and descriptions
of whatever emergent features might be necessary to describe a person (e.g., a
“soul” if naturalistic bases for personhood are ever deemed insufficient by the
relevant empirical sciences). The legal class “person” already exists and is
utilized in every legal ontology, whether explicitly or implicitly, but linkage
with the GO and other biomedical ontologies requires further clarification and
expansion, as well as incorporation of certain features of the GO.
The gap noted is not necessarily a failure in the meta-ontology of the
GO or other biological ontologies. It could conceivably be accommodated for
by a comprehensive ontology of personhood, which belongs somewhere
between biomedical and social ontologies. In fact, implicit in most existing
social ontologies is a notion of personhood, to which rights, duties, obligations,
etc. attach, but the relations and features of the entity “person” should be
clarified and expanded to include relevant relations and features from the GO
and other biomedical ontologies. Assuming, as empirical science does, a
naturalistic basis for all relevant human behaviors (intentionality, rationality,
etc.) then a bridge to legal and other social ontologies could be built into layers
of the GO and other biomedical ontologies, or a bridge ontology of personhood
could be developed. Either way, the GO and biomedical ontologies need to
have a common entity at some level to facilitate interaction at the levels
discussed in this paper. Even assuming that consciousness and other complex
personhood-features are emergent or irreducible, they are nonetheless
ontologically dependant upon genetic, molecular, biological processes which,
when fully described, should encompass those emergent phenomena. Either
approach should make clear that, given a certain set of preconditions, a
genomic string plus X is a person, and thus has a certain legal and social status,
and absent such, no person yet exists.
4. The Genome, Particular Gemones, Persons and Possessory Interests
One important but tricky problem posed by the discovery of the sequence
of the generic human genome, and the ability to sequence an individual’s
particular genome, is the problem of defining the relationships among those
entities. To what extent, for example, is your genome part of you, or is it in
fact another expression of you? [5]. It turns out that answers to these and
similar questions are both legally and socially significant as more aspects of the
genome, and particular SNPs, haplotypes and alleles come to be “owned”
through schemes such as patent and copyright.
Ordinarily, expressions are productions of human intentionality. [6].
Humans, however, are “expressions” of particular genomes. Persons, finally,
are a result of both genome and perhaps other factors (for instance, X +
[occurrent] life of X). Whatever the ultimate ontological status of persons,
there is currently no good account of the nature of the relations between
humans, persons, the human genome, and particular genomes. Do persons
stand in the relation of “owners” of their genome, given their arguably
possessory interest in the data? Does the human species stand in the role of
possessor of the generic human genome, as against, say, some alien species
wishing to utilize the genome for evil (or profit). [7].
The human — person — genome relation, whether one of ownership,
or otherwise, needs resolving to deal with a number of weighty and unresolved
ethical and legal issues, such as: patenting of genes, cloning, stem cell research,
etc. [8], [9]. The GO’s current ontology, because it does not extend to social
ontological terms, cannot capture these relations. A bridge ontology of
personhood, extending from the GO, can link this and other important
biomedical concepts to legal and ethical concepts.
5. Conclusion
The GO and other biomedical ontologies capture important data and
relations within and among species and members of species. Missing from
these ontologies is any ready manner to link these important concepts with
legal and other social ontologies, specifically regarding the critical concept of
personhood. Complex and timely ethical and legal issues are emerging from
genomic and bioinformatics research, and central to most of these is the
ontology of personhood which, if formally described, and linked to GO and
OBO concepts, could do much to clarify emerging legal and ethical issues.
Such a bridge ontology should be developed.
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