J. theor. Biol.

(1997) 186, 5563

00225193/97/090055 +09 $25.00/0/jt960335 7 1997 Academic Press Limited
What Exactly Are Genomes, Genotypes and Phenotypes? And What
About Phenomes?
M:r1iN M:nNrr* :Nb Micn:ri K:r.
*Institut fur Zoologie der Freien Universitat Berlin, Konigin-Luise-Str. 1-3, D-14195 Berlin,
Germany and Mathematics Department, Boston University, Boston, MA 02215, U.S.A.
(Received on 20 July 1995, Accepted in revised form on 24 October 1996)
The fundamental concepts of genome, genotype and phenotype are not dened in a satisfactory manner
within the biological literature. Not only are there inconsistencies in usage between various authors,
but even individual authors do not use these concepts in a consistent manner within their own writings.
We have found at least ve dierent notions of genome, seven of genotype, and ve of phenotype
current in the literature. Our goal is to clarify this situation by (a) dening clearly and precisely the
notions of genetic complement, genome, genotype, phenetic complement, and phenotype; (b) examining
that of phenome; and (c) analysing the logical structure of this family of concepts.
7 1997 Academic Press Limited
Introduction
The concepts of genotype and phenotype are among
the most fundamental in all of genetics, developmen-
tal and evolutionary biology. By now, almost 90 years
after their introduction by Wilhelm Johannsen (1909),
one would think there would be agreement over their
denitions. Such is not the case.
Consider the following selection from various
articles, dictionaries, and textbooks:
By genotype and phenotype we mean classes of
organisms satisfying some genetic or phenetic criteria.
(Lewontin, 1992, p. 139)
The physical appearance of a trait is called the
phenotype of the individual. [. . .] When alleles are
written in pairs to represent the two unit factors
present in any individual (DD, Dd, or dd), these
symbols are referred to as the genotype. This term
reects the genetic makeup of an individual whether
it is haploid or diploid. (Klug & Cummings, 1991,
p. 48)
genotypethe sum total of the genetic information
(genes) contained in the linkage structures (chromo-
somes) of the pro- and eukaryotes [. . .]; pheno-
typethe observable properties (structural and
functional) of an organism . . . (Rieger et al.,
1991, p. 230 & 376)
genotypethe specic allelic composition of a
celleither of the entire cell or, more commonly, for
a certain gene or a set of genes [. . .] phenotype(1)
The form taken by some character (or group of
characters) in a specic individual. (2) The detectable
outward manifestation of a specic genotype. (Suzuki
et al., 1989, p. 727 & 732)
The genotype is the genetic constitution of an
organism, AA, Aa, and aa are examples. [. . .] The
observable properties of an organism make up its
phenotype. (Hartl et al., 1987, p. 12)
The genotype is a blueprint for an organism, the set
of instructions for development . . . The phenotype is
the manifestation . . . of the interaction of this
information with the physical and chemical factors
the environment in the broadest sensethat enable
the blueprint to be realized. (Futuyma, 1986, p. 43)
The phenotype of an organism is its appearanceits
morphology, physiology, and ways of lifewhat we
can observe. The genotype is the sum total of
hereditary materials of the organism. (Dobzhansky
et al., 1977, p. 29)
Genotype. Genetic constitution of an organism.
Phenotype. Collection of traits possessed by a cell or
organism that results from the interaction of the
Author to whom correspondence should be addressed.
E-mail: 101773.1334.compuserve.com
x. x:nNrr :Nb x. i:r. 56
genotype and the environment. (Herskowitz, 1977, p. 723
& 729)
In addition to inter-geneticist variation, we also
nd intra: for example while Lewontins denition of
genotype and phenotype as classes of organisms
requires that the organisms themselves be members of
genotypes and phenotypes, he also wrote, on the very
next page of the same article, that
the phenotype of an organism . . . is a consequence of
the development of that individual from a zygote
through a historical sequence. That sequence is a
result . . . of the previous state of the organism, of its
genotype. and of the environment in which it is
developing . . . (p. 140)
Thus, the later passage proclaims on the contrary
the more common view that it is the genotypes and
phenotypes that belong to individual organisms. And
still later in the article he says that the DNA
sequence of the genes itself is a phenotype (p. 143),
so that phenotype now seems to be synonymous
with phenotypic character. In sum, like many
others, Lewontin uses genotype, and likewise
phenotype, to designate completely dierent
concepts in rapid succession. [For a similar assort-
ment of intra-text usage variants see Suzuki et al.
(1989, pp. 7, 727, and 732). Even Johannsen used
these terms in more than one sense, and redened
them several times during his career; see Johannsen
(1909, 1913, 1926) and Chuchill (1974)].
We encounter a similar variety of denitions of the
term genome, whereas the corresponding term
phenome is only rarely used:
The actual physical set of inherited genes, both in the
nucleus and in various cytoplasmatic particles such as
mitochondria and chloroplasts, make up the genome
of an individual . . . In like manner there is a physical
phenome, the actual physical manifestation of the
organism, including its morphology, physiology, and
behavior. (Lewontin, 1992, p. 139)
genomein eukaryotes, the basic (monoploid)
chromosome set, consisting of a species-specic
number of linkage groups and the genes contained
therein. [. . .] In prokaryotes, the complement of all
hereditary factors (genes) included in one linkage
group. (Rieger et al., 1991, p. 227)
genomethe total complement of genes contained in
a cell or virus; commonly used in eukaryotes to refer
to all genes present in one complete haploid set of
chromosomes (Hartl et al., 1987, p. 445)
genomea term used to refer to all of the genes
carried by a single gamete (King & Stanseld, 1985,
p. 156)
Who doubts that, when biologists use these terms
on a daily basis and in any given context, they
typically know what they are talking about. But as the
above lists show, when they are forced to actually sit
down and dene them, some unexpected surprises
result. Indeed, according to the preceding denitions,
the genotype is: (a) a class of organisms; (b) a set of
symbols; (c) the set of all genes (hereditary material)
of an organism; (d) the set of chromosomal genes of
an organism; (e) the set of alleles of a cell; (f) a set
of instructions (or a program); and (g) the genetic
constitution of an organism, where presumably we
are to infer that genetic constitution is somehow
dened in terms of allele-pairs. And the phenotype is:
(a) a class of organisms; (b) the physical appearance
(or form) of a character (or trait); (c) the observable
properties (or traits) of an organism; (d) the collection
of traits of a cell or organism (whether observable or
not); and (e) the manifestation of the genotype.
Finally, the genome is: (a) the set of genes of an
organism (so that, according to some of the above
denitions, genome =genotype); (b) the set of genes
of a cell; (c) the set of genes of a gamete; (d) a set of
chromosomes; and (e) the set of genes contained in a
haploid chromosome set of a eukaryotic cell.
In view of this variety of denitions, we are left with
the following questions: is there one correct denition
for each of the terms genome, genotype and
phenotype? Are the correct denitions, if any, in
the above list of citations? If not, are the quoted
denitions somehow correct, yet just incomplete and
imprecise, and possibly context-dependent? Before
we proceed though to respond to these questions,
we should ask a more fundamental one: since genetics
is apparently doing quite well despite such variety
in the denitions of central concepts, do these
conceptual and terminological issues constitute
genuine problems?
The answer depends on the scope of ones interests.
A person interested only in identifying individual
sequences of DNA and their protein products will
likely use the terms genotype and phenotype as
little more than literary relief for DNA and
protein, and have no harm come of it. But a person
interested in meaningful genetic theory, in eective
pedagogy and in conceptual clarity will of course nd
that they constitute genuine problems, and have an
interest in resolving them.
Genes and Gene Types
To begin with, in order to have precise and useful
denitions of the concepts of genome and genotype,
we need some denition of gene. The concept of gene,
however, is even more problematic than that of either
genome or genotype: see for example the overview
of the situation by Kitcher (1992), or the more
riNb:xrN1:i coNcri1s or crNoxr, crNo1.ir :Nb inrNo1.ir 57
extensive reviews by Carlson (1966) and Portin
(1993).
1
Fortunately, for our purposes it will suce to
take an individual gene to be some DNA sequence
that is somehow involved in a metabolic process,
other than its own replication, in the cell it is
part of.
What we need to be more precise about is
what exactly it means to talk about a type (or kind
or class) of gene. Two things are of the same
type if they share some common characteristic.
The type itself is the concept formed by group-
ing together in thought all the individual things
that share this characteristic. Thus kinds, types,
classes and the like are abstractions; specically,
they are sets in the mathematical sense. Hence,
in the real world, one only nds their mem-
bers, i.e., their exemplars, but never the types
themselves.
As with all idealizations, the purpose of dealing
with types instead of individuals is to simplify. While
individual pieces of DNA molecules are distinguished
by a multitude of physical, chemical, geometric and
other properties, types of genes are dened only by
essential common characteristics important for
genetic analysis. In general there are two sorts of
characteristics that stand out as fundamental in this
regard.
The rst is that of having the same base sequence
or functionfor example, being the genetic template
for mRNA molecules with the same sequence or, via
these intermediaries, for peptide chains with the
same amino acid sequence. The second is that of
having the same relative chromosomal location
(locus). Clearly when geneticists say for example
that they have discovered the gene for X, or when
an editorialist for Nature Genetics (1996) writes that
there are a total of four genes now known to be
associated with [early onset Alzheimers disease],
what has been discovered and what are now known
are one or more of the fundamental common
characteristics dening the type of gene involved,
not any one, or any four, individual pieces of
DNA.
2
Furthermore, the function or base sequence of a
gene can be discussed in either generic or specic
terms. When geneticists say, for example, that a
certain gene is a gene for eye colour, they focus
on generic function or base sequence. In this case
the terms gene and locus are used almost
interchangeably (see, e.g., Sinnott et al., 1958,
p. 183). On the other hand, when they say that a
certain gene is a gene for red eye colour, what
they have in mind is specic function or base
sequence. In this case the term gene is used in the
sense of allele.
Genome and Genotype in Haploid Organisms
These ideas form the basis of the distinctions we
suggest drawing between the various genetic concepts
in question. Consider a single organism, uni- or
multicellular. We refer to the physical totality of all
its individual genes,
3
that is, all the actual concrete
sequences of DNA distributed throughout the
organism, as its total genetic complement. (One can
also be more specic and consider only the genetic
complement of e.g. some particular organ, tissue,
cell, nucleus, mitochondrion or plastid. In the
following we shall be concerned only with the nuclear
genes.)
As an expression, genetic complement, or some
variant thereof, is fairly standard. Indeed some
authors simply use it to dene genome [e.g., Rieger
et al. (1991) and Hartl et al. (1987) in the denitions
quoted previously], and most who do not use an
expression of this sort do dene the latter as the actual
genetic material (e.g., Lewontin). This physical
genome is what is referred to when, for example,
developmental biologists speak of genomic imprint-
ing or the embryonic activation of the genome
(see, e.g., Gilbert, 1994). But we suggest that those
who wish to use the concept of genome in this sense
refer to it specically as the physical genome. For if
the genome really were the physical set of genes of
an organism (see Lewontins denition), then a
human genome would consist of roughly 10
20
genes,
or 10
30
genes for the entire genome of the population
as a whole [10
5
genes per chromosome complement
2 chromosome complements per cell 6 10
13
cells
per adult human (Czihak et al., 1992, p. 11);
optionally, 6 billion presently living humans];
whereas, fortunately for the budget of the Human
Genome Project (NIH, 1990), the entire human
genome is generally described as consisting of only
about 100000 genes. Clearly, the concept of genome
used by geneticists in their daily professional lives, as
opposed to the one most often dened in the
literature, is a detail-discarding abstraction. Instead
of being a physical set of dierent individual
1
The philosophically interested reader may also wish to consult
Waters (1994).
2
Woodger (1952, p. 168) warned long ago of the potential for
confusion arising from the failure to clearly distinguish these.
3
These include nuclear, mitochondrial, or plastidial DNA
sequences, if any, but not the genes of parasites or symbionts, if
any, which we exclude as not being parts of the organism proper.
A
+
A
+
B
+
A
+
A
+
B

x. x:nNrr :Nb x. i:r. 58

concrete genes, the genome is really just a (mathemati-
cal) set consisting of dierent types of genes, these
being distinguished according to locus and base
sequence or function.
To illustrate, consider for the sake of simplicity
the two-celled haploid organism depicted in Fig. 1.
Each cell contains three genes, two of type A and
one of type B. These generic types can be further
resolved into specic types (i.e., allele types), such
as the allelic forms A
+
and B
+
, which we assume
to represent the normal (e.g., either zygotic or else
wild type) state. We further assume that, in cell 2,
the normal B
+
allele has mutated to B

. The total
genetic complement of this organism is the mass of
DNA consisting of multiple copies of the A and
B genes, compartmentalized into the two cells. It
can (disregarding overlapping genes and other
complications) be extracted, physically collected,
weighed, cooked and even eaten. We can ask how
many calories were expended in its formation, and
what fraction it constitutes of the total organism mass.
By contrast, the normal genome of this organism
is, in standard mathematical notation, the set
4A
+
1
, A
+
2
, B
+
5, with the subscripts used where
necessary to dierentiate loci; while the genomes of
the two individual cells are 4A
+
1
, A
+
2
, B
+
5 and
4A
+
1
, A
+
2
, B

5 respectively.
1
Being a mathematical set,
a genome exists only in our minds. As an abstraction
from reality, it allows us to deal solely with the
essentials for genetic analysis, and disregard the many
aspects of the real aggregate that are not relevant,
such as the mass, the temperature, or the avour; and
disregard too other aspects which, though relevant,
are not at issue, such as the geometry of the
chromosomes or the multiplicity of cells.
This ability to abstract away from the multiplicity
of cells also allows us to abstract away from the
multiplicity of organisms in a species, and conceive of
the genome typical of all the members of an entire
species. Of course in any individual multicellular
organism, the cells are usually genetically identical,
and thus the genomes of any organ, tissue or cell are
identical tooif we disregard such complications as
somatic mutations or the restructuring of the genetic
complement that occurs in the lymphocytes during
the formation of new immunoglobulin genes (Gilbert,
1994). Unlike the cells of an individual, the organisms
of a population or a species are not, except for clones,
genetically identical, and instead exhibit allelic
Fic. 1. A two-celled haploid organism with a single chromosome
per cell, containing two genes of types A and B. Each cell has two
copies of the A
+
allele, while in cell 2, the zygotic B
+
allele has
mutated to type B

. See text.
dierences. However, individuals of the same species
still have equivalent genomes in the sense that all the
alleles involved typically have the same generic
function or base sequences and belong to the same
loci. So, for example, the species-specic genome for
the haploid organism of Fig. 1 would be the set
4A
1
, A
2
, B5.
Thus when, as in the case of the Human Genome
Project, it is said that the genome of the human
species consists of roughly 100000 genes, the genome
is actually thought of as a set consisting of the
approximately 10
5
generic types of human genes, the
types now being distinguished only according to locus
and generic function or base sequence. In practice, the
HGP also seeks to nd a representative human
genome (NIH, 1990), where, in addition to locus, the
types of genes involved will be distinguished not by
generic function or base sequence, but by specic
function or base sequence, the specic representatives
being chosen as those allele types common to most,
or at least many, human beings.
2
Thus there are two fundamental variants of the
genome concept: one involving generic types of genes,
and the other specic (i.e., allele) types. While both
are referred to as genomes, the latter can also be
identied specically as an allelome.
There is yet another concept that boils down even
further the biological reality to the essentials for
genetic analysis. This is the concept of genotype. It
discards all information about the number of copies
of each gene, not only across cells but within them as
well. The genotype, as spelled out this time in its
name, is again a set formed by collecting together only
gene types, these being distinguished now only by
base sequence or function. Thus the normal genotype
of the two-celled haploid organism of Fig. 1 is simply
4A
+
, B
+
5, while the genotypes of the individual cells
1
If useful, one can also conceive of a total genome, listing in one
set all the variants, 4A
+
1
, A
+
2
, B
+
, B

5.
2
Much like with the example mentioned in note 1, one could in
addition conceive of a more encyclopedic human genome, listing in
one set all the allelic variants.
A
+
A
+
B
+
B
+
A

A
+
A
+
B
+ B
+
A

riNb:xrN1:i coNcri1s or crNoxr, crNo1.ir :Nb inrNo1.ir 59

Fic. 2. A multicellular organism in the two-cell stage of
development with only one pair of chromosomes (chromatids) per
cell. Each chromosome contains three genes, two genes of type A
and one of type B. See text.
so that each chromosome consists only of a single
chromatid; and that each chromosome carries three
loci, two heterozygous of type A (alleles of types A
+
and A

), and one homozygous of type B (only B

+
alleles).
All together this organism has 12 nuclear genes of
two general types A and B, and three types of alleles,
distinguished according to specic function or base
sequence: A
+
, A

, B
+
. Its nuclear genetic complement
is the actual 12 genes (alleles). On the other hand,
its nuclear genome (allelome) is the set
4A
+
1
, A

1
, A
+
2
, A

2
, B
+
5, with the subscripts being used
where necessary to distinguish between loci. If we
disregard allelic variation by distinguishing the types
of genes in the genome by, in addition to locus, only
generic, and not specic, function or base sequence,
then we get what we refer to as the monoploid genome,
4A
1
, A
2
, B5. This is the notion involved when one
refers to the genomic equivalence of the individuals of
a species, and it is the same as the species-specic
genome described previously in the haploid case.
(Traditionally, monoploid genome is understood in
the sense of a monoploid genetic complement, as
found for instance in gametes, or as thought of when
diploid cells are described as possessing two
genomes.)
Disregarding next the redundant genes leaves the
set of all the allele types, 4A
+
, A

, B
+
5, which can be
called the allelotype.
2
This notion is of the same
conceptual nature as the haploid genotype. By
contrast, what is conceived of as the genotype of a
diploid cell or organism is not the set of all its allele
types, but the set of all its allele-pair types. Thus, in
our example (Fig. 2), the normal genotype is the set
of allele-pair types 4A
+
A

, B
+
B
+
5. This, then, the
diploid genotype is the second traditional signication
of the word genotype in biology.
3
In practice, geneticists usually focus their attention
on some subset of the total genotype, obtained by
considering only one or a few loci of interest. This
concept has been designated the partial genotype
(see, e.g., Suzuki et al., 1989; Lewontin, 1992). For
example, in Fig. 2, the partial genotype at the B-locus
is, in standard mathematical notation, 4B
+
B
+
5. On
the other hand, standard genetic notation for a
heterozygous two-locus partial genotype would
simply be e.g. A
+
A

B
+
B

or AaBb, instead of
4A
+
A

, B
+
B

5 or 4Aa, Bb5.
Finally, as with the notion of a species-specic
haploid genotype, we can also conceive of the concept
of a species-specic diploid genotype. In Fig. 2, this
would be the set {AA, BB}. This notion seems to be
involved when one refers to the unity of the
genotype (Mayr, 1988).
are 4A
+
, B
+
5 and 4A
+
, B

5.
1
By focusing on generic
gene types, not allele types, we can also form the
species-specic genotype, 4A, B5.
The normal haploid genotype, then, isnot
counting what we have referred to as the genetic
complement and the genomean exact denition
of one traditional signication of the word geno-
type.
In light of the preceding analysis we nd it
unsatisfactory and even inaccurate to dene either the
genome or the genotype as a set of genes or as the
sum total of hereditary material, whether of an
organism or a single cell: doing so does not
distinguish between individual genes and gene types,
and thus conates genetic complements, genomes and
genotypes.
Genome and Genotype in Diploid Organisms
In diploid organisms the situation is more
complicated, for we have to take into account the
existence of two complements of chromosomes of the
same kind and thus the existence of dierent alleles
within the same cell. Consider then a modication of
our previous example, this time a diploid organism in
the two-cell stage of development, with one pair of
chromosomes in each cell (Fig. 2). We further assume
that the two cells are in the G
1
phase of the cell cycle,
1
Again, if necessary, one can conceive of a total genotype, listing
in one set all the variants, 4A
+
, B
+
, B

5
2
Note that the concept of allelotype is commonly dened as a
populational notion, namely as the allele frequency in a breeding
population (Rieger et al., 1991, King & Stanseld, 1985).
3
Presumably this is what Hartl et al. as well as Klug &
Cummings have in mind. Yet the expressions genetic consti-
tution and genetic makeup do not necessarily imply set of
allele-pair types; nor do symbols, i.e., the letters AA, Aa, and aa,
constitute a genotype: they only name one.
x. x:nNrr :Nb x. i:r. 60
Other Versions of the Term Genotype
Even all this does not yet exhaust the usages of the
term genotype found in the literature. Particularly
in evolutionary and population genetics, we nd
phrases such as the dierential replication of
genotypes, the frequency of genotype Aa is x %,
and genotype Aa has a higher tness than the
aa-genotype. The previous concepts of genotype
cannot apply here, since it is only material objects, not
abstract sets, that replicate and multiply, and that can
be more or less t. So if expressions of this sort are
to make sense, this third usage of the word
genotype must be viewed as a shorthand for
genotypic organism, namely an organism character-
ized by some (haploid or diploid) genotype.
Accordingly, the relative frequency of the AA-, Aa,
and aa-genotypes is p
2
:2pq:q
2
simply means that, in
the given population, the organisms whose genotypes
at the A-locus are AA, Aa, and aa respectively, occur
in the proportions described. Needless to say, if there
is any danger of ambiguity, one can simply substitute
the word genotype with genotypic organism,
such as in the phrase Aa-genotypic organisms have
higher tness values than aa-genotypic organisms.
On the other hand, Lewontins rst-quoted
denition of genotype is actually a denition of a
genotypic class, namely a set consisting of all
organisms characterized by a certain genotype.
1
This
fourth signication of the term genotype is what is
meant in phrases such as the Aa-genotype has x
members, which can be translated as either there
are x organisms with the Aa genotype, or the class
of organisms with the Aa genotype has x members.
Likewise in the context of Mendelian crossings, for
example in the mating of two identical dihybrids (e.g.,
AaBb AaBb), geneticists usually say the ospring
belong to any of nine possible genotypes, meaning
actually nine possible genotypic classes, as only a few
authors state explicitly (e.g., Herskowitz, 1977).
In brief, we have to distinguish four dierent usages
of the term genotype current in biological
discourse:
(1) the set of gene types (distinguished according to
base sequence or function) of a haploid organism, or
of a gamete;
(2) the set of allele-pair types of a diploid cell or
organism;
(3) an organism characterized by a certain (usually
partial) haploid or diploid genotype;
(4) a set of organisms sharing the same (usually
partial) haploid or diploid genotype.
All four of these concepts have their place in
biological discourse, but the last two logically
presuppose one or the other of the two preceding.
That is, one cannot dene the genotype in the sense
of a genotypic class or a genotypic organism without
rst presupposing the concepts of either haploid or
diploid genotype as we have dened them here. For
example, the genetic criteria Lewontin refers to in
his denition of the genotype as a class of organisms
are precisely the possessing of genes of the same type;
in other words, the possessing of the same genotype.
If one does not select the logically basic concept as the
denition of the genotype, then one is bound to use
the many concepts of genotype in an ad hoc manner,
without making clear or even realizing the distinctions
between them.
Phenome and Phenotype
The phenetic concepts have for the most part much
in common with the genetic ones. To begin with, there
is the physical aggregate of all the organisms parts,
whether at the level of organs, tissues, cells or
molecules: its total phenetic complement or, if
preferred, physical phenome (see Lewontins denition
above). Needless to say, this concept parallels that of
genetic complement or physical genome. However,
there is in current biological usage no concept of
phenome parallel to that of genome. In fact, phenetic
traits, whether morphological, physiological, or
behavioural, are not in general classied according to
locus-like or base sequence/gene function-like charac-
teristics. For example, comparative morphology,
which is evolutionarily-oriented and thus centres
around homologies, usually prefers structurally
dened types of traits to functionally dened ones,
since a classication of phenotypic traits according to
function would not distinguish homologies from
analogies or homoplasies. (See, e.g., Amundson &
Lauder, 1994.) Moreover, functions themselves can
be regarded as phenotypic traits. Yet the structural
characterization of DNA by base sequence, being
essentially linear and one-dimensional, is of no great
use for complex multidimensional phenetic traits. Nor
1
Dening genotypes and phenotypes as classes of organisms was
also done much earlier, under the inuence of the philosophy of
operationalism: A class of organisms whose members cannot be
distinguished from one another by observation is called a
phenotype; a class which can be distinguished from another by
breeding tests is called a genotype. (Haldane, 1929, p. 485). These
construals were also adopted by Woodger (1952) in his
axiomatization of genetics. Of course, like all the so-called
operational denitions, the above is not a denition proper: it does
not tell us what a genotype is but how to recognize it. That is, it
confuses denitions with indicators or criteria. More on the
confusion of denitions and indicators in biology in Mahner (1994)
and Mahner & Bunge (1997).
riNb:xrN1:i coNcri1s or crNoxr, crNo1.ir :Nb inrNo1.ir 61
are the features that make the locus an important
genetic concept readily generalizable. For these
reasons, all the dierent ways of distinguishing
between types of traits are traditionally subsumed
under the concept of phenotype. That is, the
phenotype of an organism is just the set of all its types
of traits, however construed.
Just as partial genotypes are more tractable than
whole ones, partial phenotypes (Suzuki et al., 1989,
Rieger et al., 1991, Lewontin, 1992), namely
restrictions of the phenotype to some subset of
features that happen to be of interest, make dealing
with phenotypes more feasible. For example, in
Drosophila melanogaster, we may only be interested
in the vestigial- or Curly-phenotypes as well as in
the corresponding normal phenotype. Thus, we can
conceive of the phenotype of a particular organ, the
phenotype of a cell, or even the phenotype of some
molecule.
It is also conventional to expand the scope of the
concept and conceive of the set consisting of all the
monomorphic characters, i.e., the types of traits
common to all normal organisms of a species, and
form the concept of the species-specic phenotype.
For example, the human phenotype is the set of all
types of traits whose common characteristic is being
normally human. We can also go in both directions
at once and conceive of for example the species-
specic phenotype of the human brain.
Just as with the genetic complement and the
genome, we again emphasize the necessity of
distinguishing the phenetic complement (or physical
phenome) from the phenotype. Since an organisms
parts come in nested and functionally integrated
subsystems, we cannot physically extract its phenetic
complement in the same way as can be done (at least
in principle) with its genetic complement. We can just
dismember the organism down to a certain level of
interest, thereby destroying higher level characters.
However, we can bloodlessly conceptualize the set of
all its types of traits, namely its phenotype.
Being sets of trait types, phenotypes are abstrac-
tions of organismal attributes, not material objects.
However, the term phenotype is often used
synonymously with organism or, more specically,
organism characterized by some phenotype or
phenotypic character. For example, when we say
that selection acts on phenotypes, we can only
mean that it is organisms with certain phenotypes,
i.e., phenotypic organisms, that have certain degrees of
adaptedness determining their (dierential) reproduc-
tive success. Likewise, environmental items can only
act on genotypic organisms, not genotypes or
genotypic classes. However, since an organisms
phenotype is not uniquely specied by its genotype,
environmental items interact dierentially with
organisms according to their phenotypic properties,
and only indirectly according to their genotypic
properties. [More on levels of selection in Brandon
(1990) and Mahner & Bunge (1997)].
Lastly, Lewontins rst-quoted denition of phe-
notype is really a denition of a phenotypic class,
namely a class of organisms sharing some (usually
partial) phenotype. Obviously this notion parallels
that of a genotypic class, explained above. For
example, in a Mendelian crossing of two identical
dihybrids, AaBb AaBb, the ospring come in nine
genotypic classes, but in only four phenotypic classes
(provided the A and B alleles are completely
dominant). Again, only a few authors explicitly refer
to phenotypic classes here instead of phenotypes (e.g.,
Herskowitz, 1977).
To summarize, we must distinguish at least three
usages of the term phenotype in biology, namely
(1) the set of trait types of an organism or of one
of its subsystems;
(2) an organism characterized by a certain (usually
partial) phenotype;
(3) a class of organisms sharing the same (usually
partial) phenotype.
Note that the concepts of phenotypic organism and
class logically presuppose the concept of phenotype,
so that we must again distinguish between the
denition of the phenotype and the other, derived
usages. Though thus being the logically basic concept,
it is remarkable that the notion of phenotype has until
now been dened mostly in terms of vague notions
such as appearance or observable form.
Conclusions
Given the above denitions, it becomes obvious
that a concrete string of DNA, i.e., an individual gene
or allele, is itself a phenotypic character (Brandon,
1990, Lewontin, 1992). After all, the formerly
unobservable unit of heredity, an individual gene,
is observable nowat least indirectly. It is a concrete
subsystem of an organism, capable of interacting with
other subsystems. Thus, the genetic complement of
an organism is a physical part of its phenetic
complement. On the other hand, both the genome and
the genotype of an organism are subsets of its
phenotype, as construed here.
1
1
Note that genomes and genotypes would not be subsets of
phenotypes, if one were to dene the phenotype of an organism as
the set of its phene types, for a phene is usually dened as a
genetically controlled character (King & Stanseld, 1985, Rieger
et al., 1991).
x. x:nNrr :Nb x. i:r. 62
T:nir 1
Summary of terms and denitions
Suggested terms Commonly used terms Denition
Genome, genetic Genetic complement, Physical totality of all genes of a cell, tissue or organism
physical genome complement
Genome, (Allelome) Set of all types of genes (alleles), distinguished by locus and specic base Genome, genotype
sequence/function
Species-specic genome, Genome, species genome (e.g. Set of all types of genes, distinguished by locus and generic base
monoploid genome mouse, human genome), sequence/function
monoploid genome
Genotype (haploid) Genotype Set of all types of genes (alleles), distinguished by specic base
sequence/function
Species-specic haploid Species genotype Set of all gene types, distinguished by generic base sequence/function,
genotype common to all normal members of a species
Genotype (diploid) Set of all types of allele-pairs of a diploid organism Genotype
Species-specic diploid Species genotype Set of all types of gene-pairs, distinguished by generic base sequence/
genotype function, common to all normal members of a species
Genotypic organism Genotype Organism characterized by some (usually partial) genotype
Genotypic class Class of organisms characterized by some (usually partial) genotype Genotype, genotypic class
Physical totality of all traits of an organism or of one of its subsystems Phenetic complement, Phenome, phenotype
physical phenome
Phenotype Set of all types of traits of an organism or of one of its subsystems, however Phenotype
dened
Species-specic phenotype Species phenotype Set of all types of traits common to all normal members of a species
Phenotypic organism Organism characterized by some (usually partial) phenotype Phenotype
Phenotypic class Class of organisms characterized by some (usually partial) phenotype Phenotype, phenotypic class
We see no valid use for denitions of the genotype
and phenotype in terms of blueprints, programs, or
sets of instructions, and their realizations or
manifestations. For one thing, they oer not even a
suggestion of how to distinguish between the genetic
complement, the genome and the genotype, or
between the physical phenome and the phenotype.
For another, they do not really tell us what geno-
types and phenotypes are, but only that the two
are related, presupposing that we already know
what they are. In other words, they are at most
statements about genotypes and phenotypes, not
denitions. For example, the sentences the geno-
type is a blueprint for the phenotype and the
phenotype is a manifestation of the genotype do
tell us that genotypes and phenotypes are related,
but they are inadequate for purposes of denition
because they are too broadmany things are
blueprints for, or manifestations of, other things
and because they lead to circularity and innite
regress: one can substitute one denition into the
other, so that we obtain the genotype is a blueprint
for the manifestation of the genotype, and then
ultimately the genotype is a blueprint for the
manifestation of a blueprint for the manifestation of
. . . ad innitum; and likewise for the phenotype.
[More on adequacy rules for denitions in van der
Steen (1993).] Furthermore, the program/manifes-
tation metaphor is factually misleading, because it
suggests that the genotype uniquely determines an
organisms phenotype. However, as is well known, all
it does is specify an organisms norm of reaction to
environmental conditions (Rieger et al., 1991,
Lewontin, 1992).
In the end, such formulations are but metaphorical
relics of a Platonic metaphysics which now serve only
as obstacles to the scientic explanation of biological
processes in their own terms. After all, molecules do
not express themselves, but simply may or may not
undergo certain chemical reactions. And while it is
always tempting to describe certain features of the
reactions most relevant to biology with the word
information, a good deal of caution should be
exercised before doing so (see, e.g., Apter & Wolpert,
1965; Bunge, 1979; Kary, 1990; Mahner & Bunge,
1997). The redescription of complex biochemical
processes in terms of analogies and metaphors,
whether familiar or exotic, usually leads only to the
riNb:xrN1:i coNcri1s or crNoxr, crNo1.ir :Nb inrNo1.ir 63
illusion that one has provided a scientic explanation.
[For a critical look at the notion of a genetic program
see Moss, (1992).]
Most biologists seem to use one or more of the
previously elucidated concepts (summarized in
Table 1) in an intuitively correct manner in most
contexts, and the habit of using a single word to mean
many dierent things does not yet seem to have
seriously impeded research. (The real confusion
facing students is another matter entirely.) Yet the
fact remains that the current state of these key
concepts of biology is far from satisfactory. Our
intention here is not to advance our own proposals
for their reform as ultimate; but instead to provoke
an increased awareness of, and attention to, these
and similar foundational issues in the biological
sciences.
M.M. received funding from the Deutsche Forschungsge-
meinschaft, Bonn, Germany, while beginning this collabor-
ation at the Foundations & Philosophy of Science Unit of
McGill University, Montreal. The hospitality of the Unit
and its head, Mario Bunge, is appreciated. M.K. received
assistance from the Graduate School and the Mathematics
Department of Boston University.
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