## 1. A History of the Gene Within the History of Genetics


### 1.1 From Mendel's methods to Mendelism



The question of biological heredity emerged in the nineteenth century
in diverse fields of practice and gave rise to various theories, which
often aimed to provide a unified view of heredity, development, and
evolution (Muller-Wille & Rheinberger 2012: Chs. 2-5).
Gregor Mendel (1822-1884) did not aim at a unifying theory, nor
did he set out to discover laws governing heredity. Historians have
argued, instead, that he was concerned with specific questions
regarding the role of hybridization in evolution (Olby 1979; cf.
Muller-Wille 2018). Other hybridists had crossed plants of
different species and varieties, studied their offspring, and asked
whether new species could emerge in this process. Issues regarding the
classification of hybrids emerged: how did hybrids resulting from
crosses between pure species differ from offspring of parent organisms
that were hybrids themselves; and how could their characteristics be
interpreted with respect to those of their parents when it came to
determining their type? Mendel (1866 [2016]) aimed to address such
questions in his experiments with garden peas and in this respect was
indeed indebted to his predecessors. Nonetheless, he introduced
several changes in the experimental system employed by the hybridists
that allowed him to arrive at more specific results regarding the
distribution of types in several generations of offspring
(Muller-Wille & Orel 2007). First, he concentrated on
varieties that differed only in one or a few characteristics. This
enabled him to move from classifying the offspring according to type
to a focus on the distribution of traits that characterized the types.
Second, he made sure that he obtained offspring in numbers that
allowed for a statistical treatment of the distribution of characters.
In this way, he was able to observe regularities in the appearance of
types in the third generation (plants resulting from crosses between
hybrids) that previous hybridists where not able to detect. Finally,
he developed a notation system where letters represented types of germ
cells, which he used to record his results and compare them with
theoretical predictions. These innovations enabled Mendel to arrive at
a set of regularities regarding


1. the uniform appearance of a "dominant" character in
the first generation,
2. the segregation of the dominant and alternative,
"recessive" characters in a ratio 3:1 in the second
generation, representing one pure dominant, two hybrids, showing the
dominant character, and one pure recessive, and
3. the independent inheritance of separate character pairs.



Mendel's refined methodology was the basis for important
conceptual innovations. Next to the shift from "forms" or
"types" found in several generations in hybridization
experiments to the distribution of characters, Mendel could move from
the characterization of the contribution of gametes (also addressed as
"factors") to the "elements" by which the
gametes differed (Muller-Wille & Orel 2007). Nonetheless,
Mendel did not think of the regularities as laws of heredity. Indeed,
whether they were valid for organisms other than the garden pea he
considered subject to empirical investigation. Furthermore, Mendel
thought of his results as illuminating the behavior of characters in
hybrids, i.e., he did not generalize his results to heredity *per
se,* as it would occur in the reproduction of all characters, also
in pure varieties (Rheinberger & Muller-Wille 2018: Ch.
3).



In 1900, several botanists independently arrived at similar results in
their hybridization experiments and at the same time took notice of
Mendel's original work and stated its significance in their
respective publications (Olby 1966: Ch. 6). This brought the Mendelian
approach and way of reasoning to the attention of those who worked
with experimental crosses in contexts of either theoretical questions
regarding heredity and evolution or applied problems of horticulture
and scientific breeding (Bowler 1989a: Ch. 6). Much had changed in
biology since Mendel's days: first, the idea that the hereditary
material is passed on independently of somatic development, codified
in August Weismann's (1834-1914) germ-line theory, was
well established; second, several researchers had developed a
cytological interpretation of hereditary phenomena; third, in the late
nineteenth century various ideas on how to identify units transmitted
through germ cells had emerged. Furthermore, on a broader social and
economic scale, processes of industrialization and rationalization of
food production, vaccines, and other applications had led to an
increased demand for standardized biological materials
(Muller-Wille & Rheinberger 2012: Ch. 6). In this context,
the entities and regularities identified by hybridization experiments
were now taken to be the basis of heredity in general.



The early "Mendelians" employed and expanded
Mendel's experimental system, notation, and terminology (Shan
2020). They codified Mendel's regularities as "laws"
of heredity, while at the same time investigating exceptions to
uniformity or dominance (e.g., "blending" characters), to
the ratios of segregation (e.g., due to "composite"
characters, which came to be seen as influenced by several factors),
and to independent assortment in crosses involving several characters
(e.g., because characters appeared to be "coupled").
Mendel's experiments, perceived as exemplars for the study of
variation and heredity, named "genetics" by William
Bateson (1861-1926; 1907), played an important role for the
formation of both the field and its central concept, the gene. Bateson
emphasized the idea that discrete "unit-characters" could
be identified in organisms, which occurred in alternative forms or
"allelomorphs". In crosses these characters segregated in
Mendelian ratios. This indicated and was explained by assuming the
"purity of gametes", i.e., the fact that reproductive
cells can transmit only one form of a character. When two gametes that
were alike with respect to one character united, the resulting zygote
was "homozygous" for this character, otherwise it was
"heterozygous". While these observations were initially
discussed mainly in terms of characters and types of gametes or the
gametes' ability to transmit characters, Bateson came to think
of the dominant allelomorph as being determined by some
"factor" present in the gamete, while the recessive
character resulted when the factor was absent in both gametes (Darden
1991: Ch. 6; Schwartz 2002). "Factor" thus came to be
used by many Mendelians similarly to Mendel's
"elements". The term referred to whatever made two gametes
different regarding the inheritance of characters, but it was not
connected to any specific theory regarding the physical nature of the
hereditary material.



There were also alternatives to the Mendelian view of heredity. The
biometric approach, going back to the work of Francis Galton
(1822-1911) and further developed by W.F.R. Weldon
(1860-1906) and Karl Pearson (1857-1936), used advanced
statistical tools to investigate heredity in terms of correlations
between characters in successive generations in limited populations
(Porter 1986: Ch. 9). Weldon and Pearson adhered to an orthodox
interpretation of Charles Darwin's (1809-1882) view that
evolution proceeded by natural selection acting on gradual variation.
Mendelians, instead, focused on discontinuous variation (Bowler 1992;
Gayon 1998). Wilhelm Johannsen (1857-1927) had conducted
experiments with "pure lines", in which he selected the
plus or minus variants of quantitative characters such as seed size in
the offspring of self-fertilized beans (Johannsen 1903). Based on his
results, Johannsen distinguished between fluctuating variation, which
was due to contingent influences of the environment, and variation
between types, which remained stable unless changed in a discontinuous
manner through mutation (Roll-Hansen 2009). Around that time, Hugo de
Vries (1848-1935; 1901-1903) suggested the concept of
mutation to account for the spontaneous emergence of new stable types.
Even though many did not follow de Vries' idea of large-scale
changes affecting several characters at once, giving rise to a new
species instantaneously, most Mendelians came to think that the
character variation they observed occurred spontaneously through
changes in factors as units of the hereditary material (Bowler 1992:
Ch. 8).



Initially, some Mendelians doubted the purity of gametes and concluded
that the maternal and paternal gametes "contaminated" each
other regarding the factors by which they differed, thus allowing for
continuous variation. However, various researchers were able to
resolve the question by showing how several factors affected the same
quantitatively characterized character in cumulative manner (Carlson
1966: Chs. 4-5; Darden 1991: Chs. 6-7). Around 1910,
models of "multi-factorial inheritance" explained modes of
inheritance of continuously varying characters based on discontinuous
genetic variation. These and other developments led to a convergence
of biometric approaches and Mendelism and the emergence of
mathematical population genetics in the 1920s and 30s, a field that
laid the foundations for genetic models of the effects of selection
and other processes of evolution (Allen 1978: Ch. V, Part II; Bowler
1989b: Ch. 11; Provine 1971; entries on
 population genetics
 and
 ecological genetics).


### 1.2 Classical and physiological genetics



Much of population genetics relied on an abstract concept of the gene
as a unit inferred through character differences, represented in a
symbolism, and used in the mathematical reconstruction or prediction
of patterns of variation in theoretical, experimental, or natural
breeding populations. In the early years of genetics, there was no
agreement regarding the possibility of identifying units of the
hereditary material and characterizing their nature and function.
Considerations in this direction did not differ much from the
speculative theories of the nineteenth century and were indeed mainly
informed by them. In 1909 Johannsen coined the term
"gene", derived from de Vries's term
"pangene", to disentangle the concept of the hereditary
unit from any specific theory:



> 
> 
> It is meant to express merely the simple idea that
> "something" in the gametes can condition or take part in
> the determination of a property of a developing organism. (Johannsen
> 1909: 124, author's translation)
> 
> 
> 



With respect to his selection experiments mentioned above, Johannsen
had furthermore introduced the distinctions between phenotype and
genotype. The former concept initially captured the range of
fluctuating variation in a quantitative character centering on an
average value that characterized a pure line. Later, however, the term
was used with respect to an individual's characteristics for
both quantitative and qualitative differences in type. The genotype
was the genetically relevant constitution of the germ cells or zygote,
in other words, the sum of the genes, where genes could only be
identified as bearing differences between genotypes resulting in
phenotypic differences. The phenotype was the result of the
interaction of the genotype with the environment in ontogenesis
(Meunier 2016a; entry on
 the genotype/phenotype distinction).
 The phenotype of the parents, let alone of more distant ancestors,
thus had no effect on the offspring. The genotype was what passed from
parents to offspring. Johannsen defined heredity "as the
presence of identical genes in ancestors and descendants"
(Johannsen 1911: 159).



Paradoxically, the rejection of speculations about the nature and
functioning of hereditary units advocated by Johannsen opened the
possibility for its investigation as an epistemic object. By
separating genes and characters more clearly and treating them as
correlated in terms of differences rather than in terms of growth or
production implied in "Anlage" and similar earlier
concepts, characters could take on the epistemic function of an
"index" or "marker" informative of the genetic
composition of gametes and zygotes (Meunier 2016b; Schwartz 2000). The
gene began to take shape as a material entity when this inferential
strategy was combined with observations from microscopic studies of
reproductive cells that enabled inferences on the role of chromosomes
in heredity.



In 1910-1911, Thomas Hunt Morgan (1856-1945) observed
several mutants in his stocks of *Drosophila melanogaster*.
When he analyzed these mutants through Mendelian crosses, he found
that they were partially linked regarding their inheritance, i.e., the
characters were inherited together in more than the 50% of cases that
would be expected if genes were randomly distributed, but in less than
100% of the cases, which would have suggested that both characters
depend on the same gene. Indeed, Morgan found that his characters
could be recombined, despite the fact that they were all sex-linked,
i.e., the genes were associated with whatever determined sex in the
fruit fly. As every gene was present in two instances (later called
"alleles"), the linkage groups could be assumed to exist
in pairs and recombination thus suggested exchange between
corresponding linkage groups, or "crossing over" of genes.
This again suggested that linked genes appeared in linear order, with
the frequency of crossing over between two genes being an indicator of
their proximity. Other characters were found that also formed such
linkage groups but were not sex-linked. Based on these assumptions,
Morgan and his students were able to construct maps of four linkage
groups in *Drosophila* that represented the linear order and
relative distance as inferred from recombination frequencies (Carlson
1966: Ch. 6-7).



While this account of genes was derived from genetic evidence, i.e.,
Mendelian crosses, the results could be mechanistically explained with
reference to chromosomes. Chromosomes had been suggested as containing
hereditary material before, but evidence was not forthcoming until the
early twentieth century. Cytologists had been able to observe the
behavior of chromosomes the formation of gametes and draw analogies to
the segregation and independent assortment of Mendelian units. They
demonstrated the role of chromosomes in the determination of sex and
made observations which suggested an exchange of materials between
homologous chromosomes (Brush 1978; Carlson 1966: Ch. 6; Crow &
Crow 2002). On this basis, the Morgan group's account identified
linkage groups with chromosomes (Morgan et al. 1915; Vorms 2014). By
the 1930s, cytological observations had reached a resolution that
enabled researchers to correlate genetic linkage map loci with
physical landmarks in the chromosomes, leading to cytological maps,
which further facilitated the study of chromosomes in heredity (Falk
2004; Gannett & Griesemer 2004).



In this tradition, often referred to as "classical
genetics", genes were hypothetical material units of the genetic
material, located in the chromosomes. But unlike the material carriers
of heredity assumed in the nineteenth century, they did not give rise
to characters in a straightforward manner. Many-many relations between
genes and characters became obvious early on. All characters were
influenced by many genes (polygenic) and most genes affected many
characters (pleiotropic). The only kind of causal statement that was
justified was that a difference in a gene resulted in one or more
differences on the phenotypic level (Schwartz 2000).



Some questioned the chromosome theory of heredity and the notion of
separable corpuscular genes. For instance, in the light of the
"position effect", where genes had different effects
depending on their location in the chromosome, Richard Goldschmidt
(1878-1958; 1938) suggested a holistic view of chromosomal
agency (Allen 1974; Carlson 1966: Chs. 13-15). Furthermore,
whether justified or not, many embryologists interpreted genetics as a
form of preformationism, the view that organisms or their parts were
in some way already given or at least pre-determined in the fertilized
egg or its nucleus, such that development would be the mere
articulation of the given structures. This interpretation was at odds
with the view held by most embryologists, that the organism is the
result of a process referred to as epigenesis, in which nucleus,
cytoplasm and environment interact to transform material and
structures (see the entry on
 theories of biological development).



On their part, geneticists became increasingly interested in the
chemical nature of genes and their roles in metabolism and
development. Several researchers had emphasized analogies between gene
action and enzyme mediated chemical reactions (Ravin 1977). Using
their terminology, Hermann Muller (1890-1967) and others
observed that the gene had two characteristics that needed to be
elucidated. First, it was autocatalytic, i.e., it was capable of
reproducing itself for cell division and heredity to happen; second,
it was heterocatalytic, i.e., it was able to facilitate the production
of other chemical materials to perform its function (Muller 1922,
1947). What was peculiar regarding the first aspect was that genes
were still capable of autocatalysis when they underwent mutational
change, and they faithfully reproduced the alteration. Hence, for
Muller, mutation was the key to the material nature of the gene. In
the late 1920s, he and others were able to establish the mutagenic
agency of radiation (Muller 1927; see Campos 2015: Chs. 5-6).
The fact that genes could be "hit" and changed through
X-rays supported the idea that they were individual entities that
could be physically and chemically characterized.



To address the immediate chemical function of genes in the cell, i.e.,
their heterocatalytic properties, it was necessary to conceive of the
phenotype itself in chemical terms. In 1908 Archibald Garrod
(1857-1936; 1909) had found that some medical conditions that
could be associated with "errors in metabolism" were
inherited in a Mendelian fashion. Subsequently, physiological
geneticists studied the relation of genes and catalytic activities.
Conclusive evidence was achieved when George Beadle (1903-1989)
and Edward Tatum (1909-1975) used the bread mold *Neurospora
crassa* to search for mutants that affected known nutritional
pathways by growing the fungi on selective media that provided or
lacked certain substances. This approach established the field of
biochemical genetics and stabilized the one gene--one enzyme
hypothesis, i.e., the view that every gene was involved in the
production of a specific enzyme, which had a specific effect on
cellular metabolism (Kay 1993: Ch. 7; Kohler 1994: Ch. 7).


### 1.3 Molecular genetics: From DNA to protein



As much as these achievements of genetic analysis pushed the gene in
the biochemical or molecular domain, they were not able to elucidate
the chemical nature of the gene and its immediate action. This
required other experimental systems, which began to take shape in the
1930s to 1950s (Morange 2020, Part One). For instance, Max
Delbruck (1906-1981) and others turned to T-phages (viruses
that infect the bacterium *e.coli*) because they assumed that
viruses were essentially "naked genes". While these
researchers were able to show that genetic phenomena (mutation,
exchange of genetic material) were present in viruses and bacteria as
well and to achieve higher resolution of analysis, this work remained
as formal as *Drosophila* genetics. It was only through
integrating new technologies from physics and chemistry into the new
experimental systems that microbial genetics led to molecular
genetics. Results from biochemical work in biomedical microbiology and
from work involving radioactive isotopes to label biological molecules
provided evidence that DNA might be the genetic material.



Several researchers turned their efforts to elucidating the structure
of DNA (Judson 1979: Ch. 2; Morange 2020: Ch.11; Olby 1974: Section
V). Among them were James Watson (born 1928) and Francis Crick
(1916-2004). They used data from DNA X-ray crystallography
produced by Maurice Wilkins (1916-2004), Rosalind Franklin
(1920-1958), and co-workers, and adopted the style of reasoning
and use of ball-and-stick models of molecules pioneered by Linus
Pauling (1901-1994). DNA was already known to consist of a
sugar-phosphate structure and the four bases cytosine (C), guanine
(G), adenine (A) or thymine (T). Based on additional evidence, Watson
and Crick eventually came to consider a double helix model with the
bases on the inside and a pairing of A with T and G with C, which was
published in April 1953. Shortly thereafter they published another
paper which spelled out the consequences for genetics (Watson &
Crick 1953a,b). The model suggested a mechanism of DNA replication
according to which the two chains of the DNA separate and each
acquires a novel complementary strand on the basis of base pair
complementarity. Hence it explained the previously postulated
autocatalytic properties of genes. Seymour Benzer (1921-2007),
working with phage was able to push the resolution of genetic analysis
to a level below the gene, by mapping mutation loci within genes
(Holmes 2006). His work supported the DNA model as it showed that not
only genes, but also their components were arranged in a linear
sequence and suggested that single bases could be the locus of
mutation. Benzer concluded that the understanding of the classical
gene as unit of mutation, recombination and function needed to be
revised (Benzer 1957). He suggested the novel terms
"muton", "recon" and "cistron,"
where only the latter gained some currency to refer to genes as units
of function.



The acceptance of DNA as genetic material and of its structure brought
the search for the material basis of genes to an end. Subsequently,
the focus shifted on the question of how genes realized their
heterocatalytic capacities. At this point, the question was reframed
in terms of protein synthesis (Judson 1979: Ch. 6; Morange 2020: Ch.
12). Proteins consist of one or several polypeptide chains, which are
composed of amino acids. In the early 1950s, Frederick Sanger
(1918-2013) had determined the amino acid sequence for
polypeptides of insulin (Chadarevian 1996). On this basis, Crick
re-defined the problem by observing that



> 
> 
> [t]he actual chemical step by which any two amino acids [...] are
> joined together is probably always the same [...].
> 
> 
> 



Therefore, the aspect of protein synthesis in need of explanation
was



> 
> 
> that only a single standard set of twenty amino acids can be
> incorporated, and that for any particular protein *the amino acids
> must be joined up in the right order*.
> 
> 
> 



In other words, it was



> 
> 
> the problem of "sequentialization". (Crick 1958: 144)
> 
> 
> 



In response to this problem Crick formulated the sequence hypothesis,
which assumed



> 
> 
> that the specificity of a piece of nucleic acid [i.e., a stretch of
> DNA or RNA] is expressed solely by the sequence of its bases, and that
> this sequence is a (simple) code for the amino acid sequence of a
> particular protein. (1958: 152)
> 
> 
> 



The three-dimensional conformation of the protein was then seen as
emerging spontaneously as a function of its sequence. Additionally,
Crick formulated what he called the "central dogma",
regarding the directionality of the relation of DNA's sequence
of bases and proteins' sequence of amino acids:



> 
> 
> [The central dogma] states that once "information" has
> passed into protein *it cannot get out again*. In more detail,
> the transfer of information from nucleic acid to nucleic acid, or from
> nucleic acid to protein may be possible, but transfer from protein to
> protein, or from protein to nucleic acid is impossible. (1958:
> 153)
> 
> 
> 



The language of "information" and "code" had
entered genetics only recently and from several sources. One was Erwin
Schrodinger's (1887-1961) *What is life?*
(1944), where he spoke of a "code-script"; another was the
broader cold war techno-cultural context of cryptography, computer
science, and cybernetics (Kay 2000; Keller 2000). In this context,
before the early 1960s, most authors treated the problem of the role
of DNA in protein synthesis in a theoretical manner, relying on
mathematical and cryptographic considerations, and using computers to
solve the combinatorial puzzle. Although some theoretical insights and
much of the language developed at this time was important for later
developments, these attempts by geneticists were ultimately
unsuccessful (Sarkar 1996; Stegmann 2021).



Biochemists at the time were equally convinced that genes played an
important role in protein synthesis (Judson 1979: Ch. 6 and 8; Morange
2020: Ch. 12; Rheinberger 1997). New evidence emerged from the medical
genetics and biochemistry of sickle cell anemia, indicating the
relation of gene mutations and amino acid alterations, from *in
vitro* systems of protein synthesis based on *e.coli* cell
extracts, leading to the characterization of ribosomes and transfer
RNA (tRNA), as well as from work establishing the existence and role
of messenger RNA (mRNA) and its complementarity to DNA. The image that
resulted from this diverse evidence was that mRNA transferred
information from nuclear DNA to the cytoplasm, where ribosomes, as
largely unchanged structures, facilitated the assembly of amino acid
chains based on the sequence of mRNA. In 1961, Crick and co-workers
showed experimentally that three bases code for one amino acid, that
coding triplets do not overlap and that they are read from a fixed
starting point. In the same year, Marshall Nirenberg (1927-2010)
and Heinrich Matthaei (born 1929) published results from an experiment
in which synthetic RNA consisting only of uracil bases (RNA contains
uracil, instead of thymine) was introduced in a cell free protein
synthesis system, resulting in the production of a monotonous protein
consisting of the amino acid Phenylalanine. Thus, it was shown that
the RNA triplet UUU coded for this amino acid. This result opened the
possibility to solve the genetic code experimentally and several labs
participated in this project, leading to a complete table of
correlated codons (coding triplets) and amino acids by 1967.


### 1.4 Molecular biology: DNA technology, development, and evolution



Molecular technologies and concepts inevitably had a transforming
influence on other fields. Indeed, it might be argued, that while
molecular genetics constituted a discipline centered on a limited
number of questions regarding the molecular basis of heredity,
molecular biology is best understood as a set of techniques and
approaches that came to be applied in various disciplines (Burian
1993).



In the classical period of molecular genetics, many central mechanisms
pertaining to DNA replication, gene regulation, and protein synthesis
were described. While DNA served as a template in its own replication,
it was not self-replicating or autocatalytic; many enzymes and other
molecules were required in this process, such as DNA polymerase and
DNA ligase. Furthermore, around 1970, several enzymes specific for
bacteria or viruses were described such as reverse transcriptase,
which enabled viruses to translate RNA into DNA, and restriction
enzymes, which cleaved DNA as part of a bacterial defense system. Next
to explaining important cellular processes, taken together, these
enzymes could be used as a toolkit to manipulate DNA *in
vitro*, in bacterial systems and eventually also in eukaryotic
cells. In 1972, Paul Berg (born 1926) and colleagues published a study
demonstrating the possibility to construct DNA molecules from
fragments originating from different organisms by using these enzymes
as tools (Jackson et al. 1972). These molecular tools not only led to
recombinant DNA technology and genetic engineering, but also
facilitated the further molecular characterization of genes by
isolating and amplifying them in bacteria (molecular cloning) (Morange
2020: Ch. 16).



Molecular technologies changed the way research was done in molecular
biology. *In vitro* systems that helped among other things to
solve the genetic code, were complemented by new methods of *in
vivo* manipulation and detection (Rheinberger 2009). This in turn
led to the discovery of new cellular mechanisms involved in the
transcription and translation of genes. For instance, it had been
observed in virus-based model systems that in some cases mRNA
corresponded to non-contiguous fragments of the DNA from which it was
transcribed. Further studies revealed that in these cases parts of the
initial transcript were removed to form the mature mRNA that was
eventually translated and the segments that were removed could
separate coding regions. Much to the surprise of biologists, this was
the case for all genes in eukaryotic cells, while the mechanism was
absent in prokaryotes (Abir-Am 2020; Morange 2020: Ch. 17).
"Split genes" and the mechanism of RNA splicing led to an
important reconception of genes. As Walter Gilbert (born 1932)
wrote:



> 
> 
> The notion of the cistron, the genetic unit of function that one
> thought corresponded to a polypeptide chain, now must be replaced by
> that of a transcription unit containing regions which will be lost
> from the mature messenger which I suggest we call introns (for
> intragenic regions)--alternating with regions which will be
> expressed--exons. (W. Gilbert 1978: 501)
> 
> 
> 



Gilbert's terminology was widely accepted and it became clear
that exons could be spliced together in alternative ways, thus
multiplying the number of proteins that could be derived from a
stretch of DNA. During the 1970s and 80s, further mechanisms of RNA
processing were discovered in various organisms. For instance, mRNA
could be generated by splicing together exons from several
transcripts, from either the same or adjacent loci or even from
different chromosomes ("trans-splicing"). Furthermore, RNA
could be edited by changing several or single nucleotides, which could
have large effects on the proteins translated from the mRNA. Mobile
elements in the genome (transposons), already characterized by Barbara
McClintock (1902-1992) in Maize in the early 1950s by classical
genetic means, were also studied in bacteria and molecularly
characterized around 1980 (Comfort 2001). It was not always
immediately clear how general these and other mechanisms were (and it
is still investigated). Nonetheless, it transpired that the notion
that one gene, understood as an unequivocally localized stretch of
DNA, corresponded to one polypeptide, had to be abandoned (Fogle 2000;
Portin 2002).



Another important development concerned gene regulation. Studying the
ability of bacteria to adapt to varying food sources, Francois
Jacob (1920-2013) and Jacques Monod (1910-1976) developed
the operon model, according to which a protein called
"repressor" is permanently produced, which binds to a DNA
region called "operator" in the vicinity of the genes
required for lactose metabolism, thereby inhibiting the production of
the respective enzymes and other proteins. If lactose was present, it
(or a derivate) interacts with the repressor such that the genes are
activated, and lactose could be digested by the bacteria. This model
introduced an important distinction regarding genes. Those genes that
coded for b-galactosidase or lactose permease or other proteins
constituting cellular functions were called "structural
genes". The genes that produced the repressor and other proteins
controlling the expression of genes were called "regulatory
genes" (Jacob & Monod 1961).



This kind of mechanism was immediately interpreted as providing
answers to the question how different genes become activated at
different times and in different tissues during metazoan development
(differential gene expression). Between the 1950s and the 1980s the
concept of specific developmental genes emerged (Morange 2001: Ch. 7).
Developmental biologists identified a limited number of genes that
were essential in establishing the organization of the very early
embryo and functioned by controlling the expression of various other
genes. Molecular cloning led to the molecular characterization of
developmental genes and the discovery of their evolutionary
conservation (Weber 2004, see also the entry on 
 developmental biology).



Evolutionary biology as well became molecularized
(Suarez-Diaz 2018). One important contribution was the
theory of the molecular clock, which stated that the rate of
evolutionary change in a protein remained constant such that the time
of divergence of lineages could be estimated from data on amino acid
sequences (Morgan 1998). This lent support to and was explained by the
neutral theory of molecular evolution suggested, which was
controversially discussed between molecular and traditional biologists
in the 1960s (Dietrich 1998; entries on
 ecological genetics
 and
 genetic drift).
 In general, molecular biology opened a new perspective on
evolutionary mechanisms, for instance, the notion that evolution
builds upon events of duplication of genes, chromosomes, or whole
genomes. On this view the duplicated elements could acquire new
functions or alter the dosage of gene products (Morange 2020, Ch.
23).


### 1.5 Genomics and post-genomics



In the late 1970s, Sanger developed methods for sequencing DNA. The
1980s then saw the automation of these methods (Garcia-Sancho
2012). This made whole genome sequencing of humans and other
organisms feasible, and the Human Genome Project (HGP) commenced work
in 1990 (Bostanci 2004; entry on
 the human genome project).
 New parallel, or "next generation", sequencing methods
that emerged around 2005 made sequencing faster and cheaper.
Accordingly, the number of species and human samples sequenced
increased continually. Since the early days of protein sequencing,
sequence data was stored in digital databases, with GenBank being
among the most important sequence repositories (Strasser 2019).
Genomics, the science of analyzing and comparing genomes was thus
strongly aligned with bioinformatics. Sequence comparison once more
transformed evolutionary genetics and enabled new comparative
approaches; now the DNA sequence itself could be used to reconstruct
phylogenetic trees, and patterns of duplication events could be
tracked in more detail (Suarez-Diaz 2010). Microbial
systematics and ecology, in particular, changed significantly when
metagenomic approaches, i.e., the sequencing of whole microbial
communities, revealed not only the diversity of microbial life, but
also the amount of lateral gene transfer between organisms, including
eukaryotes (O'Malley 2014). But the availability of large data
sets on human genomes also fostered novel interest in human diversity
and history, enhanced medical genetics and the use of genetic data in
forensics, and led to the emergence of direct-to-consumer genetic
testing (Atkinson et al. 2009; Gibbon et al. 2018).



One of the unexpected results of the HGP was that the human genome
contained only about 23,000 protein-coding genes as defined based on
the concept of an open reading frame (ORF), that is, a stretch of DNA
that begins with a start and ends with stop codon that initiate and
terminate translation. Other, apparently less complex organisms, had
as many or even more genes (thus defined) in their genomes (G-value
paradox). This fact again suggested the significance of splicing
variants and other mechanisms increasing the number of proteins
derived from a given genome, of regulatory elements in the genome, and
of non-coding RNA (see entry on
 genomics and postgenomics).
 In 2003 the Encyclopedia of DNA Elements (ENCODE) project was
initiated, aiming at identifying all functional elements in the human
genome including those transcribed to non-protein-coding RNA, and
sites for protein binding or epigenetic modification (Brzovic
& Sustar 2020). The results of the consortium's work
made the already known deviations from the classic model of the
molecular, protein-coding gene appear as the rule rather than the
exception. To a large extent ENCODE researchers found overlap of
transcripts, products derived from widely separated pieces of DNA
sequence and widely dispersed regulatory sequences for a given gene.
The findings also confirm that most of the genome is transcribed and
emphasize the importance and pervasiveness of functional non-coding
RNA transcripts (Morange 2020: Ch. 25; O'Malley et al. 2010;
Veigl 2021).



These developments belong to what is commonly referred to as
"post-genomics" (Richardson & Stevens 2015). Next to
DNA, so-called "omics" research studies the transcriptome,
the proteome, the interactome, and other levels of cellular processes
and is strongly driven by new technological developments. DNA and
protein microarrays (biochips) have been instrumental in this respect,
and the investigation of RNA transcripts has been even further
enhanced by next generation RNA sequencing (Rheinberger &
Muller-Wille 2018: Ch. 9). Such high-throughput technologies
result in massive amounts of diverse types of data. Bio-ontologies,
and database infrastructures and curation, accordingly, became a
central aspect of molecular biological research (Leonelli 2016).



While relevant mechanisms were first characterized in the 1960s and
70s, omics-approaches have furthered the study of cellular
epigenetics, referring to molecular mechanisms including DNA
methylation, changes in chromatin structure, and non-coding RNA
related regulation (Buklijas 2018; Morange 2020: Ch. 26; Nicoglou
& Merlin 2017). These mechanisms can result in patterns of
differential gene expression that remain stable across mitotic cell
division, thus contributing to the explanation of development.
Epigenetic modifications have also been shown to be conserved in
meiosis, facilitating the inheritance of phenotypic variation across
generations, independently of changes in DNA sequence, a fact with
consequences for evolutionary biology (Jablonka & Raz 2009).



The availability of data sets also enabled new, technology-driven
styles of biological research (Morange 2020: Ch. 28; Rheinberger &
Muller-Wille 2018: Ch. 9; entry on
 philosophy of systems and synthetic biology).
 Systems biology emerged as a highly interdisciplinary field, which is
characterized by mathematical and computational approaches to the
topology and dynamics of interaction networks involving genes and gene
products. In a complementary manner, synthetic biology focuses on
engineering metabolic pathways and regulatory networks for
biotechnological applications such as drug or biofuel production, but
also to increase the understanding of molecular systems (Kastenhofer
2013). The CRISPR-Cas system, originally elucidated as a bacterial
immune defense mechanism, was developed into a new tool for genome
editing, which, due to its precision, also enhanced genetic
engineering approaches in multicellular organisms (Morange 2020: Ch.
24).



It becomes clear that biological research remains dynamic and that
every development sheds new light on questions of heredity and the
functioning of DNA. With the developments presented in this part in
mind, we shall now turn to some of the philosophical debates they have
engendered.


## 2. Philosophical Accounts of Scientific Change in Genetics


### 2.1 Theory change and reductionism in genetics



The developments in genetics sketched in Part 1 prompted the question
how philosophical models of scientific change could be applied to the
case of biology from the late nineteenth century to the present, as
they had been developed mainly based on cases from modern physics and
chemistry and preceding traditions in natural philosophy. Were the
major transitions in hereditary thought to be described as scientific
revolutions (see entries on
 scientific revolutions
 and
 the incommensurability of scientific theories)?
 It seems that models of change emphasizing discontinuity and
incommensurability among successive paradigms, such as Thomas
Kuhn's (1962), do not fit well with what can be observed in the
history of genetics: Much terminology and many practices seem to
remain intact despite constant theoretical novelty, and the
developments do not appear to be perceived as discontinuous in a
strong sense by the protagonists. Continuous models of change,
developed earlier by logical empiricists and centered on the notion of
reduction as a relation between earlier and later theories, were thus
discussed as possible alternatives with respect to the history of
genetics.



"Reductionism" in genetics can, on the one hand, refer to
philosophical positions regarding theory reduction or reductive
explanation. On the other hand, attitudes in biology and philosophy
that are characterized by a preference for molecular over organismic
accounts of biological phenomena or an emphasis on genes in
explanations have been labeled "reductionist" (see entry
on
 reductionism in biology).
 The latter, broader meaning overlaps with notions of "genetic
determinism" and, more generally, "gene-centrism".
This section focuses on the former, technical meanings of
"reduction". The debate on reduction got contemporary
philosophy of biology started around 1970 and is still on-going today
(Vidal & Teira 2020; Winther 2009). Theory reduction is most
prominently articulated by Ernest Nagel (1961). Put very simply, on
Nagel's account, one theory reduces to another if the former can
be logically derived from the latter, or, in terms of a
nomological-deductive model of explanation, if the reducing theory
explains the reduced theory. Since, on this view, the relation between
theories is one between sets of statements, including, most
importantly, laws or law-like generalizations, successful reduction
also requires "bridge principles" or coordinating
definitions, which indicate how the vocabularies (terms or predicates)
of the two theories relate (see entry on
 scientific reduction).



Kenneth Schaffner (1967, 1969) further develops Nagel's account
by pointing out that the candidate reduced theory typically needs to
be corrected before it can be reduced. He then applies his model to
the case of genetics. On Schaffner's view, molecular genetics
reduced or is in the process of reducing classical genetics (see
 SS1.2
 and
 SS1.3
 for an account of classical and molecular genetics). On his account,
the genes of classical genetics can be identified with DNA sequences.
Furthermore, concepts that capture law-like generalizations about
phenomena in classical genetics (e.g., dominance) can be explained
through generalizations on the molecular level. Schaffner's
account is met with criticism by David Hull (1972, 1974). Hull's
most influential objection rests on a multiple realizability argument.
He argues that the types of phenomena identified in classical genetics
(such as dominance) can be instantiated by a variety of different
molecular constellations. Furthermore, Hull points out that any
molecular entity or mechanism can be involved in various types of
situations as described in classical genetics. Accordingly, Hull
diagnoses many-many relations between molecular phenomena and
phenomena identified through cytological and phenotypic analysis.



Alexander Rosenberg (1978; 1985: Ch. 4) argues that Mendelian
properties supervene on molecular properties, i.e., that for any
difference in Mendelian properties there is a difference in molecular
properties. Thus, even if theory reduction is not available, the facts
of Mendelian genetics can be ontologically reduced to facts of
molecular genetics. Others describe this situation by observing that
while token-token reduction is possible, type-type reduction is not to
be had (Kimbrough 1979). Closer to a Kuhnian notion of
incommensurability is Michael Ruse's (1971) reconstruction,
according to which the Mendelian gene and the molecular gene are
incompatible concepts. One reason is that the former was treated as a
unit of function, recombination, and mutation, while the latter is
not. Furthermore, molecular genetics explains everything that is
explained by Mendelian genetics and more; it has more explanatory
power and is more accurate. Hence, according to Ruse, molecular
genetics does not reduce, but replaces Mendelian genetics. Others
defend the thesis that Mendelian genetics in its original version is
reduced by molecular genetics (e.g., Goosens 1978).



Another, influential set of challenges to theory reduction in genetics
is posed by Philip Kitcher (1984). The main problem, and indeed one
that is fundamental to any account of theory reduction that identifies
theories with sets of laws, is that there are no laws in classical
genetics. Even seemingly straightforward examples such as what came to
be called "Mendel's laws", as Kitcher shows, are
neither laws, nor do they play an important explanatory role in
classical genetics. Kitcher further argues that the basic predicates
of classical genetics, such as "*x* is a gene"
cannot be unequivocally connected to the vocabulary of molecular
genetics through bridge principles, as it would be required for
successful theory reduction. Finally, even if these two issues were
solved, an account based on the principles of molecular genetics would
not explain the phenomena of classical genetics any better than the
cytological explanations already in place. Others argue against this
disunified picture of Mendelian and molecular genetics that the two
fields depend on each other in their practices. This interdependence,
however, also precludes an eliminative reduction (i.e., replacement)
(Vance 1996).



Several authors suggest that the debates on in-principle reducibility
are far removed from explanatory practice in molecular genetics.
Wimsatt (1974) highlights theories of inter-level relations and how
they facilitate mechanistic explanations (see the entry on 
 mechanisms in science). 
 Pointing towards a sematic view of theory, which holds that
theories are families of related models, Waters (1990, 1994) maintains
that molecular genetics provides explanations for phenomena described
by Mendelian theory. The basis for this is that both fields rely on
the principle that only phenotypic differences in a population, rather
than the presence of traits is explained by genes (or rather by
genetic differences). While these authors still speak of theoretical
reduction, theory has changed its status. Rather than one theory
containing laws being reduced by another theory through logical
deduction, theory is conceived in terms of explanatory models which
mediate the conceptual and practical relations between Mendelian and
molecular genetics.



Subsequently, the emphasis of philosophical debates shifts more
towards explanatory reduction (Huttemann & Love 2011; Kaiser
2015; Rosenberg 2006; Sarkar 1998). The question becomes less one of
the relations between Mendelian genetics and molecular genetics, but
rather whether organismic phenomena from heredity to development to
evolution can or should be explained in molecular terms (see
 SS1.4).



This section was concerned with the relation of the theories in which
gene concepts are embedded from the perspective of scientific change.
The next section will address scientific change on the level of the
gene concept itself, where the focus is on the question to what extent
such concepts remain constant regarding reference and meaning when
theories and practices change.


### 2.2 Conceptual change and the gene concept



About the time when philosophers of science turned to biology, a new
theory of meaning was widely discussed--the causal theory of
reference (Kripke 1972; Putnam 1975; see entries on
 reference
 and
 natural kinds).
 Proponents of this view turned against earlier theories of reference,
which they took to hold that the reference of a token (an instance of
a term's use) is fixed by a description of the referent the
speaker has in mind and that represents the term's meaning.
Instead, according to the new theory, a natural kind term, and
especially a scientific term, is connected to a kind of entity when it
is used for the first time to refer to an instance as belonging to a
certain natural kind by an ostensive gesture or an equivalent.
Speakers might then use a scientific term to refer to a natural kind,
even if they are not able to identify a member of the kind in question
or have false beliefs about this kind of entity. They rely on the fact
that there are experts in their broader linguistic community who can
identify members of the kind in question in the way it was initially
introduced, and who stand in a suitable causal relation with the event
of the original naming of the kind through a series of communicative
links. The initial identification of a kind might have been based on
recognizing some salient shared properties ("nominal
essence" in Locke's terms;
 Locke on real essences).
 However, if the introduction of the term has indeed successfully
identified a natural kind, then, eventually, the "real
essence" of the kind will be identified, presumably in form of
the physical microstructure, which explains the initially recognized
properties. The latter still play a role in characterizing a
stereotype for non-expert speakers, but based on the underlying causal
properties experts can determine kind membership unequivocally in
every case (Putnam 1975).



Based on such a view, the dependence of the reference of theoretical
terms in science on a description or on its relation to a currently
accepted theory can be avoided. This is what made causal theories of
reference attractive to philosophers of biology, who saw continuity in
the use of the term "gene" despite significant theoretical
shifts in genetics during the twentieth century. This view suggests
the following narrative regarding the events presented in Part 1:
Mendel had identified a natural kind when he identified gametic
elements involved in the inheritance of characters. Early Mendelians
used a variety of terms but referred to the same entity when
performing hybridization experiments. Later the units were named
"genes" but the communicative chain connecting earlier and
later uses of the terms referring to entities belonging to the natural
kind remained intact. And even if the meaning of the concept changed,
i.e., various properties shared by the members of the kind were
suggested or dropped from the list of necessary and sufficient
criteria, eventually, a molecular characterization of genes was
achieved, which explained the most stable observed properties (or
their variation under varying conditions) and was since available for
expert geneticists to determine whether something was a gene or not.
Much of the debate sketched in the following can be described as
discussing to what extent this narrative is adequate.



Kitcher takes causal theories of reference as his starting point to
discuss conceptual change in the case of the gene concept (1982). He
introduces the notion of reference potential of a term type, which on
his account comprises several ways in which the reference of a token
is fixed. On the one hand, there are several modes of reference and
they are correlated with the intention of the speakers. Sometimes a
speaker might value clarity and hence provide a description that fixes
the reference of a term in the sense of descriptivist theories of
reference. Indeed, researchers or teachers often provide definitions
of the term "gene". The description might turn out to be
wrong, however, and hence the term might fail to refer, but at least
the speaker made it transparent in which sense the term is used. In
other situations, a speaker might want to conform to the established
use of a term in a community. In this case the reference is fixed in
the way suggested by causal theories of reference; in using the term
the speaker relies on the existence of experts in the broader language
community, who know how the term is applied correctly (i.e., how a
member of the natural kind is identified). These experts are causally
connected to the initial event of the term's introduction. This
is the way most people use the term "gene". Finally,
speakers might refer to an entity in a situation where they are in
direct causal interaction with it. This might be the case when
researchers refer to genes in research articles reporting experiments
involving genes.


 
On the other hand, and this is what expands the reference potential of
a concept, there are various descriptions available, which speakers
might use to fix the reference of the term
"gene". Furthermore, there are several causal trajectories
by which various groups of experts are connected to situations where
the term was introduced by something akin to ostension. Finally, there
are always new situations in which researchers refer by ostension in
direct interaction with genes, possibly based on new kinds of
experiments. Conceptual change for Kitcher is thus constituted by
changes in the reference potential of a concept, in this case, in the
ways tokens of the term "gene" refer to genes (if they
refer at all).



When applying theories of reference, philosophers typically commit to
realism of some form. This means that they assume that there are
natural kinds and that a concept, when it refers successfully, picks
out some natural kind. When dealing with complex matters such as the
phenomena of heredity, there are certainly several natural kinds to be
identified. Hence, according to Kitcher, not only the reference
potential of a concept changes, but also the reference of the concept
itself. Earlier as well as later uses of the term "gene"
might have referred successfully, but the extensions of the term in
earlier and later instances might nonetheless have been different.
Mendelians might have picked out the natural kind of, say, chromosomal
elements that are potential difference makers with respect to
heritable phenotypic variation when using the term. This kind
comprises protein-coding DNA sequences and some non-coding regions.
Molecular geneticists might have picked out another natural kind, say,
template for functional molecules, which did not include some of the
elements referred to as genes by Mendelians, but protein-coding DNA
sequences as well as sequences coding for functional RNA. While this
opens the door to a form of pluralism regarding genes as natural
kinds, Kitcher connects his account to a notion of progress. He
maintains that the reference potential of the gene concept improved.
Descriptions that failed to fix reference were rejected and causal
trajectories going back to the ostensive introduction of a term that
turned out to have failed to pick out a natural kind or picked a
natural kind no longer held to be significant are cut. In
Kitcher's view molecular genetics refined the concept of the
gene. The notions of failure of reference and improvement of the
reference potential are of course dependent on the status of molecular
biological knowledge at a given time, which provides the baseline for
the evaluation of concepts (Weber 2005: Ch. 7; for developments since
Kitcher's writing, see
 SS1.5).



Richard Burian (1985), like Kitcher, is concerned with the facts that
theoretical terms can pick out natural kinds even when a theory turns
out to be mistaken and that researchers who disagree in their theories
can use a concept that refers to the same natural kind. Burian
illustrates these points with the case of Bateson, who held
theoretical views that are now seen as false (e.g., regarding the
presence/absence hypothesis, see
 SS1.1),
 but who is still taken to have referred successfully to genes on most
occasions where he used the term or synonyms. Furthermore, Bateson was
able to discuss the chromosome theory held by the Morgan group (see
 SS1.2),
 despite rejecting it. This only makes sense if it is assumed that
despite disagreement, both parties used the term "gene" to
refer to the same natural kind. Burian aims at a hybrid account
combining extensionalist views based on causal theories of reference
and intensionalist views relying on the notion of theoretical
descriptions. Theoretical differences among accounts put forward by
various groups simultaneously or across time can thus be bridged by a
gene concept exhibiting "referential openness" achieved by
indefinite, rather schematic descriptions that are not committed to
the material nature of genes but nonetheless characterize them through
their causal effects and in that sense operationalize the concept.
While such concepts facilitate continuity in scientific change, any
given research project will operate with a specification of the
description that provides criteria to individuate genes and that
relies on a mix of functional and structural characterizations. How
genes are identified depends among other things on how and on what
level the phenotype is determined (e.g., as qualitative or
quantitative, molecular or morphological). Such specific gene concepts
then account for the discontinuities observed in the history of
genetics (Burian 1985; [1995] 2005). In the light of the complex
cellular processes in which DNA is involved, both Kitcher and Burian
suggest that molecular biologists ultimately study the genetic
material rather than genes, but importantly, they are still interested
in functional units; a gene then becomes "anything a competent
biologist chooses to call a gene" (Kitcher 1992: 131). Genomics
or post-genomics can be understood as enhancing this shift (see
 SS1.5;
 Dupre 2004; Stotz et al. 2006; entry on
 genomics and postgenomics).



Marcel Weber (2005: Ch. 7) begins his discussion of reference and
conceptual change in genetics by drawing on Kitcher's account of
changing modes of reference and reference potentials, following Burian
in emphasizing the important role of meaning in terms of descriptions
or theoretical beliefs. Weber then presents a more fine-grained series
of conceptual changes, driven by the introduction of new investigative
techniques or new experimental organisms (esp. bacteria and phage),
and observes that the reference potential (including theoretical
beliefs) as well as the extension of the term "gene"
changed continuously. Weber describes a situation where a broad
extension based on the causal effects observed in Mendelian crossing
experiments is narrowed down when additional criteria are introduced
in classical, chromosome-based genetics, broadened again to include
bacteria and viruses, and narrowed down again to sequences of DNA that
determine the sequence of proteins (see
 SSSS1.1-1.3).
 Furthermore, in different contexts researchers could interpret the
molecular characterization differently, for instance, including or
excluding regulatory sequences.



Because of this diachronic and synchronic variation in gene concepts,
Weber speaks of "floating reference", highlighting
permanent change in the reference potential and shifts in reference.
This fact, according to Weber, is explained by metaphysical
considerations regarding the nature of biological objects. Evolution
produces variation; this is true also for genetic material. As a
result, genetic material exhibits kinds in the sense of classes of
objects that share some causal disposition, but it can nonetheless be
divided in various ways. Hence different historical and contemporary
gene concepts identify different kinds depending on the methods and
interests of researchers. Apart from the different ways to identify
causally relevant classes of objects, any such class contains objects
none of which is exactly like the other. The gene concept is thus
comparable to the species concept (Weber 2014; see entry on
 species).



Furthermore, Weber moves from general characterizations of concepts to
an empirical study of reference to particular genes in
*Drosophila* in the context of investigative practices in
genetics, such as the molecular cloning of genes in the context of
developmental biology (see
 SS1.4).
 Even though reference and description of classical and various
versions of molecular gene concepts differ, it turns out that the
classical concept is utilized in identifying genes (e.g., those
involved in the organization of the fly embryo), which are then made
subject to molecular characterization (Weber 2005: Ch 7; see also
Waters 1994). Thus, despite a lack of complete co-extension of the
classical and the molecular gene concepts, partial referential
continuity plays a significant role in mediating investigative
practices.



The importance of investigative practices highlighted by Weber is also
emphasized by Ingo Brigandt (2010). He suggests that the content of
theoretical concepts consists of three elements: a concept's
reference; its inferential role, which he construes similarly to
Kitcher's reference potential; and its epistemic goal, which he
specifies as the theoretical, explanatory, and investigative aims that
are facilitated using a given concept. Brigandt argues that change of
or variation in the inferential role of a concept is rational when the
inferences or explanations supported by the revised concept support a
given epistemic goal better than an earlier or an alternative version.
The epistemic goals associated with a concept can change as well,
typically, according to Brigandt, in a gradual manner. From this
perspective, Brigandt reconstructs a continuous shift in the goals
pursued by researchers using the gene concept, from classical
genetics, which pursued the epistemic goal of predicting patterns of
inheritance to molecular genetics' focus on the goal of
explaining how genes bring about their molecular products, through
various intermediate goals, such as understanding the influence of
genes on cell metabolism (see
 SSSS1.2-1.3).
 Furthermore, the account addresses the variety of gene concepts
emerging in the last 30 years (see
 SS1.5).
 While the epistemic goal connected to the gene concept in
contemporary molecular genetics remains similar to that associated
with the classical molecular gene, i.e., to elucidate how DNA
contributes to functional RNA and protein, reference and inferential
role are specific to various research contexts. More recent
discussions of conceptual change in biology have not focused on genes,
but on related concepts such as dominance (Shan 2020) or lineage (Neto
2020).



The next section focuses on the simultaneous use of various gene
concepts in contemporary biology rather than the succession of gene
concepts.


### 2.3 The plurality of gene concepts in contemporary biology


#### 2.3.1 The instrumental and the molecular gene



The gene concept that structured the work of early Mendelism and
chromosomal genetics is referred to as "instrumental gene"
(Falk 1986; Griffiths & Stotz 2006). Geneticists routinely
identified genes based on phenotypic differences in hybridization
experiments or the analysis of pedigrees (see
 SS1.2).
 Differences between, first germ cells, and, later, more specifically,
between chromosomes, had to be assumed to explain patterns of
phenotypic correlation between sexually reproducing organisms and
their offspring. These units of difference in the genetic material
could also, and more importantly, be used to predict phenotypes. For
these purposes, it was not necessary to know what exactly their
physical location or material composition was. In this sense, the
concept was instrumental. In a similar way, Lenny Moss (2003: Ch. 1)
characterizes the gene-P as a gene defined by its phenotypic effect
and used for prediction (the "P" can thus stand for
"phenotype" or "prediction", but Moss also
points out that the concept is associated with instrumental
preformationism).



Once the tools of molecular genetics were in place, for each case the
genetic difference correlated with the phenotypic difference could be
located in the DNA and hence the genes of classical genetics could be
molecularized (Waters 1994). The instrumental gene (as a unit that
correlates with a phenotypic difference, segregates in a Mendelian
manner, and is subject to recombination events) can remain
indeterminate regarding DNA-sequence and need not correspond to a gene
that has an identifiable product. In many cases one of the genetic
variants consists in the absence or lack of a function of a gene
product and there are many ways in which a change in DNA can result in
the lack of a resource (Moss 2003: Ch. 1). The instrumental gene can
correspond to elements of various size, including whole chromosome
aberrations, and they might be located in coding regions as much as in
regulatory elements or even insulator regions that only function to
separate other functional elements, as long as a difference in 
the sequence is correlated with a phenotypic effect (Griffiths &
Stotz 2006).



The concept of the gene analyzed in terms of instrumental genes, or
genes-P, is still widely used in many contexts such as evolutionary
biology, agricultural breeding, or medicine (even though it might play
out differently in the identification of genetic traits and in
evolutionary theory, respectively; see Gifford 2000; S. Gilbert 2000).
The instrumental gene thus exists along-side other gene concepts which
emphasize the material basis and immediate biochemical roles of
genes.



Molecular genetics gave rise to what has been called the
"classical molecular gene" concept (Neumann-Held 1999, see
 SSSS1.3-1.4).
 The classical molecular gene was characterized both structurally and
functionally in the following way: A gene exhibits a certain structure
known as an "open reading frame" (ORF), that is, a
sequence of codons between and including a start and a stop codon,
which initiate and terminate translation respectively (i.e., they
exhibit their function in the transcribed RNA, but can be identified
in the corresponding DNA). Also, transcription and translation
initiation and determination signals, such as transcription factor
binding sites and other regulatory elements typically associated with
protein-coding genes were often seen as part of the molecular gene
(forming a "transcription unit"). The function of such a
molecularly described gene was to give rise (via mRNA) to a
polypeptide chain as the basis of a functional protein through the
processes of transcription and translation. The gene fulfilled this
function by acting as a template. Complications such as splicing or
overlapping genes were initially not seen as compromising the
structural-functional unity of the material gene. Non-coding,
functional RNA could also be assimilated to the concept, if it was
possible to identify a stretch of DNA based on linear correspondence
between the product and its gene (Griffiths & Stotz 2006).



In the molecular realm, yet another gene concept, gene-D, can be
identified, which is characterized in contrast to the gene-P and
captures a situation in which researchers identify genes as
developmental resources (Moss 2003: Ch. 1). Genes-D are typically
classical molecular genes, but here the emphasis is on function rather
than structure and especially on function beyond the initial role as
template. As pointed out by Weber (2005: Ch. 7), researchers'
attention is often initially guided towards a part of DNA sequence
conceptualized as gene-P, that is, as associated with phenotypic
variation. Once the relevant gene is cloned and the regulatory
networks in which it is involved as well as the activities of its
product are investigated, it frequently becomes clear that it is
expressed in many tissues, in different contexts and at different
times (see
 SS1.4).
 Furthermore, the locus in question often functions as template for a
large variety of products. Hence, while the gene-P is indeterminate
with respect to sequence, the gene-D is indeterminate with respect to
phenotype. Addressing a gene as gene-D means to investigate its
various roles in the process of epigenesis. The fact that the absence
of one or several of these products leads to phenotypic change does
not imply that the resource is more important in the development of
the structure exhibiting the phenotype than the large number of other
genes involved and their respective products. Instead, the phenotype
shows how the developmental process responds to the absence of a
resource. The fallacious notion of genes for a certain trait (e.g.,
blue eyes) containing developmental information (e.g., for making blue
eyes) results when biologists (or commentators) conflate the separate
notions that genes-D contain template information and that genes-P
contain predictive information (Moss 2003: Ch. 1 and 2). While
"gene for" talk is misleading in the context of
development (Kampourakis 2017), the notion has been defended in the
context of evolution (Kaplan & Pigliucci 2001).



The classical molecular gene concept was closely related to the
notions of genetic information and the genetic code (see
 SS1.3
 and entry on
 biological information).
 While some philosophers have described these terms as potentially
misleading metaphors (Sarkar 1996), many see these concepts either as
used in a literal sense and hence justified (Godfrey-Smith 2000), or
as metaphorical, but productive (Levy 2011). The details of an
adequate explication are much debated (e.g., Stegmann 2005), but on
the level of molecular phenotypes (mainly proteins) the information
concept is seen as relatively uncontroversial. More debated is the
question if information, or the notion of causal specificity that it
implies, is a unique property of DNA or if it applies to other
cellular and extra-cellular components as well (Baxter 2019; Bourrat
2020; Griffiths & Stotz 2013: Ch. 4-6; Griffiths et al.
2015; Waters 2007; Weber 2017; Woodward 2010). On the level of whole
organism phenotypes, genetic information has been explicated in terms
of teleosemantic theories borrowed from philosophy of mind and
emphasizing the selected function of genes (Maynard Smith 2000;
Sterelny et al. 1996). The parity thesis, stating that non-genetic
factors can carry information in the same sense has been suggested on
this level as well (Griffiths 2001). Other philosophers have discussed
the question of whether selected function would not be better located
on the level of the developing organism as the receiver of information
(Jablonka 2002) or if a notion of genetic representation can be
reformulated in terms of transmission in an intergenerational
information producer and consumer system (Shea 2013; cf. Koiv
2020; Planer 2016).



From a broader perspective, it has been argued that information talk
in genetics results in the persistence of genetic determinism (Oyama
[1985] 2000). The latter notion expresses the idea that an organism
will exhibit a trait if it carries certain alleles, where the role of
the environment is reduced to permitting this potential to unfold (see
entries on
 heritability
 and
 the distinction between innate and acquired characteristics).
 The question is if the influence of genes and environment can be
separated, especially when considering the often non-additive
character of genotype-environment interactions (Gray 1992; Griffiths
2006; Kitcher 2001). These issues are most controversial and have
received most attention regarding the question to what extent human
behaviors or cognitive capabilities can be described as genetically
determined (Esposito 2017; Keller 2010; Longino 2013; Schaffner 2016;
Tabery 2014; Turkheimer 2019). Interestingly, the new science of
molecular epigenetics is often framed in a deterministic language as
well (see
 SS1.5;
 Meloni 2016; Richardson 2017; Waggoner & Uller 2015).


#### 2.3.2 The molecular and the post-genomic gene



Molecular biology is not interested merely in the physical
characterization of molecules; it aims to assign biological roles to
molecules, that is, functions in highly specialized, directively
organized systems (Waters 2000). However, it becomes increasingly
questionable if molecules identified as developmental resources or
functional parts of cellular mechanisms can be identified in a
coherent manner as genes or gene products. The classical molecular
gene concept has been undermined by the accumulation of insights about
the complexities of regulation and post-transcriptional processing of
RNA (see
 SSSS1.4-1.5;
 Fogle 2000; Portin 2002). A more flexible gene concept has since
emerged, which analysts have dubbed the "post-genomic
gene" (Griffiths & Stotz 2006). In an influential article,
researchers associated with the ENCODE project suggested the following
definition:



> 
> 
> The gene is a union of genomic sequences encoding a coherent set of
> potentially overlapping functional products. (Gerstein et al. 2007:
> 677)
> 
> 
> 



In this view, several molecular products are the starting point from
which elements in the genome are identified giving rise to this set of
products (regulatory regions not included).



The post-genomic gene thus not only adds to the plurality of gene
concepts, but it is also inherently pluralistic. Many new cellular
processes have been discovered and found to be ubiquitous, such as
frameshifting, antisense DNA transcription, alternative and
trans-splicing, RNA editing, as well as an abundance of regulatory
elements in DNA, and of DNA regions transcribed to non-coding, but
functional RNA. This has created a situation in which no single or
simple set of criteria can be formulated for when a sequence of DNA
counts as a gene. While the classical molecular gene seemed to
reestablish a one-one relation of genes and phenotypes on the
molecular level (one gene - one polypeptide), the processes just
mentioned can result in a situation where one gene identified through
an ORF gives rise to various gene products (molecular phenotypes). One
can thus speak of "molecular pleiotropy" (Burian 2004).
Additionally, a given product might be synthesized from various genes
(ORFs). Accordingly, a given stretch of DNA can belong to several
genes identified more broadly as set of template resources for a
product. Furthermore, the nature of these processes implies that the
molecular phenotype is not determined by the DNA sequence but depends
on a distributed and context-dependent interaction of many cellular
and, ultimately, extracellular factors. Hence one can also speak of
"molecular epigenesis" in this respect (Burian 2004).



Again, however, it seems that just as the molecular gene concept has
not replaced the instrumental gene concept, the new, post-genomic
concept has not replaced the molecular gene concept. Indeed, empirical
research shows that groups that identify with different subfields of
biology prefer different gene concepts (Stotz et al. 2004). Referring
to genes as more or less straightforward representations of gene
products in DNA sequence plays an important role in many contexts, and
for coordinating research and integrating results from various fields.
Gene annotation, for instance, which is necessary to make genome
sequences in databases accessible in a useful way, depends on
identifying genes in a canonical manner (Baetu 2012a; see
 SS1.5).
 The persisting classical molecular gene concept can be referred to as
the "consensus" or "nominal gene" (Burian
2004; Fogle 2000; Griffiths & Stotz 2006). The post-genomic gene
concept, instead, has been proposed to capture situations where
researchers focus on the complexities of regulation, transcription,
and translation, and conceptualize genes as template resources used in
various ways in cellular processes (Griffiths & Stotz 2006). Even
in cases of complex transcription, however, the identification of
genes tends to be guided by the consensus gene concept. As opposed to
the instrumental and the nominal molecular gene, the post-genomic gene
does not entail a prescription as to how to identify a gene. In some
sense, the focus shifts more to function (the product), but at the
same time this new concept de-emphasizes the gene as a unit and
facilitates the study of the whole genome as a set of complexly
structured DNA molecules (Barnes & Dupre 2008; Falk
2010).



Because of its focus on structure and the resulting usefulness for
annotation practices in bioinformatics, the nominal gene remains the
unit of analysis in comparative genomics (see
 SS1.5).
 In these contexts, claims about similarity in terms of nominal
molecular genes are often translated into claims of similarity more
broadly construed, based on the assumption that homologous genes yield
homologous products and hence are involved in homologous functions.
Such claims are, however, often not warranted given the complexity of
gene expression (Piotrowska 2009). On the other hand, much of genomic
research seems not to be committed to any specific gene concept.
Statistical techniques of bioinformatic sequence comparison function
as discovery tools that detect relations between genome sequences,
transcripts, and proteins or between sequences on any level among
various species (Perini 2011). They can suggest candidate genes,
indicate events of post-transcriptional processing, or point to
processes of genome evolution (see
 SSSS1.4-1.5).
 Researchers in genomics (involving sequence annotation tasks), seem
to respond to the complexities of regulation and post-transcriptional
processing by operating with an extended structural characterization
("syntax-based", in the parlance of bioinformatics-driven
research) of genes and other genome elements, rather than emphasizing
the *ad hoc* identification of genes from the perspective of
products captured by the post-genomic gene concept (Baetu 2011,
2012a). A sequence thus characterized can still give rise to a variety
of products, but their processing depends on splicing signals and
similar sequence features that can be identified on a structural
level. In this view, genes appear "as modular sets of
instructions for the genome expression machinery of the cell"
(Baetu 2011: 718).



In terms of development, the genome has been described not only as a
resource, but also as reactive to the cellular context rather than as
directing cellular processes (S. Gilbert 2003; Griffiths & Stotz
2013: Ch. 4; Keller 2014). The genome is always embedded in a cellular
environment (also virus genomes become reactive in the context of
their host's cells), and cellular processes mediate between the
organismal or extra-organismal environment and the genome. The
post-genomic gene concept is thus open to integrate molecular
epigenetic processes that turn environmental cues into regulatory
signals. Molecular epigenetics has also been discussed as a pathway of
inheritance, alternative to DNA transmission and more responsive to
environmental changes (Jablonka & Raz 2009; entry on
 inheritance systems).
 Emerging knowledge of these processes re-shapes explanations in
heredity, development, and evolution and hence shifts the explanatory
status of gene concepts (Baedke 2018; Griesemer 2011; Griffiths &
Stotz 2013, Ch. 5; Le Goff et al. 2021; Stotz & Griffiths 2016).
Furthermore, next to the complexity of the regulation and genesis of
molecular products, also the interaction of products as studied in
systems biology displays a complexity that makes it difficult to
ascribe functional roles to genes (see entry on
 philosophy of systems and synthetic biology;
 see
 SS1.5).
 If genes are deleted from the genome experimentally ("gene
knock-out"), this often does not have the expected effect on
developmental processes, because the encoded molecules are part of
large interaction networks that can exhibit a high degree of
robustness and redundancy (Mitchell 2009: Ch. 4; Morange 2001: Ch. 5).
The stochasticity of gene expression and molecular interactions
emerges as another aspect complicating the role of genes and gene
products in cellular processes (Casali & Merlin 2020; Kupiec 2014;
Morange 2011; Nicholson 2019).



In the light of these developments, one might say that the
post-genomic gene was disassociated from the notion of a
"genetic program", which was criticized as embodying a
preformationist view of development (Keller 2000; Moss 1992; Robert
2004; entry on 
 theories of biological development). 
 Some have argued,
however, that the concept is still important for reasoning about
regulatory mechanisms, highlighting roles and organizational features
of genomic elements without excluding others (Baetu 2012b; Calcott
2020). Nonetheless, it appears that post-genomic explanations are
rather articulated in terms of signaling, regulatory, or interaction
networks than programs (Calcott 2014; Huneman 2019; Planer 2014). Even
though genes do not constitute a blueprint of the organism (Pigliucci
2010), DNA and its functional elements provide a form of stability
necessary for epigenetic processes to yield robust outcomes (De
Tiege et al. 2015; Meunier & Reynaud 2017; Vecchi
2020).



Suggestions have been made to use the term "gene" to refer
to the whole process that yields the functional product (the
"process molecular gene" concept, Neumann-Held 1999). But
apart from the fact that it is difficult to delineate the boundaries
of such a process, this seems to be too distant from the ways
researchers use the term. Biologists and philosophers have suggested
alternative terminologies for DNA sequences that are meant to replace
or complement the problematic term gene, for instance, regarding
genome evolution (Brosius & Gould 1992), regulation (Scherrer
& Jost 2007), and from an integrative systems perspective (Keller
& Harel 2007). While some of these interventions seem to suggest
that the gene concept has become redundant, biologists have emphasized
its explanatory value when seen in the right context, in particular,
as a cellular component (Hall 2001). It might be the case that this
component of cells has received undue attention to the expense of
others, but it must also be noted that genes (or DNA) are often in
focus because they can be most easily intervened on, while these
interventions can then also be informative about other components of
cellular processes (Gannett 1999; Waters 2008). Similarly, in the
practical contexts of synthetic biology, genes can often successfully
be constructed, conceptually and materially, as causal agents (Oftedal
& Parkkinen 2013). More generally, it has been suggested that the
gene concept is useful exactly because of its overall vagueness,
because it can be adjusted to specific epistemic needs within newly
emerging fields and at the same time facilitate connections between
disparate areas of research (Rheinberger & Muller-Wille
2018).


## 3. Conclusion



It became clear that discussions in philosophy of biology are driven
by developments in biology. At the same time, it appears that there is
no end to scientific innovation in biology. New technologies open new
windows into biological domains, make new phenomena accessible, or
shed a different light on known entities and processes. These
developments and the ensuing theoretical shifts and conceptual
transformations will require a type of conceptual reflection and
clarification for which philosophy of science has developed an
indispensable set of tools (Pradeu et al. forthcoming).