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CHAPTER 1
The Gene
A Concept in Flux
In this book we review a long century of research in biology. Our aim is to present an in-depth analysis of the history of the gene concept, which, in different instantiations, became central to all main branches of the life sciences and promoted unprecedented visions of controlling and directing life. But if the turn from the nineteenth to the twentieth century saw the coming into being of a powerful concept, it experienced an existential crisis a century later. Tracing this history will help us to better understand the changing role of the gene concept in the current age of epigenetics and data-intensive systems biology, often referred to as "postgenomics."
With this aim in mind, let us first set out what we mean by postgenomics. A genome is taken to be the totality of the hereditary material that is stored in the nuclei, as well as some other organelles like mitochondria, of living cells, usually in the form of deoxyribonucleic acid (DNA). Accordingly, genomics refers to the research field that elucidates the molecular composition and structure of whole genomes, in particular the sequence of the nucleotide base-pairs that make up the chains of DNA. The focus of genomics thus includes genes, but is not restricted to them. Technologies developed in the 1980s made it possible to characterize entire genomes at the molecular level for the first time, and since then the capacity for nucleic acid sequencing and processing the resulting sequence data has continued to grow exponentially. In the first instance, the expression postgenomics simply refers to the period that began when whole genome sequencing had become feasible and the contextualization of sequence data moved center stage.
So far, so good. The completion of large-scale genomics projects like the Human Genome Project at the beginning of the new millennium coincided with the fiftieth anniversary of the elucidation of the double-helical structure of DNA (in 1953), which in turn followed roughly half a century after the identification of the gene as the fundamental unit of inheritance. Genomics, and the ensuing era of postgenomics, may therefore seem to be a logical consequence and mere extension of these epochal discoveries. But instead of experiencing closure, researchers at the dawn of the postgenomic era faced an altogether new set of questions, concerning not only the composition and structure of the genome, but its expression and integration into cell metabolism and other nongenetic processes. What was the exact relationship between genes and their products? What kind of factors spurred genes into action, and how was gene activation achieved at exactly the right time and place in an organism? And were the conditions of gene activation not transmitted as well, thus opening the door to the existence of nonclassical inheritance systems and deposing the gene from its privileged position as the sole bearer of hereditary information? Genetics — the science of heredity begotten by the twentieth century — is currently being buffeted by rapid and profound changes in biological thought. Even long-ignored tropes such as the inheritance of acquired characteristics appear to be experiencing a renaissance (Meloni and Testa 2014). What underlying reasons brought about this cataclysmic rethink?
According to Evelyn Fox Keller, the answer is that the "very successes [of genomics] that have so stirred our imagination have also radically undermined their core driving concept, the concept of the gene" (Keller 2000a, 5). Indeed, the centrality of the gene as the fundamental unit of biological thinking is being questioned by parts of the scientific community. Statements like the following reflect the urgency of the situation as felt even in 2007: "'Gene' has become a vague and ill-defined concept. ... What is a 'gene'? Surprisingly, in the world of biology and genetics there is no longer a straightforward answer" (Scherrer and Jost 2007, 1). In view of this situation, some commentators have argued that we should abandon the gene concept and speak about genetic material and its expression instead (Kitcher as early as 1982; Burian 2005) or adopt more systems-oriented ways of talking about genes (Keller 2005), while still others have proposed that we need to accept the existence of a plurality of gene concepts (Moss 2003; Falk 2009; for a review of responses see El-Hani 2007). At the same time, ideas that were thought to be nongenetic and supposedly vanquished a long time ago — for example, that racial affiliation is of biomedical significance, or that maternal lifestyle may affect the hereditary constitution of the embryo — have once more become focal points of biomedical research. Talk about postgenomics, which so obviously echoes the notion of "postmodernity," also highlights the bewildering spectrum of coexisting and seemingly contradictory and anachronistic positions that have been bred by breathtaking advances in sequencing, expression profiling, and biocomputing in the last decades (Richardson and Stevens 2015).
Given this confusing backdrop, a survey from the vantage point of the history of science is called for. What was the gene like to researchers at various points in the history of the discipline? we ask, and we do so not to satisfy antiquarian interests, but to provide a new understanding of this intriguing concept, an understanding that may also enable us to delineate the current horizon of the life sciences. Even the most ardent recent critics of the gene concept accept that, both as a concept and as an object of experimental and of theoretical research, the gene has been an important organizing principle in twentieth-century biology (Keller 2000a; Moss 2003; Griffiths and Stotz 2013). Nor has talk about genes vanished from scientific and vernacular discourses. On the contrary, despite apparent confusion about its meaning, talk about genes continues to be omnipresent, both within and outside the biosciences. Despite the ongoing conceptual revolution in the postgenomic biosciences, the gene is as alive and well as it was a century ago.
One might surmise that this lasting significance of the gene concept can be explained by the fact that, in the last analysis, it has always had a specific and simple meaning. But as our survey of the century of genetics and molecular biology will show, a simple and universally accepted definition of the gene never existed. The current situation, we will argue, is therefore nothing new. On the contrary, the gene concept always was "in flux" — as one can expect from any seminal term in the history of science (Elkana 1970; Falk 1986; Morange 2001; Weber 2005, 194–203). Right from the start, as our historical analysis will reveal, the concept of the gene took on different meanings with respect to different domains of biological reality — transmission, development, physiological function, evolution, to name just a few. And by doing so, it opened up a range of new ways to conceptualize the relationships between these domains. Speaking metaphorically, one might say that each new meaning of the gene created an additional dimension along which life could be imagined to vary and unfold.
The Danish botanist Wilhelm Johannsen recognized this open-endedness when he introduced the term "gene" into the scientific literature at the beginning of our long century of the gene. "No particular hypothesis is attached to the term gene," he wrote in 1909. In coining a new term his goal was rather to capture the idea that there is "something" in the gametes — the male and female germ cells that unite to form the fertilized egg — that "conditions or has a determining influence on the traits of the developing organism, or has the capacity of doing so" (Johannsen 1909, 143). This definition was exceedingly vague and thus left room for all sorts of understandings of the "nature" of the gene. But that, as we claim, was precisely the point of Johannsen's "definition." As a concept, the gene referred to a distant vanishing point and connected diverse lines of research in twentieth-century biology. It did not refer to a well-defined object with a finite set of properties. Interestingly, while Johannsen denied that any hypothesis was associated with the term "gene," he also emphasized that it corresponded to a concept that already existed and "had to be named in order to become precise" (Johannsen 1909, iv). Precision and ambiguity do not exclude each other.
Attempts to give precise meanings to Johannsen's "something" proliferated throughout the twentieth century. But the operationalization of any particular definition for the purpose of experimental investigation usually only ended up revealing further puzzling phenomena that prompted ever more complex descriptions and explanations of how genes supposedly worked and influenced life (Rheinberger, Müller-Wille, and Meunier 2015). Somewhat paradoxically, one might say that the more rigidly the gene concept tried to be defined, the more questionable it became. A glance into any textbook of biology confirms that the gene can be determined in multiple frames of reference — as a unit of transmission, as a unit of mutation, as a unit of function, or as a unit of selection — and that the relations between the entities thus defined are usually not simple one-to-one but complex many-to-many relations. The much-criticized gene-centrism of the twentieth century has therefore not reduced biological reality to a purported simple core. It has revealed a forever increasing number of new entities, relations, and processes that play their role in life.
One of our overarching claims is therefore that the gene became something akin to the organizing principle of twentieth-century biology not because, once discovered, it was characterized ever more definitively, but because the object of research it referred to — the gene as an "epistemic thing" (Rheinberger 1997) — opened itself up to experimental manipulation again and again with every new turn researchers took in providing definitions for the gene. This epistemological fertility of the gene concept points to a very special role that genes play in mediating vital processes, but not necessarily to what philosophers would call a privileged ontological status of genes as somehow more "fundamental" units to which all other phenomena of life can be "reduced." The phenomena geneticists addressed were always complex, intricate, and indeed to a large degree idiosyncratic; for otherwise they would have been of little interest to biologists. What is "fundamental" about genes must therefore likewise have something to do with the complexity and idiosyncrasy of life. The following chapter outline provides a sketch of our overall argument.
The gene, like any scientific concept, did not simply fall from heaven. Chapter 2 describes the protracted convergence in the nineteenth century of initially separate strands of investigation to a point where "heredity" became a central biological problem. We emphasize that nineteenth-century thought about heredity did not concern itself with simple phenomena, least of all with the causes of similarities between parents and offspring (e.g., in skin or eye color). The adage that "like begets like" had provided a satisfactory explanation for such similarities since ancient times. When physicians, breeders, and naturalists began to discuss heredity in the early nineteenth century, they singled out a truly exceptional and intriguing phenomenon. For they invoked the notion of heredity only in connection with a deviation — such as a disease, a malformation, or any other unusual and rare feature — that reappeared generation after generation even though its initial appearance had seemed to be an individual and capricious occurrence. Phenomena of this kind provided clues to the existence of a system of microscopic "germs" or "dispositions" that somehow spanned populations and generations and appeared to obey their own laws without always fully expressing themselves — if at all — in the manifest traits of individual organisms. Only statistical or experimental analysis could reveal the properties of such a system.
Chapters 3 and 4 focus on the rise of what is commonly known as classical genetics, covering a period that began around 1900 with the so-called rediscovery of experimental results obtained by the Augustinianmonk Gregor Mendel more than thirty years earlier, and that ended with the presentation of the molecular structure of DNA by James Watson and Francis Crick in 1953. Largely unnoticed by his contemporaries, Mendel had created an experimental system during the late 1850s and early 1860s that made it possible to elucidate the genetic constitution of organisms by means of deliberate crossing experiments with plants differing in one or a small number of character pairs. In the hands of his "rediscoverers," this system rapidly evolved into a method for investigating more complex transmission processes that deviated from the ideal case described by Mendel's rules, according to which elementary hereditary factors were statistically distributed among the germ cells and passed on to offspring independently from one another. Far from being the "atom" of life, the gene even at this stage was already recognized to be deeply implicated in the complex machinery that supports organic reproduction.
Chapter 5 describes the impact of classical genetics beyond its own, originally narrow, focus on investigating the transmission of hereditary traits. Transmission and development were originally ascribed to independent levels of organization named genotype and phenotype by Johannsen, and this distinction soon pervaded contemporary thought about life. Yet, questions of evolution and embryology were at all times on the horizon of researchers who worked with genetic methods. Especially during the 1930s, the significance of genes in the evolution of populations and in the development of individual organisms was explored in mathematical models and experimentally with model organisms like the fruit fly, maize, the red bread mold, or bacteriophages, that is, viruses infesting bacteria. But the physical nature of the hereditary material, the material mechanism of its transmission from generation to generation, as well as its mode of biochemical action in the body remained inaccessible to the methods of classical genetics, despite astounding successes in elucidating the formal structure of genes, their putative arrangement on chromosomes, and their multifarious relations to the traits of the organism.
This situation changed with the molecularization of genetics around the middle of the twentieth century, which we describe in chapter 6. Biophysical and biochemical techniques that had taken hold in biology independently of the quest to study the nature of the hereditary substance from the 1930s onward began to be used to probe the material structure of genes. This created a space for a new discourse about the peculiar nature of living matter, a discourse that condensed around the metaphor of information. The rise, in the 1970s, of molecular genetic instruments for manipulating the genetic material itself had far-reaching consequences. These molecular biotechnologies are the focus of chapter 7, in which we make a general observation similar to the one we made in preceding chapters about classical genetics: Research that started with a simple assumption — the so-called "central dogma" of molecular biology, according to which genetic information only flows from genes to proteins and never in the opposite direction — produced an increasingly complicated picture of the transmission and expression of genetic information. Both in transmission and expression, one-to-one relations between genes and their products turned out to be the exception rather than the rule, and both processes revealed themselves to be subject to complex regulating networks and epigenetic mechanisms.
In chapter 8, we consider the gradual shift in perspective on development and evolution brought about by insights into the minutiae of gene transmission and expression from the early 1980s onward. As a determining factor for the expression of particular traits, "the gene" began to recede into the background. Instead, it assumed the character of a flexible molecular "resource" among a number of others that could be mobilized in different ways in evolution, development, and cell metabolism. Chapter 9 outlines the scope of the latest generation of postgenomic biotechnologies that have made it possible to generate, process, and visualize large amounts of data to capture systemic states and dynamic processes in single cells, tissues, and even organisms. The decline of the idea of genes as simple, elementary units of heredity has gone hand in hand with the recognition of a modular ensemble of genetic and epigenetic mechanisms that do not determine our fate, but rather open new avenues for human interference with vital processes. Epigenetic reprogramming, genome editing, and the synthetic production of cells have now appeared on the horizon of what may soon become technically feasible.
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