Re-Envisioning the History of Cellular and Molecular Biology

Abstract

At the turn of the twentieth century, the German cytologist Oscar Hertwig (a pioneer in the study of fertilization and the role of chromosomes in heredity) described the cell as both “a marvellously complicated organism” and “a small universe into the construction of which we can only laboriously penetrate by means of microscopical, chemico-physical and experimental methods of inquiry.”1 Hertwig, I suspect, would not have been surprised by the “molecular turn” taken by biology in the mid-twentieth century, nor that it revealed both a great deal of order and organization within the cell (think the genetic code, the central dogma, the cell cycle), and that it would amplify our appreciation of the cell’s complexity.For various reasons historical study of the development of cytology into cell and molecular biology has been dominantly focused on molecular genetics and understanding of the structure and function of DNA. Whereas cytology and cellular biology traditionally relied on techniques of observation with light microscopy, molecular biology refers to the description of living organisms and cells with methods from physics and chemistry, initially and most importantly the use of X-ray crystallography (and later spectroscopy and electron microscopy) to create three-dimensional models of various macromolecules such as the double-helical DNA, single-stranded RNA or proteins, and biochemical analysis of enzymes and other proteins. From within the perspective of molecular genetics, the cell and organism have been at risk of being reduced to the site where DNA is found. (As one of the founders of molecular biology, Jacques Monod, once said: “What is true for E. coli is true for the elephant.”2)One could speculate that the fascination with molecular genetics and the story of the discovery of the structure of DNA and the genetic code mid-twentieth century is at least in part the result of modern society’s having been more or less contemporaneously transformed and absorbed by the computer revolution. Codes, programs, and information are now omnipresent—within us and without us—and we are both fascinated and blinded by the age of information. To be fair, the resolution of the molecular structure of DNA and its role in heredity and genetics was exciting, momentous, and of lasting significance for the development of biology and the life sciences to come. Talk of using molecular technologies like CRISPR to “edit” our genomes for medical and therapeutic purposes illustrates how deeply this framework continues to structure our thinking about life and health. But a near obsession with DNA as the “master molecule” and “secret of life” has meant that other features of how cells function and the scientific figures who have worked on problems outside of this narrow focus have received much less attention.In one sense science and the history of science are necessarily selective, since as individuals we cannot productively cast our vision simultaneously in all directions. Constrained as we are by our human anatomy and neurophysiology, we must focus on one thing at a time. Hence the prevalence of visual metaphors in science, history, and philosophy of focusing on x or putting x under the microscope. This can, however, lead to a myopia in our understanding. Fortunately, we can collectively address this narrowness of perspective when individuals choose to focus their attention on previously understudied topics. And if we understand “revision” as taking a second look, we can say that each of the books under consideration here attempts in its own way a revisionist history of molecular and cellular biology. Each author asks us to shift our focus for a moment from DNA and molecular genetics to other components and aspects of modern cell and molecular biology.To that end, de Chadarevian puts “chromosomes under the microscope,” Grote focuses on explaining the rise of “the molecular-mechanical vision of life” (1), while Lyons asks us to “re-envision cell theory.” The first two authors seek to expand our vision and understanding of modern molecular biology beyond the narrow focus on DNA, the macromolecule whose personality has proven to be “larger than life.” Lyons’s perspective is broader still, encompassing the cell as a whole, and yet at the same time, she seeks to revoke the cell’s status as fundamental unit of life, and to award that title to what the plant biologist František Baluška and colleagues call the cell body,3 a currently subservient and less well recognized sub-cellular constituent. There is an attempted coup afoot! And in an unusual move for a historian, Lyons does not restrict herself to a dispassionate chronicle of the affair (then again—does any historian remain truly objective?), instead joining sides with the conspirators.In short, we have here three very interesting books asking us to look at the history of cellular and molecular biology with fresh eyes.***Soraya de Chadarevian’s Heredity under the Microscope: Chromosomes and the Study of the Human Genome uses chromosomes as an “analytical lens to gain insight into where human heredity mattered and genetic knowledge was embraced, debated or rejected” (4). It deals specifically with the history of human cytogenetics in the postwar period. Although the twentieth century may have been, as Evelyn Fox Keller described it, “the century of the gene,”4 de Chadarevian reminds us that you can’t see genes, but you can see chromosomes. Consequently, before the double helix became iconic of heredity and genetics, photographs of human chromosomes symbolized the scientific promise of understanding the biological keys that not only make each of us human, but also indicate our sex, our health and disease, and possibly even aberrant behavior. Contemporaneously with the birth of molecular genetics, images of chromosomes, known as karyotypes, made visible the complete human genome. De Chadarevian explains how concerns about the effects of atomic radiation at the close of the Second World War were a key impetus for the study of chromosomes, the hope being that mutations would be visible at the whole-chromosome level.It was their visibility that helped chromosomes assume diagnostic significance. Through their inspection, clinicians and medical researchers hoped to detect and to understand medical conditions like radiation poisoning and birth defects. But before images of chromosomes could be pressed into these services, it was necessary to know what a “normal” set of human chromosomes looked like. It is somewhat surprising that, as she explains, a consensus that most humans possess 46 chromosomes, consisting of 23 pairs of consistently identifiable individual chromosome types, did not come about until the late 1950s. When the Indonesian-American Joe Hin Tjio and the Swede Albert Levan (both originally plant geneticists) published their landmark paper in 1956, the number was still commonly thought to be 48, the count offered by Theophilus Painter in 1923. Why it was so difficult to establish what seems such a basic observational fact is very telling. Karyotype images of “the human genome” have become so familiar that most people are unaware of the difficulties that had to be overcome to produce them. Chromatin, the genetic material consisting of DNA coiled around histone proteins, condenses into the distinct bodies that can be observed under the microscope only when dyed (hence the term “colored bodies” or chromo-somes) during mitosis or cell division. Most of the cell’s time is spent in interphase, a stage during which the chromatin is loosely organized and appears as a filamentous network.Consequently, to study chromatin in the stage at which chromosomes are formed, one needs cells undergoing division. The preferred material, de Chadarevian explains, was from human testes (where new sperm cells are always being formed), but access to this tissue was limited to operating rooms or places of execution. Moreover, earlier researchers like Painter worked with tissue extracts that were then embedded in paraffin and sectioned, a technique that often mixed the contents of several nuclei together. Tjio and Levan worked with cells from culture (allowing them to inspect a single layer of cells rather than a thicker section) and used the plant poison colchicine to freeze cell division in metaphase, when chromatid pairs are in a highly condensed state. They also applied hypotonic solution to swell the cells and to help separate the chromosomes, and then pressed down on the cover slips to further spread them out as distinct and non-overlapping bodies. What this illustrates is that learning about chromosomes is not simply a matter of looking and seeing what the facts are. Even optical microscopy involves intervention and manipulation.De Chadarevian recounts the rise of chromosomes’ diagnostic and clinical significance, for instance as markers of birth defects due to abnormal chromosome numbers, such as trisomy 21 or Down syndrome. Once the existence of so-called sex chromosomes (X and Y) in humans was established (and XX and XY associated with female and male characteristics, respectively), the presence of Barr bodies (a small darkly stained round object that turned out to be an inactivated X chromosome typically seen in females) was used to help clarify the sex of ambiguous cases. For example, those diagnosed with Turner syndrome were determined to be females lacking two normal X chromosomes, while cases of Klinefelter syndrome were designated to be males with an extra X chromosome. Tests for genetic sex also featured in disputes about the “true” gender of female Olympic athletes.The realities of cell division and phenotypic expression, however, often proved to be more complicated than many hoped or imagined. Cases of mosaicism (different numbers of chromosomes in different cells of the same body), so-called “superfemales” (XXX), and other combinations (XXY, XXYY) challenged assumptions of a tidy binary sex category. The purported discovery (eventually debunked) that a higher than average number of prison and mental institution inmates possessed an extra Y chromosome (XYY) that explained their aberrant behavior created a media stir in the 1960s. As de Chadarevian describes, it was through the appeal and promise of chromosomes that medicine first became geneticized. Collection of data in registries of abnormal karyotypes raised ethical questions about consent and the uses to which such information would be put. Surprisingly, the scientists carrying out this research, even in the 1950s and 1960s, were not cold-blooded technocrats looking to reduce human sexuality and experience to simplistic biological formulae. Rather, they often showed real compassion and concern for how the patients referred to them might be impacted by the diagnoses and test results they had to offer, and were critical of their indiscriminate application.De Chadarevian details the techniques required to make chromosomes visible, so they can all be seen as separate objects on a flat plane, either drawn by camera lucida or photographed. If photographed through the microscope, the images were magnified, cut out with scissors, then arranged by hand and glued to a page, to assume one or the other of the now familiar conventional arrangements of chromosomes: in numerical sequence (1–23), either aligned “clothesline” style with the centromeres serving as midpoint across the page, or with the bottom tip of each “lower” chromosome arm lined up in rows (arms are not always of even length because the centromere is not always situated dead-center in the chromosome). In this way the karyotype made chromosomes the visible and orderly epistemic objects with which we have all become so familiar. De Chadarevian does an excellent job describing how chromosome studies featured in the effort to impose visible order—both literal and figurative—on the mysteries of human genetics, sex, disease, and even criminal behavior.At the 1977 International Chromosome Conference, however, Francis Crick, a leading figure of molecular biology, declared, “It’s not enough, in order to understand the Book of Nature, to turn over the pages looking at the pictures. Painful though it may be, it will also be necessary to learn to read the text. Only with the assistance of molecular biology will this be possible” (156). De Chadarevian contrasts the quantitative approach of how molecular biologists like Crick used chromosome images to make calculations of finer details with the more qualitative approach of human cytogeneticists. Modern-day microscopes, she notes, rely on number-crunching software algorithms to convert data into crisp and colorful imagery. But in closing de Chadarevian points out how attention to chromosomes is making a significant comeback, for understanding how genes are regulated requires understanding how the three-dimensional structure of chromatin (the DNA and the histone proteins around which it is wound and packaged) reacts to various internal and external cellular signals. “Then and now,” she writes, “chromosomes stand at the crossroads of a cellular and molecular understanding of life” (185). (I can’t help but note how fitting a metaphor this is, given the chromosome’s shape.) This is a very useful study, based on extensive archival and interview work with some of the key research figures, of the diagnostic, clinical, and cultural significance attributed to chromosomes and how they helped geneticize medicine the first time around.***In Membranes to Molecular Machines: Active Matter and the Remaking of Life, Mathias Grote seeks to understand how the “molecular-mechanical vision of life” arose starting in the 1970s, resulting in the now commonplace description of cell function in terms of protein “motors,” “switches,” “transducers,” “pumps,” and other machine language. This stands in contrast to the choice of information metaphors that helped to create the field of molecular genetics, e.g., codes, books, blueprints, and programs. Those metaphors were a rather natural fit for scientists interested chiefly in the heritable transmission of traits from one generation of cells or organisms to the next. Scientists, encouraged by the development of a formal mathematical information theory by people like Norbert Wiener, Claude Shannon, and Warren Weaver in the late 1940s, fastened onto the idea that what was transmitted from one generation to the next was information in some form. But like de Chadarevian, Grote wishes to draw our attention to aspects of postwar laboratory biology other than molecular genetics. By choosing as his topic the cell membrane and the proteins responsible for admitting molecules into and out of the cell, he focuses on “active matter” rather than the comparatively inert instructions encoded in nucleic acids. Grote notes that the study of cell membranes is an understudied topic in the history of biology. Emphasis is placed on the importance of chemistry and chemical techniques in the study of proteins as active matter, in contrast to the roles of molecular genetics and structural biology in the dominant narrative about the “molecularization of life” centered on Watson, Crick, et al. and the double-helical structure of DNA.In particular, Grote concentrates on investigations into bacteriorhodopsin, a light-sensitive, membrane-bound protein that gained attention in the 1960s for its role in a visible purple reaction first observed in Halobacteria, microbes of the Archaea distinctive for their tolerance of extreme salinity, acidity, temperature, etc. This was a reliably reversible reaction from purple to yellow color in the presence of light, which could be isolated to the bacterial cell membrane, thereafter referred to as “purple membrane.” Bacteriorhodopsin (BR) is among the family of G-coupled protein receptors and is similar in structure to rhodopsin proteins that make possible vision in humans and other vertebrates. Absorption of a light photon causes a series of conformational changes in the shape of the protein that spans the cell membrane. Its function was first described in 1973 by the membrane microscopist Walther Stockenius and chemist Dieter Oesterhelt as a light-energy-driven “pump” that transports protons (H+ ions) across the cell membrane, and subsequently powers the synthesis of ATP (adenosine triphosphate), the cell’s favored energy “currency.” This was an early example of scientists using a machine metaphor and analogy to describe and understand a vital function at the molecular level, and Grote employs it as an exemplar of the molecular machine vision of life to come that brought us turbines, rotors, switches, and other protein machines.But Grote is concerned not just with scientists’ use of machine metaphor to describe this and other molecular complexes in the cell, but also with how conceiving of them as such is implicated in consequent attempts to manipulate them—by devising proton-pump inhibitors, for instance, that reduce the level of stomach acid as a treatment for indigestion. What Grote calls “the materialization of molecular machines” refers to how these little machines have become, in one sense, intensely real. Drawing on Ian Hacking’s argument for entity realism, Grote suggests that if the proton pump can be switched on and off, this would explain why so many scientists today regard talk of molecular machines as more than metaphor and as referring to something quite real. He makes clear, however, that he is not taking a stance in the scientific realism debate, but wishes only to explain why scientists have become so comfortable with all the molecular machine talk that has emerged in and transformed modern cellular and molecular biology.Grote describes what he calls a “plug and play” approach assumed by those working within the molecular-mechanical vision of life, according to which cells are composed of modular protein units that can themselves be disassembled into amino acid components and rearranged like computer software, which can then be run on different hardware systems. In order to understand their function better, scientists extracted the protein pumps from their natural membrane environment and reconstituted them in artificial liposomes intended to simulate cell membranes, or using recombinant DNA spliced the BR gene into the more lab-hardy E. coli so they could be probed in the test tube with various reagents. In this way, BR “became a ‘molecular component’ of life since it could be unplugged from its original environment, the cell membrane, and plugged into novel environment [sic] of a cell simulacrum apparently without loss of function” (127). Similar experiments carried out with other protein modules (“machines”) sought to re-engineer them to increase or alter their original function.In what he suggests can be understood as an important anticipation of the “biobricks” and other “standardised parts” of current synthetic biology, Grote discusses efforts in biocomputing undertaken in the 1980s to engineer BR as an electronic switch in so-called biochips. This attempt to merge molecular biology with computing ultimately ended in failure, largely because the meager successes attained in the lab could not be scaled up to any commercially viable results. It demonstrates, however, that although scientific metaphors may begin as creative and promissory flights of fancy, they remained tethered to and constrained by reality. These machine and engineering metaphors have served particularly well the interests of those guided by the engineering ideal that continues to drive synthetic biology, and those business-savvy researchers looking to “translate” their research into commercially marketable products and techniques. (Think of how CRISPR and its associated endonuclease enzymes—Cas 9, 13, etc.—are commonly described as “programmable scissors” for performing what is now commonly referred to as “molecular surgery.”5)In addition to the analysis of the conceptual and technical developments that led to the “materialization of molecular machines,” From Membranes to Molecular Machines also provides an excellent history of the scientists and institutions devoted to this research based on the author’s own interviews with many of the key players.***Sherry Lyons’s From Cells to Organisms: Re-envisioning Cell Theory takes a much broader historical sweep than the previous two studies, ranging from the seventeenth century to the present. It also offers three distinct perspectives: a history of cell theory from Robert Hooke to the present; an argument for revising our understanding of the ontological and epistemic status of the cell as the fundamental unit of life; and an apologia for two scientists in particular who Lyons thinks deserve greater recognition for their prescient vision of this purportedly more adequate scientific conception, Thomas H. Huxley (1825–1895) and Daniel Mazia (1912–1996).Regarding the first perspective, Lyons provides a thorough history of cell theory from its conceptual (and terminological) beginnings in the seventeenth century to the present, covering its relevance for anatomy, embryology/developmental biology, cytology (with focus on heredity and chromosomes), molecular genetics and DNA, to current ideas about symbiogenesis and the possible endosymbiotic origins of the nucleus and associated microtubule organizing center. In doing so Lyons includes discussions of some lesser-known scientific figures, most significantly the cell biologist Daniel Mazia, who worked on the role of the centrosome and microtubule organizing center in mitosis and the cell cycle in eukaryotes. This is a very interesting history of scientific developments, most not covered in other sources. Although Mazia’s research focused on mitosis, Lyons aptly explains that he did not approach the problem as a geneticist, and so, like the other two volumes reviewed here, his research provides another example of how molecular biology is broader than molecular genetics.Mazia (in collaboration with Katsuma Dan) was at base interested in the question of how one cell becomes two. His research focused naturally enough, therefore, on the centrosome, the organelle lying just outside the nucleus that contains the centrioles, from which the mitotic spindles are formed, the microtubule fibers that attach to the centromere of chromosomes and pull the sister chromatids apart during mitosis. But in some cases, such as in syncytia (Drosophila eggs, muscle tissue, plasmodial slime molds), replication and division of the nucleus (karyokinesis) occurs independently of and without replication and division of the whole cell (cytokinesis). Mazia became convinced, therefore, that the complex of nucleus and centrosome, which he proposed to call the cell body, was more fundamental than the entire cell with its cytoplasm and peripheral enclosing membrane.Lyons explains that a similar idea had been proposed earlier in the nineteenth century by the plant biologist Julius von Sachs. Sachs was a critic of the cell theory—on the basis that at the time a single nucleus was considered characteristic of a cell, so multinucleated syncytia appeared to be a counter example to the claim that all organisms are composed of a multitude of single, well-defined cells. Sachs proposed the term “energide” to denote a nucleus and the surrounding cytoplasm under its direct influence. The energide was primary, and individual characteristic cells consisting of a single nucleus enclosed in its own membrane would be a secondary and non-essential phenomenon. Lyons is similarly interested in Huxley because of his criticisms of the cell theory. Huxley famously endorsed the protoplasmic theory of life, according to which the jelly-like substance was fundamental for life, not its morphological arrangement into a mononucleated membrane-bound unit. But Lyons also approves of Huxley’s refusal to separate questions of heredity from development, for she, like many others, believes the tendency to do so in the twentieth century has not been beneficial for biology as a whole.Lyons’s third perspective concerns her insistence on the need to “re-envision cell theory” (as the book’s subtitle proclaims). This seems to be motivated by the question “What is the fundamental living unit?” It’s not the cell, she argues, but Mazia’s cell body. (Lyons has collaborated with the plant cell biologist František Baluška, who also advocates a revision of cell theory centered on the cell body or energide concept.6) Early in the book, Lyons presents the Cell Theory as comprised of three theses: (1) All life is made up of cells; (2) The cell is the smallest independent unit of life; and (3) All cells arise from pre-existing cells. Much is made (perhaps too much) of the cell’s lack of true “independence,” which is key to Lyon’s complaint against cell theory.The cell is indeed often called the “basic” or “fundamental” unit of life (as Lyons herself does in the book), but it is crucial not to confuse the issue of independence with fundamentality. An analogy will illustrate the point. A team may be the fundamental unit of sport in a league—teams are composed of individual players, and no player can on her own successfully play a game of soccer, say. But no team is entirely independent, in the sense that in order to carry out the activity of playing a match, it must interact with at least one other team and with officials (referee and linesmen). So, fundamentality and independence are two separate logical categories. Likewise, the cell may be considered the fundamental unit of life (in the sense that it is the least minimal unit capable of being alive), but that is not to say that a cell is entirely independent and self-sufficient, especially if it is a member of a multicellular organism (cells differentiate or cease living on the reception of signals from the environment and other cells with which they are directly in communication).In fact, Theodor Schwann himself—one of the chief architects of the cell theory—had anticipated this confusion when he remarked that a honey bee is no more able to live independent of its colony than an animal cell is able to live outside of the body to which it belongs (this was before the discovery of cell culture technique), but that doesn’t prove the bee is not the fundamental living unit of the bee colony.7 Moreover, the very same criticism Lyons makes of the cell can be made of the cell body, which is in no way entirely independent of the rest of the cell or the external environment. It does not exist on its own in nature or in the lab, and is unable to function without the assistance of the cell’s other accoutrement, such as the cell membrane and cytoplasmic contents. Lyons does note that accepting the cell body as the real fundamental unit requires accepting an endosymbiotic origin for the eukaryote nucleus, an originally autonomous cell-microbe having taken up residence inside a larger prokaryote. This, she concedes, is not a popular idea at present.Not coincidentally, Lyons also argues in favor of a range of other “extended synthesis” ideas promoted by Lynn Margulis and others.8 This includes an interpretation of endosymbiogenesis (the merging of prokaryote cells to form eukaryotes) as somehow posing a challenge to both the cell theory and natural selection as a chief mechanism of evolution. Yet the comparatively rapid increase in complexity made possible by events of endosymbiosis are no challenge to natural selection per se, since these new cooperative mergers between previously autonomous cells (and Lyons seems to admit they do qualify as cells) will either be favorable for further survival and replication or not. Nature and the environment will sort out which mergers work and which don’t. The target of her criticism ought not to be natural selection, but Darwin’s mistaken idea that new traits and structures must be built up gradually, in a series of small and improbable steps due to random mutation. On this matter Huxley rightly cautioned Darwin about insisting too much on the thesis natura non facit saltum.9At the heart of Lyons’s concerns seems to be the problem of biological individuality: What exactly is an individual? What is the correct definition to use? Recent scholarship suggests that the answer(s) depends on the organism/system and questions being asked. As for selecting which is the most fundamental (or important) bit of the cell (whether genes, chromosomes, proteins, or the cell body), that is a task informed by philosophical assumptions about causation and the relationship between parts and whole.Lyons describes how Mazia extolled the gifts wrought by the light microscope for our understanding of cells and organisms; but the gift of the great microscopist, he pronounced, is to “think with the eyes and see with the brain” (223). This is a rather obscure apothegm for sure, and unless I am mistaken about what seems to me to be a logical confusion at the heart of Lyons’s argument for re-envisioning cell theory, there is perhaps reason to question its counsel. Although I disagree with the more philosophical argument of the book, I recommend it for its excellent historical treatment of cell biology broadly construed.***October 25, 2022. will mark one hundred years since Oscar Hertwig’s death. In that time the creation of new investigative tools and techniques have played both an ampliative and a constraining role on what scientists can see and how they view (i.e., understand) it. Innovative microscope technology, cell fractionation, X-ray crystallography, spectroscopy, polymerase chain reaction, recombinant DNA, radioisotope and fluorescent tagging, and single-cell analysis etc., all guide the scientist’s gaze in particular directions and lead them to view life from particular perspectives. By putting chromosomes under the microscope, explicating the rise of the molecular-mechanical vision, and re-envisioning cell theory, these three histories demonstrate the breadth and complexity remaining in our understanding of life, despite attempts to simplify it down to one dominant narrative about the almighty gene.In closing, I draw from these three books, three lessons: (1) Molecular biology may best be understood as a set of tools and techniques, not a specific and comprehensive view of life—for if the cell theory is indeed correct, no molecule or molecules are alive on their own, only the cell as an organized whole, or multicellular aggregates, is capable of manifesting all the properties characteristic of life. (2) Cells are wondrously rich and complex systems, which allow a plurality of investigative perspectives and interpretative visions. (3) Seeing always involves more than just looking, which is what makes doing the history and philosophy of science so interesting and rewarding.