Today, the lipid bilayer structure is nearly ubiquitous, taken for granted in even the most rudimentary introductions to cell biology. Yet the image of the lipid bilayer, built out of lipids with heads and tails, went from having obscure origins deep in colloid chemical theory in 1924 to being “obvious to any competent physical chemist” by 1935. This chapter examines how this schematic, strictly heuristic explanation of the idea of molecular orientation was developed within colloid physical chemistry, and how (...) the image was transformed into a reflection of the reality and agency of lipid molecules in the biological microworld. Whereas in physical and colloid chemistry these images considered secondary to instrumental measurement and mathematical modeling of surface phenomena, in biology the manipulable image of the lipid on paper became an essential tool for the molecularization of the cell. (shrink)

The molecular genetic age can be said to have begun with the letter in Nature in 1953 by Watson and Crick, describing the helical structure of DNA. Some outstanding scientific work preceded that discovery, including especially the recognition by Chargaff of base-pair complementarity, but no discovery quite captured the imagination of the biomedical world as a few understated words by Watson and Crick in their famous one-page paper: "It has not escaped our notice that the specific pairing we (...) have postulated immediately suggests a possible copying mechanism for the genetic material". The manner in which genetic material was passed on from generation to generation had been decoded.That discovery was... (shrink)

"A person is not explainable in molecular, field-theoretical, or physiological terms alone." With that declaration, Nobel laureate Gerald M. Edelman goes straight to the heart of Nature's Imagination, a vibrant and important collection of essays by some of the world's foremost scientists. Ever since the Enlightenment, the authors write, science has pursued reductionism: the idea that the whole can be understood by examining and explaining each of its parts. But as this book shows, scientists in every discipline are (...) reaching for a new paradigm that accounts for the whole--from the individual person to the universe itself. Nature's Imagination gathers together the work of thirteen leading mathematicians, astronomers, neuroscientists, and philosophers, as they discuss the revolution sweeping the sciences. Here Roger Penrose, Oliver Sacks, John Barrow, Gregory Chaitin, Maragret Boden, and others explore how and why classic reductionism is falling by the wayside in their own fields. As Freeman Dyson writes in the introduction, science is an art form, not a philosophical method, and it is always in search of new tools. Reductionism has done its work, and scientists are in search of another. Roger Penrose offers a fascinating account of irreducibility in mathematics, starting with the example of an impossible triangle--a drawing of a triangular object twisted so that could not exist in three dimensions. He breaks the triangle into three parts, showing that each corner is physically possible; only in combination is the triangle impossible. Both Penrose and mathematician Gregory Chaitin explore Godel's incompleteness theorem--as does John Barrow, who explains that Chaitin's proof of the theorem shows that, if we ever arrive at a Theory of Everything, there may be a still deeper and simpler unifying theory beyond that. Other contributors discuss the changing thinking in neuroscience, and the limitations of a mechanical view of the mind: as Oliver Sacks writes, "if we are to have a model or theory of mind as this actually occurs in living creatures in the world, it may have to be radically different from anything like a computational one." In addition, this volume includes staunch defenders of the classic scientific approach, such as Peter Atkins ("The omnicompetence of science, and in particular the simplicity its reductionist insight reveals, should be accepted as a working hypothesis until, if ever, it is proved inadequate"). The advance of science has been so startlingly swift in the last century that it has begun to approach limits never dreamed of before. This remarkable volume captures the latest thinking on where we must turn if we are to truly understand oursevles and the universe we live in. (shrink)

The objective of the new series, "Molecular Biology, Biochemistry and Biophysics", of which this brochure forms the first volume, is to produce more than another compilation of data. It is hoped that the new series will help the individual "specialist" keep abreast of important developments in the natural sciences at the molecular and subcellular level in fields complementary to his own. The predominant aim is not so much to increase the ever-growing body of information in an encyclopedic fashion (...) but rather to give, in addition to a well rounded factual presentation of subjects which have reached a degree of maturation, a leitmotiv developed by the individual authors from a more personal point of view. The reader should thus be able to use these mono graphs not only for acquisition of knowledge but as a source of further motiva tion in his own work. This latter and more consequential aim of the monograph series is one of the reasons for presenting here a most unusual talk which should enable the reader to sit back and view his own efforts in the context of science and creative attempts as a whole. The lecture is the virtually unknown inaugural address of the Dutch physical chemist JACOBUS HENRICUS VAN'T HOFF. As is shown in his short biography presented on pages 3 and 4 the principal thoughts of the molecular biologist of today are akin to his own and he clearly recognized the universality of molecular life processes. (shrink)

Images are at the heart of strategies of persuasion. They render certain aspects visible and leave others unrepresented; and they may shape processes of scientific reasoning and imagination. By tracing diagrammatic images in the anthropological sciences throughout the 20thcentury, the contributions to this special issue highlight some dominant pictorial traditions for rendering human evolution and diversity visible. This article aims to provide an overview of and an introduction to the special issue ‘Visibility Matters’.

The rapidly changing field of genetics affects society through advances in health-care and through implications of genetic research. This study addresses the impacts of new genetic discoveries and technologies on different segments of today's society. The book begins with a chapter on genetic complexity, and subsequent chapters discuss moral and ethical questions arising from today's genetics from the perspectives of health care professionals, the media, the general public, special interest groups and commercial interests.

Recent philosophy of science has seen a number of attempts to understand scientific models by looking to theories of fiction. In previous work, I have offered an account of models that draws on Kendall Walton’s ‘make-believe’ theory of art. According to this account, models function as ‘props’ in games of make-believe, like children’s dolls or toy trucks. In this paper, I assess the make-believe view through an empirical study of molecular models. I suggest that the view gains support when (...) we look at the way that these models are used and the attitude that users take towards them. Users’ interaction with molecular models suggests that they do imagine the models to be molecules, in much the same way that children imagine a doll to be a baby. Furthermore, I argue, users of molecular models imagine themselves viewing and manipulating molecules, just as children playing with a doll might imagine themselves looking at a baby or feeding it. Recognising this ‘participation’ in modelling, I suggest, points towards a new account of how models are used to learn about the world, and helps us to understand the value that scientists sometimes place on three-dimensional, physical models over other forms of representation. (shrink)

In this thesis I examine a number of topics that bear on explanation and understanding in molecular and cell biology, in order to shed new light on explanatory practice in those areas and to find novel angles from which to approach relevant philosophical debates. The topics I look at include mechanism, emergence, cellular complexity, and the informational role of the genome. I develop a perspective that stresses the intimacy of the relations between ontology and epistemology. Whether a phenomenon looks (...) mechanistic, or complex, or indeed emergent, is largely an epistemic matter, yet has an objective basis in features of the world. After reviewing several concepts of mechanism I consider the influential recent account of Machamer, Darden and Craver (MDC). That account makes interesting proposals concerning the relationship between mechanistic explanation and intelligibility, which are consistent with the results of the investigation I undertake into the science surrounding protein folding. In relation to a number of other issues pertaining to biological systems I conclude that the MDC account is insufficiently nuanced, however, leading me to outline an alternative approach to mechanism. This emphasizes the importance of structure—function relations and addresses issues raised by reflection on the nature of cellular complexity. These include the distinction between structure and process and the different possible bases on which system organization may be maintained. The account I give of emergence construes the phenomenon in terms of psychological deficit: phenomena are emergent when we lack the capacity to trace through and model their causal structures using our cognitive schemas. I conclude by developing these ideas into a preliminary and partial account of explanation and understanding. This aspires to cover the significant fraction of work in molecular and cell biology that correlates biological structures, processes and functions by visualizing phenomena and making them imaginable. (shrink)

Molecular and developmental studies of limb pattern formation have recently gained widespread attention. The fact that vertebrate limbs are amenable to both genetic and embryological manipulations has established this model system as a valuable paradigm for studying vertebrate development. Limb buds are polarised along all three major axes and the establishment of the dorso‐ventral (DV) polarity is dependent upon cues localised in the trunk, where a DV ectodermal interface is produced by confrontation of dorsal and ventral identities. By analogy (...) to Drosophila imaginal disc development, this interface has been proposed to determine and position an ectodermal organising centre, the Apical Ectodermal Ridge (AER), controlling limb bud outgrowth. Recent fate mapping studies(1) and studies of genes regulating DV limb polarity(2‐6), AER formation(7,8) and differentiation(9) suggest, however, that DV patterning and AER induction, though coordinately regulated during limb bud outgrowth, may early on be more dissociated than expected. (shrink)

Molecular models are typical topics of chemical research depending on the technical standards of observation, computation, and representation. Mathematically, molecular structures have been represented by means of graph theory, topology, differential equations, and numerical procedures. With the increasing capabilities of computer networks, computational models and computer-assisted visualization become an essential part of chemical research. Object-oriented programming languages create a virtual reality of chemical structures opening new avenues of exploration and collaboration in chemistry. From an epistemic point of view, (...) virtual reality is a new computer-assisted tool of human imagination and recognition. (shrink)

Drosophila imaginal discs (appendage primordia) have proved invaluable for deciphering cellular and molecular mechanisms of animal development. By combining the accessibility of the discs with the genetic tractability of the fruit fly, researchers have discovered key mechanisms of growth control, pattern formation and long‐range signaling. One of the principal experimental attractions of discs is their anatomical simplicity — they have long been considered to be cellular monolayers. During larval stages, however, the growing discs are 2‐sided sacs composed of a (...) columnar epithelium on one side and a squamous ‘peripodial’ epithelium on the other. Recent studies suggest important roles for peripodial epithelia in processes previously assumed to be confined to columnar cell monolayers. BioEssays 23:691–697, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

Recent advances in molecular genetics, plant physiology, and biochemistry have opened up the new biotechnology of herbicide resistant crops (HRCs). Herbicide resistant crops have been characterized as the solution for many environmental problems associated with modern crop production, being described as powerful tools for farmers that may increase production options. We are concerned that these releases are occurring in the absence of forethought about their impact on agroecosystems, the broader landscape, and the rural and urban economies and cultures. Many (...) of the benefits and risks associated with HRCs are not apparent to either the public, farmers, policy makers, or the scientific community. HRC technology raises moral issues in three areas: our duties toward the natural environment; our political and economic responsibilities to each other; and our communal character as one generation among many. We also need a rational basis on which to make evaluations of this new biotechnology. The technical aspects of their release require a logical guide to the ecological, environmental, and biological effects the release might have in sustainable agroecosystems. The initial step should include an assessment of the intrinsic qualities of the crop, the herbicide, and the resistance mechanisms. The second step should include an assessment of effects associated with population ecology, population genetics, environmental degradation, consumer health, and farm economic viability due to the resistant crop-herbicide pair. Herbicides have been used in crop production for nearly a half a century. There has been a tremendous increase in the use of these chemicals in that time. Society has seen the use of these chemicals not only help to feed many people, but also to bring costs not anticipated before the introduction of the chemicals. We need to draw on that long history of use and learn the lessons it can provide us as we approach the introduction and commercialization of the next generation of weed control technology, herbicide resistant crops. We also need to reflect on the lessons we missed during that half century because we spend more time imagining the possible benefits that would come from the technology than scrutinizing the possible harm. (shrink)

Some of the most imaginative analyses in contemporary science have been fostered by the paradox of irreversibility. Rendered as a question the paradox reads: How can the anisotropic macrophysical behavior of a system of molecules be reconciled with the underlying reversible molecular model? Attempts to resolve and dissolve the paradox have appealed to large numbers of particles, jammed correlations, unseen perturbations, hidden variables or constraints, uncertainty principles, averaging procedures (e.g., coarse graining and time smoothing), stochastic flaws, cosmological origins, etc. (...) While acknowledging these efforts as important articulations of basic ideas of statistical mechanics, we question their relevance to irreversibility as it occurs in nature. It seems to us that once the emergence of the phenomenon of equilibrium is understood in terms of molecular dynamics, the macroscopic appearance of irreversibility can also be understood in terms of the frequency of forced withdrawals from young equilibria. We believe that the paradox of irreversibility can be resolved in a simple, logically clear, and aesthetically pleasing manner. (shrink)

Scientists and historians have often presumed that the divide between biochemistry and molecular biology is fundamentally epistemological.100 The historiography of molecular biology as promulgated by Max Delbrück's phage disciples similarly emphasizes inherent differences between the archaic tradition of biochemistry and the approach of phage geneticists, the ur molecular biologists. A historical analysis of the development of both disciplines at Berkeley mitigates against accepting predestined differences, and underscores the similarities between the postwar development of biochemistry and the emergence (...) of molecular biology as a university discipline. Stanley's image of postwar biochemistry, with its focus on viruses as key experimental systems, and its preference for following macromolecular structure over metabolism pathways, traced the outline of molecular biology in 1950.Changes in the postwar political economy of research universities enabled the proliferation of disciplines such as microbiology, biochemistry, biophysics, immunology, and molecular biology in universities rather than in medical schools and agricultural colleges. These disciplines were predominantly concerned with investigating life at the subcellular level-research that during the 1930s had often entailed collaboration with physicists and chemists. The interdisciplinary efforts of the 1930s (many fostered by the Rockefeller Foundation) yielded a host of new tools and reagents that were standardized and mass-produced for laboratories after World War II. This commercial infrastructure enabled “basic” researchers in biochemistry and molecular biology in the 1950s and 1960s to become more independent from physics and chemistry (although they were practicing a physicochemical biology), as well as from the agricultural and medical schools that had previously housed or sponsored such research. In turn, the disciplines increasingly required their practitioners to have specialized graduate training, rather than admitting interlopers from the physical sciences.These general transitions toward greater autonomy for biochemistry and allied disciplines should not mask the important particularities of these developments on each campus. At the University of Caliornia at Berkeley, agriculture had provided, with medicine, significant sponsorship for biochemistry. The proximity of Lawrence and his cyclotrons supported the early development of Berkeley as a center for the biological uses of radioisotopes, particularly in studies of metabolism and photosynthesis. Stanley arrived to establish his department and virus institute before large-scale federal funding of biomedical research was in place, and he courted the state of California for substantial backing by promising both national prominence in the life sciences and virus research pertinent to agriculture and public health. Stanley's venture benefited significantly from the expansion of California's economy after World War II, and his mobilization against viral diseases resonated with the concerns of the Cold War, which fueled the state's rapid growth. The scientific prominence of contemporary developments at Caltech and Stanford invites the historical examination of the significance of postwar biochemistry and molecular biology within the political and cultural economy of the Golden State.In 1950, Stanley presented a persuasive picture of the power of biochemistry to refurbish life science at Berkeley while answering fundamental questions about life and infection. In the words of one Rockefeller Foundation officer,There seems little doubt in [my] mind that as a personality Stanley will be well able to dominate the other personalities on the Berkeley campus and will be able to drive his dream through to completion, which, incidentally, leaves Dr. Hubert [sic] Evans and the whole ineffective Life Sciences building in the somewhat peculiar position of being by-passed by much of the truly modern biochemistry and biophysics research that will be carried out at Berkeley. Furthermore, it seems likely that Dr. S's show will throw Dr. John Lawrence's Biophysics Department strongly in the shade both figuratively and literally, but should make the University of California pre-eminent not only in physics but in biochemistry as well.101Stanley, Sproul, Weaver, and this officer (William Loomis) all testified to a perceptible postwar opportunity to capitalize on public support for biological research that relied on the technologies from physics and chemistry without being captive to them, and that addressed issues of medicine and agriculture without being institutionally subservient. What is striking, given the expectation by many that Stanley would ‘be able to drive his dream through to completion,” was that in fact he did not. Biochemists who had succeeded in making their expertise valued in specialized niches were resistant to giving up their affiliations to joint Stanley's “liberated” organization. Stanley's failure was not simply due to institutional factors: researchers as well as Rockefeller Foundation officers faulted him for his lack of scientific imagination, which made it difficult for him to gain credibility in leading the field. Moreover, many biochemists did not share Stanley's commitment to viruses as the key material for the “new biochemistry.”In the end, Stanley's free-standing department did become a first-rate department of biochemistry, but only after freeing itself from Stanley's leadership and his single-minded devotion to viruses. Nonetheless, the falling-out with the Berkeley biochemists was rapidly followed by the establishment of a Department of Molecular Biology, attesting to the unabating economic and institutional possibilities for an authoritative “general biology” (or two, for that matter) to take hold. In each case, following Stanley's dream sheds light on how the possible and the real shaped the (re)formation of biochemistry and molecular biology as postwar life sciences. (shrink)

Are living organisms--as Descartes argued--just machines? Or is the nature of life such that it can never be fully explained by mechanistic models? In this thought-provoking and controversial book, eminent geophysicist Walter M. Elsasser argues that the behavior of living organisms cannot be reduced to physico-chemical causality. Suggesting that molecular biology today is at the same point as Newtonian physics on the eve of the quantum revolution, Elsasser lays the foundation for a theoretical biology that points the way toward (...) a natural philosophy of organic life. Explicitly repudiating "vitalism" (the notion that the laws of nature need to be modified when applied to living organisms), Elsasser argues instead that the structural complexity of even a single living cell is "transcomputational"--that is, beyond the power of any imaginable system to compute. Beginning from this insight, Elsasser leads the reader through a step-by-step process that ultimately arrives at the conclusion that living and non-living matter are separated by "a no-man's land of irrationality." Trained in Germany as a physicist, Elsasser first pondered the implications of quantum mechanics for biology as early as 1951. The more closely he studied the inherent complexity of life, the more skeptical he became of the reductionist view of organisms as tiny machines. "An organism," he concluded, "is a source of causal chains which cannot be traced beyond a terminal point because they are lost in the unfathomable complexity of the organism." Like the physicist who works within the bounds of an unfathomable universe, Elsasser argues, the biologist must seek answers within a system that is no less unfathomable. (shrink)

Degeneracy is a poorly understood process, essential to natural selection. In the 18th and 19th centuries, the concept of degeneracy was commandeered by the colonial imagination. A rigid understanding of species, race, and culture grew to dominate the normative thinking that persisted well into the burgeoning new industrial age. A 20th-century reconfiguration of the concept by George Gamow highlighted a form of intraorganismic variation that is still underexplored. Degeneracy exists in a population of variants where structurally different components perform (...) a similar, but not necessarily identical, function with respect to context. The presence of degeneracy increases a system’s complexity and robustness against perturbations. The loss of a genetic component in biological systems, for example, can be compensated by redundant elements , or by degenerate elements . A historical survey of the use of the term “degeneracy” reveals how and why the processes it once designated, and the mechanisms it now represents, have largely escaped the purview of contemporary science. Despite confusion and general oversight, degeneracy has been characterized by select researchers at the molecular, genetic, and neuronal levels. The concept is a potent analytical tool to understand selection, variation, and transmission. (shrink)

I address this talk to anyone who believes in the possibility of an informative empirical science about sensory qualities. Potentially this is a large audience. By "sensory quality" I mean those qualities manifest in various sensory experiences: color, taste, smell, touch, pain, and so on. We should include sensory modalities humans do not share, such as electro-reception in fish, echolocation in bats, or the skylight compass in birds. Those pursuing empirical science about this large domain might pursue it in the (...) halls of experimental psychology, psycho-physics, psychometrics, psycho-physiology, sensory physiology, neuroscience, neuro-biology, comparative psychology, neuro-anatomy, and so on and on. These days even molecular genetics has kicked in with some notable recent contributions to the sequencing of genes for photopigments and for olfactory receptors. But to all those investigators in all those halls I bring bad news. Your discipline is _a priori_ impossible. Philosophers whom you do not know have uncovered _a priori_ proofs that empirical investigation which proceeds along the lines currently underway, or which will proceed along lines that are currently _imaginable_, does not, will not, and cannot explain the sensory qualities of experience. Or at least so they say. You might as well give up now. (shrink)

This article develops a framework for analysing how digital software and models become mediums for creative imagination in architectural design. To understand the hermeneutics of these relationships, we develop key concepts from Material Engagement Theory (MET) and Postphenomenology (PP). To push these frameworks into the realm of digital design, we develop the concept of Digital Materiality. Digital Materiality describes the way successive layers of mathematics, code, and software come to mediate enactive perception, and the possibilities of creative material engagement (...) actualised in work with software. Just as molecular materials come to transform action with material objects, so digital materiality comes to enable and transform creative practices with computers. Digital architectural design form a new space for ongoing enactive discovery and creativity through manipulation of digital models and their underlying software environments. By shifting relationships within their digital models, architects can direct their attention, intention, and imagination towards widely different aspects of the model. Here, creative imagination becomes a fundamentally situated activity where mind emerges through dynamic interaction between a variety of embodied, material, and cultural domains. (shrink)

The classical model of the molecule assumes that it has a definite shape and structure like a mechanical object in the world of possible experience. This study deals with this assumption so as to shed some light on the foundations of the model. Arguments based on Kant’s theory of transcendental idealism suggest that neither shape nor structure are attributes of the molecule, but are rather contributions of the subject. This claim has great relevance to the questions of whether or not (...) a quantum treatment of the molecule can derive structure without recourse to any approximation, and the possible existence of emergence and downward causation. The answer to the first question is in the negative, and to the second is that agnosticism is the only possible attitude to have toward this problem. We are creatures who can only imagine what is going on by observing phenomena. All that is accessible to us is the modal structure of the model. The causal structure of the real system is not. From the same point of view and taking the concept of the affordance into account, the adequacy of the concept of molecular structure will be argued. The point is to specify what objects the concept can legitimately be applied to. Also briefly discussed in relation to shape and structure is the idea that molecular chirality might be a probe to reveal the nature of space. (shrink)

Genomics is increasingly considered a global enterprise – the fact that biological information can flow rapidly around the planet is taken to be important to what genomics is and what it can achieve. However, the large-scale international circulation of nucleotide sequence information did not begin with the Human Genome Project. Efforts to formalize and institutionalize the circulation of sequence information emerged concurrently with the development of centralized facilities for collecting that information. That is, the very first databases build for collecting (...) and sharing DNA sequence information were, from their outset, international collaborative enterprises. This paper describes the origins of the International Nucleotide Sequence Database Collaboration between GenBank in the United States, the European Molecular Biology Laboratory Databank, and the DNA Database of Japan. The technical and social groundwork for the international exchange of nucleotide sequences created the conditions of possibility for imagining nucleotide sequences as a “global” objects. The “transnationalism” of nucleotide sequence was critical to their ontology – what DNA sequences came to be during the Human Genome Project was deeply influenced by international exchange. (shrink)

Wolf Totem is not a novel which advocates ‘molar’ wolf characteristics such as violence, brutality and bloodthirstiness, and ‘molar’ wolf laws such as the law of the jungle and the law of profiting at others’ expense, but a novel which reveals to readers a brand new life experience, different affects possessed by the ‘molecular’ wolf, and the becoming-wolf of human beings. Becoming-wolf is not to imitate the above-mentioned characteristics of the ‘molar’ wolf, but to see or imagine what affects (...) the ‘molecular’ wolf has, and make the life force or the assumed life force possessed by the ‘molecular’ wolf transverse a person, so that he or she can also have those affects. Becoming-wolf is to find a line of flight between man and wolf, to get rid of all the restraints imposed by the Confucian culture on the law-abiding, abjectly obedient people, and thus regaining the force of the ‘impersonal, inorganic’ life, so as to become different by endless desiring productions, and enhance mankind's power. (shrink)

The Drosophila compound eye is an excellent experimental system for analysing fate induction of identifiable single cells. Each ommatidium, a unit eye, contains eight photoreceptors (R1‐R8), and the differentiation of these photoreceptors occurs in the larval eye imaginal disc in discrete steps: first R8 is determined, then R2/R5, R3/R4, R1/R6 and finally R7. Induction of R7, in particular, has been extensively studied at the molecular level. The R8 photoreceptor presents on its surface a ligand, Bride of Sevenless, that binds (...) and activates Sevenless receptor tyrosine kinase in the R7 precursor. Autophosphorylated Sevenless initiates a Ras1‐mediated cascade, which eventually activates transcription factors in the nucleus via Raf1 and MAP kinases, resulting in R7 development. However, recent studies indicate that Sevenless (Sev) functions just to neuralize the cell and has no role in R7 fate determination per se. It appears that the R7 fate may represent the lowest rung of a ‘neuronal ground state’, which is attained without any specific inductive cue. It is plausible that the R7 precursor is actively prevented from taking on the neuronal fate and this inhibition is removed by activation of Sev. (shrink)

Unlike in physics, the category of thought experiment is not very common in biology. At least there are no classic examples that are as important and as well-known as the most famous thought experiments in physics, such as Galileo’s, Maxwell’s or Einstein’s. The reasons for this are far from obvious; maybe it has to do with the fact that modern biology for the most part sees itself as a thoroughly empirical discipline that engages either in real natural history or in (...) experimenting on real organisms rather than fictive ones. While theoretical biology does exist and is recognized as part of biology, its role within biology appears to be more marginal than the role of theoretical physics within physics. It could be that this marginality of theory also affects thought experiments as sources of theoretical knowledge. Of course, none of this provides a sufficient reason for thinking that thought experiments are really unimportant in biology. It is quite possible that the common perception of this matter is wrong and that there are important theoretical considerations in biology, past or present, that deserve the title of thought experiment just as much as the standard examples from physics. Some such considerations may even be widely known and considered to be important, but were not recognized as thought experiments. In fact, as we shall see, there are reasons for thinking that what is arguably the single most important biological work ever, Charles Darwin’s On the Origin of Species, contains a number of thought experiments. There are also more recent examples both in evolutionary and non-evolutionary biology, as we will show. Part of the problem in identifying positive examples in the history of biology is the lack of agreement as to what exactly a thought experiment is. Even worse, there may not be more than a family resemblance that unifies this epistemic category. We take it that classical thought experiments show the following characteristics: They serve directly or indirectly in the non-empirical epistemic evaluation of theoretical propositions, explanations or hypotheses. Thought experiments somehow appeal to the imagination. They involve hypothetical scenarios, which may or may not be fictive. In other words, thought experiments suppose that certain states of affairs hold and then try to intuit what would happen in a world where these suppositions are true. We want to examine in the following sections if there are episodes in the history of biology that satisfy these criteria. As we will show, there are a few episodes that might satisfy all three of these criteria, and many more if the imagination criterion is dropped or understood in a lose sense. In any case, this criterion is somewhat vague in the first place, unless a specific account of the imagination is presupposed. There will also be issues as to what exactly “non-empirical” means. In general, for the sake of discussion we propose to understand the term “thought experiment” here in a broad rather than a narrow sense here. We would rather be guilty of having too wide a conception of thought experiment than of missing a whole range of really interesting examples. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:A Chance to CutBruce H. CampbellMy gloved hand reaches for progressively sharper surgical instruments. The prior radiation therapy and recurrent cancer [End Page E3] have made his neck tissues as stiff and hard as an old block of wood; everything appears too dull and feels too dry under the bright operating room lights. I push, dissect, urge, divide, prod, and spread with little effect.The nursing staff keeps to its (...) routine—completing computer entries, retrieving supplies, counting sponges—only intermittently aware that things are not going well at the point of attack. Nondescript music plays softly and the anesthesia machine continues to emit its gentle sounds. The junior resident—assisting me with the first of many neck dissections she will see during her five years of training—grips the retractor as she has been told and dabs the wound periodically to clear any blood or fluid.I glance up to recheck the CT scan. It confirms that this man’s recurrent cancer is just below the next layer of neck muscles. There are also some large blood vessels and major nerves nearby. I am confident, though, that I will be able to expose the mass, protect all of the critical structures, and safely remove the cancer.Curing cancer with surgery is no small feat, mind you. Cancer is, after all, a molecular disease not easily confined to an obvious lump, even though we sometimes refer to a malignant mass being “like a walnut” or “as hard and round as a marble.” The actual disease rests deep inside each cancer cell where the genetic code—the DNA—makes mistake–after–mistake. If cancer is to be cured with a surgical procedure, the surgeon must remove every last cell that is capable of making the same nonsensical, life–threatening error. Given Science’s rudimentary knowledge of cancer cell dynamics and signaling, it’s a miracle that surgery ever works. Yet, we continue to try. And we succeed just often enough to keep on trying.I rearrange the retractors and alter my approach. My mentors would have known what to do next, I imagine. My training included time well–spent with brilliant and technically–gifted surgeons. How would they have approached this case? Their experience and instincts might have told them to open the wound more widely, work the lateral and deep margins first, or position the instruments differently.Perhaps, one of my mentors would have attacked this man’s tumor using the same approach I am attempting but would have known exactly where to exploit some area of weakness that I cannot locate. A few swift, confident moves and he would have held the mass in his hands. “That’s it. We’re done,” he would have said.I met this patient several months ago when his cancer was first discovered and have seen him throughout his course of treatment. Recently, his daughter had accompanied him to the office to review his options. “Treatment has been rugged, Doc,” he reminded me. “The cancer’s still there and they said I can’t get any more radiation. Chemo would only prolong things. I don’t really want surgery, but what choice do I have if I want to be cured?”“Supportive care is an option, but the only curative approach is surgery.”“Well, I’m not ready to quit yet, Doc. I got grand-kids, y’know. I want to watch them grow up.” He nodded to his daughter. “I’m in charge of spoiling her little boys.”The daughter smiled. We crowded around the computer screen to look at the scans. I showed them how the tumor was invading and destroying surrounding structures. I described the surgery and the risks.“There are many things I will not know about your tumor until we are actually in the operating room,” I explained. Surgery in the setting of recurrent disease involves a series of on–the–spot decisions and course corrections. The odds of success are unknowable. “Sometimes, the only way to find out if we can remove the cancer is simply to try.”He took a deep breath and looked at his daughter. “Well then, Doc, if surgery is the only... (shrink)

A cell's biochemistry is now known to be the biochemistry of molecular machines, that is, protein complexes that are assembled and dismantled in particular locations within the cell as needed. One important element in our understanding has been the ability to begin to see where proteins are in cells and what they are doing as they go about their business. Accordingly, there is now a strong impetus to discover new ways of looking at the workings of proteins in living (...) cells. Although the use of fluorescent tags to track individual proteins in cells has a long history, the availability of laser-based confocal microscopes and the imaginative exploitation of the green fluorescent protein from jellyfish have provided new tools of great diversity and utility. It is now possible to watch a protein bind its substrate or its partners in real time and with submicron resolution within a single cell. The importance of processes of self-organisation represented by protein folding on the one hand and subcellular organelles on the other are well recognised. Self-organisation at the intermediate level of multimeric protein complexes is now open to inspection. BioEssays 22:180–187, 2000. ©2000 John Wiley & Sons, Inc. (shrink)

The introduction of recombinant DNA technology into the field of genetics has led to a rapid advancement of our knowledge of genes and genome structure. Such technology, applied to the human genome, has provided valuable information concerning the nature and possible treatment of inherited disorders. The possibility that this knowledge will pave the way for the correction of at least some of these disorders has captured the imagination of the informed public. In this review we look at the accomplishments (...) of molecular pathologists to date and how new techniques are being applied to the study of inherited disease. (shrink)

Tendencies and efforts have shifted from genome description, DNA mapping, and DNA sequencing to active and profound re-programming, repairing life on genetic and molecular levels in some parts of contemporary life science research. Mirroring and materializing this atmosphere, various life engineering technologies have been used and established in many areas of life sciences in the last decades. A contemporary progressive example of one such technology is DNA editing. Novel developments related to reproductive technologies, particularly embryo editing, prenatal human life (...) engineering, and germline engineering need to be analyzed against the broader social and structural background. The crucial analytical scope for this paper is a specific field: the life-editing technologies used in reproductive medicine and performed experimentally on viable human embryos, particularly CRISPR/cas9 technology. This text argues that germline editing technologies, as a representative part of contemporary biomedicine, are merging ideas of treatment and enhancement to avoid future risks. Using this specific life manipulation of embryos and gametes, the text analyzes these processes within the concept of power over life—biopower and the specific governing rationality that imagines, classifies, and governs contemporary societies. The text specifically focuses on the potential to create, define, and manage future risks and uncertainties related to prenatal life. (shrink)

An adequate account of how inferences and discoveries are made in modern biology is a difficult prospect for a philosopher. Do we really deduce conclusions from Darwin’s principles? Once Darwinian biology is integrated with molecular biology, can we deduce the organism from its DNA? What does induction look like in an era where data sets are often too large to be processed by a human being? What is the role of abductive explanatory claims that try to define the biological (...) individual in relation to the microbiome with which it may be associated, or to revise the notion of evolution when the interaction of organism and environment comes to seem much more complex than earlier generations imagined. How should we evaluate “origins of life” experiments conducted in the laboratory, where chemistry shifts to biology and we try to recreate early conditions on earth to which we have no empirical access? How are the carefully controlled conditions in the lab to be brought into productive relationship with the messy, contingent outdoor work of biologists in the field, studying crabs or eelgrass at the edge of the Pacific Ocean, or prairie plants at the end of woods, on the plains of the Midwest. To answer these questions, I sent my graduate student Tano Posteraro to work with Ted Grosholz, a marine biologist at the University of California / Davis, and my undergraduate student Alex Grigas to work with Ruth Geyer Shaw, a population geneticist at the University of Minnesota. They came back with complex and interesting answers to these questions. (shrink)

While for the majority of physicists the problem of the deciphering of the brain code, the intelligence code, is a matter for future generations, the author boldly and forcefully disagrees. Breaking with the dogma of classical logic he develops in the form of the conversion postulate a concrete working hypothesis for the actual thought mechanism. The reader is invited on a fascinating mathematical journey to the very edges of modern scientific knowledge. From lepton and quark to mind, from cognition to (...) a logic analogue of the Schrodinger equation, from Fibonacci numbers to logic quantum numbers, from imaginary logic to a quantum computer, from coding theory to atomic physics - the breadth and scope of this work is overwhelming. Combining quantum physics, fundamental logic and coding theory this unique work sets the stage for future physics and is bound to titillate and challenge the imagination of physicists, biophysicists and computer designers. Growing from the author's matrix operator formalization of logic, this work pursues a synthesis of physics and logic methods, leading to the development of the concept of infophysics. The experimental verification of the proposed quantum hypothesis of the brain is presently in preparation in cooperation with the Cavendish Laboratory, Cambridge, UK, and, if proved positive, would have major theoretical implications. Even more significant should be the practical applications in such fields as molecular electronics and computer science, biophysics and neuroscience, medicine and education. The new possiblities that could be opened up by quantum level computing could be truly revolutionary. The book aims at researchers and engineers in technical sciences as well as in biophysics and biosciences in general. It should have great appeal for physicists, mathematicians, logicians and for philosophers with a mathematical bent. (shrink)

This is the third, penultimate volume in the Toward a Theoretical Biology series. The contributors agree that there is a major problem in finding methods of dealing with the great complexity of biological systems. Molecular biology has given us considerable insight into the nature of the elementary units and processes of life, but to understand how these are put together to form systems that are usually too complicated to be analyzed completely, but exhibit global properties of simplicity, presents biologists (...) with an intellectual challenge that physical sciences and chemistry must also face. The problem is approached from several different angles: quantum physics, topology, and statistical mechanics. A stimulating discussion is recorded: that the behavior of randomly constructed networks exhibits simplicity. Thoughtful analyses of complexities in such basic biological processes as the genetic control of differentiation, evolution, and ecology is also included. Some of the questions dealt with are: What kinds of theories should we wish to have in connection with developmental biology? And have we got them? The subject matter of Organization Stability and Process is defined as the basic concept of biology. None of the contributors herein contained is a molecular biologist in the modern sense, but molecular biology casts a shadow over this work, at least in so far as they challenge its interpretative aggressiveness and its enthusiastic but unendearing self-confidence and self-sufficiency. This volume inaugurates a new and authentic style of scientific literature. The contributions are thoughtful, imaginative, illuminating, and exceptionally well written. (shrink)

IntroductionThe identity thesis asserts that for every psychological state P there is a neural state N such that P=N. In the hope of rendering IT clear and plausible many identity theorists have compared psycho-neural identity claims to such theoretical identities as temperature is identical with molecular mean kinetic energy. However such a comparison admits a weak and a strong interpretation. According to the weak interpretation, psycho-neural identities are said to be like theoretical identities in the sense that the former (...) are contingent claims just as the latter are presumed to be. Identity theorists have appealed to the contingent status of IT in order to meet prima facie objections of the following sort. We can imagine ourselves undergoing a pain, although we are not undergoing the neural process which the identity theorist claims is identical with the pain. Indeed we can imagine ourselves being in pain and yet not having a brain at all. Hence IT is false. Identity theorists have replied by arguing that this objection merely shows that IT is not a necessary truth, or that psychological and neurological terms do not have the same meaning. (shrink)

In this fascinating and bold discussion, a renowned neurobiologist serves as guide to the most complex physical object in the living world: the human brain. Taking into account the newest brain research—morphological, physiological, chemical, genetic—and placing these findings in the context of psychology, philosophy, art, and literature, Changeux ventures into the unexplored territories where these diverse disciplines intersect. Changeux's book draws on Plato's notion that the Good, the True, and the Beautiful are celestial essences or ideas, independent but so intertwined (...) as to be inseparable. Placing these essences within the characteristic features of the human brain's neuronal organization, the author addresses unsolved questions in neuroscience today. With imagination and deep insight, Changeux illuminates the evolution of the brain and deciphers what new developments in neuroscience may portend for the future of humanity. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:The Maternal Imprint: The Contested Science of Maternal-Fetal Effects (2021) by Sarah RichardsonQuill KuklaQuill Kukla, review of Sarah Richardson's The Maternal Imprint: The Contested Science of Maternal-Fetal Effects (2021)I had been eagerly anticipating the release of Sarah Richardson's meticulously researched The Maternal Imprint: The Contested Science of Maternal-Fetal Effects (2021) for several years, and I was not disappointed. A leading feminist scholar of the history and philosophy of (...) science, Richardson traces the scientific history of the idea that pregnant people's bodies control the future health, character, and well-being of their offspring. She also explores how this science is translated into social messaging and shaped by social ideology. Richardson delves into the details of the methodology, motivations, results, and communication of the science of maternal influences. She reveals a history of shaky results, contested methods, and socially loaded messaging, unified by a sustained interest in framing maternal bodies as sites of risk and responsibility for birth outcomes.A central narrative of the book is that the perceived location and mechanism through which pregnant bodies control fetal development keeps shifting around; over time, scientists have located this maternal influence in the uterine environment, the cytoplasm, the methylation of DNA, maternal nutrition, and even in the emotions, thoughts, and imagination of the mother, among other locations.1 Each time a version of the maternal influence hypothesis re-emerges, targeting a different bodily location and mechanism, it comes along with similar social messaging: pregnant people are distinctively responsible for the 'quality' of their children; their bodies are distinctive sites of risk, in need of social management; and their influence can be understood and controlled independent of the context in which they live. Given how many times this scientific hypothesis and its accompanying social messaging has died and been reborn, it is hard not to conclude, with Richardson, that background ideology compels us to keep searching for new stories that take this same form. The idea that pregnant people's bodies are understood as decontextualized and heightened sites of risk and responsibility for birth outcomes, in need of systematic discipline (both self-discipline and social discipline) in order to ensure their production of proper offspring, is one that has been explored [End Page e-1] in quite a bit of depth within feminist theory and reproductive ethics over the last thirty years. To name just a few, Barbara Duden's Disembodying Women: Perspectives on Pregnancy and the Unborn (1993), Deborah Lupton's "Risk and the Ontology of Pregnant Embodiment" (1999), Lisa Mitchell's Baby's First Picture: Ultrasound and the Politics of Fetal Subjects (2001), and my own Mass Hysteria: Medicine, Culture, and Mothers' Bodies (2005) are all works firmly within this tradition. What is new about Richardson's book is not the development and exploration of this cultural narrative and imaginary, but rather her rigorous and skillful analysis of the science that has grown out of and undergirded it. Richardson is a masterful writer, who makes scientific details comprehensible and fascinating. Her historical and epistemological analyses of exactly what shaped the science at each stage, what each scientific iteration did and didn't manage to show, and how these different scientific movements were translated into public messaging, is sharp and compelling. Richardson shows us the inner workings of how scientific programs build momentum; how scientists make methodological decisions; and how results feed into ongoing research programs. From this book, we also develop a rich sense of just how much uncertainty is baked into the science of human development, and how both scientific and public excitement about a given research program are mostly independent of the success and security of the science that comes out of it. The book traces 150 years of the history of the science of maternal influences, culminating in the current focus on epigenetics—which, like various past maternal influence theories, has ignited our broader social imagination. Epigenetics, roughly, is the study of molecular changes outside our DNA that control how genes express themselves. Environmental stimuli (such as stress) can cause changes in methylation, and thereby influence the expression of the genome: "Epigenetic markers that help determine whether a... (shrink)

Whether or not quantum physics can account for molecular structure is a matter of considerable controversy. Three of the problems raised in this regard are the problems of molecular structure. We argue that these problems are just special cases of the measurement problem of quantum mechanics: insofar as the measurement problem is solved, the problems of molecular structure are resolved as well. In addition, we explore one consequence of our argument: that claims about the reduction or emergence (...) of molecular structure cannot be settled independently of the choice of a particular resolution to the measurement problem. Specifically, we consider how three standard putative solutions to the measurement problem inform our under- standing of a molecule in isolation, as well as of chemistry’s relation to quantum physics. (shrink)

What role does the imagination play in scientific progress? After examining several studies in cognitive science, I argue that one thing the imagination does is help to increase scientific understanding, which is itself indispensable for scientific progress. Then, I sketch a transcendental justification of the role of imagination in this process.

This essay argues that there are theoretical benefits to keeping distinct—more pervasively than the literature has done so far—the psychological states of imagining that p versus believing that in-the-story p, when it comes to cognition of fiction and other forms of narrative. Positing both in the minds of a story’s audience helps explain the full range of reactions characteristic of story consumption. This distinction also has interesting conceptual and explanatory dimensions that haven’t been carefully observed, and the two mental state (...) types make distinct contributions to generating emotional responses to stories. Finally, the differences between the mental states illuminate how a given story can be both shared with others and at the same time experienced as personal. (shrink)

Between the radical, creative capacity of our imagination and the social imaginary we are immersed in is an intermediate space philosophers have termed the imaginal, populated by images or (re)presentations that are presences in themselves. Offering a new, systematic understanding of the imaginal and its nexus with the political, Chiara Bottici brings fresh perspective to the formation of political and power relationships and the paradox of a world rich in imagery yet seemingly devoid of imagination. Bottici begins by (...) defining the difference between the imaginal and the imaginary, locating the imaginal's root meaning in the image and its ability to both characterize a public and establish a set of activities within that public. She identifies the imaginal's critical role in powering representative democracies and its amplification through globalization. She then addresses the troublesome increase in images now mediating politics and the transformation of politics into empty spectacle. The spectacularization of politics has led to its virtualization, Bottici observes, transforming images into processes with an uncertain relationship to reality, and, while new media has democratized the image in a global society of the spectacle, the cloned image no longer mediates politics but does the act for us. Bottici concludes with politics' current search for legitimacy through an invented ideal of tradition, a turn to religion, and the incorporation of human rights language. (shrink)

There is consensus within the chemosciences that olfactory perception is of the molecular structure of chemical compounds, yet within philosophical theories of smell there is little agreement about the nature of smell. The paper critically assesses the current state of debate regarding smells within philosophy in the hopes of setting it upon firm scientific footing. The theories to be covered are: Naïve Realism, Hedonic Theories, Process Theory, Odor Theories, and non-Objectivist Theories. The aforementioned theories will be evaluated based on (...) their explanations of the (a) the olfactory quality of a smell, (b) smells as distal entities, and (c) our experience of smells as intentional objects. The paper concludes with a defense of Molecular Structure Theory that demonstrating its superiority in accounting for each of these three aspects of smell. (shrink)

Despite the transformation in biological practice and theory brought about by discoveries in molecular biology, until recently philosophy of biology continued to focus on evolutionary biology. When the Human Genome Project got underway in the late 1980s and early 1990s, philosophers of biology -- unlike historians and social scientists -- had little to add to the debate. In this landmark collection of essays, Sahotra Sarkar broadens the scope of current discussions of the philosophy of biology, viewing molecular biology (...) as a unifying perspective on life that complements that of evolutionary biology. His focus is on molecular biology, but the overriding question behind these papers is what molecular biology contributes to all traditional areas of biological research.Molecular biology -- described with some foresight in a 1938 Rockefeller Foundation report as a branch of science in which "delicate modern techniques are being used to investigate ever more minute details" -- and its modeling strategies apparently argue in favor of physical reductionism. Sarkar's first three chapters explore reductionism -- defending it, but cautioning that reduction to molecular interactions is not necessarily a reduction to genetics. The next sections of the book discuss function, exploring how functional explanations pose a problem for reductionism; the informational interpretation of biology and how it interacts with reductionism; and the tension between the unifying framework of molecular biology and the received framework of evolutionary theory. The concluding chapter is an essay in the emerging field of developmental evolution, exploring what molecular biology may contribute to the transformation of evolutionary theory as evolutionary theory takes into account morphogenetic development. (shrink)

It is widely believed, among philosophers of literature, that imagining contradictions is as easy as telling or reading a story with contradictory content. Italo Calvino’s The Nonexistent Knight, for instance, concerns a knight who performs many brave deeds, but who does not exist. Anything at all, they argue, can be true in a story, including contradictions and other impossibilia. While most will readily concede that we cannot objectually imagine contradictions, they nevertheless insist that we can propositionally imagine them, and regularly (...) do, simply by entertaining a text which prompts us to do so. I argue that this narrative does not bear scrutiny for two main reasons. First, because propositional imagining is beside the point, where truth in fiction is concerned; evaluating truth in fiction engages the cognitive architecture in ways that prohibit the mobilization of merely propositional imagination to that end. And second, because it is not obvious, given the strategies usually suggested, that we ever propositionally imagine contradictions in the first place—in fact, it seems we go out of our way to avoid directly imagining them. (shrink)

With Imagining Karma, Gananath Obeyesekere embarks on the very first comparison of rebirth concepts across a wide range of cultures. Exploring in rich detail the beliefs of small-scale societies of West Africa, Melanesia, traditional Siberia, Canada, and the northwest coast of North America, Obeyesekere compares their ideas with those of the ancient and modern Indic civilizations and with the Greek rebirth theories of Pythagoras, Empedocles, Pindar, and Plato. His groundbreaking and authoritative discussion decenters the popular notion that India was the (...) origin and locus of ideas of rebirth. As Obeyesekere compares responses to the most fundamental questions of human existence, he challenges readers to reexamine accepted ideas about death, cosmology, morality, and eschatology. Obeyesekere's comprehensive inquiry shows that diverse societies have come through independent invention or borrowing to believe in reincarnation as an integral part of their larger cosmological systems. The author brings together into a coherent methodological framework the thought of such diverse thinkers as Weber, Wittgenstein, and Nietzsche. In a contemporary intellectual context that celebrates difference and cultural relativism, this book makes a case for disciplined comparison, a humane view of human nature, and a theoretical understanding of "family resemblances" and differences across great cultural divides. (shrink)

Fragmented thinking, broken world -- Toward recovery of wholeness: the radical humanities and traditional wisdom -- Toward recovery of wholeness: another look at science -- Insight-imagination -- Living thinking, living world: toward an education of insight-imagination.

One of the most plausible and widely discussed examples of strong emergence is molecular structure. The only detailed account of it, which has been very influential, is due to Robin Hendry and is formulated in terms of downward causation. This paper explains Hendry’s account of the strong emergence of molecular structure and argues that it is coherent only if one assumes a diachronic reflexive notion of downward causation. However, in the context of this notion of downward causation, the (...) strong emergence of molecular structure faces three challenges that have not been met and which have so far remained unnoticed. First, the putative empirical evidence presented for the strong emergence of molecular structure equally undermines supervenience, which is one of the main tenets of strong emergence. Secondly, it is ambiguous how the assumption of determinate nuclear positions is invoked for the support of strong emergence, as the role of this assumption in Hendry’s argument can be interpreted in more than one way. Lastly, there are understandings of causation which render the postulation of a downward causal relation between a molecule’s structure and its quantum mechanical entities, untenable. (shrink)

Biologists and historians often present natural history and molecular biology as distinct, perhaps conflicting, fields in biological research. Such accounts, although supported by abundant evidence, overlook important areas of overlap between these areas. Focusing upon examples drawn particularly from systematics and molecular evolution, I argue that naturalists and molecular biologists often share questions, methods, and forms of explanation. Acknowledging these interdisciplinary efforts provides a more balanced account of the development of biology during the post-World War II era.

If a work of literary fiction prescribes us to imagine that the Devil made a bet with God and transformed into a poodle, then that claim is true in the fiction and we imagine accordingly. Generally, we cooperate imaginatively with literary fictions, however bizarre, and the things authors write into their stories become true in the fiction. But for some claims, such as moral falsehoods, this seems not to be straightforwardly the case, which raises the question: Why not? The puzzles (...) such cases raise are sometimes grouped under the heading “imaginative resistance”. In this paper, I argue against what I take to be the best attempts to dismiss the puzzles and solve them. I also tease out subtleties not sufficiently addressed in the existing literature and end by defending a unified solution of my own. According to this solution, the puzzling phenomena occur when literary works offer inadequate and exhaustive grounds for claims. The solution’s novelty lies in its giving a normative rather than psychological or alethic explanation for the puzzling phenomena, the relevant norms being those of proper artistic appreciation. (shrink)