Interlevel Relations in Biology

The organism against its environment. The organism against other organisms, competing and struggling for life. Antagonism and confrontment as the only possible relation in nature. The tendency to anthropomorphize nature and explain it using concepts and facts from the human sphere. A stroll through the worlds of Uexküll and Merleau-Ponty in the search of alternative knowledge that allow us to understand relation from another point of view. A counterpoint and identification of common tonalities between the research programs from both thinkers (...) as a way to demonstrate the possibilities of a more fruitful approach. Umwelt as a generative system of meaningful relations in which its participants are not mutually exclusive, but express a melody that include them all. (shrink)

Life is the center of our existence. One would be tempted to say that first of all we live. However, our existence does not seem to pass in that modality. The exacerbated materialism in which our existence takes place, displaces life from the center of the scene. Our society is organized around production, consumerism, exploitation, efficiency, trade and propaganda. That is to say, our existence seems to have economy as the center of organization of our activities. The struggle of this (...) century that is beginning is to put life at the center of our existence, and to put economy in its proper place, that is, in the service of life. (shrink)

Over the last decades, network-based approaches have become highly popular in diverse fields of biology, including neuroscience, ecology, molecular biology and genetics. While these approaches continue to grow very rapidly, some of their conceptual and methodological aspects still require a programmatic foundation. This challenge particularly concerns the question of whether a generalized account of explanatory, organisational and descriptive levels of networks can be applied universally across biological sciences. To this end, this highly interdisciplinary theme issue focuses on the definition, motivation (...) and application of key concepts in biological network science, such as explanatory power of distinctively network explanations, network levels, and network hierarchies. (shrink)

The subject of this edited volume is the idea of levels of organization: roughly, the idea that the natural world is segregated into part-whole relationships of increasing spatiotemporal scale and complexity. The book comprises a collection of essays that raise the idea of levels into its own topic of analysis. Owing to the wide prominence of the idea of levels, the scope of the volume is aimed at theoreticians, philosophers, and practicing researchers of all stripes in the life sciences. The (...) volume’s contributions reflect this diversity, and draw from fields such as developmental biology, evolutionary biology, molecular biology, ecology, cell biology, and neuroscience. The book presents wide-ranging novel insights on causation and levels, the hierarchical structure of evolution, the role of levels in biological theory, and more. (shrink)

Despite its pervasiveness, the concept of ‘levels of organization’ has received relatively little attention in its own right. I propose here an emerging approach that posits ‘levels’ as a fragmentary concept situated within an interest-relative matrix of operational usage within scientific practice. To this end I propose one important component of meaning, namely the epistemic goal motivating the term’s usage, which recovers a remarkably conserved and sufficiently unifying significance attributable to ‘levels’ across different instances of usage. This epistemic goal, to (...) provide structure to scientific problems, delegates tasks whose execution generates the term’s expressed content in a given instance. This treatment of levels does not diminish the concept’s general importance to science, but rather allows for its use in, and usefulness for, scientific practice to be better contextualized to particular tasks encompassing varying breadths of activity. (shrink)

Many researchers consider cancer to have molecular causes, namely mutated genes that result in abnormal cell proliferation (e.g. Weinberg 1998); yet for others, the causes of cancer are to be found not at the molecular level but at the tissue level and carcinogenesis would consist in a disrupted tissue organization with downward causation effects on cells and cellular components (e.g. Sonnenschein & Soto 2008). In this contribution, I ponder how to make sense of such downward causation claims. Adopting a manipulationist (...) account of causation (Woodward 2003), I propose a formal definition of downward causation, and discuss further requirements (in light of Baumgartner 2009). I then show that such an account cannot be mobilized in support of non-reductive physicalism (contrary to Raatikainen 2010). However, I also argue that such downward causation claims might point at particularly interesting dynamic properties of causal relationships that might prove salient in characterizing causal relationships (following Woodward 2010). (shrink)

"Brower explores the way philosophers were inspired by entomological social systems and communication to reflect on human psyche, social behavior, community organization, communication, and inter-individual relationships. His essay rehearses the swarms of insects embedded in contemporary philosophy and literary theory, not only showing how many of the major concepts (or philosophemes) in continental philosophy – sexuality, politics, thinking, time, interdependence, and language – draw lessons from the world of insects, but also illustrating again how the insect world spurred human reflection.".

Darwin described biological species as groups of morphologically similar individuals. These groups of individuals can split into several subgroups due to natural selection, resulting in the emergence of new species. Some species can stay stable without the appearance of a new species, some others can disappear or evolve. Some of these evolutionary patterns were described in our previous works independently of each other. In this work we have developed a single model which allows us to reproduce the principal patterns in (...) Darwin’s diagram. Some more complex evolutionary patterns are also observed. The relation between Darwin’s definition of species, stated above, and Mayr’s definition of species is also discussed. (shrink)

The concept of 'levels of organization' has come under fire recently as being useless for scientific and philosophical purposes. In this paper, we show that 'levels' is actually a remarkably resilient and constructive conceptual tool that can be, and in fact is, used for a variety of purposes. To this effect, we articulate an account of the importance of the levels concept seen in light of its status as a major organizing concept of biology. We argue that the usefulness of (...) ‘levels’ is best seen in the heuristic contributions the concept makes to treating and structuring scientific problems. We illustrate this with two examples from biological research. (shrink)

Bence Nanay has argued that we must abandon the etiological theory of teleological function because this theory explains functions and functional categories in a circular manner. Paul Griffiths argued earlier that we should retain the etiological theory and instead prevent the circularity by making etiologies independent of functional categories. Karen Neander and Alex Rosenberg reply to Nanay similarly, and argue that we should analyze functions in terms of natural selection acting not on functional categories, but merely on lineages. Nanay replies (...) that these lineages cannot be individuated except by reference to functional categories. Worryingly, Neander and Rosenberg themselves have previously argued persuasively that homology often depends on function. This article addresses their arguments and shows how to escape them: Regardless whether the arguments are right about long-term homological categories, they do not apply to generation-to-generation homology. The latter, moreover, is sufficient for individuating the lineages needed to explain teleological functions. (shrink)

The paper offers a partial vindication of Sterelny’s view on the role of error rates and reliability in his theory of decoupled representation based on modelling techniques borrowed from the biological literature on evolution in stochastic environments. In the case of a tight link between tracking states and behaviour, I argue that in its full generality Sterelny’s account instantiates the base-rate fallacy. With regard to non-tightly linked behaviour, I show that Sterelny’s account can be vindicated subject to an adequate evolutionary (...) model and a suitable notion of reliability. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

We sketch the mechanistic approach to levels, contrast it with other senses of “level,” and explore some of its metaphysical implications. This perspective allows us to articulate what it means for things to be at different levels, to distinguish mechanistic levels from realization relations, and to describe the structure of multilevel explanations, the evidence by which they are evaluated, and the scientific unity that results from them. This approach is not intended to solve all metaphysical problems surrounding physicalism. Yet it (...) provides a framework for thinking about how the macroscopic phenomena of our world are or might be related to its most fundamental entities and activities. (shrink)

Explanations in the life sciences frequently involve presenting a model of the mechanism taken to be responsible for a given phenomenon. Such explanations depart in numerous ways from nomological explanations commonly presented in philosophy of science. This paper focuses on three sorts of differences. First, scientists who develop mechanistic explanations are not limited to linguistic representations and logical inference; they frequently employ diagrams to characterize mechanisms and simulations to reason about them. Thus, the epistemic resources for presenting mechanistic explanations are (...) considerably richer than those suggested by a nomological framework. Second, the fact that mechanisms involve organized systems of component parts and operations provides direction to both the discovery and testing of mechanistic explanations. Finally, models of mechanisms are developed for specific exemplars and are not represented in terms of universally quantified statements. Generalization involves investigating both the similarity of new exemplars to those already studied and the variations between them. (shrink)

In a recent article “From Epistemology to Ontology,” Tihamer Margitay argues, in addition to other things, that the ontological arguments Polanyi provided for his ontological realism with respect to the levels of reality are insufficient. Although Margitay shows this correctly in the case of arguments from boundary conditions, his arguments are not that convincing against the unidentifyability thesis, the thesis that entity kinds on higher levels cannot be identified with descriptions given on lower levels. I argue that here Polányi relies (...) on a version of the multiple realizeability thesis and this argument can be reformulated in a stronger version against which the counterargument Margitay provides is insufficient. (shrink)

The groups of problems that fall under the titles ‘reduction’ and ‘emergence’ appear at the boundaries of seemingly independent and well-established scientific disciplines, such as chemistry and biology, biology and psychology, biology and political theory, and so on. They arise in this way.

The Somatic Mutation Theory has been challenged on its fundamentals by the Tissue Organization Field Theory of Carcinogenesis. However, a recent publication has questioned whether TOFT could be a valid alternative theory of carcinogenesis to that presented by SMT. Herein we critically review arguments supporting the irreducible opposition between the two theoretical approaches by highlighting differences regarding the philosophical, methodological and experimental approaches on which they respectively rely. We conclude that SMT has not explained carcinogenesis due to severe epistemological and (...) empirical shortcomings, while TOFT is gaining momentum. The main issue is actually to submit SMT to rigorous testing. This concern includes the imperatives to seek evidence for disproving one’s hypothesis, and to consider the whole, and not just selective evidence. (shrink)

Understanding the organization of an organism by individuating meaningful parts and accounting for organismal properties by studying the interaction of bodily parts is a central practice in many areas of biology. While structures are obvious bodily parts and structure and function have often been seen as antagonistic principles in the study of organismal organization, my tenet is that structures and functions are on a par. I articulate a notion of function (functions as activities), according to which functions are bodily parts (...) just as structures are. Recognizing part-whole relations among an organism’s various structures and functions permits fruitful investigation and multilevel explanation of organismal properties and functioning, across both developmental and evolutionary time. I show how my perspective clarifies debates surrounding homology and evolutionary novelty that stem from an alleged structure-function dichotomy. My approach favors a pluralism about individuation, where the criteria of what counts as a meaningful bodily part depend on the particular epistemic aims pursued in a scientific context. (shrink)

Large sets of elements interacting locally and producing specific architectures reliably form a category that transcends the usual dividing line between biological and engineered systems. We propose to call them morphogenetically architected complex systems. While taking the emergence of properties seriously, the notion of MACS enables at the same time the design of operational means that allow controlling and even, paradoxically, programming this emergence. To demonstrate our claim, we first show that among all the self-organized systems studied in the field (...) of Artificial Life, the specificity of MACS essentially lies in the close relation between their emergent properties and functional properties. Second, we argue that to be a MACS a system does not need to display more than weak emergent properties. Third, since the notion of weak emergence is based on the possibility of simulation, whether computational or mechanistic via machines, we see MACS as good candidates to help design artificial self-architected systems but also harness and redesign living ones. (shrink)

Philosophers have proposed various kinds of relations between Mendelian genetics and molecular biology: reduction, replacement, explanatory extension. This paper argues that the two fields are best characterized as investigating different, serially integrated, hereditary mechanisms. The mechanisms operate at different times and contain different working entities. The working entities of the mechanisms of Mendelian heredity are chromosomes, whose movements serve to segregate alleles and independently assort genes in different linkage groups. The working entities of numerous mechanisms of molecular biology are larger (...) and smaller segments of DNA plus related molecules. Discovery of molecular DNA mechanisms filled black boxes that were noted, but unilluminated, by Mendelian genetics. (shrink)

The topic of this article is the analysis of the relations between different levels of reality. The core argument is based on considerations of both an epistemology of action and manipulative causality as a criterion of object identity. The argumentation is extended towards the concepts of self-organization and self-regulation. Finally, several views on reduction and the problems of emergence and complexity are discussed.

A recent evolution of computer simulations has led to the emergence of complex computer simulations. In particular, the need to formalize composite objects (those objects that are composed of other objects) has led to what the author suggests calling pluriformalizations, i.e. formalizations that are based on distinct sub-models which are expressed in a variety of heterogeneous symbolic languages. With the help of four case-studies, he shows that such pluriformalizations enable to formalize distinctly but simultaneously either different aspects or different parts (...) or different scales of the same object or system. From an epistemological standpoint, he suggests that this kind of computer-aided complex formalization of composite objects renew the traditional relations between computer simulations, theoretical models and operational models. (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)

According to many biologists, explaining the evolution of morphological novelty and behavioral innovation are central endeavors in contemporary evolutionary biology. These endeavors are inherently multidisciplinary but also have involved a high degree of controversy. One key source of controversy is the definitional diversity associated with the concept of evolutionary novelty, which can lead to contradictory claims (a novel trait according to one definition is not a novel trait according to another). We argue that this diversity should be interpreted in light (...) of a different epistemic role played by the concept of evolutionary novelty—the structuring of a problem space or setting of an explanatory agenda—rather than the concept’s capacity to categorize traits as novel. This distinctive role is consistent with the definitional diversity and shows that the concept of novelty benefits ongoing investigation by focusing attention on answering different questions related to comprehending the origins of novelty. A review of recent theoretical and empirical work on evolutionary novelty confirms this interpretation. (shrink)

Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological, and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modeling, and representation.

Griffiths and Stotz’s Genetics and Philosophy: An Introduction offers a very good overview of scientific and philosophical issues raised by present-day genetics. Examining, in particular, the questions of how a “gene” should be defined and what a gene does from a causal point of view, the authors explore the different domains of the life sciences in which genetics has come to play a decisive role, from Mendelian genetics to molecular genetics, behavioural genetics, and evolution. In this review, I highlight what (...) I consider as the two main theses of the book, namely: genes are better conceived as tools; genes become causes only in a context. I situate these two theses in the wider perspective of developmental systems theory. This leads me to emphasize that Griffiths and Stotz reflect very well an on going process in genetics, which I call the “epigenetization” of genetics, i.e., the growing interest in the complex processes by which gene activation is regulated. I then make a factual objection, which is that Griffiths and Stotz have almost entirely neglected the perspective of ecological developmental biology, and more precisely recent work on developmental symbioses, and I suggest that this omission is unfortunate in so far as an examination of developmental symbioses would have considerably strengthened Griffiths and Stotz’s own conclusions. (shrink)

The fundamental concept of structured chemical system has been introduced and analysed in this paper. This concept, as in biology but not in physics, is very important in chemistry. In fact, the main chemical concepts (molecule and compound) have been identified as systemic concepts and their use in chemical explanation can only be justified in this approach. The fundamental concept of “environment” has been considered and then the system concept in mechanics, chemistry and biology. The differences and the analogies between (...) the use of the systemic approach in these disciplines have been analyzed and correlated to the general problem of reductionism and complexity perspectives. The inanimate–animate dichotomy can be reconsidered in this new approach. Since the chemical systemic concepts of molecule and compound can be dated to the nineteenth century, chemistry can be considered the first true systemic science and its historical evolution can be a model for other sciences (such as the humanities) where the systemic concepts are important. (shrink)

I show that the recent account of levels in neuroscience proposed by Craver and Bechtel is unsatisfactory since it fails to provide a plausible criterion for being at the same level and is incompatible with Craver and Bechtel’s account of downward causation. Furthermore, I argue that no distinct notion of levels is needed for analyzing explanations and causal issues in neuroscience: it is better to rely on more well-defined notions such as composition and scale. One outcome of this is that (...) apparent cases of downward causation can be analyzed away. (shrink)

Unlike Aristotelian physics with its teleological notions, modern physics was developed exclusively in relation to the nonliving domain. This raised the question as to whether mechanics applies to organisms, and if so, to what extent. From the seventeenth century on, mechanistic ideas became prominent in biological and medical theory. Contemporary biology explains essential features of life on the basis of physical laws and processes. This does not prove, however, that the early mechanists were essentially right. In the eighteenth century, following (...) Cartesian notions of mind-body separation and preformation theories of organismic development, they tended to exclude major biological questions rather than answering them. It was those who insisted on the organizational features of organisms, like Stahl and Wolff, who paved the way for solutions to such crucial problems as the psychological basis of human nature and behavior and the generation of form in the course of reproduction. Though they underrated the potentials of a future, extended physics for understanding biology, their case against reductionist exclusion should not be considered outdated even today. (shrink)

Two senses of ‘ontology’ can be distinguished in the current literature. First is the sense favored by information scientists, who view ontologies as software implementations designed to capture in some formal way the consensus conceptualization shared by those working on information systems or databases in a given domain. [Gruber 1993] Second is the sense favored by philosophers, who regard ontologies as theories of different types of entities (objects, processes, relations, functions) [Smith 2003]. Where information systems ontologists seek to maximize reasoning (...) efficiency even at the price of simplifications on the side of representation, philosophical ontologists argue that representational adequacy can bring benefits for the stability and resistance to error of an ontological framework and also for its extendibility in the future. In bioinformatics, however, a third sense of ‘ontology’ has established itself, above all as a result of the successes of the Gene Ontology (hereafter: GO), which is a tool for the representation and processing of information about gene products and their biological functions [Gene Ontology Consortium 2000]. We show how Basic Formal Ontology (BFO) has established itself as an overarching ontology drawing on all three of the strands distinguished above, and describe applications of BFO especially in the treatment of biological granularity. (shrink)

Probably the most distinctive feature of synthetic biology is its being “synthetic” in some sense or another. For some, synthesis plays a unique role in the production of knowledge that is most distinct from that played by analysis: it is claimed to deliver knowledge that would otherwise not be attained. In this contribution, my aim is to explore how synthetic biology delivers knowledge via synthesis, and to assess the extent to which this knowledge is distinctly synthetic. On the basis of (...) distinctions between knowledge-how and knowledge-why, and between syntheses that succeed and syntheses that fail, I argue that the contribution of synthesis to knowledge is best understood when syntheses are construed as experimental interventions that aim at probing causal relationships between properties of the entities that are combined through these syntheses and properties of their target products. The distinctiveness of synthetic biology in its quest for knowledge through synthesis stems from its ability to sample at will a space of empirical possibilities that is not only huge but also that has been so scarcely sampled by nature. (shrink)

If the problem of the origin of life is conceptualized as a process of emergence of biochemistry from proto-biochemistry, which in turn emerged from the organic chemistry and geochemistry of primitive earth, then the resources of the new sciences of complex systems dynamics can provide a more robust conceptual framework within which to explore the possible pathways of chemical complexification leading to living systems and biosemiosis. In such a view the emergence of life, and concomitantly of natural selection and biosemiosis, (...) is the result of deep natural laws (the outlines of which we are only beginning to perceive) and reflects a degree of holism in those systems that led to life. Further, such an approach may lead to the development of a more general theory of biology and of natural organization, one informed by semiotic concepts. (shrink)