Interlevel Relations in Biology

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)

"Theoretical pluralism" obtains when there are good evidential reasons for accommodating multiple theories of the same domain. Issues of "relative significance" often arise in connection with the investigation of such domains. In this paper, I describe and give examples of theoretical pluralism and relative significance issues. Then I explain why theoretical pluralism so often obtains in biology--and why issues of relative significance arise--in terms of evolutionary contingencies and the paucity or lack of laws of biology. Finally, I turn from explanation (...) to justification, and raise questions about the purpose and value of concerns and disagreements about relative significance. (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)

Die Frequenzkurven, die die lebendige Substanz charakterisieren, können als eine statische Beschreibung oder als das Ergebnis einer Entwicklung betrachtet werden.Im ersten Falle akzeptiert man ohne weiteres die gegebenen Verteilungen und man versucht, ihnen durch mathematische Gleichungen, die keine unmittelbare Wirklich-keitsbedeutung haben, nahezukommen. Das kausale Denken wird hier ausgeschaltet oder man gibt sich wenigstens mit nur sehr groben Analogien zufrieden.Verschiedene Methoden über die Genese der Frequenzkurven werden besprochen; dabei wird gezeigt, dass die Mehrheit der Fälle auf Hypothesen beruht, die biologisch wenig (...) begründet sind. Eine Ausnahme davon macht die Theorie vonJ. C. Kapteyn, weil er den Vorgang des Wachstums in die Genese einbezieht. Seine Methode weiter ausbauend kann man sich vorstellen, dass die Genese einer Frequenzkurve in erblich homogenem Pflanzenmaterial durch Variation der Wachstumsgeschwindigkeit zustandekommt.Auf solche Weise kann man in einem Koordinatensystem mit Länge und Zeit als Koordinaten ein “Deviationsraster” konstruieren.In einem experimentell untersuchten Fall ergab die graphische Methode mit völlig ausreichender Genauigkeit die schon gefundene Frequenz.Les courbes de fréquence qui caractérisent la matière vivante, peuvent être considérées ou comme une description statique ou bien comme le produit d'un développement.Dans le premier cas on accepte les distributions obtenues et on essaie de s'en rapprocher par des équations mathématiques qui n'ont pas une réalité effective. On ne recherche plus la causalité ou alors on se contente le plus souvent d'analogies très grossières.Les auteurs traitent des diverses méthodes de la genèse des courbes de fréquence et démontrent que la plupart des cas reposent sur des hypothèses qui ont peu de fond biologique. La théorie deM. J. C. Kapteyn fait exception parcequ'il introduit le processus de croissance dans la genèse. En poursuivant plus loin dans sa méthode on peut se figurer que la genèse d'une courbe de fréquence de plantes homogènes par hérédité s'expliquerait par des variations de vitesse de croissance.De cette façon on peut construire une “grille de déviation” dans un système en prenant longueur et temps comme coordonnées.Dans un cas essayé expérimentalement ce graphique donnait avec une exactitude assez grande la distribution de fréquence déjà trouvée. (shrink)

In the first part of my analysis, I wish briefly to clarify the different modes of relation found in the living being, and point out the multiplicity of disciplines in which biologists use (explicitly or implicitly) the notion of laws. In the second part, I shall analyse the notion of universal laws in biology and examine successively: (1) accidental generalizations; (2) non-causal biological correlations; (3) the meaning of 'necessity' in these correlations; and (4) causal connections. Finally, in the third part, (...) I shall examine statistical laws and probabilistic laws in biology, in particular: (1) chance in biology; (2) probabilistic theories; and (3) relations between logical probability and statistical probability. (shrink)

The view known as animalism asserts that we are human animals—that each of us is an instance of the Homo sapiens species. The standard argument for this view is known as the thinking animal argument . But this argument has recently come under attack. So, here, a new argument for animalism is introduced. The animal ancestors argument illustrates how the case for animalism can be seen to piggyback on the credibility of evolutionary theory. Two objections are then considered and answered.

Introduction -- Light and life -- Biology and atomic physics -- Natural philosophy and human cultures -- Discussion with Einstein on epistemological problems in atomic physics -- Unity of knowledge -- Atoms and human knowledge -- Physical science and the problem of life.

In this article, two issues regarding mechanisms are discussed. The first concerns the relationships between “mechanism description” and “mechanism explanation.” It is proposed that it is rather plausible to think of them as two distinct epistemic acts. The second deals with the different molecular biology explanatory contexts, and it is shown that some of them require physics and its laws.

In this paper the common association between ontological reductionism and a methodological position called 'Mechanism' is discussed. Three major points are argued for: (1) Mechanism is not to be identified with reductionism in any of its forms; in fact, mechanism leads to a non-reductionist ontology. (2) Biological methodology is thoroughly mechanistic. (3) Mechanism is compatible with at least one form of teleology. Along the way the nature and value of scientific explanations, some recent controversies in biology and why reductionism has (...) proven to be such an attractive position are discussed. (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)

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)

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)

Beller, Bender, and Medin argue that a reconciliation between anthropology and cognitive science seems unlikely. We disagree. In our view, Beller et al.’s view of the scope of what anthropology can offer cognitive science is too narrow. In focusing on anthropology’s role in elucidating cultural particulars, they downplay the fact that anthropology can reveal both variation and universals in human cognition, and is in a unique position to do so relative to the other subfields of cognitive science. Indeed, without cross-cultural (...) research, the universality of any aspect of human cognition cannot truly be established. Therefore, if the goal of cognitive science is to understand the cognitive capacities of our species as a whole, then it cannot do without anthropology. We briefly review a growing body of anthropological work aimed at answering questions about human cognition and offer suggestions for future work. (shrink)

In many of the special sciences, mathematical models are used to provide information about specified target systems. For instance, population models are used in ecology to make predictions about the abundance of real populations of particular organisms. The status of mathematical models, though, is unclear and their use is hotly contested by some practitioners. A common objection levelled against the use of these models is that they ignore all the known, causally-relevant details of the often complex target systems. Indeed, the (...) objection continues, mathematical models, by their very nature, abstract away from what matters and thus cannot be relied upon to provide any useful information about the systems they are supposed to represent. In this paper, I will examine the role of some typical mathematical models in population ecology and elsewhere. I argue that while, in a sense, these models do ignore the causal details, this move can not only be justified, it is necessary. I will argue that idealising away from complicating causal details often gives a clearer view of what really matters. And often what really matters is not the push and shove of base-level causal processes, but higher-level predictions and (non-causal) explanations. (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)

T he term emergence is used to describe the appearance of new properties that arise when a system exceeds a certain level of size or complexity, properties that are absent from the constituents of the system. It is a concept often summed up by the phrase that “the whole is greater than the sum of its parts,” and it is a key notion in the burgeoning field of complexity science. Life is often cited as a classic example of an emergent (...) phenomenon: no atoms of my body are living, yet I am living (see, for example, Morowitz [1]). Biological organisms depend on the processes of their constituent parts, yet they nevertheless exhibit a degree of autonomy from their parts (see, for example, Kauffman [2]). How can this be? These seem to be contradictory properties. (shrink)

To what degree has biology influenced and shaped the development of moral systems? One way to determine the extent to which human moral systems might be the product of natural selection is to explore behaviour in other species that is analogous and perhaps homologous to our own. Many non-human primates, for example, have similar methods to humans for resolving, managing, and preventing conflicts of interests within their groups. Such methods, which include reciprocity and food sharing, reconciliation, consolation, conflict intervention, and (...) mediation, are the very building blocks of moral systems in that they are based on and facilitate cohesion among individuals and reflect a concerted effort by community members to find shared solutions to social conflict. Furthermore, these methods of resource distribution and conflict resolution often require or make use of capacities for empathy, sympathy, and sometimes even community concern. Non-human primates in societies in which such mechanisms are present may not be exactly moral beings, but they do show signs of a sense of social regularity that—just like the norms and rules underlying human moral conduct—promotes a mutually satisfactory modus vivendi. (shrink)

According to the so-called Quantum Darwinist approach, the emergence of "classical islands" from a quantum background is assumed to obey a (selection) principle of maximal information. We illustrate this idea by considering the coupling of two oscillators (modes). As our approach suggests that the classical limit could have emerged throughout a long and progressive Evolution mechanism, it is likely that primitive living organisms behave in a "more quantum", "less classical" way than more evolved ones. This brings us to seriously consider (...) the possibility to measure departures from classicality exhibited by biological systems. We describe an experimental proposal the aimed at revealing the presence of entanglement in the biophotonic radiation emitted by biological sources. (shrink)

The evolutionary emergence of biological processes in organisms with inner, qualitative aspects has not been explained in any sufficient way by neurobiology, nor by the traditional neo-Darwinian paradigm — natural selection would appear to work just as well on insentient zombies (with the right behavioral input-output relations) as on real sentient animals. In consciousness studies one talks about the ‘hard problem’ of qualia. In this paper I sketch a set of principles about sign action, causality and emergent evolution. On the (...) basis of these principles, I characterize a concept of cause that would allow for a naturalistic explanation of the origin of consciousness. The suggested account of causation also turns the ‘hard problem’ of qualia into the easier problem of relating experimental biology to experiential biology. (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)

Biological reality does not consist of chemistry and physics of organism alone. It also includes their information content. This information regulates developmental and reproductive processes. Its quantity is finite. We observe mixing of information (mating patterns, reduction division, hybridisation, genetic engineering), its loss (species extinction, reduction of genetic diversity in domestication, isolation, inbreeding) and increase of useless or injurious information (duplications, neutral and harmful mutations, genetic load). On the other hand we do not observe new useful biological information arising (positive (...) mutations). New useful information does not appear by accident. Nature and man made selections reduce the information resources, mutations debilitate them, population reduction and its isolation cause accidental losses of information. Acquired resistance to antibiotics or herbicides, which is often presented as an example of increase of information, is only a defence mechanism against loss of functionality of an organism or population (e.g. by immunological adaptation). Such mechanisms belong to the already existing information content. No new organs or functions are produced. Until natural sciences come up with an indication of the mode by which useful information resources can be increased in nature, by which new functions or organs are produced, the theory of evolution will remain a hypothesis without substantiation in facts. (shrink)

The cell theory of Schleiden and Schwann is generalized to the effect that throughout the natural world, in physics, biology, and sociopsychology, there is a widespread phenomenon of the existence of organized cells, whose organization is usually protected by barriers. These barriers exist not only in space, but in time and even in other domains. These barriers typically not only protect the organization within the cell from external disturbance, but they actively participate in reducing the internal disorganization. It appears that (...) the quantum phase cell or its equivalent, the discrete quantum state, may be a physical analog of the organized biological cell. The sampling and ambiguity theorems of communication theory throw new light on phase cells. The quantum phase cell has both configuration and momentum elements, which are analogous respectively to the somatic elements in the cytoplasm of a cell and the genetic elements in the DNA. A biological cell or organism, a physical quantum state, and a human being as a sociopsychological entity each has a natural individuality. A natural individuality is a somewhat mysterious thing, since in addition to specificity, it also involves stochasticity and complementarity. There are some striking and unexplained spin-analog characteristics in biology which have a relation to boson- and fermion-analog characteristics in biology that corresponds with the known relation in physics. The hypothesis suggested in our earlier paper, that quantum mechanical entropy is diminished in interaction, is clarified and sharpened in this paper. (shrink)

We argue that genuine biological autonomy, or described at human level as free will, requires taking into account quantum vacuum processes in the context of biological teleology. One faces at least three basic problems of genuine biological autonomy: (1) if biological autonomy is not physical, where does it come from? (2) Is there a room for biological causes? And (3) how to obtain a workable model of biological teleology? It is shown here that the solution of all these three problems (...) is related to the quantum vacuum. We present a short review of how this basic aspect of the fundamentals of quantum theory, although it had not been addressed for nearly 100 years, actually it was suggested by Bohr, Heisenberg, and others. Realizing that the quantum mechanical measurement problem associated with the “collapse” of the wave function is related, in the Copenhagen Interpretation of quantum mechanics, to a process between self-consciousness and the external physical environment, we are extending the issue for an explanation of the different processes occurring between living organisms and their internal environment. Definitions of genuine biological autonomy, biological aim, and biological spontaneity are presented. We propose to improve the popular two-stage model of decisions with a biological model suitable to obtain a deeper look at the nature of the mind-body problem. In the newly emerging picture biological autonomy emerges as a new, fundamental and inevitable element of the scientific worldview. (shrink)

To make possible the integration proposed by Domjan et al., psychologists first need to close the research gap between behavioral ecology and the study of Pavlovian conditioning. I suggest two strategies, namely, to adopt more behavioral ecological approaches to social behavior or to co-opt problems already addressed by behavioral ecologists that are especially well suited to the study of Pavlovian conditioning.

Niels Bohr's arguments indicating the non-applicability of quantum methodology to the study of the ultimate details of life, given in his bookAtomic Physics and Human Knowledge, conflict with the commonly held opposite view. The bases for the usual beliefs are examined and shown to have little validity; significant differences do exist between the living organism and the type of system studied successfully in the physics laboratory. Dealing with living organisms in quantum-mechanical terms with the same degree of rigor as is (...) normal for non-living systems would seem not to be possible without considering also questions of the origins of life and of the universe. (shrink)

An explicit formal-ontological representation of entities existing at multiple levels of granularity is an urgent requirement for biomedical information processing. We discuss some fundamental principles which can form a basis for such a representation. We also comment on some of the implicit treatments of granularity in currently available ontologies and terminologies (GO, FMA, SNOMED CT).

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)

Nanoscience has enabled the understanding of organisation of the atomic and molecular world. Due to the unique chemical, electronic and magnetic properties nanomaterials have wide applications in the chemical, manufacturing, medical sector etc., Single walled carbon nanotubes, buckyballs, ZnSe quantum dots, TiO 2 nanoparticle based products are nearing commercialisation. Research is on-going worldwide on suitable delivery systems for nanomaterial based drugs. Nanomaterials are highly reactive in biological systems due to the large surface area. While the benefits of nanomaterials are evident (...) there are studies which indicate the potential risk to biological systems. Substances known to be harmless in bulk can be potentially toxic in certain fibrous and nanoparticle form. Risk assessment studies with nanomaterials largely focus on mouse models. There are very few studies on their effects on aquatic species and plants which form the largest in the productivity chain with respect to the ecological pyramid. This study reviews the research done worldwide in the area of risk assessment of nanomaterials, particularly the effects on aquatic and plant systems. Risk assessment is the foundation for regulatory decision making. A general comparison of the regulatory regime in nanotechnology is performed to understand the extent of development. (shrink)