The Organizational View of Biological Functions and Hegel’s Teleological Conception of Life

In this paper I return to Hegel's dispute with Kant over the conceptual ordering of external and internal purposiveness to distinguish between two conceptions of teleology at play in the contemporary function debate. I begin by outlining the three main views in the debate (the etiological, causal role and organizational views). I argue that only the organizational view can maintain the capacity of function ascriptions both to explain the presence of a trait and to identify its contribution to a current system, for it is the only view that considers teleology as a natural cause. To establish how teleology can be considered as a natural cause, advocates of the organizational view return to Kant's analysis of internal purposiveness. However, while Kant identifies the requirements that an object must meet to satisfy the demands of teleological judgment, I suggest that he denies that we can know whether they are truly met. I argue that Hegel's philosophy of nature is better equipped to determine how internal purposiveness can be considered as a natural cause, for it grounds organization in a form of purposiveness that is more fundamental than a designer's intention.

In this paper, we develop an organizational account that defines biological functions as causal relations subject to closure in living systems, interpreted as the most typical example of organizationally closed and differentiated self-maintaining systems. We argue that this account adequately grounds the teleological and normative dimensions of functions in the current organization of a system, insofar as it provides an explanation for the existence of the function bearer and, at the same time, identifies in a non-arbitrary way the norms that functions are supposed to obey. Accordingly, we suggest that the organizational account combines the etiological and dispositional perspectives in an integrated theoretical framework. 1. Introduction 2. Dispositional Approaches 3. Etiological Theories 4. Biological Self-maintenance 4.1. Closure, teleology, and normativity 4.2. Organizational differentiation 5. Functions 5.1. C1: Contributing to the maintenance of the organization 5.2. C2: Producing the functional trait 6. Implications and Objections 6.1. Functional versus useful 6.2. Dysfunctions, side effects, and accidental contributions 6.3. Proper functions and selected effects 6.4. Reproduction 6.5. Relation with other ‘unitarian’ approaches 7. Conclusions

In the previous issue, I offered some thoughts on how to think about evolution (Eldredge 2008). It turns out that how “we” collectively think about evolution, starting with the most basic, fundamental conceptualization about what evolution is, has differed dramatically depending on when a given evolutionist was active, what her subdiscipline is— and even to some degree on what country she was born in. For example, a systematist or paleontologist might prefer a one-sentence definition of “evolution” as “the idea that all species that have ever lived on earth are descended from a single common ancestor.” In contrast, a geneticist might prefer to define evolution as “any permanent change in genetic information.” In addition, while both definitions may suffice for some systematists or geneticists, others (such as myself) would insist on adding “and the causal processes underlying such patterns of descent and/or change in genetic information.” And while there may be still other definitions of evolution, these two seem to constitute a dichotomy that has pervaded biological evolutionary theory at least since Darwin. One of them is about the origin and fates of species—and, by extension, higher taxa such as genera, families etc. The other focuses on the origin and further modification of genetically based properties of organisms (morphology, physiology, behavior). And although such nondeterministic causes of genetic change as Sewall Wright’s “genetic drift” (see Eldredge 2008) are in operation, basically theories of genetic change (i.e., over and above mutational and related sorts of changes in individual organisms) are theories of adaptation through natural selection—and have been so throughout the history of evolutionary thought. What’s more, the distinction between these two fundamentally different ways of defining evolution—the “taxic” vs. the “transformationist” approach (as I initially called them in Eldredge 1979) are seldom acknowledged. The tendency (probably ever since Darwin published the Origin in 1859) is to see the “origin of species” as the simple and direct consequence of the ongoing transformation of the heritable properties of organisms via adaptation through natural selection. The thought goes: If natural selection modifies a species enough, over the course of time a new species will inevitably emerge. But, as I will explore in detail in the next issue (dedicated to Charles Robert Darwin on the occasion of his 200th birthday), Darwin himself initially saw evolution as a “taxic” phenomenon: ancestral species give rise to descendant species, much as mothers give birth to infant children. He was thinking in these terms even on the Beagle and continued to do so after he returned home in 1836. Later, he essentially dropped this line of thought—but only after he had come up with the idea of natural selection—and switched over to thinking of evolution as essentially the simple modification of adaptations through natural selection. Today, we have theories of “speciation”—how new species are “born” from ancestral species (see Thanukos 2008, for a useful review in these pages), and we also have theories of adaptation through natural selection. And it is clear that the two fundamentally different ways of thinking about evolution I have sketched out above are intimately related to one another: This is not an either/or dichotomy, but rather two equally valid ways of looking at evolution that resonate with one another in more of a dialectical than a dichotomous way. For though it is possible to have a descendant species arise with hardly much genetic change Evo Edu Outreach (2008) 1:355–357 DOI 10.1007/s12052-008-0070-7

Functionality is essential to any form of anticipation beyond simple directedness at an end. In the literature on function in biology, there are two distinct approaches. One, the etiological view, places the origin of function in selection, while the other, the organizational view, individuates function by organizational role. Both approaches have well‐known advantages and disadvantages. I propose a reconciliation of the two approaches, based in an interactivist approach to the individuation and stability of organisms. The approach was suggested by Kant in the Critique of Judgment, but since it requires, on his account, the identification a new form of causation, it has not been accessible by analytical techniques. I proceed by construction of the required concept to fit certain design requirements. This construction builds on concepts introduced in my previous four talks to these meetings.

The spatial organization in the cell nucleus is tightly linked to genome functions such as gene regulation. Similarly, specific spatial arrangements of biological components such as macromolecular complexes, organelles and cells are involved in many biological functions. Spatial interactions among elementary components of biological systems define their relative positioning and are key determinants of spatial patterns. However, biological variability and the lack of appropriate spatial statistical methods and models limit our current ability to analyze these interactions. Here, we developed a framework to dissect spatial interactions and organization principles by combining unbiased statistical tests, multiple spatial descriptors and new spatial models. We used plant constitutive heterochromatin as a model system to demonstrate the potential of our framework. Our results challenge the common view of a peripheral organization of chromocenters, showing that chromocenters are arranged along both radial and lateral directions in the nuclear space and obey a multiscale organization with scale-dependent antagonistic effects. The proposed generic framework will be useful to identify determinants of spatial organizations and to question their interplay with biological functions.

Chromosomes are giant chain molecules organized into an ensemble of three-dimensional structures characterized with its genomic state and the corresponding biological functions. Despite the strong cell-to-cell heterogeneity, the cell-type specific pattern demonstrated in high-throughput chromosome conformation capture (Hi-C) data hints at a valuable link between structure and function, which makes inference of chromatin domains (CDs) from the pattern of Hi-C a central problem in genome research. Here we present a unified method for analyzing Hi-C data to determine spatial organization of CDs over multiple genomic scales. By applying statistical physics-based clustering analysis to a polymer physics model of the chromosome, our method identifies the CDs that best represent the global pattern of correlation manifested in Hi-C. The multi-scale intra-chromosomal structures compared across different cell types uncover the principles underlying the multi-scale organization of chromatin chain: (i) Sub-TADs, TADs, and meta-TADs constitute a robust hierarchical structure. (ii) The assemblies of compartments and TAD-based domains are governed by different organizational principles. (iii) Sub-TADs are the common building blocks of chromosome architecture. Our physically principled interpretation and analysis of Hi-C not only offer an accurate and quantitative view of multi-scale chromatin organization but also help decipher its connections with genome function.

Chromosomes are giant chain molecules organized into an ensemble of three-dimensional structures characterized with its genomic state and the corresponding biological functions. Despite the strong cell-to-cell heterogeneity, the cell-type specific pattern demonstrated in high-throughput chromosome conformation capture (Hi-C) data hints at a valuable link between structure and function, which makes inference of chromatin domains (CDs) from the pattern of Hi-C a central problem in genome research. Here we present a unified method for analyzing Hi-C data to determine spatial organization of CDs over multiple genomic scales. By applying statistical physics-based clustering analysis to a polymer physics model of the chromosome, our method identifies the CDs that best represent the global pattern of correlation manifested in Hi-C. The multi-scale intra-chromosomal structures compared across different cell types uncover the principles underlying the multi-scale organization of chromatin chain: (i) Sub-TADs, TADs, and meta-TADs constitute a robust hierarchical structure. (ii) The assemblies of compartments and TAD-based domains are governed by different organizational principles. (iii) Sub-TADs are the common building blocks of chromosome architecture. Our physically principled interpretation and analysis of Hi-C not only offer an accurate and quantitative view of multi-scale chromatin organization but also help decipher its connections with genome function.

Darwin at Orchis Bank: Selection after the Origin

Editorial

The relationship between structure and function is a major constituent of the rules of life. Structures and functions occur across all levels of biological organization. Current efforts to integrate conceptual frameworks and approaches to address new and old questions promise to allow a more holistic and robust understanding of how different biological functions are achieved across levels of biological organization. Here, we provide unifying and generalizable definitions of both structure and function that can be applied across all levels of biological organization. However, we find differences in the nature of structures at the organismal level and below as compared to above the level of the organism. We term these intrinsic and emergent structures, respectively. Intrinsic structures are directly under selection, contributing to the overall performance (fitness) of the individual organism. Emergent structures involve interactions among aggregations of organisms and are not directly under selection. Given this distinction, we argue that while the functions of many intrinsic structures remain unknown, functions of emergent structures are the result of the aggregate of processes of individual organisms. We then provide a detailed and unified framework of the structure-function relationship for intrinsic structures to explore how their unknown functions can be defined. We provide examples of how these scalable definitions applied to intrinsic structures provide a framework to address questions on structure-function relationships that can be approached simultaneously from all subdisciplines of biology. We propose that this will produce a more holistic and robust understanding of how different biological functions are achieved across levels of biological organization.

In a written test investigating the level of understanding of the concept of natural selection, only 18 per cent of a group of first-year university students with an Advanced-level biology background were consistently able to apply this concept to common environmental problems. In their explanations, over half the students mistakenly formulated a ‘theory of adaptation by induced mutation’ instead of a ‘theory of evolution by natural selection’. On further analysis, many students had a poor understanding of adaptation, immunity, the origin of mutations, and the laws of inheritance. A major cause of these interrelated errors was students extrapolating from changes occurring within the lifetime of an individual, to account for evolutionary changes altering populations over many generations.

What can recent theories in evolutionary biology about the problem of altruism contribute to a Christian perspective on the nature of humanity?Altruism is considered a ‘problem’ because Darwin’s theory of natural selection leads us to expect all organisms, including humans, to be selfish. According to the theory of natural selection those traits which we expect to see in the natural world are the ones which have conferred on their bearers the greatest reproductive success. As altruism means the giving of aid, a preliminary reading of Darwinism suggests that altruism poses a challenge to the whole theory of adaptation by natural selection. Sociobiology has a great deal to say about the evolution of altruism in non-humans. How far does the study of altruism in non-humans help us to understand altruism in us?Sociobiological theories for the evolution of altruism Sociobiology, the systematic study of the biological basis of all social behaviour, dates as a named discipline from only 1975, when E.O. Wilson’s now much-discussed book, Sociobiology: The New Synthesis, was published. As altruism manifestly requires social behaviour—an organism cannot be altruistic on its own!—theories for the evolution of altruism lie at the centre of sociobiology.The first biological explanation for altruism was, however, proposed by none other than Darwin himself. Having developed the theory of natural selection, Darwin went on to consider how the sterile castes in many social insects could have evolved. He realised that it might be argued that such castes could not have evolved by natural selection because the bearers of traits associated with sterility leave, by definition, no offspring, but he proposed that sterility in such circumstances could evolve by a process he termed ‘family selection’.

Speciation—the origin of new species—is the source of the diversity of life. A theory of speciation is essential to link poorly understood macro-evolutionary processes, such as the origin of biodiversity and adaptive radiation, to well understood micro-evolutionary processes, such as allele frequency change due to natural or sexual selection. An important question is whether, and to what extent, the process of speciation is ‘adaptive’, i.e., driven by natural and/or sexual selection. Here, we discuss two main modelling approaches in adaptive speciation theory. Ecological models of speciation focus on the evolution of ecological differentiation through divergent natural selection. These models can explain the stable coexistence of the resulting daughter species in the face of interspecific competition, but they are often vague about the evolution of reproductive isolation. Most sexual selection models of speciation focus on the diversification of mating strategies through divergent sexual selection. These models can explain the evolution of prezygotic reproductive isolation, but they are typically vague on questions like ecological coexistence. By means of an integrated model, incorporating both ecological interactions and sexual selection, we demonstrate that disruptive selection on both ecological and mating strategies is necessary, but not sufficient, for speciation to occur. To achieve speciation, mating must at least partly reflect ecological characteristics. The interaction of natural and sexual selection is also pivotal in a model where sexual selection facilitates ecological speciation even in the absence of diverging female preferences. In view of these results, it is counterproductive to consider ecological and sexual selection models as contrasting and incompatible views on speciation, one being dominant over the other. Instead, an integrative perspective is needed to achieve a thorough and coherent understanding of adaptive speciation.

Chapter 17 - Bridging Microscopes: 3D Correlative Light and Scanning Electron Microscopy of Complex Biological Structures

This chapter considers a major reconstruction of Williams’s theory of adaptation in Natural Selection: Domains, Levels, and Challenges (1992), in light of increasingly subtle theories about genetic information, and macroevolution, evolutionary history on a grand scale. He explores the ways genetic information might be edited, as if it were a text, by evolutionary processes. Most notably, Natural Selection introduces historicity as a doctrine that allows him to explore how evolutionary processes, especially of adaptation, are limited by historical constraint and historical contingency, and how these processes can lead to extinctions of species. His focus often reveals “features that are functionally arbitrary or even maladaptive” in organisms.