Ulrich Krohs

Niches and mechanisms are two important but contested elements in the study of organism-environment interactions. Although they are closely interrelated, with niches playing a crucial role in theorizing about ecological and evolutionary mechanisms such as niche construction, facilitation, and species invasion, philosophical discussions about each issue have been largely disconnected. This collection addresses this gap, bringing together contributions from philosophers and biologists about the niche concept, niche construction theory, and ecological and evolutionary mechanisms. In this introduction we provide some background to the collection, which arose out of two workshops organized within an interdisciplinary research consortium. We also summarize each contribution, organized roughly into three groups with considerable overlap and interrelations: niche construction and evolutionary theory, niches, and ecological and evolutionary mechanisms.

With this Editorial, we’d like to inform our readers about some news concerning the editorship of the Journal for General Philosophy of Science:Since its foundation by Alwin Diemer , Lutz Geldsetzer and Gert König in 1970, JGPS was edited by the three founders until 2004. In 2005 and 2008, respectively, Helmut Pulte and Gregor Schiemann joined JGPS as new editors, while Lutz Geldsetzer and Gert König retired by the end of 2008. In 2013, Ulrich Krohs joined the editorial team and thereby restored the ‘trinity’ of the starting years of JGPS.Gregor Schiemann has decided to resign from his editorship with the end of 2014 and has assigned Claus Beisbart as his successor in consultation with the other editors and the publisher. Since 2012, Prof. Dr. Dr. Beisbart is working as a philosopher of science at the University of Bern . His areas of expertise include philosophy of physics, particularly of cosmology, epistemology of model building and simulation ..

Darwin’s claim about natural selection is reconstructed as an empirical claim about a causal connection leading from the match of the physiology of an individual and its environment to leaving surviving progeny. Variations in this match, Darwin claims, cause differences in the survival of the progeny. Modern concepts of fitness focus the survival side of this chain. Therefore, the assumption that evolutionary theory wants to explain reproductive success in terms of a modern concept of fitness has given rise to the so-called tautology problem. It is shown that the tautology problem reappears in the treatment of fitness proxies in today’s experimental evolutionary biology when these proxies are considered to indicate fitness only. Taking Darwin’s empirical claim seriously suggests, by contrast, that fitness proxies are first of all measures of the match between organism and environment, which I call the organism’s ‘fittedness’. At the same time, they are indeed related to reproductive success. Thus looking in both directions, at fitness and at fittedness, they are janiform. Acknowledging this situation not only allows for rejection of the tautology objection, but also for integration of Darwin’s argument into current evolutionary biology. It is suggested that this helps reframe and alleviate the dispute between the Modern Synthesis and the Extended Evolutionary Synthesis.

Form follows function, but it does not follow from function. Form is not derivable from the latter. To realize a desired technical function, a form must first be found that is able to realize it at all. Secondly, the question arises as to whether an envisaged form realizes the function in an appropriate way. Functions are multiply realizable—various different forms can bear the very same function. One needs to find a form of a technical artifact that realizes an envisaged function sufficiently efficient, robust, or whatever criteria might be imposed. This paper scrutinizes biomimetics as one way to find a good solution to the realization problem. Drawing on an approach from the philosophy of simulations, it reconstructs the biomimetic relation as being mediated by a theoretical model. It is shown that the robustness of the functioning system is usually reached in different ways in biological and in technological systems, which explains differences in morphogenetic mechanisms or principles found in these fields. This reconstruction helps to understand problems with robustness in synthetic biology that occur when technical design principles are implemented in a biological system. The mimetic relation between the biological and the technical realm is found to be asymmetric.

Technical artifacts are embedded in social systems and, to some extent, even shape them. This chapter inquires, then, whether designing artifacts may be regarded as a contribution to social design. I explicate a concept of general design that conceives design as the type fixation of a complex entity. This allows for an analysis of different contributions to the design of social systems without favoring the intended effects of artifacts on a system over those effects that actually show up. First, the clear-cut case of socio-technical systems is considered. Here, functions of artifacts can be planned fairly precise. In societies, in contrast, the actual functions of an artifact can hardly be predicted, which is due to strong self-organizing processes. Nevertheless artifact design can be shown to contribute to the design of the system also in this case.

occurs first. The biological debate is conducted largely on a theoretical level. In this paper, I undertake to locate
the reason for the difference in temporal ordering. The question is whether the difference depends on alternative
interpretations of empirical data, on differing views about evolutionary mechanisms, or on different conceptual
frameworks. It will turn out that the latter is the case and that discerning two different notions of novelty solves
the apparent contradiction. Both concepts may apply to different cases in evolution. To settle the dispute by
judging whether any of both concepts is empty or not has to be recommitted to science.

Part of the scientific enterprise is to measure the material world and to explain its dynamics by means of models. However, not only is measurability of the world limited, analyzability of models is so, too. Most often, computer simulations offer a way out of this epistemic bottleneck. They instantiate the model and may help to analyze it. In relation to the material world a simulation may be regarded as a kind of a “non-material scale model”. Like any other scale model, it does not per se give any scientific explanation but is first in itself an object of scientific enquiry, a world. Since this world is numerical, it is a priori measurable. Its role in scientific explanation will be discussed.

There is a trend within philosophy of biology to concentrate on questions that are strongly related to particular biological research programs rather than on the general scope of the field and its relation to other sciences. Projects of the latter kind, of course, are followed as well but will not be the topic of this review. Shifting the focus to particular research programs reflects philosophers’ increased interest in knowledge of, and contribution to, actual biological research, which is organized in such programs. It is accompanied by the increasing enthusiasm of biologists to involve philosophers in the conceptual work of theoretical biology. I concentrate on the philosophies of four biological research programs, three of which are devoted to evolutionary biology, which is still the main field of interest among philosophers of biology: adaptationism, EvoDevo, and the developmental systems approach. In addition, a short sketch of the newly emerging philosophy of systems biology is given. Several lines of philosophical inquiry can be found in all of the fields considered here: philosophy contributes to the conceptual development of biological research programs, it analyzes structures and delineations of particular research programs, and sometimes it is involved in a comparative assessment of biological programs as well. Philosophical projects that start from the level of a particular research program may give rise to a bottom-up perspective on biology and allow for an integrative view of biological research. This may open up the opportunity to tackle “larger” questions again in an altered and fruitful manner.

Systems biology is largely tributary to genomics and other “omic” disciplines that generate vast amounts of structural data. “Omics”, however, lack a theoretical framework that would allow using these data sets as such (rather than just tiny bits that are extracted by advanced data-mining techniques) to build explanatory models that help understand physiological processes. Systems biology provides such a framework by adding a dynamic dimension to merely structural “omics”. It makes use of bottom-up and top-down models. The former are based on data about systems components, the latter on systems-level data. We trace back both modeling strategies (which are often used to delineate two branches of the field) to the modeling of metabolic and signaling pathways in the bottom-up case, and to biological cybernetics and systems theory in the top-down case. We then argue that three roots of systems biology must be discerned to account adequately for the structure of the field: pathway modeling, biological cybernetics, and “omics”. We regard systems biology as merging modeling strategies (supplemented by new mathematical procedures) from data-poor fields with data supply from a field that is quite deficient in explanatory modeling. After characterizing the structure of the field, we address some epistemological and ontological issues regarding concepts on which the top-down approach relies and that seem to us to require clarification. This includes the consequences of identifying modules in large networks without relying on functional considerations, the question of the “holism” of systems biology, and the epistemic value of the “systeome” project that aspires to become the cutting edge of the field.

Darwin’s explanation of biological speciation in terms of variation and natural selection has revolutionised biological thought. However, while his principle of natural selection, the fitness principle, has shaped biology until the present, its interpretation changed more than once during the almost 150 years of its history. The most striking change of the status of the principle is that, in the middle of the 20th century, it transmutated from an often disputed, groundbreaking insight into a tautology. Moreover, not only the interpretation of the fitness principle, but the whole body of biological knowledge was subjected to significant modifications. In this paper, I relate modifications of the fitness principle to those of the respective body of biological knowledge. This body of knowledge is conceived as a Quinean web of belief. After an exposition of Darwin’s conception of the principle, which equated fitness with adaptedness to the environment, several of its changes are analysed with respect to different webs of biological knowledge. It is concluded that the different interpretations and the reshaping of the fitness principle are rational responses to the modified systems of background knowledge, which saved the coherence of the web of biological knowledge in each single case.

Scientists of many disciplines use theoretical models to explain and predict the dynamics of the world. They often have to rely on digital computer simulations to draw predictions fromthe model. But to deliver phenomenologically adequate results, simulations deviate from the assumptions of the theoretical model. Therefore the role of simulations in scientific explanation demands itself an explanation. This paper analyzes the relation between real-world system, theoretical model, and simulation. It is argued that simulations do not explain processes in the real world directly. The way in which simulations help explaining real-world processes is conceived as indirect, mediated by the theoretical model. Simulacra are characterized further, and turn out to be a priori measurable. This gives a clue to a better understanding of the epistemic role of computer simulations in scientific research.

A technical artefact is often described in two ways: by means of a physicalistic model of its structure and dynamics, and by a functional account of the contributions of the components of the artefact to its capacities. These models do not compete, as different models of the same phenomenon in physics usually do; they supplement each other and cohere. Coherence is shown to be the result of a mapping of role-contributions on physicalistic relations that is brought about by the concept of function. It results a sandwich-like structure of the two models, which can be reconstructed as a two-sorted theory element.

Looking for an adequate explication of the concept of a biological function, several authors have proposed to link function to design. Unfortunately, known explications of biological design in turn refer to functions. The concept of general design I will introduce here breaks up this circle. I specify design with respect to its ontogenetic role. This allows function to be based on design without making reference to the history of the design, or to the phylogeny of an organism, while retaining the normative aspect of function ascriptions. The concept is applicable to the function and design of technical artifacts as well. Several problems well known with other definitions can be overcome by this approach.