Organisms interact with their environments in various ways. We present a conceptual framework that distinguishes three mechanisms of organism–environment interaction. We call these NC3 mechanisms: niche construction, in which individuals make changes to the environment; niche choice, in which individuals select an environment; and niche conformance, in which individuals adjust their phenotypes in response to the environment. Each of these individual-level mechanisms affects an individual's phenotype–environment match, its fitness, and its individualized niche, defined in terms of the environmental conditions under which the individual can survive and reproduce. Our framework identifies how individuals alter the selective regimes that they and other organisms experience. It also places clear emphasis on individual differences and construes niche construction and other processes as evolved mechanisms. The NC3 mechanism framework therefore helps to integrate population-level and individual-level research.

No abstract

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 from the 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 realworld 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.

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.

Are we in the midst of a paradigm change in biology and have animals and plants lost their individuality, i.e., are even so-called 'typical' organisms no longer organisms in their own right? Is the study of the holobiont-host plus its symbiotic microorganisms-no longer optional, but rather an obligatory path that must be taken for a comprehensive understanding of the ecology and evolution of the individual components that make up a holobiont? Or are associated microbes merely a component of their host's environment, and the holobiont concept is just a beautiful idea that does not add much or anything to our understanding of evolution? This article explores different aspects of the concept of the holobiont. We focus on the aspect of functional integration, a central holobiont property, which is only rarely considered thoroughly. We conclude that the holobiont comes in degrees, i.e., we regard the property of being a holobiont as a continuous trait that we term holobiontness, and that holobiontness is differentiated in several dimensions. Although the holobiont represents yet another level of selection (different from classical individual or group selection because it acts on a system that is composed of multiple species), it depends on the grade of functional integration whether or not the holobiont concept helps to cast light on the various degrees of interactions between symbiotic partners.

Systems biology aims at explaining life processes by means of detailed models of molecular networks, mainly on the whole-cell scale. The whole cell perspective distinguishes the new field of systems biology from earlier approaches within molecular cell biology. The shift was made possible by the high throughput methods that were developed for gathering 'omic' (genomic, proteomic, etc.) data. These new techniques are made commercially available as semi-automatic analytic equipment, ready-made analytic kits and probe arrays. There is a whole industry of supplies for what may be called convenience experimentation. My paper inquires some epistemic consequences of strong reliance on convenience experimentation in systems biology. In times when experimentation was automated to a lesser degree, modeling and in part even experimentation could be understood fairly well as either being driven by hypotheses, and thus proceed by the testing of hypothesis, or as being performed in an exploratory mode, intended to sharpen concepts or initially vague phenomena. In systems biology, the situation is dramatically different. Data collection became so easy (though not cheap) that experimentation is, to a high degree, driven by convenience equipment, and model building is driven by the vast amount of data that is produced by convenience experimentation. This results in a shift in the mode of science. The paper shows that convenience driven science is not primarily hypothesis-testing, nor is it in an exploratory mode. It rather proceeds in a gathering mode. This shift demands another shift in the mode of evaluation, which now becomes an exploratory endeavor, in response to the superabundance of gathered data.

No abstract

Halobacteria usually respond to repellent light stimuli by reversing their swimming direction. However, cells seem to be in a refractory state when stimulated immediately after performance of a reversal. I found that in this case, a special type of response is exhibited rather than spontaneous behavior. A strong stimulus induced a rhythmic pattern of successive reversals. On stimulation immediately after a reversal of swimming direction, the first of these reversals was skipped without influence on the rhythm. The results suggest that the stimulus evokes an oscillating signal which alters reversal probability but which is itself independent of the state of the motor apparatus. The oscillation has a period length of about 5 s and is damped out within a few cycles. It does not depend on the special sensory photosystem through which the stimulus is applied. The consequences of these findings for the model description of swimming behavior control in halobacteria are discussed.Under constant conditions, Halobacterium salinarium (formerly Halobacterium halobium) reverses its swimming direction every 3 to 50 s by switching the rotational sense of its flagellar motors from clockwise (CW) to counterclockwise (CCW) or vice versa. The distribution of the interval length is highly asymmetric, with the maximum at short times of about 10 s (for a comparative compilation of different results, see reference 14; original data are presented in references 5, 7, 9, 10, and 15). Light stimuli alter the length of a swimming interval. The effect of stimulation depends on the wavelength and on the sign of the light intensity change, which is sensed by the retinal proteins sensory rhodopsins I and II (9,20,21,23,24). Stimuli which prolong a swimming interval are called attractants, and stimuli which cause a shortening of a swimming interval are called repellents. After strong repellent stimuli, all bacteria reverse their swimming direction within a few seconds. However, this response fails to occur if the stimulus is applied during the first half-second after a reversal has taken place, during the so-called refractory period. Cells regain responsiveness within the following 2 s (10, 15).It has been postulated that the swimming behavior of H. salinarium is controlled by an intracellular deterministic oscillator, which triggers a switching event after completion of each cycle. It was assumed to alter sensitivity to attractant light stimuli during the cycle (15, 16). Such an oscillator would be one of the very few examples of the occurrence of a biological clock in procaryotes, besides the circadian rhythms in certain cyanobacteria (2,11,18). But the original results in favor of the oscillator hypothesis were recently rejected as being based on inadequate methods, and constancy of the sensitivity to attractant light stimuli during a swimming interval could be demonstrated (5). There is no evidence for oscillations in the unstimulated state.In an alternative description of the system, the transition between the CW and CCW rotating states of...