Models,mechanisms and pathways of succession

The study of succession has been hampered by the lack of a general theory. This is illustrated by confusion over basic concepts and inadequacy of certain models. This review clarifies the basic ideas of pathway, mechanism, and model in succession. Second, in order to prevent inappropriate narrowness in successional studies, we analyze the mechanistic adequacy of the most widely cited models of succession, those of Connell and Slatyer. This analysis shows that models involving a single pathway or a dominant mechanism cannot be treated as alternative, testable hypotheses. Our review shows much more mechanistic richness than allowed by these widely cited models of succession. Classification of the mechanisms of specific replacement, called for by existing models, is problematic and less valuable than the search for the actual mechanisms of particular seres. For example, the “tolerance” mechanism of succession has at least two contrasting meanings and is unlikely to be disentangled from the “inhibition” mechanism in field experiments. However, the understanding of particular species replacements through experiment and knowledge of the conditions of a particular sere and species life histories is a reasonable and desirable goal. Finally, we suggest the need for a broad mechanistic concept of succession. Thus, based on classical causes of succession that have survived recent scrutiny, we erect a framework of successional mechanisms. This framework aims at comprehensiveness, and specific mechanisms are nested within more general causes. As a result of its breadth and hierarchical structure, the framework performs two important functions: First, it provides a context for studies at specific sites and, second, is a scheme for formulating general and testable hypotheses. The review of specific successional mechanisms and the general mechanistic framework can together guide future work on succession, and may foment the development of a broad theory.     

Mechanisms, determination and the metaphysics of neuroscience

In this paper, I evaluate recently defended mechanistic accounts of the unity of neuroscience from a metaphysical point of view. Considering the mechanistic framework in general (Sections 2 and 3), I argue that explanations of this kind are essentially reductive (Section 4). The reductive character of mechanistic explanations provides a sufficiency criterion, according to which the mechanism underlying a certain phenomenon is sufficient for the latter. Thus, the concept of supervenience can be used in order to describe the relation between mechanisms and phenomena (Section 5). Against this background, I show that the mechanistic framework is subject to the causal exclusion problem and faces the classical metaphysical options when it comes to the relations obtaining between different levels of mechanisms (Section 6). Finally, an attempt to improve the metaphysics of mechanisms is made (Section 7) and further difficulties are pointed out (Section 8).     

Mechanistic models of population-level phenomena

This paper is about mechanisms and models, and how they interact. In part, it is a response to recent discussion in philosophy of biology regarding whether natural selection is a mechanism. We suggest that this debate is indicative of a more general problem that occurs when scientists produce mechanistic models of populations and their behaviour. We can make sense of claims that there are mechanisms that drive population-level phenomena such as macroeconomics, natural selection, ecology, and epidemiology. But talk of mechanisms and mechanistic explanation evokes objects with well-defined and localisable parts which interact in discrete ways, while models of populations include parts and interactions that are neither local nor discrete in any actual populations. This apparent tension can be resolved by carefully distinguishing between the properties of a model and those of the system it represents. To this end, we provide an analysis that recognises the flexible relationship between a mechanistic model and its target system. In turn, this reveals a surprising feature of mechanistic representation and explanation: it can occur even when there is a mismatch between the mechanism of the model and that of its target. Our analysis reframes the debate, providing an alternative way to interpret scientists’ “mechanism-talk”, which initially motivated the issue. We suggest that the relevant question is not whether any population-level phenomenon such as natural selection is a mechanism, but whether it can be usefully modelled as though it were a particular type of mechanism.     

A cross-scale framework to support a mechanistic understanding and modelling of marine climate-driven species redistribution,from individuals to communities

Climate-driven species redistribution is pervasive and accelerating, yet the complex mechanisms at play remain poorly understood. The implications of large-scale species redistribution for natural systems and human societies have resulted in a large number of studies exploring the effects on individual species and ecological communities worldwide. Whilst many studies have investigated discrete components of species redistribution, the integration required for a more complete mechanistic understanding is lacking. In this paper, we provide a framework for synthesising approaches to more robustly understand and predict marine species redistributions. We conceptualise the stages and processes involved in climate-driven species redistribution at increasing levels of biological organisation, and synthesize the laboratory, field and modelling approaches used to study redistribution related processes at individual, population and community levels. We then summarise links between scales of biological organisation and methodological approaches in a hierarchical framework that represents an integrated mechanistic assessment of climate-driven species redistributions. In a rapidly expanding field of research, this framework provides direction for: 1) guiding future research, 2) highlighting key knowledge gaps, 3) fostering data exchange and collaboration between disciplines and 4) improving shared capacity to predict and therefore, inform the proactive management of climate impacts on natural systems.     

Effects of product inhibition in metabolic pathways: stability and control

The effect of product inhibition in metabolic pathways is examined using (a) an unbranched pathway in the absence of endproduct inhibition and (b) an unbranched pathway with endproduct inhibition. It is shown that product inhibition may be considered an alternative mechanism to endproduct inhibition for reducing the overall logarithmic gain of an unregulated pathway. When product inhibition and endproduct inhibition are both present, they act in concert with each other to lower the overall logarithmic gain and alleviate parameter sensitivities. Product inhibition is also found to exert a stabilizing influence that competes with the destabilizing effect of endproduct inhibition in controlling the dynamic behavior.     

Function and organization: comparing the mechanisms of protein synthesis and natural selection

In this paper, we compare the mechanisms of protein synthesis and natural selection. We identify three core elements of mechanistic explanation: functional individuation, hierarchical nestedness or decomposition, and organization. These are now well understood elements of mechanistic explanation in fields such as protein synthesis, and widely accepted in the mechanisms literature. But Skipper and Millstein have argued (2005) that natural selection is neither decomposable nor organized. This would mean that much of the current mechanisms literature does not apply to the mechanism of natural selection. We take each element of mechanistic explanation in turn. Having appreciated the importance of functional individuation, we show how decomposition and organization should be better understood in these terms. We thereby show that mechanistic explanation by protein synthesis and natural selection are more closely analogous than they appear--both possess all three of these core elements of a mechanism widely recognized in the mechanisms literature.     

“Essentially,all models are wrong,but some are useful”<Emphasis Type="Italic">—</Emphasis>a cross-disciplinary agenda for building useful models in cell biology and biophysics

Intuition alone often fails to decipher the mechanisms underlying the experimental data in Cell Biology and Biophysics, and mathematical modeling has become a critical tool in these fields. However, mathematical modeling is not as widespread as it could be, because experimentalists and modelers often have difficulties communicating with each other, and are not always on the same page about what a model can or should achieve. Here, we present a framework to develop models that increase the understanding of the mechanisms underlying one’s favorite biological system. Development of the most insightful models starts with identifying a good biological question in light of what is known and unknown in the field, and determining the proper level of details that are sufficient to address this question. The model should aim not only to explain already available data, but also to make predictions that can be experimentally tested. We hope that both experimentalists and modelers who are driven by mechanistic questions will find these guidelines useful to develop models with maximum impact in their field.     

Biological hierarchies and the nature of extinction

Hierarchy theory recognises that ecological and evolutionary units occur in a nested and interconnected hierarchical system, with cascading effects occurring between hierarchical levels. Different biological disciplines have routinely come into conflict over the primacy of different forcing mechanisms behind evolutionary and ecological change. These disconnects arise partly from differences in perspective (with some researchers favouring ecological forcing mechanisms while others favour developmental/historical mechanisms), as well as differences in the temporal framework in which workers operate. In particular, long‐term palaeontological data often show that large‐scale (macro) patterns of evolution are predominantly dictated by shifts in the abiotic environment, while short‐term (micro) modern biological studies stress the importance of biotic interactions. We propose that thinking about ecological and evolutionary interactions in a hierarchical framework is a fruitful way to resolve these conflicts. Hierarchy theory suggests that changes occurring at lower hierarchical levels can have unexpected, complex effects at higher scales due to emergent interactions between simple systems. In this way, patterns occurring on short‐ and long‐term time scales are equally valid, as changes that are driven from lower levels will manifest in different forms at higher levels. We propose that the dual hierarchy framework fits well with our current understanding of evolutionary and ecological theory. Furthermore, we describe how this framework can be used to understand major extinction events better. Multi‐generational attritional loss of reproductive fitness (MALF) has recently been proposed as the primary mechanism behind extinction events, whereby extinction is explainable solely through processes that result in extirpation of populations through a shutdown of reproduction. While not necessarily explicit, the push to explain extinction through solely population‐level dynamics could be used to suggest that environmentally mediated patterns of extinction or slowed speciation across geological time are largely artefacts of poor preservation or a coarse temporal scale. We demonstrate how MALF fits into a hierarchical framework, showing that MALF can be a primary forcing mechanism at lower scales that still results in differential survivorship patterns at the species and clade level which vary depending upon the initial environmental forcing mechanism. Thus, even if MALF is the primary mechanism of extinction across all mass extinction events, the primary environmental cause of these events will still affect the system and result in differential responses. Therefore, patterns at both temporal scales are relevant.     

Stability and synchrony across ecological hierarchies in heterogeneous metacommunities: linking theory to data

Understanding stability across ecological hierarchies is critical for landscape management in a changing world. Recent studies showed that synchrony among lower‐level components is key to scaling temporal stability across two hierarchical levels, whether spatial or organizational. But an extended framework that integrates both spatial scale and organizational level simultaneously is required to clarify the sources of ecosystem stability at large scales. However, such an extension is far from trivial when taking into account the spatial heterogeneities in real‐world ecosystems. In this paper, we develop a partitioning framework that bridges variability and synchrony measures across spatial scales and organizational levels in heterogeneous metacommunities. In this framework, metacommunity variability is expressed as the product of local‐scale population variability and two synchrony indices that capture the temporal coherence across species and space, respectively. We develop an R function ‘var.partition’ and apply it to five types of desert plant communities to illustrate our framework and test how diversity shapes synchrony and variability at different hierarchical levels. As the observation scale increased from local populations to metacommunities, the temporal variability of plant productivity was reduced mainly by factors that decreased species synchrony. Species synchrony decreased from local to regional scales, and spatial synchrony decreased from species to community levels. Local and regional species diversity were key factors that reduced species synchrony at the two scales. Moreover, beta diversity contributed to decreasing spatial synchrony among communities. We conclude that our new framework offers a valuable toolbox for future empirical studies to disentangle the mechanisms and pathways by which ecological factors influence stability at large scales.     

The causal structure of mechanisms

Recently, a number of philosophers of science have claimed that much explanation in the sciences, especially in the biomedical and social sciences, is mechanistic explanation. I argue the account of mechanistic explanation provided in this tradition has not been entirely satisfactory, as it has neglected to describe in complete detail the crucial causal structure of mechanistic explanation. I show how the interventionist approach to causation, especially within a structural equations framework, provides a simple and elegant account of the causal structure of mechanisms. This account explains the many useful insights of traditional accounts of mechanism, such as Carl Craver’s account in his book Explaining the Brain (2007), but also helps to correct the omissions of such accounts. One of these omissions is the failure to provide an explicit formulation of a modularity constraint that plays a significant role in mechanistic explanation. One virtue of the interventionist/structural equations framework is that it allows for a simple formulation of a modularity constraint on mechanistic explanation. I illustrate the role of this constraint in the last section of the paper, which describes the form that mechanistic explanation takes in the computational, information-processing paradigm of cognitive psychology.     

Cell biology of embryonic migration

Cell migration is an evolutionarily conserved mechanism that underlies the development and functioning of uni- and multicellular organisms and takes place in normal and pathogenic processes, including various events of embryogenesis, wound healing, immune response, cancer metastases, and angiogenesis. Despite the differences in the cell types that take part in different migratory events, it is believed that all of these migrations occur by similar molecular mechanisms, whose major components have been functionally conserved in evolution and whose perturbation leads to severe developmental defects. These mechanisms involve intricate cytoskeleton-based molecular machines that can sense the environment, respond to signals, and modulate the entire cell behavior. A big question that has concerned the researchers for decades relates to the coordination of cell migration in situ and its relation to the intracellular aspects of the cell migratory mechanisms. Traditionally, this question has been addressed by researchers that considered the intra- and extracellular mechanisms driving migration in separate sets of studies. As more data accumulate researchers are now able to integrate all of the available information and consider the intracellular mechanisms of cell migration in the context of the developing organisms that contain additional levels of complexity provided by extracellular regulation. This review provides a broad summary of the existing and emerging data in the cell and developmental biology fields regarding cell migration during development.