This issue of The Journal of Physiology is devoted to the integration of evolutionary biology with physiological science. The immediate trigger was a very successful symposium on this theme held during the IUPS Congress in Birmingham in July 2013. The symposium followed an opening plenary lecture based on an article that had recently been published by one of us in the sister journal Experimental Physiology (Noble, 2013) and previously in The Journal of Physiology (Noble, 2011). The title of that article was ambitious, describing physiology as ‘rocking the foundations’ of biology. Strong language, perhaps? Yes, but that title was merely reflecting a rising tide of recently published articles in major scientific journals, including Nature Reviews Genetics (Müller, 2007), Proceedings of the National Academy of Sciences of the USA (Mattick, 2012), Nature (Ball, 2013), Biological Journal of the Linnean Society (Bateson, 2014) and Science (Rosenberg & Queitsch, 2014). It was also prompted by important books that have appeared recently (Margulis & Sagan, 2003; Jablonka & Lamb, 2014; Noble, 2006; Beurton et al. 2008; Pigliucci & Müller, 2010; Bateson & Gluckman, 2011; Gissis & Jablonka, 2011; Shapiro, 2011). Those books also propose either significant extensions of existing evolutionary theory or the replacement of the Modern Synthesis by a new synthesis. Despite the radical presentation of the Experimental Physiology article, therefore, it contains little that was not already known to those biologists who have been keeping abreast of recent literature. It is becoming increasingly difficult to keep up with this literature because it is widely spread amongst very many scientific journals. A focused issue of a journal, like this one, can therefore be very valuable. We intend that this should be a seminal resource for future research and teaching. Why have these questions become important? One answer is that they change the way in which physiological function is relevant to evolutionary biology. We define function here as the role that a part, a process or a mechanism plays within an encompassing system, a role that contributes to the goal-directed behaviour of that system. This definition covers different notions, such as those presented by Wright (1973), Cummins (1975) and Kitcher (1993). There is a possible confusion in discussing function in the context of evolution because current utility is not necessarily how the trait evolved. Further reading on these issues can be found in the articles by Tinbergen (1963), Bateson & Laland (2013) and the one in this issue by Roux (2014). We are also using a broad definition of physiology as a discipline at the intersection of ecology, behavioural biology, developmental biology and molecular biology. As will be evident in the articles of this focused issue, the new developments encompass all these fields, often in combination. In standard selection theory, usually called the Modern Synthesis (MS) and sometimes called Neo-Darwinism, function is relevant only to postgenomic change in populations through determining which individuals are successful in reproducing. One of the dogmas of the Modern Synthesis is the impossibility of the inheritance of acquired developmental dispositions. Genomic change, which is seen within the MS framework as a synonym to hereditary change, is assumed to be random with respect to function. Function therefore plays a role only in so far as it determines the fitness of the individual organism in its reproductive success after genomic mutations have created the possibility of an advantage. In contrast, the inheritance of some acquired epigenetic characteristics and other forms of non-DNA inheritance enables function to be involved in pregenomic change by influencing hereditary change more directly before selection could play a role. Furthermore, mechanisms of genomic change have been identified that were not envisaged by the founders of the Modern Synthesis, including symbiogenesis and natural genetic engineering. Making a categorical prohibition a central part of a theory can be useful for a time. The Modern Synthesis served an important function in the mid-20th century in stimulating much mathematical work in population genetics, for example. But we have to recognize that by encouraging a dogmatic use of the theory it may also have inhibited many lines of research that have now been found to be important. Theories with categorical prohibitions court their own demise, requiring either fundamental extensions or even complete replacement when contrary experimental evidence emerges. The articles in this issue demonstrate that evidence. The mechanism of random change followed by selection becomes only one of many possible mechanisms of evolutionary change. Moreover, all those mechanisms can interact. We have entered a period of a systems approach to evolution science that contrasts markedly with the parsimonious reductionism of the Modern Synthesis. In this respect, it echoes the move towards a systems approach in many other areas of biology (Melham et al. 2013). The genotype–phenotype relation, which is at the heart of our view of heredity and development, has turned out to be much more subtle than what the Modern Synthesis made room for, and it is increasingly acknowledged that a better understanding of this relation is key to understanding a range of evolutionary phenomena beyond the explanatory reach of the Modern Synthesis. Considering that the disciplinary goals of physiology are ‘the study of the functions and activities of living matter (as of organs, tissues, or cells) as such and of the physical and chemical phenomena involved’ (Webster's Third New International Dictionary), it is clear that the mechanistic aspects of the genotype–phenotype relation lie within the explanatory domain of physiology. Hence, physiology must of necessity become the backbone of any mature evolutionary theory pretending to merge the proximate and ultimate explanatory domains. The consequence is that we will have to go back to a broader, more inclusive view of heredity, which was captured by William Bateson's original definition of genetics as ‘The Physiology of Descent’ (Bateson, 1906; see Olby, 2000). A physiological view of heredity enables the integration of the extended evolutionary synthesis view of evolution with the physiological sciences. More specifically, the genotype–phenotype concept that is currently in wide use within evolutionary theory conceals the facts that it is an abstraction of a relation that is the outcome of very complex dynamics that in many cases are intimately connected to the environment (Gjuvsland et al. 2013), and that DNA does not have the privileged place in the chain of causality many attribute to it. As described in more detail by Omholt (2013), if one tries to interpret the function of DNA in systemic terms one finds that DNA allows a system to induce perturbations of its own dynamics as a function of the system's own state (its phenome). In this systems view, the causality flows from the system state through a change in use of DNA that results in a change in the production of RNA and protein, which in turn perturbs the system's dynamics. In those cases where variations in DNA cause changes in the perturbation regimen, it may lead to different system dynamics and thus physiological variation. Thus, the genotype–phenotype relation cannot be understood outside a systems-physiology framework, whatever causes variations in DNA. And any evolutionary theory aiming to explain the manifestation of biological form across time and space needs to be highly articulate about this relation. Physiology in a broad sense, therefore, now moves to centre stage in evolutionary biology as we are finally in a position to step conceptually and technologically out of the narrow frames of the Modern Synthesis and take explanatory responsibility for a much wider set of evolutionary phenomena and patterns across time and space. Some of the articles in this issue address the consequences that this new intellectual spotlight has for the discipline of physiology itself, including possible consequences for health and disease; it is noteworthy that some of the new mechanisms manifest themselves in the inheritance of the chances of acquired disease states. The ways in which a systems approach can be applied to the complex dynamics and evolution of organisms are addressed in this issue by Badyaev (2014), who explores ‘whether epigenetic effects facilitate adaptive modulation of complex phenotypes by effectively reducing the dimensionality of their deterministic networks’; Baverstock & Rönkkö (2014), who regard the cell ‘as a complex dissipative natural process’ that ‘minimizes the free energy of their ecosystems’, a process where genetic variation is largely irrelevant; Jaeger & Monk (2014) showing ‘how dynamical systems theory can provide a unifying conceptual framework for evolution of biological regulatory systems’; Lamm (2014), who ‘applies the conceptual toolkit of Evolutionary Developmental Biology (evo–devo) to the evolution of the genome and the role of the genome in organism development’; Levin (2014), who analyses ‘the control of anatomy by bioelectricity and the evolutionary implications of its top-down causal efficacy’; and Danchin & Pocheville (2014), who discuss the ways in which ‘non-genetic inheritance shatters the frontier between physiology and evolution’. The molecular mechanisms by which non-standard inheritance can occur are diverse. Natural genetic engineering refers to reorganization of genomes. The mechanisms discovered since McClintock (1950, 1984) first demonstrated mobile genetic elements in plants are many. As Beurton et al. (2008) write, ‘it seems that a cell's enzymes are capable of actively manipulating DNA to do this or that. A genome consists largely of semi-stable genetic elements that may be rearranged or even moved around in the genome thus modifying the information content of DNA.’ In this issue, Shapiro (2014) shows that ‘the genome is best modelled as a read–write (RW) data storage system rather than a read-only memory (ROM)’. Symbiogenesis has been involved in the most dramatic examples of genome re-organization, i.e. the acquisition of DNA from other organisms through lateral gene transfer. As is now well known, this is thought to explain the origin of mitochondria, chloroplasts and other organelles. Lateral gene transfer is now recognized to be much more extensive and widespread than it was previously assumed to be; occurring in most orders and often among them. Recent examples include mechanisms of transfer from prokaryotes to eukaryotes generally (Redrejo-Rodríguez et al. 2012) and transfer from bacteria to insects (Acuña et al. 2012). Epigenetic mechanisms that lead to persistent developmentally induced changes in gene activity include diverse processes and factors. One type of system, the chromatin marking system, includes methylation of cytosines and histone modifications, which interact with each other and with other epigenetic control as were thought to be during between It is now clear that this is not Moreover, recent work has epigenetic changes for and were after through the et al. 2012). induced epigenetic changes a wide range of characteristics were for to et al. and to an was for in & 2014). of epigenetic variations through the not for inheritance between can be across by marking the genome in the through their physiological and behavioural to the of developmental in the genomic marking may also et al. and effects et al. non-standard inheritance system, the inheritance system, which with the chromatin marking the of many important characteristics in plants and of to has been to be for in et al. 2011). In this issue, et al. (2014) demonstrate that to the of in the and this contributes to the inheritance of induced in this issue, Bateson et al. (2014) discuss a form of developmental the adaptive which in the of a that is to the of et al. (2014) the different epigenetic effects by with and therefore the and the The physiological of organisms to changes in within and between epigenetic for the of the physiological can lead to the selection of epigenetic changes that are between to the selection of genetic changes that or the physiological This genetic was first demonstrated by who also the not with its current A more inclusive was by This process can lead to the and of developmentally induced to an in and to the of In all the processes are usually by developmental changes that induce new patterns of gene activity in that already in the population not in that in any and the new to natural new mutations are in this a new can to it. that it is gene and developmental that are the of genetic is process showing the of on of rather than on individual to the definition of through the process of genetic of the between different developmental mechanisms at different of biological genetic the inheritance becomes standard DNA therefore, it be difficult to from genomic this process had of chromatin marking and RNA in populations that are at the of evolutionary can the epigenetic of the physiological that genetic and can to epigenetic that are and to the of the new Further on these questions can be found in the article in this issue by Bateson et al. (2014). changes can and and are phenomena that may have physiological living in in of and such as are to be to and which can their epigenetic and and their This is by data from the of which has that a in environment can have including the of many et al. 2011; et al. 2012). effects also in the from to as is now in and with consequences for the of type The physiology of and of inheritance as a new and The of physiological may also lead to to their environment at many that a it has been that selection to an in the of the of the in the This is with function et al. 2013), and the is that it and thus in a This to for the that is highly in and that can with only a of et al. & (2014) in this issue the of the view in the study of that provide system to study the role and between and in that ‘the developmental process should be in a systemic rather than in a way that on the role of The therefore, is not developmental and non-standard forms of inheritance occur but how often they occur and to what they to evolutionary change. It is also important to these changes mathematical et al. 2010; Danchin et al. and to define the in the regulatory that for broad and narrow et al. 2013). It will be important to the these regulatory mechanisms may have made to the of evolution and how between the such as genetic are all and difficult Nature is even more than the of the Modern Synthesis and processes we thought were The Modern Synthesis has also been a of research and experimental and since at the on which in A key was that genetic and molecular to these could be identified and with could be This view is now and is seen as a far more complex many by or behavioural with only evidence for genetic in & 2008; 2013). in the on have largely been through most In a the genome a between and with major with known genetic based on gene or other forms of genetic engineering more such as and heart gene explain much of the of the disease and lead to In other could be for and either or to This has been by a to gene that place of at for a of with have been In the of genetic information in does little to beyond and for such as and disease & 2010; et al. 2013). The current in seems so by the of and physical activity that some have that the for is 2011). even if such information were the change their behaviour or individuals free generally to health issues are with in more detail in the article by & (2014) in this There is also a for In the of the for a genotype–phenotype & 2012) has been to and to in most by genetic have & even within the with the gene do not manifest the some research by the Modern Synthesis is The is that gene new for A recent is the of with the gene & to The to which this new is more than the on genetic engineering or the to be on the it be that the by the Modern Synthesis have or at In contrast, in and with more evidence showing the effects of environment and on health et al. & 2003; 2012). The to which the genome has not is recent have little or of genetic to the of the the to to based on individual genetic is The and of epigenetic inheritance has implications for disease and the to New for and the of epigenetic variation in populations are One for this has been by et al. who have a genetics approach with information about the of for epigenetic between and about to the epigenetic and epigenetic The of this or to data can to the epigenetic and causes of complex and and in Further relevant can be found in the article on the in this issue et al. 2014). It is therefore, that evolutionary theory is in the and conceptual to evolution a of the of processes in evolutionary change, to an framework beyond the standard population genetic (Margulis & Sagan, 2003; Beurton et al. 2008; Pigliucci & Müller, 2010; Gissis & Jablonka, 2011; Shapiro, 2011). science has an important role in this encompassing of evolutionary theory, because of major it can the of the of and an of systems In the view of the Modern Synthesis, function in was all but from any role in the of the of evolutionary change was assumed to be the consequence of selection or the of information from one to the The to this issue demonstrate that this view is on all Hence, a of is in the evolutionary and evolutionary were as since the function has been in terms of on the of variation et al. More have to be addressed evolutionary of gene development, systems in physiology. The trigger for this was the to a better mechanistic understanding of the genotype–phenotype relation in the evolutionary It is that the has and on the molecular of gene through and genetic engineering. this a of experimental of the made by genetic & 2007), thus a new of to evolutionary science. these aspects of function our mechanistic understanding of the genotype–phenotype relation, physiology function to evolution also in a different through the control that physiological systems molecular or to but a physiological systems that are not to gene but the behaviour of and developmental processes at systems may themselves be a of more they can also the and of evolutionary change. In these the outcome is not an immediate consequence of natural but a consequence of the of the system. physiological activity during development, such as when through to the or of elements (Müller, Moreover, the of already in when in a may the possible of et al. systems evolutionary processes also through their on epigenetic marking or gene Epigenetic that the and of evolutionary change can markedly from that from population genetic & 2011; & 2012), and epigenetic inheritance may genetic processes et al. 2013). epigenetic changes may also and genomic and to change, for in & Lamb, 2014). Furthermore, epigenetic DNA which to gene can the of of mutations 2012) and adaptive evolution by gene et al. effects the standard of evolutionary theory and induce questions about the role and the evolutionary of epigenetic mechanisms during the major in evolution & Lamb, way in which systems evolution is through their Biological functions at many different of from to some aspects of which can now be through systems biological such as the et al. & & (2014) in this issue of with the of physical to molecular and processes within these to the on evolution’. (2014) also how the of physical in biology can that changes in form now a scientific other than natural selection based on adaptive In developmental processes that biological for physiological and gene play in any privileged of Evolutionary of such be it through natural selection or will the system. such systems and effects that the outcome et al. et al. 2014). the evolutionary such can lead to dynamics in population change et al. 2012). of and by the and for among the physiological can a major towards the of evolutionary dynamics and Thus, function in and physiological function in does the of the of evolutionary change and the of genetic and Hence, evolutionary biologists should be in the physiological are and a synthesis between molecular biology and evolutionary biology has been & we here is not only does molecular function to be with gene but the of to become part of a major of the evolutionary framework that is currently place through the of new from the article by Laland et al. (2014) in this epigenetic inheritance and other areas & Müller, of function the integration of this extended synthesis view of evolution with physiology. The of such a is a of any privileged of in the evolutionary process and a replacement of gene reductionism by systems (Noble, 2013). of the that many of the relevant processes now have become to ‘the for a of and evolutionary biology have we some consequences for the of key elements and on the concept of the The articles by (2014), (2014) and Roux (2014) in this issue should be for important on the and of the relevant and for their of the The concept of is amongst because the Modern Synthesis is a theory of There has been a between its original definition as a and the molecular biological definition of a gene as a for a Noble, The was for so as it was thought that the between and were at even if up ‘the was made that is a relation between genetic and to that many are involved in each physiological function. a physiological even this is not are well DNA changes through in In the mechanisms so that any one may in only changes in et al. & Noble, 2011). In of are in physiological et al. The relation between DNA and the is better as by in which not all the are in DNA et al. this we to that by genetic as we cannot be in terms of individual but rather as of to which we can the also to that DNA provide a of disease There has therefore been a new within the Modern Synthesis view to this as a of or et al. 2012). This the in terms that have role in scientific The better way is to that we a much better of inheritance through a systemic understanding of the genotype–phenotype relation. such understanding we for be to explain how the of broad and narrow of are functions of regulatory anatomy and the environment et al. 2013). It is also important to between different of in physiology and in evolutionary biology. are different but often As Roux (2014) the of a trait to its and not its current these are with the concept of function in other terms in the also in the of these such as and of The set of articles published in this issue a major for the physiological and for evolutionary biology. As the integration between the can Evolutionary theory or even physiological science needs to address the up for the We that our article, and those published will to effectively to that