The morphogenesis of evolutionary developmental biology

The early studies of evolutionary developmental biology (Evo-Devo) come from several sources. Tributaries flowing into Evo-Devo came from such disciplines as embryology, developmental genetics, evolutionary biology, ecology, paleontology, systematics, medical embryology and mathematical modeling. This essay will trace one of the major pathways, that from evolutionary embryology to Evo-Devo and it will show the interactions of this pathway with two other sources of Evo-Devo: ecological developmental biology and medical developmental biology. Together, these three fields are forming a more inclusive evolutionary developmental biology that is revitalizing and providing answers to old and important questions involving the formation of biodiversity on Earth. The phenotype of Evo-Devo is limited by internal constraints on what could be known given the methods and equipment of the time and it has been framed by external factors that include both academic and global politics.     

A semiotical reflection on biology,living signs and artificial life

It is argued, that theory sf signs, especially in the tradition of the great philosopher Charles Sanders Peirce (1839–1914) can inspire the study of central problems in the philosophy of biology. Three such problems are considered: (1) The nature of biology as a science, where a semiotically informed pluralistic approach to the theory of science is introduced. (2) The peculiarity of the general object of biology, where a realistic interpretation of sign- and information-concepts is required to see sign-processes as immanent in nature. (3) The possibility of an artificial construction of life, hereby discussed as a conceptual problem in the present form of the artificial life project and its implied definition of life.     

Synthesizing insight: artificial life as thought experimentation in biology

What is artificial life? Much has been said about this interesting collection of efforts to artificially simulate and synthesize lifelike behavior and processes, yet we are far from having a robust philosophical understanding of just what Alifers are doing and why it ought to interest philosophers of science, and philosophers of biology in particular. In this paper, I first provide three introductory examples from the particular subset of artificial life I focus on, known as ‘soft Alife’ (s-Alife), and follow up with a more in-depth review of the Avida program, which serves as my case study of s-Alife. Next, I review three well-known accounts of thought experiments, and then offer my own synthesized account, to make the argument that s-Alife functions as thought experimentation in biology. I draw a comparison between the methodology of the thought-experimental world that yields real-world results, and the s-Alife research that informs our understanding of natural life. I conclude that the insights provided by s-Alife research have the potential to fundamentally alter our understanding of the nature of organic life and thus deserve the attention of both philosophers and natural scientists.     

Ashbya gossypii: a model for fungal developmental biology

Ashbya gossypii is a riboflavin-overproducing filamentous fungus that is closely related to unicellular yeasts such as Saccharomyces cerevisiae. With its close ties to yeast and the ease of genetic manipulation in this fungal species, A. gossypii is well suited as a model to elucidate the regulatory networks that govern the functional differences between filamentous growth and yeast growth, especially now that the A. gossypii genome sequence has been completed. Understanding these networks could be relevant to related dimorphic yeasts such as the human fungal pathogen Candida albicans, in which a switch in morphology from the yeast to the filamentous form in response to specific environmental stimuli is important for virulence.     

Chironomid midges: a forgotten model of developmental biology research

For more than a century, embryologists have been exploring various model systems to gain insights into developmental processes. This article presents an overview of the role of chironomid midges in embryology research since their introduction as model organisms in the 19th century. We present the vestiges of bibliography since the days of Weismann (1834–1914), who raised preliminary queries to unravel many unique features of insect embryogenesis using midges as a crucible. Unfortunately, over the years, chironomid midges got lost into obscurity as a model for developmental biology, which is evident from the paucity of developmental biology–related literature on midges in the past decades. Through this essay, the authors intend to share reminiscences of the heydays of chironomid research with the wider community of zoologists with an aim of reviving chironomid embryology. Midges not only possess the basic qualities essential for an ideal model system, but being one of the ancestral dipteran stocks, they can also prove an excellent test system for evo‐devo, transgenetic, and embryogenomic investigations that utilize methodologies at the interface of developmental biology and high‐throughput molecular genetic and genomics approach. An introspection of re‐introducing chironomid midgesas model system will be rewarding for the contemporary developmental biologists.     

Ecological developmental biology: developmental biology meets the real world

The production of phenotype is regulated by differential gene expression. However, the regulators of gene expression need not all reside within the embryo. Environmental factors, such as temperature, photoperiod, diet, population density, or the presence of predators, can produce specific phenotypes, presumably by altering gene-expression patterns. The field of ecological developmental biology seeks to look at development in the real world of predators, competitors, and changing seasons. Ecological concerns had played a major role in the formation of experimental embryology, and they are returning as the need for knowledge about the effects of environmental change on embryos and larvae becomes crucial. This essay reviews some of the areas of ecological developmental biology, concentrating on new studies of amphibia and Homo.     

Molecular biology of feather morphogenesis: a testable model for evo-devo research

Darwin's theory describes the principles that are responsible for evolutionary change of organisms and their attributes. The actual mechanisms, however, need to be studied for each species and each organ separately. Here we have investigated the mechanisms underlying these principles in the avian feather. Feathers comprise one of the most complex and diverse epidermal organs as demonstrated by their shape, size, patterned arrangement and pigmentation. Variations can occur at several steps along each level of organization, leading to highly diverse forms and functions. Feathers develop gradually during ontogeny through a series of steps that may correspond to the evolutionary steps that were taken during the phylogeny from a reptilian ancestor to birds. These developmental steps include 1) the formation of feather tract fields on the skin surfaces; 2) periodic patterning of the individual feather primordia within the feather tract fields; 3) feather bud morphogenesis establishing anterio-posterior (along the cranio-caudal axis) and proximo-distal axes; 4) branching morphogenesis to create the rachis, barbs and barbules within a feather bud; and 5) gradual modulations of these basic morphological parameters within a single feather or across a feather tract. Thus, possibilities for variation in form and function of feathers occur at every developmental step. In this paper, principles guiding feather tract formation, distributions of individual feathers within the tracts and variations in feather forms are discussed at a cellular and molecular level.     

Evolutionary developmental biology and vertebrate head segmentation: A perspective from developmental constraint

Summary The question of vertebrate head segmentation has become one of the central issues in Evolutionary Developmental Biology. Beginning as a theory based in comparative anatomy, a segmental theory of the head has been adopted and further developed by comparative embryologists. With the use of molecular and cellular biology, and in particular analyses of the Hox gene complex, the question has been addressed at new levels, but it remains unresolved. In this review, vertebrate head segmentation is reevaluated, by introducing findings from experimental embryology and evolutionary biology. Developmental biology has shown that pattern is generated through hierarchically organized and causally linked series of events. The question of head segmentation can be viewed as a question of generative constraint, that is whether segmentation in the head is imposed by underlying segmental patterns, as it is in the trunk. In this respect, amphioxus appears to be segmented along the entire anteroposterior axis, with myotomes and peripheral nerves repeating with the same rhythm (somitomerism). Similarly, in the vertebrate trunk, the segmental patterns shared by myotomes, peripheral nerves and vertebrae are derived from the somites. However, in the head of vertebrates there is no such mesodermal pattern, although neuromerism and branchiomerism do indicate the presence of constraints derived from rhombomeres and pharyngeal pouches, respectively. These data fit better the concept of dual metamerism of the vertebrate body proposed by Romer (1972), than the traditional head cavity-based segmental model by Goodrich (1930).     

Pattern formation and morphogenesis: A reaction-diffusion model

The problem of cellular differentiation and consequent pattern generation during embryonic development has been mathematically investigated with the help of a reaction-diffusion model. It is by now a well-recognized fact that diffusion of micromolecules (through intercellular gap junctions), which is dependent on the spatial parameter (r), serve the purpose of ‘positional information’ for differentiation. Based on this principle the present model has been constructed by coupling the Goodwin-type equations for RNA and protein synthesis with the diffusion process. The homogeneous Goodwin system can exhibit stable periodic solution if the value of the cooperativity as measured by the Hill coefficient (ρ) is greater than 8, which is not biologically realistic. In the present work it has been observed that inclusion of a negative cross-diffusion can drive the system into local instability for any value of ρ and thus a time-periodic spatial solution is possible around the unstable local equilibrium, eventually leading to a definite pattern formation. Inclusion of a negative cross-diffusion thus makes the system biologically realistic. The cross-diffusion can also give rise to a stationary wave-like dissipative structure.     

Acute lymphoblastic leukemia and developmental biology: A crucial interrelationship

The latest scientific findings in the field of cancer research are redefining our understanding of the molecular and cellular basis of the disease, moving the emphasis toward the study of the mechanisms underlying the alteration of the normal processes of cellular differentiation. The concepts best exemplifying this new vision are those of cancer stem cells and tumoral reprogramming. The study of the biology of acute lymphoblastic leukemias (ALLs) has provided seminal experimental evidence supporting these new points of view. Furthermore, in the case of B cells, it has been shown that all the stages of their normal development show a tremendous degree of plasticity, allowing them to be reprogrammed to other cellular types, either normal or leukemic. Here we revise the most recent discoveries in the fields of B-cell developmental plasticity and B-ALL research and discuss their interrelationships and their implications for our understanding of the biology of the disease.Key words: leukemia, hematopoietic development, leukemic stem cells, lymphopoiesis, developmental plasticity, B cells, stem cells, cancer, B-ALL     

Driving developmental and evolutionary change: A systems biology view

Embryonic development is underpinned by ～50 core processes that drive morphogenesis, growth, patterning and differentiation, and each is the functional output of a complex molecular network. Processes are thus the natural and parsimonious link between genotype and phenotype and the obvious focus for any discussion of biological change. Here, the implications of this approach are explored. One is that many features of developmental change can be modeled as mathematical graphs, or sets of connected triplets of the general form <noun><verb><noun>. In these, the verbs (edges) are the outputs of the processes that drive change and the nouns (nodes) are the time-dependent states of biological entities (from molecules to tissues). Such graphs help unpick the multi-level complexity of developmental phenomena and may help suggest new experiments. Another comes from analyzing the effect of mutation that lead to tinkering with the dynamic properties of these processes and to congenital abnormalities; if these changes are both inherited and advantageous, they become evolutionary modifications. In this context, protein networks often represents what classical evolutionary genetics sees as genes, and the realization that traits reflect the output processes of complex networks, particularly for growth, patterning and pigmentation, rather than anything simpler clarifies some problems that the evolutionary synthesis of the 1950s has found hard to solve. In the wider context, most processes are used many times in development and cooperate to produce tissue modules (bones, branching duct systems, muscles etc.). Their underlying generative networks can thus be thought of as genomic modules or subroutines.     

Molecular biology of hair morphogenesis: development and cycling

In mammals, hair follicles produce hairs that fulfill a number of functions including thermoregulation, collecting sensory information, protection against environmental trauma, social communication, and mimicry. Hair follicles develop as a result of epithelial-mesenchymal interactions between epidermal keratinocytes committed to hair-specific differentiation and cluster of dermal fibroblasts that form follicular papilla. During postnatal life, hair follicles show patterns of cyclic activity with periods of active growth and hair production (anagen), apoptosis-driven involution (catagen), and relative resting (telogen). During last decade, substantial progress has been achieved in delineating molecular mechanisms that control hair follicle development and cyclic activity. In this review, we summarize the data demonstrating that regulation of hair follicle development in the embryo and control of hair follicle growth during postnatal life are highly conserved and both require involvement of similar molecular mechanisms. Since many of the molecules that control hair follicle development and cycling are also involved in regulating morphogenesis and postnatal biology of other ectodermal derivatives, such as teeth, feathers, and mammary glands, basic principles and molecular mechanisms that govern hair follicle development and growth may also be applicable for other developmental systems.     

Environmental and endogenous control of sexuality in a rotifer life cycle: developmental and population biology

Induction of mictic females, and hence initiation of sexuality, in the life cycle of some Brachionus requires an environmental stimulus associated with crowding. The inducing stimulus appears to be a taxonomically specific chemical released into the environment by the rotifers. Oocytes are induced to develop into mictic females before they are oviposited by their amictic mothers and begin cleavage divisions. Thus, the inducer affects the oocyte in the maternal body cavity either directly or indirectly by altering the physiology of its mother. The level of sexual reproduction expressed in populations of a Florida strain of B. calyciflorus is controlled by two types of endogenous factors and by the degree of crowding. First, some fraction of genetically identical oocytes in a clonal population fails to respond to even extreme crowding conditions, thus ensuring some potential for continued population growth by female parthenogenesis. Second, the propensity of amictic females to produce mictic daughters is extremely low when they hatch from fertilized resting eggs and then gradually increases to an asymptote after about 12 parthenogenetic generations. This multigenerational parental effect likely is due to a cytoplasmic factor in fertilized eggs that inhibits expression of the mictic-female phenotype and that is gradually diluted in successive parthenogenetic generations. The effect may increase a clone's genetic contribution to the resting-egg bank by increasing its population size through parthenogenetic generations before mictic females are induced.     

A sugar rush for developmental biology

The EMBO Workshop on Glycoscience and Development, organised by Philippe Delannoy, Yann Guérardel, Tony Merry and Jean-Claude Michalski, was held in the picturesque, contemplative environment of Les Minimes, a converted seventeenth century Flemish convent in Lille, France, in December 2007. A cross-section of researchers, both confirmed ;glycomaniacs' and those newer to the field, discussed and debated recent advances in the field of glycobiology. Presentations ranged from the clinical applications of glycobiology to novel approaches for unravelling carbohydrate biosynthesis in developmental settings and models, such as the fruit fly, nematode and zebrafish.     

Cavefish as a model system in evolutionary developmental biology

The Mexican tetra Astyanax mexicanus has many of the favorable attributes that have made the zebrafish a model system in developmental biology. The existence of eyed surface (surface fish) and blind cave (cavefish) dwelling forms in Astyanax also provides an attractive system for studying the evolution of developmental mechanisms. The polarity of evolutionary changes and the environmental conditions leading to the cavefish phenotype are known with certainty, and several different cavefish populations have evolved constructive and regressive changes independently. The constructive changes include enhancement of the feeding apparatus (jaws, taste buds, and teeth) and the mechanosensory system of cranial neuromasts. The homeobox gene Prox 1, which is expressed in the expanded taste buds and cranial neuromasts, is one of the genes involved in the constructive changes in sensory organ development. The regressive changes include loss of pigmentation and eye degeneration. Although adult cavefish lack functional eyes, small eye primordia are formed during embryogenesis, which later arrest in development, degenerate, and sink into the orbit. Apoptosis and lens signaling to other eye parts, such as the cornea, iris, and retina, result in the arrest of eye development and ultimate optic degeneration. Accordingly, an eye with restored cornea, iris, and retinal photoreceptor cells is formed when a surface fish lens is transplanted into a cavefish optic cup, indicating that cavefish optic tissues have conserved the ability to respond to lens signaling. Genetic analysis indicates that multiple genes regulate eye degeneration, and molecular studies suggest that Pax6 may be one of the genes controlling cavefish eye degeneration. Further studies of the Astyanax system will contribute to our understanding of the evolution of developmental mechanisms in vertebrates.