Network design meets in silico evolutionary biology

Cell fate is programmed through gene regulatory networks that perform several calculations to take the appropriate decision. In silico evolutionary optimization mimics the way Nature has designed such gene regulatory networks. In this review we discuss the basic principles of these evolutionary approaches and how they can be applied to engineer synthetic networks. We summarize the basic guidelines to implement an in silico evolutionary design method, the operators for mutation and selection that iteratively drive the network architecture towards a specified dynamical behavior. Interestingly, as it happens in natural evolution, we show the existence of patterns of punctuated evolution. In addition, we highlight several examples of models that have been designed using automated procedures, together with different objective functions to select for the proper behavior. Finally, we briefly discuss the modular designability of gene regulatory networks and its potential application in biotechnology.     

Embryogenomics: developmental biology meets genomics

Fundamental questions in developmental biology are: what genes are expressed, where and when they are expressed, what is the level of expression and how are these programs changed by the functional and structural alteration of genes? These questions have been addressed by studying one gene at a time, but a new research field that handles many genes in parallel is emerging. The methodology is at the interface of large-scale genomics approaches and developmental biology. Genomics needs developmental biology because one of the goals of genomics – collection and analysis of all genes in an organism – cannot be completed without working on embryonic tissues in which many genes are uniquely expressed. However, developmental biology needs genomics – the high-throughput approaches of genomics generate information about genes and pathways that can give an integrated view of complex processes. This article discusses these new approaches and their applications to mammalian developmental biology.     

How to be an anti-reductionist about developmental biology: Response to Laubichler and Wagner

Alexander Rosenberg recently claimed (1997) that developmental biology is currently being reduced to molecular biology. cite several concrete biological examples that are intended to impugn Rosenberg's claim. I first argue that although Laubichler and Wagner's examples would refute a very strong reductionism, a more moderate reductionism would escape their attacks. Next, taking my cue from the antireductionist's perennial stress on the importance of spatial organization, I describe one form an empirical finding that refutes this moderate reductionism would take. Finally, I point out an actual example, anterior-posterior axis determination in the chick, that challenges the reductionist's belief that all developmental regularities can be explained by molecular biology. In short, I argue that Rosenberg's position can be saved from Laubichler and Wagner's criticisms and putative counter-examples, but it would not survive a different kind of counter-example.     

Fluctuating asymmetry and developmental instability in evolutionary biology: past, present and future

The role of developmental instability (DI), as measured by fluctuating asymmetry (FA), in evolutionary biology has been the focus of a wealth of research for more than half a century. In spite of this long period and many published papers, our current state of knowledge reviewed here only allows us to conclude that patterns are heterogeneous and that very little is known about the underlying causes of this heterogeneity. In addition, the statistical properties of FA as a measure of DI are only poorly grasped because of a general lack of understanding of the underlying mechanisms that drive DI. If we want to avoid that this area of research becomes abandoned, more efforts should be made to understand the observed heterogeneity, and attempts should be made to develop a unifying statistical protocol. More specifically, and perhaps most importantly, it is argued here that more attention should be paid to the usefulness of FA as a measure of DI since many factors might blur this relationship. Furthermore, the genetic architecture, associations with fitness and the importance of compensatory growth should be investigated under a variety of stress situations. In addition, more focus should be directed to the underlying mechanisms of DI as well as how these processes map to the observable phenotype. These insights could yield more efficient statistical models and a unified approach to the analysis of patterns in FA and DI. The study of both DI and canalization is indispensable to obtain better insights in their possible common origin, especially because both have been suggested to play a role in both micro- and macro-evolutionary processes.     

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.     

Typology now: homology and developmental constraints explain evolvability

By linking the concepts of homology and morphological organization to evolvability, this paper attempts to (1) bridge the gap between developmental and phylogenetic approaches to homology and to (2) show that developmental constraints and natural selection are compatible and in fact complementary. I conceive of a homologue as a unit of morphological evolvability, i.e., as a part of an organism that can exhibit heritable phenotypic variation independently of the organism’s other homologues. An account of homology therefore consists in explaining how an organism’s developmental constitution results in different homologues/characters as units that can evolve independently of each other. The explanans of an account of homology is developmental, yet the very explanandum is an evolutionary phenomenon: evolvability in a character-by-character fashion, which manifests itself in phylogenetic patterns as recognized by phylogenetic approaches to homology. While developmental constraints and selection have often been viewed as antagonistic forces, I argue that both are complementary as they concern different parts of the evolutionary process. Developmental constraints, conceived of as the presence of the same set of homologues across phenotypic change, pertain to how heritable variation can be generated in the first place (evolvability), while natural selection operates subsequently on the produced variation.

浅谈发育生物学实验教学改革及创新能力培养

实验教学是培养具有创新精神和实践能力的应用型人才的重要途径.发育生物学是一门新兴学科,其实验教学存在教学内容参差不齐和教学环节薄弱等诸多问题,实行教学改革迫在眉睫.通过对发育生物学实验教学改革的实践经验进行总结,以期对同类高校该课程实验教学有所借鉴和参考,共同完善发育生物学实验教学环节.     

Toward a new synthesis: population genetics and evolutionary developmental biology

Despite the recent synthesis of developmental genetics and evolutionary biology, current theories of adaptation are still strictly phenomenological and do not yet consider the implications of how phenotypes are constructed from genotypes. Given the ubiquity of regulatory genetic pathways in developmental processes, we contend that study of the population genetics of these pathways should become a major research program. We discuss the role divergence in regulatory developmental genetic pathways may play in speciation, focusing on our theoretical and computational investigations. We also discuss the population genetics of molecular co-option, arguing that mutations of large effect are not needed for co-option. We offer a prospectus for future research, arguing for a new synthesis of the population genetics of development.     

Morphology and behaviour: functional links in development and evolution

Development and evolution of animal behaviour and morphology are frequently addressed independently, as reflected in the dichotomy of disciplines dedicated to their study distinguishing object of study (morphology versus behaviour) and perspective (ultimate versus proximate). Although traits are known to develop and evolve semi-independently, they are matched together in development and evolution to produce a unique functional phenotype. Here I highlight similarities shared by both traits, such as the decisive role played by the environment for their ontogeny. Considering the widespread developmental and functional entanglement between both traits, many cases of adaptive evolution are better understood when proximate and ultimate explanations are integrated. A field integrating these perspectives is evolutionary developmental biology (evo-devo), which studies the developmental basis of phenotypic diversity. Ultimate aspects in evo-devo studies--which have mostly focused on morphological traits--could become more apparent when behaviour, 'the integrator of form and function', is integrated into the same framework of analysis. Integrating a trait such as behaviour at a different level in the biological hierarchy will help to better understand not only how behavioural diversity is produced, but also how levels are connected to produce functional phenotypes and how these evolve. A possible framework to accommodate and compare form and function at different levels of the biological hierarchy is outlined. At the end, some methodological issues are discussed.     

Porphyra monospore system (Bangiales, Rhodophyta): A model for the developmental biology of marine plants

We have developed an experimental system of cohort monospores from clonal culture of leafy gametophytes in Porphyra yezoensis Ueda (strain TU-1). This system is quite different from traditional systems for algal protoplast experimentation, which require expensive enzymatic treatment and utilize an ineffective method of preservation. Cohort monospores were obtained by utilizing a mode of asexual reproduction in the culture strain (monospores) and artificial regulation (thallus length, temperature, light, etc.) of monospore release. When the leafy gametophytes that formed monospores were frozen at - 20°C in a cryoprotective solution composed of 5% DMSO and 5% dextran in 100% seawater, about 98% survived for 3 months. When stored at 5°C without cryoprotectants, these leafy gametophytes could be kept without monospore release for 1 week. Maximum monospore yield was about 3000 spores per 100 gametophytes, and germination rate was about 70%, This system will accelerate developmental biology studies in Porphyra.     

Annelids in evolutionary developmental biology and comparative genomics

Annelids have had a long history in comparative embryology and morphology, which has helped to establish them in zoology textbooks as an ideal system to understand the evolution of the typical triploblastic, coelomate, protostome condition. In recent years there has been a relative upsurge in embryological data, particularly with regard to the expression and function of developmental control genes. Polychaetes, as well as other annelids such as the parasitic leech, are now also entering the age of comparative genomics. All of this comparative data has had an important impact on our views of the ancestral conditions at various levels of the animal phylogeny, including the bilaterian ancestor and the nature of the annelid ancestor. Here we review some of the recent advances made in annelid comparative development and genomics, revealing a hitherto unsuspected level of complexity in these ancestors. It is also apparent that the transition to a parasitic lifestyle leads to, or requires, extensive modifications and derivations at both the genomic and embryological levels.     

How evolutionary biology challenges the classical theory of rational choice

A fundamental philosophical question that arises in connection with evolutionary theory is whether the fittest patterns of behavior are always the most rational. Are fitness and rationality fully compatible? When behavioral rationality is characterized formally as in classical decision theory, the question becomes mathematically meaningful and can be explored systematically by investigating whether the optimally fit behavior predicted by evolutionary process models is decision-theoretically coherent. Upon investigation, it appears that in nontrivial evolutionary models the expected behavior is not always in accord with the norms of the standard theory of decision as ordinarily applied. Many classically irrational acts, e.g. betting on the occurrence of one event in the knowledge that the probabilities favor another, can under certain circumstances constitute adaptive behavior. One interesting interpretation of this clash is that the criterion of rationality offered by classical decision theory is simply incorrect (or at least incomplete) as it stands, and that evolutionary theory should be called upon to provide a more generally applicable theory of rationality. Such a program, should it prove feasible, would amount to the logical reduction of the theory of rational choice to evolutionary theory.     

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.     

The role of developmental plasticity in evolutionary innovation

Explaining the origins of novel traits is central to evolutionary biology. Longstanding theory suggests that developmental plasticity, the ability of an individual to modify its development in response to environmental conditions, might facilitate the evolution of novel traits. Yet whether and how such developmental flexibility promotes innovations that persist over evolutionary time remains unclear. Here, we examine three distinct ways by which developmental plasticity can promote evolutionary innovation. First, we show how the process of genetic accommodation provides a feasible and possibly common avenue by which environmentally induced phenotypes can become subject to heritable modification. Second, we posit that the developmental underpinnings of plasticity increase the degrees of freedom by which environmental and genetic factors influence ontogeny, thereby diversifying targets for evolutionary processes to act on and increasing opportunities for the construction of novel, functional and potentially adaptive phenotypes. Finally, we examine the developmental genetic architectures of environment-dependent trait expression, and highlight their specific implications for the evolutionary origin of novel traits. We critically review the empirical evidence supporting each of these processes, and propose future experiments and tests that would further illuminate the interplay between environmental factors, condition-dependent development, and the initiation and elaboration of novel phenotypes.     

Evolutionary biology and feminism

Evolutionary biology and feminism share a variety of philosophical and practical concerns. I have tried to describe how a perspective from both evolutionary biology and feminism can accelerate the achievement of goals for both feminists and evolutionary biologists. In an early section of this paper I discuss the importance of variation to the disciplines of evolutionary biology and feminism. In the section entitled “Control of Female Reproduction” I demonstrate how insight provided by participation in life as woman and also as a feminist suggests testable hypotheses about the evolution of social behavior—hypotheses that are applicable to our investigations of the evolution of social behavior in nonhuman animals. In the section on “Deceit, Self-deception, and Patriarchal Reversals” I have overtly conceded that evolutionary biology, a scientific discipline, also represents a human cultural practice that, like other human cultural practices, may in parts and at times be characterized by deceit and self-deception. In the section on “Femininity” I have indicated how questions cast and answered and hypotheses tested from an evolutionary perspective can serve women and men struggling with sexist oppression. Patricia Adair Gowaty studies the evolution of social behavior, particularly mating systems and sex allocation, primarily in birds. She is most well-known for her long-term studies of eastern bluebirds, which began in 1977 and are on-going. She was an undergraduate at H. Sophie Newcomb College of Tulane University (1963–1967). In the late sixties and early seventies, while employed at the Bronx Zoo (New York Zoological Society), she belonged to a feminist “consciousness-raising” group. She started graduate school in 1974 at the University of Georgia and received her Ph.D. from Clemson University (1980). She had a postdoctoral position at the University of Oklahoma (1982–1983) and a visiting faculty position at Cornell University through the Visiting Professorships for Women NSF program (1983–1984) before returning to her bluebird study sites at Clemson in 1985. She has supported herself and her research efforts throughout her academic career on a series of awards and grants. She is currently (1990–1995) supported by a Research Scientist Development Award from The National Institute of Mental Health.     

Evolving cell models for systems and synthetic biology

This paper proposes a new methodology for the automated design of cell models for systems and synthetic biology. Our modelling framework is based on P systems, a discrete, stochastic and modular formal modelling language. The automated design of biological models comprising the optimization of the model structure and its stochastic kinetic constants is performed using an evolutionary algorithm. The evolutionary algorithm evolves model structures by combining different modules taken from a predefined module library and then it fine-tunes the associated stochastic kinetic constants. We investigate four alternative objective functions for the fitness calculation within the evolutionary algorithm: (1) equally weighted sum method, (2) normalization method, (3) randomly weighted sum method, and (4) equally weighted product method. The effectiveness of the methodology is tested on four case studies of increasing complexity including negative and positive autoregulation as well as two gene networks implementing a pulse generator and a bandwidth detector. We provide a systematic analysis of the evolutionary algorithm’s results as well as of the resulting evolved cell models.     

A developmental approach to the problem of variation in evolutionary rates

Certain general features are widely recognized in evolution, one of which is the variability in the rate at which morphological characters evolve and taxa are replaced by others. Although some rate-variability in evolution no doubt arises because of different rates of ecological change, it is proposed that some of the variability also arises from developmental, rather than ecological, sources. A theory is outlined whereby early-acting genes influencing the course of development evolve more slowly, but have individually larger effects, than genes affecting development at a later stage in the life-cycle. The erratic course of morphological evolution that results is illustrated by computer simulation. It is suggested that the applicability of the theory is restricted to long-term evolution and that variability in the rate of evolution over shorter periods may be of an entirely different nature.