Biology

Metabolic reprogramming is a critical phenomenon in cellular processes associated with development, morphogenesis and cancer. In addition to the alteration of metabolites concentration, the method of dynamic optimization is capable of providing the dynamic profile of metabolic enzymes in the cells. However, the application of this method in the systems as large as metabolic networks suffers from drastic computational challenges. Here, we use techniques derived from distributed optimal control theory to set up a comprehensive landscape of metabolism during cellular reprogramming and differentiation. The proposed approach and the expected outputs introduce potential targets for controlling metabolic plasticity and help for directing cell-level evolution and engineering biological circuits. We introduce distributed optimal control (DOC) as a mathematical framework for dynamical control of large scale metabolic models. This approach tackles the network components as separate dynamic obj...

Molecular methods have revolutionised virtually every area of biology, and metazoan phylogenetics is no exception: molecular phylogenies, molecular clocks, comparative phylogenomics, and developmental genetics have collectively transformed our understanding of the evolutionary history of animals. Moreover, the diversity of methods and models within molecular phylogenetics has resulted in significant disagreement among molecular phylogenies as well as between these and traditional phylogenies. Here, I argue that tackling this multifaceted problem lies in integrating evidence to infer the best evolutionary scenario. I begin with an overview of recent developments in early metazoan phylogenetics, followed by a discussion of key conceptual issues in phylogenetics revolving around phylogenetic evidence and theory. I then argue that integration of different kinds of evidence is necessary for arriving at the best evolutionary scenario rather than the best-fitting cladogram. Finally, I discuss the prospects of this view in stimulating interdisciplinary cross-talk in early metazoan research and beyond.

This thesis is about the complicated and multifaceted problem of the evolution of the eumetazoan body plan and its key role in the emergence of organismal complexity in the animal kingdom. As such, it draws on a very broad range of topics and discussions including empirical research programmes in palaeontology, comparative morphology, classical and genetic developmental biology, and morphological and molecular phylogenetics; as well as theoretical/philosophical research around the conceptual bases of phylogenetics, homology, scientific integration, and biological complexity and individuality. In the following chapters, I first provide background on and an outline of the thesis (chapter 1); I then propose an overarching conceptual framework for the integration of different kinds of evidence in macroevolutionary biology (chapter 2), with a special emphasis on the integration of morphological and developmental genetic evidence in inferring morphological homology (chapter 3); followed by providing a phylogeny of the major animal groups incorporating the two Ediacaran fossils Dickinsonia and Yorgia (chapter 4) and building on this phylogenetic placement to propose a novel evolutionary scenario for the evolution of key features of the eumetazoan body plan—namely the gastric cavity and bilateral symmetry—in light of Dickinsonia and other Ediacaran fossils (chapter 5). I finish with a discussion on the evolution of complexity in the animal kingdom in light of preceding chapters and the multilevel selection literature (chapter 6), and a brief final conclusion.

A number of recent biologists have used multilevel selection theory to help explain the major transitions in evolution. I argue that in doing so, they have shifted from a ‘synchronic’ to a ‘diachronic’ formulation of the levels of selection question. The implications of this shift in perspective are explored, in relation to an ambiguity in the meaning of multilevel selection. Though the ambiguity is well-known, it has never before been discussed in the context of the major transitions.

Molecular methods have revolutionised virtually every area of biology, and metazoan phylogenetics is no exception: molecular phylogenies, molecular clocks, comparative phylogenomics, and developmental genetics have collectively transformed our understanding of the evolutionary history of animals. Moreover, the diversity of methods and models within molecular phylogenetics has resulted in significant disagreement among molecular phylogenies as well as between these and traditional phylogenies. Here, I argue that tackling this multifaceted problem lies in integrating evidence to infer the best evolutionary scenario. I begin with an overview of recent developments in early metazoan phylogenetics, followed by a discussion of key conceptual issues in phylogenetics revolving around phylogenetic evidence and theory. I then argue that integration of different kinds of evidence is necessary for arriving at the best evolutionary scenario rather than the best-fitting cladogram. Finally, I disc...

Reconstructing ancestral species is a challenging endeavour: fossils are often scarce or enigmatic, and inferring ancestral characters based on novel molecular approaches (e.g. comparative genomics or developmental genetics) has long been controversial. A key philosophical challenge pertinent at present is the lack of a theoretical framework capable of evaluating inferences of homology made through integration of multiple kinds of evidence (e.g. molecular, developmental, or morphological). Here, I present just such a framework. I start with a brief history and critical assessment of attempts at inferring morphological homology through developmental genetics. I then bring attention to a recent model of homology, namely Character Identity Mechanisms (DiFrisco, Love, & Wagner, 2020), intended partly to elucidate the relationships between morphological characters, developmental genetics, and homology. I utilise and build on this model to construct the evaluative framework mentioned abov...

The transition to multicellularity is perhaps the best-studied of the “major evolutionary transitions”. It has occurred independently multiple times within the eukaryotes alone, and multicellular organisms comprise virtually the entirety of Earth’s macrobiota. However, the theoretical framework used to study the major evolutionary transitions does not neatly accommodate the evolution of complex multicellularity as a process distinct from the evolution of multicellularity more generally. Here, I attempt to fill this explanatory gap. I will first give an overview of research on the major evolutionary transitions, focusing on multicellularity, and demonstrate that the theoretical framework so far utilised does not provide us with sufficient conceptual tools to explain crucial phenomena that call for explanation, such as the evolution of organs and organ systems. I will then discuss our current understanding of early metazoan evolution as paradigmatically exemplifying the evolution of c...