Arsham Nejad Kourki

This paper examines the early evolution of cognition in animals through the lens of the Transitions in Structural Complexity approach. By focusing on the emergence and transformation of coordination systems, the study identifies three progressive stages: collective, specialised, and integrated coordination. Each stage is characterised by distinct structural innovations—ranging from contractile epithelia and cytoskeletal coupling to the development of neurons, neurosecretory cells, and integrated nervous tissues—and is shaped by the processes of modularisation, subfunctionalisation, and integration. By conceptualising coordination as a transferable biological function, this approach offers an analysis of the evolution of this capacity without presupposing specific mechanisms or structures. Rather than defining cognition in advance, this approach tracks how functions associated with cognition become structurally embodied in multicellular systems through the progressive reorganisation of coordination across levels of biological organisation. Besides offering a general schema for analysing the early stages of cognitive evolution in metazoans, this approach has broader implications for the comparative study of cognition and the structural focus within the major evolutionary transitions framework.

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 complex organisation in a multicellular system, specifically regarding three core processes enabling it, namely modularisation, subfunctionalisation, and integration, allowing the provision of a general account of the evolution of complex from simple multicellularity that is potentially applicable to other such cases such as the evolution of land plants. This paves the way for a revised account of major evolutionary transitions which incorporates the evolution of complex organismal traits following the evolution of minimal autonomous reproducers while marking a shift of emphasis from reproducers to organisms.

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 generated a plethora of molecular data spanning numerous taxa and collectively transformed our understanding of the evolutionary history of animals, often corroborating but at times opposing results of more traditional approaches. Moreover, the diversity of methods and models within molecular phylogenetics has resulted in significant disagreement among molecular phylogenies as well as between these and earlier phylogenies. How should this broad and multifaceted problem be tackled? I argue that the answer lies in integrating evidence to infer the best evolutionary scenario. I begin with an overview of recent development in early metazoan phylogenetics, followed by a discussion of key conceptual issues in phylogenetics revolving around phylogenetic evidence, theory, methodology, and interrelations thereof. I then argue that the integration of different kinds of evidence (e.g. molecular, morphological, ecological) is necessary for arriving at the best evolutionary scenario (causal explanation) rather than merely the best-fitting cladogram (statistical explanation). Finally, I discuss the prospects of this view in stimulating interdisciplinary cross-talk in early metazoan research and beyond, and challenges that need to be overcome.

Reconstructing ancestral species is a challenging endeavour: fossils are often scarce or enigmatic, and inferring ancestral characters based on novel molecular approaches 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. 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, 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 above, which judges the epistemic value of evidence of each kind in each particular case based on three proposed criteria: effectiveness, admissibility, and informativity, as well as providing a generalised guideline on how it can be scientifically operationalised. I then point out the evolution of the eumetazoan body plan as a case in point where the application of this framework can yield satisfactory results, both empirically and conceptually. I will conclude with a discussion on some potential implications for more general philosophy of biology and philosophy of science, especially surrounding evidential integration, models and explanation, and reductionism.