17.0: Introduction

In which we consider the basic molecular & cellular processes involved in the behavior of groups of cells, including those involved in the transformation of a single cell, the fertilized egg, into a complex multicellular organism composed of multiple and integrated cell types.

By this point, you have been introduced to many and perhaps most of the core molecular and cellular ideas needed to understand the facts and mechanisms involved in the behavior of biological systems.^[566] We will call upon these to build models of specific processes. With modification, these ideas serve as the basic toolkit that working biologists and biology students call upon to design models of a process, and design experiments to test the model's assumptions and either refine or abandon the model and development new ones. The ability to generate plausible (rather than correct) models, and understand the model's predictions is a high level skill that involves recognizing and applying relevant facts and concepts and ignoring irrelevant and distracting ideas.^[567] It allows us to simplify and focus our thinking on what is important. Given the complexities of biological systems, which may be beyond what a human brain can readily comprehend, simplification can be necessary.^[568] It starts by reflecting on what ideas apply to specific situations; a skill that takes practice and informed feedback - one reason that manuscripts written by the most experienced scientists often benefit from peer review leading to thoughtful response and revision, and sometimes new experiments. Here we consider how fundamental ideas are applied to understanding the behaviors of developing (animal) systems.

By developing systems we mean a cell or group of cells and how they change over time in response to various signals and perturbations, including their interactions with one another. Cells monitor their external and internal environments; their regulatory networks are critical to maintaining the living state (a process known as homeostasis), adapting to changing conditions, as well as decisions on whether to grow and divide, or to "differentiate". These decisions involve interconnected molecular and cellular networks that control all aspects of cellular behavior, including coordination with surrounding cells - together they produce the emergent behaviors we referred to as the living state. Emergent behaviors are those that "cannot be predicted through analysis at any level simpler than that of the system as a whole".^[569]

When we think about emergent behaviors, an obvious example is the development of multicellular organisms. In these systems a fertilized egg, formed by the fusion of haploid gametes, goes on to form a multicellular embryo composed of multiple cell types in specific juxtapositions, and controlled by a combination of intracellular and extracellular asymmetries and cellular responses to those asymmetries. Similar processes are found among unicellular organisms. Microbes of various types sense their neighborhood, including the numbers (concentration) of related and unrelated organisms. They can alter their cooperative, competitive, and adaptive behaviors in various ways through quorum sensing, positive and negative feedback interactions, and molecular cascades that produce changes in gene expression, morphology, and behaviors (phenotypes).

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