6
1 Introduction
values are chosen. There may be some truth to this statement if the model is
purely mathematical in the sense that the equations are not based on the laws of
nature. However, when a model is constrained by physical law, and if all parameters
are physically meaningful and have realistic values, comparing computational and
experimental results provides a rigorous test of the underlying proposed mechanism.
Therefore, it may be more appropriate to call such a model theoretical rather than
mathematical.
1.4 Developmental Biology Background
This section provides a brief introduction to some of the biology considered in this
book, with an emphasis on embryonic development, the focus of Chap. 8. Further
details will be provided as needed, and more information can be found in the
references included below. 5
1.4.1 Cells, Tissues, and Organs
The cell is the fundamental building block of biological structures. The book by
Alberts et al. (2014) is an exquisitely detailed reference for all aspects of cell
biology.
Eukaryotic cells consist of a nucleus and cytoplasm, enclosed by a cell (plasma)
membrane that allows the transport of nutrients and waste products (Fig. 1.1a).
(Prokaryotic cells have no nucleus.) The nucleus, also surrounded by a porous
membrane, contains DNA, a nucleolus, and other proteins. The genetic material in
the DNA carries instructions to regulate growth, development, and protein synthesis.
The cytoplasm comprises gel-like cytosol, organelles, and the cytoskeleton.
Major organelles include the mitochondria for energy production, the endoplasmic
reticulum for protein synthesis, and the Golgi apparatus for packing proteins into
vesicles to be transported elsewhere (Fig. 1.1a).
The cytoskeleton is an interconnected network of structural proteins that control
cell shape. Structural proteins in cells comprise three main types (Fig. 1.1b): actin
filaments, microtubules, and intermediate filaments. Actin is involved in numerous
cell activities, including cell crawling, intracellular transport, and cell division.
Interactions between actin and myosin, a motor protein, 6 drive contraction of muscle
and other contractile constituents, e.g., stress fibers. Microtubules are hollow tubes
that bind to the motor proteins kinesin and dynein to transport cargo-containing
5 Additional biology specific to growth and remodeling will be included in chapters that focus on
these subjects.
6 Motor proteins move along filaments using energy provided by ATP hydrolysis.
1 Introduction
values are chosen. There may be some truth to this statement if the model is
purely mathematical in the sense that the equations are not based on the laws of
nature. However, when a model is constrained by physical law, and if all parameters
are physically meaningful and have realistic values, comparing computational and
experimental results provides a rigorous test of the underlying proposed mechanism.
Therefore, it may be more appropriate to call such a model theoretical rather than
mathematical.
1.4 Developmental Biology Background
This section provides a brief introduction to some of the biology considered in this
book, with an emphasis on embryonic development, the focus of Chap. 8. Further
details will be provided as needed, and more information can be found in the
references included below. 5
1.4.1 Cells, Tissues, and Organs
The cell is the fundamental building block of biological structures. The book by
Alberts et al. (2014) is an exquisitely detailed reference for all aspects of cell
biology.
Eukaryotic cells consist of a nucleus and cytoplasm, enclosed by a cell (plasma)
membrane that allows the transport of nutrients and waste products (Fig. 1.1a).
(Prokaryotic cells have no nucleus.) The nucleus, also surrounded by a porous
membrane, contains DNA, a nucleolus, and other proteins. The genetic material in
the DNA carries instructions to regulate growth, development, and protein synthesis.
The cytoplasm comprises gel-like cytosol, organelles, and the cytoskeleton.
Major organelles include the mitochondria for energy production, the endoplasmic
reticulum for protein synthesis, and the Golgi apparatus for packing proteins into
vesicles to be transported elsewhere (Fig. 1.1a).
The cytoskeleton is an interconnected network of structural proteins that control
cell shape. Structural proteins in cells comprise three main types (Fig. 1.1b): actin
filaments, microtubules, and intermediate filaments. Actin is involved in numerous
cell activities, including cell crawling, intracellular transport, and cell division.
Interactions between actin and myosin, a motor protein, 6 drive contraction of muscle
and other contractile constituents, e.g., stress fibers. Microtubules are hollow tubes
that bind to the motor proteins kinesin and dynein to transport cargo-containing
5 Additional biology specific to growth and remodeling will be included in chapters that focus on
these subjects.
6 Motor proteins move along filaments using energy provided by ATP hydrolysis.