Mathematical and theoretical biology

Mathematical and theoretical biology, or biomathematics,

is a branch of biology which employs theoretical analysis,
mathematical models and abstractions of the living organisms
to investigate the principles that govern the structure,
development and behavior of the systems, as opposed to
experimental biology which deals with the conduction of
experiments to prove and validate the scientific theories.[1] The
field is sometimes called mathematical biology or
biomathematics to stress the mathematical side, or theoretical
biology to stress the biological side.[2] Theoretical biology
focuses more on the development of theoretical principles for
biology while mathematical biology focuses on the use of
mathematical tools to study biological systems, even though
the two terms are sometimes interchanged.[3][4]
Yellow chamomile head showing the
Fibonacci numbers in spirals consisting of
Mathematical biology aims at the mathematical representation
21 (blue) and 13 (aqua). Such
and modeling of biological processes, using techniques and
arrangements have been noticed since
tools of applied mathematics. It can be useful in both
the Middle Ages and can be used to make
theoretical and practical research. Describing systems in a
mathematical models of a wide variety of
quantitative manner means their behavior can be better
plants.
simulated, and hence properties can be predicted that might not
be evident to the experimenter. This requires precise
mathematical models.

Because of the complexity of the living systems, theoretical biology employs several fields of
mathematics,[5] and has contributed to the development of new techniques.

History

Early history

Mathematics has been used in biology as early as the 13th century, when Fibonacci used the famous
Fibonacci series to describe a growing population of rabbits. In the 18th century, Daniel Bernoulli applied
mathematics to describe the effect of smallpox on the human population. Thomas Malthus' 1789 essay on
the growth of the human population was based on the concept of exponential growth. Pierre François
Verhulst formulated the logistic growth model in 1836.

Fritz Müller described the evolutionary benefits of what is now called Müllerian mimicry in 1879, in an
account notable for being the first use of a mathematical argument in evolutionary ecology to show how
powerful the effect of natural selection would be, unless one includes Malthus's discussion of the effects of
population growth that influenced Charles Darwin: Malthus argued that growth would be exponential (he
uses the word "geometric") while resources (the environment's carrying capacity) could only grow
arithmetically.[6]
The term "theoretical biology" was first used as a monograph title by Johannes Reinke in 1901, and soon
after by Jakob von Uexküll in 1920. One founding text is considered to be On Growth and Form (1917) by
D'Arcy Thompson,[7] and other early pioneers include Ronald Fisher, Hans Leo Przibram, Vito Volterra,
Nicolas Rashevsky and Conrad Hal Waddington.[8]

Recent growth

Interest in the field has grown rapidly from the 1960s onwards. Some reasons for this include:

The rapid growth of data-rich information sets, due to the genomics revolution, which are
difficult to understand without the use of analytical tools[9]
Recent development of mathematical tools such as chaos theory to help understand
complex, non-linear mechanisms in biology
An increase in computing power, which facilitates calculations and simulations not
previously possible
An increasing interest in in silico experimentation due to ethical considerations, risk,
unreliability and other complications involved in human and animal research

Areas of research
Several areas of specialized research in mathematical and theoretical biology[10][11][12][13][14] as well as
external links to related projects in various universities are concisely presented in the following subsections,
including also a large number of appropriate validating references from a list of several thousands of
published authors contributing to this field. Many of the included examples are characterised by highly
complex, nonlinear, and supercomplex mechanisms, as it is being increasingly recognised that the result of
such interactions may only be understood through a combination of mathematical, logical,
physical/chemical, molecular and computational models.

Abstract relational biology

Abstract relational biology (ARB) is concerned with the study of general, relational models of complex
biological systems, usually abstracting out specific morphological, or anatomical, structures. Some of the
simplest models in ARB are the Metabolic-Replication, or (M,R)--systems introduced by Robert Rosen in
1957–1958 as abstract, relational models of cellular and organismal organization.

Other approaches include the notion of autopoiesis developed by Maturana and Varela, Kauffman's Work-
Constraints cycles, and more recently the notion of closure of constraints.[15]

Algebraic biology

Algebraic biology (also known as symbolic systems biology) applies the algebraic methods of symbolic
computation to the study of biological problems, especially in genomics, proteomics, analysis of molecular
structures and study of genes.[16][17][18]

Complex systems biology

An elaboration of systems biology to understand the more complex life processes was developed since
1970 in connection with molecular set theory, relational biology and algebraic biology.

Computer models and automata theory

A monograph on this topic summarizes an extensive amount of published research in this area up to
1986,[19][20][21] including subsections in the following areas: computer modeling in biology and medicine,
arterial system models, neuron models, biochemical and oscillation networks, quantum automata, quantum
computers in molecular biology and genetics,[22] cancer modelling,[23] neural nets, genetic networks,
abstract categories in relational biology,[24] metabolic-replication systems, category theory[25] applications
in biology and medicine,[26] automata theory, cellular automata,[27] tessellation models[28][29] and complete
self-reproduction, chaotic systems in organisms, relational biology and organismic theories.[16][30]

Modeling cell and molecular biology

This area has received a boost due to the growing importance of molecular biology.[13]

Mechanics of biological tissues[31][32]

Theoretical enzymology and enzyme kinetics
Cancer modelling and simulation[33][34]
Modelling the movement of interacting cell populations[35]
Mathematical modelling of scar tissue formation[36]
Mathematical modelling of intracellular dynamics[37][38]
Mathematical modelling of the cell cycle[39]
Mathematical modelling of apoptosis[40]

Modelling physiological systems

Modelling of arterial disease[41]

Multi-scale modelling of the heart[42]
Modelling electrical properties of muscle interactions, as in bidomain and monodomain
models

Computational neuroscience

Computational neuroscience (also known as theoretical neuroscience or mathematical neuroscience) is the

theoretical study of the nervous system.[43][44]

Evolutionary biology

Ecology and evolutionary biology have traditionally been the dominant fields of mathematical biology.

Evolutionary biology has been the subject of extensive mathematical theorizing. The traditional approach in
this area, which includes complications from genetics, is population genetics. Most population geneticists
consider the appearance of new alleles by mutation, the appearance of new genotypes by recombination,
and changes in the frequencies of existing alleles and genotypes at a small number of gene loci. When
infinitesimal effects at a large number of gene loci are considered, together with the assumption of linkage
equilibrium or quasi-linkage equilibrium, one derives quantitative genetics. Ronald Fisher made
fundamental advances in statistics, such as analysis of variance, via his work on quantitative genetics.
Another important branch of population genetics that led to the extensive development of coalescent theory
is phylogenetics. Phylogenetics is an area that deals with the reconstruction and analysis of phylogenetic
(evolutionary) trees and networks based on inherited characteristics[45] Traditional population genetic
models deal with alleles and genotypes, and are frequently stochastic.

Many population genetics models assume that population sizes are constant. Variable population sizes,
often in the absence of genetic variation, are treated by the field of population dynamics. Work in this area
dates back to the 19th century, and even as far as 1798 when Thomas Malthus formulated the first principle
of population dynamics, which later became known as the Malthusian growth model. The Lotka–Volterra
predator-prey equations are another famous example. Population dynamics overlap with another active area
of research in mathematical biology: mathematical epidemiology, the study of infectious disease affecting
populations. Various models of the spread of infections have been proposed and analyzed, and provide
important results that may be applied to health policy decisions.

In evolutionary game theory, developed first by John Maynard Smith and George R. Price, selection acts
directly on inherited phenotypes, without genetic complications. This approach has been mathematically
refined to produce the field of adaptive dynamics.

Mathematical biophysics

The earlier stages of mathematical biology were dominated by mathematical biophysics, described as the
application of mathematics in biophysics, often involving specific physical/mathematical models of
biosystems and their components or compartments.

The following is a list of mathematical descriptions and their assumptions.

Deterministic processes (dynamical systems)

A fixed mapping between an initial state and a final state. Starting from an initial condition and moving
forward in time, a deterministic process always generates the same trajectory, and no two trajectories cross
in state space.

Difference equations/Maps – discrete time, continuous state space.

Ordinary differential equations – continuous time, continuous state space, no spatial
derivatives. See also: Numerical ordinary differential equations.
Partial differential equations – continuous time, continuous state space, spatial derivatives.
See also: Numerical partial differential equations.
Logical deterministic cellular automata – discrete time, discrete state space. See also:
Cellular automaton.

Stochastic processes (random dynamical systems)

A random mapping between an initial state and a final state, making the state of the system a random
variable with a corresponding probability distribution.

Non-Markovian processes – generalized master equation – continuous time with memory of

past events, discrete state space, waiting times of events (or transitions between states)
discretely occur.
 Jump Markov process – master equation – continuous time with no memory of past events,
discrete state space, waiting times between events discretely occur and are exponentially
distributed. See also: Monte Carlo method for numerical simulation methods, specifically
dynamic Monte Carlo method and Gillespie algorithm.
Continuous Markov process – stochastic differential equations or a Fokker–Planck
equation – continuous time, continuous state space, events occur continuously according to
a random Wiener process.

Spatial modelling

One classic work in this area is Alan Turing's paper on morphogenesis entitled The Chemical Basis of
Morphogenesis, published in 1952 in the Philosophical Transactions of the Royal Society.

Travelling waves in a wound-healing assay[46]

Swarming behaviour[47]
A mechanochemical theory of morphogenesis[48]
Biological pattern formation[49]
Spatial distribution modeling using plot samples[50]
Turing patterns[51]

Mathematical methods

A model of a biological system is converted into a system of equations, although the word 'model' is often
used synonymously with the system of corresponding equations. The solution of the equations, by either
analytical or numerical means, describes how the biological system behaves either over time or at
equilibrium. There are many different types of equations and the type of behavior that can occur is
dependent on both the model and the equations used. The model often makes assumptions about the
system. The equations may also make assumptions about the nature of what may occur.

Molecular set theory

Molecular set theory (MST) is a mathematical formulation of the wide-sense chemical kinetics of
biomolecular reactions in terms of sets of molecules and their chemical transformations represented by set-
theoretical mappings between molecular sets. It was introduced by Anthony Bartholomay, and its
applications were developed in mathematical biology and especially in mathematical medicine.[52] In a
more general sense, MST is the theory of molecular categories defined as categories of molecular sets and
their chemical transformations represented as set-theoretical mappings of molecular sets. The theory has
also contributed to biostatistics and the formulation of clinical biochemistry problems in mathematical
formulations of pathological, biochemical changes of interest to Physiology, Clinical Biochemistry and
Medicine.[52]

Organizational biology

Theoretical approaches to biological organization aim to understand the interdependence between the parts
of organisms. They emphasize the circularities that these interdependences lead to. Theoretical biologists
developed several concepts to formalize this idea.
For example, abstract relational biology (ARB)[53] is concerned with the study of general, relational models
of complex biological systems, usually abstracting out specific morphological, or anatomical, structures.
Some of the simplest models in ARB are the Metabolic-Replication, or (M,R)--systems introduced by
Robert Rosen in 1957–1958 as abstract, relational models of cellular and organismal organization.[54]

Model example: the cell cycle

The eukaryotic cell cycle is very complex and is one of the most studied topics, since its misregulation leads
to cancers. It is possibly a good example of a mathematical model as it deals with simple calculus but gives
valid results. Two research groups [55][56] have produced several models of the cell cycle simulating several
organisms. They have recently produced a generic eukaryotic cell cycle model that can represent a
particular eukaryote depending on the values of the parameters, demonstrating that the idiosyncrasies of the
individual cell cycles are due to different protein concentrations and affinities, while the underlying
mechanisms are conserved (Csikasz-Nagy et al., 2006).

By means of a system of ordinary differential equations these models show the change in time (dynamical
system) of the protein inside a single typical cell; this type of model is called a deterministic process
(whereas a model describing a statistical distribution of protein concentrations in a population of cells is
called a stochastic process).

To obtain these equations an iterative series of steps must be done: first the several models and observations
are combined to form a consensus diagram and the appropriate kinetic laws are chosen to write the
differential equations, such as rate kinetics for stoichiometric reactions, Michaelis-Menten kinetics for
enzyme substrate reactions and Goldbeter–Koshland kinetics for ultrasensitive transcription factors,
afterwards the parameters of the equations (rate constants, enzyme efficiency coefficients and Michaelis
constants) must be fitted to match observations; when they cannot be fitted the kinetic equation is revised
and when that is not possible the wiring diagram is modified. The parameters are fitted and validated using
observations of both wild type and mutants, such as protein half-life and cell size.

To fit the parameters, the differential equations must be studied. This can be done either by simulation or by
analysis. In a simulation, given a starting vector (list of the values of the variables), the progression of the
system is calculated by solving the equations at each time-frame in small increments.

In analysis, the properties of the equations are used to investigate the behavior of the system depending on
the values of the parameters and variables. A system of differential equations can be represented as a vector
field, where each vector described the change (in concentration of two or more protein) determining where
and how fast the trajectory (simulation) is heading. Vector fields can have several special points: a stable
point, called a sink, that attracts in all directions (forcing the concentrations to be at a certain value), an
unstable point, either a source or a saddle point, which repels (forcing the concentrations to change away
from a certain value), and a limit cycle, a closed trajectory towards which several trajectories spiral towards
(making the concentrations oscillate).

A better representation, which handles the large number of variables and parameters, is a bifurcation
diagram using bifurcation theory. The presence of these special steady-state points at certain values of a
parameter (e.g. mass) is represented by a point and once the parameter passes a certain value, a qualitative
change occurs, called a bifurcation, in which the nature of the space changes, with profound consequences
for the protein concentrations: the cell cycle has phases (partially corresponding to G1 and G2) in which
mass, via a stable point, controls cyclin levels, and phases (S and M phases) in which the concentrations
change independently, but once the phase has changed at a bifurcation event (Cell cycle checkpoint), the
system cannot go back to the previous levels since at the current mass the vector field is profoundly
different and the mass cannot be reversed back through the bifurcation event, making a checkpoint
irreversible. In particular the S and M checkpoints are regulated by means of special bifurcations called a
Hopf bifurcation and an infinite period bifurcation.

Societies
Jan van der Hoeven Society for Theoretical Biology
Dutch Society for Theoretical Biology (http://www.theoreticalbiology.nl/)
Society for Mathematical Biology
European Society for Mathematical and Theoretical Biology (ESMTB) (http://www.esmtb.or
g/)
The Israeli Society for Theoretical and Mathematical Biology (https://web.archive.org/web/20
040109164805/http://bioinformatics.weizmann.ac.il/istmb/)
Société Francophone de Biologie Théorique (https://web.archive.org/web/20080911022733/
http://www.necker.fr/sfbt/)
International Society for Biosemiotic Studies (https://web.archive.org/web/20160118072627/
http://www.biosemiotics.org/)

Institutes
National Institute for Mathematical and Biological Synthesis (NIMBioS), University of
Tennessee Knoxville
Mathematical Biosciences Institute (MBI), Ohio State University
School of Computational and Integrative Sciences (https://jnu.ac.in/scis), Jawaharlal Nehru
University
Santa Fe Institute
NSF-Simons National Institute for Theory and Mathematics in Biology (NITMB) (https://beta.
nsf.gov/funding/opportunities/nsf-simons-collaboration-national-institute-theory)

Journals [year established]

Acta Biotheoretica [1935]
Bulletin of Mathematical Biology [1939]
Journal of Theoretical Biology [1961]
BioSystems [1967]
Mathematical Biosciences [1967]
 Theoretical Population Biology [1970]
Journal of Mathematical Biology [1974]
Artificial Life [1993]
Theory in Biosciences (https://www.springer.com/journal/12064#:~:text=Theory%20in%20Bi
osciences%20focuses%20on%20new%20concepts%20in,%3B%20Bioinspired%20Modeli
ng%3B%20Complexity%3B%20Embodied%20Cognition%3B%20Evolutionary%20Biology)
[2000]
Biological Theory [2005]
Theoretical Ecology (https://www.springer.com/journal/12080) [2008]
Philosophy, Theory, and Practice in Biology (https://journals.publishing.umich.edu/ptpbio/)
[2009]

See also
Biological applications of bifurcation theory Metabolic network modelling
Biophysics Molecular modelling
Biostatistics Morphometrics
Entropy and life Population genetics
Ewens's sampling formula Spring school on theoretical biology
Journal of Theoretical Biology Statistical genetics
Logistic function Theoretical ecology
Mathematical modelling of infectious Turing pattern
disease

Notes
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Further reading
Hoppensteadt F (September 1995). "Getting Started in Mathematical Biology" (https://www.a
ms.org/notices/199509/hoppensteadt.pdf) (PDF). Notices of the American Mathematical
Society.
May RM (February 2004). "Uses and abuses of mathematics in biology". Science. 303
(5659): 790–3. Bibcode:2004Sci...303..790M (https://ui.adsabs.harvard.edu/abs/2004Sci...3
03..790M). doi:10.1126/science.1094442 (https://doi.org/10.1126%2Fscience.1094442).
PMID 14764866 (https://pubmed.ncbi.nlm.nih.gov/14764866). S2CID 24844494 (https://api.s
emanticscholar.org/CorpusID:24844494).
Murray JD (1988). "How the leopard gets its spots?" (http://www.resnet.wm.edu/~jxshix/math
490/murray.doc). Scientific American. 258 (3): 80–87. Bibcode:1988SciAm.258c..80M (http
s://ui.adsabs.harvard.edu/abs/1988SciAm.258c..80M). doi:10.1038/scientificamerican0388-
80 (https://doi.org/10.1038%2Fscientificamerican0388-80).
Reed MC (March 2004). "Why Is Mathematical Biology So Hard?" (http://www.resnet.wm.ed
u/~jxshix/math490/reed.pdf) (PDF). Notices of the American Mathematical Society.
Kroc J, Balihar K, Matejovic M (2019). "Complex Systems and Their Use in Medicine:
Concepts, Methods and Bio-Medical Applications" (https://www.researchgate.net/publicatio
n/330546521). doi:10.13140/RG.2.2.29919.30887 (https://doi.org/10.13140%2FRG.2.2.2991
9.30887).

External links
The Society for Mathematical Biology (http://www.smb.org/)
The Collection of Biostatistics Research Archive (https://web.archive.org/web/20080827161
431/http://www.biostatsresearch.com/repository/)
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