review;articles
Doi: 10.1145/2001269.2001289
Exploring the connection of biology with
reactive systems to better understand
living systems.
BY Jasmin fisheR, DaViD haReL, anD thomas a. henzinGeR
Biology as
Reactivity
BIoLoGY IS No T an exact science. Biological systems are
messy and noisy, and our understanding of many
biological scenarios remains extremely vague and
incomplete. We cannot assign precise rules to the way
cells behave and interact with one another, and we often
cannot quantify the exact amounts of molecules, such
as genes and proteins, in the resolution of a single cell.
To make matters worse (so to speak), the combinatorial
complexity observed in biological networks (for
example, metabolic and signaling pathways) is
staggering, which renders the comprehension and
analysis of such systems a major challenge.
One way to explain a certain class of complex
dynamical systems is to view them as highly
concurrent reactive systems.
42 We argue that this
perspective is a natural fit for many biological
systems.
40 A reactive system is characterized by the
way it responds to its inputs, as they arrive over time,
sequentially, or concurrently. The system’s behavior
and outputs are not just a function of the input values
but also of the order in which the inputs arrive, their
arrival times, speeds, and locations, and so forth.
A living cell, we claim, is not only reactive in nature, but is the ultimate example of a reactive system, and so are collections thereof. As explained in Cohen
and Harel 2007,
16 a cell succeeds by being robust and resilient. It reacts to inputs and perturbations and continues
to survive thanks to its reactive dynamics. The cell is a reactive system that expresses a dynamic narrative, in which
the DNA code is one of many formative
inputs. Structural proteins, enzymes,
carbohydrates, lipids, hormones, and
other molecules also play key roles in
forming and informing the system.
Biological systems are also highly
adaptive, to both internal and external
changes; they use signals coming in
from receptors and sensors, as well as
emergent properties to fine-tune their
functioning. This adaptivity is another
facet of the reactivity of such systems.
We are well aware of the fact that
there are many aspects of biology that
are not reactive, or that reactivity is not
the best way to view them. These include, for example, structural aspects
of chemicals. While we point to the importance of combining other modeling methods with reactive models, the
main thrust of this article is to explain
the connection of biology with reactive
systems, and the benefits that can be
gained from adopting such a view.
Viewing biology as reactivity is not
just an illustrative analogy, but has
key insights
;;; Living cells, and collections thereof, can
be viewed as reactive systems.
;;; Reactive models emphasize important
aspects of biological systems, such
as executability, concurrency and
interaction, multiple scales, and
combinatorial complexity.
;;; concepts, languages, and tools for the
description and analysis of reactive
systems can help in the process
of biological discovery, ultimately
by providing biologists with virtual
experimentation environments.
;;; Biological experimentation needs to
obtain quantitative data across different
levels, and reactive modeling needs
to focus on incorporating and linking
such data.
