- author = "Nadav Kashtan",
- title = "Evolution in varying environments : rapid emergence of modular systems",
- school = "Weizmann Institute of Science",
- year = "2008",
- address = "Israel",
- month = mar,
- keywords = "genetic algorithms, genetic programming",
-
URL = "
http://lib-phds1.weizmann.ac.il/Dissertations/Kashtan_Nadav.pdf",
- size = "107 pages",
-
abstract = "The design of biological systems is shaped by
evolution. There are several general features of
biological design that seem to occur again and again
across levels of biological organisation. One such
central feature is modularity, biological systems can
often be decomposed into nearly independent subsystems.
Modularity can be seen on several levels, from the
design of organisms (tissues, limbs, sensory organs),
through the design of regulatory networks in the cell
(signalling pathways, transcription modules) and down
to the design of many bio-molecules (protein domains).
Despite its presence on all of these levels, the
evolutionary origin of modularity is currently
considered as an open question.
The first part of my Ph.D. research aimed at understanding the evolutionary origin of modularity. We used computer simulations that mimic natural evolution to study the evolution of simple model systems such as Logic circuits, neural networks and RNA secondary structure. We find that evolution under constant goals (i.e. that do no change over time) typically lead to highly optimal systems with non-modular structure. In contrast, we find that evolution under environments that change over time in a modular fashion, such that each new goal is a different combination of the same set of subgoals, lead to the spontaneous emergence of modularity and network motifs. The evolved systems developed a specific module for each of the sub goals. Although sub-optimal the modular systems were able to adapt rapidly when the environment changed. We suggest that such switching between related goals may represent biological evolution in a changing environment that requires, at different times or conditions, different combinations of the same set of basic biological functions (such as eating, moving, and mating). This study therefore may help to explain some of the evolutionary forces that promote structural simplicity in biological systems.
A second well-known puzzle which is known in evolution studies is whether the theory can explain the speed at which the present complexity of life evolved. My second research objective was to try to find mechanisms, compatible with natural evolution, which can speed up evolution. We studied the effect of varying environments on the speed of evolution, defined as the number of generations needed for an initially random population to achieve a given goal. We find that varying environments can dramatically speed up evolution compared to evolution in constant environment. A consistent speedup was found under modularly varying goals. Importantly, we find that the speedup scales with the complexity of the goal: the harder the goals the larger the speedup. This study suggests that varying environments might significantly contribute to the speed of natural evolution. In addition, it suggests a way to accelerate optimisation algorithms and improve evolutionary approaches in engineering.
We then tried to understand the underlying reasons for the observed speedup. We suggested a simple mathematical model that can be solved analytically. This model seems to explain the reasons for a rapid evolution of modular structures under modularly varying goals. It helps us understand the effects found in simulations of more complex systems described above.",
-
abstract = "In the last part of my research we studied the effects
of extinctions in a spatially distributed environment.
We demonstrate that extinctions can impact the design
of evolved organisms. Specifically, extinctions in
heterogeneous environment lead to the emergence of
modular species. This is because modular species can
better adapt when they encounter niches freed by
extinction events. We further show how lack of
extinctions tends to result in distinct specialist
species in each niche, whereas extinctions lead to
formation of multi-niche species with modular and
evolvable design.
In summary, this thesis has extended our understanding of the role of varying environments in generating biological structure and in speeding up evolution. It used detailed simulations and analytical models to test hypothesis, rather than the more commonly used method of well-argued prose. The main idea is that over time, organisms learn, in their genome, the shared subgoals common to different environments, and evolve modules to solve these different subgoals. This modular design makes it much easier to rewire and adapt when environments change. The present results also suggest new ways to accelerate optimization algorithms, and open the way to studying additional relationships between environmental variation and biological structure.",
-
notes = "MOLECULAR CELL BIOLOGY Supervisor: Uri Alon
chapter 1 \cite{Kashtan:2005:PNAS} chapter 2 \cite{Kashtan:2007:PNAS}
In english.",
