Current Research and Interest -1: Biology-related problems
- Origin of Heredity (Information):
Among many chemicals in a cell, only some specific chemicals (e.g., DNA) are
regarded to carry genetic information. Why do only some specific
molecules play the role of genetic information carrier? How were the
roles of molecules separated into information carrier and metabolism?
Is the separation a necessary consequence for a system to make recursive
production of a cell with internal biochemical reaction dynamics?
As a first step in investigating the origin of genetic information, we
study how some species of molecules are preserved over cell generations
and play an important role in controlling the growth of a cell. We
have proposed a minority control theory for the origin of heredity.
K. Kaneko and T. Yomo"
On a kinetic origin of heredity :minority control in
" J. Theor. Biol. 214 (2002) 563-576 (nlin.AO/0105031)
K. Kaneko "
Kinetic Origin of Heredity in a
Replicating System with a Catalytic Network
" J Biol. Phys., in press
- Universal Feature of a Cell with Recursive Growth
Questions: A cell consists of several replicating molecule species that,
through mutual interaction, help the synthesis of new molecules and
maintain some synchronization for replication. The very least, a
membrane that partly separates a cell from the outside has to be
synthesized, and this process must keep some degree of synchronization
with the replication of other internal chemicals. How can such
recursive production and chemical diversity be maintained at the same
time? Is there some universal feature in these reaction dynamics?
Furthermore, this recursive production is not exact and slow
`mutational' changes appear over the generations in an evolutionary
process. How is this evolvability possible in the presence of recursive
We found Zipf's law in the abundance of chemicals for a reproducing
cell, which is also confirmed in real data in a cell, as Zipf's law
in gene expressions. Next, we have studied fluctuations of abudnances of each chemical,
to show ubiquity of the log-nromal distribution. This is also confirmed
C. Furusawa and K. Kaneko "
Zipf's law in Gene Expression
" Phys. Rev. Lett., 90 (2003) 088102
(pdf file )
C. Furusawa, T. Suzuki, A. Kashiwagi, T. Yomo and K. Kaneko;
- General Theory for Fluctuations and Stability of a Cell
Relationship between fluctuation and response in a biological system
is proposed by extending the fluctuation-disspiation theorem in physics.
This proposition is applied to evolution experiments. We are also discussing
relatoinship between genotypic and phenotypic fluctuations.
K. Sato et al., PNAS 2003
- Theory for Cell differentiation
Questions: How do identical cells diversify into discrete types through
development and how can these distinct cell types be maintained by
recursive production? How are the characteristics of each cell type
stabilized in the presence of molecular fluctuations, and how can the
number distribution of cell types stably be maintained?
We proposed isologous diversifictaion theory, based on the study of
coupled dynamical systems.
K. Kaneko and T. Yomo,
``Isologous Diversification: A Theory of Cell Differentiation ",
Bull.Math.Biol. 59 (1997) 139-196;
K. Kaneko and T. Yomo,
``Isologous Diversification for Robust Development of Cell Society",
J. Theor. Biol.,
- Context-dependent rule for cell differntiation from a stem cell
Questions: In the development of multi cellular organisms, so-called
stem cells that either proliferate or differentiate into other cell
types play an essential role. What are the rules for differentiation
from multipotent stem cells and how are these differentiation rules
generated? How can such rules and several cell types coexist stably
Using chaotic intracellular dynamics, we showed that a rule for
hierarachical differentiations gnerally emerges, and proposed `chaotic
stem cell hypothesis'. We have made several predictions on the
characteristics for differentiations from stem cells, some of which are
C. Furusawa and K. Kaneko"Theory of Robustness of Irreversible Differentiation in a Stem Cell
System: Chaos Hypothesis"
J. Theor. Biol. (2001) 209 (2001) 395-416
C. Furusawa and K. Kaneko
``Emergence of Rules in Cell Society: Differentiation, Hierarchy, and Stability",
Bull.Math.Biol. 60 (1998) 659-687
- Stability and Irreversibility in the Development of Cell Societies
Questions: In the development of multi-cellular organisms, there is a
successive determination from totipotent ES cell, to multipotent stem
cells, and finally to several determined cell types. A clear temporal
direction in the loss of potency for forming a variety of cell types
exists in the normal course of development. How is such irreversibility
generated and how is it characterized quantitatively? Is such
irreversibility related to developmental stability?
Kunihiko Kaneko and Chikara Furusawa ``Robust and Irreversible
Development in Cell Society as a General Consequence of Intra-Inter
Dynamics", Physica A 280 (2000) 23-33 (also available at http://arXiv.org/abs/chao-dyn/9912005)
- Pattern Formation and the Origin of Positional Information
Question: Biological pattern formation (morphogenesis) is understood as
a change of genetic expression that depends on the spatial gradient of
chemicals. This gradient supposedly provides information on the
position of each cell. The positional information then leads to a change
in the concentration of the signal molecules, and thus finally to a
change of the genetic expressions. Still the question remains: How is
such positional information generated? In order to form gradients,
spatial differentiation of cells is necessary.
Extending the theory for cell differentiation, generation of positional
information is demonstrated, which turns out to be robust against
C. Furusawa and K. Kaneko ``Generation of Positional Information
..", to be submitted to J Tneo. Biol.
C. Furusawa and K. Kaneko ``Origin of complexity in multicellular organisms",
Phys. Rev. Lett. i84 (2000) 6130-6133
C. Furusawa and K. Kaneko"
Complex Orgnization in multicullarity as a necessity in evolution"
Artificial Life, 6(2000) 265-281
- Origin of Multicellular Organisms
Questions: In order for a multicellular organism to exist over
successive generations, the cell aggregates themselves have to be
replicated recursively (i.e., recursiveness at the cell ensemble level
is a necessity). How is this recursive replication at the ensemble
level achieved? Furthermore, the offspring of a multicellular organism
usually does not begin its life by inheriting all the cell types of the
mother (parents) but by the fertilization of a single specific cell
type, called germ cell. Why does the development of multicellular
organisms have to pass through such narrow bottleneck? Is this related
to the mechanism of recursive generation?
C. Furusawa and K. Kaneko " Origin of Multicellular Organisms
as an Inevitable Consequence of Dynamical Systems " Anatomical
Record, in press
- Evolution; in particular in relatiohship with development and phenotypic plasticity
Questions: Darwin asked why organisms are separated into distinct
groups, rather than their character being continuously distributed. If
two organisms, due to minor genetic changes, differ only slightly in
phenotype, then they share a common niche and compete for survival.
Consequently, it is difficult for two groups with only slight genetic
differences to coexist. Then how is sympatric speciation possible when
organisms live in the same space interacting each other?
We showed that ionteraction-induced phenotype plasticty leads to genetic
diversification. In particular, when phenotype separate into two groups,
genetic separation into the two groups follows, leading to sympatric speciation.
Hybrud sterility is resulted, and the premating isolation also follows
as a result of postmating isoloation.
K. Kaneko and T. Yomo "Genetic Diversification through Interaction-driven Phenotype
Evol Eco. Res., 4 (2002) 317-350
K. Kaneko "
Symbiotic Sympatric Speciation:
Compliance with Interaction-driven Phenotype
Differentiation from a Single Genotype
" Population Ecology, 44 (2002) 71-85
K. Kaneko and T. Yomo
``Sympatric Speciation: compliance with
phenotype diversification from a single genotype"
Proc. Roy. Soc. B, 267 (2000) 2367-2373
- Evolution of Genetic System:
How has genetic system evolved to make correspondence with genotype and phenotype?
In relationship, we are interested in the evolution of genetic code.
H. Takagi, K. Kaneko, and T. Yomo
``Evolution of genetic code through isologous diversification of cellular states",
Artificial Life, 6(2000) 283-305
Questions: Individual biological units sometimes join to form a new
unit. For example, endosymbiosis is believed to have played an
essential role in the origin of the eucaryotic cell. Such joining of
systems must generally be difficult. For example, consider two
independent logical systems, say two separately written, independent
computer programs. Then it would be almost impossible for a mere
composite system of the two to work without error. On the other hand,
in biological systems such joining seems to have occurred sometimes
during the course of evolution, as, for example, is discussed in the
endosymbiosis theory. Then, how can two independent biological systems
(with independent biochemical networks) join to form a new composite
system without damaging (killing) each system?
- Dynamic Memory and Learning
The emergence of memory is ubiquitous in biological systems and not
limited to neural networks. Cells generally are able to store the
history of the external influences that they have experienced in their
internal state up to some extent. In order to form a memory, external
changes that occur at relatively fast time scales have to be transformed
into internal changes that have much longer time scales. Changes of the
internal state at such longer time scales may alter later responses of
the internal state against further external stimuli. This alteration
can be regarded as learning. Hence the question is: under what
conditions can external stimuli at faster time scales be transformed
into long-term changes of the internal state? In other words, under
what conditions can a system have memory and learn?
- Energy Transduction in Interacting Molecules, in partial relationship with Molecular Motor
N. Nakagawa and K. Kaneko " A dynamic mechanism of energy
conversion to a mechanical work " Phys. Rev. E; also in Phyisca A
- Consturction of `Complex Systems Theory' for Biological System in general
( so far mostly in relationship with development and cell differentiation)
``Organization through Intra-Inter Dynamics",
to appear in ``Organizations" (MIT press) eds. G. Mueller and S. Newmann
K Kaneko ``From Coupled Dynamical Systems to Biological Irreversibility",
Adv in Chem Phys. (2002)
Reserch interests 2
Documents about Kaneko Lab