Biology Reference
In-Depth Information
ribons.
Thus, Statement 12.18 can be interpreted as the prediction of the existence
of
ribons
as both the RNA trajectories in the living cell and as the cooperative or
coordinated system of
transcriptosome and degradosome underlying such
trajectories:
¼
þ
Ribons
Transcriptosome
Degradosome
(12.19)
Defined in this manner,
ribons
are examples of dissipative structures or
dissipatons
, since ribons cannot exist without yeast cells dissipating free energy.
Ribons are also examples of SOWAWN machines (Sect.
2.4.4
) composed of
transcriptosome
and
degradosome
. Unlike transcriptosome and degradosome
which can be isolated and purified, ribons cannot be isolated just as the flame of a
candle cannot be isolated and studied. Interestingly, the term
ribons
tend to
emphasize the shapes of RNA trajectories (i.e., kinematics) and
dissipatons
highlights the free energy cost of maintaining such trajectories (i.e., dynamics).
Thus, ribons embodies two complementary aspects - kinematics and dynamics (see
Sect.
2.3.5
).
Since there are obviously many different
dissipatons
(RNA trajectories, protein
trajectories, metabolite trajectories, ion gradients, cytoskeletal stress gradients, cell
migratory path, etc.) (i.e., dynamics) (see Sect.
2.3.5
), it would be necessary to have
a means to differentially represent them as different species of
dissipatons
. One
such method would be to attach a prefix to different kinds of dissipatons. For
example, ribons may be referred to as “RNA-dissipatons” and the ion gradients
across the cell membrane as “ionic dissipatons,” etc.
12.8 Visualizing and Analyzing
RNA-Dissipatons
12.8.1 ViDaExpert
The concept of dissipative structures (or
dissipatons
) has been around in the
scientific literature for more than three decades (Prigogine 1977, 1980); Kondepudi
and Prigogine 1998; Kondepudi 2008), but the experimental methods for studying
them in the context of cell biology had been limited until the ViDaExpert became
available about a decade ago (Zinovyev 2001; Gorban and Zinovyev 2004, 2005).
My experience in analyzing budding yeast transcriptome (i.e., the genome-wide
RNA metabolism) with this method (see below) induces me to speculate that
ViDaExpert
(and
equivalent computer programs
) may well turn out to be for
the
cell biology
in the twenty-first century what the
X-ray crystallography
was to
the
molecular biology
in the twentieth century. This speculation is based on one
assumption - Cell biology is (and should be) mainly concerned with the study of
dissipative structures
(
dissipatons
) in contrast to molecular biology which has
mainly been the study of
equilibrium structures
(
equilibrons
)
.
