Biology Reference
In-Depth Information
Self-Replicator Space
(or
EvoDevo Space
)
Development
in
Synchronic
Time
Evolution
in Diachronic Time
Fig. 14.3 A diagrammatic representation of the orthogonalities 1) between
development
and
evolution
on the one hand and (2) between
synchronic
and
diachronic
times on the other. The
series of the
gray
disks symbolizes a spiral motion (see the
curved red arrow
) advancing from
left
to
right
consisting of (1) the
cyclical motions
in the plane of each disk which is orthogonal to the
x
-axis and parallel to the
y
-axis, and (2) the
translational motion
of the disk along the
x
-axis. When
viewed at low resolution, the spiral appears as the arrow of time (see the
straight red arrow
). Each
circular disk, therefore, may be thought of as the “atom of evolutionary time (AET).” See text
4. The
EvoDevo space
may be analogous to the
phase space
in physics (consisting
of the position axis and the momentum axis that are orthogonal). Just as each
point in the phase space represents the state of a system of many particles and the
evolution of such a system is depicted as a bundle of line trajectories, each point
in the EvoDevo space represents an organism, clusters of points represent groups
of organisms, bundles of line trajectories represent the development of
organisms (groups, taxons, clades), and bifurcating bundles of line trajectories
represent the tree of life.
5. Just as the phase space is essential for
statistical mechanics
in physics, so
the EvoDevo space may be essential for
infostatistical mechanics
(defined in
Sect.
4.9
) that accounts for living structures and processes, that is, life.
An interesting analogy may be drawn between the
evolutionary debate
between
anti-Darwinians (favoring the
variation generation
as the cause of evolution) and
neo-Darwinians
(claiming the
natural selection
as the evolutionary cause) on the
one hand and the controversy, on the other hand, about interpreting DNA
microarray data based on the
transcriptional control
or on both the
transcrip-
tional/transcript-degradation controls
Ji et al. 2009a). It is well established that
RNA levels measured with DNA microarrays are determined by two opposing
processes - “transcription” and “transcript degradation” (Figs. 12.5 and 12.27)
(Sect.
12.8
), which can be schematically depicted as in Fig.
14.4
.
Before Perez-Ortin and his group in Valencia (Garcia-Martinez et al. 2004) and
others measured both
RNA levels
(or
transcript levels
, TL) and
transcription rates
(TR) simultaneously in budding yeast (see Fig.
12.6
), most experimenters utilizing
microarrays assumed that RNA levels were determined by transcription rates alone
