Whole Cells - Molecular Theory of the Living Cell - page 409

Table 12.5 A comparison between molecular spectra and ribonic spectra
Molecular spectra Ribonic spectra

1. Objects under
study

Subatomic structural transitions
of a group of identical
molecules

Kinetic trajectories (or ribons) of a
group of heterogeneous RNA
molecules catalyzing a
common metabolic function

2. Stability
of the object

Equilibrium structures
( equilibrons )

Dissipative structures ( dissipatons )

3. Internal

organization

Electronic energy levels Pathway-forming RNA molecules

Distances between RNA pairs a Vibrational energy levels

Rotational energy levels Individual RNAs

4. X -axis Wavelengths of light absorbed

( energy )

Node numbers encoding the shapes
of RNA trajectories
( Information )

5. Y -axis Absorbance (or amount of light

absorbed by a given number
of molecules)

Number of RNA molecules
possessing a given shape of
their trajectories or waves

DNA microarrays + PCA b 6. Experimental

method

Spectrophotometers

7. Measured Molecular spectra RNA spectra, or “ribonic spectra”

8. Mechanics Dynamics Kinematics

9. Field of study
( Alternative
names )

Molecular spectroscopy “Ribonoscopy” (or “RNA

spectroscopy”, “ribonics”,
transcriptomics, “RNA
interactomics”)

10. Theory Quantum mechanics (1900-1925) Molecular theory of the living cell

(1985-2010)

a The dissimilarity between two RNA trajectories or wave forms
b Principal component analysis, a mathematical procedure by which high-dimensional data can be
projected onto a lower-dimensional space with a minimal loss of information. For example,
this can be accomplished by using the ViDaExpert program developed by Zinovyev (2001)
(see Sect. 12.8.1 )

subfields of mechanics that are complementary to each other (Sect. 2.3.5 ) (Murdoch
1987; Plotnitsky 2006).
The methodology of molecular spectroscopy is based on spectrophotometers
that can produce molecular spectra in most cases without having to rely on
computers or mathematical analysis (Row 6, Table 12.5 ). The methodology of
ribonoscopy , however, depends not only on DNA microarrays invented in the mid-
1990s (Sect. 12.1 ) but also on computer-based visualization techniques that reduce
high-dimensional microarray data (e.g., six in the case of the data displayed in
Figs. 12.1 , 12.11 ) to low dimensions (e.g., to three in Fig. 12.11 and two in
Fig. 12.12 ) utilizing the mathematical procedure of principal component analysis
(Gorban and Zinovyev 2004). Therefore, just as the invention of spectrophotomers
(i.e., the device measuring the absorption or emission of photons by molecules as
functions of wavenumbers or wavelengths) in the nineteenth century led to the
emergence of a vast field of “molecular spectroscopy,” so I am here predicting that
the combination of DNA microarrays and computer software implementing the