Cell Language Theory, The: Connecting Mind And Matter

Applications of the Cell Language Theory to Biomedical Sciences 309

“6x9” b2861 The Cell Language Theory: Connecting Mind and Matter

imTI = (4 + 8)/(2 + 6), (7.15)

where the Arabic numeral x represents the number of the open read-

ing frames (ORFs) whose transcripts exhibit mechanism x in a given

patient, i.e., the number of times x appears in the M column in a given

patient in Table 7.2.

(4) Plot the imTI values against the SM (survival month) values from

Table 7.2 to obtain the “survival month vs. imTI” plot and the associ-

ated repression line (Figure 7.13, upper panel).

(5) Find an objective method (e.g., the PDE-based method shown in

Figure 7.17) to remove those ORFs whose transcripts exhibit mecha-

nisms 2, 6, 4, or 8 in a given patient so that the unfiltered imTI vs.

SM plot in Figure 7.13 (upper panel) can be transformed into the

fimTI vs. SM plot shown in the lower panel of Figure 7.13, where

fimTI indicates “filtered micro-therapeutic index”. Discovering what

is here referred to as “filtering” would constitute one of the major

objectives of ribonomics (i.e., the study of genome-wide RNA levels)

as applied to cancer research. One such method, which is based on

utilizing PDE, is described in Sections 7.3.2 and 7.3.3 (see especially

Figures 7.18, 7.20, and 7.22).

Figure 7.13 lists the results of analyzing 30 genes randomly selected

out of 4,740 genes from each of the 20 patients. Mechanisms 2 and 6

indicate that both the breast tumor and doxorubicin induce the RNA level

changes that are in the same direction in the mechanisms circle (Figure 7.11)

and hence are likely to be harmful (but not proven) thus being colored red

(symbolizing a potential danger), while Mechanisms 4 and 8 indicate that

both breast tumor and the drug induce the RNA level changes that are in

the opposite directions in the mechanisms circle and hence are likely to be

beneficial (although not proven) thus being colored green (symbolizing a

potential benefit). In the absence of independent evidence, the words

“harmful” and “beneficial” may be better replaced with the terms such as

“parallel” and “anti-parallel” or with “red” and “green” that are non-

committal as to the clinical (in contrast to molecular-theoretical) signifi-

cance of these mechanisms.

The mechanisms defined in Table 7.2 represent the phenotypes on

whole cell levels, since the effects of tumor and drug treatment on the

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