Biology Reference
In-Depth Information
where X is the name of S such as “ORF (open reading frame)” or “ATPase,” etc.,
and the symbol “A ~ B” reads “A is associated with B” or more specifically “A is
the necessary condition for B.” To emphasize the latter sense which is “hierarchi-
cal” or “ordinal” (i.e., without Gene X, no mRNA X; without mRNA X, no Cell
Function X), Eq.
11.12c
can be rewritten as:
<
<
Gene X
mRNAX
CellFunctionX
(11.12d)
where the symbol “
<
” indicates the hierarchical or ordinal relation. Because of the
importance of Inequality (
11.12d
) in interpreting microarray data, it may be
justified to refer to Inequality (
11.12d
) as the
Principle of the Ordinal Relation
among Genes, RNAs, and Cell Functions
or
PORAGRF
. One practical consequence
of PORAGRF is this: Although genes, RNAs, and cell functions are often given the
same name (e.g., “glycolysis gene,” “glycolysis mRNA,” “glyclysis proteins”),
they cannot be
equated
or
interchanged
, ultimately because a gene and its products
are not one dimensional entities but two-dimensional so that, although they have the
same S, they can have different CNs (see Eqs.
11.12
,
11.12a
,
11.12b
).
Most of the papers on microarray data experiments that have been published
since the beginning of the microarray era in the mid-1990s have made false positive
and false negative conclusions (Ji et al. 2009a). The reason for such errors may be
traced ultimately to the following two erroneous assumptions which are
interconnected:
1. “Gene X” can be replaced by “mRNA X” (violating PORAGRF, Inequality
(11.12d)).
2. Microarrays measure the expression of “gene X” because “gene X” is synony-
mous with “mRNA X.”
11.2.6 DNA and RNA as Secondary and Primary
Memories of the Cell
To understand the role of RNAs in cell functions, it may be instructive to use the
digital computer as a model, in agreement with the so-called Simpson thesis
discussed in the Preface that biology is the study of phenomena to which all
principles apply, including most likely the architectural principles of modern-day
digital computers. It is interesting in this connection to point out that Wang and
Gribskov's (2005) made a theoretical comparison between the digital computer and
the living cell in a complementary way to the comparison made in Ji (1999a).
According to Wang and Gribskov, DNA is analogous to the
secondary
memory and
RNA to the
primary
memory of computers (Fig.
11.11
).
One of the crucial differences between the primary and secondary memories
of the computer is that the former is dynamic and disappears when the computer is
turned off, whereas the secondary memory (e.g., stored in hard drives, CDs, etc.)
