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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Asunto:
</th>
<td>Re: [Fis] Informatics of DNA</td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Fecha: </th>
<td>Thu, 30 Nov 2017 23:33:09 +0000</td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">De: </th>
<td>Sungchul Ji <a class="moz-txt-link-rfc2396E" href="mailto:sji@pharmacy.rutgers.edu"><sji@pharmacy.rutgers.edu></a></td>
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<th align="RIGHT" nowrap="nowrap" valign="BASELINE">Para: </th>
<td>FIS Group <a class="moz-txt-link-rfc2396E" href="mailto:fis@listas.unizar.es"><fis@listas.unizar.es></a>, <a class="moz-txt-link-abbreviated" href="mailto:yxs@pku.edu.cn">yxs@pku.edu.cn</a>
<a class="moz-txt-link-rfc2396E" href="mailto:yxs@pku.edu.cn"><yxs@pku.edu.cn></a></td>
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<p style="margin-top:0;margin-bottom:0">Hi Xueshan,</p>
<p style="margin-top:0;margin-bottom:0"><br>
</p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
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<span style="font-family: "Times New Roman", serif;
color: rgb(255, 0, 0);" lang="EN-US">1. I highly appreciate
your informational parsing on cell language and the
comparative study of cell language and human language. By
the end of last century, the main topics of (Human)
Linguistics have been basically completed. It is not known
whether human language study can get any inspiration from
cell language study.</span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
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EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="font-family: "Times New Roman", serif;
color: rgb(255, 0, 0);" lang="EN-US"><span style="color:
rgb(0, 0, 0);">The concept of the third articulation that
emerged in cell biology around 2012 (the reference to be
provided upon request) is useful in understanding cell
metabolism and hence perhaps in linguistics too: </span></span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
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<span style="font-family: "Times New Roman", serif;
color: rgb(255, 0, 0);" lang="EN-US"><span style="color:
rgb(0, 0, 0);"><br>
</span></span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
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<span style="font-family: "Times New Roman", serif;
color: rgb(255, 0, 0);" lang="EN-US"><span style="color:
rgb(0, 0, 0);">1st articulation = words ---->
sentences; </span></span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
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EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="font-family: "Times New Roman", serif;
color: rgb(255, 0, 0);" lang="EN-US"><span style="color:
rgb(0, 0, 0);">2nd articulation = letters ----> words; </span></span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
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EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="font-family: "Times New Roman", serif;
color: rgb(255, 0, 0);" lang="EN-US"><span style="color:
rgb(0, 0, 0);">3rd articulation = sentences ---->
texts (e.g., the syllogism) <br>
</span><br>
</span></p>
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<br>
</p>
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<span style="font-family: "Times New Roman", serif;
color: rgb(255, 0, 0);" lang="EN-US"><span style="color:
rgb(0, 0, 0);">
<table class="MsoTableGrid"
style="background:#EEECE1;mso-background-themecolor:background2;border-collapse:
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4.3pt 5.75pt" border="1" cellpadding="0" cellspacing="0">
<tbody>
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.5pt;padding:4.3pt 5.75pt 4.3pt 5.75pt"
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<span style="font-size: 12pt; font-family:
"Times New Roman", serif;"> <b>Table
1.</b> The isomorphism between the human
and cell languages<o:p></o:p></span></p>
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<td style="width:118.25pt;border:solid windowtext
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<b><span style="font-size: 12pt; font-family:
"Times New Roman", serif;">Human
Language </span></b><span
style="font-size: 12pt; font-family:
"Times New Roman", serif;"><o:p></o:p></span></p>
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<td style="width:3.25in;border-top:none;border-left:
none;border-bottom:solid windowtext
1.0pt;border-right:solid windowtext 1.0pt;
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<p class="MsoNormal"
style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal">
<b><span style="font-size: 12pt; font-family:
"Times New Roman", serif;">Cell
Language </span></b><span
style="font-size: 12pt; font-family:
"Times New Roman", serif;"><o:p></o:p></span></p>
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<td
style="width:127.25pt;border-top:none;border-left:
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<p class="MsoNormal"
style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal">
<b><span style="font-size: 12pt; font-family:
"Times New Roman", serif;">Function<o:p></o:p></span></b></p>
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<p class="MsoNormal"
style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal">
<span style="font-size: 12pt; font-family:
"Times New Roman", serif;"><br>
Letters<o:p></o:p></span></p>
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<td style="width:3.25in;border-top:none;border-left:
none;border-bottom:solid windowtext
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width="312">
<p class="MsoNormal"
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<span style="font-size: 12pt; font-family:
"Times New Roman", serif;"><br>
A. C, G, T or U<br>
<!--[if !supportLineBreakNewLine]--><br>
<!--[endif]--><o:p></o:p></span></p>
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<td
style="width:127.25pt;border-top:none;border-left:
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width="170">
<p class="MsoNormal"
style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal">
<span style="font-size: 12pt; font-family:
"Times New Roman", serif;"><br>
to build <o:p></o:p></span></p>
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<p class="MsoNormal"
style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal">
<span style="font-size: 12pt; font-family:
"Times New Roman", serif;"><br>
Words<br>
<!--[if !supportLineBreakNewLine]--><br>
<!--[endif]--><o:p></o:p></span></p>
</td>
<td style="width:3.25in;border-top:none;border-left:
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<br>
</p>
<p class="MsoNormal"
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normal">
genes/mRNA/proteins</p>
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<p class="MsoNormal"
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<span style="font-size: 12pt; font-family:
"Times New Roman", serif;"><br>
to denote<o:p></o:p></span></p>
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<td style="width:118.25pt;border:solid windowtext
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valign="top" width="158">
<p class="MsoNormal"
style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal">
<span style="font-size: 12pt; font-family:
"Times New Roman", serif;"><br>
Sentences<br>
<!--[if !supportLineBreakNewLine]--><br>
<!--[endif]--><o:p></o:p></span></p>
</td>
<td style="width:3.25in;border-top:none;border-left:
none;border-bottom:solid windowtext
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<p class="MsoNormal"
style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
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<span style="font-size: 12pt; font-family:
"Times New Roman", serif;"><br>
metabolic pathways<o:p></o:p></span></p>
</td>
<td
style="width:127.25pt;border-top:none;border-left:
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<p class="MsoNormal"
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normal">
<span style="font-size: 12pt; font-family:
"Times New Roman", serif;"><br>
to decide and judge<o:p></o:p></span></p>
</td>
</tr>
<tr>
<td style="width:118.25pt;border:solid windowtext
1.0pt; border-top:none;mso-border-top-alt:solid
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.5pt; padding:4.3pt 5.75pt 4.3pt 5.75pt"
valign="top" width="158">
<p class="MsoNormal"
style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal">
<span style="font-size: 12pt; font-family:
"Times New Roman", serif;"><br>
Texts<br>
<!--[if !supportLineBreakNewLine]--><br>
<!--[endif]--><o:p></o:p></span></p>
</td>
<td style="width:3.25in;border-top:none;border-left:
none;border-bottom:solid windowtext
1.0pt;border-right:solid windowtext 1.0pt;
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<p class="MsoNormal"
style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal">
<span style="font-size: 12pt; font-family:
"Times New Roman", serif;"><br>
functional networks of metabolic pathways<o:p></o:p></span></p>
</td>
<td
style="width:127.25pt;border-top:none;border-left:
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<p class="MsoNormal"
style="margin-bottom:0in;margin-bottom:.0001pt;line-height:
normal">
<span style="font-size: 12pt; font-family:
"Times New Roman", serif;"><br>
to reason and compute<o:p></o:p></span></p>
</td>
</tr>
</tbody>
</table>
<br>
</span></span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="font-family: "Times New Roman", serif;
text-indent: 21pt;">We recently discovered that what we came
to refer to as the "</span><b style="font-family:
"Times New Roman", serif; text-indent: 21pt;">Planck-Shannon
plot</b><span style="font-family: "Times New
Roman", serif; text-indent: 21pt;">" can be used to
identify the cell-linguistic counter-parts of </span><b
style="font-family: "Times New Roman", serif;
text-indent: 21pt;">sentences</b><span style="font-family:
"Times New Roman", serif; text-indent: 21pt;"> and
</span><b style="font-family: "Times New Roman",
serif; text-indent: 21pt;">texts</b><span
style="font-family: "Times New Roman", serif;
text-indent: 21pt;"> based on mRNA data measured from,
e.g., human breast tissues. I will be detailing this
finding shortly in a later post.</span><br>
</p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="font-family: "Times New Roman", serif;
color: rgb(255, 0, 0);" lang="EN-US"><br>
</span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="font-family: "Times New Roman", serif;
color: rgb(255, 0, 0);" lang="EN-US">2. What kind of
information definition and principle(s) have you got from
the cell language study? To what extent are they applicable
to other information fields? Exactly, your conclusions are
mainly from the analysis of genetic cell. Among the
biological information, the second major field of
information application is neural cell. Are they effective
in Neuroscience?</span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="font-family: "Times New Roman", serif;
color: rgb(255, 0, 0);" lang="EN-US"><span style="color:
rgb(0, 0, 0);">A good question. We have not yet extended
our cell-linguistic approach to neural network. When we
do, we may find evidence for higher-order articulations
such as the fourth, fifth, sixth articulations, etc. </span><br>
</span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="font-family: "Times New Roman", serif;
color: rgb(255, 0, 0);" lang="EN-US"><span style="color:
rgb(0, 0, 0);"></span><span style="color: rgb(0, 0, 0);"></span><br>
</span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="font-family: "Times New Roman", serif;
color: rgb(255, 0, 0);" lang="EN-US">3. At the macro level,
in your seven (six) steps of information flow scheme, we can
consider all the content as "cell information / genetic
information". But on the step 6, what you call it: Cell
Functions→Human Behaviors, they transform cell information /
genetic information into human information. If some
information can be understood by a cell, it must not be
understood by a (human) brain, and vice versa. How do you
think of it?</span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="font-family: "Times New Roman", serif;
color: rgb(255, 0, 0);" lang="EN-US"><span style="color:
rgb(0, 0, 0);">An excellent point.</span><br>
</span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="font-family: "Times New Roman", serif;
color: rgb(255, 0, 0);" lang="EN-US"><span style="color:
rgb(0, 0, 0);">I often wonder if I do understand cell
information biologically but not linguistically, i.e., I
feel and communicate with every cell in my body but cannot
articulate that experience due to the limited expressive
power of human language. The study of the phenomenon of
such communication that can occur without linguistic signs
has recently been referred to as "neo-semiotics" that was
formulated by extending Peirce's semiotics by including a
new category called "Zeroness" (see the attached).</span></span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="font-family: "Times New Roman", serif;
color: rgb(255, 0, 0);" lang="EN-US"><span style="color:
rgb(0, 0, 0);"></span></span><span style="color: rgb(255,
0, 0); font-family: "Times New Roman", serif;
text-indent: 21pt;">4. In your information flow scheme of
DNA→pre-mRNA→mRNA→proteins→IDS→Cell Functions→Human
Behaviors, should the leftmost DNA be molecule? So far, we
have seen that many researches thought that there are
communication between molecules. From your research
experience, are there any real examples of information
communication took place between molecules?</span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="color: rgb(255, 0, 0); font-family: "Times
New Roman", serif; text-indent: 21pt;"><span
style="color: rgb(0, 0, 0);">According to Peirce
(1839-1914), communication is irreducibly triadic. I have
found ti useful to use this definition of communication in
my research in biology. So I am currently of the opinion
that whenever there is an irreducible triadic relation,
there is communication: i.e.,</span><br>
</span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="color: rgb(255, 0, 0); font-family: "Times
New Roman", serif; text-indent: 21pt;"><span
style="color: rgb(0, 0, 0);"><br>
f g</span></span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="color: rgb(255, 0, 0); font-family: "Times
New Roman", serif; text-indent: 21pt;"><span
style="color: rgb(0, 0, 0);">A ------> B ------>
C<br>
| ^<br>
| |<br>
|_________________|</span></span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="color: rgb(255, 0, 0); font-family: "Times
New Roman", serif; text-indent: 21pt;"><span
style="color: rgb(0, 0, 0);"> h</span></span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="font-family: "Times New Roman", serif;
text-indent: 21pt;"><b>Figure 1</b>. A diagrammatic
representation of the
</span><b style="font-family: "Times New Roman",
serif; text-indent: 21pt;">irreducible triadic relation</b><span
style="font-family: "Times New Roman", serif;
text-indent: 21pt;"> (ITR) or
</span><b style="font-family: "Times New Roman",
serif; text-indent: 21pt;">communication.</b><span
style="font-family: "Times New Roman", serif;
text-indent: 21pt;"> A = source; B = message; C =
receiver; f = encoding; g = decoding; h = grouding or
information flow. </span><br>
</p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
There is no reason why A, B and C cannot be all molecules,
e.g., A = DNA/RNA, B = proteins, and C = chemical reactions,
but this does not mean that molecules A is communicating with
molecule C, because without the third and the rest of the
communication system, no communication would be possible.</p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="color: rgb(255, 0, 0); font-family: "Times
New Roman", serif; text-indent: 21pt;">5. Before 1952,
the concept of "information" was rarely used in the works of
Genetics. After Molecular Genetics, or after Crick's
"central dogma", in Genetics research, many places used to
use "gene" were replaced by "information". Do you think is
it feasible to replace all "gene" with "information"
completely at last?</span><br>
</p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="color: rgb(255, 0, 0); font-family: "Times
New Roman", serif; text-indent: 21pt;"><span
style="color: rgb(0, 0, 0);">I don't think so, because all
genes carry information but not all information carriers
are genes.</span><br>
</span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="color: rgb(255, 0, 0); font-family: "Times
New Roman", serif; text-indent: 21pt;"><span
style="color: rgb(0, 0, 0);"><br>
</span></span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="color: rgb(255, 0, 0); font-family: "Times
New Roman", serif; text-indent: 21pt;"><span
style="color: rgb(0, 0, 0);">All the best.</span></span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="color: rgb(255, 0, 0); font-family: "Times
New Roman", serif; text-indent: 21pt;"><span
style="color: rgb(0, 0, 0);"><br>
</span></span></p>
<p class="x_MsoNormal" style="margin-top: 4.65pt; font-family:
Calibri, Helvetica, sans-serif, EmojiFont, "Apple Color
Emoji", "Segoe UI Emoji", NotoColorEmoji,
"Segoe UI Symbol", "Android Emoji",
EmojiSymbols; font-size: 16px; text-indent: 21pt;">
<span style="color: rgb(255, 0, 0); font-family: "Times
New Roman", serif; text-indent: 21pt;"><span
style="color: rgb(0, 0, 0);">Sung</span></span></p>
<br>
<br>
<br>
<div style="color: rgb(0, 0, 0);">
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>From:</b>
Fis <a class="moz-txt-link-rfc2396E" href="mailto:fis-bounces@listas.unizar.es"><fis-bounces@listas.unizar.es></a> on behalf of
Xueshan Yan <a class="moz-txt-link-rfc2396E" href="mailto:yxs@pku.edu.cn"><yxs@pku.edu.cn></a><br>
<b>Sent:</b> Thursday, November 30, 2017 8:35 AM<br>
<b>To:</b> FIS Group<br>
<b>Subject:</b> Re: [Fis] Informatics of DNA</font>
<div> </div>
</div>
<div link="blue" vlink="purple" style="background-color:white"
lang="ZH-CN">
<div class="x_WordSection1">
<p class="x_MsoNormal" style="margin-top:3.6pt"><span
style="font-family:"Times New Roman",serif"
lang="EN-US">Dear Sungchul,</span><span
style="font-size:10.5pt; font-family:"Times New
Roman",serif; color:windowtext" lang="EN-US"></span></p>
<p class="x_MsoNormal" style="margin-top:4.65pt;
text-indent:21.0pt"><span style="font-family:"Times
New Roman",serif" lang="EN-US">1. I highly
appreciate your informational parsing on cell language
and the comparative study of cell language and human
language. By the end of last century, the main topics
of (Human) Linguistics have been basically completed.
It is not known whether human language study can get
any inspiration from cell language study.</span></p>
<p class="x_MsoNormal" style="margin-top:4.65pt;
text-indent:21.0pt"><span style="font-family:"Times
New Roman",serif" lang="EN-US">2. What kind of
information definition and principle(s) have you got
from the cell language study? To what extent are they
applicable to other information fields? Exactly, your
conclusions are mainly from the analysis of genetic
cell. Among the biological information, the second
major field of information application is neural cell.
Are they effective in Neuroscience?</span></p>
<p class="x_MsoNormal" style="margin-top:4.65pt;
text-indent:21.0pt"><span style="font-family:"Times
New Roman",serif" lang="EN-US">3. At the macro
level, in your seven (six) steps of information flow
scheme, we can consider all the content as "cell
information / genetic information". But on the step 6,
what you call it: Cell Functions→Human Behaviors, they
transform cell information / genetic information into
human information. If some information can be
understood by a cell, it must not be understood by a
(human) brain, and vice versa. How do you think of it?</span></p>
<p class="x_MsoNormal" style="margin-top:4.65pt;
text-indent:21.0pt"><span style="font-family:"Times
New Roman",serif" lang="EN-US">4. In your
information flow scheme of
DNA→pre-mRNA→mRNA→proteins→IDS→Cell Functions→Human
Behaviors, should the leftmost DNA be molecule? So
far, we have seen that many researches thought that
there are communication between molecules. From your
research experience, are there any real examples of
information communication took place between
molecules?</span></p>
<p class="x_MsoNormal" style="margin-top:4.65pt;
text-indent:21.0pt"><span style="font-family:"Times
New Roman",serif" lang="EN-US">5. Before 1952,
the concept of "information" was rarely used in the
works of Genetics. After Molecular Genetics, or after
Crick's "central dogma", in Genetics research, many
places used to use "gene" were replaced by
"information". Do you think is it feasible to replace
all "gene" with "information" completely at last?</span></p>
<p class="x_MsoNormal" style="margin-top:4.65pt"><span
style="font-family:"Times New Roman",serif"
lang="EN-US"> </span></p>
<p class="x_MsoNormal" style="margin-top:4.65pt"><span
style="font-family:"Times New Roman",serif"
lang="EN-US">Best wishes,</span></p>
<p class="x_MsoNormal" style="margin-top:4.65pt"><span
style="font-family:"Times New Roman",serif"
lang="EN-US">Xueshan</span></p>
<p class="x_MsoNormal"><span style="font-family:等线;
color:black" lang="EN-US"> </span></p>
<div>
<div style="border:none; border-top:solid #E1E1E1 1.0pt;
padding:3.0pt 0cm 0cm 0cm">
<p class="x_MsoNormal"><b><span
style="font-size:11.0pt;
font-family:"Calibri",sans-serif;
color:windowtext" lang="EN-US">From:</span></b><span
style="font-size:11.0pt;
font-family:"Calibri",sans-serif;
color:windowtext" lang="EN-US">
<a class="moz-txt-link-abbreviated" href="mailto:fis-bounces@listas.unizar.es">fis-bounces@listas.unizar.es</a>
[<a class="moz-txt-link-freetext" href="mailto:fis-bounces@listas.unizar.es">mailto:fis-bounces@listas.unizar.es</a>] <b>On
Behalf Of </b>Pedro C. Marijuan<br>
<b>Sent:</b> Wednesday, November 29, 2017 9:41 PM<br>
<b>To:</b> 'fis' <a class="moz-txt-link-rfc2396E" href="mailto:fis@listas.unizar.es"><fis@listas.unizar.es></a><br>
<b>Subject:</b> [Fis] Informatics of DNA (Sungchul
Ji)</span></p>
</div>
</div>
<p><span style="font-family:"Times New
Roman",serif" lang="EN-US">Hi FISers,</span><span
style="font-family:"Calibri",sans-serif"
lang="EN-US"></span></p>
<p><span style="font-family:"Times New
Roman",serif" lang="EN-US">We may have in DNA a
golden opportunity to define what
<b>information</b> is. </span><span
style="font-family:"Calibri",sans-serif"
lang="EN-US"></span></p>
<p class="x_xxxxxxxmsonormal" style=""><span lang="EN-US"> </span><b><span
style="font-family:"Times New
Roman",serif" lang="EN-US">(1)</span></b><span
style="font-size:7.0pt; font-family:"Times New
Roman",serif" lang="EN-US"> </span><span
style="font-family:"Times New Roman",serif"
lang="EN-US">We now know that we are different from
mice because our <span class="x_highlight">DNA</span> sequences
are different from those of mice [1]. That is, we are
different from mice because our <span
class="x_highlight">DNA</span> carries different
kinds (both with respect to <i>quality</i> and <i>quantity</i>)
of </span><span class="x_highlight"><span
style="font-family:"Times New
Roman",serif; color:red" lang="EN-US">INFORMATION</span></span><span
style="font-family:"Times New Roman",serif;
color:red" lang="EN-US"> </span><span
style="font-family:"Times New Roman",serif"
lang="EN-US">from the mouse <span class="x_highlight">DNA:</span></span><span
lang="EN-US"></span></p>
<p class="x_xxxxxxxmsolistparagraph"
style="margin-right:0cm; margin-bottom:0cm;
margin-left:38.25pt; margin-bottom:.0001pt;
text-indent:-20.25pt; background-image:initial">
<span style="font-family:"Calibri",sans-serif"
lang="EN-US"> </span>”<span lang="EN-US">When it comes
to protein-encoding genes, mice are 85% similar to
humans. For non-coding genes, it's only about 50%.
The National Human Genome Research <span
class="x_highlight">In</span>stitute attributes this
similarity </span><span style="font-family:"Times
New Roman",serif; color:#212529" lang="EN-US">to
a shared ancestor about 80 million years ago.” </span><span
lang="EN-US"><a moz-do-not-send="true"
href="https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.thisisinsider.com%2Fcomparing-genetic-similarity-between-humans-and-other-things-2016-5&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7C65e6d35da38f42a35c0608d537f75fe4%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636476457988945872&sdata=jpAs7QGzTxeIP6qyqUV1jcjOk1OWwKERTNK8V%2FHrg0E%3D&reserved=0"><span
style="font-size:10.0pt; font-family:"Times
New Roman",serif">http://www.thisisinsider.com/comparing-genetic-similarity-between-humans-and-other-things-2016-5</span></a></span></p>
<p class="x_xxxxxxxmsonormal" style=""><span lang="EN-US"> (<b>2</b>)
We also know that our properties or behaviors are at
least <span class="x_highlight">in</span> part
determined by both <span class="x_highlight">DNA</span> sequences
(i.e., <i>genetics</i>) and the way they are turned on
or off by environment-sensitive cells constituting
our body (i.e., <i>epigenetics</i>): We are the
products of both our <i>genes</i> and our <i>environment</i>. The
causal link between <span class="x_highlight">DNA</span> and our
behaviors can be briefly summarized as follows: </span></p>
<p class="x_xxxxxxxmsonormal" style=""><span lang="EN-US"> </span><span
style="font-size:10.0pt" lang="EN-US"> <b>1
2 3
4 5
6</b></span><span lang="EN-US"></span></p>
<p class="x_xxxxxxxmsonormal" style=""><span
class="x_highlight"><b><span style="font-size:10.0pt"
lang="EN-US">DNA</span></b></span><b><span
style="font-size:10.0pt" lang="EN-US"> ---->
pre-mRNA -----> mRNA -----> proteins
-----> IDS -----> Cell Functions ----->
Human Behaviors<br>
^
|<br>
|
|<br>
|
|<br>
|
|<br>
|_________________________________________________________________________________|</span></b><span
lang="EN-US"></span></p>
<p class="x_xxxxxxxmsonormal" style=""><b><span
style="font-size:10.0pt" lang="EN-US">
7</span></b><span lang="EN-US"></span></p>
<p class="x_xxxxxxxmsonormal" style=""><b><span
style="font-size:10.0pt" lang="EN-US"> </span></b><span
lang="EN-US"> </span><b><span
style="font-family:"Calibri",sans-serif"
lang="EN-US">Figure A. </span></b><span
style="font-family:"Calibri",sans-serif"
lang="EN-US">The flow of genetic and epigenetic <span
class="x_highlight">information</span>s between <span
class="x_highlight">DNA</span> and the human
behavior. IDS stands for the </span><span
class="x_highlight"><i><span
style="font-family:"Times New
Roman",serif" lang="EN-US">In</span></i></span><i><span
style="font-family:"Times New
Roman",serif" lang="EN-US">tracellular
Dissipative Structures </span></i><span
style="font-family:"Calibri",sans-serif"
lang="EN-US">(also called the </span><i><span
style="font-family:"Times New
Roman",serif" lang="EN-US">Dissipative
Structures of Prigogine</span></i><span
style="font-family:"Calibri",sans-serif"
lang="EN-US">) such as ion gradients across cell
membranes and within the cytoplasm without any
membrane barriers. According to the Bhopalator, a
molecular model of the living cell proposed <span
class="x_highlight">in</span> 1985 <span
class="x_highlight">in</span> a meeting held <span
class="x_highlight">in</span> Bhopal, <span
class="x_highlight">In</span>dia, IDS's are
postulated to be the immediate or the proximal causes
for all cell functions [2]. The seven steps <span
class="x_highlight">in</span> the scheme are </span></p>
<p class="x_xxxxxxxmsonormal" style=""><b><span
style="font-family:"Times New
Roman",serif" lang="EN-US">1</span></b><span
lang="EN-US"> = transcription</span></p>
<p class="x_xxxxxxxmsonormal" style=""><b><span
lang="EN-US">2</span></b><span lang="EN-US"> =
splicing</span></p>
<p class="x_xxxxxxxmsonormal" style=""><b><span
lang="EN-US">3</span></b><span lang="EN-US"> =
translation (explained <span class="x_highlight">in</span> (3) <span
class="x_highlight">in</span> more detail.)</span></p>
<p class="x_xxxxxxxmsonormal" style=""><b><span
lang="EN-US">4</span></b><span lang="EN-US"> =
enzyme catalysis</span></p>
<p class="x_xxxxxxxmsonormal" style=""><b><span
lang="EN-US">5</span></b><span lang="EN-US"> = cell
motions</span></p>
<p class="x_xxxxxxxmsonormal" style=""><b><span
lang="EN-US">6</span></b><span lang="EN-US"> = body
motions<br>
<b>7</b> = the effect of human behavior or emotion on
gene expression, e.g., see the phenomenon of the <i>conservedtranscriptional response
to adversity</i> (CTRA) [3].</span></p>
<p class="x_xxxxxxxmsonormal" style=""><span lang="EN-US"> I hope
that the <span class="x_highlight"><i>information</i></span><i> flow
scheme</i> shown <span class="x_highlight">in</span><b> Figure
A</b> can serve as a concrete example of <span
class="x_highlight">information</span> <span
class="x_highlight">in</span>action as <span
class="x_highlight">information</span> scientists strive
to come up with a generally acceptable definition
of what <span class="x_highlight">INFORMATION</span>is. </span></p>
<p class="x_xxxxxxxmsonormal" style=""><span lang="EN-US"> (<b>3</b>)
Unlike <span class="x_highlight">in</span> Steps 1
and 2 where the same kinds of molecules, i.e.,
the nucleic acids, <span class="x_highlight">DNA</span> and RNA, directly <span
class="x_highlight">in</span>teract (or contact
or touch each other) via the Watson-Crick base-paring
mechanism (see the second row <span
class="x_highlight">in </span><b>Figure 1</b> below), <span
class="x_highlight">in</span> Step 3, there is no
such direct <span class="x_highlight">in</span>teraction
between mRNA and amino acids, but rather their <span
class="x_highlight">in</span>teractions are mediated
by tRNA which recognizes mRNA at its <i>anti-codon
arm</i> and amino acids at its 3<i>'-acceptor stem</i>,
about 60 angstroms away (see the blue region <span
class="x_highlight">in</span> the mechanism of
translation shown at <a moz-do-not-send="true"
href="https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.quora.com%2FWhy-are-ribosomes-so-important-in-plant-cells&data=02%7C01%7Csji%40pharmacy.rutgers.edu%7C65e6d35da38f42a35c0608d537f75fe4%7Cb92d2b234d35447093ff69aca6632ffe%7C1%7C0%7C636476457988945872&sdata=JWXFYri%2BEXQzF3%2B2nfzklANJlXbKYoP2sEmgk9l%2BUs8%3D&reserved=0"
id="LPlnk275136" previewremoved="true">https://www.quora.com/Why-are-ribosomes-so-important-in-plant-cells</a>).
The universality of the wave-particle duality
demonstrated <span class="x_highlight">in</span> [4]
suggest that the tripartite coupling among </span><span
style="font-family:"Times New Roman",serif;
color:red" lang="EN-US">codon</span><span
style="font-family:"Times New Roman",serif"
lang="EN-US">,</span><span
style="font-family:"Times New Roman",serif;
color:red" lang="EN-US"> anticodon</span><span
lang="EN-US">, and amino acid <span
class="x_highlight">in</span> the ribosome-mRNA-tRNA
complex may be mediated by <i>resonant vibrations</i> or <i>standing
waves</i> (also called <i>resonance</i> or <i>resonant
waves</i>) generated within the complex, just as the
vibratioal patterns located at distant regions on
the Chladni (1756-1827) plate [5, 6] are coordinated
via resonance. </span></p>
<p class="x_xxxxxxxmsonormal" style=""><span lang="EN-US"> </span><span
style="font-family:"Times New Roman",serif;
color:#222222" lang="EN-US">The Chladni plate [5,
6] is an ideal model for illustrating the role of
resonance <span class="x_highlight">in</span></span><span
style="font-family:"Times New Roman",serif"
lang="EN-US"> molecular biology. At a given resonance
frequency, the particles on remote regions of the
Chaldni plate </span><span style="color:#222222"
lang="EN-US">are coordinated without any direct <span
class="x_highlight">in</span>teractions between them
and yet form ordered patterns. To me this is
similar to what happens <span class="x_highlight">in</span> the
ribosome system when a peptide molecule is
synthesized; i.e, different components of the
ribosome-mRNA-tRNA complex execute their motions that
are so coordinated as to achieve the peptide
synthesis. The ribosome and the Chladni plate are
compared at several levels <span class="x_highlight">in</span> <b>Table
1.</b>
</span><span lang="EN-US"></span></p>
<p class="x_xxxxxxxmsonormal" style=""><span
style="font-family:"Times New Roman",serif;
color:#222222" lang="EN-US">.....</span><span
lang="EN-US"></span></p>
<p class="x_xxxxxxxmsonormal" style=""><span
style="font-family:"Times New Roman",serif;
color:#222222" lang="EN-US">Sungchul Ji
</span><span lang="EN-US"><a moz-do-not-send="true"
href="mailto:sji.conformon@gmail.com"><span
style="font-family:"Times New
Roman",serif"><sji.conformon@gmail.com></span></a></span></p>
<p class="x_xxxxxxxmsonormal" style=""><span
style="color:#CC0000" lang="EN-US">The message
continues at:</span><span lang="EN-US"><br>
<a moz-do-not-send="true"
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<pre><span lang="EN-US">------------------------------------------------- </span></pre>
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