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</o:shapelayout></xml><![endif]--></head><body bgcolor=white lang=ZH-CN link=blue vlink=purple><div class=WordSection1><p class=MsoNormal style='margin-top:3.6pt;mso-para-margin-top:.3gd'><span lang=EN-US style='font-family:"Times New Roman",serif'>Dear Sungchul,</span><span lang=EN-US style='font-size:10.5pt;font-family:"Times New Roman",serif;color:windowtext'><o:p></o:p></span></p><p class=MsoNormal style='margin-top:4.65pt;text-indent:21.0pt'><span lang=EN-US style='font-family:"Times New Roman",serif'>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.<o:p></o:p></span></p><p class=MsoNormal style='margin-top:4.65pt;text-indent:21.0pt'><span lang=EN-US style='font-family:"Times New Roman",serif'>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?<o:p></o:p></span></p><p class=MsoNormal style='margin-top:4.65pt;text-indent:21.0pt'><span lang=EN-US style='font-family:"Times New Roman",serif'>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?<o:p></o:p></span></p><p class=MsoNormal style='margin-top:4.65pt;text-indent:21.0pt'><span lang=EN-US style='font-family:"Times New Roman",serif'>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?<o:p></o:p></span></p><p class=MsoNormal style='margin-top:4.65pt;text-indent:21.0pt'><span lang=EN-US style='font-family:"Times New Roman",serif'>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?<o:p></o:p></span></p><p class=MsoNormal style='margin-top:4.65pt'><span lang=EN-US style='font-family:"Times New Roman",serif'><o:p> </o:p></span></p><p class=MsoNormal style='margin-top:4.65pt'><span lang=EN-US style='font-family:"Times New Roman",serif'>Best wishes,<o:p></o:p></span></p><p class=MsoNormal style='margin-top:4.65pt'><span lang=EN-US style='font-family:"Times New Roman",serif'>Xueshan<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-family:等线;color:black'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext'>From:</span></b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext'> fis-bounces@listas.unizar.es [mailto:fis-bounces@listas.unizar.es] <b>On Behalf Of </b>Pedro C. Marijuan<br><b>Sent:</b> Wednesday, November 29, 2017 9:41 PM<br><b>To:</b> 'fis' <fis@listas.unizar.es><br><b>Subject:</b> [Fis] Informatics of DNA (Sungchul Ji)<o:p></o:p></span></p></div></div><p><span lang=EN-US style='font-family:"Times New Roman",serif'>Hi FISers,</span><span lang=EN-US style='font-family:"Calibri",sans-serif'><o:p></o:p></span></p><p><span lang=EN-US style='font-family:"Times New Roman",serif'>We may have in DNA a golden opportunity to define what <b>information</b> is. </span><span lang=EN-US style='font-family:"Calibri",sans-serif'><o:p></o:p></span></p><p class=xxxxxxxmsonormal style='0.0001pt;background-image:initial'><span lang=EN-US> </span><b><span lang=EN-US style='font-family:"Times New Roman",serif'>(1)</span></b><span lang=EN-US style='font-size:7.0pt;font-family:"Times New Roman",serif'> </span><span lang=EN-US style='font-family:"Times New Roman",serif'>We now know that we are different from mice because our <span class=highlight>DNA</span> sequences are different from those of mice [1]. That is, we are different from mice because our <span class=highlight>DNA</span> carries different kinds (both with respect to <i>quality</i> and <i>quantity</i>) of </span><span class=highlight><span lang=EN-US style='font-family:"Times New Roman",serif;color:red'>INFORMATION</span></span><span lang=EN-US style='font-family:"Times New Roman",serif;color:red'> </span><span lang=EN-US style='font-family:"Times New Roman",serif'>from the mouse <span class=highlight>DNA:</span></span><span lang=EN-US><o:p></o:p></span></p><p class=xxxxxxxmsolistparagraph style='mso-margin-top-alt:0cm;margin-right:0cm;margin-bottom:0cm;margin-left:38.25pt;margin-bottom:.0001pt;text-indent:-20.25pt;background-image:initial'><span lang=EN-US style='font-family:"Calibri",sans-serif'> </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=highlight>In</span>stitute attributes this similarity </span><span lang=EN-US style='font-family:"Times New Roman",serif;color:#212529'>to a shared ancestor about 80 million years ago.” </span><span lang=EN-US><a href="http://www.thisisinsider.com/comparing-genetic-similarity-between-humans-and-other-things-2016-5"><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><o:p></o:p></span></p><p class=xxxxxxxmsonormal style='0.0001pt;background-image:initial'><span lang=EN-US> (<b>2</b>) We also know that our properties or behaviors are at least <span class=highlight>in</span> part determined by both <span class=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=highlight>DNA</span> and our behaviors can be briefly summarized as follows: <o:p></o:p></span></p><p class=xxxxxxxmsonormal style='0.0001pt;background-image:initial'><span lang=EN-US> </span><span lang=EN-US style='font-size:10.0pt'> <b>1 2 3 4 5 6</b></span><span lang=EN-US><o:p></o:p></span></p><p class=xxxxxxxmsonormal style='text-indent:5.25pt;0.0001pt;background-image:initial'><span class=highlight><b><span lang=EN-US style='font-size:10.0pt'>DNA</span></b></span><b><span lang=EN-US style='font-size:10.0pt'> ----> pre-mRNA -----> mRNA -----> proteins -----> IDS -----> Cell Functions -----> Human Behaviors<br> ^ |<br> | |<br> | |<br> | |<br> |_________________________________________________________________________________|</span></b><span lang=EN-US><o:p></o:p></span></p><p class=xxxxxxxmsonormal style='text-indent:5.25pt;0.0001pt;background-image:initial'><b><span lang=EN-US style='font-size:10.0pt'> 7</span></b><span lang=EN-US><o:p></o:p></span></p><p class=xxxxxxxmsonormal style='text-indent:5.25pt;0.0001pt;background-image:initial'><b><span lang=EN-US style='font-size:10.0pt'> </span></b><span lang=EN-US> </span><b><span lang=EN-US style='font-family:"Calibri",sans-serif'>Figure A. </span></b><span lang=EN-US style='font-family:"Calibri",sans-serif'>The flow of genetic and epigenetic <span class=highlight>information</span>s between <span class=highlight>DNA</span> and the human behavior. IDS stands for the </span><span class=highlight><i><span lang=EN-US style='font-family:"Times New Roman",serif'>In</span></i></span><i><span lang=EN-US style='font-family:"Times New Roman",serif'>tracellular Dissipative Structures </span></i><span lang=EN-US style='font-family:"Calibri",sans-serif'>(also called the </span><i><span lang=EN-US style='font-family:"Times New Roman",serif'>Dissipative Structures of Prigogine</span></i><span lang=EN-US style='font-family:"Calibri",sans-serif'>) 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=highlight>in</span> 1985 <span class=highlight>in</span> a meeting held <span class=highlight>in</span> Bhopal, <span class=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=highlight>in</span> the scheme are <o:p></o:p></span></p><p class=xxxxxxxmsonormal style='0.0001pt;background-image:initial'><b><span lang=EN-US style='font-family:"Times New Roman",serif'>1</span></b><span lang=EN-US> = transcription<o:p></o:p></span></p><p class=xxxxxxxmsonormal style='0.0001pt;background-image:initial'><b><span lang=EN-US>2</span></b><span lang=EN-US> = splicing<o:p></o:p></span></p><p class=xxxxxxxmsonormal style='0.0001pt;background-image:initial'><b><span lang=EN-US>3</span></b><span lang=EN-US> = translation (explained <span class=highlight>in</span> (3) <span class=highlight>in</span> more detail.)<o:p></o:p></span></p><p class=xxxxxxxmsonormal style='0.0001pt;background-image:initial'><b><span lang=EN-US>4</span></b><span lang=EN-US> = enzyme catalysis<o:p></o:p></span></p><p class=xxxxxxxmsonormal style='0.0001pt;background-image:initial'><b><span lang=EN-US>5</span></b><span lang=EN-US> = cell motions<o:p></o:p></span></p><p class=xxxxxxxmsonormal style='0.0001pt;background-image:initial'><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].<o:p></o:p></span></p><p class=xxxxxxxmsonormal style='0.0001pt;background-image:initial'><span lang=EN-US> I hope that the <span class=highlight><i>information</i></span><i> flow scheme</i> shown <span class=highlight>in</span><b> Figure A</b> can serve as a concrete example of <span class=highlight>information</span> <span class=highlight>in</span>action as <span class=highlight>information</span> scientists strive to come up with a generally acceptable definition of what <span class=highlight>INFORMATION</span>is. <o:p></o:p></span></p><p class=xxxxxxxmsonormal style='0.0001pt;background-image:initial'><span lang=EN-US> (<b>3</b>) Unlike <span class=highlight>in</span> Steps 1 and 2 where the same kinds of molecules, i.e., the nucleic acids, <span class=highlight>DNA</span> and RNA, directly <span class=highlight>in</span>teract (or contact or touch each other) via the Watson-Crick base-paring mechanism (see the second row <span class=highlight>in </span><b>Figure 1</b> below), <span class=highlight>in</span> Step 3, there is no such direct <span class=highlight>in</span>teraction between mRNA and amino acids, but rather their <span class=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=highlight>in</span> the mechanism of translation shown at <a href="https://www.quora.com/Why-are-ribosomes-so-important-in-plant-cells" id=LPlnk275136>https://www.quora.com/Why-are-ribosomes-so-important-in-plant-cells</a>). The universality of the wave-particle duality demonstrated <span class=highlight>in</span> [4] suggest that the tripartite coupling among </span><span lang=EN-US style='font-family:"Times New Roman",serif;color:red'>codon</span><span lang=EN-US style='font-family:"Times New Roman",serif'>,</span><span lang=EN-US style='font-family:"Times New Roman",serif;color:red'> anticodon</span><span lang=EN-US>, and amino acid <span class=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. <o:p></o:p></span></p><p class=xxxxxxxmsonormal style='0.0001pt;background-image:initial'><span lang=EN-US> </span><span lang=EN-US style='font-family:"Times New Roman",serif;color:#222222'>The Chladni plate [5, 6] is an ideal model for illustrating the role of resonance <span class=highlight>in</span></span><span lang=EN-US style='font-family:"Times New Roman",serif'> molecular biology. At a given resonance frequency, the particles on remote regions of the Chaldni plate </span><span lang=EN-US style='color:#222222'>are coordinated without any direct <span class=highlight>in</span>teractions between them and yet form ordered patterns. To me this is similar to what happens <span class=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=highlight>in</span> <b>Table 1.</b> </span><span lang=EN-US><o:p></o:p></span></p><p class=xxxxxxxmsonormal style='0.0001pt;background-image:initial'><span lang=EN-US style='font-family:"Times New Roman",serif;color:#222222'>.....</span><span lang=EN-US><o:p></o:p></span></p><p class=xxxxxxxmsonormal style='0.0001pt;background-image:initial'><span lang=EN-US style='font-family:"Times New Roman",serif;color:#222222'>Sungchul Ji </span><span lang=EN-US><a href="mailto:sji.conformon@gmail.com"><span style='font-family:"Times New Roman",serif'><sji.conformon@gmail.com></span></a><o:p></o:p></span></p><p class=xxxxxxxmsonormal style='0.0001pt;background-image:initial'><span lang=EN-US style='color:#CC0000'>The message continues at:</span><span lang=EN-US><br><a href="http://fis.sciforum.net/wp-content/uploads/sites/2/2014/11/Sung_informatics-of-DNA.pdf">http://fis.sciforum.net/wp-content/uploads/sites/2/2014/11/Sung_informatics-of-DNA.pdf</a></span><span lang=EN-US style='color:black'><o:p></o:p></span></p><pre><span lang=EN-US>-------------------------------------------------<o:p></o:p></span></pre><pre><span lang=EN-US>Pedro C. Mariju</span>á<span lang=EN-US>n<o:p></o:p></span></pre><pre><span lang=EN-US>Grupo de Bioinformaci</span>ó<span lang=EN-US>n / Bioinformation Group<o:p></o:p></span></pre><pre><span lang=EN-US>Instituto Aragon</span>é<span lang=EN-US>s de Ciencias de la Salud<o:p></o:p></span></pre><pre><span lang=EN-US>Centro de Investigaci</span>ó<span lang=EN-US>n Biom</span>é<span lang=EN-US>dica de Arag</span>ó<span lang=EN-US>n (CIBA)<o:p></o:p></span></pre><pre><span lang=EN-US>Avda. San Juan Bosco, 13, planta 0<o:p></o:p></span></pre><pre><span lang=EN-US>50009 Zaragoza, Spain<o:p></o:p></span></pre><pre><span lang=EN-US>Tfno. +34 976 71 3526 (& 6818)<o:p></o:p></span></pre><pre><span lang=EN-US><a href="mailto:pcmarijuan.iacs@aragon.es">pcmarijuan.iacs@aragon.es</a><o:p></o:p></span></pre><pre><span lang=EN-US><a href="http://sites.google.com/site/pedrocmarijuan/">http://sites.google.com/site/pedrocmarijuan/</a><o:p></o:p></span></pre><pre><span lang=EN-US>------------------------------------------------- <o:p></o:p></span></pre></div></body></html>