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<p class="MsoNormal">But going back to Dave’s original proposition: What are the limiting factors in bundling up new stretches of DNA in chromatin? The fossils of viruses are in there, so apparently it is possible.<o:p></o:p></p>
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<p class="MsoNormal"><b>From:</b> Friam <friam-bounces@redfish.com> <b>On Behalf Of
</b>thompnickson2@gmail.com<br>
<b>Sent:</b> Monday, January 25, 2021 10:00 AM<br>
<b>To:</b> 'The Friday Morning Applied Complexity Coffee Group' <friam@redfish.com>; Peter and Janet Lailey <PeterLailey@yahoo.co.uk><br>
<b>Subject:</b> Re: [FRIAM] tangent from uncanny valley<o:p></o:p></p>
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<p class="MsoNormal">Like I said. DNA is not just a code. It’s a bit of meat. It has geometry. The silent DNA is presumably crucial to that dynamic geometry.
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<p class="MsoNormal">Nick Thompson<o:p></o:p></p>
<p class="MsoNormal"><a href="mailto:ThompNickSon2@gmail.com"><span style="color:#0563C1">ThompNickSon2@gmail.com</span></a><o:p></o:p></p>
<p class="MsoNormal"><a href="https://wordpress.clarku.edu/nthompson/"><span style="color:#0563C1">https://wordpress.clarku.edu/nthompson/</span></a><o:p></o:p></p>
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<p class="MsoNormal"><b>From:</b> Friam <<a href="mailto:friam-bounces@redfish.com">friam-bounces@redfish.com</a>>
<b>On Behalf Of </b>David Eric Smith<br>
<b>Sent:</b> Monday, January 25, 2021 11:20 AM<br>
<b>To:</b> The Friday Morning Applied Complexity Coffee Group <<a href="mailto:friam@redfish.com">friam@redfish.com</a>><br>
<b>Subject:</b> Re: [FRIAM] tangent from uncanny valley<o:p></o:p></p>
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<p class="MsoNormal">It’s good that Marcus said specifically “doesn’t express as proteins”, because that can capture both the small fraction that does, and the fact that indeed, the word “junk” is now rather characteristically embarrassing. At the least, we
have small regulatory RNAs of several kinds (I am not a specialist in this), and probably elaborate regions for the control of gene expression modulated by many transcription factors. I feel sure that somewhere I have seen a paper with a graph to the effect
that the number of regulatory (SOMETHING: what? sites? protein-protein interactions?) grows quadratically in the number of protein-coding exons. I know Peter Stadler in Leipzig has worked in this area a lot, but I have asked, and that paper is not by him.<o:p></o:p></p>
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<p class="MsoNormal">I believe I have also seen that spatial proximity in the nucleus is relevant to regulation of rates and coordination of gene expression. Proximity in space may come from proximity in a chromosomal sequence, but can also be non-local on
the chromosome. Erez Lieberman, perhaps 15 years ago or longer, when he was working at Martin Nowak’s Program for Evolutionary Dynamics at Harvard, was using new imaging methods to identify what the proximity arrangements were for transcribed regions, to
conclude that they were reproducible, and then to work toward how that was being controlled when they were not necessarily contiguous in sequence. <o:p></o:p></p>
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<p class="MsoNormal">Eric<o:p></o:p></p>
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<p class="MsoNormal">On Jan 25, 2021, at 11:09 AM, Barry MacKichan <<a href="mailto:barry.mackichan@mackichan.com">barry.mackichan@mackichan.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Arial",sans-serif">There used to be a lot of talk about “junk DNA” which doesn’t do anything, but I’ve gotten the impression (sorry, I can’t give references)
that more recently the “junk DNA” does play a role.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Arial",sans-serif">Also, adjacency or propinquity of genes on a chromosome affects evolution (if I get one of the genes from a parent, I’m highly likely
to get the other also). I have no idea if it plays a role during the life of a cell. I don’t know anything about how sexual reproduction goes about building a new chromosome by selecting pieces from the chromosomes of the parents, but on the face of it, changing
the layout (or in mathematical terms, the metric) could lead to omission or duplication errors in the result.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Arial",sans-serif">TL;DR Be careful what you wish for.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Arial",sans-serif">—Barry<o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Arial",sans-serif">On 22 Jan 2021, at 18:37, Marcus Daniels wrote:<o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="font-family:"Arial",sans-serif;color:#777777">Most of the human genome doesn't express as proteins, so there should be lots of room to store stuff.<br>
Such technology is hardly science fiction, it's even FDA approved!<br>
<br>
<a href="https://www.fda.gov/news-events/press-announcements/fda-approves-novel-gene-therapy-treat-patients-rare-form-inherited-vision-loss"><span style="color:#777777">https://www.fda.gov/news-events/press-announcements/fda-approves-novel-gene-therapy-treat-patients-rare-form-inherited-vision-loss</span></a><br>
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-----Original Message-----<br>
From: Friam <<a href="mailto:friam-bounces@redfish.com">friam-bounces@redfish.com</a>> On Behalf Of Prof David West<br>
Sent: Friday, January 22, 2021 2:43 PM<br>
To: <a href="mailto:friam@redfish.com">friam@redfish.com</a><br>
Subject: [FRIAM] tangent from uncanny valley<br>
<br>
The idea of posthuman came up (yes it was me) in another thread. This article <a href="https://www.nature.com/articles/s41589-020-00711-4">
<span style="color:#777777">https://www.nature.com/articles/s41589-020-00711-4</span></a> opens an interesting door: "reprogramming" DNA by inserting new data into living DNA. After all a program is just another form of data. This might be orthogonal to genetic
(re)engineering.<br>
<br>
davew<br>
<br>
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