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Can one apply the “Goldilocks Principle” of fine-tuning to DNA structure?

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From ScienceDaily:

Inspired by ideas from the physics of phase transitions and polymer physics, researchers in the Divisions of Physical and Biological Sciences at UC San Diego set out specifically to determine the organization of DNA inside the nucleus of a living cell. The findings of their study, recently published in Nature Communications, suggest that the phase state of the genomic DNA is “just right” — a gel poised at the phase boundary between gel and sol, the solid-liquid phase transition.

Think of pudding, panna cotta — or even porridge. The consistency of these delectables must be just right to be ideally enjoyed. Just as the “sol-gel” phase transition, according to the scientists, seems just right for explaining the timing of genomic interactions that dictate gene expression and somatic recombination.

“This finding points to a general physical principle of chromosomal organization, which has important implications for many key processes in biology, from antibody production to tissue differentiation,” said Olga Dudko, a theoretical biophysicist and professor in the Department of Physics at UC San Diego, who collaborated with colleague Cornelis Murre, a distinguished professor in the Section of Molecular Biology, on the study. Paper. (open access) – Nimish Khanna, Yaojun Zhang, Joseph S. Lucas, Olga K. Dudko, Cornelis Murre. Chromosome dynamics near the sol-gel phase transition dictate the timing of remote genomic interactions. Nature Communications, 2019; 10 (1) DOI: 10.1038/s41467-019-10628-9 More.

From what these researchers report, yes, one can definitely apply the principle. But then one must accept that biology shows evidence of design. “Just right” is rarely an accident.

See also: Carbon dioxide and the Goldilocks Principle

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A single-celled organism walks into a casino ... ScuzzaMan
A few notes:
Cross section of DNA compared to the Rose window at York Minster (the largest Gothic cathedral in northern Europe) – picture https://reflectionsfrommyporchswing.files.wordpress.com/2012/01/dna-2.jpg Unwinding the Double Helix: Meet DNA Helicase – Jonathan M. February 20, 2013 – article with video Excerpt: With a rotational speed of up to 10,000 rotations per minute, the helicase rivals the rotational speed of jet engine turbines. http://www.evolutionnews.org/2013/02/unwinding_the_d_1069371.html DNA Packaging: Nucleosomes and Chromatin each of us has enough DNA to go from here to the Sun and back more than 300 times, or around Earth’s equator 2.5 million times! How is this possible? http://www.nature.com/scitable/topicpage/DNA-Packaging-Nucleosomes-and-Chromatin-310 The Chromosome in Nuclear Space – Stephen L. Talbott Excerpt: “If you arranged the DNA in a human cell linearly, it would extend for nearly two meters. How do you pack all that DNA into a cell nucleus just five or ten millionths of a meter in diameter? According to the usual comparison it’s as if you had to pack 24 miles (40 km) of extremely thin thread into a tennis ball. Moreover, this thread is divided into 46 pieces (individual chromosomes) averaging, in our tennis-ball analogy, over half a mile long. Can it be at all possible not only to pack the chromosomes into the nucleus, but also to keep them from becoming hopelessly entangled? Obviously it must be possible, however difficult to conceive — and in fact an endlessly varied packing and unpacking is going on all the time.,,, http://natureinstitute.org/txt/st/mqual/genome_2.htm Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome – Oct. 2009 Excerpt: At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, polymer conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. http://www.sciencemag.org/cgi/content/abstract/326/5950/289 Information Storage in DNA by Wyss Institute – video https://vimeo.com/47615970 Quote from preceding video: “The theoretical (information) density of DNA is you could store the total world information, which is 1.8 zetabytes, at least in 2011, in about 4 grams of DNA.” Sriram Kosuri PhD. – Wyss Institute Demonstrating, Once Again, the Fantastic Information-Storage Capacity of DNA – January 29, 2013 Excerpt: researchers led by molecular biologists Nick Goldman and Ewan Birney of the European Bioinformatics Institute (EBI) in Hinxton, UK, report online today in Nature that they’ve improved the DNA encoding scheme to raise that storage density to a staggering 2.2 petabytes per gram, three times the previous effort.,,, http://www.evolutionnews.org/2013/01/how_do_you_peta068641.html Second, third, fourth… genetic codes – One spectacular case of code crowding – Edward N. Trifonov – video https://www.youtube.com/watch?v=fDB3fMCfk0E
In the preceding video, Trifonov elucidates codes that are, simultaneously, in the same sequence, coding for DNA curvature, Chromatin Code, Amphipathic helices, and NF kappaB. In fact, at the 58:00 minute mark he states, “Reading only one message, one gets three more, practically GRATIS!”. And please note that this was just an introductory lecture in which Trifinov just covered the very basics and left many of the other codes out of the lecture. Codes which code for completely different, yet still biologically important, functions. In fact, at the 7:55 mark of the video, there are 13 codes that are listed on a powerpoint. And that is not even taking into account alternative splicing which adds yet even another level of complexity on top of all that,,
Time to Redefine the Concept of a Gene? - Sept. 10, 2012 Excerpt: As detailed in my second post on alternative splicing, there is one human gene that codes for 576 different proteins, and there is one fruit fly gene that codes for 38,016 different proteins! While the fact that a single gene can code for so many proteins is truly astounding, we didn’t really know how prevalent alternative splicing is. Are there only a few genes that participate in it, or do most genes engage in it? The ENCODE data presented in reference 2 indicates that at least 75% of all genes participate in alternative splicing. They also indicate that the number of different proteins each gene makes varies significantly, with most genes producing somewhere between 2 and 25. - per networked blogs

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