A genetic switch

What Hacker News says

1. koengSep 2022
   “A Genetic Switch” is one of the best books in my field. The entire book is about a single genetic switch in a bacterial virus, starting off high level before going down into the nitty gritty, all for this single switch. Highly recommend for a deep dive into how genetics can actually be controlled, down to the physics level.
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2. kkylinApr 2022
   Not just spacing. The sequence also matters as they serve as binding sites for enzymes that can promote or repress the expression of downstream genes. As just one (relative simple) example of how complicated genetic circuitry can be, I really enjoyed & recommend Mark Ptashne's A Genetic Switch: Phage Lambda for anyone who doesn't mind doing some slightly technical reading.

   Disclaimer: not a biologist, and would be interested in hearing from someone more knowledgeble than I, both about the Ptashne book and about recommended reading.

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3. vibrioMar 2022
   This had great impact on me…and the quick read of Ptashne’s “a genetic switch” really pulled me into molecular biology. They helped me start to conceptualize how a group of inanimate objects (eg proteins, lipids, nucleic acid) can collectively be “alive”, including reproduce, and “make decisions”.
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4. dalyApr 2024
   I've been looking at yeast to see if it is possible to create a NOR gate. Then the game is to use the CPU that someone created in Conway's game of life to create a yeast-based computer.

   The CRISPR stuff:

   "We demonstrate the world’s first successful editing of the human genome using a gene editing system where every component is fully designed by AI. Our most performant AI-generated editor, OpenCRISPR-1, achieves similar activity and higher specificity than SpCas9, an exemplar gene editor, while being highly dissimilar in sequence. Moreover, our platform is capable of generating many more gene editing systems at-will; OpenCRISPR-1 is just the tip of the iceberg. We publicly release OpenCRISPR-1 to facilitate broad, ethical usage across research and commercial applications. In making this molecule available to the broader community, we hope to lower the costs and barrier to entry for therapeutic, agricultural, and scientific applications of CRISPR-based technologies." https://www.profluent.bio/blog/editing-the-human-genome-with...

   Conway's Game of Life CPU: https://www.youtube.com/watch?v=Kk2MH9O4pXY&ab_channel=AlanZ...

   Yeast-based NOR gate: https://www.nature.com/articles/ncomms15459

   I've finished one textbook on yeast so far. I've looked at doing CRISPR at home: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9053061/

   There is an ongoing effort on "yeast evolution" to create new kinds of yeast behavior https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9225242/ and, in particular, yeast seem to self-specialize when, through "directed evolution" they start to cooperate https://www.sciencedirect.com/science/article/pii/S200103702...

   There already is known machinery to do switching in cells: https://www.amazon.com/Genetic-Switch-Third-Lambda-Revisited...

   This form of epigenetics allows all kinds of interesting responses to external stimuli. In particular, it would allow "chemical questions" to be asked.

   It would be possible to create a cellular "display":

   "Scientists from Trinity College Dublin, in collaboration with the Royal College of Surgeons in Ireland (RCSI), have developed special fluorescent, color-changing dyes that, for the first time, can be used to simultaneously visualize multiple distinct biological environments using only one singular dye.

   When these dyes are encapsulated in delivery vessels, like those used in technologies like the COVID-19 vaccines, they “switch on” and give out light via a process called “aggregation-induced emission” (AIE). Soon after delivery into the cells their light “switches off” before “switching on” again once the cells shuttle the dyes into cellular lipid droplets."

   So when your Petri dish "yogurt" "sees you" open the fridge it can change the surface to say "Hello". Coming to a fridge near you...

   I suspect it gives more weight to "a gut feeling" when your stomach can argue for a viewpoint in actual words. We'll leave off the question of how to avoid angry mutterings from your toilet :-)

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5. dalyJul 2023
   <speculation>

   1) cells share a large portion of DNA sequences

   2) cells change their behavior based on their environment (Mark Ptashne "A Genetic Switch: Phage Lambda Revisited") (Mark Ptashne and Alexander Gann "Genes & Signals)

   3) The technology exists to edit the genome (Ali Movahedi "One Introduction of Genome Editing (CRISPR))

   4) modify yeast genome so that based on the sugar concentration they produce barley rather than yeast

   5) combine regular yeast and "barley yeast" in a sugar concentration

   ... beer!

   </speculation>

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