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Sorry for being cryptic. Mr. Levin uses this metaphor [1]: just as in the 1950s in order to change the state of a computer you would have to physically change t
by ly3xqhl8g9 4y ago
Sorry for being cryptic. Mr. Levin uses this metaphor [1]: just as in the 1950s in order to change the state of a computer you would have to physically change the wires, in a proportional manner, today, when we play with genes we try to alter state at a hardware level, and from the past 70+ years of software development we simply know there is a better way to control state. Imagine you'd have to pull a soldering iron each time you wanted to switch between Adobe Photoshop and Microsoft Word, to paraphrase Mr. Levin's remark.
Therefore, there might not be any morphological secret in the DNA, junk or not: DNA encodes a recipe for the building tools to be used in the eventuality of development. Imagine I would extract the exact state of the transistors from my computer, a ridiculously long string of 0s and 1s. Which strings of 0s and 1s codify this very textbox, its background color, the position of the cursor, the cursor itself? The questions are simply at the wrong level of abstraction, even if of course the state of the textbox is certainly somewhere in that string, but if I wanted to alter state at this wrong level then I would have to move very carefully a lot of 0s and 1s, in a very particular manner, with almost no room for errors, in order to add a simple "a" character to this very textbox. Isn't it much more simple and much more interesting, in the waterfall of effects through the abstraction layers if not in action, to push the key "A" on the keyboard? The question then becomes what is and how do we press the keyboard to alter the morphospace location of a cell, a tissue, an organism. A possible answer researched by Mr. Levin's group is voltage-gated ion channels controlling bioelectrical gradients [2].
Of course, at the lowest level, we are all stardust, a collection of femtoevents between femtoparticles, but we simply do not have to operate at that level to understand and control biology: biology itself has done the work, for at least the past 4+ billions of years of evolution, to increase the level of abstraction, from bonds between carbon and sulfur [3], to rotary motors to store and transfer energy [4], to organisms capable of running some kind of simulation of the world in which their reflected self becomes an agent in the world which sometimes knows they are an agent.
[1] Michael Levin | Cell Intelligence in Physiological and Morphological Spaces https://youtu.be/jLiHLDrOTW8?t=1201 https://youtu.be/jLiHLDrOTW8?t=1201
[2] Exploring the Behavior of Bioelectric Circuits Using Evolution Heuristic Search, https://www.liebertpub.com/doi/epub/10.1089/bioe.2022.0033 https://www.liebertpub.com/doi/epub/10.1089/bioe.2022.0033
[3] At the very beginning of life on Earth: the thiol-rich peptide (TRP) world hypothesis, https://pubmed.ncbi.nlm.nih.gov/29139533 https://pubmed.ncbi.nlm.nih.gov/29139533
[4] ATP synthase — a marvellous rotary engine of the cell, https://www.nature.com/articles/35089509 https://www.nature.com/articles/35089509
- graderjs 4y agoYou know a lot about this. Although I think gradients are mechanism of how a body implements shape, I don't think they are (nor contain) the design. I understand your computer analogy, but I think it's misapplied because the opaque string of 01s requiring exquisite manipulation is exactly like what DNA was before we had modern genetic engineering, CRISPR, etc. And we walked the path your analogy suggests is ridiculous and impossible, to arrive with the contemporary genetic tools we now have. I think "junk" is morphogenetics (and more), just in a different language that published science does not yet understand.
- ly3xqhl8g9 4y agoFalling back again to the research done by Levin lab, they are able to shape 2-headed or 2-tailed flatworms by altering electric potential differences, and these flatworms have the same DNA as the regular one head, one tail flatworm [1]. See them in video [2]. One other lesson to be learned from the planarian flatworms is that their DNA is a complete mess, yet they are able to fully regenerate without any issues, and are functionally immortal, they do not age [3]. DNA is certainly important and interesting and needs more research, my initial comment just pointed out that if DNA is a "CAD model", the computational layer, the basal cognition in cell/tissue/organ(ism), is even more enticing, and probably we don't even need to alter genes in order to shape morphology, giving another analogy, if a pocket calculator "knows" what 5 + 7 is, we probably don't need to build another pocket calculator just to compute 6 + 8. [1] A Computational Approach to Explaining Bioelectrically Induced Persistent, Stochastic Changes of Axial Polarity in Planarian Regeneration, https://www.liebertpub.com/doi/10.1089/bioe.2021.0036 https://www.liebertpub.com/doi/10.1089/bioe.2021.0036 [2] Endogenous Bioelectric Networks & Regenerative Medicine, https://www.youtube.com/watch?v=HKWyB9qLP_s https://www.youtube.com/watch?v=HKWyB9qLP_s (Impossible Biological Objects, 2-headed flatworms at 52:30) [3] Planarians as a model of aging to study the interaction between stem cells and senescent cells in vivo, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4696462/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4696462/