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Increasingly it's becoming clear that DNA is only a small part of the picture. Cellular electrical dynamics are the forefront of morphogenesis research atm. Loo
by TaupeRanger 6y ago
Increasingly it's becoming clear that DNA is only a small part of the picture. Cellular electrical dynamics are the forefront of morphogenesis research atm. Look at any recent high profile work out of Michael Levin's lab for an example.
- bigtones 6y agohttps://en.wikipedia.org/wiki/Bioelectricity https://en.wikipedia.org/wiki/Bioelectricity
- fktnktofk 6y agoAren't those electrical field patterns still somehow encoded in the DNA?
- ethbr0 6y agoEverything is deterministic if you're omniscient. In our more limited experience, certain levels of complexity mean unpredictable outcomes. As for why-not-DNA, I think about it in terms of "If there were some way that was faster able to adapt organisms than DNA changes, wouldn't most organisms accumulate substantial functionality via that pathway over time?"
- sssilver 6y ago> Everything is deterministic if you're omniscient Is this true, given https://en.wikipedia.org/wiki/Uncertainty_principle https://en.wikipedia.org/wiki/Uncertainty_principle ?
- deleted 6y ago[deleted]
- frutiger 6y agoIt is indeed not true, even omniscient beings can only produce probability distributions. However it is not clear if quantum effects are relevant at a biomolecular scale. Some experts[1] suggest so but these ideas are considered fringe by the mainstream. 1. Sir Roger Penrose
- Ixio 6y agoI'm of the mind that randomness is only an approximation of complexity, if you're omniscient then randomness doesn't exist and everything is deterministic. However it seems to me the deterministic vs randomness debate is of the same order as the existence of god(s) : we will never be able to prove or disprove it and we aren't able to make useful predictions out of the information one way or the other so we might as well just agree to disagree and move on.
- TeMPOraL 6y agoThey don't need to be. I'm not sure what the conclusion of biologists is today, but I have a feeling a lot of important mechanisms aren't encoded in the DNA - or, at least, not anymore. The key insight here is that cell reproduction doesn't happen out of nothing, it's always an existing mechanism working on a new mechanism. The seminal paper of Ken Thompson, "Reflections on Trusting Trust" (1984)[0], demonstrates how you can encode a backdoor in a compiler in such a way that the compiler embeds this backdoor in every program it builds, and embeds the backdoor-embedding machinery in every new compiler binary it builds. You can use it to build a "vanilla" compiler and make it backdoor-embedding, even though the source code doesn't have backdoor-embedding instructions in it. I suspect similar things happen in biology - there is computationally relevant information embedded in the runtime state, that's not explicitly encoded in the DNA - but it carries on, because every new living cell is built by a previous living cell. -- [0] - https://www.cs.cmu.edu/~rdriley/487/papers/Thompson_1984_ReflectionsonTrustingTrust.pdf https://www.cs.cmu.edu/~rdriley/487/papers/Thompson_1984_Ref...
- fktnktofk 6y agoI get your point and I agree, the DNA runs on hardware, which is why you can't take cat DNA and put it in a salamander cell and expect to get a cat. The resulting cell will just die since the hardware is not compatible with the DNA. My point was that there is only so much information capacity in the cell if you exclude DNA, surely much less than needed to store electrical fields patterns for a whole embryo.
- deleted 6y ago[deleted]
- FartyMcFarter 6y agoA cell has a lot of atoms, which may store a lot of information?
- Robotbeat 6y agoBut not error corrected like DNA.
- WClayFerguson 6y agoDNA is basically digital information. Every rung on the helix ladder is either an AT or GC. Nature found the simplest say to store information in our chemistry set. Couldn't really store any field patterns though.
- Robotbeat 6y agoRNA is simpler but doesn’t error correct as much like DNA. It’s possible the first life forms had only RNA.
- oconnor663 6y agoSpeculating for fun based on what scientist people have told me at parties :) I think the idea is that DNA will directly and literally encode things like "the genes for proteins A and B tend to get activated together". But the next thing that happens is that protein B catalyzes some chain of chemical reactions that winds up activating a different gene for protein C. And then maybe protein C causes some sort of mechanical change in the cell, and the resulting mechanical stress triggers the production of protein D in adjacent cells. Mapping the mechanical relationships between cells in an animal with developing bones and muscles gets super complicated. So the question of "does the DNA encode the relationship between A and D" ends up depending on what you mean by "encode".
- jcims 6y agoNot sure if this is included in 'cellular electrical dynamics' but it's still amazing: Neuronal Signaling and Sodium-Potassium Pump (from PDB-101) https://www.youtube.com/watch?v=ZKE8qK9UCrU https://www.youtube.com/watch?v=ZKE8qK9UCrU
- navan 6y agoThis reminded me of a beautiful animation of "Mitochondria: the cell's powerhouse" which I recently watched. https://www.youtube.com/watch?v=vkYEYjintqU https://www.youtube.com/watch?v=vkYEYjintqU
- ChuckMcM 6y agoExcellent reference. Bio papers with electricity in them, that is new for me. This one [1] is currently blowing my mind :-) [1] https://www.the-scientist.com/features/how-groups-of-cells-cooperate-to-build-organs-and-organisms-67881 https://www.the-scientist.com/features/how-groups-of-cells-c...
- yalok 6y agoTotally. And kind of explains why some electrophoresis therapies may be working.
- lurquer 6y agoDuring the initial boredom of Covid, I got very interested in Levin’s lab’s work and morphogenesis in general. I made a program to implement some of my theories. You’re welcome to try it. cycell2d.com My pet theory — morphogenic fields — is described in their on one of the pages. (Caveat: I’m neither a biologist nor a ‘real’ programmer. But, I was able to come up with a system to ‘grow’ certain animals and found it a fun way to spend the lockdown... almost as much fun as posting ‘Covid is a hoax’ comments on HackerNews... ahhh... those were the days.)
- dgellow 6y agoYou should submit your website as its own on HN :)
- plancien 6y agoI'm very impressed, this made my day (my month ?). Too bad your site lacks some nice video demos on the front page. To other HN readers, look what I found in it's tutorial : https://www.youtube.com/watch?v=dkvB4nb8PXw https://www.youtube.com/watch?v=dkvB4nb8PXw
- koeng 6y agoSmall part of the picture is an exaggeration, IMO. Cellular electrical dynamics matter, but we already know that surface physics matter (see: any mammalian lab with those flat little red bottles). Those dynamics (physical, electrical, chemical) are all derived from genes coded in DNA, and so long as you have the basic ribosomes / mitochondrial structures, you can re-instantiate an entire organism from just the DNA.
- TaupeRanger 6y agoDNA is certainly necessary and integral, but not at all sufficient for a full scientific understanding. Just like quantum mechanics is to rocket science. The heavy focus on genetics has hindered our understanding until very recently IMO.
- koeng 6y ago> hindered our understanding until very recently IMO Any specific examples of how it hindered our understanding? Like maybe some grants or something? Because as a synthetic biologist, I've never seen a heavy emphasis on genetics take away from other causes of cellular dynamics - in fact, exactly the opposite, because genetic engineering has allowed tinkering of those cellular dynamics (for example, cardio tissue surface physics). I don't know of any serious biologist that (even historically) disregarded the importance of other physical factors in favor of DNA, but I would love to know compelling counter examples.
- abandonliberty 6y agoRather than "small part of the picture", you would get less disagreement with something like "beginning of the story." I doubt many people would agree that computer hardware is a small part of the picture of modern computation. They're the foundations that everything else is built on, and with.
- kaba0 6y agoDNA can’t bootstrap itself, so to say. So previous cell-functionality is required for everything, so you can only re-instantiate an entire organism if you have a denucleated pluripotent cell from an evolutionary close enough organism. (But correct me if I’m wrong)
- abledon 6y agohave you read "Spark in the Machine"? Its an attempt to connect bioelectric science with ancient notions of 'chi', it goes over neural crest cells, organization centers for cell growth, and the electrosensitive pericardium cage near the heart. They definitely didn't get 100% of it right, buts its quite uncanny how the ancient texts were so accurate at predicting certain things that are only becoming evident in morphogensis research.
- sriku 6y agoLink to talk - https://www.youtube.com/watch?v=HwtOZ_WfMw0 https://www.youtube.com/watch?v=HwtOZ_WfMw0 - in which my mind was blown.