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Comment by TaupeRanger | Hacker News Reader

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.

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During 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.)

You should submit your website as its own on HN :)

I'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

Excellent 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-c...

Totally. And kind of explains why some electrophoresis therapies may be working.

Not 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

This reminded me of a beautiful animation of "Mitochondria: the cell's powerhouse" which I recently watched.

https://www.youtube.com/watch?v=vkYEYjintqU

Small 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.

DNA 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.

> 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.

Rather 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.

DNA 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)

Link to talk - https://www.youtube.com/watch?v=HwtOZ_WfMw0 - in which my mind was blown.

https://en.wikipedia.org/wiki/Bioelectricity

Aren't those electrical field patterns still somehow encoded in the DNA?

Everything 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?"

> Everything is deterministic if you're omniscient

Is this true, given https://en.wikipedia.org/wiki/Uncertainty_principle ?

It 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

I'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.

They 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_Ref...

I 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.

A cell has a lot of atoms, which may store a lot of information?

But not error corrected like DNA.

Can single atom store more information than a bit?

Each electron present in one of the atom's orbitals is a bit, so yeah.

More realistically, the simplest atom- one proton, one electron- has 3 integer numbers associated with the state of the electron. You need more than a bit to describe the state of that system, so yeah.

DNA is made up of 4 main components (G,C,A and T). Very generally these encode instructions for making proteins.

Those blocks are very small, less than 20 Atoms.

https://en.m.wikipedia.org/wiki/Adenine

They’re working on using it for storage. (very slow read write times). Duplicating shouldn’t be a problem.

https://en.m.wikipedia.org/wiki/DNA_digital_data_storage

https://en.wikipedia.org/wiki/Tuatara

https://asunow.asu.edu/20200806-dragon-dna-sequencing-genome...

https://phys.org/news/2020-08-dinosaur-relative-genome-linke...

I really recommend Anton's segment on the Tuatara, https://www.youtube.com/watch?v=PWywZyzmBDE MindBlown!

The issue is you’re going to get massive mutations building up in anything that doesn’t have the significant error correcting capability of DNA. So while the coding is not direct, it still has to somehow be in DNA so that the trait will be conserved over the generations. Shorter term changes could conceivably be stored in other molecular structures, though. (Think patterns of methylation in epigenetics or even the fringe idea of RNA memory.)

I would suspect really basic things like replication would be stored somehow in DNA (nuclear DNA, mitochondrial DNA, etc) as they must be highly conserved and mutation resistant in order for organisms to survive and reproduce.

Computationally relevant information is sometimes embedded in runtime state (for example, yeast prions), but this is very rare. For small bacteria, you can switch out the entire genome with a new genome and have them continue living just fine. For all intents and purposes on an engineering level, everything is/can be encoded in DNA.

DNA 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.

Speculating 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".

have 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.

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