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.)
[1] https://www.the-scientist.com/features/how-groups-of-cells-c...
Neuronal Signaling and Sodium-Potassium Pump (from PDB-101)
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.
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.
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.
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[0] - https://www.cs.cmu.edu/~rdriley/487/papers/Thompson_1984_Ref...
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.
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.
Like the difference between a silicon microchip and just a silicon block. Same stuff, bit the microchip one has intricate patterns.
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!
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.
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.
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?"
Is this true, given https://en.wikipedia.org/wiki/Uncertainty_principle ?
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
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 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.
From something much simpler, and which has been iterating for approx 4 billion years.
Here's my best analogy: If you take one mole of "random" Rubik's Cubes (the number of molecules in a glass of water), then search for 'Solved' ones you'll find 512 are magically solved, merely by the power of large numbers. The ways molecules can 'snap together' are similarly 'finite', just like a puzzle.
Now think how many glasses of water are on earth. A replicating molecule would have existed probably on the FIRST DAY earth had cooled enough to form water.
If we knew what the shortest sequence if DNA is that can replicate, we'd be able to mathematically state the probability of it existing in any 'random' length of DNA of that length as 1/(4^N) where N is DNA length (number of AT/GC pairs).
Take it as 200 bases and you won't find another life in the observable universe. Avogadro's number is no match for exponential growth.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3943892/
"The present study describes the directed evolution of replicating RNA enzymes that operate with an exponential growth rate of 0.14 min−1, corresponding to a doubling time of 5 min. Each parental enzyme can give rise to thousands of copies per hour, and each of these copies in turn can do the same, all the while transmitting molecular information across the generations."
According to my math 10 million moles of random sequence 50-base pair RNA segments would be required to ensure a correct 'Hit' on a replicator, assuming only one of those 50-long sequences can replicate. 4^50=10^30. 10^30/Avogadro=10^7. Assuming each enzyme is the size of a water molecule, that would be about one large swimming pool of water.
In actual evolution this number of RNA molecules can be thought of as 'diluted' across the entire oceans, and not magically sitting in single pond.
But do you? If elements A and B tend to form compound A-B, and compound A-B can attach a further set of A and B, forming B-A-B-A which under certain circumstances will split into A-B and A-B, you have basic reproduction, and perhaps the occasional presence of element C will expedite the process. Game of life. In my [very] layman's view of the world, given a billion years or two, some such infinitely simple process should be enough to get the ball rolling, as long as it can somehow produce an ever so slightly errorprone copy.
To make an analogy, what you describe would be only the electronic chips or the logic gates of a computer. There are a still the CPU, RAM, and the whole software stack from the OS that runs our bodies (and mind you, there is a different one for each species) to the yet unknown abstractions from which human general intelligence emerges.
I think people underestimate how difficult it is for all the above to get started by accident.
For molecules that are a linear chain of only 2 possible items in the chain, it becomes a 'brute force search' of a 'puzzle space' to find a chain that 'does something like computer code', and the earth has the computing power to solve that brute force problem in 30 seconds, not 30 million years.
Nature is statistically guaranteed to find the simplest patterns first and that's why our life is built on 'binary' (two kinds of 'cards' AT/GC). Life on all planets will likely use binary "information storage", especially because of it's modularity (i.e. it can be cut-n-pasted together in different patterns)
And since life was presumably started with RNA, we are still talking about 4 base elems
However there's always at least one stickler who wants to quibble that the orientation is also a "binary bit" of information. Congratulations, you're him today!!
A code with a 4 letter alphabet would be 2 letter, if it happened to use a parity “bit” or other error correction info?
However there may be slightly more requirements like the sequence has to be found in an oil film (bubble) up until it can form a skin/membrane, to protect itself, so even if it was happening on earth trillions of times every day no one would be there to discover it, and other life on the planet with a head start (bacteria, etc) would consume it before it made more 'progress' by evolution.
In the early planet there was nothing to "eat up" life as it was starting. Everything was on an equal footing.
For example, if I understand this correctly, a random jumble of DNA as you describe would have a 50/50 chance of twisting to the right or twisting to the left. And yet all life on earth uses DNA that is "right handed" twisting to the right.
It's already experimentally proven you can mix up N, H, and O and it spontaneously forms RNA. We've even found entire RNA and sugars on meteorites. It's not rare in nature, it's abundant and self-emergent from the raw atoms themselves.
Now, either there were some naturally formed impermeable areas with an abundance of base material (yet again, I’m not saying life emerged because the UFOs created it), or we are talking about many orders of magnitude less statistical chances. I am willing to believe that many, not individually extraordinary thing had to happen at the same time, that made life possible - but that pretty much makes their combined presence extraordinary, which is my claim.
(Some form of underwater volcanic caves or whatever could sound like a possibility, especially because last I checked, starting sticked to a surface with certain catalytic activities is a plausible theory. Especially due to the reduced statistical chances due to a 2D surface instead of a 3D one! What I have a bit of trouble seeing, is how did organic materials form - I am aware of the famous experiment with lightning bolts that created ammonia and some other chemicals, but it would only slowly increase their uniform distribution in the oceans. Perhaps some chemical reaction with gases that made them accumulate? )
That's well known. It is the key driver for the global contraceptives market, which generated revenue of $28,175 million in 2015 and is estimated to reach $43,812 million by 2022.
We are familiar with downs syndrome, 3 rather than the intended 2 copies of chromosome 21, only because it's comparatively viable.
Software programming or biological programming ?
These things have the same names but they're not really comparable