how much information is *outside* of the genome? e.g. does the developmental code live in the genome, or does the embryo have behaviour that is not reducible to genes ?
"DNA is a “blueprint” for a cell. But information is needed to interpret that blueprint. Imagine a machine that could take in a DNA sequence and build a human cell. How many bits would be needed to describe that machine? A lot, right?
Of course, there’s a recursive “chicken and the egg” issue here: The machines that actually make human cells from DNA are… other human cells. But you need some information to get the loop started!"
I guess it depends on your reference.. the zygote obviously has everything it needs. The information or potential is...somewhere. “embodied information” as you say. But an external observer trying to define the full information content of that program - across development, physiology, etc.. they would need to capture basically every activity and state of every cell/tissue/organ at every time point through development? feel like it could be OOM beyond however many bytes we say are in DNA
do you thnk it will be possible for software to simulate development just from genome + perfect simulation of zygote ?
I certainly agree that if you're thinking about an adult human, information comes from everywhere. But I think it's reasonable to think about how much of that comes from (A) DNA in the gametes, (B) the physical structure of the gametes, and (C) everything else. So I guess the "phenotypic Kolmogorov complexity" would only be looking at category A, category B seems hard, and category C seems REALLY hard?
Pretty informative! This reminds me of a paper entitled : "The Genomic Code: The genome instantiates a generative model of the organism".
They argue that the genome is a latent representation of an organisms. Conceptually similar to this compressed view of DNA. Interestingly, some stretch of "useless" DNA could be there for structural regulation (TADs, LADs, etc).
If you take (say) lungfish DNA, they have much more repetitive elements / jumping genes than humans. The exact cause of this seems to be unclear. But the impact in terms of information is that while they have more "storage space", I doubt they actually have more "information". That is, I speculate that you could theoretically engineer DNA to create a lungfish-like organism with vastly smaller DNA.
how much information is *outside* of the genome? e.g. does the developmental code live in the genome, or does the embryo have behaviour that is not reducible to genes ?
I believe it's substantial!
"DNA is a “blueprint” for a cell. But information is needed to interpret that blueprint. Imagine a machine that could take in a DNA sequence and build a human cell. How many bits would be needed to describe that machine? A lot, right?
Of course, there’s a recursive “chicken and the egg” issue here: The machines that actually make human cells from DNA are… other human cells. But you need some information to get the loop started!"
(Although I have no idea how to quantify it.)
https://dynomight.net/data-wall/#its-not-just-dna
I guess it depends on your reference.. the zygote obviously has everything it needs. The information or potential is...somewhere. “embodied information” as you say. But an external observer trying to define the full information content of that program - across development, physiology, etc.. they would need to capture basically every activity and state of every cell/tissue/organ at every time point through development? feel like it could be OOM beyond however many bytes we say are in DNA
do you thnk it will be possible for software to simulate development just from genome + perfect simulation of zygote ?
I certainly agree that if you're thinking about an adult human, information comes from everywhere. But I think it's reasonable to think about how much of that comes from (A) DNA in the gametes, (B) the physical structure of the gametes, and (C) everything else. So I guess the "phenotypic Kolmogorov complexity" would only be looking at category A, category B seems hard, and category C seems REALLY hard?
If only someone had written a book about that subject. We wouldn't have to guess so much. A book like this one perhaps. https://press.princeton.edu/books/paperback/9780691241142/the-evolution-of-biological-information
Pretty informative! This reminds me of a paper entitled : "The Genomic Code: The genome instantiates a generative model of the organism".
They argue that the genome is a latent representation of an organisms. Conceptually similar to this compressed view of DNA. Interestingly, some stretch of "useless" DNA could be there for structural regulation (TADs, LADs, etc).
I think some simple organisms have much more DNA than humans. Any idea why that is and how that fits with your information estimates?
If you take (say) lungfish DNA, they have much more repetitive elements / jumping genes than humans. The exact cause of this seems to be unclear. But the impact in terms of information is that while they have more "storage space", I doubt they actually have more "information". That is, I speculate that you could theoretically engineer DNA to create a lungfish-like organism with vastly smaller DNA.
Nice, tightly compressed bit of information here.