11 ms·

It's a slight exaggeration of the information content to report the data size using an ASCII encoding. Since there are 4 bases, each can be encoded using 2 bits

by cvoss 3y ago

It's a slight exaggeration of the information content to report the data size using an ASCII encoding. Since there are 4 bases, each can be encoded using 2 bits, rather than 8. So we're really talking 750 megabytes. But still mind-blowing.

khazhoux 3y ago
Yes, and if you gzip it it's even smaller. But the big takeaway is that the amount of info that fully defines a human, is what we consider "not much data," even in its plainest encoding.
- astrange 3y ago
  We don't know that it fully defines a human until we can create one without the starting condition of being inside another human. It's prototype-based inheritance.
  - hotnfresh 3y ago
    Some of the research about being able to make simple animals grow structures from other animals in their evolutionary “tree” by changing chemical signaling—among other wild things like finding that memories may be stored outside the brain, at least in some animals—makes me think you need more than just the “code” to get the animal that would have been produced if that “code” were in its full context (of a reproductive cell doing all sorts of other stuff). Even if the dna contains the instructions for that reproductive cell, too, in some sense… which instructions do you “run”? There might be multiple possible variants, some of which don’t actually reproduce the animal you took the dna from.
    - astrange 3y ago
      My favorite trivia here is that flamingos aren't actually "genetically" pink but "environmentally" pink because they pick up the color from eating algae. Except of course "genetics" and "environment" aren't actually separate things; sure, people's skin color isn't usually affected by their food, but only because most people don't eat colloidal silver. https://en.wikipedia.org/wiki/Paul_Karason https://en.wikipedia.org/wiki/Paul_Karason
      - hotnfresh 3y ago
        AFAIK most poisonous frogs also aren’t “naturally” poisonous—they get it from diet. Ones raised in captivity aren’t poisonous unless you go out of your way to feed them the things they need to become poisonous.
- dekhn 3y ago
  bzip2 is marginally better, and then genome-specific compressors were developed, and then finally, people started storing individual genomes as diffs from a single reference, https://en.wikipedia.org/wiki/CRAM_(file_format) https://en.wikipedia.org/wiki/CRAM_(file_format) Since genome files contain more data than just ATGC (typically a comment line, then a DNA line, then a quality score line), and each of those draws from a different distribution, DEFLATE on a FASTA file doesn't reach the full potential of the compressor because the huffman table ends up having to hold all three distributions, and the dictionary backlookups aren't as efficient either. It turns out you can split the file into multiple streams, one per line type, and then compress those independently, with slightly better compression ratios, but it's still not great.
borissk 3y ago
I'm curious if these 750MB + the DNA of mitochondria + the protein metagenomics contain all the information needed to build a human, or if there's extra info stored in the machinery of the first cell. That is if we transfer the DNA to an advanced alien civilization - would they be able to make a human.
- ejstronge 3y ago
  > That is if we transfer the DNA to an advanced alien civilization - would they be able to make a human. You'd need a cell to start the process, with the various nucleic acids distributed correctly and proteins/energy with which to create further proteins using the information encoded by the DNA. Thus the civilization would need information about cells and a set of building blocks before being able to use the DNA.
  - borissk 3y ago
    The DNA contains all the code that creates and regulates the proteins.
    - penteract 3y ago
      Including code for the proteins that read DNA to produce proteins. You might hit similar problems trying to understand C given the source code for a C compiler - a non-standard environment could reproduce itself given the source code, meaning the code alone doesn't strictly determine the output.
      - kibibyte 3y ago
        I'll torture this DNA and C source code analogy a bit. Epigenetics is missing in this discussion about reproducing a human from just the DNA. These are superficial modifications (e.g. methylation, histone modification, repressor factors) to a strand of DNA that can drastically alter how specific regions get expressed into proteins. These mechanisms essentially work by either hiding or unhiding DNA from RNA polymerases and other parts of the transcription complex. These mechanisms can change throughout your lifetime because of environmental factors and can be inherited. So it's like reading C source code, except there so many of these inscrutable C preprocessor directives strewn all throughout. You won't get a successful compilation by turning on or off all the directives. Instead, you need to get this similarly inscrutable configuration blob that tells you how to set each directive. I guess in a way, it's like the weights for an ML model. It just works, you can't explain why it works, and changing this weight here produces a program that crashes prematurely, and changing a weight there produces a program with allergic reactions to everything.
dekhn 3y ago
And since the data is highly redundant the 750MB can be compressed down even further using standard approaches (DEFLATE works well, it uses both huffman coding and dictionary backreferences). Or, you could build an embedding with far fewer parameters that could explain the vast majority of phenotypic differences. the genome is a hierarchical palimpsest of low entropy. My standard interview question- because I hate leetcode- walks the interviewee through compressing DNA using bit encoding, then using that to implement a rolling hash to do fast frequency counting. Some folks get stuck at "how many bits in a byte", others at "if you have 4 symbols, how many bits are required to encode a symbol?", and other candidates jump straight to bloom filters and other probabilistic approaches (https://github.com/bcgsc/ntHash https://github.com/bcgsc/ntHash and https://github.com/dib-lab/khmer https://github.com/dib-lab/khmer are good places to start if you are interested).
- deleted 3y ago
  [deleted]

by cvoss 3y ago

khazhoux 3y ago

Yes, and if you gzip it it's even smaller. But the big takeaway is that the amount of info that fully defines a human, is what we consider "not much data," even in its plainest encoding.

astrange 3y ago
We don't know that it fully defines a human until we can create one without the starting condition of being inside another human. It's prototype-based inheritance.
- hotnfresh 3y ago
  Some of the research about being able to make simple animals grow structures from other animals in their evolutionary “tree” by changing chemical signaling—among other wild things like finding that memories may be stored outside the brain, at least in some animals—makes me think you need more than just the “code” to get the animal that would have been produced if that “code” were in its full context (of a reproductive cell doing all sorts of other stuff). Even if the dna contains the instructions for that reproductive cell, too, in some sense… which instructions do you “run”? There might be multiple possible variants, some of which don’t actually reproduce the animal you took the dna from.
  - astrange 3y ago
    My favorite trivia here is that flamingos aren't actually "genetically" pink but "environmentally" pink because they pick up the color from eating algae. Except of course "genetics" and "environment" aren't actually separate things; sure, people's skin color isn't usually affected by their food, but only because most people don't eat colloidal silver. https://en.wikipedia.org/wiki/Paul_Karason https://en.wikipedia.org/wiki/Paul_Karason
    - hotnfresh 3y ago
      AFAIK most poisonous frogs also aren’t “naturally” poisonous—they get it from diet. Ones raised in captivity aren’t poisonous unless you go out of your way to feed them the things they need to become poisonous.
dekhn 3y ago
bzip2 is marginally better, and then genome-specific compressors were developed, and then finally, people started storing individual genomes as diffs from a single reference, https://en.wikipedia.org/wiki/CRAM_(file_format) https://en.wikipedia.org/wiki/CRAM_(file_format) Since genome files contain more data than just ATGC (typically a comment line, then a DNA line, then a quality score line), and each of those draws from a different distribution, DEFLATE on a FASTA file doesn't reach the full potential of the compressor because the huffman table ends up having to hold all three distributions, and the dictionary backlookups aren't as efficient either. It turns out you can split the file into multiple streams, one per line type, and then compress those independently, with slightly better compression ratios, but it's still not great.

borissk 3y ago

I'm curious if these 750MB + the DNA of mitochondria + the protein metagenomics contain all the information needed to build a human, or if there's extra info stored in the machinery of the first cell. That is if we transfer the DNA to an advanced alien civilization - would they be able to make a human.

ejstronge 3y ago
> That is if we transfer the DNA to an advanced alien civilization - would they be able to make a human. You'd need a cell to start the process, with the various nucleic acids distributed correctly and proteins/energy with which to create further proteins using the information encoded by the DNA. Thus the civilization would need information about cells and a set of building blocks before being able to use the DNA.
- borissk 3y ago
  The DNA contains all the code that creates and regulates the proteins.
  - penteract 3y ago
    Including code for the proteins that read DNA to produce proteins. You might hit similar problems trying to understand C given the source code for a C compiler - a non-standard environment could reproduce itself given the source code, meaning the code alone doesn't strictly determine the output.
    - kibibyte 3y ago
      I'll torture this DNA and C source code analogy a bit. Epigenetics is missing in this discussion about reproducing a human from just the DNA. These are superficial modifications (e.g. methylation, histone modification, repressor factors) to a strand of DNA that can drastically alter how specific regions get expressed into proteins. These mechanisms essentially work by either hiding or unhiding DNA from RNA polymerases and other parts of the transcription complex. These mechanisms can change throughout your lifetime because of environmental factors and can be inherited. So it's like reading C source code, except there so many of these inscrutable C preprocessor directives strewn all throughout. You won't get a successful compilation by turning on or off all the directives. Instead, you need to get this similarly inscrutable configuration blob that tells you how to set each directive. I guess in a way, it's like the weights for an ML model. It just works, you can't explain why it works, and changing this weight here produces a program that crashes prematurely, and changing a weight there produces a program with allergic reactions to everything.

dekhn 3y ago

And since the data is highly redundant the 750MB can be compressed down even further using standard approaches (DEFLATE works well, it uses both huffman coding and dictionary backreferences). Or, you could build an embedding with far fewer parameters that could explain the vast majority of phenotypic differences. the genome is a hierarchical palimpsest of low entropy. My standard interview question- because I hate leetcode- walks the interviewee through compressing DNA using bit encoding, then using that to implement a rolling hash to do fast frequency counting. Some folks get stuck at "how many bits in a byte", others at "if you have 4 symbols, how many bits are required to encode a symbol?", and other candidates jump straight to bloom filters and other probabilistic approaches (https://github.com/bcgsc/ntHash https://github.com/bcgsc/ntHash and https://github.com/dib-lab/khmer https://github.com/dib-lab/khmer are good places to start if you are interested).

deleted 3y ago
[deleted]