5 ms·

I've always thought of DNA as mere "data". "This goes here, that goes there", etc. And I've always wondered how such a relatively small amount of data could des

by _bxg1 7y ago

I've always thought of DNA as mere "data". "This goes here, that goes there", etc. And I've always wondered how such a relatively small amount of data could describe the massive complexity of a full-size organism. But this makes it sound like DNA is data the way Lisp is data: it can contain procedures and transformations and meta-statements about itself, and even mutate during the course of being interpreted. That would explain so much. The use of the term "virus" in software seems to be more apt than I'd thought.

freepor 7y ago
You’ve got half of it, but the other half is the existence of the cell to interpret the data. The DNA is like a Lisp program, but how much good would a Lisp program be without a computer to run it?
- UncleOxidant 7y ago
  But in this case the program also creates the computer it runs on.
  - mjg59 7y ago
    You can't bootstrap a cell from DNA - you need a functioning cell to start with. There's a lot of semantic data that's embodied in the existing set of proteins and other functional elements, and I don't think it's clear that the DNA of any moderately complex organism actually expresses that state.
    - c22 7y ago
      You can't bootstrap a self-hosting compiler from a language you just made up either. You'll need to first write a compiler in another language then use it to compile the compiler you wrote in your new language. I think the compiler/program dichotomy is a more apt metaphor for cells and dna than the computer/program one.
      - TeMPOraL 7y ago
        See https://news.ycombinator.com/item?id=22515015 https://news.ycombinator.com/item?id=22515015, in particular the "Reflections on Trusting Trust". You can bootstrap your target language from almost nothing by incrementally compiling more complex compilers, and all the intermediary complexity is stored in the compiler, not in the source code of the language you're trying to bootstrap. Notably, life did proceed like this - incrementally, from the first replicator. (Another way to look at it: a piece of code, be it DNA or a program written in a programming language, is just a bunch of symbols. You can't divine what these symbols mean from looking at the piece of code alone; you have to understand the mechanics of your compiler and your runtime. And these can evolve separately to the code you're looking at.)
    - deleted 7y ago
      [deleted]
  - Relys 7y ago
    With a very complex CPU architecture and ISA (chemistry, laws of physics, protein folding, etc).
3pt14159 7y ago
I had a thought the other day. It's theoretically possible for a computer virus to lead to a biological virus. Corrupting the data of a computer responsible for manufacturing a vaccine, for example.
- taylorfinley 7y ago
  Or the converse of this, malicious DNA has been used to exploit sequencing computers. (https://dnasec.cs.washington.edu/ https://dnasec.cs.washington.edu/) I swear I heard Mikki Hypponen talk of a self-replicating version of this that exploited the sequencers to encode the exploit into other sequenced DNA, making this self-replicating, but I can't find a link.
  - mattkrause 7y ago
    The DNA-based attack was a little contrived. They deliberately introduced a vulnerability into a post-processing tool, then generated a DNA sequence that abused it. It’s a creative idea but it would be fairly difficult find and use exploits in the wild. Sequencing has gotten a lot cheaper but it’s still going to cost tens-to-thousands of dollars per attempt, so you can’t do the genomic equivalent of packet stuffing on the cheap. (Nevertheless, it is true that a lot of biology-related code is not great but...)
- bionhoward 7y ago
  Since protein folding is “solved,” you can make pathogen proteins with wildly different DNA to fool algorithms used to identify bioweapons. No bueno because baddies can order nasty germs printed cheap! There are no bug bounties for bio bugs
inimino 7y ago
> how such a relatively small amount of data could describe the massive complexity of a full-size organism The busy beaver numbers are an interesting connection here. https://en.m.wikipedia.org/wiki/Busy_beaver https://en.m.wikipedia.org/wiki/Busy_beaver
Ericson2314 7y ago
Modern cells are something first order like Harvard architecture. Crisper or RNA organisms you could maybe call von Neumann architecture. (rRNA actually containing vestigal tRNA and many coding sequences containing vestigial rRNA is very interesting.)
dehrmann 7y ago
> I've always wondered how such a relatively small amount of data could describe the massive complexity of a full-size organism I'm not convinced it fully does. Remember that DNA is never in isolation; there's always a cell that's been replicated and passed down to offspring, so there's interplay between the hardware cell and software DNA. I also don't know much about biology and only took a high school class, so don't read into this beyond it being an idea.
- shijie 7y ago
  I think what you’re describing here is called “epigenetics,” or how different genes are expressed or not expressed due to environmental and other outside factors such as stress, etc...
  - rolph 7y ago
    the big deal about epigenetics is that those [methylation and histone binding] are modifications that dont alter the sequence of the DNA but are also inherited by subsequent generations. https://www.thieme-connect.de/products/ejournals/abstract/10.1055/s-0029-1237423 https://www.thieme-connect.de/products/ejournals/abstract/10... https://sci-hub.se/10.1038/542406a https://sci-hub.se/10.1038/542406a
  - ryankemper 7y ago
    For those that aren't familiar, this principle is known as gene expression: https://en.wikipedia.org/wiki/Gene_expression https://en.wikipedia.org/wiki/Gene_expression To make an analogy to software, a common pattern is to have a monolithic repo with many different "personalities" (codepaths / configurations) that utilize different subsets of the monolith. DNA seems to work under a similar principle, a given cell will preferentially transcribe parts of the DNA based on epigenetic factors.
  - enchiridion 7y ago
    Maybe in a way. I think they are driving at an orthogonal argument. The DNA is more or less useless without cells. It seems like the machinery of the cell carries information about the whole of the organism in an abstract sense.
swiley 7y ago
You should read some of the genetic computing papers (I think the one on computing paths on a graph was posted here the other week.). My understanding is that DNA oligimers can interact with each other directly and perform what are essentially string operations. Like most systems that can perform string operations on themselves this appears to be capable of universal computation.
refurb 7y ago
Yes, there are several layers of complexity that go beyond just the genetic sequence of a given gene. The sequence of the DNA also impacts thing like folding of DNA which impacts expression. And the intermediaries between the DNA and the protein (RNA), can also interact with the DNA itself to promote or retard expression. It’s incredibly complex really.
- neuronic 7y ago
  And I suspect that CRISPR and other tools will be far harder to use than expected by many, especially laymen. Simply due to the combinatorics involved when exchanging sequences in DNA, for example introduced by resulting new epigenetic dynamics.
  - refurb 7y ago
    Agreed! Seems like most of the focus has been on correcting single nucleotide errors. That’s more straightforward than trying to insert a new gene.
    - bionhoward 7y ago
      you could add a new loop of DNA with a new gene, without an update to existing code. That might be easier than changing one letter Append only immutable biotech
pergadad 7y ago
Just in case this is not known, human generic code is more than just DNA. Most important parts of what encodes us are: - DNA - epigenetic markers on the DNA which modulate which parts of the DNA are active. You influence these and pass them on to your children (as men) and grandchildren (as women, as girls are born with all egg cells they'll ever have) - cell organelles which copy the DNA, ensure the cell has food and lives, etc. These tend to be independent cells that were at some point captured by our own cells. So they have their own genetic code. These you only inherit from your mother (dad gives half the DNA with epigenetic markers, mom the other half (also with markers) and everything else. And of course much of what we are is shaped through gestation as well, I.e. the mother's body sends not just nutrients but also hormones etc that regulate gestation (and vice versa the child sends various messages to mom, up to even own cells in case of serious illness or accident or the mother). Fascinating stuff.
- thaumasiotes 7y ago
  > independent cells that were at some point captured by our own cells It makes a little more sense to think of them as "domesticated" rather than "captured".
  - JulianMorrison 7y ago
    Domesticated and implanted, unable to survive outside the host, we're talking full H.R. Giger here.
- loufe 7y ago
  I found the egg claim interesting so I gave it a quick search: looks like there may be cases where these eggs can be replaced (https://www.nationalgeographic.com/news/2012/3/120229-women-health-ovaries-eggs-reproduction-science/ https://www.nationalgeographic.com/news/2012/3/120229-women-...) but your claim does generally hold true. Wow! It gave me a weird feeling thinking that men would be procreating directly in a sense with their partner's mother.
- taneq 7y ago
  DNA isn’t data, or even code. DNA is a machine that builds things.
agumonkey 7y ago
also genes are influenced by a ton of context ecm, womb. if dna is code i'm still looking for eval semantics
hinkley 7y ago
My read on the situation is that the analogy for computer viruses holds if, in the process of getting and removing the virus, it creates lots of little memory leaks. They don’t kill you, rarely do they help you, the rest of the time they are just a very subtle drag on an important resource. At some point when we understand these systems much much better, we might go so far as to try to surgically remove them, but we can’t be absolutely sure there are no consequences. Turns out the rebooting (ie children) fixes the problem sometimes, but nowhere near all the time.
xg15 7y ago
> I've always thought of DNA as mere "data". "This goes here, that goes there", etc. And I've always wondered how such a relatively small amount of data could describe the massive complexity of a full-size organism. I believe this is the wrong way to think about this. From what I understand, DNA (plus epigenetics, etc) is more like a firmware that encodes the behaviour of a single cell. ("If this happens, build that protein"). Out of trillions of cells, each following its respective copy of that "program", plus all the interactions between the cells, plus physics and plus effects from the environment, a complex organism emerges. So, the complexity of the organism is the result of what is encoded in the DNA, but the DNA does not directly store it.
dreamcompiler 7y ago
Yes, DNA is a programming language and ribosomes are the interpreter.

by _bxg1 7y ago

freepor 7y ago

You’ve got half of it, but the other half is the existence of the cell to interpret the data. The DNA is like a Lisp program, but how much good would a Lisp program be without a computer to run it?

UncleOxidant 7y ago
But in this case the program also creates the computer it runs on.
- mjg59 7y ago
  You can't bootstrap a cell from DNA - you need a functioning cell to start with. There's a lot of semantic data that's embodied in the existing set of proteins and other functional elements, and I don't think it's clear that the DNA of any moderately complex organism actually expresses that state.
  - c22 7y ago
    You can't bootstrap a self-hosting compiler from a language you just made up either. You'll need to first write a compiler in another language then use it to compile the compiler you wrote in your new language. I think the compiler/program dichotomy is a more apt metaphor for cells and dna than the computer/program one.
    - TeMPOraL 7y ago
      See https://news.ycombinator.com/item?id=22515015 https://news.ycombinator.com/item?id=22515015, in particular the "Reflections on Trusting Trust". You can bootstrap your target language from almost nothing by incrementally compiling more complex compilers, and all the intermediary complexity is stored in the compiler, not in the source code of the language you're trying to bootstrap. Notably, life did proceed like this - incrementally, from the first replicator. (Another way to look at it: a piece of code, be it DNA or a program written in a programming language, is just a bunch of symbols. You can't divine what these symbols mean from looking at the piece of code alone; you have to understand the mechanics of your compiler and your runtime. And these can evolve separately to the code you're looking at.)
  - deleted 7y ago
    [deleted]
- Relys 7y ago
  With a very complex CPU architecture and ISA (chemistry, laws of physics, protein folding, etc).

3pt14159 7y ago

I had a thought the other day. It's theoretically possible for a computer virus to lead to a biological virus. Corrupting the data of a computer responsible for manufacturing a vaccine, for example.

taylorfinley 7y ago
Or the converse of this, malicious DNA has been used to exploit sequencing computers. (https://dnasec.cs.washington.edu/ https://dnasec.cs.washington.edu/) I swear I heard Mikki Hypponen talk of a self-replicating version of this that exploited the sequencers to encode the exploit into other sequenced DNA, making this self-replicating, but I can't find a link.
- mattkrause 7y ago
  The DNA-based attack was a little contrived. They deliberately introduced a vulnerability into a post-processing tool, then generated a DNA sequence that abused it. It’s a creative idea but it would be fairly difficult find and use exploits in the wild. Sequencing has gotten a lot cheaper but it’s still going to cost tens-to-thousands of dollars per attempt, so you can’t do the genomic equivalent of packet stuffing on the cheap. (Nevertheless, it is true that a lot of biology-related code is not great but...)
bionhoward 7y ago
Since protein folding is “solved,” you can make pathogen proteins with wildly different DNA to fool algorithms used to identify bioweapons. No bueno because baddies can order nasty germs printed cheap! There are no bug bounties for bio bugs

inimino 7y ago

> how such a relatively small amount of data could describe the massive complexity of a full-size organism The busy beaver numbers are an interesting connection here. https://en.m.wikipedia.org/wiki/Busy_beaver https://en.m.wikipedia.org/wiki/Busy_beaver

Ericson2314 7y ago

Modern cells are something first order like Harvard architecture. Crisper or RNA organisms you could maybe call von Neumann architecture. (rRNA actually containing vestigal tRNA and many coding sequences containing vestigial rRNA is very interesting.)

dehrmann 7y ago

> I've always wondered how such a relatively small amount of data could describe the massive complexity of a full-size organism I'm not convinced it fully does. Remember that DNA is never in isolation; there's always a cell that's been replicated and passed down to offspring, so there's interplay between the hardware cell and software DNA. I also don't know much about biology and only took a high school class, so don't read into this beyond it being an idea.

shijie 7y ago
I think what you’re describing here is called “epigenetics,” or how different genes are expressed or not expressed due to environmental and other outside factors such as stress, etc...
- rolph 7y ago
  the big deal about epigenetics is that those [methylation and histone binding] are modifications that dont alter the sequence of the DNA but are also inherited by subsequent generations. https://www.thieme-connect.de/products/ejournals/abstract/10.1055/s-0029-1237423 https://www.thieme-connect.de/products/ejournals/abstract/10... https://sci-hub.se/10.1038/542406a https://sci-hub.se/10.1038/542406a
- ryankemper 7y ago
  For those that aren't familiar, this principle is known as gene expression: https://en.wikipedia.org/wiki/Gene_expression https://en.wikipedia.org/wiki/Gene_expression To make an analogy to software, a common pattern is to have a monolithic repo with many different "personalities" (codepaths / configurations) that utilize different subsets of the monolith. DNA seems to work under a similar principle, a given cell will preferentially transcribe parts of the DNA based on epigenetic factors.
- enchiridion 7y ago
  Maybe in a way. I think they are driving at an orthogonal argument. The DNA is more or less useless without cells. It seems like the machinery of the cell carries information about the whole of the organism in an abstract sense.

swiley 7y ago

You should read some of the genetic computing papers (I think the one on computing paths on a graph was posted here the other week.). My understanding is that DNA oligimers can interact with each other directly and perform what are essentially string operations. Like most systems that can perform string operations on themselves this appears to be capable of universal computation.

refurb 7y ago

Yes, there are several layers of complexity that go beyond just the genetic sequence of a given gene. The sequence of the DNA also impacts thing like folding of DNA which impacts expression. And the intermediaries between the DNA and the protein (RNA), can also interact with the DNA itself to promote or retard expression. It’s incredibly complex really.

neuronic 7y ago
And I suspect that CRISPR and other tools will be far harder to use than expected by many, especially laymen. Simply due to the combinatorics involved when exchanging sequences in DNA, for example introduced by resulting new epigenetic dynamics.
- refurb 7y ago
  Agreed! Seems like most of the focus has been on correcting single nucleotide errors. That’s more straightforward than trying to insert a new gene.
  - bionhoward 7y ago
    you could add a new loop of DNA with a new gene, without an update to existing code. That might be easier than changing one letter Append only immutable biotech

pergadad 7y ago

Just in case this is not known, human generic code is more than just DNA. Most important parts of what encodes us are: - DNA - epigenetic markers on the DNA which modulate which parts of the DNA are active. You influence these and pass them on to your children (as men) and grandchildren (as women, as girls are born with all egg cells they'll ever have) - cell organelles which copy the DNA, ensure the cell has food and lives, etc. These tend to be independent cells that were at some point captured by our own cells. So they have their own genetic code. These you only inherit from your mother (dad gives half the DNA with epigenetic markers, mom the other half (also with markers) and everything else. And of course much of what we are is shaped through gestation as well, I.e. the mother's body sends not just nutrients but also hormones etc that regulate gestation (and vice versa the child sends various messages to mom, up to even own cells in case of serious illness or accident or the mother). Fascinating stuff.

thaumasiotes 7y ago
> independent cells that were at some point captured by our own cells It makes a little more sense to think of them as "domesticated" rather than "captured".
- JulianMorrison 7y ago
  Domesticated and implanted, unable to survive outside the host, we're talking full H.R. Giger here.
loufe 7y ago
I found the egg claim interesting so I gave it a quick search: looks like there may be cases where these eggs can be replaced (https://www.nationalgeographic.com/news/2012/3/120229-women-health-ovaries-eggs-reproduction-science/ https://www.nationalgeographic.com/news/2012/3/120229-women-...) but your claim does generally hold true. Wow! It gave me a weird feeling thinking that men would be procreating directly in a sense with their partner's mother.
taneq 7y ago
DNA isn’t data, or even code. DNA is a machine that builds things.

agumonkey 7y ago

also genes are influenced by a ton of context ecm, womb. if dna is code i'm still looking for eval semantics

hinkley 7y ago

My read on the situation is that the analogy for computer viruses holds if, in the process of getting and removing the virus, it creates lots of little memory leaks. They don’t kill you, rarely do they help you, the rest of the time they are just a very subtle drag on an important resource. At some point when we understand these systems much much better, we might go so far as to try to surgically remove them, but we can’t be absolutely sure there are no consequences. Turns out the rebooting (ie children) fixes the problem sometimes, but nowhere near all the time.

xg15 7y ago

> I've always thought of DNA as mere "data". "This goes here, that goes there", etc. And I've always wondered how such a relatively small amount of data could describe the massive complexity of a full-size organism. I believe this is the wrong way to think about this. From what I understand, DNA (plus epigenetics, etc) is more like a firmware that encodes the behaviour of a single cell. ("If this happens, build that protein"). Out of trillions of cells, each following its respective copy of that "program", plus all the interactions between the cells, plus physics and plus effects from the environment, a complex organism emerges. So, the complexity of the organism is the result of what is encoded in the DNA, but the DNA does not directly store it.

dreamcompiler 7y ago

Yes, DNA is a programming language and ribosomes are the interpreter.