The human genome is full of viruses • Hacker News Board

Re: The human genome is full of viruses

#11

Post by Ericson2314 » Sat, Mar 07, 2020, 7:36 PM UTC

_bxg1 wrote: post #3

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 wo…

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.)

Re: The human genome is full of viruses

#12

Post by mjg59 » Sat, Mar 07, 2020, 7:37 PM UTC

UncleOxidant wrote: post #10

freepor wrote: post #5

Earlier quoted context omitted.

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?

But in this case the program also creates the computer it runs on.

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.

Re: The human genome is full of viruses

#13

Post by superkuh » Sat, Mar 07, 2020, 7:39 PM UTC

Mammals could not and would not exist without the membrane fusion protein given to their ancestors by a retrovirus. This protein is essential for forming the multiple nucleus cells that make up the placenta.

Re: The human genome is full of viruses

#14

Post by dehrmann » Sat, Mar 07, 2020, 7:53 PM UTC

_bxg1 wrote: post #3

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 wo…

> 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.

Re: The human genome is full of viruses

#15

Post by shijie » Sat, Mar 07, 2020, 8:03 PM UTC

dehrmann wrote: post #14

_bxg1 wrote: post #3

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 wo…

> 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…

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...

Re: The human genome is full of viruses

#16

Post by swiley » Sat, Mar 07, 2020, 8:09 PM UTC

_bxg1 wrote: post #3

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 wo…

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.

Re: The human genome is full of viruses

#17

Post by rolph » Sat, Mar 07, 2020, 8:11 PM UTC

shijie wrote: post #15

dehrmann wrote: post #14

Earlier quoted context omitted.

> 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…

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...

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...

https://sci-hub.se/10.1038/542406a

Re: The human genome is full of viruses

#18

Post by Relys » Sat, Mar 07, 2020, 8:12 PM UTC

UncleOxidant wrote: post #10

freepor wrote: post #5

Earlier quoted context omitted.

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?

But in this case the program also creates the computer it runs on.

With a very complex CPU architecture and ISA (chemistry, laws of physics, protein folding, etc).

Re: The human genome is full of viruses

#19

Post by mattkrause » Sat, Mar 07, 2020, 8:20 PM UTC

taylorfinley wrote: post #9

3pt14159 wrote: post #6

Earlier quoted context omitted.

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.

Or the converse of this, malicious DNA has been used to exploit sequencing computers. ( 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.

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...)

Re: The human genome is full of viruses

#20

Post by ryankemper » Sat, Mar 07, 2020, 8:21 PM UTC

shijie wrote: post #15

dehrmann wrote: post #14

Earlier quoted context omitted.

> 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…

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...

For those that aren't familiar, this principle is known as 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.