4 ms·

I find genome sequences fascinating, life's binary code has only 4 opcodes, a, c, g and t. I wonder if any computer VM will ever be able to actually fully run i

I find genome sequences fascinating, life's binary code has only 4 opcodes, a, c, g and t. I wonder if any computer VM will ever be able to actually fully run it. Still, the massively parallel capacity needed to run it "realtime" is not quite here just yet.

TomMarius 7y ago
I'm not sure I would call a/c/g/t the opcodes, I deem them to be the equivalents of 0 and 1. Opcodes could probably be some proteins?
- deleted 7y ago
  [deleted]
- maze-le 7y ago
  Or probably the genes and proteins are the actual execution of the opcodes in this analogy.
- samatman 7y ago
  Codons are close enough to opcodes to share an etymology. There are other 'opcodes' such as the initiation factor, but codons are the main ones.
dddddaviddddd 7y ago
There's also lots of information at other layers, e.g. epigenetics, that is difficult to capture and adds additional complexity to interpreting a genome, in addition to elaborate post-processing and other aspects of the 'compiler'.
- teshier-A 7y ago
  The 'compiler' is also built from DNA. The amount of epigenetics inheritance is subject to debate AFAIK. In the end look at what's being passed on to carry the information through generations. It's (almost) just the DNA !
deleted 7y ago
[deleted]
gilbetron 7y ago
The genomic machinery is incredible complex and messy. Imagine some code, that is interpreted by little machines not created by that code, that then create other machines, that read that code in a different way, to create other machines, that copy that code, which is then read by other machines, etc, etc. These "machines" are chunks of molecules that require quantum mechanics to fully understand, and also tend to have a lot of issues with them. As an example of the weirdness, look at motor proteins: https://www.youtube.com/watch?v=9RUHJhskW00 https://www.youtube.com/watch?v=9RUHJhskW00 It's amazing how utterly mad it all is, and yet not only does it work, our simple models of how it works have actually been helpful even though they were wrong. I mean, it's not like there's actually a single value in your DNA that is looked up by some "eyeball creation" machine when it determines the color of your eyes. Rather, there's a whole slew of genes that, when used as a map to build proteins and then, over a cascade of complex reactions, ends up with an eyeball that is also blue (and, additionally, probably more light sensitive, more tolerant to alcohol, and also more likely to have alcohol use disorder) Source: work for genomenon.com which is like a search engine for genetic research papers)
- wlesieutre 7y ago
  I like this xkcd on the subject: https://xkcd.com/1605/ https://xkcd.com/1605/
graycat 7y ago
Yes, amazing stuff: (1) If we have a rock, can we expect slowly by small modifications to make it into a hammer? (2) If we have a horse, can we expect slowly by small modifications to make it into a Model T? (3) ... a mechanical adding machine into an iPhone? (4) ... a log cabin into the Empire State Building? (5) ... a pocket knife into a computer numerically controlled milling machine? (6) ... any software from the earliest operating system or simplest application into to all the software we have now? Especially for software, we believe that lots of little modifications will lead to technical debt, need for refactoring, to throwing out and starting over with a clean sheet of paper, to "plan to throw one away because you will anyway". In software, often it seems that there is no reasonable way to get from here to there and, instead, have to start over. Well, with DNA, on this planet apparently the first version of life able to reproduce at all significantly was based on DNA, and all versions of life since then, including us, have also been based on DNA. Moreover we got here by small modifications of the DNA. So, maybe the point is, DNA is not really life but just a design for a life, not a species but just a design for one. And we do believe that easily enough we could go to an architect and building engineer with standard tools for generating blue prints and doing the engineering for buildings, and they could use the same tools for a log cabin or a floating city. Okay, but for life there hasn't been any design means, hasn't been any alternatives, other than just DNA. Moreover, the simplest design tools for life have also been sufficient for the life to understand the design tools, life, the earth, and the universe. Moreover, we are about the first, one of the first graduating classes of life that understands DNA, life, ..., and the universe: It's been about 14 billion years since the big bang, and our solar system was made about 5 billion years ago from the results of exploding stars that grew and exploded in the first 9 billion years which is not much longer than it took for the first stars to form and explode. So, apparently to get life able to understand the universe had to take about 14 billion years from the big bang and we are among the first instances of such life. YMMV, but looks amazing to me! Hmm ....
- tigershark 7y ago
  > Well, with DNA, on this planet apparently the first version of life able to reproduce at all significantly was based on DNA, and all versions of life since then, including us, have also been based on DNA. Moreover we got here by small modifications of the DNA. Are you sure? I remember that life started as RNA not DNA.
pp19dd 7y ago
In no way can this explain any of the complexity of life, but, I found the DNA walk graphs very fascinating to look at anyway. You assign a direction to each letter (a=up, c=down, g=left, t=right) and plot pixels in a sequence. For example: https://academic.oup.com/view-large/figure/139941708/bty1021f1.tif https://academic.oup.com/view-large/figure/139941708/bty1021... There was also a partly functioning interactive at http://www.g-language.org/g3/ http://www.g-language.org/g3/ (click on DNA walk tab) and zoom in.
panda88888 7y ago
The code is simple, but the runtime is incredibly complex and every implementation is slightly different ;)
nostrademons 7y ago
Gene sequences are easy. Methylation, expression, and protein folding are hard. You can sequence a human genome with a single computer in a day or two; sequencing generates about 30G of data. By contrast, protein folding has its own distributed crowdsourcing project (Folding@Home), with collected computational power of 98.7 petaflops, and it still has barely scratched the surface of our understanding for how specific proteins generate their biological effects.

TomMarius 7y ago

I'm not sure I would call a/c/g/t the opcodes, I deem them to be the equivalents of 0 and 1. Opcodes could probably be some proteins?

deleted 7y ago
[deleted]
maze-le 7y ago
Or probably the genes and proteins are the actual execution of the opcodes in this analogy.
samatman 7y ago
Codons are close enough to opcodes to share an etymology. There are other 'opcodes' such as the initiation factor, but codons are the main ones.

dddddaviddddd 7y ago

There's also lots of information at other layers, e.g. epigenetics, that is difficult to capture and adds additional complexity to interpreting a genome, in addition to elaborate post-processing and other aspects of the 'compiler'.

teshier-A 7y ago
The 'compiler' is also built from DNA. The amount of epigenetics inheritance is subject to debate AFAIK. In the end look at what's being passed on to carry the information through generations. It's (almost) just the DNA !

deleted 7y ago

[deleted]

gilbetron 7y ago

The genomic machinery is incredible complex and messy. Imagine some code, that is interpreted by little machines not created by that code, that then create other machines, that read that code in a different way, to create other machines, that copy that code, which is then read by other machines, etc, etc. These "machines" are chunks of molecules that require quantum mechanics to fully understand, and also tend to have a lot of issues with them. As an example of the weirdness, look at motor proteins: https://www.youtube.com/watch?v=9RUHJhskW00 https://www.youtube.com/watch?v=9RUHJhskW00 It's amazing how utterly mad it all is, and yet not only does it work, our simple models of how it works have actually been helpful even though they were wrong. I mean, it's not like there's actually a single value in your DNA that is looked up by some "eyeball creation" machine when it determines the color of your eyes. Rather, there's a whole slew of genes that, when used as a map to build proteins and then, over a cascade of complex reactions, ends up with an eyeball that is also blue (and, additionally, probably more light sensitive, more tolerant to alcohol, and also more likely to have alcohol use disorder) Source: work for genomenon.com which is like a search engine for genetic research papers)

wlesieutre 7y ago
I like this xkcd on the subject: https://xkcd.com/1605/ https://xkcd.com/1605/

graycat 7y ago

Yes, amazing stuff: (1) If we have a rock, can we expect slowly by small modifications to make it into a hammer? (2) If we have a horse, can we expect slowly by small modifications to make it into a Model T? (3) ... a mechanical adding machine into an iPhone? (4) ... a log cabin into the Empire State Building? (5) ... a pocket knife into a computer numerically controlled milling machine? (6) ... any software from the earliest operating system or simplest application into to all the software we have now? Especially for software, we believe that lots of little modifications will lead to technical debt, need for refactoring, to throwing out and starting over with a clean sheet of paper, to "plan to throw one away because you will anyway". In software, often it seems that there is no reasonable way to get from here to there and, instead, have to start over. Well, with DNA, on this planet apparently the first version of life able to reproduce at all significantly was based on DNA, and all versions of life since then, including us, have also been based on DNA. Moreover we got here by small modifications of the DNA. So, maybe the point is, DNA is not really life but just a design for a life, not a species but just a design for one. And we do believe that easily enough we could go to an architect and building engineer with standard tools for generating blue prints and doing the engineering for buildings, and they could use the same tools for a log cabin or a floating city. Okay, but for life there hasn't been any design means, hasn't been any alternatives, other than just DNA. Moreover, the simplest design tools for life have also been sufficient for the life to understand the design tools, life, the earth, and the universe. Moreover, we are about the first, one of the first graduating classes of life that understands DNA, life, ..., and the universe: It's been about 14 billion years since the big bang, and our solar system was made about 5 billion years ago from the results of exploding stars that grew and exploded in the first 9 billion years which is not much longer than it took for the first stars to form and explode. So, apparently to get life able to understand the universe had to take about 14 billion years from the big bang and we are among the first instances of such life. YMMV, but looks amazing to me! Hmm ....

tigershark 7y ago
> Well, with DNA, on this planet apparently the first version of life able to reproduce at all significantly was based on DNA, and all versions of life since then, including us, have also been based on DNA. Moreover we got here by small modifications of the DNA. Are you sure? I remember that life started as RNA not DNA.

pp19dd 7y ago

In no way can this explain any of the complexity of life, but, I found the DNA walk graphs very fascinating to look at anyway. You assign a direction to each letter (a=up, c=down, g=left, t=right) and plot pixels in a sequence. For example: https://academic.oup.com/view-large/figure/139941708/bty1021f1.tif https://academic.oup.com/view-large/figure/139941708/bty1021... There was also a partly functioning interactive at http://www.g-language.org/g3/ http://www.g-language.org/g3/ (click on DNA walk tab) and zoom in.

panda88888 7y ago

The code is simple, but the runtime is incredibly complex and every implementation is slightly different ;)

nostrademons 7y ago

Gene sequences are easy. Methylation, expression, and protein folding are hard. You can sequence a human genome with a single computer in a day or two; sequencing generates about 30G of data. By contrast, protein folding has its own distributed crowdsourcing project (Folding@Home), with collected computational power of 98.7 petaflops, and it still has barely scratched the surface of our understanding for how specific proteins generate their biological effects.