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I remember several years ago reading about "junk DNA" or "useless DNA" in sequences. Even then, I was certain that it probably wasn't "junk", we were just yet t

I remember several years ago reading about "junk DNA" or "useless DNA" in sequences. Even then, I was certain that it probably wasn't "junk", we were just yet to understand it. I wish we'd take that attitude a bit more with science journalism. "It doesn't make sense..... YET".

andai 4y ago
We need a few more copies of this gene before we can recognize all the patterns ;)
- VeninVidiaVicii 4y ago
  Hello, ChatGPT
User23 4y ago
That was born of the widely held metaphysical position that evolution is purposeless. Given that assumption one would expect to find plenty of “junk” DNA.
- Geezus-42 4y ago
  I don't think that follows as well as you think. If the primary goal is survival based primarily on efficient use of energy. A lot of evolution is about organisms becoming more efficient by adapting to their environment. So then keeping unnecessary junk around is inefficient and we would expect orgasms that lose to would benefit and out breed the others.
  - User23 4y ago
    Having our optic nerve run right through our retina producing a blind spot in order to capture an upside down and backwards image is pretty inefficient too. Evolution doesn't maximize efficiency, it maximizes good-enough-to-reproduce-ity.
  - alpaca128 4y ago
    Better adapted organisms are just that - better. Not perfect, or free of inefficiencies. And even a perfectly adapted organism might not be as good at adapting to changes in the very long term compared to one with "junk" DNA. Also, does unused junk in the DNA really hurt energy efficiency?
- deleted 4y ago
  [deleted]
dekhn 4y ago
There are parts that are almost certainly not under functional selection and provide no benefit whatsoever- with Alu sequences being the best candidate. Even in tthe case of Alu, they do seem to have some vague effect on regulation of transcription... although they're not what we would call "genes" or "regulatory regions". In other cases, there are just lots and lots of duplicates of the same genes over and over. Other parts appear to be forges of gene creation- either through gene duplication and divergent evolution, or through some other mysterious mechanism we don't know yet. Certainly, we've had parts that looked like they were nothing at all and ended up being very important, and other parts that looked like they were incredibly important, but were really just the side effect of some effective parasite. It's sort of not even an interesting debate any more, as most of the initial positions everybody held were changed when we interrogated more, and better data.
- gaboot 4y ago
  There are also fairly strict limits, given human mutation and reproductive rates, on the amount of information that can be preserved in the genome. Most of the genome is therefore meaningless (although not necessarily useless). As this article points out, these regions allow for random creation of novel proteins
- jl6 4y ago
  Even for the “no benefit whatsoever” parts, is it not possible that they influence (and are possibly crucial to) the rest of the system just by providing spacing between other more-apparently-functional parts? I’m thinking by analogy of executable programs that have runs of zeros. The zeros don’t necessarily do anything, but remove them and everything else is out of alignment.
  - dekhn 4y ago
    I am open to the idea that "boring duplicated regions" performance some vague function through spacing. Some folks have proposed doing experiments where the spacers are removed, or replaced with other sequences, but they are extremely hard experiments to properly do (in a way that convinces the field). We already know that enhancers "work at a distance" and it's not clear what "distance" exactly means, and it gets into complicated 3D structure of the genome inside a cell; see https://en.wikipedia.org/wiki/Enhancer_(genetics) https://en.wikipedia.org/wiki/Enhancer_(genetics) Personally I think that the best way to think about the genome is to unlearn most of the preconceptions you learned in genetics and instead think about it in terms of biophysics and development and machine learning: you'll never realyl be able to understand the true function of every little bit, but you cvan probably create an approximate model that explains the vast majority of biology with relatively few variables, and some deep models that contain all the necessary statistics to model these systems accurately.
taneq 4y ago
"Junk DNA" brought to you by the same geniuses that brought you "we only use 10% of our brain cells" and "the heart is where the spirit resides, the brain is just useless grey goo."
- seydor 4y ago
  Those two are not of the same league
nathias 4y ago
people just need to understand that useless can become useful and vice versa
retrac 4y ago
I'm not sure where I encountered this hypothesis but I find it compelling. As noted by many, junk DNA, acquired from viruses and mutations and genome shuffling, is quite a puzzle. Why does it persist? It takes energy to copy, and misreading it can cause fatal or maladaptive mutations. From that perspective, it shouldn't persist (with slowly accumulating drift) for billions of years, as some shared junk sequences have across species. But it does. Obviously, because it isn't junk; it is of value to the organism. Even if it's not of any use right now, even if it's completely biologically inactive at present. Because it is still extremely high entropy information. They're remnants of solutions other living systems once used, at some point, to solve the problem of staying alive. If I were going to try and exploit genetic mutation to produce novel solutions to biological problems, I would start from an existing genome. In fact, I'd start with as much data, from as many organisms, as I could get my hands on and store. Perhaps we carry junk DNA because mutations in existing coded sequences, even mutated, currently useless ones, are far more likely to be functional, and so potentially a useful adaptation, than literal randomness. It's life's portfolio of solutions, badly photocopied little snippets accumulated over the years, and we all carry it around for future generations that might live in an environment where it's useful.
- yAak 4y ago
  I feel like me keeping copies of all the code I've ever written is a awkwardly good analogy here.
  - lowdose 4y ago
    Git commitments to your autocomplete library?
- tedunangst 4y ago
  We should also consider that simply copying everything, even the junk, leads to fewer errors than selectively trying to identify only the good parts.
  - systems_glitch 4y ago
jeremiep 4y ago
Read "The Structure of Scientific Revolutions" recently, science ignoring what it does not understand is far from a new phenomenon. Science is fantastic to dig into areas it can already see, and terrible at seeing new areas from the greater unknown.
- aeonik 4y ago
  We studied "The History of Science in Society" by Andrew Ede and Lesley Cormack, which left a big impression on me. ISBN-13: 978-1442634992, ISBN-10: 1442634995
kzuberi 4y ago
For folks interested in understanding the subject of junk DNA a bit better, there's an upcoming book [1] that might be worth checking out. The authors blog seems also to be interesting on this and related subjects. [1] https://utorontopress.com/9781487508593/whats-in-your-genome/ https://utorontopress.com/9781487508593/whats-in-your-genome...
vbezhenar 4y ago
Junk DNA is a junk DNA. It's not used in any way. We understand it.
- svnt 4y ago
  This is entirely untrue.
deleted 4y ago
[deleted]
bell-cot 4y ago
Junk DNA, or near-junk DNA (active in theory, but with minimal effects) both: - Is extremely difficult to remove, at a worthwhile scale, from the genome of any large & long-lived organism - Can be thought of as a huge pile of tickets for the Extremely Favorable Random Mutation lottery
- folex 4y ago
  pile of tickets is a very nice metaphor
rockinghigh 4y ago
Non-coding sequences have been understood as having some functions at least since the early 1990s. Because genome expression is dynamic, tracking the exact mechanisms of action of these sequences is challenging.

andai 4y ago

We need a few more copies of this gene before we can recognize all the patterns ;)

VeninVidiaVicii 4y ago
Hello, ChatGPT

User23 4y ago

That was born of the widely held metaphysical position that evolution is purposeless. Given that assumption one would expect to find plenty of “junk” DNA.

Geezus-42 4y ago
I don't think that follows as well as you think. If the primary goal is survival based primarily on efficient use of energy. A lot of evolution is about organisms becoming more efficient by adapting to their environment. So then keeping unnecessary junk around is inefficient and we would expect orgasms that lose to would benefit and out breed the others.
- User23 4y ago
  Having our optic nerve run right through our retina producing a blind spot in order to capture an upside down and backwards image is pretty inefficient too. Evolution doesn't maximize efficiency, it maximizes good-enough-to-reproduce-ity.
- alpaca128 4y ago
  Better adapted organisms are just that - better. Not perfect, or free of inefficiencies. And even a perfectly adapted organism might not be as good at adapting to changes in the very long term compared to one with "junk" DNA. Also, does unused junk in the DNA really hurt energy efficiency?
deleted 4y ago
[deleted]

dekhn 4y ago

There are parts that are almost certainly not under functional selection and provide no benefit whatsoever- with Alu sequences being the best candidate. Even in tthe case of Alu, they do seem to have some vague effect on regulation of transcription... although they're not what we would call "genes" or "regulatory regions". In other cases, there are just lots and lots of duplicates of the same genes over and over. Other parts appear to be forges of gene creation- either through gene duplication and divergent evolution, or through some other mysterious mechanism we don't know yet. Certainly, we've had parts that looked like they were nothing at all and ended up being very important, and other parts that looked like they were incredibly important, but were really just the side effect of some effective parasite. It's sort of not even an interesting debate any more, as most of the initial positions everybody held were changed when we interrogated more, and better data.

gaboot 4y ago
There are also fairly strict limits, given human mutation and reproductive rates, on the amount of information that can be preserved in the genome. Most of the genome is therefore meaningless (although not necessarily useless). As this article points out, these regions allow for random creation of novel proteins
jl6 4y ago
Even for the “no benefit whatsoever” parts, is it not possible that they influence (and are possibly crucial to) the rest of the system just by providing spacing between other more-apparently-functional parts? I’m thinking by analogy of executable programs that have runs of zeros. The zeros don’t necessarily do anything, but remove them and everything else is out of alignment.
- dekhn 4y ago
  I am open to the idea that "boring duplicated regions" performance some vague function through spacing. Some folks have proposed doing experiments where the spacers are removed, or replaced with other sequences, but they are extremely hard experiments to properly do (in a way that convinces the field). We already know that enhancers "work at a distance" and it's not clear what "distance" exactly means, and it gets into complicated 3D structure of the genome inside a cell; see https://en.wikipedia.org/wiki/Enhancer_(genetics) https://en.wikipedia.org/wiki/Enhancer_(genetics) Personally I think that the best way to think about the genome is to unlearn most of the preconceptions you learned in genetics and instead think about it in terms of biophysics and development and machine learning: you'll never realyl be able to understand the true function of every little bit, but you cvan probably create an approximate model that explains the vast majority of biology with relatively few variables, and some deep models that contain all the necessary statistics to model these systems accurately.

taneq 4y ago

"Junk DNA" brought to you by the same geniuses that brought you "we only use 10% of our brain cells" and "the heart is where the spirit resides, the brain is just useless grey goo."

seydor 4y ago
Those two are not of the same league

nathias 4y ago

people just need to understand that useless can become useful and vice versa

retrac 4y ago

I'm not sure where I encountered this hypothesis but I find it compelling. As noted by many, junk DNA, acquired from viruses and mutations and genome shuffling, is quite a puzzle. Why does it persist? It takes energy to copy, and misreading it can cause fatal or maladaptive mutations. From that perspective, it shouldn't persist (with slowly accumulating drift) for billions of years, as some shared junk sequences have across species. But it does. Obviously, because it isn't junk; it is of value to the organism. Even if it's not of any use right now, even if it's completely biologically inactive at present. Because it is still extremely high entropy information. They're remnants of solutions other living systems once used, at some point, to solve the problem of staying alive. If I were going to try and exploit genetic mutation to produce novel solutions to biological problems, I would start from an existing genome. In fact, I'd start with as much data, from as many organisms, as I could get my hands on and store. Perhaps we carry junk DNA because mutations in existing coded sequences, even mutated, currently useless ones, are far more likely to be functional, and so potentially a useful adaptation, than literal randomness. It's life's portfolio of solutions, badly photocopied little snippets accumulated over the years, and we all carry it around for future generations that might live in an environment where it's useful.

yAak 4y ago
I feel like me keeping copies of all the code I've ever written is a awkwardly good analogy here.
- lowdose 4y ago
  Git commitments to your autocomplete library?
tedunangst 4y ago
We should also consider that simply copying everything, even the junk, leads to fewer errors than selectively trying to identify only the good parts.
- systems_glitch 4y ago

jeremiep 4y ago

Read "The Structure of Scientific Revolutions" recently, science ignoring what it does not understand is far from a new phenomenon. Science is fantastic to dig into areas it can already see, and terrible at seeing new areas from the greater unknown.

aeonik 4y ago
We studied "The History of Science in Society" by Andrew Ede and Lesley Cormack, which left a big impression on me. ISBN-13: 978-1442634992, ISBN-10: 1442634995

kzuberi 4y ago

For folks interested in understanding the subject of junk DNA a bit better, there's an upcoming book [1] that might be worth checking out. The authors blog seems also to be interesting on this and related subjects. [1] https://utorontopress.com/9781487508593/whats-in-your-genome/ https://utorontopress.com/9781487508593/whats-in-your-genome...

vbezhenar 4y ago

Junk DNA is a junk DNA. It's not used in any way. We understand it.

svnt 4y ago
This is entirely untrue.

deleted 4y ago

[deleted]

bell-cot 4y ago

Junk DNA, or near-junk DNA (active in theory, but with minimal effects) both: - Is extremely difficult to remove, at a worthwhile scale, from the genome of any large & long-lived organism - Can be thought of as a huge pile of tickets for the Extremely Favorable Random Mutation lottery

folex 4y ago
pile of tickets is a very nice metaphor

rockinghigh 4y ago

Non-coding sequences have been understood as having some functions at least since the early 1990s. Because genome expression is dynamic, tracking the exact mechanisms of action of these sequences is challenging.