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This is a pet peeve of mine - the common misconceptions that "junk DNA" is just DNA with an unknown function. By far most junk DNA really is junk. We know this

This is a pet peeve of mine - the common misconceptions that "junk DNA" is just DNA with an unknown function. By far most junk DNA really is junk. We know this because we know its nonfunctional origin (transposons, pseudogenes and similar), because we can do studies of conservation between species, and because there is a huge range of junk DNA content in otherwise similar species. The misconception come from media bias: You'll never hear a story about "junk DNA really is junk, researchers find"

vbezhenar 4y ago
Does it mean that mutations in the junk DNA are evenly distributed among the population because supposedly they don’t affect anything?
Fubwubs 4y ago
Transposons and pseudogenes may be nonfunctional for an individual organism, but aren't they useful for evolution to create new genes? Wikipedia suggests some usefulness: "While some TEs confer benefits on their hosts, most are regarded as selfish DNA parasites" (https://en.wikipedia.org/wiki/Transposable_element#Evolution https://en.wikipedia.org/wiki/Transposable_element#Evolution) "Pseudogene sequences may be transcribed into RNA at low levels, due to promoter elements inherited from the ancestral gene or arising by new mutations. Although most of these transcripts will have no more functional significance than chance transcripts from other parts of the genome, some have given rise to beneficial regulatory RNAs and new proteins." (https://en.wikipedia.org/wiki/Pseudogene https://en.wikipedia.org/wiki/Pseudogene) I would define truly junk DNA as any DNA that if removed would be beneficial or not harmful to the majority of organisms in a species, and be beneficial or not harmful to the ability of a species to adapt and evolve its genome.
- xg15 4y ago
  > Transposons and pseudogenes may be nonfunctional for an individual organism, but aren't they useful for evolution to create new genes? Ok, but by that definition, nothing is really junk: Even our own junkyards are still home to all sorts of animals and microorganisms which feed on the junk. Not even starting with the recycling/upcycling movement. Doesn't change the fact that it's junk in the sense of its original purpose and immediate utility to us. In the same way, if junk DNA really has no effect on the body it's currently part of (like freed but uncleared memory in RAM), then I think the name is appropriate. What I'm really missing in popular reporting about genetics though is more focus on the "regulatory elements". The understanding of DNA as given by pop-science articles is mostly that DNA is either instructions for building proteins or "junk", nothing else. This completely leaves out the question how the cell decides when/if a particular protein should be built - which is of course integral for understanding how a number of protein building instructions can result in a complex organism. It's like describing a programming language as consisting only of instructions and comments but completely leaving out branches and loops. (even though gene regulation does not happen through branches and loops)

vbezhenar 4y ago

Does it mean that mutations in the junk DNA are evenly distributed among the population because supposedly they don’t affect anything?

Fubwubs 4y ago

Transposons and pseudogenes may be nonfunctional for an individual organism, but aren't they useful for evolution to create new genes? Wikipedia suggests some usefulness: "While some TEs confer benefits on their hosts, most are regarded as selfish DNA parasites" (https://en.wikipedia.org/wiki/Transposable_element#Evolution https://en.wikipedia.org/wiki/Transposable_element#Evolution) "Pseudogene sequences may be transcribed into RNA at low levels, due to promoter elements inherited from the ancestral gene or arising by new mutations. Although most of these transcripts will have no more functional significance than chance transcripts from other parts of the genome, some have given rise to beneficial regulatory RNAs and new proteins." (https://en.wikipedia.org/wiki/Pseudogene https://en.wikipedia.org/wiki/Pseudogene) I would define truly junk DNA as any DNA that if removed would be beneficial or not harmful to the majority of organisms in a species, and be beneficial or not harmful to the ability of a species to adapt and evolve its genome.

xg15 4y ago
> Transposons and pseudogenes may be nonfunctional for an individual organism, but aren't they useful for evolution to create new genes? Ok, but by that definition, nothing is really junk: Even our own junkyards are still home to all sorts of animals and microorganisms which feed on the junk. Not even starting with the recycling/upcycling movement. Doesn't change the fact that it's junk in the sense of its original purpose and immediate utility to us. In the same way, if junk DNA really has no effect on the body it's currently part of (like freed but uncleared memory in RAM), then I think the name is appropriate. What I'm really missing in popular reporting about genetics though is more focus on the "regulatory elements". The understanding of DNA as given by pop-science articles is mostly that DNA is either instructions for building proteins or "junk", nothing else. This completely leaves out the question how the cell decides when/if a particular protein should be built - which is of course integral for understanding how a number of protein building instructions can result in a complex organism. It's like describing a programming language as consisting only of instructions and comments but completely leaving out branches and loops. (even though gene regulation does not happen through branches and loops)