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Paragraph 4: “Slowly, slowly, slowly, the terminology of ‘junk DNA’ [has] started to die,” Rest of the article: continues to use the term "Junk DNA".

by rflrob 5y ago

hateful 5y ago
I think more than any other group, programmers can understand the gut reaction of calling code that they don't understand "junk".
- delecti 5y ago
  Normally it means "poor quality" though. I think "junk DNA" is more analogous to "dead code". Not all code labeled "dead" is actually unreachable/unused.
  - im3w1l 5y ago
    Well we do have "comments" that are actually interpreted by tooling.
f6v 5y ago
Everyone doing biology professionally already knows the non-coding DNA has function. It’s only logical since we know that resource-intensive mechanisms don’t survive the evolutionary pressure if there’s no benefit for them to exist. So it’d be wasteful to replicate 98% of DNA if it’s not functional. Keep in mind it’s not only replicated, there’s error-correction as well.
- dekhn 5y ago
  it's wasteful to replicate non-functional DNA, yet there are organisms whose genomes are 10X-100X larger than any others (literally ten copies of a genome), and they do just fine (https://en.wikipedia.org/wiki/Paris_japonica https://en.wikipedia.org/wiki/Paris_japonica). The cost of DNA replication isn't that strong a functional selection afaict.
  - taneq 5y ago
    Sounds like "non-functional DNA" might in fact have a function, hm?
    - dekhn 5y ago
      Probably not in the context of the example I gave; that's more likely to just be a totally random genome duplication which will eventually be functionally selected away.
    - thaumasiotes 5y ago
      Non-functional DNA is to all DNA as source code that doesn't call I/O is to all source code.
  - IncRnd 5y ago
    You're conflating the size of a genome with the amount of DNA that is non-functional.
    - dekhn 5y ago
      I'm not conflating anything. Those details are scientifically conflated (IE, they are functionally related) in a very interesting way. For exmaple, new genes probably arise from gene or genome duplications.
      - IncRnd 5y ago
        DNA that doesn't encode proteins is not necessarily non-functional.
        dekhn 5y ago
        Yes, I know that. It's unclear what aspects of those duplications are "functional but not coding for genes, enhancers, promotors, or other well-known and understood coding and regulator elements", and which are "functional because if you remove it the organism dies but we can't explain what the cause is". Everything in my terminology is entirely correct within the current mainstream understanding and it encapsulates much of the ongoing confusion about what "role" non-coding functional elements play, and how they play it. See http://cryptogenomicon.org/encode-says-what.html http://cryptogenomicon.org/encode-says-what.html and https://www.cell.com/current-biology/comments/S0960-9822(13)00289-3 https://www.cell.com/current-biology/comments/S0960-9822(13)... for the strongest arguments against ENCODE's more wide definition of functional elements, as well as https://www.pnas.org/content/110/14/5294 https://www.pnas.org/content/110/14/5294 and https://www.mun.ca/biology/scarr/MGA2_02-10.html https://www.mun.ca/biology/scarr/MGA2_02-10.html I am of the opinion that nearly everybody in this field is overly dogmatic in their views of how genomes work at the macro scale, and that these squabbles demonstrate that clearly. For more context, please understand that as a researcher in this field, much of what I say may not make sense to casual readers. I decided it's better to think about minimal organisms, than ones that have 500 copies of the ribosome (http://citeseerx.ist.psu.edu/viewdoc/download?rep=rep1&type=pdf&doi=10.1.1.209.118 http://citeseerx.ist.psu.edu/viewdoc/download?rep=rep1&type=...)
- otherme123 5y ago
  If the organism is pressured, the non-coding DNA slowly fades. There are some parasitic organisms (eg Nasuia deltocephalinicola) that have highly compacted DNA: no introns, no regulatory regions, no transposable elements and even overlapping genes.
taneq 5y ago
Introduction: Introduces term. Early text: Details evidence that term is misguided. Late text: Continues to use early term so as to provide a consistent interface to readers. Might use 'scare quotes' if term is particularly egregious but still conserves familiarity of terminology.
- burnished 5y ago
  What would you have them do instead? Naming stuff is hard. The authors get their point across quite nicely without also trying to coin more terminology.

Paragraph 4: “Slowly, slowly, slowly, the terminology of ‘junk DNA’ [has] started to die,” Rest of the article: continues to use the term "Junk DNA".

by rflrob 5y ago

Paragraph 4: “Slowly, slowly, slowly, the terminology of ‘junk DNA’ [has] started to die,” Rest of the article: continues to use the term "Junk DNA".

hateful 5y ago

I think more than any other group, programmers can understand the gut reaction of calling code that they don't understand "junk".

delecti 5y ago
Normally it means "poor quality" though. I think "junk DNA" is more analogous to "dead code". Not all code labeled "dead" is actually unreachable/unused.
- im3w1l 5y ago
  Well we do have "comments" that are actually interpreted by tooling.

f6v 5y ago

Everyone doing biology professionally already knows the non-coding DNA has function. It’s only logical since we know that resource-intensive mechanisms don’t survive the evolutionary pressure if there’s no benefit for them to exist. So it’d be wasteful to replicate 98% of DNA if it’s not functional. Keep in mind it’s not only replicated, there’s error-correction as well.

dekhn 5y ago
it's wasteful to replicate non-functional DNA, yet there are organisms whose genomes are 10X-100X larger than any others (literally ten copies of a genome), and they do just fine (https://en.wikipedia.org/wiki/Paris_japonica https://en.wikipedia.org/wiki/Paris_japonica). The cost of DNA replication isn't that strong a functional selection afaict.
- taneq 5y ago
  Sounds like "non-functional DNA" might in fact have a function, hm?
  - dekhn 5y ago
    Probably not in the context of the example I gave; that's more likely to just be a totally random genome duplication which will eventually be functionally selected away.
  - thaumasiotes 5y ago
    Non-functional DNA is to all DNA as source code that doesn't call I/O is to all source code.
- IncRnd 5y ago
  You're conflating the size of a genome with the amount of DNA that is non-functional.
  - dekhn 5y ago
    I'm not conflating anything. Those details are scientifically conflated (IE, they are functionally related) in a very interesting way. For exmaple, new genes probably arise from gene or genome duplications.
    - IncRnd 5y ago
      DNA that doesn't encode proteins is not necessarily non-functional.
      - dekhn 5y ago
        Yes, I know that. It's unclear what aspects of those duplications are "functional but not coding for genes, enhancers, promotors, or other well-known and understood coding and regulator elements", and which are "functional because if you remove it the organism dies but we can't explain what the cause is". Everything in my terminology is entirely correct within the current mainstream understanding and it encapsulates much of the ongoing confusion about what "role" non-coding functional elements play, and how they play it. See http://cryptogenomicon.org/encode-says-what.html http://cryptogenomicon.org/encode-says-what.html and https://www.cell.com/current-biology/comments/S0960-9822(13)00289-3 https://www.cell.com/current-biology/comments/S0960-9822(13)... for the strongest arguments against ENCODE's more wide definition of functional elements, as well as https://www.pnas.org/content/110/14/5294 https://www.pnas.org/content/110/14/5294 and https://www.mun.ca/biology/scarr/MGA2_02-10.html https://www.mun.ca/biology/scarr/MGA2_02-10.html I am of the opinion that nearly everybody in this field is overly dogmatic in their views of how genomes work at the macro scale, and that these squabbles demonstrate that clearly. For more context, please understand that as a researcher in this field, much of what I say may not make sense to casual readers. I decided it's better to think about minimal organisms, than ones that have 500 copies of the ribosome (http://citeseerx.ist.psu.edu/viewdoc/download?rep=rep1&type=pdf&doi=10.1.1.209.118 http://citeseerx.ist.psu.edu/viewdoc/download?rep=rep1&type=...)
otherme123 5y ago
If the organism is pressured, the non-coding DNA slowly fades. There are some parasitic organisms (eg Nasuia deltocephalinicola) that have highly compacted DNA: no introns, no regulatory regions, no transposable elements and even overlapping genes.

taneq 5y ago

Introduction: Introduces term. Early text: Details evidence that term is misguided. Late text: Continues to use early term so as to provide a consistent interface to readers. Might use 'scare quotes' if term is particularly egregious but still conserves familiarity of terminology.

burnished 5y ago
What would you have them do instead? Naming stuff is hard. The authors get their point across quite nicely without also trying to coin more terminology.