5 ms·

The trend of discovering biological purposes for what were once termed 'junk' DNA (which these RNA are transcribed from) continues. In addition to the improved

The trend of discovering biological purposes for what were once termed 'junk' DNA (which these RNA are transcribed from) continues. In addition to the improved understanding of our physical nature, it will be exciting to see what applications are developed for targeting or tricking-out these novel cellular components for pharmaceutical and biotechnological purposes. They are sure to be significant, if our experience with the RNA tech employed in the modeRNA and Pfizer vaccines are any indication. Personally, as someone who finished his biochemistry degree 2 decades ago (and has mostly worked on the software side of things since), I'm excited for what we'll be able to do with fuller understanding of this molecular machinery, and plan to pivot back into biotech over the next decade.

UncleOxidant 5y ago
It seems that we find more and more 'junk' DNA to not be junk. Whoever was quick to label it 'junk DNA' did so in haste. It would have been a lot more humble to label it 'DNA of unknown function'.
- 1cvmask 5y ago
  Well we did rename swamps to wetlands.
  - J5892 5y ago
    A swamp is a type of wetland. They weren't renamed.
    - thaumasiotes 5y ago
      Well, there is supposedly a distinction between swamps (which are dominated by trees), marshes (which are dominated by grass) and bogs (which have a pH differing from 7). This is already kind of a weird classification scheme, since the trait that defines a bog is so wildly different from the trait that defines swamps and marshes. And then, if you believe in this scheme, "wetlands" is the generic term referring to all of them. But 1cvmask is actually correct that the generic term was (and still is, outside of specialized scientific terminology) "swamp", and pushing the approach of my earlier paragraph constitutes a renaming.
      - mc32 5y ago
        Where does muskeg fit in all of this? Also salt marshes which while they may have grasses, are different ecosystems.
        sdenton4 5y ago
        Sometimes a riparian estuary is just a riparian estuary... Let's call a fen a fen and be done with it... Would not a bayou by any other name be as mucky?
- uplifter 5y ago
  You made me curious and some quick duckduckgo-ing led me to a biologists involved-if-not-comprehensive investigation of the origins of the term [0]. Long story short, it probably dates to late 1950s Cambridge and may have originated with Francis Crick, co-discoverer of the structure of DNA. Of relevance is that it preceded the discovery of mRNA, dating to a time when all RNA was thought to be ribosomal DNA. At that time the prevailing theory was that DNA codes for RNA that is incorporated into the ribosome (which then makes proteins). Because the amount of RNA code in the ribosome was clearly much less than the amount of DNA code in the genome, the implication was that much of the genome did not code anything, simply as a matter of mathematical difference. The term was controversial early on, and it might even have been coined to be so, though that's less clear. [0] https://judgestarling.tumblr.com/post/667709690372849664/the-origin-of-the-term-junk-dna-a-scientific https://judgestarling.tumblr.com/post/667709690372849664/the...
- smegsicle 5y ago
  "dark dna"
  - m3kw9 5y ago
    If most dna were junk
- bigodbiel 5y ago
  IIRC it was in jest, and then taken as "serious" by mainstream audience, like "god paricle" or "al gore invented the internet".
  - msla 5y ago
    > "al gore invented the internet" This is politics: If you can claim the Other Guy said something stupid, you can score points against the Other Side.
    - refurb 5y ago
      I mean Al Gore did say something stupid. I don't think he intended it to come across the way it did, but he did say it.
      - pklausler 5y ago
        “ During my service in the United States Congress, I took the initiative in creating the Internet. I took the initiative in moving forward a whole range of initiatives that have proven to be important to our country’s economic growth and environmental protection, improvements in our educational system.” That’s what he said. It was not stupid or inaccurate.
        refurb 5y ago
        "I took the initiative in creating the Internet" That's stupid and inaccurate. It infers the internet would not exist without his efforts. That's clearly not true. If he had said "I took the initiative to drive development of the internet" then sure. But "creating" it? No.
- questiondev 5y ago
  you are right about this, i think HN posted an article on “junk” dna not being “junk” dna after all. this was about a month ago, it may have been on news.google.com if it was not on here, having read science breakthrough stuff throughout the years i was never convinced of that term and was more than cautious when tech subs started talking about how crispr alters “junk” dna, the general consensus before the pandemic was, “this is cool, but we must be careful, this technology may cause unexpected side effects” but during the pandemic or the peak of it, people were like “canon ball”, all caution to the wind. or seemed like caution was thrown to the wind. it’s surprising how fast we adopted this technology but we still gotta question if there is gonna be long term issues. there’s nothing wrong with questioning science, that’s actually what science is about.
- kzuberi 5y ago
  While new discoveries of biological function are fascinating, I don't think it follows that we are overturning the idea of junk DNA (however the phrase was coined). More likely we are converging towards an understanding where most of the genome really is non-functional. Here's a recent accounting [1] of known function suggesting 90% is junk. I wonder how much this differs from our understanding of decades ago, it really may not have changed much at least in terms of broad accounting. Now the potential significance of those little fractional bits of recently uncovered function, well that's a different discussion and more aligned with the original article, which I don't think mentioned junk anyway. [1] https://sandwalk.blogspot.com/2021/11/whats-in-your-genome-2021.html https://sandwalk.blogspot.com/2021/11/whats-in-your-genome-2...
ampdepolymerase 5y ago
Molecular biology education needs more funding. Teaching it at scale (and more importantly, communicating new discoveries outside of textbooks) still remains a challenge. Keeping up with the field without reading papers is much harder compared to CS/ML where almost every ML engineer maintains a blog.
shigawire 5y ago
I'm in a similar situation but a decade removed. I'm not sure I even remember what I learned previously - how have you retained anything after 2 decades?
- uplifter 5y ago
  I try to read journal papers every now and then, usually when investigating the source of some news story, or when digging down into the molecular details of a personal health interest. Somewhat contrary to the theme of TFA, I've found that my 20 year old training has provided good mileage in terms of understanding current research. Much of the overarching theory of molecular biology hasn't changed in that time, and a lot of the same techniques are still used, if often miniaturized and scaled, e.g. microarray methods for things I learned to do using blots. For when I find a gap in my knowledge, modern literature search tech facilitates digging down to find related papers that describe newer theories or ones that describe new methods. Often I'll find references to review papers which are essentially designed to get one up to speed on a topic. If anything papers are easier to access now than back when I was in university, wink wink. Oh, and there are definitely quite a few bored biochemists contributing serious detail to select wikipedia articles. With grain of salt in hand, I've found some pretty high quality descriptions (in terms of detail and ease of understanding) of molecular pathways peppered throughout articles on various topics, which can serve as decent starting points for diving into the literature on those topics. I'm a far cry from considering myself current on the latest research, but I feel not too far behind and that I can catch up quickly when needed.

UncleOxidant 5y ago

It seems that we find more and more 'junk' DNA to not be junk. Whoever was quick to label it 'junk DNA' did so in haste. It would have been a lot more humble to label it 'DNA of unknown function'.

1cvmask 5y ago
Well we did rename swamps to wetlands.
- J5892 5y ago
  A swamp is a type of wetland. They weren't renamed.
  - thaumasiotes 5y ago
    Well, there is supposedly a distinction between swamps (which are dominated by trees), marshes (which are dominated by grass) and bogs (which have a pH differing from 7). This is already kind of a weird classification scheme, since the trait that defines a bog is so wildly different from the trait that defines swamps and marshes. And then, if you believe in this scheme, "wetlands" is the generic term referring to all of them. But 1cvmask is actually correct that the generic term was (and still is, outside of specialized scientific terminology) "swamp", and pushing the approach of my earlier paragraph constitutes a renaming.
    - mc32 5y ago
      Where does muskeg fit in all of this? Also salt marshes which while they may have grasses, are different ecosystems.
      - sdenton4 5y ago
        Sometimes a riparian estuary is just a riparian estuary... Let's call a fen a fen and be done with it... Would not a bayou by any other name be as mucky?
uplifter 5y ago
You made me curious and some quick duckduckgo-ing led me to a biologists involved-if-not-comprehensive investigation of the origins of the term [0]. Long story short, it probably dates to late 1950s Cambridge and may have originated with Francis Crick, co-discoverer of the structure of DNA. Of relevance is that it preceded the discovery of mRNA, dating to a time when all RNA was thought to be ribosomal DNA. At that time the prevailing theory was that DNA codes for RNA that is incorporated into the ribosome (which then makes proteins). Because the amount of RNA code in the ribosome was clearly much less than the amount of DNA code in the genome, the implication was that much of the genome did not code anything, simply as a matter of mathematical difference. The term was controversial early on, and it might even have been coined to be so, though that's less clear. [0] https://judgestarling.tumblr.com/post/667709690372849664/the-origin-of-the-term-junk-dna-a-scientific https://judgestarling.tumblr.com/post/667709690372849664/the...
smegsicle 5y ago
"dark dna"
- m3kw9 5y ago
  If most dna were junk
bigodbiel 5y ago
IIRC it was in jest, and then taken as "serious" by mainstream audience, like "god paricle" or "al gore invented the internet".
- msla 5y ago
  > "al gore invented the internet" This is politics: If you can claim the Other Guy said something stupid, you can score points against the Other Side.
  - refurb 5y ago
    I mean Al Gore did say something stupid. I don't think he intended it to come across the way it did, but he did say it.
    - pklausler 5y ago
      “ During my service in the United States Congress, I took the initiative in creating the Internet. I took the initiative in moving forward a whole range of initiatives that have proven to be important to our country’s economic growth and environmental protection, improvements in our educational system.” That’s what he said. It was not stupid or inaccurate.
      - refurb 5y ago
        "I took the initiative in creating the Internet" That's stupid and inaccurate. It infers the internet would not exist without his efforts. That's clearly not true. If he had said "I took the initiative to drive development of the internet" then sure. But "creating" it? No.
questiondev 5y ago
you are right about this, i think HN posted an article on “junk” dna not being “junk” dna after all. this was about a month ago, it may have been on news.google.com if it was not on here, having read science breakthrough stuff throughout the years i was never convinced of that term and was more than cautious when tech subs started talking about how crispr alters “junk” dna, the general consensus before the pandemic was, “this is cool, but we must be careful, this technology may cause unexpected side effects” but during the pandemic or the peak of it, people were like “canon ball”, all caution to the wind. or seemed like caution was thrown to the wind. it’s surprising how fast we adopted this technology but we still gotta question if there is gonna be long term issues. there’s nothing wrong with questioning science, that’s actually what science is about.
kzuberi 5y ago
While new discoveries of biological function are fascinating, I don't think it follows that we are overturning the idea of junk DNA (however the phrase was coined). More likely we are converging towards an understanding where most of the genome really is non-functional. Here's a recent accounting [1] of known function suggesting 90% is junk. I wonder how much this differs from our understanding of decades ago, it really may not have changed much at least in terms of broad accounting. Now the potential significance of those little fractional bits of recently uncovered function, well that's a different discussion and more aligned with the original article, which I don't think mentioned junk anyway. [1] https://sandwalk.blogspot.com/2021/11/whats-in-your-genome-2021.html https://sandwalk.blogspot.com/2021/11/whats-in-your-genome-2...

ampdepolymerase 5y ago

Molecular biology education needs more funding. Teaching it at scale (and more importantly, communicating new discoveries outside of textbooks) still remains a challenge. Keeping up with the field without reading papers is much harder compared to CS/ML where almost every ML engineer maintains a blog.

shigawire 5y ago

I'm in a similar situation but a decade removed. I'm not sure I even remember what I learned previously - how have you retained anything after 2 decades?

uplifter 5y ago
I try to read journal papers every now and then, usually when investigating the source of some news story, or when digging down into the molecular details of a personal health interest. Somewhat contrary to the theme of TFA, I've found that my 20 year old training has provided good mileage in terms of understanding current research. Much of the overarching theory of molecular biology hasn't changed in that time, and a lot of the same techniques are still used, if often miniaturized and scaled, e.g. microarray methods for things I learned to do using blots. For when I find a gap in my knowledge, modern literature search tech facilitates digging down to find related papers that describe newer theories or ones that describe new methods. Often I'll find references to review papers which are essentially designed to get one up to speed on a topic. If anything papers are easier to access now than back when I was in university, wink wink. Oh, and there are definitely quite a few bored biochemists contributing serious detail to select wikipedia articles. With grain of salt in hand, I've found some pretty high quality descriptions (in terms of detail and ease of understanding) of molecular pathways peppered throughout articles on various topics, which can serve as decent starting points for diving into the literature on those topics. I'm a far cry from considering myself current on the latest research, but I feel not too far behind and that I can catch up quickly when needed.