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Personally I think it's both naive and arrogant to assume that because something is called "junk DNA", that means that the scientific community as a whole have

by cyphar 7y ago

Personally I think it's both naive and arrogant to assume that because something is called "junk DNA", that means that the scientific community as a whole have decided to never consider whether it has any impact. There are all sorts of weird terms-of-art in science and I find it quite frustrating that armchair-scientists think they know better purely based on the words that happen to be used.

refurb 7y ago
Actually, “junk DNA” was assumed to have no function decades ago. That’s why it got the name. That’s what I was taught in college 15 years ago. Subsequently it was discovered it does have a very important function. Scientific understanding evolves.
- klmr 7y ago
  What you were taught in college 15 years ago is still correct. Junk DNA does not have “a very important function”. The “subsequent discoveries” were, by and large, just a failure in science communication. Junk DNA is still non-functional, very little has changed. We know this because it’s not preserved evolutionarily. By contrast, “important” DNA is preserved from mutation (this is called “negative” or “purifying” selection) because mutating it is almost always bad for the individual. What has changed is twofold: * We have a better handle on what constitutes noncoding, non-junk DNA. The proportion of DNA thus labelled has grown slightly (but only slightly!). We were always aware of its existence but we previously couldn’t study it easily. There are very good reasons to think that the proportion won’t grow much further. The rest is still junk DNA. * We know more about how new genetic function can evolve using the raw genetic material in junk DNA, and how junk DNA might interfere with the proper function of cells, in particular in the presence of pathogens. But, again, the principle of this was already known (or, partially, at least strongly suspected) decades ago. It was just not studied, and we’re now able to study it better. But our fundamental understanding of junk DNA hasn’t changed.
  - refurb 7y ago
    Many noncoding DNA sequences must have some important biological function. This is indicated by comparative genomics studies that report highly conserved regions of noncoding DNA, sometimes on time-scales of hundreds of millions of years. This implies that these noncoding regions are under strong evolutionary pressure and positive selection.[47] For example, in the genomes of humans and mice, which diverged from a common ancestor 65–75 million years ago, protein-coding DNA sequences account for only about 20% of conserved DNA, with the remaining 80% of conserved DNA represented in noncoding regions.[48]
    - klmr 7y ago
      Noncoding DNA ≠ junk DNA! In fact, the latter is a subset of the former. Confusing the two is understandable since even scientists occasionally play fast and loose with the terms but scientists nevertheless understand that they are different. To cite from the same article you’ve cited: > When there is much non-coding DNA, a large proportion appears to have no biological function, as predicted in the 1960s. Since that time, this non-functional portion has controversially been called "junk DNA". And this is by no means a new discovery, functional noncoding DNA has been known for as long as junk DNA.
dkoston 7y ago
Maybe my wording wasn’t clear. I never implied that everyone is ignoring non coding DNA. My point was that it seems naive or arrogant to label something as “not useful” rather than “use unknown”. It makes it less likely that a larger amount of people will investigate it. I think you should also use some data to back up your point because it’s my understanding that the majority of DNA sequencing ignores non coding DNA and the article makes the same point. You also have no idea what field I work in so I’d suggest perhaps asking before coming to the conclusion without any data.

by cyphar 7y ago

refurb 7y ago

Actually, “junk DNA” was assumed to have no function decades ago. That’s why it got the name. That’s what I was taught in college 15 years ago. Subsequently it was discovered it does have a very important function. Scientific understanding evolves.

klmr 7y ago
What you were taught in college 15 years ago is still correct. Junk DNA does not have “a very important function”. The “subsequent discoveries” were, by and large, just a failure in science communication. Junk DNA is still non-functional, very little has changed. We know this because it’s not preserved evolutionarily. By contrast, “important” DNA is preserved from mutation (this is called “negative” or “purifying” selection) because mutating it is almost always bad for the individual. What has changed is twofold: * We have a better handle on what constitutes noncoding, non-junk DNA. The proportion of DNA thus labelled has grown slightly (but only slightly!). We were always aware of its existence but we previously couldn’t study it easily. There are very good reasons to think that the proportion won’t grow much further. The rest is still junk DNA. * We know more about how new genetic function can evolve using the raw genetic material in junk DNA, and how junk DNA might interfere with the proper function of cells, in particular in the presence of pathogens. But, again, the principle of this was already known (or, partially, at least strongly suspected) decades ago. It was just not studied, and we’re now able to study it better. But our fundamental understanding of junk DNA hasn’t changed.
- refurb 7y ago
  Many noncoding DNA sequences must have some important biological function. This is indicated by comparative genomics studies that report highly conserved regions of noncoding DNA, sometimes on time-scales of hundreds of millions of years. This implies that these noncoding regions are under strong evolutionary pressure and positive selection.[47] For example, in the genomes of humans and mice, which diverged from a common ancestor 65–75 million years ago, protein-coding DNA sequences account for only about 20% of conserved DNA, with the remaining 80% of conserved DNA represented in noncoding regions.[48]
  - klmr 7y ago
    Noncoding DNA ≠ junk DNA! In fact, the latter is a subset of the former. Confusing the two is understandable since even scientists occasionally play fast and loose with the terms but scientists nevertheless understand that they are different. To cite from the same article you’ve cited: > When there is much non-coding DNA, a large proportion appears to have no biological function, as predicted in the 1960s. Since that time, this non-functional portion has controversially been called "junk DNA". And this is by no means a new discovery, functional noncoding DNA has been known for as long as junk DNA.

dkoston 7y ago

Maybe my wording wasn’t clear. I never implied that everyone is ignoring non coding DNA. My point was that it seems naive or arrogant to label something as “not useful” rather than “use unknown”. It makes it less likely that a larger amount of people will investigate it. I think you should also use some data to back up your point because it’s my understanding that the majority of DNA sequencing ignores non coding DNA and the article makes the same point. You also have no idea what field I work in so I’d suggest perhaps asking before coming to the conclusion without any data.