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Comment by xyzelement | Hacker News Reader

Had the exact thought when I read the headline.

What arrogance. "I don't understand what these genes do. Must be junk"

Well, it was the 70s. The "start" and "stop" codons were known. They could work out that transcription proteins would seek out those codons, produce a strip of mRNA of the DNA bases between those codons, zip it on over to the ribosome, and crank out a protein.

Then there's the rest of the genome. Vast stretches of DNA that don't have the signals needed to transcribe proteins. Why?

They didn't know. They had no idea. It would be decades before they even had a complete copy of the genome. It was years of grinding effort, of trying to work out the big picture by staring through a straw. DNA methylation, gene expression, histone stuff, the entire field of epigeneics-- non-coding DNA playing an active role in cellular operation without directly producing proteins-- was still in the future.

Hah, they would kill for a straw.

Like the old particle physics joke: trying to figure out how a mechanical watch works by pouring a hundred of them into a bucket, smashing them up with a hammer, sorting the fragments by size, and speculating how they fit together when intact.

Now they call it "non-coding DNA": https://en.wikipedia.org/wiki/Non-coding_DNA

That's not what your reference says. Briefly, "non-coding" means it doesn't code for proteins, while "junk" means it serves no function at all.

When the term "junk DNA" was first used it was used for everything that didn't map to proteins, because the other functions weren't yet known.

Actually no, that's not the intellectual level at which any science is performed, let alone population genetics and molecular genetics. Do you perhaps see the irony in making such a grotesquely arrogant suggestion yourself? People working on population genetics and molecular genetics, who came to the conclusion that much DNA has no phenotypic relevance, were doing so based on several decades of literature and 10-20+ years of their own education and scientific training. Would you care to give your own qualifications in this field?

> Would you care to give your own qualifications in this field?

I am a programmer, and I trust my ability to call out junk code. Except if I am reading code from someone like Carmack or Linus. In those cases, I am gonna assume whatever I don't understand is my fault. What hubris would it be for me to call Linus' code junk, even if I really can't make sense of it despite my best effort?

Same here. It's fine to say "we did our best to understand this and as far as we can tell, these genes are not utilized" to go like "yeah it's junk" is quite different. You're a mere mortal, and DNA has been the foundation of all life for millennia. You don't get to judge so easily.

> It's fine to say "we did our best to understand this and as far as we can tell, these genes are not utilized" to go like "yeah it's junk" is quite different.

That’s not how junk DNA was defined. Junk DNA regions have no coding regions. No genes. There’s no easily recognized feature or pattern that would allow you to derive or even propose a function, despite decades of advances in the area. In this particular example the analogy with computer code won’t take you far.

Have you considered that there might be methods that you are not aware of for inferring whether a region of DNA has phenotypic consequences? There’s a huge literature on this. I can’t believe you’re so arrogant as to imagine that you can just intuit the contents of that literature in a few seconds thought before writing a comment on HN.

If a section of DNA has no phenotypic consequences then that means that when we look at a sample of genomes from a population, then the stochastic process underlying the evolution of that region of the genome features random genetic drift, but natural selection is only involved via statistical associations with nearby functional regions due to limited recombination. In contrast, non-junk regions of DNA have natural selection involved directly in the stochastic process underlying their evolution. That difference gives rise to a research program where we seek to infer whether or not a region is “junk” by developing statistical models of DNA sequence evolution and fitting them to data sets comprising samples of DNA sequences from multiple individuals in a population.

That’s just one example of how the question of junk vs. non- junk is studied. There’s also comparative genomics which compares genomes of related species, taking the phylogeny into account in the analysis.

You’re not expected to know any of this; it’s evidently not your field. What is expected however, as a reader of an intelligent website such as this, is for you to understand that there might actually be an entire research field lying behind a question, and not to think that everything is so simple that you can understand it without any study at all on your part.

peak Hacker News.

not exactly; many of those regions that we knew were junk weren't genes, but long regions of repitition of archaic junk that was inserted by viruses and replicated unnecessarily tens of thousands to millions of years ago. Generally, most scientists don't think that (for example) alu sequences really have strong function that you could measure in an experiment.

For example junk DNA was described before we really understood that RNA genes were common and so large regions of the genome that are RNA genes were just treated as totally non-functional.

Sean Eddy proposed an interesting experiment called the Random Genome to address these questions but I don't think anybody is seriously considering running the experiment.

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