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Comment by msandford | Hacker News Reader

Does anyone remember the days when some geneticists were saying that 98% of DNA is "junk" DNA? When I heard it I knew it couldn't be true but it's probably going to take another 50 years to figure out how much really does get used.

I can't help but suspect that a lot of the genome is a part of the boot sequence that helps you go from one cell up to all the differentiated organs and tissues and systems.

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FWIW the study focuses on the coding region of the human genome, i.e., the other 2%.

It is also important to point out that the fraction of non-coding DNA in a genome depends on the organism and is not correlated to complexity. There are multicellular organisms with less than 5% of it as well as unicellular organisms with amounts of DNA orders of magnitude higher than humans.

the marbled lungfish has the largest recorded genome of any eukaryote. One haploid copy of this fish's genome is composed of a whopping 132.8 billion base pairs, while one copy of a human haploid genome has only 3.5 billion

http://www.nature.com/scitable/topicpage/eukaryotic-genome-c...

DNA developers these days just use electron and don’t care about efficiency. That lungfish is ripe for a refactoring.

Bet I could implement a new lungfish with only a few million base pairs in a weekend.

640 kbp should be enough for anybody.

Is electron some sort of synthetic genome compiler?

It’s a (not well executed) joke about electron’s memory consumption and how developers refuse to use anything better.

I think the joke may be about binary size and not memory, which would make sense when talking about DNA.

> not well executed

Aw! :(

For the record I like Electron a lot and am usually the one to defend it on HN, but it indeed was a comment on binary size, needless duplication and copy-paste culture ;)

To be specific, it is Javascript based desktop application platform. Each finished app ships its own version of Chrome which affects the size and arguably adds quite a lot of overhead. It also makes developing cross-platform desktop applications much more accessible, thus making it easier for more developers to make slow, unoptimized applications. Overall it has become a meme for bulky, slow desktop apps with Visual Studio Code being the notable exception.

> I can't help but suspect that a lot of the genome is a part of the boot sequence that helps you go from one cell up to all the differentiated organs and tissues and systems.

Boot sequence. Amazing. I've always been interested in how the DNA transcription looks like a Turing machine with the RNAP being the head and the one DNA strand being the tape. Is there any research in that kind of computational analogy or is it just a coincidence?

I mean, it could be except that the tape in this case has 3D structure and can change shape (and thereby expression) depending on histone modification. So its close to a good analogy, but in some ways DNA is more interesting and complex than a reel to reel tape.

There are many similarities between information processing in biology and information processing in computing, but the analogies only stretch so far. It's worth reading the basic textbooks in this area to get an idea of what mainstream science currently thinks; speculating too far outside the mainstream is a guarantee you will never be successful.

Turing did actually make a significant contribution to biology, but unfortunately he died right around the time the structure of DNA was discovered. Can you imagine what might have been?

https://www.dna.caltech.edu/courses/cs191/paperscs191/turing...

That is not bad intuition. Another analogy is that coding DNA is like all the function calls - the parts of the code that change data. Non coding DNA is like the all the flow control, conditionals, constants, etc. They don’t directly operate on the data, but have a huge impact on how the program behaves given some input.

Had the exact thought when I read the headline.

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

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.

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.

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.

That hypothesis is a little dated, but it should be noted that the exome (the thing being discussed in this article) is 1% of the overall human genome.

Bio-electrics are starting to look at biology the way you describe.

Michael Levin and team at Tufts are instigating regenerative healing by “boot strapping” the process through manipulation of electric fields surrounding cells.

Understanding the extent of network effects will be a big idea in the future. Proving our statistics are probable causes versus mathematical object identification and social debate over the effects.

We’re moving beyond mere taxonomy and catalog of reality into seriously weird science.

Tumor treating fields are a thing that apparently extend survival for folks with glioblastoma. Amazing.

Citation? Open minded, but this sounds like hogwash.

Here’s a recent review: https://www.frontiersin.org/articles/10.3389/fonc.2020.57599...

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