I remember talking to my colleagues about 15 years ago about trying to do research on some noncoding polymorphisms and was ridiculed. The basic response was something along the lines of "those are noncoding, why would you look at those?" as if I was an idiot who didn't understand current genetics.

It's been long ago enough that I don't remember all the details, but my perspective was that it was naive and arrogant to assume we had a good handle on everything about DNA, especially then as it was all new, and there was evidence then that a lot of the noncoding DNA had function.

Dogmatic attitudes are surprisingly prevalent in academics. There's definitely a weird hubris accompanying published findings that goes something like peer reviewed -> established fact as if the point of academics isn't to understand things but to score points like on a test. Some skepticism about certain things seems warranted but other times there's really nothing but overly simplistic models that were really never evaluated to begin with. I wish there was more awareness of the topography of uncertainty in research findings.

> Dogmatic attitudes are surprisingly prevalent in academics.

https://en.m.wikipedia.org/wiki/Planck%27s_principle

“Science progresses one funeral at a time.”

The idea of junk DNA never made sense to me.

Having a list of proteins (coding DNA) does nothing to tell an organism how to combine those proteins to form working systems.

It's like claiming that the parts list in an assembly manual is the only information of importance. And the step-by-step instructions are junk, because they don't describe a useful part in the box.

Did we think that the whole organism just self-assembles once it makes the tens of thousands of individual parts described in coding DNA?

"Junk DNA" was a terrible terrible phrase to begin with.

Disclaimer: I believe in a creator. (https://www.jw.org/en/bible-teachings/science/)

No creator necessary.

Imagine a big machine run by paper tape. On the tape are two possible holes. Punch one and feed it in, the machine makes a man. Punch the other, it makes a mouse.

Does the tape 'encode' the essence of 'human being'? (or even 'mouse'?) Of course not.

The machine is a vital part of the equation. Likewise, dna in a jar is just a molecule. It has to have a cell, evolved over a billion years, ready to make something of it.

So no self-assembly, no magic in the DNA.

Yes you're right, we know that DNA is inert and used as a storage device by an organism.

What we don't know is how an organism with no intelligence (cell), could develop code (DNA), archive it, rehydrate it and then parse and copy it like someone with intelligence.

Without getting too deep into it, it's just not convincing anymore to appeal to vast amounts of time and random chance to do something which is fundamentally within the realms of engineering.

Sure we do. It's littered with history, fragments from all over. And organisms today are more complex than organisms of the past, some of which still have remnants existing. So many stages of development as examples. There's no magic to it.

You're entitled to your opinion, but what you're suggesting is wrong. What you've said are some observations made and some interpretations based on evidence gathered but none of it concludes that cellular organisms invented DNA, that suggestion is still stuck in a chicken vs egg scenario.

The fact is, we don't know how these systems could have created themselves or been created abiogenesis. There are wildly different theories, but it's far from a closed case.

I used to think the same thing as you because that's all I was taught to think, but perhaps if you looked at what synthetic chemists think about abiogenesis you may find it interesting / informative to see what they have to say about the challenges involved in it. An interview with a synthetic organic chemist on the topic: youtube.com/watch?v=r4sP1E1Jd_Y

While an interesting thought experiment, no one is proposing that you will get self-assembly of an organism by expressing 10,000 genes. We really don't know what the beginning steps of this process were - since it only happened once (or however many times life arose). Once an organism was made, now it can just express whatever proteins it currently needs, based on lifecycle/nutrients/metabolic requirements/etc.

Besides its DNA, every living thing has at least one whole functioning cell to use as a template, since they all start as dividing cells.

Natural selection doesn't care about what looks pretty, only that it works. A modern operating system is millions of lines of code. Do you think it is possible that some of the code are no longer used but nobody dares remove it?

That would presuppose an intelligent designer who doesn't dare to try and remove the code. (Unless that's what you are saying)

Are you saying god is working in two-week sprints and has no control over the backlog? That would explain a lot.

That'd be the case if a conscious entity was not daring to remove code.

An evolutionary process, on the other hand, doesn't fear removing random sections so their continued presence indicates the "junk" must (somehow) be important to the organism's fitness.

Or not. Since a random process doesn't care, its easy to carry around indefinitely. Like that closet you never bother to clean.

The fact that enhancers can be transcribed is quite interesting. I’m not sure what’s the function of these transcripts though. It seems like the transcription is terminated prematurely once RNA pol realizes it’s not a functional gene.

There's a lot of literature on this, but you are quite right as there are tons of open questions. Some enhancer RNAs are non-functional. Others seem to help stabilizing chromosome contacts. Some do seem to encode secondary structures, so they are probably functional ncRNAs.

Irrespective of this, enhancer RNA transcription is very useful to track active regulatory regions and to perform QTL studies.

For starters, junk DNA is a fuzzy term. I would never include regulatory regions or introns in junk DNA, just non-coding. To me, junk are tranposons and friends, or pseudogenes: they rarely have any purpose, and sometime they cause troubles.

I should update this:

https://jacquesmattheij.com/junk-dna-no-way/

with the newly found insights. Still: No Way. Just not-yet-understood-DNA.