Three cheers for Dan Nichol's paper.
Here's a direct link to the PDF found on Philpapers.org.

The cell isn't a machine.

What do you mean by this? I feel like you think the meaning is obvious after everything you've said, but it's not.

Even if we accept that everything you said is true, all it means is that the cell is a very, very complex machine. More complex than current models account for. It's just chemistry, after all. The chemicals behave in predictable fashion or else life wouldn't be possible at all. Molecules moving around, transforming, causing other molecules to transform, etc, etc, to turn food into shit and babies. You can always use the word "machine" to describe that, no matter how complex it is. Just like the word "algorithm" can be used to describe the function of code no matter how complex it is, whether it's a simple path finding algorithm, or the newest machine learning one.

But I probably shouldn't use the word "function" because that implies purpose, and, as you say, no part of the chemistry of life has purpose. I hope you can detect my snark. That's a pretty lame argument that's philosophical at best. The purpose of the machinations of the cell is to maintain life and reproduce. No mater how many times you say it, your words won't change the fact that that is the purpose of the chemistry of life.

You've twisted around the word "purpose" in your head until it has no useful meaning. Nonsense. A molecule can many overlapping, hard to discern purposes. That does not mean it doesn't have a purpose.

A pretty deus ex machina approach.

How would the size of this plants genetic code be justified I wonder?

https://en.m.wikipedia.org/wiki/Paris_japonica

There are plenty of plants that execute the exact same functions with code thousands of times smaller.

To say every codon has a purpose is to be ignorant of how evolution works. There are start triplicate pairs and stop triplicate pairs, the regions between stop and start don't need to have function, even structurally, otherwise why would chromosomes come in different lengths? There was no creator of the genome, there was no efficiency driven outcome, there's only descent with modification, things just happen to with the way they work, and that's beautiful in it's own way.

@TempermentalAnomaly @morphballganon
Junk dna was junk science from the start for ignoring that evolution often eliminates or reduces useless things, like eyes in cave fish, so there’s little likelihood that there’s useless parts of the genome.

Junk DNA is repeating codons, or codons that occur in areas that are outside of the "start/stop" codon triplicate pairs.

Those sequences do things and have effects. In fact, the coding regions are often less functional than the non-coding ones.

They aren't there for structural reasons, all DNA is the same 4 codons linked together over and over, all the different chromosomes are different sizes.

Sometimes they ARE there for structural reasons? Read: enhancers, or CTCF binding sites? Among many other myriad examples of functional noncoding regions? Also, nucleotides =/= codons. There are 64 codons.

All of this DNA is reported when the cells divide, that's the only time those regions between the stops and starts actually come into play. This is very easily proven, we know the structure of the reading proteins down to the molecule (indeed there are starts and stops and triplicate base pairs that design these transcribing proteins).

That's bull. You're out of your depth. A contemporary college molecular biology course would show your examples to the contrary.

The "important" junk DNA that has significance while not being in a "start->stop" zone are the codons that occur before the first start codon on either side of a DNA strand, when DNA is replicated the protein that starts replicating it has to start at 1 end of 1 side of the DNA in order to be able to read it

I feel like a broken record but Enhancers! lncRNAs! siRNAs! Binding sites! Other gene regulatory regions! Epigenetic nucleosome modifications! Chromatin remodeler sites!

except it needs to find the end first, and to make sure it's all the end it "clips" the first 6 (? Maybe more maybe less, it's been decades since I've studied this)

Oh, there's your problem. A lot has changed. You refuse to see the sea change happening around you because it means you're out of date.

Sorry for the wall of text, but there's plenty of examples of blatantly junk DNA, and there are known methods of how it occurs. Anyone who says every codon pair has a purpose has a screw loose and is ignorant to the mechanics of evolution.

I was happy to reply to you and engage pleasantly originally but you are only engaging with people that know less about biology than you do. You are not an expert if you last studied biology decades ago and can't remember the details. You certainly aren't enough of an authority on the subject to question a contemporary article published in Science or the work of other researchers currently in the field.

I really, really encourage you to read these papers thoroughly. You are the target audience-- people who learned the machine model of the cell and who are gripping it so tightly that they are blind to the nuance that we've uncovered. I also encourage you to not write insults about people who disagree with you, especially people with more domain knowledge than you have.

If a gene becomes disabled (a start triplicate pair gets changed to a nonsense triplicate), and it turns out that gene was no longer useful so there's no impact on survivability/reproduction, what happens to the rest of the pairs before the next start triplicate? That stop triplicate and everything before it is now useless. Except evolution doesn't understand useless, there's just as much chance of flipping that gene back on as there is of shortening all of that non readable DNA by just 1 codon length, DNA replicators are very good at not dropping codons. But not you have a gene that isn't being read (outside of replication) or transcribed, and it really isn't costing the individual any significant amount of extra resources to continue to produce that set of code in that strand, so it just hangs out.

There are dozens of other mechanisms to control the rate of protein synthesis, why would junk DNA be the controlling mechanism for it when there are epigenetics, gates, chemical limits, so many different ways rare limit down the path.

"It's there so it must have function" is spitting in the face of the theory of evolution. "It's still in the genetic code so it must've been selected for" is barely less offensive. Evolution does not select for efficiency, it's descent with modification, there is no pressure that says the genetic information must be as efficiently contained as possible. Example: https://en.m.wikipedia.org/wiki/Paris_japonica

Also I'm not at all arguing that proteins are junk (also not saying they're peak efficiency, but "junk" in a 'read' section of DNA is clearly not 'junk'), I'm arguing there are sections of DNA, especially repeating sections outside of start stop sections, that are without purpose.

Sure large proteins have multiple forms and functions, but we do know the exact makeup shape and function of a lot of the smaller ones, like the ones that are small enough to get between either strand of an opened helix to read, transcribe, and send for translation the code for the larger proteins (anything inside the nucleus). Saying all proteins are inherently not understandable because there are large proteins that we don't have full understanding of, is just as incorrect as saying we know every function of every synthesized protein.

Also I can't stand veritasium, he gives over simplified, easy to latch onto, "explanations" of questions and misses out on a lot of minutia that would actually lead to a better understanding of why these questions exist. But people on the Internet love that stuff because they get an answer and are enabled to say "well actually" next time the topic comes up even though they've barely gotten any of the details of the problem itself. Pop science at it's worst. Him and numberphile both