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The Complex Truth About ‘Junk DNA’

quantamagazine.org

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Re: The Complex Truth About ‘Junk DNA’

#31

Post by throw3849 »

nitrogen wrote: post #26
throw3849 wrote: post #22

Earlier quoted context omitted.

Not really. Smaller DNA means smaller surface, and less total accidents.

Hypothetically, let's suppose risk of damage correlates with cross sectional area of DNA. It's conceivable that scaling up length with less critical segments reduces risk faster than the increasing cross section increases it. It's an interesting idea from the OP. I'm basically imagining a box full of rope and someone is poking the box with a stick. The length of rope that can fit in the box increases faster than the…

It is not square area, but cubic area (mass).

Re: The Complex Truth About ‘Junk DNA’

#32

Post by im3w1l »

delecti wrote: post #11
hateful wrote: post #4

Earlier quoted context omitted.

I think more than any other group, programmers can understand the gut reaction of calling code that they don't understand "junk".

Normally it means "poor quality" though. I think "junk DNA" is more analogous to "dead code". Not all code labeled "dead" is actually unreachable/unused.

Well we do have "comments" that are actually interpreted by tooling.

Re: The Complex Truth About ‘Junk DNA’

#33

Post by ijidak »

nextos wrote: post #5

Most genetic variants associated with common diseases fall in non-coding DNA areas, previously thought to be junk DNA. Many of these non-coding areas are actually enhancer elements. These elements produce enhancer RNA, previously thought to be noise, and regulate distant genes thanks to chromosome conformation. Chromosome conformation means DNA folds in complex 3D patterns. The interplay between chromosome conformati…

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/)

Re: The Complex Truth About ‘Junk DNA’

#34

Post by andi999 »

dekhn wrote: post #28
phkahler wrote: post #18

Earlier quoted context omitted.

And yet we probably don't know why they have so many copies. Maybe it's a crude method of regulating the ratio of activation on genes. If a few genes are either on or off, and you want to have ratios other than 1:0 1:1 or 0:1, maybe independently activating N of the M copies can achieve that. Just speculating as to how multiple copies might be useful. You can't prove that they are "extra copies" until you understand…

While I agree in principle, it does look like in most cases, these 100X large genomes are just due to random events that haven't been selected away. Often, what you see looking at evolutionary processes at a point in time, you want to find a "reason for why it's this way", when the reason is "it was random chance". Compare deinococcus radiodurans, where there's a whole mechanism for exploiting multiple copies of the…

If it didn't give an advantage it shouldn't have become dominant (that all individuals of that species have that) or not?

Re: The Complex Truth About ‘Junk DNA’

#35

Post by dekhn »

IncRnd wrote: post #29
dekhn wrote: post #20

Earlier quoted context omitted.

I'm not conflating anything. Those details are scientifically conflated (IE, they are functionally related) in a very interesting way. For exmaple, new genes probably arise from gene or genome duplications.

DNA that doesn't encode proteins is not necessarily non-functional.

Yes, I know that. It's unclear what aspects of those duplications are "functional but not coding for genes, enhancers, promotors, or other well-known and understood coding and regulator elements", and which are "functional because if you remove it the organism dies but we can't explain what the cause is".

Everything in my terminology is entirely correct within the current mainstream understanding and it encapsulates much of the ongoing confusion about what "role" non-coding functional elements play, and how they play it.

See http://cryptogenomicon.org/encode-says-what.html and https://www.cell.com/current-biology/comments/S0960-9822(13)... for the strongest arguments against ENCODE's more wide definition of functional elements, as well as https://www.pnas.org/content/110/14/5294 and https://www.mun.ca/biology/scarr/MGA2_02-10.html

I am of the opinion that nearly everybody in this field is overly dogmatic in their views of how genomes work at the macro scale, and that these squabbles demonstrate that clearly.

For more context, please understand that as a researcher in this field, much of what I say may not make sense to casual readers. I decided it's better to think about minimal organisms, than ones that have 500 copies of the ribosome (http://citeseerx.ist.psu.edu/viewdoc/download?rep=rep1&type=...)

Re: The Complex Truth About ‘Junk DNA’

#36

Post by dekhn »

andi999 wrote: post #34
dekhn wrote: post #28

Earlier quoted context omitted.

While I agree in principle, it does look like in most cases, these 100X large genomes are just due to random events that haven't been selected away. Often, what you see looking at evolutionary processes at a point in time, you want to find a "reason for why it's this way", when the reason is "it was random chance". Compare deinococcus radiodurans, where there's a whole mechanism for exploiting multiple copies of the…

If it didn't give an advantage it shouldn't have become dominant (that all individuals of that species have that) or not?

that's now how evolution works. evolution tolerates enormous amounts of things that don't 'give advantage', and 'advantage' is a fairly subjective term anyway. Any number of possible events could have occurred to lead to the scenario we see. Population bottlenecks often lead to strange outcomes.

Re: The Complex Truth About ‘Junk DNA’

#37

Post by shpongled »

ijidak wrote: post #33
nextos wrote: post #5

Most genetic variants associated with common diseases fall in non-coding DNA areas, previously thought to be junk DNA. Many of these non-coding areas are actually enhancer elements. These elements produce enhancer RNA, previously thought to be noise, and regulate distant genes thanks to chromosome conformation. Chromosome conformation means DNA folds in complex 3D patterns. The interplay between chromosome conformati…

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-ass…

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.

Re: The Complex Truth About ‘Junk DNA’

#38

Post by callesgg »

To me the hole notion of junk DNA seamed wrong or even ludicrous the first time I heard of it.

I have a hard time understanding that anyone with a proper education in the field would ever believe the junk dna thesis.

Could it be that it has something to do with me being educated in computers before being educated in biology? The analogy’s a person with computer knowledge would use might make it hard to see these things as junk.

Re: The Complex Truth About ‘Junk DNA’

#39

Post by favoritecolor »

I don't think this article gives the pro-"Junk DNA" arguments fair treatment.

Check out Larry Moran's blog [1, 2] if you want to to hear the other side of the story. He maintains that most of the human genome IS junk, and I find his arguments compelling.

[1] A representative article: https://sandwalk.blogspot.com/2013/07/five-things-you-should...

[2] Rabbit hole warning, all of his Junk DNA posts: https://sandwalk.blogspot.com/2008/02/theme-genomes-junk-dna...

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