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Butterfly wing patterns emerge from ancient ‘junk’ DNA

news.cornell.edu

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Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#71

Post by dkural »

goodmachine wrote: post #20
dkural wrote: post #18

Earlier quoted context omitted.

One man's junk is another's treasure. The truth is, a large chunk of it is somewhat "junky". I have a huge problem of using the word "junk" itself, as the word itself comes with so much baggage. When you really think about junk in the real world, it is not truly always junk - things can be recycled in some ways, and the matter itself is usually not destroyed... earth + energy gets used in some way, and then gets toss…

Thank you for this excellent explanation.

Thank you!

Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#72

Post by rolph »

johnnylambada wrote: post #63

Junk DNA is like dead code your IDE greys out for you in a large code base. They’re still there even though nothing uses them anymore.

it would be closer to say this is legacy code lock-in.

the system is legacy dependent for early boot configurations then changes mode to runtime with recently versioned modules and libraries

Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#73

Post by rolph »

tragomaskhalos wrote: post #61
dkural wrote: post #18

Earlier quoted context omitted.

One man's junk is another's treasure. The truth is, a large chunk of it is somewhat "junky". I have a huge problem of using the word "junk" itself, as the word itself comes with so much baggage. When you really think about junk in the real world, it is not truly always junk - things can be recycled in some ways, and the matter itself is usually not destroyed... earth + energy gets used in some way, and then gets toss…

On the assumption that there are big areas that can be skipped or deleted without any effect on the phenotype though, I've often wondered why there doesn't seem to be evolutionary pressure to delete them. Is it that the energy or other costs of duplication of those regions are not significant, or are there other factors that oppose it?

DNA, and many other biological polymers are structure as well as storage, some of these regions are about structure and modification of structure, to facilitate modality of function. they act as recognition sites, consensus sequences, torsion limiters, process interference selectors, user defined variables.

picture if you will, a big mass of magtape, no spool just a disaster, and you have to scan accross this mess until you find an accessible loop of it with a particular flag or type readable- likehow magtape works, except you have the mechanical challange of reading the tape in the form of a quivering, dynamic mass of spaggetti being read at mutiple locations and having to remain undamaged.

some of these regions make the biggest contribution by simply allowing mechanical slack and positioning of contact sites.

Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#74

Post by can16358p »

wruza wrote: post #35
can16358p wrote: post #31

I'm not a biologist but the whole term "junk DNA" always felt a bit off to me. Millions of years of evolution and having a significant portion of DNA in all living organisms being "junk" doesn't make sense at all.

Why? If it can copy, junk just sits there for eons. Think of free-again sectors on your old hdd that were not overwritten due to how fs driver allocates them.

Perhaps. Still, my gut feeling tells me that there is much more to it that we haven't even scratched the surface as humanity.

Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#75

Post by xg15 »

To add to the stash of dangerously simplifying computer analogies, this almost sounds like separate "code" and "data" sections: The coding DNA sort of interpreting the non-coding part as "data".

The advantage is the same: The coding parts can evolve only slowly, because a wrong mutation can mess up the entire functioning of the wings and would seriously reduce the individual's chance of survival. Meanwhile, a mutation in the non-coding part can only change the color pattern and nothing else. Therefore, the non-coding part can evolve a lot faster.

Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#76

Post by xg15 »

Fubwubs wrote: post #67
jakobnissen wrote: post #26

Earlier quoted context omitted.

This is a pet peeve of mine - the common misconceptions that "junk DNA" is just DNA with an unknown function. By far most junk DNA really is junk. We know this because we know its nonfunctional origin (transposons, pseudogenes and similar), because we can do studies of conservation between species, and because there is a huge range of junk DNA content in otherwise similar species. The misconception come from media bi…

Transposons and pseudogenes may be nonfunctional for an individual organism, but aren't they useful for evolution to create new genes? Wikipedia suggests some usefulness: "While some TEs confer benefits on their hosts, most are regarded as selfish DNA parasites" ( https://en.wikipedia.org/wiki/Transposable_element#Evolution ) "Pseudogene sequences may be transcribed into RNA at low levels, due to promoter elements in…

> Transposons and pseudogenes may be nonfunctional for an individual organism, but aren't they useful for evolution to create new genes?

Ok, but by that definition, nothing is really junk: Even our own junkyards are still home to all sorts of animals and microorganisms which feed on the junk.

Not even starting with the recycling/upcycling movement.

Doesn't change the fact that it's junk in the sense of its original purpose and immediate utility to us.

In the same way, if junk DNA really has no effect on the body it's currently part of (like freed but uncleared memory in RAM), then I think the name is appropriate.

What I'm really missing in popular reporting about genetics though is more focus on the "regulatory elements". The understanding of DNA as given by pop-science articles is mostly that DNA is either instructions for building proteins or "junk", nothing else. This completely leaves out the question how the cell decides when/if a particular protein should be built - which is of course integral for understanding how a number of protein building instructions can result in a complex organism.

It's like describing a programming language as consisting only of instructions and comments but completely leaving out branches and loops.

(even though gene regulation does not happen through branches and loops)

Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#77

Post by naniwaduni »

tragomaskhalos wrote: post #61
dkural wrote: post #18

Earlier quoted context omitted.

One man's junk is another's treasure. The truth is, a large chunk of it is somewhat "junky". I have a huge problem of using the word "junk" itself, as the word itself comes with so much baggage. When you really think about junk in the real world, it is not truly always junk - things can be recycled in some ways, and the matter itself is usually not destroyed... earth + energy gets used in some way, and then gets toss…

On the assumption that there are big areas that can be skipped or deleted without any effect on the phenotype though, I've often wondered why there doesn't seem to be evolutionary pressure to delete them. Is it that the energy or other costs of duplication of those regions are not significant, or are there other factors that oppose it?

You can't have an evolutionary pressure to delete stuff in general, because then you'll oops out stuff that needs to be there. Short of that, building the mechanisms to figure out what to delete would be far more short-term expensive than copying everything around for one more generation.

Re: Butterfly wing patterns emerge from ancient ‘junk’ DNA

#78

Post by TeMPOraL »

zeristor wrote: post #34
TeMPOraL wrote: post #13

Earlier quoted context omitted.

The problem isn't classification, as much as undoing the effect of a generation of academic and pop-sci publishing, which popularized the term "junk DNA" - and groups that perpetuate this term today, e.g. creationist/anti-evolution groups that use it to argue biologists are full of hubris (and thus wrong about evolution), and inadvertently keep the term itself alive.

Do you mean “Junk DNA” is a junk term? At least until it gets repurposed. Apologies for getting too meta.

> Do you mean “Junk DNA” is a junk term?

Junk gene is a junk meme? Yeah, that's about right.

> At least until it gets repurposed.

Like all memes do. And genes, for that matter.

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