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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

#61

Post by tragomaskhalos »

dkural wrote: post #18
photochemsyn wrote: post #15

Earlier quoted context omitted.

The even use the better term throughout the article (non-coding regulatory DNA) but someone thought they should stick 'junk' in the headline. The whole saga of 'junk' DNA is pretty interesting, and serves as a cautionary tale for those who want to use science to prop up their metaphysical ideologies. These non-coding regions of the genome were long thought to be the detritus of evolution, nothing but extra baggage ca…

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?

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

#62

Post by tragomaskhalos »

xeonmc wrote: post #19
fuckstick wrote: post #6

Earlier quoted context omitted.

We need to stop using the term “junk” DNA - it’s an outmoded term based on the wrongheaded assumption that DNA directly encoding proteins was the be all end all.

Maybe they are opening and closing parentheses of a lambda program.

Maybe God is still trying to exit vim.

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

#64

Post by Mizza »

Pigalowda wrote: post #58
Mizza wrote: post #44

Why don't we give genes names like functions? Seems like the whole thing might be easier to understand if we called a gene "butterflyStripeWidth" rathern than "WntA". It's like we're writing a new core library but only using obfuscated function names.

You want Wnt to be named after butterfly stripes? Last sentence below gives away wnt and lack of it leading to colon polyps/cancer. It does a million other things though. Might as well call it signaling molecule 145626. The activation of the pathway occurs at the cellular membrane, where Wnt ligands bind to the seven transmembrane-domain protein receptors Frizzled (Fzd) and/or to the low-density lipoprotein receptor-…

The name of the gene, not the protein, but yeah you're right that butterflyStripeWidth is far too abstract. But something like, I don't know, decarboxylizeOrnithine would make a genome more "readable".

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

#67

Post by Fubwubs »

jakobnissen wrote: post #26
lmpdev wrote: post #21

I feel like at this point I need a browser plugin which changes the phrase "junk DNA" to literally any other phrase One of the worst names I've come across for a concept

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 inherited from the ancestral gene or arising by new mutations. Although most of these transcripts will have no more functional significance than chance transcripts from other parts of the genome, some have given rise to beneficial regulatory RNAs and new proteins." (https://en.wikipedia.org/wiki/Pseudogene)

I would define truly junk DNA as any DNA that if removed would be beneficial or not harmful to the majority of organisms in a species, and be beneficial or not harmful to the ability of a species to adapt and evolve its genome.

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

#68

Post by rolph »

haimez wrote: post #12

This sounds really neat, from the layman’s perspective. Are they saying that the neighboring non coding genes are acting as a kind of entropy source for the coding genes? If so, are there other known examples?

you and Oarch both get the idea, its not a pattern for butterfly wings, its a pattern. the pattern is conserved across species, and reused to direct morphogenesis.

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

#69

Post by dkural »

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?

It's exactly as you say it - the energy costs are negligible. Most mutation is neutral drift.

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

#70

Post by rolph »

Mizza wrote: post #44

Why don't we give genes names like functions? Seems like the whole thing might be easier to understand if we called a gene "butterflyStripeWidth" rathern than "WntA". It's like we're writing a new core library but only using obfuscated function names.

we kind of do that to an extent but that confuses things.

for example tumor suppressor genes, actually produce a product that, among many other things, leads to suppression of tumor activity or viability.

the gene function [depending on the gene] would really be something hypothetically like -immuno signaling factor modulator gene number 9-

this makes things harder to mentally catalog for a lot of people, so we use name like SONIC; KRUPPEL; HEDGEHOG; SONIC HEDGHOG.

these are developmental pattern genes, and the names are subjective based on phenotype appearance, or what a researcher was doing when they observed it, etc.

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