Butterfly wing patterns emerge from ancient ‘junk’ DNA

https://news.cornell.edu/stories/2022/10/butterfly-wing-patterns-emerge-ancient-junk-dna

by hhs • 4 years ago

114 76 4 years ago

news.cornell.edu

hbbio• 4 years ago

Thinking of DNA as code, with the particularity that outdated versions of the code are kept in "binaries", it's a creative use to recycle them as a random pattern generator!

djbusby• 4 years ago

The Ghost in the Machine is beautiful.

fuckstick• 4 years ago

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.

pests• 4 years ago

Right. Its like someone reverse-engineered an executable file and discovered the .data section while calling the .text junk.

LAC-Tech• 4 years ago

Working Effectively with Legacy DNA

photochemsyn• 4 years ago

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 carried around by the genome. Richard Dawkins and others famously settled on this as a means of discrediting the ideology of 'intelligent design' because, as they saw it, an intelligent designer wouldn't leave all this junk sitting in the genome. The later realization that this junk was actually playing all kinds of roles in large-scale regulation, cell differentiation, three-dimensional structure of the genome, and was often being actively transcribed (to regulatory RNA), etc. tossed that whole notion out the window and then it became (for a few years) something the intellectual creationists tried to use to discredit Dawkins and co. There was something called the 'Encode controversy' over a decade ago which featured centrally and which is well described here:

https://www.science20.com/adaptivecomplexity/our_genomes_enc...

Most people seem to have forgotten all that and accepted that large non-protein-gene-coding regions of eukaryotic genomes have various essential functional roles.

xeonmc• 4 years ago

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

daguava• 4 years ago

Man, butterflies relying on all this old shit smh.... [ indiscriminate murmuring.... ] Yo hey [hallway scuffling] Yo PM, can't we just deprecate butterflies already? Ah he- I know I kno- yes I understand the boss likes butterflies, pretty and what no- no stop. Butterflies are a cost center, can we just deprecate and phase them out? Deprecation Plan? Cost Center Optimization? Ah shit ah- yeah, we keep the butterflies....

zakki• 4 years ago

If some part of DNA is classified as code DNA, why not classify this as data DNA instead of junk?

JohnJamesRambo• 4 years ago

Journalists don’t understand data but they understand junk.

pyinstallwoes• 4 years ago

I’m a junk engineer to these journalists.

TeMPOraL3• 4 years ago

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.

hsn9152• 4 years ago

Creationists only weaponize the term because it really is used by journalists and pop-scientists to argue against design.

zeristor• 4 years ago

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

At least until it gets repurposed.

Apologies for getting too meta.

haimez• 4 years ago

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?

Oarch• 4 years ago

(From another layman) this sounds a bit like Turing Patterns, which are found all over nature.

rolph4• 4 years ago

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.

supernova87a• 4 years ago

It would've been nice if the article could have even shown a single image of how knocking out a certain sequence caused some wing pattern to disappear. But I guess that's hidden behind a paywall.

taneliv• 4 years ago

The first image, before the text of the article, has this caption: "Wings of the painted lady butterfly – Vanessa cardui, modified by deletion of non-coding DNA sequence."

(I'm definitely not paying for this content, and it is available in a fresh incognito browser session, so I suppose it should be available to all readers.)

olejorgenb• 4 years ago

The "materials and methods" attachment is free and includes some images: https://www.science.org/doi/suppl/10.1126/science.abi9407/su...

(paper is not yet available on scihub)

lmpdev• 4 years ago

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

epistasis• 4 years ago

True enlightenment is when you realize that junk DNA is actually a great term, because evolution is great at building things out of junk and repurposing them.

The "junk" areas of repetitive DNA were actually identified as cauldrons of evolution in the early days of research, so we have known since the beginning that the junk was actually crucial.

Barbara McClintock's Nobel for this was awarded way back in 1983

https://en.wikipedia.org/wiki/Barbara_McClintock

jakobnissen• 4 years ago

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 bias: You'll never hear a story about "junk DNA really is junk, researchers find"

vbezhenar• 4 years ago

Does it mean that mutations in the junk DNA are evenly distributed among the population because supposedly they don’t affect anything?

Fubwubs• 4 years ago

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.

pwdisswordfish9• 4 years ago

How about "cloud computing"?

thanatos519• 4 years ago

How about "legacy DNA" or "retired DNA" or just "leftovers"?

Gatsky• 4 years ago

Of course, nobody who does biological sciences actually believes it is junk.

lrhegeba• 4 years ago

"deprecated DNA" seems a good fit ;-)

hsn9152• 4 years ago

Not knowing much about DNA, it seems weird to me that it's assumed the primary purpose of DNA is to encode for proteins. Sure, that's one of its functions, but it would be just as misguided as assuming that bits only exist to encode text, and when they encode anything else, it's seen as some extraordinary exception to the norm.

amphitoky• 4 years ago

people like to forget DNA has a 3D structure. A lot of the DNA that doesnt encode proteins might be involved, for example, in the association of 3D topological domains or conformational switches that impact chromatin accessibility. Interesting also is when sufficient factors bind to a local region of DNA to change the local chemistry and initiate phase separated domains where regulatory factors might preferrentially bind and thus drive the transcription of the few coding regions, and that's pretty cool too. Just to add some context to your bits-analogy.

can16358p2• 4 years ago

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.

wruza• 4 years ago

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.

can16358p2• 4 years ago

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

jasmer• 4 years ago

It's all 'junk' from a scientific materialist perspective.

It's a chemical reaction just like any other - it's random noise.

There's no (scientific materialist) reason to attribute 'junk' or 'not junk' to a sequence of random bits of information. There can be no 'purpose' to random noise.

Now, it is a bit odd that the most ardent secular scientific materialists do, truly in their own living experiences, tend strongly to attribute such anthropological attributes to such things, by calling some of these processes 'life', using terms such as 'evolution' instead of what is just 'random changes some of which persist in time', isn't it? It's almost like they 'believe' in some metaphysical orientation or principle which is a bit different than their stated 'belief' of materialism and the odd bunch of equations we posit to govern 'everything'?

Perhaps we can avoid going all the way down the intellectual rabbit hole by shifting these kinds of discussions into the evolving (pun intended) field of 'emergence' ...

endymi0n• 4 years ago

Pretty ingenious, reminds me a bit about how Elite double used its own program code as a lookup table for building a procedurally generated universe in order to conserve memory.

I figured it was ingenious back then but I had no clue it‘s biomimetic :)

https://en.m.wikipedia.org/wiki/Elite_(video_game)

karmaniverous• 4 years ago

Sooo... Not "junk". :) <ducks>

smusamashah• 4 years ago

Don't we have similar terminology for some of human organs. Appendix or some other organs are assumed useless. Personally I feel it's insane to call DNA or organs useless instead of acknowledging that we don't yet understand there true purpose.

Hendrikto• 4 years ago

Not everything serves a purpose. Onions have more DNA than humans.

throwamon• 4 years ago

Has it been demonstrated that that extra DNA has no function or are you just assuming "onions are less complex than us"?

RugnirViking• 4 years ago

Iirc appendix is now known to harbour gut microflora/bacteria when you have diarrhea, to keep them safe etc while your body clears whatever it deems unwanted

melagonster2• 4 years ago

This term used almost twenty years ago.

Mizza6• 4 years ago

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.

nguyenkien2• 4 years ago

We can only guess it functions. Give concrete name like that is not very good idea

Mizza6• 4 years ago

But I can't get anything at all from the name now. BRCA1 isn't descriptive at all, but suppressBreastTumor is more helpful even it's not 100% accurate. I'd rather it be our best guess description than some random letters.

Pigalowda• 4 years ago

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-related protein (LRP) 5/6. This interaction leads to the inhibition of the axin degradasome destruction complex, which is a multiprotein complex that controls the cytoplasmic amount of β-catenin via phosphorylation, and, thereby, triggers β-catenin degradation by the proteasome in the absence of Wnt [10]. The destruction complex comprises the tumor suppressor adenomatous polyposis coli (APC), the axin scaffold protein, and two Ser/Thr kinases: glycogen synthase kinase 3 (GSK3) β and casein kinase 1 (CK1). In the absence of Wnt ligands, CK1 phosphorylates β-catenin at Ser45 residue and GSK3β at Ser33/Ser37/Thr41 residues. Then, the β-transducin repeats-containing protein (β-TrCP), an E3-ubiquitin ligase, ubiquitinates phosphorylated β-catenin, which becomes a target for proteasomal degradation [10]. When Wnt binds to Fzd and/or LRP5/6 receptors, the Wnt/β-catenin pathway is activated and the axin degradasome is inhibited [9]. As a consequence, Dishevelled (Dvl) is activated and recruits the degradasome complex to the plasma membrane, and, thereby, promotes the interaction between LRP5/6 and axin [11,12]. Consequently, LRP5/6 is phosphorylated at specific amino acidic residues (Ser1490, Thr1530, Thr1572, Ser1590, Ser1607) [13], acting as a direct competitive inhibitor of GSK3β [14]. Moreover, inactivation of GSK3β through Akt-dependent Ser9 phosphorylation prevents the phosphorylation of β-catenin, which allows its stabilization and accumulation in the cytoplasm. Stabilized β-catenin translocates to the nucleus where it binds to transcription factors, notably T-cell factor (TCF) and lymphoid enhancing factor (LEF), TCF/LEF. This interaction displaces the co-TCF/LEF repressor Groucho, whose function under basal conditions is to compact chromatin [15]. Groucho and TCF/LEF form a multiprotein complex, which is also termed Wnt enhanceosome, that recruits transcriptional co-activators and histone modifiers such as the ATP-dependent helicase Brahma-related gene 1 (BRG1, also known as SMARCA4), cyclic adenosine mono phosphate response element (CREB)-binding protein (CBP), p300, B-cell lymphoma 9 (BCL9), and pygo [15,16]. The Wnt enhanceosome regulates chromatin remodeling and activates the transcription of β-catenin-dependent genes involved in cell growth and survival, including C-MYC, CCND1, BIRC5, and CDKN1a [9]. C-myc is a proto-oncogene that activates cyclin D1 and simultaneously inhibits p21 and p27, which leads to uncontrolled cell proliferation

Mizza6• 4 years ago

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".

rolph4• 4 years ago

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.

johnnylambada• 4 years ago

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.

alrlroipsp• 4 years ago

False. Read the article and learn what they found out in this case.

rolph4• 4 years ago

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

xg152• 4 years ago

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.

Butterfly wing patterns emerge from ancient ‘junk’ DNA

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