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Butterfly wing patterns emerge from ancient ‘junk’ DNA
- hbbio 4y agoThinking of DNA as code, with the particularity that outdated versions of the code are kept in "binaries", it's a creative use to recycle them as a random pattern generator!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 4y agoThe Ghost in the Machine is beautiful.
- fuckstick 4y agoWe 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 4y agoRight. Its like someone reverse-engineered an executable file and discovered the .data section while calling the .text junk.
- LAC-Tech 4y agoWorking Effectively with Legacy DNA
- photochemsyn 4y agoThe 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_encode_and_intelligent_design 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.
- dkural 4y agoOne 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 tossed aside.. Moving on to biology, we have ~2500 smell receptor genes in various states of decay. We also have a lot of deactivated smell receptor genes, with a lot of polymorphism across humans.. as it's in free drift. Perhaps a long time ago when we shared a common ancestor with rats, many of these were far more useful, with strong selection pressure to preserve working copies, but not so much anymore.. Perhaps the trash man didn't come yet, but it's definitely stored away in our basements. A more concrete example would be the roughly 40% of our genome that consists of repetitive elements, transposons, and retrotransposons. One of them, the ALU sequence, is 300 basepairs long, and yet is about %10 of our genome. There are about ~1 million copies of this sequence across our genome. It's spread has slowed down recently. Out of about a million copies, most of them are "inert", with no further ability to copy themselves. Sure, given just how much of our genome is this one thing being repeated over and over again, it has some function in some places - causes various splicing events here and there, helps shuffle genes (which is a bit of a meta function across evolutionary timescales), but overall, if you had children with these parts mutated, 99.9% of the time nothing of significance would happen. 10% is huge, given the protein coding region is about 1%, and the regulatory regions influencing transcription & RNA expression with some sort of identifiable action is about ~10% (if we're being very, very generous). DNA is promiscuously transcribed, but this doesn't mean much of that has any particular function. A lot of is transcribed at very low copy numbers, and degraded as fast as possible. A lot of things are stochastic, so there is a "long tail" of what gets transcribed, and at very low numbers at that. Another good chunk of that 40% of repetitive sequence is is old retroviruses we got infected with (not dissimilar to HIV) that totally raided our DNA and became endogenous - in fact they're called HERVs - human endogenous retroviruses. These mostly stopped spreading in our DNA as well. Also, large streches of our DNA is the same couple of bases repeated ad nauseam for no particular reason.. let's say AT... there are these massive streches that go ATATATATATATA and you find people are highly polymorphic and tolerate a lot of mutations in these sequences. Some people have it deleted with no ill effect. There are rare examples of this occuring inside a gene, where having the repeat go on for too long is bad for you ("Huntingtin" (no it's not a mis-spelling) is the paradigmatic example). This is the exception rather than the rule, considering we have more repeats than the entire % of coding regions in the genome. Junk is a bad word, but it's not like there is a "clean rewrite", or "clean refactor" either... so things accumulate, get shuffled around, get forgotten.. randomly get deleted in snippets... most mutations are either neutral or detrimental, with happy accidents happening here and there. Overall, it is nonsensical to force things into this binary of "junk", "not junk", but beware of thinking of the genome as one would a design schematic for a microprocessor, or an aircraft for that matter. There is a lot of stuff in it that's like meh... doesn't really matter if it's there or not.
- xeonmc 4y agoMaybe they are opening and closing parentheses of a lambda program.
- tragomaskhalos 4y agoMaybe God is still trying to exit vim.
- daguava 4y agoMan, 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 4y agoIf some part of DNA is classified as code DNA, why not classify this as data DNA instead of junk?
- deleted 4y ago[deleted]
- JohnJamesRambo 4y agoJournalists don’t understand data but they understand junk.
- pyinstallwoes 4y agoI’m a junk engineer to these journalists.
- TeMPOraL 4y agoThe 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.
- hsn915 4y agoCreationists only weaponize the term because it really is used by journalists and pop-scientists to argue against design.
- TeMPOraL 4y agoSome journalists and pop-science writers are creationists themselves; the whole debate is still self-sustaining feedback loop, and one of its side effects is that the term "junk DNA" remains in use.
- zeristor 4y agoDo you mean “Junk DNA” is a junk term? At least until it gets repurposed. Apologies for getting too meta.
- haimez 4y agoThis 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?
- supernova87a 4y agoIt 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 4y agoThe 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 4y agoThe "materials and methods" attachment is free and includes some images: https://www.science.org/doi/suppl/10.1126/science.abi9407/suppl_file/science.abi9407_sm.pdf https://www.science.org/doi/suppl/10.1126/science.abi9407/su... (paper is not yet available on scihub)
- lmpdev 4y agoI 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 4y agoTrue 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 https://en.wikipedia.org/wiki/Barbara_McClintock
- jakobnissen 4y agoThis 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 4y agoDoes it mean that mutations in the junk DNA are evenly distributed among the population because supposedly they don’t affect anything?
- Fubwubs 4y agoTransposons 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 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 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.
- hsn915 4y agoNot 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 4y agopeople 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.
- can16358p 4y agoI'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 4y agoWhy? 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.
- can16358p 4y agoPerhaps. Still, my gut feeling tells me that there is much more to it that we haven't even scratched the surface as humanity.
- jasmer 4y agoIt'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 4y agoPretty 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) https://en.m.wikipedia.org/wiki/Elite_(video_game)
- karmaniverous 4y agoSooo... Not "junk". :) <ducks>
- smusamashah 4y agoDon'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 4y agoNot everything serves a purpose. Onions have more DNA than humans.
- throwamon 4y agoHas it been demonstrated that that extra DNA has no function or are you just assuming "onions are less complex than us"?
- melagonster 4y agoplant like double their genome, and become stronger.
- tragomaskhalos 4y agoOk now I'm afraid to look in that bottom drawer in the kitchen, who knows what those devious bloody alliums are up to in there.
- RugnirViking 4y agoIirc 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
- melagonster 4y agoThis term used almost twenty years ago.
- Mizza 4y agoWhy 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.
- Pigalowda 4y agoYou 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
- johnnylambada 4y agoJunk 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 4y agoFalse. Read the article and learn what they found out in this case.
- rolph 4y agoit 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
- xg15 4y agoTo 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.