18 ms·
I’m bothered by the description of the history of “junk” dna. Going by this article dna, researchers labeled it junk just because they couldn’t analyze it well
by mint2 5y ago
I’m bothered by the description of the history of “junk” dna. Going by this article dna, researchers labeled it junk just because they couldn’t analyze it well and prioritized the easier 92% and thus didn’t understand it. Calling it junk just seems like trying to compensate for not understanding it like “I don’t understand it but that’s fine because it’s junk anyway”
And the scientist quote seems so wrong. if missing almost 10% of something when that ~10% is not like the other 90% then it seems like a very bad assumption to assume that it doesn’t show a lot of important features.
The quote: “ You would think that, with 92 percent of the genome completed long ago, another eight percent wouldn’t contribute much“
- swayvil 5y agoIt's a common trope. Anything that cannot be intellectually digested is labeled "junk", ignored and, eventually, becomes invisible. You would be astonished at how much of reality falls into that category.
- robwwilliams 5y agoWrong. It is not called junk DNA out of ignorance but because we know much of it is ancient viral insertion. There is no way to cleanse the genome effectively.
- sterlind 5y agothere must be some genome-cleaning processes active, surely. otherwise wouldn't the size of all genomes slowly ratchet up in every species, until organisms just can't cope anymore and everything goes extinct? also, do you consider introns to be junk DNA? those didn't evolve from viral insertion (probably?) so though they might end up hosting "junk", presumably they're not all "junk."
- asdff 5y agoThere is a balance to genome size in terms of selection. If you have a smaller genome, mutations are more likely to have an effect, which means faster evolution (good if you are a pathogen for example). There are smaller energy requirements with replicating a smaller genome, and fewer atoms needed from the environment with shorter DNA. There is probably some optimal physical size to the nucleus, which gets larger as there is more DNA inside. Deletions can occur during cell division. A deletion bias is observed over a duplication bias: https://en.wikipedia.org/wiki/Bacterial_genome#Deletional_bias https://en.wikipedia.org/wiki/Bacterial_genome#Deletional_bi...
- swayvil 5y agoYet the trope exists, my fervent friend.
- shadowgovt 5y agoIt would have been wise to declare it "the unknown regions" or "the frontier," I think. Something to more closely indicate that our gap of understanding was wider than indicated by the moniker the project chose. And I also agree with the bad assumption on the remaining 8% not being significant when we knew that it was structurally different. Less than 8% of an ELF is the header, but boy howdy will that thing not run well if you cut it off.
- TheJoeMan 5y agoCalling the "junk DNA" a "header" is closer to what it may do, but still slightly different because in computer software a header is still read with the same codec (bits) as the data, much like DNA is usually read with the protein codec. Instead, we are learning the "unknown" DNA performs biological functions due to its physical nature, such as physically blocking things from binding. Imagine if a small section of a hard drive was so strongly magnetized that it repulsed the read head - if you were trying to translate it into binary it would appear to be nonsense.
- robwwilliams 5y agoWe are not learning that. Much unknown DNA is repetitive crufts. Get used to it. Biology is even messier than coding.
- xenadu02 5y agoIm not sure which of your many comments to respond to here but we certainly have learned that a small part of "junk" DNA (as that term was originally meant) performs useful functions not directly related to protein coding. So the comment you replied to is absolutely accurate. Of course you are accurate as well: if we subtract the protein coding and the known non-coding but useful bits the rest is almost certainly absolute junk... duplications, bits of retroviruses, etc. But it would be inappropriate to claim we are absolutely certain none of it is useful. Will we find out 50% is useful? Obviously not. But I would rather say "current evidence suggests at least 97% is true junk; we are not likely to find large sequences with hidden uses at this point".
- tehchromic 5y agoI think it's more that the geneticists have the sense of humor.
- robwwilliams 5y agoYep: especially the Drosophila geneticists: sonic hedgehog is a seriously important gene (even in humans).
- aaaronic 5y agoJunk DNA is, AFAIK, not actively expressed (used to create proteins). It's important, though, in the sense that spacing between gene expression sites is a control on which genes get expressed under which conditions (so the junk adds necessary spacing between important genes). I did _some_ research on epigenetics during my MS degree. Spacing between sites was an important factor in our modeling of gene expression.
- grishka 5y agoI remember reading how some of the "junk" DNA turned out to be important because while it doesn't make proteins, the "non-coding" RNA it gets transcribed into regulates something.
- ShroudedNight 5y ago> spacing between gene expression sites is a control on which genes get expressed under which conditions This makes it sound like it represents control flow rather than data. If its presence does / can make a material difference on the output encoding, it strikes my non-expert ears as actively perilous to label such DNA 'junk'
- chaxor 5y agoWhat research have you seen on modeling gene expression? I'm genuinely curious, as I haven't really seen many convincingab initio studies towards this. I could see finding certain features like this spacing as predictive of perhaps some other feature, but I haven't seen any research that really tackles generation of gene expression data from first principles and input of DNA sequence. It's my understanding that modeling the kinetics is difficult, as we really haven't tried making the full network of differential equations. Does anyone have a project that points to the 'final solution' to this? I know recently there was a paper in cell that modeled the cell with the smallest viable genome to predict cell division, but that's a bit further away from complete modeling of our 30k genes' (much less isoforms) dynamics.
- dudeinjapan 5y agoDidn't you watch the move Twins? Arnold got all the good DNA and Danny DeVito got the junk DNA.
- Lammy 5y agoOr play Metal Gear Solid https://metalgearsaladblog.wordpress.com/2016/10/28/liquid-snakes-misunderstood-genes/ https://metalgearsaladblog.wordpress.com/2016/10/28/liquid-s...
- robwwilliams 5y agoLoL: will have to watch.
- fabian2k 5y agoThere is a very clear difference between "junk" DNA and "non-junk" DNA, the latter encodes proteins. That doesn't mean that the DNA parts that don't encode proteins are junk, this is more of an exaggeration or misunderstanding that is often repeated, but not what scientists thought. There are clearly parts of DNA that are not essential, this is clear if you compare genome sizes between different organism. They can vary enormously, and not in a way correlated with any complexity of the organism. There are also parts of DNA that are remnants of viruses inserting many copies of their DNA, which are the parts that could be considered junk. Even those might have an effect simply due to their presence, but essentially everything in the cell has some effects if you look closely enough.
- panabee 5y agoor the viral DNA might have an effect if demethylated.
- robwwilliams 5y agoNot really. Effect sizes that are small are not subject to selection in most metazoan species because of a small effective population size. These types of variant either drift to fixation or extinction. See Michael Lynch for details.
- asdff 5y agoThis is why in school these days they say noncoding DNA or noncoding regions of the genome.
- oofbey 5y agoThe term "junk DNA" was coined very early in our understanding of DNA. Even when we had no idea what it was for, very few respectable geneticists actually believed it was "junk" - basic evolutionary theory argues pretty strongly against it. But the name has stuck around for far longer than it deserves to.
- mateo1 5y ago>basic evolutionary theory argues pretty strongly against it. That's not true. Over millenia leftover chunks of DNA can accumulate for no good reason. Duplication mistakes, viral infections etc. The term junk dna originated from the initial assumption that all noncoding dna was useless. Evolutionary theory has nothing to do with this.
- fabian2k 5y agoThere is a huge difference between "large parts of it are useless" and "all of it are useless". And large parts of the non-coding DNA are probably useless, unless you're extremely generous with what counts as "function" when examining this.
- robwwilliams 5y agoYep!
- robwwilliams 5y agoAnother voice of reason.
- oofbey 5y agoEvolutionary theory says that it would not be preserved if it wasn't being used. If it was never read or relied on, then random errors would accumulate dramatically faster than in coding DNA. Because in coding DNA mutations generally lead to problems and so they're selected against. IIRC, much of these non-coding sequences (so-called "junk DNA") are preserved in a way that shows they are being relied upon for something.
- 5y ago
- hetspookjee 5y agoHa, they might as well call it high yield DNA as in other nomenclature.
- Vladimof 5y ago
- ncmncm 5y agoThe usual expression nowadays is "non-coding DNA". Undoubtedly much of it could be pruned out with no undesirable result, but there does not seem to be any ongoing process to do that, so stuff piles up. As it will.
- robwwilliams 5y agoYes, but too simple—there are many types of non-coding DNA, some very important, others truly jun. Promotors, enhancers, insulators, CpG regions, 5’ and 3’ UTRs, splice junctions in introns, transposons, retrotransposons, LTRs, …
- deleted 5y ago[deleted]
- sockpuppet_12 5y ago>Undoubtedly much of it could be pruned out with no undesirable result Such hubris as this is what led us to: - define DNA we didn't and still don't understand as useless "junk" - call the appendix a useless vestigial organ - declared "silenced" b-cells useless The list goes on and on and on... When will somebody compile a list of how often science is wrong just to slap the arrogance out of people before they cost more time and lives with such reckless and impatient reasoning?
- epgui 5y agoThis perspective is true to some extent, but it’s counter-productive to think of science as being wrong. You should think of science as the “least wrong” set of beliefs we have at any point in time. It will never be perfectly right, and every day it’s less and less wrong. The reason it’s so reliable is because it embraces (and doesn’t dismiss) this uncertainty.
- post_below 5y agoI don't think it's counter productive at all. There was a period of time, when the appendix was (absurdly) considered vestigial, that surgeons would remove the appendix as a side quest if they happened to have the area opened for some other purpose. That was a terrible idea, but one that was supported by science at the time. There are practical reasons to be skeptical about scientific assumptions. Science becomes less wrong faster if we allow history to remind us that a lot of what we believe will likely turn out to be wrong.
- deleted 5y ago[deleted]
- axg11 5y agoContext: I have a PhD in genomics The label “junk DNA” was one of the biggest mistakes in the history of genetics. A lot of high school textbooks still reference this term and it’s worse than misleading. In many ways, non-coding DNA is just as important as the parts of the genome that code for proteins. Non-coding DNA determines expression levels, genome confirmation (shape), and replication efficiency among other things. The term junk DNA misleads students into thinking that these sections of DNA play little part in how a cell functions. Quite the opposite, the “junk DNA” is responsible for orchestrating the “non-junk” bits.
- deleted 5y ago[deleted]
- alfiedotwtf 5y agoQuestion from the peanut gallery: if you were to flip a single bit in this junk DNA, are the outcomes only slightly different or could they be wildly variable depending on which bit was flipped?
- axg11 5y agoWildly variable. That’s true for all DNA including protein coding DNA. It’s much more likely that changing a base in a protein coding region will result in an effect, but still nowhere near guaranteed. Statistically, the average human has ~1 base variant (SNP) in a protein coding region somewhere in their genome. In almost all people the effect of that SNP is no more apparent than the effect of SNPs in “junk DNA”.
- robwwilliams 5y agoNot true at all. So much charming and well intentioned misinformation on this thread; as much as if I were to weigh in on the pros and cons of MariaBD versus PostgreSL. Coding sequence is under significantly higher levels of active “purifying” selection than regulatory DNA, and much higher than de novo mutations in repetitive mobile elements that only rare perturb phenotypes.
- robwwilliams 5y agoJunk is an appropriate easy-access word. Would you be happier if geneticists told you junk DNA was mainly highly repetitive mobile element DNA derived originally from exogenous viruses? In general this junk does not make proteins and its expression as RNA is often actively suppressed. The human genome is littered with cruft and dumb code comments just like you would expect for very very old code.