[HN Gopher] 'Useless specks of dust' turn out to be building blo... ___________________________________________________________________ 'Useless specks of dust' turn out to be building blocks of vertebrate genomes Author : georgecmu Score : 231 points Date : 2021-11-03 12:18 UTC (10 hours ago) (HTM) web link (www.sciencealert.com) (TXT) w3m dump (www.sciencealert.com) | worik wrote: | This seems to be another nail in the coffin of "DNA is Code" | idea. | | We do not know how life organises itself. DNA is involved. We | have some knowledge. | | But what we do not know matters much more than what we do know. | ramraj07 wrote: | Blowing out of proportions a bit are we? This is still dna, | just in another form elsewhere. And it doesn't uproot anything, | most of the important genes are still in the main chromosomes, | we just don't have the full picture and studies like this help | us inch closer towards it. | [deleted] | MichaelZuo wrote: | "Not only are they the same in each species, but they crowd | together in the center of the nucleus where they physically | interact with each other, suggesting functional coherence," | | If there truly is some sort of functional interaction going on | then this is a very profound observation. As it implies the close | spacing is for some kind of mechanical/electrical mechanism | within the core of every cell's nucelus. | 0des wrote: | Surely nobody was under the impression that detail stops at the | nucleic level, right? It's small machines and complex systems | the entire way down, ad infinitum. Our ability or inability to | render or understand these increasingly small systems does not | negate their existence. | dekhn wrote: | I don't completely understand what you are saying; the | information encoded at the nucleic level does not have any | analogy at the sub-molecular level (IE there is no biological | information stored using subatomic particles or quantum | tricks), nor do there seem to be any functional contributes | to non-information molecular mechanisms. | EvanAnderson wrote: | I interpreted the parent comment as: Artifacts of the | virtual machine that physics / biology / chemistry | "executes" on (i.e. the universe and potentially minute | physical properties we aren't aware of) may be reflected at | the macro-scale in the "output" (life). | dekhn wrote: | That doesn't make any sense from a scientific | perspection, and reality is not a virtual machine that | physics executes on. | [deleted] | panda-giddiness wrote: | I assume they were referring to emergence. | | https://en.wikipedia.org/wiki/Emergence | neuronic wrote: | Yes, if the word 'complexity' falls then emergence is | inevitable to be mentioned alongside. | Tagbert wrote: | Reminds me of... | | The Vermin only teaze and pinch | | Their Foes superior by an Inch. | | So, Nat'ralists observe, a Flea | | Hath smaller Fleas that on him prey, | | And these have smaller yet to bite 'em, | | And so proceed ad infinitum: | | Thus ev'ry Poet, in his Kind | | Is bit by him that comes behind. | | -Swift | gus_massa wrote: | There are some known subparts of the nucleus, in particular | the Nucleolus [1], and that link discuss a few additional | subparts. | | I'm not an expert in biology, so I don't know if this is a | new part, or it's a part that we already know but in mammals | is made by small areas of the big chromosomes and in this | animals this areas are on their own. | | [1] https://en.wikipedia.org/wiki/Nucleolus | | Edit: nucleolus -> nucleus | saghm wrote: | > There are some known subparts of the nucleolus, in | particular the Nucleolus | | I think you meant "known subparts of the nucleus", right? | gus_massa wrote: | Thanks. I fixed it now, because my typo made the sentence | very confusing. | vanderZwan wrote: | I agree with your general sentiment, but I don't see why we | should expect "machines and complex systems" (as related to | life) to exist at the level below molecules and atoms. If | that was the case then we should expect otherwise identical | organic molecules to have differences when they're created by | living things and synthesis in the lab (ok, ok, there's | chirality and carbon-14, but you get what I mean). | 0des wrote: | I get what you're trying to say, however this is a flawed | assumption right up there with just getting an FTP account, | mounting it locally with curlftpfs, and then using SVN or | CVS on the mounted filesystem. Time and innovation are both | not on your side, in this case. Complex systems are complex | and extend far beyond the focal depth of our squinting. | vanderZwan wrote: | I genuinely don't understand what your analogy is | supposed to convey, could you elaborate? | WastingMyTime89 wrote: | Wohler proved in 1828 that there was nothing special with | organic molecules by synthesising urea. | | I guess you could view molecular formation as a complex | system involving atoms and atoms as a complex system | involving quarks. That would define chemistry and | particle physics as the study of said complex systems | which makes sense to me. Still at that level that's not | generally viewed as the study of organisms. What we view | as biology, the study of the mechanisms of life, really | starts at the molecular level. If you go lower, things | stop being specific enough. | ramblenode wrote: | There is an emerging subfield "quantum biology" that | studies biological systems under quantum mechanical | influence [0]. Photoreceptor systems seem to be a prominent | example. | | [0] https://quantum.ch.ntu.edu.tw/ycclab/wp- | content/uploads/2015... | vanderZwan wrote: | I guess my issue was more with the implication that we'll | find more fundamental building blocks of life. | 0des wrote: | Are you more comfortable with the implication that we | won't? | vanderZwan wrote: | Comfortable or uncomfortable doesn't even enter the | discussion. You can't go down much further without | entering the domain of high-energy physics. Which is not | the domain of life. | 0des wrote: | How so? | goldenkey wrote: | It's hard for structure to form in burning hot plasmas. | But hell, we only know about ourselves. That's the flaw | in all the dogmatic thinking about what life is. Life is | after all, just structured computation, and computation | is just action, and action..just the passage of observer | time: | | https://www.youtube.com/watch?v=Q_CQDSlmboA | vanderZwan wrote: | Before we go into the discussion of whether life may or | may not be able to exist in hot plasmas (which is fine, | in a speculative hypothetical physics kind of way), the | point is that we are talking about the building blocks of | _our_ form of life. Which is _not_ the kind that exists | in hot plasmas. | washadjeffmad wrote: | I'm reminded of an early machine learning experiment where | a system self-trained to perform a certain task on a piece | of dedicated hardware did so unexpectedly. The researchers | "knew" the solution but wanted to learn how their project | solved it. | | At some point, the sensing for analog effects became the | most efficient way to achieve the result by exploiting | flaws or unique properties in the individual components, | sort of like that inductance backdoor where a particular | set of instructions in a certain circuit leaks into another | until it's energized enough to trigger it like a relay. | Anyway, the result was unintuitive but worked. | | Anyway, there's no doubt that after millions and millions | of years, there are natural principles at the quantum and | atomic levels that biologics are taking advantage of that | we're basically only at the "allegory of the cave" level of | understanding. | | The micro is very much relative. | dr_dshiv wrote: | Individual atoms and molecules are identical in a vacuum. | Are they in context? They at least have quantum degrees of | freedom, which is quite a lot. But whether that has | functional value is tbd | vanderZwan wrote: | A statement like "complex machines all the way down" | implies precisely that molecules would be different | _without context_ because of some lower-level machinery | that forms a more fundamental building block of life. | This is what I am skeptical of. | _ihaque wrote: | > As it implies the close spacing is for some kind of | mechanical/electrical mechanism within the core of every cell's | nucelus. | | It is interesting, but not for the reasons you may be | imagining. And not a mysterious electrical mechanism. | | It's well-known in the field that (e.g., in humans), | chromosomes fold in on themselves in structured ways [1,2]. The | functional consequence is not precisely mechanical or | electrical -- rather, these folds bring regulatory domains | close in 3D space to the sequences which they regulate (which | may be far in 1-D sequence distance). These can be elements | like "enhancers", which increase the level of transcription | (DNA->RNA copying, the first step of gene expression); | "insulators", which break up coherent blocks of gene | regulation, etc. One of the mediating mechanisms is that | regulatory proteins bind to these particular sequences; | bringing them together in 3D space allows the assembly of a | protein complex that actually carries out the relevant process | (eg, transcription). | | So, what's interesting here? There is extensive evidence of | these contacts within mammalian chromosomes, but limited | evidence _between_ different chromosomes. Insofar as the paper | shows that mammalian macrochromosomes have homology to multiple | reptile/avian microchromosomes (really, to their most recent | common ancestor), it may be (speculation alert) that intra- | chromosome contacts recapitulate contacts and organization seen | in the ancestral microchromosomes. | | (There are also "simple" interactions like wrapping of DNA on | protein complexes called nucleosomes, like string on beads, but | that's less interesting in this context.) | | [1] | https://en.wikipedia.org/wiki/Nuclear_organization#DNA_loopi... | [2] | https://en.wikipedia.org/wiki/Nuclear_organization#Chromosom... | est31 wrote: | It's interesting how much variation there is even within mammals | when it comes to number of chromosomes, even though so much of | the genome is conserved. This points to chromosomes being a major | factor on the grander scales of evolution. | gumby wrote: | > This points to chromosomes being a major factor on the | grander scales of evolution. | | Or, alternatively, that chromosomal-level organization is | happenstance. | | I agree though with your implication that it's an interesting | area of study. Perhaps there is an interesting mechanism to be | learned or disproven. | notTheAuth wrote: | Check out bio electrical regeneration research | | If you haven't come across it, the teams inject drugs that do | nothing to cells but instigate an electrical field effect. | What happens is regrowth of a limb to the correct "spec" even | though that physical information is gone (limb amputated). | | This suggests to me an equalizing effect exists, where fields | and matter feed each other just enough to reach structural | equilibrium. | | Relativistic information network effects, proving what math | objects create which field effects, and the social impacts, | are going to become huge and blow away our current | engineering goals of making hard silicon computers. | | We might be able to use nature itself as our CPU. | IAmGraydon wrote: | I understand some of these words. Can someone explain this in | layman's terms? | RyEgswuCsn wrote: | It's a legacy codebase. The default assumption should be "DO NOT | DELETE THIS". | | Jokes aside, I wonder if we actually know enough to safely meddle | with genetic materials, e.g. with mRNAs vaccines. | wizzwizz4 wrote: | mRNA vaccines are barely meddling with genetic materials. We | know that lots of viruses are barely harmful; mRNA vaccines are | basically just: | | * take out most of the steps | | * change the payload | | * substitute one of the ingredients to trick the immune system. | | If you said CRISPR, I'd agree - but we do know enough for mRNA | vaccines. | | To use a CS analogy, mRNA vaccines aren't Turing-complete, but | CRISPR is. We understand both fairly well, but the implications | of mRNA are much simpler than the vast, vast, vast implications | of CRISPR. | what_is_orcas wrote: | I'm curious why you question CRISPR. I've worked with CRISPR; | I've seen some very unexpected results from its use; I've | also not really kept up with the science in the past few | years. | | Do you have experience working with CRISPR? Is there a study | or set of studies that concerns you, or is it the reality | that negative results don't get really get published? | wizzwizz4 wrote: | CRISPR is basically find-and-replace with DNA. DNA | expression is weird and complicated, and some bits do | different things depending on the environmental context. | There's a lot of potential for things to go wrong. | | mRNA vaccines are injecting simple, engineered mRNA. This | mRNA is expressed 100% of the time; what it does is very | simple. I'd be confident using a new mRNA vaccine on day 1, | so long as they're certain they picked the right protein, | but I wouldn't be confident using a CRISPR treatment | without a full medical trial. | tazjin wrote: | There's nothing in the comment that "questions" CRISPR, | it's just pointing out that due to the larger space of | possibilities more care needs to be taken with it. | dekhn wrote: | CRISPR is not "turing complete", I'm not sure where you got | this impression. You could build a pseudo-turing machine | (finite memory, measurable but small error rate) with enzymes | and DNA, but CRISPR is not sufficient to implement turing | complete computation. | singlow wrote: | He did not try to say it was turing complete. He was making | an analogy: CRISPR:mRNA::Turing Complete:Non-Turing | Complete. Not sure how deep that analogy is, since non- | turing complete systems can still be very powerful. But I | think it gits the idea across OK. | dekhn wrote: | OK, it was written very misleadingly. Further, the | comparison doesn't even make sense. RNA molecules can | fold into ribozymes and carry out activity. In principle, | you could make a turing machine with RNA molecules, | although the error correciton would be fantastically | hard. | | Computer scientists, please stop making CS/biology | analogies. | tazjin wrote: | That's also not what they wrote, they used it as an analogy | - in the sense that mRNA can express one very specific | thing, and CRISPR can express a much wider variety of | things. It's not about literal turing-completeness. | RyEgswuCsn wrote: | I guess my point is that our understanding of how mRNA | vaccines operate (or any other methods for manipulating | genetic materials, for that matter) might prove incomplete, | just like how we underestimated the importance of | microchromosomes, as stated in the article. | | The current generation of mRNA vaccines may be simple enough | for the scientists to analyse, but I feel it will only be a | matter of time before the complexity of such technologies | grow to the point that it resembles art more than science. (I | am looking at you, deep neural networks!) | caymanjim wrote: | mRNA's mechanism of action is trivially simple. There's a | known gene that codes for a known protein, and they create | a snippet of mRNA to codify it. It doesn't change your DNA, | it's not a virus, it's not able to replicate in any way. | There aren't any unknowns waiting to be discovered. The | mechanism is fully-understood and easy and safe. | | The complications with mRNA vaccines like this have to do | with keeping the mRNA intact during delivery and getting it | into the cell so the protein gets built. That's the hard | part, and the focus of all the patented engineering that | differentiates BioNTech and Moderna vaccines. And the | delivery mechanism, while complicated, doesn't involve | anything genetic; it's a mechanical problem. | RyEgswuCsn wrote: | > There aren't any unknowns waiting to be discovered. The | mechanism is fully-understood and easy and safe. | | I am sure many people felt that we had figured it all out | w.r.t. planet motions etc. with Newton's law of physics | :) | | You are mistaken if you think I am anti-vaccine or | something. I merely tried to point out that there are | always unknown unknowns and that we should remain | cautious when it is people's health that are at risk. | nicktelford wrote: | mRNA vaccines don't meddle with your DNA. They inject mRNA in | to cells that _temporarily_ instruct the cell to produce a | specific protein. Once the mRNA is exhausted, the cell stops | producing that protein. | Zababa wrote: | So in that case the mRNA is more like printer ink than like a | blueprint? Or both at the same time? Is it possible for a | cell to still produce the protein when it runs out of mRNA? | pjc50 wrote: | It's a print _job_. The cell is printing more bits of cell | all the time, we just slip in some extra messages that | print foreign proteins. The immune system identifies the | proteins as foreign and produces antibodies to destroy | them, which primes it to destroy matching COVID viruses. | m00x wrote: | As an ex-biologist, this is the best analogy. | | mRNA is "messaging" RNA. It sends the message to the | protein factory to make more of a protein structure | defined by the DNA, just like a print job sends the | message to the printer. | chriswarbo wrote: | The "ink" would be amino acids that are always floating | around in the cell, the "printer" would be a ribosome. | | The mRNA would be something like the print buffer that | stores the currently printing document. DNA would be the | document file stored on disk. | nicktelford wrote: | I'm not an expert in this but... If DNA is like a | blueprint, mRNA is like an email sent from the architect to | the contractor to instruct them to carry out specific work. | sp332 wrote: | If DNA is a blueprint, mRNA is a photocopy that's used as a | working memory of it for a ribosome to use while making a | protein. It's chemically unstable and soon falls apart. | (The individual nucleotides night be recycled into other | mRNA strands that the cells make.) Since the vaccine mRNA | does not have any corresponding DNA to make more copies | from, that's the end of it. | Zababa wrote: | > It's chemically unstable and soon falls apart. | | Thanks, that was the part that the others answers didn't | cover. | vaylian wrote: | Watch out, your computer is using electricity that could | potentially kill you. | | mRNA vaccines don't modify your dNA. They provide a volatile | blueprint of the corona-specific spike protein, so that spike | proteins can be synthesized for a short time, analyzed and then | discarded by the body. | [deleted] | feoren wrote: | One problem with mRNA is that 75% of its name is what it's | built out of, and only 25% what it _does_. It 'd be like if we | called HTTP packets "hBits", flash memory words "mBits", text | files "tBits", and OS kernel instructions "kBits". I can see | how someone would be worried that putting tBits on their | computer could potentially modify their kBits! What if all | those bits got all jangled up!? | | If we called mRNA a "protein print job" like pjc50 came up | with, and we called our chromosomal DNA our "kernel | instructions", etc., I think it'd be more obvious how silly it | is to worry that mRNA is going to somehow alter your | chromosomal DNA. The point is that there are a _lot_ of | different functional things and data structures made out of | bits, and a _lot_ of different functional things and data | structures made out of adenosine, guanine, cytosine, and | thymine /uracil. | telotortium wrote: | To be fair (not trying to imply mRNA vaccines modify your | DNA), there are a _lot_ of systems, especially past but also | present (with vulnerabilities), where the right (wrong) print | job could end up permanently modifying your system 's kernel | instructions. | umvi wrote: | Maybe we should use the word "use unknown" instead of "useless" | when dealing with things we don't fully understand. | | History has humbled us countless times. I recall a recent | Veritasium video wherein famous mathematicians of centuries past | labelled the concept of negative numbers "useless" (because they | didn't understand how they could be useful). My high school bio | teacher confidently claimed that the appendix was a "useless | organ". | OneLeggedCat wrote: | The first sentence of the article: | | "Originally, they were thought to be just specks of dust on a | microscope slide." | jfrunyon wrote: | > My high school bio teacher confidently claimed that the | appendix was a "useless organ". | | So does the Encyclopedia Brittanica, Healthline, and any number | of other sources: | | > appendix, formally vermiform appendix, in anatomy, a | vestigial hollow tube | 323 wrote: | They are wrong. | | > The appendix has been identified as an important component | of mammalian mucosal immune function, particularly B cell- | mediated immune responses and extrathymically derived T | cells. | | https://en.wikipedia.org/wiki/Appendix_(anatomy)#Functions | neuronic wrote: | Do we have data on COVID in people without appendix? | echelon wrote: | If the appendix truly serves no function and isn't | developmentally required, then selection pressures would tend | to remove it. | | It likely has some complex purpose, such as a reservoir for | microbiome. | hinkley wrote: | Others have said this using different words, but evolution | relies on the preservation of low-cost mutations. It took | many mutations to get from photoreceptors to the mammalian | eyeball. | | If the cost is small enough that other factors dominate | your ability to procreate, it will spread to all of your | descendants. If other genes in your genome make you | reproductively successful, that gene edit will spread and | spread. | | It's a good thing these cheap changes are preserved, or | viruses and bacteria would have wiped out all multicellular | life early on by practicing patience. We all have genes | that make us less susceptible to some pathogens than others | and if a bad enough variant comes around, suddenly we are | over represented in the next generation. If the hits keep | coming eventually our family reunion may be the only one | being held. | robbiep wrote: | This is a profound misunderstanding of the driving forces | of evolution. | | Why do we have wisdom teeth? Just because something is | useless doesn't mean it's eliminated | fastaguy88 wrote: | This is a widely held misconception. Mammalian genomes | contain about 50% of their DNA as repeated sequences, and | although there are people who can imagine uses for those | sequences, there is no evidence that they are required or | even evolutionarily advantageous. | | The idea that modern higher organisms have been "optimized" | so that every part is essential is not well supported by | evidence, and there are many examples of features that | simply are historical artifacts or "not-sufficiently | harmful". Many evolutionary biologists are comfortable with | neutral theories consistent with the idea that large | portions of the genome are not under strong (or perhaps | even moderate) selection. | pbh101 wrote: | You're talking about messiness in the genotype, but | selection pressure happens to the phenotype. The latter I | think controls more of what ends up in the former. | | Which is what we see all the time in programming: | software wins because of its effect, not usually the | lines of code needed (or not) to get there. | fastaguy88 wrote: | I'm not sure I understand your argument, but if large | portions of the genome have no effect on phenotype, then | perhaps we can both agree that those regions would not be | under selection. Pressure on the phenotype cannot | directly alter the genotype (no Lamarkism), but it could | select for or against the fraction of the population with | a particular genotype. But only if the genotype produces | a phenotype. | cma wrote: | Wouldn't assuming a one-copy rule end state is natural | cause immense issues with recessive genetic disorders | (which could in turn select against it), and also make | chromosomal-crossover produce sterilized but viable young | at a much higher rate? | echelon wrote: | > This is a widely held misconception. Mammalian genomes | contain about 50% of their DNA as repeated sequences, and | although there are people who can imagine uses for those | sequences, there is no evidence that they are required or | even evolutionarily advantageous. | | If you remove noncoding "junk DNA", you alter the higher | level spatial configuration of DNA. Histone winding | changes which promoter regions are accessible, gene | dosing is altered, binding affinity and kinetics change, | etc. These are dynamical equations you're dramatically | altering. | | Non-coding DNA also likely shields against several | classes of random point mutations, base substitutions, | transposition, etc. preventing cancer and cell | physiological disease states. | | It's also important for maintaining alignment during | crossover. | | If it truly served no purpose, it would be gone. | | > The idea that modern higher organisms have been | "optimized" so that every part is essential | | Essential is the wrong word here. Relying on every part | for survival would put us at risk. We have plenty of | built in redundancies to support degradation, failure, | and loss of multiple systems and functions. | | I get your argument, but I still disagree. At the species | / population level, we have been optimized as wholesale | organisms as best as development and body plans will | allow. Everything not subject to pressure will get washed | away. | | Despite our vestigial tails, the coccyx supports our | weight while we are seated. As I postulated before, the | appendix probably has a net positive function in | supporting gut microflora and our "junk DNA" plays a role | at the molecular level. | gwright wrote: | biological version of dead code with no time allocated in | the roadmap for cleanup and refactoring? | frenchyatwork wrote: | Only vaguely. If the DNA was to be compared with our | programming languages, it would be like INTERCAL, but a | million times worse. | | Sections of the genome interact not only with the code | right around them, but also with code far away, as a | result of the chromosomal folding. So a section of 100 | nucleotides might not do anything if you splice it out | and throw various enzymes and other chemicals at it, and | it might not even matter that much which nucleotides they | are, but if you remove them and change the shape of the | chromosome, it might not work the same way. | | A lot of our knowledge of genetic is limited to the | things that are easy to test. | UnFleshedOne wrote: | Except our machines are designed around the idea of | isolating components and minimizing unintended side | effects, while biology has no such compulsion. | | Imagine if an extra semicolon in one of your unused files | shifted electrical distribution on storage media and that | had all kinds of downstream effects on unrelated systems | and those effects were critical for multiple other | functions. | | Only increase complexity enough so the whole contraption | is NOT brittle. | dwaltrip wrote: | You yourself gave the answer. "Tend to" means it is likely, | not that it will always happen. | jfrunyon wrote: | That's not how selection works. If something doesn't | _decrease_ survivability, then there is no reason why | evolution would get rid of it. | beebmam wrote: | This is a common misunderstanding. | | The same logic would apply to male nipples. It's a flawed | logic. | wwwwewwww wrote: | Nipples are used by female mammals for feeding their | young, so this logic does not apply to nipples. | beebmam wrote: | It certainly does apply: why do men have nipples? Likely | for reasons similar to why we have an appendix. | | Fundamentally, natural selection and evolution are models | that help explain general biological processes, to help | us comprehend a bigger picture. Around the edges of that | picture, it's not fully clear. | | The truth is that the universe is governed by laws that | are deeply unintuitive: general relativity and the | standard model. Each layer of abstraction on these makes | the periphery of the image fuzzier, but allows us to make | more sense of the part of the image that we're focusing | in on. | echelon wrote: | Genes to turn off development of the nipples would cost | more. The same body plan is used until sex hormones cause | sex characteristics to develop. | | Many females also find male nipples attractive. | bmeski wrote: | That's only if the gene's to express an appendix ever go | away. | | I always think back to Richard Dawkins explaining how a | particular vein in a Giraffe's neck is wrapped around a | lower neck bone and has grown 2x to accommodate the long | neck instead of regrowing in a more efficient way (not | wrapping). | freedomben wrote: | I believe you're talking about the laryngeal nerve! | | And I don't think it's just giraffes, it's all mammals, | which also points to a common ancestor. | roywiggins wrote: | The recurrent laryngeal nerve is actually common to all | tetrapods, not just mammals. Birds have it, probably | dinosaurs had it. | | https://bioone.org/journals/acta-palaeontologica- | polonica/vo... | bmeski wrote: | Nature's billion dollar mistake? | elliekelly wrote: | Can't an inherited trait be "neutral"? By that I mean it | confers neither a benefit nor a detriment? It's my | understanding that the baby toe, for example, isn't | particularly useful anymore. But having or not having the | baby toe(s) isn't likely to help or hinder a person's | ability to reach adulthood and reproduce. There must be a | lot of traits like that, right? Like eye color or maybe | wisdom teeth. No one (as far as I know) is selecting a sex | partner based on whether their wisdom teeth were impacted | or not. | bluepizza wrote: | > selection pressures would tend to remove it. | | A person born without an appendix has no actual advantage | over a person who has one, so selection doesn't really | influence it. | | The human body is full of things that truly serve no | function, and it's also full of detrimental things, such as | genetic diseases. | | As long as it does not impact reproduction, selection has | no impact. | consp wrote: | > A person born without an appendix has no actual | advantage over a person who has one | | Untreated appendicitis is quite deadly. I would say there | is definitely some advantage. | blacksmith_tb wrote: | That's true, but untreated cardiomyopathy is potentially | deadly too, yet that isn't enough pressure to cause us to | not have hearts... | joconde wrote: | Good idea but bad example. Something needs to fulfill a | heart's role, but we can live without an appendix just | fine. | blacksmith_tb wrote: | Oh sure, it was reductio ad absurdum, just pointing out | that the possibility of appendicitis wasn't by itself an | argument against its continued existence - I don't know | anyone personally who has ever been diagnosed with it... | bluepizza wrote: | Unless it is widespread deadly before breeding age, it | doesn't make much difference. | | See: dementia, cancer. | [deleted] | awillen wrote: | It looks like the only person who described them as useless is | the editor who wrote the headline, and they did it in an | incredibly disingenuous (and grammatically incorrect way) by | putting quotes around it. That implies that someone in the | study used the word useless, which doesn't actually appear to | be the case. | ConcernedCoder wrote: | It is difficult to imagine a system of evolution where | "useless" survives in successful iterations. | BurningFrog wrote: | I find it difficult to imagine a system of evolution where | useless code is reliably removed. | baruch wrote: | Presumably there is a cost to carrying the DNA, if it gets | removed by chance and the cost was high enough the useless | part will disappear. | | That however hinges on the cost being high enough, if the | cost is negligible then there is no real pressure either | way. | dekhn wrote: | this cost of "DNA size" is a long and ongoing argument in | biology with no clear answer. Here's the strongest straw | man argument in favor of "there are large amounts of non- | funcitonal DNA which has zero evolutionary cost": | https://www.cell.com/current- | biology/pdf/S0960-9822(12)01154... | epistasis wrote: | Your point of view in evolution is called Adaptionism, but | there are those who believe otherwise, and use the term | "spandrel" to talk about the "useless" things that evolution | carries along. | | https://en.m.wikipedia.org/wiki/Spandrel_(biology) | | Of course, something that is currently useless may become | useful as the environment changes. Or it may not. Personally, | I find a healthy sense of detachment from purpose, and | certainly from any sort of teleology, is necessary to become | philosophically consistent with the evidence from | evolutionary biology. | ConcernedCoder wrote: | Thanks for the rabbit hole ( I've never really studied | evolution outside of CS applications ). | | Your point of view about detachment makes quite a bit of | sense to me, and if the spandrel idea proves true I guess | we (Homo sapiens) will just have to take it on the chin... | elliekelly wrote: | This is quite interesting! Thanks for sharing! So might it | be that a species, as a whole, benefits from carrying | around a certain amount of "spandrels"? A genetic insurance | policy of sorts to protect against/quickly adapt to | unforeseen changes? Has there been any research into the | prevalence (or absence) of spandrels in species that have | gone extinct? | epistasis wrote: | I'm not sure if there's much research in evolution about | species that have gone extinct versus extant species, or | at least I haven't encountered it. | | The human genome carries around a massive amount of | spandrels, in the form of what is called "selfish DNA." | About 15% of the human genome consists of repeats of a | single sequence: the Alu gene, which seems to primarily | exist to replicate itself in the genome. This is part of | a class of genes called transposable elements: | | https://en.m.wikipedia.org/wiki/Transposable_element | | And when discovered in corn, accounted for 85% of the | genome. Barbara McClintock, their discoverer, | hypothesized that they serve as a growth bed for | evolution. And over the years it has indeed been found | that individual transposable elements can serve as the | seeds for new control sequences that coordinate when to | turn genes on and off. The major forces of evolution in | vertebrates are not big changes in proteins, but rather | changes in when and how various proteins get activated, | and transposable elements serve a big function in | allowing that sort of evolutionary change in genomic | sequences. | | Does most repetitive DNA in the genome seem to be | useless, in that its deletion or replacement have little | effect on the genome? Probably! But all that fluff also | facilitates more easy rearrangement of the genome, | because if every part of the genome was essential, | randomly moving a chunk of DNA into a new spot would | likely kill off some useful stuff. But if there's a bunch | of stuff that is useless, randomly copying some stuff | into a random spot is less likely to disrupt something. | If the genome is a hard drive, there's no "free list" or | file system for the genome, so random writes are less | likely to be disastrous if there's nothing of importance | on most of the drive. | | I used to get upset at the term "junk DNA" but I don't | really care one way or the other now. One cell's junk is | another's treasure. | enkid wrote: | Certainly there are thing that formerly had a use but are | less useful now. I'd be careful calling something useless, | but if there isn't an advantage to getting rid of a feature, | I see no reason it would be gotten rid of. | nextaccountic wrote: | It depends on the cost of carrying vestigial stuff around vs | the time required to make such changes (thousands of years? | millions of years?) | | Sometimes organisms carry things not very useful anymore for | a looong time. | roywiggins wrote: | Evolution is not that ruthless. Useless but neutral traits | can just stick around, if there's no selection pressure to | get rid of them. | micromacrofoot wrote: | not to mention the perception of some organisms in ecosystems | as "useless" only to discover their absence causes the system | to collapse | bruce343434 wrote: | The video in question, for those curious: | https://www.youtube.com/watch?v=cUzklzVXJwo | gus_massa wrote: | I agree, but note that the title of the research article is " | _Microchromosomes are building blocks of bird, reptile, and | mammal chromosomes_ ". | mrfusion wrote: | So they're saying we have chromosomes floating around in our | cells? Outside the nucleaus? How do they get replicated? | roflc0ptic wrote: | They're saying birds and reptiles and other animals have micro | chromosomes, and that mammals have incorporated these micro | chromosomes into their macro-chromosomes. | | Per the Wikipedia page, Micro chromosomes are replicated the | same way as other chromosomes - mitosis. | vaylian wrote: | The original scientific article says that mammals don't have | the microchromosomes. And they are located inside the nucleus | in other species. | greatjack613 wrote: | Ha, I though this was an article on useless crypto - | https://uselesscrypto.com since my skim reading of the title came | up with Useless + building blocks. | | Little did I know....... | beckerdo wrote: | A fascinating article. David Quammen's book "The Tangled Tree: A | Radical History of Life" also has stories how DNA changes through | more mechanisms than just mutation. | mcbishop wrote: | > The exception is the platypus, which has several chromosome | sections line up with microchromosomes... | | Even at this level, the platypus is a strange creature. | feoren wrote: | One really has to wonder if we're all missing something with | the platypus. Did some extremely unlikely gene transfer happen | at a scale, and across taxonomic distances, that nobody has | ever thought possible? There is some N where repeating the | argument "it's just a quirk that they're so different" N | different times starts to not feel like the simplest | explanation any more. Are we _absolutely certain_ there 's no | way a frisky duck-oid forced itself on an unlucky shrew-oid and | in a one-in-a-billion stars-aligning miracle, managed to | produce a viable offspring? (Edit: I guess they'd have to | produce at least two ...) ___________________________________________________________________ (page generated 2021-11-03 23:00 UTC)