[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 ...)
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