[HN Gopher] Tiny fern has the largest genome of any organism on ...
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Tiny fern has the largest genome of any organism on Earth
Author : PaulHoule
Score : 102 points
Date : 2024-06-08 11:02 UTC (11 hours ago)
(HTM) web link (phys.org)
(TXT) w3m dump (phys.org)
| beretguy wrote:
| My man Anton made a video about it
|
| https://invidious.private.coffee/watch?v=QhEfAHNREmM
| chairhairair wrote:
| Awful summary video, in my opinion. Takes 5 minutes to get to
| the new discovery, then spends 3 minutes repeatedly claiming
| that we don't have any explanations for the wide range of
| genome sizes, then 2 mins of Patreon credits to get over the 10
| minute mark. There might be 30 seconds of actual content in
| this video.
|
| I'd give a highschooler a bad grad on this, why do so many
| people give this guy money to make low quality content like
| this?
|
| He could have just picked any section of this Wikipedia page
| and read it verbatim and he would have transmitted more
| information: https://en.m.wikipedia.org/wiki/Genome_size
| p1esk wrote:
| I found that video pretty interesting.
| 1234554321a wrote:
| Bad channels which've accumulated views and subscribers
| getting recommended by the youtube algorithm. Hence why he
| has a filler segment to get the video to 10 minutes. That's
| just how youtube works nowadays.
| unutranyholas wrote:
| is it a memory leak?
| 2OEH8eoCRo0 wrote:
| memory leek?
| Animats wrote:
| Many plants have huge genomes. Maybe they didn't evolve macros or
| subroutines or something. Anyone know anything about this?
| jameshart wrote:
| Weird, since ferns' fractal growth plan lends itself so well to
| simple recursion.
|
| Maybe most of the genome is just a long comment explaining why
| they can't use recursion.
| pantalaimon wrote:
| Or maybe the simple growth plan allowed it to accumulate lots
| of cruft that's basically doing nothing
| idiotsecant wrote:
| Biology only cares about elegance when it substantially
| contributes to fitness, otherwise entropy is the natural way
| of things!
| jameshart wrote:
| Natural selection leaving review comments: lgtm
| throwup238 wrote:
| It's an active area of research but there's no consensus on
| _why_ this happens other than hand wavy evolutionary biology
| stuff. The most interesting mechanism is paleopolyploidy [1]
| where the whole genome of the organism is doubled due to
| hybridization or DNA replication errors and from that point on
| the duplicates start diverging. It has occurred at least once
| in most flowering plants and it must have happened several
| times with this fern. Normally after this kind of event, the
| genome is paired down and duplicate genes are "silenced" in a
| process called diploidization [2] but if there are a bunch of
| transposable element, they might differentiate the copies
| enough to keep them before the process completes.
|
| [1] https://en.wikipedia.org/wiki/Paleopolyploidy
|
| [2] https://en.wikipedia.org/wiki/Diploidization
| PartiallyTyped wrote:
| There's a recent veritasium video on jumping spiders. Turns
| out some of them evolved red colour eyesight in multiple
| independent ways, one example involves replicating a green
| colour vision gene and then mutation, another one adding a
| filter on top of green colour receptors, forcing neurons to
| activate on red instead!
| brnaftr361 wrote:
| We touched on polyploidy in genetics of course but I don't
| recall anything that was particularly salient insofar as
| resistances. In humans xploidy typically results in either
| excessive protein expression or compromised (<=50%) protein
| expression - in many cases this is fatal or seriously damaging
| in terms of fertility/development. There are exceptions, for
| instance the mammalian liver has polyploidal cells.
|
| But plants are _way_ different in terms of habit, think about
| evolving to sit in the same place for a hundred years...
|
| These for example could have epigenetic crosstalk between their
| environment (epiphytic nature) and their hosts. E.g. a special
| chromosome for birch vs oak. Or drought vs monsoon. Given the
| endpoint of the species is purportedly 350mn years it stands to
| reason that a highly specialized and nuanced system of
| regulatory pathways may have emerged. Sequence data and
| genomics would be revelatory.
|
| It wouldn't surprise me if there was specialized information
| per-host which was regulated by signal produced by the host, I
| think this would explain redundancy pretty well. Different
| epigenetic pathways operating on different x1 chromosomes
| yielding differential response to discrete small
| molecules/proteins/hormones produced by host species which
| prove beneficial in the _looong_ run. This could have a whole
| cascade of effects or just subtle SNP differences which yield
| fitness enhancements. Essentially each one being a subroutine
| for each host case producing local optimums.
|
| But I'm just a scrubby undergrad so with a grain of salt.
| There's probably many other more reasonable explanations, it's
| biology, biology seeks to find exceptions to every rule by its
| nature.
| photochemsyn wrote:
| Plants are tolerant of gene duplication, possibly related to
| the fact that their stem cells are permanently active (which is
| why you can take a branch tip and get it to grow into a whole
| plant, quite unlike the efforts needed to clone Dolly the
| sheep). Their development is thus remarkably plastic (so you
| can get trees at the snowline that look like small shrubs,
| while the same species grows into tall straight trees a few
| thousand feet lower). In contrast, gene duplication at a large
| scale in any animal would probably fundamentally mess up body
| plan development in non-survivable ways.
|
| Plants might be under active selection for gene duplication
| since it does allow rapid evolution and facilitates spread into
| new environments:
|
| Evolution of Gene Duplication in Plants (2016)
| https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4972278/
| samatman wrote:
| > _In contrast, gene duplication at a large scale in any
| animal would probably fundamentally mess up body plan
| development in non-survivable ways._
|
| While unusual, polyploidy in mammals is survivable, there's a
| species which is tetraploid:
|
| https://en.wikipedia.org/wiki/Plains_viscacha_rat
|
| The wiki exaggerates the degree to which this claim is
| controversial, fwiw. Better than the alternative, probably.
| layla5alive wrote:
| This is like template metaprogramming :)
|
| You're confusing the difference between macros and functions,
| only functions fully avoid duplication (except when they are
| inlined!)
|
| Macros are expanded into text by the preprocessor. Templates
| are expanded by the compiler instead.
| kevindamm wrote:
| Real macros (lisp-style not C-style) are more like template
| metaprogramming, too. It's not clear which source language GP
| comment is referring to.
| Tuna-Fish wrote:
| Interestingly, warm-blooded animals (including humans!) tend to
| have simple genomes compared to cold-blooded ones or similar
| complexity. It's just much easier to get repeatable results
| during development when you can do all the trickiest parts at
| fixed temperature, a human can use a single gene to achieve
| what a frog needs half a dozen for.
| thelastgallon wrote:
| Humans outsource a lot to the microbiome. We have to add up
| all that too!
| throwup238 wrote:
| As far as we know, all complex organisms have an
| accompanying microbiome of commensurate species, even the
| most basic ones like marine sponges [1]. Plants nurture
| these symbionts in their roots while animals do it in their
| digestive tracts (mostly, both have surface microbes too
| that do various things too).
|
| [1] https://www.nature.com/articles/s41396-020-0591-9
| lend000 wrote:
| The reason for this is that chemical reaction rates are
| temperature dependent, and cold blooded animals need
| different systems of chemicals/proteins to keep them
| operating over significantly different temperatures.
|
| I wonder to what degree the competitive advantage of being
| warm blooded consists of the smaller genome vs. more obvious
| advantages like ability to stay active in colder climates.
| magicfractal wrote:
| This is super interesting! Can you share more info/resources?
| thih9 wrote:
| Moral of the story, if you notice you have to deal with a
| multitude of states, get out of that swamp first, get some
| foundations right and then iterate. Applies to both biology
| and coding.
| idiotsecant wrote:
| On the other hand, the human body is super-reliant on very
| nearly exact temperature regulation. A few degrees can kill
| us easily. Cold blooded systems are substantially less
| reliant on pristine conditions.
| thih9 wrote:
| Warm blooded systems though can power high energy
| activities like maintaining a large brain, which could
| figure out how to get warm.
|
| A few degrees can kill a human only in theory, in
| practice a human would wear a jacket or seek shade.
| simmerup wrote:
| Octopi are cold blooded and smart
| colechristensen wrote:
| Plants are considerably simpler than animals so they tolerate a
| lot more genetic nonsense. Crazy things like duplications which
| would simply result in non viable animals most often don't have
| nearly the harmful effects in some plants so they survive and
| aren't nearly so aggressively pruned out by evolution.
| kleton wrote:
| Article doesn't mention ploidy, source paper says octoploid.
| bloak wrote:
| No explanation of why this tiny fern has such a huge genome?
| chmod775 wrote:
| Because it somehow survived millions of years despite that
| massive inefficiency holding it back. Quite remarkable luck not
| getting out-competed to extinction.
| dustfinger wrote:
| > despite that massive inefficiency holding it back
|
| I assume you are referring to the size of the genome. Has
| anyone been able to prove that it is causing an inefficiency?
| Maybe it isn't. In classical computer programming languages
| sometimes more code is more efficient, such as unrolled
| loops. That analogy may not apply here. I am far from
| knowledgeable in this realm.
| wongarsu wrote:
| If it's really just inefficiency, wouldn't a mutation that
| removes some of the surplus genome bring an evolutionary
| advantage? Those mutations are probably rare and the
| advantage miniscule, but anything adds up over a long enough
| timeframe
| analog31 wrote:
| Not ferns specifically, but I've read a simplistic explanation
| that plants lack behavioral defenses, so they rely on chemical
| defenses. And more chemical defenses requires more genes.
| novalis78 wrote:
| Clunky code. Slow growing. Makes sense.
| amelius wrote:
| At least they should have mentioned:
|
| https://en.wikipedia.org/wiki/Junk_DNA
| kvdveer wrote:
| "we don't know what it does, therefore is is junk" feels like a
| very arrogant and/or short sighted way of thinking to me.
| knodi123 wrote:
| "We don't know what it does, but junk DNA is a real thing,
| and that's one possible explanation" is a lot more
| reasonable. And I think that's a more charitable reading of
| the comment you replied to.
| jszymborski wrote:
| As you'll often hear from geneticists these days, one
| person's junk is another person's treasure.
|
| There certainly was an attitude for a long period of time
| that our DNA was full of junk[0], but the field has since
| characterized much of what we once thought was junk (i.e.
| non-functional DNA) actually is just non-coding DNA[1] that
| serves one or more of a wide array of biological functions.
|
| In many ways, you can't really blame scientists of the 70s
| for thinking that much of what we now know is ncDNA was
| inscrutable junk. In many ways, given the technology at the
| time, it was.
|
| It's a super interesting area of study.
|
| [0] https://pubmed.ncbi.nlm.nih.gov/5065367
|
| [1] https://en.wikipedia.org/wiki/Non-coding_DNA
| rpozarickij wrote:
| > junk (i.e. non-functional DNA)
|
| Perhaps people should use the term "non-functional DNA"
| instead of "junk DNA" more often. Calling something as
| "junk" has unnecessarily dismissive connotations.
| pretendscholar wrote:
| They should call it non-translating-to-protein-but-
| probably-has-some-function DNA
| darby_nine wrote:
| Even non-functional isn't nearly as good as "genetic data
| with unknown function or expression".
| ijidak wrote:
| I don't know. The concept of junk DNA never made sense to
| me because, besides proteins, you need to know how to
| assemble everything and when.
|
| The idea behind junk DNA was that the rest of it didn't
| code for proteins and therefore was junk.
|
| But if I give you a list of parts for a Boeing 747 that's
| not enough information to build the jet.
|
| I never understood how this was not obvious to scientists.
|
| I still remember being taught the concept of junk DNA in
| high school, and didn't believe it then.
| akira2501 wrote:
| They're not calling it junk as part of an effort to down play
| it or to cause the rest of the field to deprecate or ignore
| it.
|
| They're calling it that because the result is baffling. It's
| meant to be a call to action, not an affront to reason.
| kvdveer wrote:
| "Mystery DNA", or "enigmatic basepairs" might have conveyed
| a call to action. "Junk" definitely has a dismissive vibe
| to it.
| rob74 wrote:
| How about "uncharted" or "here be dragons"
| (https://en.wikipedia.org/wiki/Here_be_dragons) DNA?
| gweinberg wrote:
| "Junk DNA" was a terrible name. But the article really should
| have mentioned something about how much of it actually codes
| for proteins (for both the fern and us).
| kkoncevicius wrote:
| Might be relevant and interesting:
|
| https://www.thenewatlantis.com/publications/getting-over-the...
| playingalong wrote:
| What share of the total organism weight would be the DNA? Is it
| something non trivial in this case?
| s0rce wrote:
| I can't imagine its very much, probably still mostly water and
| structural polysaccharides.
| playingalong wrote:
| How do they know it's the largest? They should rather say it's
| the largest known if anything.
| John23832 wrote:
| I think that is pedantic and goes without saying. There are
| always unknown unknowns.
| eikenberry wrote:
| Yes and no. Scientists throw out these sorts of terms and
| know what they mean but the general population doesn't and
| doesn't get the ramifications of the real meaning. Just see
| how many people think that when a scientist says "the
| universe" that they mean the entire universe and not, as
| scientists mean, the observable universe. For general, "pop"
| cosmology those have very different meanings and lead to all
| sorts of bad thinking.
| Swizec wrote:
| > Just see how many people think that when a scientist says
| "the universe" that they mean the entire universe and not,
| as scientists mean, the observable universe
|
| We once pestered our physics professor to explain what's
| outside the universe. He finally said that's a dumb
| question, the universe is definitionally everything, if we
| find anything beyond the edge of the universe, we'll just
| call that universe too.
|
| Always liked that framing.
| tsimionescu wrote:
| In many contexts, "the universe" means "the whole universe
| [to the best of our knowledge]". For example, when
| scientists talk about the age of the universe or the start
| of the universe or the ultimate fate of the universe, they
| really do mean the whole universe, not just the observable
| universe.
| eikenberry wrote:
| So sometimes scientists are just talking out of their
| ass. They are people after all, so it should be expected
| sometimes.
| exo-pla-net wrote:
| Plants ain't got brains. Gotta use their genome to process
| information.
|
| /Wild speculation.
| the_gipsy wrote:
| Long term strategy
| SomeoneFromCA wrote:
| Cats have longer genomes than dogs too FYI.
| swarnie wrote:
| Is that why they taste better?
| SomeoneFromCA wrote:
| Not even comparable to good old bats and pangolines.
| 2OEH8eoCRo0 wrote:
| Weren't the first plants on land ferns or fern-like?
| bastawhiz wrote:
| The first land plants were likely similar to mosses or
| liverworts.
| DonHopkins wrote:
| Maybe it's recursively encoding JSON as JSON strings many levels
| deep, and it's mostly backslashes and double quotes.
| saddat wrote:
| So bloat-ware ?
| darby_nine wrote:
| It'd be a hell of a job to demonstrate that all that
| information couldn't be useful in the right environment, very
| much unlike bloatware.
| jes5199 wrote:
| sounds _exactly_ like bloatware. it was designed for
| something, it just doesn't happen very often
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