once a year or so a study makes the
rounds that supposedly ends the idea of
junk DNA like we thought most of our
genome was garbage but this time we're
sure that it's not see it the human
genome is 3.2 billion base pairs long
and contains around 20,000 genes
stretches of DNA that code for protein
but those genes only make up about one
to two percent of our DNA the other 99%
of our genome is non-coding and the
question of whether it's useless or not
has been hotly debated by biologists
since the term junk DNA was coined in
the 1960s so is there really a bunch of
DNA that doesn't do much of anything or
does it all do something and we just
haven't figured out what it seems like
our genomes shouldn't be mostly junk it
takes energy to copy and maintain large
amounts of DNA so it seems like we
should get rid of any extra baggage and
well it's pretty easy for biologists to
say that coding DNA does something it's
tricky to make the call about different
types of non-coding DNA protein coding
DNA has a clear and elegant function a
stretch of DNA is transcribed to RNA and
a cell's nucleus and then translated
into a protein proteins do things that
you can pretty easily study like helping
with chemical reactions are building a
cellular structure and humans are made
up of thousands of types of cells which
each need different kinds and amounts of
proteins to do their jobs so every cell
needs a way of handing out instructions
for how much to make of what stuff enter
transcription factors proteins that
increase or decrease the chance that a
gene will be transcribed into RNA they
can be switched on in response to all
kinds of things like chemical signals
from outside the cell or a certain stage
in the organisms development and this is
where a couple important types of
non-coding DNA come into play with a
clear purpose transcription factors bind
to DNA but not directly to genes instead
they bind to stretches of DNA that don't
code for anything but have a direct
effect on genes for instance promoters
are right in front of genes there where
the machinery that transcribes RNA
actually
comes together and gets to work when a
transcription factor binds to a promoter
it helps everything get going now naming
all of the different kinds of non-coding
DNA and what they do would be a little
much but let's talk about a couple you
might have heard of before like there
are introns gaps in coding regions that
seem kind of like junk but actually a
cell can cut them out to mix and match
segments of coding regions and create
variants of a protein from a single gene
there are also bits of non-coding DNA
that get transcribed into RNA that never
gets translated into a protein
collectively called non-coding RNAs the
structures that directly assemble
proteins called ribosomes are partially
made up of non-coding rnas and transfer
RNAs shuttle around the building blocks
of proteins some others like micro RNAs
and long non-coding rnas act more like
transcription factors they change the
expression of a certain gene or region
of the genome in indirect ways so
molecular biologists are interested in
studying things like all the
nitty-gritty functions of transcription
factor binding sites and non-coding RNAs
and by some definitions any DNA that
binds to a transcription factor or gets
transcribed into RNA is considered
functional which seems like a victory
for the anti junk way of thinking this
idea peaked in 2012 thanks to the
publication of a lot of research by an
international consortium known as encode
it's short for encyclopedia of DNA
elements they made a remarkable claim
that 80% of the human genome is
functional in some way encode used a
variety of molecular biology techniques
to support this idea most of them had
something to do with whether a
transcription factor binds to a given
piece of DNA for example chips seek is a
way to isolate segments of DNA where a
particular transcription factor binds
which scientists can then sequence the
idea behind encode is really cool it was
meant to help anyone who wanted to study
specific stretches of DNA like a
database of what binds there and what
non-coding RNAs are produced but there
was immediate push back against that 80%
of the human genome is functional idea
it wasn't that encodes research was bad
this was a huge international group of
reputable scientists their definition of
functional was just way too generous as
even some of the authors admit it's like
great you found places where
transcription factors stick to DNA but
some regions of DNA can be kind of
sticky certain proteins might tend to
bind there purely by chance and that
doesn't necessarily mean anything is
happening there other than stickiness
that's only one criticism of many but
you get the idea saying 80% of our
genome is functional is probably too
generous now different fields of biology
work with different scientific tools
molecular biologists research very small
biochemical reactions and the like as
their name suggests meanwhile
evolutionary biologists are studying
genome function through a broader lens
like trying to figure out why different
organisms have vastly different genome
sizes for instance onions and African
lungfish have way more DNA than humans
do meanwhile tougher fish seem to have
weirdly little no one's complaining that
humans are better than onions and that
they somehow deserve to have more DNA
it's just that being a human and being
an onion are two very different things
and it shouldn't take five times more
DNA to be an onion even if they are very
tasty and have all those layers like
ogres the simplest answer to this puzzle
is that a lot of DNA just isn't doing
anything it's junk
even though maintaining extra DNA might
be a little more energetically costly
the process of natural selection might
not stop it from piling up unless it
seriously affects survival and turns out
having extra DNA could also maybe help
in some cases consider pseudogenes which
led to the coining of the term junk DNA
pseudo genes are what happened when a
gene gets duplicated initially both
copies probably work if one of them
picks up a beneficial mutation tada you
got a brand new gene thanks evolution
but if one picks up a detrimental
mutation the duplicated gene stops
working while the original chugs on
normally the messed up version doesn't
get pruned from the genome though it
hangs around as a non-functional bit of
DNA that still mostly looks like a gene
hence pseudo gene a junky left over our
genome is also littered with viral
sequences from old infections loss there
are transposons which encode proteins
that
let that segment of DNA cut itself out
of the genome and squeeze in somewhere
else
that's all they seem to do they just
jump around because they listen to House
of Pain too much every now and then a
paper assigns a function to some viral
gene or transposon but those seem to be
in the vast minority and there are a
handful of other types of junk that
don't seem to do anything for us it's
hard to estimate how much of the genome
is non-functional because these elements
are pretty repetitive repetition tends
to throw off our sequencing methods
because those methods rely on looking at
a bunch of copies of the genome at once
it's like throwing 600 copies of Hamlet
into a blender the unique parts like
alas poor Yorick they're fairly easy to
spot but how many times does Shakespeare
use the word the' if you just get a the
you don't know where to put it overall a
lot of the data in support of junk DNA
comes from population genetics which
involves a lot of math big one paper
published in 2017 in the journal genome
biology and evolution instead of looking
at where transcription factors bind
their definition of functional hinged on
whether a DNA sequence could be acted on
by natural selection in a positive or
negative way most mutations that are
subject to natural selection are bad
because they break some cellular system
and make survival less likely the
study's author estimated their rates
that harmful mutations build up in
humans compared to our rate of
reproduction and effective population
size that's a statistical term that
refers to how much of the population is
finding mates and making babies
basically natural selection can only
eliminate harmful mutations as fast as a
species can breed or they would slowly
die out but mutations in junky regions
wouldn't have bad consequences so they
would stick around this paper tried to
calculate what it would take to maintain
a human genome that's 80 percent
functional even using a conservative
estimate of mutation rate it concluded
that every human couple would have to
have 15 children 13 of which would
survive and have children of their own
which is super unrealistic an earlier
paper published by UK researchers in
2014 in PLoS genetics used a similar
definition of functional they compared
the rates of change of mammalian genomes
to one another genes
come and go across evolutionary time but
by comparing related groups side-by-side
researchers can figure out the most
important regions a subject natural
selection
they found that protein coding genes and
certain non-coding elements were pretty
stable for example promoters were less
stable than coding regions but mostly
stayed put but other non-coding
stretches like transposons weren't
really preserved across species and
therefore they might not do much
interestingly both of these studies
independently came up with similar
estimates for how much of the genome is
functional the 2017 studies suggested
the absolute upper limit for how much of
the genome has a function is around 25%
but favored a more conservative figure
of 10 to 15% in the 2014 study landed at
8.2 percent that's obviously way less
than encodes sweeping 80 percent claim
and those estimates still leave room for
functional non-coding elements on top of
the coding stuff so we still don't have
a clear answer for what's junk DNA and
what's not because how scientists define
functional varies a lot and we're still
trying to understand everything our
genomes can do there's a lot of
complexity and those 3.2 billion base
pairs and we'd be foolish to think we
know every trick but it's also foolish
to think that evolution is so elegant
that there's barely any room for
messiness evolution has no end goal and
no sense of aesthetics it's a whole lot
of probability
so sometimes stuff piles up like DNA
that doesn't do anything in the end we
may have to meet in the middle ground to
reconcile both of those ideas and of
course keep learning thank you for
watching this episode of scishow I
thought it was really good I liked it if
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