Non-Coding DNA preserved by genetic drift?



I don't know if the following is accurate. If so it raises many
interesting questions and possibilities:

"The data suggest it is genetic drift (an evolutionary force whose main
component is randomness), not natural selection, that preserves junk
DNA and other extraneous genetic sequences in organisms. When
population sizes are large, drift is usually overpowered by natural
selection, but when population sizes are small, drift may actually
supersede natural selection as the dominant evolutionary force, making
it possible for weakly disadvantageous DNA sequences to accumulate.
Junk DNA costs energy to duplicate and to carry around as part of each
cell. So natural selection operates against it. But if junk DNA gets
generated by errors in replication faster than natural selection can
select against it then junk DNA can accumulate."

A Few questions. If mutations caused by genetic drift are neither
harmful or beneficial then what use are they? I get the impression they
can be possibly disadvantageous. Secondly, it seems to me natural
selection is the most important in evolution, not genetic drift or
anything else. I surmise to a biologist this is a simple headed and
erroneous way of looking at evolution. Rather the whole picture should
be viewed. However, it does seem genetic drift operates the most in
small populations and therefore it had more evolutionary importance in
the past. Assuming, "The data suggest it is genetic drift (an
evolutionary force whose main component is randomness), not natural
selection, that preserves junk DNA and other extraneous genetic
sequences in organisms" what role does natural selection play in junk
DNA? Is it largely decoupled from genetic drift and junk DNA? The
article states, "The researchers found that a consistent pattern
emerged when genomic characteristics of bacteria and various eukaryotes
were plotted against the species' total genome sizes. Bigger species,
such as salmon, humans and mice, tended to have small, long-term
population sizes, more genes, more junk DNA and longer-lived gene
duplications. Almost without exception, the species found to have
large, long-term population sizes, fewer genes, less junk DNA and
shorter-lived gene duplications were bacteria. The data suggest it is
genetic drift (an evolutionary force whose main component is
randomness), not natural selection, that preserves junk DNA and other
extraneous genetic sequences in organisms. When population sizes are
large, drift is usually overpowered by natural selection, but when
population sizes are small, drift may actually supersede natural
selection as the dominant evolutionary force, making it possible for
weakly disadvantageous DNA sequences to accumulate."

So my questions are what role does genetic drift play in "junk" DNA and
what role does natural selection (the coding region) play in "junk
DNA". And how the two may effect "junk DNA".

Michael Ragland



November 25, 2003
Junk DNA Result Of Slowness Of Natural Selection
Species that replicate at a slower rate and that are fewer in number do
not experience enough selective pressure to prevent junk DNA from
accumulating

Genetic mutations occur in all organisms. But since large-scale
mutations -- such as the random insertion of large DNA sequences within
or between genes -- are almost always bad for an organism, Lynch and
University of Oregon computer scientist John Conery suggest the only
way junk DNA can survive the streamlining force of natural selection is
if natural selection's potency is weakened.

When populations get small, Lynch explained, natural selection becomes
less efficient, which makes it possible for extraneous genetic
sequences to creep into populations by mutation and stay there. In
larger populations, disadvantageous mutations vanish quickly.

Most experts believe that the first eukaryotes, which were probably
single-celled, appeared on Earth about 2.5 billion years ago.
Multicellular eukaryotes are generally believed to have evolved about
700 million years ago. If Lynch's and Conery's explanation of why
bacterial and eukaryotic genomes are so different is true, it provides
new insights into the genomic characteristics of Earth's first
single-celled and multicellular eukaryotes.

A general rule in nature is that the bigger the species, the less
populous it is. With a few exceptions, eukaryotic cells are so big that
they make most bacteria look like barnacles on the side of a dinghy. If
the first eukaryotes were larger than their bacterial ancestors, as
Lynch believes, then their population sizes probably went down. This
decrease in eukaryote population sizes is why a burgeoning of
large-scale mutations survived natural selection in the first
single-celled and multicellular eukaryotes, according to Lynch and
Conery.

To estimate long-term population sizes of 50 or so species for which
extensive genomic data was available, Lynch and Conery examined
"silent-site" mutations. Silent-site mutations are single nucleotide
changes within genes that don't affect the gene product, which is a
protein. Because of their unique characteristics, silent-site mutations
can't be significantly influenced by natural selection. The researchers
were able to calculate rough estimates of the species' long-term
population sizes by assessing variation in the species' silent-site
nucleotides.

Of the original group of sampled organisms, Lynch and Conery selected a
subset of about 30 and calculated, for each organism, the number of
genes per total genome size as well as the longevity of gene
duplications per total genome size. They also calculated the
approximate amount of each organism's genome taken up by DNA sequences
that do not contain genes.

The researchers found that a consistent pattern emerged when genomic
characteristics of bacteria and various eukaryotes were plotted against
the species' total genome sizes. Bigger species, such as salmon, humans
and mice, tended to have small, long-term population sizes, more genes,
more junk DNA and longer-lived gene duplications. Almost without
exception, the species found to have large, long-term population sizes,
fewer genes, less junk DNA and shorter-lived gene duplications were
bacteria.

The data suggest it is genetic drift (an evolutionary force whose main
component is randomness), not natural selection, that preserves junk
DNA and other extraneous genetic sequences in organisms. When
population sizes are large, drift is usually overpowered by natural
selection, but when population sizes are small, drift may actually
supersede natural selection as the dominant evolutionary force, making
it possible for weakly disadvantageous DNA sequences to accumulate.

Junk DNA costs energy to duplicate and to carry around as part of each
cell. So natural selection operates against it. But if junk DNA gets
generated by errors in replication faster than natural selection can
select against it then junk DNA can accumulate..

At some point in the 21st century, barring some natural or human-caused
disaster, biotechnology will advance far enough to make it possible to
edit out junk sequences from cells. So it should become possible to
have offspring that have far fewer junk DNA sequences. Therefore junk
DNA may eventually disappear from the human species. Also, replacement
organs will eventually be genetically enhanced with more beneficial
variants of genes that play important roles in each organ type. It
seems reasonable to expect that at least some people will opt to have
their DNA edited to eliminate junk DNA sequences from cells that will
be used to grow replacement organs. So even some of us who today are
walking around with junk DNA will have less of it once we are able to
have replacement organs grown for us.

Update: Carl Zimmer raises a number of specific objections against the
idea of removing junk DNA but he also sees one point in favor of doing
so: some junk DNA sections can hop around the genome and cause
mutations when they embed in new locations.

There are also arguments for getting rid of junk DNA that Futurepundit
doesn't mention. When mobile elements jump around to new homes, they
can trigger diseases as they mutate the genome.

As for mobile elements that jump around the genome: Yes, note that this
reason for removing junk DNA is especially strong in the case of stem
cells that are going to be used to grow replacement organs. The cells
in those replacement organs (with the exception of testes and ovaries)
are not going to have their DNA passed along to progeny and therefore
the ability of their junk DNA to mutate to create new environmental
adaptations provides no benefit while the junk DNA does pose a
mutational threat that can result in cancer and other diseases.

The effects of removing various junk sequences will be testable by
producing organs without them and then seeing how those organs perform.
This will be relatively less risky to experiment with in the case where
humans have two of an organ. So, for instance, one could have just one
kidney replaced with a junk-free kidney and then, with the other kidney
still available as back-up, the functionality of the junk-free kidney
could be monitored over time. The same could be done with many muscles.
Replace a thigh muscle with a junk-free thigh muscle. If the thigh
muscle fails the result is unlikely to be fatal. There would still be
risks from such an experiment as one could imagine fatal failure modes
where, for instance, an organ releases toxins or clotting factor or
something else that damages some other more critical part of the body.

Next he raises the point that what seems like junk DNA might not really
be junk DNA.

Junk-free genomes may indeed become possible in the future, but they're
probably not a wise idea. Even if junk DNA doesn't benefit us in any
obvious way, that doesn't mean that we can do without it. Many
stretches of DNA encode RNA which never become proteins, but that
doesn't make the RNA useless--instead, it regulates the production of
other proteins. Some broken genes (known as "pseudogenes") may no
longer be able to encode for proteins, but they can still help other
genes produce more of their proteins

Well, my response to this is pretty simple: Yes, it is hard to be
certain that some DNA section has no benefit to the cell. But suppose
at some point in the future we can assign a really high probability to
the idea that some chunk of DNA has no value and that it actually is
far more likely to cause disease than benefit? Why not then remove it?

This reminds of another point: Some genetic theorists make the argument
that we each have dozens and perhaps hundreds of purely harmful
mutations because natural selection can't select out hamful mutations
as fast as they are generated by mutations that occur during
reproduction. If this argument is correct (and I believe it is) then we
should also have junk DNA that is either of no value or harmful.
Someone who holds this more pessimistic view of our genomes as full of
flaws and parasitic DNA sections is going to tend to be more willing to
decide to throw out the suspected junk with the view that the odds are
great that the suspected junk really is junk. Of course, there's no
rush here and we ought to wait a couple of decades for a lot more
evidence to accumulate before acting on this belief.

Zimmer also brings up the argument that simply by making the genome
bigger that junk DNA may serve a useful function by making cells the
correct size. I'm skeptical of this argument mostly because an
assortment of different kinds of intracellular components cross-react
with each other in undesirable ways and turn into compounds that the
cell can not eject or destroy. As a result, cells accumulate junk and
this junk accumulation robs the cells of needed space and decreases the
efficiency of cells as they age as well. The junk also serves as a
source of free radical generation. This problem with junk accumulation
has even led Aubrey de Grey to argue for the transfer of lysosomal
enzymes from other species into humans as a rejuvenation treatment.
Analogously, genomal junk is taking up space that could be used by
cells to do useful work. Get rid of it and the cells might become ever
so slightly more efficient.

Next Zimmer brings up the value of junk DNA and, in particular,
pseudogenes, as potential sources of future beneficial mutations:

It's on this evolutionary scale where purging junk DNA makes the least
sense. The pasting and copying of junk DNA is a major source of new
genetic variation. Instead of changing a nucleotide here or there,
mobile elements can shuffle big stretches of DNA into new arrangements,
taking regulatory switches and other genetic components and attaching
them to different genes. While some of this variation may lead to
diseases, it also prepares our species to adapt to new environmental
challenges. (Similarly, pseudogenes that are truly broken still have
the potential to become working genes again. Some scientists have
proposed calling them "potogenes.")

Here's my problem with that argument: Natural selection is going to
cease to be the major source of new beneficial mutations in humans
within 20 or 30 years. We are going to have our genomes changed by
bioengineering. Therefore junk DNA will have no value to us. Going into
future centuries our bioengineering techniques will advance even
further and we will be able to simulate the effects of variations
orders of magnitude more quickly than mutations occur naturally.

There's another point about junk DNA that especially holds for
agricultural plants and animals: to the extent that junk DNA can be
removed from crops and livestock a source of variability is removed
that essentially serves as noise. If someone develops some ideal dairy
cow and wants to clone it he does not want jumping genes creating
variations that cause some of them clones to produce less milk.
Similarly, jumping genes could create variations in the growth of corn
or wheat that would be undesirable.

It should be possible to grow up replacement organs in other species
first and to try out junk removal in organs and whole genomes in other
species before trying it out in humans. This will provide an important
way to discover functional purposes served by parts of genomes that are
mistakenly thought to be junk. The mechanisms by which those parts
serve useful functions will then be able to be searched for in humans
as well. In my view, the discovery of which sections of the genome
really are junk is a technical challenge that will be solved with time.
Once purely junk sections are identified with a fairly high probability
of correct classification and techniques for removing it are developed
it seems inevitable that more daring individuals will opt to try to
have the junk removed from their replacement organs and progeny.

By Randall Parker at 2003 November 25 01:39 AM Evolutionary History


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Relevant Pages

  • Re: Non-Coding DNA preserved by genetic drift?
    ... > supersede natural selection as the dominant evolutionary force, ... > Junk DNA costs energy to duplicate and to carry around as part of each ... > were plotted against the species' total genome sizes. ... > population sizes, more genes, more junk DNA and longer-lived gene ...
    (sci.bio.evolution)
  • Re: Non-Coding DNA preserved by genetic drift?
    ... DNA" is very important and has to be seen as a part of the genetic ... by genetic drift, how if at all does that throw in a monkey wrench to ... For Darwin it was natural selection. ... drift and there is very little "junk DNA". ...
    (sci.bio.evolution)
  • Re: Non-Coding DNA preserved by genetic drift?
    ... "Assuming non-coding DNA is preserved ... > by genetic drift, how if at all does that throw in a monkey wrench to ... For Darwin it was natural selection. ... > drift and there is very little "junk DNA". ...
    (sci.bio.evolution)
  • Re: Ultraconserved Elements in the Genome: Are They Indispensable?
    ... Junk DNA is simply enough defined. ... evolution, mutations just randomly drifting to extinction or fixation. ... Sometimes natural selection may speed ... not a biology type. ...
    (talk.origins)
  • Re: Role of Junk DNA
    ... When researchers began mapping the genome, ... startled to find that humans have only 25,000 active genes. ... But researchers are now finding this junk DNA, ... by geneticists, may actually not be junk at all. ...
    (talk.origins)