Three Reasons Why Junk DNA Makes Evolutionary Sense

By Ashutosh Jogalekar 
September 13, 2012 
http://blogs.scientificamerican.com/the-curious-wavefunction/2012/09/13/three-reasons-to-like-junk-dna/

The recent dustup over the ENCODE project and its
confusing finding that “80% of DNA is functional”
surprises me greatly. What surprises me especially is
that people are surprised by junk DNA. Unfortunately
this time the scientists are also culpable since, while
the publicity surrounding ENCODE has been a media
disaster, the 80% claim originated in the scientific
papers themselves. There is no doubt that the project
itself – which represents a triumph of teamwork, dogged
pursuit, technological mastery and first-rate science –
has produced enormously useful data, and there is no
doubt it will continue to do so. What is in doubt is how
long it will take for the public damage to be repaired.

There’s a lot written about the various misleading
statements about the project made by both scientists and
journalists and I cannot add much to it. All I can do is
to point to some excellent articles: Larry Moran has
waged a longstanding effort to spread the true wisdom
about junk DNA for years on his blog. Ed Yong
exhaustively summarizes a long list of opinions, links
and analysis. T. Ryan Gregory has some great posts
dispelling the myth of the myth of junk DNA. And John
Timmer has the best popular account of the matter. The
biggest mistake on the part of the scientists was to
define “functional” so loosely that it could mean pretty
much all of DNA. The second big mistake was not in
clarifying what functional means to the public.

But what I found astonishing was why it’s so hard for
people to accept that much of DNA must indeed be junk.
Even to someone like me who is not an expert, the
existence of junk DNA appeared perfectly normal. I think
that junk DNA shouldn’t shock us at all if we accept the
standard evolutionary picture.

The standard evolutionary picture tells us that
evolution is messy, incomplete and inefficient. DNA
consists of many kinds of sequences. Some sequences have
a bonafide biological function in that they are
transcribed and then translated into proteins that have
a clear physiological role. Then there are sequences
which are only transcribed into RNA which doesn’t do
anything. There are also sequences which are only bound
by DNA-binding proteins (which was one of the
definitions of “functional” the ENCODE scientists
subscribed to). Finally, there are sequences which don’t
do anything at all. Many of these sequences consist of
pseudogenes and transposons and are defective and
dysfunctional genes from viruses and other genetic
flotsam, inserted into our genome through our long,
imperfect and promiscuous genetic history. If we can
appreciate that evolution is a flawed, piecemeal,
inefficient and patchwork process, we should not be
surprised to find this diversity of sequences with
varying degrees of function or with no function in our
genome.

The reason why most of these useless pieces have not
been weeded out is simply because there was no need to.
We should remember that evolution does not work toward a
best possible outcome, it can only do the best with what
it already has. It’s too much of a risk and too much
work to get rid of all these defective and non-
functional sequences if they aren’t a burden; the work
of simply duplicating these sequences is much lesser
than that of getting rid of them. Thus the sequences
hung around in our long evolutionary history and got
passed on. The fact that they may not serve any function
at all would be perfectively consistent with a haphazard
natural mechanism depending on chance and the tacking on
of non-functionality to useful functions simply as extra
baggage.

There are two other facts in my view which should make
it very easy for us to accept the existence of junk DNA.
Consider that the salamander genome is ten times the
size of the human genome. Now this implies two
possibilities; either salamanders have ten times
functional DNA than we do, or that the main difference
between us and salamanders is that they have much more
junk DNA. Wouldn’t the complexity of salamander anatomy
of physiology be vastly different if they really had so
much more functional DNA? On the contrary, wouldn’t the
relative simplicity of salamanders compared to humans be
much more consistent with just varying degrees of junk
DNA? Which explanation sounds more plausible?

The third reason for accepting the reality of junk DNA
is to simply think about mutational load. Our genomes,
as of other organisms, have undergone lots of mutations
during evolution. What would be the consequences if 90%
of our genome were really functional and had undergone
mutations? How would we have survived and flourished
with such a high mutation rate? On the other hand, it’s
much simpler to understand our survival if we assume
that most mutations that happen in our genome happen in
junk DNA.

As a summary then, we should be surprised to find
someone who says they are surprised by junk DNA. Even
someone like me who is not an expert can think of at
least three simple reasons to like junk DNA:

1. The understanding that evolution is an inherently
messy and inefficient process that often produces junk.
This junk may be retained if it’s not causing trouble.

2. The realization that the vast differences in genome
sizes are much better explained by junk DNA than by
assuming that most DNA is truly functional.

3. The understanding that mutational loads would be
prohibitive had most of our DNA not been junk.

Finally as a chemist, let me say that I don’t find the
binding of DNA-binding proteins to random, non-
functional stretches of DNA surprising at all. That
hardly makes these stretches physiologically important.
If evolution is messy, chemistry is equally messy.
Molecules stick to many other molecules, and not every
one of these interactions has to lead to a physiological
event. DNA-binding proteins that are designed to bind to
specific DNA sequences would be expected to have some
affinity for non-specific sequences just by chance; a
negatively charged group could interact with a
positively charged one, an aromatic ring could insert
between DNA base pairs and a greasy side chain might
nestle into a pocket by displacing water molecules. It
was a pity the authors of ENCODE decided to define
biological functionality partly in terms of chemical
interactions which may or may not be biologically
relevant.

The dustup from the ENCODE findings suggests that
scientists continue to find order and purpose in an
orderless and purposeless universe which can nonetheless
produce structures of great beauty. They would like to
find a purpose for everything in nature and are
constantly looking for the signal hidden in the noise.
Such a quest is consistent with our ingrained sense of
pattern recognition and has often led to great
discoveries. But the stochastic, contingent, haphazard
meanderings of nature mean that sometimes noise is just
that, noise. It’s a truth we must accept if we want to
understand nature as she really is.

About the Author: Ashutosh (Ash) Jogalekar is a chemist
interested in the nature of the "central science" and
its intersection with philosophy, history and culture.
He is also more generally interested in the history and
philosophy of science and is particularly fascinated by
how science tries to mirror reality by building models.
Follow on Twitter @[log in to unmask]

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