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Three reasons why junk DNA makes evolutionary sense

The views expressed are those of the author and are not necessarily those of Scientific American.

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ENCODE (Image: Ed Yong)

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.

Ashutosh Jogalekar About the Author: Ashutosh (Ash) Jogalekar is a chemist interested in the history and philosophy of science. He considers science to be a seamless and all-encompassing part of the human experience. Follow on Twitter @curiouswavefn.

The views expressed are those of the author and are not necessarily those of Scientific American.

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  1. 1. vapur 10:09 pm 09/13/2012

    I appreciate the Occam’s Razor argument, but I find a flaw in making assumptions that just because it is a smaller creature then it should essentially have a less complex genome. What if that ‘junk’ was meant to be translated and leave the incomplete RNA fragments behind in the environment to recombine into something else?

    Link to this
  2. 2. THEMAYAN 10:40 pm 09/13/2012

    It seems that the poster hit the nail on the head when he entitled this thread…”Three reasons why junk DNA makes evolutionary sense”

    And I say that because all this underlying anger and hostility seems to be the real reason, i.e. the reason being a culture war. It seems so many scientist over the years have dug themselves in a hole by preaching this usles vestigial junk paradigm to students and to the general public, and now it has come back to bite them in the ass! Let me just speak on a couple of issues. T. Ryan Gregory’s argument is that we have known about function for a long time and that it’s dishonest for people like John Mattick to say that there has never been any scientific research on junk DNA. First off, this is false. Mattick never used those words.

    Secondly, while it is true, in the earlier days, there were a small handfull who found at least some hints of function but it is also true their research was largely ignored by the Status quo, and in much the same way Barbera Mcclintocks work on maize and transposons was ignored, and for many years, until she was finally redeemed decades later. It seemed that for many years, the junk DNA paradigme was held up as a poster child for bad design. Kenneth Miller and Richard Dawkins (just to name a few) both claimed it made sense from an evolutionary perspective and was predicted by evolutionary theory.

    The poster cited Gregory and Moran which is interesting, because on one hand you have Gregory admonishing others who claim that we were surprised at the amount of function, when he rightfully claims that we have known this for years. Of course again, at the same time he refuses to acknowledge how much of this work was ignored by the status quo. His thoughts are echoed by Mike Eisen who also criticizes ENCODE (but not because they have reported function, but again for at least some of the same reasons Gregory uses.

    E.g. Mike Eisen …”The hundreds of researchers working on the ENCODE project have revealed that much of what has been called ‘junk DNA’ in the human genome is actually a massive control panel with millions of switches regulating the activity of our genes. Without these switches, genes would not work – and mutations in these regions might lead to human disease. The new information delivered by ENCODE is so comprehensive and complex that it has given rise to a new publishing model in which electronic documents and datasets are interconnected”

    Larry Morans response to this is as follows…..”Here’s the interesting thing. Many of us are upset about the press releases and the PR because we don’t think the ENCODE data disproves junk DNA. Michael Eisen’s perspective is entirely different. He’s upset because, according to him, junk DNA was discredited years ago. Eisen is wrong, junk DNA is alive and well. In fact almost 90% of our genome is junk”

    Moran also goes on to say…….”Eisen is wrong, junk DNA is alive and well. In fact almost 90% of our genome is junk”

    It seems even the critics cant agree on this topic. In the end, Gregory and Moran have every opportunity to critique the data, but do it in peer review, and not from your personel blogs where your many minions can cheer you on with un critical adulation. The genome is a highly dynamic and highly complex structure with layer and layers of underlying complexity, and there is no simple “one size fits all” answer in terms of function.

    The deeper story lies within this extremely complex work itself. You cannot convey the kind of complexity involved in press releases, but what is certain, is that just because we may have a better handle on 20%, and may not know all the specifics of the other 40% (at least at this time), does not mean that we should continue to write off these non protein coding region as useless junk, especially when even critics of the article such as the good folks at Eddy/Rivas lab, as in the words of one one of their anonymous staff bloggers admitted…..”Nobody should bet against finding more and more regulatory noncoding DNA, either”

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  3. 3. Metridia 11:14 pm 09/13/2012

    Actually, T. Ryan Gregory has been a font of misunderstanding on genome complexity. Try reading others such as this seminal paper
    by Lynch and Conery. It’s a bit more counterintuitive but is more explanatory, well-supported and theoretically sound than the explanations forwarded by Gregory and others.

    Link to this
  4. 4. AGibson 1:01 am 09/14/2012

    So if you assume DNA is a stored computer program and its been edited at least a couple of hundred million times (with defective versions purged), having a large percentage of code that does not produce printable text (proteins) is no great surprise. A look through a program on your PC would produce similar results of readable text vs executable code (a good percentage of which may no longer be used but hasn’t been removed (DLL’s in windows are typical of that)).

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  5. 5. zzap999 1:17 am 09/14/2012

    ID is truth.

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  6. 6. THEMAYAN 1:36 am 09/14/2012

    Correction, meant to say…….”but what is certain, is that just because we may have a better handle on 20%, and may not know all the specifics of the other 60% (at least at this time), does not mean that we should continue to write off these non protein coding region as useless junk”

    Link to this
  7. 7. phalaris 1:53 am 09/14/2012

    Surely there are problems with reason no. 3?

    It implies that larger genomes are better protected against mutational load, which would give larger genomes an evolutionary advantage. How then the apparently random differences in the amount of junk DNA (the onion test)?

    Also, what is mutational load? If it were the risk of mutation per so many base pairs, having extra junk would provide no benefit to the important parts of the genome.

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  8. 8. Symonas79 6:41 am 09/14/2012

    Basically a good point, however the part of Salamanders might specifically not be the best example as they are in fact quite complex, perhaps more complex than humans as they go through a larval phase as part of their life cycle. (I don’t know we humans seem to need to think of ourselves as being complex)

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  9. 9. curiouswavefunction 7:07 am 09/14/2012

    I don’t mean to imply that humans are vastly more complex than salamanders (in fact I rather admire their regenerative abilities) and I would be the last to buy into a solipsistic argument. What I mean to say is that, presented with so many diverse species with such significant differences in genome sizes, I find an explanation based on differing levels of non-coding and junk DNA simpler and more satisfying.

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  10. 10. t0mmy 7:46 am 09/14/2012

    Or maybe having a higher junk/functional DNA ratio allows increased resistance to DNA damage?

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  11. 11. t0mmy 7:48 am 09/14/2012

    functional DNA damage I should add

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  12. 12. password 3:47 pm 09/14/2012

    Ultimately we will know if there really is junk by finding out. That’s how science works. We constantly look for opportunities to test out theory and if the tests don’t bear out the theory the theory has trouble. I for one fail to see how junk can according to Evolution have an opportunity to get passed down via natural selection. If you want to argue something became junk it’s one thing. Perhaps it is the imperfect interpreters of Evolution who stand to lose in this one rather than Evolutionary theory itself.

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  13. 13. VivaLaEvolucion 4:39 pm 09/14/2012

    I don’t like the term Junk DNA.

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  14. 14. Bill_Crofut 5:01 pm 09/14/2012

    Re: “[W]hat 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.”

    There seems to be contradictory information on SCIENTIFIC AMERICAN web pages:

    “Should we be retiring the phrase “junk DNA” now?”

    “Yes, I really think this phrase does need to be totally expunged from the lexicon. It was a slightly throwaway phrase to describe very interesting phenomena that were discovered in the 1970s. I am now convinced that it’s just not a very useful way of describing what’s going on.”

    Ewan Birney of the European Bioinformatics Institute in Cambridge, England

    Hidden Treasures in “Junk” DNA

    Link to this
  15. 15. hungry doggy 5:19 pm 09/14/2012

    Although a certain amount of so-called “junk” DNA could be expected for all the reasons cited, too much has to be a metabolic burden for the organism. Making DNA isn’t metabolically free. It takes energy and uses resources. Creating and then endlessly copying large stretches of useless DNA in trillions of cells must be costly. There should be a selective pressure to eliminate unneeded DNA.

    Unless of course most of it isn’t really junk, it’s just that we don’t understand it yet.

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  16. 16. Laroquod 10:46 am 09/28/2012

    Although science can prove that a particular sequence of DNA has some effect, I seriously doubt that science will ever be able to prove that a particular sequence of DNA has NO effect. Therefore, calling it ‘junk DNA’ was inadvisable in the first place, since that phrase contains an unfalsifiable assertion. Rather they should have called it ‘dark DNA’ — then there be no argument today, or at least the argument would have been a lot more narrow with less extraneous semantic nonsense that it is pointless, really to discuss. Arguing over whether a particular phenomenon has no effect is a fool’s game; one should argue over whether any effect can be detected, instead. In the absence of that evidence, a rational person should suspend judgement NOT declare that there is no effect.

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  17. 17. ralvesson 8:34 am 01/18/2015

    I need some help: One of my students asked me this question and I had no answer for it (yet). I need some help. Here is the question: “If the so called “Junk DNA” now has the “computer code” like function of controlling the “cascading”, step-by-step (meaning that each step depends on the results of the preceding one) expression of genes involved in the development and growth of the Embryo…then if you change any of these DNA instructions via non-directed, random mutations as Evolution holds the code gets ruined…so then it would follow that all cells emerged or surged with its own species-specific DNA from the beginning and did not evolve….wouldn’t this conclusion seem correct given the results of the ENCODE prohject ? What would you answer my student…Thanks

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