Junk and Jewels in the Genome

In this Sunday’s issue of the New York Times Magazine, I have a feature about clashing visions of the genome. Is it overwhelmingly made up of “junk”–pieces of DNA that provide us with no useful function–or is it rife with functional pieces that we have yet to understand? Or is the reality of the genome a confusing mixture of the two?

To research this story, I shed some blood so that I could compare my genome to that of an onion. This print-out, annotated by T. Ryan Gregory, shows that an onion has five times more DNA in its genome than mine. I also spent time in the lab of John Rinn at Harvard, where scientists are discovering hints that our genome encodes exotic molecules that may be essential for our well-being. And I talked to a range of scientists about the challenges of understanding what any given piece of DNA is “for,” and what sort of assumptions one should bring to the challenge. Finally, I dug deep into the history of this question, which has roots reaching all the way back to Darwin. Check it out.

Courtesy of T. Ryan Gregory
Courtesy of T. Ryan Gregory

P.S. This is an incredibly rich topic, and I welcome readers to discuss it (especially the stuff I didn’t have room to get to in my feature) in the comment thread below. I’ll also post some interesting papers here, too.

The Genomic Challenge to Adaptationism, by Sahotra Sarkar. British Journal for the Philosophy of Science, 2014. [subscription required]

Junk or Functional DNA? Germain et al., Biology and Philosophy, 2014. pdf

An Evolutionary Classification of Genomic Function, by Dan Graur et al. Genome Biology and Evolution 2015.

Discovery and Annotation of Long Noncoding RNAs. Mattick and Rinn. Nature Structural & Molecular Biology 2015. [subscription required]

5 thoughts on “Junk and Jewels in the Genome

  1. I have a slightly odd question.

    Watching certain organisms like Amoeba Proteus, I see a lot of what seem to be fairly sophisticated behaviours from a creature that is, by definition, less than a single neuron.

    And that same single-celled organism also has an absurdly large genome.

    That leaves me wondering if our little friend is using part of it’s DNA not to create physical structures and proteins, but actually uses some of that ‘junk’ DNA as…operating code?

    [CZ: Great question. I’d say scientists don’t really have a firm handle on the relationship between genomic complexity and behavioral complexity. Even bacteria with much smaller genomes can display some impressive behavior. The giant size of A. proteus’s genome is the result of many duplications of an original genome, so it has lots of copies of each gene. Those copies may become disabled by mutations, carry on the same function as the original gene, or evolve to take on a new job.]

  2. I accept that large portions of non-coding DNA of the sort that is called ‘junk’ DNA is mistakenly amplified in eukaryote genomes and not be removed because of weak negative selection. However, I strongly feel that this idea still needs to be tested experimentally.

  3. MOTORING METAPHORS. There are many metaphors indicating why two organisms, with apparently equal demands on the quantity of information their genomes should carry, might bear quite disparate genomic loads. The car tyre metaphor is one.

    One car may just have a puncture repair kit and a pump. Another may have one spare tyre. A more pessimistic other in remote parts may trail a van with 100 spares. Another may just have a spare inner-tube. Apparently, it is possible to bleed sufficient high pressure air out of three tyres to inflate the replacement tube. A wandering minstrel once put it thus:

    Some cars escape sans dent,
    But strategies are different.
    Some alas have accident,
    And not just bumper bent.

    Same for tyres that go flat,
    That get us into such a spat.
    Some carry just one spare,
    Others far from base,
    Trail a hundred just in case.

    Others have tricks und’ belt,
    No baggage, we go svelt.
    So we use our humble wit,
    Zero tyres, just repair kit.

    Others in land of sun,
    With tube empty,
    Take air from three,
    To give to one!

    No one-fits-all,
    No excess fattegy,
    But what recalls,
    Evolution’s strategy!

  4. Re: (CZ’s response)

    Oooh, yeah. I suppose it makes sense that they could keep them around as long as they weren’t hindered passing it on, right?

    Though that does leave one question…where do all those behaviors come from without their being any thinky bits? I get how they can sense they’re touching (or just near, if there are chemicals leaking about for them to follow), but am a bit baffled as to how they turn a triggered sensor into something that looks pretty complicated and selective.

    Amoeba.Proteus might not be the best example there (an argument for your argument, which is of course correct!), but there are lots of those little single-celled critters who can do some apparently complicated things (picking food sources, measuring things to engulf (or give up on), spitting out certain things, following ‘prey’ once contacted, and so on)

    What part of that fascinating inner biology of those little guys is the actual mechanism that runs their ‘code’ so to speak?

    I’m a total amateur and my fascination with all things alive has drifted into the tiny (and it just keeps getting a new sort of awesomely weird, doesn’t it?), and a few of these concepts boggle me!

  5. Recently I read a paper in which the authors showed that the same patterns of biochemical activity that identify mammalian enhancers with a reasonable degree of accuracy can also be used to identify enhancers in sea anemone. (Enhancers are short regions of DNA generally buried in non conserved sequence that are important for regulating when and where genes are expressed.) So while 90% of the activity identified by ENCODE and similar projects may be noise, it seems likely that it will be rather useful in identifying and understanding the evolution of gene regulatory regions.

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