Evolution, Perfection and Life

Mar 10 2015 Published by under Uncategorized

Carl Zimmer has an excellent piece in Sunday's NYTimes on Junk DNA, which I have learned is an unacceptable term in some circles, particularly to some of our most favorite NIH directors.

I would say, in terms of junk DNA, we don't use that term any more 'cause I think it was pretty much a case of hubris to imagine that we could dispense with any part of the genome as if we knew enough to say it wasn't functional. There will be parts of the genome that are just, you know, random collections of repeats, like Alu's, but most of the genome that we used to think was there for spacer turns out to be doing stuff and most of that stuff is about regulation and that's where the epigenome gets involved, and is teaching us a lot.- Francis Collins

Zimmer talks to a number of scientists who present some pretty convincing evidence about the lack of correlation between genome size and biological complexity, including the plant with the biggest genome.  The article presents the tension between those, like T. Ryan Gregory from University of Guelph (one of the stars of Zimmer's article) who see lots of junk, and those, such as John Rinn, who are busy looking for things that non-coding DNA do.

As background for the current dispute, Zimmer goes back to Gould and Lewontin and their view of evolutionary mechanisms. Gould in particular, was frequently represented as "not believing in natural selection" because he believed that it wasn't all of evolution. What Gould (read closely) was saying  was that of course, natural selection worked, but it, and evolution didn't make perfection. Exaptation, in his paper with Elizabeth Vrba, succinctly points out that selection often works with what already exists when a new structure evolves. Examples include skull sutures which make significant brain growth possible in mammals exist as joints in ectotherms that have neither large brains nor live birth. The Panglossian concept of perfection, as generated by natural selection, is something that has been argued about for years. The debates about junk DNA are just its current incarnation.

What fascinates me are the folks who object to the concept of junk DNA. Zimmer points out that even if John Rinn finds that "junk genes" have an important purpose, its much more like looking for gold in the sand on the beach. He quotes Alex Palazzo from University of Toronto:  “probably what you found is a little bit of noise.” Zimmer, at the end of the article, comes down firmly on the side of some DNA being junk, and in fact not "a sign of evolution’s failure. It is, instead, evidence of its slow and slovenly triumph". As Zimmer implies, part of this defense of the Human Genome Project, but perhaps there is more going on.

The idea that there is junk, or waste, or nonsense in nature is tough for some people. They may or may not be overtly or classically religious, but slovenly nature, to use Zimmer's word, is an anathema to them. Many people who are in awe of nature, be it towering redwoods, or the intricate dance of genes, find stuff that doesn't serve a purpose, well, unsettling. The explanations of the accumulation of junk DNA, just like the accumulations of non-functional bits of anatomy, just happens. Zimmer, as Steve Gould famously did every year, goes back to Darwin for defense of both other forces of evolution beyond natural selection. What is tough is when the data, be it in the natural world, one's laboratory or genome, don't conform to one's preconceptions of the world.

 

12 responses so far

  • dr24hours says:

    I don't know a damn thing about DNA. But I have found that over and over and over scientists are wrong when they declare that "X has no function" in a system. So it will not surprise me in the slightest if we discover that what looks like junk now turns out to be useful later.

    But, "Nature/God doesn't make junk!" seems like a pretty silly argument that it must be productive.

    • potnia theron says:

      part of the argument about junk is the quantity- the size of the genome is not at all correlated with biologic complexity. Further the ratio of junk vs. functional is pretty large. Read Zimmer's article and then tell me what you think. He makes the arguments far better than I do.

      • dr24hours says:

        I'm not even qualified to judge it. I don't see that an onion is any more/less "biologically complex" than a person or a bird or a mushroom or an orchid (or a virus). I last took biology in high school and got a C. I don't even know what "biological complexity" means, nor have I the tools to grasp even a basic explanation.

        From a systems perspective, the complexity I see at a higher level than the DNA is not obviously different from one organism to another.

        • potnia theron says:

          there are ways to judge complexity, including things like number of cells, number of physiologic processes, etc.

  • girlparts says:

    I think I react viscerally, not to the notion that there might be a lot of nonfunctional DNA, but to the hubris of thinking "I don't know what that does, so it must not be important." As dr25hours points out, scientists usually do that at their peril.

    • potnia theron says:

      I think its a kind of hubris to assume everything must have a function and a role. No one said "not important".

  • AEMcDonald says:

    One of the reasons that I love Biology is that there is always an exception to the rule. While I don't expect that all "junk DNA" will have a purpose or be useful, I do expect that some of it will be important for regulation, structure, function, or perhaps only serve as a space holder or bookmark in genomes.

  • Mikka says:

    I like Eric Lander's metaphor (might have been someone else): When you are exploring an attic that serves as storage for anything that has been thrown in there, it is hard to say that a particular stack of papers has a function or a purpose. But if you go and set your coffee mug on it, there it has just acquired a function. I think this goes with the exaptation and spandrels arguments.
    The cool question is where all this raw material for exaptation of functional elements comes from. Transposons, genome duplications, viruses etc probably all contribute. I think we will eventually develop a more quantitative notion of "function" for a particular element.

  • The junk DNA just seems to be the genomic extension of the arguments over whether most protein variation (yes, these debate go back well before DNA sequencing) is neutral or under selection. Much of it is neutral, but I remember how difficult it was (a while ago) to convince molecular biologists that not every (or really most) amino acid variant must be under selection–"It's there, it must do something".

    Same song, different beat.

  • Would add that I touch on this here (#1):

  • […] Evolution, Perfection and Life Across the USA, flu season winding down Insurance companies are slow to cover next-generation sequencing Largest Risk for Diabetes With Statins Yet Seen, in New Study Genetics of Why Finns Are Less Anxious Than Italians […]

  • Kaleberg says:

    Back in the early 1980s some researchers (Kollar & Fisher) reported that they had managed to express a chicken gene for a protein found in dental enamel. They argued that this was an example of a fossil gene, as no recent birds have teeth. Presumably this gene has mutated a bit since it hasn't been critical to survival and reproduction for some time. It might even mutate more and start providing some advantage. This could be considered junk DNA in the sense that I have a junk drawer full of odd screws and bolts and partially disassembled gizmos. I have no immediate need for any of this stuff, but now and then something breaks and some piece of junk or another finds itself useful again.

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