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Virtual ecology in the genome

December 15, 2011

The idea of virtual life is commonplace in science fiction. In real life, the closest thing we may find is parasitic DNA–sequences of DNA that may jump, copy, and/or get stuck in a genome. Some called HERVs form virus particles out of our own genome. Fully half the human genome consists of sequences that got there as transposable elements, viruses, or degenerative forms called retroelements. Retroelements descend from HIV-like retroviruses; some still encode their reverse transcriptase, making DNA off an RNA template and putting it somewhere in the human genome. Other retroelements such as the famous Alu sequence depend on some other element’s transcriptase to put them into the genome.

In a given person, most of these elements are quiescent. But over many generations, these genetic elements move around, seething and interacting in our genome; a virtual ecosystem of DNA sequence. How do they interact with their host?  Some selfish genetic elements enhance their own transmission at the expense of host progeny that fail to include them. Other genetic elements eventually evolve into functioning parts of the host. It’s as if someone left a bolt rattling around in the engine, and the mechanic took it up and fastened it to a part somewhere, then added such a bolt forever after in that place. Whether “alive” or not, these sequence elements may be the closest thing to the evolving virus codes in computer software.

11 Comments
  1. December 15, 2011 10:39 pm

    Fascinating. I love the way there are different life-forms, like those little guys with their own DNA–mitchondria, I think–and the life of the DNA within a species, and now your disclosure: life within DNA! It’s too cool.

  2. SFreader permalink
    December 16, 2011 3:06 pm

    Will be interesting to see how and which types of retro-elements most impact various species’ evolution. For example, if the great white shark’s genome is less permeable-to-RE inclusion, this would help explain why great whites seem to have not changed much in 16 million years and the shark lineage extends back almost a quarter billion years.

  3. December 16, 2011 4:12 pm

    Retroelements and transposons impact evolution in various ways: By providing raw material (DNA) to evolve into new control sites; by carrying new genes from one species to another (such a herbicide resistance from a crop plant to a weed); and by inserting within existing genes, knocking them out or drastically altering their function.

    I’m not sure about the great white shark. The elephant shark genome reportedly shows slower evolution of protein sequences than other vertebrates:
    http://www.sciencedaily.com/releases/2009/03/090317162844.htm
    But it still had time to evolve, for example, three-color vision, independently of the line that led to ape three-color vision.

    • SFreader permalink
      December 16, 2011 5:09 pm

      I appreciate your clarification — but what I was trying to get at was whether different RE and transposons had different ‘weights and directions’ in driving evolution (i.e., forward vs. backward vs. sideways; and, do not change vs. change) sort of like how subatomic particles have specific properties (or amount of a particular property) that makes their participation in certain reactions more likely. If so, then knowing a species genome’s predisposition to change could be valuable in either preserving its current status or accelerating further changes. For example, if potatoes are less change resistant than corn then it would probably be faster, easier and less expensive to concentrate efforts on genetically tweaking potatoes to make them better able to grow in different climates and soils.

      Is there a branch of genetics ‘math’?

  4. December 16, 2011 7:57 pm

    “Genetics math” — yes there are multiple fields of math used for genetics! For example, to make and use genomic DNA chips (one chip contains all the genes of a species) requires about ten different kinds of math. No one person knows all of them, so interpreting the results is highly controversial. I’ve published some myself:
    http://biology.kenyon.edu/slonc/maurer304.pdf

    What drives evolution rate–it’s not just one thing. Different RE and DNA transposons move at different rates, and have different effects when they do. Genome size and DNA mutation rate affect evolution–in microbes, mutation rate is especially important.

    Generation time also–the shorter your generation time, the faster you evolve:
    http://news.nationalgeographic.co.uk/news/2009/01/090126-bird-evolution-missions.html

    Brain size: The larger your brain, the more plastic your behavior, and the wider range of environments you will colonize. Therefore, the wider extremes of genetic selection you will experience:
    http://www.sciencedaily.com/releases/2008/08/080814210006.htm

  5. December 16, 2011 8:20 pm

    I’ve seen suggestions that humans came about because our primate lineage has a heavier load of transposons than other mammals do. Whether that’s true or proved, I don’t know. More transposons would increase the mutation rate, though.

    Another good point is that DNA has other functions than holding data. For example, one of the functions of junk DNA may be as a transposon trap. The stuff never codes for anything, so a transposon that inserts itself into junk is functionally dead. Another of my favorite sequences, ITS2, doesn’t code for anything either. However, its function when transcribed is to loop three or four times, to bring two subunits of a ribosome together. Since the only thing that’s conservative about it is the need to bring the ends together (its sequence doesn’t matter, only the folding does), paradoxically it serves as a fairly useful barcode for identifying eukaryotic species.

    Oh well: cells are ecosystems of former symbiotes bound together by traded DNA, DNA is an ecosystem of sequences, bodies are ecosystems that often contain more bacterial cells than self cells, as well as containing rogue cells (cancer) that act as parasites or predators, white blood cells act a bit like a trainable superorganism predator on both cancer and foreign pathogens, and so forth. Instead of turtles all the way down, it’s more like ecosystems, all the way down

    The amusing thing in all this is that most physicians’ remedies are on the order of spraying DDT (antibiotics) and planting eucalyptus and reed canary grass (the standardized probiotics they routinely give hospital patients to re-establish their gut microbiomes, even though at least one probiotic has already been pulled due to the harm it caused). Since it’s a dark time of year, I predict it will be at least 50 years before physicians start taking ecology and evolution seriously. After all, it took them about that long to accept the germ theory in the first place, even though they cling to it now.

    • December 16, 2011 9:24 pm

      The ecology model of organism is a fascinating field of research; your description is lots of fun. Physicians are beginning in many ways to take a more ecological approach. The most dramatic example is fecal transplant, where you actually transplant a genuine “ecosystem” (someone else’s feces) to replace lost intestinal microbes. This actually works, and is accepted practice.

      Transposons are all over the place; I think the primate evolution had more to do with the “big brain” promoting diverse environments, as in my earlier post about the big-brained birds. I don’t know about the “transposon trap”, since bacteria get just as many transposons without junk DNA. But it’s true that some sequences have structural content without encoding protein. In fact, several thousand human genes express RNA that folds up and functions as if it were a protein. Remnant of our long-lost ancestry in the RNA world.

    • SFreader permalink
      December 17, 2011 6:07 pm

      Has anyone tried to reduce the amount of ‘junk DNA’ in any genome or part of a chromosome to see what happens? I’ve read ScienceDaily articles that describe research where bits of DNA are removed or silenced, but this appears restricted to the coding DNA only. I’ve sometimes wondered whether the junk DNA provides ballast, spare-parts and/or even sufficient heft/weight so that the chemistry of the coding DNA might proceed at a predetermined/necessary pace.

  6. December 16, 2011 11:07 pm

    Joan, I wish I was that sanguine. I know they’ve done fecal transplants, but I also know a hospital pharmacist. When I suggested that someone would start doing intestinal bacterial assays to figure out how they would affect drug metabolism, her comment was, “You know what they’ll do? Create a standardized gut flora, clean out patients’ guts, and dose them with the standardized one.” (which will cost a lot, she tactfully didn’t add. Those standardized probiotics they use now aren’t that cheap, nor are they always effective).

    I have a number of friends who work in hospitals. They’re great people, but most of them suffer from a real dearth of ecological knowledge, coupled both with a strong belief in their own abilities and a willingness to uncritically do what a doctor tells them to do. Because of that, I think the medical profession will have to make every single mistake land managers have made with ecosystems, because they show little interest in learning from ecologists.

  7. December 17, 2011 9:09 pm

    SFreader:
    “Has anyone tried to reduce the amount of ‘junk DNA’ in any genome”
    That’s a good question. It turns out to be exceedingly complicated, because the “junk DNA” can be found inbetween genes, or within introns that interrupt genes. Removing it all would be an enormous task.

    However, it’s clear by studies of phylogeny (comparison of related sequences in a family tree) that certain non-coding (“junk”) sequences change less often than you would expect by random mutation. This means that although the sequences do not encode protein, they do contain regulators, such as DNA binding sites for regulatory proteins that direct the expression of a gene product. These regulator sites are short, often less than ten bases, so they can evolve easily out of any piece of DNA, even defunct viral DNA (see earlier post). If you’re interested, an example of the research is here:
    http://genome.cshlp.org/content/20/3/311.full

    As I said, it’s hugely complicated, but the bottom line is that what looks like junk actually is sprinkled with tiny bits of essential regulatory DNA (which evolved from the junk). It’s like when you try to throw out stuff from the attic but keep finding things that could be useful.

    • December 20, 2011 10:19 am

      ObSF: Bruce Sterling, Distraction – the protagonist is the result of an experiment in editing out all the introns in a human genome (in order to make the maths easier and facilitate spoiler spoiler). It sort of works but he’s kinda almost, in a number of different ways, some positive and some negative.

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