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I Can Haz Genes for Hole Biosphere?

October 27, 2011

As Max pointed out (no doubt with help from tabby friends), “Adapting ourselves would be expensive enough, but there’s no way we could afford to adapt all the species that would be wiped out by catastrophic climate change.”

Humans depend on all kinds of organisms out there that we don’t even know about. For instance, the marine microbes that recycle oxidized nitrogen back to N2 and NH3–without them we’d be gone. Not to mention the plants and animals we feed on, and all their assorted microbial friends.

It turns out the Sharers not only engineered themselves–they engineered their entire biosphere, to stabilize it. What looks like a “natural” ecosystem is in fact gene-modified, down to the last raft branch. In fact the raft branches are their IT “cloud,” storing all their known data in the genome of every cell.

This would be “far” science fiction, but could we actually make a vector (or small set of vectors) to carry genes into all organisms on Earth?  There are heat shock proteins that restore heat-damaged proteins; they act pretty much the same way in all organisms, from E. coli to plants to us. Could we devise super-heat shock proteins and transfer the genes encoding them into all life forms, to help protect life from rising temperature?  We would need viral carriers.  HIV only works for humans, but other viruses can infect many different species, for instance rabies virus, influenza, and (in plants) cauliflower mosaic virus.

If we put recombinant genes into all life on Earth–would “nature” or “wilderness” even exist as such anymore?  Or does it even now?

  1. October 27, 2011 10:45 pm

    Isn’t that simply making eukaryotes more like prokaryotes, in that we’re making it easier for genes to jump among bodies?

    It’s a fun question that I’ve played with a bit: what’s the minimum set of organisms you need for a functioning biosphere.

    One thing I did figure out is that you can actually shrink your data storage requirements substantially by saving, not the genome, but a standard genome, annotated to show which sequences vary and how. After all, many genes are strongly conserved, and there’s little reason to save multiple, identical copies of all of them. By saving a model plus variations, you can actually store much more diversity in a smaller memory. This is an in vitro solution, not in vivo. However, if you want to colonize the stars with machines that will then build a new Gaian biosphere at the other end, shrinking the genomic data down is useful.

    • October 27, 2011 10:53 pm

      Oops. Meant in silico when I said in vitro. Silly latin: glass and chips are the same material…Anyway, my bad.

  2. October 28, 2011 2:07 am

    My cats are big ocean activists because they are concerned about the possible extinction of tuna through overfishing.

    If you were terraforming a planet from scratch, you could design an ecosystem where all life forms are effectively plugged in to the network and can pass updates around, but retrofitting that into an existing biosphere would be incredibly difficult. Sure, you pass a gene around for heat shock proteins; how much does that gene need to be expressed in any given species for it to be effective, but not so much that it renders the creature unfit because it’s devoting too many resources to manufacturing the protein?

    Tinkering with evolved systems is very tricky; you can even observe this with evolved computer software, which is vastly simpler than living beings. They re-use the same bit of genetic code in multiple ways, and making a change that affects one path can accidentally screw up another path. That’s why I think synthetic biology, which is trying to strip bacteria down to the minimum and then build up from there, is going to show useful results long before we can do major tweaking to macroscopic organisms.

  3. Esebian permalink
    October 28, 2011 8:43 am

    IIRC one of the big challenges of gengineering is to make the new genes insert in the right places, so mass-modification of hundreds of millions/billions of organisms seems to harbor many dangers. It might take another century till the methods have matured enough to ensure that they do things as intended.

    The interactions of the mods with the dark part of the biosphere are quite possibly a loose cannon, though.

    • October 28, 2011 8:02 pm

      Yes, it’s hard to do a repeatable experiment when you have only one biosphere.
      And we don’t even know what organisms we can’t “see” out there will be modified.

      That’s also a problem with modifying crops. Actually, I’m in favor of modifying crops generally; we’ve done that for tens of thousands of years, and the test tube is just more efficient. But when herbicide resistance genes are put in, the same genes show up soon in the weeds near by.

  4. October 28, 2011 6:32 pm

    I’m reminded of Janet Kagan’s Mirabile. It”s out of print, but she postulated that organisms on a colony ship would contain “secondary and tertiary DNA helices” that would code for other organisms. In the stories, a patch of petunias might suddenly breed up cockroaches.

    Unfortunately, reality doesn’t work this way, but I suppose you could hide subsidiary genomes inside cells using some artificial equivalent of methylation that you could control with some sort of drug. Such a technology would allow you to switch, say, corn to wheat or bamboo, or potatoes to tomatoes. Of course, cells in such organisms would have monstrous nuclei, and mitosis and meiosis would have high failure, but theoretically you could do it. Plants such as wheat are hexaploid, and most of those genes are silenced anyway. Why not hide something in them?

    • October 28, 2011 8:05 pm

      The Mirabile stories were a great take on DNA in development. I used them in teaching years ago, and included them in this education piece for HHMI:

    • alex tolley permalink
      October 28, 2011 10:26 pm

      Is it really so different from different life stages in animals? So many invertebrates have 2-3 stages, and even amphibians manage 2 stages. If it is gene silencing, it cannot be permanent, and under some sort of genetic control.

      • October 28, 2011 11:07 pm

        Alex, that’s a good question. Some developmental biologists argue that different life stages of metamorphosis represent different kinds of creatures that merged their genomes. In plants, some genome mergers have occurred, though they don’t end up with metamorphosis.

        The genome merger view lacks evidence, however. We think it’s more likely that successive genome duplications led to multiple organism segments and multiple life stages. The Homeobox genes that determine pattern in insects and in humans can be traced back statistically to a long series of duplications an original Homeobox gene.

        • alex tolley permalink
          October 29, 2011 10:41 am

          Whether Margulis is correct about genome merging doesn’t matter. Different life stages which undergo metamorphosis must be coordinated under some sort of control system. The genes involved in each stage may be overlapping to some extent. I would guess that it is the gene control regions that are being regulated, and these are possibly the targets of the hormonal control of metamorphosis. But it may well be that the genes are different, in effect mostly complete genomes for each stage, even if they are mixed as the origin is gene duplication rather than from horizontal transfer in the past.
          Either way, it suggests that one could insert genomes that are triggered under certain circumstances.

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