The Loom

bacteriophage2.gifIf you took a census of life on Earth, you’d probably find that the majority of life forms looked like this. It’s a virus known as a bacteriophage, which lives exclusively in bacteria. There are about 10 million phages in every milliliter of coastal sea water. All told, scientists put the total number of bacteriophages at a million trillion trillion (10 to the 30th power). Bacteriophages not only make up the majority of life forms, but they are believed to have existed just about since life itself began. Since then, they have been evolving along with their hosts, and even making much of their hosts’ evolution possible by shuttling genes from one host to another. Thanks in large part to bacteriophages, more and more bacteria are acquiring the genes they need to defeat antibiotics. Bacteriophages also kill off a huge portion of ocean bacteria that consume greenhouse gases. If you suddenly rid the world of all bacteriophages, the global climate would lurch out of whack.

It may seem strange that the world’s most successful life form looks a bit like the ship-drilling robots that swarmed through The Matrix. But the fact is that the bacteriophage is nanotechnology of the most elegant, most deadly sort. To get a real appreciation of its mechanical cool, check out the movie from which this picture comes. (Big and small Quicktime.) The movie is based on the awesome work of Michael Rossmann of Purdue University and his colleagues. (Their most recent paper appears in the latest issue of Cell, along with even more cool movies.) Rossmann and company have teased apart pieces of a bacteriophage and have gotten a better understanding of how they work together. The phage extends six delicate legs in order to make contact with its host, E. coli.. Each leg docks on one of the bacteria’s receptors, giving the phage the signal that it is time to inject its DNA. The legs bend so that its body pulls towards the bacterium. The pulling motion makes the base of the phage begin to spin like the barrel of a lock. A set of shorter legs, previously held flush against the base of the virus, unfold so that they can clamp onto the microbe’s membrane. The phage’s sheath, shown here in green, shrinks as its spiralling proteins slide over one another. A hidden tube emerges, which in turn pushes out a needle, which rams into the side of the bacterium. The needle injects molecules that can eat away at the tough inner wall of the microbe, and the tube then pushes all the way into the microbe’s interior, where it unloads the virus’s DNA.

It has taken a while, historically speaking, for scientists to come to appreciate just how sophisticated parasites such as bacteriophages can be, a subject I explored at length in my book Parasite Rex. The best human-designed nanotech pales in comparison to bacteriophages, a fact that hasn’t been lost on scientists. Some have been using bacteriophages to build nanowires and other circuitry. Others see them as the best hope for gene therapy, if they can be engineered to infect humans rather than bacteria. In both cases, evolution must play a central role. By allowing the phages to mutate and then selecting the viruses that do the best job at whatever task the scientists choose, the scientists will be able to let evolution design nanotechnology for them. From the depths of deep time, one of the next great advances in technology may come. And perhaps some more work in Hollywood, I hope.

Comments

  1. #1 Seth
    August 26, 2004

    Bacteriophages are a truly incredible species of viral-like “organisms”, but even more spectactular is their ability to be used for DNA delivery or transport of other nucleic acids as part of a treatment of attempt of gene therapy. Bravo for bringing them up and discussing their brillianc!

  2. #2 Seth
    August 26, 2004

    Despite the glaring errors in spelling and grammar in my previous post, I think I got the idea across….just wanted to save a little face here…

  3. #3 Paul Orwin
    August 27, 2004

    Not to mention their use as anti-microbial therapeutics, as was done almost 100 years ago by the Russians, was forgotten about or relegated to textbooks, and then rediscovered and repopularized by Fischetti and the group at Rockefeller (I think). I would pick the same nit as Seth over the term “life” or “organism”, but I think is is arguably a matter of opinion.

  4. #4 Jim Bartek
    August 27, 2004

    Hello,

    Myself and one other member of Seyet LLC, Lee Gooding, created the 3D visualizations for Purdue University.

    It was a great experience and I love working on scientifically accurate visualizations because of the advanced research and discoveries I have to learn about in the process.

    I agree that these bacteriophages are quite amazing. When we first had a completed model of the bacteriophage built it was so incredible to see such a small biological structure that looks mechanical in nature. Also, that model was built directly from their research so it is highly accurate. It is not a representation. It still amazes me to look at that animation and know that I am seeing precisely how a virus can inject its DNA into e-coli.

    The Structural Biology group at Purdue seems to be doing a lot of different work on DNA docking and delivery. It will be great to see what comes of the research over the years. Instead of taking pills filled with drugs maybe someday they will be filled with living organisms that can do a specific task inside our body such as dock to cancer cells.

    If anyone has questions on the creation of the visualization feel free to ask.

    Also, I have probably read many of Carl’s articles without even knowing it since I am a big Popular Science and Discover fan. Look’s like I will picking up a copy of his books as well.

  5. #5 Bas Burger
    August 27, 2004

    Great article, only I disagree on one point though, sticking a needle into tisue and inject some chemical bond is not considered sophisticated when done by men, then why is it when a bacteriophage does a similar thing? (and probably infringes some hotheads patent in the process :-) )
    It only shows that the process of doing such thing is a proven tactic in our evolution as we all share each others evolution to thrive ourselfs, oops sharing is forbidden nowadays, one wonders how patent laws will stop evolution in the end… lol… we just mutate lawyers into green goo… lol…

    But on a serious note, nature works because of it’s simplicity, don’t let yourself fool by things that look complicated closeby, it’s behaviour paterns are often simple and because of that they work.
    A bacteriophage sticking a tube into tisue
    to inject manipulating chemicals to reach it’s goals is simple and expected behaviour.

  6. #6 Jim Bartek
    August 27, 2004

    I like your viewpoint, but I think it is a complex process and it is more advanced than a doctor and a needle.

    This bacteriophage only sticks its needle into e-coli when its “legs” come across a specific receptor.

    Imagine putting a ton of these little guys in your system and they can only attach to HIV and they carry something to kill it.

    Also, for cancer treatment the toxic drug would only be able to go into the cancer cell and would not be able to invade healthy cells as well. Cancer patients would not have to live through the grueling side effects of chemotherapy.

    Perhaps one day there will be a whole army of “helper” organisms in our bodies that act as a secondary immune system.

    On a less serious note, you comments remind me of the movie Pi, where everything is simply and complexly mathematical and predictable.

    -Jim

  7. #7 Noumenon
    August 30, 2004

    Yeah, my experience with nature is that it _looks_ simple until you start peeling back the layers, because our brains are simple and so we assume other things must be simple. When a human being wants to inject something into something, we put a straight metal needle onto a glass tube with a plunger. When nature wants to do it, it builds an assembly of rotating proteins, a six-part docking assembly, creates solvents to eat through the walls… and when you look up even closer it’s probably even more complicated, because this is the version that’s been simplified for us to understand by a professional writer. Atoms are not billiard balls, our eyes don’t just take a picture like cameras, and being able to describe something briefly doesn’t make it simple.