Friday, March 1, 2013

Still alive, still kicking, and so are viruses, too.

The last few months for me have been a total whirl-wind, and have caused me to neglect my blog! I feel terrible! I'm sure that, since then, all of my (not so) dedicated readers have turned to bland multi-topic science quick-fixes, like those posted by the "I fucking love science" page on Facebook, or io9, who tried to say that NASA was covering up knowledge of alien existence a few months ago. Laughable! Anyway, we'll just forget I abandoned my blog as I planned out the next few steps in my life. It's not important!

Let's jump right in, shall we?

The hottest topic in virology these days is the sudden reemergence of the age old "are viruses alive?" debate. The basic properties used to describe something as "living" are:
  • Does it have the ability to grow? 
  • Does it have the ability to reproduce? 
  • Can it maintain an internal homeostasis
  • Can it respond to stimuli, and carry out various metabolic processes? 
  • Has it, and can it evolve over time?
 Such criteria make sense when you apply them to things that we've already determined to be alive, but when it comes to viruses, we're still searching for some solid answers. The most common quest to find an answer to whether or not viruses can be classified as living things is to consider the origin of viruses.

There are three theories for the origin of viruses that have been respectfully agreed-upon: (1) the progressive hypothesis, (2) the regressive hypothesis, and (3) the virus-first hypothesis. Let's discuss, shall we?

The progressive hypothesis:
The progressive hypothesis states that mobile genetic elements found the ability to leave one cell and enter another, progressively picking up additions as they traveled, forming infectious agents. The progressive hypothesis is supported by the existence and they behaviors of retrotransposons. Retrotransposons are the essence of the progressive hypothesis, as they are genes that move along the genome with the aid of RNA intermediates. While transitive within a single cell's genome, retrotransposons are currently limited to the confines of that cell. We've seen retrotransposons in many eukaryotic genomes, and attribute them to assisting with evolution.

The progressive hypothesis, which leans so heavily on retrotransposons for support, also has a viral example: retroviruses (which as you know, are some of my favorites). The single stranded RNA genome of a retrovirus utilizes a number of enzymes to fuel reverse transcription and integration into the host's genome. But, while retrotransposons are limited to one cell, retroviruses are able to bud from the host cell and move to another.

The regressive hypothesis:
The regressive hypothesis states that the formation of viruses occurred due to reductive evolution. Regressive evolution is not as common, but is supported. On a singular cell level, the best example of regressive evolution is that of the mitochondria. Mitochondria are organelles in eukaryotic cells that are responsible for the generation of most of the cell's energy. Mitochondria are comprised of multiple layers and membranes, and have their own set of DNA that is handed down through maternal ties. Due to their complex structure and their individual set of DNA, researchers believe that mitochondria were once bacteria that devolved to become an organelle.

The virus-first hypothesis:
The virus-first hypothesis takes a completely different approach to the origin of viruses, as it suggests that viruses originated before other cellular life. This hypothesis is really hard for some people to grasp, since we currently identify viruses by their dependency on a host for continued replication and existence. But what if viruses existed first? The simplistic design of a virus and the high rate of mutations that occur within viral replication are both promising reasons for the virus-first hypothesis.

Why am I talking about this?

A study published in Nature seems to have illustrated an adaptive quality in bacteriophages, wherein they begin to express somewhat of an "immune response" to the host's innate immune response. Researchers have shown that specific short palindromic repeats and associated proteins (CRISPR/Cas, for those who are interested) protect vital regions of the bacteriophage genome when exposed to potential threats, like invading amino acids or other bacteriophages.

Now, this article on Discovery News jumps the gun a little bit in the headline alone. "Viruses Pass Major Test to Enter Ranks of Living"? Now just hold on a gosh darned second.

Well, actually, I think I might let you decide. What do you think? Does this mean viruses are living things? Additionally, how do you think people will react to hearing that viruses may be living?

Or do you even care?

1 comment:

  1. I have always loved this ongoing debate. The part that I find difficult is that it may not only be a debate about what a virus is, but also beg a thourough re-evaluation of what the definition of life is, as well as an overhaul of our current theory on genetics.

    The five rather simplistic qualifications for living organisms always boggles my mind, and inevitably there will come a time when they become insufficient. Even our rather rudimentary dabbling in gene splicing may give way to or possibly eliminate some of these qualities if applied properly (or IMproperly as some moralistic viewpoints may claim). Additionally the field of nanotechnology could easily replicate any and all of these qualifications after sufficient developments have been made. At the current point of our species intellectual and technological advancement, our own involvement in these biological systems will begin to alter the foundational theories that we rely upon to understand them and ultimately ourselves.

    Remember that super exciting breakthrough project where some rich guy mapped his own genome? Yeah the Human Genome Project, that's the one. Funny how nobody ever talks about that anymore. The results of that project were quite literally the opposite from what we had hoped, rather than illuminating the fine details of our species intrinsic programming it proved that the very theory we use to study and manipulate genetics is flawed at its very foundation. The human genome does not actually contain enough of what we currently consider "genes" to express the variety of proteins and biological functions that we know exist in most every human body. Some researchers responded with multitudinous theories of "dynamic genetics" but unless I missed some earth-shaking announcement from within the scientific community, no resolution was ever reached.

    I love that you laugh about the accusastions against NASA's alien cover up. Personally I could care less if it is known or hidden, but the one thing on our planet that always makes me wonder how involved another, more advanced species was in the seeding of our planet with living creatures is the virus. It is so elegent and effective. A structure smaller and simpler then a single cell that can move, alter and proliferate genetic codes just screams of advanced design. It is almost like a next level nanotechnology in action. All that junk DNA that our and so many other species contain may very likely be the result of millions of viruses that have taken up permanent residency in our genomes over the course of our evolutionary development. And of all the theories on what sparks evolutionary changes, doesn't viral intervention seem to make the most sense?

    Feel free to call me old fashioned or distracted with sci fi fantasy out of touch with modern science, after all I am old and grey by now and it has been a long time since my years in the ivory towers of academia. However my own close pesonal relationship with these intriguing vessels, be they living creatures or conicidental gene bombs or intentional vessels of evolutionary opportunity, has taught me that they are not the only conundra to be considered.