Map of life expectancy at birth from Global Education Project.

Monday, June 02, 2008

The Unalive

It's time to wind up my little tour of biology with an odd little subplot. You can find plenty of arguments over the definition of life, what it is exactly that makes us call something alive. This is all very interesting as we think about what we might encounter out there, beyond the earth; and it was at one time all very interesting back when we didn't understand very much about life here on our little rock. But nowadays, the answer to what constitutes life on earth is simple and unequivocal: life is cells.

A cell is a comparment enclosed by a phospholipid bilayer containing a chemical system in a salty solution that includes polypeptides -- long chains of chemical units called amino acids -- shorter peptide chains, and polymers of varying length called RNA and DNA, among other important kinds of chemicals. Some cells, such as your own, also have smaller membrane-enclosed comparments within the larger compartment, in which specific processes take place, but that's optional. Y'all ought to know by now about the system in which information stored in DNA is read out onto RNA and translated into polypeptides. If you don't, look it up. Cells use a chemical process to extract energy from sugar to fuel all that chemistry. They get the sugar in various ways, and they can burn it with or without oxygen, but those are just details.

That's life. (And I can't deny it, many times I thought of cutting out, but my heart won't buy it . . .) But there are these other things floating around, teeny weeny particles with no cell membrane, no salty solution, no sugar burning, no nuthin' -- except DNA or RNA, in a teeny tiny compartment made of a few protein molecules. Are they alive?

Take it from me. No. No way. Nohow. Absolutamente no. Not. Never. Not a chance. Why do I say that? No chemical processes take place in a virus. Viruses do not and cannot eat, metabolize, or even reproduce. They don't do anything. Put a bunch of viruses on a nutrient solution and they'll just sit there for a little while, then they'll dissolve and be gone. That's it. So why are there so many of them around?

They're around because that DNA or RNA inside the little compartment consists of the instructions for making more of them, should it somehow get inside a cell. And the protein jacket is of a nature that it can dock with one or more of the various kinds of receptors that stick out through cell membranes in order to selectively let stuff in, and have the genetic material of the virus slip through. Most viruses contain DNA. The ones with RNA are called retroviruses, because in cells, RNA is usually constructed on a DNA template, but retroviral RNA serves as a template for creating DNA, which gets inserted into the host cells genome. In other words they work backwards, i.e. retro.

Now, as you can readily imagine, if a cell starts getting wrong instructions -- in this case, instructions to just start making virus particles -- that's bad news for the cell. Instead of doing whatever it does, it's just manufacturing bajillions of virus particles until it's full to bursting and then POW! it busts apart and all those viruses are out there. If the cell is one of yours, the viruses are now floating around in your bloodstream or your lymph or your cerebrospinal fluid or whatever. If one of them should happen to bump into the right cellular receptor, in goes the genetic material and another one of your cells is done for. As a result, you are sick.

Note that people talk in metaphorical terms about viruses all the time, in ways that make them seem alive, even purposeful. They talk about viruses "attacking cells," for example, but that really isn't accurate. Viruses just float around, and if they happen to bump into the right receptor, chemical forces cause them to dock and insert the viral genetic material. But they aren't actually doing anything, it's just chance. Similarly, because the cells don't reproduce the viral genetic material perfectly, the viruses mutate, and that means they can evolve. But that also is a random process.

I got very annoyed a few years back when I heard somebody I admire, the founder of the AIDS Action Committee of Massachusetts, saying on the radio that HIV is "intelligent," that it can "figure out how to get around the drugs." I wrote to Larry and complained, but he didn't seem to understand why I was so ticked off with him. (Hey, he said it in public.) A lot of people living with HIV have this idea that it's somehow malevolent and wily, and out to get them. One guy I interviewed even told me he decided not to take his nutritional supplements, because he didn't want to feed the virus. Nope. It's just like a little piece of computer tape, just some simple instructions for making a few proteins, consisting of 9 genes and about 10,000 genetic "words." That's all it is. (And here's a picture, and a description. Pretty interesting, so check it out.)

Since what really defines the virus is just the set of instructions, the DNA inserted into a cellular genome by a retrovirus is the virus, fundamentally. The free floating virus particle is called a virion. The virus as it exists in the host cells genome is called a provirus. A very interesting discovery in recent years is that eukaryotic genomes, including our own, appear to include quite a lot of junk that has been inserted by retroviruses over the eons and ended up stowing away for the long term. Most of this doesn't do anything, but it's quite possible that some DNA that gets inserted by viruses actually does end up functioning in the cell and its descendants, which means that there is a previously unknown mechanism of evolution. In addition to mutation, genes just might get moved around from one organism to another by viruses, which opens up all sorts of interesting possibilities.

But here's the tough question. Where in tarnation did these awful little things come from in the first place? If they were intelligently designed, that's a pretty nasty trick, don't you think? Actually, there would seem to be two basic possibilities, and quite likely both of them have happened:

a) A bit of genetic material gets loose from a cell, stuck to a piece of protein in such a way that it can persist long enough to get into another cell, and off you go;
b) A phage -- a parasitic bacterium that infects other cells -- goes through an evolutionary process called degeneration in which it gives up more and more of its own functions to its infected hosts, until it's whittled all the way down to a virus.

Either way, once a virus is out there, even though it isn't alive, it can evolve, and diversify. So from a small number of beginnings, you can ultimately get a huge diversity of viruses. The DNA viruses and the retroviruses are sufficiently different in principle that they must have different origins, I would say, but beyond that, there don't need to have been many originating events. So viruses really are not improbable. But even though they aren't alive, they are an important part of the biome.

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