Stardate 20010430.1750 (On Screen): When there's a war, I suppose there's a natural tendency on some level to treat it sort of like a sporting event, to follow the play-by-play and to root for your own team. But of course deep down there's guilt in doing this, because real people are out there fighting and  getting killed. So I must admit that there's non-guilty pleasure in watching this particular war (though "border skirmish" might be more appropriate) because no-one's really getting hurt on either side. In actuality, it's little more than a vandalism contest. This is really sort of like what American Indians used to call counting coup: defeat your enemy in war by humiliating him. Now that I can get into.

Stardate 20010430.1550 (On Screen): I suppose a quick review is needed of how we deal with relatively harmless viruses like influenza.

A virus can enter your body any of a number of different ways, and once inside you what it does is to invade cells and take over their reproductive mechanisms. It hijacks the tools there which ordinarily would be making new proteins and nucleic acids for the cell's normal operation, and instead reprograms them to make new viruses instead. Eventually there are a huge number of viruses in the cell and its own function is thoroughly disrupted. The cell bursts and releases a swarm of new viruses into the blood, which then attack and co-opt other cells.

Our bodies have a strong defense against this kind of thing, but it's reactive and it is slow. The immune system has white cells which eventually recognize the viruses as invaders. They have a sort of toolkit of DNA, about a thousand fragments of them, which they rearrange to create antibodies (through a process which is not yet well understood). Such a cell will become primed to recognize and respond to that virus. It then reacts to the presence of the virus by reproducing like mad, by generating certain signal chemicals, and by creating antibodies which are released into the blood plasma.

Antibodies are extremely small and primitive; they are little more than customized proteins. But they're designed to stick to specific other proteins like those in the jacket of a specific virus. Not only does this largely prevent that virus from infecting another cell (because the jacket is a tool to invade a cell membrane and it can't do it with all those pesky antibodies in the way), but it also tags the virus so that it can be recognized by another kind of white cell which will engulf it and destroy it with enzymes.

That takes care of the viruses in the plasma, but not the ones buried in cells. To assist in that, most cells have a mechanism known as the endoplasmic reticulum. What it does is to take random proteins from inside the cell, break them into pieces, and shove those pieces partially through the cell wall. If the protein is "self" it gets ignored. If the protein is "invader" (because there are viruses inside it being reproduced) then antibodies will hook to it, and the cell itself will be attacked and destroyed by a white blood cell. The cells aid in their own destruction.

Once you've gotten over a given strain of flu, you'll never get it again. That's because your immune system retains white blood cells which are sensitized to it. The process of identifying an invader in the first place is slow (about two days) but once some of the white blood cells are primed for it the response is extremely rapid (because it isn't necessary to go through the "identify and learn" part), and if you're ever infected with that particular strain of virus again the response will be so fast and efficient that you'll never even notice that you were sick. The viruses will be defeated before their numbers achieve the quantity necessary to make you feel ill.

A vaccine works by priming the immune system to create that pool of white blood cells. There are a number of ways this is done. In some cases a virus which is harmless but similar to a harmful one can be used, since the resulting immune response will stop them both. That's how the smallpox vaccine works; it uses a virus called vaccinia which is similar to, but not the same as, the smallpox virus. (This was the first successful vaccine, and the word "vaccine" derives from the name vaccinia.) In other cases a dead virus or a weakened virus is used, which is how polio vaccines work. Some modern vaccines simply consist of proteins. In all cases the effect is to fool the immune system into thinking there's been an invasion, resulting in the immune system creating that all-important pool of pre-trained white blood cells. When the real infection comes, then the response is swift and sure.

Which brings us to the point: a vaccine doesn't prevent infection. What it does is to defeat the infection rapidly after it's taken place. But invading viruses do enter the blood and do infect cells and do reproduce; it's just that they don't get to do very much of that. While they're making their initial attack, the relevant white blood cells have skipped the "identify and learn" step (which already happened at the time of the vaccination) and go straight to the "reproduce like mad and create antibodies" step. Even that, though, takes a while (a few hours) and during that time the viruses are still largely able to go about their business. Absent a response, the population of viruses grows exponentially. On first infection, the first adequate immune response takes about 3 days. Once your immune system is sensitized, it takes maybe six hours. This doesn't mean "1/12th the number of viruses"; because the exponential curve works in your favor. So the peak blood concentration of viruses is really a lot lower than 1/12th.

Why, then, are there viruses we don't get over, such as herpes or papillomavirus (which causes warts)? It's because the immune system doesn't go everywhere. Not all cells have an endoplasmic reticulum (red blood cells don't), and the immune system doesn't have access to all areas of the body anyway. In particular, the immune system doesn't have access to nerve cells (which is a good thing, because nerve cells don't reproduce, so if the immune system were killing them at the same rate they kill epithelial cells, you'd be dead before you were 20). Herpes and papillomavirae have a pitched battle with the immune system during the initial invasion which the immune system wins. But while this is going on, some of the viruses hav