Carl_Sagan42

Jick, I just wanted to let you know that my girlfriend and I furiously F5 http://videogameshotdog.com/ every thursday night/friday morning.

For an actual semi-related question: I have to say, the weekly podcasts/radio shows have been some of my favorite things about KoL. Having a two-hour window into the minds of the people developing a game you're playing is a really awesome thing. How did you guys ever end up making something like that a standard way of interacting with the community, and do you think more games would benefit from this sort of thing?

I'm a PhD student who does this sort of recombinant DNA work.

To expand a little bit on the discussion, here's some background on viruses that might help. Viruses essentially consist of a protective protein shell which surrounds their genetic material (RNA or DNA). Viruses need to get inside of the cells of other organisms in order to hijack their protein creation machinery to make more viruses. This process of gaining access to a cell, called viral entry, is carried out by various proteins on the surface of the virus that interact with the cell the virus is going to infect. Some viruses puncture the cell and directly inject their genetic material inside, some viruses fuse with the cell dumping their viral DNA/RNA inside, some viruses trick the cell into uptaking the virus, and other strategies exist too -- viruses are sneaky.

Because viruses are so small and have so little DNA compared to most other organisms, the majority have had their genomes sequenced for quite some time. Once the sequence for the virus is known, then you can pretty much find all the proteins that the virus makes by reading the DNA -- for the most part, we know what genes look like at this point. Most viruses only encode a single protein, or a small number, that are responsible for viral entry.

If you're interested in how people discover what a gene does, a simple way is by deleting or altering the gene and seeing what happens. In the case of viral entry, you could test whether the virus can still get inside cells after altering the gene. This might be tested by electron microscopy or using fluorescent markers that can be seen visually (among many other techniques) to actually see if the viruses can be found inside the cells.

Once a viral entry gene is identified in a particular virus, by using the methods described by /u/nowpleasure you could use that gene to replace the entry gene of a different virus. Because many viruses function very similarly, this hybrid virus actually works in many cases, or works well enough to study viral entry anyway (if not anything beyond that). This is useful to do if one virus is extremely dangerous (see Ebola), as it allows you to test its entry proteins using a much safer virus.

I'd be happy to answer any related questions if you have more!