This is not unlike how where there's biological life, there's parasites and viruses.
Perhaps some sort of a similar homeostasis will also be reached by software.
1) A virus provides some additional benefit. For example, if a virus' first stage acts as a sort of installer and pulls in some additional libraries for use, at some point of public infection rate there's a pretty good chance those libraries are available to anyone targeting programming for those systems. This becomes more feasible if AV cleaned the infectious and malicious portion while leaving libraries. Imagine, every system has libpcap one it...
2) Viruses start opening previously locked down portions of the OS to achieve their goals, and developers start taking advantage of these opening to extract more value for what they provide (in fact, being somewhat malicious themselves). This is already the case to some small degree with browser exploits. Keygen utilities that install malware seem to fit this somewhat.
This all presupposes a much more computer integrated and yet less computer aware society, which is where I think we are heading. More and more items have integrated computers and operating systems, yet we are much less aware of when this is the case (of course certain groups, such HN regulars, are more likely to be a aware of these items).
Edit: Here's a sample scenario for you: You turn on your new computer and attempt to use it to watch videos on your favorite site, but it doesn't work. You try again tomorrow and it does. What happened is that between then and now, a virus has infected your system and installed a hacked divx codec and made some changes in your browser to redirect you to some specific sites often. The author gets information about your system far beyond what is normally allowed, and you get access to videos as you normally did (possibly illegally).
I work as a malware and enterprise security analyst, and I can certainly see no current or future benefits to malware. I think the "cons" of them harvesting your email, banking, and social networking credentials, abusing your system resources to spam and DoS, and siphoning important information from your hard drive to a remote server certainly outweigh any incidental benefits that may occur.
Edit: s/Stephens/Stephenson/, + classic
Additionally, for point 2, locked down OSes usually have a locked down app store. This means those app store tester machines would also need to be compromised, as well as the app store testing suite. Otherwise the testing suite would notice a dependency on not-allowed functionality.
As for OS lockdown, while I can see why you went towards that interpretation, and on re-reading it does make sense, I was actually thinking of something much more general (so OS is a bit of a red herring). Any hole that allows root/administrator access (so any multi-user secured OS), or even something that loosens security in the browser to make more, probably less safe, access available to web pages.
You made me curious to know if we would literally die without gut bacteria.
The answer is no: "humans can live without gut flora"[1].
[1] http://www.sciencedirect.com/science/article/pii/S0165247805...
(Note: no criticism is intended. I understand the larger point you're making.)
In nature, a virus or parasite can't spread too fast or hurt its host too much or its reproductive cycle will not be able to sustain itself. We see this in software too: a virus that is too nasty will attract too much attention and everyone will end up installing tools to detect and remove it.
So, while you may find the occasional symbiosis in nature between host and parasite, there is little reason for that to happen in the software world. It's far easier, safer, and potentially more lucrative to fly under the radar. For example, once your software infects a computer and you get access to their bank account, you only take $7.69 out once every couple months or so instead of draining it in one go.
Moreover, a virus could be deliberately designed to mutate, so as to evade anti-virus software. In fact, isn't this already being done since ages?