"My favorite was in Mass Effect when I went to talk to the Reapers and they were all 'you cannot hope to understand us' and I'm like, 'dude, you're a big thing that likes to smash little things, what's not to get?'" -- as seen on a forum
I totally can't sleep, so I'm going to lay this little essay on you about a common science fiction trope that just doesn't work for me. There will be huge spoilers in this essay for the novel Bloom by Wil McCarthy, and I guess some spoilers for Stephen Baxter's Xeelee series.
So here's the summary of Bloom. In the backstory of the novel, an uncontrolled nanotechnological "gray goo" release has devastated not just the Earth but the entire inner solar system, turning it into a vast unliving horror called the Mycosystem. A tiny fraction of the Earth's population managed to escape to underground colonies on Jupiter's moons, where they eke out a regimented, hardscrabble existence called the Immunity which lives in constant terror of nanotech infestation -- the "bloom" of the title -- a single one of which, if unresisted, could consume a whole town. (The Mycosystem cannot survive below a certain ambient temperature, so fortunately spores can only survive if they somehow penetrate one of the heated underground cities; various countermeasures are deployed by the Immunity whenever that happens.)
The novel itself describes a space mission sent down from the Immunity into the Mycosystem to monitor it and determine if the spores are learning to survive at low temperatures, something which would obviously be devastating to humanity's chances for survival. After various shenanigans and crises, the crew find themselves contacted by a human personality living within the Mycosystem. It explains that actually, the Mycosystem contains the uploaded personalities of everyone thought to have been consumed by it, and they're all pretty happy with the situation. They've apparently been baffled by how violently the Immunity has been resisting their attempts to draw them into the system, but now that they understand how the colonists feel they promise to refrain from any more "invitations." At the end of the novel, the Immunity has become able to coexist with the Mycosystem and everyone lives happily ever after, more or less.
I don't really want to slam the book here. It's a pretty good SF novel. Although it's only sketched out, McCarthy does a good job of describing the Immunity's regimented society as seen from the inside (the narrator is a freelance reporter -- a blogger, effectively -- who's been invited along to document the space mission.) The characterization is decent, interesting things happen on the ship's descent into the Mycosystem, and said Mycosystem is described with appropriate levels of horror.
The problem I'm getting at is with the resolution of the story; the explanation of why the Mycosystem has been so determinedly attacking the Immunity with its spores, and why they decide to stop. It's made clear that they understand what's been happening in the Immunity -- the spores they send are resolutely attacked and destroyed with a variety of sophisticated weapons. So... if they care enough to keep sending the spores and developing more and more advanced versions... surely they'd care enough to find out why the spores are being attacked? How about, you know, asking? A radio message would do. Heck, they don't even need to send a message; the Immunity doesn't keep secrets (mostly) and eavesdropping on its communications for a few hours would probably make it clear why they do what they do. All this is assuming that the humans in the Mycosystem wouldn't just recall how scary it was to get consumed in the first place, and conclude that perhaps the Immunity is just acting on that fear.
McCarthy kind of handwaves this point by asserting that the human minds in the Mycosystem think at a very slow rate and have largely transcended to a higher mode of thought. But even so, a) they evolved from humans and b) they are smarter than humans, so they ought to be able to figure out human thought processes. Even if they can't, the fact that after thirty years of living right next door they can't make this connection does not speak well for the Mycosystem's smarts. Ultimately this plot point is just not sustainable: the Mycosystem is perfectly capable of communicating with the Immunity, it should have done so right away. The end.
This same flaw hollows out a major plot element in Stephen Baxter's Xeelee series. In these stories, the Xeelee are a bunch of unbelievably advanced beings capable of astounding feats of cosmic engineering. They don't communicate; from humanity's perspective, they just do random, incomprehensible things. Eventually we go to war with them for some reason, smash up a bunch of their megastructure thingies by throwing planets and stars at them, and manage to seize the Milky Way Galaxy (the Xeelee control all the rest of the Universe, so this isn't as big an achievement as you might think.) It ultimately turns out that what's really going on is that the Universe is infested by dark matter creatures that are eating all the stars, and the Xeelee are battling them on behalf of baryonic life everywhere. Humanity's war on the Xeelee is therefore not just hopeless but in fact fantastically counterproductive.
...Yep, you're way ahead of me here. At no point during the millions of years we humans are jumping around and nipping their ankles do the Xeelee attempt to inform us what's going on. A couple of powerful radio beacons scattered through the galaxy constantly beaming out the message "Hey, jerkwads, we're trying to save baryonic life here, back off" would be perfectly adequate, and trivally within Xeelee capabilities: surely much less expensive than battling humans for millions of years and dealing with the resulting damage to the war effort against the enemy that actually matters. But somehow the simple concept of picking up a phone never occurs to anyone, and the great cosmic tragedy creaks relentlessly on.
This is indeed the very nub of my gist, as it were. In science fiction we constantly get pummeled with mega-advanced alien societies that we allegedly can't hope to understand. And perhaps it's true that there's another level of thought beyond the consciousness and intellect of human beings, something that we can no more comprehend than a dog can comprehend human-level intellect; at the very least it's a perfectly reasonable science fictional concept. But if the point of misunderstanding between the aliens and humans is something that can be communicated on a human level ("we didn't realize you didn't want the spores, sorry about that," "we're fighting mega-bad guys who will destroy you, stay out of our way") then there's absolutely no justification for the failure of communication that so often underpins these types of stories.
Put it another way: It's true that you can't explain representative democracy or fractional reserve banking to your dog. But you most definitely can make it understand that it should stay off the couch.