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Barkley said:
StarOcean said:

I'm more concerned by the diseases they carry than their weapons

Any diseases they carry would have evolved specifically around their biology, it would be surprising if it would be effective against humans.

Yes their biology could be completely different but if still carbon based I'm sure there could be insects, microscopic life that we have no resistance to. Life is a delicate balance of new strains of viruses, bacteria vs larger animals immune system.  Present a bacteria that causes a immune system shock, is highly poisonous, more effective in our atmosphere. I suspect if two animals meet evolved from 2 different planets one will be susceptible to the other. Yes viruses seem less likely to be effective but viruses are constantly mutating with each new generation and our viruses are something like 20 minutes to 2-3hrs per generation. 

Admittedly though aliens are much likely to be exterminating us so they can make use of our resources. All aliens will have evolved on planets where creatures have to consume each other to survive. They will be I'm sure used to killing on their own world.  We like to think of ourselves as civilised but lets face it you only have to look at an abbatoir to see the true horror's of humanity.