Likewise, one can feel lonely or empty due to insufficient social contact, wrong kind of social contact, insufficient exercise, or due to physical or psychological conditions.
Healthy empiricism is vital: like you said, our senses are telling us something for a reason (our ancestors wouldn't get far on the savannah if the predator they saw with their eyes was just as likely to be a fantom as the real thing, or if feelings of loneliness or isolation were just as likely to suggest eating more of a certain berry instead of joining a hunter gatherer pack), but it's important examine evidence impartially and in total (like a physician would do) as well as to make falsifiable hypotheses (one can never say "i have this specific pain due to a twisted wrist from an accident" with full certainty, but one can say that this is not the case if the wrist is not fractured in the first place and thus avoid treatment specific to a twisted wrist.)
I'd advice the OP to quantify the social contact one is getting and to describe its qualities (with evidence for and against) and make an action plan that tests the hypothesis, rules out some common alternatives (e.g., if one has family history of depression or physiological conditions like thyroidism, see a doctor first; if one is also not getting insufficient physical exercise, try that as well.) and a fall back plan if those aren't the case (perhaps taking a vacation to see if one needs a change of scenery, going to a conference and talking to others in the industry to see if a different group of colleagues might help.)
One somewhat bad advice I keep hearing is to enter into something that involves a long term commitment (e.g., get a pet, change jobs, or most commonly and more dangerously go to a dating site) as the first and/or only thing to try. All of these things are good and in many case help (e.g., now that I'm married and have two dogs, I find myself feeling less lonely than I did prior to this, even some of my closest friends have moved away recently), but have the tendency to act as short term distractions from a deeper or more difficult problem. It may end up doing little to help or might make things worse in the long term (neglecting a pet, hurting one's long term career, or getting into a codependent relationship) IF done without any reflection beforehand, that is "just because" it seemed at the time that to be the easiest and most obvious thing to do.