Okay, I’ve had a pretty severe cold the last 5 days. I don’t know why in 52 years I haven’t noticed it before, but despite the heavy nasal congestion, one nostril always remains relatively clear. but throughout the day as I blow my nose, the clear nostril is sometimes on the left and sometimes on the right. That is not to say that I can’t produce mucus from both nostrils. Is this normal and what gives with this alternating phenomenon?
It’s probably normal. IANAD (I’m Not A Doctor) but as I understand it, our sinuses are a big (mostly)hollow space behind our noses. This space contains most of the mucus when we’re sick, and like any other container, it’s affected by how its held.
<re-reads OP. Darn you probably mean when we’re up and about>
I’m not sure if it explains much about congestion when our heads are upright, but it does explain why you can breath out of the side of your nose away from the pillow when you’re lying down.
I can only confirm this strange and annoying phenomenon. I figure hey, at least ONE of them is working…
I am also not a doctor, but I think this is normal. The airflow through the nose is partially controlled by “swell bodies” (which I’m sure turns up some interesting Google results if you don’t qualify with +nose, +respiratory, or similar), which partially close one nostril, maybe so that it can recover from partially drying out. They switch your dominant nostril every half-hour or so.
IANAD(yet) but the blood flow to the nares is not symmetric or constant. One side is perfused more and it alternates (IIRC about every half hour). Congestion (in simplified form) comes from fluid leaking out of the blood vessels and engorging the tissue (that’s how decongestants decongest- by tightening up the vessels so they don’t leak so much). So, basically, the side with more blood flow gets more congested. I don’t remember if we learned a teleologic explanation (it was in a lecture 8 years ago- I don’t know why I remember it :)).
PC
I’m glad that some people have spoken with a bit of authority on this. I suspect it has something to do with the idea that nobody holds their head perfectly vertically, and the drainage goes to the “down side.” But I can confirm that yes, it happens to me too.
What I want to know is, why is it the nostril that’s clear is always the one on the side I’m lying on, so that the weight of my head against the pillow pinches it shut so I can’t breathe? I choke and gasp for about half an hour, then roll over, and it’s the other nostril’s turn… gaah…
That’s easy: medical Murphy’s law. 
As others have said the bloodflow to the membranes in the nose is not constant or symmetrical, causing the phenomonen of having one blocked and one open nostril. This seems to be a reasonable evolutionary adaptation since the nose is used both for breathing and for smelling.
Breathing through the nose requires a good fast flow of air to supply the lungs, but this will tend to dry out the nasal membranes and may cause them to crack or suffer other problems. Smelling, on the other hand, is best served by a slow, turbulent flow of air that would not dry the mucus so. It seems a logical solution to have nostrils that alternate the performance of these tasks. Exactly how this nasal cycling is regulated remains, as far as I know, a mystery.
Research on the phenomonon is often contradictory. Different studies have claimed that as many as 80% (Flanagan P, Eccles R. Spontaneous changes of unilateral nasal airflow in man. A re- examination of the ‘nasal cycle’. Acta Oto-Laryngologica 1997; 117: 590-595.), or as few as 13% (Gilbert AN, Rosenwasser AM. Biological rhythmicity of nasal airway patency: a re-examination of the ‘nasal cycle’. Acta Otolaryngol 1987 Jul-Aug;104(1-2):180-6) , of the population experience a classic alternating cycle. There have also been some (unpublished, to my knowledge) studies that correlated left and right handedness with the frequency of the corresponding nostril being the “dominant” one.
There was some (research published about a year ago by Dr Larry Cahill from the University of California that suggested we perceived smells differently through each nostril. His team found that smells inhaled through the right nostril were thought to be more pleasant. Smells inhaled through the left nostril were identified more accurately.
If the correlation between handedness and nostril dominance is true then lefties should find the world to have a more pleasant aroma while righties would be better at identifying what they’re smelling.