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My beer has been in the primary for about 5 days now. I can only assume fermentation has stopped as its reached peak krauzen and the froth seems to be subsiding.

I attempted to seal up my primary as best as possible after I added a new bung through which to feed a wire for my thermostat but there was inevitably going to be gaps as I didn't have the proper tools - as a result gas has not been exiting through the bubble air lock but I don't see this as a problem in itself.

I would like to take a sample for FG testing but this will draw air in through the hole(s) - is this okay? Can I assume that very little, if any, CO2 will escape meaning that there will still be a CO2 layer on top of the beer to stop it oxygenating?

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    The answers below are good, I'll just toss my two-cents in that the timeframe we're talking about (a couple of weeks) and the volumes of O₂ (opening the bung, taking a sample, &c.) are simply not worth worrying about. So long as you're not aggressively shaking or otherwise forcibly introducing O₂, you're fine. – jsled Jun 15 '15 at 16:07
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Any way you take a sample (unless it's from a pressurized vessel with an outlet) will draw air in. As you suspect, it should be a small amount, and given that your beer A) may still be fermenting (which CO2 will help strip any introduced oxygen out of the beer) and B) definitely still has yeast in it (which will scavenge oxygen, as long as it's still alive), it should be just fine. If you prime and bottle-condition as well, the re-fermentation will give an added layer of protection from oxygen.

However, it's always best practice to avoid contact of any kind with air, as even small amounts of oxygen can be damaging to the beer's flavor. The 'CO2 blanket' often referred to is not a viable solution for keeping beer exposed to air (even just by small gaps around the lid/bung) safe from oxidation. While CO2 is indeed heavier than air, it, along with oxygen (and all other gasses), will always diffuse to take up the whole volume available for it, eventually making a homogenous mixture of the gasses present. Gasses also travel from areas of higher concentration to lower concentration (meaning CO2 will tend to diffuse out the gaps and air will tend to diffuse in). In other words, any air that gets in will not simply sit atop the CO2, but will rather mix with it until the whole head-space volume is an even mixture of CO2 and any introduced air (letting air touch the beer/head-space boundary and hence enter the beer), and this will continue until the gasses on either side of the leak are in equilibrium (these behaviors are described by the ideal gas law). Luckily, this takes a while and may be of little consequence to the quality of your beer if you don't leave it too long.

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Since CO2 is heavier than oxygen, it won't escape the container unless you have a wind blowing over the opening. Also, the beer will be generating more CO2 as i ferments, so even if any escapes, more will replace it. I don't think it would be a problem to leave a small hole.

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    While CO2 is technically heavier than air, the small forces that cause it to occupy its whole volume vastly outweigh the force of gravity. This is why the gases present in ordinary air in a sealed room at STP (standard temperature and pressure) don't layer into their individual components. In fact, O2 will slowly infiltrate into "sealed" beer bottles against two or more volumes of pressure, which is one reason why crown-capped bottles of vintage ale age over time. – Chino Brews Jun 15 '15 at 18:57
  • the reason for beer aging - interesting! – Phizzy Aug 28 '15 at 15:09

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