Lions in a Cage
rossboucher.com
rossboucher.com
There's a difference between an environment where something is missing (and having it would make you happier, but the lack of it doesn't hurt you) and a toxic environment which by definition means "Harmful, destructive or deadly to living things." (at least one of the definitions).
It seems to me that Paul's essay claims that working in a company is detrimental to programmers and the way they're "supposed to work". This means everyone should quit working for big companies and start working the way they're supposed to (since programming has so much in common with hunting...).
But then Paul and several others jump to defend the essay and claim that this isn't really the message, that working in a company is fine and that some people would thrive and do better in a startup environment. I fully agree with this point, but if this is the intended message the article fails to deliver it. Drop the toxic, lions in cages and constant references to how you think people should live (society has greatly advanced since the days people used to roam around in groups of 10, and has primarily done so by organizing in large groups and figuring out way to function and work together).
I can see how someone might have difficulty making the connection, but I think the food analogy addresses it. Most food that people eat is in fact toxic to humans. However, its toxicity, on average, is fairly low; it is only in aggregate over an extended period of time that the consequences become apparent. In some cases, it will never even cause a problem.
Eating this "toxic" food doesn't cause anyone unhappiness in the short term, it may even cause a great deal of happiness, but it can have long term consequences.