Meta question....What are these penalties you are referring to?
My understanding was the only ban hacker news imposed on sites was a binary one. ie a domain was banned or treated as an equal to all other allowed domains.
> Some submissions get automatically penalized based on the title, and others get penalized based on the domain. It appears that any article with NSA in the title gets an automatic penalty of .4. I looked for other words causing automatic penalties, such as awesome, bitcoin, and bubble but they do not seem to get penalized.
> I observed that many websites appear to automatically get a penalty of .25 to .8: arstechnica.com, businessinsider.com, easypost.com, github.com, imgur.com, medium.com, quora.com, qz.com, reddit.com, rt.com, stackexchange.com, theguardian.com, theregister.com, theverge.com, torrentfreak.com, youtube.com. I'm sure the actual list is longer. (This is separate from "banned" sites, which were listed at one point.
Page ranking also decays with time, and I think also once you reach a discussion threshold. (I haven't re-read the entire article as thoroughly just now.) I highly recommend reading the article, as it's VERY interesting and well presented.
[0] http://www.righto.com/2013/11/how-hacker-news-ranking-really...
A good description of the math behind penalties (and a list of some penalized domains) is here: http://www.righto.com/2013/11/how-hacker-news-ranking-really...