I think I don't have the correct background to understand fully. However, I think it makes a little more sense than when I originally read it. 

An analogue to what you're talking about (referential containment) with the medical knowledge would be something like PCA (principle component analysis) in genomics, right? Just at a much higher, autonomous level.

I didn't understand everything completely, however when you mentioned "relevance realization" it reminded me of a recent post which gave labels to data which was of different levels of usefulness. The exact labels he used isn't particularly important, but the categories that they represent are extremely useful. He outlines, more or less, that there are three types of information: 

1. Unsorted, unfiltered data. Without a way to discriminate the signal from the noise, this data is basically useless. One example he gives are unsorted error logs for a given computer.

2. Highly relevant, well processed data. When the raw data is filtered, modified, and processed into a hyper usable form, that's when it is it's most useful. The ways to slice and dice the data are subjective in the sense that it depends on the goals of the user. 

3. Misleading or incorrect data. Some data may be correct, but misleading. The example given is a ticket created because a "website loaded slowly". Because this ticket was submitted, a lot of time may be taken to determine what may be wrong with a server. However, it turns out that the page loaded slowly because it was accessed via an old machine! 

I wonder if the two of you might be interested in exploring these concepts together. Or apologies if I misunderstood!

Reading your post, the idea of Concept Dependency reminded me of the way that some people implement their Zettelkasten systems using Obsidian software. This software uses wiki-type links, and has the native ability that if you press control while hovering over one of these links, that you get a preview. These previews render (mostly) normally, except they are smaller than usual. They can still be scrolled like usual, links clicked internally, and so on.

I sometimes see people using these links in a way similar to how you are describing concept dependency posts. For example, if something contained a quote where a word is being used in an unusual way (like philosophers love to do), when you "peek" at the link you might see, for example, how the author previously defined the term.

I saw one implementation where the author would link to where they had previously justified the assumptions they were using in their research. Unfortunately I don't have any good resources specifically for this kind of implementation, though I think that my comments likely explained it well enough.|

For a similar idea regarding making scientific research (or any kind of academic paper, really) more modularly accessible in the context of storage or writing, you might be interested in some of the work that Joel Chan has done on Discourse Graphs. He has used a few other names as well, for example "iTunes for papers". 

I think that "information architecture" is an interesting concept. These two ideas seemed the most closely related to what you're describing.

McDonald's on the other hand... changes their frying oil every two weeks. 8 hours by 14 days

As a quick point— McDonald’s fryers are not turned off as much as you think. At a 24 hour location, the fry/hash oil never turns off. The chicken fryer might be turned off between 4am and 11am if there’s no breakfast item containing chicken. Often it just gets left on so no one can forget to turn it on.

One thing to consider also, is the burnt food remaining in the fryers for many hours. Additionally, oil topped up between changes.

I don’t remember how often we changed the oil but I thought it was once per week. It was a 24 hour location

I know that you said comments should focus on things that were confusing, so I'll admit to being quite confused. 

• Early in the article you said that it's not possible to agree on definitions of man and woman because of competing ideological needs -- directly after creating a functional evo-psych justification for a set of answers that you claim is accepted by nearly every people group to have ever existed. I find this confusing. Perhaps it is better to use a different example, because the one you used seemed so convincing that it overshadowed your point. 
• There is, in my opinion, and unreasonably large distance between when you talk about "uncertainty" and when you talk about the fact that it can be almost completely ignored in daily life. If it's not so important in general daily life, then mentioning this early will help people understand better as you show examples where it actually does matter. 
• As far as choiceless mode goes, you say something to the effect of "if people can have any (moral?) choice at all, then it's not actually choiceless mode at all". However, this would imply that choiceless mode has actually never existed, as there has always been some degree of choice in morality and worldview. Either what people were yearning for wasn't choiceless mode, or that there is some threshold of moral choice that cannot be exceeded. 
• I believe it would be less confusing if you mentioned earlier that "moral uncertainty" refers to an individual being uncertain about any specific moral judgment, rather than a sense of "morality doesn't exist" or "morality is unknowable". 
• I feel that, as a chapter, I'm not completely sure what I'm supposed to take away from it. Perhaps the use of some progressive summarization or some signposting would help in that regard. It's not that any of the points made are bad or something like this, and I'm not talking about individual sentence structure. But overall, there doesn't really feel like a huge connection between the sections. Logically, I can see what the connection is supposed to be, but when reading it feels more like mini essays arranged on a topic than a chapter. 

Overall, I found the chapter interesting. And as I said, I was actually very convinced by the evo-psych answer to "man" and "woman" and plan to write on it in the near future. 

I think that ideas are not very clearly presented here, and I become a bit confused. I will try to explain what I understood from the article followed by some comments. 

1. It is possible that we have no free will. That our minds try to interpret our actions, but have no control over our body's action. 

2. Some people believe that if they have no control over their physical actions, there would be no need to use our mind to determine right or wrong -- because that information cannot "go backwards" to the brain that controls physical actions.  

3. When people choose not to explore the possibility we might lack free will, this is called an "unimportant possibility"

4. In this situation, it doesn't matter if the mind explores right or wrong, fact or fiction, but it does matter what the brain believes and the actions the body takes. 

5. Conversations happen between brains by the use of bodies, so brains should use their bodies to spread knowledge about what is correct and incorrect, what is fact and fiction. 

-- Unfortunately, in this case, it still does not matter what the mind thinks or believes. It is the brain engaging in communication, not the mind. So the mind considering right or wrong has no effect on this. There being no free will, brains cannot choose (or not choose) to share information, they are merely compelled by stimulus. 

But, regardless of this, we have evidence showing that belief in free will increases goal directed behavior, self reported satisfaction, and so on. 

If free will is false, then no amount of arguing will change it, because everything was set in motion long before you were ever born, and you are not free to change them. However, deterministically telling people they have free will will make them feel better and perform better. So, deterministically, promoting belief in free will is important. 

If, however, free will is true, then telling people that it isn't is robbing them of an essential agency. You are creating harm. If free will is true, and you tell people that it is, then you're empowering them with the truth -- allowing them to make better choices and to improve themselves. Therefore, under free will, promoting belief in free will is important. 

To put it plainly: Belief in determinism is an info hazard.

I'm inclined to agree with other commenters: While the concepts presented in the article are very useful, the name "garbage" information is itself cursed  information, because if we tried to talk to someone about garbage information, they already have a very strong preconception that will be called up, which doesn't align with what you're trying to communicate.

You're using "garbage" to mean that the noise to signal ratio is fundamentally unusable. However when others think of "garbage" information, they think of something like a malfunctioning sensor, where all of the data collected is useless and should be thrown away. Instead, you mean that there is good data there, but it gets lost under a pile of irrelevant information. 

I would say the distinction is important to avoid incorrect intuitions.