The general stroke of "Here's an empirical cure that people won't use because they have a differing theory (that this deficiency disease is actually due to infectious agents)" is of course similar. But the beriberi story seems more just like people foolishly ignoring an empirical cure due to, well, having a contradicting theory; it doesn't seem to have the same component of "here's a series of coincidences that seems to undermine the empirical evidence for the cure in the first place".
Also, note that while Takaki correctly identified beriberi as a deficiency disease, he misidentified it as a protein deficiency! Yet his cure still worked well enough, when he could get people to follow it -- which, note, was on top of the difficulty of getting it officially implemented. That's another difference -- if there was any problem getting individual sailors to drink their lemon juice once the British navy started serving it, Cegłowski doesn't mention it.
The switch to limes resulted in many more cases of scurvy. The citrus cure for scurvy was lost until the discovery of vitamin C. I recall an article about this being on HN. The Brits switch to limes because they were cheaper than lemons.
The most interesting part of the disease is that corn actually contains vitamin B3, but it cannot be absorbed by humans when eaten by itself. Native people always treated corn meal with lime, which allowed the vitamin B3 to be digested. When Europeans came to the Americas and learned about corn from the native people, they thought it was stupid to put lime in their food so they left that part out. Thus, causing a disease that afflicted 3 million people and killed over 100,000.
· the “lime” we’re talking about here is not the fruit, but the strong alkali slaked lime, i.e. whitewash or mortar, made by roasting limestone. You can apparently also use lye (Drano), and I wouldn’t be surprised if fermented urine (lant) also worked, but I really recommend that you know what the fuck you’re doing before you start trying to cook with Drano or construction materials. This may help understand the Europeans’ reluctance.
· nixtamalization is done on the whole corn, not on the corn meal. Nixtamalized corn is also known as “hominy”, and if you’re from the US you’ve probably heard of it under that name. It’s been common in the US since colonial times.
· When you nixtamalize corn, you don’t leave the lime in your food. You have to rinse it out after the long, slow nixtamalization process. Otherwise, the result is really bitter.
· Nixtamalization is indeed a traditional practice with a broad pre-Columbian distribution, but it is almost unknown in South America, even though the native cultures here in South America are much more intact and in many ways less assimilated than in North America; this suggests to me that it may not be true that “Native people always treated corn [...] with lime”. I mean, maybe Tawantinsuyu universally nixtamalized its corn, and then the Spanish stamped out the practice so thoroughly that you can’t find nixtamalized corn in the grocery stores there today, even as a special holiday product like chuño; but it seems much more likely to me that nixtamalization just was not universal or even common there in pre-Columbian times.
The pellagra epidemic is one of my favorite examples of how ignorance kills people.
They can just have a cold hard study where they isolate 100 people in a lab, and half only get white rice, while have get rice and barley. Then see what happens.
This is were epidemiology gets very useful: you look at data for correlations, and from there you can design experiments to check for causation.
My main point is that it seems the real problem wasn't so much one approach over another, as one side having an unjustified commitment to bacteria/virus as a root cause.
But back in the 1870s, he didn't know that. He only knew that something in barley was helping to prevent beriberi, and he was in fact mistaken about what that something was. (He thought it was proteins when it was actually vitamin B1.) So the Antibiotic Barley Theory could have been a reasonable hypothesis.
Vitamin C is named "ascorbic" (i.e. anti-scurvy) acid because the people who discovered it were looking for a substance that prevented scurvy, no matter what the mechanism of action. The mechanism of action was only known for sure after the substance was identified.
A lot of it must be to do with taste and quality, but also a desire to not eat like a poor person or barbarian.
(A little bit of mixed barley (and other grains) is fine, but it doesn't take a huge leap to see why people would prefer pure rice.)
As a kid, my parents would make me Mochi. They were hippies, so it was the brown rice mochi. Lately, I've been craving the stuff, and every time I ask my asian friends, they get me white rice based mochi, a very different (and in my opinion, much less flavorful) food.
I eventually figured out where I could mail-order the brown rice mochi from. So good! but, again, made for hippies, so unlike the white rice mochi, which comes in individual plastic packs, this stuff comes in big sheets you need to cut up. Hippies. grumble.
But yeah, I think a lot of this is just cultural factors. I can't imagine eating tofu with nutritional yeast if I didn't have it for breakfast nearly every day of my childhood. Or nutritional yeast at all, for that matter. That stuff looks like fish food, and really, what else do you put in your mouth that is that color? But it's so good on popcorn.
(Well, I guess the way some people refuse to have even 5% barley is probably cultural...)
I can't speak for Japan, but in case of Korea, generally people don't consider barley horrible. They just find it a bad substitute for rice.
- a diet consisting of white rice lacks in vitamin B1, which causes a debilitating disease called "beriberi"
- a naval officer named Kanehiro Takaki discovered this (indirectly) using epidemiology techniques, determining that those who ate more balanced diets did not catch the disease
- mixing barley in with rice basically eliminated the disease from the Japanese navy
- due to some combination of politics, and worry that the solution was "superstition" (ie, it was similar to a folk remedy, and was not laboratory-tested; many Japanese academics of the time did not trust epidemiological/statistical techniques) the Japanese army rejected the solution and continued to have serious beriberi outbreaks, up until 1905 when they finally decided to give it a chance
The two clans put their rivalries aside temporarily to overthrow the Tokugawa Shogunate, but from the Meiji Era the rivalry was responsible for the lack of coordination between the Army, and Navy through the Second World War. 
The article had a one sentence paragraph about this attitude:
Stubborn and blind to the truth,
the army was marching towards its
biggest beriberi disaster ever.
Stubborn and blind to the truth
Science advances one funeral at a time.
It's clear HN appreciates this sort of thing -- the last time I had a comment as heavily upvoted, it was another summary. 
I don't find articles that have a vague dramatic opening that gets you wondering where it's going works anymore.
Inform me, don't try to "entice" me towards your embellishments. Ain't nobody got time for that.
The headline of this article, in my opinion, should have been "too monotonic diet", not "too much rice".
One reason we see so many tl;dr comments even on a very technically inclined place like HN is that articles very often bury their content. We want a thesis out front; we don't want to be strung along for 1600 words and then find the interesting bit between 1601 and 1700.
However, I also think that the phrase “too long; didn’t read” represents a dysfunctional attitude that turns this blessing that is the abundance of information into a curse: if you spend three hours reading 100-word abstracts (let’s say, 300 of them), at the end you will probably have learned almost nothing. If you instead spend three hours reading 1000-word articles (let’s say, 40 of them), you will probably have learned a small amount, which is an improvement. If, by contrast, you spend three hours reading 50 000 words (say, a few chapters of a Murakami book), or a quarter of Olin Shivers’s dissertation, you will probably acquire some new ideas that will stay with you for the rest of your life. There’s a point at which this becomes counterproductive; if you read a book in a day, it won’t stay with you as well as if you read it over the course of a week, and the week also gives you time to reflect on other connections.
My thesis: being able to focus your attention on interesting things is only valuable if you then do actually focus your attention on them. The attitude expressed in “tl;dr” is that focusing your attention is itself undesirable.
It's not about low attention spans, it's about there only being so many hours in a day. It's about helping people find what they want to read because there is just too much content being produced every day.
What analogous contemporary ideas will people be laughing about in the 22nd century? What parts of how we view science and medicine are costing lives?
I think a lot of what is taken as gospel in the field of nutrition will probably be looked back on as barmy or the result of ignorance. The low-fat thing already seems to be going that way.
Takaki most likely had to contend with thinking his cure for beriberi was similarly "monumentally stupid" and "based on poor 'science' and scaremongering", which prevented an objective examination of his experiments.
Yet the American Heart Association treated this study as a curiosity, and doctors deemed it only worthy of snide comments about using it to justifying conference trips to hospital administrators.
As for science, the two examples I'll trot out yet again are Pluto, and kibibytes. Pluto, is of course, not a planet, yet many cling to the nomenclature simply because that's what they learned growing up. More relevant for HN's is usage of kibibytes for 1024 bytes and kilobytes for 1000 bytes. Uptake on replacing the more traditional usage is similarly slow, for some reason.
The ramifications of that aren't clear, though, as it could be something so simple as the risky/difficult procedures being delayed when the best docs are out of the hospital.
Pluto is sort of the same, though at least there's an empirical justification in that there are other similarly sized bodies that shouldn't qualify as planets, so a consistent definition was chosen to exclude them and Pluto. But because it's a definitional change rather than a new discovery, people can be slow to adopt it.
In my opinion, the unsolvable nature of this kind of problem is a lesson in the importance of humility. After a lot of hard work and rigorous investigation, it is easy to conclude that some conclusion must be correct. Unfortunately, as science can only works within the range of known observations. New evidence can completely undermine supposedly "certain" conclusions. Much to the annoyance of the people reporting on scientific discoveries, or the people that demand certainty in any report so they can rely on it (e.g. for military purposes), there is no "final" conclusion in science.
I assumed the OP was submitted as a parallel to the (possible) connection of some mental illnesses to inflammation and infection, just seen on HN: https://news.ycombinator.com/item?id=9388176
Both feature doctors noticing weird chains of causation that accidentally cure mysterious ailments.