How to survive boiling water

4 days ago (taxa.substack.com)

> about 7 out of 10 people in the U.S. were prescribed antibiotics in 2024 according to <CDC data>.

This blew my mind so I double checked the source. It links to https://www.cdc.gov/antibiotic-use/hcp/data-research/antibio... which contains some numbers but not the claim. It links to various reports, the latest one (2024 at the time of writing) https://www.cdc.gov/antibiotic-use/media/pdfs/2024-Annual-Re... says at the top of page 2 that the prescription rate is 679 and 775 doses per 1000 people in 2024, depending on the gender. That matches the 7-in-10 number so I'm guessing this is where the statistic comes from

Doesn't that reflect how many prescriptions there were rather than what number of people got it prescribed? See also page 3 where Mississippi has 1167 doses per 1000 persons. Either the number of people is wrong (if the prescription given to a tourist and counted towards this statistic, the tourist should also be counted as person, but the CDC says they take the population count from a census) or it's about doses and not about what part of the population got an antibiotic in the last year. In both of these cases, you can't conclude 116.7% of people got antibiotics prescribed. The claim in the article based on that CDC data sounds to me like saying 520% of the people drink alcohol when, in reality, 10% drinks a bottle a week and the rest nil

I'm probably misunderstanding the CDC report but I'm not sure how I should be able to tell that

  • There's no way 7 in 10 people were prescribed antibiotics in 2024. This looks like a simple and egregious misinterpretation of the data, which seem to be all too common. I could believe there were 700 prescriptions given in the US per 1000 people in the US population. But many of those would be repeats to the same smaller number of people. I still would say there's way too much antiobiotic use - every time doctors have wanted to give me antiobiotics it wasn't necessary.

    • My wife isn't with me to answer directly, so I am going off memory. She is a nurse. But I am pretty she when telling me about her day at the hospital she also mentions needing to change antibiotic for patients for various reasons. I am guessing that also counts as 1 person, multiple antibiotics. Probably considered "separate" prescriptions.

    • This would be my read.

      Hell - my children just this year would have counted for 10+ doses (my daughter 6 all by herself for a series of severe ear infections).

  • Yes, it's "number of prescriptions" (but not "number of people prescribed" or "number of doses"). One person could be prescribed an antibiotic (or multiple) several times a year.

    I'm amazed that there are 1216 antibiotic prescriptions per 1000 people per year in West Virginia though (2.5x the rate of California or Colorado, which itself frankly seems pretty high). Are large parts of the South just awash with bacterial infections, are people being prescribed antibiotics for viral illnesses, or are they just taking antibiotics prophylactically?

  • Yes I stopped reading there after checking the source myself and seeing the same discrepancy. I had also noticed earlier in the article she wrote, "This finding was great news for Napoleon. The French were losing money, and perhaps more alarmingly, their reputation, exporting wine to the British – the wine would “spontaneously” go bad during shipping."

    Pasteur was born after Napoleon was exiled. Maybe she is referring to Napoleon III, but then it's misleading to just write "Napoleon." Two factual mistakes in the first couple pages and I can't trust the rest. Especially on a topic I know little about so I can't be discerning regarding.

    • There seems to be some original research in the post as well though. I'm not assuming they faked their test results or anything at all. I think the article is worth the read, just yeah this (if the replies and I are not reading it wrong) seems like a strange error to make so maybe the not-really-relevant background facts are just not as rigorous. And to err is human

  • Wait is that individual doses? Like one prescription would commonly be for 20-30 doses.

    • Can't imagine; then the figure should be much higher. If the source had agreed with the claim, I wouldn't have trouble believing 7 in 10 people in the USA get told to take at least one set of antibiotics a year (ageing population, it's prescribed almost as frequently as water and rest.. one can rationalise it together), but conversely a 25th of 70% would be ~3% which seems on the low side again. I got it prescribed way more than 3% of the years I've been alive and I'm not yet middle aged

      It's probably just as the CDC document says: number of prescriptions. If you are told to take it for 3 weeks thrice a day and later in the year a second time, that's two prescriptions (per my non-native understanding of English medical terms anyway)

People interested in this: if you are ever in Amsterdam, I recommend to visit the Micropia museum: https://www.artis.nl/en/artis-micropia

Among many stunning things, they have a shelf full of foods and drinks (behind glasses) with age labels, ranging from days to years. It is fascinating to see how they evolve over time.

In case anyone else is curious about the current status:

> The Milk was declared missing on August 20th, 2022.

> The dorm’s extended mailing list of over 300 current students, alumni, and other assorted Random-adjacent humans was contacted, twice.

> In the end, no Milk.

https://mitadmissions.org/blogs/entry/guest-post-the-random-...

A great read from the author. It reminded me of my previous life as a bioprocess engineer, where I led investigations into biologically contaminated batches in biotech. It was fun stuff and I still remember some of the best advice I received from an Executive Vice President to never underestimate a microbe.

On this subject, I once led an investigation in which Bacillus cereus somehow survived in situ media sterilisation for 30 minutes and >121.1°C, despite there being no cold spots. At the end we realised it was the bioburden load of a media component and water temperature used during compounding.

  • > it was the bioburden load of a media component and water temperature used during compounding.

    In English, please ;-)

    • I put it in AI and even that couldn't fix the sentence sufficiently for me to understand it completely.

      "So, in ordinary language:"

      "One dirty raw ingredient introduced far more spores than expected, and the way it was mixed into the water made the sterilization cycle less effective against them. The autoclave itself was probably not broken."

      "The exact relationship to water temperature remains somewhat ambiguous because the HN commenter did not provide the detailed investigation findings."

      2 replies →

Spore forming bacterium are notoriously resistant to most ways of killing them. There's even a species that can resist radiation amounts that are 1000x the dose needed to kill a human.

https://en.wikipedia.org/wiki/Deinococcus_radiodurans

That was a fun read. The author has a really good storytelling style.

I dont understand why the cold brew test had fewer bacteria than the steeped teas. If the bacteria are shielded in spores, shouldnt it be expected that they have the same amount of bacteria?

  • I think it’s just that the bacteria in the hotter container woke up to a warmer, nicer environment. Warm temperatures are much better for bacterial growth. While it was too hot they didn’t seem to care at all since their spores protect them completely from damage.

  • Agreed - I really enjoyed the writing. I'd have normally skimmed for the conclusion but ended up reading it all. Shame that that's so rare these days.

  • They could have some coating that make them stick to the content of the tea bag, basically affecting their solubility.

This almost throwaway line from the article struck me as an example of what we can do with technology, if we choose to put our billions of dollars towards it: "I downloaded the BC30 genome".

So under most brewing conditions a nonzero amount of this microbe survive, but that count is 3 orders of magnitude lower what might be termed a “therapeutic dose?”

What even is a good experimental design for probiotic tea? Brew -> agitate in hydrochloric acid & digestive enzymes for X minutes -> mix with billions of existing gut microbes (that may kill this microbe or out-compete it for resources) and incubate at body temperature -> count the number of new colonies of this particular microbe?

  • The author does mention that a synthetic digestive system was used in another experiment, so you may be correct!

Learning that MIT has an ancient bottle of rotting milk reminded me of my 9th grade science teacher. He had been teaching for decades and had a tremendously messy little office attached to his classroom. The pièce de résistance of his menagerie of scientific oddities was a large fish tank filled with many strata of mottled goos. I asked what it was and he said it used to be an ordinary aquarium, filled with fish and water, and he just left it alone for 20 years.

Another organism that survives pasteurization is paratuberculosis, in milk. It is commonly found in commercial dairy herds. In my opinion, this is alarming.

Many consider it to be a candidate for the cause of Crohn’s disease. Johne’s disease, which occurs in a subset of cattle infected by paratuberculosis, bears many similarities to Crohn’s disease.

When Crohn’s disease was first described, it was believed to be an intestinal tuberculosis, though tests seemed to counter this idea; to this day, it remains difficult to test humans for paratuberculosis infections.

[0] https://www.sciencedirect.com/science/article/abs/pii/S07400...

[1] https://www.journalofdairyscience.org/article/S0022-0302(19)...

spores are the reasons that labs use autoclaves instead of boiling to sterilize things. autoclaves are pressurized so can reach much higher temperatures

  • I didn't know pressure is used in sterilisation. Trying to look up why that helps, the Wikipedia article on autoclaves does not explain why but says it uses 1 bar, which would be equivalent to ambient pressure (atmosphere at sea level is ~1.01 bar). Does it maybe mean an additional bar, so twice atmospheric pressure?

    Wikipedia also says it uses steam, not just hot air, and again doesn't say anything as to why

    Do you know why pressure and steam help?

    Edit: I may have found it while looking at what I thought was an unrelated part of the rabbit hole. Gravity displacement sounds like antigravity technology but it's apparently the cheapest autoclave type and means "displace using gravity" (by letting gravity do its thing; not adding in a vacuum pump). What it's displacing is air. This matters because

    > Steam at 134 °C can achieve a desired level of sterility in three minutes, while achieving the same level of sterility in hot air requires two hours at 160 °C. (—Wikipedia)

    I'm now assuming that pressure must help push the air out, and steam is used for having better heat conductivity. Neither is quite spelled out but that's my best guess currently

Fascinating post. Why did the author steep the tea at home?

"It was at this point I realized I needed a sterile-ish way to transport the steeped tea and tea bags from my house to the lab."

Was steeping the tea at home somehow relevant to the experiment?

  • If I had to guess, it would be because that's exactly the environment and process that consumers will use, so it would capture variables such as "what if the probiotic was out-competed by a bacteria living on your mug?"

    And then I would assume the sterile transfer was to preserve this state of the tea as-made without changing it on the way to the lab.

  • Probably frowned on to bring in food stuff and make it in a bio lab.

    • This makes sense. Even if you're not going to drink the tea in the office, even the appearance of making food in a lab space might well be enough hassle that it's easier to just bring sampling equipment home.

>This is one of the most polarizing choices one can make as a biomedical research scientist. The alternative to the hockey stick is to use glass beads that you autoclave then sprinkle on the plate and roll around. People are very passionate about their chosen method and will attempt to convert you.

It turns out vim vs emacs is a universal phenomenon.

Cool story with an interesting ending (to me at least).

Just a tiny nit... Should "Brewed as directed for 4 minutes in boiling water." be "Brewed as directed for 4 minutes in boiled water." Was the tea sitting in water that was boiling or placed in water that just boiled? The later is how I brew my teas.

  • Isn't boiled water what goes up into the air?

    • The boiled water (assuming even heating throughout) is what reaches boiling temperature, 100°C, which is the entire pot. Additional energy applied to the pot/water after that point turns at some rate the already-at-100°C-boiled-water into water vapor/gas/steam. If you stop heating before all the already-at-100°C-boiled-water disappear, you have left what is or will have been "boiled water".

Hockey stick? Glass beads? What happened to the good old inoculating loop?

  • Loops are good for streaking. It's hard to get even coverage with a loop, so loops would make it hard to get accurate CFU/ml counts. Loops are more likely to get you single colonies even if you're inoculating from a high density culture, so loops are usually used when picking single colonies is the goal. Sterilized cheap flat toothpicks work pretty well for streaking too.

This is kinda disgusting but I think applies to this discussion.

Blue cheese. Its living mold. I think it tastes good.

BUT.. when I eat it, I notice a few days later that my excrement smells more like blue cheese as well. My guess is that I'm inoculating my own digestive tract with blue cheese molds.

Another mishap happened with my cat too. I gave her some beef from our supper. Some of the gorgonzola blue cheese sauce got on it, but I thought I cut and kept the blue cheese off. Nope, I didnt, not enough. She had diarrhea for the next 2 days cause it wrecked with her digestive tract.

Maybe this will help a microbiologist.

> While unhappy microbiomes can be unhappy in their own way, we do not have a consensus on what a “healthy” gut microbiome looks like, either. In collaboration with a continent-wide consortium in Africa, our lab helped catalogue the species found in healthy adult women across the continent. We found over 1,000 new species relative to what had been previously described in studies focused on Western countries.

>Companies trying to introduce targeted combinations of microbes into the gut are thus forever shooting at a moving target.

IIRC, the only semi-reliable way to "adjust" one's microbiome is to find someone who is healthy (and preferably your target body composition/energy levels/psychological profile; and, even more preferably - and possibly paradoxically - who is as close to "you", genetically and physiologically, as possible), harvest and freeze their feces, and take a daily, months-long course of the resulting poop pills, hoping that their gut microbes colonize your own digestive system.