Hello!

Yes, the !biology@mander.xyz community is a community for general biology-related content.

There are also more specific communities that focus in more specialized topics, such as such as !palaeontology@mander.xyz.

If you have an interest in a specific topic, feel free to create a community that reflects that interest. Some instances are very general while others try to limit communities to those that fit a range of topics, so it is best to create a community in an instance for which the topic is in scope.

• In the general case, I think that we would not be able to tell. Unless the programmers explicitly program into the simulation the tools for us to interact with the external world, we would not be able to collect evidence of something external to the simulation. We are limited.

• I am agnostic to whether we live in a simulation or not, but I don’t think that this hypothesis brings a lot in terms of answering existential questions. We could live in a simulation inside of a simulation inside of a simulation inside of a simulation… meaning that there is an infinite depth of simulations when we choose to consider this possibility. In my view, being the first rung of existence or being a million simulations deep is the same. Discovering that we are in a simulation just shifts the existential question one universe higher.

• I have been reading some texts about theories of how the brain thinks (predictive coding), and it seems like what we experience as “consciousness” might be the result of our brain simulating what our next sensory experience will be. So, in that sense, we are all experiencing our brain’s predictive simulation.

Ooh, cool! 😁 That detector seems to be working only in “Geiger mode”, which means that it can count the number of X-rays/Gamma particles but it does not estimate their energy. So, the dedicated devices are still better in that they allow you to identify the source of the radiation by measuring the counts and the energy distribution simultaneously.

It probably would not be too difficult to build the open gamma detector into something like a pinephone. I don’t think that has been done yet.

My experience with phone zoom has been underwhelming so far, but I would like to check out the Samsung S2x’s 10x zoom when I have the chance!

Still, I really like using binoculars because they transport me next to what I am looking at and do so in very high definition. I do have >100€ binoculars though, colors look very nice through them. I think it will be difficult to replicate via a screen.

I think it would be an interesting hypothesis to test.

I looked a bit more and extended my search into brines, and was able to find another set of data in the following paper:

Roupas, P., Keogh, J., Noakes, M., Margetts, C., & Taylor, P. (2010). Mushrooms and agaritine: A mini-review. Journal of Functional Foods, 2(2), 91-98.

This one is not freely available, but it is found in SciHub and I can also share the PDF if needed.

This relevant section discusses that mushrooms canned in liquid and in brine were measured to have less agaritine, which makes sense. I think that lactofermentation helps degrade even more due to the acid, additional metabolic activity, and possibly a bit more oxygen.

I agree that it would be nice to research. I am surprised that it hasn’t been (or at least it is not easy to find). I did find research on other methods such as heating and drying, but I could not find lacto fermentation…

Agaritine content of mushrooms

The agaritine content in fresh A. bisporus mushrooms in Swit- zerland has been reported to be in the range of 94–629 mg/kg fresh weight. Canned mushrooms contained 1–55 mg/kg drained weight with 3–103 mg/L in the liquid. The highest agaritine values were reported in dried commercial mush- rooms amounting to 2110–6905 mg/kg (Fischer et al., 1984). In Sweden, Andersson et al. (1999) measured agaritine in fresh mushrooms and 35 canned mushroom products (A. bisporus). Two fresh samples contained 212 and 229 mg/kg, respectively. Agaritine levels in brine were generally slightly lower than the levels detected in canned mushrooms. Canned whole mushrooms contained 14.9 ± 6.7 mg agaritine per kg product whereas cut mushrooms contained 18.1 ± 7.8 mg/kg. The wet canning process was shown to reduce the level of agaritine in A. bisporus by 10-fold resulting in lower levels in canned products. On a portion basis, somewhat higher amounts of agaritine may be found in some other food prod- ucts (mushroom soup and pasta sauce) containing A. bisporus (Andersson et al., 1999).

Yes. The camera pixels generate a current in response to light. You can add some filters to block certain wavelengths of light (like UV) from getting to the camera sensor, and tune the pixels so that they respond more to to specific colors. But X-rays and gamma rays can just pass through the filter. Often they will pass through sensor as well, but, in the cases that they do get absorbed by the sensor, they can also produce a current that to the camera’s readout electronics looks like other light would.

The gamma detectors I mentioned are very very sensitive. They respond to single X-ray/Gamma ray particles. These detectors can count how many individual particles collide with a small crystal cube every second. These crystals are special in that they produce a very tiny flash of light when an X-ray or gamma particle collides with them. As an added bonus, these sensors can directly measure the energy of the particles by measuring the strength of the flash, and from this information they can construct not only the total counts but also a spectrum. With this extreme sensitivity these detectors can measure small quantities of radiation that come from space, from rocks, and from other materials.

I looked for a video of a phone going through an X-ray machine, and found these:

https://www.youtube.com/watch?v=E8iSoPhtY3s

https://www.youtube.com/watch?v=V1YaroH6lHA

The white specks that you can see near second 25 (first video) and second 34 (second video) could be a result of the X-rays. I am not sure, but it seems reasonable to me. On contrast, when I put my radiacode through the X-ray machine in the airport the radiacode reacts very strongly and becomes saturated.

Radiation detectors. Such as the Radiacode or the Open Gamma Detector.

Binoculars are quite portable, very useful, and phones don’t do a good job at zooming in like that.

Smart watches integrate with phones but the phones by themselves are not so good at measuring the heart rate and other parameters directly.

Mini projectors. UV flashlights. Tools in general… There is so much actually. What type of gadgets are you looking for?

Only those who complete life without believing in a God pass into the next stage of the simulation.

Yes, this is what I mean.

As for (3), this is how I am reasoning about this. The mushroom cells are surrounded by a soft cell membrane made out of lipids, and a hard cell wall made out of a network of sugar filaments (primarily chitin). The cell membrane serves as a chemical barrier that separates the chemistry outside of the cell from the chemistry inside of the cell, and it has many mechanisms to allow specific chemicals to flow from one side to the other. This cell membrane is very dynamic and it needs continuous maintenance to remain functioning as intended. When a cell dies, the cell membrane is no longer kept under maintenance, and it basically dissolves.

After the cell membrane disintegrates, the cell wall remains. This cell wall is much tougher and does not require constant maintenance. The wall also has its own filtering capacity as well the ability to absorb and retain chemicals, but it is a lot more porous and this porosity allows water, nutrients, and other water-soluble chemicals to move more freely.

So, my reasoning is: The mushroom dies. The cell wall disintegrates. The more permeable cell wall remains. Agaritine is soluble in water, and water and small water-soluble molecules can usually move freely through the cell wall. So, within a short period of time the water outside of the mushrooms will mix with the water inside of the mushrooms, and the agaritine will distribute throughout the whole volume. At this point, even if the mushroom’s environment had provided some form of protection, the now-mixed agaritine will experience an environment similar to the environments discussed in the papers I from the previous comments.

It is not as simple as I describe here, because the specific properties of the cell wall can be complex, and they can change due to chemical modifications. For example, some molecules can be absorbed into the sugar matrix such that they are protected from degradation - but I could not find any data to suggest that this likely a significant factor for agaritine. There are some recent articles that review the fungal cell wall, I will paste the citations below, in case you want to look at some of this in more detail.

Gow, N. A., & Lenardon, M. D. (2023). Architecture of the dynamic fungal cell wall. Nature Reviews Microbiology, 21(4), 248-259.

Latgé, J. P., & Wang, T. (2022). Modern biophysics redefines our understanding of fungal cell wall structure, complexity, and dynamics. Mbio, 13(3), e01145-22.

My question has to do about the agaritine content in mushrooms that are subjected to fermentation. That agaritine might behave differently when contained in a mushroom. What answer to my question does the articles give you?

It is true. I am not sure, the articles do not address this specific question. It would depend on the process and the amount of time that you let it ferment. Over a period of weeks, it is likely that the mushrooms will have died, the cell membranes will have broken down, and the chemistry of degradation described in those papers will have taken place.

Fresh mushrooms are still alive at the beginning of the process. Until they die, the mushroom’s cells may continue to produce agaritine, and the chemistry inside of the cells is not necessarily going to be the same as in tap water. The amount of time that it will take for the cells to die depends on the process. If you are submerging the mushrooms into a brine, I don’t think that they will survive for long because of the osmotic pressure.

No problem! I searched “Agaritine degradation” in Google Scholar and selected to those two articles from the results page as they seemed relevant. I also searched for more specific fermentation based papers but did not find any - this is what I mean when I say quick search.

I did not use an LLM chat bot to formulate the answer, but I did copy and paste it to ChatGPT and asked whether it agreed. I often do this in case it catches some obvious mistake. But it did not suggest any corrections, and it did not affect my answer. So an LLM chatbot did assist me in validation.

If you want I can explain some of the reasoning in more detail. Figures 1 and 3 of the first paper have data on what happens when agaritine is dissolved in water in the presence of air (‘open vial’), no air (‘closed vial’), and at a low pH with a closed vial. I think that these two figures are the most relevant to this particular question, as they give you an estimate to how fast agaritine will break down due to conditions that are easy to control and measure. Other types of microbiological activity can have an effect, but in this case it is not essential to invoke these more complicated processes.

Short summary from a quick search in the literature: Agaritine in water degrades quickly if oxygen is present, so if you can have an extended amount of time during which the mixture of water and ground mushroom is exposed to fresh air, that will help. As the mixture becomes acidic, degradation speeds up again even if the the atmosphere becomes oxygen poor. If the fermentation is meant to take more than 3 weeks, the acidic environment will probably be enough. Enzymes from the microbes are likely to have a combined effect that ultimately speeds up degradation as well, but that is a more complicated process and so it is not so easy to estimate the rates.

Low pH, exposure to water, oxygen, and time will help. It seems like it degrades quite quickly in water if oxygen is present, but in lacto fermentation you do want to create an anaerobic environment so you might have a quick degradation followed by the formation of a protective atmosphere.

The lowering of the pH will then help speed up the degradation again, but not as much as oxygen does.

Have a look at the following paper to see curves of how agaritine degrades in water in the presence of fresh air, in a closed vial, at different pH levels:

Hajšlová, J., Hajkova, L., Schulzova, V., Frandsen, H., Gry, J., & Andersson, H. C. (2002). Stability of agaritine-a natural toxicant of Agaricus mushrooms. Food Additives & Contaminants, 19(11), 1028-1033.

Since you have a microbiologically active community, you also have access to the enzymatic pathways. I have not found a specific paper about agaritine during fermentation. I can find other articles describing enzymatic transformations and degradation. Some of these transformations can change the molecule into more toxic forms, and other enzymes move it towards a degraded product. What I expect that you will see is that the net effect of having a complex enzymatic mixture will be faster degradation, even if the pathways may cross the more active toxic intermediates (which would also probably form in your intestine), these will only form for a short time and degrade.

You can refer to the paper below for specific examples of the enzymatic transformations that I am referring to. In this paper, the enzymes come from mushrooms that are ground into a liquid, and so they are mushroom enzymes. In the context of fermentation the source of the enzymes would be excreted by the fermenters into the ferment. These enzymes would likely not be specifically evolved for agaritine but instead represent general classes of enzymes that affect functional groups that are present in agaritine. It is difficult to make specific predictions.

Walton, K., Coombs, M. M., Walker, R., & Ioannides, C. (2001). The metabolism and bioactivation of agaritine and of other mushroom hydrazines by whole mushroom homogenate and by mushroom tyrosinase. Toxicology, 161(3), 165-177.

I have used XMPP for some time now and I tried Matrix for a bit, but have stuck with XMPP until now.

I found it practically very easy to set up a prosody XMPP server in a raspberry pi. In XMPP you have the core standard that is kept quite minimal and then you can extended your implementation using XMPP extension protocols (XEPs) in a highly modular fashion. This approach of building on top of a light core using well-documented extensions I like very much.

With Matrix, JSON is used instead of XML. I think that JSON is a nice format when trying to look under the hood at how the message data is structured. XML is a bit of a pain to look at in my opinion. And I think JSON might be more efficient in how it moves the data around. So, that is a big positive for me. But I Matrix appears to be more focused on being feature rich than on having a flexible modular structure. While it does have extensions, successful extensions do have a chance of being eventually integrated into the core protocol. This makes the core feel bloated to me, because I have very minimal requirements.

In terms of security, in XMPP you start with the core and then you select the type of encryption that you like (OpenPGP, OMEMO, etc). OMEMO encryption has plausible deniability built into its design, and for me, plausible deniability is a property that I consider important for messaging. The modular approach to XMPP also means that these are choices that one gets to make in an active manner, and the protocols are open protocols that come from outside of XMPP. With Matrix you get their encryption protocol as part of the core - it is a protocol that they designed and that you need to accept to use their tool with encryption. It is probably a good protocol, but I don’t think it has plausible deniability built in, and that’s a choice you did not get to make.

As for moderation, I don’t know. Do they mean moderation tools, or the actual absence of moderators and unmoderated communities? Because the latter is more a property of the people using the tool that the tool itself. You can have your own private communities.

If someone asks me, I could recommend Matrix but would rather recommend XMPP, depending on what they are looking for specifically.

Snowden’s Permanent Record book was a strong motivator for me.

Ah, bidding technology has advanced since I sniped Tony Hawk Pro-Skater for the Nintendo 64 on ebay. Why start bidding over a week early, though?

I find it strange that they are out-bidding each other like this when there are over 8 days left. I am not too experienced with bidding, but I thought that the normal strategy was to maybe place a placeholder bid if there is no activity, but more generally one waits until the last second to set a reasonably high bid. Going on a 1v1 with fast out-bidding over a week early seems bad for everyone except the seller. Perhaps someone can explain.

Very cool!

Someone needs to explain to Musk how to debug with the JSON so that the ipv6 GUI does not overflow into the git API front-end

Good squirrel. Similar to a tan egg

Doesn’t the executive order specify the ‘Gulf of America’ as the sub-secion of the Gulf of Mexico that is bordering the US states? If so, should’t that name appear only when you zoom into that specific sub-region?

I’m from Mexico so my opinion on this whole thing is pretty obvious.