Sal

joined 3 years ago
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[–] Sal@mander.xyz 7 points 1 day ago

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.

[–] Sal@mander.xyz 2 points 2 days ago
  • 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.

 

Abstract

Cognitive maps confer animals with flexible intelligence by representing spatial, temporal and abstract relationships that can be used to shape thought, planning and behaviour. Cognitive maps have been observed in the hippocampus1, but their algorithmic form and learning mechanisms remain obscure. Here we used large-scale, longitudinal two-photon calcium imaging to record activity from thousands of neurons in the CA1 region of the hippocampus while mice learned to efficiently collect rewards from two subtly different linear tracks in virtual reality. Throughout learning, both animal behaviour and hippocampal neural activity progressed through multiple stages, gradually revealing improved task representation that mirrored improved behavioural efficiency. The learning process involved progressive decorrelations in initially similar hippocampal neural activity within and across tracks, ultimately resulting in orthogonalized representations resembling a state machine capturing the inherent structure of the task. This decorrelation process was driven by individual neurons acquiring task-state-specific responses (that is, ‘state cells’). Although various standard artificial neural networks did not naturally capture these dynamics, the clone-structured causal graph, a hidden Markov model variant, uniquely reproduced both the final orthogonalized states and the learning trajectory seen in animals. The observed cellular and population dynamics constrain the mechanisms underlying cognitive map formation in the hippocampus, pointing to hidden state inference as a fundamental computational principle, with implications for both biological and artificial intelligence.

[–] Sal@mander.xyz 3 points 1 week ago

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.

[–] Sal@mander.xyz 3 points 1 week ago (2 children)

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.

[–] Sal@mander.xyz 1 points 1 week ago

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).

[–] Sal@mander.xyz 2 points 1 week ago* (last edited 1 week ago)

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.

[–] Sal@mander.xyz 27 points 1 week ago (12 children)

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?

18
submitted 1 week ago* (last edited 1 week ago) by Sal@mander.xyz to c/taneggs@lemmy.ca
 

A spy tan egg pretends to be on the same emotional wavelength as other tan eggs

[–] Sal@mander.xyz 1 points 1 week ago

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

[–] Sal@mander.xyz 3 points 1 week ago (2 children)

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.

[–] Sal@mander.xyz 2 points 1 week ago (4 children)

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.

[–] Sal@mander.xyz 2 points 1 week ago* (last edited 1 week ago) (6 children)

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.

[–] Sal@mander.xyz 2 points 1 week ago* (last edited 1 week ago) (8 children)

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.

 
 

Sietske A.L. van Till and Eline M. Bunnik (2024) have recently expressed a concern about science miscommunication regarding human brain organoids. They worry that the mereological fallacy is often being committed when the possibility of brain organoid psychological capacities such as consciousness and intelligence are considered, especially by bioethicists discussing the moral status of human brain organoids. Focusing specifically on one psychological capacity, namely consciousness, this article begins with a brief introduction to van Till and Bunnik’s concern about the mereological fallacy as it relates to brain organoids. It is then shown that whether the mereological fallacy is being committed depends on commitments in philosophy of mind about how consciousness relates to the brain and its neural mechanisms. This is demonstrated by appealing to two different example views about the ontology of consciousness embraced by J.J.C. Smart’s type identity theory and a version of hylomorphism. The article ends with a discussion of how neurobiological theories of consciousness can be intertwined with ontological commitments about consciousness that have significant implications for HBOs. An awareness of this can yield a philosophically informed application of neurobiological theories to the topic of whether HBOs could be conscious.

 

Abstract

While observational studies and small pilot trials suggest that vitamin D, omega-3 and exercise may slow biological aging, larger clinical trials testing these treatments individually or in combination are lacking. Here, we report the results of a post hoc analysis among 777 participants of the DO-HEALTH trial on the effect of vitamin D (2,000 IU per day) and/or omega-3 (1 g per day) and/or a home exercise program on four next-generation DNA methylation (DNAm) measures of biological aging (PhenoAge, GrimAge, GrimAge2 and DunedinPACE) over 3 years. Omega-3 alone slowed the DNAm clocks PhenoAge, GrimAge2 and DunedinPACE, and all three treatments had additive benefits on PhenoAge. Overall, from baseline to year 3, standardized effects ranged from 0.16 to 0.32 units (2.9–3.8 months). In summary, our trial indicates a small protective effect of omega-3 treatment on slowing biological aging over 3 years across several clocks, with an additive protective effect of omega-3, vitamin D and exercise based on PhenoAge.

 

Abstract

Cacao and chocolate production is a global industry worth around $133 billion. Full sun cultivation is a modern approach aimed at increasing yields. We evaluated six cacao clones (PS 1319, CCN 10, CCN 51, PH 16, SJ 02, and CP 49) grown under full sun conditions to assess their leaf physiology, leaf structure, yield, and yield components. Leaf physiology was measured through seven gas exchange parameters, while leaf structure was analyzed using eight measurements. For fruit and seed, we evaluated seven yield components. The clones showed differences in gas exchange. Clones PH 16 and PS 1319 had higher net photosynthetic rates per unit of leaf area (A), transpiration rates, and lower leaf internal CO2 concentrations. These A high values suggest the clones are well-acclimatized to full sun cultivation. Water availability, nutrient supply, and appropriate plant architecture also contributed to this acclimatization. Under high light intensity, the potential quantum yield of photosystem II indicated no photoinhibition, and adaptations in the photosynthetic apparatus were observed, such as lower pigment concentration in clone PH 16. Clones differed in specific leaf area (SLA) and stomatal density (SD). CCN 51 had a higher SLA, while SJ 02 had a higher SD. A significant negative correlation (-0.89) was found between dry bean yield and leaf-to-air water vapor pressure deficit (VpdL), suggesting that VpdL is a crucial parameter for selecting high-performance clones for fertigated full sun cultivation. Yields ranged from 1,220 kg/ha (CCN 10) to 2,900 kg/ha (CCN 51). Full sun cacao farms have high yield potential due to a combination of cloning, management practices, and adequate water and nutrient availability.

 

Abstract

This paper presents design and analysis of an optical memory and counter based on ultra-compact temporal integrators (INTs) using a graphene hybrid plasmonic add-drop ring resonator (GHP-ADRR) and pulley-type ring resonator (GHP-PRR) for optical signal processing. Due to the valuable features of graphene hybrid plasmonic technology, the footprint of these INTs is equal to 4 × 3.5 µm2 for GHP-ADRR and 5.4 × 3.6 µm2 for GHP-PRR. Also, the performance of the INTs has been analyzed by the three-dimensional finite-difference time-domain method in the frequency and time domains, and the accuracy of the results has been compared with those of the math counterparts and also key specifications of the first-order temporal INTs including phase jump, insertion loss, 3 dB bandwidth, rise time, integration time window, and energy efficiency have been investigated. Based on the results, both circuits have better performance than the photonic counterparts. Furthermore, the performance of these INTs has been evaluated in detail as a high-speed optical memory and counter. It has been illustrated that due to the greater quality factor of the GHP-PRR, this circuit has more accuracy for realizing the first-order integration, optical memory, and counter than the GHP-ADRR-based INT.

 

Found a photos of ferns that I took during a visit to Cascadas Tulimán, in Puebla, Mexico, back in 2022.

Here is the biome:

I never got to identifying them, so any any input on potential IDs is welcome!

 

Abstract

We present ErAs:In(Al)GaAs-based terahertz transceiver modules, comprising transmitter and receiver components integrated on a single chip. The transceiver module is employed in a two-port single-path (TxRx-Rx) or 1.5-port pulsed free space photonic vector network analyzer setup, wherein the second receiver is an individual ErAs:InGaAs photoconductor. This configuration allows for simultaneous extraction of transmission and reflection coefficients or scattering parameters S21 and S11. The system achieves a peak dynamic range of ~59 dB for S21 and ~43 dB for S11 at a bandwidth reaching ~3.5 THz for the transmission and ~2.5 THz for the reflection path. These values are obtained by averaging over 500 traces at a scan rate of 4 Hz. The system exhibits superior frequency coverage compared to commercially available electronic vector network analyzers, thus offering a compact, cost-effective, broadband characterization solution for the benchmarking of terahertz devices and components.

 

Abstract

Efficient single-photon generation remains a big challenge in quantum photonics. A promising approach to overcome this challenge is to employ active multiplexing—repeating a nondeterministic photon pair generation process across orthogonal degrees of freedom and exploiting heralding to actively route the heralded photon to the desired single output mode via feedforward. The main barriers of multiplexing schemes, however, are minimizing resource requirements to allow scalability and the lack of availability of high-speed, low-loss switches. Here, we present an on-chip temporal multiplexing scheme utilizing thin-film lithium niobate (TFLN) photonics to effectively address these challenges. Our time-multiplexed source, operating at a rate of 62.2 MHz, enhances single-photon probability by a factor of 3.37 ± 0.05 without introducing additional multi-photon noise. This demonstration highlights the feasibility and potential of TFLN photonics for large-scale complex quantum information technologies.

 
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