@lykos, what LucH said. Along with fatigue and poor copper metabolism, having low iron despite adequate intake is another sign of an under-active thyroid. Despite my intake of iron-rich foods like red meat and supplementing with food-based iron, my ferritin was down to 6 and didn’t budge until I started taking thyroid (Armour). I was also diagnosed with mold toxicity and gut dysbiosis (SIBO), which cleared up when I targeted my thyroid. To rule out your symptoms being thyroid related, if you haven’t done so already, you may find it useful to track your temps (including extremities) first thing in the morning, and before and 20–30 minutes after you eat, and also your pulse rate, for two weeks. And in case you haven’t read it, here is Ray Peat’s article on TSH, temperature, pulse rate, and other indicators in hypothyroidism:

https://raypeat.com/articles/articles/hypothyroidism.shtml

Milk and oj as a base. B vitamins or liver sometimes. Mildronate or purycet. Walking. Enviroment is important.

@RandomUser I’ve tried both and think it’s worth trying both Cynomel and Tyronene. Ideally crush (pulverize) Cynomel then start off with no more than about a 1/16th of the powder with food and only very gradually increase the dose.
Cyproheptadine initially will make people sluggish or sleepy coz it reduces the stress hormones. Once (after weeks or months) the proper hormones start kicking in, eg thyroid, then it’ll still be working but not making you so tired.
As far as the aspirin maybe try starting taking it in smaller doses and not on an empty stomach. Taking it with baking soda, diluted in a little warm water, with gelatin or caffeine might also be things worth trying.
I’m cautious about MB and have only .once or twice tried a small dose because of Ray’s caveats. So can’t really tell any thing about it. I might try a little again at some point if i run out of other things that work.

Youtube Video

album_art.jpg
*There is. It's just art. Stop thinking, start making sense to 'me'.

@lobotomize-me said in "The dopamine system of healthy, highly creative people is similar to that found in people with schizophrenia":

antipsychotic medicine increases D2 density and lowers dopamine, so one can argue that high baseline dopamine reduces D2 density

BTW, I had some doubts about the statement above, so I've asked gpt to refine it...

"Antipsychotics block D2 receptors, which can lead the brain to upregulate D2 density over time. This suggests that the brain responds to dopamine levels dynamically: when dopamine signaling is low (due to receptor blockade), D2 density may increase; when dopamine signaling is chronically high, the brain may compensate by reducing D2 receptor density. Thus, baseline dopamine levels may influence D2 receptor availability through feedback mechanisms."

@Osteo said in Coffee and AMPK:

That's why I'm confused reading articles about how coffee diminishes cerebral blood flow... Or how coffee changes behavior..

Context matters.

Coffee is beneficial if you maintain a proper diet and a healthy lifestyle.

For someone (most average people?) who eats junk food, fast, or does keto, and undersleeps, coffee may be problematic...

@Mossy said in The peatiest fruit suggestions:

@Jennifer said in The peatiest fruit suggestions:

@Mossy, those are the two main varieties we have where I live. I don’t know if it’s because they’re often unripe, but I find them to be fibrous, especially compared to the ataulfo—its flesh is buttery, IMO—and pine-like/resinous in flavor, something I never taste with ataulfos. But how nice to have access to a guava orchard. I haven’t tried freezing guava before, but I’ve been successfully juicing and freezing fruit for at least 20 years now, including tropical varieties, and frozen fruit was a staple of mine the roughly 8 years in total that I followed Dr. Graham’s 80/10/10 diet and Dr. Morse’s protocol so my guess is it freezes just as well as all other fruit.

Ok, interesting. Indeed, I also would call those two varieties fibrous; and the longer I let them ripen the smoother they get, and less fibrous. I will definitely have to try the ataulfo. I think another reason I probably go for the larger variety is they are larger for the same price, if not cheaper. But, I will try the ataulfo when I get a chance. I don't always see them.

Yes, it is nice having the orchard relatively close. I didn't even know the orchard was by me all these years. I found it by accident, searching for local growers. Actually, I haven't been there in years, due to the quantity requirement, but I think I'll attempt it again. Though, I could imagine it's past harvest time currently (P.S. seems like the harvest may still be happening, but the tail end).

Good to know about your success with freezing fruit. Your diet, and food planning and management, all seem very good. I have a bit of a love-hate relationship with it — haha. The more real and whole foods it is, the more time consuming; but no doubt, the better. It's just a matter of finding a balance and making room for yet another from scratch, so to speak, additional process.

That’s good to know. I’ll try letting them ripen longer then. In this climate there’s a fine line between ripe and rotten when it comes to tropical fruit and overall, it has been less hit and more miss, for me. I hope you get a chance to try some good ataulfos and fingers crossed guavas are still available—I love happy accidents, especially those involving food. lol

I have a love-hate relationship with it, too. I’m all for quality nutrition, but this level of organization was born purely out of necessity. I don’t thrive on a diet native to this region or my family (mainly Swiss-French), and I meal plan, shop and cook for two and our diets are different—mine is fruit-based and his is meat-based—so I have to be organized if I want a life outside of a kitchen. lol

@Kilgore Sick, thanks.

@CrumblingCookie said in Chris Masterjohn: Salicylates are Toxic:

I dare say could Travis have followed this up he would have delivered a coherently explained and backed-up piece of work.

Thanks for your input and the warning (inflammation). I appreciate. I'll try to find Travis post on old RP forum, though I have to proceed indirectly. I no longer go there if I can avoid it 😉
No need t explain why, I think.
Bye. 😉

@lobotomize-me - Reuteri yogurt is a very good suggestion. I have been making it since Nov 2023. I have it for breakfast.

@gg12 - There are videos on YouTube describing how to make the Reuteri containing yogurt. Search YouTube for "SIBO yogurt".

The theory behind how and why it works for SIBO is that pharmaceutical antibiotics can permanently disrupt the balance of bacteria in the GI tract and the naturally occurring reuteri that resides in the small intestine is one of the bacterial species that is permanently lost (along with other species). The imbalance of bacteria creates a situation that allows bacteria that normally only reside in the colon and large intestine to spread or "overgrow" into the small intestine, thus the term SIBO (small intestinal bacterial overgrowth).

The reuteri yogurt reintroduces the lost species and some balance is restored. Digestive issues associated with the imbalance are resolved within about 30 - 45 days. Unfortunately, if you stop eating the yogurt the digestive issues return over time.

@gg12 I think that is kinda specific to what you life looks like and what your goals. For many people being social is simply part of work. For others it's part of resting. For someone who either wants to be a great orator or is socially anxious it would be part of self-improvement.

I personally don't think you can force being social. How social we are heavily depends on our physical health. If we don't have the energy for the interaction then it will always feel shallow and fake and not lead anything further.

However as I mentioned prolonged boredom/being in the default mode network does change your perception of time and as consequence how we judge social interactions. In the end it makes one more open, after all you are bored, if you don't have anything else to do you might just chat around.

Obesity is a fibroblast growth factor 21 (FGF21)-resistant state
https://pubmed.ncbi.nlm.nih.gov/20682689/

In EU, Biogena B Komplex is quite good and well dosed. Contains active form of B6, and methylated b9 and b12.

Infinite Canvas app gallery

Lilex is another excellent option for those who prefer to use monospaced fonts. It resembles IA Writer Mono because both are based on IBM Plex Mono.

Some monospaced fonts are too thin, so it's worth experimenting varying their weight to your preference. For example, from the default 400 to slightly bolder 400–450.

'Andrey Churkin':

Principles of Beautiful Figures for Research Papers How to Create Beautiful Research Figures

Figshare | Wikipedia

"Users can upload files in any format, and items are attributed a DOI."

Can I use Donorbox if I am not a nonprofit? Ko-fi | Make money doing what you love

Digital Books wear out faster than Physical Books | Internet Archive

PDF: Still Unfit for Human Consumption, 20 Years Later | NN Group

Journals sometimes offer downloads in EPUB format, making it easier to reflow text to your liking.

You can vary these terms for many relevant results:

metastasis "complete remission" metabolic | Google Scholar

This post covers additional details about the function of Complex III and how it relates to other respiratory complexes, starting with nomenclature:

Complex III is also referred to as Cytochrome b-c1 complex, Ubiquinol–cytochrome c Oxidoreductase, or Cytochrome c Reductase.

Cytochrome b-c1 complex highlights the electron-transfer cytochromes representing each chain:

High-potential chain (↑) Cytochrome c1 (+230 mV) Iron-sulfur Protein (ISP) (+250 mV) Low-potential chain (↓) Cytochromes b Cytochrome bL (low-potential heme: −30 mV) Cytochrome bH (high-potential heme: +100 mV)

⠀
f56dbb6e-df24-45dc-973f-9e794ceae17b-image.png
⠀(10.1016/j.bbabio.2012.11.008)

[It's a bacterial Complex III, but the core components in evidence remain the same. FeS clusters (ISC) are part of ISPs.]

Ubiquinol–cytochrome c Oxidoreductase highlights the overall reaction, where ubiquinol is the electron donor and cytochrome c the acceptor, and indicates the role of Complex III as oxidant to one and reductant to the other.

Cytochrome c Reductase emphasizes only its function as a cytochrome c reductant. Electrons can reach cytochrome c from sources other than Complex III, making this term less specific.

Then, Complex III reduces and Complex IV oxidizes cytochrome c :

Cytochrome c Reductase (Complex III) ↻ Cytochrome c Cytochrome c Oxidase (Complex IV) Calling Complex IV 'cytochrome c' for short is comparable to calling succinate dehydrogenase (SDH) 'succinate'.

Complex III is often used interchangeably with III₂. Both notations refer to the same enzyme, which exists as a dimer needed for proper function. A figure from an earlier post highlights one monomer in pink and the other in yellow:

528b59bc-fff9-4059-b87b-d60e0defc96b-image.png
⠀(10.1038/s42255-023-00956-y)

These monomers are sometimes called protomers, implying that they are part of a larger complex and don't occur in isolation.

A Complex III dimer has 4 Q-sites in total (red circles), 2 per monomer, but located on different levels:

Qp (positive) [sometimes called Qo (outside)] Qn (negative) [sometimes called Qi (inside)]

dfd0c642-edd3-4bec-8f7b-cf0c14ab50eb-image.png
⠀(10.1016/j.bbabio.2012.11.008)

Electrons from UQH₂ oxidized at Qp-sites bifurcate into the high- and low-potential chains:

UQH₂ (2e⁻)
↳ 1e⁻ → [ISP → Cyt c1 →] Cyt c
↳ 1e⁻ → [Cyt bL → Cyt bH →] UQ/UQH•

So, one electron moves 'upward' (toward cyt c) and the other 'downward' (toward UQ/UQH•) from a Qp-site.

The short distance separating the two cytochromes bL allows electron transfer between monomers.

f56dbb6e-df24-45dc-973f-9e794ceae17b-image.png

f1e9aed8-4263-4734-ad00-733b0713702b-image.png
⠀(10.1016/j.bbabio.2008.04.022)

(Here they call the Qp-site 'Center P' and the Qn-site 'Center N'. Damn it.)

This bL–bL interaction lets the Complex III dimer reroute electrons when needed, preventing incomplete oxidation of UQH₂ at the Qp-site and consequently reducing the risk of ROS production.

Complex III releases superoxide to the matrix and the cytosol, but most of it originates from the susceptible Qp region:

adcfbb6f-e999-46d6-99fa-5e11e0823374-image.png
⠀(10.1074/jbc.M407715200)

However, electron accumulation anywhere can affect the Qp regions indirectly, so increasing the number of possible electron acceptors through inter-monomer communication gives Complex III flexibility.

Monomer A Monomer A Monomer B Monomer B UQH₂ ⚫⚫ {Qp/Qo} (Empty) 1e⁻ ↙ 1e⁻ ↓ ↓ ↘ ISP ◯ bL ◯ ⇄ ◯ bL ◯ ISP ↓ ⇅ ⇅ ↓ c1 ◯ bH ◯ ◯ bH ◯ c1 ↓ ⇅ ⇅ ↓ c ◯ UQ ◯◯ {Qn/Qi} ◯◯ UQ ◯ c c ⚫ ↵ UQH• ⚫◯ ↵ or ↳ ◯⚫ UQH• High-potential chain Low-potential chain Low-potential chain High-potential chain

To avoid mixing up the order of cytochromes b, this may help:
Qo - bL - bH - Qi

Which reads:
oL-Hi

An inverted Low next to a High. Let the trauma sink in.

I find the obsession with reverse electron flow at Complex I out of proportion. It does happen, but is energetically unfavorable, needing an excess of electrons in the UQ pool along with elevated membrane electrical and chemical potentials to force Complex I to run in reverse. In contrast, it doesn't seem to bother the obsessed how the same excess electrons in the UQ pool might affect other UQ-dependent respiratory complexes that operate nearer the UQH₂/UQ potential, making them less resistant to backflow than Complex I.

Like Complex I, Complex III relies on UQ (the oxidized form) to function. As redundant as it may seem, Complex III uses UQ to oxidize UQH₂, but only partially because the other half of electrons go to cytochrome c. Whether UQH₂ is produced at Complex I or III, its protons (H⁺) are derived from the matrix of mitochondria.

Qp-sites are traditionally viewed as UQH₂-oxidizing centers (where electrons enter Complex III), while Qn-sites are viewed as UQ-reducing centers (where electrons leave Complex III). However, electrons can also enter via Qn-sites, especially when UQH₂ is in excess.

The redox state of cyt bH changes the behavior of its Qn-site:

Oxidized cyt bH is an acceptor and favors UQH₂ binding to gain an electron. Cyt bH³⁺ ◯ ↶ ⚫⚫ UQH₂ Reduced cyt bH is a donor and favors UQ binding to lose an electron. Cyt bH²⁺ ⚫ ↷ ◯◯ UQ

This change in affinity according to the state of cyt bH reduces Complex III dependence on appropriate levels of UQH₂ and UQ. In either case an ubisemiquinone [⚫◯ UQH•] is formed and stabilized at the Qn-site.

The occupancy of Qn-sites affect the activity of Qp-sites via ISP. Possible scenarios:

Qn-site A Qn-site B Outcome Qp-sites A and B UQH• UQH• → 1 active Empty Empty → 1 active UQH• Empty → 2 active Empty UQH• → 2 active

Due to intense activity, the first scenario is more common, which limits oxidation capacity but prevents incomplete UQH₂ oxidation and premature electron leakage to oxygen around the problematic Qp-sites.

Since monomers interact, an electron entering via a Qn-site can transfer to the opposite monomer, promoting UQ binding there to accept it. This clears the original monomer for unimpeded electron flow from a Qp-site while stabilizing another terminal acceptor on the neighboring monomer. The result is technically known as 'bi-winning': win here, win there.

15b46985-2907-420a-99c7-03fa33ed151b-image.png
⠀(10.1016/j.bbabio.2008.04.008)

The figure below shows UQH₂ again entering a Qp‑site for oxidation, but in contrast to before, the low-potential chain of this monomer wasn't primed for oxidation. The path to its Qn‑site is now blocked, but the electron can divert to the opposite monomer to complete the process.

37ed3c35-9d0a-4efd-aca3-33e68c65fa49-image.png
⠀(10.1016/j.bbabio.2008.04.008)

These inter-monomer interactions often take place within larger structures, as it's common for a Complex III dimer to associate with other respiratory complexes. For example, most Complex I occurs with Complex III in a supercomplex:

0c20f30f-de55-49c8-b13b-79ab85e9f389-image.png
⠀(10.1074/jbc.M106474200)

Composition Frequency I+III₂+IV ~54% I+III₂ ~17% I+III₂+IV₂ ~9% I+III₂+IV₂+IV ~3% I+III₂+IV₂+IV₂ ~1% I (free) ~16%

This is how Complex III₂ associates with Complex I, in the presence or absence of Complex IV:

e937442c-42b7-4427-8e2d-fc27b6d01249-image.png
⠀(10.1038/nature19774)

I+III₂+IV (a,b) I+III₂ (c)

As you can tell, the 'heel' of Complex I isn't fully turned against Complex III (as often represented in figures), nor is the heel directly facing Complex III. Instead, Complex I and Complex III are arranged in parallel, and one of the Complex III monomers ends up adjacent to Complex I, gaining privileged access to the Q-tunnel of Complex I:

640d7f1c-dbeb-464c-9ad9-df72b0407156-image.png
⠀(10.1016/j.molcel.2019.07.022)

From the legend, this is a cross-section of the I+III₂ supercomplex through the membrane domains and viewed from the matrix.

Proximal and distal refer to two lipid-filled cavities on opposite sides of the Complex III dimer: each cavity gives access to the Qp-site of one monomer and Qn-site of the other, shown by the alternate 'dashed wedges' on a lower plane and the 'solid wedges' on a higher plane (which includes the Q-tunnel). The proximity is relative to the Q-tunnel (a source of UQH₂ for Complex III to oxidize).

It helps to picture the Q‑tunnel at the heel of Complex I, but the tunnel and its opening are oriented more to the side than to the back:

84e43691-17e6-4e4d-b11f-c8c7ed628448-image.png
⠀(10.1080/09168451.2020.1747974)

When Complex IV joins the supercomplex, it forms an autonomous respiratory unit capable of completing respiration, hence the term 'respirasome'.

9fa6d06c-e80f-4f1a-be10-d6c1b57c571d-image.png
⠀(10.1016/j.sbi.2020.01.004)

1ac3fa39-599c-458a-8893-418bf8b6f94a-image.png
⠀(10.1038/nature19774)

Rotating it to coincide with the view of the previous figure:

8c23a569-d87e-4298-94b0-b89052a70d52-image.png

IV: pink IIIb: dark green IIIa: light green I: blue

The authors speculate that occlusion of the distal cavity by Complex IV may be advantageous: because the Q-cycle involves formation of ubisemiquinone radicals, partial closure of the cavity while Complex IV consumes local oxygen may protect unstable intermediates from adverse reactions. However, they also acknowledge that the occluded Qn-site is not a major ROS producer and that the Qp-site in the same cavity may be inactive.

For mobile carriers that connect these respiratory complexes, some argue for the existence of dedicated UQ pools for NAD-linked and FAD-linked respiration.

c97d77bb-e630-4c8c-9dba-3224505d1b89-image.png
⠀(10.1016/j.freeradbiomed.2021.03.010)

Relying only on UQ trapped within I+III₂(+IV) would limit reoxidation of Complex I–derived UQH₂ to the proximal cavity of Complex III₂, because of its exclusive access to the Q-tunnel. Nonetheless, these respiratory complexes have their quinone sites exposed to the supercomplex exterior and can exchange with the free UQ pool, so they're not restricted to local UQ and can respond to mitochondrial conditions. This flexibility is particularly important given that Complex I can outpace Complex III. More information here.

Because the Qp-site of monomer A shares a cavity with the Qn-site of monomer B, reoxidized UQ can return to Complex I to bring in more electrons, exchange with the free UQ pool around the supercomplex (and indirectly affect the distal cavity), or perhaps be reused in the same cavity as an electron acceptor. This last possibility isn't futile, since part of electrons are removed via cytochrome c.

Monomer A Monomer A Monomer B UQH₂ ↷ UQ 1e⁻ ↙ 1e⁻ ↓ ⇅ ISP bL bH ↓ ⇅ ↘↖ ⇅ c1 bH bL ↓ ⇅ c UQH• High-potential chain Low-potential chain Low-potential chain

If UQ turnover is insufficient, an elevated UQH₂/UQ ratio can favor ROS production and reversibly deactivate Complex I or promote its degradation for supercomplex remodeling, freeing some of the III₂+IV to serve FAD-dependent complexes. These can be adaptive. Recall that substrates more reliant on FAD-linked respiration (↓ATP/O) demand additional UQ turnover.

I 💥 ↮ III₂+IV ↘ SDH/ETFDH/etc. + III₂+IV

023b11f6-9806-4f94-90f2-049cb214d084-image.png
⠀(10.1016/j.bbabio.2023.148977)

It's complicated at times, but when a problem appears to run counter to the oversimplified and sensationalist take of bioenergetic gurus, it's probably a good sign.

⠀

Herrero Martín, J. C., Salegi Ansa, B., Álvarez-Rivera, G., Domínguez-Zorita, S., Rodríguez-Pombo, P., Pérez, B., ... & Formentini, L. (2024). An ETFDH-driven metabolon supports OXPHOS efficiency in skeletal muscle by regulating coenzyme Q homeostasis. Nature metabolism, 6(2), 209-225. https://doi.org/10.1038/s42255-023-00956-y

Muller, F. L., Liu, Y., & Van Remmen, H. (2004). Complex III releases superoxide to both sides of the inner mitochondrial membrane. Journal of Biological Chemistry, 279(47), 49064-49073. https://doi.org/10.1074/jbc.M407715200

Murai, M. (2020). Exploring the binding pocket of quinone/inhibitors in mitochondrial respiratory complex I by chemical biology approaches. Bioscience, biotechnology, and biochemistry, 84(7), 1322-1331. https://doi.org/10.1080/09168451.2020.1747974

Hernansanz-Agustín, P., & Enríquez, J. A. (2021). Functional segmentation of CoQ and cyt c pools by respiratory complex superassembly. Free Radical Biology and Medicine, 167, 232-242. https://doi.org/10.1016/j.freeradbiomed.2021.03.010

Covian, R., & Trumpower, B. L. (2008). Regulatory interactions in the dimeric cytochrome bc1 complex: the advantages of being a twin. Biochimica et Biophysica Acta (BBA)-Bioenergetics, 1777(9), 1079-1091. https://doi.org/10.1016/j.bbabio.2008.04.022

Parey, K., Wirth, C., Vonck, J., & Zickermann, V. (2020). Respiratory complex I—structure, mechanism and evolution. Current opinion in structural biology, 63, 1-9. https://doi.org/10.1016/j.sbi.2020.01.004

Xia, D., Esser, L., Tang, W. K., Zhou, F., Zhou, Y., Yu, L., & Yu, C. A. (2013). Structural analysis of cytochrome bc1 complexes: implications to the mechanism of function. Biochimica et Biophysica Acta (BBA)-Bioenergetics, 1827(11-12), 1278-1294. https://doi.org/10.1016/j.bbabio.2012.11.008

Letts, J. A., Fiedorczuk, K., Degliesposti, G., Skehel, M., & Sazanov, L. A. (2019). Structures of respiratory supercomplex I+ III2 reveal functional and conformational crosstalk. Molecular cell, 75(6), 1131-1146. https://doi.org/10.1016/j.molcel.2019.07.022

Letts, J. A., Fiedorczuk, K., & Sazanov, L. A. (2016). The architecture of respiratory supercomplexes. Nature, 537(7622), 644-648. https://doi.org/10.1038/nature19774

Guaras, A., Perales-Clemente, E., Calvo, E., Acín-Pérez, R., Loureiro-Lopez, M., Pujol, C., ... & Enríquez, J. A. (2016). The CoQH2/CoQ ratio serves as a sensor of respiratory chain efficiency. Cell reports, 15(1), 197-209. https://doi.org/10.1016/j.celrep.2016.03.009

Covian, R., & Trumpower, B. L. (2008). The dimeric structure of the cytochrome bc1 complex prevents center P inhibition by reverse reactions at center N. Biochimica et Biophysica Acta (BBA)-Bioenergetics, 1777(7-8), 1044-1052. https://doi.org/10.1016/j.bbabio.2008.04.008

Schägger, H., & Pfeiffer, K. (2001). The ratio of oxidative phosphorylation complexes I–V in bovine heart mitochondria and the composition of respiratory chain supercomplexes. Journal of Biological Chemistry, 276(41), 37861-37867. https://doi.org/10.1074/jbc.M106474200

Nesci, S., Algieri, C., Trombetti, F., Fabbri, M., & Lenaz, G. (2023). Two separate pathways underlie NADH and succinate oxidation in swine heart mitochondria: Kinetic evidence on the mobile electron carriers. Biochimica et Biophysica Acta (BBA)-Bioenergetics, 1864(3), 148977. https://doi.org/10.1016/j.bbabio.2023.148977

On this website they offer a chart with methionine levels of all kinds of foods.

Apparently people in need of it, can also order methioniase.

Also lots of studies on methionine and cancer .

https://howtostarvecancernaturally.com/

@BearWithMe said:

what CT means in this context

Calcitonin, in the context of (GI) hormones.
Running celiac diagnostics makes sense.

Internet is healing.