QUANTUM ENGINEERING #55: CELLULAR TIME STAMPING
Added 2023-09-22 20:57:34 +0000 UTCPost translational time stamping is present from cyanobacteria to mammals. All organisms have evolved timing mechanisms to adapt to environmental changes in order to optimize survival and improve fitness for an environment. To anticipate these regular daily electromagnetic cycles of light and dark, many organisms manifest near 24-h cell-autonomous oscillations that are sustained by transcription–translation-based or post-transcriptional negative feedback loops that control a wide range of biological processes. With an eye to identifying emerging common themes among cyanobacterial, fungal and animal clocks, some major recent developments in the understanding of the mechanisms that regulate these oscillators and their output need to be discussed. These include roles for antisense transcription, intrinsically disordered proteins, codon bias in clock genes, and a more focused discussion of post-transcriptional and translational regulation as a part of both the oscillator and output.
Circadian rhythms in every organism are cell autonomous, appear to have arisen only a few times in evolution, and can be driven by one of a few lineage-specific but otherwise highly conserved central oscillators. While oscillators driving bacterial and plant clocks are distinct from each other and from other known clocks, fungal and animal cells share circadian oscillators of conserved regulatory architecture: transcription-translation feedback loops (TTFLs) comprised of two parts.
Specifically, 1) a positive arm with a heterodimeric complex at its core that behaves as the activator of the system, promoting the transcription of 2) one or more components of the negative arm, which when translated inhibit the activity of the positive arm.
WHAT IS THE TTFL?
Transcription-translation feedback loop (TTFL) is THE cellular model for explaining circadian rhythms in behavior and physiology. It is widely conserved across species, and the TTFL is largely auto-regulatory with the assistance of the sun & moon and dark periods on Earth, in which transcription of clock genes is regulated by their own protein products. This implies that light and dark control genetic expression and not the other way around. The TTFL is a negative feedback loop, in which clock genes are regulated by their protein products. Generally, the TTFL involves 2 main arms: positive regulatory elements that promote transcription and protein products that suppress transcription. When a positive regulatory element binds to a clock gene promoter, transcription of DNA proceeds, resulting in the creation of an mRNA transcript, and then translation proceeds, resulting in a semiconductive protein product. There are characteristic delays between mRNA transcript accumulation, protein accumulation, and gene suppression due to translation dynamics, post-translational protein modification, protein dimerization, and intracellular travel to the nucleus. Across species, proteins involved in the TTFL contain common structural motifs such PAS domains, involved in protein-protein interactions, and bHLH domains, involved in DNA binding.
The two overarching areas characteristic of circadian systems in general: 1) the negative arm and its regulation of the core clock; 2) the control of output by the positive arm and its environment.
In ALL mammals the heterodimeric BMAL1-CLOCK complex positively regulates expression of negative arm component genes, the Periods and Cryptochromes(encoding PER1, PER2, PER3, CRY1 and CRY2), that combine with CK1 and several other proteins to make the repressive complex that depresses BMAL1-CLOCK activity and alters periodicity of the mammalian clock which alters its accuracy. Remember all circadian clocks are flow meters for entropy in a cell.
Solar light input into mammal TTFLs begins with dedicated non visual photoreceptors that elicit signaling that acts to induce (in fungi and mammals) or reduce (insects) the amounts of negative arm proteins mentioned above. In broad outline, Output occurs when the positive Arm heterodimer binds to DNA and activates expression of genes whose products do not impact the TTFL. The key take away is the clock gene actions are PROXIMAL to DNA translation and gene activation. This tells you that light inputs controls gene expression in mammals and it is not the other way around. Altering your genome will not improve your illness or disease if the light and dark environment is repair first.
HOW DOES TIME STAMPING WORK BY LIGHT AND DARK WORK?
Once enough modified protein products accumulate in the cytoplasm of a cell, they are transported into the nucleus where they inhibit the positive element from the promoter to stop transcription of clock genes. The clock gene is thus transcribed at low levels until its protein products are degraded, allowing for positive regulatory elements to bind to the promoter and restart DNA transcription. The negative feedback loop of the TTFL has multiple properties important for the cellular circadian clock. First, it results in daily rhythms in both gene transcription and protein abundance and size, caused by the delay between translation and negative regulation of the gene. The cycle's period, or time required to complete one cycle, remains consistent in each individual and, barring mutation, is typically near 24 hours. This enables stable entrainment to the 24 hour light-dark cycle that Earth experiences from the sun & moon.
Additionally, the protein products of clock genes control downstream genes that are not part of the feedback loop, allowing clock genes to create daily rhythms in other processes, such as metabolism, within the organism. Light and dark cycles are the decentralized controllers of the TTFL.
THE TTFL USES MELANIN TO ELECTROCHEMICALLY TIME STAMP YOUR CELLS. This occurs in the retinohypothalamic pathways anterior to the SCN and it modifies what the SCN signals to all the other molecular clock genes it links to in tissues.
WHY IS MORNING LIGHT SO CRITICAL TO GET RIGHT?
CSP-1 (conidial separation 1) is a morning induced transcriptional repressor with a phosphorylation gated half-life is a key cog in driving EVENING gene expression in mammals. If you do not get AM sun your evening genomic expression will be AWRY. People have forgotten that leptin is released by fat cells and can only enter the hypothalamus under darkness after 4 hours. This should happen at night time. It cannot happen when CSP-1 is not created by AM light. These are the new recent insights into how circadian clocks in your eye and skin achieve phase-specific gene expression. This is how and why leptin resistance exists.
The negative element of the core circadian feedback loop is the frq or frequency gene. The frequency (frq) gene controls the morning-specific rhythmic transcription of a sense RNA encoding FRQ segment. As a result of this action, a long noncoding antisense RNA, qrf, is rhythmically transcribed in an evening-specific manner. It has been reported in the literature that the qrf rhythm relies on transcriptional interference with frq transcription and that complete suppression of qrf transcription impairs the circadian clock. The biological function of qrf transcription and its impact on the circadian clock are not understood in centralized science because centralized science has no light controls at night in labs.
CSP-1 expression is induced by light and glucose, and this finding suggests a rhythmic coordination of qrf transcription with metabolism. Because it is light and glucose we know POMC, ACTH, and melanin are the key to understanding CSP-1 biology. It also means that artificial light during the day or night is especially toxic when you know this is how the mechanism operates.
There are three type of melanins in humans and only one ACTH in humans. All three are used to time stamp the atomic lattice of cells to create an internal map of space time domains to be accurate measuring sticks for the flow of entropy inside of cells. This links melanin biology to Noether's theorem directly. You have blogs on all these ideas now and it is time for you to link them all to comprend what I have been teaching your for 20 years. Light causes modern diseases.
These 3 melanins are ALL extended heterogeneous biopolymers composed of molecular subunits with ambiguous macromolecular topology to modern centralized science. In the literature, an electrochemical fingerprinting technique has been described for melanin, which suggests that natural melanin pigments which contain indole-based tetramers seem to be always arranged into porphyrin-like domains to capture light and measure it in some way useful to the system.
Spectroscopy and density functional theory calculations suggest that sodium ions undergo occupancy-dependent stepwise insertion into the core of porphyrin-like tetramers in natural melanins at discrete potentials that time stamp the internal atomic lattice that allow it to act like a clock to measure the flow of entropy in the cellular system accurately just using light and dark as the feedback loops. It is fully decentralized because light and dark control this process. One is not more important than the other. A loss of melanin implies a loss of accurate time keeping inside the cell or tissue.
Lastly, in humans, the TTFL is a limit cycle, meaning that it is a closed loop that will return to its fixed trajectory even if it is disturbed by its environment, maintaining the oscillatory path on its fixed 24-hour period. It appears this is only true if the melanin structures it uses on surfaces and endogenously remain intact and are chronically replaced and renovated. If the endogenous electrochemical time stamping mechanism is damaged, the TTFL loses its periodicity and chronic modern disease results without any alteration to the DNA or RNA of a cell. These are diseases do not mimic genetic diseases like Tay Sach's. These diseases are far more common than mutational diseases of DNA which are relatively rare. It means our circadian mechanism is open to the environment, and as such is not subject to calories measurement for metabolism because calories only is useful in closed thermodynamic loops.
CITES
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Comments
TIMESTAMPING = PROOF OF TIME mechanism. As Einstein has shown us, time is not static. There is no such thing as a universal time to rely upon. Time is relative, and simultaneity is nonexistent. This fact alone makes all timestamps—especially across large distances—inherently unreliable, even without adversarial actors. This is why timestamps of GPS satellites have to be adjusted constantly, by the way. The same thing is true in the mammalian SCN. The sunrise provides the SCN and the leptin-melanocortin pathway its daily adjustment. In the Bitcoin network, the difficulty-adjustment ensures that the rate at which new blocks are created remains constant, regardless of changes in energy expenditure. This allows for a reliable and secure system that cannot be easily manipulated or inflated. Time is the ultimate decider in this system because time cannot be changed or manipulated. This concept may seem abstract, but it is essential in creating a trustworthy and robust monetary system. Cells are decentralized just in the same way using proof of time. This is done by the circadian mechanism. Light captured by chlorophyll, hemoglobin, or any nonvisual photoreceptor like cholesterol is slowed down tremendously. During that small moment of time, time dilation allows for food to manifest on Earth. Buried in food is an electromagnetic bar code. This makes food a form of optical information on time. This is where the proof of time shows up. The dilation of time is a job for mitochondria to decipher. The data/information is then sent to the circadian clock mechanism controlled by Rev-erb Alpha and beta, which are themselves non-visual red light chromophores. Why are they redlight chromophores? Like hemoglobin and cytochrome C oxidase, they are heme-based proteins. They are time crystals that pulse and act as a red light clock. As a result, our tissue begins to experience time in our cells. When the fidelity of the light signal is not purely solar and nonnative or artificial, Proof of time fails, and time is experienced to speed up for the person, and they tend to get sicker faster and die sooner. How sensitive is this signal to the mitochondria in the leptin-melanocortin pathway in the eye? Think about what any lens or tarp can do to light. It acts as a filter. Those lenses change the frequency of light in some small way, but that slight change induces an altered signal in your retina where the leptin-melanocortin pathways lie. Leptin is also created in your skin, so this pathway exists in other places globally and has to be accounted for in GPS fashion. Proof of time mechanism comes into play here again. As a result of this dance, the eyes and brain get an altered signal and this altered light stimulus (PoW) is what is used to time stamp the circadian mechanism in every cell of your body. That light alters the spin cycle of the TCA cycle in you. Unfiltered sunlight makes it go clockwise. Any other spectra of light make the TCA cycle spin counter-clockwise. Now, think about Bitcoin and your cells for a moment. It would help if you thought of the TCA cycle as a cellular auditor for light and dark cycles. Auditors need to be able to go over the books —backward in time — to keep ledgers honest and functioning. Without reliable circadian timestamps in our DNA ledgers, verifying the internal consistency of a ledger is impossible. When this occurs, due to unusual alien markings made in the Rev-erb alpha and beta genes by nnEMF/blue light stimulus, timestamping is made nonsensical, and only an improper audit is created. This is how all chronic disease epidemics begin. The value in life, time, is subtracted from your ledgers. Telomeres can and should be thought of as a ledger of time. As this blog shows you, so is the TTFL. If you could read the doctor portion of my form you'd see amazing threads of how ROR gamma and the Vitamin A liberated by opsins all act to ruin timestamping and cause disease. This is why free Vitamin A ruins sleep.
Dr. Jack Kruse
2024-05-02 04:42:02 +0000 UTCBlue light increases blood glucose.
Dr. Jack Kruse
2023-10-01 12:01:59 +0000 UTCCentralized medicine treats the eye as a camera when its most important physiologic role is as an optical clock. Glucose is fully capable of braking ubiquitin when ubiquitin is coupled to the cell cycle, but not when it is uncoupled and isolated. This occurs when the eye is fed a strict diet of blue light from modern tech gear, TVs, and LED lights where humans live. The reason glucose has this ability because the glucose molecule contains a strong blue light fingerprint in its molecular structure and it interacts with POMC biology in the eye. This occurs because of how Nature designed the retina to operate. It happens because of how the red and blue photons built it via photosynthesis via chloroplasts. This is why carbohydrates electrons are fed into NAD+/NADH in mitochondrial respiration and no where else. The SCN in the eye provides the negative feedback loops for the SCN using diurnally changing solar frequencies. This ability is lost when light cycles are uncoupled in the retina from the nitrogen cycle in cells of the eye or gut. When these cycles are isolated, glucose/insulin/AMPK levels go through the roof to stop the PER 1 and PER 2 clock genes from turning over proteins by ubiquitin marking in cells. This changes the NAD+ and oxygen level and the resultant hypoxia destroys melanin all over the body plan of mammals. This makes them impotent to use sunlight properly. PROTEIN turnover is increased when there is more ubiquitin marking and protein creation is the most energy costly thermodynamic activity a living thing experiences. Since energy is a zero sum game in humans the organs with the highest oxygen consumption begin to fail. This is why nnEMF/blue light drives insulin levels, AMPk, and is pro-growth when you live under their influence 24/7. Eukaryotes spend 80% of their total energy budget on protein synthesis. That process is controlled by ubiquitination. This is why you need to understand ubiquitin. Once you master ubiquitin you can use that recovered energy to reverse illnesses. Each peptide bond requires 5 ATP's to seal the bond. That amount is 5 times as much that is needed to polymerize nucleotides into DNA!! Ponder what that means to mitochondrial biology where ATP is made. Each protein is reproduced from RNA/DNA in thousands of copies, which are continuously turned over by ubiquitin to repair wear and tear. If you alter the balance of predator or prey of the clock genes the result is always the EXTINCTION of both animals. I have told you that in aging and neolithic disease generation that NAD+ becomes altered in relation to NADH. The chronic loss of NAD+ is the critical sign of a loss of negative feedback control of the ubiquitin cycle and a great marker for cellular hypoxia. All circadian clock genes operate after translation. This tells us most diseases are not due to DNA alterations. They are due to post translational events that are epigenetic. Now for how this scales to your molecular circadian clock and your peripheral clock genes (CCG's). The current model of the mammalian circadian clock includes two interlocking transcription-translation feedback loops (TTFL) comprised of several so-called “clock” genes and their protein products, which ultimately regulate the transcription of “clock-controlled” genes. These feedback loops consist of positive and negative components = predator and prey The positive components include the basic helix-loop-helix-PAS domain transcription factors, CLOCK, and BMAL1. These transcription factors heterodimerize, translocate from the cytosol to the nucleus, and bind to circadian E-box promoter elements that enhance the transcription of genes encoding the negative components PERIOD 1 & 2 and CRYPTOCHROME 1 & 2. The CRYPTOCHROME and PERIOD protein's feedback inhibit the transcription of the Cryptochrome and Period genes by blocking CLOCK/BMAL1-mediated trans-activation. The second feedback loop involves the trans-activation of the Rev-Erbα and Rora genes by CLOCK/BMAL1. The protein products of these genes compete for binding to RRE elements in the Bmal1 promoter, driving a daily rhythm of Bmal1 transcription and closing the second feedback loop. Rhythmic expression of these clock gene products produces circadian clock outputs by regulating transcription of clock-controlled genes (CCGs). At least some of these CCGs, including aanat, the gene encoding the penultimate enzyme in the melatonin biosynthetic pathway, contain circadian E boxes, which have a core nucleotide sequence of CACGTG and are activated rhythmically by CLOCK/BMAL1. Post-translational regulation, including phosphorylation, acetylation, ubiquitination, sumoylation, and proteasomal degradation are also important in the regulatory mechanisms generating the circadian oscillation. Once you SCN goes haywire it is a matter of time before your circadian clock genes in tissues the SCN controls go haywire. What will be the ultimate result? EXTINCTION of both sides of the circadian coupling and cancer is that result. The normal relationship of predator and prey is lost in the clock mechanism and modern chronic diseases manifest. My decentralized PSA for the day is done. 1. Herzog ED. Neurons and networks in daily rhythms. Nat Rev Neurosci. 2007;8:790–802. 2. Yamazaki S, Numano R, Abe M, Hida A, Takahashi R, et al. Resetting central and peripheral circadian oscillators in transgenic rats. Science. 2000;288:682–685. 3. Ko CH, Takahashi JC. Molecular components of the mammalian circadian clock. Hum Mol Genet. 2006;2:R271–277. 4. Munoz E, Baler R. The circadian E-box: when perfect is not good enough. Chronobiol Int. 2003;20:371–88. 5. Gatfield D, Schibler U. Proteasomes keep the circadian clock ticking. Science. 2007;316:1135–1136. http://dx.doi.org/10.1038/nrn2215
Dr. Jack Kruse
2023-10-01 12:01:15 +0000 UTCJack, I'm trying to understand the relation, if light has impact on TTFL that induces BMAL1-CLOCK genes that in turn increases anabolic processes which promote glucagon release, then blue light should decrease glucose level in blood, am I right? I'm confused since other research showed that blue light increases glucose levels
Sebastian Miedziak
2023-10-01 11:42:33 +0000 UTCDoes anyone know the clothing line that doesn't block UV? I remember seeing some brand in one of Dr Kruse's comment sections a long time ago.
Antony
2023-10-01 10:59:19 +0000 UTCCriminal, isn't it? It seems like mainstream medicine is so corrupt that in most things - one is truly best doing the opposite of what they say. Of course I wish I knew 20 years ago what I know now. Unfortunately I now rely on glasses for near and far vision. I learned too late how opthalmology sets thing up so we will need a stronger prescription year after year; so of course they require a new RX every year. It is impossible to find lenses without UV blocking in them -if anyone is aware of a source, please let me know. Of course, once one needs the lenses to replace the cataracts, you are stuck with the things permanently on your eyeball, never allowing UV light to enter. Last I heard, there are no lenses available without UV blocking. I don't know what would be worse, living with a cataract or having a lense like that. Is anyone aware of cataract reducing protocols? I know many who are told they have early signs. Opthalmologist told my father (after receiving his increased magnification eyeglasses to wear over his UV blocking cataract lenses), that he should buy a very intensely bright LED light to use in the evening. Which he does, while using his Ipad. I hate that I have to use these people and give them money - as I prepare to replace my glasses; but i can't see at all with out them and isn't another immediate option.
Ellen aka Scooby
2023-09-25 20:23:56 +0000 UTCEspecially if you are taking Farxiga and having fourniers gangrene!
Brian G
2023-09-24 23:12:32 +0000 UTCAha but Does red light on the perineum actually have a beneficial effect. I'm sure it does but I just need to understand the mechanics of it all.
Rohen Kapur
2023-09-24 18:01:21 +0000 UTCLaura where can I find the red light on the perineum writings ?
Rohen Kapur
2023-09-24 17:58:18 +0000 UTCMade my day with these: your ICD-10 code “Circadian Dysrhythmia“ & Red Light on the Perineum” - classics!
Laura Kissmann
2023-09-24 16:08:25 +0000 UTCJust refreshed on this: https://www.nature.com/articles/s41514-022-00092-z - looks like 1) the older folk are at the top of the carbon list they want to reduce 2) Older folk MUST prioritize artificial blue light blocking. Ironic when it is centralized Ophthalmology recommending UV light blocking. Again thank you Dr Kruse for continuing to challenge our brains and beliefs with these articles!
Laura Kissmann
2023-09-24 16:06:40 +0000 UTCThat is because you do not understand how Operation Paperclip and MK Ultra were formed. My tribe members do.
Dr. Jack Kruse
2023-09-23 12:48:31 +0000 UTCIn a thermodynamic system that is open calries cannot be the unit of measure. PERIOD.
Dr. Jack Kruse
2023-09-23 12:47:32 +0000 UTCIn Australia we have been indoctrinated to fear the sun. People are getting all these medical skin cancer treatments and massive incisions removing cancers and are told to avoid sun and plaster on sunscreen. It is nuts!
Rebel
2023-09-23 02:49:24 +0000 UTCUnfortunately Calories in, calories out isn’t accurate. The intellectual laziness, even of us doctors, like to push that because I can make a hashtag out of that. What we have to consider is that 1 calorie that you take in, has many potential effects based on your current energy balance in the system, your current latitude/altitude, your mitochondrial haplotype (where your ancestors migrated from around 150,000 years ago, the season, the time of day, the type of electron, the photospectral environment you are currently STANDING IN , your skin/eye exposure, etc. Jump on the JK roadway my friend and don’t forget to buckle up. LOL
Brian G
2023-09-22 23:44:46 +0000 UTCHonestly I don’t give the powers that be credit in being able to have the foresight to understand mitochondrial photobiology when even the greats are still adhering to Paleolithic mechanisms of chemiosmosis, ATP, lock and key biochemistry. I’ve had the similar discussions with UCLA ER residents and unfortunately they flat out still say things like “We are doing EVERYTHING wrong, and most of us don’t know it”. The blank stares that i get when discussing medical treatment when i SUGGEST LESS pharmaceuticals and more photoendocrinology/circadian science is very concerning. The idea of Ozempic being the answer to all of our problems. I still think its funny when I put on my ICD-10 code “Circadian Dysrhythmia” and my colleagues ask me what that is. I think you, Jack, are attempting to shine a necessary “Red Light on the Perineum” of the medical establishment. I also think I may need to move to El Salvador. LOL. But I digress.
Brian G
2023-09-22 23:32:07 +0000 UTCDifferent reactions are possible. Hypersensitivity reactions is the “allergic reaction” but it can make people more sensitive. To the sun resulting in photosensitivity reactions. The mechanism behind sulfa-induced photosensitivity primarily involves the interaction of the drug or its metabolites with ultraviolet (UV) light, mainly UVA rays. Sulfa drugs tend to accumulate in the skin. When the skin, impregnated with the drug, is exposed to sunlight, particularly UVA rays, a photochemical reaction occurs. Exposure to UVA light leads to the formation of reactive oxygen species (ROS) and reactive drug intermediates. These reactive intermediates can bind to cellular components, damaging cellular membranes, proteins, and DNA in the skin cells. The damage to cellular components triggers an inflammatory response, attracting immune cells to the site of damage, leading to the symptoms of photosensitivity such as redness, inflammation, and blistering of the skin. There's evidence to suggest that sulfa drugs can also alter apoptosis (programmed cell death) in skin cells upon exposure to sunlight, contributing to the damage seen in photosensitive reactions. Hope that helps.
Brian G
2023-09-22 23:10:31 +0000 UTCIs this at all related to why some antibiotics cause reactions to sun exposure? I know some antibiotics are called ‘sulfa’ antibiotics… I am allergic to these, apparently.
Christopher Jones
2023-09-22 22:27:39 +0000 UTChttps://www.nature.com/articles/s41514-022-00092-z NOW do you see why they banned incandescent light bulbs and why they want to BLOCK THE SUN!?!?! When you understand the basics of how humans are meant to function and what causes Dis-Ease you understand how the pieces fit together and how they fall apart. You can see how "the powers that be" whether it's "Big Pharma," our government, The World Health Organization, etc. call the shots and make moves for one stated reason. You are the carbon they want to reduce. . . yet there are hidden agendas at play. Case in point here. It feels like we're saving the earth by banning incandescent light bulbs, and it's all for the stated goal of improving energy consumption. With energy, I've learned it's a zero-sum game. . . With this example in particular where we may save some energy by switching out all our lighting, it's depleting your mitochondria of energy!!!! (READ THAT AGAIN!) What happens when you deplete your mitochondria of energy you ask? Weight gain, Dis-EASE of all types, neurodegeneration and brain fog, and the list goes on. . . h/t to Skip for this.
Dr. Jack Kruse
2023-09-22 21:49:10 +0000 UTCCalories, as a measure of energy, is technically measuring electrons and bonds in the food we eat, right? Light and it’s coworker photosynthesis is ultimately responsible for bonding all those the atoms in the first place… right? When you say “we’re not a closed thermodynamic system”… you are meaning that we lose energy to the environment all the time, right? It takes energy to keep us warm, and we’re constantly losing electrons to the environment, right? Excuse all the noob questions, please! “Calories in, calories out” actually IS correct, but just not in the way meant by all the norm-core ‘gurus’, right? Thanks… this is all changing my paradigms.
Christopher Jones
2023-09-22 21:23:00 +0000 UTCI can’t help to contemplate how cysteine (sulfa) plays a role with this time stamping, considering it is basically the “decider” to produce pheomelanin instead of eumelanin. And how having pheo in specific locations allows for increased UV absorption in these areas. Those areas ALSO tend to have more vascular flow as well (think lips, genitals etc). From a sulfation standpoint within the vascular system being so important, i bet that is something i need to focus on. Thanks for the post.
Brian G
2023-09-22 21:16:43 +0000 UTC
