BIOLOGICAL MESH NETWORKS

 Biological Mesh Networks

 

We are a collection of cells. We never think about it or probably don’t know that each one of those cells is individual unicellular organism with its own innate intelligence. These cells come together to build a higher life form to improve chances of survival. All evolution is about survival. Individually each cell is much more vulnerable but collectively it can build attributes that would protect it better. But ironically to be part of such collective self it has to sacrifice its own life for the betterment of the whole whereas if it was not part of such collective self it would use its innate intelligence and desire to survive to make itself immortal. We call such cells that break free from the collective self cancer cells. For the higher form to remain operationally and collectively stable the cells are bound together with ‘mesh’ networks. The cell towers that give signal to our millions of cell phones have an interesting architecture where each tower is not just connected to its neighbour but all cell towers are connected to each other like a mesh. This is done to create automatic, intelligent load sharing between them. That way if there is conference or a festival at a certain area it won’t overwhelm the cell towers in its vicinity. Instead the extra load is shared with whichever towers that have much lower utilization regardless of how far or near they are. That way every cell tower helps the other.

 

Mesh Network Topology

 

In our biological mesh networks cell completely changes its persona and priorities to that of the collective organism. This may not be its natural state and so is held tightly on a leash by multiple mesh networks. One of the most recently discovered mesh network is bioelectrical by a brilliant scientist called Professor Michael Levin at Tufts University. I would encourage everyone to see his fascinating videos available on YouTube.

Michael Levin PhD

Another one is a physical mesh network connected by filaments protruding from each cell connecting to each other in a 3D network. The one that my own research works on is Extracellular Messaging Network. Each cell secretes tiny bubbles with various molecules which find another cell and inject that cargo of molecules in the receiving cell. This exchange too is constantly happening amongst and between our more than 30 trillion cells.

Michael Levin has proposed a major change in how we treat diseases. He suggests that the way we currently do so with our obsession with DNA and single molecules and CRISPR gene editing is similar to how programmers changed programs on computers in the 1960s:

By repatching the hardware every time the program needed to be changed. But now it can easily be done systemwide without touching the hardware using only the operating software and recoding it. What we have managed with these manual repatching of hardware is mostly management of symptoms with hardly any full cures of chronic diseases. No wonder 90% of the drugs fail to be approved. It would be much more powerful and effective to reprogram cells through the mesh networks that hold them tightly together. He demonstrates this by taming the most difficult disease ever: cancer. In a young, healthy body the cells are polarized in the bioelectrical network. They are always depolarized in disease and aging. Cancer cells too are depolarized. Michael Levin’s lab hyperpolarized the cancer cells and voila! Like magic they become normal cells. When cells break free from the collective organism all other cells become their host cells and they multiply and proliferate rapidly to ensure survival. They use their innate intelligence to outwit their hosts collective defense networks and tools. But as soon as they are pulled back into the collective self then they lose that independent selfish desire to thrive and survive and become a slave of the collective will. By changing them from depolarized state to hyperpolarized they come back to what we would term as normal behaviour but in reality there is no right or wrong behavior just different personas depending on whether they are part of a collective society or individual single cell organism like an amoeba. Can you imagine us as collection of amoebas? J

What this highlights is the future of medicine: Using any of the mesh networks to resolve a disease state. One can also consider aging as a disease state that we can also resolve in a similar manner.

So there are three levels of intelligence: innate intelligence of each cell, collective intelligence of the mesh networks and neurological intelligence of the higher organism. Although we call multicellular organisms a higher form the distributed innate adaptive intelligence that cells have seems far more superior to the higher form. Without having a central neural network to have the ability to analyze and take complex decisions the cell is able to use its internal, individual bioelectrical, biochemical and genetic/epigenetic networks to become a distributed intelligence. What incredible, incredible engineering in such a tiny, crowded space! Levin showed us through experiments that the bioelectrical network hosts sequential information about spatial organization of a higher form which builds us from a tiny single egg to a complex adult: the program of development.  But where is the sequential information stored on the program of aging? The collective intelligence has a group plan for building a multicellular life form and also a group plan for its operations. Cells that have partial disruption in their mesh network connections manifest into a disease and when they are completely disconnected from the group mesh networks and group identity they become selfish and cancerous.

Professor Michael Levin gives an amazing example of the collective intelligence: He loves to research with Planaria worm because it has evolved some astounding abilities. If it is cut into pieces, each piece is able to grow into a full, exactly same proportioned worm. What is in that cut off piece of that worm that has the distributed memory of its own full architecture and also instructions of how to regenerate exactly the parts needed at exactly the correct location to conform to the original worms architecture. Levin has shown evidence that this information is stored in its bioelectrical mesh network. In another example of collective intelligence: When planaria is inserted in barium its head blows off because it can not survive in barium. In a few days it regrows a head that can survive in barium. How does it activate only those genes that would allow its head to adapt to barium? So not only does it’s collective intelligence design a brand new head and position it correctly but it also changes its tissue material and properties so that it can survive in barium. Think about it: such a tiny worm without its head making decisions about which tissue material would be able to withstand barium! and then which genes to activate and close to produce that tissue as part of the regenerative scaffold! Beyond belief! This same collective intelligence also builds us in correct proportions into a full blown adult starting from a single fertilized egg. Imagine the power we would have if we can code or manipulate this collective intelligence stored in a mesh network? Our current tools like CRISPR seem so advanced and revolutionary but are primitive and unidimensional compared to this tiny worm's collective intelligence. We are so used to intelligence associated with dense neural networks in our brains that it’s very difficult to imagine such brilliant collaborative intelligence without any ‘brain’ or neurons. Where would such analytical computing machine be residing?

This tiny worm's mesh networks are more evolved and more advanced than us humans.

Another mesh network is what I call Extracellular Messaging Network or EMN. YUVAN uses this mesh network to make system wide changes. 

Extracellular vesicles derived from young plasma rejuvenates aging cells through multi-modal improvements by hacking the EMN. It’s like inserting new code to correct operating software errors in a computer. 

Besides bioelectrical network and chemical exchange through physical filament network, cells also communicate with each other via lipid enclosed molecules like proteins and RNAs. Almost all cells constantly secrete these messages in extracellular vesicles (EVs) or in protein conjugates. These EVs naturally do a molecular ‘handshake’ with other cells and inject their cargo of proteins, RNAs and more not only into the recipient cell but also into its nucleus. This cargo then executes their function: for example, a miRNA may bind to a protein and neutralize it or a non coding RNA may make epigenetic change which could affect a gene’s expression. This exchange again is like a mesh, so not just between neighboring cells but across distances with cells in far off locations transported there in circulating plasma. This intercellular messaging is constantly going on from even before we are born till death. Each cell is influencing the epigenome, transcriptome, proteome and gene expression of other cells through this messaging network. Some exchange is targeted to a particular cell through surface proteins called tetraspanins regardless of how far the recipient cells are located.

 

Next generation of medicine will hack into or leverage these intercellular mesh networks to gain system wide results. Levin is developing actuators/switches to manipulate the bioelectrical network to gain Planar worm type of regenerative superpowers. YUVAN has been harvesting EVs and some more plasma constituents from the plasma of the young mammals around puberty. As at that age the messaging cargo is supporting a near homeostatic efficiency in cells. As I have mentioned in my previous posts aging and disease result from ‘epigenetic drift’. A quick recap: all cells have the same DNA then why some cells become a heart cell and another becomes a liver cell – both so different. This is due to epigenetic configuration. Each cell type has its own unique epigenetic template that shuts down around 80% of the genes and keeps open the balance. Which gene is shut and which is left open decides the cells form and function. During embryogenesis these epigenetic marks are wiped clean and a fresh template is installed for each cell type during differentiation. But in almost all multicellular organisms this epigenome begins to lose it’s configuration in some places leading to what some scientists call ‘epigenetic drift’. This can result in partial or full loss of cellular function. As more and more cells progressively get misorganized parts of their epigenome, their tissue or organ can lapse into a disease. Aging is another manifestation of this epigenetic drift. Around puberty such epigenetic drift has not started and body is at its peak to support reproduction. So YUVAN harvests EVs and other plasma constituents around puberty and injects them into older recipients. This basically hacks into the EMN. As per natural process these EVs inject their cargo into older recipients cells. Now the proteins and RNAs circulating in the young influence the epigenome, transcriptome, proteome and gene expression of the older cell. This reverses the epigenetic drift and resets the epigenetic configuration closer to it’s pristine template found around puberty. And voila! the cell begins to function like a young cell.

Modern medicine has been priceless for so many infections and diseases that used to kill us previously but it hardly gives us any full cures. Mostly managing symptoms. Focusing on a single gene or a few genes or a single protein or antibody doesn’t produce a full transformation or regeneration of the diseased tissue or organ. That’s why 90% of the drugs fail to get regulatory approval. Whereas a drug that can influence any of these mesh networks can reprogram the entire network or any part of it to a more efficient form. A tiny worm has adapted its survival mechanism, won during evolution, to regenerate and repair any epigenetic disorganization instantly as we would heal a small wound. This results in a stable epigenome the importance and benefits of which is the subject of my previous blog post titled Stability = Lifespan. A stable epigenome keeps the cells healthy and efficient leading to youthful immortality of the Planar worm. We can see a similar ability to keep its epigenome stable in Ginkgo Biloba tree which is much bigger than the worm. It too has been called immortal. We are a collection of cells. Of all the parts of a cell why is epigenome the most important? Because it is what gives each cell its identity and function. In aging and disease we see a gradual loss of both leading to various painful complications and eventually to death. Reprogramming our biological software to cure epigenetic disorganization is the future of our medicine. Can we learn from the worm and the tree to modulate our endogenous mesh network softwares to stabilize epigenome in each of our cells and then maintain that stability forever?

 

STABILITY 🔀⏩️LIFESPAN

 STABILITY 🔀⏩️LIFESPAN

 

The lifespan of objects in the universe is dependent on the stability of its unit ©2023 akshay Sanghavi 

 

All matter moves towards stability.

 

Atom is more stable when it is in a lower energy state and so it tries to move towards the lesser energy state.

 

 Unstable atom isotopes will spontaneously decay and change to another more stable element. The rate of radioactive decay is inversely proportional to the stability of the isotope. Radon-222 has a half life of just 4 days so every 4 days it will reduce to half. Which creates the spontaneous move towards a more stable form. Universal law of survival: a stable atom can exist for billions of years. Xenon-124’s half life is 18 billion trillion years. Despite its incredible lifespan and stability, it’s not immortal: it will also eventually die and turn to tellurium-124. 

 

Atom of Xenon-124 from Descopera.ro

 

I have been thinking about the different lifespans of biological species on our planet. My fascination and desperate curiosity to unravel the mystery of variable lifespans has obsessed me with constantly researching the potential causes. I have been sharing my findings in some of my previous posts like Mechanism of Aging, Headwaters, Autologous Regulation and Agents of Time. In the last few posts I have shared the realization that a cell’s destiny is strongly linked to regulatory changes enforced by regulators like non coding RNAs. Of course, there is incredible complexity to this process. Nothing else on this planet has brilliant, complex, autonomous engineering like our biology. But can there be one simple factor behind the variance that we see in the lifespans? It’s not size for example as the exceptions demonstrate. My mind is blown by the study by Professor Richard Dixon on Ginkgo Biloba tree. So much that it features in all my longevity related posts since it was published. If these hardcoded transcription plans are making deliberate changes starting after puberty setting off a cascade that ends in death, then how did Ginkgo Biloba make adaptive changes to bypass such a universal recycling mechanism of Nature? Professor Dixon called it almost immortal. The best part is that not only is it almost immortal but it’s almost immortal in a youthful state! Who wants to live a thousand years looking like shrunken bag of bones and crumpled skin? So, what is this one single cause of lifespan variance? We will arrive at that after some more deliberation. 

 

As we read in a paper by Morimoto and Labbadia called ‘Repression of the heat shock response is a programmed event at the onset of reproduction’ that just after puberty there is a change that reduces the ability of chaperones, that are key to the protein production process in our cells, by 60%-70%. This results in higher number of malformed proteins. This starts a cascade of many other drops in important functions in the cell and these drops snowball making us age. For example, as we read in Agents of Time, the debris of the 450 billion cells that die every single day in our body is cleared by phagocytes. But thanks to various regulatory changes and their ensuing cascades their mitochondrial batteries begin to fail them. This leads to accumulating number of sharp debris that enters cells and causes 1 quadrillion double strand DNA breaks everyday! In this chain of events germline cells triggered epigenetic changes that resulted in the fall of efficiency of protein production chaperones. What if these epigenetic changes were not allowed to be made or after they were made they were ‘repaired’ back to their original epigenetic configuration. In order to prioritize reproduction the germline stem cells trigger epigenetic repression of heat shock proteins which act as chaperones to support protein production and as stress response. When we get a hurt while playing sports the injury is repaired over a period of time. What if similarly the epigenetic mark that germline stem cells make after puberty is demethylated or removed to restore back the full strength of heat shock proteins? That would stop the chain of events that eventually cause so many double strand DNA breaks every day. Just to demonstrate how this cascade snowballs when those breaks keep happening in the DNA, even though almost all are repaired, they succeed in creating roadblocks in the hurtling train of transcription in our DNA. This than has serious repercussions as many transcription programs get blunted. In the Agents of Time blog another change causing aging is mentioned wherein our long, coding and noncoding, transcripts begin to fade. The authors of the cited paper also mentioned that these longest transcripts were activating prolongevity genes. Thereby repressing or silencing the genes associated with making us live longer. So when we prevent or significantly reduce the huge number of double strand DNA breaks we restore smooth transcription and thereby prevent the loss of longer transcripts and silencing of longevity genes. Do you see where this is leading us? 

1,400 year old Gingko Biloba Tree

 

The mechanism that Ginkgo Biloba tree has figured out is probably how to keep its epigenome stable! We are a collection of cells and all cells have the same DNA and yet they are transformed into 200 types to form eye and stomach and liver and skin etc. The DNA is the same but each type of cell has its own configuration of epigenetic marks on its DNA. These marks do not change the DNA physically but result in silencing majority of the genes and activating only the10%- 20% that transform it into its type of cell.  Around puberty we achieve our homeostatic peak where all our systems are working at their best. But due to the changes mentioned above we experience what is called as ‘epigenetic’ drift where the beautiful epigenetic configuration found around puberty is slowly changing leading to unwanted genes being activated and wanted genes becoming silent. This epigenetic drift manifests into what we know as aging. The Ginkgo Biloba tree does not seem to succumb to this epigenetic drift which can be seen in almost all multicellular life forms leading to cell nuclear instability that slowly grows into cellular, tissue and organ instability. In a fascinating paper titled ‘Multifeature analyses of vascular cambial cells reveal longevity mechanisms in old Ginkgo biloba trees’ by Professor Richard Dixon and Dr. Jinxing Lin et.al. the authors try to reveal the longevity mechanisms of Ginkgo Biloba trees. The table below shows the miraculous stability of really old Ginkgo Biloba trees:

The authors selected nine trees for further study and divided them into three groups: 20 y (15Y, 20Y, and 22Y, young trees; VC20), 200 y (193Y, 211Y, and 236Y, older trees; VC200), and 600 y (538Y, 553Y, and 667Y, oldest trees; VC600). Below we can see the comparison of the average leaf area, seed germination rates, efficiency of stress resistance, photosynthetic capacity and chlorophyll content of the 3 groups:

 Ginkgo Biloba Trees Comparison of 20 year olds, 200 olds and 600 year olds

 

Unlike almost all plants and trees that grow old and die Ginkgo Biloba’s environmental stress resistance, photosynthesis capacity, autophagy, sexual fertility and immune defense doesn’t drop with age! It’s cambial cells equivalent of our stem cells remain active even in oldest trees in the group but tempered with reduction in cell division, expansion and differentiation allows it to remain young without any uncontrolled growth or senescence. In human aging we begin to lose stability of the epigenome and our transcription track and its machinery leading to loss of beneficial genes and activation of unwanted genes. The exact opposite is happening with Ginkgo Biloba tree. In the same paper authors compared around 27,500 genes of the three groups: 20 year old, 200 year olds and 600 year olds there was only 4.4% difference in gene expression between the young trees and the older trees! How does Ginkgo Biloba tree maintain such stability of its epigenome, transcription, gene and protein expression???

This kind of beneficial stability is quite different then the longer lived species: the latter like Naked Mole Rats or Bowhead whales have some protective genes that are overexpressed even in old age. That does give longer than average life span associated with their species but they do grow old and die. Whereas Gingko Biloba trees seem to live forever in youthful prime. 

 

As I had shared in my post Mechanism of Aging, Nature manages optimum levels of various activities and functions in our biology by the triage of activators and inhibitors and sensors. This works like a tap of hot water and cold water and a thermometer. Equilibrium is when taps are turned just the right amount to create ideal temperature of water. Any disturbance in this ratio can cause either too hot water or too cold water causing damage. In our prime, just after puberty, we enjoy optimum equilibrium or homeostasis between the activators, inhibitors and sensors. But soon after starts the slow offsets in this balance leading to all the accumulation of unrepaired damage and nuclear instability which manifests as age related changes. We can see and feel this happening especially after our 50s but since it’s not overnight and since we see others too showing similar negative changes we accept them. Ginkgo Biloba has been around longer than us: for more than 270 million years. Whereas we humans have been around only 200,000 to 300,000 years. Ginkgo Biloba has had 270 million more years to win the adaptation lottery. We humans too have won another genetic lottery: of higher intelligence that is compounding rapidly like an umbrella curve. We are developing great technologies and tools like CRISPR and AI and will soon figure out how to safely inculcate stability in our epigenome and nucleus. Then we too will have the option to live for thousands of years in the prime of our youth. Every known thing in observable universe seems to be recycled. The stars too die and leave behind a super dense spinning ball with no fusion or light just fading heat. These white dwarfs or neutron/pulsar remnants and planets and their debris all get recycled by black holes. All of the galaxies are probably held together by the gravitational pull of the super massive black hole at their core. This central black hole eventually will eat up the entire galaxy and break it down into fresh units of matter and radiation and spew them out as astrophysical jets long distances into space. So all the different bodies in a galaxy are broken down to sub atomic particles in the intense gravitational crush of the super massive black hole and slowly recycled into basic units of matter and radiation which then forms new stars and planets. So to outwit such a pervasive norm of recycling in the universe is a phenomenal achievement of Ginkgo Biloba. 

Super massive black hole spewing recycled matter and radiation deep into space. By Newsweek. 

 

Has Ginkgo Biloba developed some technology based in the futuristic world of science fiction? No. We see some mindblowing processes in biology all around us. During early embryogenesis there is global epigenetic reprogramming. For example in male embryos 96% of the methylation is wiped out to clear all accumulated errors from parents and later globally re-methylated as per template to create a brand new error free baby. This is the reason why Nature has created a program of aging so that continuous recycling will ensure cleaning out of errors every generation. So such an all encompassing and powerful epigenetic reprogramming technology is already being used in every embryo. Second technology is of self repair. Everyone of us would have got various degrees of hurt as a child while playing and see how over a few days or weeks it’s fully healed. Third technology is seen in some reptiles that regrow limbs even after they are fully severed. So biology already has some incredible engineering technologies to reset and restore any disturbance back to its optimum configuration. Can these technologies be harnessed to restore any erosion in our epigenome so that after every disturbance, whether it is stochastic or programmed, the epigenome is reset back to its optimum, youthful pattern? 

To understand the cause of nuclear and cellular instability further let us borrow from my last post Agents of Time: We read that Aging is associated with loss of longer transcripts including long non coding RNA: https://www.nature.com/articles/s43587-022-00317-6

Plus they found: ‘we find that in humans and mice the genes with the longest transcripts enrich for genes reported to extend lifespan, whereas those with the shortest transcripts enrich for genes reported to shorten lifespan’

This is one of main reasons why longer transcripts fade away with aging:

https://www.nature.com/articles/s41588-022-01279-6

‘The drops were not due to drop in promoter activity or drop in RNAP II activity. Even the launch of transcription was unaffected. The authors postulate that DNA breaks interrupted and stalled transcription – and as longer genes/transcripts have greater chances of being broken somewhere they can be the primary cause of their reduced transcription during aging.’

A recent paper gives us glimpse of one of the ways this loss of long non coding RNAs cause the damage to tissues and organs during aging:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10834948/

“LncREST localises to chromatin (the structure in which DNA is organised in the cell). Its main function is to facilitate the localisation of key proteins in the process of DNA replication and DNA damage repair where they are needed. In fact, the absence of lncREST has been shown to cause impaired stress signalling, leading to the accumulation of severe DNA defects and, ultimately, cell death“

A few deliberate changes like the sudden massive drop in heat shock chaperone efficiency just after puberty start this cascade of errors leading to the instability of epigenome, genome, nuclear architecture and the cell. If these errors can be stopped/repaired as soon as they occur we too can’ live forever’ in youth like the Ginkgo Biloba tree. E5 does this partially by feeding older cells and its nucleus suffering from epigenetic drift with regulatory workers like longer transcripts from a youthful system that fill in some of the gaps or missing pieces in the old cell/nucleus. This restores the broken epigenetic pattern partially back to its original template. The amazing part is that old, damaged cells bounce back to youthful healthy fitness once it’s epigenetic pattern is reversed closer to its optimum design. This is a safer engineering intervention than any that needs the cell to move towards pluripotent state. As it creates a fluid epigenetic state which can lead to tripping into loss of cell identity and loss of controls which can result in development of cancerous growth. The idea is to create stability in the epigenome not fluidity.

We already have the engineering peak around puberty where our biology works beautifully. But there are a thousand negative changes that occur as we age. We have to now learn how not to slip into the epigenetic drift and to keep our cell stable at its homeostatic peak as long as we want. Ultimately, we want to install a Ginkgo Biloba type of mechanism that restores the cell and its nuclear architecture after any disturbance. The secret to long youthful lifespan is achieving long lasting nuclear stability after reaching adult biology. We just have to observe the Universe to unmask this secret. Stability is the difference between a lifespan of 4 days and 18 billion trillion years. 

 

 

AGENTS OF TIME

 AGENTS OF TIME

 

Human biology is finite and yet so incredibly complex. We are constantly surprised by new components and systems being discovered. So far we relied on ‘Hallmarks of Aging’ as a reference for what all changes in us with aging but there have been a flood of papers recently that go much more deeper or upstream, closer to the source of these macro changes. They are giving us another perspective on the changes occurring in us with aging.

All of them not only sit very well with but also embellish what I shared in my two previous posts: Headwaters and Autologous Regulation. 

So let’s go over some of them here:

Cell-free chromatin particles from dead cells accumulate in our plasma and cut DNA in healthy cells making 1 Quadrillion double strand DNA breaks everyday in each of us as we grow older!

https://www.nature.com/articles/s41598-022-21388-w

A Shocking discovery of how shrapnel from exploding dead cells cause Double Strand DNA fractures in healthy cells and a simple oral supplement may protect against that. 

Dr. Indraneel Mittra is a brilliant scientist and a cancer surgeon with Tata Memorial Center for cancer research. He worked against all odds for 20 years to confirm, with evidence of 150,000 volunteers, the importance of regular low cost screening for breast and cervical cancers thereby saving lives of millions of women. Recently he was perplexed by the very high occurrence of double strand DNA breaks in our cells: 10 to 50 per cell per day! These DDBs are constantly repaired to maintain the viability of the cell but any error leads to cell death or worse cancer. So he and his team began to investigate the cause. They were surprised by what they found. Every day around 450 billion cells die in our body (our body is a collection of avg 33 trillion cells). This huge number of dead cells leave fragments or debris which circulates in our blood. Phagocytes work relentlessly to ‘eat’ this debris and digest it - clear it. But Dr. Mittra found that cell free chromatin particles released from the dead cell fragments enter healthy cells and cause double strand DNA breaks which basically snaps both the strands of the DNA. He found that the plasma consists of large quantities of these dangerous bullets circulating all across our bodies as we age they inflict dsDNA breaks, activate apoptotic pathways and induce inflammatory cytokines. This could be one of key causes of rising chronic inflammation during aging. Chronic inflammation is a precursor to most of our mortal diseases. Their group has successfully isolated and characterised cfChPs from human serum, which upon EM examination revealed extensive size heterogeneity ranging between ~ 10 and ~ 1000 nm13. They have also reported that blood levels of cfChPs increase with age. No surprise there. This is a BIG discovery! Dr. Mittra hypothesizes that the that lifelong assault on healthy cells by cell- free chromatin particles or cfChPs is the underlying cause of aging. Again a very major discovery if it turns out to be true. I personally do not fully attribute the circulation of these dangerous particles as the cause of aging because I am sure in the young, healthy body they can be more or less cleared by our amazing phagocytes. What happens with aging is that the efficiency of the phagocytic cells goes down which would leave accumulating amounts of this harmful circulating debris. An example of why phagocytes may lose their efficiency is the disruption of mitochondria seen in aging. Phagocytes especially require huge amount of energy provided by the mitochondria. Here is a paper on that: https://www.cuimc.columbia.edu/news/change-mitochondria-critical-clearing-dead-cells

Regardless of whether cfChPs are the cause of aging or result of aging Dr. Mittra also found that just by taking a combination of resveratrol and copper in a particular ratio one can drastically reduce the cfChPs and in his experiment he saw reversal of many key pathologies of aging. Basically this combination which is absorbed from the stomach after an oral pill generated oxygen radicals that degraded cfChPs. I always like to share some way one could intervene against age related damage whenever something was available. Dr. Mittra’s lab found that oxygen radicals that are generated upon oral administration of R–Cu are apparently absorbed from the stomach to have systemic effects in the form of deactivation/eradication of extracellular cfChPs. In that  study they have taken advantage of cfChPs deactivating property of R–Cu to investigate whether prolonged administration of R–Cu to aging mice will retard the hallmarks of aging and neurodegeneration. The dose of Resveratrol used in our study was 1 mg/kg, and that of Copper was 0.1 μg/kg, given by oral gavage twice daily. This dose of Copper was 20,000 times less, and that of Resveratrol 5 times less, than those that have been used in pre-clinical studies to investigate their health promoting properties by other investigators.

Using confocal microscopy and antibodies against DNA and histone they detected copious presence of extra-cellular cfChPs in brain of aging mice, and observed that cfChPs were deactivated/eradicated following prolonged oral administration of R–Cu. Deactivation/eradication of cfChPs was associated with down-regulation of multiple biological hallmarks of aging in brain cells. At a systemic level, R–Cu treatment led to significant reduction in blood levels of glucose, cholesterol and C-reactive protein. Such a combination in the ratio discovered by Dr. Mittra can be an inexpensive, non-toxic solution which can be easily incorporated into our daily supplement regimen.

 

Global loss of Heterochromatin and disorganization of nuclear architecture in aging

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3414389/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7253059/

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8673774/

During youth DNA is tightly packed in heterochromatin but in aging we see rising disorganization in the heterochromatin leading to loosely packed DNA and aberrant transcription of silenced genes. We have 200 types of cells but to create a particular type of cell and maintain that identity nearly 80% of the DNA needs to be permanently silenced and made inaccessible in tightly packed heterochromatin. Aging causes global disorganization of chromatin architecture. Disruption of nuclear lamina/INM proteins and decondensation of associated heterochromatin are common features of normative aging. This initially leads to transcription of genes that should not have been transcribed and later leads to loss of cellular identity causing pro inflammatory secretions and loss of function. Nuclear envelope dysfunction leads to alterations in nuclear transport, chromatin organization, and telomere maintenance and  are correlated with nuclear protein alterations, namely nucleoporins, nuclear transport factors, lamins, INM proteins, chromatin‐associated factors, histones modifications, and sheltering complex proteins, revealing that NE proteins are essential determinants of aging. There are also morphological changes that are observed of the nucleus. For example in the young the nuclear periphery is smooth but over time, an increasing number of nuclei started to show a rather convoluted nuclear periphery, with multiple folds. As we grow older we see nuclei that showed increasingly abnormal shape and/or extensive stretching and fragmentation. 

 

 

Lipotoxic accumulation of lipid droplets in cellular nuclear compartments during aging

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10086520/

The authors say: Age‐dependent deterioration of lipid metabolism and nuclear morphology are common features in evolutionary divergent organisms. Nuclear lipid droplet (nLDs) deposition and LMN‐1/LMNA accumulation lead to cellular dysfunction and, subsequently, to tissue homeostasis collapse, with age. Nothing is kept by Nature and evolution without a purpose. Nuclear lipid droplets would have beneficial functions during embryogenesis, development and youthful homeostasis but during aging they begin to accumulate abnormally within the nucleus causing lipotoxic and mechanospatial damage to nuclear compartments and membrane. The authors found that longevity interventions like fasting and inhibition of IGF-1 reduced such lipotoxic burden. They also examined long lived nematodes and found some commonality with longevity mediation. HLH-30 is a crucial regulator of autophagy and it was found to reduce lipid accumulation in the nucleus in both cases. Specifically an enzyme ATLG-1 which is transcriptionally regulated by HLH-30 maintains lipid droplet homeostasis in nuclear compartments. ATLG-1 deficiency is seen in aging cells of normal worms but not in long lived works and is also upregulated during longevity interventions like fasting in normal worms. This interesting research paper shows how we could investigate further upregulation of ATLG-1 during aging by a natural extract called Oridonin: https://www.nature.com/articles/s41419-023-05613-6

Another deficiency they found in patients suffering from metabolic syndrome is deficiency in Phosphatidylethanolamine PE. Supplementation of PE or Oridonin led to restoration of lipid homeostasis by activating LXRa which in turn activated ATLG-1 and another enzyme EPT-1.

The loss of cellular bioelectricity and polarity in aging

https://www.sciencedirect.com/science/article/abs/pii/S1568163712000992

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3896621/

A fundamental need of our cells is bioelectricity otherwise it would shut down just like any mobile phone when batteries run out. Similarly cells in our body progressively loose polarity as we age (or during cancer and disease). Polarity is important for the spatial organization of a cell. We read above what happened when a tight, stable configuration of heterochromatin and nucleus becomes loose and unstable in aging and the damage it can cause. So cell polarity plays an important role in maintaining that tight configuration. 

https://journals.biologists.com/jcs/article/121/8/1141/30524/Cell-polarity-and-cancer-cell-and-tissue-polarity As this paper adds to new evidence that restoration of cell polarity may differentiate the dedifferentiated cancer cells and normalize them. As we age we lose proteins that support bioelectrical

 generation and cell polarity. This leads to the fading of both and  further leading to eventual loss of the cell. 

Cell transcription speed increases with age and leads to more errors in transcription

https://www.nature.com/articles/s41586-023-05922-y

A very interesting paper by Andreas Beyer et. al. Shows us that Transcription of genes is fast but sloppy with age. Six research groups from the University of Cologne Cluster of Excellence on Cellular Stress Responses in Age-Associated Diseases (CECAD), the Max Planck Institute for Biology of Aging (MPI) in Cologne and the University of Göttingen discovered a new molecular mechanism that contributes to ageing by studying the transcription process in five different model organisms and in a wide variety of tissues. 26 scientists investigated genome-wide, age-related changes in transcription processes in nematodes, fruit flies, mice, rats and humans, including diverse tissues. And they discovered that the average speed at which the transcript grows through the attachment of RNA building blocks, the nucleotides, increased with age in all five species. With this increase in the speed of transcription they also saw increase in transcriptional and splicing errors. They observed that increase in transcription speed led to decrease in unspliced exons and intron retention. Basically increased splicing and splicing errors were seen with aging. In my previous blog post Headwaters I have written about how transcription is the beginning of the cascade of biological changes through out our life. So errors in transcription and splicing leads to multiple missexpression of genes which would further lead to cell, tissue and organs becoming impaired and diseased as we see with progressive aging. The authors also found that  calorie restriction and inhibition of IGF signaling led to slowing down of transcription speed and corresponding reduction in errors. This also extended their lifespan. Another finding shared by the authors was that overexpression of histones led to reduction transcription speed and increase in lifespan. Also the genes affected were not completely random, as they observed consistent changes across replicates for a subset of introns. As the speed increase in transcription and rise in errors in splicing are global and occur in all 

the 5 species including humans studied by the authors and they are not random one can conclude that these age related changes 
are encoded in our DNA deliberately causing the biological  deterioration we see during aging. 

 

Changes in plasma extracellular vesicles, volume and content, with aging

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5430958/

Cells release lipid-bound extracellular vesicles (EVs; exosomes, microvesicles and apoptotic bodies) containing proteins, lipids and RNAs into the circulation. Vesicles mediate intercellular communication between both neighboring and distant cells. Here the authors analyzed circulating plasma EVs in a cross-sectional and longitudinal study in order to address age-related changes in circulating EVs. They found that EV concentration decreases with advancing age. They also observed increased internalization of EVs by B cells which are immune cells. They found more tumorigenous surface proteins and cargo with age and also more misfolded proteins as cargo. Loss of proteostasis is also cited as a reason by the authors for the reduction of circulating secretome in aging. There are some papers that mention the opposite by showing how EVs increase with age. They cite increase in senescent cells and their EVs increasing the overall volume. But these are harmful EVs and carry cargo that leads to turning an healthy cell into a senescent cell a little like Zombies. That may not change the fact that secretome from healthy cells may decrease with age. 

Another paper: 

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7811845/

Sort of corroborates this. The same authors of the paper cited above Eitan et. al. state in this paper that

 They examined whether mtDNA (mitochondrial DNA) can be detected in human plasma EVs and whether mtDNA levels are altered with human age. They found that Plasma EV mtDNA was significantly and negatively associated with age in their cross‐sectional analyses. Basically mtDNA in EVs reduced with age. Did this have any consequences? To determine whether age‐related changes in plasma EV mtDNA affect mitochondrial function, they pooled EV populations of young and old EVs and measured the cell’s respiration rate. They found that cells treated with young EVs had significantly higher levels of both basal and maximal respiration compared to those cells treated with old EVs. So the reduction of mtDNA in EVs in aging did hamper mitochondrial functions. 

 

Longer transcripts decrease with age and shorter transcripts increase with age

https://www.nature.com/articles/s43587-022-00317-6

This has been one of the most interesting papers recently in the aging research field. Not only did they find that longer transcripts seem to fade away as we age and shorter transcripts seem to be of higher abundance but they also found the correlation of longest transcripts with pro-longevity genes and shortest transcripts with genes reported to shorten life. 

https://www.nature.com/articles/s41588-022-01279-6

This paper by Joris Pothof et.al. also finds in old mice (2year old) liver cells that there is 40% drop in transcription. This change was pronounced especially in longer transcripts. They did not find any changes or drops due to drop in promoter activity or drop in RNAP II activity. Even the launch of transcription was unaffected. They postulate that DNA breaks interrupted and stalled transcription – and as longer genes/transcripts have greater chances of being broken somewhere they can be the primary cause of their reduced transcription during aging. If we see the first listed change in aging in this post it is talking about rising Double Strand DNA breaks due to cell-free chromatin shards from dead cells which explains why the authors found a 40% drop in transcription. This may also explain what we read above where transcription errors increase with age. Breaks in DNA could stall transcription or create an error in transcription. 

 

 

The role of retrotransposable elements in aging

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8600649/

There is an on going war from 100s of thousands of years within us. It’s not just against outside pathogens and parasites but also against parasites that have virus like capabilities that have inserted in our genome – not just our genome but it seems in all living life forms-in a big way. These foreign invaders that have made our genome their permanent home since the dawn of life are called Transposons. Scarily they also have the ability to fly from one genomic location to another and insert themselves there. Transposons belong to two main groups: those that move using a DNA intermediate (‘DNA transposons’) in a ‘cut and paste’ mechanism, and retrotransposable elements (retrotransposons) that move using a ‘copy and paste’ mechanism that involves an RNA intermediate. Thirty five percent of the human genome is comprised of retrotransposon DNA sequence! Retrotransposons are further divided into Long Terminal Repeat (LTR) elements, derived from exogenous retrovirus infections, and more primitive and ancient non-LTR elements with an obligate intra-cellular life cycle. Non-LTR retrotransposons consist of two main groups: the Long INnterspersed Elements (LINEs), which encode their own proteins necessary for retrotransposition, and the Short INnterspersed Elements (SINEs), which are short, non-coding RNAs that hijack the LINE protein machinery. Our original genome continues to build tools and mechanisms to silence these elements and the transposons keep trying to outrun them. Both try to outsmart each other but also coexist and adapt from each other. A retrotransposon onslaught can be profoundly deleterious and hence the germline is guarded with multiple defenses. Host defenses are highly effective, and hence the majority of retrotransposons in our genome are passive passengers, slowly accumulating mutations, deletions or other rearrangements. While some older elements can still affect host function through cis-acting gene regulatory or recombinational mechanisms,  the deleterious effects of retrotransposons increasingly being linked with aging appear to be largely dependent on the activities of their encoded proteins, and fall into three general mechanisms: genetic and epigenetic effects associated with retrotransposition, DNA damage associated with active or abortive retrotransposition, and activation of immune pathways associated with detection of retrotransposon nucleic acids. One of the key defense mechanisms is heterochromatization which represses these elements. The other retrotransposon silencing mechanism is through methylation. Our genome has proteins that activate these repressive mechanisms on transposons. One example is KRAB domain containing Zinc Finger proteins or KZFPs. KZFPs, of which there are over 400 in the human genome, co-evolve with retrotransposons as part of an ongoing ‘arms race’. Many of these KZFPs bind to retrotransposon elements in the genome and promote their heterochromatinization via the recruitment of KAP1.  Retrotransposons mutate to avoid this surveillance, and the host organisms evolve variant KZFPs that can again repress the new generation of retrotransposons. Other such transposon surveillance and repression elements are siRNAs and piRNAs, we have CRISPR like RNA editing enzymes like APOBEC and ADAR, MOV10, BRCA1, SAMHD1 and TREX1. 

Some of these factors are defenses against exogenous viruses and act by diverse mechanisms such as editing of viral/retrotransposon genomes to mis-code the protein sequences (APOBEC), decreasing nucleotide triphosphate pools to limit viral/retrotransposon cDNA synthesis (SAMHD1) or degrading viral/retrotransposon nucleic acids (TREX1). These are our intelligent weapons to watch over and overpower transposons. As we read above aging is associated with loss of heterochromatin in various locations in the genome. Decreases of heterochromatin or heterochromatin-establishing factors contribute to elevated retrotransposon activity with age. Genetic interventions that promote heterochromatin formation and/or retrotransposon silencing, remarkably, can increase life span. Aging also sees loss of methylation which also derepresses transposons. Mobilisation of transposons can lead to genomic instability: if a transposon jumps into a functional (coding or regulatory) region of the genome, the insertion often results in loss of function, thereby, facilitating the death of the affected cell. The mass occurrence of transposition events can lead to various degenerative processes. Unwanted  activation of transposons in aging can lead to diseases even cancer. Their activation also led to immune response which is part of rise of chronic inflammation seen in aging. Studies suggest that retrotransposons causally contribute to the aging process, and that interventions that oppose retrotransposon activity might improve healthy longevity and lifespan. To quote the authors further: The most proximal approach to inhibiting retrotransposons would be to strengthen the epigenetic mechanisms responsible for their silencing, especially those that become compromised with age. One such epigenetic regulator is SIRT6. Male mice overexpressing SIRT6 show increased life span, which may be due in part to more efficient silencing of L1 elements and reduced inflammation. SIRT6 is involved in multiple processes which include DNA repair, telomere maintenance and metabolism. Small molecule activators of SIRT6 are being developed and may provide an array of health benefits, including improved retrotransposon silencing. Several experiments also show that that a key intervention already known to increase lifespan, a low-calorie diet, dramatically delays the onset of increased transposon activity.

 

 

 

The decline of the extracellular matrix begins just after puberty

https://karger.com/ger/article/66/3/266/148307/The-Matrisome-during-Aging-and-Longevity-A-Systems

 

We assume that ECM begins to deteriorate due to accumulation of AGE’s and cross linking of collagen over decades but actually ECM is deliberately hurtled towards destruction much earlier: During development and growth, cells constantly remodel the ECM by degrading parts of their ECM and through de novo synthesis of matrisome components in order to maintain homeostasis. This dynamic and energy-intensive process declines  after reproduction. Either because natural selection, as defined as reproductive fitness, is ineffective after reproduction, or because of a shift in resource allocation from somatic to germline tissue during the onset of reproduction. Irrespective of the etiology, this predicts that after reproduction the homeostasis of matrisome components, that is, de novo synthesis and ECM remodeling, would decline and should be reflected in the temporal change of matreotypes during aging. Thus, the matreotype of a young ECM is different compared to an old ECM. In this paper the authors also give  an explanation of the kind vicious cycle such early decline would lead to: During aging, either through collagen fragmentation or loss of adherence proteins,  cells detach from the ECM potentially leading to cell dysfunction and loss of ECM synthesis and turnover. In fact, the loss of ECM-to-cell connection might start a vicious downward spiral. For instance, during aging, there is an increase in activity of ECM-degrading enzymes, such as matrix metalloproteases (MMP). Increased MMP activity leads to collagen fragmentation, causing cell detachment, which leads to altered -integrin signaling and an increase in mitochondrial -reactive oxygen species, which in turn promotes the -expression of more MMPs, leading to further ECM fragmentation. 

So the aging program seems to select our most important components and systems for early start in deterioration -another example is 60% loss of heat shock protein chaperone support to protein product also happening just after puberty. ECM is as important as protein production because it makes up a staggering 50–70% of the human body mass and any change in that would be felt systemically. Another way to estimate importance of decline of ECM in aging is from this paper: 

https://www.aginganddisease.org/EN/10.14336/AD.2022.1116

The authors found that 12 most established longevity-promoting transcription factors (i.e., CREB1, FOXO1,3, GATA1,2,3,4, HIF1A, JUN, KLF4, MYC, NFE2L2/Nrf2, RELA/NF-κB, REST, STAT3,5A, and TP53/p53), directly and indirectly transcriptionally regulate ECM genes. 

Healthy cell-ECM crosstalk is vital for cellular homeostasis

Cells synthesize their own surrounding ECM. Each type of cell has its own unique type of EVM. Throughout the life of a cell there is constant cross talk with its ECM-in fact during aging when the damage to ECM is so great that a cell detached from it, which is called anoikis leading to the cell either dying or turning cancerous. A fascinating finding is that placing senescent cells or aged stem cells in a “younger ECM” has been shown to rejuvenate these old cells. The ECM provides instructive signals that change cellular function and identity. For instance, placing tumor cells into an embryonic ECM reprograms them to lose their tumorigenicity and become normal cells. Furthermore, the lost regenerative potential of old muscles is rejuvenated by grafting them into young, but not old hosts. And so a young and healthy ECM is vital for the survival of the cell it surrounds. During aging, components of the ECM become damaged through fragmentation, glycation, crosslinking, and accumulation of protein aggregation, all of which contribute to age-related pathologies. Since ECM is pervasive throughout our body it’s decline is linked to catastrophic tissue failure and multiple organ failure. ECM is a dynamic structure that is continuously built and remodeled but in aging Advanced Glycation End products that build up on the ECM blocking remodeling enzymes making it stiff. This leads to diseases like fibrosis seen in various organs like heart, lungs, kidneys, etc. So far it was believed that once formed AGEs can not be destroyed. But in 2020 Nam Y Kim et.al. published this paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6768434/

In which they shared about an altered enzyme and it’s variant were able to reverse AGEs. This is a great breakthrough and hopefully all types of AGEs can soon be eliminated. 

 

  

These are just a few of the thousands of changes occurring during aging. From this we can see why addressing one or a few of these changes will not be able to reverse aging. Only those interventions that work to reverse all these changes back to normal or youthful configuration can actually reverse aging. The entire universe is made up of only one building material: atoms. Atoms are incredibly mysterious full of magical forces but atomic, nuclear and quantum physics deserve a separate blog post. What is fascinating is what happened on Earth: these mystical atoms in different configurations formed molecules. From these molecules came living forms and their unit is cells. Cells are intricately beautiful with their components and engineering. Along with other tiny life forms like microbes and and another mysterious object: virus-it’s like a non-living zombie code that can jump from living cells to living cells housed in various bodies. Various collections have developed of these three to form a variety of life forms including us humans. Another principle of the universe seen in everything, living or inanimate, is recycling. May fly lives just 24 hours and our Sun 4.5 billion years but despite that difference both have one thing in common: both will perish and be recycled into something else. And there is black holes from which nothing seems to escape: the ultimate recycler of the known universe. On Earth cells have DNA and RNA which is DNA’s master and servant. But emerging evidence over the last few decades points to a recycling code embedded in the DNA which is altered due to various paths of adaptationary changes adopted by each life form or each unique collection of cells, microbes and viruses. No matter what alterations almost all seem to participate in the universal principle of recycling. In some life forms reproduction is asexual and automatic as part of their life journey. In other forms with higher intelligence where a factor of choice comes in reproduction is incentivized with pleasurable sensations. So the birth and death cycle continues millions of times. In life forms with even more complex engineering, like humans, we can witness an army of agents of time which chip away at a thousand different locations till one day the life form succumbs and dies. Our awareness of our biology is growing rapidly and every now and then we keep discovering another agent of time. Our gift from adaptions to survive is highest intelligence amongst all life forms on Earth due to which we have come to totally dominate Earth just like our predecessors the dinosaurs. This intelligence will also allow us at some point to synthesize our own adaptation to overpower these agents of time. We have the potential to become one of the first forms in the universe to bypass the principle of recycling at least from our own short recycling cycles. Although eventually one of the powerful forces of the universe would end our run. If we reach the point of immortality who knows we may get enough time to avoid or prevent total oblivion through interstellar travel and building our own defenses manipulating matter. Becoming biologically immortal is not such a big jump as we think now because as I have said in my previous posts there are complex life forms on Earth not gifted with our intelligence that have already achieved this by way of adaptation lottery win. So our intelligence will surely allow us to create indefinite lifespan in perpetual youthful homeostasis. We are going to build technologies which we can’t even imagine today. Tempted to throw in just one example of possibility: The virus that recently created a global epidemic is considered an enemy but we have the capability to turn an enemy into our greatest weapon. One song that all agents of time sing is dialing down of our amazing repair systems so imagine tiny nano robotized virus like codes that continuously repair damage as it occurs in our 30 trillion cells and their microenvironment. We can literally blow this virus from various points in a city to ensure everyone remains infected. The virus can be engineered to sit in a cell and get activated at any sign of damage and repair it. Similar virus can also be created to prevent or treat cancer our other great enemy. May be we can learn from cancer cell and reengineer it to make us young – after all a cancer cell makes itself immortal. It would be technologies we can’t even begin to comprehend now.