The Fountain of Youth
The Fountain of Youth
In this rabbit hole, we learn how our DNA replaces all the atoms in our bodies every 12 months. So our “hardware” never ages, only our “software”. Now that we have the technology to edit our own source code, future generations will live indefinitely. 😳
This story is part 2 of “The BioLogical Robot”. In part 1, we learned that our DNA software is mirrored for redundancy and duplicated for performance. We can still make proteins from either of our parents at any time. Our DNA software is stored in chromosomes, which use physical encryption to protect our source code. They constantly spool and unspool the DNA tape only where it needs to be read. We also learned that our DNA software is packaged into genes that work in bacteria, plants, animals, and aliens.
At the end of part 1, we learned that some of our genes have a 0.00% mutation rate in 1,000 million years. So if you believe in Darwinian Evolution, you may be surprised to learn that some segments of our DNA have never mutated. Ever. But just as surprising, other segments of our DNA will perpetually mutate throughout our lifetimes to better fit us into our environments.
Computer scientists have a similar process for updating software while it’s running called Runtime Patching. There are so many things that can go wrong when runtime patching, that software designers generally avoid it at all costs. If even a single bit gets corrupted, it can sometimes crash the entire machine.
Runtime Patching DNA
There are several ways that our DNA modifies itself during our lifetimes. The simplest method is Horizontal Gene Transfer (HGT). Our chromosomes not only acquire genes from our parents, but they can also download genes from any foreign invaders they encounter. Bet you didn’t learn that in high school Biology.
Horizontal Gene Transfer is the most prolific source of mutation in bacteria. When a larger bacteria eats a smaller bacteria, they try out its software. This is another reason Darwinian Evolution doesn’t make sense. If bacteria mutate aggressively while they are alive, and they have the shortest lifespans to increase their rate of natural selection, then why are they at the bottom of life’s hierarchy? E. coli bacteria can divide every 20 mins. Why don’t they ever evolve into anything else?
HGT isn’t as common in animals, but there are plenty of examples of bacteria-to-bacteria HGT, bacteria-to-animal HGT, and animal-to-animal HGT. To learn more, check out “Horizontal gene transfer between bacteria and animals”.
Our ability to download new genes is incredible, but it creates vulnerabilities in our design. Geneticists have determined that roughly 1% of our DNA is actually viruses, called Human Endogenous Retroviruses. Viruses are just strings of RNA, floating around the universe, looking for “protein factories” to hijack. Retroviruses come with a special Reverse Transcriptase protein that can insert their RNA into another organism's DNA, just like a computer worm.
However, when we take a closer look at the Human Endogenous Retroviruses, not all of them are “infections”. Check out this quote from the National Institute of Health,
Over 20 HERV families have been identified during the past two decades. Although many are defective through the accumulation of mutations, deletions, and termination signals within coding sequences, a limited number of HERVs have the potential to produce viral products and, indeed, to produce viral-like particles.
As a computer scientist looking at DNA as software, these code snippets with “deletions and termination signals within coding sequences” sound just like Antivirus Software. For example, if we looked at the machine code of Norton Antivirus in a text editor, we would see sequences of code from the StuxNet computer virus. But that doesn’t mean Norton Antivirus is infected with StuxNet. Norton retains bits and pieces of StuxNet to quickly identify and kill the virus on sight in the future.
The mRNA vaccine from Moderna works the exact same way. Their mRNA platform manufactures a synthetic RNA sequence for just the “protein spike” of the COVID-19 virus. Our immune systems “train” on this data to quickly identify and kill the virus on sight in the future.
This is where the line between biology and computer science really begins to blur. When COVID-19 was first sequenced, geneticists from the World Health Organization sent the RNA sequence to Moderna in Microsoft Word. I received the Moderna vaccination, so that means somewhere inside of me is DNA source code that was originally copy pasted from an email.
Error Correcting Memory
So our DNA deliberately mutates through horizontal gene transfers and viral attacks, but it also mutates by accident. Occasionally extra nucleotides get inserted or deleted from DNA sequences during replication. Geneticists call this “strand slippage”. Our DNA software uses a process known as Mismatch Repair (MMR) to prevent these mistakes. Here is a diagram from Khan Academy to explain how MMR works.
Kudos to Khan Academy for making this look simple, because the MMR system is incredibly sophisticated. It has to be. Our very lives depend on it. Every minute, our bodies have 10 million cells individually replicating 3 billion letters. If even just 1 of those 30 quadrillion letters is wrong, it causes us to age.
Every time a cell makes a mistake, its daughter cell will lose some ability, which is called Cell Senescence. When enough of these errors accumulate, they cause Cancer. This is another reason Darwinian Evolution doesn’t make any sense—our DNA is disintegrating, not integrating.
@mathnerds: Here is a video that discusses why our lifespans have decreased so rapidly since the first two humans were spawned on this planet. If you plot the lifespans of people in the Old Testament, each data point fits a power law curve with an R-squared of 0.9537, meaning 95% of the datapoints fit the curve. If the Bible was made up, then those ancient scribes had some next level understanding of logarithms.
The genetic bottleneck after the global flood caused our mutations to exponentially increase, which caused our lifespans to exponentially decrease—perfectly following a biological decay curve. So again, our DNA is disintegrating, not integrating. (7 mins)
Here is a quote from Cell Research magazine to explain the role of the MMR system in preventing cancer:
MMR corrects DNA mismatches generated during DNA replication, thereby preventing mutations from becoming permanent in dividing cells. Because MMR reduces the number of replication-associated errors, defects in MMR increase the spontaneous mutation rate. Inactivation of MMR in human cells is associated with hereditary and sporadic human cancers, and the MMR system is required for cell cycle arrest and/or programmed cell death in response to certain types of DNA damage. Thus, MMR plays a role in the DNA damage response pathway that eliminates severely damaged cells and prevents both mutagenesis in the short term and tumorigenesis in the long term.
So whenever our cells have defects, the MMR system sends them instructions to commit suicide. This is known as apoptosis, or Programmed Cell Death. In the average adult, 50 to 70 billion cells commit suicide every single day to keep us healthy. The contents of these cells are swallowed up by our immune systems, chopped up for parts, and then reused by other cells looking to replicate their stronger DNA.
Failures of the MMR system are the single largest cause of all cancers. If you want to learn more about MMR, checkout “Role of DNA Mismatch Repair Defects in the Pathogenesis of Human Cancer” from the Journal of Clinical Oncology.
Remember, 98% of the atoms in your body right now are less than 12 months old. That means 98% of your body was regenerated by fresh copies of your DNA within the last year. So whatever you eat in the next 12 months will contain the atoms that WILL BE YOU one year from now.
In Vivo Evolution
The genes that continuously regenerate our bodies are called “Protein Coding Genes”. Surprisingly, they only make up about 3% of our genome. For decades, geneticists called the rest of our genome “Junk DNA”, but we now have modern evidence that it’s not so junky after all. Check out this quote from Medical News Magazine,
In a Nature review published in the 1980, Leslie Orgel and Francis Crick stated that junk DNA ‘had little specificity and conveys little or no selective advantage to the organism’. However, over the years, researchers have found evidence to suggest that junk DNA may provide some form of functional activity. Some lines of evidence suggest that fragments of what were originally nonfunctional DNA have undergone the process of exaptation throughout evolution. Exaptation refers to the acquisition of a function through means other than natural selection. In 2012, a research program called the ENCODE project concluded that around three quarters of the noncoding DNA in the human genome did undergo transcription and that almost 50% of the genome was available to the proteins involved in genetic regulation such as transcription factors.
What this means is more than half our genome is dedicated to making logical decisions about how each cell should respond to its environment, including which combination of proteins to make. The reason our junk DNA gains function “through means other than natural selection” is because our DNA edits itself. Yes, our DNA constantly reconfigures itself using transposons, or “Jumping Genes”, to better fit us into our environments.
To understand how this works, let’s start at the beginning. You, me and everyone we know began as an Ovum, or egg cell, inside our mothers. To create a person, the ovum must encounter a sperm cell to become a zygote. A Zygote is a single living cell that contains the original diploid DNA source code donated from each parent. A zygote is the only time a human being is in “mint condition”.
When a zygote begins interacting with the universe, it immediately gets smarter. Its DNA might download foreign genes living within the mother, it might get hacked by RNA worms, and it will definitely update its own source code to improve cell regulation. Geneticists have detected transposing jumping genes in embryos as young as 5 days old.
Eventually, when the zygote is ready to divide, its DNA software undergoes a process that computer programmers call a “Project Fork”. Here’s Wiki to explain.
In software engineering, a project fork happens when developers take a copy of source code from one software package and start independent development on it, creating a distinct and separate piece of software. The term often implies not merely a development branch, but also a split in the developer community; as such, it is a form of schism. Grounds for forking are varying user preferences and stagnated or discontinued development of the original software.
All 37 trillion cells in your body forked from code, that forked from code, that forked from code, that forked from your original zygote and none of those forks are by mistake. The best reason to constantly fork software like this is to A/B test its performance. Software engineers do this all the time. For example, the Facebook app on your phone doesn’t just have source code to make the little navigation bar along the bottom of your screen. The Facebook app has source code to create 60 different versions of that little navigation bar, and they live test which versions are the best performers ON YOU. Whichever version you have, is the one that makes you do what they want you to do the most.
It might seem weird that all the DNA in your body doesn’t match at the same time, but it doesn’t. There’s a chance that some of your DNA didn’t even come from you at all. Here is a fascinating story in Time magazine about a dad who is actually his own kid’s uncle. Using the miracle of modern genetics, this dad learned he suffered from vanishing twin syndrome. 10% of the sperm he produces today actually carries the DNA of his twin brother who was cannibalized in utero. The attacking DNA never quite finished the job because the dead twin not only lives on inside him, it reproduced a new human. This dad only shares 25% of his genes with his own son.
In Vivo Natural Selection
With billions of DNA variations to manage, the decisions of the MMR system are critically important to our health. The MMR system decides which of our DNA variations live and which of our DNA variations die.
The best example of this are the egg cells in women. Check out this quote from the book “Genome: The Autobiography of a Species in 23 Chapters” by Matt Ridley. He writes,
In the ovary of a five-month-old human fetus, for example, there are nearly seven million germ cells. By birth, there are only two million, and of those two million, just 400 or so will be ovulated during the coming lifetime. Most of the rest will be culled by apoptosis, which is ruthlessly eugenic, issuing strict orders to cells that are not perfect to commit suicide (the body is a totalitarian place).
So the MMR system culls 5 million eggs from each female fetus before they are born. That’s crazy. The culling within our bodies also takes place in our brains. Ridley writes,
The brain is born with far too many connections between cells; many are lost as it develops. For example, at first each side of the visual cortex is connected to one half of the input from both eyes. Only by fairly drastic pruning does this change so that one slice of the brain receives input from the right eye and another slice receives input from the left eye. Experience causes the unnecessary connections to wither away and thereby turns the brain from a general to a specific device. Like a sculptor chipping away at a block of marble to find the human form within, so the environment strips away the surplus neurons to sharpen the skills of the brain. In a blind, or permanently blindfolded young mammal, this sorting out never happens.
This is yet another reason why Darwinian Evolution doesn’t fit the evidence. Mutation and natural selection are not happening between generations by accident. Mutation and natural selection are happening on the cellular level every day on purpose because our DNA was designed to A/B tests its own source code continuously. When the MMR System works perfectly, it culls underperforming DNA from our “software repository”, which allows us to become perpetually fitter to our environment indefinitely.
In Vivo Forever
This is why most longevity research is focused on the MMR system. At the forefront of longevity research is David Sinclair and his Information Theory of Aging. Sinclair’s theory, like many others in this book, is built upon Information Theory by Claude Shannon. He explains it all in his book, “Lifespan: Why We Age and Why We Don't Have To”.
Sinclair summarizes his longevity research in this TED Talk, “Is Aging Reversible?”. (15 mins)
Here is a more in-depth interview with Dr. Lee Hood, MD, PhD. (71 mins)
Here are a few of Dr. Hood’s notes from the conversation:
Sinclair asserts that the replicating efficiency of DNA codes degenerates over time as “noise” enters the system. This noise leads to “breaks” in DNA sequences. It is these breaks in DNA sequences, not the DNA itself, that cause aging.
Degeneration occurs in “reader” cells: Genes and their epigenetic expression propel cell development and differentiation. The body contains two basic types of cells. The first type contains each individual’s genetic data or DNA. The second type reads and directs DNA application. Throughout the translation process, the archival DNA copies remain pristine, but the “reader” cells degrade over time from the signaling noise described above. Sinclair equates these degenerating DNA “reader” cells to “scratched CDs” that don’t play music as well as they once did. Fix the “scratches” and aging slows.
Aging is a disease: Sinclair’s research suggests that these “scratched” reader cells are treatable. From a medical perspective, he believes it is easier to slow or even reverse cell degeneration (i.e., aging) than to treat many forms of cancer. If true, this represents a monumental shift in medical reasoning. Aging causes 85% of all human suffering, including most major diseases. The ability to treat aging as a disease and slow its detrimental impacts has the potential to extend healthy human life well into the 100s.
Practical advice: Throughout the discussion, and especially during the audience Q&A segment, Sinclair discussed his own strategies for managing his immune system and extending his lifespan. They include eating one meal a day, exercising big muscle groups and taking supplements to enhance his longevity genes. These supplements include metformin, rapamycin and resveratrol. It’s never too late to start combating aging. Upon retirement, Sinclair’s 81-year-old father changed lifestyle behaviors and now is in better shape than Sinclair himself.
What's fascinating about David Sinclair’s research is that his team can artificially age a living mouse by introducing intentional errors during DNA replication. These young mice get fat, slow down, and their hair turns gray just like the rest of us. More importantly, his team can reverse age a living mouse by “polishing out the scratches” in its DNA record with a process called DNA methylation. All the information we need to stay alive forever is already present in our DNA. David Sinclair argues that we’ll cure cancer as a by-product of curing aging itself. With improved DNA methylation and MMR management, future generations of people will finally drink from the fountain of youth.
@americans: When we eliminate aging, we will eliminate one of the strongest certainties of our world. Benjamin Franklin 🤩 once wrote,
Our new Constitution is now established, everything seems to promise it will be durable; but, in this world, nothing is certain except death and taxes.
Well I’m not certain death is going to be around much longer. We’ll have to update his famous quote to,
Our old Constitution is still established, everything but social media seems to promise it will be durable; but, in this world, nothing is certain except uncertainty and taxes.
Taxes aren’t going anywhere, taxes are way more certain than death. Even if there were only two humans left on this planet, the weaker one would get taxed.
@biologists: The core of biology is digital, Matt Ridley said it himself. Richard Dawkins agrees. Humans are artificial intelligence, not accidental intelligence, which is why Darwinian Evolution doesn’t fit any of the evidence in our DNA. How can you believe in Darwinian Evolution and the Information Theory of Aging at the same time? Our random source code randomly assembled to randomly live forever through the process of selectively dying?
Darwinian Evolution annoys me more as a computer scientist than it does as a Christian. It makes no sense. For more scientific evidence that contradicts Darwinian Evolution, read:
@computerscientists: Just imagine designing software to produce artificial general intelligence that is as sophisticated as our DNA . What does that teach you about the mind of “He Who Programs in DNA”?
@christians: There’s a very important reason why the Messiah had to be born from a virgin—his DNA is different than ours. It’s uncorrupted, which is why Paul calls Jesus “the second Adam” in 1 Corinthians 15.
If you want to learn more about DNA, checkout the book, “Traced: Human DNA’s Big Surprise” by Nathaniel Jeanson. He used Y-chromosomal DNA to trace every man alive today back to one man, Noah.
In Vivo Software Upgrades
Remember earlier, when I joked about Moderna updating my DNA source code from Microsoft Word? Well DNA editing is about to get a whole lot crazier using CRISPR based gene repair.
@chatGPT: How does crispr work in less than 100 words?
CRISPR works by utilizing a guide RNA (gRNA) that is designed to match a specific DNA sequence within the genome. The gRNA directs the Cas9 enzyme to the target sequence. Once the Cas9 enzyme binds to the DNA, it makes a precise cut, creating a double-strand break. The cell then attempts to repair the break, allowing for the insertion, deletion, or modification of genes. This system enables highly specific and efficient gene editing for research, therapeutic, and biotechnological applications.
This technology is mind boggling. Here is the Ted Talk from one of its inventors, Jennifer Doudna. (16 mins)
And here is her follow up 8 years later. Evidentially biologists can now gene edit our entire microbiomes, which is bonkers. (7 mins)
CRISPR enables scientists to reprogram our DNA just like a computer, which allows them to cure incurable diseases. The first notable example of this was Sickle Cell Anemia, which is caused by a single letter mutation in the gene for hemoglobin.
Patient zero for this cure was a woman named Victoria Gray. Geneticists took out some of her stem cells, edited them with CRISPR, and then basically gave her a bone marrow transplant with herself to propagate the change. Over the next 12 months, she naturally replaced all the atoms in her body, so today there are no more sickle cells in her blood. Here is a video to learn more about this revolutionary moment in history. (14 mins)
Millions of people will upgrade their DNA in the future. In ten years, changing the color of your eyes, growing full lips, or switching to thick curly hair might just be a CRISPR shot in the arm. All we’ll have to do is wait 12 months for our DNA to replace all the atoms in our bodies. You know those people who are addicted to cosmetic surgery? Well they will be even more addicted to Cosmetic DNA.
How many future NBA hopefuls will upgrade their DNA software to become Shaquille O’Neal’s size? They might even be able to license Shaq’s DNA to do it. Corporations like Monsanto are already copyrighting and licensing DNA for fruits and vegetables that “outperform” their wild counterparts.
As crazy as this sounds, the world may eventually be full of augmented mutants like the X-Men movies because of two key inventions.
The first is the desktop DNA printer, which produces synthetic genes of any kind using nucleotide reagents as the “printer ink”. The genes that grow wings on birds and gills on fish will work in humans and every other animal. So now everyone from scientists to terrorists can try out whatever DNA sequences they want. Here is a photo of what desktop DNA printers look like today:
The second breakthrough technology is DeepMind’s artificial intelligence program, AlphaFold. Knowing a protein’s 3D structure tells us a lot about what it does and how it works. It has taken 60 years for scientists and drug companies to identify the 3D structure of 170,000 different proteins, but it only took AlphaFold a year to identify the 3D structure of the remaining 200 million proteins known to nature in all forms of life. DeepMind has open sourced these structures for the betterment of mankind. To learn more, here is a TED interview about AlphaFold with DeepMind founder, Demis Hassabis. (26 mins)
Continue reading…
Table of Contents
HUGE THANKS 🙏
to the sponsors of this story. Your support helps us reach new academics, scholars, and scientists all around the world.
If this story was helpful to you, please consider supporting our foundation. All your gifts are tax deductible.
Help us improve this story. Send me an email or leave a comment.
What did you love the most?
What did you hate the most?
What surprised you the most?
What confused you the most?
