Time to read: 30 minutes
“DNA Design and Replication Simplified | Source of Digital Encoded In-formation | Simulation Hypothesis Revisited” by Jeffrey Thayer (August 2024)
First Principles:
IF we can now model DNA replification of 3 billion base pairs of each human; occurring millions of times each second; and IF … we can digitally simulate this process; THEN … what is the source of the in-formation in this intelligent design? … AT the beginning of life about 3.8 billion years ago? Did the intelligent designer require; at a minimum, the type of digital technologies we have developed in the past 50 years … but 3.8 billion years ago? And if we can simulate the codes of in-formation today, are we not simulating a small portion of a much greater Simulation in which we now live? After reading and digesting this article, please consider this question: What’s in it for our DNA? What is the intelligent design intention for it; for the “continuous” digital stream of encoded in-formation activating and animating DNA?
[NOTE TO READERS: The structure of this article, like other posts made by Change the Thoughts, is created from one video on DNA Replication embedded below; and a full TRANSCRIPT of the video beneath it. It is not simply a “transcript”; but I have taken the time to punctuate it with helpful graphics, and links to articles by other parties, which support and expand upon what is presented in the video. In [COMMENTS AND ANNOTATIONS], readers will discover much more information on the subject matter; all well documented by physicists and scientists in the field of synthetic biology, biochemistry, and holographic DNA.
ABSTRACT:
This article explores, in simple easy-to-understand terms, the biochemical foundation of life on Earth, specifically DNA replication. Yes! DNA is a helical polymer that stores information and instructions necessary for building proteins. It is also the basis for all growth, motion, and the entire business of life on Earth. A complex of around a dozen molecular processors work in perfect coordination to ensure that one set of DNA in one of trillions of cells can turn into two sets of DNA. This process occurs ahead of one small cell division happening all across the molecular landscape, millions of times every second.
DNA is also a sequence of letters, encoding information that cells used to build. The four DNA letters are adenine, guanine, thymine, and cytosine, which are similar in shape, allowing these bases to bond with each other. Understanding DNA replication can provide a profound understanding of one's place in the unbroken, 3.8 billion-year chain of life on Earth.
https://youtu.be/lv89fSt5jBY?feature=shared
If readers watch below the entirety of the video, they will know toward the end, the narrator mentions the phrase, I AM three times in a row. It may seem strange to hear that that phrase in a video describing DNA and digital biology. Although this article is not intended to be religious, nor dogmatic in any way, there is a context for the phrase I AM (as a verb, i.e a “process” and not a static or frozen noun) which at times is thematic in other articles posted by Change the Thoughts.
There is indeed a relationship, which is empirically proven in science, between the process of conscious thoughts; and our personal reality perceived. On an empiracal and deeper level, perception of the world by an individual cannot get much more real … than when perceptions are described by a thinker or speaker; and, when those perceptions are preceeded by the words I AM. Not only does I AM convey a sense of personal responsibility for what is perceived; but, it also reveals an ancient wisdom echoing down the halls of our common history.
The video below clearly demonstrates that DNA has a purpose, which has existed for at least 3.8 billion years; where, every second, every minute, and throughout one’s life, DNA demonstrates it’s continuous preprogrammed “choice” to replicate life at a molecular level with an accuracy, and pristine design, which is nothing short of profound.
In Proverbs 23.7, its author reveals a simple statement of reality. As a man thinks in his heart, so is he. That statement is expressed in the phrase: I AM; in both thought and speech; being followed by some “attribute” you either now embody or wish to embody. Furthermore, it is the same word, Moses uses; translated “life“ (Hebrew HYH hayah). It may answer also the questions posed above; as to the purpose of DNA; at the appearance of life on Earth through the very moment you are reading these words.
“11 For this commandment which I command thee this day, it is not hidden from thee, neither is it far off. 12 It is not in heaven, that thou shouldest say, Who shall go up for us to heaven, and bring it unto us, that we may hear it, and do it? 13 Neither is it beyond the sea, that thou shouldest say, Who shall go over the sea for us, and bring it unto us, that we may hear it, and do it? 14 But the word is very nigh unto thee, in thy mouth, and in thy heart, that thou mayest do it. 15 See I have set before thee this day life and good, and death and evil; … 19. I call heaven and earth to record this day against you, that I have set before you life and death, blessing and cursing: therefore choose life, that both thou and thy seed may live: …” (Deut. 30.11-15, 19, KJV) [Emphasis added.]
“That your seed may live” describes, in a short phrase, our intelligent designer’s intention for DNA replication … that is: reproducing life for gene-erations (hyphen added for emphasis).
Video title: Your Unstoppable Copy Machine｜DNA Replication
Video URL: https://youtu.be/lv89fSt5jBY?feature=shared
TRANSCRIPT EXCERPTS OF VIDEO WITH ANNOTATIONS AND COMMENTS:
“Okay. Quick question. How long have you been alive? And no, I'm not asking you how old you are. I want you to really think about this for a second.
“This is a video about you at the smallest scale. …”
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[COMMENTS AND ANNOTATIONS]:
“Smallest scale” means here “nano scale” and even smaller scales of atoms. What was known about “nano” scale biology in 2005 may surprise readers, as will the very clear unheeded warnings of many scientists reported in “NanoRX, The Big Downturn, Nanogeopolitics” by ETC GROUP. “The Big Downturn? Nanogeopolitics, ETC Group’s new 68-page report on global governance of nanoscale technologies, is an update of our 2005 Nanogeopolitics survey. In the intervening five years, policymakers – some kicking and screaming – have begun to acknowledge that fast-tracking nanotech has come at a price and that some sort of regulation is needed to deal with at least some of the risks nanoscale technologies pose. …Nanotechnology refers to the manipulation of matter on the scale of the nanometer (one billionth of a meter). Nanoscale science operates in the realm of single atoms and molecules. At present, commercial nanotechnology involves materials science (i.e. researchers have been able to make materials that are stronger and more durable by taking advantage of property changes that occur when substances are reduced to nanoscale dimensions). …”
https://etcgroup.org/sites/www.etcgroup.org/files/publication/pdf_file/nano_big4web.pdf
“What is Synthetic Biology? Engineering Life and Livelihood”. ETC GROUP: https://etcgroup.org/sites/www.etcgroup.org/files/files/synbio_comics-complete_letter_size_rev.pdf
Bioengineering Report over Seeds, Food, Health, Knowledge of the Earth by Navdanya International: https://navdanyainternational.org/wp-content/uploads/2020/10/GATES-TO-A-GLOBAL-EMPIRE-REPORT-SYNTHESIS-13.10.2020-3.pdf ]
Consider the following questions for a moment. If we recently discovered nanoscale materials and their properties, is it reasonable to conclude nano scale processes existed 3.8 billion years ago as part of intelligent design in the Simulation in which we observe? If not … then exactly WHAT are we simulating now?
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THE TRANSCRIPT CONTINUES:
“So my actual question here is how long have the processes that make you, you know, you been working when you come at this from the biochemical angle, the answer here can get a little hazy.
“This is your biochemical ground floor. Take the time to explore your DNA and pull apart the mechanics of DNA replication, and you'll come away with a pretty profound understanding of your place in this unbroken, 3.8 billion year chain of life on Earth.
“It's time to explore the eukaryotic rip Elysium, y'all. Let's get into it. And hey, welcome back to Clockwork. (Stories from cutting edge life sciences)
https://clockwork.beehiiv.com/
“This is the first episode in a long series where we'll explore your DNA and how it powers everything you do.
“And I guess we should start with the basics, right? So what even is DNA? This is deoxyribonucleic acid or, you know, DNA. This helical polymer is how your body stores information, all the instructions necessary to build.”
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[COMMENTS AND ANNOTATION]:
Its from bits. Physicist John Wheeler (1930’s)
“Researchers discovered that, unlike a classical computer that codes information as 0s and 1s, a brain cell uses 26 different ways to code its "bits." They calculated that the brain could store 1 petabyte (or a quadrillion bytes) of information.
"This is a real bombshell in the field of neuroscience," Terry Sejnowski, a biologist at the Salk Institute in La Jolla, California, said in a statement. "Our new measurements of the brain’s memory capacity increase conservative estimates by a factor of 10."
“What's more, the human braincan store this mind-boggling amount of information while sipping just enough power to run a dim light bulb. [Top 10 Mysteries of the Mind]
“By contrast, a computer with the same memory and processing power would require 1 gigawatt of power, or "basically a whole nuclear power station to run one computer that does what our 'computer' does with 20 watts, said study co-author Tom Bartol, a neuroscientist at the Salk Institute. …” https://www.livescience.com/53751-brain-could-store-internet.html
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TRANSCRIPT OF VIDEO CONTINUES.
“You live in your DNA. In order to carry out the business of keeping you alive, every single one of your cells needs to constantly synthesize proteins to do basically everything you need to do. … The instructions to build those proteins that lives in these DNA molecules, and we're not even going to cover how DNA does that work, right? We're not even leaving the ground floor here before your cells can carry out any of that work, your DNA needs to be copied first.
“Your cells are constantly growing and dividing to maintain … Well, you.
“And so each and every time one of your cells divides, your cells have to completely copy all 3 billion base pairs of your genetic information.
“That helical structure helps DNA become extremely stable, but it hides the true purpose of this polymer. If we unwind the strand, we'll see. DNA is real magic. DNA is a sequence of letters, like a sentence. These colorful bases encode information that your cells used to build. You know, you all the business of you being alive is hidden in these letters.”
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[COMMENTS AND ANNOTATIONS]:
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VIDEO TRANSCRIPT CONTINUES:
“What's really wild here is that you only get four letters to encode all that information, though your four DNA letters are adenine, guanine, thymine and cytosine. If you look carefully, you'll see that adenine and guanine are kind of similarly shaped with thymine and cytosine also looking kind of similar.”
“Principles of Linguistic-Wave Genetics” by Peter P. Gariaev*, Mark J. Friedman & Ekaterina A. Leonova-Gariaeva
“… To create an organism, two genetic programs are required. The first one is geometric, i.e. a scheme, how to design the body. The second program is in the form of a meaningful text which contains instructions and explanations how to use the first program, how to understand and build the organism. These programs exist in the form of "DNA video tapes", which are used by the genetic apparatus, acting like a bio-computer. When the bio-computer reads these video tapes, sound and light images appear that constitute the movie program of the development of the organism. When the creation of a grown-up organism is completed, the movie ends.
Then the second movie starts, which contains the instructions for maintenance of the organism for indefinitely long time. Unfortunately, the videotapes containing information about a perfectly healthy organism, get corrupted with time, errors accumulate (DNA mutations). The instructions accumulate errors and the organism gets sick, grows old and dies. It is very likely that these DNA video tapes can be renewed and corrected. With this new understanding of how our genetic apparatus works, completely new technologies for healing a person and extending a person"s life become feasible. And this is the essence of wave genetics and its practical applications to come.
See also: Institute of Linguistics of Wave Genetics: https://wavegenetics.org/en/issledovania/
DNA Decipher Journal papers by Peter Gariaev: https://dnadecipher.com/index.php/ddj/search/search?simpleQuery=gariaev&searchField=query
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Self Correcting Codes | Double Proof Reading | Why?
“DNA Proofreading, Correcting Mutations during Replication, Cellullar Self Directed Engineering” by John D. Lieff, MD (2012)
“… To pass on the code of life to the next cell, DNA copies itself. This process is called replication. Much is made of the mutations, or errors in DNA replication. Evolutionary theory relies in part on these mutations to explain the development of the dramatic diversity of nature; however, what is most dramatic about DNA is not its errors but its accuracy. Many levels of proofreading and error correction ensure near-perfect fidelity in replication.
Current theory suggests DNA somehow directs the entire replication process, perhaps through RNA messages. But, since there is editing and error correction involving the DNA itself, it is hard to imagine exactly how this is done. Regulation for these processes is massively complex; currently, there is no obvious source of direction.
DNA Errors and Proofreading
During replication, nucleotides, which compose DNA, are copied. When E coli makes a copy of its DNA, it makes approximately one mistake for every billion new nucleotides. It can copy about 2000 letters per second, finishing the entire replication process in less than an hour. Compared to human engineering, this error rate is amazingly low. E coli makes so few errors because DNA is proofread in multiple ways.
An enzyme, DNA polymerase, moves along the DNA strands to start copying the code from each strand of DNA. This process has an error rate of about one in 100,000: rather high. When an error occurs, though, DNA polymerase senses the irregularity as a distortion of the new DNA’s structure, and stops what it is doing. How a protein can sense this is not clear.
A Second Round of Proofreading
There are still some errors, however, that escape the previous mechanism. For those, three other complex proteins go over the newly copied DNA sequence. The first protein, called MutS (for mutator), senses a distortion in the helix shape of the new DNA and binds to the region with the mistaken nucleotides. The second protein, MutL, senses that its brother S is attached and brings a third protein over and attaches the two. The third molecule actually cuts the mistake on both sides. The three proteins then tag the incorrect section with a methyl group.
Meanwhile, another partial strand of DNA is being created for the region in question, and another set of proteins cut out the exact amount of DNA needed to fill the gap. With both the mistaken piece and newly minted correct piece present, yet another protein determines which is the correct one by way of the methyl tag. That is, the correct one does not have the methyl tag on it. This new, correct section is then brought over and added to the original DNA strand.
This second proofreading is itself 99% efficient and increases the overall accuracy of replication by another 100 times. …”
See also: Quantum Rainbow Codes
Thomas R. Scruby,1, ∗ Arthur Pesah,2, † and Mark Webster.
https://arxiv.org/pdf/2408.13130
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THE TRANSCRIPT CONTINUES:
“… These shapes make it so that these bases can bond with each other.
“Adenine can always stick to thymine, and it turns out that guanine can only stick decidedly. It's always a short letter bonded to a long letter. And, you know, wow, there's some great symmetry here. Actually, if you clean these shapes up a little bit, you might have yourself a pretty solid logo, maybe something to stick on, a hat or a shirt or something. Make a whole identity out of it. I don't know.
Anyway. Let's zoom in on adenine to look at how this chain gets built. Adenine is held on to the DNA strand by this little ribose sugar, and this phosphate group on the back end. Because of that shape, new letters can get stacked on top of DNA in a linear sequence. The real super power here lies in how these letters always pair off. Since each letter only binds to one other letter, you can split these strands apart, add new nucleotides, and have two identical copies of your DNA with no errors. This is one of those little perfections in life.
DNA is fine tuned specifically to be copied.”
“That’s where we are now, at the phase of cell division, where it's time to copy your DNA and get ready for some good old fashioned mitosis. So this is happening inside you at every level effectively millions of times a day. Like I can practically pick a spot at random here and catch a cell in s phase. So let's meet our machines.
How on earth can we copy the roughly 3 billion letters in each copy of your DNA at a time? It comes down to this incredible complex of molecular machines working together with incredible speed and accuracy. This is your replica home, one of the most foundational and most powerful forces of nature.
This thing looks like a beast, but we can assemble this thing one piece at a time and get a pretty solid understanding of how this all works. So let's just go ahead and jump in. At the moment your cell kicks off replication, it'll assemble the first piece of your realism right on this DNA strand. This is CMG helicase, a brilliant little motor that unwinds your DNA. Up top here, we've got timeless Tippin and Claspin, which appear to help guide the parent DNA strand into the CMG helicase to help speed up the rate of replication. Once these are built, support structures like agains get attached to the CMG helicase. These stabilize the motor and actually kickstart the whole thing, letting it start pulling your DNA apart.
“If we go down to the business end of CMG, we can see kind of how one half of the parent's DNA strand is getting blocked from entering helicase while the other one gets continuously pulled down. Over here is the lagging strand of your DNA. We'll get back to this complicated little goofus in a second. If we move down to the core of helicase, we can see how this little motor works. Its magic helicase is constantly using these little arms to walk this single strand of DNA down through the motor.
“And by the way, this strand also has a label. This is your leading strand of DNA. But if, like the DNA strands are complementary, why do we even bother with a distinction between the leading and lagging strands? You know what that's called?
Foreshadowing, folks. For now, we're going to follow the leading strand down through helicase to its next stop, and eukaryotes like us, the leading strand is pulled all the way down through helicase.
“And then based on our current understanding of realism structures, has a surprisingly long distance to travel before it hits the real business end of DNA replication. Down here is DNA polymerase one other one of the most powerful forces in all of nature.
“Specifically, though this is DNA polymerase epsilon. In school, you might have learned about DNA polymerase as a single enzyme.
“… And eukaryotes, we love making things just a little more complicated. We've got three DNA polymerase variants all working together to copy this genome, at least at the first stage. There's actually kind of a lot of DNA polymerases. And we're going to cover all of them. Across the course of this playlist, DNA polymerase epsilon works exclusively on the leading strand and is where we're going to learn about the magic of DNA replication. As the leading strand is wound down here, it's going to come in contact with poly right in front of poly is our PKA sliding clamp. Basically, when DNA replication gets kicked off, PC clamps onto the DNA strand right in front of poly to help hold everything together. But let's move back to Pol E's active site and check out how this DNA print actually happens. If I turn DNA polymerase on its side, you see, it's got this U shape that perfectly fits DNA. But the main thing to keep in mind is that polymerase holds on to DNA in the exact right position to allow a complementary nucleotide to bind to the template strand. This little hole back here is a tunnel that only the next correct letter in a DNA sequence can fit through and watch carefully. Low nucleotides are a little bit different before they get attached to the DNA. Instead of just one phosphate on their backbone, these letters actually have three phosphates as they come in contact with their complement letter on the other side of the chain, the other two phosphates will pop off, securing this letter onto the growing DNA strand. Breaking these two phosphate bonds releases a ton of energy, which helps push the whole polymerization process along. And you know, if that sounds familiar, well, it should. I mean, just check back with adenine over here. Adenine plus two extra phosphates is just adenosine triphosphate. You know, ATP the energy currency that your body uses to power literally everything you do. Your body literally repurposes DNA letters to move energy around your cells. I just love that little bit of symmetry. Nothing goes to waste inside your cellular landscape. Heck, even guanine gets in on the action by being an important energy carrier for transmitting signals around your cells. But that's something we need to save for another video. And for the leading strand, that's pretty much it. And that’s all that really happens here. DNA printer go. No drama. Awesome. Technically, though, we're in the middle of the replication process, and at the very start, this leading strand needed to have an RNA primer attached to it. So that pole E had something to latch onto and extend. But we're about to see that play out like dozens of times with the lagging strand. So we don't need to talk about it right now.
“Instead, let's buckle up and talk about how this gets super complicated. The way this replication fork is oriented is perfectly tuned for the leading strand. Just feed more DNA in and pull. You can just churn out more nucleotides with blazing speed. And so like the lagging strand, I mean, we're just adding more DNA letters onto it as well, right?
“Why have I been like foreshadowing how complicated this is? Let's go ahead and go back to our original models we used to show how new letters get added on to a DNA molecule. Like I said, it's super easy for DNA to polymerize just to get the backbone sugars in contact and boom, they bind. Easy. But what if I try to add new nucleotides from the other direction? They're not going to attach. Remember, we need to break those two phosphate bonds to power this reaction. So in a way, the opposite end of this rung is the glue we need to polymerize DNA.
These letters have glue only on one side. You can't just flip it around and attach from the other side, which means the DNA can only be built in one direction. That's why each end of the DNA molecule has a label. This side is the five prime, and that's the three prime end.
DNA can only be synthesized from the five prime to the three prime direction. Are you starting to see the problem? We can only build DNA in one direction, but these two DNA strands flow in opposite directions.
So to bring this all together, the helix is moving the red blossom along this DNA strand from the three prime to the five prime end. This is great for poly right because the DNA is flowing in the right direction for them. They're just going to keep churning out new DNA with no drama. However, up here the lagging strand is basically moving backwards entirely in the wrong direction. The blossom is pretty clever here. We can get around this catastrophic misalignment. We're just going to build the lagging strand in fragments. So let's just get into it as the lagging strand gets kicked out of helicase.
“So it's going to hit this beautiful subunit called the primer zone. This is technically two different molecular processors. We've got primase over here. And DNA polymerase alpha right here. Like I said before, we can't synthesize new DNA without something for the polymerase to hook onto.
“That's what the primer zone builds. The prime example. We need to do this one time on the leading strand, but it has to continuously do so on the lagging strand. Every 200 nucleotides, give or take.
“The process is pretty wild here, and I am shaving a bunch of details off to keep this video from going on way too long. But basically, as the lagging strand exits helicase, it will run right into the business end of primase. Primary superglue eight small ten letter RNA primer onto the lagging strand and then disengage, allowing polymerase alpha to swoop in and extend this primer by about 20 more letters before it, too, pops off.
“So after the primeism does its business, this little section is going to spool out about 200 nucleotides downstream from the replace zone before our final contributor shows up. This is polymerase delta, the lone wolf DNA replicator. Poldy is loaded onto the lagging strand one primer at a time, synthesizing the lagging strand in the correct direction until it hits the next primer, and then it gets disengaged, allowing this cycle to repeat for each little fragment of the lagging strand.
“And if we take a deep breath and pull back, we can see this whole process in action. The leading strand is synthesized in one fluid reaction. While we have all this machinery over here to put the lagging strand together 200 letters at a time. What we're left with is a complete and accurate copy of your genome. And if this feels exhausting, no big deal.
“This only happens every time your cells divide, which means it's happened in your body about 20 billion times over the course of this video alone.
You know, give or take a few billion, given your age and whatever. And incredibly, this all happens with very few mistakes, all in perfect time with the rest of your cellular growth processes. It is so small, yet such a staggeringly large process. And that's what I want you to think about. This little loop has played out endlessly across all your cells, every single microsecond that you've been alive. But the question is, when did it start? Or maybe a better way of thinking about it ois does it ever stop?
“And that's really the question I want you to ask now that we're thinking at the biochemical level, because the argument I want to make here is a bit of a reach. How long have you been alive?
When did your DNA start replicating? Well, I mean, replication can pause depending on what's going on in the cell cycle, but as long as you're alive, it never actually stops. Right? This replication process is genuinely endless, and this very physical process happening in you right now has been going on for way longer than you've been alive. Everything else on this channel, every other part of biochemistry, is just a way to help keep this story, this DNA replication process, going. And if you really think about the totality of it, let your mind reach out and try to connect to the actual scale of what the endlessness of DNA replication means. Your DNA dividing right now and just the latest iteration of a story and a process that has gone on unbroken for a single instant for nearly 4 billion years. And sure, maybe you can push back and say that your initial set of DNA was created whole cloth from your parents, but in reality, you got two sets of chromosomes from your parents that were created through a process similar to DNA replication.
“We think about DNA in the abstract so much that we forget it's a physical object, the DNA that eventually became you was replicated and then stood waiting until the moment that it combined and, you know, began process that is now you. It is still a part of this nearly endless chain of DNA replication going back all the way to the dawn of time. DNA replication pauses, but it has never stopped.
“You are not separate from the whole history of life on Earth. 3.8 billion years ago. Somehow, this process appeared on Earth and DNA started replicating itself, and it has never stopped. If you understand all the ins and outs of DNA replication, it gives you a little window into your billion year history. You aren't an island.
“You're the latest link in an unbroken chain that reaches back across the whole history of life on Earth. There is a tangible line that connects you. Watching this video all the way back to the very first time the original cells started replicating their genes at the very dawn of life on Earth. You're standing on top of a foundation billions of years in the making, and all the while, your replica homes are dutifully copying your DNA and a constant chemical little mantra your cells copying your code over and over again, constantly whispering all over you I am, I am, I am, I am, I am, I am, and so you are. There's so much more to explore here.
“We haven't even scratched the surface of how your DNA powers the work of keeping you alive. But this is a good foundation to stand on for now. I really appreciate your time. Thank you so much for watching. And again, thank you so much for watching. If you liked this video, please consider subscribing to this channel. I'd also appreciate it if you check us out over at Watch clockwork.com, or over at our Patreon as well. Find all those links in the bio below. Feel free to sign up for our newsletter, which is going to be a weekly exploration of all the biggest news in biochemistry that honestly helps the channel quite a lot. Either way, we've got new episodes on the way monthly for now, but we're slowly ramping up with our new style. If you like the new style of Clockwork videos, if you like us going 3D, please leave a comment. I really appreciate any feedback you have. Otherwise I really appreciate your time and as always, we like to leave you with peace, love and nucleoside triphosphate. Everyone be well. Thank you so much.
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