Nanobots and Microbots

@midjourneybot: /imagine: a human cell with all the organs inside drawn as cartoons

Nanobots and Microbots

In this chapter, “The BioLogical Robot”, we are exploring the technology inside our own body to decide if humans are either Accidental Intelligence or Artificial Intelligence. Are we this way from random mutations after a cosmic explosion, or are we this way because we were designed by “He Who Programs in DNA”? 🤔

In the first essay, "DNA Tape Drives”, we looked at the sophistication of our DNA Storage. The “software” that makes a human is stored on “tape drives” in each cell of our body that can make decisions and make proteins from either of our parents. DNA also has a second form of redundancy, the double helix, which ensures that our “DNA Reader” can reconstitute damaged DNA. We also learned that the DNA that makes the “spools” to hold our DNA tape haven’t mutated even 1 letter in 1,000 million years.

In the second essay of this chapter, “Micro Deaths Create Eternal Life”, we plunged further into the Mismatch Repair (MMR) System that repairs damaged DNA. We learned several reasons the MMR System chooses suicide, or “programmed cell death”, for the variations of our DNA software that is underperforming. Most of our cells die this way. Our cells die from programmed cell death so rapidly, that humans have to replace all the atoms in their bodies every seven years. Every BODY of everybody you know is only 7 years old, even the people who are 70. The reason they look so old is because their DNA software has been damaged by the sun and our environment. So the software of a 70-year-old is 70 years old, but their hardware is only 7. Our DNA was DESIGNED TO LIVE FOREVER. We finished that essay with the longevity research from David Sinclair at Harvard University, who is inventing new ways to keep our software young indefinitely.

Our grandchildren may have to choose to die.

In this third essay, we discuss how our DNA software creates all the hardware in our bodies using Proteins. Proteins are way more sophisticated than we learned about in ninth-grade biology. Proteins are molecular machines. Proteins have little legs that walk, little motors that spin, and perform massive construction projects inside and outside their cells.

For a quick introduction, here’s a 6-min video from Veritasium called, “Your Body’s Molecular Machines”. Seeing is believing.

About a minute into the video, you will see our DNA Reader in action. The motor in that little “nanobot” spins faster than a commercial jet engine. Think about that. When we zoom in to Life on this scale, it doesn’t look like “life” at all. It looks like machinery.

Proteins are more than just the choice of meat that goes with your salad. In fact, when we eat meat, we are ingesting that organisms' collection of micromachines. Our digestive system chews, ferments, sieves, and strains the meat to get to the little robots inside. Our bodies chemically strip these proteins down for parts, then use the parts to make our “better, stronger” micromachines from our “better, stronger” software (DNA). This is why the law of the jungle is eat, or be eaten. As each animal lives their life, they slowly re-organize the world into these little micromachine proteins.

The average human is 62% water, 16% fat, 16% protein, 6% minerals, less than 1% carbohydrates, and very small amounts of vitamins. So every part of your body that you can touch that isn’t water or fat, is made out of proteins. These little nanobots lock together to make bone and muscle. They combine to make organs that process our food and pump our blood. These little nanobots are even used as neurotransmitters in our brains.

How Our Software makes Hardware

In the previous essay, we discussed how some sections of our DNA are used in environmental regulation (logical decision making), some sections are used for antivirus protection, and some sections manage error handling. So most of the software in our chromosomes don’t produce mechanical hardware. In fact, only 1-3% of our DNA is made up of protein-coding genes.

For comparison, protein-coding genes make up 98% of the DNA inside bacteria. If you recall from the last essay, bacteria use horizontal gene transfer to constantly try out new competitive advantages in their environment. They try out all the genes of the bacteria they “eat”. This is where Darwin stops making sense at smaller scales. The average bacteria lives for only 12 hours. If humans and bacteria are “accidental intelligence”, shouldn’t a life form that mutates and replicates every 12 hours have an exponentially competitive advantage against a life form that lives 50 years? If life was created by accident and “survival of the fittest” means organisms need to die to evolve, it sure seems like the hierarchy of the animal kingdom should be ruled by animals who live the shortest lives.

The 1-3% of our genes that make proteins, make every protein the exact same way. Molecular biologists call this The Central Dogma. This fundamental theory was invented by Francis Crick in 1958 and states, “Genetic information flows only in one direction, from DNA, to RNA, to Protein”.

@cybernerds: Our DNA software has a build process just like our modern computer languages. DNA is basically the “human.c” file that holds our source code. MessengerRNA is basically the “human.o” object file that gets created by the C compiler. Proteins are the “human.exe” output that does real stuff in the real world.

Chromosomes store our DNA letters in logical groups of 3, called Codons. A codon is like a byte in computer science. A byte holds 8 bits of uncertainty that are either 1 or 0 to produce 256 possible states. A codon, by contrast, can have 4 different values in each position to produce 64 possible state. This may seem limiting, but protein coding genes don’t even need all 64 possibilities. That’s because every nanobot, in every life form, is constructed from the same 20 “Lego blocks” we call Amino Acids.

Matt Ridley illustrates this point well in his book, “Genome: The Autobiography of a Species in 23 Chapters” (paid link).

Ridley writes, “The three-letter words of the genetic code are the same in every creature. CGA means arginine and GCG means alanine – in bats, in beetles, in beech trees, in bacteria. They even mean the same in the misleadingly named archaebacteria living at boiling temperatures in sulphurous springs thousands of feet beneath the surface of the Atlantic ocean or in those microscopic capsules of deviousness called viruses. Wherever you go in the world, whatever animal, plant, bug or blob you look at, if it is alive, it will use the same dictionary and know the same code. All life is one.”

When our DNA is ready to build a protein micromachine, it doesn’t just take a stretch of DNA and send it to the “printer”. Our DNA splices together multiple sections from the gene’s source code, editing out any superfluous data. We aren’t sure exactly how it knows which DNA letters to keep, but the subsequent messengerRNA is then sent to the Ribosome. The ribosome is an integral part of every cell that turns any messengerRNA into proteins. The ribosomes in each cell are basically our “nanobot factories”.

Ribosomes are not in our cell’s nucleus (the data center), because it doesn’t contain any logic. Ribosomes are kinda dumb. When the ribosome first encounters free floating messengerRNA, it begins a new string of amino acids. For each codon (byte) it reads in the messengerRNA, the ribosome appends a corresponding amino acid to the chain. There’s even a stop command in the code. Molecular biologists have a codon lookup table that shows the relationship between codons and amino acids. They replace the letter ‘T’ with ‘U’ to indicate that the codon is messengerRNA, and not DNA.

Computer geeks might recognize this as something like an ASCII lookup table to convert binary to alphabet. If there is a “He who programs in DNA”, this mapping is a very deliberate choice.

How a string of amino acids turns into a sophisticated nanobot with legs, motors, valves, and pumps was a big mystery for 50 years in Biochemistry. The best explanation I’ve found for how this works is in a TED Talk from Ken Dill. It is titled, “The protein folding problem: a major conundrum of science”. This 16-min video also does a great job depicting how these nanobots use mechanical leverage to power the systems in our bodies.

The reason amino acids can transform into nanobots is because they are self similar. They have an amino group of molecules on one end and a carboxyl group on the other that are polarized. This enables them to connect to each other with magnets, just like a little toy train. What makes each amino acid unique is their side chains. Some side chains are polar which allows for more than just the two connections from the amino and carboxyl groups. Some side chains are nonpolar and vary in shape. These side chains are what provide the three dimensional structure to the string of amino acids. Changing the sequence of amino acids will change the overall structure of the protein once it’s folded up.

To learn a little about each amino acid, I’ve asked ChatGPT to step in. What’s important to remember about his responses is that amino acids don’t perform any direct function in our body, but some functions in our body have high concentrations of certain amino acids.

@ChatGPT: “Can you list the amino acids and describe where in the body we can find it in high concentrations?”

ChatGPT: “Certainly! Here's a list of amino acids and a brief description of where they are found in the body in high concentrations:

  1. Alanine (Ala/A): Abundant in muscle tissue, plays a role in glucose production.

  2. Arginine (Arg/R): Found in high levels in the kidneys, involved in immune function.

  3. Asparagine (Asn/N): Concentrated in the brain and nervous system, vital for neural processes.

  4. Aspartic acid (Asp/D): Abundant in the brain and various tissues, important for energy metabolism.

  5. Cysteine (Cys/C): Found in high concentrations in the liver, involved in detoxification.

  6. Glutamic acid (Glu/E): Abundant in the brain, serves as a neurotransmitter.

  7. Glutamine (Gln/Q): High levels in the muscles, contributes to protein synthesis.

  8. Glycine (Gly/G): Abundant in connective tissues and muscles, important for collagen production.

  9. Histidine (His/H): Concentrated in hemoglobin, essential for red blood cell function.

  10. Isoleucine (Ile/I): Found in high levels in muscle tissue, important for energy production.

  11. Leucine (Leu/L): Abundant in muscle tissue, crucial for protein synthesis and muscle growth.

  12. Lysine (Lys/K): Found in high concentrations in muscle tissue, essential for protein stability.

  13. Methionine (Met/M): Concentrated in the liver, crucial for sulfur-containing compounds.

  14. Phenylalanine (Phe/F): Found in high levels in the brain, precursor to neurotransmitters.

  15. Proline (Pro/P): Abundant in collagen, important for connective tissue structure.

  16. Serine (Ser/S): Found in high concentrations in the brain and spinal cord, involved in metabolism.

  17. Threonine (Thr/T): Abundant in the heart, central nervous system, and skeletal muscles.

  18. Tryptophan (Trp/W): Found in high levels in the brain, precursor to serotonin.

  19. Tyrosine (Tyr/Y): Abundant in the brain, precursor to neurotransmitters and hormones.

  20. Valine (Val/V): Concentrated in muscle tissue, important for energy metabolism.

These concentrations can vary, and amino acids often serve multiple functions in different tissues throughout the body.”

If you haven’t been convinced you live in “The Matrix” yet, here’s 7 more minutes to watch our nanobots in action. This is what is going on inside all of your cells, RIGHT NOW. Notice how large the gateways are in the physical firewall guarding the nucleus.

The Cellular Computer

Each of the 100,000 various nanobots in our bodies are produced in cells. Cells are many orders of magnitude larger than proteins and they are many orders of magnitude smarter.

Inside each cell are all the functions you would expect in a computer.

The Lysosome is The Recycle Bin. From its wiki: “A lysosome is a membrane-bound organelle found in many animal cells. They are spherical vesicles that contain hydrolytic enzymes that can break down many kinds of biomolecules. A lysosome has a specific composition, of both its membrane proteins, and its lumenal proteins. The lumen's pH (~4.5–5.0) is optimal for the enzymes involved in hydrolysis.”

So each of our “computing cells” comes with its own “amino acid shredder” that uses acid to strip proteins down for parts.

Vesicles are used to manage partitions. Programmers use partitions when they are trying out new software and don’t want it to contaminate their working code. From its wiki: “vesicles are a basic tool used by the cell for organizing cellular substances. Vesicles are involved in metabolism, transport, buoyancy control, and temporary storage of food and enzymes. They can also act as chemical reaction chambers.”

This is so smart. How can humans be “accidental intelligence”?

The Endoplasmic Reticulum is essentially the system’s bus. A bus, or omnibus, is essentially the data highway of a computer that feeds into its microprocessor. Any components that need to send or receive data are plugged into it. If you recall from the videos above, the endoplasmic reticulum runs right through the nucleus. For some reason, the nucleus perpetually creates new endoplasmic reticulum while it destroys the old. The nucleus perpetually paves its own information highway.

We’ve already discussed the Ribosome. What we didn’t mentioned is that ribosomes are usually attached to the endoplasmic reticulum. But once a ribosome starts processing messengerRNA, it can sometimes “decide” to untether itself and travel to a specific part of the membrane known as the Golgi Apparatus. The ribosome somehow knows that the protein it is making is destined for a location outside of its cell. So ribosomes have the ability to “finish the job offsite”. The golgi apparatus can “secrete” the new nanobot outside its cell walls without getting any yucky cytoplasm on it.

Our cells have intricate hardware manufacturing techniques so advanced, we are still learning from them.

The other thing we didn’t mention about ribosomes is our cell’s total capacity to produce these nanobots. Some mammalian cells, have 10,000,000 nanobot factories ready to go. Ribosomes can join 200 amino acids per minute, so most proteins are created fairly quickly. But massive proteins, like the muscle protein titin, have 30,000 amino acids in their sequence and need 2-3 hours to construct.

The Centrosome is “an organelle that serves as the main microtubule organizing center (MTOC) of the animal cell, as well as a regulator of cell-cycle progression.” The centrosome decides when it’s time for a cell to divide and when it’s time to die. We don’t really know what microtubules do in cells, although I do like the OrchOR theory from Sir Roger Penrose and Stuart Hameroff. If you recall their OrchOR theory from our previous chapter, “The Quantum Neural Network”, our brains perform quantum computation using microtubules, just like little vacuum tubes resonating with the quantum vibes of the universe.

The last computer part to mention is Mitochondrion. Star Wars fans might confuse them with “midi-chlorians”, the mysterious life form that lives inside everyone’s cells and gives Jedi access to “the Force”. Mitochondria do the same thing, only this time the Force is called Adenosine Triphosphate. From its wiki: “Adenosine triphosphate (ATP) is an organic compound that provides energy to drive and support many processes in living cells, such as muscle contraction, nerve impulse propagation, condensate dissolution, and chemical synthesis. Found in all known forms of life, ATP is often referred to as the "molecular unit of currency" of intracellular energy transfer. The human body recycles its own body weight equivalent in ATP each day. It is also a precursor to DNA and RNA, and is used as a coenzyme.”

Mitochondria are essentially little battery packs that power every cell. One liver cell might have 2000 mitochondria. What’s so unusual about them is they are the only cellular component to has its own DNA. In fact, mitochondria DNA is more closely related to bacteria DNA than human DNA.

Mitochondria produce the ATP our little proteins need through aerobic respiration. Yes, mitochondria breathe. In fact, the harder our muscles have to work, the harder our lungs huff and puff, right? But all that oxygen isn’t going to “us”, it goes to our mitochondria. That oxygen is fed to our mitochondria because aerobic metabolism (with oxygen present) yields 15 times more ATP than anaerobic metabolism (which only yields 2 molecules of ATP per 1 molecule of glucose). The waste products from mitochondria are carbon dioxide and water. So every time we exhale, we are releasing the breath from trillions of mitochondria.

The fact that mitochondria have their own DNA that looks like a bacterial genome has led to the Endosymbiotic Hypothesis. It states, “free-living prokaryotic ancestors of modern mitochondria permanently fused with eukaryotic cells in the distant past, evolving such that modern animals, plants, fungi, and other eukaryotes are able to respire to generate cellular energy.”

This theory is widely accepted among microbiologists and really only makes sense if humans are “Accidental Intelligence”. But if the universe was designed this way on purpose, then mitochondria were a very critical design choice. There’s a really good reason that a computer programmer would choose to have a second genome produce all the ATP for the human body…

Our source code was designed to work on more than one planet or in more than one reality.

Think about it. All 3 BILLION letters of DNA were written to create an organic robot powered by adenosine triphosphate, not oxygen. So mitochondria create an Interface for our DNA to thrive in this world. Here’s the wiki for computing interface: “In computing, an interface is a shared boundary across which two or more separate components of a computer system exchange information. The exchange can be between software, computer hardware, peripheral devices, humans, and combinations of these. Some computer hardware devices, such as a touchscreen, can both send and receive data through the interface, while others such as a mouse or microphone may only provide an interface to send data to a given system.”

By swapping out the DNA in our mitochondria, our robot bodies could work in multiple planetary environments. Instead of using “local” oxygen to turn 1 glucose molecule into 30 ATP molecules, we might inhale nitrogen or carbon dioxide and exhale sulfur. Our neural networks adapt our “taste preferences” to the local physics the same way the neural networks for coffee drinkers learn to love coffee. Our bodies could even work with mitochondrial DNA that ingests carbon dioxide, as long as it produces ATP.

I don’t know how many changes would have to be made to our lungs or red blood cells, but that may have already happened to us. Our red blood cells are the only cells in our body that don’t have a nucleus. Red blood cells don’t even have mitochondria batteries. They have RNA, just like a virus. Red blood cells are a virus we give to ourselves. We make and discard so many of these little organic computers that they turn our poop brown. If we ever meet aliens from this universe or another dimension, the color of their blood, skin, and poop will also be determined by the molecules they harvest from the air.

@biblenerds: This idea makes Genesis 1:26 in the Torah pretty interesting. In English, it reads, “Then God said, “Let Us make man in Our image, according to Our likeness. They will rule the fish of the sea, the birds of the sky, the livestock, all the earth, and the creatures that crawl on the earth.”

In Hebrew, the word “man” is “a-dam”. It means “ruddy” or “red”. So “Adam” isn’t the name that Adam gave himself. Adam got to name all the creatures of our world, but he received the name “red” from beings known as the Elohim (translated as God in English). Elohim is the plural of Eloah, which means “Ruler”. So the Torah reads something more like, “Then said The Rulers, “We make red in our design””.

Genesis 5:2 doubles down on this idea. Translating Elohim and adam the same way it reads, “The Rulers created them male and female. When they were created, The Rulers blessed them and called them red.”

We’ll explore these “Rulers” more in the next chapter.

We close this essay on Nanobots and Microbots with a short video from BioVisions at Harvard University. Here’s another 4-minute tour through the entire organic computer. As Morpheus said to Neo in the Matrix, “Welcome to the desert of the real”.

Continue reading

➡️: Carbon Fiber, Fiber Optics, and Pneumatics

⬅️: Micro Deaths Create Eternal Life 

⬆️: Table of Contents

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