Micro Machines and Micro Computers

@midjourneybot: /imagine: an underwater scene with a wide variety of advanced nanobots

Proteins are way more sophisticated than we learned about in ninth-grade biology. Proteins are molecular machines. They have little legs that walk, little motors that spin, and they perform massive construction projects on behalf of their cells. Life on this scale doesn’t look like life at all—it looks like machinery.

Check out this video from Veritasium called, “Your Body’s Molecular Machines”. Seeing is believing. (6 mins)

Proteins are more than just the choice of meat that goes on your salad. In fact, when we eat meat, we are ingesting that animal’s collection of micro machines. Our digestive system chews, ferments, sieves, and strains the meat to get to all the little robots inside. Our bodies chemically strip those proteins down for parts, then use those parts to make “better, stronger” micro machines from our “better, stronger” DNA software. That’s 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 micro machines.

The average human is 50-60% water, 15-30% fat, 10-20% protein, and 6% minerals, like salts and metals. So almost every part of your body that you can touch that isn’t water or fat, is made out of proteins. These little micro machines lock together to make bones and muscles. They combine to make organs that process our food and pump our blood. These little micro machines are even used as neurotransmitters in our brains.

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How Our Software Makes Hardware

In “The BioLogical Robot”, we discussed how various sections of our DNA were used for various purposes. Some sections are used for environmental regulation and logical decision making. Other sections are used for error handling and antivirus protection. 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 previous story, bacteria use Horizontal Gene Transfer to try out genes from other bacteria they meet and other bacteria they eat. This helps bacteria find competitive advantages in their environments.

@biologists: This is where Darwin stops making sense to me. The average bacteria only lives for 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 over a life form that mutates and replicates every 25 years? If life was created by accident and “survival of the fittest” means species need to die to evolve, it sure seems like the hierarchy of the animal kingdom should be ruled by organisms who live the shortest lives.

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Maybe they are. Maybe my gut bacteria are farming me, but it sure feels like it’s the other way around.

The 1-3% of our DNA that make proteins, make every protein the exact same way. Molecular biologists call this The Central Dogma. This fundamental theory was defined by Francis Crick in 1958 who said,

Genetic information flows only in one direction, from DNA, to RNA, to Protein.

So here’s how that works.

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, which produces 256 possible states. A codon, by contrast, can have 4 different values in 3 positions, which only produces 64 possible states. This may seem limiting, but protein-coding genes don’t even need all 64 possibilities because every protein, in every life form, is constructed from the exact same 20 “Lego blocks” we call Amino Acids.

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

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.

Here’s a “Codon lookup table” that shows how each three-letter word maps to the 20 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.

When a gene is ready to build a protein micro machine, it doesn’t just send a stretch of DNA to the “micro machine printer”. The DNA splits in half, and the gene splices together multiple sections of its source code, editing out any superfluous data. We aren’t really sure how genes know which DNA letters to keep and which to ignore. The assembled DNA is called messengerRNA and that is what gets sent to the “micro machine printer”. ✉️

All of this data processing happens inside a cell’s Nucleus, which is its data center. Each nucleus has its own physical firewall to keep the rest of the cell’s machinery from mucking up all its data. So after the messengerRNA is assembled, the nucleus exports it to the “micro machine printer”. 🖨️

The “micro machine printer” is called a Ribosome. When a ribosome first encounters any free floating messengerRNA, it begins a new chain of amino acids. For each codon (byte) it reads from the messengerRNA, the ribosome appends the corresponding amino acid to the chain from the “Codon lookup table”. Have a second look at the table above. Did you notice the Stop commands in the code? ‘UAA’, ‘UAG’, and ‘UGA’ all mean Stop. Molecular biologists replaced the DNA letter ‘T’ with ‘U’ in the table to indicate that the codon is messengerRNA.

How these chains of amino acids turn into sophisticated micro machines with legs, motors, valves, and pumps was a big mystery in Biochemistry for 50 years. My favorite explanation is a TED Talk from Ken Dill called, “The protein folding problem: a major conundrum of science”. Dill does a great job depicting how these micro machines use mechanical leverage to power all the systems in our bodies. (16 mins)

The reason amino acids can transform into micro machines is because they are self similar. They all have an amino group of molecules on one end and a carboxyl group on the other end 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 its side chain. Some side chains are polar, which allows for more than two magnetic connections. Some side chains are non-polar and vary in shape. Side chains are what provide the three dimensional structures to any chain of amino acids. Changing the sequence of amino acids changes the overall structure of the protein once it’s folded up.

@biblenerds: Amino acids are basically “God’s Lego blocks”.


Here’s an example of what these chains of amino acids can be once they fold up. This is a “flagellar motor” that allows bacteria to swim around.

That “thing” on the left is a protein. It’s manufactured by a gene in a bacteria.

If you haven’t been convinced you live in “The Matrix” yet, here is 7 more minutes of watching our micro machines 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.

You have trillions and trillions of cells doing this right now. Is that real life or are we real life? Why are we always the last to know what’s going on? You gotta admit, whoever or whatever can design intelligent life in DNA is a bajillion-trillion times smarter than us. 😳

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@cybernerds: Our DNA software has a build process just like 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 assembled by the C compiler. Proteins are the “human.exe” output that does real stuff in the real world.


The Micro Computer

There are about 100,000 different protein micro machines in the human body, and all of them are manufactured by our Cells. Cells are many orders of magnitude larger than proteins and they are many orders of magnitude smarter than proteins. The average adult male has around 36 trillion cells in their body, while the average adult female has 28 trillion. Inside each cell, there are all the functions you would expect in any “micro computer”:

Lysosome - This is the Recycle Bin of our micro computers. From 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.

Vesicles - These manage Partitions. Computer programmers use partitions when they want to try out new software, but don’t want to risk contaminating their existing 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.

Endoplasmic Reticulum - This is the System Bus of our micro computers. A bus, or omnibus, is essentially the data highway of a computer that feeds into its microprocessor. Any components in a computer that need to send or receive data are plugged into its system bus. If you recall from the videos above, the endoplasmic reticulum runs right through the nucleus. For whatever reason, the nucleus perpetually creates new endoplasmic reticulum while destroying the old. The nucleus perpetually paves its own information highway. 🛣️

Ribosome - Remember the micro machine Printers? Some mammalian cells, have 10,000,000 ribosomes ready to go at all times. They all hang out on the endoplasmic reticulum which gives some of it a “rough” appearance under a microscope. 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 so they need 2-3 hours to construct.

Golgi Apparatus - Ribosomes somehow know when a protein is destined for a location outside the cell. So ribosomes can untether themselves and travel to the Gogli apparatus along the cell’s outer walls to finish the job offsite. The Golgi apparatus then secretes the new protein outside the cell walls without getting any yucky cytoplasm on it.

Cell Nucleus - This is obviously the Microprocessor, right? The nucleus must also be some kind of Database. In the previous story, I mentioned how I was vaccinated with Moderna’s mRNA vaccine, which means somewhere inside of me there is DNA source code that was originally cut-and-pasted from Microsoft Word. Well, there aren’t a lot of other places to store the DNA sequence for that COVID-19 protein spike other than a cell nucleus. 🤔

Centrosome - This is the BIOS or UEFI of our micro computers. UEFI stands for Unified Extensible Firmware Interface. The UEFI in a computer is responsible for powering on all the components, connecting them to the bus, and loading the operating system into memory. The UEFI is very limited in its decision-making compared to a microprocessor, but nothing happens in a computer without permission from the UEFI. Now check out this quote from wiki,

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 provides structure for the cell.

The centrosome tells the cell where to go, how to orient itself in space, when to replicate itself, and when to die from programmed cell death. The centrosome also does some amazing things with microtubules that biologists are just starting to understand. If you recall the OrchOR theory by Sir Roger Penrose and Stuart Hameroff from “The Quantum Neural Network”, our brains perform quantum computation using microtubules. Microtubules are like little vacuum tubes resonating with the quantum vibes of the universe. 😎

Here’s a video called, “Clarifying the Tubulin bit/qubit” where Stuart Hameroff makes a strong case that microtubules also store our memories. If you like biology, this presentation is fascinating. (46 mins)

Mitochondria - These are the Power Supply Units (PSU) of our micro computers. One liver cell will have 2,000 mitochondria. Star Wars fans might confuse mitochondria with “midi-chlorians”—the mysterious life form living inside all our cells that give the Jedi power from the Force.

Well, the real Force is called Adenosine Triphosphate. From 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.

What’s so unusual about mitochondria is that they are the only cellular components that have their own DNA. In fact, mitochondrial DNA is more closely related to bacterial DNA than to human DNA. So mitochondria actually are the mysterious life form living inside all our cells that give us power. 🔋

Mitochondria batteries produce ATP power for our proteins through Aerobic Respiration, which means they breathe oxygen. The harder our muscles work, the harder our lungs huff and puff, right? But all that oxygen isn’t going to “us”, it is fed directly to our mitochondria because their metabolism yields:

  • 30 molecules of ATP per 1 molecule of glucose with oxygen

  • 2 molecules of ATP per 1 molecule of glucose without oxygen

The waste products from our mitochondria batteries are carbon dioxide and water. So every time we exhale, we are releasing the waste products from trillions of mitochondria batteries. 🚮

Modularity By Design

The fact that mitochondria have their own DNA that looks like a bacterial genome has led to the Symbiogenesis Hypothesis which 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, but it doesn’t even make evolutionary sense to me. Remember how we have 100,000 different protein micro machines in our body with amazing turbine motors that spin faster than commercial jet engines? NONE of those genes are powered by oxygen, which means all 3 billion letters of our DNA “evolved” after our cells permanently fused with mitochondria. That’s not really symbiogenesis, that’s more like, “In the beginning there were mitochondria producing ATP, and then there was everything else”.

I understand why symbiogenesis makes sense if you believe humans must be accidental intelligence. But if humans are artificial intelligence, then we were designed with mitochondria batteries on purpose, which makes them a very critical design choice. 🤔

I don’t really know why our Intelligent Designer gave us mitochondria batteries, but I know why a computer programmer would do it: to make all 3 billion letters of our DNA “Plug and Play”. By swapping out the DNA in our mitochondria batteries, the rest of our DNA could work in other atmospheres on other planets without a lot of modification. Instead of using oxygen to turn 1 glucose molecule into 30 ATP molecules, we could inhale nitrogen or carbon dioxide to perform the same function.

This is total speculation and I don’t know how many changes would have to be made to our lungs and Red Blood Cells, but that may have already happened to us. Mature red blood cells are the only cells in our body that don’t have a nucleus. They don’t even have mitochondria batteries. They have RNA, which means red blood cells are kind of like a virus that we give to ourselves.

Red blood cells are red for the same reason that rust is red—iron is the central atom in the hemoglobin protein. Our bodies make 2,000,000 red blood cells per second. We discard so many that they turn our poop brown. If we ever meet aliens from this universe or any other dimension, the color of their blood, the color of their skin, and the color of their poop will most certainly be determined by the molecules they harvest from the air. 🩸

@biblenerds: This idea makes Genesis 1:26 really 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 the original Hebrew, the word translated as “man” is “a-dam”. Adam is not a name, it means “red” or “ruddy”. So technically, the first man got to name all the creatures in the Garden of Eden except himself. He received the name “red” from beings known as the Elohim, which is translated as “God” in English. Elohim is the plural of Eloah, which means “Ruler”. So Genesis 1:26 in the Torah reads something more like,

Then The Rulers said, “Let us make red in our design, according to our form”.

Genesis 5:2 doubles down on this idea,

The Rulers created them male and female. The Rulers blessed them and called them red on the day they were created.

To learn more about “The Rulers” check out:

We close with a short video from BioVisions at Harvard University. Here’s another 4-minute tour through our micro computing bodies. As Morpheus said to Neo in the Matrix, “Welcome to the desert of the real”.

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