Our Cell Machinery
Our Cell Machinery
In this story, we learn how protein “micro machines” construct cells that have all the components we would expect in a modern computer.
TLDR: I’ll summarize this story for you.
Proteins are way more sophisticated than we learned about in high school 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. For example, here is a flagellum motor protein:
Does this look “organic” to you?
Here is a kinesin motor protein. They deliver supplies all around your cells like postal workers.
To see more of your proteins in action, check out this video from Veritasium called, “Your Body’s Molecular Machines”. (6 mins)
Proteins are way more than just the choice of meat that goes on your salad. When we eat, we are ingesting all the little micro machines of those plants and animals. Our digestive system chews, ferments, sieves, and strains our food to extract all the little robots inside. We chemically strip them down for parts to make our “better, stronger” micro machines from our “better, stronger” DNA. That’s why the law of the jungle is eat, or be eaten—as each animal lives their life, they slowly reorganize the world into these little micro machines.
The average person is approximately 60% water, 20% fat, 15% protein, and 5% minerals like salts and metals. So almost every part of your body that isn’t fat or water, is made out of micro machines. They construct all the components of our cells. They lock together to make bones and muscles. They work as hormones in our blood and enzymes in our guts. They are even used as neurotransmitters in our brains.
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. Only 1-3% of our genomes are protein coding genes. For comparison, 98% of the genomes in bacteria are protein coding genes.
Protein coding genes build all their proteins the exact same way. According to Francis Crick, discoverer of the double helix, “Genetic information flows in one direction: from DNA, to RNA, to Protein.” This is called The Central Dogma of Molecular Biology.
So when a gene is ready to build a protein, 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 segments of its source code to produce messengerRNA. We aren’t really sure how genes decide which letters to keep and which letters to ignore.
The messengerRNA, or mRNA, is what gets sent to the micro machine printer, called a Ribosome. Whenever ribosomes encounter any free floating mRNA, they automatically begin a new chain of Amino Acids. The 20 amino acids are the “Lego blocks” of life. Here’s what they look like:
They may look simple, and they are, but you have already seen the kind of machines we build with them.
Ribosomes know which amino acid to add next by reading 3 letters at a time from the mRNA. Each 3 letter group is called a Codon, which works like a byte in computer science. A byte holds 8 bits of uncertainty that are either 1 or 0, which produces 256 possible states (2^8). A codon, by contrast, has 4 different values in only 3 positions, which produces 64 possible states (4^3). Here is a “Codon lookup table” to illustrate how each three-letter word maps to the 20 amino acids.
Geneticists replace the DNA letter ‘T’ with ‘U’ to indicate this is mRNA. Also, did you notice the “Stop” commands in the code? ‘UAA’, ‘UAG’, and ‘UGA’ all mean stop, which tells the ribosome to cut the chain free so that it can fold up into a micro machine like a transformer.
All known life in the universe use these 20 simple building blocks. 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 is another diagram to illustrate The Central Dogma of molecular biology.
How the chains of amino acids transform into sophisticated micro machines with legs, motors, valves, and pumps was a big mystery in biochemistry for 50 years. My favorite explanation for how this works is a TED Talk from Ken Dill called, “The protein folding problem: a major conundrum of science”. (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.
If you haven’t been convinced that you are artificial intelligence yet, here is 4 more minutes of watching your “nanobots” in action. This is happening inside all of your cells, RIGHT NOW.
@programmers: Our DNA software has a build process just like our computer software. 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.
Cell Computing
There are about 100,000 different protein micro machines in the human body, and all of them are manufactured in Cells. Cells are many orders of magnitude larger than proteins and many orders of magnitude smarter than proteins. Inside each cell are all the functions you would expect in a modern computer:
Cell Nucleus - This is obviously the Microprocessor. We discussed how this works in the previous two essays. Check out this video one more time to notice the size of the gateways in the firewall. Cells are high tech. (7 mins)
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 the 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, so the nucleus perpetually paves its own information highway.
Ribosome - These are our micro machine Printers. Some mammalian cells, have 10,000,000 ribosomes ready to go at all times. They hang out on the endoplasmic reticulum which gives it the “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 - This works like a Modem. 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 exports the new protein outside the cell walls without getting any yucky cytoplasm on it.
Lysosome - This is the Recycle Bin of our micro computers. After proteins serve their purpose, they are sent to the lysosome, which breaks them down into amino acids to be reused in new proteins. Here’s 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.
Vesicle - This is a Partition. Computer programmers use partitions when they want to try out new software, but don’t want to risk contaminating their existing code. According to 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.
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 each component, connecting them to the system bus, and loading the operating system into memory. The UEFI is limited in its decision making compared to a microprocessor, but nothing happens in a computer without permission from the UEFI. Here’s 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 each cell where to go, how to orient itself in space, when to replicate, and when to die from programmed cell death.
The centrosome also does some amazing things with microtubules that microbiologists are only beginning 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 that resonate with the vibes of the quantum universe. 😎
Here is a presentation called, “Clarifying the Tubulin bit/qubit” where Stuart Hameroff makes a strong case that microtubules store our memories. If you like biology, this video is fascinating. (46 mins)
Mitochondria - These are the Power Supply Units (PSU) of our micro computers. Every cell has multiple power supply units. Liver cells, for example, have around 2,000 mitochondria each. Star Wars fans might naturally confuse mitochondria with “midi-chlorians”, the mysterious life form that gives a Jedi power from the Force. Well, the real power is called Adenosine Triphosphate. Here’s 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 “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 into our mitochondria because their metabolism yields:
30 molecules of ATP per 1 molecule of glucose when oxygen is present, but only
2 molecules of ATP per 1 molecule of glucose when oxygen is not present.
The waste products from mitochondria are carbon dioxide and water. So each time we exhale, we are releasing the waste products from trillions of mitochondria batteries. 😮💨
Plug and Play by Design
Mitochondria are unique because they are the only cellular component that have their own DNA. In fact, mitochondrial DNA is more closely related to bacterial DNA than human DNA. So mitochondria actually are the mysterious life form who live inside our cells to give us power. This 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. Remember how we have 100,000 different protein micro machines in our body? NONE of those genes evolved to use 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”.
Symbiogenesis is the only explanation if you are committed to the belief that humans are accidental intelligence from millions of years of evolution and natural selection. 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 presume to know why God gave us mitochondria batteries, but a software designer on Earth would do it to make all 3 billion letters of our DNA software “Plug and Play”. By swapping out the DNA in our mitochondria batteries, the rest of our DNA could work on multiple planets with multiple atmospheres without any other modifications.
None of our DNA was designed for oxygen. 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. Maybe we would need some changes 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 our hemoglobin protein. Our bodies make 2,000,000 red blood cells every second and discard so many that they turn our poop brown. When we meet other aliens from this universe, the color of their blood, the color of their skin, and the color of their poop will most certainly be determined by which molecules they harvest from the air. 🩸
@biblenerds: This plug and play mitochondria idea makes Genesis 1:26 even more intriguing. 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.”
But in the original Hebrew, the word translated as man is “adam”. Adam isn’t a name, it’s a color. It means red or ruddy. So technically, the first man spawned on this planet got to name all the creatures 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 from above”. We obviously look like these “Rulers from above” because we were made in their image. So maybe somewhere else in the universe are beings who look like us, but have yellow blood, blue blood, or green blood. Why else would we be distinguished by the color red?
Genesis 1:26 in the Torah literally reads,
Then the Rulers from above said, “Let us make red in our design, according to our form”.
Genesis 5:2 confirms the name,
He created them male and female. He blessed them and called them red on the day they were created.
To learn more about the “Rulers from above”, read:
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