The purpose of this essay is to introduce you to the internal structure of the living cell. I will show you it has been designed by divine intelligence with such precision it will leave you breathless. If you currently believe in evolution and doubt the case for an intelligent designer who created life then please go to this link and watch this very revealing video interview with Richard Dawkins. If still in doubt please reserve judgement until you have finished this essay.
I must acknowledge the work of Dr Fazele Rana in constructing this essay. His book, The Cell’s Design took me beyond the realm of high school biology and into the fascinating world of the most recent scientific discoveries concerning the cell. His book was my launch pad to a mountain of additional research. I have verified all information in his book before adding it to the essay.
After the introduction, the essay will follow this order:
- The cell as a living city
- The cell as a living factory
- The cell as a living computer
- The cell as a living messenger
From 1949 until 2004, professor Antony Flew was the worlds most celebrated atheist. He wrote dozens of books on atheism and attacked theistic philosophy relentlessly from his position as a professor of philosophy at Oxford and other universities. He argued that the onus of proof lay with the theist and that the case for divine intelligence, if any, must only come from scientific evidence.
Very early in Flew’s stellar career, in 1953 to be exact, Watson and Crick published their famous findings on the double helix structure of DNA. For the next 51 years, as the complexity of biochemistry became more widely known and understood, Flew became increasingly anxious. In 2004 Antony Flew finally told the world that he was no longer an atheist. The vast amount of intelligence built into the structure of genetics and the cell convinced him otherwise. Here is what he said on page 75 of his last book, There is a God:
“What I think the DNA material has done is that it has shown, by the almost unbelievable complexity of the arrangements which are needed to produce (life), that intelligence must have been involved in getting these extraordinarily diverse elements to work together.”
Antony Flew followed the evidence to a very costly conclusion. He was viciously attacked by his colleagues for his honesty. However, unlike Richard Dawkins, he was consistent with his belief that you must go where the evidence leads. So what exactly was the evidence of divine design that Flew saw?
When we see something made by humans we instinctively know it is different from that which surrounds it. There are familiar and recurring patterns, significant information, deliberate design, obvious construction, purpose, eloquence and efficiency of function. Objects shaped and built by natural processes may have one, perhaps two at the most of these qualities, but fall abundantly short of the rest, especially in the area of information. Now, if there is a divine origin to life then we should also see these same features when we investigate the building block of life, the cell. Any argument, naturalistic research or essay that acknowledges the above qualities in the cell, but denies an intelligent designer is by definition, self-contradictory.
The cell was first discovered in 1665AD by Englishman Robert Hooke. In his published work, Micrographia, he described over sixty objects he observed under a crude compound microscope. One of those observations was of large numbers of identical shapes from a sliver of cork. He named the small objects “cells” as they resembled honeycomb. These empty cell walls of dead plant tissue were the first human observations of what we now know to be the most important aspect of all biological life, the living cell. In 1676 Anton van Leeuwenhoek used a superior microscope to observe cells and found them to be the building blocks of all life. Leeuwenhoek was the true father of cellular biology.
So what exactly is the cell? It is the most basic from of independent life on planet earth. It is made of molecules, liquids, chemicals and organelles. But is infinitely more, being able to feed itself, expel waste, store and print out construction plans, build and repair internal structures, self-replicate, carry out repairs, communicate with other cells, defend itself against threats and co-operate with trillions of others to create superstructures that we call humans, plants, animals, fungi, protista or bacteria. Perhaps the most astounding aspect of the cell is that it is alive, it LIVES!
There are two types of cells. The cells of all single-celled organisms are called prokaryotic cells. This means they do not have a nucleus or organelles. Eukaryotic cells make up all multi-cellular organisms. They have both a nucleus and organelles. For the purposes of simplicity and length, this essay will only talk about eukaryotic cells. We will also give little attention to plant cells as the differences between plant and animal cells are not the focus of this essay. I will also often refer to human cells as they are what make up you and I, and this will make the essay more personal.
I will now work my way through some of the features of cells to show you patterns, information, design, construction, purpose, eloquence, efficiency and function. I will use the analogy of a city, a factory, computer and messenger to help you understand the structure of the cell.
THE CELL AS A LIVING CITY
I once asked a Spanish scientist, whose job was figuring out the purpose of a short segment of RNA, how complicated a cell was. His reply shocked me. He said the cell is “far, far, FAR more complicated than Brisbane”, a city of 2 million people not far from where I live. Imagine that for a second. Imagine every physical movement, external and internal communication, energy supply, waste disposal, building project, computer function in Tokyo, then multiply it. That’s the cell! It’s mind-bogglingly complicated. Let’s now investigate how a cell resembles a city.
You as a human being are a single and independent functioning unit with a mind, will and body. On a physical level you are made of organs and these organs are made of tissue which is made of cells. There are somewhere between 30 and 50 trillion cells in the average human body, but nobody really knows for sure the precise figure. A healthy liver for example has around 240 billion cells. Your brain has about 100 billion cells and a thousand trillion neural connections. It is by far the most complex piece of matter in the universe.
The products we consume that build cells are proteins, fats, water, carbohydrates, nucleic acids, and some inorganic ions (called electrolytes) which include sodium, potassium, magnesium, calcium, phosphate, chloride, and bicarbonate. The proteins, fats, carbohydrates and nucleic acids mentioned above are made of different combinations of elements such as carbon, hydrogen and oxygen, with carbon being by far the most common. Elements themselves are made of atoms, which are in turn made of mathematically precise sub-atomic particles called quanta. There are approximately 50 trillion atoms in a typical cell. In another essay I delve into this sub-atomic world, but here we will stick to the stunning marvels of the cell. Inside the cell all of the products in atomic form listed above are recombined into functional molecules, which are held together by either sharing electrons or electro-static attraction.
Cells are small, usually between 5 and 40 millionths of a metre in size, or one twentieth to one third the width of a human hair. Cells have a seal around them called a membrane. Without it, life’s functions would be in jeopardy. Inside, a combination of water, bio-molecular machines and salts make up the cytoplasm. The cytoplasm is the fluid in which internal cellular structures function. A flexible scaffold of hair-like microtubules is attached to the cell membrane. This scaffold criss-crosses the cell and holds it in its correct shape. These microtubules also function as railway lines for transporting all sorts of cargo around the cell.
Inside the cytoplasm are a number of very large conglomerations of functional protein molecules, called organelles. Just as we have a heart, liver, intestine etc, they are the “organs” of the cell. Organelles help the cell reproduce, consume energy, duplicate, repair and build all that is needed and take out waste.
It is important to understand as you read on that organelles do not think. They don’t decide anything that takes place in the cell. They simply react according to the laws of chemistry and physics. Using only instructional information transferred into amino acid chains and then into protein molecules, the laws of physics and chemistry automatically and almost magically combine proteins by the millions into all the unique and functional organelles of the cell. This staggering process continues all the way up from the cell to the consciousness and senses you are using to read this essay. Everything that you read from this point on about the cell is just physics and chemistry responding to information-dense instructions. It is the genius of the original instructions that is the true miracle of the cell. A vast amount of information is the genius of the cellular machine, as it is with all machines.
The largest and most important organelle is the nucleus. It is like the city computer network. It houses most of the above mentioned vast instructional software needed to build everything according to very specific plans. This information is chemically stored in a molecule called deoxyribonucleic acid, or DNA. DNA determines every “what”, “when”, “where” and “how” in the cell. The nucleus is protected from the rest of the cell by a double shell-like membrane called the endoplasmic reticulum. Where the two parts of this membrane connect there are portals for transporting all material in and out of the nucleus.
For anything to be built outside the nucleus, the DNA must be copied into a segment of RNA software code. These short lengths of RNA code are then used to continually build protein molecules in little factories called ribosomes. There can be millions of ribosomes in a single cell.
These ribosomes are built inside the nucleus but are then usually attached at a precise spacing on specific sections of the endoplasmic reticulum. Ribosomes function as an assembly line that processes RNA instructions into amino acid chains, the first step in making protein molecules. Ribosomes are like the city steel works. After the ribosomes have finished their work, proteins that cannot shape themselves, which is most of them, are absorbed back into the endoplasmic reticulum through a special portal for final shaping and moulding into functional molecules. Thus the endoplasmic reticulum determines the exact function of each cell in the context of billions of other almost identical cells. It does this through the unique shaping of each unique protein molecule. There are between 50,000-100,000 different types of protein molecules in the 50 trillion human cells, with a few thousand different types of protein molecules in each individual cell.
Small transporter proteins called vesicles transport a special group of those folded protein molecules directly to an organelle called the Golgi apparatus via those railway lines, the microtubules. Vesicles do the job of a city transport system. The Golgi apparatus looks like a stack of layered pancakes. As the vesicles pass through these “pancakes” the proteins within are successively modified, with lipids and carbohydrates added for their ultimate function in the cell cytoplasm. Transfer from one compartment to the next is very delicate and the whole process is completely controlled by the vesicles themselves. This final folding and joining of these complicated protein molecules is handled by chaperone proteins which stabilise and fold the assembling proteins, or send them to the chaperonin, a barrel-like structure that finishes folding the most difficult proteins. The Golgi apparatus then sends all completed molecules to their assigned workstations. It is like a postal and delivery system.
Cellular waste is also handled by the Golgi apparatus. Special vesicles, called lysosomes, break off from the Golgi apparatus and digest recyclable materials including unneeded molecules, damaged cells and food waste using about forty different acid-based enzymes that, it just so happens, cannot survive anywhere else in the cell but in the lysosome. Other vesicles, called peroxisomes, destroy any harmful and toxic foreign materials, such as poisons, by using an oxidising enzyme similar to household bleach. The two processes are not dissimilar to two city garbage bins, one used for throwing out waste and the other for recycling useful materials!
Floating elsewhere in the cell’s cytoplasm are many energy conversion and generation organelles called mitochondria. Mitochondria are the power stations of the cell. They convert incoming oxygen and biochemical sugars called saccharides to energy intense molecules in a process called cellular respiration. The energy is stored as an Adenosine Tri-Phosphate (ATP) molecule for future use in all parts of the cell. The conversion ratio is at the exact rate of two to one, and this has been found to be the perfect “goldilocks” conversion rate.
ATP molecules are like batteries being discharged around the cell and recharged by the mitochondria. Because the muscle and liver use more energy than most, they will have up to several thousand mitochondria in each of their cells. Mitochondria are unique in that they have their own smaller circular piece of DNA. Unlike all other organelles, cells don’t make their mitochondria from scratch via DNA, RNA, ribosomes and the Golgi apparatus. Mitochondria come from previous mitochondria through a process of direct replication and division. This is similar to cellular replication but on a smaller scale and is controlled by the nucleus.
Footnote: Plant cells do not have mitochondria as they produce their own energy from the sun. Plant cells have an organelle called a chloroplast for converting sunlight to energy. Like mitochondria, chloroplasts have their own DNA and self-replicate on command from the nucleus. Membrane sacs inside the chloroplast absorb light energy and value-add it to carbohydrate molecules to form glucose in a process called photosynthesis. It is basically the opposite of what our cells do as we then consume and burn this plant-produced glucose in some form of plant-based or higher value-added food material.
The organelles described above are the major macro structures inside a human cell. It is very obvious already that the cell is much like a city. All the same functions are present but with one proviso; what I have described to you is an astronomically simplistic version of what really happens inside the cell! The cell also does all these biochemical functions of life perfectly, without the vast amounts of human intelligence we need for our cities to function. To put it in perspective, if the cell arose without an intelligent designer it would be like the city of Tokyo constructing itself from raw materials and functioning impeccably without a single human being present.
Now let’s dig a little deeper to have a look at the molecular building blocks and machinery of the cellular city to see how they are built.
THE CELL AS A LIVING FACTORY
Digging below the already amazing macro-structure of the cell organelles, we come to the molecular level of complexity and design in the cell. In many ways the cell is similar to a factory that takes in raw materials and produces sophisticated finished products. The raw materials coming in to the cell include water, inorganic ions, amino acids, oxygen, sugars, hydrogen, fats, salts and carbon…lots of carbon. These inputs are used to build the thousands of molecular machines needed to run the cell. We are what we eat. We break down our food through digestion. Then, by the most complex chemical processes in the known universe, we weave them back into functional molecular machines, organelles, cells, human tissue, organs and bodies.
We will now dive into a discussion on the function of these molecular building blocks and take a very cursory look at the “weaving process” that recreates them into human beings…or fish, or plants, or fungi, or any of the other 9 million species of life on earth!
Proteins are by far the most important molecular machines in the cell. Their production is paramount to the cells survival. Protein molecules are the slaves, trucks, taxis, foot soldiers and workhorses of the cellular world. Without them the cell would simply not exist. The basic structures and activity of the cellular city described above all depend on the production of protein molecules to function. Producing sophisticated proteins are what DNA codes are all about. DNA does not store information for fats or carbohydrates, just protein molecules. Fats and carbohydrates are added later.
Proteins are combinations of twenty amino acids. Amino acids are specific molecular combinations of oxygen, carbon, nitrogen and hydrogen atoms. The carbon atom is central to the others. That’s why we are called a carbon-based life form. Nine amino acids make their way into the cell through the digestion of protein-based foods, while the other eleven can be synthesised by the body if they are missing from the rest of our diet.
When formed into a protein, these 20 different amino acids are first joined together like thousands of beads on a string. At this point it is called a polypeptide. Polypeptides are always built in exact and unique combinations which are determined by their specific DNA assembly instructions, copied to the messenger RNA and sent to the ribosomes for processing. More on that process later. Each amino acid in its unique position gives the whole protein molecule a distinct chemical and physical blueprint. This automatically determines how it can be folded, creating a unique structure. Structure determines function.
There are four levels to a proteins structure. First there is the linear or primary structure of amino acids themselves, the polypeptide. The secondary structure refers to the way these polypeptides are bent into coils, sheets or helixes. The tertiary structure then goes a step further, folding the coils, sheets and helixes into larger exact molecular shapes. The final quaternary structure occurs when anything from a few to several million tertiary proteins are combined into a single molecular machine or organelle. That final step may also involve the addition of lipids, or carbohydrate molecules.
This whole process is exacting physics, moving beautifully from code to chemistry to corporal structure. Individual cells have between two and four thousand different types of protein molecules, and millions of individual protein machines floating around inside the cytoplasm. The human body as a whole is capable of creating between 50,000-100,000 different types of protein molecules. Twenty per cent of your body is made up of protein molecules.
So what do proteins do in the cell? Well most everything, but here are a few: They create the cell’s structures such as the membrane and the cytoskeleton. The also create the “fabric” between cells. Proteins called enzymes speed up otherwise slow chemical processes by dragging molecules together, as do others like steroids and hormones. Other proteins harvest chemical energy inside the mitochondria. Some operate the cell’s defense system by combining to form antibodies. Others are transporters such as hemoglobin. Receptor proteins decide what enters and leaves a cell. Many others are essential for reading and duplicating DNA and the cell. They are also vital in the creation of RNA and transcribing it to amino acid chains. The list goes on and on…and on!
The next few paragraphs will describe in a little more detail just six of these many thousands of different types of protein functions found in a single typical human cell. These are the astonishingly sophisticated machines produced by the cells factory assembly line system.
- Receptor proteins are like the cell’s eyes and ears. At lightning speed they can receive messages from within the cell, package the information in special hormones and neurotransmitters called ligands, and send them to other cells. That’s how you just blinked! Alternatively they can be receiving messenger molecules from other cells and bringing them into the cell. Thus receptors are constantly listening to the lightning fast chemical chatter that swirls around both inside and outside each cell. Without receptor proteins there would be no multi-celled organisms…and no pharmaceutical industry! The processes involved are so complex that entire scientific careers are dedicated to finding out what specific chemical pathways are involved in receiving and sending one specific piece of information to and from the cell.
- Carrier Proteins are the gate keepers and guards of the cell membrane. Carrier proteins actively transport molecules across the membrane. Carrier proteins are naturally closed to either the outside or inside of the cell. When they “collect” molecules from one side, they seal off that opening behind the incoming or outgoing molecule, hold the molecule in transit, open the opposite seal, and release the molecule. All the work that carrier proteins do against the natural chemical and electrical gradient of the cell and its exterior requires them to engage in active pumping, and this involves the consumption of ATP energy from the mitochondria.
- Channel proteins on the other hand, are permanently open on both sides of the cell membrane, like a pore in human skin. They make up a large part of the membrane and their job is to transport water, oxygen and other molecules freely across it. Scientists have been amazed at how channel proteins can transfer their cargos at massive speed and in massive quantities. These proteins instinctively know which molecules to let through and which to stop by the use of ion selectivity filters that stop the flow of substances with ions of the wrong electrical charge. Water-based molecules and others like oxygen don’t need to be pumped into a cell. They will naturally diffuse through the channel proteins through osmosis.
- Mitochondria are the power stations of the cell and proteins are heavily involved in the production of ATP “batteries”. ATP is generated when a large number of proteins in the inner mitochondria oxidise the major products of glucose in the presence of oxygen. It is a hugely complex sequence requiring the presence of vast numbers of enzyme proteins. This is the reason why we breathe in oxygen and breathe out carbon dioxide.
- Enzyme Proteins speed up chemical reactions all through the cell, and all through the body. They are especially active at the cells interior and exterior membrane surfaces where substances have to enter and exit quickly. Enzymes are perhaps the most important type of protein because they act on over 5,000 different chemical processes within the cell and they speed up the rate of each of these by many million-fold. Without enzymes the cell would starve in seconds. This is why many drugs and poisons are enzyme enablers and inhibitors. Enzymes work by any or all of the following mechanisms: They sometimes have a shape with the exact angle that locks on perfectly to the molecule needed, like a lock and key. They sometimes use a specific electrical charge to attract molecules, like a magnet. They may also use water attraction/repulsion properties to operate. All three types of mechanisms are needed in different functions of the cell. Amazingly enzymes are not consumed in the chemical process they initiate the process but can then be used many times over.
- Antibodies are Y shaped proteins produced mostly by plasma blood cells of the immune system. They are either secreted to float freely in the blood stream as guards, or bind by the thousands to the membranes of plasma cells to act as receptors. Their job is to police the blood stream and extra-cellular environment looking for foreign bodies, or antigens. When they find an antigen that fits their uniquely specific docking mechanism at the end of their two arms, they lock on. If it is a free-floating antibody it will try to neutralise the target directly. Receptor anti-bodies on the other hand will alert their plasma cell to an antigen’s presence. Some plasma cells then initiate mass reproduction to go into battle to destroy it. Others embed the “memory” of the specific antigen so they can repel it more quickly in the future. It must be remembered that there are thousands of different types of antibodies and each will only lock on to a single type of antigen. This is why it is important to build up the immune system in young children.
The second of the four major raw materials used in the various factories of the cell are fat molecules. The word lipid is an ancient Greek name for a substance made of animal fat or vegetable oil. Lipids contain carbon, hydrogen and oxygen but have far less oxygen proportionally than carbohydrates. This renders them insoluble in water, or hydrophobic. Together with carbohydrates and proteins, lipids are the main constituents of plant and animal cells. Some well-known lipid molecules include cholesterol, steroids, fatty acids and vitamins A, D, E and K. The three main biological functions of lipids are in creating the cell or organelle membrane, storing energy and in transferring information.
The cell membrane that encloses the cell is made mainly of lipids interspersed with the receptor and channel proteins mentioned above. The lipids that make up the cell membrane are a compound of both lipids and phosphate called phospholipids. They look like a round head with twin kite tails. The phosphate head is water attracting, while the lipid tail is water repellent. This combination is of great biological significance as there is water both inside and outside the cell. Thus the millions of phospholipid heads instinctively align with water on each side of the membrane, while the tails turn away from the water to face each other. The attraction of the tails to each other is stronger than the attraction of the heads to water. So, by using only forces of attraction, these molecules create a tiny parallel layer around the cell that keeps extra-cellular fluids outside, and the cytoplasm inside. Degeneration of the phospholipid membrane plays a key role in the onset of Alzheimer’s disease.
Phospholipid construction takes place on an area of the endoplasmic reticulum membrane that is studded with proteins that direct their production. Eventually a vesicle will bud off from the endoplasmic reticulum and carry several phospholipids bound for the internal cellular membrane on its exterior leaflet, and several phospholipids destined for the external cellular membrane in its interior leaflet.
Evolutionary scientists used to think the cell membrane was the first part of the cell to evolve as it is a natural chemical bond. However, as more has become known about the cell membrane this view has diminished. We now know there are many different types of phospholipids in the cell membrane. Some of them activate the receptor and channel proteins. Some activate the proteins involved in DNA replication. Others play a key role in cell division. This diverse function requires diverse structure and immense information.
Importantly, the phospholipid cell membranes are only stable at critical temperatures, which happen to be the exact temperatures of their respective organisms. The cell membrane can even adjust its composition in reaction to changing temperatures or salinity, producing more of the types of phospholipids that can handle the new condition.
Finally, contrary to the standard Fluid Mosaic model of membrane structure which held that phospholipid distribution was random, we now know that distribution of phospholipids is not a random chemical bond. Some groups of phospholipids deliberately bond around receptor and channel proteins and stay there permanently to seal off the connection to the membrane. We also know that the inner and outer membranes are designed to perform very different functions. Both of these functions argue strongly against an evolutionary origin for the cell membrane.
Lipid rafts are specialised and stiffer sections of the cell membrane that protrude 50% above the membrane wall. They contain up to five times the cholesterol of the surrounding membrane wall. This holds the raft together. The purpose of these rafts is to enhance inter-cellular recognition and communication by embedding many receptor proteins into the raft and protecting many types of incoming and outgoing signals from non-raft enzymes. They perform a similar function to a tower of communications antennas on a hill. Lipid rafts in the Golgi apparatus are also crucial for the formation of vesicles.
Triglyceride, or what we commonly refer to as fat, is the major form of energy storage in multi-cellular organisms as it is over twice as energy dense as carbohydrate and protein. Fat is stored in special adipose (fat) tissue which is designed for continuous storage or burning of triglycerides. This process is controlled by our old friends the enzymes. On a macro level adipose tissue will cushion, heat and insulate your body. Adipose tissue also generates immune cells called macrophages.
Lipids are also heavily involved in inter-cellular signaling via hormone production. Hormones are often released by the cell into the bloodstream for long distance signaling right around the body. Lipid-based hormones control functions such as male and female sexual development and function, metabolism, cell growth, calcium regulation, inflammation levels, immunity to disease, blood pressure and the clearance of dead or damaged cells.
Carbohydrates are the sugars, starches and grains of our diets. In chemistry carbohydrates are called saccharides and they are biological molecules made from carbon, hydrogen and oxygen in the ratio of 1:2:1. They are basically a combination of carbon and water, making them easily dissolvable in the watery cellular environment. These saccharide molecules come in four forms. Monosaccharides are the hexagonal base-units. They include glucose and fructose. Di-saccharides are two of these base-unit molecules joined together. Examples are sucrose and lactose. Oligosaccharides consist of up to ten hexagonal base-unit molecules and this category includes human milk. Poly-saccharides can have base units numbering in the thousands. Any saccharide above monosaccharide will need an enzyme to help our body break it down. This is where some food intolerances come from.
The saccharides perform numerous roles in living organisms. Combinations of saccharides with lipids and proteins create many important molecules that play key roles in the immune system, fertilization, preventing pathogen invasion, blood clotting, and physical development. Glucose is produced by plants for their own fuel supply and, because it dissolves readily in blood, we animals are designed to use it as a major source of food leading to the production of ATP. The ribose monosaccharide is the backbone of RNA. A similar monosaccharide, deoxyribose, is the backbone of DNA. Oligosaccharides include the glycoproteins that are crucial to the immune system (blood type and blood coagulation), inter-cellular communication (enzymes and steroids), digestion (flavour detection and secretion of digestive juices) and our reproductive system (testosterone and estrogen). This is why human milk is so good for a baby. Glycolipids help attach each cell to the extra-cellular matrix. Polysaccharides perform the roles of storage molecules such as glycogen which stores starch in the liver, or structural molecules such as cellulose in plants.
The role of glycoproteins as an inter-cellular “smartphone” is particularly interesting. For this role they are positioned on the external surface of the cell to interact with other cells. DNA and RNA store information in sequential fashion on “rungs” of their spiral. Glycoproteins, however, can store information in a much more complex fashion via the types of chemicals that are used to bind the sugar subunits, the types of bonds used in the sugar subunits and also in the branching that occurs in the molecule. For example, glucose and galactose can be combined in 36 different ways on one just one glycoprotein, sending 36 different messages.
You can now see how this discussion of the cell as a molecular factory has uncovered a production system of exquisite order and precision. And, once again, I have only shown you the tip of the iceberg! The chemistry of each and everything described above is hundreds of times more complex than I have explained. The cell produces molecular machines far more eloquent and functional than an Airbus A380 aircraft, the space shuttle, Rolls Royce jet engines or Audi cars. According to evolutionary theory, no intelligence directed the design, construction production and application phases of these machines. As you can see, the deeper we delve into the cell, the more improbable the theory of evolution becomes.
Now we go one step further, looking at the computer system that controls the cellular city, the many factories the cellular city contains, and the machines that work so well in those factories. This computer system is the brain of the cellular world.
THE CELL AS A LIVING COMPUTER
When all else is said and done, the difference between a naturally occurring object and one crafted by an intelligent being is information. Entire human civilisations are simply the taking of raw materials and transforming them using information. The computer you are looking at now is basically a bit of dirt + information. The difference between a randomly occurring single amino acid and a functioning protein, lipid or carbohydrate molecule is likewise transformation via vast amounts of precise information. Life took a lot more than a few bolts of lightning!
Because it is alive, DNA is obviously not a computer, but when it comes to the way it operates and the storage of information, the analogy is relevant and accurate with one proviso; DNA is superior to our most advanced computers, and superior in the extreme! Bill Gates, the founder of Microsoft once said “DNA is like a computer program but far, far more advanced than any software ever created.” (The Road Ahead, page 188). The book, Biological Information: New Perspectives, which is a compilation of research papers from Cornell University, described the DNA of our cells as like the hard drive of our computers, the millions of RNA molecules like the active memory, communication between them like the internet, gene function like an executable computer program, and protein molecules like a computer algorithm.
Our biggest supercomputers cannot match the storage capacity of the DNA. Our genetic code would pack billions of gigabytes of information into a single gram of pure DNA. A mere milligram of DNA could encode the complete text of every one of the 16 million books in the American Library of Congress, and have plenty of room to spare.
From Gregor Mendel’s first experiments on hereditary, to the Spanish friend of my daughter who was recently trying to figure out the purpose of six strands of RNA, humans are sinking vast funding, time and effort into finding, analysing and recording this universe of genetic information. However, It is one thing to figure out how something works, quite another to have built it in the first place. The original source of the genetic information inside the cell must have involved a process many orders of magnitude higher and complex than the best human minds have achieved until now in activities of mere description.
Our journey now takes us into the information software systems of the cell. We will investigate the structure of the two codes of life, deoxyribonucleic acid, called DNA, and ribonucleic acid, called RNA. These two nucleic acids are the fourth and final type of matter in the cell after proteins, lipids and saccharides. Let’s start with DNA, the instruction manual for the cell.
1. Understanding DNA
Think of a spiral staircase or twisting ladder. That is the shape of DNA at its most fundamental level. Scientists call it a double helix and have found it is much more stable and compact than a straight DNA “ladder” would have been. The distinctive spiral shape comes from the highly specific hydrogen bonds between the structural side-framing molecules. The double helix is actually two copies of the one genetic code/language running down each side of the ladder, one in reverse to the other!
The two side-frames of the ladder are made from inter-connected sugar (deoxyribose) and phosphate molecules. The rungs straddling the two sides are made of any two of the following four nitrogen molecules; adenine, thymine, guanine or cytosine. We will call them A, T, G and C. The chemical properties of attraction of the DNA molecules alone determine that an A will always match with a T, while a G will always match with a C. We call them base pairs, or nucleotides. So, reading the genetic code will look something like …GGTCAATCGTAATCG… etc.
Why this particular and unique combination of chemicals? One of the many reasons why adenine, thymine, guanine and cytosine are used to construct the DNA molecule is that they absorb ultraviolet light at the same wavelength as ozone shields it from earth. This results in minimal UV damage and resultant mutations. In addition, phosphates are perfect for building the DNA spiral frame as they can form bonds with the deoxyribose molecule on both sides at the same time. They also stop water breaking down the deoxyribose sugar molecule. Deoxyribose is much more stable than ribose so that is why it is used to construct the DNA, while ribose is used to make the RNA, which needs to break down after use.
When molecular machines are reading a DNA code for copying purposes, the basic unit of information they are looking for is a three letter grouping called a codon. Each codon links to one specific amino acid. There are 64 possible three-letter codons for the twenty amino acids used for protein construction. This means that anything from one to six codons can code for an amino acid. Why this redundancy? It is a design feature that vastly reduces the likelihood of mutations because mutations occur far more frequently in highly repetitive codon sequences.
Now for some mind-boggling statistics to demonstrate the volume of information stored in our DNA: Humans have about 3 billion base pairs of genetic “letters” in their genome, which, at five letters per average English word, equates to about 500 million words of English. That’s a lot of information to fit inside a tiny cell that is 1/20th the thickness of a human hair. A gram of pure DNA would contain as much information as a trillion CD’s. If the DNA molecule was unraveled, every 2.5cm would hold 25 megabytes of equivalent computer information. There is about 2 metres of unraveled DNA in a single cell, so each cell contains about 1.5 gigabytes of information. This means there is about 75 trillion gigabytes of information inside you right now. Oh, and by the way, there are two copies of each DNA molecule inside you, so you can double all those figures! Feeling tired or smart? What we are talking about is simply the most efficient information storage system in the universe. It is so good that the best brains on earth are currently scrambling to build DNA computers. Yet we are in collective denial as to its origins and its designer.
The entire 2 meter DNA sequence is called a genome and it codes for about 23,000 specific sub-units called genes. These genes can be thousands or millions of nucleotides long. Each gene codes for a specific combination of up to 50,000 proteins and therefore a distinct feature of you, or any other living organism. This is why we talk about genes so much. It’s where we can literally see the difference in each other.
Just when they thought we understood DNA and gene sequencing, scientists discovered another layer of complexity in the genetic information storage system. Biochemists have now learnt that there are overlapping genes in some bacteria, fish and mammals. One study found just under a thousand in humans. By “overlapping” they mean that the DNA letter sequence, which is normally very exact, can be moved along one or two base pairs, read again and produce a another perfect message for coding a different protein. This is equivalent to moving the reading frame of this sentence one or two spaces to the left and the sentence still being perfect grammatical English…T hisi sequivalen tt omoving….Th isis equivale nt tomovi…!!!The best minds on earth can’t match this feat of the humble cell.
How is this astronomical amount of information stored in such a small space? Well, the already spiraled DNA ladder is first of all wrapped around a special protein binder called a histone, like a thread wound around a spool. Each histone will wrap around DNA exactly 2.5 turns. Are you surprised to learn that the initiation sites for gene replication or translation are always perfectly positioned between histones so they can be accessed?! This exact placement is driven by a histone placement code embedded in the DNA that repeats every ten nucleotides. Histones are further wrapped around larger protein binders called nucleosomes. This process goes on up through nine ever larger levels until we finally come to a complete chromosome housing a specific section of DNA about 5cm long. Given that there are between 30 and 50 trillion cells in an adult human, this means there could be 50 billion kilometres of DNA inside us. This is enough to go to the sun 300 times!
Humans have 23 duplicate pairs of chromosomes, so that makes 46 in total. Twenty two of these pairs are identical in males and females. The final pair of chromosomes are made up of an X and a Y for males, and two X chromosomes for females. This difference forms the basis of all sexual reproduction and gender development.
The reason why we have 23 separate pairs of chromosomes instead of one exceptionally long one is threefold:
First, access to genetic information is far and far easier. As part of its everyday functioning, the cell is constantly transcribing a genetic strand of DNA into RNA. These genes are then taken to a ribosome for the manufacturing of proteins. Quick access to the exact strand of DNA required is therefore vital.
Second, transcribing shorter sections minimises copying mistakes. In fact the protein molecules that control the copying process are so accurate, and can multi-level proofread so well, that only one mistake occurs for every 100 million nucleotides copied. This is truly fantastic. As an example Chromosome Number 1 has 246 million base pairs of A, T, G, and C. This is the equivalent of 200,000 pages of information.
Third, sexual reproduction requires the mixing of genes from two parents. This is why only one of each chromosome pair is passed on through sperm-and-egg fertilisation. The offspring then becomes a perfect genetic mix of the two parents. This sexual mixing of the genes is vital for our survival since genetic entropy, which is the build-up of genetic mutations over generations, would otherwise wipe out a species more rapidly than is happening at present. Yes, mutations are currently sending us down the road to extinction quite rapidly. For more on this phenomena please read my essay called Human Genetic Entropy.
2. Cell Division
When the cell is ready to divide, a protein-based molecular machine called a topoisomerase begins to unzip the coiled DNA inside each chromosome. The DNA is then both unwound and split open, like a ladder being cut down the middle. Other protein machines then come in and stitch new A, T, C and G molecules to both exposed sides of the DNA ladder, and they do this while spinning at the speed of a jet turbine. This sounds fast, but the whole process still takes about eight hours! If this process doesn’t sound difficult enough, one side, the lagging side, has to be copied backwards and in sections as it comes out as a mirror image of the leading side.
To illustrate the genius involved in this process, the lagging side has to have a special RNA protein drop a few base letters into a codon of the unzipped strand to get the process started. Then a DNA polymerase protein copies several thousand letters backwards. The whole process is repeated again and again until the job is done. Then each new disconnected section has to be stitched back together with ligase proteins to form a complete whole.
Why does DNA replication use a primer-dependent, bi-directional, mirror image duplication process? This does not speak of evolution but is a megaphone announcement that our creator has used untold intelligence and power to build the most exquisite information copying system in the universe.
Evolutionists will counter-argue that copying mistakes in the system speak of unguided consolidation rather than design, and these copying mistakes form the basis of evolution itself. Yes, copying mistakes do indeed occur on both the leading and lagging sides between every hundred thousand to a million nucleotides copied. However, to eliminate these mistakes, many built-in automatic proof-reading features constantly come to the rescue. The DNA polymerase is equipped with a proofreading system that checks the hydrogen bonds between all the molecules. When, for example, a T mistakenly attaches to a C, the polymerase backs up, spits it out and corrects it. It then continues on at lightning speed. Thus the error rate is reduced to about one in a 100 million by the time a protein molecule has been built. The culling of errors at this first and vital step in cell replication and RNA translation is crucial to the smooth functioning of the cell. The more we know about the cell, the more we see a perfectly designed machine.
Normal cellular division outside of sexual reproduction is called mitosis and nearly two trillion cells undergo this process every day in a mature human body. Mitosis has five distinct stages. First of all signals from special proteins called cyclins tell the cell when to divide. Then each chromosome pair is “told” to begin to form a supercoil from their normal linear shape. They then form a “H” shape; two identical single chromosomes hinged in the middle by a protein coupling system. All the chromosomes are then checked for readiness to proceed by more protein machines. After checking, the hinge couplings are broken and the chromosomes are dragged away to the opposite ends of the cell by mitotic spindles that are aided by dozens of motor proteins that literally walk along the microtubule cell scaffold, dragging all the chromosomes with them with perfect timing. When the cell finally divides, the cell membranes close in behind the two sets of chromosomes. The chromosomes then disappear into two new cell nuclei of two new identical daughter cells and begin to uncoil so that RNA transcribing can begin. This is the cell division process often seen on documentaries.
Mitosis is almost infinitely more complicated than this simplistic description and relies on a multitude of molecular signals and machines performing their jobs perfectly on time and in order. Just to make life more interesting, in sexual reproduction the cellular division process is completely different again. It is little short of a miracle to put it bluntly. Without it we would not exist. Unguided chemistry and physics, yeah right!
The DNA master-code never leaves the nucleus of the new cell. Its job is to house and keep safe all the instructions for the building of the protein, lipid and carbohydrate-based molecular machinery that enable the cell to do everything described above, and below in this essay. There is a vast amount of software in that little DNA hard drive so it is vital it is kept safe. So, just how does the information get from the nucleus to the rest of the cell where it is needed for all those cellular functions? This is where we begin our discussion of RNA.
3. Understanding RNA
Ribonucleic acid, or RNA, is the cell’s ingenious system of transferring instructions from the DNA code to the rest of the cell. It’s the computer downloading system of the cell. The process is called transcription and it all begins when the chromosome housing the gene to be copied is dragged over to the nuclear membrane. Part of the supercoil is then unwound, exposing just the exact section to be copied. Then one of three special RNA polymerase protein molecules creates a replication bubble enveloping this section of DNA. It then splits the DNA with a replication fork, while other proteins hold the DNA back from recoiling again. A gene sized sequence of the DNA molecule is then split open revealing a length of DNA code.
One of six sub-units of one of those three polymerase proteins has the job of finding the exact spot in the DNA code that is to be copied. After this spot has been found and properly primed by a primosome protein, the machinery of the polymerase proteins cleverly collect complimentary base letters and match them with the three letter codons of the master DNA code. As this process unfolds the polymerase spits out a copy of a short section of a new RNA molecule. The process proceeds in a stop-start fashion as the replication bubble is slower moving than the transcribing machinery. Each time the procedure stops, a short strand of daughter RNA code is produced and released from the machines to be taken away. During the transcription process the original DNA is single-stranded and vulnerable to damage so special protein machines bind to each of the two single strands to stop them from breaking.
After the transcription of the RNA is complete, the DNA is re-zipped and the chromosome dragged away from the nuclear pore. As with DNA translation in cell mitosis, the RNA transcription process is subject to intricate and complex proofreading checks and balances, making the copy as perfect as possible. How does the cell know the exact spot to copy on the incredibly long DNA strand? The answer is beyond the scope of this essay. Learning genetics has been like peeling an onion, every time I took off a layer, the process became more complicated by a factor of ten!
The timing of this DNA copying process is also exquisite. Only when the cell directly needs a new protein is RNA transcription initiated. This is made a little simpler by the fact that a cell goes through a regular process of life so there is an ordered series of stages it progresses through and only about 20% of all genes are being switched on for division at any one time. The cell thus avoids waste and the consumption of excess energy by producing protein machinery only when it is needed. It is a beautiful microscopic version of the “just in time” manufacturing system perfected by Japanese car manufacturers in the late 20th century. In addition, genes from different chromosomes coding for proteins that are all needed at the same time in the cell cycle are always switched on and copied to RNA at the same time. Proteins called transcription factors control this wave of RNA production. RNA is continuously produced for those proteins that are constantly in use. It is only produced just in time for all other proteins.
Just when you thought things couldn’t get more complicated, they do. The molecular machines do not use thymine (T) molecules when transcribing DNA to RNA. They use uracil (U) in its place. So A, T, G, and C now becomes A, U, G and C. This begs the question why? It turns out that thymine is much less likely to suffer from copying mistakes in the DNA, while uracil is much more energy efficient. Go figure!
After transcription is complete the RNA molecule is still far from ready to exit the nucleus. Parts of its length will code for proteins (exons) and parts will not (introns). The introns are spliced out and the exons joined together to form a continuous protein coding length of RNA. The reason for the introns goes back to the fact that our 23,000 genes can produce 100,000 protein molecules. The dicing and splicing of exons from different regions of the gene enables novel sections of code to be joined from a distance and then produce those other 77,000 proteins. It is like getting instructions from pages 3 and 54 of a manual for one structure and then pages 3 and 19 to build another structure. The space-saving benefits are obvious. The design behind it is beyond brilliant.
Scientists used to believe that the introns were part of what was called “junk DNA” and a result of eons of evolution. However, scientists have recently found out that introns are used for making multiple copies of the same RNA, for the variation in splicing from cell to cell needed to account for the different proteins expressed in different cell types, for changes in splicing patterns over time as the organism proceeds from fertilized egg to adult, and for seeding mitochondria with DNA. Not much junk there!
Scientists also used to think that “junk DNA” amounted to a whopping 97% of our genes. As well as junk introns there were junk pseudo-genes and endogenous retroviruses, all left over from previous evolutionary advancement. However, through our increased understanding of the human genome via the US$400 million dollar ENCODE research project, we now know this to be a false claim and we are down to 20% “junk DNA”. Can you see where this is going? In time we will eventually find out what the remaining 20% does. We now know that many pseudo-genes and retroviruses have uses. Some of them regulate gene expression simply through a function of their length, some code for protein function, some help pull the chromosomes apart in cellular duplication, others regulate embryonic development. In fact the scientific community no longer uses the term “junk DNA”. The more we learn, the more humility is emerging.
Once splicing and connection of the RNA molecule is complete, it is tagged by yet another protein machine for transport out of the nucleus. Before it leaves, specialist protein enzymes place a cap at one end and a tail at the other end so the RNA becomes more stable and protected from molecular garbage collectors. RNA is then moved by transporter proteins out through a nucleus portal to a protein-based ribosome.
Up until this point we have been referring simply to RNA. However, the entire RNA transcription process until now has been dealing with what is specifically called messenger RNA, or mRNA. The conversion of mRNA to amino acid chains is called translation, and for good reason. The procedure is like translating from English to Spanish and printing it off a computer, all in real time.
Once inside the ribosome, initiation proteins bind and prepare the mRNA sequence at exactly the right codon to begin the next stage of the journey from DNA to protein molecule. As all of the codons of the mRNA are subsequently read, specialist protein molecules act like taxis, bringing in transfer RNA molecules (tRNA) to the mRNA and locking them into position. Each tRNA has a three-pronged codon at one end that will only match a specific codon in the mRNA.
At the other end of the tRNA is a specific amino acid that only chemically bonds to that tRNA. When the reading of the three letter codon occurs at the business end of the protein, the amino acid at the other end is electrostatically released and bonds onto a growing chain of other amino acids. The amino acids string together because they naturally exchange certain electrons, creating another electrostatic bond. This “daisy chain” grows at about 3-5 amino acids per second. During this whole process many separate proofreading systems ensure that there are no mistakes
And, by the way, there is no water inside the ribosome as water destroys amino acid chains when they are being formed. This is the only water-free part of the cell. This is yet another design feature that, if missing, would destroy life.
Intriguingly, all of these hundreds and sometimes thousands of amino acids being strung together into chains are “left-handed”. This means they are not symmetrical and have a hydrogen molecule protruding from one specific side. In nature there are equal numbers of right-handed and left-handed amino acids and all unguided chemical reactions relying on pure chance always result in an equal number of left and right handed molecules. The fact that those used by the cell to make proteins are all left-handed is therefore clearly impossible and is another hint that someone way smarter than us has had fun playing with the design processes of life. You just can’t toss heads two thousand times in a row! Do I need to add that all the sugar molecules in DNA and RNA are all right-handed, and if they weren’t the helix would collapse? It just gets better and better!
The precise order of the amino acids determines the type of protein that will be built. It is this application of incredibly complex informational order and rigor to an dumb chemical object that creates the true building blocks of life. As a high school student, I was told that in the 1950’s Miller and Urey had created amino acids in a lab and were on the verge of creating life itself. What we were not told was that experiments were rigged, and that amino acids were both right and left handed, the side products were noxious and the amino acids are useless without the information to bind them, sequence them in perfect order and shape them into exquisite molecular machines. Human DNA can code for 100,000 different protein molecules in the human body. Scientists now know they will NEVER duplicate a single one if they start from scratch.
Once the amino acid chains are linked and completed inside the ribosome, they can sometimes naturally bend into a functional protein molecule on their own. However most are packaged in another vesicle and taken by a chaperone protein to the Golgi apparatus. Remember him, the garbage disposal organelle? Inside the Golgi apparatus the amino acid “daisy chain” is bent, twisted, shaped and moulded through the primary, secondary, tertiary and quaternary levels mentioned earlier into incredibly complex protein molecules. It is here that the most complex protein molecules of all will have carbohydrates and/or lipids added to form much of the essential molecular machinery of the cell. When this process is complete yet more vesicles take the completed machines to the place in the cell where they start their working life of…drumroll…about two days! The amino acids are then recycled and the process starts all over.
How energy efficient is this entire process of protein construction? Scientists at the University of Washington combined the amino acids from 108 different protein molecules using all possible permutations to see which was the most energy efficient. They found that those combinations being used by the cell always used the least amount of energy during construction. They also found they were also the most stable. In addition, those protein molecules that need the least amount of energy to construct are the most used by the cell.
To take this wonderful economy of design a step further, consider the fact that the tRNA proteins that transport a particular amino acid will never have that same amino acid in their own structure. This solves the problem of amino acid depletion. If an amino acid was in critically short supply then there would be no way to make the protein needed to transport that amino acid.
If a protein, after all the quality control and proof-reading measures mentioned above, is still mistakenly folded incorrectly in manufacture, a special enzyme will tag it with a few small protein molecules. Then a massive protein-eater called a proteasome swallows it up. This process of deliberate destruction once again preserves the cell from mutational damage and unwanted garbage. But it gets better. If the protein is not actually damaged at all and somehow accidently tagged for destruction incorrectly, the lid of the proteasome protein eater will save it from destruction. Coincidently, correctly folded proteins withstand the breakdown of oxygen and the release of free radicals (oxidation) far better than faulty folded proteins.
The mRNA molecule is inherently unstable in comparison to DNA. When it has finished its task the mRNA molecule will then begin to break down under the control of the cell recycling machinery. Fascinatingly, an mRNA molecule and the proteins it codes for have exactly the same decay rate; fast for functions in the cytoplasm and slow for functions in the nucleus.
THE CELL AS A LIVING MESSENGER
Throughout this essay I have described the astonishing internal world of the human cell from the perspective of a city, a factory and a computer. The cell screams DESIGN! to any and all who investigate its genius. Can a mega-city like New York build itself without vast intelligence? Can a factory self-assemble and then produce Mercedes Benz cars? Can a computer self-assemble and design its own software? The ridiculousness of an affirmative answer is the current position evolutionary arguments for the self-assembly of life find themselves in. This is why Richard Dawkins, in the video clip link at the start of this essay, seriously suggests the plausibility of life being seeded by aliens. Francis Crick, co-discoverer of the DNA double helix, has also had to fall back on this same pseudo-scientific explanation in order to deny a divine origin for the cell.
As the decades have rolled by, an army of atheistic but otherwise intelligent scientists have followed. They desperately and religiously search for a naturalistic invisible hand that somehow causes random chemicals to self-assemble into information-dense DNA, DNA to self-replicate, RNA to spontaneously appear, amino acids to self-assemble into functional proteins and a million other just-so events to occur so that a cell can self-generate. They will search fruitlessly forever.
This final section of the essay will deal with the sheer volume of logic that now emanates from our collective knowledge of the cell. Not only is DNA and RNA a code that gives life to the cell, the miraculously improbable existence of the cell itself leads to a clear and common sense conclusion that it is the result of an infinite mind. Antony Flew saw it. I see it. Here I will summarise the message of the cell so that you can see it too.
1. Masterful Proofreading
The prime axiom of evolutionary theory says copying mistakes, or mutations, cause onward and upward genetic complexity. However, in the real world copying mistakes always destroy, jam or add interference to existing genetic information. The scientific literature is silent on the topic of observed increases in genetic complexity via mutations. Only one in a million mutations is deemed beneficial, but they will always result in a loss of genetic information. Recorded increases in genetic complexity do not exist in the scientific literature.
On the other hand, if the cell was the product of design then you would expect there to be excellent error correction systems to prevent the cascading destruction that runaway mutations would have on the survival of the cell. As you can see from the 30 error eradication processes listed below, the cells is indeed perfectly designed to remove faults and keep itself mutation-free. While you read the list consider what would happen if a single one of these stages did not proceed perfectly, all the time. Consider also that the system was designed to find errors as early as possible, thus minimising wasted resources. Consider also that an evolutionary primitive cell would have had none of these error correction systems in place:
- The DNA information code is stored safely in the nucleus. It never leaves.
- Only when it is transcribed perfectly to mRNA can the information leave the nucleus
- If transcription is faulty, the copying stops. The error is corrected immediately
- Sections of the mRNA that do not code for protein production are spliced out
- The mRNA is then given a tail and a cap so it does not unravel
- So-called “discard pathways” eliminate any faulty mRNA in the nucleus
- All mRNA is tagged, then read by a protein that transports it to the nuclear pore
- Only mRNA with the correct splicing is allowed through the nuclear pore
- A special protein, called EF-Tu, guides the tRNA to a ribosome
- The mRNA is guided to the perfect place in the ribosome to start transcribing.
- If the mRNA is faulty it will stall the ribosome. Special proteins will then destroy it
- The enzymes that attach amino acids to tRNA rarely ever attach the wrong amino acid
- When they do attach the wrong amino acid, editing enzymes eliminate the mistakes
- If the EF-Tu detects a faulty amino acid on the tRNA, it tags it for destruction
- tRNA proteins carrying amino acids always arrive in the exact order they are needed.
- The tRNA knows exactly when to unlock its amino acid, and itself from the ribosome
- Ribosomes transcribe between 3 and 5 amino acids a second, the perfect speed
- All tRNA proteins are stable enough to be reused again and again
- All mRNA molecules are only as stable as the proteins they code for
- If any tRNA is incorrectly built it is immediately tagged for destruction
- Transporters take completed protein chains into the endoplasmic reticulum (ER)
- The ER folds all amino acid chains into many complex molecules with high precision.
- The ER will always tag any rare miss-folded proteins for destruction or recycling
- If miss-folding does build up then the ER slows production down till it is fixed
- The ER can distinguish between partially folded molecules and miss-folded molecules
- The ER uses sugar molecules as “sensors” to monitor the accuracy of all folding
- A special trigger sugar tells the transporter vesicle that construction is complete
- Vesicles then take proteins to the Golgi apparatus for additions and modifications
- The Golgi apparatus then sends the completed molecules to their work station
- If a faulty molecule still makes it to the cytoplasm it will be tagged for destruction.
This 30 point summary is a very simplified version of what actually involves hundreds of quality assurance and proofreading steps. The point should now be obvious: The cell was exquisitely designed and built by our creator to eliminate mutations. Evolutionist Francis Crick, Nobel Prize winning co-discoverer of the double helix, admits the genetic code “cannot have undergone significant evolution. A single error in codon reading would lead to wholesale errors in every process from that point on”(The Origin of the Genetic Code, Journal of Molecular Biology 38 (1968): 367-79). I agree. Perhaps this is why he believes that the DNA was seeded here by aliens, an argument that just pushes back the hard questions. Let me finish with a quote from page 20 of eminent evolutionist Stephen J. Gould’s book, The Panda’s Thumb: “Textbooks like to illustrate evolution with examples of optimal design…but ideal design is a lousy argument for evolution, for it mimics the postulated actions of an omnipotent creator.” Duh!
2. The Chicken and Egg Dilemma
In the list above and throughout this essay, did you notice the essential role protein molecules play in the process of making RNA and protein machinery from DNA? Now, here’s the giant chicken-and-egg dilemma: Which came first, the protein or the DNA and RNA? DNA and RNA need protein machinery to unzip, replicate, transfer, proofread, rebuild and thousands of other functions. Yet the protein needs the DNA for its very sequence, shape, purpose and existence. Which came first? The answer is neither, as it is structurally and causally impossible to have one without the other. They both had to be formed together, at once, and at a level of complexity far beyond the simple summary that has been described in this essay. A home cannot draw its own plans, and house plans cannot build a house. We call this the dilemma of irreducible complexity, where you cannot go beyond a certain point without the entire apparatus collapsing. We simply cannot escape a divine designer and builder.
3. Mutations Don’t Create New Genetic Material
Evolutionists appeal to two mechanisms as causal agents in the progress of evolution; natural selection and mutations. Natural selection can be easily dismissed as it has always been, and always will be, a net loss of genetic information. It gets rid of unfit individuals, losing all their genetic diversity in the process. Polar bears have lost the genetic information for black fur and small dogs lack the genetic material for size. It is gone forever from those individuals. There is never an increase of genetic material with natural selection. It is a one way street. In addition, natural selection cannot be invoked for the initial creation of life as, by definition, it can only act on living things, favouring the survival of the fittest living thing.
Mutations are different story. They involve a definite change in the structure and transmission of genetic information to the cell via proteins. They are genetic spelling mistakes so it is theoretically possible that they could create new genetic information, like accidently spelling a new and better word. Mutations are the only possible and plausible explanation that exists for the macro-evolution of life. Mutations supposedly added extra useful genetic material to the gene pool over millions of years, allowing organisms to become more complex.
However we now know that deleterious mutations outnumber beneficial mutations by the order of up to 1:1,000,000 (Gerrish and Lenski 1998). In addition, if the deleterious mutation rate is over one per person per generation then it guarantees eventual human extinction (Muller 1950, Crow 1997). We now know that the rate is a bare minimum of 75-175 per generation (Nachman and Crowell 2000, Campbell and Eichler 2013). The true rate is actually closer to 300. In summary; mutations did not build us, they are destroying us. And fast.
There are mutations happening every time reproduction occurs today. So we can test the evolutionary thesis by looking for examples of mutations producing specific benefits, more complex genetic sequences, and new biologic features. But we can’t find any. We do find some exceedingly rare beneficial mutations, but these are still corruptions of existing genetic material. We never find mutations adding positive genetic information to a genome anywhere in nature. The central problem with mutational change is that it always leads to biological degradation. The cell “knows” this and goes to great lengths to avoid them. Like natural selection, mutations are a one way street going in the opposite direction to evolution. Mutations will always result in defective protein production, leading to faulty cells, faulty tissue, faulty organs, and almost always to a myriad of diseases at the host level. In medical circles mutations are universally regarded as disastrous. The World Health Organisation now lists over 10,000 genetic diseases and the list grows every year. Spelling mistakes do not make better English and dents on a car do not produce spare parts. The prime axiom of evolutionary theory is a big fat lie.
Intriguingly, the vast majority of the 100-300 mutations per individual human per generation are very minor. They are not bad enough to prevent sexual reproduction. So they accumulate in the gene pool in a linear fashion. So the older the species, the more mutational drag exists in its gene pool. This is the exact opposite of evolution. It is degenerative devolution. To illustrate this point, humans are currently de-generating at the rate of at least 1-2% per generation, with an extra 100-300 or so more mutations in your children being added to the millions already in you. The problem is currently so bad that it is estimated that humans will be extinct within thousands, not millions of years. Genetic entropy, in layman’s language this means extinction, is a one way ticket for all species. Life on earth is not evolving, it was designed and made perfect, but is now cursed and heading toward extinction. Large long-lived organisms will die out first as they have more cells and more life time for mutational build. If humans had been on this planet for millions of years we should have died out a hundred times over. Try telling that to a biology professor.
4. Bio-Chemical Repetition
If all the inordinately complex biochemical systems described in this essay were indeed the product of chance and evolution, then how did they evolve identically and independently of each other multiple times throughout nature. There would be hundreds of thousands of improbable improvements proceeding down hundreds of thousands of improbable pathways preventing such an outcome. Evolution, by definition, is a non-repeatable event.
Yet we do find repetition again and again and again. The first was discovered in 1943 when it was found the same enzyme existed in yeast and rabbit muscles. With the exponential growth in knowledge of genomics, we can now document hundreds of examples of five distinct and different types of identical but supposedly independent “evolution”. The list is growing rapidly. How can it be that the very same identical bio-molecular systems evolved independently many times over in separate species? If evolution is true then this development is not just impossible, it’s absurd. If life came from a divine mind, then it is entirely logical and probable.
5. Information Never Arises Through Chance
The DNA language/code transfers vast amounts of highly specific information via sequences of code. That’s what languages and codes do. The DNA language/code comes to us in a format like Morse code or braille, but with chemistry instead of dots and dashes. However, the format that the language arrives in is not the purpose of the language. Take the combination of three lines that create this letter: R. This visual shape has a specific meaning only to those who understand English. The meaning behind the letter R has nothing to do with the ink and paper, computer screen, braille book or Morse code on which it is sent. It matters little how it was sent, it matters what it means.
What must always be remembered when studying DNA is that, just as the letter R conveys much more than a few random lines of ink on a page, so the actual message contained within DNA is completely separate from the chemical “ink” on which it is written. Evolutionary theories for origins have no explanation for this conundrum as information never arises by chance, only through applied intelligence. The origin of vast amounts of information inside life itself cannot be explained if matter, energy, chemistry and physics, is all there is to existence. To avoid this unsurmountable problem, evolutionists will often say their theory is about what happened after the construction of the first cell. In the words of Dawkins “Nobody knows how it started.”
6. Probability or Impossibility?
All evolutionary explanations for the origin of life lead people to believe life was somehow destined to begin through the guiding hand of chance and natural selection, with no divine intelligence needed. “Mother Nature” did it. Evolutionists do at least admit the probability of life arising this way is extremely low. But it must have happened once because we are here. This reasoning, by the way, is a circular argument. Evolutionists maintain that the cellular proteins and organelles we now have are the result of a long process in which favoured genes are preserved, so things are gradually built up to the complexity we now see in today’s living species. The fundamental problem with this argument is that it invokes natural selection, a process that only involves the existing reproduction process of living species as a mechanism for eliminating unfit mutations. That the vast majority of mutations are minor and passed on to the next generation is conveniently ignored. Genetic entropy is a taboo topic among evolutionary biologists, but an open secret among leading geneticists.
This leads us to a more objective discussion of the probability of amino acid sequences and proteins arising by chance. In the real world of today’s chemical laboratories things work very differently than in the world evolutionary just-so theory. Chemical processes, physics and time have never shown the remotest tendency to assemble anything complex as they are never subject to natural selection, and natural selection only ever acts on existing life forms! In the process of the sequencing of amino acids to form proteins and the first life form, there was absolutely no significant chemical preference which forced a particular sequence. So it is quite valid to calculate the true probability that a protein full of left-handed amino acids fully assembled itself purely by chance into a perfect information-dense sequence of genetic code.
Let’s demonstrate the odds of a single complete 100 amino acid length protein molecule assembling itself by pure chance by examining the probability of spelling the 23 part phrase “the theory of evolution” by pure chance. This would simply involve the random selection of letters and sequencing of those letters and spaces in the correct order. It turns out that it is not simple at all and that, at the rate of billion attempts every microsecond, chance will spell the phrase above correctly only once every 25 billion years! This phrase is infinitely simpler than the smallest protein, let alone life form!
For the entire genetic code, Biophysicist Hubert Yockey determined that the evolutionary process of natural chemical selection (which as we have just seen, cannot even be invoked) would have to produce and explore some 1.4 x 1070 different genetic codes inside 6.3 x 1017 seconds before settling on the genetic code now found in nature. This would require sorting 1055 entire genetic codes per second to have found it in the timeframe of evolutionary history.
You are far, far, far, far, far, far, far better off buying a lotto ticket!
7. The simplest Life is Still Complex
So, even if we could actually climb Mount Impossible and miraculously produce a simple protein molecule by pure chance, we still have not produced life. Life in its simplest form requires a fantastic array of irreducibly complex, and interlocking machinery to function. Scientists now know that their simplest theoretical first life form had to contain between 250-600 genes to function and self-replicate. We are talking here of about half a million nucleotides or base pairs housing vast amounts of information, duplicating this information for reproduction, transferring this information to amino acid chains, turning them into functional proteins inside an enclosed safe space, self-reproduction, and doing it all with energy obtained from outside itself. To get to this point consider the following essential simultaneous and accidental assembly requirements as the bare minimum for that organism:
- The self-assembly of boundary membranes
- The self-formation of energy capturing abilities by this boundary
- The self-creation of DNA, RNA and all the hundreds of proteins used to process them
- The introduction of pores into the membrane for respiration and access to resources
- The self-generation of production systems to allow proteins to be assembled
- The self-generation of catalysts that dramatically speed up all cellular functions
- The accidental introduction of vast amounts of information into the system
- The accidental ability of this information to perfectly replicate chemically
- The self-generation of mechanisms that allow for duplication of all vital functions
- The self-formation of replication system safeguards to avoid mutations
All these processes require a functional DNA, while DNA requires all these functions to survive. We are now looking at a probability factor of many orders of magnitude greater than the simple sentence exercise we went through above. It’s all now getting super-astronomically improbable! Impossible actually.
To give you an idea how impossible the building this structure would be, in 2012 scientists from Stanford University constructed the world’s first real time computer simulation of all of the internal functions of the bacteria Mycoplasma genitalium, considered to be one of the simplest independent life forms on earth. It took 128 computers to handle the information flow that continually takes place inside this little bacteria. Please note that this is just for the functioning of this organism, not its unguided construction from inorganic components.
9. Early Earth, Early Death
So, let’s assume, for argument sake, that life did actually surmount all the obstacles discussed above and was birthed by pure chance in an early ocean, either here or on any other planet! What are the chances of this very first life form surviving more than a few seconds before being destroyed by its very surroundings? Here are a few of the reasons why the survival of the first hypothetical evolutionary cell is highly improbable given its hostile environment:
- The atmosphere of earth when life is supposed to have evolved was devoid of oxygen. If there was no oxygen there would be no ozone and ultraviolet light would instantly destroy all bio-chemicals.
- The conditions that were alleged to lead to the formation of adenine (the letter A in a DNA nucleotide) can occur only in the presence of oxygen. There was no oxygen.
- All solar and chemical energy sources that produce bio-chemicals destroy them even faster.
- Sugars react destructively with amino acids, but both must be present for a cell to form as they help build DNA, proteins and RNA.
- Metal ions readily form complexes with amino acids, hindering them from involvement in other reactions.
- Water is a poor medium for condensation of chemical chains. In fact it destroys amino acid chains and sugar molecules.
- Heating to evaporate water tends to destroy some vital amino acids.
- The alkaline conditions needed to form sugars are incompatible with acid conditions required to form polypeptides.
- Life requires molecules with all the same handedness. Proteins have only left-handed amino acids, while DNA and RNA have only right-handed sugars.
- No geological evidence has been found anywhere on earth for the alleged primordial soup.
10. Then There’s the Big Picture
In all my discussion about the cell so far I have deliberately not engaged with the issue of multicellular life, until now. Evolutionary arguments for the existence of multicellular organisms must account for the vast and almost infinite complexity of millions of species of life interacting with their environment, communicating, surviving, reproducing, relating, colonising, sensing and thinking. All this from the starting position of never-ending copying mistakes and blind selection, no intelligence allowed!
Then there is the “minor” issue of trillions of cells, each one almost identical to its neighbour and being able combine into a team to maintain homeostasis, breathe air, absorb oxygen, eat, digest, excrete, pump blood, remove toxins, communicate, think, fight infection, move, stand up using bones, grow, sexually reproduce, see, hear, touch, fly, swim, breathe water, defend, and much more. Any transitional life form that did not have a single one of these functions working perfectly would have been removed by our dreaded enemy natural selection. To illustrate the point, imagine how many intermediary stage mutations it would take to produce an eye. At every step along the way the emerging blob is a huge hindrance to survival and the individual much more likely not to survive the natural selection process. Multiply this problem by thousands for all the other functions of the body.
Evidence for transitional forms is as rare as beneficial mutations, even more so. Doctor Colin Patterson, once head paleontologist at the British Museum of natural History famously admitted he can’t find any. Stephen J Gould, professor of paleontology at Harvard University likewise admitted that the lack of transitional fossils was a trade secret within his profession. Transitional forms are a concept that has no basis in evidence.
So, the causal mechanisms of evolution, mutations and natural selection, are a myth not reality. Which makes perfect sense if you remember that they are not intelligent, have no IQ and have no predisposed direction. How then can they produce perfection in every life from on earth? A global level of perfection in motion, survival, breeding and LIFE does not come from chance, chemistry and continual error.
11. Darwin or God?
As I have clearly demonstrated in this essay, the cell contains all the hallmarks of an intelligent origin. It easily passes the test of possessing fantastic patterns, significant information, near perfect design, obvious construction, precision, purpose, amazing eloquence and efficiency of function. Study of the cell is like entering Alice’s rabbit hole. It just gets “curiouser and curiouser” the more you delve into its fascinating world. I could continue with many more reasons why the cell is a divine messenger as I have barely scratched the surface of cellular chemistry, physics, function and structure.
However, most people become very uncomfortable when confronted with evidence that demands they change their worldview, beliefs and lifestyle. At the end of the day people, no matter how educated, are stubborn. They believe what they want to believe, what they are told to believe and what suits their lifestyles. There are none so blind as those who will not see.
All the obvious pointers to a divine origin for life and the cell cannot perform the job of convincing someone who is determined not to be convinced. Few and far between are the brave souls like Antony Flew, determined to go where the evidence leads. There are many excuse makers, like Richard Dawkins and Francis Crick, who resort to pseudo-science and plead for an alien origin to DNA and the cell. They remind us of why Darwinian evolution became the cornerstone of western intellectualism, it simply appealed to a growing desire for an atheistic religion. Charles Darwin, totally ignorant of genetics, then became the poster child of this new worldview.
Knowledge will eventually lead to truth, so I will end this essay with a prediction: Sometime in the future, probably before 2100AD, our increasing knowledge of the cell will create a crisis of faith in Darwinian evolution and global atheism, destroying them both.
Romans 1: 20
For since the creation of the world God’s invisible qualities, his eternal power and divine nature, have been clearly seen, being understood from what has been made, so that people are without excuse.
Thank you for reading this far!