Protein Synthesis in The Cell
The proteins that humans ingest for their nutrition are not all used by the body in the same form. First of all, they are decomposed into smaller molecules called amino acids. Later on, these amino acids are brought together in new arrangements to make any one of the 200,000 different types of protein encoded in the DNA which may be needed at that particular time. The name given to this complex process, each step of which is a miracle in itself, is protein synthesis. Each step is broken down into tens of other steps. Without even realizing it, during your daily routine, these processes are repeated over and over again in the 100 trillion cells throughout your body.
A Giant Factory that can't Be Seen with the Naked Eye
In order to understand this topic more fully, let's remember that the cell's organizational setup for protein production can be compared to a giant factory that can manufacture hundreds of different products all at the same time. Obviously, no factory on Earth can perfectly manufacture such a wide range of products. In order to understand the cell's perfect production methods, we can imagine a science-fiction model factory that possesses similar features and abilities.
Such a theoretical factory would work as follows: An external command arrives at the factory, and the decision is made to manufacture (for instance) a fighter plane. The plane's technical details are stored in the factory's computer, along with all its other measurements and specifications. The computer presents all these calculations and measurements into a plan that the production-and-assembly robots can understand, and sends these plans to them by special transport systems.
Carefully, the assembly system begins to manufacture the plane. Its every part is brought by an assembly robot responsible solely for that particular piece and then is assembled in the correct location. The smallest error will later result in the plane falling out of the sky; but the system makes no mistake. On the rare occasion a defective product is produced, it passes through sensitive quality-control checkpoints and is removed from the assembly line, whereupon the defective product is disassembled and its parts are used for new products. Nothing is wasted. At the same time, the factory is able to produce hundreds of other products such as dialysis machines, computers, and cars. Some of these products it uses for itself, and others it exports outside.
The cell's organization is actually much more perfect than this science-fiction analogy suggests. As mentioned before, the human body uses more than 200,000 different types of proteins, and all of these are synthesized in the cell. The plans for all of these proteins are also found in the cell. But the cell selects from its DNA only the information needed to make the proteins it will use for itself or it will export outside, and then makes only these proteins. The functional differences between the proteins it produces are at least as great as the differences between those of a plane and a television.
How Is the Synthesis of Proteins Realized?
- Whenever the body needs a protein, a cell or a group of cells goes into action to implement a series of complex processes. This may be a type of protein that the cell may need to use in its own structure or that it will export for outside use. The cell itself decides which proteins it will use within its own structure, but when it comes to making proteins for outside use, special messenger proteins are sent to the cell.
- All information about the particular protein's structure is encoded in the nucleus within the DNA. All instructions relevant to the protein to be made are copied from the DNA with the aid of many enzymes and a strand of RNA molecule produced from this DNA. The protein will be produced according to the information in this RNA, which has been copied from the DNA. And so, this RNA is referred to as messenger RNA (mRNA; Figure 3.1 ).
- The mRNA, having received its instructions, heads towards the ribosomes-the cell's main production units. The ribosomes read the instructions, starting from the beginning of the RNA strand. Each code in the DNA is made up of three bases called a codon, and represents one amino acid in the protein chain.
- Using the order it has obtained from the RNA, the ribosome joins together the amino acids to form a chain.
- One by one, the amino acids are brought to a molecule called the transfer RNA, or tRNA. Every tRNA carries its own special amino acid. The tRNA carries the amino acid on one end and on the other, the code with the address where the tRNA will deposit its load (the anticodon; Figure 3.2).
- The tRNA that arrives at the ribosome aligns along the mRNA transcript at the described address. There it deposits the amino acid it is carrying and moves away from the ribosome. The ribosome moves one codon (three bases) along the mRNA transcript. Another tRNA molecule arrives at the new address and aligns along the mRNA, depositing its amino acid. Once all of the codons have been "read," the amino acids join together to form a protein molecule.
As you can imagine, the event crudely outlined in a few sentences above, in reality occurs as a result of processes that are miraculously complex, beyond the limits of what the mind can conceive. But they do leave us facing some important questions.
The first has to do with the beginnings of protein synthesis. How does a cell-which cannot be seen with the naked eye, formed from mindless molecules-make the decision to start producing something? The ability to decide, think, and evaluate is a feature of conscious living things. Obviously, unconscious molecules of carbon, hydrogen, oxygen and nitrogen atoms don't possess the ability to make decisions. There must be another power inspiring the cell to make these decisions and then directing it accordingly.
Once a decision is made, the next step is for the messenger RNA to read the instructions encoded within the DNA. The enzyme responsible for producing RNA finds in the DNA only the instructions needed for the desired protein-but in reality, the process is extremely difficult. Finding the relevant information in the DNA means locating and extracting an instruction consisting of 900 base pairs from a store of 5 billion. This is like trying to find one particular sentence in a 20-volume encyclopedia, without any help. However this problem has been made easy in an awe-inspiring way: The relevant portion of the DNA has been marked by "start" and "stop" labels that the enzyme can find.
Who has placed these labels, understood only by enzymes, in the relevant places? Who gave these enzymes the ability to recognize these labels?
The undoubted answer to these questions is clear: the One Who made these faultless systems and the One Who placed every detail where it needs to be, and Who has allowed all of this to proceed in harmony is the Creator of all living things, God, the Possessor of infinite knowledge.
All Manner of Precautions
Enzymes do not stop once they've found the relevant information. They facilitate its being copied at great speed, but some enzymes keep any problems from arising during the replication of DNA's highly complex structure. You'll recall that the DNA molecule is coiled, and shaped like a spiral ladder. During the replication stage, the rungs of the ladder need to open up so that their information can be read, and this is done by an enzyme. This unwinding process is so fast that friction might cause the DNA molecule to heat up and disintegrate. But this danger is overcome by precautions that have been taken beforehand. A special enzyme holds both sides of the helix apart, preventing any friction. Again with the help of special enzymes, the DNA molecule is prevented from getting tangled and messed up while being unwound during replication.
Remember, the enzymes that carry out such complicated and difficult tasks are just proteins themselves, also produced by the same method: protein synthesis inside the cell. In order for this production to be carried out, all of the required enzymes, the vitamins that help the enzymes, helper proteins and energy sources, the required genetic instructions and production organelles-are all needed at once, and in the same place. The lack of just one of these components will render the whole mechanism ineffective.
Consequently, the first cell that ever appeared on Earth had to have formed in its entirety, all at once. Undoubtedly, this means that the cell was created-a situation that evolutionists can never explain, proposing that living things formed step by step as a result of coincidences. Two evolutionary scientists Fred Hoyle and Chandra Wickramansinghe express the quagmire within which evolutionists have fallen:
The Enigma of Unwanted Sequences
During the copying of DNA by RNA in some cells, amazing events take place. The enzyme that produces RNA reads and copies the code in the DNA relevant to the protein it will produce, but it sometimes runs across codes that aren't needed for this production. Because during replication, the enzyme reads the DNA fragments in order, it has to read the irrelevant instructions as well. But remember, even one irrelevant instruction can render an entire synthesized protein completely worthless.
Let's examine in more detail the problem this enzyme encounters. Say a protein of 1,000 amino acids is to be produced. If each amino acid is represented by three bases (a codon), then in order to perform this duty, the enzyme needs to read a 3,000 base pair DNA sequence-in order. But within this 3,000-base pair sequence is a complete sequence of say 500 base pairs for which the enzyme has no need. But in order to reach the instructions that follow, the enzyme cannot just skip over these 500 base pairs without copying them. It must copy them whether it wants to or not. The enzyme cannot cut the giant DNA molecule, nor can it skip over it. What would you-a human being, possessed of intellect-do to solve this problem?
In recent years, scientists have observed the fascinating way in which this problem is solved. The DNA molecule, made up of simple materials like phosphate, sugar, and carbon, acts in a way which leaves one dumbfounded. The unwanted sequence, called an intron, is coiled into a loop outside of the main sequence (see Figure 3.4). In this way, the ends of the codons that need to be read one after the other, but which are separated by irrelevant information, are brought together. The regions containing the necessary information are called exons. The enzyme that reads the DNA sequence passes by without reading the instructions contained outside in the loop and continues reading on the other side. As you can imagine, many different chemical reactions occur at each stage of this event. But in the nucleus of the tiny cell, there is not the slightest confusion or chaos arising from these reactions.
A second method is used to prevent the problem of the introns. The RNA first copies the entire DNA molecule from start to finish, including the irrelevant sequences. Later on, as if obeying a command, it coils out the unnecessary sequences in loops, which are then broken off and removed (see Figure 3.5). But who tells the RNA that the sequences it has coiled up and broken off are irrelevant and unnecessary?
The enzyme that brings about these events must be very familiar with both the DNA and the RNA molecules. It must have received special training for such a specific job, know its responsibilities and work in a cooperative manner with the other enzymes to carry out its duty. On the other hand, the DNA, like a separate living entity, must have the ability to make decisions and, according to the situation, present certain instructions to the enzyme while keeping others from it and guiding the enzyme to what it needs to do. And of course both the enzymes and the DNA need to know the function of the protein they are manufacturing. First of all, they need to know what protein needs to be made, then must make the necessary plans and all the complex calculations to bring this about.
But it is clear that such abilities as knowing, calculating, wanting, and creating cannot exist in this heap of tiny molecules. These functions are attributes of God, the Master of Infinite Power. As He displays these attributes throughout the whole universe, so does He display them in the lifeless molecules in the nucleus of a tiny cell. A person of any intelligence would understand that this system has been created and, just like all of the other systems in the universe, the cell is also under God's absolute control.
His dominion over all of creation is given in the Qur'an as follows:
I have put my trust in God, my Lord and your Lord. There is no creature He does not hold by the forelock. My Lord is on a straight path. (Qur'an, 11:56)
Getting the Order Ready
As a result of the processes enumerated in the previous section, the instructions needed for the order for the particular protein are transferred by enzymes from the DNA to the messenger RNA (mRNA). Now it's the ribosomes' turn to manufacture the particular protein, according to orders given them by the DNA. The ribosome manufactures a substance to the exact specifications desired. The structural plan of the ordered protein is also found in the mRNA. The mRNA, together with the instructions it has copied from the DNA, moves out of the nucleus and towards one of the ribosomes found in the cytoplasm, to which it binds. An amino acid, corresponding to each codon in the mRNA, is brought to the ribosome by transfer RNA (tRNA), and attached to the relevant site. To one end of the tRNA is attached the anticodon of one of the codons in the mRNA, and on the other end is the amino acid represented by the codon. As the tRNA binds to the codon in the mRNA that corresponds to its own anticodon, the amino acid it bears is automatically placed in the correct sequence.
There are 20 different tRNA molecules for the 20 different amino acids used. Each amino acid can bind only to its own tRNA. This is because in order for them to bind to each other, their three-dimensional shapes have to fit together exactly (see Figure 3.7). The fact that the tRNA and the amino acids, composed of thousands of atoms, have been made to fit together is a proof of the harmony and perfection in God's creation. God is the Creator, the Maker, the Giver of Form (al-Bari) (Qur'an, 59:24).
Thousands of amino acids join together to form the desired polypeptide chain (or protein molecule), according to the thousands of instructions found on the mRNA arriving at the ribosomes on which the protein is synthesized. Not even one extra amino acid is included in the mRNA plan to be attached to this molecule. No amino acid attaches to a different site than what the plan requires, and no amino acid is left out. If any of these mistakes occur, the desired protein will not be made, and a different, unwanted protein will be synthesized. But cells and organisms will not generally tolerate foreign proteins. They will make antibodies against them and demonstrate an allergic reaction.
Like other elements in the cell, ribosomes are formed from lifeless atoms. But this heap of protein succeeds in manufacturing thousands of different products by numerous complicated processes, with an intelligence that cannot be its own, but which is possible through the creation of God.
The synthesis of just one protein, according to instructions given in the DNA, requires at least 75 helper molecules in the cell working together in harmony. The enzymes carrying out the duty of copying the instructions in the DNA are not included in this number.
Each protein molecule is made, the last amino acid is attached, and the protein is complete. But the synthesis is not considered finished until the cell (or more correctly, its ribosomes) go through one more control checkpoint. If any fault is found at the last minute, the cell does not just say, "That's good enough. Let this one go through," and produce a molecule like this outside of the plan. Such tolerance, allowing the construction of a protein that's not the one originally planned, will degenerate the cell's control system and drive it towards dis
order and destructive anarchy-a state that comes about only in pathologic conditions or when the cell is dying.
Under normal, healthy circumstances, a protein molecule that is incomplete and imperfect is delivered to destructive enzymes that break many or all of its peptide bonds. They reduce the protein to its constituent amino acids or into short, harmless polypeptide chains and leave them available as structural building blocks for other protein syntheses.
This cellular process amazes even Prof. Muammer Bilge, a Turkish evolutionist academician and cell specialist:
Life cannot Arise by Coincidence
How does evolutionary theory explain how proteins, the first stage of life, were first formed?
The answer is simple: it cannot. The evolutionists' claim is nothing more than that proteins came about by chance, as a result of a series of coincidences. Examining their claim's inconsistency, we can see how strikingly deceitful evolution really is.
How could the first protein molecule have come about by coincidence, under such uncontrolled conditions as-according to the claim of evolutionists-existed on our primitive Earth? How could the ordering of amino acids have come about "by chance" despite all the negative factors present on that primitive planet?
What's more, it's not enough for just this one protein to have formed itself. In this wildly uncontrolled environment, it had to wait for another protein molecule to form just like itself-by coincidence under the same conditions-without anything destroying it in the meantime. This had to occur again and again until at last, millions of appropriate and necessary proteins had come together "coincidentally" in the same place to form the cell. The very first proteins that formed had to wait patiently for thousands and millions of years for other proteins to form right next to them-without being destroyed in the meantime despite ultraviolet radiation and a harsh environment. Then these proteins, assumed to have formed by coincidence in enough numbers and in the same place, had to have come together in a meaningful way to form the organelles in the cell. No foreign substance, harmful molecule, or useless protein should have been incorporated into the chain. These organelles had to come together in the most organized fashion, with all the necessary enzymes, and had to have been surrounded by a membrane, containing a special fluid that constituted the most ideal environment.
But even if all of these implausible events took place, the pile of molecules that resulted still would not have come to life.
Research has shown that the mere coming together of substances necessary for living things is not sufficient enough for life to come about. Even if all of the proteins needed for life were placed in a test tube, they still wouldn't result in a living being, because life is much more than just a few molecules being found together.
Life is a metaphysical concept. Life is a reflection of the al-Hayy (The Living) attribute of God. Only with His will does life begin, continue and then cease. Just like everything else, life comes about through the mere command of Be from God.
The theory of evolution cannot explain how the necessary substances for life formed, nor how they came together, nor how life first started.
Let's for a moment accept all of these impossibilities: that billions of years ago, all of the substances needed for life came together as a living entity. Alas, the theory of evolution is still destined to collapse! Even if the cell became alive, eventually it would have died. There would have been nothing left, and we would have been back where we started. Because this first living had no genetic system in place, cell would have died not having been able to replicate itself and therefore, could not have left behind a new generation. Life would have expired along with the cell.
The genetic system is not made up of just DNA. Vital components include enzymes that read the code in the DNA, the production of mRNA from the reading of this code, ribosomes upon which the mRNA with its codons binds, the tRNAs that carry to the ribosomes the amino acids to be used in production, and innumerable other complex enzymes that facilitate these processes. All had to be found in the same environment-which, moreover, had to have been completely isolated and controlled. Only in the cell itself are found all of the needed raw materials and energy sources. Consequently, an organic substance can replicate itself only if there first exists a completely functional cell with all its organelles in place. This means that the cell, with its all incredibly complex structure, was created in one instant.
But for a complex structure to come into being instantaneously, what are the implications?
We can compare the cell's complexity to that of a highly developed car (even though the cell actually constitutes a much more complex and highly developed system). Now, suppose you went for a walk through an untouched forest one day and found the latest model car among the trees. All the raw materials making up the car-iron, plastic, rubber, etc.-are made from substances that occur naturally. But would you believe that such a sophisticated, user-friendly machine came about as a result of the coincidental coming together of different elements in the forest over millions of years? Would you think that these various substances were also made coincidentally, and then came together to make such a car?
Of course, you know that any car is the product of conscious design-by engineers working in a factory. And you would wonder what it was doing in the middle of a forest.
For such a complex structure as the cell to come into being in one instant indicates that it was created by a conscious Being. The probability that one useful, meaningful protein could come about by chance is zero, so how impossible is the coming together of millions of these various proteins to form a cell?
Moreover, this chain of impossibilities does not end there. Even if the millions of proteins needed came about by coincidence and gathered at the same point, this is still the equivalent of simply heaping bricks and cement onto a site where a sophisticated skyscraper is to be built. Only with a plan of utmost complexity, after the most sensitive measurements, calculations, and assuming a chain of order and command among intelligent builders, can such a skyscraper be erected.
But some people, on seeing a skyscraper, will ask, "Who built this?" yet still wonder about the "coincidences" that brought about living things. This blindness is really difficult to understand. To understand this is possible only with the advice given in the Qur'an because, as the Qur'an informs us, some people "have hearts they do not understand with. They have eyes they do not see with. They have ears they do not hear with. Such people are like cattle. No, they are even further astray! They are the unaware." (Qur'an, 7:179)
The fact that some people cannot see clear truths that are in front of their eyes and their denial of their Creator is one of the miracles of God. And like other miracles, it too is astonishing. Just as the creation of the Earth, the Sun and everything in the universe is a sign of God's infinite power and knowledge, so too is the creation of one who denies, even though surrounded by an infinite number of proofs-another sign that God has power over all things.
If you are surprised at their blindness, what could be more surprising than their words: "What, when we are turned to dust, shall we then be created all anew?" These are the people who reject their Lord. Such people have iron collars round their necks. Such people are the Companions of the Fire, remaining in it timelessly, for ever. (Qur'an, 13:5)
Some Other Examples of Discrepancies
The living cell possesses the most complex structure the scientific world has ever come across. Even the single cell of tiny prokaryotic bacterium-the simplest organism capable of living as a separate entity-has developed such complexity that the technology of a space shuttle is simple by comparison.
To accept the impossible, suppose that the cell did form coincidentally and then let's consider the plausibility of this supposition. In this situation, most of the innumerable objects and tools we see around us, which are much simpler in structure than the cell, would have to have been formed a thousand times easier than the cell. According to the rules of simple logic, the formation of a less complex object by chance is much easier than the formation of a more complex object by chance. If this highly complex structure could have formed on its own, then simpler ones in the same environment would have to have formed much more easily and in greater numbers. Consequently, if we accept for a second that coincidences have the power to create, then the probability that a television, a car, a microchip or a walkman could form at random, with no creative mind, in a primitive environment, is much higher than a cell theoretically forming by chance. (Without a doubt, in reality, the possibility that these formed by coincidence is zero, and this is a solely imaginary example, the cell included).
Consider another discrepancy.
For a living cell to form, multiply, and continue the next generation, the proteins making up a major part of the cell's components and the DNA that facilitates genetic transmission must have been found together at the same time. If all the proteins and enzymes, organelles, cell membrane, and DNA all came together at random, even this is not enough to form a cell because of one great danger: DNA can in no way come into contact with these proteins since DNA is acidic, and proteins are bases. Whenever they come in contact, they will immediately react and neutralize each other. Even if the DNA nucleotides and the proteins came together in the "primitive soup"-the imaginary environment so named by evolutionists-they would have destroyed each other and never moved on to the next step.
Another miraculous aspect is that although an acid and a base naturally react together when brought in contact, in the cell these two substances display perfect cooperation and work together in harmony to facilitate production-yet their coming together freely outside of the cell spells destruction for both of them.
As always, this system has been planned in great detail, with all manner of precaution. The DNA has been placed in the nucleus, the safest of all places in the cell, and isolated by very sensitive and special means from surrounding structures that might harm it. During the DNA replication process, contact between the DNA and the enzyme proteins occurs in such a controlled and measured manner that no molecule is damaged, and both substances enjoy the highest productivity.
Molecules have No Consciousness
Biology books by evolutionist authors commonly emphasize that the elements of the processes we have discussed apparently act with conscious intent. Whether writing about the cell, the RNA or the DNA, the enzymes or the organelles, we too frequently used verbs like reads, decides, chooses, tries, repairs. Quite clearly, these verbs can only follow a noun that possesses knowledge, intelligence and will. But the cells we have written about up to this point are composed of mere atoms and molecules that in no way possess the ability to think, make decisions, or reason.
As made clear in previous sections, however complex and amazing a structure the cell may have, it can in no way possess intelligence or consciousness. For this cell or any of its components to desire, decide or control anything is consequently not an issue.
For this reason, verbs such as decides, controls and repairs, assumed to apply to the cell, need in reality to be attributed to the knowledge and intelligence of the Creator.
For example, when we say "this book is trying to say that…" it is obvious that we are talking about what the author of the book is trying to say. Otherwise it is clear that it cannot be understood from this expression that the book itself, its pages and its ink, thought about something and then tried to explain it. (For this to be understood by someone would indicate that that person has a serious mental health problem).
In the same way, expressions such as wants, decides, calculates, which are used in many parts in this book, are just analogies chosen to practically describe and depict the events that take place. To attribute false meanings to the words other than what they mean will lead man into a deep misconception. It's obvious that the will to desire and decide does not come from this heap of unconscious molecules. These characteristics, the creative power that allows this pile of molecules to carry out such conscious and calculated acts and that creates these according to their duties belong only to God. The One Who desires, and decides and makes to happen is God.
That substances we cannot normally form a connection with such concepts carry out these extraordinary acts is a means whereby we can perceive more easily and clearly the true possessor of power and intelligence behind them all.
Up to now, we have explained just a few of the miracles that take place in the cell and in the human body. Anyone with a conscience can perceive the perfection in the creation of his own body and by thus knowing God's handiwork, can grow closer to Him. In contrast, those at a lower level of intelligence will of course maintain the perspective that "However all of this happens, it happens. I care only about what goes in my pocket and down my throat."
But a person of knowledge and conscience will ask, "Why was this perfect system created? And who made it?" There is only one purpose behind this system in each of the trillions of cells in the human body: so that man can perceive and comprehend God's infinite knowledge, intelligence, power and perfection in His creation, and His close attention… Man must realize that not even one molecule within a cell can act without His permission and knowledge, let alone behave like a conscious human being who walks and talks.
Even if we assume that there were no other miracles on the face of the Earth, the fact that 5 billion instructions have been stored in a single cell is enough proof for a person of knowledge and conscience to have faith. And the same proof will this time be proof against those people who, having received such knowledge, turn their faces from God-proof that will drive them to punishment on the Day of Judgment.
God, the Possessor of infinite mercy, displays an infinite number of proofs not just in the tiny cell but also right throughout the universe. Those who believe can further strengthen their guidance with the number of these proofs. Those who deny, however, will receive their punishment for rejecting all of this and thinking it was all just empty and without purpose. One verse in the Qur'an states the following:
We did not create heaven and Earth and everything between them to no purpose. That is the opinion of those who disbelieve. Woe to those who disbelieve, because of the Fire! (Qur'an, 38:27)
8- Sir Fred Hoyle-Chandra Wickramasinghe, Evolution from Space (New York: Simon & Schuster, 1984), p. 148; http://www.evolutionisdead.com/quotes.php?QID=343&er=62
9- Muammer Bilge, Hucre Bilimi (Cellular Science) (Istanbul: Cerrahpasa Medical Faculty Physiology and Biophysics Chairs, 3rd edition), pp. 131-132.