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Chapter 05. Proteins: The Miracle Molecules

protein, hemoglobin

Figure 5.1
The three-dimensional shape of the hemoglobin protein found in human blood. Hemoglobin facilitates the transport of vitally important oxygen to cells via blood circulation.

Life without proteins is impossible. Not only the basic building blocks of the body, they also compose the enzymes and hormones that are vitally important to human life. These complex protein molecules are specialized for vital duties and reactions in the body, such as facilitating coordination and continuing the basic functions of life.

This chapter will look at the extraordinary structure of proteins and the incredibly difficult processes in the body facilitated by mechanisms that they carry out.

Consider that billions of these processes are going on at every second, and you can more clearly understand that complexity of this system within the body is beyond our comprehension.

Twenty different types of amino acids found in nature are used in protein structure. Actually, depending on the number used and their order, an infinite number of proteins can be made from only these 20 different amino acids. If you compare any protein to a chain, amino acids are the links in the chain. The number of amino acids in different protein types within living things is between 100 and 3,000. Random removal, addition, or changing of the order of just one amino acid in the chain would render the protein completely useless, and in fact harmful.

Along with the location and number of amino acids, the three- dimensional geometry of the protein they form is also extremely important (see Figure 5.1). It's not enough for the amino acids to be of the right number and in the right place, they also need to fold at certain points to form a shape that lets the protein carry out its duty. To allow these folds to take place, amino acids located at sites to be folded are joined by much weaker bonds, which facilitates folding at the right angle. If this weren't so and all amino acid bonds were of equal strength, the protein formed would be straight, without function-in fact, useless.

In short, a protein's three-dimensional shape is highly important. Only because of their 3-D shape can enzymes in particular direct, regulate, and accelerate many reactions. Even if the protein possessed the right number of amino acids in the correct order, its lack of correct geometric shape would render it useless. In order to facilitate folding, the bonds of attraction between amino acids need to be individually regulated with incredible control and sensitivity. Even the slightest detail must be determined with care (see Figure 5.2).

Since the formation of even one protein molecule requires so many processes and controls, today's technology has not been able to synthesize a protein molecule under laboratory conditions. Yet evolutionists, with their usual insensitivity and blindness, claim that such a molecule came about in the primitive atmosphere as a result of coincidences.

Let us look at the likelihood of a protein forming by chance, and then contrast this impossibility with the hopeless position of the evolutionists.

One Possibility in Infinity

hemoglobin, protein

Figure 5.2 The structure of the oxyhemoglobin protein

In his book Origin of Life, Russian scientist, A. I. Oparin, one of the most famous proponents of evolution, has this to say about the impossibility of proteins forming as a result of chance:

But even the simplest of these substances represent extremely complex compounds, containing many thousands of atoms of carbon, hydrogen, oxygen, and nitrogen arranged in absolutely definite patterns, which are specific for each separate substance. To the student of protein structure the spontaneous formation of such an atomic arrangement in the protein molecule would seem as improbable as would the accidental origin of the text of Virgil's "Aeneid" from scattered letter type.10

However much he appears to be on the side of evolution, this famous scientist's admission completely nullifies the theory he advocates. This is an important example of the discrepant logic that evolutionists advance. Because as Oparin states, it really is impossible for a protein to come about as a result of a series of coincidences. But even though evolutionists admit this, still they do not concede one inch when it comes to their superstitious beliefs in coincidence.

Prof. Nevzat Baban, one of Turkey's famous scientists, has the following to say about the mathematical impossibility of proteins forming coincidentally:

It has been calculated that 10300 different proteins could theoretically be formed for a protein with a molecular weight of 34,000, and 288 amino acids in its chain selected from 12 different types of amino acids. If just one of each of these different molecules came together, the total mass would be 10280 grams. But the total mass of the earth is only 1027 grams… Calculations have shown that there are 5 x 1079 possible polypeptide isomers for a polypeptide of 61 amino acids, made from 20 different amino acids… this would mean that there would be 6 of these polypeptide isomers for every atom in the universe.11

As Baban states, for a small protein of 61 amino acids, there aren't enough atoms in the universe to cover all of the possible versions of proteins that would form by blind chance. Moreover, the average protein is made up not of 61, but of about 400 amino acids. Even if all of the atoms in the whole universe stopped whatever they're doing and occupied themselves only with forming this protein at random, the billions of years that the universe has been in existence and all the atoms in it would not be sufficient for this protein to form coincidentally.

In short, for an average protein of about 400 amino acids to come about as a result of coincidence is not possible. What's more, when we go one step further in the development of life, we see that the one single protein doesn't amount to much. Even one of the smallest bacteria known today, Mycoplasma Hominis H 39, contains 600 different proteins. So in this situation we would have to apply the above probability by an exponent of 600, and be faced with a number that exceeds the limits of human understanding.

It's impossible for even one of these proteins to have formed by coincidence, but a billion times more impossible it is for a million of these to coincidentally come together and form a complete human cell. Besides proteins, in the cell structure there are carbohydrates, lipids, water, electrolytes (anions and cations), and vitamins. All of these are used as helper molecules and as the building blocks of many different organelles.

And so it is very difficult to express the impossibility of having 100 trillion of these cells coming together accidentally, but faultlessly and completely, to form the inner and outer organs of a human being.

Coincidence, the sole "explanation" that evolution offers is powerless to explain even one of the millions of proteins found in the cell. So how can it explain the entire cell? The reliability of a theory that cannot even solve the problem at the stage of proteins, yet continues to write scenarios of how living beings came into being, is open for all to see.

At whatever stage or component of life we examine, claims of so-called "coincidence" are turned into crazy nonsense.

As an example, let's look at levo (left-handed) proteins.

All amino acids have a central core comprising a carbon atom with a hydrogen and nitrogen atom bound to it. This core structure in all amino acids is exactly the same. However, attached to this core is a side group, given the name of R group, which is different in each amino acid. This R group gives each amino acid its particular identity. The R group atoms can be found on either the right- or left-hand side of the amino acid's central core. Those with the R group on the left hand side are called L-levo (left handed) amino acids, and the ones with the R group on the right are called D-dextro (right handed) amino acids. The probability that each will occur is 50%. Though they arise from the same atoms and the same parts, and come together in the same way, these molecules have a different symmetry. The two forms, the left handed and right handed forms of the same molecule are called optical isomers, or mirror images, of each other.

In the inanimate world, these isomers are found in roughly equal amounts (50-50). And all of the 20 basic amino acids used in the human body can be found in both forms, levo or dextro, in nature.

But research has come up with a striking fact: From the simplest organism to the most complex, the proteins in all plants and animals are only of the levo form. In certain experiments, in fact, dextro amino acids were given to bacteria, and the bacteria immediately broke them down, and sometimes they rebuilt from the remains levo amino acids that they could use.

Evolutionists can in no way explain such a special, seemingly deliberate differentiation. (If life really did arise by coincidence, then there would have been no reason for this differentiation to exist.) Both forms of amino acids are found in equal amounts in nature, and each is able to bind with the other perfectly. Then how can we explain that only levo amino acids are found in the proteins in all living things?

As you would anticipate, this characteristic of proteins has led the evolutionists even deeper into their dead end of "coincidence." For a relevant protein to be formed, as explained before, it's not enough for the amino acids that compose it to be of a certain number, in a certain order, and have a special 3-D shape. Besides this, the left-handed amino acids must be selected and not even a single right-handed one will be tolerated. This situation places the concept of coincidence completely out of the picture.

The Britannica Science Encyclopaedia, an outspoken defender of evolution, states that the amino acids of all living organisms on Earth, and the building blocks of complex polymers such as proteins, have the same left-handed asymmetry. It adds that this is tantamount to tossing a coin a million times and always getting heads. The same article states that it's impossible to understand why molecules become left- or right-handed, and that this choice is fascinatingly related to the origin of life on Earth.12

If a coin is tossed into the air a million times, and it always comes down heads, wouldn't it be logical to accept that somebody is consciously intervening with the coin? Clearly there is a conscious intervention. But despite this obvious fact, evolutionists continue to cling to "coincidence," just because they do not want to accept God's sovereignty over living beings-and this is nothing more than an obsession.

A similar situation can be found in nucleotides, the building blocks of DNA and RNA: In all living organisms, nucleotide molecules are right-handed, as opposed to the left-handed amino acids.

All of these impossible events make it equally impossible to explain the origins of life by coincidences. If we try to calculate the probability that only L amino acids will be selected for an average-sized protein of about 400 amino acids, we come up with a figure of 2400-that is, a probability of 1 in 10120. For comparison, the number of electrons in the universe-approximately 1080-is much smaller than this. The probability of amino acids forming in the correct order and functional structure would lead to much larger numbers. If we extend this improbability to the fact that we need to form more than just one protein, we'll get bogged down in the calculations.

In the light of all of this, let us leave you with one last reminder.

Despite all these impossibilities, let's accept that a functional protein molecule did happen to come about by chance. Alas, evolution is at a loss once again! Because for this protein to continue its existence, it must isolate itself from its environment and protect itself, or else it will be broken down by natural conditions, react with other amino acids or chemical agents, and lose its identity, turning into a useless, even harmful substance.

Up to this point, we have demonstrated the impasse which evolution has met in terms of its claims in regard to the origins of life and the formation of proteins required to form a living cell. This leaves us the plain fact that God, Possessor of infinite knowledge and power, has established this extraordinary balance, allows this system to continue, and created all of the necessary substances in the necessary locations to form proteins.



1) The enzyme fits snugly around the substrate-the substance it is to act upon-as shown in the diagram.

2) The 3-D shape of the enzyme has been created to perfectly fit the substrate, just like a lock and key.

3) It carries out its reaction on the substance using ATP energy at each stage.

4) After converting the substance into a wholly new form, it comes away from the reaction unchanged, ready to take part in another reaction.

Figure 5.3

Diagrams aim to show the snug fit between the enzyme and the substrate.

Many complex events take place in our bodies every second. So detailed are they, that at every step, their complex reactions need to be regulated by super overseers to bring about order: the enzymes. In every living cell, hundreds of enzymes are found, each with its own special duty: breakdown of nutrients, production of energy from nutrients, production of macromolecular chains from simple molecules, and innumerable other similar processes.

Enzymes play a vital role in all cellular functions, from protein synthesis to energy production. If not for these enzymes, not one of your bodily functions, from the simplest to the most complex, would operate; or else they would slow down and stop altogether. You would not be able to breathe, eat or digest anything, see, or speak. The result in either case would be death.

We can compare enzymes' speeding-up of body processes to an example from everyday life. The few seconds' time it takes to read a sentence under normal circumstances would, without any enzymes, take ten years. The enzymes that play a role in bodily reactions are at least as rapid as this example.

The relationship between an enzyme and the substance it affects is like that between a lock and key. An enzyme and the substance it binds to, join together in a complex three-dimensional manner (see Figure 5.3). Each has been created to fit the other in the most appropriate ways (see Figure 5.4). What's more, this harmony comes about at a speed so dizzying that in one second, one enzyme can bind to 300 substances, one after the after, changing each one into the desired form and then separating from it (see Figure 5.5).

In short, cells live thanks to enzymes, and each cell produces the enzymes it needs for itself, in the required amounts.

All of this should cause an intelligent person to ask how it is that a cell can tell when a substance is needed and calculate its requirements? Does the cell itself design these enzymes that work faster than machines and facilitate so many complex reactions? Where is the intelligence that carries out this plan?

Clearly, a person of intelligence would come to the conclusion that none of this can be the product of a microscopic structure, the cell, or a product of the smaller components found within it. The truth is clear: All of this has come about as a result of God's creation:

You will not find any flaw in the creation of the All-Merciful. Look again-do you see any gaps? (Qur'an, 67:3)


enzim, subsrat

1. Molecule after undergoing change
2. Molecule to be changed

Figure 5.4
This diagram shows the perfect three-dimensional fit between an enzyme (hexokinase) and the substance it acts on. The hexokinase enzyme converts ATP into ADP, then ADP into ATP. In the first box, the enzyme closes in on the molecule it's going to act upon. In the second box, different parts of the enzyme separate, and the molecule is released, having been changed into its new state.



E. Enzyme
1. Affected molecules
2. Section subjected to change

Figure 5.5
An enzyme joins two different molecules together, thereby forming a new molecule. The reaction between the molecules and the enzyme is very short, and it comes out unchanged at the end of the reaction, ready to act on new molecules.


Multicellular organisms like animals and humans are composed of cells that have different structures and functions. The body depends on these cells' complex yet highly cooperative functions. The 100 trillion cells in the human body work together as if they all know each other. To the end, they carry out the functions assigned to them without any neglect or laziness. And within this perfect coordination are messenger chemicals called hormones, whose function is to carry orders between cells. The growth and internal balance of the body, control of reproduction, coordination of the nervous system, and many other processes are realized because of the messages carried by hormones to the relevant cells. Without you even knowing it, a superb command system is at work, as an unseen intelligence sends its orders to cells throughout your body (See Figure 5.6).

This superior intelligence keeps everything under control without you even knowing it. You do not have any say in this system. For instance, you cannot make your body grow as much as you want, no matter how much you may wish so. Whatever you do, you cannot order your cells to divide, multiply and make you grow. Only your cells know the pre-determined height and shape for your body. They will multiply until they reach that target and then stop growing, at just the right time.

Cells cannot, of course, carry these out through their own intelligence and will. God inspires this flawless chain of commands in them and enables them to carry out their duties to perfection.

Figure 5.6

a) In the first cell, calcium ions are present in low concentrations. With the binding of certain hormones (peptide or protein hormones, or hormones such as epinephrine), the order is given to increase the calcium ion concentration.

b) Certain hormones (steroids, thyroxin) delivered via blood circulation and carried by protein transporter molecules, enter into the cell. By binding to special receptors in the cell nucleus, they facilitate the reading of certain genes, allowing for production of the desired proteins.

1. Surface receptors
2. Hormones that bind to the surface receptors
3. Calcium ions in low concentrations  
4. Calcium ions in high concentrations
5. Transport proteins in the blood
6. Hormone
7. Receptors
8. Structure of the receptor/hormone complex
9. Nucleus

hücre, hormonlar

Mysterious Control

For life to continue, the amount of sugar in the human body needs to stay within certain limits. But when you eat nutrients containing sugar, obviously you cannot control this sensitive balance. This control is made on your behalf. When your level of blood sugar rises, an organ called the pancreas secretes a special substance called insulin, which orders the cells of the liver and elsewhere in the body to take up sugar from the blood and store it. In this way, blood sugar does not reach dangerous levels.

Let's do an experiment. Command all of the cells in your body, the liver cells in particular, to take up the sugar from your blood and start to store it.

Forget controlling them. This is impossible, of course.

You aren't even aware of your pancreas, your insulin, or your liver. You don't even realize that your blood sugar level has gone up. In fact, if two tubes of blood with differing levels of sugar were placed in front of you, you wouldn't be able to tell the difference between them. For this, you would need a laboratory with highly developed instruments. But some cells in your body, which you never see or know about, measure your blood sugar level with a higher degree of sensitivity than the instruments in a laboratory, and decide what needs to be done. Then they take the necessary measures, isolating the sugar in the blood and removing it. Thanks to this perfect system, someone who could eat a piece of cake, fall into a sugar coma and die, is made to live.

deri hücresi, deri

Figure 5.7
God has absolute control over every part of the human body, from the cells that make up the skin, to the organelles found in the cell, to the membrane of that organelle, to the proteins found on that membrane, to the molecules that make up those proteins. Though he may sometimes consider himself independent of Him, if mankind analyzes his own creation he will realize God's control more clearly.

So whom do we have to thank for this perfect system? As always, evolutionists claim that this system came about as a result of a series of coincidences.

But on the basis of logic and reason, it is not possible to accept this claim. As with other evolutionists' claims, this one too is nonsense.

Evolution proposes that the human body reached its present day form over millions of years. This means that at some stage, some organs in the human body were not around but later evolved. In that case, we have to assume that the pancreas, which controls the level of sugar in the blood and the insulin it secretes, "evolved" over stages.

However, this is defective logic, because a person with neither a pancreas nor insulin wouldn't have been able to live. Let's imagine that millions of years ago, there were half-human beings without a pancreas who walked the Earth. They would have eaten large amounts of the first source of sugar they found (sugar cane, for example), gone into a sugar coma and died on the spot. The same thing would have happened to all others like them: They would have died from a sugar coma, but without knowing the reason.

Let's assume that some of them stayed alive by strictly controlling their diets. (Though this is not really possible, because there is sugar in practically everything we eat.) This leaves us with the following question: How did these "ancestors of human beings" come to possess a pancreas and insulin?

Did one of them say one day, "You know, this sugar problem needs to be solved! The best thing to do is place an organ underneath the stomach that will secrete a hormone to balance the level of sugar in our blood"? And with an extreme effort of will, did he then place a pancreas underneath his stomach, work out the chemical structure of insulin and teach this to his pancreas?

Or did a very successful mutation come about one day, as a result of a flaw in the DNA of one of these half-human beings, and then suddenly form a perfectly functioning pancreas, producing insulin hormone? But such a mutation could not have occurred because as we explained in a previous section, mutations do not have such beneficial effects. And even if such a situation did come about, it would still not be enough to keep these half-humans alive. There needed to have formed-by coincidence, of course-a mechanism somewhere in the brain that would constantly control the level of blood sugar, command the pancreas to produce insulin, and then give the command to stop once enough insulin had been secreted.

These two "explanations" are obviously illogical. The evolutionists' beliefs are exactly like this, but because they themselves know how great a lie it is, they prefer not to bring it up and try to sweep it under the carpet.

With this example of insulin, the hopeless impasse into which evolutionary logic has fallen brings us to one conclusion: The first person who ever existed had a pancreas just as we do. The "evolution" of this organ is in no way possible.

Undoubtedly the same insight can be applied to other organs, different systems and processes in the body. Because thousands of other hormones and enzymes in the body are just as vital as insulin, if not more so. All of these avert critical situations, and most entail adjustments much more complex than maintaining the control of insulin. The system that regulates blood pressure, for instance, is made up of much more complicated measurements and processes than the pancreatic system.

Wherever you look in the body, you will be faced with the same situation. A person with no kidneys will live three days, at the most. Someone with no lungs, on the other hand, won't survive for more than one or two minutes. For anyone without a digestive system, even without just a small intestine, to live a week would be considered a miracle. It would be impossible to last one or two hours without the liver and its nearly 200 different functions. It would be impossible to withstand the absence of a heart for even three to five seconds, to say nothing of the brain, obviously.

None of these organs could have formed "step by step" as a result of evolution. No human body could have waited for millions of years to receive a kidney as a result of a chance mutation. Consequently, the clear truth that stares us in the face is that the very first person possessed the exact same body structure we have today; that man was created by God together with a perfect, faultless body.

Certainly this applies to all other living creatures as well. There is no difference between the first tiger to have walked the Earth and ones alive now. The elephant, whale, eagle and snake were all created in the first beginning, the same as they are now.

A Life Spent on the Unknown

endokrin sistem

1. Endocrine signals
2. Blood vessel
3. Target cell

Figure 5.8
Cells that secrete hormones carry out their production to suit target cells that would lie the equivalent of many kilometers away if they were the size of a human being. The diagram shows the hormone produced in the endocrine glands, reaching their target cells.

The insulin molecule, which constitutes an impasse for evolutionists, is only one of the many hormones in the human body. And those other hormones present proofs at least as striking as insulin's.

Some of the hormones and enzymes that cells make but don't use are exported out, to be used by other cells at a considerable distance, which the original hormone-generating cells cannot recognize or know about in any way. Were the cells enlarged to the size of a man, the distances between them would be measured in kilometers. The cell does not know where and how the substances that it's produced with such care and effort will be used. But for its whole life, it continues producing these complex products, not knowing to what use they will be put (see Figure 5.8).

For example, cells that lie below the pituitary gland, which is found just under the brain, produce a very special hormone that controls kidney function. A cell in the pituitary does not know what the kidneys are, nor what they need. So how can it produce a substance so suitable to the structure of the kidneys, an organ of which it will have no knowledge, for as long as it lives? The undoubted answer is that it has been created by God specially to carry out this duty.

miyoglobin proteini

Figure 5.9 3-D shape of the myoglobin protein

We can further explain this hormone production for reasons unknown with an analogy: People in a factory work their whole lives making a special complex circuit for an important electronic gadget. But these people have never seen the gadget, nor do they know what purpose it serves. In fact, they have never seen anything beyond the factory, yet they have dedicated their lives to making these complex finished circuits, which they then leave outside the factory to be picked up. Someone comes along and transports the circuits thousands of kilometers away to another factory, where they are combined with some new parts to form the gadget in question. The people in the first factory work 24 hours a day, not knowing why, with tireless, faultless obedience.

How were these factories formed? The only answer is that without a doubt, there is a will that knows and directs both factories, who has planned a certain division of labor, given the first factory the sole duty of making this particular electronic circuit, and also described in great detail how this is to be done. (It is impossible for the first factory, which cannot know what the final product looks like, to facilitate its production all by itself.)

Enzymes and hormones work in a similar way. They constantly produce substances for purposes they will never know, and devote their whole lives for this. They display not the slightest selfishness, boredom, caprice because they have been taught in a special way-or more accurately, they have been created for this. Just like everyone and everything else in the universe, they too submit to God, the Lord of all the worlds. They have no other choice. One verse expresses this submission in the following way:

... No, everything in the heavens and Earth belongs to Him. Everything is obedient to Him. The Originator of the heavens and Earth. When He decides on something, He just says to it, "Be!" and it is. (Qur'an, 2:116-117)



10-Oparin, The Origin of Life, pp. 132-133.

11-Nevzat Baban, Protein Biyokimyası (Protein Biochemistry) (Istanbul: Cerrahpaşa Medical Faculty), p. 32.

12-Fabbri Britannica Science Encyclopedia, Vol. 2, No. 22, p. 519.


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