Protein Synthesis is Impossible to Explain Through Evolutionary Mechanisms

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10 November, 2013

As evolutionists also well know, it is impossible that even a single protein, which is the smallest building block of life, could come into existence on its own by coincidence. Even the tiniest protein molecule has a superior creation, a striking mechanism and characteristics. It is impossible that inanimate atoms could organize and form this perfect structure through coincidence.

In order to better understand this impossibility, let’s summarize the stages in protein production shortly:

Elements in protein synthesis

When the information for the protein to be produced is found, a code for protein synthesis is collected from the DNA molecule.
This code is a copy-molecule and named mRNA (messenger RNA).
mRNA is the copy taken from part of the DNA (gene) but actually there are very important differences between DNA and RNA.
Three of the 4 letters DNA and RNA use as a code are the same but one is different (Timine-Urasil).
There is only a single oxygen molecule different among the sugar molecules to which this single letter is attached.
This new mRNA copy molecule is much more active but unstable as a result of this small difference, which means that it has more tendency to enter into new reactions than the DNA.
Since DNA is a data bank, it must have a determined and stable structure.
mRNA, on the other hand, must be mobile and must transfer the copy molecule and be destroyed when required.
Therefore, this unstable structure of mRNA is very important for the cell.
Thanks to its unstable structure, mRNA can be produced in the cell at any time, can move in any way and can be degraded at will.

RNA polymerase

RNA polymerase is an enzyme, meaning a protein and it takes a role in protein synthesis.
RNA polymerase is the greatest translator in the world.
It reads the code on the DNA and forms the mRNA by translating it into a completely new language.
What this enzyme does is very surprising. It understands the text it reads and writes a similar version of this to someplace else.
This enzyme also detects any defects that take place –even though they are few in number- and corrects these.
What this enzyme does is quite amazing and scientists cannot even approach duplicating these processes in a lab environment.
DNA is composed of a double helix. These helixes rotate on top of one another to form strong bonds. However, the hydrogen bonds, which hold the chain intact, must be degraded to use the information kept in here. RNA polymerase degrades these bonds. RNA polymerase (RNAP) is an enzyme, but what it does is so high-tech that we can compare it to a factory because a separate unit is required to identify the section that will be added to the DNA chain, a separate unit to bond, to move ahead, to copy, to synthesize RNA, and cut DNA bonds. RNA can do these easy to say but difficult to do processes in the blink of an eye. It was discovered that only the E-coli bacteria has 100 sub-units for RNAP to do all these tasks (different proteins).[i]

The code in the DNA

The alphabet in the DNA is only four letters. The derivatives of these four letters form a perfect coding system in the DNA:
The beginning and end points of the genes are defined with special codes.
During protein synthesis, RNA polymerase finds the required code instantly in a single book inside a library of 1,000 books inside 46 chromosomes that belong to the human genome. This code is only a couple of sequences of information within this book.
When RNA polymerase reaches this region, DNA finds the beginning point of the protein it will make a copy of using the coding system mentioned above. This finding process is a significant problem for the world of science because this brings with it many unknowns, such as how to find the beginning and end points of the gene to be copied in the DNA and how the timing of the copying is regulated.
Every protein begins with an amino acid called methionine and the code for this on the DNA is TAC (Timine-Adenine-Citozine).
When the RNA polymerase enzyme comes to the TAC code in a specific region, it understands that it has reached the beginning point of the required copy for the protein and opens the DNA helix.
ATT, ATC and ACT are used as the ending sequences. When one of these is reached, it understands that it has reached the end of the required copy and finishes the copying process.

Promoters

There are special coded sequences in the parts of the DNA called promoters.
While the first line is -35 bases before the protein begins and the second line is -10 bases before.
The first of these sequences is named as the- 35 sequence or recognition area.
A counterpart for this sequence is created on the RNA polymerase.
RNA polymerases connect to this special sequence on the promoter sections of the gene and detect the production information of the protein.
After the RNA polymerase attaches to the recognition area on the DNA, they move on the DNA and close up to where the protein information begins.
This is just like a plane reaching the airport and closing in on the landing strip with lights and signs on it.
Promoter sections show the location searched to the RNA polymerases just like arrow signs. A group of atoms telling the place of another group of atoms is a clear evidence of Creation.
The -10 sequence, which points 10 bases before where the protein begins, points to the place where the RNA polymerase begins to open the DNA double helix.
This section in the DNA is like a door that opens to information. It is the place the DNA double helix begins to open for protein synthesis.
Even if everything were there for protein production, the system would collapse and no being could survive, had the promoter section of the DNA or the part of the RNA polymerase that will identify the promoter section not existed.

Regulator gene

The RNA polymerases must be attached to promoter sections and control code production for protein synthesis: For this Allah created a very special system.
A protein to “stop” the RNA polymerase is produced in a special section called the “Regulator Gene.” This protein attaches to the DNA, exactly where the code that needs to be copied for the protein that will be produced ends.
It holds onto the RNA. While the RNA polymerase continues to make copies, it stops as soon as it sees this protein. This is the terminus point of the copy at hand.
In this way, no codes more than needed are copied.
We can compare this to putting an obstacle between the gear wheels to halt excess production in a factory.
However, if the cell still needs protein production, the inhibitor proteins are sent away from the DNA and so the way ahead for protein production is clear.
Coding systems are often used in stores. Thanks to devices that can read codes, we are able to read what is bought. It is amazing that our coding system is through molecules in the DNA.

One must not forget that all these actions, which require wisdom, caution, precision and knowledge, are carried out by unconscious molecules. It is great foolishness to claim that this perfect system comes into existence through coincidence.

The details in protein production are not limited to what’s presented here.

Accelerators and attenuators

There are two special sequences in the DNA called accelerator and attenuator. These help adjust the speed of protein production.
It is a manifestation of the perfection in Allah’s creation that some special sequences in the DNA adjust the speed of protein production just like the mechanisms adjusting a car’s speed.

Additional information in the beginning and end of the code

mRNAs take the code they have, meaning the photocopy, to ribosomes, which are production facilities.
However, different than a normal photocopy, there are some signals in the beginning and end of the mRNA other than protein information. These signals are some special nucleotide sequences.
Here there is a great miracle of Creation because this structure is the basis of the discipline, which is today called computer networks and telecommunication. Sending data by adding control transcriptions and additional information at the beginning and end of the data is a very common application.
These special signal sequences are similar to codes. When the recipient gets this it understands that there is new information coming in.
These signs, which are used in addition to the data, include information about where the package will be sent to, error checking, details to prevent confusion with other data packages and prioritization .
A sign placed right before the protein code has a special section to attach to the related ribosome. mRNA can only be attached to the ribosome in this way. Thanks to this sign, the ribosome understands that mRNA contains information about itself.
There is a sign at the end of mRNA. This is attached to the sign sequence with special proteins and mRNA is protected from destruction.
Moreover, this sign attached at the end of mRNA helps mRNA get out of the nucleolus and go to the ribosome area and recognize the ribosome.
This situation is like this: Let’s say that you are going to send a page inside a book from a library of 920 book volumes to a friend. Of course it will not be enough to take a photocopy of the related book. This must be transmitted much like a mailing system. The recipient name and mailing details on the paper are like this sign on the mRNA.
Proteins tied with this sign are like a mail coach that transmits this information. They carry out the related mission.

Ribosome

Ribosomes are special units that carry out protein synthesis.
They are approximately 20-30 nanometers in diameter (1nm= one in one billionth of 1 meter)
The discovery of the three dimensional structures of ribosomes measured in nanometers is accepted as one of the most important success stories in the field of biology in 2000s.
Two third of ribosomes are composed of RNA and the remaining one third is composed of proteins. The RNAs in the ribosome are called RNA or rRNA.
We stated that ribosomes are composed of rRNAs and proteins. What’s interesting is that proteins that make up the ribosomes are also synthesized in ribosomes.
In other words, without proteins, ribosomes cannot exist but ribosomes also make proteins.
Ribosome re-writes the information, which is formed by structuring the four letters that come from the DNA in several ways by using the 20-letter amino acid alphabet.
Sometimes the cell may need more than one copy of the same protein but it is not possible to synthesize the required amount of protein in a single ribosome.
Then many ribosomes are needed.
For this reason, ribosomes are aligned one after the other and form sets called polysomes.
During protein synthesis, mRNA passes through the ribosomes and when its tip leaves the first ribosomes, it is taken in by the second ribosome and a new copy of the same protein is synthesized.
At the same time, the first ribosome continues to read the rest of the mRNA.
When the tip of the mRNA leaves the second ribosome, it is taken in by the third ribosome and this action continues successively.
Thus, a single mRNA chain is read by many ribosomes at the same time and the required amount of proteins is synthesized in a short time.

Importance of cell nucleus

DNA of prokaryote bacteria is inside the cell fluid; in eukaryote beings, the DNA is separated from the cell fluid by the nuclear membrane.
The nuclear membrane is a system with additional protection and control of entrance and exit.
Even though the cell itself is covered with a single membrane, the nucleus is covered with a double membrane. There is a thin space in between the two membranes and the structures and functions of the interior and exterior membranes are different from one another.
There are approximately 3,000-4,000 doors on the nuclear membrane and 500 molecules enter and exit through each of these doors every second. This is a akin to a highway where 500 vehicles pass in bi-directional traffic and there are no traffic accidents.
The building material of this membrane system and the doors (pores) on it are utterly perfect.
The average size of these doors (pores) is almost 30 times that of a ribosome and they are composed of hundreds of different sorts of proteins.
Only building blocks with special codes can enter through these pores into the nucleus. There is very strict control at these doors and it is still a great mystery for the world of science how these pores work.
These guards at the nuclear membrane always allow the proteins that belong to the nucleus enter so only nucleus proteins can enter the nucleus.
For a protein to pass through a pore it needs a special five-letter amino acid sequence. This five-letter special sequence, lysine- lysine - lysine -arginine- lysine, is the code the protein needs to enter the nucleus.
Special code -detecting proteins that wait at the doors detect the special code on the cargo. Entrance and exist can only be made in this way. But there is another miracle here: Scientists have found that pores open for every protein only as large as that protein to pass through. So if we can give an example, this is like an automatic door with a specific numerical password opening for everyone who enters the password according to the person’s width. It is one of the unknowns in microbiology that proteins with no eyes can know about the width of a single protein inside the cell, which is a very dark place.
These proteins are like a doorman that helps a passenger with a ticket who doesn't know the way.
The receptor protein, which detects the code of the opposite party, doesn't leave the passenger alone either during exit from the nucleus or entering the nucleus. If there will be entry into the nucleus, they move along the passage channel together with the passenger. At the point of entry into the nucleus, it leaves the passenger and turns back to the channel and gets ready to take in new proteins.
This system is meaningful only if it is complete with all these details and sub-units. It is not possible for this system to have come into existence over time in stages.
The nucleus works like a brain. Under normal circumstances, all messages that are sent from the outside world are not transmitted to the nucleus. A majority of these messages is replied to by the cell membrane and ribosome.
However, when important jobs are concerned, the message is transmitted to the nucleus. Despite the initial elimination the nucleus is very busy; 500 pass throughs in one second is important evidence for this.

Protein production with packaged DNA

The flawless databank in the cell, called the DNA, is a two meter long code when it is opened up. This code fits into an area much smaller than itself and this is a clear miracle.
For this packaging system, histone proteins are used.
Histone proteins have five varieties. When these five proteins are brought together in an orderly way, a sort of molecular reel is made. The DNA is wrapped around these reels to be packaged.
Every package unit is called a nucleosome.
Histone proteins are special proteins wrapped around the DNA. It is very interesting that the information of these proteins is also kept inside the DNA.
The DNA being wrapped around reel proteins to be ordered as nucleosomes prevents the wrapped information from being read. In this case, protein production cannot be done under normal conditions. However for the survival of the cell protein production must continue. Therefore, nucleosomes are not fixed unchanged structures but dynamic structures that can be changed when needed. For example, when there will be a process in that part of the DNA, an enzyme called the ATP-Dependent Chromatin Remodeling Complex[ii] is catalyzed and this allows nucleosomes to open. We can compare the nucleosome-enzyme adaptation observed at this point to a key with a very special three-dimensional shape holding onto the histone proteins’ specific parts and loosening it without harming the DNA string.
Therefore, histone proteins must exist together with the systems that allow the information from the DNA to be read from histone proteins at the very beginning.
For this, Almighty Allah created robot molecules.
The research done shows that several molecules like methyl, acetyl, phosphate are added to and extracted from histone proteins. As a result, with these additions some additional codes are formed, and these codes are read by other enzymes.
For example, histones with methyl added to them symbolize parts that cannot carry out production in the DNA.
Such a flawless structure is no doubt a clear miracle of Creation. Evolutionists have to explain not only how a single protein molecule has come into existence but also how this perfect organization has come to be. Even if evolutionists were provided with all the materials required for life to come into existence, it is impossible that this organization could exist on its own, or that molecules could form such a perfect system. It is abundantly clear and completely certain that every detail of life is the work of Almighty and All-Knowing Allah.

[i] Molecular Biology of the Cell, fifth edition Sf.215

[ii] Akira Ishihama (2000). Functional modulation of Escherichia coli RNA polymerase. pp. 499–518. doi:10.1146/annurev.micro.54.1.499)

Protein synthesis