Evolution Hoax

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Transcriptions of the Talks 5/8

Carlo Alberto Cossano - “Informatics Records and Proteins Production”

We’re living in the Digital Age. It’s really hard, if not impossible, to find a process that is not in some way managed, controlled, administered or enhanced through the use of a computer program or a database or any software application.

In these contexts, the computer, database or system programmer or operator has often a pleasure and pain to live with: “the record”, defined in the usual jargon.

Very simply put, the record is a collection of information, that can be both complex and simple, ample or reduced, structured in one or more field or parts, the base unit of a computer archive.

Making an example: in a set called “people”, formed by several records, the single record may contain two fields, the field “name” and the field “surname” but even the “sex” and the “date of birth” fields.

When we add a record similar to another introducing a variation in its content we use quite often a codified information, usually quite simple, that allows us to organize and interpret the information already or potentially present in the record itself: the “state”.

Introducing another example that we will recall later, supposing that I want to insert a record for every new account in the archive or database of a bank and I have to maintain a record of every closed account, I need at the very least one field in which to write “O” or “C” for identifying both the “open” and the “closed” states. If I should need to consult the archive for a feedback on the number of closed or open accounts it would be enough just to create the above field in the record, (b) fill it with the correct information in the correct moment and (c) recall that information, that specific record “state” at the very same moment in which I need an “output” to my “query”.

Record
number

Account
code

Account
owner

Account
type

Start
date

Account
state

1

AA132989

JOHN SMITH

A

15/01/2013

OPEN

2

AG234456

SIMON WATERS

A

01/04/2010

OPEN

3

CR267539

JOHN MILTON

C

15/09/2014

CLOSED

It’s normal to come upon these considerations and logics examining details of the information management approach regarding computer programs and databases: we have these solutions today, having reached the peak of the information age, thanks to decades of enhancements applied by intelligent beings with that specific purpose, so what we have is the best of what intellectual and technological growth can develop in years and years.

But it may seem less “normal” to find out that these very same logics and considerations, that we’ve just described as the product of years and years of applications by the most clever being of the planet, are fully adopted in biological processes operating in the cells inside our body, as in those of every living organism.

And this happens since the appearance of the first so-called “simple” –supposedly named by evolutionistsunicellular life forms, with logics and processes fundamentally unchanged from the extant ones.

Protein Production Requires a State Management

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Every living being is made of cells; every cell is made of proteins (or of their products). Proteins aren’t “substances”, as how sometimes are simplistically defined; granted, from a certain point of view everything is a “substance”, even the computer that we use when we surf the Internet, since substances are constituted by atoms, and atoms are the fundamental building blocks of matter.

Proteins are rather electrochemical mechanical (and, as we will see, even information processing) mechanisms that constitute, assemble, regulate, maintain, manage, transform create and destroy (and much more) cells and tissues of any living organism (and even of any “non-living” one, like viruses).

Their almost boundless diversity is remarkable: it’s been estimated that inside of the human body there are at least 25.000 different kind of proteins, every one with its specificity that can be connected to a moment, a purpose, a quantity essential or concurrent to the completion of a certain function.

What prepares and produces proteins in the cell? Very simple: other proteins, themselves prepared and produced in the same way.

But, if we make an analogy, it will be easy to grasp that; for a production line that must continually and according to specific and highly variable requirements churn out something as 25.000 different pieces, you need to manage the production flow, in some way. the amount and diversity are so high that a “production problem” in such a “factory” would mean not only a halt in the production line, but a following money loss. the same would cost the life of the cell and maybe of the entire organism.

It becomes clear that it’s essential to have the pieces production line under control, managing the different phases, maybe having the information of the point at which the single piece is in the production phase: a state management.

State Management and Information

When a software program must control records variations it’s essential that a programmer assigns semiotically a condition to information and structures the software to allow the management of that condition.

If I would want to use my program to manage the production of a car in the final steps of its construction, say for example during the painting process, I may ensure that (a) some optical sensors recognize the entrance of the car bodies in the painting basin, that (b) other proximity sensors activate drying fans for the bodies that are already painted, that (c) a timer stops the drying process and (d) a weight sensor involves the activation of carrying robots designate for moving the painted models to the next production step.

If my program would follow every car body passing this phase, I could create a specific field named “Painting State” in the database used by my program, in which it will be saved the information received from the various transducers with four different letters, “A”, “B”,”C”, ”D”: with a simple function that compares the records with the state “A” with the ones having the others I could know in real time how many cars I still have to paint, how many are painted and how many I deliver to the next phase.

I believe that this simple example could adequately represent the usefulness of the state management in informatics and its countless applications.

This powerful tool of assigning “meaning” and “purpose” to simple letters though used within the appropriate context and the proper tools, allows to increase tremendously the amount of feedback information from a process managed with it: I can control every aspect of the quality in my production, as speed and precision, calibrating it on the requests flow, of the personnel, the environmental context, the raw material supply, and so on.

Potential is almost limitless if behind those “letters” there’s a need, a project and a mechanism that allows its management: to utilize to the full this potential it’s clearly essential that an intelligent and competent being modifies the program inserting the instruction needed.

A Record State in the ER and in the Golgi Apparatus

Cells are constituted by several discrete components that perform different functions, called organelles. Among them, endoplasmatic reticulum (ER) and the Golgi apparatus (GA) are very important on proteins production and dispatching inside the cell. Proteins being “wrought” and distributed through these two electrochemical mechanical marvels, ER and GA, circulate inside them using vesicles that become detached from and attached to the organelles membranes using others protein functions that we will not consider in this present lecture.

Simplifying with another analogy taken from the previous ones (inevitably a little more complex), proteins could correspond to a car that must be completed in an assembly line, ER and GA to the assembly line and the vesicles to the transporter robots designated for the circulation of the car “under construction”. How can all this flow of preparation, mounting and distribution be controlled?

 PLANT CELL

An informatics engineer today would propose to do it with a software program, which easily allows a state management in the various phases of the car production. At this point let’s introduce the heart of the matter: the real incredible thing is to find that this solution, resulted from decades of enhanced applied intelligence, thought and proposed by an expert and competent intelligent human being, is exactly what happens inside the cell through the use of specific sugar chemical compounds, called oligosaccharides or N-glycans, able to provide semiotics, a precise and straight information on the state i.e. the phase at which a protein is arrived in a certain moment.

Let’s compare so the proteins to the records and these sugars to the field that contains the information related to the state of the record itself and let’s see if the analogy fits.

These sugar chains are prepared and “attached” on the folding protein as some kind of a “mounting diary” that will accompany them through all the following phases till they will become detached as unnecessary.

 CHEMICAL STRUCTURE OF OLIGOSACCHARIDE

Before being used as “mounting diary”, these chemical structures must be built and connected to the nascent protein or the protein in some production phase; only for preparing the oligosaccharide, 15 different proteins intervene, all coordinated in precise moments and designated to perform specific modifications to the sugar chain.

Once concluded, this huge work of synthesis allows the carrying out of the state management function, an essential function added to those that constitute what is defined by biologists and biochemists as a real “Quality Control” system, working inside the cell in the ER and GA, system that is described in a technical paper as it follows [2]:

“The QC system is adapted to handling virtually any condition that results in a protein conformation other than the native state. Accordingly, multiple scenarios of QC arise from the many ways in which proteins can fail to achieve their native conformation”.

Therefore a system highly complex, able to manage and act automatically on the “quality” of the production in relation to every possible scenario that would materialize, an extraordinary thing for a process capable to produce more than 20.000 different “pieces”. For example, some proteins require oligosaccharides for the folding properly in the ER. Furthermore, oligosaccharides even confer stability to several secreted protein structures, as well as favor their preparation and transport.

In addition, cells adhesions are facilitated if there are oligosaccharides on the proteins that serve as “hooks”.

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 CHEMICAL STRUCTURE OF OLIGOSACCHARIDE’S

In short, every oligosaccharide’s modified form has both chemical, “structural” and “semiotical” characteristics that are, recalling our main theme, essential to the nascent protein production process.

Sugar structure is transferred on to the protein and linked to a special part of the constituting amino acids sequence, acting then as a block or as a “promoter” for others proteins adhesion, proteins used for sorting and management like lectins homologues calreticulin and calnexin, thus even indicating at which “point” of the production the nascent protein has arrived.

Additionally, exactly as it would happen in our car painting example described above, there’s no guarantee that the painting process would not be completed if the transducers that signal the car body passage would be inactivated, but anomalies on the final result quality may occur, as well as management problems of the entire process, resulting in unsellable products.

In fact, in laboratory experiments where synthesis of oligosaccharides portions is inhibited, proteins are still produced but they don’t fold properly (so they result to be not functional), accumulate in the ER and are less stable: in short, “unsellable”.

Adaptation or Irreducibly Complex Innovation?

The paragraph cited above describing the quality control system, has used a term to indicate how a set of these kinds of systems may have appeared in living organisms (assuming that it may have done so after the same living organism itself): that term is “adapted”.

Actually we don’t want to raise doubts on the fact that organisms are able to adapt to environment changes, selecting the more fitting “versions” depending on the wvarious context. But adaptation doesn’t create biological novelties: at these level of complexity, nothing that wasn’t pre-existing has been observed experimentally “arise” from precedent or different systems. Indeed, biological novelty so complex, with functional constraints requiring simultaneously and holistically expressed functions, it’s described by intelligent design theorists as “irreducibly complex”, as a whole or in its parts.

After all, in an evolutionary context, to explain why oligosaccharides are used for state management as it occurs in informatics one should not only invoke prohibitive probabilistic arguments of selection of the correct sugar structure useful to manage all the various “transitions” but even for all the systems that prepare that specific structure (and we’ve seen how this process is complex and structured) as well as for all the machineries that utilize the information that it represents and its biochemical design, with their stability characteristics.

It is true that [allegedly] evolutionary adaptation operates step by step, selecting the most beneficial “version” of the “program” using informatics terms but it’s exactly this condition that makes extremely difficult to demonstrate logically and experimentally evolutionary “jumps” essential to these transitions. a complete function which brings advantage at every single hypothetical step must be identified, steps to obtain the oligosaccharides structure and all the specificities of the hundreds of molecular machines connected to them and which operate behind a system like this. It’s easy to understand how the sum of all these probabilities that must bring an advantage at every single selective “step” makes too far implausible an hypothetical scenario in which the required biological information parameter is overlooked, even without analyzing the details behind these steps. Exactly as you would refuse to believe someone that would try to convince you to have guessed your phone number making casual phone calls, the factors of (i) scientifically accepted available time since the appearance of life on earth, (ii) the mode of “exploration” of the probabilistic space that evolution adopts, (iii) holistic complexity of the systems to obtain render a hazardous fairy tale assume the appearance of such a process without being able to observe it or prove it, but just because it has to be the only way to achieve a result.

It should be noted too that these molecules are “conserved” practically in every complex form of living organism, namely we don’t find noteworthy variations in their structure among living things, so it’s very complicated to define an “evolutive line” related to their appearance which is scientifically satisfying, although hypothetical or speculative.

KINESIN (A MOTOR PROTEIN) PULLING A VESICLE ALONG CYTOSKELETAL FILAMENT SCIENCE.

So, can we assume a simpler oligosaccharide, with less managed “states”, to place in the “evolutive ladder” as a precursor of the extant forms? Very complicated, for several reasons that we can summarize resuming our analogies. How could a quality control system work if it would verify, for example, just the entrance and the exit of the car bodies? How could a computer program, recompiled after the casual insertion of letters, numbers, spaces and symbols in its code, create all the needed structures for implementing the management of the state from one or two at the very best to fourteen, knowing that behind every state there are dozens of others part of the program that you would need to exist simultaneously an contextually as to carry out specific and complex functions? An oligosaccharide composed of one or two sugars is not so probabilistically prohibitive, but adding just another single sugar to the chain means at least that (i) this biological information must be semiotically connected to a certain specific condition in the protein production phase (possibly one of the biggest hurdles for the evolution of this sugar structure), that (ii) the enzyme which attaches it (and which carries out yet others functions) would “appear” or “come to aid” (we’re talking about another complex protein, specifically formed by hundreds of amino acids), that (iii) the enzymes and the proteins which “read” that “state” would exist, would be structured for “reading it” and for acting once activated by it and finally that (iv) the structural stability which the oligosaccharides concur to create would be so, even with such a different or smaller structure.

Oligosaccharides are not an analogy with the state of an informatics record and all that surrounds it: they are real molecular support for biological information management, being automatically prepared by the very same proteins, which they help to build.

INDEED, BIOLOGICAL NOVELTY SO
COMPLEX, WITH FUNCTIONAL CONSTRAINTS
REQUIRING SIMULTANEOUSLY AND HOLISTICALLY
EXPRESSED FUNCTIONS, IT’S DESCRIBED BY INTELLIGENT
DESIGN THEORISTS AS “IRREDUCIBLY COMPLEX”, AS A WHOLE OR IN ITS PARTS.
CARLO ALBERTO COSSANO

Adnan Oktar Says

Intracellular Molecular Machines That Perform Protein Care and Cleanup

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Cells spring to life with the proteins and the functions of the cells actualize through proteins specially made for each task.

In a typical mammal cell, there are approximately ten to twenty thousand different functioning protein varieties. For a cell to be healthy, these proteins need to be healthy first. For this reason, the existence of intracellular quality control mechanisms is crucial.

The latest studies revealed a quality control system made up from proteins, which again control the proteins inside the cell. According to this, defective or damaged proteins are identified first, and then removed from the environment

Proteins Create a Toxic Effect If They Are Misfolded

A protein leaves the ribosome as a chain formed by thousands of amino acids, however it can’t fulfill its functions without transforming into the threedimensional state folded onto itself. Proteins called chaperons transform these amino acid chains into their designed final state in seconds and turn them into functional nano-machines. However, during this folding phase, which requires sensitive connections at molecular level, errors can be made and broken amino acid aggregates can be formed. Faulty proteins such as these can pose a great danger to the health of the cell. Because there is a high possibility for these incorrectly folded proteins to chemically bond with other molecules in the environment due to their exposed linkups.

All manner of dysfunctional proteins that are ready for uncontrolled chemical bonding are in fact quite hazardous for the cell. Accumulation of this waste material poses a health risk for the cell and the entire body. Alzheimer’s and Parkinson’s diseases, where permanent neuron damage develops, various heart diseases, diabetes and certain cancers arise due to improper handling of the intracellular protein balance. Faulty proteins cause “accumulation” by sticking to each other and other proteins and therefore a cytotoxic effect, in other words, intracellular intoxication ensues. These aggregates, which are comprised of faulty proteins, are in the form of fibrils (or filaments) and are also defined as amyloid accumulations.1

An Intracellular Monitoring and Control System That Functions 7/24

For a cell to fulfill its functions in a healthy way, a broad and effective quality control network has to be in process at any given time. For this, faulty proteins should be collected and immediately removed from the cell. Due to proteins’ dynamic structure, they have to be continuously monitored. For this purpose, chaperon molecules and protein breakdown mechanisms that work in combination with each other have to be on continuous duty.

While proteins called chaperons enable folding, they also play a role in repair and maintenance tasks. Due to their critical purpose, chaperons are defined as a cells’ “technical inspection authority”. They inspect other proteins for errors in quality. When chaperons identify a misfolded broken protein, they engage the protein-breakdown mechanism. This is the ubiquitin-proteasome (protein degradation) system.

A Nano-Sized Garbage Disposal System

Protein breakdown is an annihilation process kept under tight control through consecutive steps. In addition to chaperons, Doa10 ligase enzyme was discovered to also detect faulty proteins. When a Doa10 enzyme detects a faulty protein, it marks that protein with the ubiquitin molecule. However, when generating the degradation signal, Ubc6 enzyme first has to attach the ubiquitin molecule to the faulty protein. Following this initial step, another enzyme, Ubc7 steps in and forms a homogeneous chain consisting of many ubiquitin molecules. Once the chain is completed, the annihilation process begins. As it is seen, two separate enzymes are needed for the break down signal to be triggered.2

At this phase, proteasome, which consists of 33 subunits and two sub-complexes, detects the ubiquitin and immediately breaks the marked protein’s peptide bonds. the faulty protein has now been separated into its amino acids.

When we consider the fact that the 30% of the proteins produced within the cell are defected, we can understand how vital a role this garbage disposal system plays better. Faulty production aside, in time, all properly functioning proteins wear down and are replaced by new ones and that means proteins, which have reached the end of their lifespan, are likewise marked and annihilated.

Each Detail In Our Body Is An Indication of a Magnificent Creation

If it were not for the precise control system we briefly summarized here that monitors the protein world, we could never speak of cellular health at all. This vital balance system has to function with the same perfection inside each one of the almost 100 trillion cells that constitute our body, which can only be explained by a superior management and coordination.

Mindless proteins overseeing other proteins that are essentially molecules like themselves, again different unconscious molecules acting systematically in a specific order as well as the degradation system being activated only when and where it is needed, can be explained neither with coincidences or other idle reasoning.

It is obvious that the absence of even one step in this precise process would lead to the cell’s death, this indicates that there should be no deficiency in the entire system and all should be working in coordination at the same time. This evidently guides us to the truth that there is only a single “Power” Who has knowledge of all things and created life and all living things. the Owner of this marvelous and breathtaking Power is Almighty God, Who knows and has dominion over all things in the heavens and the earth.

References:
____________________________________

  1. In vivo aspects of protein folding and quality control, David Balchin, Manajit Hayer-Hartl and F. Ulrich Hartl (June 30, 2016) Science 353 (6294), [doi: 10.1126/science.aac4354]

     

  2. Sequential Poly-ubiquitylation by Specialized Conjugating Enzymes Expands the Versatility of a Quality Control Ubiquitin Ligase. Annika Weber et al, Molecular Cell 63. DOI: 10.1016/j.molcel.2016.07.020

The Perfect Distribution of Organelles in the Cell

The basic structural unit of creatures, the cell, is incredibly complex enough to leave people amazed. Just like the existence of a single cell, the harmony and cooperation in the cell is very impressive. As the structure of the cell and systems in it are further investigated and new details are found, this perfect order is seen more clearly.

A single cell may be said to resemble a large city with its operation systems, communication networks, transportation and administration. the power plants generate the power used by cells; the plants generate the enzyme and hormones which are essential for life; the data bank including all information regarding the products to be manufactured; the complex transportation systems and pipelines transferring the raw materials and products from one region to the other; the laboratories and refineries separating the raw materials taken from outside into the useful parts; the expert cell membrane proteins executing the enter and exit controls of materials to be taken in or sent out of the cell create only a part of this structure.

Just like cities, there is a dense traffic flow caused by the molecules like “moving on the boats”, “walking” and “taking hands” like people and by the “trucks carrying the organelles” in the cells. However, there is a great order in cells against the traffic congestion in these cities.

An investigation demonstrating this smooth order was made in Exeter University in recent days and the results were published in the journal Nature Communications. This study has shown one more time that the dispersion of organelles in the cell is not random at all, and is caused by a motion depending on en- ergy.

As is known, organelles are specialized func- tional units of cells. the organelles for the cell are the same as organs in the body. Each organelle has special duties to ensure the sustaining of the cell. the order in the ar- rangement of organelles inside the cell is also exceptional. Let us review the results of the research showing how this positioning occurs in the cell.

The distribution of organelles is executed by a special molecule named ATP (adenosine triphosphate). the energy attained from food items is first packaged in ATP. Later on, this energy is used in all the production and trans- portation processes that take place inside the cell. Actually, ATP is like the fuel for molecular motors, which transport its cargo along the fibers of the cytoskeleton. Just like trucking rigs carrying a load, organelles are also carried by means of this fuel from one place to the other as to the needs. During the transporta- tion process, other organelles are also both dragged and kept under the impact of a turbu- lence increasing their motion. However, these motions never occur randomly. Organelles do not get clustered in a certain part of the cell, or become dispersed randomly; in short, their distribution does not cause any disorder. Quite the contrary, such organization of the cell’s components is essential to ensure their interaction and persistence of the cell. Lead researcher Professor Gero Steinberg, Chair in Cell Biology and Director of the Bioimaging Centre at the University of Exeter, said the fol- lowing on this matter:

“Many people had previously assumed that organelles are randomly-distributed, as that’s how they appear. Our research has revealed a new fundamental principle of the way cells organize themselves -- that they use energy to create this seemingly random, even distribu- tion. This allows the organelles to interact with each other throughout the cell.” 1

If organelles were distributed randomly during their transportation as claimed prior to this research, certain diseases would arise. In fact, organelle clustering without proper distri- bution inside the cell is found in some human disorders, such as Zellweger Syndrome, which is a fatal disease. Children born with this disorder may only live until the age of one”. 2

This new scientific research carried out by Exeter University makes evident that organ- elles in the cell are not dispersed randomly and they cannot be moved from one place to another without an intelligence that directs them. There is no doubt that this perfect or- der in the cell is not the coincidental ability of organelles that lack intellect or conscious- ness. On the contrary, that is one of the most profound instances of Almighty God’s infinite power and His artistry in Creation. God reveals the following in a verse:

“That is God,your Lord.Thereisnogodbut Him, the Creator of everything. So worship Him. He is responsible for everything.” (Qur’an, 6:102)

While evolutionists cannot even explain the origin of a single protein molecule, they keep up with their allegations that the cell came into existence through coincidences. the im- passe of evolutionists is not limited with their not being able to explain how the protein and cell originated: Just like the order in the distribution of organelles in the cell, they are obliged to give an account for the existence of thousands of other mechanisms, and how in- organic molecules could give structure to such organizations that necessitate confounding consciousness, information and intelligence.

  1. University of Exeter. “How to organize a cell: Novel insight from a fungus.” ScienceDaily, 2 June 2016. www.sciencedaily.com/releas- es/2016/06/160602083246.htm 
  2. Femke C. C. Klouwer, Kevin Berendse, Sacha Ferdinandusse, Ronald J. A. Wanders, Marc Engelen and Bwee Tien Poll-The. “Zellweger spectrum disorders: clinical overview and management approach.” Orphanet Journal of Rare Diseases

Protein Synthesis Is Impossible to Explain Through Evolutionary Mechanisms

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 cre- ation, 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 imortant 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).1

DNA Replication

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 God 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 God’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.

RNA POLYMERASE

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 under stands 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 ribo some 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 sepa rated 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 mi crobiology 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 passes through 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 Complex2 is catalyzed and this allows nucleosomes to open. We can compare the nucle- osome-enzyme adaptation observed at this point to a key with a very special three-di- mensional shape holding onto the histone proteins’ specific parts and loosening it with- out 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 God 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 organiza- tion has come to be. Even if evolutionists were provided with all the materials required for life to come into ex- istence, 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 God.

References:
____________________________________

  • 1. Molecular Biology of the Cell, fifth edition p. 215
  • 2. Akira Ishihama (2000). Func- tional modulation of Esche- richia coli RNA polymerase. pp. 499–518. doi:10.1146/annurev. micro.54.1.499)

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.

 

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