Interpreting science through the eyes of faith

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  • Say: ‘He is God, Absolute Oneness, (Surat al-Ikhlas, 1)
  • God, the Everlasting Sustainer of all. (Surat al-Ikhlas, 2)
  • He has not given birth and was not born. (Surat al-Ikhlas, 3)
  • And no one is comparable to Him.’ (Surat al-Ikhlas, 4)

The Qur’an is a great miracle applicable to all centuries. It fully describes the essence of many problems that exist today and sets out the truth of those problems in the finest manner. Mankind came under the influence of various erroneous philosophies in the last two centuries, which inflicted great sufferings on people. These verses from Surat al-Ikhlas are excellent guides for mankind.

This wondrous universe we inhabit, our Earth with its many lovely plants, fruits and animals and every detail in living things awake the greatest amazement in people, without exception. We are astonished by these as believers, and that amazement is of course for God, Who creates them all. Unbelievers may also be amazed by nature, the universe, plants and animals; but dialectical materialism and the theory of evolution and its application to nature, blunts that appreciation in those people. They therefore seek to portray all these wondrous phenomena as the work of a simple conflict of opposites and chance.

Of course, a rational analysis and a perspective based on good conscience immediately show that no marvelous phenomenon can come into being by chance. The conscience, the soul and the subconscious mind all know and admit to that fact. Yet many people have become unable to see these truths over the last 150 years because of the aforementioned philosophies. It is therefore very important to consider the difference between scientific data and the non-scientific claims made by deniers with great care and for this difference to be described in detail.

Let us now see, through technical knowledge we have attained over the last two centuries, how we are endowed with the most amazing blessings and how none of these marvels could have come into being by chance.

Also, let us consider just two of the hundreds of subjects that could be cited as evidence in this article:

  1. Unity, not conflict, lies at the basis of life

When we look at the smallest unit of life, the cell, we see that chance has no place in any stage. The things that happen in this minute structure, organized just like a factory, are literally incomparable. Whichever detail of the cell we look at, we see mutual aid and solidarity going on.

Let us take proteins as an example and reflect on what is needed for a protein to be able to form:

In order for a protein to be able to form, there has to be

  • The coding of information in the DNA;
  • Regions showing where this information starts and ends;[i]
  • Transcription factors for this information to bind to and to allow production to begin based on the requirements in the cell and promoter regions for these to bind to in DNA;[ii]
  • Enzymes and proteins to permit the reading of what is in DNA;[iii]
  • The template known as mRNA obtained from that reading; The ribosomes produced from that structure, which are themselves made up of proteins;
  • And starting factors to ensure that ribosome production starts at the right time and under the right conditions are also required, and these starting factors are also proteins.

Let us continue; in order for a protein to form there also need to be

  • Elongation factors enabling the ribosome to enlarge the protein chain;
  • Termination factors that become involved when the ribosome’s work is done;[iv]
  • Amino acids required by the ribosome;
  • tRNAs to transport these amino acids to the ribosome;
  • Enzymes to bind the amino acids to the tRNAs;[v]
  • Structures monitoring the level of these amino acids inside the cells and that produce them if they are insufficient – and these also consist of proteins – or proteins that permit them to be transported inside the cell from outside the cell – and proteins are again required for these to be transported to the cell membrane;[vi]
  • Chaperon proteins that help the manufactured proteins to be folded into 3-D structures;
  • Enzymes that cause additional changes so the proteins can function in the regions to which they go – and more than 1,150 of these have been identified to date; [vii]
  • Many proteins are able to discharge their functions with additional structures also containing metals: Other proteins are needed for the production of these and to transport the metals to the proteins;[viii]
  • Labels determining where each protein is to work are needed, and these show the presence of a vast postal and address system within the cell; [ix]
  • In addition, there need to be proteins working like postmen to carry these labels to the right locations;
  • Proteins that receive these postmen at their destination and cause additional form changes;[x]
  • Enzymes that cut out and remove labels that need to be removed once their work is done; [xi]
  • Proteins that make placement to the right places;
  • Packets that prevent them from being affected by occasional adverse conditions inside the cell during their journey;
  • Proteins that hand these packets on;
  • Systems that check where the amounts of proteins produced are adequate or not;
  • Structures that check whether the proteins manufactured have become corrupted over the course of time;
  • There is also a need for proteins to repair any such damage and determine whether or not it is in repairable limits;[xii]
  • Some proteins monitor proteins immediately after their manufacture from ribosomes. These proteins surround corrupted proteins and gradually fold them back into the correct shape;[xiii]
  • If the damage in a protein cannot be repaired, then systems are required that decide that this protein will be harmful to the cell and begin destroying it. These damaged proteins first need to be labeled, and labeling systems and machinery to break these proteins down are needed, and these are again made up of proteins;[xiv]
  • None of this could happen without small energy packets like miniature batteries (ATP, GTP) used in all these processes.

The protein system will work smoothly in a cell in which all such conditions, of which we have listed only a very few and only in brief, are met, and then the cell will be able to survive. Any defect in these interconnected systems will lead not to improvement or evolution, but on the contrary to sickness, cancer and death.

As we have seen, numerous complex systems work hand in hand inside the cell, with great devotion and for the benefit of the cell, and literally with consciousness and enormous technical skill. From the moment a protein first begins to be manufactured to the moment of its destruction, it needs numerous different structures with a great many technical properties.

It is of course completely wrong to refer to these technical facts as a “clash of opposites.” There is no question of any such thing in any stage of the process summarized here. Yet the achievement of these structures made up of unconscious atoms is utterly amazing.

All these details exist so that we can see that all power belongs to God and that our Lord is mighty enough to do anything. Many people are unaware of these marvels that are absolutely essential for their survival. The difference with believers is that they reflect on these details and bow their heads when they see the artistry of God.

He directs the whole affair from heaven to earth. Then it will again ascend to Him on a Day whose length is a thousand years by the way you measure. (Surat al-Sajdah, 5)

 

Let us consider the arrangement within DNA as a second example:

  1. The theory of evolution tries to bring chance into the origin of life. Yet the details of life, such as when we examine the structure of DNA, show that there is no room for chance at all and that on the contrary, a magnificent control prevails.
  • All the data about us is encoded in a DNA chain. That chain is created with a spare (sibling chain) against the possibility of damage that may occur.
  • The enzyme DNA polymerase that reproduces the information checks every letter that DNA makes. If an error is made, it puts it right;[xv]
  • Errors occurring in DNA are corrected on the basis of the sibling chain:  The absence of such a sibling chain would lead to all genes eventually becoming corrupted, even if they were perfect to begin with; [xvi]
  • There needs to be robot molecules and enzymes sensitive to errors in DNA. Each one of these marvelous structures identifies and repairs a different type of error. They do not leave the DNA to become corrupted. For example, the enzyme photolyase repairs the impairment known as “thymine dimer” in bacteria 300-400 times a day. Otherwise, in the absence of this enzyme, the bacteria would not evolve but die;
  • Breaks in DNA are repaired by special enzymes; [xvii]
  • No gene production occurs haphazardly. Production always takes place in line with the level of proteins. If they are present in large numbers in the cell, those numbers are reduced, or vice versa;
  • The enzymes involved have to be deactivated when not needed. There has to be such a control system. For example, some enzymes are active when bound to phosphate and lose their activity when the phosphate is taken away. The addition or depletion of phosphate by enzymes takes place according to the requirements in the cell at that time. Enzymes without such a control system also lead to cancer under certain circumstances; [xviii] [xix]
  • A great many gates of different types are needed for entry into and exit from the cell, and all correct from the beginning. These gates have to work, not haphazardly, but in a controlled manner;
  • Systems are also needed that increase the numbers of these gates if they are insufficient or to remove them from the cell membrane if they are too numerous;
  • Systems that store critical substances inside the cell are also needed. This has to take place in a controlled manner. For example, cellular fluid possessing too many iron ions leads to a large number of free radicals and as a result to mutations in DNA and to impairments in fats and proteins. Special structures are needed to store these when there are too many of them; [xx]
  • As described above, mRNA in the form of a template is first manufactured from DNA, and ribosomes and proteins from that. In addition to control at the genetic level and the protein level, control is also required at the mRNA level. But this is not left to chance, either. Let us consider mRNA responsible for manganese ions absorbed into the cell. If there is no longer any need for a large number of manganese ions in the cell and their number is too high, manganese gates at the cell membrane are packaged and sent inside the cell. At the genetic level, the relevant gene is inactivated. However, there are still mRNA templates in the cell permitting the manufacture of gates. These are not left to their own devices either, and a destruction system involving structures such as miRNA and siRNA goes into operation. There is nothing haphazard here, either;
  • Gates on the cell membrane require fine adjustment depending on changing circumstances. For example, some gate proteins are phosphatized and their electrical properties increased, as in the learning process;
  • As described above, proteins in cells sometimes deteriorate despite being in a sheltered environment. Impairment leads to various disorders in cells. Such proteins are marked into order to prevent this and are broken down at the right location. Interestingly enough, the protein known as ubiquitin that labels such proteins is not touched. Only defective proteins are broken down by the machinery in the cell. The presence of such differentiation shows that there is a special system and surveillance in the cell. It is impossible for anyone of good conscience to say that this came about by chance: It is also dishonest to maintain that a system, the like of which we could never design, came about spontaneously by chance and through the unconscious laws of nature; [xxi]
  • As also mentioned above, all amino acids, proteins, metals and energy-giving molecules have to be present within very delicate balances inside the cell. There also have to be systems to monitor as to whether their levels have gone up or down. There needs to be sensitive sensor molecules to monitor these delicate balances and systems to take the appropriate precautions. Any cell without such a control system cannot live, and will die. [xxii] [xxiii]

 

God keeps a firm hold on the heavens and earth, preventing them from vanishing away. And if they vanished no one could then keep hold of them. Certainly He is Most-Forbearing, Ever-Forgiving. (Surat al-Fatir, 41)

Every detail we look at in the cell reveals a glorious artistry, intelligence, knowledge, skill, attention, control, collaboration and obvious planning. Yet all these structures consist of atoms that are themselves wholly unconscious and unaware of their own existence. The sublime characteristics in these atoms introduce us to our Creator, Who created them. We realize His great love and compassion for us, and how the universe came into being with a special creation.

Every point in the cell shows us the manifest presence of God. These glorious structures, in which there is no room for chance, are actually themselves helpless. However, as God reveals in Surat al-Ikhlas, God is the As-Samad, the Everlasting Refugee and Sustainer, the One in Whom all created things are in need. Everything is condemned to oblivion without His help. This is something calling for great reflection.

Our universe, in which very different phenomena are bound together through very delicate balances, exists through God, Who sees and knows all and Who keeps all things under His control right down to the tiniest detail. As we are told in Surat al-Ikhlas, our Creator is the One.

Science, which reveals all this truth, is made obligatory for us by God in the Qur’an because “science” is one of the ways of examining the universe and everything in it and explaining it to mankind through discovering the creative artistry of God. Religion therefore adopts science as one way of accessing the details inherent in God’s creation, and therefore encourages science.

In the same way that religion encourages scientific research, scientific research conducted on the basis of the truths inherent in Islam will lead to much faster and more definitive results, as religion provides the most definitive answer to the question of how the universe and life came into being. Therefore, research conducted on a sound basis from the beginning will very quickly reveal the secrets of how life and the universe came into being, with the expenditure of far less energy and effort.

As Albert Einstein, regarded as one of the greatest scientists of the 20th Century, said, "science without religion is lame.” In other words, science that is not guided by faith cannot exhibit any progress and will take much longer to obtain definitive results. Indeed, most of the time, it will be quite impossible to obtain any results at all.

Those who remember God, standing, sitting and lying on their sides, and reflect on the creation of the heavens and the earth: ‘Our Lord, You have not created this for nothing. Glory be to You! So safeguard us from the punishment of the Fire. (Surat al-Imr’an, 191)

There is thus a truth that must absolutely be known: the sole aim of science is to investigate the infinite might of God and the proofs of creation in the universe, and accurate results can only be obtained if it operates in the light of that aim. If the right course is taken, and if it is directed properly, science can attain its true end in a very short span of time.

Learning details such as this is instrumental in bringing forth  a zealous and awe-filled love and fear of God in people’s hearts. It is therefore of the greatest importance to tell people of, and encourage discussion of, the signs leading to faith.

 

References and Detailed Notes:



[i]             D. Voet and J. G. Voet, “Biochemistry,” 4th Edition, 2011, p. 367

           Proteins consist of amino acids. Each amino acid is encoded in DNA with 3-letter codons. Sixty-four different words can be written with 3 letters. Three of these letters, UAA, UAG and UGA, are in mRNA. These mean that the end of the protein has been reached. The codon AUG encodes the amino acid methionine. This is the first amino acid of proteins. The other amino acids are coded with the remaining 60 letters. This is a very intelligent system, because the coding system thus has a reserve and is also used as a marking sequence for other than amino acids. Every coding system requires intelligence. No language comes into being by chance. Consciousness is essential. The wondrous data system in each of our cells is not of course the work of chance, either.

[ii]         Rédei, George P., ed. Encyclopedia of Genetics, Genomics, Proteomics, and Informatics. Vol. 1. Springer, 2008, p. 1564

[iii]         Alberts, B. et al. "The cell cycle." Molecular Biology of the Cell. 5th Edition. Garland Science, New York, NY (2008): p. 263-328

           Various types of proteins that assist with the reading process need to be present. For example, the enzyme topoisomerase breaks the DNA chain from one or two chains in order to reduce the tension that develops as DNA is opened up and rejoins it at another region of DNA. The tension that forms is thus reduced. It enables another interesting structure, the enzyme polymerase, to remain bound to DNA. Some proteins are used to keep the opened up chains separate. The enzyme that performs replication due to to these two groups of proteins thus has room to work.

[iv]         D. Voet and J. G. Voet, “Biochemistry,” 4th Edition, 2011, p. 1375

           For example, bacteria need 3 initial factors, 3 elongation factors and 4 termination factors.

[v]          D. Voet and J. G. Voet, “Biochemistry,” 4th Edition, 2011, p. 1349

[vi]         Nelson, David L., Albert Lester Lehninger, and Michael M. Cox. Lehninger Principles of Biochemistry. MacMillan, 2008, p. 851-900

           Tens of enzymes using substances which are the product of other enzymes are responsible for the production of 20 amino acids. The functions of these enzymes are kept under delicate balance with feedback mechanisms depending on the level of energy and amount of amino acids in the cell.

[vii]        Walsh, Christopher T., Sylvie Garneau Tsodikova, and Gregory J. Gatto. "Protein posttranslational modifications: the chemistry of proteome diversifications." Angewandte Chemie International Edition 44.45 (2005): 7342-7372

           Identification of the number of the 1150 enzymes producing changes in amino acids in the post-ribosomal stage came in a paper published in 2005.

[viii]       Rosenzweig, Amy C. "Metallochaperones: bind and deliver." Chemistry & biology 9.6 (2002): 673-677

           This analysis from 2002 revealed that approximately one in three proteins contain metals. For example, they have key functions in vital processes such respiration, photosynthesis, nerve transmission and defense against toxic substances. There are special compartments to allow metals to bind to proteins. Enzymes are also needed to transmit the metals to these compartments.

[ix]         http://www.nobelprize.org/nobel_prizes/medicine/laureates/1999/press.html

[x]          Alberts, B., et al. "The cell cycle." Molecular Biology of the Cell. 5th Edition. Garland Science, New York, NY (2008): pp 713-717

           In order for proteins going to such complex structures as mitochondria to be able to settle in the right place, they are coded with interconnected postal systems. The first code involves the sending to the mitochondria, and the other indicates where it will operate in the organelle. In addition, in order for proteins to be able to pass through the narrow cell gates, they are first prevented from being folded by other proteins. For example, in order for a protein that will pass through the mitochondrial gate to do so, it has to meet these conditions. A protein complex that attracts the protein serving as a motor at the gate is also needed in order to pass through it. After that, in order for the protein that passes through to function it needs another chaperon protein that folds it up appropriately.

[xi]         Alberts, B. et al. "The cell cycle." Molecular Biology of the Cell. 5th Edition. Garland Science, New York, NY (2008), p. 701-704

[xii]         Alberts, B. et al. "The cell cycle." Molecular Biology of the Cell. 5th Edition. Garland Science, New York, NY (2008), p. 388

           For instance, the production of heat shock proteins (HSP) increase immensely when temperature in the cell increases (for example from 37°C to 42°C) and they help folding the proteins again.

[xiii]        Alberts, B., et al. "The cell cycle." Molecular Biology of the Cell. 5th Edition. Garland Science, New York, NY (2008): p. 390

[xiv]        D. Voet and J. G. Voet, “Biochemistry,” 4th Edition, 2011, p. 1409-1423

           Proteins that should be dissolved are labeled with a protein named ubiquitin with the help of three enzymes, E1, E2 and E3. A protein having a multitude of ubiquitin molecules would indicate it is a structure that needs to be destroyed in the cell. Such a labeled entity is turned into pieces in a grinding plant named proteasome which is again made of proteins itself.

[xv]         Alberts, B., et al. "The cell cycle." Molecular Biology of the Cell. 5th Edition. Garland Science, New York, NY (2008): pages 268-271

[xvi]        D. Voet and J. G. Voet, “Biochemistry,” 4th Edition, 2011, page 1214

           For example, every day about 10,000 sugar nucleotide bonds are detached with no reason. This means 10,000 letters are dismantled from DNA every day. Also, especially some nitrogen on DNA is oxidized. Again, with no enzymes, these letters are bonded with methyl groups. In addition, even if nothing occurs, 120 of the thymine turns into another molecule named uracil, which is not a part of the DNA coding.

[xvii]        D. Voet and J. G. Voet, “Biochemistry,” 4th Edition, 2011, page 1223

           Oxygen respiration in the cell may result in production of chemically active products. Such reactive material cause breaks on DNA. It has been found that while cells are dividing at 5-10% of the time there is a break on one of the chromosomes. There are special sensor proteins that become aware of such severing. This sensor protein informs other proteins for repairing the broken structure.

[xviii]       Alberts, B., et al. "The cell cycle." Molecular Biology of the Cell. 5th Edition. Garland Science, New York, NY (2008): page 175-176

[xix]        Alberts, B., et al. "The cell cycle." Molecular Biology of the Cell. 5th Edition. Garland Science, New York, NY (2008): page 175-176

           God has created tumor suppressor genes in our cells. These genes prevent uncontrolled multiplication of our cells that would cause cancer. During this process a great number of proteins subsequently trigger the other. On one of these, any mutation on the signal path TGFβ would make these proteins stop their activity and cause cancer in pancreas or other organs.

           Or, let us consider the Rb proteins that are responsible for cell-cycle control. This protein prevents the cell to enter cell division stage. In cancerous cells, these proteins do not exist, or deficiencies in proteins that control that one lead to cancer. Another reason why Rb protein does not function is the addition of phosphate to its composition. However, this should be done under control and at the right time. Because, any cell where Rb does not function would lead to cancer. The phosphorylation of the Rb protein is carried out with Cyclin D – Cdk4 complex. But existence of a control system for this complex is a requirement right from the start. Because this complex will make Rb lose its activity through phosphorylation and result in cancer. The quantity of these materials is also important. Therefore, their amount should be kept under control. For instance in breast cancer since Cyclin D – Cdk4 proteins are produced in excess, that results in more division of the cell. Also, Cyclin D – Cdk4 proteins should not function at wrong times when cell is under stress. In such circumstances, p16 protein that is produced prevents Cyclin D – Cdk4 protein complex from attaching to Rb protein. That impedes phosphorylation of Rb protein. That keeps Rb protein in active status. This way it intervenes in division of the cell, which is its assignment. This way cell does not divide. It is obvious that these are critical decisions to make and steps described here are difficult to comprehend. Is it not clear that such arrangements that require close attention would never be an act of coincidence? As a matter of fact, when p16 gene is out of control that also results in cancer.

           Mutations that take place in genes of a system that acts in a chain reaction one triggering the other would lead to cancer in a cell, not evolution.

[xx]        Andrews, Simon C., Andrea K. Robinson, and Francisco Rodríguez-Quiñones. "Bacterial iron homeostasis." FEMS microbiology reviews 27.2-3 (2003): 215-237.

           Based on Fenton reactions, iron ions result in the formation of free radicals. Free radicals harm the cell, therefore the excess amount of iron ions are stored in the cell. For example, 2000-3000 iron ions are stored in the storage protein named ferritin. Despite existence of all these storage proteins, free radicals form in the cell due to the mentioned reactions. These are neutralized by means of other protective enzymes (like SOD). The presence of such protective enzymes is a requirement for a healthy cell.

[xxi]        D. Voet and J. G. Voet, “Biochemistry,” 4th Edition, 2011, page1409-1423

[xxii]       Andrews, Simon C., Andrea K. Robinson, and Francisco Rodríguez-Quiñones. "Bacterial iron homeostasis." FEMS microbiology reviews 27.2-3 (2003): 215-237

           For instance in this article there are examples about the Fur protein that has an effect on 35 other proteins when bonded with iron. When Fe2+ ion (the iron atom lost two of its electrons) is attached to the Fur protein that would indicate there are excess of iron ions in the cell. At that instant Fur protein turns on the Bfr gene (bacterioferritin is responsible for storing iron) that is used for storing iron. This way, proteins are manufactured for storing the excessive iron in the environment. The same Fur protein also blocks the gate proteins that allow iron access into the cell. Obviously there is a perfect artistry here. We could never come close to this artistry, or imitate it.

[xxiii]       Rowbury, Robin J. "Extracellular Sensors and Extracellular Induction Components in Stress Tolerance Induction." Bacterial Physiology. Springer Berlin Heidelberg, 2008. 263-292

           It may use very interesting capabilities for sensing the physical conditions of the environment. For example in certain bacteria sensor molecules that are active in eight different levels of acidity are found for measuring its ratio.

2014-04-08 02:44:39

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