Tuesday, January 17, 2012

4. Holy Quran Explains the Phenomena of Life and Death Challenging the Molecular Gene (Genome) Concept

Holy Quran is the only source of information on the phenomena of life and death. Demolishing the molecular gene (genome) concept, the foundation of modern biology, the Quran reveals the nonmaterial basis of life (rooh or nafs) elegantly, which can be understood with the help of computer model of organism. The revelations proclaim it is impossible to create life from non-life. This is falsifiable. Atheists can take up this challenge and prove Quran wrong by creating life from chemical molecules without involving living cell or organism in the process. The revelation implies every attempt biologists make to synthesize life from non-life by chemical means is destined to fail. The failures already witnessed in this field and those bound to occur in future confirm the divinity of the Quran and existence of God. The biggest irony is that it is through atheist scientists God proves His existence!


For nearly six decades now, biologists have been promoting molecular gene (DNA) as the blueprint of life. The world now believes that it is a chemical molecule that decides the development, heritable traits and behaviour of an organism. Last century has been famously called ‘the century of the gene’. The molecular gene was born, christened, and brought up during that period.

In 1865, the Austrian monk Johann Gregor Mendel proposed three laws governing heredity, which however did not see light of the day until after 30 years when in 1900 three botanists independently and almost simultaneously rediscovered them. Bateson coined the term “genetics” for the then emerging science of heredity in 1906. Subsequently in 1909, Danish botanist Wilhelm Johannsen introduced the notions of “genotype” and “phenotype”. In addition, he proposed the term “gene” for the elements of the genotype. Johannsen had reservations with respect to gene’s particulate nature and had also warned against assuming genes for a particular character [1]. Thus the gene remained a hypothetical nonphysical entity.

Thomas Hunt Morgan and his group contributed substantially to the understanding of the mechanism of heredity. In the year 1933, on the occasion of his Nobel address, Morgan observed: “At the level at which the genetic experiments lie it does not make the slightest difference whether the gene is a hypothetical unit, or whether the gene is a material particle.” [2]. Nevertheless, many geneticists like Herman J. Muller (Morgan’s student), believed that genes had to be material particles. In 1950, on the occasion of the fiftieth anniversary of the rediscovery of Mendel’s work, Muller however admitted: “[T]he real core of gene theory still appears to lie in the deep unknown. That is, we have as yet no actual knowledge of the mechanism underlying that unique property which makes a gene a gene… its ability to cause the synthesis of another structure like itself, [in] which even the mutations of the original gene are copied. [We] do not know of such things yet in chemistry.” [3]. The growing success of various studies relating to classical genetics led to hardening of the belief that the gene is discrete, material entity [4, 5]. It has been known since about 1913 that the individual active units of heredity - the genes - are strung together in one-dimensional array along the chromosomes, the threadlike bodies in the nucleus of the cell. It has also become apparent that the information-containing part of the chromosomal chain is the DNA molecule [6]. George Beadle and Edward Tatum during the late 1930s and early 1940s established the connection between genes and metabolism. They proposed the “one gene, one enzyme hypothesis”. Since chemical reactions occurring in the body are mediated by enzymes, and since enzymes are proteins and thus heritable traits, it is supposed that the gene and proteins are related. These views of gene function strengthened the idea of genetic specificity leading to molecularization of the gene. In the early 1940s, Oswald Avery and his colleagues purified the deoxyribonuleic acid (DNA) of one strain of bacteria, and demonstrated that it was able to transmit the infectious characteristics of that strain to another, harmless one [4]. The elucidation of the structure of DNA as macromolecular double helix by Francis Crick and James Watson in 1953 and in vitro characterization of the process of protein biosynthesis led to the idea that it was the linear sequence of ribonucleic acid derived from one of the DNA strands that directed the synthesis of a linear sequence of amino acids, or a polypeptide, and that this process was mediated by an adaptor molecule (RNA template). In 1958 Francis Crick formulated the “sequence hypothesis” (triplet code or codon, i.e., three bases at a time specified one amino acid) and the “central dogma” of molecular biology. All these considerations ultimately led to defining the molecular gene. According to the classical molecular concept, a gene is a stretch of DNA that encodes a functional product, a single polypeptide chain or RNA molecule. The entire collection of genes encoded by a particular organism is the “genome” that is supposed to constitute the genetic program. The assumption of “one gene, one protein” makes the genes generally synonymous with proteins. Thus the term “gene” refers to the gene that codes for protein. Johannsen’s non-particulate gene thus metamorphosed into particulate gene (Figure 1). The molecular gene was born!

Figure 1. DNA double helix, the only structure in the whole universe, which biologists think encodes not only chemical information but also biological information

Molecular biology opened the floodgates of boundless optimism about the ability of the super molecule DNA to decipher the mechanism of life as well as the potential of gene for genetic manipulation. In his classic and influential textbook, The Molecular Biology of the Gene, James Watson stated: “We have complete confidence that further research of the intensity given to genetics will eventually provide man with the ability to describe with completeness the essential features that constitute life.” [7]. But he was grossly wrong. Peter Cook reflects: “Watson and Crick must have thought that the sequence was everything. But life is much more complicated than that.” [8]. Today biology is drifting in the ocean of genomics like a ship that has lost its direction. The gene remains undefined and obscure to say the least.

Atheistic underpinnings of the molecular gene concept

The material gene is not strictly a concept prompted by research findings; rather it is more a product of the conviction of geneticists that the gene has to be material entity. The nonphysical gene originally proposed by Johannsen had divine connotation sufficient to cause discomfort to atheistic minds. The molecular gene concept was therefore developed to oust the nonphysical gene. This is not the first time a theory because of its divine implication is overthrown by the scientific community to plant atheism-based theory in its place.  We have precedent in steady state cosmology. Steady state theory was proposed to counter the big bang theory, which indicated a beginning for the universe and time. This in turn implied existence of Creator God for the universe.  While discussing the big bang model, Stephen Hawking wrote: “Many people do not like the idea that time has a beginning, probably because it smacks of divine intervention.…There were therefore a number of attempts to avoid the conclusion that there had been a big bang. The proposal that gained widest support was called the steady state theory….Another attempt to avoid the conclusion that there must have been a big bang, and therefore a beginning of time, was made by two Russian scientists, Evangenii Lifshitz and Isaac Khalatnikov, in 1963.” [9]. In 1949 Hermann Bondi and Thomas Gold (two Austrian scientists) along with the British astronomer Fred Hoyle proposed the steady state model. According to this theory, the universe does not evolve or change with time. There was no beginning in the past and there will be no change in the future. This model is based on the perfect cosmological principle which states that the universe is the same everywhere on the large scale, at all times. This theory attracted a lot of attention as it avoided the big bang event and hence a beginning for the universe which implied divine hand. The steady state universe postulates creation of matter out of vacuum so that the perfect cosmological principle (i.e., density is constant) is satisfied. The theory held the centre stage for nearly two decades. The prediction of continual matter creation from nothing is a violation of the law of conservation of the mass and energy. Added to that, discovery of the cosmic microwave background strengthening the validity of the big bang cosmology came as fatal blow to the theory [10]. Thus the big bang theory, which upholds existence of God, remains as the acceptable theory in cosmology despite the efforts of atheist lobby to overthrow it. When we examine the present scenario in biology against this background, it appears that molecular gene is bound to meet with the same fate as steady state theory.

Nonmaterial basis of life

The Quran is the only source that gives information on the phenomena of life and death. The Quran reveals that life is caused by nonmaterial (invisible) entity called rooh (the term nafs is also used in the Quran).

وَإِذْ قَالَ رَبُّكَ لِلْمَلَائِكَةِ إِنِّي خَالِقٌ بَشَرًا مِّن صَلْصَالٍ مِّنْ حَمَإٍ مَّسْنُون فَإِذَا سَوَّيْتُهُ وَنَفَخْتُ فِيهِ مِن رُّوحِي فَقَعُوا لَهُ سَاجِدِينََ
Behold! Your Lord said to the angels: I am about to create a man from sounding clay (made) from sticky mud. When I have fashioned him and breathed into him from My rooh, you fall down in obeisance to him.”  (Q. 15:28-29).

وَلَوْ تَرَىٰ إِذِ الظَّالِمُونَ فِي غَمَرَاتِ الْمَوْتِ وَالْمَلَائِكَةُ بَاسِطُو أَيْدِيهِمْ أَخْرِجُوا أَنفُسَكُمُ
“…If you could see the wicked in their panicky state at death when the angels stretch forth their hands (saying), “Release your nafs”….” (Q. 6:93).

The Quranic revelation of non-molecular basis of life can be explained with the help of computer model of organism. 

Organism – natural biocomputer or biorobot

An organism is natural biocomputer or biorobot whose development and functioning are determined by an integrated divine biosoftware (bioprogram). The cell, the basic unit of a living system, is a biochip. The structures in the cell (organelles and nuclear structures including DNA), tissues and organs at the level of the organism constitute the hardware. Since the hardware components (chemical structures) are intended for the execution of the bioprogram, they are produced in the cell in accordance with the program and therefore, cell structures including DNA show differences among the tissues of the body. In computer parlance the biosoftware is an integrated program or sets of instructions in the right sequence for the development of the organism, execution of various bioprocesses, its behaviour, instincts, habits and every other task performed by the organism. The biological program is not coded in the form of a molecule. It has no chemical structure or visible features and is comparable with a computer program stored on a physical medium (e.g., disk). The storage device for biological information in the cell is chromosome. It is the hard disk of organism. The biosoftware is stored on the chromosome in sectors (Figure 2).

Figure 2. Illustration of biomemory organization on the chromosome (the hard disk of biosystem) as many sectors each storing one or more biomemes

The non-particulate biological program stored on the chromosome can be perceived in terms of biomemetic concept. Biomeme is the smallest unit of biological information that can be transmitted from parent to offspring and that can take part in natural biosoftware engineering processes like cutting and splicing of chromosomal sectors, deletion, replication, translocation, crossing over (recombination), etc. These phenomena lead to alteration of the biosoftware via rearrangement of the biomemetic sectors on the chromosome (Figure 2). All these processes, which biologists treat as ‘errors’ or ‘mistakes’ are in fact program-driven functions to bring about the required alterations in chromosome organization and thereby, in bioinformation content. A detailed discussion of the biocomputer concept may be found elsewhere [11, 12, 13].

The Quran reveals the nonphysical nature of biosoftware in the context of describing the creation of man (Q. 15:26-29 quoted above). Man was created by God by ‘breathing rooh’ into the clay model of man. The Bible also describes the process similarly using the phrase ‘breathing of life’ (Genesis 2:7). The phrases ‘breathing of rooh’ used in the Quran  and ‘breathing of life’ used in the Bible are metaphors referring to the installation of divine biosoftware in the clay model of man. Upon installation of the rooh in the non-living clay model, it sprang to life much like a lifeless computer springs to “life” when software is installed. Thus the nonphysical entity called rooh is the divine biosoftware (or bioprogram). Like the nonmaterial computer program, biosoftware also needs a physical medium for storage, which is the chromosome.

Quran further states that it is from the nafs (biosoftware) of Adam, woman (Eve) was created (Q. 4:1, 7:189). The Bible says that it is from Adam’s rib, Eve was created. The rib mentioned in the Bible corresponds to the X chromosome of Adam [14]. The word ‘rib’ is used in the Bible metaphorically to mean chromosome (for the obvious reason that chromosome was unknown to the people of Prophet Moses’s time). Ribs are the only part of human body that morphologically resembles the chromosome. As two arms of a chromosome are joined on either side of the centromere, two ribs are joined on either side of a vertebra (Figure 3). The arms of a chromosome may be curved, straight or anywhere in between. It is not the curved or straight shape of the arms that is taken to indicate the similarity (as is misunderstood by some critics) but the resemblance in their structures; i.e., two arms of chromosomes are fixed on either side of centromere like two ribs are fixed on either side of the vertebra.  Of the two sex chromosomes (X and Y), Adam’s rib must be referring to the X chromosome because XX combination determines femaleness. Further, the arms of the X chromosome are more nearly equal in length than those of the Y chromosome. This characteristic of X chromosome makes it more comparable with the ribs on either side of a vertebra.  Since the Bible mentions only one rib, the biomeme for femaleness might be located on one of the arms of X chromosome.

Figure 3. Morphological semblance between human ribs and chromosome.
Note: Chromosome can take any shape from curved to straight. But the morphological semblance lies in the fact that as two ribs are attached on either side of the vertebra, two arms of the chromosomes are attached on either side of the centromere.

The analogy of rib used in the Bible for chromosome also confirms that the biosoftware is stored on the chromosome.  

The invisible soul of a computer or robot is its nonphysical software stored on its hard disk. Similarly the invisible soul of an organism is its nonphysical biosoftware stored on the chromosomes (hard disk of the organism). The Quran further reveals that it is the removal (or in computer parlance ‘deletion’) of nafs (biosoftware) from the biosystem that results in death (Q. 6:93 quoted above). That is, the biosoftware is irreversibly lost from the body at death. A dead body is like a computer without software. This will explain why life cannot be created from non-life (without involving a living organism), why a dead cell cannot be cultured, and why the material gene (genome) concept is wrong. Based on these divine revelations, the phenomenon of life can be defined as the manifestation of the execution of the biosoftware, and death as permanent loss of biosoftware from the body cells.

Scientific evidence for the non-molecular nature of biosoftware

Findings of several studies in molecular genetics support the Quranic revelation of non-molecular basis of life. In this context it is pertinent to note that the two warnings given by Johannsen namely against particulate nature of the gene and that against considering gene for particular character, have been proven true. This fact is made clear in the following quotes.

According to geneticist Peter Portin, “The gene is no longer a fixed point on the chromosome, producing a single messenger RNA. Rather, most eurkaryotic genes consist of split DNA sequences, often producing more than one mRNA by means of complex promoters and/or alternative splicing. Furthermore, DNA sequences are movable in certain respects, and proteins produced by a single gene are processed into their constituent parts. Moreover, in certain cases the primary transcript is edited before translation, using information from different genetic units and thereby demolishing the one-to-one correspondence between gene and messenger RNA. Finally, the occurrence of nested genes invalidates the simpler and earlier idea of the linear arrangement of genes in the linkage group, and gene assembly similarly confutes the idea of a simple one-to-one correspondence between the gene as the unit of transmission and of genetic function....” [15]. Richard Burian remarks: “There is a fact of the matter about the structure of DNA, but there is no single fact of the matter about what the gene is. [Genetics today] provides strong, concrete support for the claim that the concept of the gene is open rather than closed with respect to both its reference potential and its reference.” [16]. “Today, in the era of genomic sequencing and intense effort to identify sites of expression, the declared goal is to search for genes, entities assumed to have physical integrity. Ironically, the sharper resolving power of modern investigative tools make less clear what, exactly, is meant by a molecular gene, and therefore, how this goal will be realized and what it will mean”, observes Fogle [17]. An important objective of genome projects is the identification of genes. Current estimates of human genes arrived at from genome sequencing is 30,000–40,000, with occasional excursions to 100,000 or more. One reason for the continuing ambiguity is that genes are neither well defined nor easily recognizable [18]. According to Hardison, “knowledge of the DNA sequence does not tell us directly how this genetic information leads to the observable traits and behaviors (phenotypes) that we want to understand.” [19]. Geneticist William Gelbart writing on databases in genomic research notes:  “For biological research, the twentieth century has arguably been the century of the gene. The central importance of the gene as a unity of inheritance and function has been crucial to our present understanding of many biological phenomena. Nonetheless, we may well have come to the point where the use of the term “gene” is of limited value and might in fact be a hindrance to our understanding of the genome. Although this may sound heretical, especially coming from a card-carrying geneticist, it reflects the fact that, unlike chromosomes, genes are not physical objects but are merely concepts that have acquired a great deal of historic baggage over the past decades.” [italics added, 20]. Horace Freeland Judson writing in Nature notes: “The phrases current in genetics that most plainly do violence to understanding begin “the gene for: the gene for breast cancer, the gene for hypercholesterolaemia, the gene for schizophrenia, the gene for homosexuality, and so on. We know of course that there are no single genes for such things.” [21]. (See also post 4 at http://atheismpseudoscienceblog.blogspot.com for more.) 

Discovery of cell-induced mutation of DNA is another clear proof that the molecule (genome) does not constitute biological program. Exposure of living organisms to natural radiation is supposed to be the major cause of DNA mutations. It is well known that irradiation of propagation materials like seed can bring about heritable changes in the offspring. In fact irradiation is an important method adopted in mutation breeding trials in plants. But the irradiation dose used in such trials far exceeds the natural background level. The annual dose of background radiation received by a human being is 2 to 3 mSv. Whether this too low a dose is sufficient to change a chemical structure in the body cells particularly gonads is doubtful. Change in cell DNA is invariably attributed to background radiation ignoring the fact that cell itself has the mechanism to bring about that change. When such mechanism is present in the cell, how is it possible to distinguish the irradiation-induced mutation from the cell-directed one? Even if the background radiation damages the DNA molecule, how can it make rearrangement of the bases and create new ‘viable’ DNA molecule is another question that has been overlooked by biologists. Thirdly there is also no explanation as to why no other cell structure is similarly affected by background radiation.

In 1970 Miroslav Radman discovered that the phenomenon of mutation is cell-directed. He found that bacteria harboured information to make mutations [22]. In 1988 Cairns et al. confirmed that genetic mutations are induced from within the cell. They found cell-induced changes of various elements of the lac operon in Escherichia coli bacteria [23]. According to Chicural, “…depending on their environmental conditions, bacteria might be able to direct mutations to particular genes….Outraged, a number of evolutionary biologists quickly embarked on their own studies to test the notion” [22]. Goodman described the studies conducted by Joshua Lederberg at the University of Wisconsin which showed that mutations for resistance to some antibiotics occurred spontaneously in cells that had never been exposed before to the antibiotics [24]. A recent report of resistance of bacteria to antibiotics further confirms cell-induced mutation [25, 26]. Reviewing the works in this area, Pennisi remarked: “Genetic change, and hence the evolution of new species, is commonly thought to result from small, random mutations in individual genes, but a growing wealth of data emphasizes that the perception is wrong. Indeed the mutations leading to evolutionary change can involve the wholesale shuffling or duplication of the genetic material, changes that can affect the expression of genes or free up duplicated genes to evolve new functions. What’s more, these changes may not be totally random….mainstream biologists need to consider genomes, and the kinds of evolutionary changes they undergo, in a much different light.” [27]. The phenomenon of cell-directed mutation refutes the particulate gene concept but supports the Quranic revelation of nonphysical rooh (biosoftware) existing in the cell (as stored information). DNA mutations have to be seen as appropriate hardware changes directed by the cell itself to execute the program.  

Atheists poised to prove God

In this era of computer technology, we cannot treat nonphysical phenomenon as something non-existing, superstitious and improbable. Information is fundamentally nonphysical. Information stored on computer disk is intangible and nonphysical. Ironically, molecular biologists cannot bring themselves to believe that biological information also exists in non-particulate form. It appears that the atheist lobby in the scientific community is rather worried about the divine implications of the nonmaterial nature of biosoftware. The molecular biologists continue to chase a chemical trail (DNA) assuming that it is the source of biological information. Using DNA-technology they are unwittingly trying to find hardware solution for software problem. More than sixty years of intensive research has gone into molecular biology worldwide and yet biologists know precious little about the gene and phenomenon of life!  

Excepting the traditional areas like taxonomy, anatomy, physiology, cytology and biochemistry, every other field in biology where the tentacles of molecular gene pervade leaves much to be desired. The ludicrous fact about biology is that although it is the science of life, biologists have not been able to define and understand what “life” is; molecular gene is the fundamental entity in genetics but geneticists do not know what the gene is; species is the unit of evolution but evolutionists (including Darwin) do not know what species is! It is without knowing these fundamental entities, theories of origin of life, theory of evolution, and molecular gene theory have been proposed! It is time we realized biology is on wrong path, rejected the molecular gene, and turned to the revelation of God – the Quran.

Atheists and skeptics may note that the Quranic revelation of nonmaterial basis of life is scientifically verifiable. It predicts that it is impossible to create life from non-life without involving living cell at any stage of the process. It also predicts that it is impossible to restore life to a dead cell or dead body. These predictions are falsifiable. In fact biologists are doing exactly that in one way or the other. The ever-increasing problems with the molecular gene and genomics, and failure of experiments to chemically synthesize “life” without involving a living organism have already given enough proof about the nonmaterial nature of life thereby upholding the divine revelations.

Biologists are trying to synthesize living cell chemically (i.e., without involving a living cell at any stage) from scratch. This is an impossible proposition with the available molecular tools.  However, biologists can adopt an alternative approach. They can as well try to restore life to a dead cell by chemical means. A dead cell is equivalent to a prosthetic cell or a synthetic cell. It has all the material ingredients and components of a living cell (including DNA) except life. By bringing a dead cell back to life through chemical means, biologists can prove that life is a material phenomenon. Thereby, they can falsify the Quranic revelation also. This method is more practical than synthesizing a cell from scratch. On the other hand, the failure of experiments to chemically restore life to a dead cell will confirm the validity of the Quranic revelation that at death biosoftware (nafs) is deleted (i.e., irreversibly lost) from the biosystem.

The Quran further reiterates that death is a certainty ordained for all (Q. 3:185, 4:78) and the term of every individual has been fixed as if by writing (Q. 3:145) implying lifespan and  death are programmed for each individual in the biosoftware (nafs).

كُلُّ نَفْسٍ ذَائِقَةُ الْمَوْتِ ۗ
“Everyone will taste death….” (Q. 3:185).

أَيْنَمَا تَكُونُوا يُدْرِككُّمُ الْمَوْتُ وَلَوْ كُنتُمْ فِي بُرُوجٍ مُّشَيَّدَةٍ ۗ
“Wherever you are, death will find you out, even if you are in forts built strong and high!...” (Q. 4:78).

وَمَا كَانَ لِنَفْسٍ أَن تَمُوتَ إِلَّا بِإِذْنِ اللَّهِ كِتَابًا مُّؤَجَّلًا ۗ
“None can die without Allah’s consent, the term being fixed as by writing.” (Q. 3:145).

These revelations indicate man will never be able to conquer death. The divine proclamations also imply that studies now going on in several institutes to enhance longevity and ultimately to conquer death, are certain to fail. For instance, the goal of Immortality Institute (www.imminst.org) is exactly that. As can be seen the Quranic challenge is two-pronged; one against molecular gene and the other against conquering death. The nonmaterial basis of life is the divine challenge that is put across to the scientific community to think and accept Allah – the only God – and His revelation, the Quran. The continued failure of experiments to create life from non-life is the unequivocal proof of divinity of the Quran and the existence of God. More failures in this field in future will further confirm the existence of God. This is not just prediction of a probability but proclamation of a certainty by the Lord of the Worlds!   


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