Friday, January 6, 2012

5. Programmed Biological Evolution – A Probable Method of Creation of Organisms

The creation of biological species (excepting man) by God can be thought of as a programmed phenomenon. It can never be a hypothetical chance phenomenon driven by random mutation and natural selection as suggested by Darwin’s theory. There were no gradations either between any two organisms created by Allah. All of them are perfectly designed ones meeting the requirements of the overall divine scheme of things. Based on the natural existence of biosoftware engineering mechanisms as well as cell-directed hereditary changes, a theory of programmed organic evolution within the framework of the Quran has been proposed earlier [1]. The theory is briefly presented here. 

Natural biosoftware engineering

An important breakthrough in molecular biology is the discovery of molecular mechanisms available in the cell itself for bringing about biomemetic changes. There are several mechanisms and processes occurring in the cell that can produce tailor-made chromosome compositions (Figure 1). The ability of the chromosome to store the biosoftware and the existence of cell-mediated mechanisms for cutting and splicing chromosome sectors thereby altering chromosome composition and hence its bioinformation content provide ample support to the proposal of programmed evolution of biological species. A couple of examples of these are:

(a) The phenomenon of crossing over (biomemtic recombination)

                                                     (b) Chromosomal aberrations                        

Figure 1. Examples of natural biosoftware engineering mechanisms. (a) Crossing over, (b) Chromosomal aberrations

a) Biomemetic recombination: This occurs during meiosis. Through a process of ‘crossing over’, the segments of non-sister chromatids of a homologous pair of homologous dyads are exchanged (Figure 1a). This swapping of portions leads to alteration of biological information content in the resulting chromosomes. This produces phenotypic differences in siblings.  

b)  Chromosomal aberrations: Aberrations are changes encountered in the chromosomes during cell division (Figure 1b).  Although many types of aberrations are found, the more commonly observed are deletion (loss of small segment of a chromosome usually in only one homologue) leading to loss of information, translocation (a segment of one of the two homologous chromosomes breaks and binds to the other), duplication (occurrence of the same sectors twice on the same chromosome), inversion (a particular sector is reversed in the chromosome), insertion (a new sector is inserted into the chromosome) and substitution (a certain chromosome sector is replaced with another). Duplication of the whole complement of the chromosomes in the same cell (a consequence of lack of disjunction between the daughter chromosomes following replication leads to polyploidy) is also seen in nature. This phenomenon is widespread in plant kingdom. Mitosis and meiosis, two kinds of cell division, observed in biological organisms are in fact biosoftware engineering processes. All these processes are programmed phenomena occurring in the cell.

Origin of biological information

What modern biology treats as origin of life is in fact origin of biological information. It is without finding out the source of biological information (or the so-called genetic information) biologists deal with life and forms of life. Every phenomenon in nature is governed by chemical or biological information, which is nothing but Allah’s instructions. We find a baby is developed with diverse tissues in mother’s womb through execution of bioprogram stored in the zygote. Without that information baby cannot develop. The evolution of baby is reflection of sequential execution of the bioprogram carried in the zygote. In effect the execution leads to the resolution of specific number of programs each representing a tissue. The hardware (cell structure in a given tissue) is produced in accordance with the program to suit its functions. We can also think of the origin of diverse biological species in a similar way as the consequence of execution of a divine bioprogram carried in a primordial cell. The execution of the bioprogram involving biosoftware engineering processes resulted in the production of specific number of cells carrying microbioprograms each representing a species. The theory of programmed organic evolution does not view the origin of species as the result of random mutations (supposed to be caused by the action of certain agents external to the cell) followed by natural selection. It also does not support the current belief that life originated as an emergent phenomenon from non-living matter. Instead, it postulates the creation of biological species as programmed evolution through partitioning and differentiation of the bioprogram carried in a primordial cell. First the primordial cell carrying the divine bioprogram marking the origin of life appeared on the Earth. Following that, the bioprogram started operating leading to the creation of specified number of diverse biosoftware each representing a species. The term “programmed evolution” refers to the sequential execution of Allah’s instructions (bioprogram) carried in the primordial cell, which is comparable to the zygote.

Origin of the primordial biochip (PBC)

A multicellular biosystem (e.g., a human individual) evolves (develops) through a series of transformations from a microscopic cell (zygote) carrying the bioprogram. The organic evolution might also have got off similarly from a single cell. Evolutionists believe that the first organism that evolved on Earth was a single cell. Contrary to that, the theory of programmed evolution proposes that the first cell formed on this planet could not have been an organism or a species but a cell similar to zygote, which carried the divine bioprogram necessary for the evolution of the various species. This cell, which carried the divine bioprogram may be called the primordial biochip (PBC). Availability of biological information is an essential prerequisite for the evolution of organisms. Without that, biological organisms cannot evolve. But this most important requirement of biological evolution is comfortably ignored by the evolutionists by supposing genetic mutation will bring new information; but from where or which source? This is a fundamental drawback of Darwinism-based evolutionary theory. Origin of life or biogenesis is in effect origin of biological information on the earth.

Woese [2] proposed the concept of the ‘universal ancestor’ to look at the rooting of the evolutionary tree. It was a genetic annealing model to develop a picture of the universal ancestor. The ancestor according to this model could not have been a particular organism, a single organismal lineage. It was communal, a loosely knit, diverse conglomeration of primitive cells that evolved as a unit, and it eventually developed to a stage where it broke into several distinct communities, which in turn became the three primary lines of descent. The primary lines, however, were not conventional lineages. Each represented a progressive consolidation of the corresponding community into a smaller number of more complex cell types, which ultimately developed into the ancestor(s) of that organismal domain. The universal ancestor is not an entity, not a thing. It is a process characteristic of a particular evolutionary stage. Woese [3] advanced a theory of evolution of cellular organization based on the dynamic of horizontal gene transfer. According to him, horizontal gene transfer is one of the important keys to understand cellular evolution. If a cell was simple and highly modular in organization, horizontal gene transfer would play a stronger role in its evolution than otherwise and the cellular evolution would have been driven in the main by horizontal gene transfer at its beginnings. The universal tree has no root in the classical sense. The root is actually a Darwinian Threshold, the first point at which we can begin to give tree representation to the organismal evolutionary course. A certain ‘symmetry of descent’ is inherent in the classical view that is totally lacking here, because the root is not classical root, the sister lineages resulting from the earliest branchings are in no sense ‘sisters’. They differ in fundamental ways. He proposed a framework for conceptualizing cellular evolution involving evolution of translation process in an RNA-world populated by what he called ‘supramolecular aggregates’ (higher-order architectures designed around nucleic acid componentry) and a variety of other stages and conditions ultimately producing not one but three distinctly different cell types from which the extant life on the earth had descended.

Molecular evolutionists gave the name LUCA (last universal common ancestor) for the common ancestor of all life [4]. Despite the wealth of genomic data, LUCA has remained elusive. Whether it is a simple or a complex one is not yet understood. Genome sequencing has given hope to find out the answers to many such questions, and the general thinking is that LUCA may be a pool of genes shared by a host of primitive organisms [5]. According to Gary Olsen, a microbiologist at the University of Illinois at Urbana-Champaign, “the naïve picture that a group of organisms got all their genes from a simple last common ancestor is breaking down”. Moreover, the communal LUCA notion does not fit the way evolution works. “To think of LUCA in terms of a community is to remove the idea of Darwinism from early evolution”, says Patrick Forterre of the Paris-Sud University in Orsay [5]. Obviously, LUCA is a misfit in the Darwinian model, but the fact that LUCA is looked upon as a more likely take-off point for the organic evolution is a disturbing signal to the supporters of Darwinism.

The LUCA concept comes close but not identical to the concept of PBC. How did the PBC with divine bioprogram to guide the evolution of diverse species originate on the earth? There are certain verses in the Quran that indicate how biosoftware is transmitted to earth by God. The creation of the zygote in the womb of Mary carrying the biosoftware of Prophet Jesus Christ is illustration of the divine mode of transmission of biosoftware to earth. This will be clear from the following discussion.

Prophet Jesus was created from a word (software) from Allah (Q. 3:45). “Behold! The Angels said: “O Mary! Allah gives you glad news of a word from Him. His name will be Jesus Christ son of Mary, held in honour in this world and in the Hereafter and one of those nearest to Allah.” (Q. 3:45). Allah’s word is software (see also post 2 on process of creation). The ‘word’ mentioned in the verse 3:45 is the rooh (biosoftware) to create Prophet Jesus Christ (Q. 19:16-22). “And remember Mary in this Book when she retreated from her family to a place in the east. She placed a screen (to separate herself) from them. Then We sent to her Our rooh and he (the angel through whom the rooh was sent) appeared to her as man in all respects. She said: “I seek refuge in Most Gracious (Allah) from you (i.e., the angel in human male form), if you fear Allah. He (i.e., the angel) said: “Indeed I am only a messenger from your Lord to gift to you a pure son.” She said: “How can I have a son as no man has (ever) touched me and I have not been an unchaste (woman)?” He (i.e., the angel) said: “It is like that. Your Lord says, “It is a simple thing for Me (Allah) and (We wish) to make him (i.e., her son Jesus) a sign to mankind and a Mercy from Us (Allah). It is a matter ordained.” So she conceived him (i.e., her son Jesus) and she retired with him to a remote place.” (Q. 19:16-22). Although not explicitly mentioned in these verses that the rooh was sent through an angel, the messenger mentioned therein could be an angel as can be understood from other verses. The Quran informs at another place Allah sends angels as messengers (Q. 35:1) with rooh (Q. 16:2). Therefore conception of Prophet Jesus Christ by Mary occurred from the rooh (biosoftware) sent by Allah through an angel who appeared as male messenger before Mary, mother of Jesus Christ. The angel transmitted the biosoftware (rooh) into her womb through her genital organ (Q. 66:12). And Mary the daughter of Imran, who guarded her genital organ; and We breathed into it (i.e., her genital organ) from Our rooh; and she testified to the truth of the words of her Lord and of His Revelations, and was one of the devout (servants).”      (Q. 66:12). These revelations indicate that the biosoftware (rooh) transmitted by the angel into the genital organ of Mary transformed into the cell (zygote) that developed into Prophet Jesus Christ. The entire phenomenon can be scientifically described as teleportation event in which biological information transmitted by God materialized in the form of zygote carrying biosoftware (of Prophet Jesus Christ) in the genital tract of Mary (Q. 66:12).

Teleportation involves what is called “quantum entanglement”, a less understood concept of entwining two or more particles without physical contact. In 2004, physicists in Austria [6] and the US independently demonstrated quantum teleportation with atoms for the first time [7]. In October 2006, Eugene Polzik and his team at the University of Aarhus in Denmark, successfully conducted a teleportation experiment involving a microscopic atomic object containing thousands of billions of atoms [8]. They teleported the information to a distance of half a metre. For the first time, it involved teleportation between light and matter, two different objects.  In effect, in a teleportation event, the information transmitted to a faraway place transforms into the corresponding material. The PBC or the first cell with biological information necessary for the creation of millions of species would have been formed on the earth in the same way as the creation of zygote in Mary’s womb from the rooh sent by Allah. The appearance of the PBC marked the biogenesis (origin of life) on this planet. It would have materialized in aqueous milieu as the Quran puts it: “…We made from water every living thing. Will they not then believe?” (Q. 21:30). There are no two opinions among biologists as to the most probable location of origin of life; it is water. Alfred Russel Wallace emphasized at the beginning of the twentieth century that the first requirement for life is liquid water; without it, as far as we know, life is impossible [9]. Although an aqueous medium is believed to be essential for the origin of life, Darwin’s theory of evolution does not indicate aqueous milieu essential for subsequent evolution of diverse species. But the Quran asserts that it was from water all species were created (Q. 21:30). That all animals were also created from water was particularly made clear through another verse (Q.  24:45). “And Allah created all animals from water. Of them there are some that creep on their bellies; some that walk on two legs; and some that walk on four. Allah creates what He wills, for verily Allah has power over all things.” (Q. 24:45). These revelations unambiguously make it clear that all living beings from unicellular organisms like bacteria to multicellular organisms like plants and animals were created from water. This however does not apply to human beings. Man was created by Allah not from water but through a special process by breathing rooh into clay model of man (Q. 15:28-29).

Programmed evolution of species from the PBC

Development of a human individual from the zygote is a natural demonstration of how the bioprogram stored in a cell can differentiate and create tissues carrying different programs. The programmed evolution of species refers to the evolution of specified number of microbioprograms each representing a species from a common bioinformation source, the divine bioprogram carried in the PBC. The ultimate result of the programmed evolution is the production of as many microbioprograms as specified in the bioprogram carried in the PBC. This would have been achieved through the operation of appropriate software engineering mechanisms, systems like mobile elements, and enzymes (Figure 1). A wide range of tasks like cutting and splicing of chromosomal sectors, shuffling of the sectors, replication, deletion and copying of the sectors with remarkably high fidelity would have been performed to ultimately accomplish the mission of producing cells each carrying the microbioprogram of a species. All these cellular functions are program-directed phenomena carried out with extreme specificity and accuracy. These processes might have been triggered into operation in the sequences and time schedules specified in the bioprogram stored in the PBC, which served as the source of biological information for the entire process.

We may now examine the probable pathways through which the PBC could have produced millions of microbioprograms each representing a species (Figure 2). The execution of the bioprogram carried in the PBC might have initially produced mother cells representing evolutionary lineages (domains of life). As per the modern phylogenetic classification, there are three domains namely, Bacteria, Archaea (microbes living in extreme environments) and Eukarya (or sometimes termed Eukaryota) [4]. Each of the domain mother cells produced kingdom mother cells. For example, the three kingdoms – animals, plants and fungi – are just three of about a dozen extant major branches of the eukaryote domain [10]. Each of these mother cells might have undergone further differentiation of the biosoftware in successive steps creating different lineages in accordance with the program to produce the end cells under the kingdom. In this way, programmed evolution of species can be broadly understood in comparison with the programmed evolution of tissues in a human adult from the zygote although the mechanisms of biosoftware differentiation are different. With the production of the end cells the programmed evolution of biodiversity is effectively complete. The entire process had occurred in an aqueous environment as revealed by the Quran. It would not have taken much time either, if the speed with which natural software engineering processes and cell division taking place is any indication. Nor would it have required so much space or quantity of water.

Figure 2. Programmed evolution of microbioprograms of diverse species from a common source of biological information carried in the primordial biochip (PBC)

The end cells produced by the animal mother cell might have been in the form of eggs while those originated from the other mother cells might have been in the form of single cells, spores, seeds, etc. Whatever the form in which they emerged, these cells might have been dispersed over the water and land areas by natural processes resulting in their widespread distribution on the earth. The development of individuals from the end cells representing species might have been programmed to take place on different time schedules. This is reflected in the sequence and chronology of appearance of the various species in the fossil record. Depending on the species, sexually dimorphic, polymorphic, asexual and other forms of individuals would have developed from the end cells, which through further reproduction increased their population and perpetuated their species. It may be noted that programmed evolution does not require intermediate stages to create a fully designed, perfect organism. It is creation in one go through a programmed evolutionary process. Therefore the theory is consistent with the natural evidence of lack of transitional forms in the fossil record.

The theory of programmed evolution proposed here differs in several respects from the traditional theories of evolution based on Darwinism. These are: 
  • Life did not originate as emergent phenomenon from non-living matter.
  • A divine software ‘bioprogram’ (the source of biological information on this planet) is supposed to be the driving force behind the organic evolution.
  • The origin of species is viewed as the creation of diverse software packages (microbioprograms) from a common bioinformation pool, the bioprogram, through a process of software differentiation.
  • The organisms that developed from the microbioprograms are in perfect form and required no intermediate forms.
  • Programmed evolution does not assume a common ancestor for all the species.
  • Programmed evolution is a deterministic phenomenon. The species so created are in accordance with the divine biosoftware to suit the multifarious purposes for which they are created by Allah.

The number of steps indicated in the biosoftware differentiation process (Figure 2) discussed above is purely arbitrary and is intended to explain the process in a broad sense. The number of steps through which the differentiation process might have taken place would be as specified in the program. Only through a process of biosoftware differentiation in a programmed sequence, biodiversity of very high magnitude as observed in nature can be created.

Geologic record indicates sudden appearance of new species punctuated by long periods of stasis (Punctuated Equilibrium). Darwin’s theory fails to explain this natural evidence of appearance of full-fledged species. The proposed theory of programmed evolution, however, allows such pattern in the appearance of species. According to Douglas Futuyma, a prominent evolutionary biologist, “Organisms either appeared fully developed or they did not. If they did not, they must have developed from preexisting species by some process of modification. If they did appear in a fully developed state, they must indeed have been created by some omnipotent intelligence” [11]. The proposed theory of programmed evolution supports the latter. Almost all groups at all taxonomic levels first appear in the fossil record as ‘type’ forms, and then ‘explode’ into a large number of diverse lineages with a mix of related but not identical potentials for adaptive morphological change [12, 13, 14]. This pattern is suggestive of partitioning of a very large common genetic package with a large number of alternate morphological potentials. But no known mechanism is so far available for generating such information-dense primordial source. According to Grasse, evolving species acquire a new store of genetic information through “a phenomenon whose equivalent cannot be seen in the creatures living at the present time (either because it is not there or because we are unable to see it)” [15]. These observations are fully consistent with the proposed theory of programmed evolution because it recognizes the divine bioprogram in the PBC as the source of biological information and the driving force behind the evolution of species.

Insofar as chromosomes form the storage device of the cell (biochip) and the bioprogram is stored in parts (program bits) in different sectors of the chromosomes of the PBC, microbioprograms specific to different species can be created by generating the required sectors through natural software engineering mechanisms and assembling and reorganising them into viable sets of instructions on the chromosomes in a programmed manner. In this way ‘new’ biosoftware (microbioprogram) can be created. This aspect is the most important and unique feature of the theory of programmed evolution as it describes how new biosoftware can be created from an original biomemetic pool through natural biosoftware engineering processes. The current scientific theories are silent about the source of biological information. Further, biologists consider phenomena like crossing over (recombination), chromosomal aberrations, etc., which create new chromosome compositions and hence bioinformation content, not as programmed mechanisms but as random errors and mistakes.

The theory of programmed organic evolution based on the differentiation of an original bioprogram (biosoftware) and its reorganisation into viable sets of millions of microbioprograms predicts extensive mixing of chromosomal regions and the possibility of finding identical program bits in the microbioprograms of the species. Physically these program bits will be represented by identical chromosomal sectors, which store them. Since DNA is part of the chromosomal material, the existence of identical sequences in the genomes of different species is a reflection of the existence of identical chromosomal sectors in them. This can be taken as confirmatory proof of the biosoftware engineering processes that occurred during the programmed evolution of microbioprograms from the original bioprogram in the PBC. Studies relating to molecular evolution provide considerable evidence of chromosome rearrangement, shuffling, reorganisation, etc., during the evolution of species. These findings support the proposed theory of programmed evolution. Little wonder that Philippe and Forterre [16] found the phylogenies as highly confusing due to the combining effects of gene duplication, gene loss, lateral gene transfer, etc. Experimental evidence for the occurrence of biosoftware engineering processes can also be obtained from several studies in comparative genomics. Wide variations are observed in karyotypes (number, size and shape of chromosomes in a somatic cell) of organisms. Comparison of karyotypes within and between species reveals that the differences are due to chromosome rearrangements. These rearrangements had played a major role in organic evolution [17]. Cases of genes in the same phylogenetic clade occurring in different chromosomal regions and genes belonging to distantly related phylogenetic clades occurring very closely in a chromosomal region are quite common [18]. These observations were explained as the result of several chromosomal rearrangements occurred at the regions of these genes and the shuffling of genes (physically chromosomal regions) contained in different genomic clusters. All these findings do support the proposed theory of programmed evolution of biodiversity.


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